gebhart/patrepeval huggingface dataset:
Differential genetic interactions of yeast stress response MAPK pathways (2015)

Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell. However, most studies have been performed under optimal growth conditions even though many functional interactions are known to occur under specific cellular conditions. In this study, we have performed a large-scale genetic interaction analysis in Saccharomyces cerevisiae involving approximately 49 × 1,200 double mutants in the presence of five different stress conditions, including osmotic, oxidative and cell wall-altering stresses. This resulted in the generation of a differential E-MAP (or dE-MAP) comprising over 250,000 measurements of conditional interactions. We found an extensive number of conditional genetic interactions that recapitulate known stress-specific functional associations. Furthermore, we have also uncovered previously unrecognized roles involving the phosphatase regulator Bud14, the histone methylation complex COMPASS and membrane trafficking complexes in modulating the cell wall integrity pathway. Finally, the osmotic stress differential genetic interactions showed enrichment for genes coding for proteins with conditional changes in phosphorylation but not for genes with conditional changes in gene expression. This suggests that conditional genetic interactions are a powerful tool to dissect the functional importance of the different response mechanisms of the cell.
Effects of Cyclophosphamide on the Pathogenesis of Cytomegalovirus-Induced Labyrinthitis (1990)

Cyclophosphamide was used in this study to define the contribution of the inflammatory response relative to direct cytopathic effects of guinea pig cytomegalovirus (GPCMV) in inducing sensorineural hearing loss in the guinea pig. The eighth nerve compound action potential (CAP) threshold on day 7 after inoculation of GPCMV into the scala tympani was an average of 35 dB greater for control animals than for those that were immunosuppressed with daily intraperitoneal injections of cyclophosphamide (20 mg/kg body weight). The amount of GPCMV antigen in the cochlea, detected immunohistochemically did not correlate with the CAP threshold. However, the greater the inflammatory response to GPCMV in the cochlea, the higher the CAP threshold and thus the greater the hearing loss. This study demonstrates that the inflammatory response to GPCMV may be more important than direct cytopathic effects of the virus in producing sensorineural hearing loss in GPCMV-induced labyrinthitis.
Solution‐Processed Wafer‐Scale Ag2S Thin Films: Synthesis and Excellent Charge Transport Properties (2022)

Abstract Monoclinic α‐Ag 2 S is an intriguing member of transition metal sulfides with great potential for all‐inorganic flexible optoelectronics and thermoelectrics. Fabrication of large‐area, high‐quality α‐Ag 2 S thin films and understanding their charge transport properties are critical for device operations yet have remained largely unexplored. Here, a novel two‐step, the solution‐processed approach is reported to produce wafer‐sized, highly crystalline α‐Ag 2 S thin films. Ultrafast terahertz (THz) conductivity measurements reveal that photogenerated charge carriers undergo efficient band transport, with room‐temperature mobility of ≈ 150 cm 2 V ‐1 s ‐1 and a diffusion length exceeding 500 nm. Furthermore, introducing poly(vinyl alcohol) (PVA) as the rigid component into the aqueous silver thiolate precursor enables the synthesis of free‐standing α‐Ag 2 S thin films with a mobility of ≈ 35 cm 2 V ‐1 s ‐1 , demonstrating their potential for flexible optoelectronics. This study provides a facile synthesis route for high‐quality, large‐area α‐Ag 2 S thin films with good charge transport properties, relevant for their integration into optoelectronics and wearable electronics.
Classification, structural biology, and applications of mucin domain-targeting proteases (2021)

Epithelial surfaces throughout the body are coated by mucins, a class of proteins carrying domains characterized by a high density of O-glycosylated serine and threonine residues. The resulting mucosal layers form crucial host-microbe interfaces that prevent the translocation of microbes while also selecting for distinct bacteria via the presented glycan repertoire. The intricate interplay between mucus production and breakdown thus determines the composition of the microbiota maintained within these mucosal environments, which can have a large influence on the host during both homeostasis and disease. Most research to date on mucus breakdown has focused on glycosidases that trim glycan structures to release monosaccharides as a source of nutrients. More recent work has uncovered the existence of mucin-type O-glycosylation-dependent proteases that are secreted by pathogens, commensals, and mutualists to facilitate mucosal colonization and penetration. Additionally, immunoglobulin A (IgA) proteases promote bacterial colonization in the presence of neutralizing secretory IgA through selective cleavage of the heavily O-glycosylated hinge region. In this review, we summarize families of O-glycoproteases and IgA proteases, discuss known structural features, and review applications of these enzymes to glycobiology.
The Histone Deacetylase Inhibitor Trichostatin A Sensitizes Human Renal Carcinoma Cells to TRAIL-Induced Apoptosis through Down-Regulation of c-FLIPL (2015)

Histone acetylation plays a critical role in the regulation of transcription by altering the structure of chromatin, and it may influence the resistance of some tumor cells to tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) by regulating the gene expression of components of the TRAIL signaling pathway. In this study, we investigated the effects and molecular mechanisms of trichostatin A (TSA), a histone deacetylase inhibitor, in sensitizing TRAIL-induced apoptosis in Caki human renal carcinoma cells. Our results indicate that nontoxic concentrations of TSA substantially enhance TRAIL-induced apoptosis compared with treatment with either agent alone. Cotreatment with TSA and TRAIL effectively induced cleavage of Bid and loss of mitochondrial membrane potential (MMP), which was associated with the activation of caspases (-3, -8, and -9) and degradation of poly (ADP-ribose) polymerase (PARP), contributing toward the sensitization to TRAIL. Combined treatment with TSA and TRAIL significantly reduced the levels of the cellular Fas-associated death domain (FADD)-like interleukin-1β-converting enzyme (FLICE) inhibitory protein (c-FLIP), whereas those of death receptor (DR) 4, DR5, and FADD remained unchanged. The synergistic effect of TAS and TRAIL was perfectly attenuated in c-FLIPL-overexpressing Caki cells. Taken together, the present study demonstrates that down-regulation of c-FLIP contributes to TSA-facilitated TRAIL-induced apoptosis, amplifying the death receptor, as well as mitochondria-mediated apoptotic signaling pathways.
Estimation of the effective medium for planar microstrip antennas on a dielectric and magnetic substrate (2012)

This paper proposes a simple formula to estimate the effective medium for planar microstrip antennas printed on a quasi-infinite magneto-dielectric substrate. The proposed empirical formulas shown in this study yield a good accuracy with a maximum error of less than 6%. These proposed empirical models are validated by electromagnetic simulations and measurements.
Growth and characterization of oxide buffer layers for YBCO coated conductors (1999)

Metal oxide films were grown on single crystal oxide substrates and deformation textured metal substrates by a metal organic deposition technique using metal alkoxides as the starting precursor materials. The crystallinity, grain alignment, and morphology of the oxide films depend on the process conditions and the substrate properties. Epitaxial oxide films were grown under a range of oxygen partial pressures and temperatures required for film formation on technologically important metal substrates. YBCO films grown on epitaxial LaAlO/sub 3/ buffer layers on single crystal SrTiO/sub 3/ had J/sub c/'s of 2.2 MA/cm/sup 2/ (77 K, self-field) demonstrating the quality of the MOD derived oxide films.
The Ubiquitous Signal Processing: Applications to Communications, Spectral Analysis and Array Processing (2002)

This dissertation is concerned with statistical signal processing and its applications. The thesis consists of three parts: I) applications to wireless communications, II) applications to spectra ...
Intracellular Roles of Microbial Aminotransferases: Overlap Enzymes Across Different Biochemical Pathways (1981)

(1981). Intracellular Roles of Microbial Aminotransferases: Overlap Enzymes Across Different Biochemical Pathways. CRC Critical Reviews in Microbiology: Vol. 8, No. 3, pp. 229-266.
Integrated optical device for Structured Illumination Microscopy (2022)

Abstract Structured Illumination Microscopy (SIM) is a key technology for high resolution and super-resolution imaging of biological cells and molecules. The spread of portable and easy-to-align SIM systems requires the development of novel methods to generate a light pattern and to shift it across the field of view of the microscope. Here we show a miniaturized chip that incorporates optical waveguides, splitters, and phase shifters, to generate a 2D structured illumination pattern suitable for SIM microscopy. The chip creates three point-sources, coherent and controlled in phase, without the need for further alignment. Placed in the pupil of a microscope’s objective, the three sources generate a hexagonal illumination pattern on the sample, which is spatially translated thanks to thermal phase shifters. We validate and use the chip, upgrading a commercial inverted fluorescence microscope to a SIM setup and we image biological sample slides, extending the resolution of the microscope.
Low levels of vitronectin and clusterin in acute meningococcal disease are closely associated with formation of the terminal-complement complex and the vitronectin-thrombin-antithrombin complex (1994)

Patients with terminal complement deficiencies and thus impaired lytic efficiency have a highly increased likelihood of contracting invasive meningococcal infections but generally experience a mild disease course. Deficiencies of lysis inhibitors might therefore be associated with severe disease. We have quantified the complement lysis inhibitors vitronectin and clusterin, as well as complexes containing the proteins, in plasma from patients with acute meningococcal disease. At hospital admission, the median vitronectin concentrations were 0.10 (range, 0.04 to 0.17) g/liter in 10 septic patients and 0.19 (0.09 to 0.47) g/liter in 14 nonseptic patients (P = 0.001). The corresponding clusterin concentrations were 0.09 (0.01 to 0.13) and 0.14 (0.06 to 0.29) g/liter (P = 0.005). The vitronectin-thrombin-antithrombin complex concentration was 1.8 (0.22 to 35.6) arbitrary units (AU)/ml in septic patients, but the complex was not detectable in most nonseptic patients (< 0.10 to 0.16 AU/ml) (P < 0.0001). The corresponding levels of the terminal complement complex (contains vitronectin and clusterin) were 4.4 (3.6 to 20.1) and 2.6 (1.6 to 4.7) AU/ml (P = 0.0005). We found no evidence of constitutively low levels of vitronectin or clusterin in patients contracting meningococcal disease. The low levels of the proteins may partly be explained by hemodilution, extravasation, and increased consumption due to incorporation into complexes which are quickly removed from circulation.
Differential renal gene expression in prehypertensive and hypertensive spontaneously hypertensive rats (2005)

Development of hypertension stems from both environmental and genetic factors wherein the kidney plays a central role. Spontaneously hypertensive rats (SHR) and the nonhypertensive Wistar-Kyoto (WKY) controls are widely used as a model for studying hypertension. The present study examined the renal gene expression profiles between SHR and WKY at a prehypertensive stage (3 wk of age) and hypertensive stage (9 wk of age). Additionally, age-related changes in gene expression patterns were examined from 3 to 9 wk in both WKY and SHR. Five to six individual kidney samples of the same experimental group were pooled together, and quadruplicate hybridizations were performed using the National Institute of Environmental Health Sciences Rat version 2.0 Chip, which contains approximately 6,700 genes. Twenty two genes were found to be differentially expressed between SHR and WKY at 3 wk of age, and 104 genes were differentially expressed at 9 wk of age. Soluble epoxide hydrolase (Ephx2) was found to be significantly upregulated in SHR at both time points and was the predominant outlier. Conversely, elastase 1 (Ela1) was found to be the predominant gene downregulated in SHR at both time points. Analysis of profiles at 3 vs. 9 wk of age identified 508 differentially expressed genes in WKY rats. In contrast, only 211 genes were found to be differentially expressed during this time period in SHR. The altered gene expression patterns observed in the age-related analysis suggested significant differences in the vascular extracellular matrix system between SHR and WKY kidney. Together, our data highlight the complexity of hypertension and the numerous genes involved in and affected by this condition.
Observation of Atom Images by Means of Field Emission Stem (1976)

A number of studies of single atom image observation utilizing either scanning transmission electron microscope ( STEM ) or conventional electron microscope ( OEM ) have been reported. For this purpose, the dark field image observation seems more promising because the scattering cross-section of an atom is extremely small. Much attention has been paid to decreasing background noises resulting from the supporting film. A thin amorphous carbon film is often utilized as a supporting film. However, many high contrast spots appear even in the dark field image when OEM is used. Matsuda and Nagata3 applied an incoherent illumination technique to the bright field image observation of OEM, and succeeded, in removing the phase contrast effects from the image.
Utility Of Revised International Prognostic Scoring System (R-IPSS) To Predict Outcome Of Myelodysplastic Syndromes (MDS) Patients After Allogeneic Hematopoietic Stem Cell Transplantation (AHSCT) (2013)

Abstract Introduction The R-IPSS at time of diagnosis was recently proposed and validated as a superior prognostic tool refining the original IPSS. The new model recognized further cytogenetic heterogeneity of the disease, and importance of the depth of cytopenia. The value of R-IPSS at time of AHSCT to predict post-transplant outcomes is not known. We examined the utility of R-IPSS prior to AHSCT in our cohort of MDS patients. Methods This was a retrospective study. We identified MDS patients who underwent AHSCT in our MDS database. Individual patient charts were reviewed. R-IPSS was calculated at time of transplant using data obtained from tests performed within 30 days of transplant. The R-IPSS karyotype was based on the new proposed 5 groups. The study main objective was to compare overall survival (OS) from time of AHSCT among R-IPSS groups and R-IPSS karyotype groups. Kaplan Meier estimates were used to calculate OS; log rank test was used to compare groups. Results Out of 1259 MDS patients in our database, 175 received AHSCT, and we excluded 65 patients who had AHSCT at any point after AML transformation. The median duration of follow up was 46 months (mo) (95% CI 39-53). Table-1 summarizes baseline characteristics of the cohort (n=110). All patients received a reduced intensity AHSCT using fludarabine and IV-busulfan. The rate of acute graft versus host disease (GVHD) II-IV was 68% and 72% for chronic GVHD. The median OS for the whole cohort was 22 mo (95% 10-33 mo.). The IPSS at time of AHSCT did not predict OS. Based on R-IPSS, 24 pts (22%) were very low, 26 (24%), low, 16 (15%) intermediate, 21 (19%) high, and 23 (21%) were very high. The R-IPSS at time of AHSCT did not predict OS. The median OS was not reached, 14, 52, 20 and 23 mo for very low, low, int, high and very high respectively. (p= 0.1). The R-IPSS karyotype groups did predict OS. The median OS was 29 mo, 26 mo, 19 mo, and 9 mo for good, intermediate, poor and very poor karyotype risk groups respectively (p=0.047) No other factors prior to AHSCT including age, myeloblasts percentage, Hemoglobin, platelets, treatment before AHSCT had impact on OS in univariate analysis. Conclusions IPSS and R-IPSS prior to AHSCT did not predict OS in our cohort of MDS patients. The R-IPSS karyotype group was the only statistically significant prognostic factor prior to AHSCT. Disclosures: List: Celgene: Membership on an entity’s Board of Directors or advisory committees.
The Ins and Outs of Rust Haustoria (2014)

Rust diseases caused by fungi of the order Pucciniales afflict a&#13;\nwide range of plants, including cereals, legumes, ornamentals, and&#13;\nfruit trees, and pose a serious threat to cropping systems and global&#13;\nfood security. The obligate parasitic lifestyle of these fungi and&#13;\ntheir complex life cycles, often involving alternate hosts for the&#13;\nsexual and asexual stages, also make this group of pathogens of&#13;\ngreat biological interest. One of the most remarkable adaptations&#13;\nof rust fungi is the specialized infection structure that underpins&#13;\nthe sustained biotrophic association with hosts; the haustorium.
Automatic Detection of Auroral Substorms from a CubeSat Platform Using Machine Learning (2020)

With the growth of auroral tourism and the desire to validate space weather predictions, a need has arisen to image the entire polar crown to understand spatial and temporal evolution of auroral substorms. Project Highly Elliptical Polar Constellation for Auroral Transport Studies (HEPCATS), in collaboration with DigitalGlobe and the University of Colorado Space Weather Center, seeks to provide automatic imaging and classification of the Aurora Borealis in the visible spectrum from a CubeSat in a Molniya orbit. Due to a limited downlink budget from this platform, a pre-trained, deep neural network (PTDNN) is used in conjunction with a custom classifier network to classify image data as containing an aurora or not, thus reducing the required number of downlinked images. The technique of supervised machine learning was used to train the classifier network to learn the classification of image features such as color and shape. Training data consists of approximately 2,000 manually labeled ultra-violet (UV) images from the POLAR and IMAGE missions. The composite neural network model was then verified on this labeled data. In the future, in-flight re-training of the classifier model can be utilized to improve classification accuracy with the extra computational cost being achievable on a CubeSat platform.
Antibody semorinemab reduces tau pathology in a transgenic mouse model and engages tau in patients with Alzheimer’s disease (2021)

Semorinemab shows beneficial effects in preclinical models and engages tau in a phase 1 study of patients with Alzheimer’s disease.
Commonsense Reasoning for Conversational AI: A Survey of the State of the Art (2023)

Large, transformer-based pretrained language models like BERT, GPT, and T5 have demonstrated a deep understanding of contextual semantics and language syntax. Their success has enabled significant advances in conversational AI, including the development of open-dialogue systems capable of coherent, salient conversations which can answer questions, chat casually, and complete tasks. However, state-of-the-art models still struggle with tasks that involve higher levels of reasoning - including commonsense reasoning that humans find trivial. This paper presents a survey of recent conversational AI research focused on commonsense reasoning. The paper lists relevant training datasets and describes the primary approaches to include commonsense in conversational AI. The paper also discusses benchmarks used for evaluating commonsense in conversational AI problems. Finally, the paper presents preliminary observations of the limited commonsense capabilities of two state-of-the-art open dialogue models, BlenderBot3 and LaMDA, and its negative effect on natural interactions. These observations further motivate research on commonsense reasoning in conversational AI.
Identification of a Gene Essential for Sheathed Structure Formation in Sphaerotilus natans , a Filamentous Sheathed Bacterium (2002)

Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in substrate-rich media it grows as single rod-shaped cells, whereas in substrate-limited media it grows as filaments. To identify genes responsible for sheath formation, we carried out transposon Tn5 mutagenesis. Of the approximately 20,000 mutants obtained, 7 did not form sheathed structures. Sequencing of the Tn5-flanking regions showed that five of the seven Tn5 insertions converged at the same open reading frame, designated sthA. The deduced amino acids encoded by sthA were found to be homologous to glycosyltransferase, which is known to be involved in linking sugars to lipid carriers during bacterial exopolysaccharide biosynthesis. Disruption of the gene of the wild-type strain by inserting a kanamycin resistance gene cassette also resulted in sheathless growth under either type of nutrient condition. These findings indicate that sthA is a crucial component responsible for sheath formation.
The Domain Restriction Hypothesis: Relating Term Similarity and Semantic Consistency (2007)

In this paper, we empirically demonstrate what we call the domain restriction hypothesis, claiming that semantically related terms extracted from a corpus tend to be semantically coherent. We apply this hypothesis to define a post-processing module for the output of Espresso, a state of the art relation extraction system, showing that irrelevant and erroneous relations can be filtered out by our module, increasing the precision of the final output. Results are confirmed by both quantitative and qualitative analyses, showing that very high precision can be reached.
A 200mV to 1.2V, 4.4MHz to 6.3GHz, 48&#x00D7;42b 1R/1W programmable register file in 65nm CMOS (2007)

This paper describes a 48times42b 1-read, 1-write ported register file which operates at supply voltage range of 1.2 V (6.1-6.3 GHz, 47 mW) down to 0.2 V (4-4.4 MHz, 0.01 mW) in 65 nm CMOS. Two programmable techniques, triple stacking and forced stacking are proposed which enable register files to operate at ultra low supply voltages while maintaining the performance comparable to conventional design at high supply voltages.
Optical Transceivers for Mobile Front-Haul and PON Applications (2017)

Low-cost tuneable lasers for PON transceivers are reviewed. Laser tuning is based on a remote signal from the OLT. The message channel is realized by envelope modulation with limited impact on the payload signal.