gebhart/patrepeval huggingface dataset:
Evasion of a Human Cytomegalovirus Entry Inhibitor with Potent Cysteine Reactivity Is Concomitant with the Utilization of a Heparan Sulfate Proteoglycan-Independent Route of Entry (2020)

The dependence of viruses on the host cell to complete their replicative cycle renders cellular functions potential targets for novel antivirals. We screened a panel of broadly acting cellular ion channel inhibitors for activity against human cytomegalovirus (HCMV) and identified the voltage-gated chloride ion channel inhibitor 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS) as a potent inhibitor of HCMV replication. Time-of-addition studies demonstrated that DIDS inhibited entry via direct interaction with the virion that impeded binding to the plasma membrane. Synthesis and analysis of pharmacological variants of DIDS suggested that intrinsic cysteine, and not lysine, reactivity was important for activity against HCMV. Although sequencing of DIDS-resistant HCMV revealed enrichment of a mutation within UL100 (encoding glycoprotein M) and a specific truncation of glycoprotein RL13, these did not explain the DIDS resistance phenotype. Specifically, only the introduction of the RL13 mutant partially phenocopied the DIDS resistance phenotype. Serendipitously, the entry of DIDS-resistant HCMV also became independent of heparan sulfate proteoglycans (HSPGs), suggesting that evasion of DIDS lowered dependence on an initial interaction with HSPGs. Intriguingly, the DIDS-resistant virus demonstrated increased sensitivity to antibody neutralization, which mapped, in part, to the presence of the gM mutation. Taken together the data characterize the antiviral activity of a novel HCMV inhibitor that drives HCMV infection to occur independently of HSPGs and the generation of increased sensitivity to humoral immunity. The data also demonstrate that compounds with cysteine reactivity have the potential to act as antiviral compounds against HCMV via direct engagement of virions.<b>IMPORTANCE</b> Human cytomegalovirus (HCMV) is major pathogen of nonimmunocompetent individuals that remains in need of new therapeutic options. Here, we identify a potent antiviral compound (4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid [DIDS]), its mechanism of action, and the chemical properties required for its activity. In doing so, the data argue that cysteine-reactive compounds could have the capacity to be developed for anti-HCMV activity. Importantly, the data show that entry of DIDS-resistant virus became independent of heparan sulfate proteoglycans (HSPGs) but, concomitantly, became more sensitive to neutralizing antibody responses. This serendipitous observation suggests that retention of an interaction with HSPGs during the entry process <i>in vivo</i> may be evolutionarily advantageous through better evasion of humoral responses directed against HCMV virions.
Arrangement-channel approach to reactive systems: Generalizations with new insight (1988)

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No Evidence of Linkage Between Familial Combined Hyperlipidemia and Genes Encoding Lipolytic Enzymes in Finnish Families (1997)

Familial combined hyperlipidemia (FCHL) is characterized by different lipid phenotypes (IIa, IIb, IV) and elevated apolipoprotein B (apo B) levels in affected family members. Despite intensive research, the genes involved in the expression of this complex disorder have not been identified, probably because of problems associated with phenotype definition, unknown mode of inheritance, and most probably genetic heterogeneity. To explore the genetics of FCHL in the genetically homogeneous Finnish population, we collected 14 well-documented Finnish pedigrees with premature coronary heart disease and FCHL-like dyslipidemia. The lipolytic enzymes lipoprotein lipase (LPL), hepatic lipase (HL), and hormone-sensitive lipase (HSL) were selected as initial candidate genes because of their central roles in apo B and triglyceride metabolism. On the basis of the pedigree structures, a dominant mode of inheritance was adopted for linkage analyses, and serum total cholesterol and/or triglyceride levels exceeding the 90th percentile level were set as diagnostic criteria (criterion 1). In pairwise linkage analyses with intragenic markers, no evidence for linkage was found. Instead, the significantly negative LOD scores suggested exclusion of all three loci for single major gene effect. LOD scores were -14.63, -5.03, and -5.70 for the three LPL polymorphisms (theta=0.00); -9.40, -6.30, and -4.74 for the three HL polymorphisms (theta=0.00); and -15.29 for the HSL polymorphism (theta=0.00). The results were very similar when apo B levels over the 90th percentile were used as criteria for affected status (criterion 2). Also, when linkage calculations were carried out using an intermediate or recessive mode of inheritance, the results of pairwise linkage analysis remained negative. Furthermore, when haplotypes were constructed from multiple polymorphisms of the LPL and HL genes, no segregation with the FCHL phenotype could be observed in the 14 Finnish families. Data obtained by the affected sib-pair method supported these findings, suggesting that the LPL, HL, or HSL genes do not represent major loci influencing the expression of the FCHL phenotype.
On Anomalous Hotspot Discovery in Graph Streams (2013)

Network streams have become ubiquitous in recent years because of many dynamic applications. Such streams may show localized regions of activity and evolution because of anomalous events. This paper will present methods for dynamically determining anomalous hot spots from network streams. These are localized regions of sudden activity or change in the underlying network. We will design a localized principal component analysis algorithm, which can continuously maintain the information about the changes in the different neighborhoods of the network. We will use a fast incremental eigenvector update algorithm based on von Mises iterations in a lazy way in order to efficiently maintain local correlation information. This is used to discover local change hotspots in dynamic streams. We will finally present an experimental study to demonstrate the effectiveness and efficiency of our approach.
The role of mass transport in laser-induced chemistry (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe role of mass transport in laser-induced chemistryToivo T. Kodas and Paul B. ComitaCite this: Acc. Chem. Res. 1990, 23, 6, 188–194Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ar00174a004https://doi.org/10.1021/ar00174a004research-articleACS PublicationsRequest reuse permissionsArticle Views109Altmetric-Citations16LEARN 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-Alertsclose Get e-Alerts
Surface Pasteurization with Hot Water and Steam (2005)

The demand by consumers for fresh and fresh-cut fruits and vegetables hassteadily increased due to nutritious qualities associated with fresh produceand the convenience of ready-to-eat fresh foods. This increased demand hasresulted in increased per capita consumption of fresh produce. Althoughfresh produce is generally considered safe, it has been implicated in numerous foodborne outbreaks in recent years. The Centers for Disease Control and Prevention reported that foodborne outbreaks associated with fresh produce doubled between the period 1973 to 1987 and 1988 to 1992 [1]. Contamination of fresh produce, often grown on the ground and/or in areas adjacent to animal production, with human pathogens may occur during growth, harvesting, handling, and processing. Conventional washing and sanitizing treatments have limited efficacy in inactivating and/or removing pathogens on the surface of produce. Survival of human pathogens and other bacteria during washing and sanitizing treatments is attributed to their attachment to inaccessible sites on produce surfaces such as within the netting of a cantaloupe [2], infiltration within the stem scar of tomatoes and the calyx region of apples [3,4], and incorporation into biofilms, as seen with apples [3], cantaloupes [2], and leaf surfaces [5,6]. Inadequate decontamination of fresh produce can result in the survival of human pathogens on the surface with the possibility of subsequent transfer of the pathogen from the surface, such as the rind of a cantaloupe or the peel of an orange, to the flesh during fresh-cut processing or juice extraction, respectively. Thus, the safety of fresh and fresh-cut produce in supermarkets and salad bars, as well as the safety of freshly squeezed unpasteurized juices, especially those served in fresh juice bars, is of concern. Although experimental approaches to washing produce, such as vacuum infiltration of sanitizers and application of abrasives during washing, have resulted in greater microbial reductions compared to conventional treatments [7], these new treatments are not capable of adequately inactivating the pathogenic bacteria in their protective attachment states on produce surfaces. Furthermore, inactivation of sanitizing agents by organic material such as soil and debris in the washing solution, prior to contact with microorganisms, may limit their sanitizing effectiveness [8].
Supplementary Figure 2 from A Multi-Institution Phase I Trial of Ruxolitinib in Patients with Chronic Myelomonocytic Leukemia (CMML) (2023)

&lt;p&gt;Quantification of quality of life score. (A-F) EORTC-Q30 parsed by predefined subgroups (bottom panel) FACT-Leu trial outcome index (TOI)&lt;/p&gt;
Supplemental Figure 10 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Figure S10&lt;/p&gt;
The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types (2015)

Enhancing pre-existing anti-tumor immunity leads to therapeutic benefit for some patients, but why some tumors are more immunogenic than others remains unresolved. We took a unique systems approach to relate patient survival to immune gene expression in >3,500 tumor RNAseq profiles from a dozen tumor types. We found significant links between immune gene expression and patient survival in 8/12 tumor types, with tumors partitioned by gene expression comprising distinct molecular subtypes. T/NK cell genes were most clearly survival-related for melanoma, head and neck, and bladder tumors, whereas myeloid cell genes were most clearly survival-related with kidney and breast tumors. T/NK or myeloid cell gene expression was linked to poor prognosis in bladder and kidney tumors, respectively, suggesting tumor-specific immunosuppressive checkpoints. Our results suggest new biomarkers for existing cancer immunotherapies and identify targets for new immunotherapies.
Evaluation of Single-Lap and Block Shear Test Methods in Adhesively Bonded Composite Joints (2021)

Adhesive bonding is increasingly being used for composite structures, especially in aerospace and automotive industries. One common joint configuration used to test adhesive strength is the single-lap shear joint, which has been widely studied and shown to produce significant normal (peeling) stresses. When bonding composite structures, the normal stresses are capable of causing delamination before the adhesive bond fails, providing inconclusive engineering data regarding the bonding strength. An alternative test is the block shear joint, which uses a shorter sample geometry and a compressive-shear loading to reduce normal stresses. Analytical models proposed by Goland and Reissner and Hart-Smith are used to compare the edge-bending moment for the two joint configurations. The stress distributions along the bondline are also compared using finite element analysis. Experimental tests are conducted to evaluate these analyses and the failure modes of each configuration are recorded. Block shear samples demonstrate a joint strength over 100% higher than single-lap shear specimen bonded with the same adhesive material. The lower joint strength measured in single-lap shear is found to be potentially misleading due to delamination of the composite adherend.
A Broadband Fully Integrated Power Amplifier Using Waveform Shaping Multi-Resonance Harmonic Matching Network (2021)

In this article, we propose a broadband fully integrated power amplifier (PA) using a waveform shaping harmonic matching network. A comprehensive theory is developed for the proposed multi-resonance harmonic matching network to derive design criteria for achieving wide bandwidth, low insertion loss, and optimum load impedances in the second- and third-harmonic frequency bands. Furthermore, it is shown that this network can be realized using a lower total inductance compared to a standard bandpass network which is an important feature in reducing chip area and fabrication cost. A fully integrated PA prototype is implemented using a 250-nm GaN-on-SiC process with 28-V supply. The PA provides 33.9&#x2013;36.1dBm output power (at 2&#x2013;3dB gain compression), 42&#x2013;51&#x0025; drain efficiency (DE), 38&#x2013;48&#x0025; power-added efficiency (PAE), and 10&#x2013;12.2dB power gain, across 4.0&#x2013;6.0GHz. The output-power 1-dB bandwidth is 3.6&#x2013;5.6GHz (44.5&#x0025;). For a 64-QAM signal with 8dB peak-to-average power ratio (PAPR) at 5.0GHz, the PA can provide 30.2dBm average output power and 32&#x0025; average PAE with RMS error vector magnitude (EVM) of &#x2212;34.0/&#x2212;32.4/&#x2212;28.4dB (2.0/2.4/3.8&#x0025;) for 50/100/200MHz modulation bandwidth, without using digital predistortion (DPD). The maximum average output power and average PAE, under the linearity constraint EVM &#x003C;&#x2212;28dB, are respectively 32.1/32.0/30.2dBm and 39/38/32&#x0025;, for modulation bandwidth of 50/100/200 MHz.
Expression and Regulation of the Arabidopsis thaliana Cel1 Endo 1,4 beta Glucanase Gene During Compatible Plant-Nematode Interactions. (2006)

The root-knot nematode Meloidogyne incognita is an obligate endoparasite of plant roots and stimulates elaborate modifications of selected root vascular cells to form giant cells for feeding. An Arabidopsis thaliana endoglucanase (Atcel1) promoter is activated in giant cells that were formed in Atcel1::UidA transgenic tobacco and Arabidopsis plants. Activity of the full-length Atcel1 promoter was detected in root and shoot elongation zones and in the lateral root primordia. Different 5' and internal deletions of regions of the 1,673 bp Atcel1 promoter were each fused to the UidA reporter gene and transformed in tobacco, and roots of the transformants were inoculated with M. incognita to assay for GUS expression in giant cells and noninfected plant tissues. Comparison of the Atcel1 promoter deletion constructs showed that the region between -1,673 and -1,171 (fragment 1) was essential for Atcel1 promoter activity in giant cells and roots. Fragment 1 alone, however, was not sufficient for Atcel1 expression in giant cells or roots, suggesting that cis-acting elements in fragment 1 may function in consort with other elements within the Atcel1 promoter. Root-knot nematodes and giant cells developed normally within roots of Arabidopsis that expressed a functional antisense construct to Atcel1, suggesting that a functional redundancy in endoglucanase activity may represent another level of regulatory control of cell wall-modifying activity within nematode feeding cells.
Atomically Precise Noble Metal Cluster-Assembled Superstructures in Water: Luminescence Enhancement and Sensing (2020)

We present an example of host–guest complexes of atomically precise noble metal nanoparticles with cucurbit[7]uril (CB) in water, specifically concentrating on Ag29(LA)12 (where LA is α-lipoic acid), a well-known red luminescent silver cluster. Such host–guest interactions resulted in enhanced luminescence of about 1.25 times for the modified system, compared to the parent cluster. We extended our study to cyclodextrins (CDs), where about 1.5 times enhanced luminescence was estimated compared to the parent cluster. The formation of supramolecular complexes was confirmed using high-resolution electrospray ionization mass spectrometry (HRESI MS) and nuclear magnetic resonance spectroscopy. Molecular docking and density functional theory calculations supported our experimental results and showed that while CB formed inclusion complexes by encapsulation of one of the LA ligands of the cluster, CD formed supramolecular adducts by interaction with the cavity built by the ligands on the cluster surface. The complexation was favored by geometrical compatibility. Consequently, these superstructures are labeled as Ag29LA12∩CBn and Ag29LA12@CDn (n = 1–3), where ∩ and @ indicate the inclusion complex and supramolecular adduct, respectively. Solution-phase Ag29LA12@CDn complexes were employed to detect dopamine (10 nM). Luminescent Ag29LA12@CDn and Ag29LA12∩CBn complexes in water could be potential candidates for organic pollutant sensing and biomedical applications.
Organocatálisis: Hacia una nueva generación de catalizadores para la síntesis de polímeros (2013)

The demanding requirements of new materials in our society and concern for greener chemistry, has led to the revelation of a new generation of highly selective and sustainable catalysts (organic catalysts) as a useful tool for the synthesis of polymers. The advantages that these catalysts offer versus traditional organometallic catalysts in terms of toxicity and versatility makes the organocatalysis and their appli- cation in polymerization reactions a continuously expanding field. This work provides a current view of the possibilities of organocatalysis in polymerization processes and our opinion on the future challenges in the XXI century.
Progress in theoretical approach to InGaN and InN epitaxy: In incorporation efficiency and structural stability (2014)

The surface stability, growth process, and structural stability of InGaN and InN are reviewed from a theoretical viewpoint. In 2001, a new theoretical approach based on an ab initio calculation was developed. This theoretical approach enables the investigation of the influence of growth conditions such as partial pressure and temperature on the surface stability. The theoretical approach is applied to the research on the In incorporation efficiency in InGaN grown on nonpolar and semipolar surfaces. The calculation results suggest that the N–H layer formed on such surfaces has a crucial role in In incorporation. Moreover, the structural stability of InN grown by pressurized-reactor MOVPE is reviewed. It was found by the theoretical approach that facet formation causes the spontaneous formation of islands with the zinc-blende structure.
Analysis of time, frequency and time-frequency domain features from acoustic emissions during Laser Powder-Bed fusion process (2020)

Sensor integration for in situ monitoring during additive manufacturing promises to enhance control over the process and assures quality in the fabricated workpieces. Acoustic emissions from the process zone of the laser powder-bed fusion process carry information about the events and failure modes of the printed workpiece. Analysis of acoustic signals emitted during different laser regimes, such as conduction, keyhole, etc. in time, frequency and time-frequency domains could provide quantitative information about the underlying physical mechanisms. This article reports a statistical analysis of the features in acoustic signals to perceive the characteristics of failure modes occurring during layering of stainless steel 316L. The visualization of the feature space distribution that corresponds to different failure modes shows the potentials of applying machine learning for in situ classification. The paper also proposes strategies in terms of data acquisition and preprocessing for building a comprehensive monitoring system.
Broadband Acoustical MEMS Transceivers for Simultaneous Range Finding and Microphone Applications (2019)

This work presents capacitive ultrasonic transceivers based on a dual-backplate MEMS microphone technology. The transducers exploit mechanical and acoustical system resonances in the low ultrasonic frequency range up to 100 kHz for both sending and receiving of ultrasonic signals. Requiring below 10V bias voltage and using standard MEMS microphone housings with dimensions of 4x3x1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , the proposed system allows an integration into space and power critical systems like e.g. smartphones. While the ultrasonic transceiver functionality enables proximity sensing and presence detection applications, state-of-the-art audio performance of 68 dB(A) signal-to-noise ratio (SNR) is maintained.
Micro-climate Prediction - Multi Scale Encoder-decoder based Deep Learning Framework (2021)

This paper presents a deep learning approach for a versatile Micro-climate prediction framework (DeepMC). Micro climate predictions are of critical importance across various applications, such as Agriculture, Forestry, Energy, Search & Rescue, etc. To the best of our knowledge, there is no other single framework which can accurately predict various micro-climate entities using Internet of Things (IoT)data. We present a generic framework (DeepMC) which predicts various climatic parameters such as soil moisture, humidity, windspeed, radiation, temperature based on the requirement over a period of 12 hours - 120 hours with a varying resolution of 1 hour - 6hours, respectively. This framework proposes the following new ideas: 1) Localization of weather forecast to IoT sensors by fusing weather station forecasts with the decomposition of IoT data at multiple scales and 2) A multi-scale encoder and two levels of attention mechanisms which learns a latent representation of the interaction between various resolutions of the IoT sensor data and weather station forecasts. We present multiple real-world agricultural and energy scenarios, and report results with uncertainty estimates from the live deployment of DeepMC, which demonstrate that DeepMC outperforms various baseline methods and reports 90%+ accuracy with tight error bounds.
Isolation and Characterization of Novel Geldanamycin Analogues. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.