gebhart/patrepeval huggingface dataset:
Efficient protein production inspired by how spiders make silk (2017)

Membrane proteins are targets of most available pharmaceuticals, but they are difficult to produce recombinantly, like many other aggregation-prone proteins. Spiders can produce silk proteins at huge concentrations by sequestering their aggregation-prone regions in micellar structures, where the very soluble N-terminal domain (NT) forms the shell. We hypothesize that fusion to NT could similarly solubilize non-spidroin proteins, and design a charge-reversed mutant (NT*) that is pH insensitive, stabilized and hypersoluble compared to wild-type NT. NT*-transmembrane protein fusions yield up to eight times more of soluble protein in Escherichia coli than fusions with several conventional tags. NT* enables transmembrane peptide purification to homogeneity without chromatography and manufacture of low-cost synthetic lung surfactant that works in an animal model of respiratory disease. NT* also allows efficient expression and purification of non-transmembrane proteins, which are otherwise refractory to recombinant production, and offers a new tool for reluctant proteins in general.
Mode-locking in an optical microresonator via soliton formation (2012)

Dissipative solitons can emerge in a wide variety of dissipative nonlinear systems throughout the fields of optics, medicine or biology. Dissipative solitons can also exist in Kerr-nonlinear optical resonators and rely on the double balance between parametric gain and resonator loss on the one hand and nonlinearity and diffraction or dispersion on the other hand. Mathematically these solitons are solution to the Lugiato-Lefever equation and exist on top of a continuous wave (cw) background. Here we report the observation of temporal dissipative solitons in a high-Q optical microresonator. The solitons are spontaneously generated when the pump laser is tuned through the effective zero detuning point of a high-Q resonance, leading to an effective red-detuned pumping. Red-detuned pumping marks a fundamentally new operating regime in nonlinear microresonators. While usually unstablethis regime acquires unique stability in the presence of solitons without any active feedback on the system. The number of solitons in the resonator can be controlled via the pump laser detuning and transitions to and between soliton states are associated with discontinuous steps in the resonator transmission. Beyond enabling to study soliton physics such as soliton crystals our observations open the route towards compact, high repetition-rate femto-second sources, where the operating wavelength is not bound to the availability of broadband laser gain media. The single soliton states correspond in the frequency domain to low-noise optical frequency combs with smooth spectral envelopes, critical to applications in broadband spectroscopy, telecommunications, astronomy and low phase-noise microwave generation.
A wavelet based de-noising technique for ocular artifact correction of the electroencephalogram (2003)

This paper investigates a wavelet based denoising of the electroencephalogram (EEG) signal to correct for the presence of the ocular artifact (OA). The. proposed technique is based on an over-complete wavelet expansion of the EEG as follows: i) a stationary wavelet transform (SWT) is applied to the corrupted EEG; ii) the thresholding of the coefficients in the lower frequency bands is performed; iii) the de-noised signal is reconstructed. This paper demonstrates the potential of the proposed technique for successful OA correction. The advantage over conventional methods is that there is no need for the recording of the electrooculogram (EOG) signal itself. The approach works both for eye blinks and eye movements. Hence, there is no need to discriminate between different artifacts. To allow for a proper comparison, the contaminated EEG signals as well as the corrected signals are presented together with their corresponding power spectra.
Utility-function-driven energy-efficient cooling in data centers (2010)

The sharp rise in energy usage in data centers, fueled by increased IT workload and high server density, and coupled with a concomitant increase in the cost and volatility of the energy supply, have triggered urgent calls to improve data center energy efficiency. In response, researchers have developed energy-aware IT systems that slow or shut down servers without sacrificing performance objectives. Several authors have shown that utility functions are a natural and advantageous framework for self-management of servers to joint power and performance objectives. We demonstrate that utility functions are a similarly powerful framework for flexibly managing entire data centers to joint power and temperature objectives. After showing how utility functions can capture a wide range of objectives and tradeoffs that an operator might wish to specify, we illustrate the resulting range in behavior and energy savings using experimental results from a real data center that is cooled by two computer room air-conditioning (CRAC) units equipped with variable-speed fan drives.
Regulation and Function of the Arabidopsis<i>ABA-insensitive4</i>Gene in Seed and Abscisic Acid Response Signaling Networks (2000)

We have characterized developmental, environmental, and genetic regulation of abscisic acid-insensitive (ABI)4 gene expression in Arabidopsis. Although expressed most strongly in seeds, ABI4 transcripts are also present at low levels in vegetative tissue; vegetative expression is not induced by abscisic acid (ABA) or stress treatments. Comparison of transcript levels in mature seeds of ABA-insensitive, ABA-hypersensitive, ABA-deficient, or heterochronic mutants indicates that ABI4 expression is altered in only two of the backgrounds, the ABA-insensitive mutants abi1-1 and abi3-1. To determine whether ABI4 is necessary and/or sufficient for ABA response, we assayed the effects of loss of ABI4 function and ectopic ABI4 expression on growth and gene expression. We examined genetic interactions among three ABA response loci, ABI3, ABI4, and ABI5, by comparing phenotypes of mutants, ectopic expression lines, mutants carrying an ectopically expressed transgene, and the corresponding wild-type lines. Our results indicate some cross-regulation of expression among ABI3, ABI4, and ABI5 and suggest that they function in a combinatorial network, rather than a regulatory hierarchy, controlling seed development and ABA response.
The <i>Drosophila melanogaster</i> Seminal Fluid Protein Acp62F Is a Protease Inhibitor That Is Toxic Upon Ectopic Expression (2002)

Drosophila melanogaster seminal fluid proteins stimulate sperm storage and egg laying in the mated female but also cause a reduction in her life span. We report here that of eight Drosophila seminal fluid proteins (Acps) and one non-Acp tested, only Acp62F is toxic when ectopically expressed. Toxicity to preadult male or female Drosophila occurs upon one exposure, whereas multiple exposures are needed for toxicity to adult female flies. Of the Acp62F received by females during mating, approximately 10% enters the circulatory system while approximately 90% remains in the reproductive tract. We show that in the reproductive tract, Acp62F localizes to the lumen of the uterus and the female's sperm storage organs. Analysis of Acp62F's sequence, and biochemical assays, reveals that it encodes a trypsin inhibitor with sequence and structural similarities to extracellular serine protease inhibitors from the nematode Ascaris. In light of previous results demonstrating entry of Acp62F into the mated female's hemolymph, we propose that Acp62F is a candidate for a molecule to contribute to the Acp-dependent decrease in female life span. We propose that Acp62F's protease inhibitor activity exerts positive protective functions in the mated female's reproductive tract but that entry of a small amount of this protein into the female's hemolymph could contribute to the cost of mating.
Nakshatra: Towards Running Batch Analytics on an Archive (2014)

Long term retention of data has become a norm for reasons like compliance and data preservation for future needs. With storage media continuing to become cheaper, this trend has further strengthened and is testified with introduction of archival solutions like Amazon Glacier and Spectra Logic Black Pearl. On the other hand, analytics and big data have become key enablers for business and research. However, analytics and archiving happens on separate storage silos. This generates additional costs and inefficiencies when part of archived data needs to be analyzed using batch analytics platforms like Hadoop because a) We need additional storage for data transferred from archive to analytics tier and b) Transfer time costs are incurred due to data migration to analytics tier. Moreover, accessing archived data has high times to first byte, as much of the data is stored in offline media like tapes or spun down disks. We introduce Nakshatra, a data processing framework to run analytics directly on an archive based on offline media. To the best of our knowledge, this is the first work of its kind available in literature. We leverage batched pre-fetching and scheduling techniques for improved retrieval of data and scalable analytics on archives. Our preliminary evaluation shows Nakshatra to be upto 81% faster than the traditional ingest-then-compute workflow for archived data.
Photoactivated Luminescence Method for Rapid Screening of Polychlorinated Biphenyls (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotoactivated Luminescence Method for Rapid Screening of Polychlorinated BiphenylsT. Vo-Dinh, A. Pal, and T. PalCite this: Anal. Chem. 1994, 66, 8, 1264–1268Publication Date (Print):April 15, 1994Publication History Published online1 May 2002Published inissue 15 April 1994https://pubs.acs.org/doi/10.1021/ac00080a011https://doi.org/10.1021/ac00080a011research-articleACS PublicationsRequest reuse permissionsArticle Views158Altmetric-Citations12LEARN 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
Quantifier elimination via clause redundancy (2013)

We consider the problem of existential quantifier elimination for Boolean formulas in conjunctive normal form. Recently we presented a new method for solving this problem based on the machinery of Dependency sequents (D-sequents). The essence of this method is to add to the quantified formula implied clauses until all the clauses with quantified variables become redundant. A D-sequent is a record of the fact that a set of quantified variables is redundant in some subspace. In this paper, we introduce a quantifier elimination algorithm based on a new type of D-sequents called clause D-sequents that express redundancy of clauses rather than variables. Clause D-sequents significantly extend our ability to introduce and algorithmically exploit redundancy, as our experimental results show.
Alda‐1 shields mitochondrial dynamic proteins from hyperoxia via Aldh2 activation (2019)

Rationale Acute respiratory distress syndrome (ARDS) is associated with fluid filled lungs and hypoxia. Thus, ARDS patients are placed on supplemental oxygen; however, hyperoxia can damage the lungs, cause mitochondrial dysfunction, and ultimately lead to acute lung injury in animal models of ARDS. Mitochondrial aldehyde dehydrogenase 2 (Aldh2) metabolizes dangerous, reactive products, such as 4‐hydroxynonenal, that otherwise causes oxidative stress. The focus of this research is to determine if Alda‐1, an Aldh2 activator enhances the activity of Aldh2, thus alleviating hyperoxia damage by preventing mitochondrial dysfunction and reducing immune cell infiltration. It also determined if administration of Alda‐1 recovers mitochondrial dynamics and reduces cytokine levels and immune cell infiltration. Methods C57BL/6 mice were exposed to hyperoxia for 48 hours with DMSO (Control) and Alda‐1 (20 mM) via alzet pumps on the dorsal side of mice. The mice were divided into four groups: normoxia + DMSO (room air), normoxia + Alda‐1, hyperoxia + DMSO, and hyperoxia + Alda‐1. The lungs were harvested and the bronchoalveolar lavage (BAL) fluid was collected and analyzed by immunoblot and cytokine levels. Results Immunoblot analysis of lung lysate demonstrates that mice treated with Alda‐1, compared to mice treated with DMSO, during hyperoxia have decreased levels of OPA1 and Drp1, indicating that Alda‐1 shields against oxidative stress for proteins associated with mitochondrial dynamics. Moreover, the BAL fluid analysis reveals less infiltration of macrophages in mice treated with Alda‐1 versus mice treated with DMSO alone. These results indicate that activation of Aldh2 via Alda‐1 is protective against hyperoxia‐induced acute lung injury and may be a viable therapeutic agent for ARDS. Conclusion These findings suggest that Alda‐1, an Aldh2 activator, maintains mitochondrial homeostasis and reduces immune cell infiltration in this mouse model of ARDS and may be a novel therapeutic agent in ARDS. Support or Funding Information This work is supported by NIH RO1 grant (HL105932) to N.K. and AHA grant (#17SDG32780002) to L.G. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Genetic control of programmed cell death in the <i>Caenorhabditis</i> elegans hermaphrodite germline (1999)

Development of the nematode Caenorhabditis elegans is highly reproducible and the fate of every somatic cell has been reported. We describe here a previously uncharacterized cell fate in C. elegans: we show that germ cells, which in hermaphrodites can differentiate into sperm and oocytes, also undergo apoptotic cell death. In adult hermaphrodites, over 300 germ cells die, using the same apoptotic execution machinery (ced-3, ced-4 and ced-9) as the previously described 131 somatic cell deaths. However, this machinery is activated by a distinct pathway, as loss of egl-1 function, which inhibits somatic cell death, does not affect germ cell apoptosis. Germ cell death requires ras/MAPK pathway activation and is used to maintain germline homeostasis. We suggest that apoptosis eliminates excess germ cells that acted as nurse cells to provide cytoplasmic components to maturing oocytes.
Improving carbon capture from power plant emissions with zinc- and cobalt-based catalysts (2014)

A carbonic anhydrase mimic converting CO<sub>2</sub> to carbonic acid, deprotonated under highly basic conditions, and being converted to a carbamate upon reaction with monoethanolamine, a solvent reported for carbon capture reactions.
Protecting publicly-available images with an invisible image watermark (2002)

A method is presented for marking high-quality digital images with a robust and invisible watermark. A broad definition of robustness, stated as fundamental, is used. It requires the invisible mark to survive and remain detectable through all image manipulations that in themselves does not damage the image beyond useability. These manipulations include JPEG "lossy" compression and, in the extreme, the printing and rescanning of the image. The watermark is imparted onto an image as a random, bur reproducible, small modulation of its pixel brightnesses, and becomes a permanent part of the marked image. Detecting the imparted watermark, especially after image manipulation, is a daunting task. It is one of detecting the presence of a known small modulation of a random carrier where the carrier is composed of the pixel brightness values of the unmarked image. The method presented exploits the not well understood but superb ability of the human visual system to recognize a correlated pattern in a scatter diagram called a "visualizer-coincidence image." Results of application of the method are presented.
Comments on hybrid-polarity SAR architecture (2007)

Recent work on compact polarimetry is reviewed in the context of the fifty-year history of polarimetric diversity. One promising form of this genre is hybrid-polarity (CL-pol), in which a synthetic aperture radar (SAR) transmits circular polarization and receives on two orthogonal mutually-coherent linear polarizations. The CL-pol technique is compared and contrasted to alternative compact polarimetric schemes. Useful characteristics that are unique to the hybrid-polarity architecture are described, especially rotational invariance and polarimetric calibration.
Data from Phase I Hepatic Immunotherapy for Metastases Study of Intra-Arterial Chimeric Antigen Receptor–Modified T-cell Therapy for CEA<sup>+</sup> Liver Metastases (2023)

<div>Abstract<p><b>Purpose:</b> Chimeric antigen receptor–modified T cells (CAR-T) have demonstrated encouraging results in early-phase clinical trials. Successful adaptation of CAR-T technology for CEA-expressing adenocarcinoma liver metastases, a major cause of death in patients with gastrointestinal cancers, has yet to be achieved. We sought to test intrahepatic delivery of anti-CEA CAR-T through percutaneous hepatic artery infusions (HAIs).</p><p><b>Experimental Design:</b> We conducted a phase I trial to test HAI of CAR-T in patients with CEA<sup>+</sup> liver metastases. Six patients completed the protocol, and 3 received anti-CEA CAR-T HAIs alone in dose-escalation fashion (10<sup>8</sup>, 10<sup>9</sup>, and 10<sup>10</sup> cells). We treated an additional 3 patients with the maximum planned CAR-T HAI dose (10<sup>10</sup> cells × 3) along with systemic IL2 support.</p><p><b>Results:</b> Four patients had more than 10 liver metastases, and patients received a mean of 2.5 lines of conventional systemic therapy before enrollment. No patient suffered a grade 3 or 4 adverse event related to the CAR-T HAIs. One patient remains alive with stable disease at 23 months following CAR-T HAI, and 5 patients died of progressive disease. Among the patients in the cohort that received systemic IL2 support, CEA levels decreased 37% (range, 19%–48%) from baseline. Biopsies demonstrated an increase in liver metastasis necrosis or fibrosis in 4 of 6 patients. Elevated serum IFNγ levels correlated with IL2 administration and CEA decreases.</p><p><b>Conclusions:</b> We have demonstrated the safety of anti-CEA CAR-T HAIs with encouraging signals of clinical activity in a heavily pretreated population with large tumor burdens. Further clinical testing of CAR-T HAIs for liver metastases is warranted. <i>Clin Cancer Res; 21(14); 3149–59. ©2015 AACR</i>.</p></div>
Enhanced Antimicrobial Activity of Engineered Human Lysozyme (2010)

Lysozymes contain a disproportionately large fraction of cationic residues, and are thereby attracted toward the negatively charged surface of bacterial targets. Importantly, this conserved biophysical property may inhibit lysozyme antibacterial function during acute and chronic infections. A mouse model of acute pulmonary Pseudomonas aeruginosa infection demonstrated that anionic biopolymers accumulate to high concentrations in the infected lung, and the presence of these species correlates with decreased endogenous lysozyme activity. To develop antibacterial enzymes designed specifically to be used as antimicrobial agents in the infected airway, the electrostatic potential of human lysozyme (hLYS) was remodeled by protein engineering. A novel, high-throughput screen was implemented to functionally interrogate combinatorial libraries of charge-engineered hLYS proteins, and variants with improved bactericidal activity were isolated and characterized in detail. These studies illustrate a general mechanism by which polyanions inhibit lysozyme function, and they are the first direct demonstration that decreasing hLYS's net cationic character improves its antibacterial activity in the presence of disease-associated biopolymers. In addition to avoiding electrostatic sequestration, at least one charge-engineered variant also kills bacteria more rapidly in the absence of inhibitory biopolymers; this observation supports a novel hypothesis that tuning the cellular affinity of peptidoglycan hydrolases may be a general strategy for improving kinetics of bacterial killing.
Bacteriophage transfer during faecal microbiota transplantation in <i>Clostridium difficile</i> infection is associated with treatment outcome (2017)

NCT02570477.
Eine einfache und allgemeine Methode zur Herstellung von α-Disulfonen (R<sup>1</sup>SO<sub>2</sub>SO<sub>2</sub>R<sup>2</sup>) (1993)

A Facile and General Method for the Preparation of α-Disulfones (R1SO2SO2R2) Dialkyl, diaryl and alkyl aryl disulfones are easily prepared by oxidation of N,N′-disulfonylhydrazines with nitric acid. The method is compatible with a wide variety of substituents (R1,R2) on the sulfur atoms.
Dihydro‐1,3,5‐dithiazines: Unusual flavor compounds with remarkable organoleptic properties (1992)

Abstract 5,6‐Dihydro‐2,4,6‐trialkyl‐4H‐1,3,5‐dithiazines play an important role in food flavors and particularly in heated food products. They are formed from thermal interaction of aldehydes, hydrogen sulfide, and ammonia resulting from degradation components of lipids, amino acids, and thiamin. Many of them have interesting organo‐leptic properties and relatively low flavor threshold values, and deserve particular attention. This review describes all alkyl‐substituted and bicyclic 1,3,5‐dithiazines identified in the flavor of foodstuffs as well as in model systems. Furthermore, this review provides a general description of the sensory properties of 1,3,5‐dithiazines and additionally reports on new results and recent research developments in order to update information in the area of this hitherto almost overlooked chemical class of flavor compounds.
Synthetic Chromosome Platforms in Plants (2011)

Synthetic chromosomes provide the means to stack transgenes independently of the remainder of the genome. Combining them with haploid breeding could provide the means to transfer many transgenes more easily among varieties of the same species. The epigenetic nature of centromere formation complicates the production of synthetic chromosomes. However, telomere-mediated truncation coupled with the introduction of site-specific recombination cassettes has been used to produce minichromosomes consisting of little more than a centromere. Methods that have been developed to modify genes in vivo could be applied to minichromosomes to improve their utility and to continue to increase their length and genic content. Synthetic chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agricultural applications or to use plants as factories for the production of foreign proteins or metabolites.
Progress in large‐scale purification of factor VIII/von Willebrand factor concentrates using ion‐exchange chromatography (2008)

Several highly purified products, suitable for haemophilia A and von Willebrand disease management, can be obtained, through the same chromatographic process, on an industrial scale.