gebhart/patrepeval huggingface dataset:
A Single Point Mutation in ϵ-COP Results in Temperature-sensitive, Lethal Defects in Membrane Transport in a Chinese Hamster Ovary Cell Mutant (1996)

At the nonpermissive temperature of 39.5 degrees C, the Chinese hamster ovary cell conditionally lethal, temperature-sensitive (ts) mutant ldlF exhibits the following defects: rapid degradation of low density lipoprotein receptors, disruption of ER-through Golgi transport, and disintegration of the Golgi apparatus. All of these are corrected by transfection with an expression vector for wild-type epsilon-COP, a subunit of coatomers (Guo, Q., Vasile, E., and Krieger, M. (1994) J. Cell Biol. 125, 1213-1224). We now report the identification in ldlF cells of a point mutation in the epsilon-COP gene, Glu251 to Lys251, which prevents the corresponding cDNA from correcting the defects in transfected ldlF cells and the immunochemical analysis of the synthesis, structure, and stability of epsilon-COP. At the permissive temperature (34 degrees C), the steady state level of ts-epsilon-COP in ldlF cells was about half that of epsilon-COP in wild-type Chinese hamster ovary cells and the isoelectric point of ts-epsilon-COP was 0.14 pH units higher than that of the wild-type protein. The stability but not the biosynthesis of ts-epsilon-COP was temperature-sensitive (t1/2 > 6 h at 34 degrees C and approximately 1-2 h at 39.5 degrees C), and this accounts for the virtual absence of detectable ts-epsilon-COP protein in ldlF cells after incubation at 39.5 degrees C for > 6h. The steady state levels in ldlF cells of another coatomer subunit, beta-COP, and the peripheral Golgi protein ldlCp were not temperature-sensitive. Thus, a mutation in epsilon-COP that causes instability at 39.5 degrees C is responsible for all of the temperature-sensitive defects in ldlF cells, and the stability of beta-COP is not linked directly to that of epsilon-COP. ldlF cells should be useful for the future analysis of the structure and function of epsilon-COP, the assembly of COPs into coatomers, and the participation of coatomers in intracellular membrane transport.
Ultrafast Fluorescence Spectroscopy and Cell Imaging Techniques in Exploring the Caffeine Mediated Dissociation of Mutagen from Biomimetics, Nucleic Acids and Cells (2013)

3514-Pos Board B669 MdDQm Calculations Explore the Origins of Differences amongst the Red Fluorescent Proteins J. Nathan Scott1, Patrik R. Callis2. Saint Francis University, Loretto, PA, USA, Montana State University, Bozeman, MT, USA. We present a number of theoretical results concerning the properties of and differences amongst several red fluorescent proteins (RFPs). RFPs are an extraordinarily useful group of fluorescent proteins that fluoresce at red-shifted wavelengths compared to GFP, thereby extending the color palette of fluorescent proteins for use in applications like FRET and multi-channel imaging. This redder fluorescence is caused by the extension of the pi-conjugated chain through oxidation of a second backbone bond of either Phenylalanine or Isoleucine, depending on the particular RFP. Our work has focused on the RFPs mCherry, mPlum, and DsRed, which share a common chromophore. Since these RFPs share a chromophore, differences in their photophysical properties must be due to differences in their chromophore environments. We performed a series of 100 ns molecular dynamics simulations followed by ZINDO semiempirical quantum mechanical calculations in an effort to explore variables such as excitation wavelength, quantum yield, and photostability in these RFPs. The ZINDO calculations were performed on MD simulation frames at 1 ps resolution. This fine resolution allowed for the observation of rare conformational states that suggest reasons for the known differences in quantum yield amongst the proteins. Notably, the electric field contributions from every nonchromophore protein atom and ion, and the ~14,000 simulation cell water molecules, were used as a perturbation in the ZINDO calculations, which allowed us to query the electrostatic environmental influence on the chromophore.
A brief review of techniques used to estimate radiated seismic energy (2006)

This chapter contains sections titled: Introduction Basic Formulation Different Techniques Used to Estimate Radiated Energy Other Macroscopic Measurements Conclusions
Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections (2023)

The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.
Highly reliable and cost effective thick film substrates for power LEDs (2016)

This paper presents Thick Printed Copper (TPC) as substrate technology for High Brightness LEDs, which features a strongly improved reliability combined with a significant cost advantage over incumbent technologies for High Brightness LED substrates. The advantages of TPC over Direct Bonded Copper (DBC) and Direct Plated Copper (DPC) substrates will be demonstrated by thermal shock test results and a demonstration of the versatile design options. The good thermal performance of TPC is demonstrated by comparative Finite Element Modelling of TPC and DBC substrates. A detailed review is given discussing the different copper to ceramic bonding mechanisms, which prevent void formation and are responsible for the excellent thermo-mechanical reliability.
A REVIEW of PARTICLE BEHAVIOR IN TUBE FLOW: APPLICATIONS to ASEPTIC PROCESSING1 (1987)

ABSTRACT The design of holding tubes for continuous sterilization of foods containing large particulates depends heavily on knowledge of pipe flow behavior of food suspensions. Although directly related literature is limited, a considerable body of potentially useful literature is available on solid‐liquid flows. This critical review discusses literature on solid‐liquid flow in tubes, including capsule flow, effects on bends, radial migration phenomena, particle‐particle interactions, modeling studies and other topics which may have a bearing on particle velocities in holding tubes.
JPEG recompression detection (2010)

Re-quantization commonly occurs when digital multimedia content is being tampered with. Detecting requantization is therefore an important element for assessing the authenticity of digital multimedia content. In this paper, we introduce three features based on the observation that re-quantization (i) induces periodic artifacts and (ii) introduces discontinuities in the signal histogram. After validating the discriminative potential of these features with synthetic signals, we propose a system to detect JPEG re-compression. Both linear (FLD) and non-linear (SVM) classifications are investigated. Experimental results clearly demonstrate the ability of the proposed features to detect JPEG re-compression, as well as their competitiveness compared to prior approaches to achieve the same goal.
Inhibition of Fatty Acid Amide Hydrolase: A Potential Treatment for Neuropathic Pain: Figure 1. (2007)

There are limited treatment options for neuropathic pain, a debilitating condition characterized by pain hypersensitivity. There is, however, growing interest in cannabinoids because CB1- and CB2-receptor agonists are analgesic in acute and chronic pain, and increases in endogenous cannabinoids are
Product Codes for Data Storage on Magnetic Tape (2016)

For 2-D product codes used in tape storage, the mapping of error-correction-coding (ECC) blocks (EBs) into 2-D physical blocks (PBs) on magnetic tape is generalized. The 3-D product codes that have the same code rate and EB size as interleaved 2-D product codes currently used in tape storage are proposed. For 3-D product codes, a new family of mappings of EBs into 2-D PBs on magnetic tape is introduced, which fulfills the stringent burst-error-correction requirements of tape storage. The burst-error-correction capability of 2-D and 3-D product code words recorded on magnetic tape is analyzed as a function of track rotation, linear density, and ECC parameters. The performance limits of the tape-storage channel are determined based on computations of channel capacity and random coding bound. Hardware simulations of iterative hard-decision decoding of product codes implemented in a field-programmable gate array demonstrate the improved error-rate performance of 3-D product codes over 2-D product codes.
Data from The High-Mobility Group A1 Gene Up-Regulates Cyclooxygenase 2 Expression in Uterine Tumorigenesis (2023)

&lt;div&gt;Abstract&lt;p&gt;Uterine cancer is the most common cancer of the female genital tract and is the fourth most frequent cause of cancer death in women in the U.S. Despite the high prevalence of uterine cancers, the molecular events that lead to neoplastic transformation in the uterus are poorly understood. Moreover, there are limited mouse models to study these malignancies. We generated transgenic mice with high-mobility group A1 gene (&lt;i&gt;HMGA1a&lt;/i&gt;) expression targeted to uterine tissue and all female mice developed tumors by 9 months of age. Histopathologically, the tumors resemble human uterine adenosarcoma and are transplantable. To determine whether these findings are relevant to human disease, we evaluated primary human uterine neoplasms and found that &lt;i&gt;HMGA1a&lt;/i&gt; mRNA and protein levels are increased in most high-grade neoplasms but not in normal uterine tissue, benign tumors, or most low-grade neoplasms. We also found that HMGA1a up-regulates &lt;i&gt;cyclooxygenase 2 (COX-2)&lt;/i&gt; expression in transgenic tumors. Moreover, both &lt;i&gt;HMGA1a&lt;/i&gt; and COX-2 expression are up-regulated in high-grade human leiomyosarcomas. Using chromatin immunoprecipitation, HMGA1a binds directly to the &lt;i&gt;COX-2&lt;/i&gt; promoter in human uterine cancer cells &lt;i&gt;in vivo&lt;/i&gt; and activates its expression in transfection experiments. We also show that blocking either &lt;i&gt;HMGA1a&lt;/i&gt; or COX-2 in high-grade human uterine cancer cells blocks anchorage-independent cell growth in methylcellulose. These findings show that &lt;i&gt;HMGA1a&lt;/i&gt; functions as an oncogene when overexpressed in the uterus and contributes to the pathogenesis of human uterine cancer by activating &lt;i&gt;COX-2&lt;/i&gt; expression. Although a larger study is needed to confirm these results, &lt;i&gt;HMGA1a&lt;/i&gt; may be a useful marker for aggressive human uterine cancers. [Cancer Res 2007;67(9):3998–4004]&lt;/p&gt;&lt;/div&gt;
Probing the Structure and Chemistry of Perylenetetracarboxylic Dianhydride on Graphene Before and After Atomic Layer Deposition of Alumina (2012)

The superlative electronic properties of graphene suggest its use as the foundation of next generation integrated circuits. However, this application requires precise control of the interface between graphene and other materials, especially the metal oxides that are commonly used as gate dielectrics. Towards that end, organic seeding layers have been empirically shown to seed ultrathin dielectric growth on graphene via atomic layer deposition (ALD), although the underlying chemical mechanisms and structural details of the molecule/dielectric interface remain unknown. Here, confocal resonance Raman spectroscopy is employed to quantify the structure and chemistry of monolayers of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on graphene before and after deposition of alumina with the ALD precursors trimethyl aluminum (TMA) and water. Photoluminescence measurements provide further insight into the details of the growth mechanism, including the transition between layer-by-layer growth and island formation. Overall, these results reveal that PTCDA is not consumed during ALD, thereby preserving a well-defined and passivating organic interface between graphene and deposited dielectric thin films.
Sequence of visual cortex stimulation affects phosphene brightness in blind subjects (2022)

We showed evidence of temporal interactions in non-overlapping sequences of electrodes, where the direction of the effect was subject specific but consistent across a variety of electrode locations and current amplitude levels.
ChemInform Abstract: A Mild and Selective Method for the Cleavage of tert‐Butyl Esters. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Food allergy: is prevalence increasing? (2017)

It is generally accepted that the prevalence of food allergy has been increasing in recent decades, particularly in westernised countries, yet high-quality evidence that is based on challenge confirmed diagnosis of food allergy to support this assumption is lacking because of the high cost and potential risks associated with conducting food challenges in large populations. Accepting this caveat, the use of surrogate markers for diagnosis of food allergy (such as nationwide data on hospital admissions for food anaphylaxis or clinical history in combination with allergen-specific IgE (sIgE) measurement in population-based cohorts) has provided consistent evidence for increasing prevalence of food allergy at least in western countries, such as the UK, United States and Australia. Recent reports that children of East Asian or African ethnicity who are raised in a western environment (Australia and United States respectively) have an increased risk of developing food allergy compared with resident Caucasian children suggest that food allergy might also increase across Asian and African countries as their economies grow and populations adopt a more westernised lifestyle. Given that many cases of food allergy persist, mathematical principles would predict a continued increase in food allergy prevalence in the short to medium term until such time as an effective treatment is identified to allow the rate of disease resolution to be equal to or greater than the rate of new cases.
Recombinant Expression of ABCC2 Variants Confirms the Importance of Mutations in Extracellular Loop 4 for Cry1F Resistance in Fall Armyworm (2022)

Fall armyworm (FAW), <i>Spodoptera frugiperda</i>, is a highly destructive and invasive global noctuid pest. Its control is based on insecticide applications and <i>Bacillus thuringiensis</i> (Bt) insecticidal Cry toxins expressed in transgenic crops, such as Cry1F in Bt corn. Continuous selection pressure has resulted in populations that are resistant to Bt corn, particularly in Brazil. FAW resistance to Cry1F was recently shown to be conferred by mutations of ATP-binding cassette transporter C2 (ABCC2), but several mutations, particularly indels in extracellular loop 4 (ECL4), are not yet functionally validated. We addressed this knowledge gap by baculovirus-free insect cell expression of ABCC2 variants (and ABCC3) by electroporation technology and tested their response to Cry1F, Cry1A.105 and Cry1Ab. We employed a SYTOX<sup>TM</sup> orange cell viability test measuring ABCC2-mediated Bt toxin pore formation. In total, we tested seven different FAW ABCC2 variants mutated in ECL4, two mutants modified in nucleotide binding domain (NBD) 2, including a deletion mutant lacking NBD2, and <i>S. frugiperda</i> ABCC3. All tested ECL4 mutations conferred high resistance to Cry1F, but much less to Cry1A.105 and Cry1Ab, whereas mutations in NBD2 hardly affected Bt toxin activity. Our study confirms the importance of indels in ECL4 for Cry1F resistance in <i>S. frugiperda</i> ABCC2.
Enhanced Decomposition of Ammonium Perchlorate–Ethyl Cellulose–Molybdenum Disulfide Nanocomposites (2023)

Ammonium perchlorate (AP) is commonly used in propulsion technology. Recent studies have demonstrated that two-dimensional (2D) nanomaterials such as graphene (Gr) and hexagonal boron nitride (hBN) dispersed with nitrocellulose (NC) can conformally coat the surface of AP particles and enhance the reactivity of AP. In this work, the effectiveness of ethyl cellulose (EC) as an alternative to NC was studied. Using a similar encapsulation procedure as in recent work, Gr and hBN dispersed with EC were used to synthesize the composite materials Gr-EC-AP and hBN-EC-AP. Additionally, EC was used because the polymer can be used to disperse other 2D nanomaterials, specifically molybdenum disulfide (MoS<sub>2</sub>), which has semiconducting properties. While Gr and hBN dispersed in EC had a minimal effect on the reactivity of AP, MoS<sub>2</sub> dispersed in EC significantly enhanced the decomposition behavior of AP compared to the control and other 2D nanomaterials, as evidenced by a pronounced low-temperature decomposition event (LTD) centered at 300 °C and then complete high-temperature decomposition (HTD) below 400 °C. Moreover, thermogravimetric analysis (TGA) showed a 5% mass loss temperature (<i>T</i><sub>d5%</sub>) of 291 °C for the MoS<sub>2</sub>-coated AP, which was 17 °C lower than the AP control. The kinetic parameters for the three encapsulated AP samples were calculated using the Kissinger equation and confirmed a lower activation energy pathway for the MoS<sub>2</sub> (86 kJ/mol) composite compared to pure AP (137 kJ/mol). This unique behavior of MoS<sub>2</sub> is likely due to enhanced oxidation-reduction of AP during the initial stages of the reaction via a transition metal-catalyzed pathway. Density functional theory (DFT) calculations showed that the interactions between AP and MoS<sub>2</sub> were stronger than AP on the Gr or hBN surfaces. Overall, this study complements previous work on NC-wrapped AP composites and demonstrates the unique roles of the disperagent and 2D nanomaterial in tuning the thermal decomposition of AP.
Genomic Diversity of Lactobacillus salivarius (2010)

Strains of Lactobacillus salivarius are increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity of L. salivarius has been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals. L. salivarius displays a high level of genomic diversity, and while selection of L. salivarius strains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits.
Toward augmented UHF RFID passive tags (2015)

The requirement of new functions for smart tags in the Internet of Things (IoT) deployment has raised the need of additional sources of energy. Among the possible energy sources, the natural or ecologic sources such as solar, motion, human body are of first interest. Another relevant approach is the use of wasted electromagnetic energy that can constitute a suitable powering source for low power consumption devices. Indeed, as it had demonstrated in practice the minimum required power to turn on UHF passive tags is the order of 10µW and several natural or green physical effects can provide much more power. In this context, the technology that best suits the requirements of enhanced functions and additional energy is the passive RFID technology, also due to its Wireless Power Transmission (WPT) operation. Therefore, in a society leaded by the information and networking, a link is defined between our real world and a virtual scenery for all the everyday objects. The linker device used in this paper is an RFID tag, that besides the identification function, it offers to enhance its powering and operation performances in applications such as sensing, authentication or location.
Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants (2021)

The emergence of SARS-CoV-2 variants that threaten the efficacy of existing vaccines and therapeutic antibodies underscores the urgent need for new antibody-based tools that potently neutralize variants by targeting multiple sites of the spike protein. We isolated 216 monoclonal antibodies targeting SARS-CoV-2 from plasmablasts and memory B cells of COVID-19 patients. The three most potent antibodies targeted distinct regions of the RBD, and all three neutralized the SARS-CoV-2 variants B.1.1.7 and B.1.351. The crystal structure of the most potent antibody, CV503, revealed that it binds to the ridge region of SARS-CoV-2 RBD, competes with the ACE2 receptor, and has limited contact with key variant residues K417, E484 and N501. We designed bispecific antibodies by combining non-overlapping specificities and identified five ultrapotent bispecific antibodies that inhibit authentic SARS-CoV-2 infection at concentrations of <1 ng/mL. Through a novel mode of action three bispecific antibodies cross-linked adjacent spike proteins using dual NTD/RBD specificities. One bispecific antibody was >100-fold more potent than a cocktail of its parent monoclonals <i>in vitro</i> and prevented clinical disease in a hamster model at a 2.5 mg/kg dose. Notably, six of nine bispecific antibodies neutralized B.1.1.7, B.1.351 and the wild-type virus with comparable potency, despite partial or complete loss of activity of at least one parent monoclonal antibody against B.1.351. Furthermore, a bispecific antibody that neutralized B.1.351 protected against SARS-CoV-2 expressing the crucial E484K mutation in the hamster model. Thus, bispecific antibodies represent a promising next-generation countermeasure against SARS-CoV-2 variants of concern.