gebhart/patrepeval huggingface dataset:
Recycling of DNA Polymerases at the Replication Fork of Bacteriophage T7 (2007)

T7 gene 5 protein (gp5) is distributive DNA polymerase. When bound to its processivity factor, Escherichia coli thioredoxin (trx), its processivity is increased from few nucleotides to few hundreds of nucleotides. In the presence of the T7 gene 4 helicase (gp4), the processivity of gp5/trx on duplex DNA increases to thousands of nucleotides. During such processive DNA synthesis on duplex DNA we find that DNA polymerase in solution can exchange with the active DNA polymerase via a mechanism that does not affect either the rate or processivity of replisome. In these studies we have made use of a T7 gp5 in which tyrosine 526 is replaced with phenylalanine (gp5‐Y526F). The altered polymerase discriminates against the chain terminating dideoxynucleotides thus providing a probe for the exchange reaction. Using a genetically altered gp5/trx that can not interact with the C‐terminus of the helicase we show that the exchange of polymerase is mediated by the interaction of polymerases for solution with gp4. We postulate that the hexameric gp4 not only stabilizes the polymerase at the replication fork but that it also serves as a reservoir for DNA polymerases in the event that the functioning polymerase dissociates.
Isolation and Function of Allophycocyanin B of Porphyridium cruentum (1977)

Allophycocyanin B was purified to homogeneity from the eukaryotic red alga Porphyridium cruentum. This biliprotein is distinct from the allophycocyanin of P. cruentum with respect to subunit molecular weights, and spectroscopic and immunological properties. The purified allophycocyanin B has a long wavelength absorption maximum at 669 nm at room temperature and at 675 nm at -196 C while the fluorescence emission maximum is at 673 nm at room temperature and 679 nm at -196 C. The emission spectrum of allophycocyanin shifted only 1 nm, from 659 to 660 nm, on cooling to -196 C, and was the same with allophycocyanin crystals as it was with pure solutions of the pigment. Phycobilisomes from P. cruentum have a major fluorescence emission band at 680 nm at -196 C which emanates from the small amount of allophycocyanin B present in the phycobilisomes. Light energy absorbed by the bulk of the biliprotein pigments is transferred to allophycocyanin B with high efficiency.
Hermansky-Pudlak syndrome-2 alters mitochondrial homeostasis in the alveolar epithelium of the lung (2021)

In summary, our findings indicate that mitochondrial function is dramatically altered in HPS-2 lung tissues, suggesting dysfunction of this organelle might be a driver of HPS lung disease.
Accuracy of the CoaguChek XS for point-of-care international normalized ratio (INR) measurement in children requiring warfarin (2008)

Point-of-care INR (POC INR) meters can provide a safe and effective method for monitoring oral vitamin K antagonists (VKAs) in children. Stollery Children's Hospital has a large POC INR meter loan program for children requiring oral VKAs. Our protocol requires that POC INR results be compared to the standard laboratory INR for each child on several consecutive tests to ensure accuracy of CoaguChek XS (Roche Diagnostics, Basel Switzerland) meter. It was the objective of the study to determine the accuracy of the CoaguChek XS by comparing whole blood INR results from the CoaguChek XS to plasma INR results from the standard laboratory in children. POC INR meter validations were performed on plasma samples from two time points from 62 children receiving warfarin by drawing a venous blood sample for laboratory prothrombin (PT)-INR measurements and simultaneous INR determinations using the POC-INR meter. Agreement between CoaguChek XS INR and laboratory INR was assessed using Bland-Altman plots. Bland-Altman's 95% limits of agreement were 0.11 (-0.20; 0.42) and 0.13 (-0.22; 0.48) at the two time points, respectively. In conclusion, the CoaguChek XS meter appraisal generates an accurate and precise INR measure in children when compared to laboratory INR test results.
WE‐C‐224C‐04: Correlated Sampling for Accelerating CT‐Based Monte Carlo Dose Calculations for Brachytherapy Treatment Planning (2006)

Purpose: To investigate the potential of correlated sampling variance reduction technique for accelerating CT‐based Monte Carlo (MC) simulations for calculating 3D brachytherapy dose distributions. Method and Materials: Correlated MC (CMC) simulations generate photon histories in the homogeneous geometry. By recomputing particle weights to account for non‐water composition of the CT voxels and applicator and seed components, a second highly correlated set of histories is constructed, resulting in a lower variance estimate of the dose difference, ΔD=D het ‐D hom To evaluate the accuracy and efficiency of CMC, a clinical permanent prostate implant with 78 I‐125 seeds was simulated using both CMC and UMC versions of our accelerated CT‐based MC dose‐computation code, PTRAN_CT for voxel sizes ranging from 1×1×1mm 3 to 2×2×2mm 3 . Mean efficiency gains were estimated for regions with minimum doses greater than 20%, 50% and 90% of D 90 , as well as different anatomical regions. Results: Systematic differences between UMC and CMC PTRAN_CT were less than 0.4%. Efficiency gains ranged from 4.68 to 15.76 depending on the voxel size and region. CMC can achieve a 2% average precision with 2 mm cubic voxels in 23 seconds on a single P4 processor for voxels with doses &gt; 50%D 90 . Voxels with very low doses and/or large dose perturbations can experience efficiency losses. Because ΔD is a relatively smoothly varying quantity compared to D het , CMC efficiency maybe enhanced using coarser voxel sizes than UMC for the same level of volume‐averaging artifact. Conclusion: Correlated sampling MC can reduce CPU times by an additional 4–15 fold compared to accelerated uncorrelated MC. In practice, larger efficiency enhancements can be achieved because correlated sampling volume‐averaging errors are smaller. MC‐based brachytherapy treatment planning, requiring only a few seconds of CPU time, is achievable. (Supported by NIH‐R01CA46640).
Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2 (2023)

COVID-19 has stimulated the rapid development of new antibody and small molecule therapeutics to inhibit SARS-CoV-2 infection. Here we describe a third antiviral modality that combines the drug-like advantages of both. Bicycles are entropically constrained peptides stabilized by a central chemical scaffold into a bi-cyclic structure. Rapid screening of diverse bacteriophage libraries against SARS-CoV-2 Spike yielded unique Bicycle binders across the entire protein. Exploiting Bicycles' inherent chemical combinability, we converted early micromolar hits into nanomolar viral inhibitors through simple multimerization. We also show how combining Bicycles against different epitopes into a single biparatopic agent allows Spike from diverse variants of concern (VoC) to be targeted (Alpha, Beta, Delta and Omicron). Finally, we demonstrate in both male hACE2-transgenic mice and Syrian golden hamsters that both multimerized and biparatopic Bicycles reduce viraemia and prevent host inflammation. These results introduce Bicycles as a potential antiviral modality to tackle new and rapidly evolving viruses.
Methods for applying microchannels to separate methane using liquid absorbents, especially ionic liquid absorbents from a mixture comprising methane and nitrogen (2023)

Methods of using microchannel separation systems including absorbents to improve thermal efficiency and reduce parasitic power loss. Energy is typically added to desorb methane and then energy or heat is removed to absorb methane using a working solution. The working solution or absorbent may comprise an ionic liquid, or other fluids that demonstrate a difference in affinity between methane and nitrogen in a solution.
Analysis of short circuit current loss in rear emitter crystalline Si solar cell (2016)

Short circuit current (Jsc) loss in rear emitter crystalline Si solar cell is analyzed in detail by a 2D device simulation and compared with the experimental results. There is a significant loss in Jsc for the rear emitter n-Si solar cell with an n-type doped front surface field (FSF) when the base substrate resistivity is low. It is due to an increase in recombination in the FSF region led by a less barrier height for minority carriers with a lower substrate resistivity. The barrier height less than 0.1 eV causes large loss in Jsc. To achieve higher Jsc for the cells with FSF, the control of the doping concentration in FSF, the substrate thickness, and the barrier height for the minority carriers are important. A rear emitter heterojunction Si solar cell with an amorphous Si passivation layer shows no substrate resistivity dependence on Jsc since an amorphous Si possess a higher barrier height and a long bulk lifetime of more than a few milliseconds.
SPI - a system model for heterogeneously specified embedded systems (2002)

Embedded systems typically include reactive and transformative functions, often described in different languages and semantics which are well established in their respective application domains. Additionally, a large part of the system functionality and components is reused from previous designs including legacy code. There is little hope that a single language will replace this heterogeneous set of languages. A design process must be able to bridge the semantic differences for verification and synthesis and should account for limited knowledge of system properties. This paper presents the system property intervals (SPI) model, which employs behavioral intervals and process modes to allow the common representation of different languages and semantics. This model is the basis of a workbench which is targeted at the design of heterogeneously specified embedded systems.
Effect of diet on cognitive function and gut microbiota (2022)

Abstract Background Alterations in the gut microbiota have been observed in patients with mild cognitive impairment and Alzheimer’s disease. Dietary consumption directly modulates gut microbiota; therefore, the quality of a diet may impact cognitive function and susceptibility to dementia. We hypothesized that consumption of the nutrient dense Mediterranean diet (MeDi) would improve cognitive function through beneficial changes to the gut microbiota as compared to the diet primarily consumed by Americans, the Western diet (WD). Method Ten‐week‐old Sprague Dawley male rats were assigned a MeDi (n = 10) or WD (n = 9). After three months, Morris water maze (MWM) was used to assess spatial reference memory cognition. MWM data were analyzed with two‐way RM ANOVA. Fecal samples were collected prior to the MWM. Microbial composition was determined by 16S rRNA sequencing, and analyses included Mann‐Whitney with false discovery rate. Result The MeDi group also spent significantly more time in the target quadrant during probe testing (p = 0.03) and was quicker to reach the platform on reversal testing (p = 0.004), indicative of improved cognitive flexibility. Microbiota α‐diversity indices, Shannon (p = 0.053), Simpson (p = 0.054), and Chao1 (p = 0.056), had a trend to be increased in the MeDi. Microbiota β‐diversity was dissimilar between diets (p&lt;0.001). At the phylum level, Actinobacteria decreased and Patescibacteria increased with consumption of the MeDi as compared to the WD. Actinobacteria relative abundance correlated with MWM time in target quadrant (r = ‐0.58, p = 0.009). Further, relative abundance of Actinobacteria and Patescibacteria correlated with MWM reversal distance to reach platform (Actinobacteria, r = 0.77, p = 0.0001; Patescibacteria, r = ‐0.59, p = 0.007). Conclusion The MeDi maintained long‐term spatial memory, as measured by the MWM, compared to the WD. Additionally, diet‐modulated gut microbiota at the phylum level and these changes were correlated with cognitive function. Modulation of the gut microbiota through a neuroprotective diet, such as the MeDi, may serve as a method to improve cognitive function.
Nanoscale Ferroelectrics (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
An autonomous electronics system for ultrasound energy transfer and passive communication (2022)

Ultrasound is a promising method for powering of implants. It allows to transfer energy in a focused way, which leads to high efficiency and allows reaching implants deeply embedded in tissue. In addition, ultrasound can be used for communication with implants. In the present work, we developed a system combining energy transfer with a passive communication scheme based on modulating the backscattered signal amplitude. Using a receive transducer of 5 mm in radius and a 2-element 16 mm transmit aperture, up to 7 mW could be transferred, which was enough to power an LED and a circuit allowing encoding the optical sensor readout (photocurrent) into the backscatter information. By means of load modulation, amplitude variations of the backscattered signal until 35% were possible.
A role for tracheal resonances in speech perception (2005)

Acoustic coupling between the vocal tract and the trachea results in the introduction of pole-zero pairs corresponding to resonances of the uncoupled trachea. If the second formant (F2) passes through the second tracheal resonance (T2) a discontinuity in amplitude occurs. This work explores the hypothesis that the F2−T2 discontinuity affects how listeners perceive the distinctive feature [back] in transitions from a front vowel (high F2) to a labial stop (low F2). We synthesized two versions of an utterance (‘‘apter’’) with an F2−T2 discontinuity at different locations in the initial VC transition. Subjects heard portions of the utterance with and without the discontinuity, and were asked to identify the utterance. Results show that the presence of the F2−T2 discontinuity facilitated the perception of frontness in the vowel. Discontinuities of the F2−T2 sort are proposed to play a role in shaping vowel inventories in the world’s languages [K. N. Stevens, J. Phonetics 17, 3–46 (1989)]. Our results support a model of lexical access in which acoustic discontinuities subserve phonological feature identification.
Supplementary Table 1 from Multifactorial T-cell Hypofunction That Is Reversible Can Limit the Efficacy of Chimeric Antigen Receptor–Transduced Human T cells in Solid Tumors (2023)

&lt;p&gt;PDF file - 38K, CAR TILs upregulate inhibitory receptors.&lt;/p&gt;
Helix formation by the phospholipase A2 38–59 fragment: Influence of chain shortening and dimerization monitored by nmr chemical shifts (1994)

The solution structure of a peptide fragment corresponding to the 38-59 region of porcine phospholipase A2 has been investigated using CD, nmr chemical shifts, and nuclear overhauser effects (NOEs). This isolated fragment of phospholipase forms an alpha-helix spanning residues 38-55, very similar to the one found in the native protein, except for residues 56-58, which were helical in the crystal but found random in solution. Addition of triflouroethanol (TFE) merely increased helix population but it did not redefine helix limits. To investigate how the folding information, in particular that concerning eventual helix start and stop signals, was coded in this particular amino acid sequence, the helices formed by synthetic peptides reproducing sections of this phospholipase 38-59 fragment, namely 40-59, 42-59, 38-50, and 45-57, were characterized using NOEs and helix populations quantitatively evaluated on different peptide chain segments using nmr chemical shifts in two solvents (H2O and 30% TFE/H2O). A set of nmr spectra was also recorded and assigned under denaturing conditions (6M urea) to obtain reliable values for the chemical shifts of each peptide in the random state. Based on chemical shift data, it was concluded that the helix formed by the phospholipase 38-59 fragment was not abruptly, but progressively, destabilized all along its length by successive elimination of residues at the N end, while the removal of residues at the C end affected helix stability more locally and to a lesser extent. These results are consistent with the idea that there are not single residues responsible for helix initiation or helix stability, and they also evidence an asymmetry for contributions to helix stability by residues located at the two chain ends. The restriction of molecular mobility caused by linking with a disulphide bridge at Cys 51 two identical 38-59 peptide chains did not increase helix stability. The helix formed by the covalently formed homodimer was very similar in length and population to that formed by the monomer.
Electrical Frequency Multiplexing for High Symbol Rate Generation (2018)

We review the design and implementation of a digital-band-interleaved (DBI) digital-to-analog converter (DAC). We show the experimental generation of up to 1.6 Tb/s per wavelength using two synchronized 100-GHz DBI-DACs.
Machine contouring: reading between the lines (1987)

The wide availability of microcomputers and inexpensive software has encouraged geologists to use contouring programs. These programs are generally based on interpolation techniques that include inverse distance, gradient projection, polynomial fit, and triangulation. Most programs produce in contour patterns that are highly at variance to the real data and can lead to very serious and expensive mistakes. As an example, algorithms were tested on simple known geometric surfaces: inclined, unimodal, bimodal, and faulted. Surfaces were sampled using different sampling techniques: equally spaced, linear point, random, and clustered. In most cases, results showed false structural variations such as closure, nosing, and structure orientations which were erroneous. Better maps were produced with extensive manipulations of key parameters including grid size and weighting exponents. When a priori knowledge of the surface is not known, as with real data, results indicate that in some cases satisfactory contouring can be generated using the above-described surfaces as surrogate mapping horizons sampled by the real data array. In this way, values for key parameters can be estimated prior to mapping the real data. Although this method offers no guarantees, it does tend to eliminate artifacts imposed on a surface by the algorithm. Unless extreme caution is exercisedmore » when using machine contouring algorithms or better algorithms become available, one should rely on the hand contouring methods of an experienced geologist when important economic decisions are at stake.« less
ChemInform Abstract: Frontiers and Opportunities in Chemoenzymatic Synthesis. (2010)

Abstract Review: 65 refs.
A Novel Target for Migraine Therapy: the α6 Subunit-Containing GABA<sub>A</sub> Receptor (2018)

The α6 subunit-containing GABAA receptors (α6GABAARs) are mainly expressed in the cerebellum but also in trigeminal ganglia (TG), the hub of the trigeminal vascular system (TGVS). TGVS activation is a hallmark of the pathogenesis of migraine, which remains an unmet medical need with a high prevalence. Here, using pharmacological approaches in a migraine-mimicking animal model, we revealed an important role of the TG α6GABAARs in TGVS activation and this GABAAR subtype may be a druggable target for migraine therapy. TGVS activation was induced by intra-cisternal (i.c.) instillation of capsaicin in rats. Centrally, i.c.capsaicin activated the trigeminal cervical complex (TCC), which can be measured by the increased number of c-Fos-immunoreactive (c-Fos-ir) TCC neurons. Peripherally, it elevated calcitonin gene-related peptide immunoreactivity (CGRP-ir) in TG and depleted CGRP-ir in the dura mater. Pharmacological approaches included using a recently identified α6GABAAR-selective positive allosteric modulator (PAM), the pyrazoloquinolinone Compound 6, two α6GABAAR-active PAMs (Ro15-4513 and loreclezole), an α6GABAAR inactive benzodiazepine (diazepam), an α6GABAAR-selective antagonist (furosemide), and a clinically effective antimigraine agent (topiramate). We examined effects of these agents and their interactions with furosemide on both central and peripheral TGVS responses induced by i.c. capsaicin. Compound 6 (3-10 mg/kg, i.p.) significantly attenuated the TCC neuronal activation and TG CGRP-ir elevation, and dural CGRP depletion induced by capsaicin. All these effects of Compound 6 were mimicked by Ro15-4513, loreclezole and topiramate, but not diazepam. The brain-impermeable furosemide antagonized the peripheral, but not central, effects of Compound 6. These results suggest that the α6GABAAR in TG is a novel target for inhibiting TGVS activation and hence α6GABAAR-selective PAMs may be a potential anti-migraine pharmacotherapy.
T1 corrected B1 mapping using multi‐TR gradient echo sequences (2010)

This work presents a new approach toward a fast, simultaneous amplitude of radiofrequency field (B(1)) and T(1) mapping technique. The new method is based on the "actual flip angle imaging" (AFI) sequence. However, the single pulse repetition time (TR) pair used in the standard AFI sequence is replaced by multiple pulse repetition time sets. The resulting method was called "multiple TR B(1)/T(1) mapping" (MTM). In this study, MTM was investigated and compared to standard AFI in simulations and experiments. Feasibility and reliability of MTM were proven in phantom and in vivo experiments. Error propagation theory was applied to identify optimal sequence parameters and to facilitate a systematic noise comparison to standard AFI. In terms of accuracy and signal-to-noise ratio, the presented method outperforms standard AFI B(1) mapping over a wide range of T(1). Finally, the capability of MTM to determine T(1) was analyzed qualitatively and quantitatively, yielding good agreement with reference measurements.
Panel - Domain Analysis: From Tar Pit Extraction to Object Mania? (1996)

Domain Analysis has been researched, debated, and applied for fifteen years. There are many documented methods available. The collective heritage of these methods covers the spectrum from the procedurally-oriented to the object-oriented paradigms. Application focus includes re-engineering (tar pit extraction?), requirements engineering, organizational learning, reuse, class/object identification, and design pattern identification (object mania?). This panel brings together perspectives on domain analysis by five practitioner methodologists. Diverse experiences including technology insertion, stakeholder analysis, and team techniques are represented. The intent is to focus on the application of domain analysis methods. The objective of the panel is to share the experiences of the participants (both panelists and audience) and to offer practical advice.
Aortic Intima-Media Thickness is Increased in Neonates of Mothers withGestational Diabetes Mellitus: The Role of Thioredoxin-InteractingProtein as a Marker of Oxidative Stress (2023)

Increased aIMT was demonstrated in the offspring of mothers with GDM. Non-invasive measurement of aIMT could be used as a biomarker to identify children at increased risk for atherogenesis later in life. This information may encourage early preventive measures. TXNIP may be associated with GDM and/or aIMT.
Demonstration of full system reaches of 100G SR4, 40G sWDM, and 100G CWDM4 transmissions over universal fiber (2016)

A universal fiber was fabricated to have reduced coupling loss with conventional multimode fiber. We demonstrated single mode and VCSEL-based multimode transmissions including 100G SR4, 40G sWDM, and 100G CWDM4 at full system reaches for the respective transmission technology for the first time.