gebhart/patrepeval huggingface dataset:
Comparison of cloned mouse alpha- and beta-globin genes: conservation of intervening sequence locations and extragenic homology. (1978)

We have cloned and characterized a 9.7-kilobase EcoRI fragment of mouse DNA that contains an alpha-globin gene. The gene is encoded in at least three discontinous segments of DNA interrupted by two small intervening sequences that can be visualized as R-loop structures in the electron miscroscope. The size of the gene and its small intervening sequences fits well with the known size of the alpha-globin mRNA precursor, suggesting that these intervening sequences, like those of beta-globin, are transcribed. Partial sequence analysis indicates that the larger intervening sequence interrupts the alpha-globin gene at a site exactly corresponding to that interrupted by the larger intervening sequences in both the beta-globin major and minor genes. This observation suggests that these sequences were present when the alpha- and beta-globin genes diverged in early vertebrate evolution, more than 500 million years ago. Furthermore, though alpha and betamaj genes are encoded on different chromosomes, when their sequences are compared directly by visualization of heteroduplex structures, only one 150- to 200-base-pair segment of homology is recognized. These homologous sequences are located on the 3'-flanking segments of both genes, about 1.5 kilobases from each.
Channel Estimation and Data Detection Analysis of Massive MIMO With 1-Bit ADCs (2021)

We present an analytical framework for the channel estimation and the data detection in massive multiple-input multiple-output uplink systems with 1-bit analog-to-digital converters (ADCs) and i.i.d. Rayleigh fading. First, we provide closed-form expressions of the mean squared error (MSE) of the channel estimation considering the state-of-the-art linear minimum MSE estimator and the class of scaled least-squares estimators. For the data detection, we provide closed-form expressions of the expected value and the variance of the estimated symbols when maximum ratio combining is adopted, which can be exploited to efficiently implement minimum distance detection and, potentially, to design the set of transmit symbols. Our analytical findings explicitly depend on key system parameters such as the signal-to-noise ratio (SNR), the number of user equipments, and the pilot length, thus enabling a precise characterization of the performance of the channel estimation and the data detection with 1-bit ADCs. The proposed analysis highlights a fundamental SNR trade-off, according to which operating at the right noise level significantly enhances the system performance.
Voltage holding properties of bend liquid crystal cells with treatments for bend alignment stabilisation (2012)

We investigated the voltage holding property of cells with additional fabrication processes for the formation of high and low pretilt angle regions within a dot for achieving a smooth splay-to-bend transition and of π-cells with a polymer network in a liquid crystal (LC) layer to stabilise a bend state. The pretilt angle could be adjusted by irradiation of deep ultraviolet (UV) light to a vertical alignment polyimide layer. The voltage holding ratio (VHR) was above 97% even with irradiation with deep UV light of 10 J/cm2. On the contrary, the VHR was decreased with increasing concentration of photoinitiator, which was added to LC mixture to form the polymer network. The VHR was 90% at the concentration of 0.3 wt%. The results indicate that the formation of the high and low pretilt angle regions within a dot is very useful from the point of reliability of the π-cell.
Pt layer thickness dependence of magnetic properties in Co/Pt multilayers (1991)

The magnetic properties of Co/Pt multilayer films prepared by dc sputtering have been investigated using ferromagnetic resonance and a vibrating sample magnetometer. The thickness of the Co layer is constant at 25 Å while the thickness of the Pt layer varies from 0.9 to 18 Å. The saturation magnetization per unit volume of Co is nearly constant for all the films and close to that of bulk Co. In the ferromagnetic resonance spectra, the presence of two resonance modes having an amplitude ratio that varies substantially with the Pt thickness is strong evidence that a significant coupling between cobalt layers exists even at 18 Å of Pt. For Pt thicknesses greater than 3.6 Å, a uniaxial perpendicular magnetic anisotropy field component increases with Pt thickness and saturates at about 9.0 Å. If the induced anisotropy energy is attributed to a surface anisotropy energy at the Co/Pt interface, it has a value Ks of approximately 0.57 erg/cm2. The temperature dependence of the magnetic hysteresis loop and the ferromagnetic resonance spectrum indicate an increase in the uniaxial anisotropy field with decreasing temperature.
Structural basis of pheromone binding to mouse major urinary protein (MUP‐I) (2001)

Abstract The mouse major urinary proteins are pheromone‐binding proteins that function as carriers of volatile effectors of mouse physiology and behavior. Crystal structures of recombinant mouse major urinary protein‐I (MUP‐I) complexed with the synthetic pheromones, 2‐sec‐butyl‐4,5‐dihydrothiazole and 6‐hydroxy‐6‐methyl‐3‐heptanone, have been determined at high resolution. The purification of MUP‐I from mouse liver and a high‐resolution structure of the natural isolate are also reported. These results show the binding of 6‐hydroxy‐6‐methyl‐3‐heptanone to MUP‐I, unambiguously define ligand orientations for two pheromones within the MUP‐I binding site, and suggest how different chemical classes of pheromones can be accommodated within the MUP‐I β‐barrel.
J0302-1-4 Apply mesh morphing technologies to design process (2009)

We developed the parametric mesh morphing technique, which can be used to change the shape of existing analytical mesh models, and generate a mesh model for a new shape by morphing the mesh model for the previous one. Compared with conventional methods, our method preserves the geometric features of the original mesh in the morphed mesh because of geometric feature identification and parametric mesh morphing. We demonstrated the effectiveness of our method by applying it to models of a engine block and a runner.
Actin Directly Interacts with Phospholipase D, Inhibiting Its Activity (2001)

Mammalian phospholipase D (PLD) plays a key role in several signal transduction pathways and is involved in many diverse functions. To elucidate the complex molecular regulation of PLD, we investigated PLD-binding proteins obtained from rat brain extract. Here we report that a 43-kDa protein in the rat brain, beta-actin, acts as a major PLD2 direct-binding protein as revealed by peptide mass fingerprinting in combination with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. We also determined that the region between amino acids 613 and 723 of PLD2 is required for the direct binding of beta-actin, using bacterially expressed glutathione S-transferase fusion proteins of PLD2 fragments. Intriguingly, purified beta-actin potently inhibited both phosphatidylinositol-4,5-bisphosphate- and oleate-dependent PLD2 activities in a concentration-dependent manner (IC50 = 5 nm). In a previous paper, we reported that alpha-actinin inhibited PLD2 activity in an interaction-dependent and an ADP-ribosylation factor 1 (ARF1)-reversible manner (Park, J. B., Kim, J. H., Kim, Y., Ha, S. H., Kim, J. H., Yoo, J.-S., Du, G., Frohman, M. A., Suh, P.-G., and Ryu, S. H. (2000) J. Biol. Chem. 275, 21295-21301). In vitro binding analyses showed that beta-actin could displace alpha-actinin binding to PLD2, demonstrating independent interaction between cytoskeletal proteins and PLD2. Furthermore, ARF1 could steer the PLD2 activity in a positive direction regardless of the inhibitory effect of beta-actin on PLD2. We also observed that beta-actin regulates PLD1 and PLD2 with similar binding and inhibitory potencies. Immunocytochemical and co-immunoprecipitation studies demonstrated the in vivo interaction between the two PLD isozymes and actin in cells. Taken together, these results suggest that the regulation of PLD by cytoskeletal proteins, beta-actin and alpha-actinin, and ARF1 may play an important role in cytoskeleton-related PLD functions.
Principles of Maude (1996)

This paper introduces the basic concepts of the rewriting logic language Maude and discusses its implementation. Maude is a wide-spectrum language supporting formal specification, rapid prototyping, and parallel programming. Maude's rewriting logic paradigm includes the functional and object-oriented paradigms as sublanguages. The fact that rewriting logic is reflective leads to novel metaprogramming capabilities that can greatly increase software reusability and adaptability. Control of the rewriting computation is achieved through internal strategy languages defined inside the logic. Maude's rewrite engine is designed with the explicit goal of being highly extensible and of supporting rapid prototyping and formal methods applications, but its semi-compilation techniques allow it to meet those goals with good performance.
Tailoring the Mobility of a 3D Molecule Adsorbed on a Metal Surface (2005)

Because of its tetrahedral structure, spirobifluorene is an innovative molecule for molecular mechanics studies by means of scanning tunneling microscopy. On Cu(100), it was observed only anchored at defects because of its mobility at room temperature. To frustrate its diffusion, it was functionalized with phenyl and thiophene groups. Tetraphenylspirobifluorene is also mobile on Cu(100), whereas tetrathienylspirobifluorene is fixed in the middle of the terraces. This very different behavior is an original and unexpected result because both benzene and thiophene are reported to be weakly bound to Cu(100) with almost the same adsorption energy.
Strategy for Dual-Analyte Luciferin Imaging: In Vivo Bioluminescence Detection of Hydrogen Peroxide and Caspase Activity in a Murine Model of Acute Inflammation (2013)

In vivo molecular imaging holds promise for understanding the underlying mechanisms of health, injury, aging, and disease, as it can detect distinct biochemical processes such as enzymatic activity, reactive small-molecule fluxes, or post-translational modifications. Current imaging techniques often detect only a single biochemical process, but, within whole organisms, multiple types of biochemical events contribute to physiological and pathological phenotypes. In this report, we present a general strategy for dual-analyte detection in living animals that employs in situ formation of firefly luciferin from two complementary caged precursors that can be unmasked by different biochemical processes. To establish this approach, we have developed Peroxy Caged Luciferin-2 (PCL-2), a H(2)O(2)-responsive boronic acid probe that releases 6-hydroxy-2-cyanobenzothiazole (HCBT) upon reacting with this reactive oxygen species, as well as a peptide-based probe, z-Ile-Glu-ThrAsp-D-Cys (IETDC), which releases D-cysteine in the presence of active caspase 8. Once released, HCBT and D-cysteine form firefly luciferin in situ, giving rise to a bioluminescent signal if and only if both chemical triggers proceed. This system thus constitutes an AND-type molecular logic gate that reports on the simultaneous presence of H(2)O(2) and caspase 8 activity. Using these probes, chemoselective imaging of either H(2)O(2) or caspase 8 activity was performed in vitro and in vivo. Moreover, concomitant use of PCL-2 and IETDC in vivo establishes a concurrent increase in both H(2)O(2) and caspase 8 activity during acute inflammation in living mice. Taken together, this method offers a potentially powerful new chemical tool for studying simultaneous oxidative stress and inflammation processes in living animals during injury, aging, and disease, as well as a versatile approach for concurrent monitoring of multiple analytes using luciferin-based bioluminescence imaging technologies.
Structural architecture of the 1980 Mount St. Helens collapse: An analysis of the Rosenquist photo sequence using digital image correlation (2011)

Author: Walter, Thomas R.; Genre: Journal Article; Finally published : 2011; Title: Structural architecture of the 1980 Mount St. Helens collapse: an analysis of the Rosenquist photo sequence using digital image correlation
Phase II study of nivolumab and salvage nivolumab + ipilimumab in treatment-naïve patients (pts) with advanced non-clear cell renal cell carcinoma (nccRCC) (HCRN GU16-260-Cohort B). (2021)

4510 Background: The HCRN GU16-260 trial reported on the efficacy and toxicity of nivo monotherapy in treatment naïve clear cell RCC (Cohort A) and the efficacy of nivo/ipi salvage therapy in pts with tumors resistant to initial nivo monotherapy (Atkins JCO 2020.38.15_suppl.5006). Limited information is available on the effects of such an approach in pts with advanced nccRCC. Methods: Eligible pts with treatment-naïve nccRCC received nivo 240mg IV q2 wk x 6 doses followed by 360mg IV q3 wk x 4 doses followed by 480 mg q4 wk until progressive disease (PD), toxicity, or completion of 96 wks of treatment (Part A). Pts with PD prior to or stable disease (SD) at 48 wks (pSD) were potentially eligible to receive salvage nivo (3mg/kg) /ipi (1 mg/kg) q3 wk x 4 doses followed by q4 wk nivo maintenance for up to 48 wks (Part B). All pts were required to submit tissue from a metastatic lesion obtained within 12 months (mo) prior to study entry and prior to enrolling on Part B for correlative studies. Results: 35 pts with nccRCC were enrolled between 5/2017 and 12/2019 at 12 participating HCRN sites. Median age 63 (range 35-84 years); 89% male. IMDC favorable 8 (23%), intermediate 18 (51%) and poor risk 9 (26%). Of the 35 pts 19 (54%) had papillary, 6 (17%) chromophobe and 10 (29%) unclassified histology. RECIST defined ORR was 5 of 35 (14.3%) [CR 2 (5.7%), PR 3 (8.6%)], SD 16 (45.7%), PD 14 (40.0%). Immune-related ORR was 8 of 35 (22.9%). RECIST ORR by histology was: papillary - 1/19 (5%); chromophobe - 1/6 (17%); unclassified - 3/10 (30%). 9 pts (26%) had tumors with sarcomatoid features with 3 (33%) (2 unclassified, 1 papillary) responding. Median PFS was 4.0 (2.7, 4.3) mo. 21 pts remain alive. None of the responders have progressed or died. 28 pts (25 PD, 3 pSD) were potentially eligible for salvage nivo/ipi (Part B), but 12 did not enroll due to symptomatic PD (2), grade 3-4 toxicity on nivo (3), or other including no biopsy tissue (7). In the 16 Part B pts, best response to nivo/ipi was: PR (1, 6%) – (unclassified/non-sarcomatoid); SD (7, 44%); PD (8, 50%). Grade 3 Treatment-related adverse events (TrAEs) were seen in 7/35 (20%) on nivo. Grade 3-5 TrAEs were seen in 7/16 (44%) on nivo/ipi with 1 pt experiencing sudden death. Correlative studies including PD-L1 status, WES and RNAseq are pending. Conclusions: Nivo monotherapy has limited activity in treatment naïve nccRCC with most responses (4 of 5) seen in pts with sarcomatoid and/or unclassified tumors. Toxicity is consistent with prior nivo studies. Salvage treatment with nivo/ipi was provided in 16 of 28 (57%) pts with PD/pSD on nivo monotherapy, with 1 response observed. Clinical trial information: NCT03117309.
Chemical Grafted Carbon-Coated LiFePO4 Using Diazonium Chemistry (2013)

Abstract not Available.
Laparoscopic Nephropexy: Washington University Experience (1995)

Laparoscopic nephropexy appears to be a feasible treatment option for patients with symptomatic, documented nephroptosis. The procedure can be accomplished safely and effectively with satisfactory anatomical and clinical results.
Failing atrial myocardium: energetic deficits accompany structural remodeling and electrical instability (2003)

The failing ventricular myocardium is characterized by reduction of high-energy phosphates and reduced activity of the phosphotransfer enzymes creatine kinase (CK) and adenylate kinase (AK), which are responsible for transfer of high-energy phosphoryls from sites of production to sites of utilization, thereby compromising excitation-contraction coupling. In humans with chronic atrial fibrillation (AF) unassociated with congestive heart failure (CHF), impairment of atrial myofibrillar energetics linked to oxidative modification of myofibrillar CK has been observed. However, the bioenergetic status of the failing atrial myocardium and its potential contribution to atrial electrical instability in CHF have not been determined. Dogs with (n = 6) and without (n = 6) rapid pacing-induced CHF underwent echocardiography (conscious) and electrophysiological (under anesthesia) studies. CHF dogs had more pronounced mitral regurgitation, higher atrial pressure, larger atrial area, and increased atrial fibrosis. An enhanced propensity to sustain AF was observed in CHF, despite significant increases in atrial effective refractory period and wavelength. Profound deficits in atrial bioenergetics were present with reduced activities of the phosphotransfer enzymes CK and AK, depletion of high-energy phosphates (ATP and creatine phosphate), and reduction of cellular energetic potential (ATP-to-ADP and creatine phosphate-to-Cr ratios). AF duration correlated with left atrial area (r = 0.73, P = 0.01) and inversely with atrial ATP concentration (r = -0.75, P = 0.005), CK activity (r = -0.57, P = 0.054), and AK activity (r = -0.64, P = 0.02). Atrial levels of malondialdehyde, a marker of oxidative stress, were significantly increased in CHF. Myocardial bioenergetic deficits are a conserved feature of dysfunctional atrial and ventricular myocardium in CHF and may constitute a component of the substrate for AF in CHF.
Clinical Potential of Light-Activated Tissue Crosslinking (2015)

Photocrosslinking can alter biomechanical and biological properties of tissue and close surgical wounds. This contribution focuses on potential clinical applications in vascular surgery and plastic surgery.
Time-dependent Dissolution of Amalgams into Saline Solution (1987)

The dissolution of mercury, silver, and copper from polished and unpolished surfaces of low- and high-copper amalgams into saline was investigated with respect to time via atomic absorption spectrophotometry. Greater amounts of mercury and silver were released from unpolished than from polished surfaces. Ion release was greatest during the first three hours after trituration of all amalgams. The rate of dissolution of ions from amalgams into saline is considered to be very low once the amalgam has set, and is probably inhibited by the formation of a surface film formed during immersion.
Accuracy of dual-photon absorptiometry compared to computed tomography of the spine (1984)

A kind of biosurfactant rhamnolipid modified zero-valent iron nanoparticles have been synthesized and applied to evaluate the immobilization efficiency of Ni (Ⅱ) contaminated soil at three concentration levels (200Ni, 600Ni and 1800Ni). The results of SEM and XRD were clearly indicative of the well-attached phenomenon of rhamnolipid on the nZVI, featuring better stability and dispersity, and FTIR analysis proposed the interactions between rhamnolipid and nZVI through monodentate chelating between carboxylate groups and nZVI or hydrogen bonding with Fe-O groups on the surface. Sequential extraction procedures (SEP) analysis illustrated that the majority of labile fractions had been transformed into less accessible fractions (Fe-Mn oxide-bound fractions and residual fractions) after 28 days of incubation. And for low-concentrations polluted soil, soil self-remediation played a dominant role, while RL@nZVI exhibited a more significant stabilizing effect for medium and high-concentrations pollution. Furthermore, XPS and XRD analyses of Ni-adsorbed RL@nZVI identified the formation of NiO, Ni(OH)<sub>2</sub> and revealed the possible interaction mechanisms including reduction, adsorption and precipitation/co-precipitation. These results confirmed that RL@nZVI presented a promising prospect for the immobilization of Ni polluted soil.
Abstract 15791: Evaluation of Medicare Claims for Heart Failure Diagnostic Development: A Multisense-linkage Feasibility Analysis (2020)

Introduction: The validity of utilizing claims data for the development of worsening heart failure (HF) diagnostics has not been previously reported. Therefore, we linked data from the MultiSENSE study, in which the HeartLogic diagnostic was first reported, with claims data in order to validate claims HF events and compare diagnostic performance. Methods: Identifiers from 791 United States study patients were directly linked with Medicare claims to produce 320 patients with continuous Medicare Part A/B fee-for-service (FFS) coverage during study participation. Claims HF events were defined using primary HF diagnosis codes (DRG and ICD-9-CM) and included inpatient events as well as outpatient events with intravenous decongestive therapy. We matched events by patient and date, calculated agreement between events (Cohen’s kappa coefficient κ), and evaluated HeartLogic diagnostic performance using sensitivity and false positive rate (FPR). Results: The linked cohort was older than the remaining patients and had greater disease burden. Study deaths (N=14) matched exactly with claims. In contrast, matching of 207 study hospitalizations with 197 acute inpatient events resulted in a total of 239 events of which 193 matched with claims (81%), 32 (13%) were claims-unique, and 14 (6%) were study-unique. Claims HF events had substantial agreement with study adjudicated hospitalizations (observed = 93.3%, κ = 0.823). The HeartLogic algorithm detected claims-derived events with a sensitivity of 75.6% and an FPR of 1.539 alerts/pt-year, which was not different from performance derived using study events (sensitivity = 77.6% and FPR = 1.528, P = 0.82 and 0.92). HeartLogic detected events contributed to 91% of HF event costs used for performance evaluation ($605,000 out of $663,000). Conclusions: The agreement between claims and study events, and equivalence of HeartLogic diagnostic performance suggest that claims data may have utility for future diagnostic development/enhancement. Additional data are needed to demonstrate safety, efficacy, and cost-effectiveness of HeartLogic-directed interventions.
Modelling the mechanical response ofurushilacquer subject to a change in relative humidity (2012)

A hygromechanical model has been developed to simulate the in-service behaviour of the natural lacquer urushi , using a phenomenological description of viscoelasticity. The material and mechanical properties were determined as a function of the relative humidity (RH), and the relationship between RH and moisture content was determined. These properties served as inputs to a finite-element-based model that was then tested against experimental measurements of the depth-averaged stresses in a thin layer of urushi deposited on a substrate and exposed to changes in the environmental conditions. Good agreement was seen between the predicted and measured behaviour. The validated model was used to investigate the spatial and temperature variation of stress in urushi films subjected to cyclic environmental conditioning.
Topical application of nebulized human IgG, IgA and IgAM in the lungs of rats and non-human primates (2019)

Taken together our data demonstrate the feasibility of topically applying plasma-derived immunoglobulins into the lungs using a nebulized liquid formulation. Moreover, topically administered human plasma-derived immunoglobulins prevented acute respiratory infection.
Direct-Attached Disk Subsystem Performance Assessment (2007)

Direct-attached storage has historically had the reputation of being less capable than equivalently sized SAN installations. Here, we empirically demonstrate the performance achievable in multiple-terabyte, direct-attached disk subsystems. A number of parameters are explored, including file system, number of logical drives, and RAID configuration.