gebhart/patrepeval huggingface dataset:
Gas/Condensate Relative Permeabilities in Propped-Fracture Porous Media: Coupling vs. Inertia (2009)

Summary Hydraulic fracturing is one of the most common well stimulation techniques for gas/condensate reservoirs. In recent years, considerable effort has been directed toward the understanding of flow around hydraulically fractured wells, especially for tight gas reservoirs. However, there has been no report of a study of flow behavior within propped-fractured porous media for the low interfacial tension (IFT) gas/condensate fluid systems. It is now a well established finding both experimentally and theoretically that the flow of gas/condensate fluid systems in porous media is affected by both coupling (the increase of relative permeability kr as velocity increases or IFT decreases) and inertial (i.e., the reduction of kr as velocity increases) effects. However, the interaction of capillary, viscous, and inertial forces within highly conductive propped fractures is not yet understood. In this work, different series of steady-state gas/condensate kr values for a proppant-filled and a sand-packed fracture with permeability of 146 darcy and 15 darcy, respectively, are reported. These experimentally measured sets of kr data cover IFT and velocity values ranging between 0.85 and 0.15 mNm-1 and 250 to 3000 md-1, respectively. The results indicate that inertia is quite dominant at all the tested conditions albeit to a greater extent at lower IFT and higher gas fractional flow rates. In the case of the fracture with the higher permeability, some kr values measured at the higher IFT are also reported, which are higher than the corresponding values at a lower IFT. These kr measurements are also compared with the corresponding predicted kr values using the generalized kr correlation reported recently by Jamiolahmady et al. (2009). The correlation expresses the combined effect of coupling and inertia with universal parameters. The unique contribution of inertial forces, as observed in the experiments and predicted by the correlation, is mainly attributed to the velocity, petrophysical properties of the fracture, and fluid properties of the flowing phases.
Prevalence ofBacillus anthracis-Like Organisms and Bacteriophages in the Intestinal Tract of the EarthwormEisenia fetida (2010)

Stable infection of Bacillus anthracis laboratory strains with environmental bacteriophages confers survival phenotypes in soil and earthworm intestinal niches (R. Schuch and V. A. Fischetti, PLoS One 4:e6532, 2009). Here, the natural occurrence of two such B. anthracis-infective bacteriophages, Wip1 and Wip4, was examined in the intestines of Eisenia fetida earthworms as part of a 6-year longitudinal study at a Pennsylvania forest site. The Wip1 tectivirus was initially dominant before being supplanted by the Wip4 siphovirus, which was then dominant for the next 3 years. In a host range analysis of a wide-ranging group of Bacillus species and related organisms, Wip1 and Wip4 were both infective only toward B. anthracis and certain B. cereus strains. The natural host of Wip4 remained constant for 3 years and was a B. cereus strain that expressed a B. anthracis-like surface polysaccharide at septal positions on the cell surface. Next, a novel metagenomic approach was used to determine the extent to which such B. cereus- and B. anthracis-like strains are found in worms from two geographical locations. Three different enrichment strategies were used for metagenomic DNA isolation, based either on the ability of B. cereus sensu lato to form heat-resistant spores, the sensitivity of B. anthracis to the PlyG lysin, or the selective amplification of environmental phages cocultured with B. anthracis. Findings from this work indicate that B. cereus sensu lato and its phages are common inhabitants of earthworm intestines.
Vibrations of infinite plates and the mean value vibrations of finite plates excited by turbulent boundary layer flows (2002)

The vibration response of a turbulent boundary layer (TBL) excited flat plate is analyzed using a finite-element model and infinite plate theory. For the finite-element models, discretization sufficient to resolve the convective fluctuations in the flow excitation field is used for the study. Clamped boundary conditions are assumed for the finite-element models and analyses are conducted at a variety of flow speeds and structural loss factors. Two equivalent TBL wall pressure excitation models are applied to the plates: (1) a modified Corcos cross-spectrum model for the finite-element models, and (2) a wave-vector-frequency spectrum model (the Fourier transform of the modified Corcos cross spectra) for the infinite plate theory. The TBL wall pressure autospectrum is approximated using the model derived by Smolyakov and Tkachenko. The infinite plate predicts the mean value response of the finite plate very well for all speeds and loss factors considered, showing consistency with Skudrzyks mean value theory and its usefulness for generating sound and vibration estimates.
Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron (2021)

Since the outbreak of the COVID-19 pandemic, widespread infections have allowed SARS-CoV-2 to evolve in human, leading to the emergence of multiple circulating variants. Some of these variants show increased resistance to vaccines, convalescent plasma, or monoclonal antibodies. In particular, mutations in the SARS-CoV-2 spike have drawn attention. To facilitate the isolation of neutralizing antibodies and the monitoring the vaccine effectiveness against these variants, we designed and produced biotin-labeled molecular probes of variant SARS-CoV-2 spikes and their subdomains, using a structure-based construct design that incorporated an N-terminal purification tag, a specific amino acid sequence for protease cleavage, the variant spike-based region of interest, and a C-terminal sequence targeted by biotin ligase. These probes could be produced by a single step using in-process biotinylation and purification. We characterized the physical properties and antigenicity of these probes, comprising the N-terminal domain (NTD), the receptor-binding domain (RBD), the RBD and subdomain 1 (RBD-SD1), and the prefusion-stabilized spike ectodomain (S2P) with sequences from SARS-CoV-2 variants of concern or of interest, including variants Alpha, Beta, Gamma, Epsilon, Iota, Kappa, Delta, Lambda, Mu, and Omicron. We functionally validated probes by using yeast expressing a panel of nine SARS-CoV-2 spike-binding antibodies and confirmed sorting capabilities of variant probes using yeast displaying libraries of plasma antibodies from COVID-19 convalescent donors. We deposited these constructs to Addgene to enable their dissemination. Overall, this study describes a matrix of SARS-CoV-2 variant molecular probes that allow for assessment of immune responses, identification of serum antibody specificity, and isolation and characterization of neutralizing antibodies.
Electrically Erasable Optical I/O for Wafer Scale Testing of Silicon Photonic Integrated Circuits (2020)

A technique for realizing electrically erasable photonics devices using micro-heaters for localized annealing of lattice defects in silicon is presented. The lattice defects have previously been introduced by ion implantation in order to cause a refractive index change. This technique can be used to fabricate electrically erasable on-chip directional couplers (DCs) and Mach-Zehnder Interferometer (MZI) switches. These devices can be used for wafer scale testing of photonics circuits, allowing testing of individual optical components in a complex photonic integrated circuit, or components for programmable optical circuits, whilst inducing negligible additional optical loss when erased electrically. In this paper, we report the designs and experimental results of fully, rapidly annealing of these devices.
Hapten/Myristoyl Functionalized Poly(propyleneimine) Dendrimers as Potent Cell Surface Recruiters of Antibodies for Mediating Innate Immune Killing (2023)

Recruiting endogenous antibodies to the surface of cancer cells using antibody-recruiting molecules has the potential to unleash innate immune effector killing mechanisms against antibody-bound cancer cells. The affinity of endogenous antibodies is relatively low, and many currently explored antibody-recruiting strategies rely on targeting over-expressed receptors, which have not yet been identified in most solid tumors. Here, both challenges are addressed by functionalizing poly(propyleneimine) (PPI) dendrimers with both multiple dinitrophenyl (DNP) motifs, as anti-hapten antibody-recruiting motifs, and myristoyl motifs, as universal phospholipid cell membrane anchoring motifs, to recruit anti-hapten antibodies to cell surfaces. By exploiting the multivalency of the ligand exposure on the dendrimer scaffold, it is demonstrated that dendrimers featuring ten myristoyl and six DNP motifs exhibit the highest antibody-recruiting capacity in vitro. Furthermore, it is shown that treating cancer cells with these dendrimers in vitro marks them for phagocytosis by macrophages in the presence of anti-hapten antibodies. As a proof-of-concept, it is shown that intratumoral injection of these dendrimers in vivo in tumor-bearing mice results in the recruitment of anti-DNP antibodies to the cell surface in the tumor microenvironment. These findings highlight the potential of dendrimers as a promising class of novel antibody-recruiting molecules for use in cancer immunotherapy.
Hydrogen Bonding Interactions of Pyridine•+ with Water:  Stepwise Solvation of Distonic Cations (2007)

The solvation energies of the pyridine*+ radical cation by 1-4 H2O molecules were determined by equilibrium measurements in a drift cell. The binding energies of the pyridine*+(H2O)n clusters are similar to the binding energies of protonated pyridine-water clusters, (C5H5NH+)(H2O)n, which involve NH+..OH2 bonds and different from those of the solvated benzene radical cation-water clusters, C6H6*+(H2O)n, which involve CHdelta+..OH2 bonds. These relations indicate that the observed pyridine*+ ions have the distonic *C5H4NH+ structures that can form NH+..OH2 bonds. The observed thermochemistry and ab initio calculations show that these bonds are not affected significantly by an unpaired electron at another site of the ion. Similar observations also identify the 2-fluoropyridine*+ distonic ion. The distonic structure is also consistent with the reactivity of pyridine*+ in H atom transfer, intra-cluster proton transfer and deprotonation reactions. The results present the first measured stepwise solvation energies of distonic ions, and demonstrate that cluster thermochemistry can identify distonic structures.
A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice (2021)

Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly effective countermeasures against them, which could be key in the prevention and mitigation of current and future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV, bat coronaviruses WIV-1, RsSHC014, and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor-binding domain (RBD)-specific human antibody, DH1047. Prophylactic and therapeutic treatment with DH1047 was protective against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B.1.351 infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among sarbecoviruses. Thus, DH1047 is a broadly protective antibody that can prevent infection and mitigate outbreaks caused by SARS-related strains and SARS-CoV-2 variants. Our results also suggest that the conserved RBD epitope bound by DH1047 is a rational target for a universal sarbecovirus vaccine
Application of multispectral color enhancement for remote sensing (2011)

Previously, we proposed a color enhancement method, which enhances the spectral features in multispectral images without changing the average color distribution, since the natural color of the object is sometimes important. In the proposed method, a user can specify both the spectral band to extract the spectral feature and the color to be visualized, respectively. This method can visualize spectral features even if the wavelength of the specified spectral band is in non-visible range or the image has a large number of spectral bands. That is, the enhancement method is also effective for hyperspectral images which are often used in remote sensing applications. If we can find the meaningful spectral features in them, those features might be employed as novel indices. In this paper, we apply the enhancement method to hyperspectral images of rice paddy and trees. We observed the enhanced results of these images, and could find the spectral features which might be useful to discriminate different species and even the different conditions in the same species. The results showed that these features might be utilized for novel indices or other applications in remote sensing.
ChemInform Abstract: An Efficient Chiral Moderator Prepared from Inexpensive (+)‐3‐Carene: Synthesis of the HIV‐1 Non‐Nucleoside Reverse Transcriptase Inhibitor DPC 963. (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.
Analysis of T‐cell hybridomas with an unusual MHC class II‐dependent ligand specificity (1996)

We have characterized two unusual T-cell hybridomas, 1E3 and 3B8, from H-2k mice immunized with I-Ab-transfected L cells (H-2k), that are stimulated by L cells transfected with I-Ab, I-Ak or I-Eb, but not by non-transfected L cells. These hybridomas could not be stimulated by spleen cells from H-2i3, H-2k, H-2b or H-2d mice. Monoclonal anti-I-A antibodies did not block their responses, suggesting that mouse major histocompatibility complex (MHC) class II molecules may be peptide donors rather than restriction elements for them. The stimulation of these hybridomas by fibroblast targets was not blocked by an anti-H-2kk, Dk-specific monoclonal antibody. Lipopolysaccharide (LPS)-activated splenic and peritoneal exudate cells from H-2k, H-2d, H-2i3, H-2b as well as beta 2-microglobulin-deficient, TAP-1-deficient and I-A alpha-deficient H-2b mice stimulated these hybridomas. LPS could also activate a macrophage cell line, but not a B-cell line, to become stimulatory for 1E3. A rat antiserum against untransfected L cells specifically and significantly blocked the response of 1E3. Thus, 1E3 may recognize a conserved murine MHC class II peptide loaded in a TAP-1-independent fashion on a non-classical, monomorphic, beta 2-microglobulin-independent restriction element.
EARLY DIRECT PERFUSION WITH VENOUS BLOOD ENHANCES RENAL FUNCTION IN IMPENDING ACUTE RENAL FAILURE (2002)

Purpose of Study: Acute renal failure (ARF) is a major determinant of morbidity and mortality in heart failure. Early direct perfusion of the kidney with venous blood may improve renal function. Methods Used To determine the impact of early Vs late perfusion on renal function, ARF was created in 7 dogs by inducing hemorrhagic shock. Renal artery was cannulated on one side via a percutaneous catheter opposite kidney served as control. Ureters were stented to measure urine output (UO). 3 animals in the late group (LG) were perfused after 1 hour of shock. Following 4 animals in the early group (EC) were perfused within 15 minutes of shock induction. Antegrade perfusion of the kidney was performed using a roller pump at perfusion pressures between 100–160 mm Hg using venous blood. Summarize Results: In shock, mean arterial pressure (MAP) was 57.6 ± 1.9 mm Hg, mean venous saturation 46.6 ± 6.5 % and mean UO 17 ± 5.3 % of the baseline. All perfused kidneys demonstrated recovery of renal function while control kidneys remained anuric. In perfused kidneys, in spite of higher oxygen delivery (709.5 ± 157.0 ml/min Vs 414.0 ± 132.0 ml/min, p=0.008) and higher renal blood flow (119 ± 14 ml/min Vs 103 ± 38 ml/min, p = 0.15) in the LG, UO (98.5 ± 20.5 % Vs 39.4 ± 19.3 % of baseline, p < 0.001) and GFR (38 ± 4 % Vs 24 ± 12 % of baseline, p = 0.56) were higher in the EG. Conclusion: Early perfusion of kidneys with venous blood provides significantly improved renal function.
PROTEUS: a high-performance parallel-architecture simulator (1992)

PROTEUS is a high-performance simulator for MIMD multiprocessors. It is fast, accurate, and flexible: it is one to two orders of magnitude faster than comparable simulators, it can reproduce results from real multiprocessors, and it is easily configured to simulate a wide range of architectures. PROTEUS provides a modular structure that simplifies customization and independent replacement of parts of architecture. There are typically multiple implementations of each module that provide different combinations of accuracy and performance; users pay for accuracy only when and where they need it. Finally, PROTEUS provides repeatability, nonintrusive monitoring and debugging, and integrated graphical output, which result in a development environment superior to those available on real multiprocessors
Efficient and surface site-selective ion desorption by positron annihilation (2018)

We compared positron- and electron-stimulated desorption (e<sup>+</sup>SD and ESD) of positive ions from a TiO<sub>2</sub>(110) surface. Although desorption of O<sup>+</sup> ions was observed in both experiments, the desorption efficiency caused by positron bombardment was larger by one order of magnitude than that caused by electron bombardment at an incident energy of 500 eV. e<sup>+</sup>SD of O<sup>+</sup> ions remained highly efficient with incident positron energies between 10 eV and 600 eV. The results indicate that e<sup>+</sup>SD of O<sup>+</sup> ions is predominantly caused by pair annihilation of surface-trapped positrons with inner-shell electrons. We also tested e<sup>+</sup>SD from water chemisorbed on the TiO<sub>2</sub> surface and found that the desorption of specific ions was enhanced by positron annihilation, above the ion yield with electron bombardment. This finding corroborates our conclusion that annihilation-site selectivity of positrons results in site-selective ion desorption from a bombarded surface.
A moonshot approach toward the management of cancer patients in the COVID-19 time: what have we learned and what could the Italian network of cancer centers (Alliance Against Cancer, ACC) do after the pandemic wave? (2020)

Abstract If we focus our attention on seven main features of COVID-19 infection ( heterogeneity, fragility, lack of effective treatments and vaccines, “miraculous cures”, psychological suffering, deprivation, and globalization ), we may establish parallelism with the challenges faced in the steep road to the understanding and treatment of neoplastic diseases. How the similarities between these two conditions can help us cope with the emergency effort represented by the management of cancer patients in the COVID-19 era, today and in the future? In a manner similar to the Cancer Moonshot initiative in the United States, we can hypothesize a multinational moonshot project towards the management of cancer patients during COVID-19 pandemic . In particular, we believe that the main road to elaborate meaningful scientific evidence is represented by the collection of all the data on COVID-19 and cancer comorbidity that are and will become available in cancer centers, coupled with the design of large clinical studies. To address this goal, it is essential to identify the entity that can produce this scientific evidences and the potentially most successful research strategy to undertake. The largest Italian organization for cancer research, Alliance Against Cancer ( Alleanza Contro il Cancro , ACC), is called to play a scientific leadership in addressing these challenges, which requires the coordination of oncology teams at regional, national, and international levels. To fulfill this commitment, ACC will create a liaison with health government agencies in order to develop “dynamic” indications able to fight such an unpredictable pandemic.
Practical Synthesis of Shi's Diester Fructose Derivative for Catalytic Asymmetric Epoxidation of Alkenes (2005)

[reaction: see text] A practical synthesis of Shi's diester 3 for catalytic asymmetric epoxidations has been developed. The catalyst has been prepared in multigram quantities from D-fructose in four steps with a 66% overall yield. Efficiency, cost, and selectivity aspects of the reagents involved for its preparation have been taken care of during its preparation. The workup procedures have been simplified to the bare minimum, rendering a very practical preparation method. The well-known high efficiency of this catalyst 3 in the epoxidation of alpha,beta-unsaturated carbonyl compounds has also proved to be high in unfunctionalized alkenes.
GPR40 activation by high fat diet decreased bone loss in ovariectomized mouse model (2015)

National audience
RC Structures Strengthened by an Iron-Based Shape Memory Alloy Embedded in a Shotcrete Layer—Nonlinear Finite Element Modeling (2020)

Shape memory alloys (SMAs) have been widely used in civil engineering applications including active and passive control of structures, sensors and actuators and strengthening of reinforced concrete (RC) structures owing to unique features such as the shape memory effect and pseudo-elasticity. Iron-based shape memory alloys (Fe-SMAs) have become popular in recent years. Use of iron-based SMAs for strengthening RC structures has received attention in the recent decade due to the advantages it presents, that is, no ducts or anchor heads are required, friction losses do not occur and no space is needed for a hydraulic device to exert force. Accordingly, Fe-SMAs embedded in a shotcrete layer have been used for pre-stressing RC beams at Empa. The aim of this study is to present an approach to model and analyze the behavior of RC members strengthened and pre-stressed with Fe-SMA rebars embedded in a shotcrete layer. The lack of research on developing finite element models for studying the behavior of concrete structures strengthened by iron-based shape memory alloys is addressed. Three-dimensional finite element models were developed in the commercial finite element code ABAQUS, using the concrete damaged plasticity model to predict the studied beams' load-displacement response. The results of the finite element analyses show a considerably good agreement with the experimental data in terms of the beams' cracking load and ultimate load capacity. The effects of different strengthening parameters, including SMA rebar diameter, steel rebar diameter and pre-stressing force level on the beam behavior, were investigated based on the verified finite element models. The results were compared. The load-displacement response of an 18-m concrete girder strengthened and pre-stressed with iron-based SMA bars was examined by the developed finite element model as a case study.