gebhart/patrepeval huggingface dataset:
Transmission and Pathogenicity of H5N1 Influenza Viruses (2008)

The interaction between multiple viral and host factors determine the pathogenicity and transmissibility of H5N1 influenza viruses. The viral surface glycoprotein haemagglutinin (HA) plays a crucial role in attachment to the host-cell sialic acid (SA) receptor and in viral growth and tissue tropism. Other viral factors known as host range or virulence determinants include viral polymerase, particularly residue 627 in the PB2 protein, and the ability to evade the host immune response through the viral NS1 protein. Applying plasmid-based reverse genetics, we have provided a good model system to study the molecular basis for pathogenicity. Differences in the pathogenicity in mammalian species were previously observed between human (A/Vietnam/1203/04) and chicken (A/Chicken/Vietnam/C58/04) H5N1 isolates. Detailed molecular characterization by plasmid-based reverse genetics showed that the polymerase subunits PB1 and PB2 contribute to the lethality of A/Vietnam/1203/04. The polymerase complex possessed significantly higher transcription/ replication activity than the A/Chicken/Vietnam/C58/04 polymerase complex. Our results suggest that high polymerase activity acts as a molecular determinant for virulence in mammalian species. We also evaluated the transmissibility and pathogenicity of H5N1 viruses isolated from humans during the years 2003- 2006 using a ferret contact model comprising one inoculated and two contact ferrets. This animal model has been shown to support efficient transmission of seasonal human influenza viruses. At 103 TCID50, A/Vietnam/1203/04 and A/ Vietnam/JP36-2/05 viruses, which have ‘avian-like’ α2,3-linked SA receptor affinity, caused neurological symptoms and death in ferrets. A/HongKong/213/03 and A/Turkey/65-596/06 viruses, which have affinity for both ‘human-like’ (α2,6- linked) and ‘avian-like’ SA receptors, caused mild clinical symptoms and were not lethal to ferrets. No transmission of A/Vietnam/1203/04 and A/Turkey/65-596/06 viruses was detected, and transmission of A/HongKong/213/03 and A/Vietnam/ JP36-2/05 viruses was inefficient. These results demonstrate that despite their receptor binding affinity, circulating H5N1 viruses retain molecular determinants that restrict their spread among mammals.
Nonstoichiometric Copper Sulfide Nanostructures at the Brass–Rubber Interface: Implications for Rubber Vulcanization Temperature in the Tire Industry (2020)

Brass (which is an alloy of copper and zinc)-coated steel cords (BCSCs) in the form of belts are embedded in a rubber compound in radial tires (beneath the tread) to give stability and strength to the tread region of the tires. The life of the tires also depends on the strength and durability of the bond between the BCSCs and rubber. During the vulcanization process with sulfur, a series of sulfide and oxide nanostructures of copper and zinc are formed at the brass–rubber interface. These nanostructures have a dendritic morphology that can reinforce rubber primarily through mechanical interlocking created through the flow of rubber chains into the dendritic cavities followed by formation of cross-links between rubber chains during vulcanization. The strength and durability of the bonding depend on a number of parameters such as rubber compound formulation, vulcanization temperature (VT) and time, nanostructure thickness (height), and chemical composition of the nanostructures (the so-called adhesion interface). A few methods have been stated in the literature for assessing the chemical composition and thickness of the adhesion interface. However, simple, reliable, and newer methodologies are needed for a better understanding of the same. This paper details a new approach called the “brass mesh experiment” to assess the thickness of the adhesion interface formed under particular vulcanization conditions using microscopy. Raman imaging and spectroscopy were employed to determine the chemical composition of the interface with complementary data from X-ray photoelectron spectroscopy and X-ray diffraction. Using the methodologies, VT optimization was done for a tire compound formulation, and this was verified by the generally accepted pull-out force method. We believe that the methodologies outlined in this paper can trigger further research for a better understanding of the adhesion interface in radial tires.
Phase Behavior of I2S Single Graft Block Copolymer/Homopolymer Blends (2001)

This work is part of an extensive study of model nonlinear block copolymer/homopolymer blends. Effects of graft molecular architecture on the morphology of block copolymer/homopolymer blends have been examined. The single graft Y-shaped block copolymers used in the study are I2S block copolymers, which have two low polydispersity (PDI) polyisoprene arms and one low PDI polystyrene arm joint at a single junction point. Previously reported linear diblock copolymer/homopolymer blend systems showed that the order−order transitions (OOTs) occur at about the same volume fractions as in pure linear diblock copolymers. The OOT occurs at the same volume fraction regardless of the direction from which it is approached, i.e., blending homopolymer A with a diblock which forms A cylinders in a B matrix to push it toward lamella or blending B homopolymer with a lamellar diblock to push it back toward cylinders. This study shows that when a homopolymer is blended with an I2S block copolymer, the OOTs split so that they occur at different volume fractions depending up whether they are approached by blending homopolymer into the two-arm or the one-arm side of the block copolymer interface. A perforated lamellar morphology is obtained in a blend of homopolystyrene (hPS) and a lamella forming single graft block copolymer, and it is found to be stable to thermal annealing.
High-index faceted Au nanocrystals with highly controllable optical properties and electro-catalytic activity (2016)

We introduce a new and naturally abundant mild reducing agent, tannic acid, to improve the seed-mediated growth method for the synthesis of elongated tetrahexahedral Au nanocrystals enclosed with high-index (730) planes, at room-temperature. The control of the dimensions, plasmonics and electro-catalysis of such high-index faceted nanocrystals is remarkable.
High Thermoelectric Performance in Polycrystalline SnSe Via Dual‐Doping with Ag/Na and Nanostructuring With Ag8SnSe6 (2018)

Abstract Single crystalline SnSe is one of the most intriguing new thermoelectric materials but the thermoelectric performance of polycrystalline SnSe seems to lag significantly compared to that of a single crystal. Here an effective strategy for enhancing the thermoelectric performance of p‐type polycrystalline SnSe by Ag/Na dual‐doping and Ag 8 SnSe 6 (STSe) nanoprecipitates is reported. The Ag/Na dual‐doping leads to a two orders of magnitude increase in carrier concentration and a convergence of valence bands (VBM 1 and VBM 5 ), which in turn results in sharp enhancement of electrical conductivities and high Seebeck coefficients in the Ag/Na dual‐doped samples. Additionally, the SnSe matrix becomes nanostructured with dispersed nanoprecipitates of the compound Ag 8 SnSe 6 , which further strengthens the scattering of phonons. Specifically, ≈20% reduction in the already ultralow lattice thermal conductivity is realized for the Sn 0.99 Na 0.01 Se–STSe sample at 773 K compared to the thermal conductivity of pure SnSe. Consequently, a peak thermoelectric figure of merit ZT of 1.33 at 773 K with a high average ZT (ZT ave ) value of 0.91 (423–823 K) is achieved for the Sn 0.99 Na 0.01 Se–STSe sample.
Arthroscopic Latarjet Techniques: Graft and Fixation Positioning Assessed With 2‐Dimensional Computed Tomography Is Not Equivalent With Standard Open Technique (2018)

Level III, retrospective comparative study.
High-swing, high-drive CMOS buffer (1995)

The advent of analogue and hybrid VLSI circuits has created new requirements for the design of many previously known building blocks. For example, implementation of cascaded multilayer analogue/hybrid neural networks requires output drivers that can charge the large number of interconnecting lines, and remain stable in the presence of large capacitive loads. A CMOS high dynamic range, high-drive buffer suitable for driving large capacitive loads is presented in this paper. An area-efficient output stage has been used, with which a rail-to-rail drive capability into a 5000 pF load at 160 kHz is achieved. The circuit occupies only 110 mils2 in a 3 µm technology. The output range is rail to rail for R&gt;10 k Omega . The buffer is capable of driving resistive loads down to 300 Omega with acceptable THD.
Anomalous scaling of spin accumulation in ferromagnetic tunnel devices with silicon and germanium (2012)

The magnitude of spin accumulation created in semiconductors by electrical injection of spin-polarized electrons from a ferromagnetic tunnel contact is investigated, focusing on how the spin signal detected in a Hanle measurement varies with the thickness of the tunnel oxide. An extensive set of spin-transport data for Si and Ge magnetic tunnel devices reveals a scaling with the tunnel resistance that violates the core feature of available theories, namely, the linear proportionality of the spin voltage to the injected spin current density. Instead, an anomalous scaling of the spin signal with the tunnel resistance is observed, following a power-law with an exponent between 0.75 and 1 over 6 decades. The scaling extends to tunnel resistance values larger than 10$^{9}$ $Ωμm^2$, far beyond the regime where the classical impedance mismatch plays a role. This scaling is incompatible with existing theory for direct tunnel injection of spins into the semiconductor. It also demonstrates conclusively that the large spin signal does not originate from two-step tunneling via localized states near the oxide/semiconductor interface. Control experiments on devices with a non-magnetic metal (Ru) electrode, instead of the semiconductor, exhibit no Hanle spin signal, showing that spin accumulation in localized states within the tunnel barrier is also not responsible. Control devices in which the spin current is removed by inserting a non-magnetic interlayer exhibit no Hanle signals either, proving that the spin signals observed in the standard devices are genuine and originate from spin-polarized tunneling and the resulting spin accumulation. Altogether, the scaling results suggest that the spin signal is proportional to the applied bias voltage, rather than the (spin) current.
Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking (2016)

Alzheimer's disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R (2), [Formula: see text] and [Formula: see text] values in ranges of 0.66-0.93, 0.55-0.79 and 0.56-0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R (2), [Formula: see text] and [Formula: see text] values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard-Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds 13, 5 and 28 exhibited the lowest binding energies of -12.2, -12.0 and -12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding, π-π stacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors.
Separation of cancer cells using vortical microfluidic flows (2018)

Label-free separation of viable cancer cells using vortical microfluidic flows has been introduced as a feasible cell collection method in oncological studies. Besides the clinical importance, the physics of particle interactions with the vortex that forms in a wall-confined geometry of a microchannel is a relatively new area of fluid dynamics. In our previous work [Haddadi and Di Carlo, J. Fluid. Mech. <b>811</b>, 436-467 (2017)], we have introduced distinct aspects of inertial flow of dilute suspensions over cavities in a microchannel such as breakdown of the separatrix and formation of stable limit cycle orbits for finite size polystyrene particles. In this work, we extend our experiments to address the engineering-physics of cancer cell entrapment in microfluidic cavities. We begin by studying the effects of the channel width and device height on the morphology of the vortex, which has not been discussed in our previous work. The stable limit cycle orbits of finite size cancer cells are then presented. We demonstrate effects of the separatrix breakdown and the limit cycle formation on the operation of the cancer cell separation platform. By studying the flow of dilute cell suspensions over the cavities, we further develop the notion of the <i>cavity capacity</i> and the relative rate of cell accumulation as optimization criteria which connect the device geometry with the flow. Finally, we discuss the proper placement of multiple cavities inside a microchannel for improved cell entrapment.
Axialfield synchronous machine with homopolar flux in the airgap for a flywheel accumulator (2015)

Abstract: A new axial-field synchronous machine designed for a flywheel accumulator is presented herein. The armature and field windings fixed in the airgap are made with double-face printed circuits. A specific armature layout provides a sine-distributed m.m.f. and solves the problem of crossing the ends of the winding. A 2D semi-analytical model at the mean radius, using surfacic permeances, is then developed. Afterwards, inductances, torque and eddy current losses are calculated using this model and compared with experimental results.
Comparative anti-glycation and α-glucosidase inhibition studies of microbial transformed compounds of dydrogesterone. (2015)

Anti-glycation and α-glucosidase inhibition activities of microbial transformed compounds of dydrogesterone (1); 20R-hydroxy-9β,10αa-pregna-4,6-diene-3-one (2), 17β-hydroxy-9β,10α-androsta-4,6-diene-3-one (3) and 9β,10α-androsta-4,6-diene-3,17-dione (4) were evaluated. Compounds 1 and 4 showed potent α-glucosidase inhibitory activities, while 2 and 3 were found to be weak inhibitors, whereas anti-glycation activities of 1-4 were not observed.
Acridine Derivatives as Chemotherapeutic Agents (2002)

Acridine derivatives are one of the oldest classes of bioactives, widely used as antibacterial and antiprotozoal agents. Some work in these areas continues, but recent research has focused mainly on their use as anticancer drugs, because of the ability of the acridine chromophore to intercalate DNA and inhibit topoisomerase enzymes.
Field dynamics and patho-genomics of Asian soybean rust pathogen Phakopsora pachyrhizi (2017)

Soybean (Glycine max) is an important legume crop and a rich source for plant proteins and vegetable oil. A major constraint for soybean production is Asian soybean rust (ASR) which causes yield losses of up to 80%. ASR is caused by the obligate biotrophic fungus Phakopsora pachyrhizi and can only be controlled by fungicide application. Extensive efforts have been made to find genetic resistance against P. pachyrhizi however, the pathogen has rapidly overcome major resistance genes Rpp1-5. Remarkably, P. pachyrhizi infects over 153 different legume species under suitable conditions, which suggests that P. pachyrhizi maintains diverse pathogenicity factors. The degree and distribution of genetic variation in the pathogen population is key for informed deployment of novel resistance genes but is largely unknown for P. pachyrhizi. To nderstand the field variation and population structure of P. pachyrhizi, infected field samples of soybean are collected from different locations across Brazil and east Africa. We have developed a next-generation sequencing approach to explore the population structure and genetic variation of P. pachyrhizi in these very different geographic locations. Sequencing of field samples will allow us to study sequence polymorphisms in P. pachyrhizi. We will aim to obtain a detailed understanding of the effector diversity in the field population of P. pachyrhizi. We will use this information for the sustainable deployment of genes that confer resistance to Asian Soybean Rust in transgenic soybean.
Efficient Visible Photoluminescence from Carbon Nanotubes in Zeolite Templates (2004)

We have found strong visible photoluminescence (PL) from 0.4 nm carbon nanotubes embedded in the ordered channels of a zeolite crystal matrix. The PL exhibits a broad emission band with an efficiency of $\ensuremath{\sim}1%--5%$. Strong polarization dependence is observed both on the excitation and emission, indicating a preferential optical dipole along the axis of carbon nanotubes. By correlating with the absorption and Raman spectra, we identify $(3,3)$ and $(4,2)$ tubes to be responsible for the PL peaks at $\ensuremath{\sim}2.6$ and $\ensuremath{\sim}1.7\text{ }\text{ }\mathrm{e}\mathrm{V}$, respectively.
Detection and quantification of the human IgG4 half‐molecule, HL, from unpurified cell‐culture supernatants (2004)

The presence and absence of inter-heavy-chain disulphide linkages contribute to the existence of the tetrameric (H(2)L(2)) and half (HL) human IgG molecules, respectively. Reduced effector response in the human IgG4 subclass presents an alternative therapeutic platform in a monoclonal-antibody (mAb) development program. During the initial cell-selection stage, titres of the recombinant human antibody present in crude cell-culture supernatants are determined by ELISA, a technique requiring nanogram quantities of mAb. In the case of an IgG4 antibody, this material is represented mainly by the combination of the tetrameric (H(2)L(2)) and dimeric (HL) forms of the antibody. The determination of concentrations or ratios of tetramer and dimer usually requires at least one chromatographic purification step, and thus frequently this is evaluated later in the mAb development process when the number of potential clones has been reduced. In the present paper we describe a Western-blot-based method that detects and quantifies IgG4 half-molecules, HL, from crude cell-culture supernatants without purification so that H(2)L(2)/HL ratios can be included as a part of early clonal evaluation along with the screening of mAb titres. This method was demonstrated (1) to have a linear HL detection range of 0.5-10 ng, (2) to require microlitre volumes of culture and (3) to react specifically with human IgG4 produced from hybridoma and Chinese-hamster ovary cell cultures. Moreover, this protocol is applicable to evaluate and monitor potential H(2)L(2)/HL variations as a result of changes during the process-development stage of a mAb development program.
Transient acidosis while retrieving a fear-related memory enhances its lability (2017)

Attenuating the strength of fearful memories could benefit people disabled by memories of past trauma. Pavlovian conditioning experiments indicate that a retrieval cue can return a conditioned aversive memory to a labile state. However, means to enhance retrieval and render a memory more labile are unknown. We hypothesized that augmenting synaptic signaling during retrieval would increase memory lability. To enhance synaptic transmission, mice inhaled CO<sub>2</sub> to induce an acidosis and activate acid sensing ion channels. Transient acidification increased the retrieval-induced lability of an aversive memory. The labile memory could then be weakened by an extinction protocol or strengthened by reconditioning. Coupling CO<sub>2</sub> inhalation to retrieval increased activation of amygdala neurons bearing the memory trace and increased the synaptic exchange from Ca<sup>2+</sup>-impermeable to Ca<sup>2+</sup>-permeable AMPA receptors. The results suggest that transient acidosis during retrieval renders the memory of an aversive event more labile and suggest a strategy to modify debilitating memories.