gebhart/patrepeval huggingface dataset:
Role of chemical potentials in surface reconstruction: A new model and phase transition of GaAs(111)2x2 (1986)

The role of chemical potentials in surface reconstructions is examined and shown to be crucial for binary semiconductor srufaces such as GaAs(111)2\ifmmode\times\else\texttimes\fi{}2. We predict that under As-rich conditions a new model, the As triangle, is the lowest-energy geometry, whereas the Ga-vacancy model is appropriate for Ga-rich conditions. A change in the relative chemical potential of Ga and As should produce a phase transition between the two structures.
Modeling of the thermal properties of SARS-CoV-2 S-protein (2022)

We calculate the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at seven temperatures ranging from 3°C to 95°C by all-atom molecular dynamics (MD) µs-scale simulations with the objectives to understand the structural variations on the temperatures and to determine the potential phase transition while trying to correlate such findings of the S-protein with the observed properties of the SARS-CoV2. Our simulations revealed the following thermal properties of the S-protein: 1) It is structurally stable at 3°C, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; 2) Its structure varies more significantly at temperature values of 60°C-80°C; 3) The sharpest structural variations occur near 60°C, signaling a plausible critical temperature nearby; 4) The maximum deviation of the receptor-binding domain at 37°C, corroborating the anecdotal observations that the virus is most infective at 37°C; 5) The in silico data agree with reported experiments of the SARS-CoV-2 survival times from weeks to seconds by our clustering approach analysis. Our MD simulations at µs scales demonstrated the S-protein's thermodynamics of the critical states at around 60°C, and the stable and denatured states for temperatures below and above this value, respectively.
Proteomic and transcriptomic profiling reveals a link between the PI3K pathway and lower estrogen-receptor (ER) levels and activity in ER+ breast cancer (2010)

Our data suggest that luminal B tumors have hyperactive GFR/PI3K signaling associated with lower ER levels, which has been correlated with resistance to endocrine therapy. Targeting PI3K in these tumors might reverse loss of ER expression and signaling and restore hormonal sensitivity.
Reliability of CNEURO hyssops for sample collection in the SARS-CoV-2 diagnosis (2021)

Abstract Background: The detection of SARS-CoV-2 genetic material from nasopharyngeal swab samples by RT-PCR is the most specific and sensitive way to test suspected cases. However, factors such as the sampling process, type of hyssop used, and the anatomical area from which the sample is collected can distort the result and cause false negatives. Objective: to evaluate the reliability of CNUERO hyssops for sample collection in the SARS-CoV-2 diagnosis versus IMPROSWAB hyssops. Methods: To study the reliability of hyssops developed in Cuba for swabbing in the COVID-19 diagnosis, by comparing them to other hyssops successfully used for this task, 2 swabbing samples were obtained from each patient (136). One of these two samples was taken using the hyssops made in Cuba, while the other was taken employing another hyssop imported from Germany. The positive detections between both hyssops were compared using the Fisher exact test. The result of the detection of each hyssop was evaluated and compared using the ROC curve. Results: The use of CNEURO hyssops allowed detecting 45 out of 59 positive cases, while IMPROSAWAB hyssops detected 52 out of 59. Non-significant differences were detected between positive cases detected for each hyssop. The sensibility of sample detection using CNEURO hyssops was of 76.3 % and of 88.1 % when using IMPROSWAB hyssops. Hence, no significant differences are detected in the detection of cases using these two hyssops. Conclusion: CNEURO hyssops are safe and reliable to be used for nasopharyngeal samples taking of COVID-19 patients.
5G MmWave Module for the ns-3 Network Simulator (2015)

The increasing demand of data, along with the spectrum scarcity, are motivating a urgent shift towards exploiting new bands. This is the main reason behind identifying mmWaves as the key disruptive enabling technology for 5G cellular networks. Indeed, utilizing new bands means facing new challenges; in this context, they are mainly related to the radio propagation, which is shorter in range and more sensitive to obstacles. The resulting key aspects that need to be taken into account when designing mmWave cellular systems are directionality and link intermittency. The lack of network level results motivated this work, which aims at providing the first of a kind open source mmWave framework, based on the network simulator ns-3. The main focus of this work is the modeling of customizable channel, physical (PHY) and medium access control (MAC) layers for mmWave systems. The overall design and architecture of the model are discussed in details. Finally, the validity of our proposed framework is corroborated through the simulation of a simple scenario.
SVD-Based vs. Release 8 Codebooks for Single User MIMO LTE-A Uplink (2010)

The ambitious data rate target of the Long Term Evolution - Advanced (LTE-A) systems, which are currently being standardized by the 3rd Generation Partnership Project (3GPP), can only be achieved by using advanced Multiple Input Multiple Output (MIMO) antenna techniques on both uplink and downlink. In this paper, the focus is on LTE-A uplink and we discuss the suitability of two options for the closed loop precoded MIMO transmission. The first option is to use the same codebook of precoding matrices defined for LTE downlink, while the second option exploits the Singular Value Decomposition (SVD) of the channel matrix, which could theoretically achieve the MIMO capacity. Qualitative benefits of both solutions are discussed. Link level simulation results show that, the SVD-based approach only lead to a poor performance gain in terms of spectral efficiency over the LTE downlink codebook because of the losses due to the quantization of the right singular vectors of the channel matrix. Since SVD-based solution doesn't even exploit some useful properties (e.g., power balance over the antennas) which LTE Release 8 codebook offers, the latter results to be a better candidate for the closed loop MIMO transmission in LTE-A uplink.
A Survey on Peer-to-Peer Overlay Network Schemes (2008)

With the growing popularity of multimedia services such as IPTV, these P2P network overlay schemes are in the limelight and actively under studied as a good alternative or complementary solution for internet multimedia service systems. Therefore, in this paper, we review and compare the P2P overlay network schemes that have been introduced and researched recently by categorizing into two groups, i.e., "structured" and "unstructured".
Mutual benefit achieved by combining ultralow-field magnetic resonance and hyperpolarizing techniques (2018)

Ultralow-field (ULF) nuclear magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) are promising spectroscopy and imaging methods allowing for, e.g., the simultaneous detection of multiple nuclei or imaging in the vicinity of metals. To overcome the inherently low signal-to-noise ratio that usually hampers a wider application, we present an alternative approach to prepolarized ULF MRS employing hyperpolarization techniques like signal amplification by reversible exchange (SABRE) or Overhauser dynamic nuclear polarization (ODNP). Both techniques allow continuous hyperpolarization of <sup>1</sup>H as well as other MR-active nuclei. For the implementation, a superconducting quantum interference device (SQUID)-based ULF MRS/MRI detection scheme was constructed. Due to the very low intrinsic noise level, SQUIDs are superior to conventional Faraday detection coils at ULFs. Additionally, the broadband characteristics of SQUIDs enable them to simultaneously detect the MR signal of different nuclei such as <sup>13</sup>C, <sup>19</sup>F, or <sup>1</sup>H. Since SQUIDs detect the MR signal directly, they are an ideal tool for a quantitative investigation of hyperpolarization techniques such as SABRE or ODNP.
An Output VSWR Protection Circuit Using Collector/Emitter Avalanche Breakdown for SiGe HBT Power Amplifiers (2004)

An output load VSWR (voltage standing wave ratio) protection circuit for SiGe power amplifiers (PA) is presented by using the relatively low collector-emitter avalanche breakdown characteristic of SiGe HBT. Unlike the conventional diode-type switch, the new protection circuit completely eliminates the undesirable dc leakage current during the normal operation of the PA. Simulations and measurements show the proposed protection circuit enhances the ruggedness of the PA at harsh operating condition while it imposes only minor performance degradation at normal operating condition.
Prenatal exposure to environmental factors and congenital limb defects (2016)

Limb congenital defects afflict approximately 0.6:1000 live births. In addition to genetic factors, prenatal exposure to drugs and environmental toxicants, represents a major contributing factor to limb defects. Examples of well-recognized limb teratogenic agents include thalidomide, warfarin, valproic acid, misoprostol, and phenytoin. While the mechanism by which these agents cause dymorphogenesis is increasingly clear, prediction of the limb teratogenicity of many thousands of as yet uncharacterized environmental factors (pollutants) remains inexact. This is limited by the insufficiencies of currently available models. Specifically, in vivo approaches using guideline animal models have inherently deficient predictive power due to genomic and anatomic differences that complicate mechanistic comparisons. On the other hand, in vitro two-dimensional (2D) cell cultures, while accessible for cellular and molecular experimentation, do not reflect the three-dimensional (3D) morphogenetic events in vivo nor systemic influences. More robust and accessible models based on human cells that accurately replicate specific processes of embryonic limb development are needed to enhance limb teratogenesis prediction and to permit mechanistic analysis of the adverse outcome pathways. Recent advances in elucidating mechanisms of normal development will aid in the development of process-specific 3D cell cultures within specialized bioreactors to support multicellular microtissues or organoid constructs that will lead to increased understanding of cell functions, cell-to-cell signaling, pathway networks, and mechanisms of toxicity. The promise is prompting researchers to look to such 3D microphysiological systems to help sort out complex and often subtle interactions relevant to developmental malformations that would not be evident by standard 2D cell culture testing. Birth Defects Research (Part C) 108:243-273, 2016. © 2016 Wiley Periodicals, Inc.
Improving Speech Understanding in Adverse Listening Environments using Distributed Microphone Processing (2014)

References  Speech understanding in highly adverse listening environments remains a major challenge for hearing aid wearers  In natural conversations, talkers move around freely. In addition to hearing aid microphones, there are microphones on other devices such as smartphones  With wireless connectivity, it is possible to utilize not only hearing aid microphones, but also other wirelessly connected microphones to improve speech understanding in such an adverse listening environment  Goal  Preliminary illustration of the benefits using a distributed microphone processing algorithm  Discuss the challenges in deploying such an algorithm in real-world
Mass and charge transport in polyethylene – Structure, morphology and properties (2022)

Polyethylene is a model for semicrystalline polymers that provides the option to vary crystallinity within wide ranges and then to establish relationships between structure and mass and charge transport properties. Three different topics are covered: diffusion of n-hexane in polyethylene, extensive penetrant uptake kinetics, swelling and the design of a novel sensor, and finally electrical conduction in polyethylene, a field important to modern distribution of electric power (HVDC). This feature article presents past and ongoing studies at KTH Royal Institute of Technology using a variety of experimental methods and computer-aided simulation and modelling.
The Chalcone Synthase Superfamily of Type III Polyketide Synthases (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Electroglottography and microphone signals assessed by approximate entropy in normal and dysphonic subjects. (2009)

Approximate Entropy is a method which provides a model independent nonlinear measure (the index ApEn) of the “regularity” of the process generating a time-series. In recent years, ApEn has been vigorously employed in the study of several biological signals, but only a few applications in the analysis of vocal disorders have been proposed. Here, we investigate the potential usefulness of ApEn in the study of electroglottography and microphone signals in normal and dysphonic subjects. Results show that statistically significant ApEn differences between the two groups can be found, more easily detectable in the microphone signal case.
Huntingtin lowering reduces somatic instability at CAG-expanded loci (2020)

Abstract Expanded trinucleotide repeats cause many human diseases, including Huntington’s disease (HD). Recent studies indicate that somatic instability of these repeats contributes to pathogenesis in several expansion disorders. We find that lowering huntingtin protein (HTT) levels reduces somatic instability of both the Htt and Atxn2 CAG tracts in knockin mouse models, and the HTT CAG tract in human iPSC-derived neurons, revealing an unexpected role for HTT in regulating somatic instability.
A Novel Small Molecule Inhibitor of Influenza A Viruses that Targets Polymerase Function and Indirectly Induces Interferon (2012)

Influenza viruses continue to pose a major public health threat worldwide and options for antiviral therapy are limited by the emergence of drug-resistant virus strains. The antiviral cytokine, interferon (IFN) is an essential mediator of the innate immune response and influenza viruses, like many viruses, have evolved strategies to evade this response, resulting in increased replication and enhanced pathogenicity. A cell-based assay that monitors IFN production was developed and applied in a high-throughput compound screen to identify molecules that restore the IFN response to influenza virus infected cells. We report the identification of compound ASN2, which induces IFN only in the presence of influenza virus infection. ASN2 preferentially inhibits the growth of influenza A viruses, including the 1918 H1N1, 1968 H3N2 and 2009 H1N1 pandemic strains and avian H5N1 virus. In vivo, ASN2 partially protects mice challenged with a lethal dose of influenza A virus. Surprisingly, we found that the antiviral activity of ASN2 is not dependent on IFN production and signaling. Rather, its IFN-inducing property appears to be an indirect effect resulting from ASN2-mediated inhibition of viral polymerase function, and subsequent loss of the expression of the viral IFN antagonist, NS1. Moreover, we identified a single amino acid mutation at position 499 of the influenza virus PB1 protein that confers resistance to ASN2, suggesting that PB1 is the direct target. This two-pronged antiviral mechanism, consisting of direct inhibition of virus replication and simultaneous activation of the host innate immune response, is a unique property not previously described for any single antiviral molecule.
Statistical Analysis of Cellular Retention by Micro-well Arrays (2010)

An understanding of cell deposition and retention properties of micro-well arrays is required to optimize high-throughput, single-cell seeding and culture processes. This paper describes the influence of micro-well geometry and fluid shear stress on cell retention statistics. A 2-layer PDMS micro-well culture device consisting of flow-cell and micro-well layers was manufactured by soft-lithography. The micro-well layer consisted of an array of 6000 micro-wells that had a diameter of 200μm and were either 35-μm or 80-μm deep. The flow-cell plate separation was 50μm or 280μm. The deposition and retention of a KG1a cell line in the 4 types of devices were studied under conditions of creeping flow. Cells were injected as a bolus into the device and allowed to sediment into micro-wells under static conditions. Flow was then initiated to determine the retention of cells in the micro-wells at various shear stresses. Cell number in individual micro-wells before and after applied shear stress was counted using large field automated video microscopy. The mean number of retained cells was related to well depth, parallel-plate separation and shear stress. The influence of these parameters on cell retention was described by a multiple linear regression model. At higher shear stress, the cell retention number was Poisson distributed. This device demonstrates the ability to use microfluidics to study the clonal properties of stem and progenitor cells.
Dexamethasone inhibition of leucocyte adhesion to rat mesenteric postcapillary venules: role of intercellular adhesion molecule 1 and KC (1999)

Induction by IL-1beta of endogenous ICAM-1 and KC contributes to leucocyte adhesion to inflamed mesenteric vessels. Without excluding other possible mediators, these data clearly show that dexamethasone interferes with ICAM-1 expression and KC release from mast cells, resulting in suppression of leucocyte accumulation in the bowel wall, which is a prominent feature of several gastrointestinal pathologies.
Schottky barrier height reduction of NiGe/Ge junction by P ion implantation for metal source/drain Ge CMOS devices (2014)

We have demonstrated effective electron Schottky barrier height (eSBH) reduction of NiGe/Ge contacts using phosphorus ion implantation after germanidation. The eSBH was drastically reduced from 0.62 eV to 0.09 eV under optimum implantation and subsequent annealing conditions. Moreover, systematic studies of NiGe/Ge contacts with various P ion profiles indicated the variation in the eSBH at NiGe/Ge interface. This method allows us to design and control junction characteristics for future Ge-based devices.
Data from: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity (2017)

Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly lower for individuals reactive to Pfs48/45, Pfs230 or to combinations of the novel TRA-associated proteins. We also show that naturally acquired purified antibodies against key transmission-blocking epitopes of Pfs48/45 and Pfs230 are mechanistically involved in TRA, whereas sera depleted of these antibodies retain high-level, complement-independent TRA. Our analysis demonstrates that host antibody responses to gametocyte proteins are associated with reduced malaria transmission efficiency from humans to mosquitoes.
Power measurements and cooling of the DOME 28nm 1.8GHz 24-thread ppc64 &#x03BC;Server compute node (2015)

Within the IBM/ASTRON DOME μServer project, we are finishing two types of memory DIMM-like sized compute nodes. The first is based on the 4-core/4-thread 2.2 GHz P5040 45nm SoC and the second on a 12-core/24-thread 1.8 GHz T4240 28nm SoC. Both SoCs employ the 64-bit Power instruction set. We show T4240 Specbench performance results, power consumption, describe the packaging of our first P5040 based 8-way hot-water cooled cluster and provide an outlook.
Ruthenium-Catalyzed Transfer Hydrogenation of Imines by Propan-2-ol in Benzene (2002)

Transfer hydrogenation of a variety of different imines to the corresponding amines by propan-2-ol in benzene catalyzed by [Ru2(CO)4(mu-H)(C4Ph4COHOCC4Ph4)] (1) has been studied. The reaction is highly efficient with turnover frequencies of over 800 per hour, and the product amines were obtained in excellent yields. A remarkable concentration dependence of propan-2-ol was observed when the reaction was run in benzene as cosolvent. An optimum was obtained at 24 equivalents of propan-2-ol to imine, and further increase of the propan-2-ol led to a dramatic decrease in rate. Also the use of polar cosolvents with 24 equivalents of propan-2-ol gave a low rate. It was found that ketimines react faster than aldimines and that electron-donating substituents on the imine increase the rate of the catalytic transfer hydrogenation. Electron-withdrawing substituents decreased the rate. An isomerization was observed with imines having an alpha-hydrogen at the N-alkyl substituent, which is in accordance with a mechanism involving a ruthenium-amine intermediate. It was demonstrated that the ruthenium-amine complex from alpha-methylbenzylamine, corresponding to the postulated intermediate, can replace 1 as catalyst in the transfer hydrogenation of imines. A primary deuterium isotope effect of kCH/CD = 2.7 +/- 0.25 was observed when 2-deuterio-propan-2-ol was used in place of propan-2-ol in the transfer hydrogenation of N-phenyl-(1-phenylethylidene)amine.
Evaluation of lithographic benefits of using ILT techniques for 22nm-node (2010)

As increasing complexity of design and scaling continue to push lithographic imaging to its k1 limit, lithographers have been developing computational lithography solutions to extend 193nm immersion lithography to the 22nm technology node. In our paper, we investigate the beneficial source or mask solutions with respect to pattern fidelity and process variation (PV) band performances for 1D through pitch patterns, SRAM and Random Logic Standard Cells. The performances of two different computational lithography solutions, idealized un-constrained ILT mask and manhattanized mask rule constrain (MRC) compliant mask, are compared. Additionally performance benefits for process-window aware hybrid assist feature (AF) are gauged against traditional rule-based AF. The results of this study will demonstrate the lithographic performance contribution that can be obtained from these mask optimization techniques in addition to what source optimization can achieve.
Singlet depletion anisotropy decay: from nanoseconds to milliseconds (1990)

We provide a brief summary of current problems in DNA-protein interactions and argue that measurement of the elastic properties of DNA is critical to understanding these problems We discuss the ing1et depletion technique and various improvements we have been able to Achieve. Previous results using this technique are discussed, and we will present our plans for future experiments.