gebhart/patrepeval huggingface dataset:
Metabolic pathway analysis of a recombinant yeast for rational strain development (2002)

Elementary mode analysis has been used to study a metabolic pathway model of a recombinant Saccharomyces cerevisiae system that was genetically engineered to produce the bacterial storage compound poly-beta-hydroxybutyrate (PHB). The model includes biochemical reactions from the intermediary metabolism and takes into account cellular compartmentalization as well as the reversibility/irreversibility of the reactions. The reaction network connects the production and/or consumption of eight external metabolites including glucose, acetate, glycerol, ethanol, PHB, CO(2), succinate, and adenosine triphosphate (ATP). Elementary mode analysis of the wild-type S. cerevisiae system reveals 241 unique reaction combinations that balance the eight external metabolites. When the recombinant PHB pathway is included, and when the reaction model is altered to simulate the experimental conditions when PHB accumulates, the analysis reveals 20 unique elementary modes. Of these 20 modes, 7 produce PHB with the optimal mode having a theoretical PHB carbon yield of 0.67. Elementary mode analysis was also used to analyze the possible effects of biochemical network modifications and altered culturing conditions. When the natively absent ATP citrate-lyase activity is added to the recombinant reaction network, the number of unique modes increases from 20 to 496, with 314 of these modes producing PHB. With this topological modification, the maximum theoretical PHB carbon yield increases from 0.67 to 0.83. Adding a transhydrogenase reaction to the model also improves the theoretical conversion of substrate into PHB. The recombinant system with the transhydrogenase reaction but without the ATP citrate-lyase reaction has an increase in PHB carbon yield from 0.67 to 0.71. When the model includes both the ATP citrate-lyase reaction and the transhydrogenase reaction, the maximum theoretical carbon yield increases to 0.84. The reaction model was also used to explore the possibility of producing PHB under anaerobic conditions. In the absence of oxygen, the recombinant reaction network possesses two elementary modes capable of producing PHB. Interestingly, both modes also produce ethanol. Elementary mode analysis provides a means of deconstructing complex metabolic networks into their basic functional units. This information can be used for analyzing existing pathways and for the rational design of further modifications that could improve the system's conversion of substrate into product.
Genetic characterization of staphopain genes in Staphylococcus aureus (2004)

Staphylococcus aureus , a leading cause of bacterial infections in humans, is endowed with a wealth of virulence factors that contribute to the disease process. Several extracellular proteolytic enzymes, including cysteine proteinases referred to as the staphopains (staphopain A, encoded by the scpA gene, and staphopain B, encoded by sspB ), have proposed roles for staphylococcal virulence. Here we present data regarding the distribution, copy number and genetic variability of the genes encoding the staphopains in a large number of S. aureus strains. The polymorphism of the scpA and sspB genes in three laboratory strains and 126 clinical isolates was analyzed by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). Both genes were detected in all isolates by PCR amplification and, based on the PCR-RFLP patterns, classified as four types for scpA and six types for sspB . Those with the most divergent patterns were subjected to DNA sequencing and compared with genomic sequence data for the seven available strains of S. aureus . Southern blot analysis of the scpA and sspB sequences indicates that they are strongly conserved as single-copy genes in the genome of each S. aureus strain investigated. Taken together, these data suggest that the staphopains have important housekeeping and/or virulence functions, and therefore may constitute an interesting target for the development of therapeutic inhibitors for the treatment of staphylococcal diseases.
Localized Surface Plasmon Resonance in Semiconductor Nanocrystals (2018)

Localized surface plasmon resonance (LSPR) in semiconductor nanocrystals (NCs) that results in resonant absorption, scattering, and near field enhancement around the NC can be tuned across a wide optical spectral range from visible to far-infrared by synthetically varying doping level, and post synthetically via chemical oxidation and reduction, photochemical control, and electrochemical control. In this review, we will discuss the fundamental electromagnetic dynamics governing light matter interaction in plasmonic semiconductor NCs and the realization of various distinctive physical properties made possible by the advancement of colloidal synthesis routes to such NCs. Here, we will illustrate how free carrier dielectric properties are induced in various semiconductor materials including metal oxides, metal chalcogenides, metal nitrides, silicon, and other materials. We will highlight the applicability and limitations of the Drude model as applied to semiconductors considering the complex band structures and crystal structures that predominate and quantum effects that emerge at nonclassical sizes. We will also emphasize the impact of dopant hybridization with bands of the host lattice as well as the interplay of shape and crystal structure in determining the LSPR characteristics of semiconductor NCs. To illustrate the discussion regarding both physical and synthetic aspects of LSPR-active NCs, we will focus on metal oxides with substantial consideration also of copper chalcogenide NCs, with select examples drawn from the literature on other doped semiconductor materials. Furthermore, we will discuss the promise that LSPR in doped semiconductor NCs holds for a wide range of applications such as infrared spectroscopy, energy-saving technologies like smart windows and waste heat management, biomedical applications including therapy and imaging, and optical applications like two photon upconversion, enhanced luminesence, and infrared metasurfaces.
Optimized block-diagonalization precoding technique using givens rotations QR decomposition (2017)

The emerging 5G mobile communication standard aims to increase the throughput and, in the same time, to considerably increase the number of users serviced concurrently (Internet of Things). The key direction for achieving these requirements is to heavily extend the use of the spatial degrees of freedom, especially in the multi-user scenarios. Multi-User Massive MIMO (MU-MIMO) is one of the key technologies that responds well to the 5G needs. However, the use of MU-MIMO in the downlink direction raises the collaborative detection problem at the user side, thus the elimination of the inter-user interference becomes necessary. The paper presents a reduced complexity linear transmitter precoding technique that cancels the inter-user interference in a downlink MU-MIMO system. The reduced complexity is achieved through re-using as many low-level operations as possible. The method is suitable for implementation on any modern processor and proven to be scalable to a Massive MIMO scenario without any loss in performance.
Effect of Curvature on Displacement Forces Acting on Aortic Endografts: A 3-Dimensional Computational Analysis (2009)

The largest component of the force acting on the aortic endograft is in the sideways direction, with respect to the blood flow, rather than in the downward (caudal) direction as is commonly assumed. Increased curvature of the aortic endograft increases the magnitude of the sideways displacement force. The degree of angulation of the proximal and distal ends of the endograft influence the magnitude and direction of displacement force. These factors may have a significant influence on the propensity of endografts to migrate in vivo.
The ‘Developmental Origins’ Hypothesis: relevance to the obstetrician and gynecologist (2015)

The recognition of 'fetal origins of adult disease' has placed new responsibilities on the obstetrician, as antenatal care is no longer simply about ensuring good perinatal outcomes, but also needs to plan for optimal long-term health for mother and baby. Recently, it has become clear that the intrauterine environment has a broad and long-lasting impact, influencing fetal and childhood growth and development as well as future cardiovascular health, non-communicable disease risk and fertility. This article looks specifically at the importance of the developmental origins of ovarian reserve and ageing, the role of the placenta and maternal nutrition before and during pregnancy. It also reviews recent insights in developmental medicine of relevance to the obstetrician, and outlines emerging evidence supporting a proactive clinical approach to optimizing periconceptional as well as antenatal care aimed to protect newborns against long-term disease susceptibility.
Molecular computing (2003)

Molecular (or DNA) computing is founded on the idea that, given enough strands of DNA, and using certain biological operations one use DNA molecules to simulate some classic computations efficiently. The original insight is due to Leonard Adleman (1994) who showed how DNA can be used to solve the Directed Hamiltonian Path (DHP) graph problem (see GRAPH THEORY). Then Richard Lipton (1995) showed how to use DNA to solve more general problems, namely to find satisfying assignments for arbitrary Boolean formulas (see BOOLEAN ALGEBRA). Lipton's approach shows that DNA can be used to solve a large class of combinatorial search problems. Since then there have been many new ideas on DNA computation. In this article we review some of these proposals.
Systematic design of photonic crystal structures using topology optimization: Low-loss waveguide bends (2004)

Topology optimization is a promising method for systematic design of optical devices. As an example, we demonstrate how the method can be used to design a 90° bend in a two-dimensional photonic crystal waveguide with a transmission loss of less than 0.3% in almost the entire frequency range of the guided mode. The method can directly be applied to the design of other optical devices, e.g., multiplexers and wave splitters, with optimized performance.
A prospective study evaluating stereotactic body radiation therapy in unresectable, recurrent, or residual pancreatic adenocarcinoma. (2016)

454 Background: The purpose of this prospective, non-randomized phase II single-institution study was to evaluate if local control can be achieved with reasonable acute and late GI toxicity using fractionated SBRT in patients with unresectable, recurrent, or residual locally advanced pancreatic cancer (LAPC). Methods: A total of 24 patients with LAPC were enrolled from June 2013 to August 2014. Eligibility required stability after induction chemotherapy or residual disease or local failure after surgery. Induction chemotherapy regimens consisted of: (1) gemcitabine alone (8%); (2) gemcitabine-based regimens (17%); (3) FOLFIRINOX-based regimens (63%); or (4) combination regimens (13%). Chemotherapy was discontinued one week prior to SBRT. Patients received a median cumulative dose of 33 Gy in 5 fractions (5-6.6 Gy/fraction). Patients were permitted to resume chemotherapy one week post-SBRT. Toxicity was assessed using the NCI CTCAE version 4.0. Results: Of the 24 patients, 58% were male and 50% had tumors in the head of the pancreas. Median age at diagnosis was 66.8 years, and median follow-up from the date of diagnosis was 11.9 months (range, 7.4-29.7 months). There have not been any acute or late grade ≥ 2 gastritis, enteritis, fistula, or ulcer toxicities (primary endpoint). Median OS has not yet been reached, median LPFS was 19.3 months (95% CI, 12.3-14.8), median DMFS was 13.6 months (95% CI, 9.2-17.9) and median PFS was 13.6 months (95% CI, 13.5-25.2). Plasma CA 19-9 level was non-significantly reduced after SBRT, displaying a -9.15 average percent change from baseline (median time after SBRT, 1.2 months). FFLP at 1 year was 83.9%. Eight (33%) patients underwent successful surgery following SBRT, with rates of both margin- and node-negative resection being 75%. Conclusions: Chemotherapy followed by fractionated SBRT results in favorable local control and survival with minimal acute and late GI toxicity. A notable proportion of patients initially deemed unresectable underwent successful resection. This study suggests that SBRT can be safely given following more aggressive multiagent chemotherapy in patients with LAPC. Clinical trial information: NCT01781728.
Prevalence of <i>Prevotella intermedia</i> and the presence of interpain A in subgingival plaque samples. (2015)

&lt;p&gt;Prevalence of &lt;i&gt;Prevotella intermedia&lt;/i&gt; and the presence of interpain A in subgingival plaque samples.&lt;/p&gt;
Sensitive and selective detection of plutonium using high resolution x-ray (2024)

Abstract Not Provided
Fast Mode Decision and Motion Estimation for H.264 with a Focus on MPEG-2/H.264 Transcoding (2005)

The H.264 standard achieves much higher coding efficiency than previous video coding standards, due to its improved inter and intra prediction modes which come with a cost of higher computational complexity. When transcoding to H.264 from MPEG-2, motion information from MPEG-2 can be used to speed up the motion search. Fast mode decision algorithms are proposed for B and P frames, and a fast intra prediction algorithm is developed for intra coding. In addition, fast motion estimation is developed by reusing the motion information from MPEG-2. Simulation results demonstrate that we can achieve significant complexity reduction while maintaining the coding efficiency.
Efficacy of Naproxen/Fexofenadine (SJP-003) in the Prevention of Side Effects of Influenza Vaccination: Four Case Studies (2022)

The influenza virus is associated with sickness, and in particular among vulnerable populations such as elderly and those with underlying disease with hospitalization and increased mortality rates. Vaccination is an effective way to prevent infection with influenza. However, undesirable side effects of the vaccination are commonly experienced, and comprise one of the primary reasons for a substantial group of individuals to refrain from vaccination. An effective treatment against vaccination side effects could increase the overall willingness to vaccinate against influenza. Here, four cases are presented that self-administered SJP-003 (a combination of 220 mg naproxen sodium, directly followed by a single oral dose of 60 mg fexofenadine HCL), 2 h before and 10 h after influenza vaccination. No flu-like symptoms and pain at the injection site were reported. These observations warrant further investigation of SJP-003 in double-blind, placebo-controlled clinical trials.
Phase-change recording media of 20-GB capacity for system with 0.6-mm-thick substrate (2003)

We have developed phase change media of 20GB user data capacity for the next generation optical recording system using a blue-violet laser diode with the wavelength of 405nm. An objective lens with the numerical aperture of 0.65 has been used along with mm-thick substrates on which the laser is incident. We have employed the land and groove recording. A transparent film with high thermal conductivity has been adopted at the light incident side of the recording layer in order to improve the carrier to noise ratio and the erase ratio as well as to reduce the cross-erase. Bottom channel bit error rate of less than 1&times;10<sup>-6</sup> has been obtained and its wide tilt margins have successfully demonstrated the strong feasibility for the next generation rewritable system.
Reconfigurable Intelligent Surface Deployment in 5G and Beyond 5G Cellular Networks (2022)

The successful deployment of Reconfigurable Intelligent Surface (RIS) technology in cellular networks is highly dependent on the availability of existing frameworks to enable the integration and operation of RIS panels in real-world propagation environments, preferably with low standardisation impact. This paper identifies the suitability of the existing 5G-NR frameworks for channel estimation, link control and beam management. The authors address the challenges related to the control of RIS infrastructure in radio environments in which multiple cellular networks have been deployed. The impact of adjacent bands and RIS operation that includes inter-cell links of another network is also discussed. The wideband reflective properties of the RIS are considered non-separable amongst operators.
Monte Carlo simulation of differences in free energies of hydration (1985)

Perturbation theory has been applied to calculate the relative free energies of hydration of methanol and ethane in dilute soluton. It is demonstrated that only two or three Monte Carlo simulations using double-wide sampling are necessary to obtain results with high precision. The small statistical uncertainty in the computed change in free energy of hydration and the good accord with experimental thermodynamic data are most encouraging for application of the procedure to a wide range of problems. Structural effects accompanying the mutation of methanol to ethane in water are also discussed; hydrogen bonding to the solute is essentialy eliminated by only a 25% reduction in the atomic charges of methanol.
Supplementary document for Layer-based, depth-resolved computation of attenuation coefficients and backscattering fractions in tissue using optical coherence tomography - 5330499.pdf (2021)

Supplementary document
Flexible and High-Performance Electrochromic Devices Enabled by Self-Assembled 2D TiO2/MXene Heterostructures (2020)

Abstract Transition metal oxides (TMO) are promising electrochromic (EC) materials for applications such as smart windows and displays, yet challenge still exists to achieve good flexibility, high coloration efficiency and fast response simultaneously. MXenes (e.g. Ti3C2Tx) and their derived TMOs (e.g. 2D TiO2) are good candidates for high-performance and flexible EC devices because of their 2D nature and the possibility of assembling them into loosely networked structures. Here we demonstrate flexible, fast, and high-coloration-efficiency EC devices based on self-assembled 2D TiO2/Ti3C2Tx heterostructures, with the Ti3C2Tx layer as the transparent electrode, and the 2D TiO2 layer as the EC layer. Benefiting from the well-balanced porosity and connectivity of these assembled nanometer-thick heterostructures, they present fast and efficient ion and electron transport, as well as superior mechanical and electrochemical stability. We further demonstrate large-area flexible devices which could potentially be integrated onto curved and flexible surfaces for future ubiquitous electronics.
ChemInform Abstract: Reduction of Alkyl Halides by Triethylsilane Based on a Cationic Iridium Bis(phosphinite) Pincer Catalyst: Scope, Selectivity and Mechanism. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Search for charginos and neutralinos in final states with two boosted hadronically decaying bosons and missing transverse momentum in pp collisions at s=13  TeV with the ATLAS detector (2021)

A search for charginos and neutralinos at the Large Hadron Collider using fully hadronic final states and missing transverse momentum is reported. Pair-produced charginos or neutralinos are explored, each decaying into a high-${p}_{\mathrm{T}}$ Standard Model weak boson. Fully hadronic final states are studied to exploit the advantage of the large branching ratio, and the efficient rejection of backgrounds by identifying the high-${p}_{\mathrm{T}}$ bosons using large-radius jets and jet substructure information. An integrated luminosity of $139\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of proton-proton collision data collected by the ATLAS detector at a center-of-mass energy of 13 TeV is used. No significant excess is found beyond the Standard Model expectation. Exclusion limits at the 95% confidence level are set on wino or higgsino production with various assumptions about the decay branching ratios and the type of lightest supersymmetric particle. A wino (higgsino) mass up to 1060 (900) GeV is excluded when the lightest supersymmetry particle mass is below 400 (240) GeV and the mass splitting is larger than 400 (450) GeV. The sensitivity to high-mass winos and higgsinos is significantly extended relative to previous LHC searches using other final states.
Role of mu and delta receptors in the supraspinal and spinal analgesic effects of [D-Pen2, D-Pen5] enkephalin in the mouse (1988)

The opioid receptors involved in the supraspinal and spinal actions of [D-Pen2, D-Pen5]enkephalin (DPDPE) for production and/or modulation of analgesia were investigated in two thermal analgesic tests, the mouse warm water (55 degrees C) tail-withdrawal assay and the radiant heat tail-flick test. Two approaches were used at supraspinal and spinal sites: determination of possible cross-tolerance between morphine and a variety of receptor selective/nonselective agonists (DPDPE, [D-Pen2, L-Pen5]enkephalin (DPLPE), [D-Ala2, MePhe4, Gly-ol]enkephalin, [D-Ala2, Met5]enkephalin amide, [D-Ser2, Leu5, Thr6]enkephalin and [D-Thr2 Leu, Thr6]enkephalin) and possible potentiation of morphine (mu) analgesia by proposed delta agonists (DPDPE, DPLPE and [D-Ala2, D-Leu5]enkephalin) in naive and morphine-tolerant mice. Additionally, proposed mu (morphine) and delta (DPDPE) agonists were evaluated for their i.c.v. analgesic effectiveness in the absence, and in the presence, of the proposed delta antagonist ICI 174,864. The present communication now reports that after i.c.v. administration analgesic cross-tolerance could be demonstrated between morphine and a variety of relatively selective or nonselective opioids but not to the highly delta selective DPDPE and DPLPE. This result was consistent with direct antagonism of i.c.v. DPDPE, but not morphine analgesia, by ICI 174,864. Furthermore, i.c.v. DPDPE and DPLPE were able to potentiate morphine analgesia in either naive or morphine-tolerant mice. In contrast, after intrathecal administration, cross-tolerance could be demonstrated between DPDPE or DPLPE and morphine, and no potentiation of morphine by DPDPE could be observed.(ABSTRACT TRUNCATED AT 250 WORDS)
Synchronization and collision avoidance in non-linear flocking networks of autonomous agents (2016)

We introduce and discuss two novel second-order consensus networks with state-dependent couplings of Cucker-Smale type. The first scheme models flocking to synchronization over a network of agents where the alignment of the agent's states occurs over a non-trivial limit orbit that is generated by the internal dynamics of each individual agent. The second scheme models the speed alignment of a group of agents which avoid approaching each other closer than a prescribed distance. While seemingly different, both of these systems can be analyzed using the same mathematical methods. We rigorously analyze both examples and reveal their striking similarities. We arrive at sufficient conditions that relate the initial configurations and the systems' parameters that give rise to a collective common behavior. Simulation examples are presented to support our theoretical conclusions.