gebhart/patrepeval huggingface dataset:
Synthetic Routes to Polyheteroacenes:  Characterization of a Heterocyclic Ladder Polymer Containing Phenoxathiinium-type Building Blocks (2001)

The synthetic routes to ladder polymers that consist of benzenetetrayl subunits with oxo and methylsulfonio linkages are described. As the key intermediate, poly(phenylene oxide)s having pendant methylsulfenyl groups are prepared by copper-catalyzed oxidative polymerization of the corresponding phenols with O2. The oxidation of the polymer with an equimolar amount of H2O2 in the presence of acetic acid effects the high-yielding conversion of methylsulfenyl to methylsulfinyl groups without the formation of the undesired methylsulfonyl groups. The superacidified condensation of the resulting polymer (Swern reaction of aryl sulfoxides) under dilution conditions induces the polymer-analogous intramolecular electrophilic ring-closing reaction of the hydroxymethylphenylsulfonium cation onto the adjacent benzene ring to yield the required ladder polymer, which has proved to be a semiconductor with an intrinsic electric conductivity of 2 × 10-5 S/cm. A comparison of the spectroscopic properties of the ladder polymer with those of the model compounds such as 5-methylphenoxathiinium triflate and phenoxathiin discloses π-electron delocalization over the methylsulfonio linkages, demonstrating the efficacy of the ladderization for p−π/d−π interactions in arylsulfonium moieties. This synthetic approach permits the thio and alkylsulfonio ladder linkages for a variety of phenyl ethers to form in high yields.
Lassa Fever among Children in Eastern Province, Sierra Leone: A 7-year Retrospective Analysis (2012–2018) (2020)

Pediatric Lassa fever (LF) usually presents as a nonspecific febrile illness, similar to other endemic diseases in countries like Sierra Leone, where LF is considered to be hyperendemic. The nonspecificity of presentation and lack of research have made it difficult to fully understand best practices for pediatric management. We aim to describe clinical characteristics of hospitalized pediatric patients suspected or diagnosed with LF and assess factors associated with hospital outcomes among those with LF antigen-positive results. We conducted a 7-year retrospective cohort study using routine data for all children younger than 18 years admitted at the Kenema Government Hospital's LF ward. A total of 292 children with suspected or confirmed LF were analyzed. Overall, mortality was high (21%). Children with antigen-positive results had a high case fatality rate of 63% (P < 0.01). In univariate analyses, children who presented with unexplained bleeding (odds ratio [OR]: 3.58; 95% CI: 1.08-11.86; P = 0.040) and confusion (altered sensorium) (OR: 5.37; 95% CI: 1.34-21.48; P = 0.020) had increased odds of death. Abnormal serum levels of alanine aminotransferase (P = 0.001), creatinine (P = 0.004), and potassium (P = 0.003) were associated with increased likelihood of death in these children. Treatment with ribavirin was not significantly associated with survival (P = 0.916). Our findings provide insights into current pediatric LF clinical presentation and management. More evidence-based, high-quality research in creating predictive algorithms of antigen-positivity and hospital outcomes is needed in the management of pediatric LF.
An Advanced 3DTV Concept Providing Interoperability and Scalability for a Wide Range of Multi-Baseline Geometries (2006)

The paper discusses an advanced approach for 3DTV services that is based on the concept of an N× video-plus-depth data representation. It particularly considers aspects of interoperability, scalability, and adaptability for the case that different multi-baseline geometries are used for multi-view capturing and 3D reproduction. In addition, it presents a method for the creation of depth maps and an algorithm for depth-image-based rendering related to the system approach.
Lanthanides: Applications in Cancer Diagnosis and Therapy (2016)

Lanthanide complexes are of increasing importance in cancer diagnosis and therapy, owing to the versatile chemical and magnetic properties of the lanthanide-ion 4f electronic configuration. Following the first implementation of gadolinium(III)-based contrast agents in magnetic resonance imaging in the 1980s, lanthanide-based small molecules and nanomaterials have been investigated as cytotoxic agents and inhibitors, in photodynamic therapy, radiation therapy, drug/gene delivery, biosensing, and bioimaging. As the potential utility of lanthanides in these areas continues to increase, this timely review of current applications will be useful to medicinal chemists and other investigators interested in the latest developments and trends in this emerging field.
The Role of the Protein Corona in the Uptake Process of Nanoparticles (2018)

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Teamwork-centered autonomy for extended human-agent interaction in space applications (2014)

This paper summarizes our efforts to bring together and extend the best in current theory and technologies for teamwork-centered autonomy for space applications. Traditional planning technologies at the foundation of intelligent robotic systems typically take an autonomycentered approach, with representations, mechanisms, and algorithms that have been designed to ingest a set of goals and output a complete plan in the most efficient and sound fashion possible. A teamwork-centered autonomy approach, on the other hand, takes as a beginning premise that people are working in parallel alongside autonomous systems, and hence adopts the stance that the processes of understanding, problem solving, and task execution are necessarily incremental, subject to negotiation, and forever tentative. Thus, a successful approach to teamwork-centered autonomy will require that every element of the autonomous system be designed to facilitate the kind of give-and-take that quintessentially characterizes natural and effective teamwork among groups of people. We briefly describe the major components of this approach and current efforts to apply and evaluate its utility from both human-centered and cost-benefit perspectives.
Computer simulation of the free energy of peptides with the local states method: Analogues of gonadotropin releasing hormone in the random coil and stable states (1994)

The Helmholtz free energy F (rather than the energy) is the correct criterion for stability; therefore, calculation of F is important for peptides and proteins that can populate a large number of metastable states. The local states (LS) method proposed by H. Meirovitch [(1977) Chemical Physics Letters, Vol. 45, p. 389] enables one to obtain upper and lower bounds of the conformational free energy, FB (b,l) and FA (b,l), respectively, from molecular dynamics (MD) or Monte Carlo samples. The correlation parameter b is the number of consecutive dihedral or valence angles along the chain that are taken into account explicitly. The continuum angles are approximated by a discretization parameter l; the larger are b and l, the better the approximations; while FA can be estimated efficiently, it is more difficult to estimate FB. The method is further developed here by applying it to MD trajectories of a relatively large molecule (188 atoms), the potent "Asp4-Dpr10" antagonist [cyclo(4/10)-(Ac-delta 3Pro1-D-pFPhe2-D-Trp3-Asp4-Tyr5-D-Nal6-Leu7-Arg8 -Pro9- Dpr10-NH2)] of gonadotropin releasing hormone (GnRH). The molecule was simulated in vacuo at T = 300 K in two conformational states, previously investigated [J. Rizo et al. Journal of the American Chemical Society, (1992) Vol. 114, p. 2860], which differ by the orientation of the N-terminal tail, above (tail up, TU) and below (tail down, TD) the cyclic heptapeptide ring. As in previous applications of the LS method, we have found the following: (1) While FA is a crude approximation for the correct F, results for the difference, delta FA = FA (TD)-FA (TU) converge rapidly to 5.6 (1) kcal/mole as the approximation is improved (i.e., as b and l are increased), which suggests that this is the correct value for delta F; therefore TD is more stable than TU. (The corresponding difference in entropy, T delta SA = 1.3(2) kcal/mole, is equal to the value obtained by the harmonic approximation.) (2) The lowest approximation, which has the minimal number of local states, i.e., based on b = 0 (no correlations) and l = 1 (the angle values are distributed homogeneously), also leads to the correct value of delta F, within the error bars. This is important since the lowest approximation can be applied even to large proteins. (3) The method enables one to define the entropy of a part of the molecule and thus to measure the flexibility of this part.(ABSTRACT TRUNCATED AT 400 WORDS)
Combining SCCA-IgM and AFP-IgM levels increases accuracy of hepatocellular carcinoma detection (2009)

Background and AIm. The assessment of serum levels of SCCA-IgM or AFP-IgM immune complexes may improve diagnosis of HCC and may also predict the progression of cirrhosis to HCC. Simulation studies on multiple diagnostic assays of cancer biomarkers suggest to combine biomarkers by linear logistic regression in order to optimize diagnostic accuracy. Aim of the study was to evaluate the diagnostic accuracy improvement in HCC by SCCA-IgM and AFP-IgM combination in sera of HCC and cirrhotic patients.
Interrogating the effects of ion-implantation-induced defects on the energy storage properties of bulk molybdenum disulphide (2018)

The effects of implanted molybdenum and tungsten ions on the energy-storage properties of electrodes made from bulk molybdenum disulphide (MoS2) have been investigated. Six samples of crystalline MoS2 were modified by an ion-implantation strategy: three samples with Mo ions and three with W ions, at varying fluences and at an energy of 10 keV. The Stopping and Range of Ions in Matter (SRIM) software was used to determine the simulated defect density in terms of vacancies and the implanted ion-penetration depth. Raman spectroscopy and photoluminescence spectroscopy were used to determine any changes in the material as a result of irradiation. Electrochemistry showed that the ion-implanted MoS2 samples exhibited significant energy storage properties (such as capacity, cycling stability, coulombic efficiency, and electron transfer kinetics) compared to the pristine MoS2 samples, confirming the effects of defects induced by ion-implantation.
Coupling of a C2-Chiral Ferrocene with Phenylalkynyl Groups: Novel Ferrocenophanes Carrying Multiple Chiral Ferrocenyl Units (2010)

Upon treatment with CuCl/TMEDA (1:1) at a high [CuCl]/[1] ratio, enantiopure C(2)-chiral tetrasubstituted ferrocene 1 carrying phenylalkynyl groups is transformed into a novel family of chiral ferrocenophanes 2 and 3 with their ferrocenyl joints connected by a pi-conjugated rigid bridge. Compound 3, which is reminiscent of the Escher's endless staircase, is a single conformer with a one-handed helical chirality.
Spin Correlations and Finite-Size Effects in the One-Dimensional Kondo Box (2006)

We analyze the Kondo effect of a magnetic impurity attached to an ultrasmall metallic wire using the density matrix renormalization group. The spatial spin correlation function and the impurity spectral density are computed for system sizes of up to L=511 sites, covering the crossover from L<l{K} to L>l{K}, with l{K} the spin screening length. We establish a proportionality between the weight of the Kondo resonance and l{K} as a function of L. This suggests a spectroscopic way of detecting the Kondo cloud.
Nonlinear wideband optical filters for laser protection applications (2012)

With the development of more powerful lasers for applications, optical limiters and blockers are required for providing human eye and optical sensors protection. We report on passive optical power control devices based on a range of photonic nanostructures, including mainly nanostructures for spatial field localization to enhance optical nonlinearities. We present the two main optical power control mechanisms: blocking and limiting, as well as their corresponding nanoscale phenomena. We propose a dynamic protection to cameras, sensors and the human eye from laser threats.
Combined Application of Approximate Computing Techniques in DNN Hardware Accelerators (2022)

This paper applies Approximate Computing (AC) techniques to the main elements which form a DNN hardware accelerator, namely, computation, communication, and memory subsystems. Specifically, approximate multipliers for computation, link voltage swing reduction for communication, voltage over-scaling for the internal SRAM memory, and lossy compression of the external DRAM memory are considered. The different AC techniques are applied in isolation as well as in conjunction with each other. A set of representative CNN models are mapped onto the approximated hardware accelerators and the trade-offs performance vs. energy vs. accuracy are derived for the execution of CNN inferences.
Tunnel magnetoresistance oscillations in current perpendicular to plane geometry of CoAlO granular thin films (2002)

We have fabricated current-perpendicular-to-plane geometry samples consisting of a thin CoAlO granular film sandwiched by top and bottom electrodes with a submicron-sized contact area, and measured magnetotransport properties at 4.2 K. Clear Coulomb staircases due to the charging effect of Co granules are observed by the addition of an Al–O bottleneck layer which leads to an asymmetric configuration of tunnel resistances. Furthermore, tunnel magnetoresistance (TMR) shows oscillatory behavior associated with the Coulomb staircase. It is considered that the TMR oscillation is based on the interplay of spin-dependent tunneling and single electron tunneling.
Developing high safety Li-metal anodes for future high-energy Li-metal batteries: strategies and perspectives (2020)

Developing high-safety Li-metal anodes (LMAs) is extremely important for the application of high-energy Li-metal batteries (LMBs), especially Li-S and Li-O<sub>2</sub> battery systems. However, the notorious Li-dendrite growth problem results in serious safety concerns for any energy storage application. Through a recent combination of interface-based science, nanotechnology-based solutions and characterization methods, the LMA is now primed for a technological boom. In this review, the recent emerging strategies and perspectives on LMAs are summarized, following which the current huge evolution in interfacial chemistry regulation, optimizing electrolyte components, designing a rational 'host' for lithium metal, optimizing "solid-state electrolytes" and other emerging strategies for developing high-safety LMAs is highlighted. Furthermore, several state-of-the-art in situ/operando synchrotron-based X-ray techniques for high safety LMB research are introduced. With the further development of LMAs in the future, subsequent application in high energy LMBs is to be expected.
Impact of Cascade Number on the Thermal Properties of Broad‐Area Quantum Cascade Lasers (2017)

In this article the operation and thermal conductance of a series of quantum cascade lasers (QCLs) emitting at 4.6 μm grown with between 5 and 30 cascades in the active region is analyzed. A reduced number of cascades, but with fixed active region design, results in larger threshold current density but lower threshold power density. An analysis of the temperature gradient in the active region implies that for continuous‐wave QCL operation, using fewer than 15 cascades in the active region is advantageous, especially for broad‐area structures. We demonstrate a QCL with 10 cascades operating in continuous‐wave mode at room temperature emitting 0.9 W from a 4 mm × 30 μm stripe.
Contribution of ionic interactions to stationary phase selectivity in hydrophilic interaction chromatography (2022)

We compared the separation selectivities of 19 different hydrophilic interaction chromatography columns. The stationary phases included underivatized silica and hybrid particles, cyano-bonded silica, materials with neutral ligands such as amide, diol, pentahydroxy, and urea, zwitterionic sorbents, and mixed-mode materials with amine functionalities. A set of 77 small molecules was used to evaluate the columns. We visualized the retention behavior of the different columns using retention time correlation plots. The analytes were classified as cations, anions, or neutral based on their estimated charge under the separation conditions. This involved adjusting the dissociation constants of the analytes for the acetonitrile content of the mobile phase and experimentally determining the pH of the mobile phase containing 70% acetonitrile. The retention correlation plots show that the selectivity differences strongly depended on ionic interactions. Comparisons of the neutral stationary phases (e.g., diol vs. amide) showed more similar selectivity than did comparisons of neutral columns versus columns with cation or anion exchange activity (bare silica or amine columns, respectively). The zwitterionic columns did not behave as perfectly neutral. The correlation plots indicated that they exhibited either cation or anion exchange activity, although to a lesser degree than the silica and amine-containing stationary phases.
[Relationship between enteroviruses and diabetes]. (2008)

Environmental factors, especially viruses, are involved in the initiation or the acceleration of type 1 diabetes (T1D) pathogenesis. Epidemiological data strongly suggest that enteroviruses, like coxsackievirus B4 (CV-B4), can be associated with T1D. It has been demonstrated that enterovirus infections were significantly more prevalent in at risk individuals, such as siblings of diabetic patients, when they developed anti-b cells autoantibodies or T1D, and in recently diagnosed diabetic patients, compared with control subjects. The isolation of CV-B4 from the pancreas of diabetic patients strengthened the hypothesis of a relationship between the virus and the disease. Studies performed in vitro and in vivo in animal models helped in discovering mechanisms of the infection of pancreas and other tissues, able to play a role in the pathogenesis of T1D. Interestingly, it cannot be excluded that enteroviruses behave as half-devil half-angel since experimental studies suggest that, in certain conditions, these agents would be able to protect individuals against the disease.
Abstract IA-016: Metabolic deregulation drives a redox vulnerability in pancreatic cancer (2021)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is an almost universally fatal malignancy and there is an urgent need for new therapeutic targets. PDAC cells harbor genetic alterations and display metabolic changes that render them vulnerable to perturbations in redox homeostasis. Peroxiredoxin 4 (PRDX4) supports redox homeostasis by metabolizing H2O2 in the endoplasmic reticulum (ER). Based on functional genomics, we found that PDAC cell lines are dependent on PRDX4 for their growth and survival. We validated this dependency in established and primary PDAC cells, as well as in 3D models and orthotopic xenografts. PRDX4 depletion led to increased levels of reactive oxygen species (ROS). Tumor cells are exposed to fluctuating oxygen levels, which are known to augment ROS production. In line with this, PRDX4 addiction was also exacerbated in cells exposed to hypoxia and reoxygenation. Cell death induced by PRDX4 depletion was accompanied by DNA damage and a DNA-PKcs-governed DNA damage response. As such, PRDX4 depletion also sensitized cells and tumors to ionizing radiation. The source of ROS that created a dependency on PRDX4 was attributed to NADPH oxidase 4 (NOX4), which localizes to the ER membrane. The functional requirement for PRDX4 was correlated with cellular NADPH levels across different models of PDAC and could be rescued by depletion of NOX4 or NADPH. As such, this study has identified NOX4 as a link between metabolic deregulation and ER-specific redox vulnerability in PDAC. Since PRDX4 is not an essential gene in normal tissues, our work also suggests that PRDX4 represents a novel therapeutic target for pancreatic cancer that may be particularly potent in combination with radiotherapy. Citation Format: Marianne Koritzinsky, Pallavi Jain, Anna Dvorkin-Gheva, Lucie Malbeteau, Piriththiv Dhavarasa, Kevin R. Brown, Gun Ho Jang, Parth Vora, Faiyaz Notta, Jason Moffat, Paul C. Boutros. Metabolic deregulation drives a redox vulnerability in pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr IA-016.
Complement activation and cytokine response by BioProtein, a bacterial single cell protein (2007)

The bacterial single cell protein (BSCP), BioProtein, is dried bacterial mass derived from fermentation of the gram negative bacteria Methylococcus capsulatus, used for animal and fish feed. Workers in this industry suffer frequently from pulmonary and systemic symptoms which may be induced by an inflammatory reaction. The aim of the present study was to examine the effect of BSCP on inflammation in vitro as evaluated by complement activation and cytokine production. Human serum was incubated with BSCP and complement activation products specific for all pathways were detected by enzyme-linked immunosorbent assay (ELISA). Human whole blood anti-coagulated with lepirudin was incubated with BSCP and a panel of 27 biological mediators was measured using multiplex technology. BSCP induced a dose-dependent complement activation as revealed by a pronounced increase in alternative and terminal pathway activation (fivefold and 20-fold, respectively) at doses from 1 microg BSCP/ml serum and a similar, but less extensive (two- to fourfold) increase in activation of the lectin and classical pathways at doses from 100 and 1000 microg BSCP/ml serum, respectively. Similarly, BSCP induced a dose-dependent production of a number of cytokines, chemokines and growth factors in human whole blood. At doses as low as 0 x 05-0 x 5 microg BSCP/ml blood a substantial increase was seen for tumour necrosis factor (TNF)-alpha, interleukin (IL)-1-beta, IL-6, interferon (IFN)-gamma, IL-8, monocyte chemoattractant protein (MCP)-1, macrophage inflammatory protein (MIP)-1alpha, MIP-1beta, IL-4, IL-9, IL-17, IL-1Ra, granulocyte-colony-stimulating factor (G-CSF) and vascular endothelial growth factor (VEGF). Thus, BSCP induced a substantial activation of all three initial complement pathways as well as a pronounced cytokine response in vitro, indicating a potent inflammatory property of this agent.