gebhart/patrepeval huggingface dataset:
Antimicrobial combination treatment including ciprofloxacin decreased the mortality rate of Pseudomonas aeruginosa bacteraemia: a retrospective cohort study (2017)

Ineffective antimicrobial therapy of Pseudomonas aeruginosa bacteraemia increases mortality. Recent studies have proposed the use of antimicrobial combination therapy composed of a beta-lactam with either ciprofloxacin or tobramycin. To determine if combination therapy correlates to lower mortality and is superior compared to monotherapy, we investigated the effect of antimicrobial treatment regimens on 30-day mortality in a cohort with Pseudomonas aeruginosa bacteraemia. All cases of P. aeruginosa bacteraemia (n = 292) in southwest Skåne County, Sweden (years 2005-2010, adult population 361,112) and the whole county (2011-2012, 966,130) were identified. Available medical and microbiological records for persons aged 18 years or more were reviewed (n = 235). Antimicrobial therapy was defined as empiric at admission or definitive after culture results and was correlated to 30-day mortality in a multivariate regression model. The incidence and mortality rates were 8.0 per 100,000 adults and 22.9% (67/292), respectively. As expected, multiple comorbidities and high age were associated with mortality. Adequate empiric or definitive antipseudomonal treatment was associated with lower mortality than other antimicrobial alternatives (empiric p = 0.02, adj. p = 0.03; definitive p < 0.001, adj. p = 0.007). No difference in mortality was seen between empiric antipseudomonal monotherapy or empiric combination therapy. However, definitive combination therapy including ciprofloxacin correlated to lower mortality than monotherapy (p = 0.006, adj. p = 0.003), whereas combinations including tobramycin did not. Our results underline the importance of adequate antipseudomonal treatment. These data also suggest that P. aeruginosa bacteraemia should be treated with an antimicrobial combination including ciprofloxacin when susceptible.
New near-infrared dyes light up deep tissue imaging (2017)

A newly synthesized class of near-infrared dyes offers strong absorption and efficient fluorescent emission for deep-tissue molecular imaging applications.
Role of hydrogen for the elastic properties of alumina thin films (2002)

We describe the role of the presence of hydrogen on the elastic properties of AlxOyHz (0.32⩽x⩽0.4; 0.54⩽y⩽0.6; 3×10−4⩽z⩽0.14) films. The films were deposited by reactive magnetron sputtering in an Ar/O2/H2O discharge and were studied by Rutherford backscattering spectrometry, nuclear resonance analysis, selected area electron diffraction, as well as nanoindentation. As the hydrogen concentration is increased from 0.03% to 13.9% the measured elastic modulus value is reduced by approximately 53%. The measured elastic modulus is in excellent agreement with our electronic structure calculations. The large scattering in the reported values of the elastic properties of amorphous alumina thin films can readily be understood by hydrogen incorporation during synthesis.
Multi‐Site Concordance of Diffusion‐Weighted Imaging Quantification for Assessing Prostate Cancer Aggressiveness (2021)

1 TECHNICAL EFFICACY: Stage 3.
Synthesis and Antiproliferative Evaluation of 3-Chloroazetidin-2-ones with Antimitotic Activity: Heterocyclic Bridged Analogues of Combretastatin A-4 (2021)

Antimitotic drugs that target tubulin are among the most widely used chemotherapeutic agents; however, the development of multidrug resistance has limited their clinical activity. We report the synthesis and biological properties of a series of novel 3-chloro-β-lactams and 3,3-dichloro-β-lactams (2-azetidinones) that are structurally related to the tubulin polymerisation inhibitor and vascular targeting agent, Combretastatin A-4. These compounds were evaluated as potential tubulin polymerisation inhibitors and for their antiproliferative effects in breast cancer cells. A number of the compounds showed potent activity in MCF-7 breast cancer cells, e.g., compound <b>10n</b> (3-chloro-4-(3-hydroxy-4-methoxy-phenyl)-1-(3,4,5-trimethoxyphenyl)azetidin-2-one) and compound <b>11n</b> (3,3-dichloro-4-(3-hydroxy-4-methoxyphenyl)-1-(3,4,5-trimethoxyphenyl)-azetidin-2-one), with IC<sub>50</sub> values of 17 and 31 nM, respectively, and displayed comparable cellular effects to those of Combretastatin A-4. Compound <b>10n</b> demonstrated minimal cytotoxicity against non-tumorigenic HEK-293T cells and inhibited the in vitro polymerisation of tubulin with significant G<sub>2</sub>/M phase cell cycle arrest. Immunofluorescence staining of MCF-7 cells confirmed that β-lactam <b>10n</b> caused a mitotic catastrophe by targeting tubulin. In addition, compound <b>10n</b> promoted apoptosis by regulating the expression of pro-apoptotic protein BAX and anti-apoptotic proteins Bcl-2 and Mcl-1. Molecular docking was used to explore the potential molecular interactions between novel 3-chloro-β-lactams and the amino acid residues of the colchicine binding active site cavity of β-tubulin. Collectively, these results suggest that 3-chloro-2-azetidinones, such as compound <b>10n</b>, could be promising lead compounds for further clinical anti-cancer drug development.
Balancing Inter-Ring Loads on SONET Dual-Ring without Demand Splitting (1996)

In the survivability and simplicity aspect, SONET Self-healing Ring(SHR) is one of the most important schemes for the high-speed telecommunication networks. Since the ring capacity requirement is defined by the largest STS-1 cross-section in the ring, load balancing is the key issue in the design of SONET SHR. Recently, most of the research on load balancing problem have been concentrated on the SONET single-ring case. However, in certain applications, multiple-ring configuration is necessary because of the geographical limitations or the need for extra bandwidth. In this paper, the load balancing problem for SONET dual-ring is considered by assuming symmetric inter-ring demands. We present a linear programming based formulation of the problem. Initial solution and improvement procedures are presented, which solves the routing and interconnection between the two rings for each demand. Computational experiments are performed on various size of networks with randomly generated demand sets. Results show that the proposed algorithm is excellent in both the solution quality and the computational time requirement. The average error bound of the solutions obtained is 0.26 % of the optimum. 1.
Coupled nanocavity arrays (2007)

We will discuss our experimental and theoretical work on coupled photonic crystal nanocavity arrays, and their applications ranging from low-threshold, high speed lasers to nonlinear optical devices.
A Novel Energy Harvester in a Backpack via Precision Sensing of Back Electromotive Force (2020)

Abstract In this paper, swop fly-back converter, a new type of fly-back converter, was proposed. It is controlled by constant-on time, a strategy of pulse frequency modulation with boundary conduction mode. Due to the structure of swop fly-back converter and the boundary conduction mode control strategy, the energy delivery to battery is proportional to the voltage of coupled capacitor of swop fly-back converter which changed the position of the metal-oxide-semiconductor field-effect transistor and the capacitor instead of measuring input voltage and input current. Thus, the energy was estimated by measuring the voltage of coupled capacitor. The previous test shows that the voltage of coupled capacitor sensing which is measured by 10-bit ADC is good. The peak voltage is 4.036 V, the ADC value is 1009 digi, and it induced average power 1.25W for striding and 2W for jogging.
FePt–C graded media for ultra-high density magnetic recording (2010)

10.1088/0022-3727/43/18/185001
β-hydroxybutyrate and hydroxycarboxylic acid receptor 2 agonists activate the AKT, ERK and AMPK pathways, which are involved in bovine neutrophil chemotaxis (2020)

Elevated plasma concentrations of the ketone body β-hydroxybutyrate (BHB), an endogenous agonist of the hydroxycarboxylic acid receptor 2 (HCA2), is associated with an increased incidence of inflammatory diseases during lactation in dairy cows. In the early stages of this pathology, an increase in neutrophil recruitment is observed; however, the role of BHB remains elusive. This study characterized the effect of BHB and synthetic agonists of the HCA2 receptor on bovine neutrophil chemotaxis and the signaling pathways involved in this process. We demonstrated that treatment with BHB concentrations between 1.2 and 10 mM and two full selective agonists of the HCA2 receptor, MK-1903 and nicotinic acid, increased bovine neutrophil chemotaxis. We also observed that BHB and HCA2 agonists induced calcium release and phosphorylation of AKT, ERK 1/2 and AMPKα. To evaluate the role of these pathways in bovine neutrophil chemotaxis, we used the pharmacological inhibitors BAPTA-AM, pertussis toxin, U73122, LY294002, U0126 and compound C. Our results suggest that these pathways are required for HCA2 agonist-induced bovine neutrophil chemotaxis in non-physiological condition. Concentrations around 1.4 mM of BHB after calving may exert a chemoattractant effect that is key during the onset of the inflammatory process associated with metabolic disorders in dairy cows.
Inhibition of Nanoceria’s Catalytic Activity due to Ce3+ Site-Specific Interaction with Phosphate Ions (2014)

Cerium oxide nanoparticles (CNPs) exhibit superoxide dismutase (SOD) and catalase mimetic activities. Therefore, based on its catalytic activities, CNPs can potentially be used to treat diseases associated with oxidative stress. The potency of CNPs can be hindered by ion interaction due to chemical modifications. The issue is that phosphate ions are relatively ubiquitous in all biological relevance medium and body fluid. Our ventures in this study were to understand the phosphate ion interaction and fabricate CNPs that are biocompatible and simultaneously retain their catalytic properties in the presence of phosphate ions. CNPs were coated with polyethylene glycol and dextran in order to enhance biocompatibility. A series of experiments determined that maximizing the preserved catalytic responses were highly dependent on the Ce3+:Ce4+. Results have shown that the particles engineered with higher concentrations of Ce4+ on the surface are more robust and retain catalytic activity post buffer exposure.
Nanotubes Fabricated from Ni−Naphthalocyanine by a Template Method (2005)

Novel naphthalocyanine (Nc) nanotubes with special wall structures were fabricated by a template method using Nc molecules as building blocks. Thermal stabilization of the ordered columnar structures of the tetrakis(tert-butyl)naphthalocyanine (Ni-BNc) molecules, induced from the pi-pi interactions in the nanoscale channels of an alumina template, resulted in Nc nanotubes with walls consisting of well-ordered Nc molecular disks. Further thermal treatment of Ni-BNc at 600 degrees C produced carbonized Nc nanotubes containing ordered columnar, graphitic wall structures with the graphene disks arranged perpendicular to the tube axis. These nanotubes may be useful for extending the application of Nc molecules for nanodevice fabrication.
Minimum time length link scheduling under blockage and interference in 60GHz networks (2015)

In this paper we tackle the problem of minimum time length link scheduling in 60GHz wireless networks, under both traffic demand and Signal to Interference and Noise Ratio (SINR) constraints. A constrained Binary Integer Programming (BIP) problem is formulated by incorporating a flexible interference model for directional transmissions and a Markov chain based blockage model. We then propose two effective solution algorithms, including a Greedy Algorithm (GA) that finds the maximum instant throughput for each time slot, and a Column Generation based algorithm (CG) that iteratively improves the current link schedule. The performance of the proposed algorithms is validated with simulations.
Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset (2019)

Over the past two decades, the use of fragment-based lead generation has become a common, mature approach to identify tractable starting points in chemical space for the drug discovery process. This approach naturally involves the study of the binding properties of highly heterogeneous ligands. Such datasets challenge computational techniques to provide comparable binding free energy estimates from different binding modes. The performance of a range of statistically robust ensemble-based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent), is evaluated. Ligands designed to target two binding pockets in the lactate dehydogenase, a target protein, which vary in size, charge, and binding mode, are studied. When compared to experimental results, excellent statistical rankings are obtained across this highly diverse set of ligands. In addition, three approaches to account for entropic contributions are investigated: 1) normal mode analysis, 2) weighted solvent accessible surface area (WSAS), and 3) variational entropy. Normal mode analysis and WSAS correlate strongly with each other-although the latter is computationally far cheaper-but do not improve rankings. Variational entropy corrects exaggerated discrimination of ligands bound in different pockets but creates three outliers which reduce the quality of the overall ranking.
Specificity for Aminoacylation of an RNA Helix: an Unpaired, Exocyclic Amino Group in the Minor Groove (1991)

An acceptor stem G3.U70 base pair is a major determinant of the identity of an alanine transfer RNA. Hairpin helices and RNA duplexes consisting of complementary single strands are aminoacylated with alanine if they contain G3.U70. Chemical synthesis of RNA duplexes enabled the introduction of base analogs that tested the role of specific functional groups in the major and minor grooves of the RNA helix. The results of these experiments indicate that an unpaired guanine 2-amino group at a specific position in the minor groove of an RNA helix marks a molecule for aminoacylation with alanine.
Copoly(imide siloxane) Abhesive Materials with Varied Siloxane Oligomer Length (2010)

In this work, low surface energy copoly(imide siloxane)s were synthesized with various siloxane segment lengths. Characterization of these materials revealed that domain formation of the low surface energy component within the matrix was more prevalent for longer siloxane segments as indicated by increased opacity, decreased mechanical properties, and variation of the Tg. Incorporation of siloxanes lowered the polymer s surface energy as indicated by water contact angle values. Topographical modification of these materials by laser ablation patterning further reduced the surface energy, even generating superhydrophobic surfaces. Combined, the contact angle data and particle adhesion testing indicated that copoly(imide siloxane) materials may provide greater mitigation to particulate adhesion than polyimide materials alone. These enhanced surface properties for abhesive applications did result in a reduction of the tensile moduli of the copolymers. It is possible that lower siloxane loading levels would result in retention of the mechanical properties of the polyimide while still affording abhesive surface properties. This hypothesis is currently being investigated. Laser ablation patterning offers further reduction in particle retention as the available surface area for particle adhesion is reduced. Pattern variation and size dependencies are currently being evaluated. For the purposes of lunar dust adhesion mitigation, it is likely that this approach, termed passive due to the lack of input from an external energy source, would not be sufficient to mitigate surface contamination or clean contaminated surfaces for some lunar applications. It is feasible to combine these materials with active mitigation strategies - methods that utilize input from external energy sources - would broaden the applicability of such materials for abhesive purposes. Collaborative efforts along these lines have been initiated with researchers at NASA Kennedy Space Center where experiments are being conducted involving a series of embedded electrodes within polymeric matrices.
State-of-the-Art: Immunosuppression and Biologic Therapy (2010)

Azathioprine and 6-mercaptopurine are orally administered immunosuppressive drugs which are effective for the treatment of Crohn's disease and ulcerative colitis. Azathioprine is rapidly converted to 6-mercaptopurine after administration. 6-Mercaptopurine is then either converted to the putative active metabolites, the 6-thioguinine nucleotides, or inactivated by the enzyme xanthine oxidase to 6-thiouric acid or alternatively inactivated to 6-methylmercaptopurine by the enzyme thiopurine methyltransferase. Thiopurine methyltransferase activity is genetically determined, with one in 300 patients having low or absent enzyme activity, one in 10 patients having intermediate enzyme activity, and 9 in 10 patients having normal enzyme activity. Patients with intermediate or low thiopurine methyltransferase activity are at risk for early leukopenia. Higher erythrocyte 6-thioguinine nucleotide concentrations are associated with a greater likelihood of clinical response. Azathioprine is modestly effective for Crohn's disease and ulcerative colitis. Toxicity associated with azathioprine includes infection and lymphoma. Anti-TNF therapy with infliximab, adalimumab, and certolizumab pegol is effective for induction and maintenance treatment of Crohn's disease, and infliximab is effective for ulcerative colitis. Toxicity associated with anti-TNF therapy includes infection and lymphoma. Combination therapy with infliximab and azathioprine is more effective for inducing and maintaining steroid-free remission and mucosal healing then monotherapy with either drug alone. Strategies to reduce immunogenicity of anti-TNF agents include combination therapy with azathioprine and administration of a loading dose followed by systematic maintenance dosing. Higher serum trough concentrations of infliximab occur more frequently in patients receiving combination therapy with azathioprine and are associated with better clinical outcomes. Combination therapy is associated with an increased relative risk of opportunistic infection, but is not associated with an increased absolute risk of serious infection. Clinical practice should change such that combination therapy with an anti-TNF agent and azathioprine replace azathioprine in patients failing first line therapy with mesalamine and/or steroids.
Capacity Limits and Multiplexing Gains of MIMO Channels with Transceiver Impairments (2012)

The capacity of ideal MIMO channels has a high-SNR slope that equals the minimum of the number of transmit and receive antennas. This letter analyzes if this result holds when there are distortions from physical transceiver impairments. We prove analytically that such physical MIMO channels have a finite upper capacity limit, for any channel distribution and SNR. The high-SNR slope thus collapses to zero. This appears discouraging, but we prove the encouraging result that the relative capacity gain of employing MIMO is at least as large as with ideal transceivers.
Sn[sub 0.9]In[sub 0.1]P[sub 2]O[sub 7]-Based Organic/Inorganic Composite Membranes (2006)

An anhydrous proton conductor, -doped , was composed by 1,8-bis(triethoxysilyl)octane (TES-Oct) and 3-(trihydroxysilyl)-1-propanesulfonic acid and was characterized by structural and electrochemical analysis. The composite membrane with showed high proton conductivities of or more between 150 and in unhumidified air. The packing of the particles in the matrix was relatively uniform, with no formation of pinholes observed. Fuel cell tests verified that the open-circuit voltage was maintained at a constant value of regardless of the electrolyte thickness , while the Ohmic resistance was decreased to by reducing the electrolyte thickness to . The peak power densities achieved with unhumidified and air were at , at , and at . Furthermore, fuel cell performance was improved by hot-pressing an intermediate layer consisting of , , TES-Oct, and between the electrolyte and cathode.
Optical fiber cables for synchronous remoting of numerous transmitters/receivers (1998)

The relative fiber-to-fiber microwave phase changes induced in optical fiber cables by interfiber thermal and strain (bending-induced) gradients are reported. It is found that these changes are effectively minimized in cables where the fibers spin around the center member at a fast rate. Commercial "loose-tube" cables are found to preserve the fiber-to-fiber phases within 1/spl deg/ at modulation frequencies as high as 18 GHz. These cables appear well suited for fiber-optic remoting of numerous phase-matched transmitters and receivers.
Data from Transcriptional Profiling Identifies Cyclin D1 as a Critical Downstream Effector of Mutant Epidermal Growth Factor Receptor Signaling (2023)

&lt;div&gt;Abstract&lt;p&gt;Activating mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase domain determine responsiveness to EGFR tyrosine kinase inhibitors in patients with advanced non–small cell lung cancer (NSCLC). The modulation of transcriptional pathways by mutant EGFR signaling is not fully understood. Previously, we and others identified a single base pair change leading to a threonine to methionine (T790M) amino acid alteration in the ATP-binding pocket of the EGFR as a common mechanism of acquired resistance. The gefitinib-resistant, T790M-mutant H1975 NSCLC cell line undergoes prominent growth arrest and apoptosis when treated with the irreversible EGFR inhibitor, CL-387,785. We did a transcriptional profiling study of mutant EGFR target genes that are differentially expressed in the “resistant” gefitinib-treated and the “sensitive” CL387,785-treated H1975 cells to identify the pivotal transcriptional changes in NSCLC with EGFR-activating mutations. We identified a small subset of early gene changes, including significant reduction of cyclin D1 as a result of EGFR inhibition by CL-387,785 but not by gefitinib. The reduction in cyclin D1 transcription was associated with subsequent suppression of E2F-responsive genes, consistent with proliferation arrest. Furthermore, cyclin D1 expression was higher in EGFR-mutant lung cancer cells compared with cells with wild-type EGFR. EGFR-mutant cells were routinely sensitive to the cyclin-dependent kinase inhibitor flavopiridol, confirming the functional relevance of the cyclin D axis. These studies suggest that cyclin D1 may contribute to the emergence of EGFR-driven tumorigenesis and can be an alternative target of therapy. (Cancer Res 2006; 66(23): 11389-98)&lt;/p&gt;&lt;/div&gt;
Sensitivity optimisation of tuberculosis bioaerosol sampling (2020)

This study demonstrates that technical improvements in particle collection together with sensitive detection enable rapid quantitation of viable Mtb in bioaerosols of sputum positive TB cases. Increased sampling sensitivity may allow future TB transmission studies to be extended to sputum-negative and subclinical individuals, and suggests the potential utility of bioaerosol measurement for rapid intervention in other airborne infectious diseases.
Sustained Release of Tacrolimus From a Topical Drug Delivery System Promotes Corneal Reinnervation (2022)

Topically applied tacrolimus may provide a readily translatable approach to promote corneal reinnervation.