gebhart/patrepeval huggingface dataset:
Sensor-based robot deployment algorithms (2010)

In robot deployment problems, the fundamental issue is to optimize a steady state performance measure that depends on the spatial configuration of a group of robots. For such problems, a classical way of designing high-level feedback motion planners is to implement a gradient descent scheme on a suitably chosen objective function. This can lead to computationally expensive algorithms that may not be adaptive to uncertain dynamic environments. We address these challenges by showing that algorithms for a variety of deployment scenarios in uncertain stochastic environments and with noisy sensor measurements can be designed as stochastic gradient descent algorithms, and their convergence properties analyzed via the theory of stochastic approximations. This approach yields often surprisingly simple algorithms that can accommodate complicated objective functions, and work without a detailed model of the environment. To illustrate the richness of the framework, we discuss two applications, namely source seeking with realistic stochastic wireless connectivity constraints, and coverage with heterogeneous sensors.
Protective effect of a polyherbal formulation (Immu‐21) against cyclophosphamide‐induced mutagenicity in mice (2003)

The object was to evaluate the effects of a polyherbal formulation, Immu-21, against cyclophosphamide (CP)-induced chromosomal aberrations (CA) and micronuclei (MN) in mice. CP alone (40 mg/kg, i.p.) produced classical as well as non-classical chromosomal aberrations in mice, and the incidence of CA was significantly more in the CP treated group when compared with that of the control group. Immu-21, which contains extracts of Ocimum sanctum, Withania somnifera, Emblica officinalis and Tinospora cordifolia, was given at 100 mg/kg, daily, over 7 days, and 30 mg/kg daily over 14 days and inhibited both CP-induced classical and non-classical chromosomal aberrations ( approximately 40%-60% of control). A significant increase in MN was also observed in bone marrow erythrocytes of mice treated with CP, and pretreatment with Immu-21 also significantly reduced these. Cytotoxicity was evaluated by estimating the ratio of polychromatic erythrocytes (PCEs) to normochromatic erythrocytes (NCEs). The present results indicate that chronic treatment with Immu-21 prevented CP-induced genotoxicity in mice.
Chronic Electroconvulsive Treatment Augments Coupling of the GTP‐Binding Protein Gs to the Catalytic Moiety of Adenylyl Cyclase in a Manner Similar to That Seen with Chronic Antidepressant Drugs (1991)

A significant increase of guanylylimidodiphosphate (GppNHp)-, fluoride-, and forskolin-stimulated adenylyl cyclase was observed in synaptic membrane preparations from rat cerebral cortex subsequent to chronic electroconvulsive shock (ECS) treatment. This effect required at least five treatments over a course of 10 days. The inhibition of adenylyl cyclase induced by GppNHp was not affected by these treatments. The dissociation constant (KD) and maximal binding for the photoaffinity GTP analog, [32P]P3-(4-azidoanilido)-P1-5'-GTP [( 32P]AAGTP), to each of the synaptic membrane G proteins also were unchanged after ECS treatment. Nonetheless, the transfer of [32P]AAGTP from Gi to Gs, which we suggest is indicative of the coupling between Gs and the adenylyl cyclase catalytic moiety, was accelerated by chronic ECS treatment but not by acute or sham treatment. Furthermore, chemical uncoupling of Gs from adenylyl cyclase rendered membranes from treated animals indistinguishable from controls. Finally, in all cases tested, membranes prepared from animals subjected to chronic treatment with amitriptyline or iprindole showed similar changes in the Gs-mediated activation of adenylyl cyclase. Acute treatments produced effects similar to controls, and liver and kidney membranes from animals receiving chronic treatment showed no changes in adenylyl cyclase despite the marked changes seen in brain. These results suggest that chronic administration of ECS enhances coupling between Gs and adenylyl cyclase enzyme and modifies interactions between Gs and Gi.
The balance of angiotensin II and nitric oxide in kidney diseases (2008)

Disparities between the activities of angiotensin II and nitric oxide are pervasive in a variety of acute and chronic kidney diseases. A better understanding of these interactions and their net effect on renal pathophysiology can lead to therapeutic interventions aimed at preventing or correcting such imbalances.
Supplementary Figure 1 from The Mitogen-Activated Protein Kinase Phosphatase <i>Vaccinia</i> H1–Related Protein Inhibits Apoptosis in Prostate Cancer Cells and Is Overexpressed in Prostate Cancer (2023)

Supplementary Figure 1 from The Mitogen-Activated Protein Kinase Phosphatase &lt;i&gt;Vaccinia&lt;/i&gt; H1–Related Protein Inhibits Apoptosis in Prostate Cancer Cells and Is Overexpressed in Prostate Cancer
Constructing biocatalytic nanochannel membranes for unidirectional isomer conversion and separation (2023)

Abstract Isomer conversion and separation are crucial in the chemical, pharmaceutical, and food industries. However, this process remains challenging due to the reversed conversion of isomers and their similar boiling points and kinetic diameters. Herein, an enzyme‐catalyzed nanochannel membrane with a hierarchical structure is fabricated for selective and directional isomeric conversion and separation. The enzyme is embedded in a confined polymer network that shows high stability and retains 95% of its initial activity after 50 reaction cycles. Studying the transport mechanisms between isomers through the membrane shows that the hierarchical layers of the membrane impose unequal energy barriers to the forward and backward transport of products, promoting unidirectional diffusion of products and interrupting the equilibrium of the isomerization reaction to increase the conversion rate by 43%. Overall, this work opens a new avenue for the design of biocatalytic nanochannel membranes and the directional production and in situ separation of isomers.
Near‐infrared time‐resolved fluorescence lifetime determinations in poly(methylmethacrylate) microchip electrophoresis devices (2004)

High aspect-ratio microstructures were hot-embossed in polymer substrates with a molding tool fabricated using lithography/electroplating/forming (LIGA). The resulting devices were used for the electrophoretic separation of oligonucleotides labeled with near-infrared (near-IR) dyes. Near-IR time-resolved fluorescence was used as an identification method for the labeling dyes. The detection apparatus consisted of a pulsed laser diode operating at 680 nm, a single-photon avalanche diode, an integrated microscope, and a PC-board incorporating time-correlated single photon counting electronics. Investigation of the optical quality and amount of autofluorescence generated from different polymer substrates was carried out in the near-IR region for determining compatibility with time-resolved fluorescence. Our results revealed that of several poly(methylmethacrylate)(PMMA) substrates, brand Plexiglas offered minimal replication errors in the embossed features using appropriate embossing conditions with low background fluorescence contributions to the observed decay. Near-IR dye-labeled oligonucleotides were separated to determine the applicability of fluorescence lifetime discrimination between Cy5.5 (tauf = 930 ps) and IRD700 (tauf = 851 ps) labeling dyes during the microchip separation. These dyes were used to label T-fragments (thymine) of an M13mp18 ssDNA template. The DNA ladders were electrophoresed at 130 V/cm in a 4% linear polyacrylamide gel (LPA) gel matrix in a 9.5 cm long serpentine channel heated to 50 degrees C. The electropherogram revealed that the lifetimes could be accurately read well beyond 450 bases, although single-base pair resolution in the electropherogram was difficult to achieve due to potential solute-wall interactions in the polymer microdevice or the electroosmotic flow (EOF) properties of the device. The relative standard deviations secured for individual bands in the electropherogram were similar to those obtained using capillary gel electrophoresis, in spite of the lower load volume.
Phenomenological Theory of Variational Quantum Ground-State Preparation (2022)

The variational approach is a cornerstone of computational physics, considering both conventional and quantum computing computational platforms. The variational quantum eigensolver (VQE) algorithm aims to prepare the ground state of a Hamiltonian exploiting parametrized quantum circuits that may offer an advantage compared to classical trial states used, for instance, in quantum Monte Carlo or tensor network calculations. While traditionally, the main focus has been on developing better trial circuits, we show that the algorithm's success crucially depends on other parameters such as the learning rate, the number $N_s$ of measurements to estimate the gradient components, and the Hamiltonian gap $Δ$. We first observe the existence of a finite $N_s$ value below which the optimization is impossible, and the energy variance resembles the behavior of the specific heat in second-order phase transitions. Secondly, when $N_s$ is above such threshold level, and learning is possible, we develop a phenomenological model that relates the fidelity of the state preparation with the optimization hyperparameters as well as $Δ$. More specifically, we observe that the computational resources scale as $1/Δ^2$, and we propose a symmetry-enhanced simulation protocol that should be used if the gap closes. We test our understanding on several instances of two-dimensional frustrated quantum magnets, which are believed to be the most promising candidates for near-term quantum advantage through variational quantum simulations.
Controlled Generation of Double Emulsions for Laser Fusion Target Fabrication Using a Glass Capillary Microfluidic Device (2017)

We report the controllable generation of double emulsions for target fabrication using glass capillary microfluidic devices. Instead of a conventional triple-orifice droplet generator, user-friendly glass capillary devices are used to produce micrometer to millimeter-sized water-in-oil-in-water emulsions. The double emulsions have a relatively uniform size distribution with an average outer diameter of 1420 μm. The sizes of the emulsions can also be varied by changing the ratio of the inner, middle, and outer fluids. Increasing the flow rate ratio of the outer fluid to the other fluids [Qo/(Qm+Qi)] from 3 to 11, the outer radii of the emulsions decrease from 1120 to 950 μm. On the other hand, increasing the flow rate ratio of the middle fluid to the inner fluid (Qm/Qi) from 0.7 to 1.6, the aspect ratio of the emulsions increases from 4 to 8. Our experimental values are in good agreement with a simple theoretical model. These results suggest that our present method to control the generation of double emulsions can be used as an alternative approach to fabricate polystyrene targets for future laser fusion experiments.
Array matching by mutual-coupling measurements (2002)

The phenomenon of mutual-coupling between the radiating elements of a phased array antenna causes variations both of the excitation distribution over the array and of the input impedances of the radiating elements. These variations are significant in arrays with a small number of elements, arrays with short distances between elements and arrays in the vicinity of which are reflecting bodies. In the past the author has presented a method for beamforming in an active phased array (i.e. for determining its excitation vector) using measured element patterns in the presence of the other elements of the array. The paper presents an expansion of the method taking in account the active mutual coupling. The use of relatively easy to measure values, with no need of complicated theoretical models or too many assumptions in order to calculate the coupling coefficients.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The initiation of vinyl polymerization by tetrakis (trialkyl‐phosphite) nickel (o) derivatives (1988)

Abstract The study of the polymerization of vinyl monomers initiated by zero‐valent nickel phosphite derivatives in the presence of organic halides has been extended to tetrakis (triethylphosphite) nickel (o) and tetrakis (tri 2‐chloroethylphosphite) nickel (o). A kinetic study with methyl methacrylate and carbon tetrachloride shows that the polymerization proceeds by a free radical process and that the mechanism of initiation resembles that previously reported for the corresponding triphenylphosphite and carbonyl derivatives. The primary process which becomes rate determining at sufficiently high carbon tetrachloride concentration is the nonreversible S N 1 scission of an alkylphosphite ligand. These alkylphosphite initiators are considerably more active than the corresponding carbonyl derivatives, but are less active than the corresponding triphenyl‐phosphite derivative. The difference in activities between the aryl and alkylphosphite derivatives has been accounted for by differences in steric over‐crowding of these molecules.
Effects of Medical Therapies on Retinopathy Progression in Type 2 Diabetes (2010)

Intensive glycemic control and intensive combination treatment of dyslipidemia, but not intensive blood-pressure control, reduced the rate of progression of diabetic retinopathy. (Funded by the National Heart, Lung, and Blood Institute and others; ClinicalTrials.gov numbers, NCT00000620 for the ACCORD study and NCT00542178 for the ACCORD Eye study.)
Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks (2017)

In <i>de novo</i> drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active toward a given biological target, we propose to fine-tune the model with small sets of molecules, which are known to be active against that target. Against <i>Staphylococcus aureus</i>, the model reproduced 14% of 6051 hold-out test molecules that medicinal chemists designed, whereas against <i>Plasmodium falciparum</i> (Malaria), it reproduced 28% of 1240 test molecules. When coupled with a scoring function, our model can perform the complete <i>de novo</i> drug design cycle to generate large sets of novel molecules for drug discovery.
Muscle-specific deletion of BDK amplifies loss of myofibrillar protein during protein undernutrition (2017)

Branched-chain amino acids (BCAAs) are essential amino acids for mammals and play key roles in the regulation of protein metabolism. However, the effect of BCAA deficiency on protein metabolism in skeletal muscle in vivo remains unclear. Here we generated mice with lower BCAA concentrations by specifically accelerating BCAA catabolism in skeletal muscle and heart (BDK-mKO mice). The mice appeared to be healthy without any obvious defects when fed a protein-rich diet; however, bolus ingestion of BCAAs showed that mTORC1 sensitivity in skeletal muscle was enhanced in BDK-mKO mice compared to the corresponding control mice. When these mice were fed a low protein diet, the concentration of myofibrillar protein was significantly decreased (but not soluble protein) and mTORC1 activity was reduced without significant change in autophagy. BCAA supplementation in drinking water attenuated the decreases in myofibrillar protein levels and mTORC1 activity. These results suggest that BCAAs are essential for maintaining myofibrillar proteins during protein undernutrition by keeping mTORC1 activity rather than by inhibiting autophagy and translation. This is the first report to reveal the importance of BCAAs for protein metabolism of skeletal muscle in vivo.
Multiplex Antibody Measurement for Post-treatment Follow-up of Staphylococcal Prosthetic Joint Infection: A Diagnostic Pilot Study (2019)

<b>Introduction:</b> Multiplex-antibody detection has been recently proposed for the noninvasive diagnosis of staphylococcal prosthetic joint infection (PJI). We evaluated this approach for the post-treatment follow-up of patients. <b>Methods:</b> Nineteen cases of staphylococcal PJI were prospectively followed for one year after treatment. The IgG response against eight staphylococcal antigens was measured before surgery and one year post-surgery using Luminex technology (Austin, TX, USA); median fluorescence intensity values determined for each antigen were transformed into a "Total Response Index" (TRI). <b>Results:</b> Patients (11 women/8 men) had a mean (SD) age of 72.2 (12.4) years. Site of prosthesis was the knee (n=10), the hip (n=8) and the shoulder (n=1). Ten patients were infected by <i>S. epidermidis</i>, six by <i>S. aureus</i>, and three by <i>S. lugdunensis</i>. TRI values at one year were significantly lower than pre-surgery values (mean [SD]: 5.9 [1.8] <i>versus</i> 8.1 [3.4], <i>p</i>=0.02) and decreased, on average, by 21.2%. TRI values markedly increased in two patients. One patient had a relapse of <i>S. aureus</i> PJI at five months post-surgery, with a 37% increase of the TRI. The other had septic failure three months after revision for <i>S. lugdunensis</i> PJI; all intraoperative samples remained culture-negative, but the TRI increased by 51% and the antibody profile showed a marked change, suggesting a reinfection with another staphylococcal species. <b>Conclusion:</b> Multiplex-antibody measurement may be useful for the follow-up of staphylococcal PJI and may help to detect septic failure involving organisms targeted by the assay.
Going and Passing Through Community Colleges: Examining the Effectiveness of Project Lead The Way in STEM Pathways (2013)

Project Lead The Way (PLTW), which aims to create a seamless pathway from secondary education to college and career success in STEM fields, was first implemented in the state of Iowa in 2005. As a part of a statewide, longitudinal research in PLTW, this study explores the effectiveness of PLTW in college persistence by analyzing multiple data sources to examine multiple educational pathways of PLTW and non-PLTW students into higher education. Data sources included the state's K–12, community college Management Information System, and National Student Clearinghouse. More specifically, this study looks at patterns of students' educational mobility within two years after high school graduation.
On the mineral core of ferritin-like proteins: structural and magnetic characterization (2015)

It is generally accepted that the mineral core synthesized by ferritin-like proteins consists of a ferric oxy-hydroxide mineral similar to ferrihydrite in the case of horse spleen ferritin (HoSF) and an oxy-hydroxide-phosphate phase in plant and prokaryotic ferritins. The structure reflects a dynamic process of deposition and dissolution, influenced by different biological, chemical and physical variables. In this work we shed light on this matter by combining a structural (High Resolution Transmission Electron Microscopy (HRTEM) and Fe K-edge X-ray Absorption Spectroscopy (XAS)) and a magnetic study of the mineral core biomineralized by horse spleen ferritin (HoSF) and three prokaryotic ferritin-like proteins: bacterial ferritin (FtnA) and bacterioferritin (Bfr) from Escherichia coli and archaeal ferritin (PfFtn) from Pyrococcus furiosus. The prokaryotic ferritin-like proteins have been studied under native conditions and inside the cells for the sake of preserving their natural attributes. They share with HoSF a nanocrystalline structure rather than an amorphous one as has been frequently reported. However, the presence of phosphorus changes drastically the short-range order and magnetic response of the prokaryotic cores with respect to HoSF. The superparamagnetism observed in HoSF is absent in the prokaryotic proteins, which show a pure atomic-like paramagnetic behaviour attributed to phosphorus breaking the Fe-Fe exchange interaction.
Indocyanine green enhanced near‐infrared laser treatment of murine mammary carcinoma (2011)

It is well accepted that near-infrared (NIR) lasers are appropriate to ablate benign lesions and induce irreversible thermal injury in deeply seated blood vessels. At this wavelength, the laser light penetrates deep (3-5 mm) into the skin. However, many researchers have reported noticeable pain, extending from mild to severe, during and immediately after NIR laser treatment. Intravenous administration of an exogenous chromophore [indocyanine green (ICG), dye] can effectively convert NIR laser light into heat. In this approach, the presence of ICG has shown to enhance thermal injury of blood vessels in the treatment of healthy tissues. However, the effectiveness of thermal injury on the regression of cutaneous carcinomas during ICG/NIR laser therapy has not been assessed. The purpose of our study was to evaluate the potential benefit of using ICG/NIR laser therapy to regress superficial carcinoma with thermal injury. Two groups of A/J mice with subcutaneous mammary adenocarcinoma tumors (7-9 mm) were irradiated with a 808-nm NIR laser preceded by tail vein injection of ICG dye or sterile saline. Histological evaluation of the subcutaneous tissue revealed minor thermal damage and necrosis in the laser/saline group and substantial damage (up to 100% necrosis) in the laser/ICG group. The laser/ICG-treated group showed a steady reduction in tumor volume compared to the laser/saline group: 48% by day 5 (p = 0.045) and 69-70% by days 8, 9 and 10 (p values 0.0005 or less). The vascular-targeted ICG-NIR laser therapy appears to have potential for treating superficial tumors.