gebhart/patrepeval huggingface dataset:
Mitigation of autophagy ameliorates hepatocellular damage following ischemia-reperfusion injury in murine steatotic liver (2014)

Ischemia-reperfusion injury (IRI) is a common clinical consequence of hepatic surgery, cardiogenic shock, and liver transplantation. A steatotic liver is particularly vulnerable to IRI, responding with extensive hepatocellular injury. Autophagy, a lysosomal pathway balancing cell survival and cell death, is engaged in IRI, although its role in IRI of a steatotic liver is unclear. The role of autophagy was investigated in high-fat diet (HFD)-fed mice exposed to IRI in vivo and in steatotic hepatocytes exposed to hypoxic IRI (HIRI) in vitro. Two inhibitors of autophagy, 3-methyladenine and bafilomycin A1, protected the steatotic hepatocytes from HIRI. Exendin 4 (Ex4), a glucagon-like peptide 1 analog, also led to suppression of autophagy, as evidenced by decreased autophagy-associated proteins [microtubule-associated protein 1A/1B-light chain 3 (LC3) II, p62, high-mobility group protein B1, beclin-1, and autophagy-related protein 7], reduced hepatocellular damage, and improved mitochondrial structure and function in HFD-fed mice exposed to IRI. Decreased autophagy was further demonstrated by reversal of a punctate pattern of LC3 and decreased autophagic flux after IRI in HFD-fed mice. Under the same conditions, the effects of Ex4 were reversed by the competitive antagonist exendin 9-39. The present study suggests that, in IRI of hepatic steatosis, treatment of hepatocytes with Ex4 mitigates autophagy, ameliorates hepatocellular injury, and preserves mitochondrial integrity. These data suggest that therapies targeting autophagy, by Ex4 treatment in particular, may ameliorate the effects of IRI in highly prevalent steatotic liver.
Data from A Phase Ib/II Study of Ramucirumab in Combination with Emibetuzumab in Patients with Advanced Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Inhibition of the VEGFR-2 blocks angiogenesis and attenuates tumor growth, but cancers may evade this effect through activation of the hepatocyte growth factor receptor MET. Here we report results of the phase Ib/II study of ramucirumab, a monoclonal anti-VEGFR-2 antibody, plus the anti-MET mAb emibetuzumab.&lt;/p&gt;Patients and Methods:&lt;p&gt;A 3+3 dose escalation of emibetuzumab plus ramucirumab (phase Ib) was followed by tumor-specific expansion cohorts. Primary objectives were to determine the recommended phase II dose and to evaluate antitumor activity. Secondary objectives included safety, pharmacokinetics, and immunogenicity. Tumoral MET expression was explored by immunohistochemistry (IHC).&lt;/p&gt;Results:&lt;p&gt;A total of 97 patients with solid tumor [6 phase Ib, 16 gastric or gastroesophageal junction adenocarcinoma, 45 hepatocellular carcinoma (HCC), 15 renal cell carcinoma, and 15 non–small lung cancer] received emibetuzumab at 750 or 2,000 mg flat dosing plus ramucirumab at 8 mg/kg every 2 weeks. No dose-limiting toxicities were observed. Common adverse events were primarily mild or moderate and included fatigue (36.1%), peripheral edema (28.9%), and nausea (14.4%). Emibetuzumab exposures were similar as in previous studies with no apparent drug–drug interactions. Five partial responses (5.2%) were observed across all tumor types. The greatest antitumor activity was noted in HCC with a 6.7% overall response rate, 60% disease control rate, and 5.42 months (95% confidence interval, 1.64–8.12) progression-free survival (PFS). HCC with high MET expression showed improved PFS with approximately 3-fold increase in PFS (8.1 vs. 2.8 months) relative to low MET expression.&lt;/p&gt;Conclusions:&lt;p&gt;Ramucirumab plus emibetuzumab was safe and exhibited cytostatic antitumor activity. MET expression may help to select patients benefitting most from this combination treatment in select tumor types.&lt;/p&gt;&lt;/div&gt;
Shadow caster culling for efficient shadow mapping (2011)

We propose a novel method for efficient construction of shadow maps by culling shadow casters which do not contribute to visible shadows. The method uses a mask of potential shadow receivers to cull shadow casters using a hierarchical occlusion culling algorithm. We propose several variants of the receiver mask implementations with different culling efficiency and computational costs. For scenes with statically focused shadow maps we designed an efficient strategy to incrementally update the shadow map, which comes close to the rendering performance for unshadowed scenes. We show that our method achieves 3x-10x speedup for rendering large city like scenes and 1.5x-2x speedup for rendering an actual game scene.
The outer membrane porin OmpW of Acinetobacter baumannii is involved in iron uptake and colistin binding (2015)

This study was undertaken to characterize functions of the outer membrane protein OmpW, which potentially contributes to the development of colistin- and imipenem-resistance in Acinetobacter baumannii. Reconstitution of OmpW in artificial lipid bilayers showed that it forms small channels (23 pS in 1 m KCl) and markedly interacts with iron and colistin, but not with imipenem. In vivo, (55) Fe uptake assays comparing the behaviours of ΔompW mutant and wild-type strains confirmed a role for OmpW in A. baumannii iron homeostasis. However, the loss of OmpW expression did not have an impact on A. baumannii susceptibilities to colistin or imipenem.
Enhancement of Pyrroloquinoline Quinone Production and Polyvinyl Alcohol Degradation in Mixed Continuous Cultures of Pseudomonas putida VM15A and Pseudomonas sp. Strain VM15C with Mixed Carbon Sources (1985)

In a mixed continuous culture of Pseudomonas putida VM15A and Pseudomonas sp. strain VM15C with polyvinyl alcohol (PVA) as the sole source of carbon, growth of the PVA-degrading bacterium VM15C and, hence, PVA degradation were limited by the growth factor, pyrroloquinoline quinone, produced by VM15A. Feeding of a carbon source for VM15A, ethanol, with PVA enhanced pyrroloquinoline quinone production and caused increases in the VM15C population and PVA degradation in a mixed continuous culture. There was an optimum range for PVA degradation of the ethanol concentration, although pyrroloquinoline quinone concentrations in continuous mixed cultures increased with increasing ethanol concentration.
Data for the green synthesis of exceptional braided, helical carbon nanotubes and nano spiral platelets made directly from CO$_2$ (2021)

This article describes base-line data used in conjunction with the Materials Today Chemistry article: The green synthesis of exceptional braided, helical carbon nanotubes and nano spiral platelets made directly from CO$_2$. The data includes Raman, XRD, SEM, TEM, EDX and high contrast TEM of conventional carbon nanotubes (CNTs) synthesized from carbon dioxide electrolytic splitting in molten electrolyte for comparison to synthesized helical carbon nanotubes grown in the main article. This data article also presents SEM showing that uncontrolled electrolytic CO$_2$ splitting leads to bent and deformed CNTs, rather than straight or helical CNTs, and SEM that helical carbon nanotubes and helical carbon nanoplatelets can be produced with only partial control of the electrolysis current and with no defect inducing agents. A novel, cheap synthesis of high purity helical nanocarbon is discovered. A baseline and comparative experimental data for non-helical analogues is presented. Both the non-helical and helical nanocarbon are synthesized from the greenhouse gas CO$_2$ by molten carbonate electrolysis.
EFFECTIVE STIFFENING OF THIN ROTATING DISKS USING SHAPE MEMORY ALLOYS (2011)

Thin spinning disk such as saw blades are limited in their rotation speed by their critical speed. The critical speed can be lowered by heating along the periphery of the disk. To counter this phenomenon, the use of shape memory alloys is investigated as a method to stiffen the disk when heated. The disk is modeled using the finite element analysis. The design results in a thin disk that can operate at higher temperatures and speeds.
Providing Addison, Illinois with community character through downtown development (1999)

Over the past few decades, the physical forms of the Village of Addison and its neighboring communities have blended together into a series of commercial corridors serving an automobile population. The result is a loss of individual character for Addison and its neighbors. The most visible way for a municipality to obtain character is through establishing or rehabilitating its downtown. This project attempts to create a unique physical identity for the Village of Addison allowing it to stand out from typical suburban development. Since a downtown does not exist in the Village of Addison, this creative project attempts to provide one.
On the Spatial Resolution of Diffuse Optical Tomography (2000)

We examined the performance of Diffuse Optical Tomography to resolve two purely absorptive objects, 2mm in diameter embedded in a diffuse slab media simulating breast tissue using simulations in the frequency domain. We demonstrate that the technique can resolve the two objects at 6mm apart with a spatial certainty of -2mm.
Protocol for ultrarapid immunostaining of frozen sections. (1999)

Rapid immunostaining of frozen sections within a tolerable time span would be very helpful for intraoperative diagnosis. A protocol was therefore established using the enhanced polymer one-step staining (EPOS) system (Dako) with antibodies against leucocyte common antigen (LCA), cytokeratin (CK), and anti-melanoma (MEL). Best results with reliable and specific immunostaining and a labelling intensity comparable to standard immunostaining protocols were achieved with fixation of samples in 100% acetone for 20 seconds (CK, LCA) or two minutes (MEL), followed by incubation of the primary antibody and development of the chromogen reaction with 3,3'diaminobenzidine (DAB) for three and five minutes at 37 degrees C, respectively. The total procedure takes only 12 minutes, thus enabling rapid immunostaining on intraoperative frozen sections. Apart from its use in tumour classification, this method is especially useful in detecting tumour cells in sentinel lymph nodes.
Morphological Changes of a Surface of Revolution due to Capillarity-Induced Surface Diffusion (1965)

The partial differential equation describing morphological changes of a surface of revolution due to capillarity-induced surface diffusion has been derived under the assumption of isotropy of surface tension and surface self-diffusion coefficient. A stable, convergent finite-difference method has been developed for the general case of an arbitrary surface of revolution and solutions have been obtained for the specific problems of the blunting of field-emission tips and the sintering of spheres. Spheroidization of cylindrical rods, as well as field-emission tips with taper below a certain critical value, is predicted; for tapers above the critical value, steady-state shapes are predicted and equations describing the blunting and recession of the tips are presented. If the sintering results for spheres are represented by a plot of log x/a vs log t, it is found that the inverse slope varies from approximately 5.5 to approximately 6.5 for the range 0.05≤x/a≤0.3, in contrast with the constant value of 7 found by Kuczynski from an order-of-magnitude analysis. At higher values of x/a, n increases steadily and without bound.
Determination of Interfacial Bond Behavior of Composite Concrete-Asphalt Pavement Systems (2008)

Described herein is a study of the interfacial debonding behavior between concrete and asphalt pavement material as found in whitetopping pavement applications. The study includes the interfacial failure resulting from both static and dynamic loading. Studies under static conditions used interfacial fracture mechanics techniques to investigate and characterize the behavior of pre-existing cracks along the asphalt-concrete interface. Experimental laboratory testing was done on uniaxially loaded rectangular block samples using asphalt material from two different age groups. It was found that the fracture toughness and interface strength increased with aging. Experiments were conducted with interfaces both normal and inclined to the loading direction, thereby allowing variation in the shear loading component. Results indicated that as shear loading component increased, the interface strength also increased. Finite element analysis was also used to explore the stresses in the laboratory block sample geometry. Finite element results of the stress distribution near the interfacial crack compared reasonably well with predictions from an idealized analytical solution. A special lap-joint specimen geometry was developed to determine the dynamic interfacial shear strength of bonded specimens using a Split Hopkinson Pressure Bar (SHPB) loading apparatus. Because of the small sample size, no pre-existing interface crack was used in this testing. Lap-joint samples were tested under both static and dynamic loading. Results indicated that at high loading rates the shear strength of the bonded lap joint was found to be about four times its static value.
An intellectual management system for soil sample collecting (2010)

The distribution of soil fertility is a very important factor in accurate agriculture decision. How to obtain the change of soil fertility correctly and efficiently, and guiding mechanized variable fertilization in terms of this change, is the current focal point and hotspot in accurate agriculture research fields. But soil sample data contains plenty of information. And soil constituent changes complicatedly. Now there is not a very useful system to solve the problem. In this paper, GPS navigational system is used to position each soil sample accurately. By this way, we can easy to know the soil sample is from where. And we can see the change of the distribution of soil fertility in the same place. After that, C++ Builder 6.0 and related database system are used to develop an intellectual management system for soil sample storing. By using this system, automatic accurate positioning, automatic bar-code generating, information entering and standard management will be finished. By the bar-code, you can easy to find the soil sample's data which you need. This intellectual management system is easy and convenient to use. The management of soil sample will be finished efficiently by using it. It will meet the demands of current agricultural industry.
Electroactive and temperature-sensitive hydrogel composites (1999)

The composites of the polypyrrole (PPy) and polyelectrolyte copolymers (PE) were prepared by electrochemical polymerization. The various compositions of the polyelectrolyte copolymers were used as a dopant, and were composed of copolymers of water-soluble polymers and 2-Acrylamido-2-methyl-1-propane sulfonic acid (AMPS). Thermally sensitive (N-isopropyl acrylamide, NiPAAm) and insensitive (acrylamide, AAm) polymers were used as the water-soluble polymer. The electrochemical activity and mass change during the redox process of the PPy composites were investigated by potentiodynamic voltametry and electrochemical quartz crystal microbalance (EQCM). The mass change during the redox process was mainly concerned with the cation in the electrolyte solution. When the electrochemical activity of the PPy was larger than the amount of the polyelectrolyte anion (AMPS), the insertion/expulsion of the monoanion (ClO) into/from the PPy composite also occurred to ionically bond with the PPy in the redox process. The PPy/P(NiPAAm/AMPS) shows a significant mass decrease with increasing the temperature compared with the PPy/P(AAm/AMPS). The transition temperature of the PPy/P(NiPAAm/AMPS) is higher in the oxidized state than in the reduced state. The transition temperature of PPy composite increases with the composition of the hydrophilic electrolyte (AMPS). © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 74: 311–321, 1999
Principal differences analysis: interpretable characterization of differences between distributions (2015)

We introduce principal differences analysis (PDA) for analyzing differences between high-dimensional distributions. The method operates by finding the projection that maximizes the Wasserstein divergence between the resulting univariate populations. Relying on the Cramer-Wold device, it requires no assumptions about the form of the underlying distributions, nor the nature of their inter-class differences. A sparse variant of the method is introduced to identify features responsible for the differences. We provide algorithms for both the original minimax formulation as well as its semidefinite relaxation. In addition to deriving some convergence results, we illustrate how the approach may be applied to identify differences between cell populations in the somatosensory cortex and hippocampus as manifested by single cell RNA-seq. Our broader framework extends beyond the specific choice of Wasserstein divergence.
Effect of Molecular Packing on Corannulene-Based Materials Electroluminescence (2011)

The present investigation reports for the first time a detailed theoretical analysis of the optical absorption spectra of corannulene-based materials using state-of-the-art first-principles many-body GW-BSE theory. The study specifically addresses the nature of optical excitations for predictions regarding suitability for device fabrication. The well-defined structure-correlation relationship in functionalized corannulenes is used in a focused investigation of the predicted optoelectronic properties in both the isolated state and bulk crystals. The findings suggest that the excitonic properties are strongly dependent on the specific substituent group as well as the crystalline arrangement. Arylethynyl-substituted corannulene derivatives are shown to be the most suitable for device purposes.
Structural Insights into <em>Thermotoga maritima</em> FtsH Periplasmic Domain on Substrate Recognition (2016)

Prompt removal of misfolded membrane proteins and misassembled membrane protein complexes is essential for membrane homeostasis. However, the elimination of these toxic proteins from the hydrophobic membrane environment has high energetic barriers. Transmembrane FtsH is the only known ATP-dependent protease responsible for this task, unlike other well-studied soluble ATP-dependent proteases. The mechanisms by which FtsH recognizes, unfolds, translocates, and proteolyzes its substrates remain unclear. Here, we report the crystal structures of the Thermotoga maritima FtsH periplasmic domain (PD) in an associative trimeric state at a 1.5-1.95 &amp;Aring; resolution. We also describe the pH-dependent oligomerization states of the isolated PD using dynamic light scattering. These observations help us understand how FtsH recognizes membrane-anchored misfolded proteins.
Line Constrained Estimation With Applications to Target Tracking: Exploiting Sparsity and Low-Rank (2018)

Trajectory estimation of moving targets is examined; in particular, quasi-linear trajectories are considered. Background subtraction methods, exploiting low-rank backgrounds, and sparse features of interest are extended to incorporate linear constraints. The line constraint is enforced via a rotation that yields an additional low rank condition. The proposed method is applied to single object tracking in video, wherein the trajectory can be parameterized as a line. The optimization is solved via the augmented Lagrange multiplier method. An average performance improvement of 4 dB is observed over previous background subtraction methods for estimating the position and velocity of the target. Furthermore, about a 6.2 dB gain is seen over previous target tracking methods that do not exploit the linear nature of the trajectory. The Cramér-Rao bound (CRB) for background subtraction with a linear constraint is derived and numerical results show that the proposed method achieves near optimal performance via comparison to the CRB. An aggregated error is shown to converge to zero and a boundedness analysis is conducted which suggests that the iterative algorithm is convergent as confirmed by simulations. Finally, the proposed technique is applied to real video data and is shown to be effective in estimating quasi-linear trajectories.
Topology and Physics of Circular DNA (1992)

Topology and Physics of Circular DNA presents comprehensive coverage of the physical properties of circular DNA. The author examines how topological constraints arising from cyclization of DNA lead to distinctive properties that make closed molecules radically different from linear DNA. The phenomenon of supercoiling, its geometric and topological analysis, and the formation of noncanonical structures in circular DNA under the influence of supercoiling are emphasized. The combination of consistent theoretical analysis and detailed treatment of major experimental approaches make Topology and Physics of Circular DNA an important reference volume for biophysicists, biochemists, molecular biologists, and researchers and students who want to expand their understanding of circular DNA.
Low Temperature Growth GaAs on Ge (2005)

In this work, low temperature growth of GaAs epitaxial layers on Ge substrates by metalorganic vapor phase epitaxy has been studied. The experiments show that a growth temperature of 530°C and a V/III ratio of 3.5 result in smooth GaAs surfaces. Atomic force micrographs do not show any anti-phase boundaries on the surface of GaAs grown on a misoriented substrate. X-ray diffraction curves show that the layer tilt is reduced as the growth temperature is lowered. Synchrotron X-ray topography reveals very low threading dislocation densities of 300 cm -2 for the GaAs epitaxial layers. Additionally, no misfit dislocations are observed. If a single layer is deposited at low temperature, secondary ion mass spectrometry shows a considerably reduced arsenic diffusion into Ge. When an additional layer is deposited at higher temperature on top of the initial low temperature layer, a substantial increase for the deep concentration-dependent arsenic diffusion is found.
Insulin-binding peptide. Design and characterization. (1988)

The design and characterization of a six-amino acid-containing peptide that binds insulin is described. The amino acid sequence of the insulin-binding peptide (IBP) was determined from the strand of DNA complementary to the strand of DNA coding for the insulin molecule in the domain of the insulin monomer believed to interact with the insulin receptor. The IBP (Cys-Val-Glu-Glu-Ala-Ser) binds specifically to insulin in a saturable manner with a Kd of 3 nM. This binding process is time dependent and slightly temperature dependent, and the peptide appears to interact with insulin near the carboxyl terminus of the B-chain of insulin. Incubation of insulin with the peptide decreases insulin binding to the insulin receptor by 50%, with no effect on the affinity of insulin for the receptor and no effect on cellular insulin-stimulated deoxyglucose uptake. A polyclonal antibody produced against the IBP will inhibit specific insulin binding to intact cells by approximately 50%, with no effects on insulin-stimulated glucose uptake. From this data, we suggest that there are at least two domains of the insulin molecule through which it interacts with its receptor, the "binding region" of insulin, which is the domain blocked by the IBP, and the "message region" of insulin, through which insulin not only binds to the receptor, but also generates the cellular signal.