gebhart/patrepeval huggingface dataset:
Metformin modulates glucose uptake and transport in Caco-2 cell monolayers (2019)

Metformin is an anti-diabetic drug widely used to treat type 2 diabetes mellitus. Several studies have demonstrated that in vivo, metformin decreases both hepatic glucose production and intestinal glucose transport, and increases intestinal glucose utilization, all of which contribute to the blood glucose-lowering effects of metformin in diabetics. Increased intestinal glucose utilization is thought to contribute to metformin-induced intestinal lactic acidosis. Studies show that the highest accumulation of metformin occurs in the intestine following oral administration, which raises the question whether high metformin intestinal concentrations modulate cell function. Since intestinal glucose absorption occurs from the apical (AP) and basolateral (BL) membranes, it warrants investigating whether high metformin concentrations affect intestinal glucose absorption and glucose transporter (GLUT) translocation to the membranes of intestinal cells. There is little information about how metformin mediates GLUT transporters, although some evidence shows that metformin promotes translocation of GLUT transporters to the AP membrane. This study aims at elucidating the effect of metformin on glucose uptake and transport as a result of the GLUT transporters being translocated to AP and BL membranes of Caco-2 cell monolayers, a well-established model of human intestinal epithelia. Real-time polymerase chain reaction to determine relative expression of candidate glucose transporters GLUT1-3 in Caco-2 cells, and time- and concentration-dependent transport and uptake studies of the non-metabolizable radiolabeled glucose surrogate 2-deoxy-D-glucose (2DG) will provide information on the effect of metformin on intestinal glucose uptake and transport and contribute to knowledge about the risk of developing lactic acidosis.
Multi-modal human action recognition using deep neural networks fusing image and inertial sensor data (2017)

Human action recognition has been studied in many fields including computer vision and sensor networks using inertial sensors. However, there are limitations such as spatial constraints, occlusions in images, sensor unreliability, and the inconvenience of users. In order to solve these problems we suggest a sensor fusion method for human action recognition exploiting RGB images from a single fixed camera and a single wrist mounted inertial sensor. These two different domain information can complement each other to fill the deficiencies that exist in both image based and inertial sensor based human action recognition methods. We propose two convolutional neural network (CNN) based feature extraction networks for image and inertial sensor data and a recurrent neural network (RNN) based classification network with long short term memory (LSTM) units. Training of deep neural networks and testing are done with synchronized images and sensor data collected from five individuals. The proposed method results in better performance compared to single sensor-based methods with an accuracy of 86.9% in cross-validation. We also verify that the proposed algorithm robustly classifies the target action when there are failures in detecting body joints from images.
Mechanisms of Human Bladder Tumor Invasion: Role of Protease Cathepsin B (1990)

To study the biochemical mechanisms of bladder tumor invasion, we analyzed specimens of invasive transitional cell carcinoma cell line EJ and non-invasive transitional cell carcinoma cell line RT4 which had been implanted into the bladders of nude mice. Using immunoprobes specific to basement membrane laminin, we observed that superficial but not invasive tumors were surrounded by intact laminin. With immunoprobes specific to cathepsin B, a cysteine proteinase which has the ability to degrade laminin, we demonstrated that cathepsin B is localized in discrete cytoplasmic granules in the non-invasive tumors, and in a more diffuse cytoplasmic pattern in the invasive tumors. Subcellular fractionation followed by immunoblot analysis and enzymatic analysis confirmed that the invasive EJ cells had active cathepsin B localized to its plasma membrane, while non-invasive RT4 cells had cathepsin B confined to lysosomes. Furthermore, immunoblot analysis revealed that invasive EJ cells had the mature form of cathepsin B with a molecular weight of 25 kD, while non-invasive RT4 cells had predominantly precursor forms with molecular weights between 30 and 35 kD. In vitro degradation assays with plasma membrane fractions isolated from invasive EJ cells and non-invasive RT4 cells demonstrated that the plasma membrane of EJ cells but not that of the RT4 cells had the ability to degrade purified laminin, and that the degradative products were similar to those obtained with purified cathepsin B. We conclude that invasive tumor cells have enhanced cathepsin B in their plasma membranes which may be used to degrade basement membrane components such as laminin and thereby facilitate tumor invasion.
Resistance considerations for stacked small multi-junction photovoltaic cells (2013)

In this paper we propose a stacked multi-junction solar cell design that allows the intimate contact of the individual cells while maintaining low resistive losses. The cell design is presented using an InGaP and GaAs multi-junction cell as an illustrative example. However, the methodologies presented in this paper can be applied to other III-V cell types including InGaAs and InGaAsP cells. The main benefits of the design come from making small cells, on the order of 2×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Simulations showed that series resistances should be kept to less than 5 Ω for devices up to 400 μm in diameter to keep resistance power losses to less than 1%. Low resistance AuBe/Ni/Au ohmic contacts to n-type InGaP are also demonstrated with contact resistivity of 5×10-6 Ωcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> when annealed at 420°C.
Dichotomous Effects of Chronic Intermittent Hypoxia on Focal Cerebral Ischemic Injury (2014)

The influence of CIH on the ischemic brain is dichotomous and can be attributed, in part, to changes in the mitochondrial susceptibility to injury. The findings highlight a previously unappreciated complexity in the effect of CIH on the brain, which needs to be considered in evaluating the neurological effect of conditions associated with cyclic hypoxia.
Sorption of carbon dioxide, methane, and nitrogen on zeolite‐F: Equilibrium adsorption study (2017)

Carbon dioxide is a major contributor in greenhouse gases. Unswerving increase of CO 2 in atmosphere, due to growing industries and automobile field, is a wakeup call to the world as excess of CO 2 will affect humans in many ways among which greenhouse effect dominated the most. In the present work potassium based zeolite‐F was synthesized by hydrothermal method as reported by International Zeolite Association. Synthesized zeolite‐F was characterized with powder X‐Ray diffraction analysis, FT‐IR spectroscopy, scanning electron microscopy, thermo gravimetric analysis and BET surface area measurement. The equilibrium adsorption capacities of pure gases CO 2 , N 2 , and CH 4 were measured at 273, 288, and 303 K up to 850 mmHg. Although zeolite‐F possesses low CO 2 adsorption capacity (43.6cc/g) at 303 K, the selectivity towards N 2 and CH 4 reflects its potential as an efficient CO 2 adsorbent. The selectivity of CO 2 over N 2 in zeolite‐F was 38 at 303 K and 850 mmHg pressure, whereas selectivity for CO 2 over CH 4 was 30. Thus, zeolite‐F has shown potential for selective CO 2 adsorption from its gas mixture with N 2 and CH 4 . © 2017 American Institute of Chemical Engineers Environ Prog, 36: 850–856, 2017
An r-based overview of the WRW concept (2009)

The WRW model serves the geoscientists’ community as a global language dedicated to deliver a better insight into the seismic reflection experiment. In today’s numerical modeling, wave equation-based techniques such as implemented in the WRW model are used more and more, while it becomes clear that ray tracing methods do not have the required accuracy. The reflectivity matrix R is undoubtedly one of the most essential parts of the WRW model since it contains the angle dependent reflectivity information of the subsurface structures. It is this information that is to be retrieved from the seismic experiment. This paper provides insight in the formation process of this matrix. Different properties of the reflectivity matrix are investigated through the numerical modeling of three different cases. Moreover, the accuracy of the WRW approach is compared to that of ray tracing. The numerical results highlight the superiority of the WRW approach, i.e., the wave theory based approach, particularly in the case of a laterally variant reflector.
Resonant soft x-ray scattering from stripe-ordered La$_{2-x}$Ba$_x$CuO$_4$ using a transition edge sensor array detector (2019)

Resonant soft x-ray scattering (RSXS) is a leading probe of valence band order in materials best known for detecting charge density wave order in the copper-oxide superconductors. One of the biggest limitations on the RSXS technique is the presence of a severe fluorescence background which, like the RSXS cross section itself, is enhanced under resonant conditions. This background prevents the study of weak signals such as diffuse scattering from glassy or fluctuating order that is spread widely over momentum space. Recent advances in superconducting transition edge sensor (TES) detectors have led to major improvements in energy resolution and detection efficiency in the soft x-ray range. Here, we perform a RSXS study of stripe-ordered La$_{2-x}$Ba$_x$CuO$_4$ at the Cu $L_{3/2}$ edge (932.2 eV) using a TES detector with 1.5 eV resolution, to evaluate its utility for mitigating the fluorescence background problem. We find that, for suitable degree of detuning from the resonance, the TES rejects the fluorescence background, leading to a 5 to 10 times improvement in the statistical quality of the data compared to an equivalent, energy-integrated measurement. We conclude that a TES presents a promising approach to reducing background in RSXS studies and may lead to new discoveries in materials exhibiting valence band order that is fluctuating or glassy.
Design, methodological issues and participation in a multiple sclerosis case-control study (2011)

Epidemiological studies play a key role in identifying genetic and environmental factors that are associated with complex diseases like MS. Methodological issues arise in every study, and investigators need to be able to detect, respond to and correct problems in a timely and scientifically valid manner.
Hypercholesterolemia in Postmenopausal Women (1994)

Center for Human Nutrition and the Departments of Clinical Nutrition, Internal Medicine and Biochemistry University of Texas Southwestern Medical Center and the Veterans Affairs Medical Center. Dallas, Texas
Orientational order of single-wall carbon nanotubes in stretch-aligned photoluminescent composite films (2009)

Aqueous suspensions of single-wall carbon nanotubes (SWNT) are mixed with solutions of polyvinylalcohol (PVA) and dried to prepare free standing SWNT/PVA composite films (~100 μm thick). For nanotube concentrations up to 1wt %, the composites are homogeneous and the nanotubes are well dispersed both at mesoscopic scales and down to the individual scale as revealed by microscopic pictures and strong photoluminescence (PL) signals, repectively. We study the alignment of SWNT in the composites using polarized Raman and PL spectroscopies. Alignment can be continuously adjusted by hot-stretching the PVA composites. We propose a simple relation to measure the order parameter, based on the assumption that only one single component of the Raman polarizability tensor is non-zero. This assumption is validated experimentally by the observation of similar profiles for spectra measured in different polarization configurations. We modelize the orientation of the nanotubes under uniaxial stretching by a simple affine model assuming deformation at constant volume. For high nanotube concentrations, we discuss the effect of absorption on the Raman/PL results and show how it can be taken into account to measure the order parameter accurately.
A model for the hepatitis C virus envelope glycoprotein E2 (2000)

Several experimental studies on hepatitis C virus (HCV) have suggested the envelope glycoprotein E2 as a key antigen for an effective vaccine against the virus. Knowledge of its structure, therefore, would present a significant step forward in the fight against this disease. This paper reports the application of fold recognition methods in order to produce a model of the HCV E2 protein. Such investigation highlighted the envelope protein E of Tick Borne Encephalitis virus as a possible template for building a model of HCV E2. Mapping of experimental data onto the model allowed the prediction of a composite interaction site between E2 and its proposed cellular receptor CD81, as well as a heparin binding domain. In addition, experimental evidence is provided to show that CD81 recognition by E2 is isolate or strain specific and possibly mediated by the second hypervariable region (HVR2) of E2. Finally, the studies have also allowed a rough model for the quaternary structure of the envelope glycoproteins E1 and E2 complex to be proposed. Proteins 2000;40:355-366.
Functional domains in plant shoot meristems (2001)

The development of higher plants depends on the activity of a shoot apical meristem. Organs are formed on the flanks of the meristem, while pluripotent stem cells are found in a separate domain in the meristem centre. Further domains are distinguished by the expression patterns of genes that control the development of the shoot meristem. Although most plant cells are immobile, their relative position within a meristem, and therefore also their function, can change after cell divisions. To maintain an active shoot meristem throughout plant life, the cells in the meristem need constantly to assess their position, transmit this information to others, and readjust their gene expression profiles and their fate. Some of the genes that permit intercellular communication have been isolated. They enable the flow of information in and between meristem regions via ligands and receptor proteins to transcription factors, that ultimately control the fate of cells in the centre of the meristem.
Treatment of Metastatic Kidney Cancer (2010)

Therapeutic options for advanced renal cell carcinoma have expanded significantly with the introduction of several agents targeting VEGF and m-TOR pathways. Sunitinib, sorafenib, bevacizumab, temsirolimus and everolimus have been approved by the regulatory agencies in the United States and Europe and multiple news compounds are currently undergoing clinical trials for this disease. These developments signify a real progress in the management of metastatic kidney cancer and provide clinically meaningful improvements in survival and quality of life for patients; however, curative results remain elusive. Targeted agents currently represent the area of most intense clinical research in renal cancer but immunotherapy and resections of limited metastases are also being refined and applied in carefully selected clinical circumstances
Rhodococcus opacus PD630 Bioconversion of Molasses Desugarized Solubles for Fatty Acid Production (2022)

The oleaginous bacterium Rhodococcus opacus PD630 accumulates triacylglycerides (TAGs), from which the fatty acid components can be converted to biodiesel. In this work, we demonstrate the simple, robust bioconversion of the agricultural byproduct molasses desugarized solubles (MDS), a co-product of the second and final extraction of sugar from sugar beets, to fatty acids suitable for biodiesel production. In 48 hours of batch culture, R. opacus PD630 grown in dilute MDS accumulates 3.01 g/L dry biomass that is 43% fatty acids, with simultaneous growth and lipid accumulation. Palmitic (C16:0), cis-10-heptadecanoic (C17:1), and oleic (C18:1n9) acids are most abundant, representing 30%, 19%, and 18% of total fatty acids, respectively. Lowering the growth temperature causes a shift toward saturated fatty acids, as palmitic (C16:0), stearic (C18:0), and margaric (C17:0) are most prevalent. Analysis of MDS, rich in organic acids, revealed that aspartic and glutamic acids were preferentially consumed, leaving some sucrose, lactic acid, and malic acid in solution. This simple bioconversion process of an agricultural byproduct, which requires no added nutrients or buffers, could provide a robust platform for larger scale production of biodiesel precursors.
Differential Modulation of Dorsal Horn Neurons by Various Spinal Cord Stimulation Strategies (2021)

New strategies for spinal cord stimulation (SCS) for chronic pain have emerged in recent years, which may work better via different analgesic mechanisms than traditional low-frequency (e.g., 50 Hz) paresthesia-based SCS. To determine if 10 kHz and burst SCS waveforms might have a similar mechanistic basis, we examined whether these SCS strategies at intensities ostensibly below sensory thresholds would modulate spinal dorsal horn (DH) neuronal function in a neuron type-dependent manner. By using an in vivo electrophysiological approach in rodents, we found that low-intensity 10 kHz SCS, but not burst SCS, selectively activates inhibitory interneurons in the spinal DH. This study suggests that low-intensity 10 kHz SCS may inhibit pain-sensory processing in the spinal DH by activating inhibitory interneurons without activating DC fibers, resulting in paresthesia-free pain relief, whereas burst SCS likely operates via other mechanisms.
Weak consolidation model for wave propagation in ocean sediments (2006)

Within the context of Biot’s theory of poroelasticity, both effective density approximations and grain-to-grain elastic and inelastic effects are incoporated into a complete theory of acoustic propagation through ocean-bottom sands. The sedimentary material is assumed to be at best weakly consolidated. A variety of possible attenuation mechanisms are considered in order to explain ultrasonic data for both laboratory studies on glass beads saturated with water and silicon oil, as well as in situ data from the SAX99 experiment. An effective medium model is introduced to treat the weakly consolidated frame constants. Wave speeds and attenuations are explained to first order by the effective density approximation alone, but the remaining small discrepancies in velocity can be modeled successfully using the consolidation constants. Remaining attenuation discrepancies can then be fit using several methods including (a) increase of viscosity in fluid trapped between grains, (b) increase of viscosity due to high frequencies alone, and also (c) a new approach that specifically takes dynamic—but small amplitude—grain rearrangements into account. None of these mechanisms was taken into account in Biot’s original low-frequency theory.
Technology Mapping for Reliability Enhancement in Logic Synthesis (2005)

Reliability enhancements are traditionally implemented through redundancies at the system level or through the use of harden-cell-designs at the circuit level. Reliability is commonly ignored during the logic synthesis step. A major reason for this is the fact that constructing a cost function to measure sensitivity to faults at the logic synthesis level is complex. The work presented in this paper addresses one important aspect of synthesis for high reliability. It focuses on the problem of mapping a technology independent circuit to a technology specific one, using gates from a given library, with fault sensitivity as an optimization metric. We believe that the difficulty in obtaining accurate metrics of fault sensitivity at the technology independent level makes it hard to optimize at this level, thus technology dependent mapping offers a direct method to improve reliability. In this paper, we present a concept named "effective fault area" for mapping onto library gates. Along with this concept, we adopt a Markov-model based analytical method to accurately estimate fault sensitivity during mapping with a low computational overhead. Several benchmark results show that the average reliability improvement is about 20.7% at the cost of 12.1% increase in delay.
Towards temporal access control in cloud computing (2012)

Abstract—Access control is one of the most important security mechanisms in cloud computing. Attribute-based access control provides a flexible approach that allows data owners to integrate data access policies within the encrypted data. However, little work has been done to explore temporal attributes in specifying and enforcing the data owner’s policy and the data user’s privileges in cloud-based environments. In this paper, we present an efficient temporal access control encryption scheme for cloud services with the help of crypto-graphic integer comparisons and a proxy-based re-encryption mechanism on the current time. We also provide a dual comparative expression of integer ranges to extend the power of attribute expression for implementing various temporal constraints. We prove the security strength of the proposed scheme and our experimental results not only validate the effectiveness of our scheme, but also show that the proposed integer comparison scheme performs significantly better than previous bitwise comparison scheme.
Low-molecular-weight S-nitrosothiols and blood vessel injury (2007)

S-nitrosothiol signaling reactions are argued to play key modulatory roles in mediating the actions of NOS in health and disease. A report by Palmer et al. in this issue of the JCI provides new insight into the in vivo biology of S-nitrosothiols (see the related article beginning on page 2592). The authors examine the chronic effects of exogenous nitrosothiol therapy and demonstrate that the commonly used antioxidant N-acetylcysteine (NAC) induces pulmonary arterial hypertension in mice. Importantly, the authors argue that the vascular pathology they observe in the lungs of these animals is functionally and morphologically equivalent to that observed in chronic hypoxia. These findings raise the concern that chronic NAC therapy may induce similar vascular pathology in patients.
Role of Adenosine Antagonism in the Cardiorenal Syndrome (2008)

Acute decompensated heart failure (ADHF), generally related to signs and symptoms of volume overload, is one the most common reasons for hospitalization in the United States. Recently, it has been observed that the majority of patients with ADHF have baseline renal dysfunction. Moreover, heart failure (HF) treatment is limited by worsening renal function despite persistent volume overload. This connection between HF and renal dysfunction has been termed the cardiorenal syndrome and has made treatment of patients with stable and unstable HF challenging. Selective adenosine A1 receptor antagonists are novel pharmacologic agents that are currently under development to treat volume overload in HF while protecting or possibly improving renal function. In this article, we review the cardiorenal syndrome, the role of adenosine in renal function, and emerging data regarding the safety and efficacy of adenosine A1 receptor antagonists in patients with advanced HF.
Introduction (2005)

The way we live, our material well-being and the extent to which we realize our dreams for ourselves and our families are all deeply influenced by the large capitalist corporations that create most of the world's wealth and to the service of which most of us devote our skill, talent and working lives. We will argue that these large, increasingly global institutions that shape our world and our lives are themselves misshapen, because they are led and governed almost entirely by men.