gebhart/patrepeval huggingface dataset:
Protein-tyrosine Phosphatase α Regulates Src Family Kinases and Alters Cell-Substratum Adhesion (1998)

The roles of protein-tyrosine phosphatases (PTPs) in processes such as cell growth and adhesion are poorly understood. To explore the ability of specific PTPs to regulate cell signaling pathways initiated by stimulation of growth factor receptors, we expressed the receptor-like PTP, PTPalpha, in A431 epidermoid carcinoma cells. These cells express high levels of the epidermal growth factor (EGF) receptor and proliferate in response to the autocrine production of transforming growth factor-alpha. Conversely, EGF stimulation of A431 cells in vitro leads to growth inhibition and triggers the rapid detachment of these cells from the substratum. Although PTPalpha expression did not alter the growth characteristics of either unstimulated or EGF-stimulated cells, this phosphatase was associated with increased cell-substratum adhesion. Furthermore, PTPalpha-expressing A431 cells were strikingly resistant to EGF-induced cell rounding. Overexpression of PTPalpha in A431 cells was associated with the dephosphorylation/activation of specific Src family kinases, suggesting a potential mechanism for the observed alteration in A431 cell-substratum adhesion. Src kinase activation was dependent on the D1 catalytic subunit of PTPalpha, and there was evidence of association between PTPalpha and Src kinase(s). PTPalpha expression also led to increased association of Src kinase with the integrin-associated focal adhesion kinase, pp125(FAK). In addition, paxillin, a Src and/or pp125(FAK) substrate, displayed increased levels of tyrosine phosphorylation in PTPalpha-expressing cells and was associated with elevated amounts of Csk. In view of these alterations in focal adhesion-associated molecules in PTPalpha-expressing A431 cells, as well as the changes in adhesion demonstrated by these cells, we propose that PTPalpha may have a role in regulating cell-substratum adhesion.
Physiological, Productive, and Economic Benefits of Shade, Spray, and Fan System Versus Shade for Holstein Cows During Summer Heat (1987)

During the 1984 summer, effects of spray and fan in freestall areas and feeding areas on milk yield, plasma growth hormone and prolactin, freestall utilization, and economic significance for Holstein cows were studied. Weekly milk and rectal temperatures at morning and afternoon milkings were higher for cows in shade than in shade with spray and fan cooling. Compared with rectal temperature, milk temperature measured in the clawpiece provided a more reliable indicator of heat stress than in the milk meter. Diurnal pattern of rectal temperature from 4-h measurements showed an average of 12 h in which maximal rectal temperatures of cows in shade were greater than 39 degrees C, but cows in the shade plus spray plus fan group had rectal temperatures below 39 degrees C all day. Plasma growth hormone was higher and prolactin lower for cows in shade plus spray and fan than cows in shade only. Cows cooled with spray and fan under shade produced 2 kg/cow per d more than cows in shade alone. Economic analysis showed a net income of 22 cents/cow per day for spray plus fan under shade. Results suggest that milk temperature is a practical technique to assess heat stress in dairy cattle, and the use of spray plus fan is a profitable means to maximize cow comfort and lessen stress-induced decline in milk production.
Quantification of stretch‐induced cytoskeletal remodeling in vascular endothelial cells by image processing (2003)

Our method is reliable for quantifying cytoskeletal remodeling induced by mechanical force.
An Analyzer-Based Software Security Measurement Model for Enhancing Software System Security (2010)

Software security has become an increasingly important issue for computer and software system. Secure holes of software system may cause a company out of business and even destroy social normal operation. How to improve software security becomes a critical issue in software development process. In this paper, utilizing the static program analyzer and dynamic simulation analyzer to collect metrics, an Analyzer-based Software Security Measurement (ASSM) model is proposed. Applying ASSM model, the secure flaws of software system can be identified clearly. And, the security defects and security holes of software system can be efficiently controlled and improved. The security of software system can be increased concretely.
Correlation of Female Indices From Virulence Assays on Inbred Lines and Field Populations of Heterodera glycines. (2008)

A lack of diversity and durability of resistant soybean varieties complicates management of the soybean cyst nematode (SCN), Heterodera glycines, exemplified by the current overdependence on the PI 88788 source of resistance. Of interest is the effect of adaptation of a SCN population to a source of resistance on its subsequent ability to develop on others. Female indices (FI) from virulence assays (race, HG Type and SCN Type tests) for SCN field populations and inbred lines were analyzed. Female indices on PI 88788, PI 209332 and PI 548316 were highly correlated, as were those of PI 548402, PI 90763, PI 89772 and PI 438489B. Previous studies on resistant SCN-infected soybean roots indicated that the cellular resistance response was similar within these two groups of soybean genotypes. In field populations, highly significant correlations were also found between FI on PI 88788 and PI 548402 and those on PI 89772 and PI 437654. In inbred lines, FI on PI 437654 were correlated with PI 90763 and PI 438489B. To avoid further adaptation, rotation of cultivars with resistance from these groups should be carefully monitored, including those from the most promising source of resistance, PI 437654, such as CystX. In a separate test, 10 soybean varieties developed from CystX were tested against HG Type 0, HG Type 2.5.7 and HG Type 1-7. Female development occurred in all tests but one. Although identification and deployment of unique resistance is needed, management strategies to prevent and detect adaptation should be emphasized.
(Structure and stability of nucleic acids) (1991)

We study the conformations of DNA and RNA oligonucleotides in order to understand their biological roles. We have determined the structure of the most common type of hairpin loop found in ribosomal RNA--the extra-stable tetraloop. It is actually a biloop with the other two bases in the loop forming a non-Watson-Crick base pair. This is the highest resolution structure reported for an RNA molecule in solution so far. We have obtained structures of pseudoknots and we have deduced general rules for their formation. We are presently studying a pseudoknot which is necessary for the replication of a retrovirus. The research done in the laboratory has been reported in 24 publications, plus 7 manuscripts in press or submitted. The research was done by 14 graduate students and 7 postdoctoral fellows. Five graduate students have received their Ph.D.s and 4 postdoctorals have finished their stay here. There are presently 9 graduate students and 3 postdoctorals working on the project; 2 new postdoctorals are expected this summer. One undergraduate student usually participates in the research during the year; this summer two undergraduates are working on the project. 31 refs., 4 figs.
BSP-Net: Generating Compact Meshes via Binary Space Partitioning (2020)

Polygonal meshes are ubiquitous in the digital 3D domain, yet they have only played a minor role in the deep learning revolution. Leading methods for learning generative models of shapes rely on implicit functions, and generate meshes only after expensive iso-surfacing routines. To overcome these challenges, we are inspired by a classical spatial data structure from computer graphics, Binary Space Partitioning (BSP), to facilitate 3D learning. The core ingredient of BSP is an operation for recursive subdivision of space to obtain convex sets. By exploiting this property, we devise BSP-Net, a network that learns to represent a 3D shape via convex decomposition. Importantly, BSP-Net is unsupervised since no convex shape decompositions are needed for training. The network is trained to reconstruct a shape using a set of convexes obtained from a BSP-tree built on a set of planes. The convexes inferred by BSP-Net can be easily extracted to form a polygon mesh, without any need for iso-surfacing. The generated meshes are compact (i.e., low-poly) and well suited to represent sharp geometry; they are guaranteed to be watertight and can be easily parameterized. We also show that the reconstruction quality by BSP-Net is competitive with state-of-the-art methods while using much fewer primitives. Code is available at https://github.com/czq142857/BSP-NET-original.
Electrical conductivity imaging by magnetic resonance electrical impedance tomography (MREIT) (2003)

Magnetic resonance electrical impedance tomography (MREIT) is a recently developed imaging technique that combines MRI and electrical impedance tomography (EIT). In MREIT, cross-sectional electrical conductivity images are reconstructed from the internal magnetic field density data produced inside an electrically conducting subject when an electrical current is injected into the subject. In this work the results of an electrical conductivity imaging experiment are presented, along with some practical considerations regarding MREIT. The MREIT experiment was performed with a 0.3 Tesla MRI system on a phantom made of two compartments with different electrical conductivities. The current density inside the phantom was measured by the MR current density imaging (MRCDI) technique. The measured current density was then used for conductivity image reconstruction by the J-substitution algorithm. The conductivity phantom images obtained with an injection current of 28mA showed conductivity errors of about 25.5%.
A Physical Model for Stress Cages (2004)

Abstract Well designs are constrained by the variation of both the pore pressure and fracture gradients throughout the depth of the well. Each hole section is designed such that the pressure profile within the hole at any time during drilling will not exceed the fracture pressure profile at any point throughout that section. The maximum pressures catered for in the design are invariably dictated by permeable formations with the highest pore pressure gradient. The casing depths are set to put behind pipe formations with too weak a fracture gradient to resist the planned pressure profile expected during drilling. This prevents a weak formation from failing and cross flow occurring between that failed zone and any high pressure permeable formations within the same hole section. The fracture gradient is typically determined by measuring the pressure at which losses begin to occur in the hole section and converting the downhole pressure into an equivalent mud weight. Most operators and mud companies have observed that the addition of some mud additives has influenced the pressure at which these induced losses begin. However, the use of those additives has been unreliable in many instances. Recent work at BP has resulted in the development of a physical model that describes the mechanism that allows the fracture resistance to increase above conventional minimum horizontal stress through the addition of mud additives. These additives result in the formation of a "stress cage" which is a near wellbore region of high stress induced by propping open and sealing shallow fractures at the wellbore/formation interface. With the development of the physical model it is now possible to analyze the effects of different drilling practices upon the reliability and stability of those induced stress cages. The development of stress cages is influenced by a number of properties including the diameter of the borehole, the width of fractures induced in a formation, the range of particle sizes which can be used as proppant in the fracture, the sealing properties of the mud, and the permeability of the formation. The successful implementation of the stress cage mechanism is dependent upon the use of appropriate constructive drilling practices and avoidance of detrimental practices which may destabilize the stress cages.
Application of an advanced micro-propulsion system to the delffi formation-flying demonstration within the qb50 mission (2012)

The performance of several micro-propulsion systems is compared when applied to the specific needs of the DelFFi project, a formation flying technology demonstration expected to take place in the framework of the QB50 mission. The evaluated options include the T3Î¼PS cold gas micro-propulsion system developed by TNO, Delft University of Technology and the University of Twente and a silicon-based MEMS resistojet design proposed by TU Delft. The analysis clearly shows that a resistojet technology, if combined with the cool gas generator units used in the T3Î¼PS system, leads to significant advantages in terms of the total propulsion system mass and is still complaint to the stringent volume requirements of micro- And nano-satellites. These advantages are particularly evident for low values of the total velocity change required by the mission, as in the case of the DelFFi project.Â©2012 by the International Astronautical Federation.
What Is a Cytokine Storm and Should It Matter to Me? (2021)

The recent COVID-19 pandemic has brought attention to cytokines and the phenomenon of cytokine storm into mainstream discussions. In this disease specifically, a cytokine storm overwhelming immune response contributes to the pathophysiology and mortality of the COVID-19 infection. Analogous perturbed immune reactions are experienced in polytrauma patients, compromising local tissue healing while threatening multiple organ systems. The expanding field of osteoimmunology should contribute to the orthopaedic community's understanding of how the immune system response, whether normal or pathologic, affects the whole body outcome of our patients.
A case study in Gray Markets (2022)

Thesis (S.M.M.O.T.)--Massachusetts Institute of Technology, Sloan School of Management, 1998.
Anionic Liposomes Enhance and Prolong Adenovirus-Mediated Gene Expression in Airway Epithelia <i>in Vitro</i> and <i>in Vivo</i> (2011)

Adenoviral vector mediated gene therapy has received extensive attention in airway disease treatment. However, the lack of the requisite coxsackie-adenovirus receptor (CAR) on the apical surface of airway epithelium and the host immune response to adenoviruses limit their in vivo application. In our study, we developed for the first time a novel formulation composed of anionic liposomes and adenoviruses (AL-Ad5) using a calcium-induced phase change method. The obtained formulation was employed to enhance the transduction efficiency of airway gene delivery. Our results indicated that primary cultured airway epithelial cells infected by AL-Ad5 displayed higher LacZ gene expression compared to naked adenovirus. Importantly, AL-Ad5 significantly improved and prolonged LacZ gene expression in murine airway tissues when delivered in vivo by intratracheal instillation. Additionally, it was found that anionic liposomes provided immunoprotection to the adenovirus from neutralizing antibody, thus slowing down the elimination of Ad5 particles meanwhile reducing the inflammatory reaction caused by the Ad5 vector. These results suggested that the combination of anionic liposomes with adenovirus may be a useful strategy to deliver therapeutic genes into the airway epithelia and is promising in clinical application.
Mechanism of the Selective Catalytic Reduction of Nitric Oxide by Ammonia Elucidated by in Situ On-Line Fourier Transform Infrared Spectroscopy (1994)

The selective catalytic reduction reaction of nitric oxide bv ammonia over vanadia-titania catalysts is one of the methods of removing NOx pollution. In the present study, it has been possible to identify the reaction mechanism and the nature of the active sites in these catalysts by combining transient or steady-state in situ (Fourier transform infrared spectroscopy) experiments directly with on-line activity studies. The results suggest a catalytic cycle that consists of both acid and redox reactions and involves both surface V-OH (Brønsted acid sites) and V=O species. A fundamental microkinetic model is proposed, which accounts for the observed industrial kinetics performance.
Extruded erythroblast nuclei are bound and phagocytosed by a novel macrophage receptor (1995)

Resident bone marrow macrophages (RBMM) play an important role in clearance of nuclei extruded from late-stage erythroblasts (Eb). To investigate the nature of macrophage receptors involved in this process, extruded erythroblast nuclei (EEN) were purified by cultivation of erythroblasts with erythropoietin, followed by density gradient centrifugation. By electron microscopy, the majority of free nuclei had an intact plasma membrane. EEN bound avidly to RBMM in a divalent cation-independent manner at both 4 degrees C and 37 degrees C. The use of specific monoclonal antibodies (MoAbs) and inhibitors showed that this adhesive interaction was not mediated by previously characterized macrophage receptors involved in recognition of either developing hematopoietic cells or apoptotic cells. The EEN receptor was expressed on resident macrophages isolated from murine bone marrow, spleen, lymph node, and peritoneal cavity, but was completely absent from alveolar macrophages. Despite high levels of EEN binding to RBMM, few were phagocytosed even after prolonged culture. Phorbol myristate acetate (PMA) was found to stimulate phagocytosis, suggesting that this is a regulated process. These findings indicate that EEN are recognized by a novel macrophage receptor and that recognition may be triggered during the membrane remodeling that accompanies enucleation.
Critical role of both p27<sup>KIP1</sup>and p21<sup>CIP1/WAF1</sup> in the antiproliferative effect of ZD1839 (‘Iressa’), an epidermal growth factor receptor tyrosine kinase inhibitor, in head and neck squamous carcinoma cells (2003)

High expression of the epidermal growth factor receptor (EGFR) has been implicated in the development of squamous-cell carcinomas of head and neck (SCCHN). ZD1839 ('Iressa') is an orally active, selective EGFR-TKI (EGFR-tyrosine kinase inhibitor) that blocks signal transduction pathways implicated in proliferation and survival of cancer cells, and other host-dependent processes promoting cancer growth. We have demonstrated that ZD1839 induces growth arrest in SCCHN cell lines by inhibiting EGFR-mediated signaling. Cell cycle kinetic analysis demonstrated that ZD1839 induces a delay in cell cycle progression and a G1 arrest together with a partial G2/M block; this was associated with increased expression of both p27(KIP1) and p21(CIP1/WAF1) cyclin-dependent kinase (CDK) inhibitors. The activity of CDK2, the main target of CIP/KIP CDK inhibitors, was reduced in a dose-dependent fashion after 24 h of ZD1839 treatment and this effect correlated to the increased amount of p27(KIP1) and p21(CIP1/WAF1) proteins associated with CDK2-cyclin-E and CDK2-cyclin-A complexes. In addition, ZD1839-induced growth inhibition was significantly reduced in cell transfectants expressing p27(KIP1) or p21(CIP1/WAF1) antisense constructs. Overall, these results as well as the timing of the effect of ZD1839 on G1 arrest and p27(KIP1) and p21(CIP1/WAF1) upregulation, suggest a mechanistic connection between these events.
A Study of the Diffusion of Alternative Fuel Vehicles: An Agent‐Based Modeling Approach<sup>*</sup> (2011)

This paper demonstrates the use of an agent‐based model (ABM) to investigate factors that can speed the diffusion of eco‐innovations, namely alternative fuel vehicles (AFVs). The ABM provides the opportunity to consider the interdependencies inherent between key participants in the automotive industry: manufacturers, consumers, and governmental agencies. Agent‐based models allow for tackling these interdependencies in a very elegant way. Because ABMs allow convenient modeling of the interactions between multiple agents, each with unique optimization goals, it provides a method for understanding consumer and manufacturer response to diverse environmental changes. Grounding the agent‐based model on empirical data further improves the validity of the model results. We use choice‐based conjoint data of more than 7,000 respondents to elicit heterogeneous consumer preferences. Further, information about manufacturers' cost structure is available from an established vehicle design tool, AVCEM. In three experiments, mechanisms are considered for speeding the adoption of AFVs: technology push, market pull, and regulatory push. Simulation results support the idea that technology push can be an important mechanism for speeding the diffusion of AFVs. Market pull, that is, word of mouth, also has a positive impact on the diffusion of AFVs and increases the social good by decreasing the preference for fuel‐inefficient vehicles. Furthermore, word of mouth leads to a higher willingness to pay for AFVs, which indicates that the perceived value of AFVs increases with word of mouth. In contrast, a governmental push that focuses on the manufacturers (fuel economy mandates) leads to a decrease in the social good (air pollution improvement) because market share for fuel‐inefficient vehicles increases. This article provides insights into how to set up an ABM to evaluate factors that influence the diffusion of alternative fuel vehicles. These insights can be applied to other types of eco‐innovations.
Protein P4 of double-stranded RNA bacteriophage phi 6 is accessible on the nucleocapsid surface: epitope mapping and orientation of the protein (1993)

Protein P4, an early protein of double-stranded RNA bacteriophage phi 6, is a component of the virion-associated RNA polymerase complex and possesses a nucleoside triphosphate (NTP) phosphohydrolase activity. We have produced and characterized a panel of 20 P4-specific monoclonal antibodies. Epitope mapping using truncated molecules of recombinant P4 revealed seven linear epitopes. The accessibility of the epitopes on the phi 6 nucleocapsid (NC) surface showed that at least the C terminus and an internal domain, containing the consensus sequence for NTP binding, protrude the NC shell. Four of the NC-binding antibodies distorted the integrity of the NC by releasing protein P4 and the major NC surface protein P8. This finding suggests a close contact between these two proteins. The dissociation of the NC led to the activation of the virion-associated RNA polymerase. The multimeric status of the recombinant P4 was similar to that of the virion-associated P4, indicating that no accessory virus proteins are needed for its multimerization.
Dynamic Occlusion Analysis in Optical Flow Fields (1985)

Optical flow can be used to locate dynamic occlusion boundaries in an image sequence. We derive an edge detection algorithm sensitive to changes in flow fields likely to be associated with occlusion. The algorithm is patterned after the Marr-Hildreth zero-crossing detectors currently used to locate boundaries in scalar fields. Zero-crossing detectors are extended to identify changes in direction and/or magnitude in a vector-valued flow field. As a result, the detector works for flow boundaries generated due to the relative motion of two overlapping surfaces, as well as the simpler case of motion parallax due to a sensor moving through an otherwise stationary environment. We then show how the approach can be extended to identify which side of a dynamic occlusion boundary corresponds to the occluding surface. The fundamental principal involved is that at an occlusion boundary, the image of the surface boundary moves with the image of the occluding surface. Such information is important in interpreting dynamic scenes. Results are demonstrated on optical flow fields automatically computed from real image sequences.