gebhart/patrepeval huggingface dataset:
Comparative analysis of mitogenic and morphogenic effects of HGF and EGF on rat and human hepatocytes maintained in collagen gels (1993)

Hepatocytes maintained in collagen gels remain differentiated for prolonged periods of time compared to cells maintained on conventional cultures. Previous studies with other culture systems in which chemical supplements or substratum modifications enhanced hepatocyte differentiation showed that in all of these systems hepatocytes do not respond to mitogens. In this study it is shown that hepatocytes maintained between two layers of collagen gels respond to mitogens HGF (also known as scatter factor (HGF/SF)) and epidermal growth factor (EGF). Cell density did not affect the responsiveness to mitogens as in conventional cultures. In addition both mitogens (HGF more pronounced) induce characteristic morphogenic changes in which hepatocytes form processes and join in formation of cords. Hepatocytes respond to mitogens for up to 6 days in culture at which point they become refractory to further mitogenic stimulation. This occurs despite electron microscopic evidence that these cells are fully viable when they become refractory to mitogenesis. The refractory state is not modified by substitution of one growth factor for the other or by addition of growth factors at different times. Hepatocytes in the refractory state become again responsive to mitogens when the collagen gels are dispersed by collagenase and the cells are replated on conventional substrates.
Dual Interaction of JAM-C with JAM-B and α<sub>M</sub>β<sub>2</sub>Integrin: Function in Junctional Complexes and Leukocyte Adhesion (2005)

The junctional adhesion molecules (JAMs) have been recently described as interendothelial junctional molecules and as integrin ligands. Here we show that JAM-B and JAM-C undergo heterophilic interaction in cell-cell contacts and that JAM-C is recruited and stabilized in junctional complexes by JAM-B. In addition, soluble JAM-B dissociates soluble JAM-C homodimers to form JAM-B/JAM-C heterodimers. This suggests that the affinity of JAM-C monomers to form dimers is higher for JAM-B than for JAM-C. Using antibodies against JAM-C, the formation of JAM-B/JAM-C heterodimers can be abolished. This liberates JAM-C from its vascular binding partner JAM-B and makes it available on the apical side of vessels for interaction with its leukocyte counter-receptor alpha(M)beta2 integrin. We demonstrate that the modulation of JAM-C localization in junctional complexes is a new regulatory mechanism for alpha(M)beta2-dependent adhesion of leukocytes.
Growth and electrical properties of multidimensional tungsten nano-buliding blocks (2004)

We report the demonstration of tungsten nanoblocks such as nanorods, nanoblocks, and nanocylinders through a simple thermal process of sputtered W films. The formation of various types of tungsten nanostructures was based on the difference in the magnitude of the residual film stress and in its spatial distribution, which depends on the deposition pressure during the sputter deposition of self-catalytic W thin film. The resulting shapes displayed well-controlled structures that have characteristic dimensionalities such as zero-dimensional dot, one-dimensional wire, and two-dimensional nanosheet with the deposition pressure. The results demonstrate the possibility of construction of in situ multidimensional achitectures through the one-step thermal process which uses a self-catalytic function of each thin film.
The Value of Follicle-Stimulating Hormone Concentration and Clinical Findings as Markers of the Late Menopausal Transition (2006)

An annual serum FSH concentration of 40 IU/liter could be incorporated, in conjunction with bleeding markers, into the Stages of Reproductive Aging Workshop paradigm for markers of the late menopausal transition.
Molecular mechanical study of halogen bonding in drug discovery (2011)

A halogen bond is a noncovalent bond between a halogen atom (X) and a Lewis base (Y). This type of bond is attributed to the anisotropic distribution of the charge density on the halogen atom, resulting in the formation of a positive cap (called the σ-hole) centered on the A-X axis. The current research is the first reported molecular mechanical study of halogen bonding, the positive region centered on the halogen atom was represented by an extra-point (EP) of charge. The correlation between the X-EP distance and the X…Y bond length was explored to determine the optimal position of the EP. A test set of 27 halogen-containing molecules complexed to various Lewis bases was studied using molecular mechanical potentials. The molecular mechanical minimized halogen bond lengths and binding energies were in good agreement with the corresponding quantum mechanical values. The EP inclusion on the halogen atom resulted in an improvement in the accuracy of the electrostatic-potential derived charges. The solvation free energies of halobenzene molecules relative to benzene were calculated with and without EP inclusion to assess the accuracy of the developed approach. Molecular mechanical study of halo derivatives of benzotriazole complexed to cyclin-dependent protein kinase 2 (CDK2) was performed, and MM-PB(GB)SA binding energies were calculated as a case study in finding potent halogenated inhibitors that can serve as antitumor drugs.
A Biomechanical Evaluation of Cervical Spinal Stabilization Methods in a Bovine Model (1988)

A bovine model was developed for biomechanical evaluation of surgical procedures stabilizing traumatic cervical injuries disrupting the anterior and posterior spinal column. Cervical spinal segments and C4-5 functional spinal units were tested statically, and C4-5 functional spinal units were tested cyclically in evaluation of 1) the intact cervical spine, 2) Rogers' wiring method, 3) Bohlman's triple-wire technique, 4) sublaminar wiring, 5) anterior cervical plate instrumentation, and 6) posterior hook plate stabilization. Anterior cervical plate instrumentation proved inadequate, and was the least rigid, with axial and flexural loading (P less than 0.05). There was no significant difference between each of the three posterior wiring methods, and all generally restored stability to equal that of the uninjured intact cervical spine. Posterior hook plating with an interspinous bone graft serving as an extension block was the most effective method in reducing flexural stress across the injured C4-5 segment (P less than 0.05). Cyclical in vitro testing was the most sensitive method in highlighting mechanical differences between instrumentation systems, particularly with "on-line" continuous measurement of anterior and posterior strains. Anterior cervical plate stabilization does not appear to confer enough stability in cervical facet injuries to obviate the need for posterior cervical stabilization procedures. The recently developed posterior hook plate technique offers biomechanical advantages that should be weighed against the greater technical precision needed for insertion and the increased potential for neurologic and vascular complications.
CT-assisted transbronchial needle aspiration: usefulness of CT fluoroscopy. (1997)

CT-assisted transbronchial needle aspiration: usefulness of CT fluoroscopy.C S White, P A Templeton and J D HasdayAudio Available | Share
3D Cardiac Microtissues Encapsulated with the Co‐Culture of Cardiomyocytes and Cardiac Fibroblasts (2015)

Cardiac tissue engineering has major applications in regenerative medicine, disease modeling and biological studies. Despite the significance, numerous questions still need to be explored to enhance the functionalities of engineered tissue substitutes. In this study, 3D cardiac microtissues are developed through encapsulation of cardiomyocytes and cardiac fibroblasts, as the main cellular constituents of native myocardium. The geometries of the constructs are precisely controlled and assessed for their role on synchronous contraction of the cells. Cardiomyocytes exhibit a native-like phenotype when co-cultured with cardiac fibroblasts as compared to the monoculture condition. Particularly, elongated F-actin fibers with abundance of sarcomeric α-actinin and troponin-I are observed within all layers of the constructs. Higher expressions of connexin-43 and integrin-β1 indicate improved cell-cell and cell-matrix interactions. Amongst co-culture conditions, 2:1 (cardiomyocytes: cardiac fibroblasts) ratio exhibits enhanced functionalities, whereas decreasing the construct size adversely affects the synchronous contraction of the cells. Overall, the study here indicates that the cell-cell ratio and the construct geometry are crucial parameters, which need to be optimized to enhance the functionalities of the engineered tissue substitutes.
Secure Remote Control of Field-programmable Network Devices (2004)

A circuit and an associated lightweight protocol have been developed to secure communication between a control console and remote programmable network devices. The circuit provides encryption, data integrity checking and sequence number verification to ensure confidentiality, integrity and authentication of control messages sent over the public Internet. All of these functions are performed directly in FPGA hardware to provide high throughput and near-zero latency. The circuit has been used to control and configure remote firewalls and intrusion detection systems. The circuit could also be used to control and configure other distributed network applications.
Electrodeless Conductivity (1989)

The history of electrodeless conductivity is discussed from its practical beginning in 1947 to the present. This technique for measuring the concentration of electrolytes in solution utilizes a probe consisting of two toroids in close proximity which are immersed in the solution. The toroids may also be mounted externally on insulated pipes carrying the solution. One toroid generates an alternating electric field in the audio frequency range and the other acts as a receiver to pick up the current from the ions moving in a conducting loop of solution. Fouling coatings, suspensions, precipitates or oil have little or no effect. Applications are reviewed for continuous measurements include the mining, pulp and paper, and heavy chemical industries.
Liquefied Petroleum Gas (2011)

Abstract The article contains sections titled: 1. Introduction 2. Properties 3. Production and Processing 3.1. Recovery Sources 3.2. Recontacting ‐ Compression 3.3. Refrigeration 3.3.1. Low‐Temperature Separation (LTS) 3.3.2. Expander Plants 3.3.3. Combined Processes 3.4. Lean Oil Absorption 3.5. Adsorption 3.6. Production of Biopropane 4. Purification 5. Storage and Transportation 6. Uses 7. Safety Aspects 8. Economic Aspects
The Deployment Production Line (2006)

Testing and deployment can be a difficult and time-consuming process in complex environments comprising application servers, messaging infrastructure and interfaces to external systems. We have seen deployments take several days, even in cases where teams have used automated builds to ensure their code is fully tested. In this paper we describe principles and practices which allow new environments to be created, configured and deployed to at the click of a button. We show how to fully automate your testing and deployment process using a multi-stage automated workflow. Using this "deployment production line", it is possible to deploy fully tested code into production environments quickly and with full confidence that you can fall back to a previous version easily should a problem occur.
Targeted isolation and analysis of single tumor cells with aptamer-encoded microwell array on microfluidic device (2012)

Microfluidic-based single cells analysis has been of great interest in recent years, promising disease diagnosis and personalized medicine. Current technologies are challenging in bioselectively isolating specific single cells from complex matrices. Herein, a novel microfluidic platform integrated with cell-recognizable aptamer-encoded microwells was specifically developed to isolate single tumor cells with satisfied single-cell occupancy and unique bioselectivity. In this work, the designed microwell-structures enable us to encourage strong 3D local topographic interactions of the target cell surface with biomolecules and regulate the single-cell resolution. Under the optimized size of microwells, the single-cell occupancy was significantly enhanced from 0.5% to 88.2% through the introduction of the aptamer. Analysis of the target cells was directly performed in short time periods (<5.0 min) with small volumes (4.5 μL). Importantly, such an aptamer-enabled microfluidic device shows an excellent selectivity for target single cells isolation compared with three control cells. Subsequently, targeted isolation and analysis of single tumor cells were demonstrated by using artificial complex cell samples at simulated conditions, and various cellular carboxylesterases were studied by time-course measurements of cellular fluorescence kinetics at individual-cell level. Thus, our technique will open up a new opportunity in single-cell level-based disease diagnosis and personalize medicine screening.
Optical oscillator strengths and excitation energies in solids, liquids, and molecules (1977)

An examination of average dipole coordinate matrix elements and electronic excitation energies in over 140 solids, liquids, and molecules reveals simple trends related to polarity, metallicity, ionicity, anion–anion ’’contact’’, cation core hybridization, and disorder. These results point to the key roles played by metallicity and polarity in crystalline solids as expressed by the empirical relationship ?2=fdZa/30.16, where 30.16 eV Å is a fundamental constant given by e/6ε0, ? is the dimensionless coordinate matrix element introduced by Harrison and Pantelides, d is the bond length in Å, Za is the formal chemical valency of the anion, and f is a coefficient associated with first-neighbor and second-neighbor delocalization, i.e., f=4.8±0.3 eV in ’’covalent’’ crystals, f=3.0±0.2 eV in ’’ionic’’ crystals, and f=3.8±0.2 eV in ’’anion-contact’’ crystals. The latter classification includes a variety of materials with close-spaced anions such as LiF, MgS, several rutile-structure compounds, and CdI2. Wurtzite-structure chalcogenides form a transitional group between large ’’ionic’’ and ’’covalent’’ classes. Direct contributions to ?2 from valencelike d10 and s2 ’’cores’’ are evident in some cases (e.g., CuCl, TlBr, PbTe, BiI3) and can be accounted for simply by including these ’’cores’’ in the valence electron count. Such direct effects are not observed, for example, in the Zn or Cd salts. Metallicity trends (described by d) and polarity trends (described by Za) are absent in liquids and molecules, and oscillator strengths (f) are considerably larger than observed in solids although matrix elements are comparable. The primary excitation energy results relate both to an approximate power law dependence on bond length of the form E0∼d−s, where 2&lt;s&lt;3 and to a substantial reduction in E0 for materials with valencelike d10 or s2 cation ’’cores’’. In most molecules the average excitation energy E0 falls close to the first ionization potential. Finally, the implications of these results on the dielectric models of Phillips and Harrison and on the nature of the chemical bond are discussed.
Using SQL to Build New Aggregates and Extenders for Object- Relational Systems (2000)

User-defined Aggregates (UDAs) provide a versatile mechanism for extending the power and applicability of Object-Relational Databases (O-R DBs). In this paper, we describe the AXL system that supports an SQLbased language for introducing new UDAs. AXL is easy to learn and use for database programmers because it preserves the constructs, programming paradigm and data types of SQL (whereas there is an `impedance mismatch&apos; between SQL and the procedural languages of user-defined functions currently used in O-R DBs). AXL will also inherit the benefits of database query languages, such as scalability, data independence and parallelizability. In this paper, we show that, while adding only minimal extensions to SQL, AXL is very powerful and capable of expressing complex algorithms e#ciently. We demonstrate this by coding data mining functions and other advanced applications that, previously, had been a major problem for SQL databases. Due to its flexibility, SQL-compati...
Estimates of the loss of main‐chain conformational entropy of different residues on protein folding (1999)

The average contribution of conformational entropy for individual amino acid residues towards the free energy of protein folding is not well understood. We have developed empirical scales for the loss of the main-chain (torsion angles, ϕ and ψ) conformational entropy by taking its side-chain into account. The analysis shows that the main-chain component of the total conformational entropy loss for a residue is significant and reflects intrinsic characteristics associated with individual residues. The values have direct correlation with the hydrophobicity values and this has important bearing on the folding process. Proteins 1999;36:332–339. © 1999 Wiley-Liss, Inc.
Evaluation of CD44 and CD133 as cancer stem cell markers for colorectal cancer (2012)

Colorectal cancer (CRC) is a major cause of cancer-related mortality in the world. Recently, a number of studies have demonstrated that cancer stem cells (CSCs) present in colorectal cancer tissues, are responsible for resistance to conventional therapies. Therefore, effective recognition of CSCs is of great importance. In the present study, to explore the potential characterizations of CSCs by the expression of specific cell surface markers such as CD133 and CD44, we screened six CRC cell lines using western blotting, immunofluorescence and flow cytometry. SW620, one of the six cell lines analyzed, was sorted into four subpopulations by fluorescence activated cell sorting (FACS). The capability of colony formation, proliferation rate, apoptosis, drug resistance, as well as their migratory and invasion potential were detected. The results revealed that the combination of CD44 and CD133 correlates with the features of CSCs in SW620 cells. CD44 positive cells showed more robust colony formation, higher proliferation, less spontaneous apoptosis, a higher resistance to drug-induced cell death, and were enriched after drug treatment. Among CD44 positive SW620 cells, the CD133 negative subpopulation was more migratory and invasive, which means that CD44+CD133- correlates with most of features proposed for CSCs. Overall, the data presented herein showed that CRCs have a wide range of expression for CD44 and CD133; it is unlikely the CSCs can be characterized by any single marker or the same set of markers for all colon cancer cells. For SW620 cells, the CSCs are likely represented by the CD44+CD133- surface marker. This finding of CSC markers represented by one positive and one negative is in line with CSCs in other tumors, such as CD34+CD38- for acute myeloid leukemia; CD44+CD24- for breast and pancreatic tumors. The absence of surface molecule(s) on CSCs will make it even more difficult to track and target this group of minority cells.
Endoscopic ultrasound comes of age: Mature, established, creative and here to stay! (2014)

Research in endoscopic ultrasound (EUS) is alive and kicking! This paper will present recent interesting developments in EUS based on research presented at the Digestive Disease Week (DDW) held in Chicago in 2014. Endosonographers are looking at various techniques to improve yield of fine needle aspiration and core biopsies, assess circulating tumor cells, apply EUS for personalized medicine and develop devices to ensure the adequacy of sampling. EUS may open new vistas in understanding of neurogastroenterology and gastrointestinal motility disorders as discussed in this paper. EUS guided drainage of pancreatic fluid collections, bile duct and gallbladder is feasible, and many randomized trials are being done to compare different techniques. EUS guided delivery of fiducials, drugs, coils or chemo loaded beads in possible. EUS has come off age, has matured and is here to stay! The DDW in 2014 in Chicago was a very active year for EUS. There were numerous papers on different aspects of EUS, some perfecting and improving old techniques, others dealing with randomized trials and many with novel concepts. In this paper, I will highlight some of the papers that were presented. It is not possible to discuss all the abstracts in detail. I have, therefore, chosen selected papers in different aspects of EUS to give the readers a flavor of the kind of research that was presented at DDW.
A note on the use of Java in scientific computing (1999)

Java provides an easy-to-use language and platform for writing distributed, network-aware applications. For the scientific computing community, Java has the potential of extending the range and usefulness of scientific codes, as well as widening the codes current user base. However, certain features of Java may limit its usefulness as a platform in which to develop and deploy scientific codes. In this paper, we analyze where Java could be used within scientific computing, and examine several Java-based systems that aim to provide tools and runtimes suitable for programming scientific codes within distributed computing environments.
Blue Light Disinfection in Hospital Infection Control: Advantages, Drawbacks, and Pitfalls (2019)

Hospital acquired infections (HAIs) are a serious problem that potentially affects millions of patients whenever in contact with hospital settings. Worsening the panorama is the emergence of antimicrobial resistance by most microorganisms implicated in HAIs. Therefore, the improvement of the actual surveillance methods and the discovery of alternative approaches with novel modes of action is vital to overcome the threats created by the emergence of such resistances. Light therapy modalities represent a viable and effective alternative to the conventional antimicrobial treatment and can be preponderant in the control of HAIs, even against multidrug resistant organisms (MDROs). This review will initially focus on the actual state of HAIs and MDROs and which methods are currently available to fight them, which is followed by the exploration of antimicrobial photodynamic therapy (aPDT) and antimicrobial blue light therapy (aBLT) as alternative approaches to control microorganisms involved in HAIs. The advantages and drawbacks of BLT relatively to aPDT and conventional antimicrobial drugs as well as its potential applications to destroy microorganisms in the healthcare setting will also be discussed.
Cytokine profiles as markers of disease severity in sepsis: a multiplex analysis (2007)

In this exploratory analysis we demonstrated that use of a multiple cytokine assay platform allowed identification of distinct cytokine profiles associated with sepsis severity, evolution of organ failure and death.
δ-Viniferin, a Resveratrol Dehydrodimer: One of the Major Stilbenes Synthesized by Stressed Grapevine Leaves (2003)

Delta-viniferin is a resveratrol dehydrodimer, an isomer of epsilon-viniferin. This compound has been reported as a molecule produced in vitro by the oxidative dimerization of resveratrol by plant peroxidases or fungal laccases. It was also recently identified in wines and in grape cell cultures. We have now identified this dimer by NMR, high-performance liquid chromatography-diode array detection (HPLC-DAD), and HPLC-mass spectrometry (MS) in grapevine leaves infected by Plasmopara viticola (downy mildew) or UV-C irradiated. Its concentration was higher than that of epsilon-viniferin and constitutes one of the most important phytoalexins derived from resveratrol.