gebhart/patrepeval huggingface dataset:
Micropatterning of Nanoengineered Surfaces to Study Neuronal Cell Attachment in Vitro (2004)

Methods for producing protein patterns with defined spatial arrangement and micro- and nanoscale features are important for studying cellular-level interactions, including basic cell-cell communications, cell signaling, and mechanisms of drug action. Toward this end, a straightforward, versatile procedure for fabricating micropatterns of bioactive nanofilm coatings as multifunctional biological testbeds is demonstrated. The method, based on a combination of photolithography and layer-by-layer self-assembly (LbL), allows for precise construction of nanocomposite films of potentially complex architecture, and patterning of these films on substrates using a modified lift-off (LO) procedure. As a first step in evaluating nanostructures made with this process, "comparison chips," comprising two coexisting regions of square patterns with relevant proteins/polypeptides on a single substrate, were fabricated with poly(diallyldimethylammonium chloride) (PDDA) as a cell-repellent background. Using neuronal cells as a model biological system, comparison chips were produced with secreted phospholipase A2 (sPLA2), a known membrane-active enzyme for neurons, for direct comparison with gelatin, poly-l-lysine (PLL), or bovine serum albumin (BSA). Fluorescence microscopy, surface profilometry, and atomic force microscopy techniques were used to evaluate the structural properties of the patterns on these chips and show that the patterning technique was successful. Preliminary cell culture studies show that neurons respond and bind specifically to the sPLA2 enzyme embedded in the polyelectrolyte thin films and present as the outermost layer. These findings point to the potential for this method to be applied in developing test substrates for a broad array of studies aimed at identifying important biological structure-function relationships.
Haptic rendering of surface-to-surface sculpted model interaction (2005)

Previous work in haptics surface tracing for virtual prototyping and surface design applications has used a point model for virtual finger-surface interaction. We extend this tracing method for surface-to-surface interactions. A straightforward extension of the point-surface formulation to surface-surface can yield extraneous, undesirable solutions, although we rework the formulation to yield more satisfactory solutions. Additionally, we derive an alternative novel velocity formulation for use in a surface-surface tracing paradigm that exhibits additional stability beyond the Newton methods. Both methods require evaluating the surface point and first and second surface partial derivatives for both surfaces, an efficient kilohertz rate computation. These methods are integrated into a three step tracking process that uses a global minimum distance method, the local Newton formulation, and the new velocity formulation.
Rat liver acyl-coenzyme A:cholesterol acyltransferase: its regulation in vivo and some of its properties in vitro (1980)

To gain insight into the role of the enzyme acyl-coenzyme A:cholesterol acyltransferase (ACAT) in cellular cholesterol homeostasis, its regulation in rat liver was investigated both in vivo and in vitro. In vitro assay conditions were optimized and some properties of the microsomal enzyme in vitro was also studied. Arrhenius plots of microsomal ACAT activity showed discontinuities at about 28-29 degrees C and 16-17 degrees C. Detergents above their critical micelle concentrations and organic solvents both inhibited the enzyme. Addition of progesterone or SC 31769, a 7-keto-cholesterol analogue, to microsomes inhibited activity while addition of 25-hydroxycholesterol increased the rate of cholesterol esterification, suggesting that the enzyme is susceptible to both negative and positive modulation by steroids, steroid analogues, or their metabolic products. Increasing the rate of cholesterol biosynthesis had a variable effect on ACAT activity. It was higher at the circadian peak of sterol biosynthesis than at the nadir. Increasing sterol biosynthesis by intragastric administration of mevalonolactone resulted in increased activity. In contrast, increasing the rate of sterol biosynthesis by feeding cholestyramine or administration of Triton WR 1339 had little effect on ACAT. Increasing hepatic cholesterol content by feeding cholesterol, cholate, or an atherogenic diet, fasting or intragastric administration of mevalonolactone all resulted in increased ACAT activity. ACAT activity showed a positive correlation with changes in microsomal free and esterified cholesterol contents. The response of ACAT to changes in hepatic cholesterol concentration in vivo and its response to changes in the rate of cholesterol synthesis support the hypothesis that this enzyme plays an important role in maintenance of hepatic cholesterol homeostasis.
Nanoscale Clustering of RGD Peptides at Surfaces Using Comb Polymers. 1. Synthesis and Characterization of Comb Thin Films (2000)

Theoretical and experimental studies were conducted to elucidate the structure and properties of amphiphilic comb polymer thin films presenting nanoscale clusters of Arg-Gly-Asp (RGD) peptides for control of cell adhesion on biomaterials. Combs comprised of a poly(methyl methacrylate) backbone and short poly(ethylene oxide) side chains were synthesized, and peptides were tethered to the side chain ends to create nanoscale peptide clusters. In thin films, comb polymers containing ≥30 wt % six to nine unit PEO side chains completely resisted adhesion of a model fibroblast cell line in the presence of 7.5% serum over 24 h. These same polymers modified with RGD peptides elicited tunable cell adhesion when mixed with unmodified combs in varying proportion. A self-consistent field lattice model of the interface between comb polymer films and water predicts an organization of the top molecular layer of comb polymer with the backbone oriented parallel to the interface in quasi-two-dimensional confinement and hydrophilic side chains extended in a brushlike layer into solution. This picture of a quasi-2D configuration is consistent with the observed surface properties of comb films in water as well as measurements of the RGD cluster density on mixed comb surfaces using fluorescent nanosphere labeling of ligand clusters.
Effects of transient intrathoracic pressure changes (hiccups) on systemic arterial pressure (1997)

The purpose of the study was to determine the effect of transient changes in intrathoracic pressure on systemic arterial pressure by utilizing hiccups as a tool. Values of systolic and diastolic pressures before, during, and after hiccups were determined in 10 intubated preterm infants. Early-systolic hiccups decreased systolic blood pressure significantly (P < 0.05) compared with control (39.38 +/- 2.72 vs. 46.46 +/- 3.41 mmHg) and posthiccups values, whereas no significant change in systolic blood pressure occurred during late-systolic hiccups. Diastolic pressure immediately after the hiccups remained unchanged during both early- and late-systolic hiccups. In contrast, diastolic pressure decreased significantly (P < 0.05) when hiccups occurred during diastole (both early and late). Systolic pressures of the succeeding cardiac cycle remained unchanged after early-diastolic hiccups, whereas they decreased after late-diastolic hiccups. These results indicate that transient decreases in intrathoracic pressure reduce systemic arterial pressure primarily through an increase in the volume of the thoracic aorta. A reduction in stroke volume appears to contribute to the reduction in systolic pressure.
Extracellular NAD and ATP: Partners in immune cell modulation (2007)

Extracellular NAD and ATP exert multiple, partially overlapping effects on immune cells. Catabolism of both nucleotides by extracellular enzymes keeps extracellular concentrations low under steady-state conditions and generates metabolites that are themselves signal transducers. ATP and its metabolites signal through purinergic P2 and P1 receptors, whereas extracellular NAD exerts its effects by serving as a substrate for ADP-ribosyltransferases (ARTs) and NAD glycohydrolases/ADPR cyclases like CD38 and CD157. Both nucleotides activate the P2X7 purinoceptor, although by different mechanisms and with different characteristics. While ATP activates P2X7 directly as a soluble ligand, activation via NAD occurs by ART-dependent ADP-ribosylation of cell surface proteins, providing an immobilised ligand. P2X7 activation by either route leads to phosphatidylserine exposure, shedding of CD62L, and ultimately to cell death. Activation by ATP requires high micromolar concentrations of nucleotide and is readily reversible, whereas NAD-dependent stimulation begins at low micromolar concentrations and is more stable. Under conditions of cell stress or inflammation, ATP and NAD are released into the extracellular space from intracellular stores by lytic and non-lytic mechanisms, and may serve as "danger signals" to alert the immune response to tissue damage. Since ART expression is limited to naïve/resting T cells, P2X7-mediated NAD-induced cell death (NICD) specifically targets this cell population. In inflamed tissue, NICD may inhibit bystander activation of unprimed T cells, reducing the risk of autoimmunity. In draining lymph nodes, NICD may eliminate regulatory T cells or provide space for the preferential expansion of primed cells, and thus help to augment an immune response.
Adjuvant arthritis as a model of inflammatory cachexia (1997)

AA in rats is a useful model of inflammatory cachexia that mimics the human pathophysiology in important ways, and is consistent with cytokine-driven cachexia in chronic inflammatory arthritis.
Generation of Constitutively Active Recombinant Caspases-3 and -6 by Rearrangement of Their Subunits (1998)

Caspases play a major role in the transduction of the apoptotic signal and execution of apoptosis in mammalian cells. Ectopic overexpression of the short prodomain caspases-3 and -6 precursors in mammalian cells does not induce apoptosis. This is due to their inability to undergo autocatalytic processing/activation and suggests that they depend on the long prodomain caspases for activation. To investigate directly the apoptotic activity of these two caspases in vivo, we engineered constitutively active recombinant caspases-3 and -6 precursors. This was achieved by making contiguous precursor caspases-3 and -6 molecules, which have their small subunits preceding their large subunits. Unlike their wild type counterparts, these recombinant molecules were capable of autocatalytic processing in an in vitro translation reaction, suggesting that they are catalytically active. They were also capable of autoprocessing and inducing apoptosis in vivo independent of the upstream caspases. Furthermore, their autocatalytic and apoptotic activities were inhibited by the pancaspase inhibitor z-VAD-fluoromethylketone, but not by CrmA or Bcl-2, thus directly demonstrating that the targets of inhibition of apoptosis by CrmA and Bcl-2 are upstream of caspases-3 and -6. Since caspases-3 and -6 are the most downstream executioners of apoptosis, the constitutively active versions of these caspases could be used at very low concentrations in gene therapy model systems to induce apoptosis in target tissues or tumors.
Arabic handwriting recognition using baseline dependant features and hidden Markov modeling (2005)

In this paper, we describe a 1D HMM offline handwriting recognition system employing an analytical approach. The system is supported by a set of robust language independent features extracted on binary images. Parameters such as lower and upper baselines are used to derive a subset of baseline dependent features. Thus, word variability due to lower and upper parts of words is better taken into account. In addition, the proposed system learns character models without character pre-segmentation. Experiments that have been conducted on the benchmark IFN/ENIT database of Tunisian handwritten country/village names, show the advantage of the proposed approach and of the baseline-dependant features.
Churchill Livingstone's Dictionary of Sport and Exercise Science and Medicine (2008)

The dictionary is designed to be a pocket companion, for ready access by students, postgraduates, trainers, and health professionals involved in sport and exercise. It provides definitions and short accounts of terms used and techniques employed in the study and practical application of the relevant anatomy, physiology, biomechanics and psychology, and of commonly associated medical problems and treatments. Illustrations are included in the A-Z text, and appendices provide additional reference information and sources for further study. Wide coverage in A-Z text of relevant basic and applied topics relevant to sport and exercise. Full contact information for professional associations. Illustrations, graphs and tables. Team of expert contributors.
梅姬颱風（2010）轉向及對台灣降雨的遠距影響－系集模擬與不確定性探討 (2014)

當梅姬颱風（2010）通過呂宋島後，距離台灣仍有一段距離，颱風於南海地區由原本的向西移動突然往北轉向，受到颱風外圍環流與東北季風影響，台灣東北部以及其外海地區於10月19日到23日降下豪雨。由於過去許多研究顯示颱風降雨預報技術高度地受到路徑預報準確度之影響，本研究利用Advanced Research WRF模式結合ensemble Kalman filter（EnKF）資料同化技術及系集模擬，探討梅姬北轉之路徑不確定性，以及梅姬對於台灣地區所造成之遠距降雨效應。
 片段位渦診斷以及駛流分析結果顯示，副熱帶高壓之東退，加上季風槽影響範圍往西縮減，前者位於颱風東北側，後者位於颱風西南側，兩者皆提供利於颱風北轉之綜觀環境。此外，由熱帶地區逐漸發展且往北延伸至颱風東側之反氣旋系統，也提供颱風顯著的南風駛流。颱風北轉後一天，中緯度槽線系統也開始扮演增加颱風往北分量之角色。造成系集成員路徑差異之因素來自於模擬副熱帶高壓分裂時機之不確定性、反氣旋系統和季風槽勢力範圍變化，以及中緯度槽線系統之強度差異等，使得颱風駛流有所差異。
 藉由公正預兆得分檢驗定量降水模擬技術，發現梅姬颱風所伴隨的遠距強降雨事件中，定量降雨模擬之優劣與路徑平均誤差無顯著相關，並非如物理直覺一般簡單，重點是還需考慮東北風勢力範圍、颱風環流大小、潛在降雨區域盛行風向及該區山脈走向、坡度等影響。分析結果顯示，颱風外圍環流與東北季風之水氣通量輻合提供一個相對潮濕的潛在發生降雨環境，但並不是造成台灣東北角陸地區域產生強降雨之主因。盛行風將水氣從外海地區平流至宜蘭平原南側較陡峭坡度之山區，透過強烈的地形抬升作用，在迎風面近地表產生輻合並伴隨強烈的垂直運動，進而產生強降雨。地形移除實驗也顯示，海面上之降雨主要為水氣通量輻合作用所致，而宜蘭地區的降雨則必須透過地形抬升之動力過程而增強。
 藉由系集模擬分析，本研究一方面探討造成颱風北轉之成因，同時透過系集模擬檢驗在颱風遠距影響下，造成台灣東北部降雨事件的不確定性以及強降雨產生機制。此研究探討了包括颱風、季風、地形以及彼此微妙之交互作用與可能的不確定性，未來可提供在東北季風盛行季，颱風所伴隨遠距降雨預報之參考。
Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase (2004)

Group II intron-encoded proteins (IEPs) have both reverse transcriptase (RT) activity, which functions in intron mobility, and maturase activity, which promotes RNA splicing by stabilizing the catalytically active RNA structure. The LtrA protein encoded by the Lactococcus lactis Ll.LtrB group II intron contains an N-terminal RT domain, with conserved sequence motifs RT1 to 7 found in the fingers and palm of retroviral RTs; domain X, associated with maturase activity; and C-terminal DNA-binding and DNA endonuclease domains. Here, partial proteolysis of LtrA with trypsin and Arg-C shows major cleavage sites in RT1, and between the RT and X domains. Group II intron and related non-LTR retroelement RTs contain an N-terminal extension and several insertions relative to retroviral RTs, some with conserved features implying functional importance. Sequence alignments, secondary-structure predictions, and hydrophobicity profiles suggest that domain X is related structurally to the thumb of retroviral RTs. Three-dimensional models of LtrA constructed by "threading" the aligned sequence on X-ray crystal structures of HIV-1 RT (1) account for the proteolytic cleavage sites; (2) suggest a template-primer binding track analogous to that of HIV-1 RT; and (3) show that conserved regions in splicing-competent LtrA variants include regions of the RT and X (thumb) domains in and around the template-primer binding track, distal regions of the fingers, and patches on the protein's back surface. These regions potentially comprise an extended RNA-binding surface that interacts with different regions of the intron for RNA splicing and reverse transcription.
Differential inhibition of Wnt‐3a by Sfrp‐1, Sfrp‐2, and Sfrp‐3 (2006)

Secreted frizzled related proteins (Sfrps) are extracellular attenuators of Wnt signaling that play important roles in both embryogenesis and oncogenesis. Although Sfrps are generally thought to bind and sequester Wnts away from active receptor complexes, very little is known about the specificity of Sfrp family members for various Wnts. In the developing chick neural tube, sfrp-1, 2, and 3 transcripts are expressed in and adjacent to the dorsal neural tube, where Wnt-1 and Wnt-3a are expressed. To better define the possible roles of Sfrp-1, 2, and 3 in the neural tube, we first tested the ability of purified Sfrps to inhibit Wnt-3a-induced accumulation of beta-catenin in L cells. We find that both Sfrp-1 and Sfrp-2 can inhibit Wnt-3a activity while Sfrp-3 cannot. To determine where Sfrp-1 and Sfrp-2 impinge on the Wnt signaling pathway, we tested the ability of these Sfrps to inhibit Wnt signaling induced by the addition of LiCl, an inhibitor of GSK-3. Sfrp-1 and Sfrp-2 are unable to inhibit the accumulation of beta-catenin in LiCl-treated cells, suggesting that the ability of Sfrps to inhibit the accumulation of beta-catenin is GSK-3 dependent. We have further shown that Sfrp-2 inhibits the ability of ectopic Wnt-3a to stimulate proliferation in the developing chick neural tube. These results provide the framework for understanding how Sfrps function to regulate Wnt-3a activity in developing embryos and in cancer.
Flow labelled IP: a connectionless approach to ATM (2002)

A number of proposals for supporting the Internet protocol (IP) over ATM are under discussion in the networking community including: LAN emulation, classical IP over ATM, routing over large clouds, and multiprotocol over ATM. Each of these proposals hides the real network topology from the IP layer by treating the data link layer as a large, opaque, network cloud. We argue that this leads to complexity, inefficiency and duplication of functionality in the resulting network. We propose an alternative in which we discard the connection oriented nature of ATM and integrate fast ATM hardware directly with the IP, presenting the connectionless nature of the IP. We use a "soft" state in the ATM hardware to cache the IP forwarding decision. This enables further traffic on the same IP flow to be switched by the ATM hardware rather than forwarded by the IP software. We claim that this approach combines the simplicity, scalability, and robustness of the IP with the speed, capacity, and multiservice traffic capabilities of ATM.
Thrombopoietin-induced Expression of the Glycoprotein IIb Gene Involves the Transcription Factor PU.1/Spi-1 in UT7-Mpl Cells (1997)

Thrombopoietin (TPO) is the major regulator of proliferation and differentiation of megakaryocytes and their progenitors. These actions can be reproduced in the human megakaryoblastic cell line UT7 into which the murine TPO receptor, c-Mpl, was introduced. In these cells, TPO enhanced the expression of the specific megakaryocytic marker integrin glycoprotein (GP) IIb-IIIa while decreasing the expression of erythroid genes (Porteu, F., Rouyez, M. -C., Cocault, L., Benit, L., Charon, M., Picard, F., Gisselbrecht, S. , Souyri, M., and Dusanter-Fourt, I. (1996) Mol. Cell. Biol. 16, 2473-2482). We have now analyzed the effect of TPO on the transcriptional activity of the GPIIb promoter in these cells. Using transient transfection assays of a series of human GPIIb promoter fragments, we delineated a TPO-responsive element within the previously reported enhancer region of the promoter. Although this enhancer included GATA- and Ets-binding sites (EBSs), we found that only EBS -514 was important for TPO response. We identified PU. 1/Spi-1 as the endogenous Ets transcription factor that strongly and preferentially interacted with this enhancer EBS. This factor did not interact with other proximal EBSs in the GPIIb promoter. We next showed that TPO induced a strong and selective increase of PU. 1/Spi-1 expression and DNA binding activity in UT7-Mpl cells. In contrast, TPO did not affect the expression of Ets-1/2 while weakly increasing the levels of Fli-1. Overexpression of PU.1/Spi-1 was further shown to enhance GPIIb promoter activity in the absence and presence of TPO. Overall, our data indicated that, in UT7-Mpl cells, TPO increased the transcriptional activity of a GPIIb gene in part due to an enhanced expression of an unexpected transcription factor, the Ets family PU.1/Spi-1 factor. To our knowledge, this is the first evidence of a role for the PU.1/Spi-1 factor in the regulation of megakaryocytic genes.
History of xenotransplantation (2005)

The present historical review reports the clinical experiences of transplantations from animal to human. The first transplantation attempts were made without any knowledge of the species barrier. The pioneers of xenotransplantation realized xenotransfusions as early as the 16th century, then cell and tissue xenotransplantations in the 19th century. At the beginning of the 20th century, xenotransplantation of testicles became the latest craze. At the same time, and later in the 1960s, organ xenotransplantations were attempted, with disappointing results. Mathieu Jaboulay, Serge Voronoff, Keith Reemtsma, James Hardy, Denton Cooley, Thomas Starzl, Christiaan Barnard and Leonard Bailey were among the pionneers of xenotransplantation. Recent trials concerned above all tissue and cell xenotransplantations. Nowadays, with encapsulation, transgenesis, and cloning, great advances have been made for controlling xenograft rejection, but ethical questions linked to the risk of infections have become a major pre-occupation within the scientific community and the general population.
The Application of Digital Broadcast Communication to Large Scale Information Systems (1985)

A new type of information system is described that combines personal computers, broadcast data communication, and bidirectional communication. The system is designed to use broadcast communication whenever possible to deliver information to personal computers, which are used for data storage, indexing, and retrieval. This paper starts with an overview of the system, and then discuss the problem of reliable digital broadcast communication in some detail. A parameterized broadcast protocol is described, and we show how to choose protocol parameters based on observed channel error characteristics. A flexible encryption-based protection system is included in the protocol. We discuss the implementation of the system on contemporary personal computers. A broadcast system based on these ideas is now operating in Boston area homes.
Fe4S4 Clusters Functionalized with Molecular Receptor Ligands (2000)

Cubane-type Fe4S4 clusters have been functionalized with the concave dithiol ligands LXyl2H and LAc2H, derived from a diphenylglucoluril-based receptor molecule. In the monomeric cluster compounds [Fe4S4(LXyl)2](PPh4)2 (cluster A) and [Fe4S4(LAc)2](PPh4)2 (cluster B), an Fe4S4 core is combined with receptor sites for alkali metal ions and aromatic guest molecules. Molecular modelling studies show that the Fe4S4 core in compound B is tightly encapsulated by its two dithiol ligands, whereas this is not the case for compound A. However, unlike the clusters in High-Potential Iron−sulfur Proteins (HiPIP′s), the Fe4S4 core in B is still accessible to solvent molecules, as has been established by solution electrochemical studies. Both cluster compounds bind alkali metal ions and undergo anodic shifts in their 2−/3− reduction potentials upon binding of these ions. Electrochemical titrations indicate the complexation of four alkali metal ions per cluster compound. Binding by cluster B takes place preferentially at the exterior of the receptor ligands, whereas in the case of cluster A the ions also bind to the interior of the receptor. The more open structure of A allows the binding of dimethylparaquat 5 [Kass = (5.6 ± 0.6) × 103 M−1] to this cluster compound. On complexation, the first reduction potential of the guest molecule shifts in the cathodic direction, whereas the reduction potential of the cluster remains unaffected. This observation can be rationalized by assuming that the twofold positively charged guest molecule binds between the aromatic side-walls of the receptor ligands, whereas the one-electron reduced, singly charged positive species is not bound.