gebhart/patrepeval huggingface dataset:
Clustering of Escherichia coli Type‐1 Fimbrial Adhesins by Using Multimeric Heptyl α‐D‐Mannoside Probes with a Carbohydrate Core (2011)

Heptyl α-D-mannoside (HM) is a strong inhibitor of the FimH lectin that mediates the initial adhesion of the uropathogenic Escherichia coli (E. coli) to the bladder cells. We designed a set of multivalent HM ligands based on carbohydrate cores with structural valencies that range from 1 to 7. The chemical strategy used to construct the regular hydrophilic structures consisted of the repetition of a critical glucoside fragment. A primary amino group was grafted at the sugar reducing end to couple the multimers to a fluorescent label. A one-pot synthetic approach was developed to tether the ligands and the fluorescein isothiocyanate (FITC) probe to the scaffold simultaneously. Isothermal calorimetry with the monomeric FimH lectin revealed nanomolar affinities and saturation of all structurally available binding sites on the multivalent HM ligands. Direct titrations domain showed almost strict correlation of enthalpy-entropy compensation with increasing valency of the ligand, whereas reverse titration calorimetry demonstrated negative cooperativity between the first and the second binding site of the divalent heptyl mannoside. A multivalency effect was nevertheless observed by inhibiting the haemagglutination of type-1 piliated UTI89 E. coli, with a titer as low as 60 nM for the heptavalent HM ligand. An FITC-labeled HM trimer showed capture and cross-linking of living bacteria in solution, a phenomenon not previously described with low-valency ligands.
Analytic methods for slewing undamped flexible structures with on-off actuators (1997)

Methods are presented that generate command profiles for undamped flexible systems equipped with on-off actuators. The shape of the command profiles are described by analytic functions of the system's frequency, actuator force-to-mass ratio, and the desired move distance. The commands are obtained by first canceling the flexible-body response and then accounting for rigid-body requirements. Performance measures such as, move duration, fuel usage, peak transient deflection, and robustness to modeling errors indicate that the analytic commands are attractive alternatives to time-optimal commands.
Mimicry of a Cellular Low Energy Status Blocks Tumor Cell Anabolism and Suppresses the Malignant Phenotype (2005)

Aggressive cancer cells typically show a high rate of energy-consuming anabolic processes driving the synthesis of lipids, proteins, and DNA. Here, we took advantage of the ability of the cell-permeable nucleoside 5-aminoimidazole-4-carboxamide (AICA) riboside to increase the intracellular levels of AICA ribotide, an AMP analogue, mimicking a low energy status of the cell. Treatment of cancer cells with AICA riboside impeded lipogenesis, decreased protein translation, and blocked DNA synthesis. Cells treated with AICA riboside stopped proliferating and lost their invasive properties and their ability to form colonies. When administered in vivo, AICA riboside attenuated the growth of MDA-MB-231 tumors in nude mice. These findings point toward a central tie between energy, anabolism, and cancer and suggest that the cellular energy sensing machinery in cancer cells is an exploitable target for cancer prevention and/or therapy.
Complete amino acid sequences of the three collagen-like regions present in subcomponent C1q of the first component of human complement (1979)

The sequences of amino acid residues 38--51 of the A-chain, and residues 42--90 of the C-chain, of human subcomponent C1q are given. These results, along with previously published sequence data [Reid (1974) Biochem.J. 141, 189--203; Reid (1977) Biochem.J. 161, 247--251; Reid & Thompson (1978) Biochem.J. 173, 863--868] allow the presentation, and comparison with each other, of the complete amino acid sequences of the collagen-like regions found in the A-, B- and C-chains of human subcomponent C1q. Each chain has the continuity of its collagen-like Gly-X-Y repeating triplet amino acid sequence broken. The B- and C-chains have alanine residues at positions B-9 and C-36 where glycine might be expected. The A-chain has a threonine residue at position A-39, which is located between two Gly-X-Y triplets.
The Use of Optical Coherence Tomography in Intraoperative Ophthalmic Imaging (2011)

Optical coherence tomography (OCT) has transformed diagnostic ophthalmic imaging but until recently has been limited to the clinic setting. The development of spectral-domain OCT (SD-OCT), with its improved speed and resolution, along with the development of a handheld OCT scanner, enabled portable imaging of patients unable to sit in a conventional tabletop scanner. This handheld SD-OCT unit has proven useful in examinations under anesthesia and, more recently, in intraoperative imaging of preoperative and postoperative manipulations. Recently, several groups have pioneered the development of novel OCT modalities, such as microscope-mounted OCT systems. Although still immature, the development of these systems is directed toward real-time imaging of surgical maneuvers in the intraoperative setting. This article reviews intraoperative imaging of the posterior and anterior segment using the handheld SD-OCT and recent advances toward real-time microscope-mounted intrasurgical imaging.
Low-power Viterbi decoder for CDMA mobile terminals (1998)

An efficient state-sequential very large scale integration (VLSI) architecture and low-power design methodologies ranging from the system-level to the layout-level are presented for a large-constraint-length Viterbi decoder for code division multiple access (CDMA) digital cellular/personal communication services (PCS) applications. The low-power design approaches are also applicable to many other systems and algorithms. VLSI implementation issues and prototype fabrication results for a state-sequential Viterbi decoder for convolutional codes of rate 1/2 and constraint-length 9 are also described. The chip's core, consisting of approximately 65 k transistors, occupies 1.9 mm by 3.4 mm in a 0.8-/spl mu/m triple-layer-metal n-well CMOS technology. The chip's measured total power dissipation is 0.24 mW at a 14.4 kb/s data-rate with 0.9216 MHz clocking at a supply voltage of 1.65 V. The Viterbi decoder presented here is the lowest power and smallest area core in its class, to the best of our knowledge.
Physical and chemical characterization of an avian reovirus (1976)

The avian viral agent S1133 has previously been classified serologically as a member of the avian reovirus group. This viral agent grows in chicken embryo fibroblast cells, bands at a density of 1.37 g/ml in CsCl equilibrium density gradients, has a particle diameter of 75 nm, and has a morphology similar to that of human reovirus type 3. Its nucleic acid is comprised of double-stranded RNA and adenosine-rich oligonucleotides. The dsRNA is distributed among 10 segments with molecular weights of 2.7 x 10(6), 2.6 x 10(6), 1.7 x 10(6), 1.5 x 10(6), 1.3 x 10(6), 1.2 x 10(6), 0.80 x 10(6), 0.74 x 10(6), and 0.68 x 10(6) for the largest (L1) to the smallest (S4) segment, respectively, as determined by polyacrylamide gel electrophoresis. These 10 segments migrate differently on polyacrylamide gels compared to those of human reovirus type 3. The capsid proteins of avian reovirus consist of eight species of polypeptides as determined by polyacrylamide gel electrophoresis. These are lambda1, lambda2, lambda3, mu1, mu2, sigma1, sigma2, and sigma3 with molecular weights of 140, 125, 115, 85, 72, 40, 36, and 32 x 10(3), respectively. Only polypeptide sigma2, which resides in the inner capsid or core, comigrated with the sigma2 polypeptide of type 3 reovirus. Antiserum against type 3 reovirus did not neutralize avian reovirus. Avian reovirus core particles were found to possess a transcriptase and a methylase activity.
Intracellular hydrogelation preserves fluid and functional cell membrane interfaces for biological interactions (2019)

Cell membranes are an intricate yet fragile interface that requires substrate support for stabilization. Upon cell death, disassembly of the cytoskeletal network deprives plasma membranes of mechanical support and leads to membrane rupture and disintegration. By assembling a network of synthetic hydrogel polymers inside the intracellular compartment using photo-activated crosslinking chemistry, we show that the fluid cell membrane can be preserved, resulting in intracellularly gelated cells with robust stability. Upon assessing several types of adherent and suspension cells over a range of hydrogel crosslinking densities, we validate retention of surface properties, membrane lipid fluidity, lipid order, and protein mobility on the gelated cells. Preservation of cell surface functions is further demonstrated with gelated antigen presenting cells, which engage with antigen-specific T lymphocytes and effectively promote cell expansion ex vivo and in vivo. The intracellular hydrogelation technique presents a versatile cell fixation approach adaptable for biomembrane studies and biomedical device construction.
Transient absorption microscopy: advances in chemical imaging of photoinduced dynamics (2015)

Abstract This article reviews the state of the art of ultrafast transient absorption microscopy, discusses current experimental concepts and highlights future challenges. The advantages of transient absorption microscopy over other micro‐spectroscopic techniques are its high optical resolution combined with high temporal resolution as well as its ability to study non‐fluorescent and weakly fluorescent molecular species and to probe excited‐state processes. In conventional transient absorption spectroscopy the spectroscopic information usually presents a spatial average over the focal spot of the typically weakly focused probe beam. Transient absorption microscopy, however, enables investigations of the excited state dynamics in individual microscopic areas of a sample. Hence, the technique does not only yield detailed morphological information based on a label‐free molecular contrast, but also gives insight into the ultrafast morphology‐dependent photoinduced processes in heterogeneous samples. Different variations of transient absorption microscopy have found a number of applications ranging from material sciences to biology, which are discussed in this review together with different setup modifications and approaches towards transient absorption spectroscopy with spatial resolution below the diffraction limit. image
Toll-like receptor 3 inhibits memory retention and constrains adult hippocampal neurogenesis (2010)

Toll-like receptors (TLRs) are innate immune receptors that have recently emerged as regulators of neuronal survival and developmental neuroplasticity. Adult TLR3-deficient mice exhibited enhanced hippocampus-dependent working memory in the Morris water maze, novel object recognition, and contextual fear-conditioning tasks. In contrast, TLR3-deficient mice demonstrated impaired amygdala-related behavior and anxiety in the cued fear-conditioning, open field, and elevated plus maze tasks. Further, TLR3-deficient mice exhibited increased hippocampal CA1 and dentate gyrus volumes, increased hippocampal neurogenesis, and elevated levels of the AMPA receptor subunit GluR1 in the CA1 region of the hippocampus. In addition, levels of activated forms of the kinase ERK and the transcription factor CREB were elevated in the hippocampus of TLR3-deficient mice, suggesting that constitutive TLR3 signaling negatively regulates pathways known to play important roles in hippocampal plasticity. Direct activation of TLR3 by intracerebroventricular infusion of a TLR3 ligand impaired working memory, but not reference memory. Our findings reveal previously undescribed roles for TLR3 as a suppressor of hippocampal cellular plasticity and memory retention.
Evidence of Distinct Tumour-Propagating Cell Populations with Different Properties in Primary Human Hepatocellular Carcinoma (2011)

Individual HCCs can harbor different self-renewing tumorigenic cell types expressing a variety of morphological and phenotypical markers, karyotypic evolution and different gene expression profiles. This suggests that the models of hepatic carcinogenesis should take into account TPC heterogeneity due to intratumour clonal evolution.
Function of Laminins and Laminin‐Binding Integrins In Gingival Epithelial Cell Adhesion (2002)

Our results provide new information on gingival epithelial cell adhesion and extracellular matrix production and may thus aid in the understanding of periodontal physiology.
Myosin VIIB from Drosophila Is a High Duty Ratio Motor (2005)

Myosin VII is an unconventional myosin widely expressed in organisms ranging from amoebae to mammals that has been shown to play vital roles in cell adhesion and phagocytosis. Here we present the first study of the mechanism of action of a myosin VII isoform. We have expressed a truncated single-headed Drosophila myosin VIIB construct in the baculovirus-Sf9 system that bound calmodulin light chains. By using steady-state and transient kinetic methods, we showed that myosin VIIB exhibits a fast release of phosphate and a slower, rate-limiting ADP release from actomyosin. As a result, myosin VIIB will be predominantly strongly bound to actin during steady-state ATP hydrolysis (its duty ratio will be at least 80%). This kinetic pattern is in many respects similar to that of the single-molecule vesicle transporters myosin V and VI. The enzymatic properties of myosin VIIB provide a kinetic basis for processivity upon possible dimerization via the C-terminal domains of the heavy chain. Our experiments also revealed conformational heterogeneity of the actomyosin VIIB complex in the absence of nucleotide.
RNA Conformation in the Tat−TAR Complex Determined by Site-Specific Photo-Cross-Linking (1996)

Transcriptional regulation in human immunodeficiency virus type 1 (HIV-1) requires specific interactions of Tat protein with the transactivation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all mRNAs. We have used a site-specific cross-linking method based on 4-thiouracil (4-thioU) photochemistry to determine the conformation of TAR RNA and its interaction with Tat protein under physiological conditions. Three different TAR RNA constructs with a single 4-thioU residue at position 23, 38, or 40 were synthesized. Upon UV irradiation, 4-thioU at all three positions formed interstrand covalent cross-links in TAR RNA. Determination of cross-link sites by RNA sequencing revealed that 4-thioU at position 23 makes a direct contact with U40, while a 4-thoU at position 40 cross-links to C24 and C25, and at position 38, 4-thioU contacts G26 in TAR RNA. The addition of arginine did not alter the yield or the site of RNA-RNA cross-link. However, in the presence of Tat(38-72), UV irradiation of RNA modified with 4-thioU at position 23 or 38 resulted in RNA- protein cross-links, but no RNA-RNA cross-links were observed. 4-thioU at position 40 formed both RNA-RNA and RNA-protein cross-links in the presence of Tat(38-72). An intriguing finding of our studies was that a cross-linked TAR RNA with 4-thioU at position 40 retained specific Tat-binding activity. Our results establish four important conclusions about Tat-TAR structure. (1) U23 of free TAR RNA is in close contact with U40. (2) U40 is in close proximity to C24 and C25 both in free TAR RNA and in a complex with Tat. (3) Tat protein directly contacts U23, U38, and U40 in the major groove of TAR RNA. (4) Tat protein can recognize a TAR RNA structure containing an interrupted bulge which is formed by a covalent link between U40 and two bulge residues, C24 and C25. These structural studies provide new insights into tertiary folding of TAR RNA and its interaction with Tat protein.
Involvement of neutrophils in the pathogenesis of lethal myocardial reperfusion injury (2003)

Neutrophils respond to myocardial ischemia-reperfusion in a manner similar to the bacterial invasion of a host. The inflammatory-like response that follows the onset of reperfusion involves intense interactions with the coronary vascular endothelium, arterial wall, and cardiomyocytes in a very well-choreographed manner. Neutrophils have been implicated as primary and secondary mediators of lethal injury after reperfusion to coronary vascular endothelium and cardiomyocytes. The involvement of neutrophils in the pathogenesis of lethal myocardial injury has been inferred from (1) their presence and accumulation in reperfused myocardium in temporal agreement with injury induced, (2) the armamentarium of toxic agents such as oxidants and proteases that are released by neutrophils in reperfused myocardium, (3) responsivity to (recruitment by and/or activation by) inflammatory factors released by reperfused myocardium, and (4) inhibition of lethal post-ischemic myocyte or endothelial cell injury by strategies that interdict neutrophil interactions at any number of stages. However, whether neutrophils are directly involved in the pathogenesis of lethal reperfusion injury in the myocardium, are just pedestrian (first) responders to inflammatory signals released after the onset of reperfusion, or are important to an early but not clinically important phase of pathology are still points of controversy. As with the general area of myocardial protection itself, the failure to reproduce the salubrious effects of anti-neutrophil therapeutic strategies and to successfully translate these strategies into clinical practice has not only fueled the debate, but has jeopardized the further pursuit of myocardial protection therapeutics to improve post-ischemic outcomes. This review will describe the molecular responses of neutrophils to ischemia-reperfusion, discuss the cellular and tissue damage inflicted either directly or indirectly by these white cells, and discuss the physiological impact of interdiction of neutrophil-mediated interactions with myocardial cells at various levels on lethal post-ischemic injury. In addition, it will discuss the arguments for and against the involvement of neutrophils in responses to ischemia-reperfusion in experimental models, and the failure to translate experimentally successful therapy into clinical practice.
Curcumin and Liver Cancer: A Review (2011)

Primary liver cancer, also known as hepatocellular carcinoma (HCC), is one of the most lethal cancers having worldwide prevalence. Although most HCC cases are reported in the developing countries of Asia and Africa, there has been an alarming increase in HCC cases in Western Europe as well as United States. Chronic liver diseases, viral hepatitis, alcoholism as well as dietary carcinogens, such as aflatoxins and nitrosoamines, contribute to HCC. Liver transplantation as well as surgical resection at best offer limited treatment options. Thus, there exists a critical need to investigate and evaluate possible alternative chemopreventive and therapeutic strategies which may be effective in the control of liver cancer. HCC, most often, develops and progresses in a milieu of oxidative stress and inflammation. Phytochemicals, such as dietary polyphenols endowed with potent antioxidant as well as anti-inflammatory properties, provide a suitable alternative in affording alleviation of HCC. Curcumin, the principal polyphenolic curcuminoid, obtained from the turmeric rhizome Curcuma longa has long been used to cure several chronic ailments, such as neoplastic and neurodegenerative diseases. Studies suggest that curcumin may have antitumor, antioxidant, and anti-inflammatory properties. This article reviews the effects of curcumin in preclinical in vitro and in vivo models of HCC with particular emphasis to its antioxidant, apoptotic and anti-inflammatory effects as well as involvement in various molecular signaling mechanisms. This review also discusses potential challenges involved in the use of curcumin in HCC, such as bioavailability, pharmacokinetics, drug delivery as well as paucity of clinical studies.
Naive and memory T cells show distinct pathways of lymphocyte recirculation. (1990)

In this report, we have addressed two questions concerning immunological memory: the way in which naive and memory T cells recirculate through the body, and the intrinsic rate of division within the naive and memory populations. We identified naive and memory T cells in sheep by their cell surface phenotype and their ability to respond to recall antigen. Memory T cells were CD2hi, CD58hi, CD44hi, CD11ahi, and CD45R-, as pertains in man. T cells that crossed from blood to the tissues of the hind leg and accumulated in the popliteal afferent lymph were all of memory phenotype. Conversely, T cells in efferent lymph, 90% of which entered the lymph node (LN) via high endothelial venules (HEV), were mostly of the naive phenotype (CD2lo, CD58lo, CD44lo, CD11alo, and CD45R+). The marked enrichment of these two phenotypes in different recirculatory compartments indicated that memory T cells selectively traffic from blood to peripheral tissues to LN (via afferent lymph), whereas naive T cells selectively traffic from blood to LN (via HEV). We argue that the differential use of these two recirculation pathways probably optimizes lymphocyte interactions with antigen. The nonrandom distribution of T cell subsets in various recirculatory compartments may be related to the relative proportion of memory cells in each subset. In particular, gamma/delta T cells in blood were almost exclusively of memory phenotype, and accumulated preferentially in afferent, but not in efferent, lymph. Finally, using the bromo-deoxyuridine labeling technique, we found that at least a sizeable proportion of memory T cells, whether in blood or afferent lymph, were a dividing population of cells, whereas naive T cells were a nondividing population. This result supports an alternative model of lymphocyte memory that assumes that maintenance of memory requires persistent antigenic stimulation.
Artificial neural networks for computing (1986)

Recent proposals for neural network models indicate that an array of amplifiers coupled to a lattice of wires with resistive components at the crosspoints can perform calculations using collective properties similar to those observed in biological systems. Such a network can perform both memory and processing functions. The promise of the connection matrix processor lies in its very high density, fault tolerance, and massively parallel operation. This paper describes the operation of a neural network and exploratory fabrication techniques for its implementation.
Inhibition of endothelial cell proliferation by platelet factor-4 involves a unique action on S phase progression. (1994)

Modulation of endothelial cell proliferation and cell cycle progression by the "chemokine" platelet factor-4 (PF-4) was investigated. PF-4 inhibited DNA synthesis, as well as proliferation of endothelial cells derived from large and small blood vessels. Inhibition by PF-4 was independent of the type and the concentration of stimuli used for the induction of endothelial cell proliferation. Inhibition of cell growth by PF-4 was reversible. The effects of PF-4 were antagonized by heparin. Cell cycle analysis using [3H]thymidine pulse labeling during traverse of synchronous cells from G0/G1 to S phase revealed that addition of PF-4 during G1 phase completely abolished the entry of cells into S phase. In addition, PF-4 also inhibited DNA synthesis in cells that were already in S phase. In exponentially growing cells, addition of PF-4 resulted in an accumulation of > 70% of the cells in early S phase, as determined by FACS (Becton-Dickinson Immunocytometry Systems, Mountain View, CA). In cells synchronized in S phase by hydroxyurea and then released, addition of PF-4 promptly blocked further progression of DNA synthesis. These results demonstrate that in G0/G1-arrested cells, PF-4 inhibited entry of endothelial cells into S phase. More strikingly, our studies have revealed a unique mode of endothelial cell growth inhibition whereby PF-4 effectively blocked cell cycle progression during S phase.