gebhart/patrepeval huggingface dataset:
Sustained thromboprophylaxis mediated by an RBC-targeted pro-urokinase zymogen activated at the site of clot formation (2010)

Plasminogen activators (PAs) are used to treat life-threatening thrombosis, but not for thromboprophylaxis because of rapid clearance, risk of bleeding, and central nervous system (CNS) toxicity. We describe a novel strategy that may help to overcome these limitations by targeting a thrombin-activated PA pro-drug to circulating red blood cells (RBCs). We fused a single chain antibody (scFv Ter-119) that binds to mouse glycophorin A (GPA) with a variant human single-chain low molecular weight urokinase construct that can be activated selectively by thrombin (scFv/uPA-T). scFv/uPA-T bound specifically to mouse RBCs without altering their biocompatibility and retained its zymogenic properties until converted by thrombin into an active 2-chain molecule. As a result, RBC-bound scFv/uPA-T caused thrombin-induced fibrinolysis. One hour and 48 hours after intravenous (IV) injection in mice, approximately 70% and approximately 35% of scFv/uPA-T was retained in the blood, respectively, and approximately 95% of the circulating scFv/uPA-T remained bound to RBCs. A single IV injection of scFv/uPA-T provided effective prophylaxis against arterial and venous thrombosis for up to 24 hours. Thus, prophylactic delivery of RBC-targeted PA pro-drugs activated selectively at the site of clot formation represents a new approach to prevent thrombosis in clinical settings where the risk of clotting is high.
Solvent-Free Functionalization of Carbon Nanotubes (2003)

A fundamentally new single-walled and multiwalled carbon nanotube sidewall functionalization technique has been developed in which solvent is not required and the reaction times are greatly shortened (1 h at 60 degrees C). Exploiting the long linear dimension of the nanotube ropes by macroscopic mechanical deformation, reactive sites are generated merely by mechanically deforming the tubes using a stir bar. This approach eliminates the need for large volumes of solvent ( approximately 2 L/g), which were formerly considered essential due to the insolubility of carbon nanotubes. Using a series of 4-substituted anilines and a nitrite, the aryl diazonium intermediates were generated in situ and permitted to react with the tubes. Raman, IR, and UV spectroscopies, coupled with thermogravimetric analyses and solubility studies, support the assignments.
Completion of the hook–basal body complex of the Salmonella typhimurium flagellum is coupled to FlgM secretion and fliC transcription (2000)

The flhDC operon of Salmonella typhimurium is the master control operon required for the expression of the entire flagellar regulon. The flagellar master operon was placed under the tetracycline-inducible promoter PtetA using the T-POP transposon. Cells containing this construct are motile in the presence of tetracycline and non-motile without inducer present. No flagella were visible under the electron microscope when cells were grown without inducer. The class 1, class 2 and class 3 promoters of the flagellar regulon are temporally regulated. After addition of tetracycline, the class 1 flhDC operon was transcribed immediately. Transcription of flgM (which is transcribed from both class 2 and class 3 promoters) began 15 min after induction. At 20 min after induction, the class 2 fliA promoter became active and intracellular FliA protein levels increased; at 30 min after induction, the class 3 fliC promoter was activated. Induction of fliC gene expression coincides with the appearance of FlgM anti-sigma factor in the growth medium. This also coincides with the completion of hook-basal body structures. Rolling cells first appeared 35 min after induction, and excess hook protein (FlgE) was also found in the growth medium at this time. At 45 min after induction, nascent flagellar filaments became visible in electron micrographs and over 40% of the cells exhibited some swimming behaviour. Multiple flagella assemble and grow on individual cells after induction of the master operon. These results confirm that the flagellar regulatory hierarchy of S. typhimurium is temporally regulated after induction. Both FlgM secretion and class 3 gene expression occur upon completion of the hook-basal body structure.
The smart house for older persons and persons with physical disabilities: structure, technology arrangements, and perspectives (2004)

Smart houses are considered a good alternative for the independent life of older persons and persons with disabilities. Numerous intelligent devices, embedded into the home environment, can provide the resident with both movement assistance and 24-h health monitoring. Modern home-installed systems tend to be not only physically versatile in functionality but also emotionally human-friendly, i.e., they may be able to perform their functions without disturbing the user and without causing him/her any pain, inconvenience, or movement restriction, instead possibly providing him/her with comfort and pleasure. Through an extensive survey, this paper analyzes the building blocks of smart houses, with particular attention paid to the health monitoring subsystem as an important component, by addressing the basic requirements of various sensors implemented from both research and clinical perspectives. The paper will then discuss some important issues of the future development of an intelligent residential space with a human-friendly health monitoring functional system.
High-speed flow microscopy using compressed sensing with ultrafast laser pulses (2015)

We demonstrate an imaging system employing continuous high-rate photonically-enabled compressed sensing (CHiRP-CS) to enable efficient microscopic imaging of rapidly moving objects with only a few percent of the samples traditionally required for Nyquist sampling. Ultrahigh-rate spectral shaping is achieved through chirp processing of broadband laser pulses and permits ultrafast structured illumination of the object flow. Image reconstructions of high-speed microscopic flows are demonstrated at effective rates up to 39.6 Gigapixel/sec from a 720-MHz sampling rate.
Synthetic non-peptide mimetics of α-helices (2007)

Proteins in nature fold into native conformations in which combinations of peripherally projected aliphatic, aromatic and ionic functionalities direct a wide range of properties. Alpha-helices, one of the most common protein secondary structures, serve as important recognition regions on protein surfaces for numerous protein-protein, protein-DNA and protein-RNA interactions. These interactions are characterized by conserved structural features within the alpha-helical domain. Rational design of structural mimetics of these domains with synthetic small molecules has proven an effective means to modulate such protein functions. In this tutorial review we discuss strategies that utilize synthetic small-molecule antagonists to selectively target essential protein-protein interactions involved in certain diseases. We also evaluate some of the protein-protein interactions that have been or are potential targets for alpha-helix mimetics.
Mechanistic Study into the Direct Epoxidation of Propene over Gold/Titania Catalysts (2005)

The epoxidation of propene over gold/titania based catalysts was investigated using different techniques. Infrared spectroscopic information showed that one key step in the reaction mechanism is a reaction catalyzed by gold between titania surface groups and propene. In this reaction step, a bidentate propoxy species is formed on titania. This species adsorbs strongly on the catalyst, and it is the same species which is formed when propene oxide adsorbs on titania. Gravimetrical adsorption experiments and catalytic tests show that product adsorption and desorption are important factors determining the catalytic activity and the catalyst stability. By combining the information from different techniques, a kinetic mechanism is proposed.
Tumor necrosis factor-alpha expression in ischemic neurons. (1994)

These results represent the first demonstration that focal cerebral ischemia in rats results in elevated TNF-alpha mRNA and protein in ischemic neurons. The neuronal expression of peptide appears to facilitate the infiltration of inflammatory cells that can further exacerbate tissue damage in cerebral ischemia and might contribute to increased sensitivity and risk in focal stroke.
Expression of disialogangliosides GD2 and GD3 on human soft tissue sarcomas (1992)

GD2 and GD3 may indicate sites for MoAb-targeted imaging and therapy for sarcomas. The association of a diminished stainability by 3F8 and R24 with aggressive sarcomas may indicate prognostic significance.
SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation (2017)

We present a novel and practical deep fully convolutional neural network architecture for semantic pixel-wise segmentation termed SegNet. This core trainable segmentation engine consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network [1] . The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification. The novelty of SegNet lies is in the manner in which the decoder upsamples its lower resolution input feature map(s). Specifically, the decoder uses pooling indices computed in the max-pooling step of the corresponding encoder to perform non-linear upsampling. This eliminates the need for learning to upsample. The upsampled maps are sparse and are then convolved with trainable filters to produce dense feature maps. We compare our proposed architecture with the widely adopted FCN [2] and also with the well known DeepLab-LargeFOV [3] , DeconvNet [4] architectures. This comparison reveals the memory versus accuracy trade-off involved in achieving good segmentation performance. SegNet was primarily motivated by scene understanding applications. Hence, it is designed to be efficient both in terms of memory and computational time during inference. It is also significantly smaller in the number of trainable parameters than other competing architectures and can be trained end-to-end using stochastic gradient descent. We also performed a controlled benchmark of SegNet and other architectures on both road scenes and SUN RGB-D indoor scene segmentation tasks. These quantitative assessments show that SegNet provides good performance with competitive inference time and most efficient inference memory-wise as compared to other architectures. We also provide a Caffe implementation of SegNet and a web demo at http://mi.eng.cam.ac.uk/projects/segnet.
Synthesis of Poly(β-amino ester)s Optimized for Highly Effective Gene Delivery (2003)

Several families of synthetic polymers, including degradable poly(beta-amino ester)s, have been previously shown to effectively mediate gene transfer. However, the combined impact of potentially significant factors-such as polymer molecular weight, polymer chain end-group, and polymer/DNA ratio-on different gene transfer properties has yet to be systematically investigated. The elucidation of these relationships may aid in the design of nonviral vectors with greatly enhanced transfection properties. To examine these factors, two distinct poly(beta-amino ester) structures, Poly-1 and Poly-2, were generated by adding 1,4-butanediol diacrylate and 1,6-hexanediol diacrylate, respectively, to 1-aminobutanol. Twelve unique versions of each structure were synthesized by varying amine/diacrylate stoichiometric ratios, resulting in polymers with either amine or acrylate end-groups and with molecular weights ranging from 3350 to 18000. Using high throughput methods, all polymers were tested in quadruplicate at nine different polymer/DNA ratios ranging from 10:1 w/w to 150:1 w/w. Through the optimization of molecular weight, polymer chain end-group, and polymer/DNA ratio, these polymers successfully mediated gene transfer at levels that surpassed both PEI and Lipofectamine 2000 in vitro.
Risk factors for infection in the trauma patient. (1992)

The most common cause of late death following trauma is sepsis. The traumatized patient has a significant increased risk of infection. Transfusion, hypotension, and prolonged ventilatory support are predictive of septic complications. In addition, the trauma patient has a higher predisposition to pneumonia than nontrauma patients (18% versus 3% incidence of pneumonia, P < .001). Additional risk factors include the degree of nutrition status and the type of medications used during surgery. Immunologic depression may be an additional risk factor. There is mounting evidence that trauma can result in host defense abnormalities. To prevent the significant mortality caused by sepsis, close surveillance must be maintained, nutritional status must be optimal, and liberal use of antibiotics should be discouraged. Their use should be guided by appropriate cultures and sensitivities.
Megakaryocytopoiesis in the rat: response to thrombocytopenia induced by exchange transfusion. (1985)

We have studied the megakaryocytopoietic response in rats to acute thrombocytopenia induced by exchange transfusion of platelet-poor blood. Our analysis included serial determinations of peripheral blood counts, the size and number of megakaryocytes in sections of humeral marrow, the numbers of megakaryocytic (CFU-Meg) and granulocyte-macrophage (CFU-GM) colony-forming cells in marrow and spleen, and the proportion of CFU-Meg and CFU-GM in DNA synthesis. With exchange transfusion, the platelet count fell to 11% of the control value (101,000 +/- 49,000/mm3; mean +/- SD) and returned to normal by day 3; rebound thrombocytosis (peak 1,720,000 +/- 246,000/mm3) was observed on days 4 and 5. The average size of marrow megakaryocytes increased significantly on days 2 and 3 compared with normal (p less than 0.01), but the numbers of recognizable megakaryocytes did not change through day 5. The numbers of splenic CFU-Meg and CFU-GM increased significantly (p less than 0.05) on days 2-4 and on day 2, respectively, after the exchange; however, the numbers of marrow progenitors, which account for over 95% of total body progenitors, remained unchanged throughout the duration of the study. The proportion of CFU-Meg in DNA synthesis (mean +/- SD) increased from a baseline value of 17% +/- 4% to 33% +/- 11% (p less than 0.02) and 35% +/- 6% (p less than 0.001) on days 1 and 2, respectively, and returned to control values thereafter. There were no changes in the cell cycle activity of CFU-GM. Thus, acute selective thrombocytopenia induced by exchange transfusion causes an enlargement of marrow megakaryocytes and an increase in the fraction of CFU-Meg in cell cycle. These changes, occurring in the absence of immunologically mediated events, are the direct result of lowered platelet count.
Metabolism of D-[3H]threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol, an inhibitor of glucosylceramide synthesis, and the synergistic action of an inhibitor of microsomal monooxygenase (1991)

D-Threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol (D-PDMP) is an effective inhibitor of the glucosyltransferase that makes glucosylceramide. Virtually all of the hundreds of naturally occurring glycolipids are formed from this primary glycolipid, so the inhibitor acts to lower their concentrations by the process of attrition (hydrolytic catabolism). Trials with mice carrying ascites carcinoma cells showed that PDMP could produce a permanent cure in some of the animals and marked prolongation of life in the others (Inokuchi, J., I. Mason, and N.S. Radin. 1987. Cancer Lett. 38: 23-30). In order to maximize the effect, we studied the metabolism of PDMP by labeling it with [3H] on carbon one, using a labeling method that discriminated against the unwanted erythro-isomer. The active enantiomer of the inhibitor (D-) was isolated by chromatography of the camphanate esters, followed by methanolytic cleavage. Examination of the fate of the labeled drug after a single injection showed that it was very rapidly converted to several polar products that were rapidly excreted. The drug penetrated all of the organs readily and a small portion was oxidized at the C-1 position to yield 3H2O. From these findings it appeared likely that the amine is attacked by a mixed function oxidase based on cytochrome P450. This conclusion was confirmed by showing that the tissue levels of PDMP could be greatly elevated, for a much longer time, when the mice were pretreated with piperonyl butoxide or cimetidine. The amount of conversion to polar metabolites was substantially reduced and tissue levels of PDMP were maintained much longer. Analysis of mice injected with one or both drugs showed that piperonyl butoxide augmented the effects of PDMP on ceramide, glucosylceramide, and dihexosylceramide levels, as well as on the activity of glucosylceramide synthase. It is suggested that piperonyl butoxide be used as an adjuvant for the many useful drugs that are inactivated by the P450 system.
A Single Amino Acid Change (Substitution of Glutamate 3 with Alanine) in the N-terminal Region of Rat Liver Carnitine Palmitoyltransferase I Abolishes Malonyl-CoA Inhibition and High Affinity Binding (1999)

We have recently shown by deletion mutation analysis that the conserved first 18 N-terminal amino acid residues of rat liver carnitine palmitoyltransferase I (L-CPTI) are essential for malonyl-CoA inhibition and binding (Shi, J., Zhu, H., Arvidson, D. N. , Cregg, J. M., and Woldegiorgis, G. (1998) Biochemistry 37, 11033-11038). To identify specific residue(s) involved in malonyl-CoA binding and inhibition of L-CPTI, we constructed two more deletion mutants, Delta12 and Delta6, and three substitution mutations within the conserved first six amino acid residues. Mutant L-CPTI, lacking either the first six N-terminal amino acid residues or with a change of glutamic acid 3 to alanine, was expressed at steady-state levels similar to wild type and had near wild type catalytic activity. However, malonyl-CoA inhibition of these mutant enzymes was reduced 100-fold, and high affinity malonyl-CoA binding was lost. A mutant L-CPTI with a change of histidine 5 to alanine caused only partial loss of malonyl-CoA inhibition, whereas a mutant L-CPTI with a change of glutamine 6 to alanine had wild type properties. These results demonstrate that glutamic acid 3 and histidine 5 are necessary for malonyl-CoA binding and inhibition of L-CPTI by malonyl-CoA but are not required for catalysis.
Functional redundancy of acetylcholinesterase and neuroligin in mammalian neuritogenesis (1998)

Accumulated evidence attributes noncatalytic morphogenic activitie(s) to acetylcholinesterase (AChE). Despite sequence homologies, functional overlaps between AChE and catalytically inactive AChE-like cell surface adhesion proteins have been demonstrated only for the Drosophila protein neurotactin. Furthermore, no mechanism had been proposed to enable signal transduction by AChE, an extracellular enzyme. Here, we report impaired neurite outgrowth and loss of neurexin Ialpha mRNA under antisense suppression of AChE in PC12 cells (AS-ACHE cells). Neurite growth was partially rescued by addition of recombinant AChE to the solid substrate or by transfection with various catalytically active and inactive AChE variants. Moreover, overexpression of the homologous neurexin I ligand, neuroligin-1, restored both neurite extension and expression of neurexin Ialpha. Differential PCR display revealed expression of a novel gene, nitzin, in AS-ACHE cells. Nitzin displays 42% homology to the band 4.1 protein superfamily capable of linking integral membrane proteins to the cytoskeleton. Nitzin mRNA is high throughout the developing nervous system, is partially colocalized with AChE, and increases in rescued AS-ACHE cells. Our findings demonstrate redundant neurite growth-promoting activities for AChE and neuroligin and implicate interactions of AChE-like proteins and neurexins as potential mediators of cytoarchitectural changes supporting neuritogenesis.
Multi-layer parallel decoding algorithm and vlsi architecture for quasi-cyclic LDPC codes (2011)

We propose a multi-layer parallel decoding algorithm and VLSI architecture for decoding of structured quasi-cyclic low-density parity-check codes. In the conventional layered decoding algorithm, the block-rows of the parity check matrix are processed sequentially, or layer after layer. The maximum number of rows that can be simultaneously processed by the conventional layered decoder is limited to the sub-matrix size. To remove this limitation and support layer-level parallelism, we extend the conventional layered decoding algorithm and architecture to enable simultaneously processing of multiple (K) layers of a parity check matrix, which will lead to a roughly K-fold throughput increase. As a case study, we have designed a double-layer parallel LDPC decoder for the IEEE 802.11n standard. The decoder was synthesized for a TSMC 45-nm CMOS technology. With a synthesis area of 0.81 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a maximum clock frequency of 815 MHz, the decoder achieves a maximum throughput of 3.0 Gbps at 15 iterations.
cAMP Response Element-Binding Protein in the Amygdala Is Required for Long- but not Short-Term Conditioned Taste Aversion Memory (1997)

In conditioned taste aversion (CTA) organisms learn to avoid a taste if the first encounter with that taste is followed by transient poisoning. The neural mechanisms that subserve this robust and long-lasting association of taste and malaise have not yet been elucidated, but several brain areas have been implicated in the process, including the amygdala. In this study we investigated the role of amygdala in general, and the cAMP response element-binding protein (CREB) in the amygdala in particular, in CTA learning and memory. Toward that end, we combined antisense technology in vivo with behavioral, molecular, and histochemical analysis. Local microinjection of phosphorothioate-modified oligodeoxynucleotides (ODNs) antisense to CREB into the rat amygdala several hours before CTA training transiently reduced the level of CREB protein during training and impaired CTA memory when tested 3-5 d later. In comparison, sense ODNs had no effect on memory. The effect of antisense was not attributable to differential tissue damage and was site-specific. CREB antisense in the amygdala had no effect on retrieval of CTA memory once it had been formed, and did not affect short-term CTA memory. We propose that the amygdala, specifically the central nucleus, is required for the establishment of long-term CTA memory in the behaving rat; that the process involves long-term changes, subserved by CRE-regulated gene expression, in amygdala neurons; and that the amygdala may retain some CTA-relevant information over time rather than merely modulating the gustatory trace during acquisition of CTA.
Breast-feeding and respiratory syncytial virus infection. (1980)

The pattern of breast-feeding in 127 infants admitted to hospital with respiratory syncytial virus infection was compared with that in 503 age-matched controls. Thirty per cent of children with infection had been breast-fed compared with 49% of controls. The approximate relative risk of being admitted to hospital with respiratory syncytial virus infection if not breast-fed was 2.2. Several other factors were also considered, including an assessment of maternal care and home environment; the mother's age, marital state, and smoking habits; the number of siblings; and gestation. Adverse factors were all associated with an increased risk of admission with infection, but breast-feeding still appeared to provide protection after controlling for these other factors in turn. These findings provide further support for encouraging mothers to breast-feed their infants and should prompt further studies into the immune status of mothers and into the nature of the protective factors in their breast milk.