gebhart/patrepeval huggingface dataset:
Isolation and characterization of a phospholipid transfer protein (LTP-II) from human plasma. (1988)

In this report we have described the purification of a human plasma phospholipid transfer protein, designated LTP-II, which displayed the following characteristics: i) facilitated both the exchange and net mass transfer of lipoprotein phospholipids; ii) did not facilitate the transfer of lipoprotein cholesteryl esters (CE) or triglycerides (TG); iii) was not recognized by antibody to the human cholesteryl ester transfer protein (LTP-I); iv) showed no amino acid sequence homology to the cholesteryl ester transfer protein (LTP-I); v) has an apparent molecular weight (Mr) of 70,000 off Sephacryl S200, and 69,000 off sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE); vi) has an apparent isoelectric point of 5.0 by chromatofocusing; and vii) when added to an incubation mixture of VLDL, HDL3, and the human plasma cholesteryl ester transfer protein (LTP-I), enhanced the observed transfer of cholesteryl esters from HDL3 to VLDL, even though LTP-II has no intrinsic cholesteryl ester transfer activity of its own. These results show that this phospholipid transfer protein is unique from the human plasma cholesteryl ester transfer protein, and may play an important role in human lipoprotein lipid metabolism.
Microfluidic electro-sonoporation: a multi-modal cell poration methodology through simultaneous application of electric field and ultrasonic wave (2013)

A microfluidic device that simultaneously applies the conditions required for microelectroporation and microsonoporation in a flow-through scheme toward high-efficiency and high-throughput molecular delivery into mammalian cells is presented. This multi-modal poration microdevice using simultaneous application of electric field and ultrasonic wave was realized by a three-dimensional (3D) microelectrode scheme where the electrodes function as both electroporation electrodes and cell flow channel so that acoustic wave can be applied perpendicular to the electric field simultaneously to cells flowing through the microfluidic channel. This 3D microelectrode configuration also allows a uniform electric field to be applied while making the device compatible with fluorescent microscopy. It is hypothesized that the simultaneous application of two different fields (electric field and acoustic wave) in perpendicular directions allows formation of transient pores along two axes of the cell membrane at reduced poration intensities, hence maximizing the delivery efficiency while minimizing cell death. The microfluidic electro-sonoporation system was characterized by delivering small molecules into mammalian cells, and showed average poration efficiency of 95.6% and cell viability of 97.3%. This proof of concept result shows that by combining electroporation and sonoporation together, significant improvement in molecule delivery efficiency could be achieved while maintaining high cell viability compared to electroporation or sonoporation alone. The microfluidic electro-sonoporation device presented here is, to the best of our knowledge, the first multi-modal cell poration device using simultaneous application of electric field and ultrasonic wave. This new multi-modal cell poration strategy and system is expected to have broad applications in delivery of small molecule therapeutics and ultimately in large molecule delivery such as gene transfection applications where high delivery efficiency and high viability are crucial.
Endocannabinoids and the regulation of their levels in health and disease (2007)

Endocannabinoid levels appear to be transiently elevated as an adaptive reaction to re-establish normal homeostasis when this is acutely and pathologically perturbed. In some chronic conditions, however, this system also contributes to the progress or symptoms of the disorder. As a consequence, new therapeutic drugs are being designed from both stimulants and blockers of endocannabinoid action.
A Commercially Available Tantalum Catalyst for the Highly Regioselective Intermolecular Hydroaminoalkylation of Styrenes (2014)

Abstract The C–C bond‐forming catalytic hydroaminoalkylation of terminal alkenes or styrenes enables a direct and 100 % atom‐efficient synthesis of amines and can generally result in the formation of two regioisomers, the branched and the linear product. Herein, we report that high‐yielding intermolecular hydroaminoalkylation reactions of styrenes can be achieved with excellent regioselectivities in the presence of the commercially available homoleptic catalyst pentakis(dimethylamino)tantalum. In all cases, the branched regioisomer is formed almost exclusively.
Illicit Transport: The Oligopeptide Permease (1973)

The oligopeptide permease of Escherichia coli has been characterized by Payne, Gilvarg, and their colleagues. We have confirmed its existence in Salmonella typhimurium, and have isolated a series of mutants lacking the permease. We use this transport system for smuggling a histidine biosynthetic intermediate, histidinol phosphate ester, into the bacteria as its glycylglycyl derivative, Gly-Gly-histidinol phosphate. Free histidinol phosphate ester is not transported into Salmonella. Several amino-acid analogues are shown to be much more inhibitory to Salmonella when presented to the bacteria in the form of tripeptides than as the free amino acids. The implications of this work for practical purposes are discussed. The synthesis of Gly-Gly-histidinol phosphate is described.
Structural and Molecular Mechanism for Autoprocessing of MARTX Toxin of Vibrio cholerae at Multiple Sites (2009)

The multifunctional autoprocessing repeats-in-toxin (MARTX) toxin of Vibrio cholerae causes destruction of the actin cytoskeleton by covalent cross-linking of actin and inactivation of Rho GTPases. The effector domains responsible for these activities are here shown to be independent proteins released from the large toxin by autoproteolysis catalyzed by an embedded cysteine protease domain (CPD). The CPD is activated upon binding inositol hexakisphosphate (InsP(6)). In this study, we demonstrated that InsP(6) is not simply an allosteric cofactor, but rather binding of InsP(6) stabilized the CPD structure, facilitating formation of the enzyme-substrate complex. The 1.95-A crystal structure of this InsP(6)-bound unprocessed form of CPD was determined and revealed the scissile bond Leu(3428)-Ala(3429) captured in the catalytic site. Upon processing at this site, CPD was converted to a form with 500-fold reduced affinity for InsP(6), but was reactivated for high affinity binding of InsP(6) by cooperative binding of both a new substrate and InsP(6). Reactivation of CPD allowed cleavage of the MARTX toxin at other sites, specifically at leucine residues between the effector domains. Processed CPD also cleaved other proteins in trans, including the leucine-rich protein YopM, demonstrating that it is a promiscuous leucine-specific protease.
Site-specific analysis of N-linked oligosaccharides of recombinant lysosomal arylsulfatase A produced in different cell lines (2009)

Metachromatic leukodystrophy (MLD) is a lysosomal storage disease caused by a deficiency of the lysosomal enzyme arylsulfatase A (ASA). Enzyme replacement therapy (ERT) is a therapeutic option for MLD and other lysosomal disorders. This therapy depends on N-linked oligosaccharide-mediated delivery of intravenously injected recombinant enzyme to the lysosomes of patient cells. Because of the importance of N-linked oligosaccharide side chains in ERT, we examined the composition of the three N-linked glycans of four different recombinant ASAs in a site-specific manner. Depending on the culture conditions and the cell line expressing the enzyme, we detected a high variability of the high-mannose-type N-glycans which prevail at all glycosylation sites. Our data show that the composition of the glycans is largely determined by substantial trimming in the medium. The susceptibility for trimming is different for the glycans at the three N-glycosylation sites. Interestingly, which of the glycans is most susceptible to trimming also depends on production conditions. CHO cells cultured under bioreactor conditions yielded recombinant ASA with the most preserved N-glycan structures, the highest mannose-6-phosphate content and the highest similarity to non-recombinant enzyme. Notably, roughly one-third of the N-glycans released from the three glycosylation sites were fucosylated. In the last years, numerous recombinant lysosomal enzymes were used for preclinical ERT trials. Our data show that the oligosaccharide structures were very different in these trials making it difficult to draw common conclusions from the various investigations.
A Compact Multi-Band Antenna Design For Mobile Handsets (2006)

In this paper, a compact multi-band antenna design (36 /spl times/ 13 /spl times/ 6.5 mm/sup 3/) for multi-function and multi-band application on highly integrated mobile handsets is investigated theoretically and experimentally. Well measured performance on both return loss and antenna gain is achieved as predicted theoretically.
DeepDNA: a hybrid convolutional and recurrent neural network for compressing human mitochondrial genomes (2018)

Large amounts of genome data are publicly available due to the high-throughput sequencing technologies developed in recent years. This availability raises a major concern about data storage costs, given that an effective and efficient compression algorithm for genome data remains an unresolved challenge in genomic data studies. In this paper, we propose a compression method, DeepDNA, that is a hybrid convolutional and recurrent deep neural network for compressing human genome data. In the DeepDNA model, the convolutional layer captures the genome's local features, while the recurrent layer captures long-term dependencies for estimating the next base probabilities in the genomic sequence. The experimental results on human mitochondrial genome datasets show the effectiveness of the DeepDNA method.The code for DeepDNA is available at https://github.com/rongiiewang/deepDNA.
Gamma-Radiation Effects on Nestling House Wrens: A Field Study (1986)

Freshly hatched house wren (Troglodytes aedon) nestlings were acutely exposed to γ-radiation doses of 0.9, 2.6, 4.3, and 6.0 Gy from an external source to investigate radiosensitivity in a natural setting. Observed growth statistics and parameters from the Richards model were used for growth analysis. Radiation exposure did not cause any mortality over the 15-day nestling period, but it had a depressing effect on growth in body mass and primary-feather and foot lengths. At 6.0 Gy this involved a delay in development. Effects increased in severity from 0.9 to 6.0 Gy and appeared to be linear. The 6.0-Gy nestlings were noticeably stunted. Radiation exposure did not affect the basic growth pattern. House wren nestlings responded similarly to radiation exposure as tree swallow (Tachycineta bicolor) and eastern bluebird (Sialia sialis) nestlings. There was no indication that natural variability of observed growth statistics or model parameters is correlated positively with sensitivity to radiation stress.
Novel Strategy for Treatment of Inner Ears using a Biodegradable Gel (2005)

These findings indicate that biodegradable hydrogels can be used for drug delivery to the inner ear.
Active Site-labeled Prothrombin Inhibits Prothrombinase in Vitro and Thrombosis in Vivo (2011)

Mouse and human prothrombin (ProT) active site specifically labeled with D-Phe-Pro-Arg-CH(2)Cl (FPR-ProT) inhibited tissue factor-initiated thrombin generation in platelet-rich and platelet-poor mouse and human plasmas. FPR-prethrombin 1 (Pre 1), fragment 1 (F1), fragment 1.2 (F1.2), and FPR-thrombin produced no significant inhibition, demonstrating the requirement for all three ProT domains. Kinetics of inhibition of ProT activation by the inactive ProT(S195A) mutant were compatible with competitive inhibition as an alternate nonproductive substrate, although FPR-ProT deviated from this mechanism, implicating a more complex process. FPR-ProT exhibited ∼10-fold more potent anticoagulant activity compared with ProT(S195A) as a result of conformational changes in the ProT catalytic domain that induce a more proteinase-like conformation upon FPR labeling. Unlike ProT and ProT(S195A), the pathway of FPR-ProT cleavage by prothrombinase was redirected from meizothrombin toward formation of the FPR-prethrombin 2 (Pre 2)·F1.2 inhibitory intermediate. Localization of ProT labeled with Alexa Fluor® 660 tethered through FPR-CH(2)Cl ([AF660]FPR-ProT) during laser-induced thrombus formation in vivo in murine arterioles was examined in real time wide-field and confocal fluorescence microscopy. [AF660]FPR-ProT bound rapidly to the vessel wall at the site of injury, preceding platelet accumulation, and subsequently to the thrombus proximal, but not distal, to the vessel wall. [AF660]FPR-ProT inhibited thrombus growth, whereas [AF660]FPR-Pre 1, lacking the F1 membrane-binding domain did not bind or inhibit. Labeled F1.2 localized similarly to [AF660]FPR-ProT, indicating binding to phosphatidylserine-rich membranes, but did not inhibit thrombosis. The studies provide new insight into the mechanism of ProT activation in vivo and in vitro, and the properties of a unique exosite-directed prothrombinase inhibitor.
Cryptography in the Bounded Quantum Storage Model (2005)

We initiate the study of two-party cryptographic primitives with unconditional security, assuming that the adversary's &lt;em&gt; quantum&lt;/em&gt; memory is of bounded size. We show that oblivious transfer and bit commitment can be implemented in this model using protocols where honest parties need no quantum memory, whereas an adversarial player needs quantum memory of size at least n/2 in order to break the protocol, where n is the number of qubits transmitted. This is in sharp contrast to the classical bounded-memory model, where we can only tolerate adversaries with memory of size quadratic in honest players' memory size. Our protocols are efficient, non-interactive and can be implemented using today's technology. On the technical side, a new entropic uncertainty relation involving min-entropy is established.
Role of C3 Cleavage in Monocyte Activation During Extracorporeal Circulation (1999)

Blockade of complement activation early in the common pathway inhibited monocyte CD11b upregulation during SECC, suggesting that early complement components contribute most to monocyte activation during SECC. As expected, PMN and platelet activation were blocked by terminal complement inhibition. This investigation further elucidates the relation between complement and blood cell activation during simulated cardiopulmonary bypass.
PRE-ACCESSION NEGOTIATIONS OF THE CROATIA AND ADJUSTMENT TO THE EU AGRICULTURAL POLICY (2011)

European Union has been continually expanding its borders, aiming at connecting the Member States by common economic and political interests. The upcoming Croatian accession to the EU fits into this context. Croatia has been preparing for EU accession by taking the necessary institutional and policy measures, related to the regulations about the Community acquis. However, the measures for adjustment to the Community acquis cannot be an end in itself but their implementation should be the goal. The common agricultural policy of the European Union offers a range of possible options for the development of rural areas, the implementation of which should obtain a transparent structure as early as pre-accession phase. By its policy of development of agriculture and rural areas, the Union has been initiating a new approach especially for the underdeveloped rural areas, creating attractive conditions for the existence of the rural population also referring to environmental protection measures. The aim of this thesis is to provide an analysis of the present situation in the Croatian agricultural policy, to elaborate and structurally depict political fields which comprise the strategic topics for upgrading and constant improvement, to show the ways of mobilizing the neglected potential of Croatian rural areas and to display the types of financial help offered by the EU.
DNA-polycation nanospheres as non-viral gene delivery vehicles (1998)

Nanospheres synthesized by salt-induced complex coacervation of cDNA and polycations such as gelatin and chitosan were evaluated as gene delivery vehicles. DNA-nanospheres in the size range of 200-750 nm could transfect a variety of cell lines. Although the transfection efficiency of the nanospheres was typically lower than that of lipofectamine and calcium phosphate controls in cell culture, the beta-gal expression in muscle of BALB/c mice was higher and more sustained than that achieved by naked DNA and lipofectamine complexes. This gene delivery system has several attractive features: (1) ligands can be conjugated to the nanosphere for targeting or stimulating receptor-mediated endocytosis; (2) lysosomolytic agents can be incorporated to reduce degradation of the DNA in the endosomal and lysosomal compartments; (3) other bioactive agents or multiple plasmids can be co-encapsulated; (4) bioavailability of the DNA can be improved because of protection from serum nuclease degradation by the polymeric matrix; (5) the nanosphere can be lyophilized for storage without loss of bioactivity.
Proposed Experiments to Probe the Non-Abelianν=5/2Quantum Hall State (2006)

We propose several experiments to test the non-Abelian nature of quasiparticles in the fractional quantum Hall state at nu = 5/2. In a simplified version of the experiment suggested by [S. Das Sarma, M. Freedman, and C. Nayak, Phys. Rev. Lett. 94, 166802 (2005).], interference is turned on and off when the number of localized quasiparticles between the interfering paths varies between even and odd. We find analogous effects in the thermodynamic properties of closed systems.
Effects of nicotinic acid on serum cholesterol concentrations of high density lipoprotein subfractions HDL2, and HDL3, in hyperlipoproteinaemia (1990)

Nicotinic acid was given in a 4-g daily dose for 6 weeks to 41 weight-stable patients of mean age (+/- SD) 52 +/- 9 years, with type IIa, type IIb or type IV hyperlipoproteinaemia (HLP), in order to study its effects on serum cholesterol concentrations of high density lipoprotein (HDL) subfractions HDL2 and HDL3. The triglyceride and cholesterol levels of serum very low density (VLDL) and low density (LDL) lipoproteins decreased during treatment (P less than 0.001). Serum HDL and HDL2 cholesterol levels increased by 37% and 135%, respectively. These changes were positively correlated (r = 0.93; P less than 0.001). There was no significant change in mean serum HDL3 cholesterol concentration. A negative correlation existed between changes in HDL3 and HDL2 cholesterol levels (r = -0.54; P less than 0.001). Multiple stepwise linear regression analyses revealed that the initial HDL3 cholesterol predicted more than 30% of the increase in HDL2 cholesterol. Changes in the concentrations of HDL2 and HDL3 cholesterol after 6 weeks of drug treatment were not related to the type of HLP, neither were these effects of nicotinic acid correlated with changes in VLDL or LDL lipid levels. The concept has previously been proposed, on the basis of in vitro data, that HDL2 is formed from HDL3 particles in the blood. Our results suggest that, in man, this reaction is stimulated in vivo by prolonged nicotinic acid therapy.
Rate-adaptive MAC protocol in high-rate personal area networks (2004)

The specification of high-rate wireless personal area network (HR WPAN) has been standardized by the IEEE 802.15.3 task group for communications of consumer electronics and portable communication devices and a final draft standard has been completed. The physical layer in IEEE 802.15.3 standard is designed to achieve data rates of 11-55Mbps. However, a MAC protocol in IEEE 802.15.3 standard does not specify the method to choose an appropriate data rate. In this paper, we propose a rate-adaptive medium access control (MAC) protocol for HR WPAN. The data rate for the next transmission is selected by channel prediction based on the currently received frame and informs the sender about the changed rate using a rate-adaptive acknowledgement (RA-ACK) frame. By overhearing the RA-ACK frame, a piconet controller can efficiently allocate channel times. In addition, we propose a constant physical layer frame length regardless of a data rate. In this way, the channel can be more effectively utilized by squeezing more bits into one transmission. The proposed scheme is evaluated under a time-correlated fading channel model in terms of the achieved throughput Simulation results show that this scheme achieves a much higher throughput than a non rate-adaptive MAC protocol in HR WPAN does.
Array compression for MRI with large coil arrays (2007)

Arrays with large numbers of independent coil elements are becoming increasingly available as they provide increased signal-to-noise ratios (SNRs) and improved parallel imaging performance. Processing of data from a large set of independent receive channels is, however, associated with an increased memory and computational load in reconstruction. This work addresses this problem by introducing coil array compression. The method allows one to reduce the number of datasets from independent channels by combining all or partial sets in the time domain prior to image reconstruction. It is demonstrated that array compression can be very effective depending on the size of the region of interest (ROI). Based on 2D in vivo data obtained with a 32-element phased-array coil in the heart, it is shown that the number of channels can be compressed to as few as four with only 0.3% SNR loss in an ROI encompassing the heart. With twofold parallel imaging, only a 2% loss in SNR occurred using the same compression factor.
Atomistic Modeling of Amorphous Aromatic Polybenzoxazoles (1996)

Atomistic models of two different fluorinated polybenzoxazoles, 6F-PBO and 3F-PBO, were used to simulate the amorphous structures of these polymers. Molecular mechanics and molecular dynamics techniques were utilized to relax the independent structures from an initial high-energy system. The relaxed model structures showed 6F-PBOs to be more coiled relative to 3F-PBO. Conformational grid search was performed on each of the repeat units to analyze the local structure of the two polymeric backbones. The torsional angles corresponding to energy minima and rotational barrier were found to vary between the 6F and 3F structure due to differences in the pendant group at the Cα carbon atom. The Hildebrand solubility parameters and elastic constants for the two different polymers were estimated from simulation. 3F-PBO is predicted to possess a higher solubility parameter and higher moduli compared to the 6F-PBO.
HealthAware: Tackling obesity with health aware smart phone systems (2009)

Obesity prevention requires individuals to have healthy eating and physical activity awareness in their daily lives. New technological products have been explored to help monitoring individual health behaviors. Smart phones are ubiq-uitous hand-held tools with rich embedded sensors and limited computing power. A smart phone is a prospective candidate to integrate physical exercise analysis and food intake monitoring. This paper presents a novel health-aware smart phone system (HealthAware) which utilizes the embedded accelerometer to monitor daily physical activities and the built-in camera to analyze food items. The system presents the user's physical activity counts at real time to remind how much daily activity is needed to keep healthy. The user takes pictures of food items and the system provides health related information regarding to the food item intakes. The system is composed of an on-device database which holds the user specific data and food item information. HealthAware is a real time practical system to prevent obesity by enhancing individual daily healthy behavior awareness.