gebhart/patrepeval huggingface dataset:
Membrane Permeabilization by Trypanosome Lytic Factor, a Cytolytic Human High Density Lipoprotein (2009)

Trypanosome lytic factor (TLF) is a subclass of human high density lipoprotein (HDL) that mediates an innate immune killing of certain mammalian trypanosomes, most notably Trypanosoma brucei brucei, the causative agent of a wasting disease in cattle. Mechanistically, killing is initiated in the lysosome of the target trypanosome where the acidic pH facilitates a membrane-disrupting activity by TLF. Here we utilize a model liposome system to characterize the membrane binding and permeabilizing activity of TLF and its protein constituents, haptoglobin-related protein (Hpr), apolipoprotein L-1 (apoL-1), and apolipoprotein A-1 (apoA-1). We show that TLF efficiently binds and permeabilizes unilamellar liposomes at lysosomal pH, whereas non-lytic human HDL exhibits inefficient permeabilizing activity. Purified, delipidated Hpr and apoL-1 both efficiently permeabilize lipid bilayers at low pH. Trypanosome lytic factor, apoL-1, and apoA-1 exhibit specificity for anionic membranes, whereas Hpr permeabilizes both anionic and zwitterionic membranes. Analysis of the relative particle sizes of susceptible liposomes reveals distinctly different membrane-active behavior for native TLF and the delipidated protein components. We propose that lysosomal membrane damage in TLF-susceptible trypanosomes is initiated by the stable association of the TLF particle with the lysosomal membrane and that this is a property unique to this subclass of human HDL.
Characterization of the Different Dextransucrase Activities Excreted in Glucose, Fructose, or Sucrose Medium by Leuconostoc mesenteroides NRRL B-1299 (1998)

When grown in glucose or fructose medium in the absence of sucrose, Leuconostoc mesenteroides NRRL B-1299 produces two distinct extracellular dextransucrases named glucose glucosyltransferase (GGT) and fructose glucosyltransferase (FGT). The production level of GGT and FGT is 10 to 20 times lower than that of the extracellular dextransucrase sucrose glucosyltransferase (SGT) produced on sucrose medium (traditional culture conditions). GGT and FGT were concentrated by ultrafiltration before sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. Their molecular masses were 183 and 186 kDa, respectively, differing from the 195 kDa of SGT. The structural analysis of the dextran produced from sucrose and of the oligosaccharides synthesized by acceptor reaction in the presence of maltose showed that GGT and FGT are two different enzymes not previously described for this strain. The polymer synthesized by GGT contains 30% alpha(1-->2) linkages, while FGT catalyzes the synthesis of a linear dextran only composed of alpha(1-->6) linkages.
Physical characteristics of small intestinal submucosa scaffolds are location‐dependent (2005)

Using biodegradable scaffolds as an alternative to engineer new tissues has become an attractive candidate in various transplantation protocols. In particular, small intestinal submucosa (SIS), a dense connective matrix harvested from the small intestine, has gained attention due to a number of favorable properties. However, use of SIS is constrained by obtaining reliable, reproducible products in large-scale preparations that affect the regenerative process. To better understand the heterogeneous nature of SIS, this study focused on evaluating the location-dependent alterations in the physical characteristics of the matrices harvested from distal and proximal ends and processed in-house (referred as hand-made). Additionally, results were compared with a commercially available machine-made Cook SIS. Tensile properties during monotonic loading and cyclical loading were compared in wet conditions. Furthermore, permeability of these membranes to urea was analyzed using a custom-built chamber, and the microarchitecture was analyzed via scanning electron microscopy. These results showed that distal samples were more elastic and less permeable to urea relative to other samples. However, permeability in each sample was direction-dependent, that is, mucosal to serosal direction was less permeable compared to sorasal to mucosal direction in all the samples. Cook SIS was more susceptible to cyclical loading and had a shorter range of load carrying capacity. In summary, results show that physical characteristics of SIS are location-dependent.
Artistic paper-cut of human portraits (2010)

This paper presents a method to render artistic paper-cut of human portraits. Rendering paper-cut images from photographs can be considered as an inhomogeneous image binarization problem, to which ideal solutions should reproduce vivid image details with sparse cuts. Especially for portrait paper-cut, good artworks should capture impressive facial features. To achieve this goal, our approach integrates bottom-up and top-down cues to better determine the binary values. In the bottom-up phase, facial components are localized on the input photograph, and their draft binary versions are proposed. In the top-down phase, we use pre-collected representative paper-cut templates, with which we synthesize the final paper-cut image by matching them with the bottom-up proposals. Experimental results show that our approach can produce visually satisfactory results.
Mapmodulin: A possible modulator of the interaction of microtubule-associated proteins with microtubules (1997)

We have purified and characterized a 31-kDa protein named mapmodulin that binds to the microtubule-associated proteins (MAPs) MAP2, MAP4, and tau. Mapmodulin binds free MAPs in strong preference to microtubule-associated MAPs, and appears to do so via the MAP's tubulin-binding domain. Mapmodulin inhibits the initial rate of MAP2 binding to microtubules, a property that may allow mapmodulin to displace MAPs from the path of organelles translocating along microtubules. In support of this possibility, mapmodulin stimulates the microtubule- and dynein-dependent localization of Golgi complexes in semi-intact CHO cells. To our knowledge, mapmodulin represents the first example of a protein that can bind and potentially regulate multiple MAP proteins.
Compact, light weight mechanisms for high precision micro-manipulators (1998)

GALATEA
Physical layer loading algorithms for indoor wireless multicarrier systems (2005)

The demand for wireless networks has been growing rapidly over the recent past due to improved reliability, higher supported data rates, seamless connectivity between users and the access point, and low deployment costs relative to wireline infrastructure. This increase in demand started with the popular IEEE 802.11b wireless local area network standard. Many recent wireless network standards are now employing multicarrier modulation in their design. Multicarrier modulation reduces the system’s susceptibility to the frequencyselective fading channel, due to multipath propagation, by transforming it into a collection of approximately flat subchannels. As a result, this makes it easier to compensate for the distortion introduced by the channel. However, standardized wireless modems, such as the ETSI HiperLAN/2 and the IEEE 802.11a standards, employ the same operating parameters across all subcarriers, and thus do not exploit all the advantages offered by the multicarrier framework. This dissertation investigates techniques to further enhance system throughput performance by tailoring several operating parameters on a per-subcarrier basis. These parameters
Phytochrome-Deficient hy1 and hy2 Long Hypocotyl Mutants of Arabidopsis Are Defective in Phytochrome Chromophore Biosynthesis (1991)

Brian M. Parks, Peter H. Quail, Phytochrome-Deficient hy1 and hy2 Long Hypocotyl Mutants of Arabidopsis Are Defective in Phytochrome Chromophore Biosynthesis, The Plant Cell, Vol. 3, No. 11 (Nov., 1991), pp. 1177-1186
An electrochemical/photochemical information processing system using a monolayer-functionalized electrode (2006)

An electroactive and photoisomerizable monolayer associated with a Au electrode acts as a Write-Read-Erase information processing system and as a flip-flop Set/Reset memory element.
Ultra-scaled Z-RAM cell (2008)

Ultra-scaled Z-RAM cells based on MuGFETs are demonstrated for the first time. Effects of physical parameters such as channel doping concentration, fin width, and gate length on Z-RAM cell performance are discussed. Transient measurements and simulations prove that the basic operational principles are effective on Z-RAM cells with a gate length down to 12.5 nm.
Remotely powered addressable UHF RFID integrated system (2005)

This paper presents a fully integrated remotely powered and addressable radio frequency identification (RFID) transponder working at 2.45 GHz. The achieved operating range at 4 W effective isotropically radiated power (EIRP) base-station transmit power is 12 m. The integrated circuit (IC) is implemented in a 0.5 /spl mu/m silicon-on-sapphire technology. A state-of-the-art rectifier design achieving 37% of global efficiency is embedded to supply energy to the transponder. The necessary input power to operate the transponder is about 2.7 /spl mu/W. Reader to transponder communication is obtained using on-off keying (OOK) modulation while transponder to reader communication is ensured using the amplitude shift keying (ASK) backscattering modulation technique. Inductive matching between the antenna and the transponder IC is used to further optimize the operating range.
EFFECT OF INTRAVESICAL NITRIC OXIDE THERAPY ON CYCLOPHOSPHAMIDE-INDUCED CYSTITIS (1999)

Intravesical NO donors can suppress CYP-induced bladder hyperactivity. We hypothesize that the effect of NO donors is not due to smooth muscle relaxation, but rather due to an inhibitory effect on bladder afferent pathways that was manifested by an increase in intercontraction interval without changes in contraction amplitude. NO donors may be considered as a possible treatment of CYP-induced and other types of bladder inflammation.
The Diabetes Drug Liraglutide Prevents Degenerative Processes in a Mouse Model of Alzheimer's Disease (2011)

Type 2 diabetes is a risk factor for Alzheimer's disease, most likely linked to an impairment of insulin signaling in the brain. The incretin hormone glucagon-like peptide-1 (GLP-1) facilitates insulin signaling, and novel long-lasting GLP-1 analogs, such as liraglutide, are on the market as diabetes therapeutics. GLP-1 has been shown to have neuroprotective properties in vitro and in vivo . Here we tested the effects of peripherally injected liraglutide in an Alzheimer mouse model, APP swe /PS1 ΔE9 (APP/PS1). Liraglutide was shown to cross the blood–brain barrier in an acute study. Liraglutide was injected for 8 weeks at 25 nmol/kg body weight i.p. once daily in 7-month-old APP/PS1 and wild-type littermate controls. In APP/PS1 mice, liraglutide prevented memory impairments in object recognition and water maze tasks, and prevented synapse loss and deterioration of synaptic plasticity in the hippocampus, commonly observed in this model. Overall β-amyloid plaque count in the cortex and dense-core plaque numbers were reduced by 40–50%, while levels of soluble amyloid oligomers were reduced by 25%. The inflammation response as measured by activated microglia numbers was halved in liraglutide-treated APP/PS1 mice. Numbers of young neurons in the dentate gyrus were increased in APP/PS1 mice with treatment. Liraglutide treatment had little effect on littermate control mice, whose behavior was comparable to wild-type saline controls; however, synaptic plasticity was enhanced in the drug group. Our results show that liraglutide prevents key neurodegenerative developments found in Alzheimer's disease, suggesting that GLP-1 analogs represent a novel treatment strategy for Alzheimer's disease.
The Asymptomatic Newborn and Risk of Cerebral Palsy (1987)

We investigated whether infants weighing over 2500 g who had experienced one or more of 14 late pregnancy or birth complications, but who were free of certain signs in the nursery period were at increased risk of cerebral palsy (CP). The signs evaluated were decreased activity after the first day of life, need for incubator care for three or more days, feeding problems, poor suck, respiratory difficulty, or neonatal seizures. More than 90% of the infants weighing over 2500 g had none of these signs. In asymptomatic infants with one or more birth complications, the rate of CP by 7 years of age was 2.3/1000; among asymptomatic infants whose births were uncomplicated, the rate of CP was 2.4/1000. The risk for CP rose with number of abnormal neonatal signs, and children with sustained neonatal abnormalities were at higher risk than those whose abnormalities were transient. Most children with CP did not derive from groups at increased risk. The full-term infant whose birth was complicated but who was free of certain abnormal signs in the newborn period was not at increased risk of CP.
The detailed analysis of high Q CMOS-compatible microwave spiral inductors in silicon technology (1998)

We present the extensive experimental results and their detailed analysis showing the important effects of layout parameters on the frequency responses of quality factor (Q) of rectangular spiral inductors, which are fabricated on a silicon substrate by using conventional silicon CMOS technology, in order to determine the desirable values of layout parameters for designing the high Q inductors used in RF IC's applications. Analysis of the inductors on Si substrates with three kinds of resistivities has been performed by tailoring the geometric layout and varying the metal thickness. Using these results, the substrate effects on RF performance of inductors are also investigated by observing the frequency responses of Q with varying the substrate resistivity in detail.
Use ECP, not ECC, for hard failures in resistive memories (2010)

As leakage and other charge storage limitations begin to impair the scalability of DRAM, non-volatile resistive memories are being developed as a potential replacement. Unfortunately, current error correction techniques are poorly suited to this emerging class of memory technologies. Unlike DRAM, PCM and other resistive memories have wear lifetimes, measured in writes, that are sufficiently short to make cell failures common during a system's lifetime. However, resistive memories are much less susceptible to transient faults than DRAM. The Hamming-based ECC codes used in DRAM are designed to handle transient faults with no effective lifetime limits, but ECC codes applied to resistive memories would wear out faster than the cells they are designed to repair. This paper evaluates Error-Correcting Pointers (ECP), a new approach to error correction optimized for memories in which errors are the result of permanent cell failures that occur, and are immediately detectable, at write time. ECP corrects errors by permanently encoding the locations of failed cells into a table and assigning cells to replace them. ECP provides longer lifetimes than previously proposed solutions with equivalent overhead. What's more, as the level of variance in cell lifetimes increases -- a likely consequence of further scalaing -- ECP's margin of improvement over existing schemes increases.
Dependence Makes You Vulnerable: Differential Privacy Under Dependent Tuples (2016)

Differential privacy (DP) is a widely accepted mathematical framework for protecting data privacy. Simply stated, it guarantees that the distribution of query results changes only slightly due to the modification of any one tuple in the database. This allows protection, even against powerful adversaries, who know the entire database except one tuple. For providing this guarantee, differential privacy mechanisms assume independence of tuples in the database -a vulnerable assumption that can lead to degradation in expected privacy levels especially when applied to real-world datasets that manifest natural dependence owing to various social, behavioral, and genetic relationships between users. In this paper, we make several contributions that not only demonstrate the feasibility of exploiting the above vulnerability but also provide steps towards mitigating it. First, we present an inference attack, using real datasets, where an adversary leverages the probabilistic dependence between tuples to extract users' sensitive information from differentially private query results (violating the DP guarantees). Second, we introduce the notion of dependent differential privacy (DDP) that accounts for the dependence that exists between tuples and propose a dependent perturbation mechanism (DPM) to achieve the privacy guarantees in DDP. Finally, using a combination of theoretical analysis and extensive experiments involving different classes of queries (e.g., machine learning queries, graph queries) issued over multiple large-scale real-world datasets, we show that our DPM consistently outperforms state-of-the-art approaches in managing the privacy-utility tradeoffs for dependent data.
Thermal emission control with one-dimensional metallodielectric photonic crystals (2004)

We have analyzed thermal emission from one-dimensional metallodielectric periodic structures using a Green's function technique together with the fluctuation-dissipation theorem. We show that such simple structures exhibit excellent selective emission characteristics with a controllable transition frequency in the infrared and even visible range. Such simple structures should be easy to fabricate and have applications in thermophotovoltaics and potentially in incandescent bulbs.
A DFT Approach to the Mechanistic Study of Hydrozone Hydrolysis (2016)

Hydrazone chemistry is widely utilized in biomedical field as a means of bioconjugation protocol, especially in drug delivery field due to pH labile nature of this linkage. In the light of kinetics studies, the generally accepted mechanism for the hydrolysis of hydrazones involves two main steps, namely, nucleophilic addition of water molecule to the hydrazone molecule to form carbinolamine intermediate and subsequent decomposition of this intermediate into the hydrazine and aldehyde/ketone moieties. Hydrolysis of hydrazones is catalyzed in the acidic environments and is thought to proceed through several proton transfer steps. To the best of our knowledge, in the literature no detailed theoretical study has been reported related to the mechanism of hydrolysis. In this study, we evaluated the proposed mechanism with DFT calculations with M06-2X functional at the 6-311+g(d,p) level including conductor-like polarizable continuum model solvation model. We also analyzed possible proton transfer pathways and assessed energetics of each step.
Crytanalysis and Improvement on Chang et al.'s Signature Scheme (2007)

In 2004, Chang's et al. presented a digital signature scheme without using one-way hash function and message redundancy schemes. They claimed their scheme do not suffer from some forgery attacks such as Shieh's scheme. However, Fu (2005) and Zhang (http://eprint.iacr.org/2004/213.pdf) proposed several forgery attacks on it and showed that message redundancy schemes may be still needed in order to resist these attacks. In this paper, we present a new message recovery digital signature scheme without using one-way hash function, too and give another general forgery attack on Chang's signature scheme different from Fu's.
Brief Report: Liver Bypass Significantly Increases the Transduction Efficiency of Recombinant Adenoviral Vectors in the Lung, Intestine, and Kidney (2000)

Recombinant adenoviruses have great potential as gene delivery systems because of their ability to infect a wide range of target cells. However, systemic delivery of viral vectors to tissues other than liver and spleen has been inefficient because of the rapid clearance of the circulating virus by the liver. In the present study we tested the hypothesis that a systemic administration of E1-deleted recombinant adenovirus vectors that bypasses the hepatic circulation will lead to enhanced expression of these vectors in extrahepatic tissues. The portal vein and hepatic artery in B6/129 F1 mice were clamped and an E1-deleted recombinant adenovirus carrying the beta-galactosidase gene (Ad.CBlacZ) was then administered through the retroorbital venous plexus. The clamp was released 30 min after viral injection with no major chronic ischemic consequences noted. High levels of LacZ expression were detected predominantly in the vessels and capillaries of the lung, intestinal wall, and renal glomeruli 7 days after viral infusion. The transgene expression persisted for at least 21 days. Intense LacZ staining was also observed in the liver, suggesting that liver infection occurred after the portal clamp was released. A retroorbital infusion of anti-adenovirus neutralizing antibodies 5 min before the release of the portal clamp significantly reduced postclamp viral infection to the liver, while LacZ expression in lung and intestine persisted after the antibody treatment. Taken together, these results suggest that liver bypass can significantly improve the transduction efficiency in the other target organs. This method could be used to develop animal models of human diseases that predominantly affect the vessels of the lung, intestine, and kidney.
Von Willebrand factor (2003)

The adhesive protein von Willebrand factor contributes to platelet function by mediating the initiation and progression of thrombus formation at sites of vascular injury. In the last 2 years, there has been considerable progress in explaining the biologic properties of von Willebrand factor. The three-dimensional structure of specific domains has been explained, with the demonstration of distinct conformational changes in the A1 domain caused by single amino acid substitutions associated with enhanced binding to platelets. The structural and functional properties of the interaction between the von Willebrand factor A1 domain and glycoprotein Ibalpha have also been elucidated in greater detail, bringing researchers closer to understanding how this adhesive bond can oppose the fluid dynamic effects of rapidly flowing blood to initiate thrombus formation and, concurrently, contribute to platelet activation. Because hemodynamic forces greatly influence platelet responses to vascular injury in stenosed and partially occluded arteries, a detailed description of how von Willebrand factor interacts with tissues and platelets may help in the design of more specific therapeutic inhibitors of arterial thrombosis. Moreover, enlightening findings have been obtained on the link between regulation of von Willebrand factor multimer size and microvascular thrombosis. This progress in basic research has provided critical information to define with greater precision the role of von Willebrand factor in vascular biology and pathology.
Guest Editorial to the Special Letters Issue on Therapeutic Ultrasound: Trends at the Leading-Edge (2010)

Discusses the main topics of discussion in the special section on therpeutic ultrasound as well as the current status and key trends in the industry.
VEGF inhibitors for the treatment of neovascular age-related macular degeneration (2009)

Age-related macular degeneration (AMD) is the leading cause of blindness in the Western world for those patients aged 50 years or older. Neovascular AMD, a subtype characterized by the growth of new, pathologic blood vessels, results in most of the cases of severe and rapid vision loss associated with AMD. A critical activator of angiogenesis in neovascular AMD is VEGF. Several therapies have been and are now being developed for neovascular AMD, with the goal of inhibiting VEGF. These VEGF inhibitors include the RNA aptamer pegaptanib, partial and full-length antibodies ranibizumab and bevacizumab, VEGF receptor decoy VEGF Trap, small interfering RNA-based therapies bevasiranib and AGN211745, sirolimus, and tyrosine kinase inhibitors including vatalanib, pazopanib, TG100801, TG101095, AG013958 and AL39324. At present, established therapies have met with great success in reducing the vision loss associated with neovascular AMD, whereas those still investigational in nature offer the potential for further advances.