gebhart/patrepeval huggingface dataset:
Structure of the C-terminal Fragment 300-320 of the Rat Angiotensin II AT1A Receptor and Its Relevance with Respect to G-Protein Coupling (1997)

Angiotensin II AT1A receptor is coupled to G-protein, and the molecular mechanism of signal transduction is still unclear. The solution conformation of a synthetic peptide corresponding to residues 300-320 of the rat AT1A receptor, located in the C-terminal cytoplasmic tail and indicated by mutagenesis work to be critical for the G-protein coupling, has been investigated by circular dichroism (CD), nuclear magnetic resonance (NMR) and restrained molecular dynamics calculations. The CD data indicate that, in acidic water, at concentration below 0.8 mM, the peptide exists in a predominantly coil structure while at higher concentration it can form helical aggregates; addition of small amounts of trifluoroethanol induces a secondary structure, mostly due to the presence of helical elements. Using NMR-derived constraints, an ensemble of conformers for the peptide has been determined by restrained molecular dynamics calculations. Analysis of the converged three-dimensional structures indicates that a significant population of them adopts an amphipathic alpha-helical conformation that, depending upon experimental conditions, presents a variable extension in the stretch Leu6-Tyr20. An equilibrium with nonhelical structured conformers is also observed. We suggest that the capability of the peptide to modulate its secondary structure as a function of the medium dielectric constant, as well as its ability to form helical aggregates by means of intermolecular hydrophobic interactions, can play a significant role for G-protein activation.
Effect of Cavtratin, a Caveolin-1 Scaffolding Domain Peptide, on Oligodendroglial Signaling Cascades (2011)

Caveolin and caveolin containing rafts are involved in the signaling of growth factors in various cell types. Previous reports of our lab indicated a co-localization of caveolin and the high affinity nerve growth factor (NGF) receptor tyrosine kinase A (TrkA). Mutual effects have been observed among which a caveolin-1 knock-down resulted in an impairment of the NGF signaling cascade rather than in an increase of activity as expected from other growth factor reports. On the other hand, an over-expression of caveolin-1 impaired the NGF stimulated activity of p42/44 mitogen activated protein kinases (MAPK). In this study, we used a caveolin-1 scaffolding domain (CSD) peptide (cavtratin) of which an inhibitory effect on growth factor receptors was reported. Our data showed that cavtratin suppresses the NGF-induced phosphorylation of TrkA as well as the activation of MAPK in porcine oligodendrocytes significantly.
Dynamic Server Selection using Bandwidth Probing in Wide-Area Networks (1996)

Replication is a commonly proposed solution to problems of scale associated with distributed services. However, when a service is replicated, each client must be assigned a server. Prior work has generally assumed that assignment to be static. In contrast, we propose dynamic server selection, and show that it enables application-level congestion avoidance. To make dynamic server selection practical, we demonstrate the use of three tools. In addition to direct measurements of round-trip latency, we introduce and validate two new tools: bprobe, which estimates the maximum possible bandwidth along a given path; and cprobe, which estimates the current congestion along a path. Using these tools we demonstrate dynamic server selection and compare it to previous static approaches. We show that dynamic server selection consistently outperforms static policies by as much as 50%. Furthermore, we demonstrate the importance of each of our tools in performing dynamic server selection. 1 Introducti...
Mechanisms of mutations inhibiting fusion and infection by Semliki Forest virus. (1996)

Semliki Forest virus (SFV) infects cells by an acid-dependent membrane fusion reaction catalyzed by the virus spike protein, a complex containing E1 and E2 transmembrane subunits. E1 carries the putative virus fusion peptide, and mutations in this domain of the spike protein were previously shown to shift the pH threshold of cell-cell fusion (G91A), or block cell-cell fusion (G91D). We have used an SFV infectious clone to characterize virus particles containing these mutations. In keeping with the previous spike protein results, G91A virus showed limited secondary infection and an acid-shifted fusion threshold, while G91D virus was noninfectious and inactive in both cell-cell and virus-liposome fusion assays. During the low pH- induced SFV fusion reaction, the E1 subunit exposes new epitopes for monoclonal antibody (mAb) binding and forms an SDS-resistant homotrimer, the virus associates hydrophobically with the target membrane, and fusion of the virus and target membranes occurs. After low pH treatment, G91A spike proteins were shown to bind conformation-specific mAbs, associate with target liposome membranes, and form the E1 homotrimer. However, both G91A membrane association and homotrimer formation had an acid-shifted pH threshold and reduced efficiency compared to wt virus. In contrast, studies of the fusion-defective G91D mutant showed that the virus efficiently reacted with low pH as assayed by mAb binding and liposome association, but was essentially inactive in homotrimer formation. These results suggest that the G91D mutant is noninfectious due to a block in a late step in membrane fusion, separate from the initial reaction to low pH and interaction with the target membrane, and involving the lack of efficient formation of the E1 homotrimer.
Secure spread spectrum watermarking for multimedia (1997)

This paper presents a secure (tamper-resistant) algorithm for watermarking images, and a methodology for digital watermarking that may be generalized to audio, video, and multimedia data. We advocate that a watermark should be constructed as an independent and identically distributed (i.i.d.) Gaussian random vector that is imperceptibly inserted in a spread-spectrum-like fashion into the perceptually most significant spectral components of the data. We argue that insertion of a watermark under this regime makes the watermark robust to signal processing operations (such as lossy compression, filtering, digital-analog and analog-digital conversion, requantization, etc.), and common geometric transformations (such as cropping, scaling, translation, and rotation) provided that the original image is available and that it can be successfully registered against the transformed watermarked image. In these cases, the watermark detector unambiguously identifies the owner. Further, the use of Gaussian noise, ensures strong resilience to multiple-document, or collusional, attacks. Experimental results are provided to support these claims, along with an exposition of pending open problems.
The Location of Myth inCamí de sirgaby Jesús Moncada (2002)

(2002). The Location of Myth in Cami de sirga by Jesus Moncada. Journal of Iberian and Latin American Studies: Vol. 8, No. 1, pp. 41-54.
C-Peptide Levels in Latent Autoimmune Diabetes in Adults Treated With Linagliptin Versus Glimepiride: Exploratory Results From a 2-Year Double-Blind, Randomized, Controlled Study (2013)

Latent autoimmune diabetes in adults (LADA) is a slowly progressing form of immune-mediated diabetes often misdiagnosed as type 2 diabetes because of its typical clinical presentation, i.e., an adult without weight loss or ketoacidosis not initially requiring insulin (1). Prior to insulin dependence, pharmacological options for reducing hyperglycemia comprise the oral glucose-lowering drugs used in type 2 diabetes; however, none has been established as the drug of choice in LADA because of the scarcity of evidence for or against the various agents (2).

This study was a prespecified, exploratory analysis of a large ( n = 1,519) trial in which patients diagnosed with type 2 diabetes and HbA1c of 6.5–10.0% (48–86 mmol/mol) on metformin were randomized to additional once-daily linagliptin 5 mg or glimepiride 1−4 mg for 2 years (NCT00622284) (3). Fasting plasma samples taken during the study were tested for autoantibodies against GAD 65-kDa isoform (GAD65), islet cell cytoplasm, tyrosine phosphatase IA-2 (IA-2A), or insulin (IAA), and patients were classified as having LADA if positive for …
Protein A-Specific Monoclonal Antibodies and Prevention of Staphylococcus aureus Disease in Mice (2012)

Staphylococcus aureus is a leading cause of human soft tissue infections and bacterial sepsis. The emergence of antibiotic-resistant strains (methicillin-resistant S. aureus [MRSA]) has prompted research into staphylococcal vaccines and preventive measures. The envelope of S. aureus is decorated with staphylococcal protein A (SpA), which captures the Fcγ portion of immunoglobulins to prevent opsonophagocytosis and associates with the Fab portion of V(H)3-type B cell receptors to trigger B cell superantigen activity. Nontoxigenic protein A (SpA(KKAA)), when used as an immunogen in mice, stimulates humoral immune responses that neutralize the Fcγ and the V(H)3(+) Fab binding activities of SpA and provide protection from staphylococcal abscess formation in mice. Here, we isolated monoclonal antibodies (MAbs) against SpA(KKAA) that, by binding to the triple-helical bundle fold of its immunoglobulin binding domains (IgBDs), neutralize the Fcγ and Fab binding activities of SpA. SpA(KKAA) MAbs promoted opsonophagocytic killing of MRSA in mouse and human blood, provided protection from abscess formation, and stimulated pathogen-specific immune responses in a mouse model of staphylococcal disease. Thus, SpA(KKAA) MAbs may be useful for the prevention and therapy of staphylococcal disease in humans.
Energetic Zinc Ion Chemistry: The Rechargeable Zinc Ion Battery (2011)

Think zinc: An ideal aqueous energy storage device, referred to as a zinc ion battery, is presented. The device is characterized by high capacity, fast charge/discharge capability, safety, and environmental friendliness. It is composed of an α-MnO2 cathode, a zinc anode, and a mild ZnSO4 or Zn(NO3)2 aqueous electrolyte (see scheme). The battery chemistry is based on the migration of Zn2+ ions between cathode and anode.
Tell Me Where to Look: Guided Attention Inference Network (2018)

Weakly supervised learning with only coarse labels can obtain visual explanations of deep neural network such as attention maps by back-propagating gradients. These attention maps are then available as priors for tasks such as object localization and semantic segmentation. In one common framework we address three shortcomings of previous approaches in modeling such attention maps: We (1) first time make attention maps an explicit and natural component of the end-to-end training, (2) provide self-guidance directly on these maps by exploring supervision form the network itself to improve them, and (3) seamlessly bridge the gap between using weak and extra supervision if available. Despite its simplicity, experiments on the semantic segmentation task demonstrate the effectiveness of our methods. We clearly surpass the state-of-the-art on Pascal VOC 2012 val. and test set. Besides, the proposed framework provides a way not only explaining the focus of the learner but also feeding back with direct guidance towards specific tasks. Under mild assumptions our method can also be understood as a plug-in to existing weakly supervised learners to improve their generalization performance.
A Heck‐Type Coupling for the Synthesis of Novel Bridged Metallochlorin–Fullerene C60 Dyads (2005)

Abstract A short and convenient synthesis of metallochlorin–C 60 dyads based on a Heck‐type hetero coupling at the 3 2 position of a chlorin is described. p ‐Bromobenzaldehyde was treated with Zn‐metalated 13 2 ‐demethoxycarbonylmethylpheophorbide a , using a palladium acetate/LiCl catalyst mixture under phase‐transfer conditions in DMF at 70 °C. The resulting asymmetric olefin was obtained in a high trans / cis ratio. The desired trans isomer was separated and subsequently transformed into a donor–acceptor dyad by a 1,3‐dipolar cycloaddition to C 60 in the presence of sarcosine in refluxing toluene. The resulting dyads are expected to undergo efficient photoinduced electron transfer and can potentially be utilized in solar energy conversion devices. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Template-directed photoligation of oligodeoxyribonucleotides via 4- thiothymidine (1998)

Non-enzymatic, template-directed ligation of oligonucleotides in aqueous solution has been of great interest because of its potential synthetic and biomedical utility and implications for the origin of life. Though there are many methods for template-directed chemical ligation of oligonucleotides, there are only three reported photochemical methods. In the first report, template-directed photoligation was effected by cyclobutane dimer formation between the 5'- and 3'-terminal thymidines of two oligonucleotides with >290 nm light, which also damages DNA itself. To make the photochemistry of native DNA more selective, we have replaced the thymidine at the 5'-end of one oligonucleotide with 4-thiothymidine (s4T) and show that it photoreacts at 366 nm with a T at the 3'-endof another oligonucleotide in the presence of a complementary template. When a single mismatch is introduced opposite either the s4T or its adjoining T, the ligation efficiency drops by a factor of five or more. We also show that by linking the two ends of the oligonucleotides together, photoligation can be used to form circular DNA molecules and to 'photopadlock' circular DNA templates. Thus, s4T-mediated photo-ligation may have applications to phototriggered antisense-based or antigene-based genetic tools, diagnostic agents and drugs, especially for those situations in which chemical or enzyme-mediated ligation isundesirable or impossible, for example inside a cell.
Comparison of neural targets for neuromodulation of bladder micturition reflex in the rat (2012)

Spinal nerve (SN) stimulation inhibits the bladder rhythmic contraction (BRC) in anesthetized rats. This preparation was used to study the effects of electrical stimulation of the tibial nerve (TN) and the dorsal nerve of the clitoris (DNC) on BRC. Stimulation of the TN and DNC for 10 min produced a frequency- and intensity-dependent attenuation of the frequency of bladder contractions. As observed with the SN, 10-Hz stimulation of either TN or DNC produced the greatest degree of inhibition, with lower or higher frequencies being either less efficacious or inactive. In contrast to the prolonged inhibition produced by SN stimulation, both TN and DNC stimulation produced "short" lasting inhibition of bladder contractions and the maximal inhibition occurred during stimulation. TN stimulation was effective over only a narrow range of current intensities [3-4 × motor threshold current for inducing a toe twitch (T(mot))] and only at a frequency of 10 Hz. Stimulation of TN at 10 Hz, 3 × T(mot) inhibited BRC to 23% of control. Ten-hertz DNC stimulation at 2 × T(EAS), the threshold current for evoking a reflex anal sphincter contraction, decreased the frequency of contractions to 4% of control. Although compared with the respective threshold current the BRC response was more sensitive to DNC compared with TN stimulation, the absolute current required to reduce BRC using DNC stimulation appeared to be higher. Comparing the effects of TN and DNC stimulation to our previous results with SN stimulation, SN stimulation produces the largest duration and efficacy of bladder inhibition.
100-μsec pulsed CO2laser resurfacing of lower eyelids: erythema and rhytides reduction (1997)

Lower eyelid skin is very thin with a low density of adnexal structures. Attempts to remove rhytides and improve surface appearance with chemical peels and dermabrasion have been disappointing. Laser resurfacing offers a new modality that may improve the outcome. We evaluated a very short duration (100 microsecond(s) ec) pulsed carbon-dioxide laser (Tru-Pulse<SUP>TM</SUP>) in terms of healing time (duration of erythema) and efficacy (wrinkle reduction). Female patients aged 35 - 75 received laser resurfacing in a variety of cosmetic zones but only data from lower lids are reported here. Dosimetry varied from total fluences of 5 to 20 J/cm<SUP>2</SUP> (9 mm<SUP>2</SUP> spot, 250 - 500 mJ pulse, 1 to 4 passes). Patients followed a strict regime of post-op wound care. Pre-treatment and follow-up photographs were taken in a studio with constant photographic parameters. Projected 35 mm slides were evaluated side-by-side for clinical improvement and presence of erythema. Within the first 4 days post-op all (100%) lower eyelids exhibited erythema and swelling, at 7 days: 71%, 12 days: 60%, 3 weeks: 25%, and one (1) month or longer 7%. In our sample the longest duration of post-op lower lid erythema lasted 5 weeks. Most patients experienced 70 -80% wrinkle reduction with a range of 0 - 100%. Regression analysis was used to evaluate the relationships between percent wrinkle reduction and the treatment, demographic, and evaluation variables. There was a significant trend for wrinkles to improve over the 3 to 9 month evaluation period. Older patients improved slightly more than younger patients. There was no relationship between total energy density and wrinkle reduction.
Dynamic Adaptive Streaming over HTTP/2.0 (2013)

MPEG Dynamic Adaptive Streaming over HTTP (DASH) is a new streaming standard that has been recently ratified as an international standard (IS). In comparison to other streaming systems, e.g., HTTP progressive download, DASH is able to handle varying bandwidth conditions providing smooth streaming. Furthermore, it enables NAT and Firewall traversal, flexible and scalable deployment as well as reduced infrastructure costs due to the reuse of existing Internet infrastructure components, e.g., proxies, caches, and Content Distribution Networks (CDN). Recently, the Hypertext Transfer Protocol Bis (httpbis) working group of the IETF has officially started the development of HTTP 2.0. Initially three major proposals have been submitted to the IETF i.e., Googles' SPDY, Microsofts' HTTP Speed+Mobility and Network-Friendly HTTP Upgrade, but SPDY has been chosen as working draft for HTTP 2.0. In this paper we implemented MPEG-DASH over HTTP 2.0 (i.e., SPDY), demonstrating its potential benefits and drawbacks. Moreover, several experimental evaluations have been performed that compare HTTP 2.0 with HTTP 1.1 and HTTP 1.0 in the context of DASH. In particular, the protocol overhead, the performance for different round trip times, and DASH with HTTP 2.0 in a lab test scenario has been evaluated in detail.
Characteristics of calcium sparks in cardiomyocytes derived from embryonic stem cells (2001)

In embryonic stem (ES) cell-derived cardiomyocytes, spontaneous Ca(2+) sparks representing Ca(2+) release through ryanodine receptor (RyR) channels were characterized and correlated to the expression of RyRs as well as the Ca(2+) load of the sarcoplasmic reticulum (SR). In very early developmental stage (VEDS) cardiac precursor cells, global intracellular Ca(2+) concentration ([Ca(2+)](i)) fluctuations occurred, whereas Ca(2+) sparks and contractions were absent. In early developmental stages (EDS), contractions as well as Ca(2+) sparks were obvious. During the further differentiation to late developmental stage (LDS) cardiomyocytes, a marked increase in the frequency of global [Ca(2+)](i) transients, the amplitude and the frequency of Ca(2+) sparks, as well as the expression of RyRs and the volume of RyR-positive SR, was observed. Furthermore, the caffeine-releasable SR Ca(2+) load was elevated in LDS compared with EDS cardiomyocytes. A high-Ca(2+) solution raised spark frequency as well as amplitude in EDS cardiomyocytes to the levels of LDS cardiomyocytes. The characteristics of Ca(2+) sparks occurring in cardiomyocytes differentiated from ES cells may be governed by the Ca(2+) load of the SR and/or the density of RyRs.
Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data (2016)

ZIKV epidemics in South America, as well as in Africa, show complex dissemination patterns. The virus appears to have been circulating in Haiti prior to the first reported cases in Brazil. Factors contributing to transmission and the possible linkage of this early Haitian outbreak with microcephaly remain to be determined.
Zdroj vysokonapěťových pulzů pro elektroporaci buněk (2016)

Hlavním cílem této práce je vytvoření řídící desky přístroje určeného pro ireverzibilní elektroporaci a napsání řídícího firmware pro použitý procesor. V první kapitole je pojednáno o samotném principu buněčné elektroporace. Je zde popsán model buňky v elektrickém poli, účinek elektroporace na živou tkáň a také simulace metody. Dále jsou definovány požadavky na parametry pulzů ireverzibilní elektroporace a také požadavky na bezpečí pacienta ve smyslu synchronizace pulzů se signálem EKG. Na konci první kapitoly je vysvětlen princip nové vysokofrekvenční elektroporační metody H-FIRE, při které jsou do tkáně aplikovány dávky bipolárních, vysokonapěťových, velmi krátkých pulzů. Ve druhé kapitole je stručně představeno komerční elektroporační zařízení Nanoknife. Je zde popsána jeho výkonová i řídící část, včetně uvedení mezních parametrů zařízení. Ve třetí kapitole je představen nový přístroj pro ireverzibilní elektroporaci vyvinutý na VUT v Brně a stručně popsáno zapojení jeho výkonové části. Čtvrtá kapitola se týká návrhu řídící desky. Jsou zde popsány jednotlivé schematické bloky celého zapojení. V páté kapitole je charakterizován algoritmus řídícího programu, následuje stručný manuál k přístroji.
Physical Structure and Inversion Charge at a Semiconductor Interface with a Crystalline Oxide (2001)

We show that the physical and electrical structure and hence the inversion charge for crystalline oxides on semiconductors can be understood and systematically manipulated at the atomic level. Heterojunction band offset and alignment are adjusted by atomic-level structural and chemical changes, resulting in the demonstration of an electrical interface between a polar oxide and a semiconductor free of interface charge. In a broader sense, we take the metal oxide semiconductor device to a new and prominent position in the solid-state electronics timeline. It can now be extensively developed using an entirely new physical system: the crystalline oxides-on-semiconductors interface.
Comparison of Effects of Locally Infused Angiotensin I and II on Hand Veins and Forearm Arteries in Man: Evidence for Converting Enzyme Activity in Limb Vessels (1974)

1. The effects of angiotensin I (AI) and angiotensin II (AII) have been compared during local infusions into peripheral arteries and veins in man. 2. Both AI and AII produced constriction of hand veins and forearm arteries; the potency of AI was somewhat less than AII. 3. When infused into the vein, the converting enzyme inhibitor SQ 20,881 abolished or markedly attenuated the effect of AI but not that of AII. 4. The results suggest the local presence of converting enzyme in human peripheral arteries and veins.
A CNN-based chip for robot locomotion control (2005)

In this paper, the paradigm of emergent computation is applied to locomotion control in legged robots: the locomotion gait is the result of self-organization of a network of locally coupled nonlinear oscillators. This means to adopt the biological paradigm of central pattern generator (CPG), implemented by using cellular neural networks (CNNs). The whole control strategy is hybrid in the sense that the gait generation is accomplished by a fully analog CNN, while a simple logic unit modulates the behavior of the CNN-based CPG, so that the strategy is suitable to eventually include sensory feedback. The design of a VLSI chip implementing the CNN-based CPG and some experimental results on the chip are presented. The chip is designed using a switched-capacitor technique, fundamental to obtain in a simple and direct way some key features of the hybrid control discussed. The experimental results confirm the suitability of the approach.