gebhart/patrepeval huggingface dataset:
Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display (2020)

Cyclic peptides with engineered protein-binding activity have gained increasing attention for use in therapeutic and biotechnology applications. We describe the efficient isolation and characterization of cyclic peptide binders from genetically encoded combinatorial libraries using yeast surface display. Here, peptide cyclization is achieved by disuccinimidyl glutarate-mediated cross-linking of amine groups within a linear peptide sequence that is expressed as a yeast cell surface fusion. Using this approach, we first screened a library of cyclic heptapeptides using magnetic selection, followed by fluorescence activated cell sorting (FACS) to isolate binders for a model target (lysozyme) with low micromolar binding affinity (<i>K</i><sub>D</sub> ∼ 1.2-3.7 μM). The isolated peptides bind lysozyme selectively and only when cyclized. Importantly, we showed that yeast surface displayed cyclic peptides can be used to efficiently obtain quantitative estimates of binding affinity, circumventing the need for chemical synthesis of the selected peptides. Subsequently, to demonstrate broader applicability of our approach, we isolated cyclic heptapeptides that bind human interleukin-17 (IL-17) using yeast-displayed IL-17 as a target for magnetic selection, followed by FACS using recombinant IL-17. Molecular docking simulations and follow-up experimental analyses identified a candidate cyclic peptide that likely binds IL-17 in its receptor binding region with moderate apparent affinity (<i>K</i><sub>D</sub> ∼ 300 nM). Taken together, our results show that yeast surface display can be used to efficiently isolate and characterize cyclic peptides generated by chemical modification from combinatorial libraries.
Spectroscopic determination of the state-to-state differential cross section by velocity selected double resonance (1993)

We have measured the state-to-state differential scattering cross section (DCS) for a rotationally inelastic process using an entirely spectroscopic method. The system studied was ${\mathrm{Li}}_{2}$(${\mathit{A}}^{1}$${\mathrm{\ensuremath{\Sigma}}}_{\mathit{u}}^{+}$)-Xe and the method utilizes two color sub-Doppler double resonance. Analysis of the shape of the double resonance line yields the final distribution of relative velocity vectors. This represents the first measurement of a state-to-state DCS using thermal cell spectroscopy. In addition we have determined, also for the first time, the dependence of the state-to-state DCS on initial relative velocity. Results are presented for the \ensuremath{\Delta}j=6 rotationally inelastic process.
Diastereoselective Synthesis of Methylenecyclopropanes from Chiral Cyclopropene Derivatives (2006)

Directed delivery: Chiral methylenecyclopropanes were prepared from cyclopropene derivatives upon reaction with Grignard reagents. A higher-order dependence of the reaction on the concentration of the Grignard reagent was revealed, and based on this finding, it was possible to reverse the regioselectivity of the process (see scheme; MEM=methoxyethoxymethyl). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z600531_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Adult Survivors of Invasive Pneumococcal Disease Exhibit Defective B Cell Function (2011)

Adults who have recovered from an episode of invasive pneumococcal disease demonstrate defective B cell activation in response to αδ-dex, a polyclonal polysaccharide mimic, compared with matched control subjects. The defect is not overcome by CD4(+) T cell assistance and may explain the relatively poor response to pneumococcal vaccination in survivors of invasive pneumococcal disease.
Quantifying Anticholinergic Burden and Sedative Load in Older Adults with Polypharmacy: A Systematic Review of Risk Scales and Models (2021)

Variability and inconsistency exists among scales used to categorize drugs with anticholinergic or sedative burden. In this review, we provide a comprehensive table that proposes a new categorization of these drugs. A longitudinal study will be required to validate the new proposed anticholinergic and sedative burden catalog in an evidence-based manner.
ChemInform Abstract: Acid‐Base Characteristics of Cholinomimetic 3‐Alkylaminopyridazine Derivatives. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Semiconductor Lasers for Ultra High Speed Applications (1985)

There exist two important modes of modulation of semiconductor lasers: (1) direct current sinusoidal or pulse modulation, and (2) mode locking.
A frequency synthesizer based on Zero-Crossing Digital Phaselocked Loop (2013)

This paper presents an efficient hybrid frequency synthesizer, that is capable of both integer and fractional division, design based on the Zero-Crossing Digital Phase-locked Loop architecture. The design uses an efficient adaptation mechanism to maintain the in-lock state following the division process. The fast switching, locking and acquisition of the system make it an excellent candidate for synthesis even in Doppler environment. The simulation results demonstrate that the proposed synthesizer can achieve the desired frequency division.
Defective basal lamina formation by transformed mammary epithelial cells: A reduced effect of collagen on basal lamina (heparan sulfate‐rich) proteoglycan degradation (1982)

Invasive, spontaneously transformed mammary epithelial cells derived from the normal NMuMG cell line have lost the ability of their parental cells to respond in vitro to the presence of a collagen substratum by forming a continuous glycosaminoglycan (GAG)-rich basal lamina. On collagen, the cells synthesize 35S-GAG at the same rates, but the transformed cells accumulate less 35S-GAG than the normal cells because a larger fraction of their newly synthesized 35S-GAG is rapidly degraded. Chromatography of the 35SO4-containing materials from cultures on collagen indicates that the reduced accumulation of 35S-GAG by the transformed cells reflects less of a heparan sulfate-rich proteoglycan fraction which has been found in the basal lamina. On plastic substrata, however, the normal and transformed cells have near identical rates of 35S-GAG synthesis and degradation and they accumulate similar low amounts of the basal lamina proteoglycan fraction, which is rapidly degraded. Thus, transformation appears to impair the ability of the cells to reduce basal lamina proteoglycan degradation in response to collagen. This impairment may prevent the neoplastic cells from forming a complete basal lamina and, therefore, allow local invasion.
Understanding BatchNorm in Ternary Training (2019)

Neural networks are comprised of two components, weights andactivation function. Ternary weight neural networks (TNNs) achievea good performance and offer up to 16x compression ratio. TNNsare difficult to train without BatchNorm and there has been no studyto clarify the role of BatchNorm in a ternary network. Benefitingfrom a study in binary networks, we show how BatchNorm helps inresolving the exploding gradients issue.
Characteristics of Hard Dental Tissues Ablation by a Quintupled Nd:YAG (1999)

Research in the use of lasers for the removal of hard dental tissue has extended over several different laser wavelengths with varying success. Excimer lasers have been one of the primary sources of UV laser radiation, however recent developments in nonlinear optics has allowed for the development of solid state UV lasers which can output non trivial amounts of UV radiation.
Nationella rekommendationer för fysisk aktivitet : En kvantitativ studie om medvetenhet och aktivitetsmönster hos unga vuxna (2013)

Syfte och frågeställningar Syftet är att undersöka hur nationella rekommendationer för fysisk aktivitet återspeglas i aktivitetsmönster hos vuxna Facebook-användare mellan 18 och 30 år. Hur är kunskapsnivån rörande de nationella rekommendationerna för fysisk aktivitet hos vuxna Facebook-användare mellan 18 och 30 år? Hur stor andel av vuxna Facebook-användare mellan 18-30 år uppnår nationella rekommendationer för fysisk aktivitet utifrån självskattning? Hur ser sambandet ut mellan kunskap om nationella rekommendationer för fysisk aktivitet och vuxnas aktivitetsmönster hos vuxna Facebook-användare mellan 18-30 år? Metod Metoden var en kvantitativ studie som genomfördes med en webbenkät på det sociala nätverket Facebook. Urvalet var vuxna mellan 18 och 30 år. Studien genomfördes under tre veckor och länken till enkäten delades från fyra Facebookkonton som tillhörde två studerande kvinnor och två yrkesverksamma män. Enkäten undersökte aktivitetsmönster och kunskap om nationella rekommendationer för fysisk aktivitet. Frågorna hämtades från IPAQ, GIH:s hälsoenkät samt egenutformade frågor. Resultaten analyserades i Statistica 64 genom deskriptiv analys, t-test, envägs ANOVA och Spearman test. Resultat Resultatet visade att 52 procent av deltagarna angav att de inte visste vilka de nationella rekommendationerna var, trots detta valde 65 procent av dessa rätt rekommendation av olika alternativ. Det var 93 procent som uppnådde rekommendationerna enligt självskattning. Sambandet mellan kunskap och aktivitetsmönster pekade på att om en person visste vilka rekommendationerna för fysisk aktivitet var, ansåg denne sig enligt självskattning mer aktiv räknat utifrån MET:s minuter per vecka. Slutsats Det går enligt studien att se en återspegling av de nationella rekommendationerna för fysisk aktivitet i vuxnas aktivitetsmönster. På grund av olika påverkansfaktorer går det dock inte att dra några generella slutsatser för hela målgruppen. Studien visar att det ur ett hälsoperspektiv finns behov av mer riktad information till den aktuella målgruppen om vardagsmotionens betydelse för hälsa och fysiskt välmående.
Method and apparatus for in-situ drying investigation and optimization of slurry drying methodology (2023)

A method of drying casted slurries that includes calculating drying conditions from an experimental model for a cast slurry and forming a cast film. An infrared heating probe is positioned on one side of the casted slurry and a thermal probe is positioned on an opposing side of the casted slurry. The infrared heating probe may control the temperature of the casted slurry during drying. The casted slurry may be observed with an optical microscope, while applying the drying conditions from the experimental model. Observing the casted slurry includes detecting the incidence of micro-structural changes in the casted slurry during drying to determine if the drying conditions from the experimental model are optimal.
Amide proton transfer imaging with improved robustness to magnetic field inhomogeneity and magnetization transfer asymmetry using saturation with frequency alternating RF irradiation (2011)

Abstract Amide proton transfer (APT) imaging results in a representative human volunteer. a: B 0 map calculated from the low SNR z‐spectrum images by the B 0 correction algorithm. b: MTR asym map and c: MTR SAFARI map calculated from the high SNR APT images without B 0 correction. The uncorrected MTR asym map shows large spatial intensity variation over the brain, which corresponds to the water frequency shift map. The uncorrected MTR SAFARI map shows a remarkable improvement in homogeneity over the brain. From the article by Scheidegger et al (pp 1275‐1285).
A Notch updated (2009)

Cell-cell signaling mediated by the Notch receptor is iteratively involved in numerous developmental contexts, and its dysregulation has been associated with inherited genetic disorders and cancers. The core components of the signaling pathway have been identified for some time, but the study of the modulation of the pathway in different cellular contexts has revealed many layers of regulation. These include complex sugar modifications in the extracellular domain as well as transit of Notch through defined cellular compartments, including specific endosomes.
In-plane loaded CLT beams - Tests and analysis of element lay-up (2017)

Background, aim and objectivesThis work concerns in-plane loaded CLT beams, including beams with a hole or a notch.Using CLT for such structural elements is very relevant from a practical engineering point of view since the transversal layers have a reinforcing effect with respect to stress perpendicular to the beam axis.Due to the general composition of CLT, the stress state is however very complex and many failure modes need to be considered in design.The beam strength is furthermore affected not only by the basic material strength and the gross cross sections dimensions, but also affected by the ratio of the longitudinal and transversal layer widths and by the dimensions of the cross sections of the individual laminations.Many of the geometry parameters are defined by the producer, e.g. the widths t 0 and t 90 of the longitudinal and transversal layers respectively.Other parameters, such as dimensions of individual laminations and lamination placement with respect to element edges, are often not known to the engineer in an actual design situation since the beams in general are cut from larger elements.In this cutting, no consideration of the location of the beam element edges in relation to the edges of the individual laminations is made.Experimental tests on CLT beams are for example reported by Bejtka (2011) and Andreolli et al (2012).Comprehensive experimental tests and a composite beam model for stress analysis and strength verification have further been presented by Flaig (2013Flaig ( , 2014Flaig ( , 2015aFlaig ( , 2015b) ) and by Flaig and Blass (2013), including stress based failure criteria for relevant failure modes.A basic assumption for that model is that the CLT lay-up
Book reviews (1993)

K. J. Bare and J. B. Goodenough, J. Mater. Chem., 1993, 3, 115 DOI: 10.1039/JM9930300115
A systematic investigation of the association between <scp>HPV</scp> and the clinicopathological parameters and prognosis of oral and oropharyngeal squamous cell carcinomas (2017)

Human papillomavirus (HPV), the causal factor of cervical cancers, was closely linked to the etiology and prognosis of oropharyngeal squamous cell carcinoma (OPSCC), but its role in oral squamous cell carcinoma (OSCC) was unclear. In addition, few researches based on Chinese population were documented. Hence, we sought to investigate the relationship of HPV marker P16 protein to the clinicopathological parameters and survival of OPSCC and OSCC patients systematically to assess the influence of ethnic, regional difference on HPV susceptibility. Specimens from 93 OPSCC patients and 95 OSCC patients were recut, and P16 immunohistochemistry (IHC) was performed. Moreover, survival analysis was conducted to confirm the independent factors that influenced the prognosis. The P16 results were positive in 25.8% and 9.5% of patients with OPSCC and OSCC, respectively. The overall survival (OS) of HPV-positive OPSCC patients was significantly longer than that of HPV-negative OPSCC patients (P = 0.004). Conversely, statistical significance was not observed regarding the OS of OSCC patients (P = 0.343). Cox regression analysis indicated that T stage and P16 status were independent factors that affected the prognosis of OPSCC patients, and the smoking index influenced the prognosis of OSCC patients. Among OPSCC patients who received radiochemotherapy (RCT), HPV-positive patients had a better survival rate than their HPV-negative counterparts (P = 0.015). Conversely, no significant difference was observed between HPV-positive and HPV-negative OSCC patients who received RCT (P = 0.237). P16 is a credible surrogate by which to define HPV status. HPV expression had a favorable effect on OPSCC patients as opposed to their OSCC counterparts in this single center population-based study.
Removal of mercury from water by multi-walled carbon nanotubes (2010)

The removal of mercury (Hg(2+)) ions from contaminated water using multiwalled carbon nanotubes (MWCNTs) was investigated in this study. Results of the study showed that MWCNTs slurry was very efficient in removing as high as 1.0 mg/L of Hg(2+) from aqueous solutions via the adsorption mechanism. This removal efficiency was found to be a function of the aqueous pH level, dosage of CNTs, mixing rate, and contact time. The study showed that the Hg uptake by MWCNTs increased to 100% with an increase in pH from pH 4 to 8. The results also showed that higher dosage of MWCNTs, showed higher removal of Hg(2+). In a 50 mL water sample, 10 mg of MWCNTs was needed to remove all of the 0.1 mg/L of Hg(2+) ions. On the other hand, increasing the mixing rate from 50 to 150 rpm improved the removal efficiency. The experimental results also showed that mercury adsorption by MWCNTs follow a pseudo second-order reaction with a rate (k) of 0.018 and it is well described by the Langmuir isotherm model with maximum adsorptive capacity (q(max)) of 13.16.
A ΔRaf1–ER‐inducible oncogenic zebrafish liver cell model identifies hepatocellular carcinoma signatures (2011)

Although the underlying molecular mechanism of hepatocellular carcinoma remains unclear, signalling pathways essential in cell survival and growth are altered, including the Raf-MEK-MAPK pathway. This pathway can be activated by hepatitis B or C virus infections and the ectopic expression of the Raf-1 oncogene is frequently seen in hepatocellular carcinomas. In addition, the Raf-MEK-MAPK pathway was also shown to be deregulated in zebrafish liver tumours. Based on the genetic conservation between zebrafish and human liver tumours, the zebrafish was used as an animal model to better understand the molecular basis of hepatocellular carcinoma. Here we establish an inducible oncogenic zebrafish cell model, in which oncogenic human Raf-1(ΔRaf1) can be post-transcriptionally activated in zebrafish liver cells by administration of 4-hydroxytamoxifen (4HT). The ΔRaf1 activation resulted in the hyperactivation of the zebrafish MEK-ERK cascade, promoted cell growth and proliferation, and inhibited apoptosis. The mitogenic transformation of the ZFL-ΔRaf1-ER cells was confirmed by in vivo allo-transplantation and in silico microarray analyses. Gene expression profiling of cells treated with 4HT and a MEK-inhibitor identified a Raf-MEK-dependent signature set. This transcriptome response was compared to zebrafish and human liver cancer transcriptomes. We identified, and validated by quantitative PCR, a set of genes transcriptionally regulated by hyperactive MAPK signalling in ZFL-ΔRaf1-ER cells, zebrafish liver tumours and human liver tumours, suggesting that the in vitro zebrafish liver cell model can be used for further study of the molecular basis of human hepatocellular carcinoma. The molecular targeting of the commonly regulated hepatocellular carcinoma genes using the ZFL-ΔRaf1-ER cell model can be applied for high-throughput preclinical target discovery.
Towards a better-than-best-effort forwarding service for multimedia flows (1999)

A salient requirement of interactive multimedia applications is that they transmit data continuously at uniform rates with minimum possible end-to-end delay. The majority of these applications do not require hard and fast guarantees of network performance, but the current best-effort forwarding model of the Internet is frequently insufficient for realizing these requirements. Worse still, the requirement of uniform-rate transmission puts many multimedia applications at odds with current and proposed Internet network management practices that assume or require TCP-like reactions to packet loss. We are investigating router-based active queue management, specifically the use of queue occupancy thresholds to isolate TCP flows and to provide a better-than-best-effort forwarding service for flows in need of uniform-rate transmissions. Our current scheme, class-based thresholds (CBT), relies on a packet marking mechanism such as those proposed for realizing differentiated services on the Internet. CBT, when combined with existing active router queue management schemes such as random early detection (RED), provides a performance for TCP that approximates that achievable under a packet scheduling scheme and acceptable performance for multimedia flows. CBT is a simple and efficient mechanism with implementation complexity and run-time overhead comparable to that of RED.
Coilgun Acceleration Model Containing Multiple Interacting Coils (2019)

A coilgun operates by pulsing current through an axially-arranged series of independently-controlled coils inductively interacting with a small, electrically-conductive, azimuthally-symmetric projectile to accelerate it to high velocities. The electrical circuits are programmed to pulse current through the coils in such a way so as to impart further electromagnetic acceleration in each stage. A method is developed to calculate the mutual inductance between the coils and between each coil and the projectile. These terms are used to write a system of first-order ordinary differential equations governing the projectile velocity and the current flow in each coil. While the inclusion of the electromagnetic interactions between coils significantly complicates the equation set as more coil sets are included in the problem, casting the problem symbolically in mass matrix form permits solution using standard numerical Runge-Kutta techniques. Comparing a projectile with a single-turn to that comprised of nine-turns, the inductance of the former is much smaller, but this leads to a greater induced projectile current. The lower inductance and greater current appear to offset each other with little difference in the acceleration profile for the two cases. For the limited cases studied, coils with a discharge half-cycle equal to the time for a projectile to transit from one coil to the next yield increased efficiency.
Low Density Lattice Codes (2007)

Low density lattice codes (LDLC) are novel lattice codes that can be decoded efficiently and approach the capacity of the additive white Gaussian noise (AWGN) channel. In LDLC a codeword x is generated directly at the n-dimensional Euclidean space as a linear transformation of a corresponding integer message vector b, i.e., x = Gb, where H, the inverse of G, is restricted to be sparse. The fact that H is sparse is utilized to develop a linear-time iterative decoding scheme which attains, as demonstrated by simulations, good error performance within ~0.5dB from capacity at block length of n = 100,000 symbols. The paper also discusses convergence results and implementation considerations.