gebhart/patrepeval huggingface dataset:
Monte Carlo simulation of topographic contrast in scanning ion microscope (2004)

Topographic contrast of secondary-electron (SE) images in a scanning ion microscope (SIM) using a focused gallium (Ga) ion beam is investigated by Monte Carlo simulation. The SE yield of heavy materials, in particular, due to the impact of 30 keV Ga ions increases much faster than for the impact of electrons at < or =10 keV as a function of the angle of incidence of the primary beam. This indicates the topographic contrast for heavy materials is clearer in a SIM image than in a scanning electron microscope (SEM) image; for light materials both contrasts are similar to each other. Semicircular rods with different radii and steps with large heights and a small wall angle, made of Si and Au, are modeled for comparison with SE images in SEM. Line profiles of the SE intensity and pseudo-images constructed from the profiles reveal some differences of the topographic contrast between SIM and SEM. We discuss not only the incident-angle effect on the contrast, but also the effects of re-entrances of primary particles and SEs to the neighboring surface, the effect of a sharp edge on the sample surface, and the effects of pattern size and beam size.
Single-mode laser emission from a multimode core surrounded by a tailored cladding (2008)

paper CMB3
Membrane-Interacting Antifungal Peptides (2021)

The incidence of invasive fungal infections is increasing worldwide, resulting in more than 1.6 million deaths every year. Due to growing antifungal drug resistance and the limited number of currently used antimycotics, there is a clear need for novel antifungal strategies. In this context, great potential is attributed to antimicrobial peptides (AMPs) that are part of the innate immune system of organisms. These peptides are known for their broad-spectrum activity that can be directed toward bacteria, fungi, viruses, and/or even cancer cells. Some AMPs act via rapid physical disruption of microbial cell membranes at high concentrations causing cell leakage and cell death. However, more complex mechanisms are also observed, such as interaction with specific lipids, production of reactive oxygen species, programmed cell death, and autophagy. This review summarizes the structure and mode of action of antifungal AMPs, thereby focusing on their interaction with fungal membranes.
A novel micro pressurized liquid extraction method for very rapid solid sample preparation (2015)

A novel micro pressurized liquid extraction (μPLE) method is introduced, which employs rapid heating in a static mode to remove analytes from 5–10 mg samples in as little as 10 seconds using only 125 μL of solvent.
Site-Specific Cross-Linking of Proteins through Tyrosine Hexahistidine Tags (2005)

The genetic addition of hexahistidine (H(6)) tags is widely used to isolate recombinant proteins by immobilized metal-affinity chromatography (IMAC). Addition of a tyrosine residue to H(6) tags enabled proteins to be covalently cross-linked under mild conditions in a manner similar to the natural, site-specific cross-linking of tyrosines into dityrosine. A series of seven hexahistidine tags with tyrosines placed in various positions (H(6)Y tags) were added to the amino terminus of the I28 immunoglobulin domain of the human cardiac titin. The H(6)Y-tagged I28 dimerized in the presence of excess Ni(2+) with a K(D) of 200 microM. Treatment of Ni(2+)-dimerized H(6)Y-I28 with an oxidant, monoperoxyphthalic acid (MMPP) or sodium sulfite, resulted in covalent protein multimerization through chelated Ni(2+)-catalyzed cross-linking of the Y residues engineered into the H(6) tag. The protein oligomerization was observed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). The presence of dityrosine in the cross-linked proteins was confirmed by fluorescence emission at 410 nm. Proteins lacking the Y residue in the H(6) tag treated with the same oxidative conditions did not cross-link or exhibit dityrosine fluorescence, despite the presence of an endogenous Y residue. The method may have potential uses in other protein conjugation applications such as protein labeling and interfacial immobilization of proteins on artificial surfaces.
Interoperability for information systems in public urban transport security: The SECUR-ED interoperability notation. (2012)

In public transport and at large urban hubs, such as metro or train stations, transport operators and first responders collaborate in the prevention of and reaction to security issues. Within the EU demonstration project SECUR-ED a specific notation for interoperability of information systems in the domain of public transport security was developed. (In this context, the interoperability of actual operating systems is not the focus.) Based on UML (Unified Modelling Language), the notation language offers the possibility for structured modelling of system-of-systems architectures. Four interoperability object templates and their interdependencies form the underlying basis. Domain-specific annotation rules and guidelines for interoperability objects and their sub-component structures allow collaboration and interpretation of this model on various granularities and stages during a systems engineering process.
Operando X-ray Tomography Imaging of Solid-State Electrolyte Response to Li Evolution under Realistic Operating Conditions (2021)

Solid-state Li-ion conductors are a next-generation battery technology that are particularly promising for electric vehicles, offering the capacitive benefits of Li metal anodes with nonflammable electrolytes. Microstructural evolution in these solid-state batteries, especially the Li anode, requires deeper understanding of the conditions under which certain undesired behaviors are more likely to occur. This study utilizes operando X-ray computed tomography to visualize the behavior of lithium in response to device operation, considering variables that are relevant to a realistic battery: stack pressure, microscale defects such as pores, and temperature. This work demonstrates that experimental and operational conditions, especially temperature, affect the fundamental driving forces of realistic solid electrolyte systems and provides visual insight into possible mechanisms of Li migration. In particular, the effect of these variables on Li propagation from the anode through pre-existing defects and Li nucleation within the imperfectly electron-insulating electrolyte is highlighted.
Parallel turbo-TCM schemes using recursive convolutional GF(2<sup>N</sup>) encoders over frequency non-selective fading channel (2010)

In this paper, recursive convolutional encoders over Galois field GF(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sup> ) are used as constituent codes in a parallel turbo trellis coded modulation (turbo TCM) scheme. These encoders are designed using the nonlinear left-circulate (LCIRC) function. The LCIRC function performs a bit left circulation over the representation word. An optimum 1-delay GF(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sup> ) recursive convolutional encoder scheme using LCIRC (RC-LCIRC) is proposed for phase shift keying - trellis-coded modulation (PSK-TCM) schemes. The minimum Euclidian distance is estimated for these PSK-TCM schemes and it is shown that these structures offer the maximum coding gains. As advantage, the RC-LCIRC encoders are less complex than the corresponding binary encoders for a fixed encoding rate. The parallel turbo TCM transmission schemes with optimum RC-LCIRC encoder as component encoder are investigated using the iterative symbol-by-symbol log-MAP algorithm in the receiver. The considered modulations schemes are 8-PSK and 16-quadrature amplitude modulation (16-QAM). The bit error rate (BER) is estimated by simulation for the proposed turbo TCM transmissions over a frequency non-selective fading channel with additive white Gaussian noise (AWGN). The simulation results are similar to the conventional turbo TCM schemes.
Terahertz pioneers: A series of interviews with significant contributors to terahertz science and technology (2011)

As a tribute to individuals who have contributed significantly, and over many years, to the terahertz community, and as a guide and inspiration for those who are just beginning their professional association with this field of study, this TRANSACTIONS will continue to include, on a regular basis, a series of biographical interviews with technical researchers who have appreciably impacted the THz community in a positive manner. In order to go beyond a strict technical review and to take better advantage of the information and commentary only available through a direct discussion, these articles will take on a less formal style than the research articles that can be found within the remaining pages of the transactions. The Editor-in-Chief (EiC) hopes that he may be given some leeway in this regard, for the benefit of communicating more fully the character, experiences, and historic circumstances that have shaped our community and set the directions for our collective research. The EiC, with the support of the IEEE MTT Publications Committee, has chosen to incorporate these biographical articles within the more formal technical journal because of the diversity of disciplines that make up the THz community and the prior absence of a single unifying publication with sufficient outreach to extend across the whole of the RF and optical THz disciplines. The EiC hopes you will enjoy the short diversion of reading these articles as much as he himself enjoys the process of composing them. As the third article in this series, he has spoken with an individual whose experience with THz sources and detectors started in 1955 at what was to become the Royal Radar Establishment in Malvern, UK. That experience is still being tapped today. At age 79, Maurice FitzGerald Kimmitt has just put the finishing touches on a new book on Terahertz Techniques that he has completed with colleagues Erik Brundermann and Heinz-Wilhelm Hubers.
Characterization of an Extremely Thermostable Restriction Enzyme, <i>Psp</i> GI, from a <i>Pyrococcus</i> Strain and Cloning of the <i>Psp</i> GI Restriction-Modification System in <i>Escherichia coli</i> (1998)

An extremely thermostable restriction endonuclease, PspGI, was purified from Pyrococcus sp. strain GI-H. PspGI is an isoschizomer of EcoRII and cleaves DNA before the first C in the sequence 5' CCWGG 3' (W is A or T). PspGI digestion can be carried out at 65 to 85 degrees C. To express PspGI at high levels, the PspGI restriction-modification genes (pspGIR and pspGIM) were cloned in Escherichia coli. M.PspGI contains the conserved sequence motifs of alpha-aminomethyltransferases; therefore, it must be an N4-cytosine methylase. M.PspGI shows 53% similarity to (44% identity with) its isoschizomer, M.MvaI from Micrococcus variabilis. In a segment of 87 amino acid residues, PspGI shows significant sequence similarity to EcoRII and to regions of SsoII and StyD4I which have a closely related recognition sequence (5' CCNGG 3'). PspGI was expressed in E. coli via a T7 expression system. Recombinant PspGI was purified to near homogeneity and had a half-life of 2 h at 95 degrees C. PspGI remained active following 30 cycles of thermocycling; thus, it can be used in DNA-based diagnostic applications.
HIV sequence databases. (2003)

Two important databases are often used in HIV genetic research, the HIV Sequence Database in Los Alamos, which collects all sequences and focuses on annotation and data analysis, and the HIV RT/Protease Sequence Database in Stanford, which collects sequences associated with the development of viral resistance against anti-retroviral drugs and focuses on analysis of those sequences. The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail.
Lipase-Catalyzed Poly(glycerol-1,8-octanediol-sebacate): Biomaterial Engineering by Combining Compositional and Crosslinking Variables (2022)

This study examined poly(glycerol-1,8-octanediol-sebacate) (PGOS) copolymers with low-level substitution of O (1,8-octanediol) for G (glycerol) units (G/O ratios 0.5:0.5, 0.66:0.33, 0.75:0.25, 0.8:0.2, and 0.91:0.09) prepared in bulk by immobilized <i>Candida antarctica</i> Lipase B (N435) catalysis. The central question explored was the extent that exchanging less than half of poly(glycerol sebacate) (PGS) glycerol units with 1,8-octanediol can be used as a strategy to fine-tune biomaterial properties. Synthesized copolymers having G/O ratios of 0.66:0.33, 0.75:0.25, 0.8:0.2, and 0.91:0.09 have similar molecular weights, where <i>M</i><sub>w</sub> varied from 52,800 to 63,800 g/mol, <i>M</i><sub>n</sub> varied from 5100 to 6450 g/mol, and Đ<sub>M</sub> (molecular mass dispersity, <i>M</i><sub>w</sub>/<i>M</i><sub>n</sub>) values were also similar (8.4-11.4). All of the copolymers were branched, and dendritic glycerol units reached 11% for PGOS-0.91:0.09:1.0. Analysis of DSC second heating scans revealed that copolymers with higher 1,8-octanediol contents have relatively higher <i>T</i><sub>m</sub> and Δ<i>H</i><sub>f</sub> values. Over the copolymer compositional range studied herein, <i>T</i><sub>m</sub> and Δ<i>H</i><sub>f</sub> values varied from 5.3 to 21.1 °C and 8.0 to 23.1 J/g, respectively. Stress-strain curves of PGOS copolymers cured at 140 °C for 48 h exhibited either a unimodal, bimodal, or trimodal response to tensile loading. Varying G/O from 10:1 to 2:1 resulted in significant increases in the peak stress (0.26-4.01 MPa), preyield modulus (0.65-62.59 MPa), failure to strain (64-110%), and failure toughness (0.1-0.56 MPa). This demonstrates that altering the G/O ratio over a narrow compositional range provides biomaterials with widely different yet tunable mechanical properties. Further investigation of PGOS-0.75:0.25:1.0 films revealed that varying the cure conditions from 120 to 160 °C for periods of 24-72 h provides access to biomaterials with a failure strain range from 15 to 224% and Young's modulus from 1.17 to 10.85 MPa. Hence, using the dual variables of compositional variation and changes in cure conditions provides an exciting platform for PGS analogues to optimize material-tissue interactions. Increased contents of 1,8-octanediol slowed <i>in vitro</i> degradation. Slowed degradation of PGOS relative to PGS will be valuable for use in slower healing wounds.
A synthetic oligo library and sequencing approach reveals an insulation mechanism encoded within bacterial σ <sup>54</sup> promoters (2016)

Summary We use an oligonucleotide library of over 10000 variants together with a synthetic biology approach to identify an insulation mechanism encoded within a subset of σ 54 promoters. Insulation manifests itself as dramatically reduced protein expression for a downstream gene that may be expressed by transcriptional read-through. The insulation we observe is strongly associated with the presence of short CT-rich motifs (3-5 bp), positioned within 25 bp upstream of the Shine-Dalgarno (SD) motif of the silenced gene. We hypothesize that insulation is effected by binding of the RBS to the upstream CT-rich motif. We provide evidence to support this hypothesis using mutations to the CT-rich motif and gene expression measurements on multiple sequence variants. Modelling is also consistent with this hypothesis. We show that the strength of the silencing, effected by insulation, depends on the location and number of CT-rich motifs encoded within the promoters. Finally, we show that in E.coli these insulator sequences are preferentially encoded within σ 54 promoters as compared to other promoter types, suggesting a regulatory role for these sequences in natural contexts. Our findings suggest that context-related regulatory effects may often be due to sequence-specific interactions encoded sparsely by short motifs that are not easily detected by lower throughput studies. Such short sequence-specific phenomena can be uncovered with a focused OL design that filters out the sequence noise, as exemplified herein.
Collimation Of Diode Laser Arrays Using Etched Cylindrical Computer-Generated Holographic Lenses (1989)

This paper describes the fabrication of computer-generated holographic lenses in fused silica; the lenses are designed to collimate the output beams of diode lasers. The lenses are cylindrical to collimate the beams in one direction at a time and to maximize the fill factor in the laser array. The lens patterns were written into resist on the substrate using an electron beam. The lenses were transferred to the fused silica substrate via reactive ion etching. Two layers of etching were demonstrated.
Polarimetry of Light using Analysis of the Nonlinear Voltage-retardance Relationship for Liquid-crystal Variable Retarders (2017)

We present a method for using liquid-crystal variable retarders (LCVR's) with continually varying voltage to measure, both, the Stokes vector of a light beam and the complete Mueller matrix of a general sample.
Relationship between baseline resting diastolic function and exercise capacity in patients with hypertrophic cardiomyopathy undergoing treadmill stress echocardiography: a cohort study (2012)

Although baseline DD is common in patients with HCM, it does not predict maximal METs achieved beyond traditional risk factors.
Deletion of<i>Plasmodium berghei</i>-specific CD4<sup>+</sup>T cells adoptively transferred into recipient mice after challenge with homologous parasite (1998)

The immune response to malaria parasites includes T cell responses that reduce parasites by effector T cell responses and by providing help for antibody responses. Some parasites are more sensitive to antibody and others are more sensitive to cell-mediated immunity. We demonstrate that cultured CD4(+) T cells that produce interferon gamma and interleukin 2, but not interleukin 4, in response to stimulation with the rodent parasite Plasmodium berghei can reduce but not eliminate parasites in vivo after adoptive transfer. Although cells can persist in vivo for up to 9 months in uninfected mice, infection results in elimination of up to 99% of specific T cells in different tissues, as judged by tracking T cells labeled with the fluorescent dye 5-(and -6)-carboxyfluorescein diacetate succinimidyl ester. T cells specific for ovalbumin are unaffected. In vivo activation and division of transferred T cells per se are not responsible for deletion because T cells positive for 5-(and -6)-carboxyfluorescein diacetate succinimidyl ester divide up to six times within 7 days in uninfected mice and are not deleted. Understanding the factors responsible for parasite-mediated specific deletion of T cells would enhance our knowledge of parasite immunity.
CodeStruct: Design and Evaluation of an Intermediary Programming Environment for Novices to Transition from Scratch to Python (2022)

Transitioning from block-based programming environments to conventional text-based programming languages is a challenge faced by many learners as they progress in their computer science education. In this paper, we introduce CodeStruct, a new intermediary programming environment for novices designed to support children who have prior experience with block-based programming to ease the eventual transition to text-based programming. We describe the development of CodeStruct and its key design features. We then present the results from a two-week long programming class with 26 high school students (ages 12-16; M=14 years) investigating how CodeStruct supported learners in transitioning from Scratch to Python. Our findings reveal how learners used the scaffolds designed into CodeStruct to support their transition from blocks to text, and that transitioning to CodeStruct reduced completion time (1.98x) and help requests (4.63x) when compared to transitioning directly to Python. Finally, learners that used CodeStruct, performed equally well (and slightly better in 10/16 programming activities) in their final transition to fully text-based Python programming.
KTa_1-x Nb_x O_3 ferroelectric thin films grown by pulsed laser deposition on various substrates (2006)

National audience
Fact or Fiction - Hunchback hypothesis_JESP Pre_reg (2015)

In this investigation we test the existence of the 'Hunchback Stereotype' and then test whether it matches reality or not. Hunchback stereotype is the tendency for perceivers to overestimate the emotional expressivity of members of low status groups compared to their higher status counterparts.
The plant glycosyltransferase clone collection for functional genomics (2014)

The glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate-Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell-wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full-length coding sequences without termination codons and are Gateway® compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.
Does Soccer Headgear Attenuate the Impact When Heading a Soccer Ball? (2003)

There is increasing concern that repetitive blows to the head, such as those from heading a soccer ball, can cause measurable cognitive impairment. Reducing acceleration of impact could reduce neurologic sequelae.To measure the effectiveness of four different types of soccer headgear in reducing the acceleration of impact.A standard magnesium headform was instrumented with a triaxial accelerometer. A soccer ball was propelled at the headform at three different speeds known to occur in soccer play: 9, 12, and 15 m/sec (20, 26, and 34 mph). The main outcome was the peak acceleration of the headform associated with these impacts with and without protective headgear.Peak accelerations were found in a range from 144 m/s(2) to 289 m/s(2) (14.67-29.5 G, G = 9.81 m/s(2)). Using multivariate analysis of variance (MANOVA) methods to compare the headbands and controls, there was no significant difference in the measured accelerations at the center of gravity with or without headgear (p = 0.50). However, the interaction term of headbands, pressure, and speed was significant at F = 5.51 and p = 0.00001. Using contrasts within conditions, some headbands were found to cause a decrease in peak acceleration at the highest speed and pressure.Currently available headgear for soccer heading shows little ability to attenuate impact during simulated soccer heading. However, statistically significant decreases are present at the highest speeds and pressures tested, suggesting the headbands may play a role in decreasing impact for more forceful blows.