gebhart/patrepeval huggingface dataset:
Cooperative Orthogonal Macromolecular Assemblies with Broad Spectrum Antiviral Activity, High Selectivity, and Resistance Mitigation (2016)

Treatment of viral infections continues to be elusive owing to the variance in virus structure (RNA, DNA, and enveloped and nonenveloped viruses) together with their ability to rapidly mutate and garner resistance. Here we report a general strategy to prevent viral infection using multifunctional macromolecules that were designed to have mannose moieties that compete with viruses for immune cells, and basic amine groups that block viral entry through electrostatic interactions and prevent viral replication by neutralizing the endosomal pH. We showed that cells treated with the antiviral polymers inhibited TIM receptors from trafficking virus, likely from electrostatic and hydrogen-bonding interactions, with EC50 values ranging from 2.6 to 6.8 mg/L, depending on the type of TIM receptors. Molecular docking computations revealed an unexpected, and general, specific hydrogen-bonding interactions with viral surface proteins, and virus and cell binding assay demonstrated a significant reduction in infection after incubating virus or cells with the antiviral polymers. Moreover, the mannose-functionalized macromolecules effectively prevented the virus from infecting the immune cells. Representative viruses from each category including dengue, influenza, Chikungunya, Enterovirus 71, Ebola, Marburg, and herpes simplex were surveyed, and viral infection was effectively prevented at polymer concentrations as low as 0.2 mg/L with very high selectivity (>5000) over mammalian cells. The generality of these cooperative orthogonal interactions (electrostatic and hydrogen-bonding) provides broad-spectrum antiviral activity. As the antiviral mechanism is based on nonspecific supramolecular interactions between the amino acid residues and mannose/cationic moieties of the macromolecule, the ability to form the virus–polymer and polymer−cell assemblies can occur regardless of viral mutation, preventing drug resistance development.
Cover Picture: Using a Core–Sheath Distribution of Surface Chemistry through 3D Tissue Engineering Scaffolds to Control Cell Ingress (Adv. Mater. 11/2006) (2006)

Abstract The cover image shows a section through a 3D microcomputed‐tomography reconstruction of a porous polymer tissue‐engineering scaffold. Fibroblast cells (red) are encouraged to populate the interior of the disc by using a core/sheath distribution of plasma polymer (pp) coating. The background shows the cells on a flat surface, where their preference for adhesion to the pp allylamine surface (left) adjacent to a pp hexane (right) surface is readily apparent. This report by Alexander and co‐workers on p. 1406 is the first of cellular guidance within porous scaffolds using plasma polymerization, a coating method readily transferable to other scaffold materials.
Broadband image sensors for biomedical, security, and automotive applications (2007)

Detectors (sensor) having detection capability ranging from visible to near-infrared region are very much required for multi-color image sensor, necessary for next generation bio-medical, bio-chem(ical), and security applications. The capability of using broadband detection in a single sensor would help to receive real-time imaging not detectable using today's CCD or CMOS sensor. We proposed a detector structure as a single sensor element (pixel) having the detection capability ranging from visible to 1.7 &mu;m, wavelengths requiring in bio-chem, biomedical cell detection and security application. This invited paper has two-fold objectives: (a) provide a comprehensive overview of conventional photo detectors array (focal-plan array) and their types, being used in today's imaging, and (b) introduce a development of multi-color detector array (image sensor) which authors pioneered. The features of proposed multi-color detector are simple structure, low-cost, high quantum efficiency, high sensitivity, and high speed. Performance results so far attained will be presented along with its possible applications.
Association of a polymorphic variant of the Werner helicase gene with myocardial infarction in a Japanese population (1997)

The Werner syndrome (WS) is a rare autosomal recessive progeroid syndrome characterized by the premature onset of multiple age-related disorders, including atherosclerosis, cancer, non-insulin-dependent diabetes mellitus (NIDDM), ocular cataracts and osteoporosis [Epstein et al., 1966]. The major cause of death (at a median age of 47) is myocardial infarction (MI) [Epstein et al., 1966]. The WS mutation involves a member (WRN) of the RecQ family of helicases and may perturb DNA replication, repair, recombination, transcription, or chromosomal segregation [Yu et al., 1996]. We now report data on 149 MI cases and age-matched controls suggesting that a polymorphic WRN variant is associated with increased risk for MI. Based on our data, homozygosity for a cysteine at amino acid 1367 (the most prevalent genotype) predicts a 2.78 times greater risk of MI (95% confidence intervals: 1.23 to 6.86). The variant was not significantly associated with NIDDM. The two alleles (cysteine vs. arginine) could influence helicase activity, turnover, macromolecular interactions or, alternatively, could be markers for haplotypes influencing WRN regulation or reflecting gene action at linked loci. However, given the caveats implicit in genetic association studies, it is imperative that the present results be replicated in independent populations.
Anomalous doping behavior of in situ boron-doped polycrystalline silicon deposited by ultrahigh vacuum chemical vapor deposition (1993)

The deposition of in situ heavily boron-doped polycrystalline silicon (poly-Si) films was studied using an ultrahigh vacuum/chemical vapor deposition system. Fully activated carrier concentrations up to 3×1020 cm−3 were obtained for the as-deposited films grown at 550 °C. For boron concentration beyond this level, the crystallinity of poly-Si films degraded with increasing boron concentration, which resulted in an anomalous rise in resistivity. This crystallinity degradation occurred at a higher rate for films grown on a SiO2 surface than those grown on an undoped poly-Si surface. It is attributed to the preferential adsorption of boron atoms on the SiO2 surface. Under a high B2H6 flux condition, a large amount of boron atoms would accumulate on the SiO2 surface before the formation of Si nuclei, and thus disturbs the subsequent film deposition and grain growth processes.
Micromolar biosensing of nitric oxide using myoglobin immobilized in a synthetic silk film (2014)

In this work we investigate the use of coiled-coil silk proteins, produced in recombinant Escherichia coli, as a new material for immobilizing biosensors. Myoglobin was embedded in transparent honeybee silk protein films. Immobilized myoglobin maintained a high affinity for nitric oxide (KD NO=52 µM) and good sensitivity with a limit of detection of 5 µM. The immobilized myoglobin-silk protein film was stable and could be stored as a dry film at room temperature for at least 60 days. The effect of immobilization on the structure of myoglobin was fully investigated using UV/visible, Fourier Transform Infrared and Raman spectroscopy, which indicated a weakening in the strength of the iron-histidine bond. This study demonstrates that recombinant coiled-coil silk proteins provide a safe and environmentally friendly alternative to sol-gels for stabilizing heme proteins for use as optical biosensors.
ChemInform Abstract: Ligand Perturbation of the Molecular and Electronic Structures of Quadruply Bonded Dimers. The Crystal Structures of Mo2Br4(PMe3)4 and Mo2I4(PMe3)4, and the Vibrational and Electronic Spectra of a Series of M2X4L4 Complexes. (1987)

Abstract The ligand dependence of the molecular and electronic structures of the title dimers (I) are investigated by evaluating four fingerprint experimental parameters: metal‐metal distance and stretching frequency, and 1(δ → δ*) transition energy and intensity.
Polarization-independent strong Bragg gratings in Planar Lightwave Circuits from ArF laser irradiation through a phase mask. (1997)

Highly functional Planar Lightwave Circuits (PLC) can be designed using silica-on-silicon waveguide technology, 1 and the possibility of writing Bragg gratings in such waveguides further enhances their potential uses. 2 Strong Bragg gratings photoinduced in planar silica-on-silicon waveguides with a germanium-doped core are usually obtained by high pressure hydrogen loading of the glass prior to exposure. 2 , 3 In the work presented here we demonstrate that hydrogen loading is not necessary when high intensity light at 193 nm from an ArF laser is used to produce the index change, an effect originally observed in germanium-doped optical fibers. 4 , 5 The waveguides used are standard PLCs with a core index difference (Δ) of 0.75% (commercially available) and 1%. 1 One drawback of silica-on-silicon waveguides is their small strain birefringence. 6 , 7 We show here that there is a sizeable birefringence in the ArF laser-induced average index change that is large enough and of the proper sign to compensate for the initial waveguide birefringence. For demonstration, 4 mm-long Bragg grating filters with more than 30 dB of transmission loss at the Bragg wavelength are presented.
In situ 13 C solid‐state polarization transfer NMR to follow starch transformations in food (2022)

Convenience food products tend to alter their quality and texture while stored. Texture-giving food components are often starch-rich ingredients, such as pasta or rice. Starch transforms depending on time, temperature and water content, which alters the properties of products. Monitoring these transformations, which are associated with a change in mobility of the starch chain segments, could optimize the quality of food products containing multiple ingredients. In order to do so, we applied a simple and efficient in situ <sup>13</sup> C solid-state magic angle spinning (MAS) NMR approach, based on two different polarization transfer schemes, cross polarization (CP) and insensitive nuclei enhanced by polarization transfer (INEPT). The efficiency of the CP and INEPT transfer depends strongly on the mobility of chain segments-the time scale of reorientation of the CH-bond and the order parameter. Rigid crystalline or amorphous starch chains give rise to CP peaks, whereas mobile gelatinized starch chains appear as INEPT peaks. Comparing <sup>13</sup> C solid-state MAS NMR experiments based on CP and INEPT allows insight into the progress of gelatinization, and other starch transformations, by reporting on both rigid and mobile starch chains simultaneously with atomic resolution by the <sup>13</sup> C chemical shift. In conjunction with <sup>1</sup> H solid-state MAS NMR, complementary information about other food components present at low concentration, such as lipids and protein, can be obtained. We demonstrate our approach on starch-based products and commercial pasta as a function of temperature and storage.
Information System for ALICE Experiment Data Access (2018)

The main goal of this paper is the presentation of Dcs ARchive MAnager for ALICE Experiment detector conditions data (DARMA), which is the updated version of the AMANDA 3 software currently used within ALICE experiment at CERN. The typical user of this system is either a physicist who performs further analysis on data acquired during the operation of the ALICE detector or an engineer, who analyzes the detector status between iterations of experiments. Based on the experience with the current system, the updated version aims to simplify the overall complexity of the previous version, which leads to simpler implementation, administration and portability of the system without sacrificing the functionality. DARMA is realized as an ASP. NET web page based on Model-View-Controller architecture and this paper provides a closer look at the design phase of the new backend structure in comparison to previous solution as well as the description of individual modules of the system.
Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae (2011)

For years, micro-organisms have been used for the industrial production of heterologous proteins. However, the production of foreign proteins causes undesirable problems for the host organism. The analysis of this phenomenon is desirable to improve the production of relevant proteins and so far no analysis of the effects of recombinant protein production on genetic regulation has been reported. In this work, network component analysis (NCA) was used to deduce transcription factor activities (TFAs) in a recombinant strain of Saccharomyces cerevisiae that produces a foreign protein, human superoxide dismutase (SOD) and compared the behavior of this yeast strain to the wild-type host to see the effect of the expression of the protein at the regulatory level. NCA identified a network of 817 genes regulated by 87 transcription factors (TFs). From the identified TFs, 45 show significant change in their activities at least in one of the three phases of diauxic growth (glucose, ethanol, and early stationary phase). The major effect of the expression of SOD on the activity of the TFs was observed in the early stationary phase with 34 of them perturbed in comparison with 12 on glucose and 20 on ethanol. These TFs cover the main functions of the cell, such as developmental processes, cell cycle, metabolism, and environmental response. Five of them are present in all growth phases: Hal9, Mac1, Oaf3, Stp1, and Urc2. In addition, TFA analysis corroborates the hypothesis that copper plays a key role as a stress factor and suggests that YJL206C, a TF with unknown function, could be related to Ace2, a cell cycle regulator.
Effect of Tetracalcium Dimagnesium Phytate on Bone Characteristics in Ovariectomized Rats (2010)

The aim was to evaluate the influence of dietary Ca-Mg-phytate consumption on the bone characteristics of ovariectomized rats, an animal model for postmenopausal osteoporosis. Twenty ovariectomized female Wistar rats were randomly assigned to two groups fed, respectively, with a non-phytate diet (AIN-76A) or the same diet enriched with 1% phytate (as the calcium magnesium salt, phytin). After 12 weeks of feeding the rats were sacrificed, and both femoral bones and L4 vertebra were removed from each rat. Bone mass, length, width, volume, and mineral density were measured, and the phosphorus, calcium, magnesium, and zinc contents of bones were determined. Deoxypyridinoline (a bone resorption marker) was measured in urine, and osteocalcin (a bone formation marker) was measured in serum. The calcium and phosphorus contents and bone mineral density were significantly higher in both femoral bones and L4 vertebra for phytate-treated rats in comparison to rats in the non-phytate group. Deoxypyridinoline was significantly increased in rats in the non-phytate treatment group. Ca-Mg-phytate consumption reduces bone mineral density loss due to estrogen deficiency. Thus, phytate exhibits effects similar to those of bisphosphonates on bone resorption and may be of use in the primary prevention of osteoporosis if larger studies in humans confirm these findings.
Anisotropic thermal expansion of Ni, Pd and Pt germanides and silicides (2016)

Silicon or germanium-based transistors are nowadays used in direct contact with silicide or germanide crystalline alloys for semiconductor device applications. Since these compounds are formed at elevated temperatures, accurate knowledge of the thermal expansion of both substrate and the contact is important to address temperature depending effects such as thermal stress. Here we report the linear coefficients of thermal expansion of Ni-, Pd- and Pt-based mono-germanides, mono-silicides and di-metal-silicides as determined by powder-based x-ray diffraction between 300 and 1225 K. The investigated mono-metallic compounds, all sharing the MnP crystal structure, as well as Pd2Si and Pt2Si exhibit anisotropic expansion. By consequence, this anisotropic behaviour should be taken into account for evaluating the crystal unit's cell at elevated temperatures.
Interface State Density of Single Vertical Nanowire MOS Capacitors (2013)

An investigation of trap states at the semiconductor-oxide interface of single silicon nanowires is presented using vertical gate-all-around nanowire MOS capacitors. By performing highly accurate capacitance-voltage measurements at room temperature, the energetic distribution of interface traps <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> could be extracted with the quasi-static method. Although the capacitance of a single nanowire MOS capacitor with Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> gate oxide is only 2 fF, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> values were obtained with good reproducibility. For etched, vertical Si nanowires, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> in the range of (4 ±1) × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> eV <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> was obtained.
Long-pulse relativistic backward wave oscillator operation utilizing a disk cathode (2001)

It has been a tradition for pulsed power-driven intense high power microwave (HPM) sources utilizing thin-walled annular electron beams to generate such beams from a "cookie cutter" geometry cathode made from either graphite or stainless steel. When such beams are produced for pulse durations exceeding 100 ns, the accompanying microwave generation process terminates much earlier in time than the electron beam current pulse. It has been postulated that the electron beam halo caused by radial expansion of the beam is the cause of pulse shortening in the University of New Mexico (UNM) long-pulse backward wave oscillator (BWO). Recent work by Loza and colleagues has demonstrated the ability to generate intense annular electron beams of 1 /spl mu/s duration without any radial beam expansion. This was accomplished utilizing a solid disk cathode. At UNM we have integrated a disk cathode in our long-pulse BWO and have demonstrated significant lengthening of the HPM pulse.
Supplementary Figure Legends from Characterization of LY3023414, a Novel PI3K/mTOR Dual Inhibitor Eliciting Transient Target Modulation to Impede Tumor Growth (2023)

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Molecular characterisation of isogenic taxane resistant cell lines identify novel drivers of drug resistance (2014)

This study established a model system for examining taxane resistance and demonstrated that both MDR and mitosis represent common mechanism of taxane resistance.
Genetic tracing of the gustatory neural pathway originating from Pkd1l3‐expressing type III taste cells in circumvallate and foliate papillae (2011)

Polycystic kidney disease 1-like 3 (Pkd1l3) is expressed specifically in sour-sensing type III taste cells that have synaptic contacts with afferent nerve fibers in circumvallate (CvP) and foliate papillae (FoP) located in the posterior region of the tongue, although not in fungiform papillae (FuP) or the palate. To visualize the gustatory neural pathways that originate from type III taste cells in CvP and FoP, we established transgenic mouse lines that express the transneuronal tracer wheat germ agglutinin (WGA) under the control of the mouse Pkd1l3 gene promoter/enhancer. The WGA transgene was accurately expressed in Pkd1l3-expressing type III taste cells in CvP and FoP. Punctate WGA protein signals appeared to be detected specifically in type III taste cells but not in other types of taste cells. WGA protein was transferred primarily to a subset of neurons located in close proximity to the glossopharyngeal (GL) nerve bundles in the nodose/petrosal ganglion (NPG). WGA signals were also observed in a small population of neurons in the geniculate ganglion (GG). This result demonstrates the anatomical connection between taste receptor cells (TRCs) in the FoP and the chorda tympani (CT) nerves. WGA protein was further conveyed to neurons in a rostro-central subdivision of the nucleus of the solitary tract (NST). These findings demonstrate that the approximately 10 kb 5'-flanking region of the mouse Pkd1l3 gene functions as a type III taste cell-specific promoter/enhancer. In addition, experiments using the pkd1l3-WGA transgenic mice reveal a sour gustatory pathway that originates from TRCs in the posterior region of the tongue.
Development of a planar waveguide microarray for the monitoring and early detection of five harmful algal toxins in water and cultures (2015)

A novel multiplex microarray has been developed for the detection of five groups of harmful algal and cyanobacterial toxins found in marine, brackish, and freshwater environments including domoic acid (DA), okadaic acid (OA, and analogues), saxitoxin (STX, and analogues), cylindrospermopsin (CYN) and microcystins (MC, and analogues). The sensitivity and specificity were determined and feasibility to be used as a screening tool investigated. Results for algal/cyanobacterial cultures (n = 12) and seawater samples (n = 33) were compared to conventional analytical methods, such as high performance liquid chromatography (HPLC) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Detection limits for the 15 min assay were 0.37, 0.44, 0.05, 0.08, and 0.40 ng/mL for DA, OA, STX, CYN, and MC, respectively. The correlation of data obtained from the microarray compared to conventional analysis for the 12 cultures was r2 = 0.83. Analysis of seawater samples showed that 82, 82, 70, 82, and 12% of samples wer...
Determination of Significant Parameters for Eye Injury Risk from Projectiles (2005)

Background: Eye injuries affect a large proportion of the population and are expensive to treat. This article presents a parametric analysis of experimental data to determine the most significant factors for predicting ocular injuries or tissue lesions. Methods: Using logistic regression, statistical values were generated to determine significant projectile characteristics for predicting ocular injury in published studies. Projectiles included BBs, metal rods, and foam particles with velocities ranging from 2 m/s to 122 m/s. Results: A normalized energy (energy per projected area) value was found as the best predictor for ocular injury. Using this predictor, a 50% injury risk of corneal abrasion, lens dislocation, hyphema, retinal damage, and globe rupture was found to be 1,503 kg/s2, 19,194 kg/s2, 20,188 kg/s2, 30,351 kg/s2, and 23,771 kg/s2, respectively. Conclusion: Normalized energy was the most significant predictor of injury type and tissue lesion. This finding is of great value for history-taking management triaging and as a design aid to minimize the risk of ocular injury for consumer products.