gebhart/patrepeval huggingface dataset:
DNA‐Linked Nanoparticle Building Blocks for Programmable Matter (2011)

One step at a time: DNA linkers were placed at defined locations and in defined 3D orientations on a colloidal nanoparticle. Because the implemented ligand-replacement strategy was carried out sequentially, DNA linkers maximally segregated, producing a nanoparticle with linkers at 90 or 180° angles (see picture). These building blocks should enable assembly of anisotropic nanostructures with precisely designed geometry and complex functionality. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Lactobacilli intra-tracheal administration protects from Pseudomonas aeruginosa pulmonary infection in mice – a proof of concept (2019)

The spreading of antibiotic resistance is a major public health issue, which requires alternative treatments to antibiotics. Lactobacilli have shown abilities to prevent pneumonia in clinical studies when given by oral route, certainly through the gut-lung axis involvement. Rationally, respiratory administration of lactobacilli has been developed and studied in murine model, to prevent from respiratory pathogens. It allows a direct effect of probiotics into the respiratory system. To our knowledge, no study has ever focused on the effect of probiotic intra-respiratory administration to prevent from <i>Pseudomonas aeruginosa</i> (PA) pneumonia, a major respiratory pathogen associated with high morbidity rates. In this study, we evaluated the beneficial activity of three <i>Lactobacillus</i> strains (<i>Lactobacillus fermentum</i> K.C6.3.1E, <i>Lactobacillus zeae</i> Od.76, <i>Lactobacillus paracasei</i> ES.D.88) previously screened by ourselves and known to be particularly efficient <i>in vitro</i> in inhibiting PAO1 virulence factors. Cytotoxic assays in alveolar epithelial cell line A549 were performed, followed by the comparison of two lactobacilli prophylactic protocols (one or two administrations) by intra-tracheal administration in a C57BL/6 murine model of PA pneumonia. A549 cells viability was improved from 23 to 75% when lactobacilli were administered before PAO1 incubation, demonstrating a protective effect (<i>P<</i>0.001). A significant decrease of 2 log of PAO1 was observed 4 h after PAO1 instillation (3×10<sup>6</sup> cfu/mouse) in both groups receiving lactobacilli (9×10<sup>6</sup> cfu/mouse) compared to PAO1 group (<i>P</i><0.05). One single prophylactic administration of lactobacilli significantly decreased the secretion by 50% in bronchoalveolar lavages of interleukin (IL)-6 and tumour necrosis factor-α compared to PAO1. No difference of secretion was observed for the IL-10 secretion, whatever the prophylactic study design. This is the first study highlighting that direct lung administration of <i>Lactobacillus</i> strains protect against PA pneumonia. Next step will be to decipher the mechanisms involved before developing this novel approach for human applications.
Synthesis and Thrombolytic Activity of Carboline‐3‐carboxylic Acid Modified Metabolites of Ala‐Arg‐Pro‐Ala‐Lys (2004)

From the metabolism of H-Ala-Arg-Pro-Ala-Lys-OH, four metabolites, H-Pro-Ala-Lys-OH, H-Arg-Pro-Ala-Lys-OH, H-Ala-Arg-Pro-OH, and H-Ala-Arg-Pro-Ala-OH were identified. In order to find a new lead compound of thrombolytic peptide, 3S-1,2,3,4-tetrahydro-beta-carboline-3-carboxylic acid was introduced to the N- and C-terminal of the metabolites by use of the common coupling strategy. Under this condition, the pseudopeptides (5a-d and 7a-d) were obtained with a good yield. The thrombolytic activities of 3S-1,2,3,4-tetrahydro-beta-carboline-3-carboxylic acid containing oligopeptides were evaluated in vitro and in vivo. The result indicated that the thrombolytic activity of the pseudopeptide depended on the sequence and the modification pattern of the metabolites, and only when 3S-1,2,3,4-tetrahydro-beta-carboline-3-carboxylic acid was introduced into the C-terminal of H-Pro-Ala-Lys-OH or H-Arg-Pro-Ala-Lys-OH, the desirable thrombolytic activity was retained and enhanced significantly.
Oil Recovery by Sequential Waterflooding: the Effects of Aging at Residual Oil and Initial Water Saturation (2012)

Abstract Sequential waterflooding refers to cycles of flooding for which initial water saturation is re-established after a waterflood by flow of crude oil followed by further waterflooding. In previously reported examples of sequential waterflooding, cores were neither cleaned nor re-aged at high crude oil saturation between floods. Numerous core floods with different rock types showed significant decrease in residual oil saturation from one flood to the next (Loahardjo et al. 2010a). Systematic decrease in residual oil saturation by sequential waterflooding was confirmed by nuclear magnetic resonance imaging measurements of in-situ saturations (Loahardjo et al. 2010b). In this work, sequential waterflooding has been demonstrated for outcrop Berea sandstones of medium and low permeability: both showed reduction in residual oil saturation with each sequential flood. The tests have been extended to include aging periods at either residual oil saturation or initial water saturation. Aging at residual oil saturation (high water saturation) resulted in an increase in oil recovery for the subsequent flood, with larger increases observed for extended aging times. After an extended period of aging at initial water saturation (high oil saturation), decreased oil recovery was observed. The variations in oil recovery are consistent with changes in wettability that depend on oil saturation during displacement and subsequent aging conditions.
Recombination laser transitions in expanding plasmas of Mg, Ca, Cu, Zn, Ag, Cd, In, Sn, Pb, and Bi (1982)

Fifty new laser transitions in the visible and near infrared in ten metal vapors have been observed in the recombination phase of the expanding plasmas produced by a segmented-plasma laser device. Several of the strong visible transitions might be attractive for applications requiring simple lasers that operate at high repetition rates with pulse energies of the order of 0.1 mJ. All the transitions reported here suggest candidates for short-wavelength recombination lasers when isoelectronically scaled to higher ion stages.
Dispersion Penalty Reduction using a Optical Modulator with Adjustable Chirp (1991)

High bit-rate fiber transmission systems operating away from the zero-dispersion wavelength require transmitters with very low frequency chirp, such as those realized using lithium niobate waveguide electrooptic modulators [1], It has been proposed that waveguide Mach-Zehnder amplitude modulators may be operated in a perfectly chirpless mode and recently devices designed to operate chirp-free have been reported [2,3]. However, the lowest fiber dispersion penalty is generally not obtained for a frequency chirp parameter identically equal to zero [2], Indeed, it is expected that choosing a non-zero value for the chirp parameter, α, depending on the fiber dispersion coefficient and distance, so as to provide some amount of pulse compression, can be advantageous.
Unique antibody gene signature in Multiple Sclerosis (49.25) (2009)

Abstract Patients with multiple sclerosis (MS), an inflammatory, demyelinating disease of the Central Nervous System (CNS), derive the most benefit from disease modifying pharmacotherapies the earlier they are treated. Patients who have had a single episode of demyelination are at greater risk to develop clinically definite MS, but are not treated for MS, even though diagnosis of clinically definite MS could be significantly delayed if currently approved treatments are initiated immediately after the first attack. Defining biomarkers that identify patients with one demyelinating event who will convert to MS may provide a tool to allow earlier treatment of this "at risk" patient group. We have discovered a unique pattern of somatic mutations in the antibody genes of B cells isolated from the cerebrospinal fluid of patients with MS that can accurately and independently predict patients that subsequently develop definite MS after a single episode of demyelination. This antibody signature represents the first genetic biomarker candidate for MS outside of the MHC locus. If independently confirmed, our observations will have a major impact as a new diagnostic tool in patients with very early demyelinating disease of the CNS. This work was supported by the National Institutes of Health (NIH) to NLM (RO1 NS 40993) and MKR (RO1 NS 37513, RO1 AI 47133, and K24 NS 44250), the National Multiple Sclerosis Society (NMSS) to NLM (RG3267) and JLB (RG3908), the Yellow Rose Foundation (NLM and MKR), the Wadsworth Foundation (to NLM) and Howson funds (to NLM).
Unique Properties of Diamond and Its Device Applications (2012)

Diamond is a new semiconductor which has been developed in the last around 15 years. It has unique properties and the potential of unique electronic devices. The typical example is negative electron affinity (NEA) for hydrogen terminated diamond surface. The nature of diamond electron affinity was investigated using by photo-yield spectroscopy (TPYS). Using the NEA property, electron emission p-n (p-i-n) diodes were fabricated, and this diode can be used as a new principle power device; a vacuum micro switch operated by a p-n diode.
<title>Bidirectional printing method for a thermal ink transfer printer</title> (1991)

All thermal transfer serial printers currently use one-directional printing. A new bidirectional printing method for a thermal transfer printer is proposed. The new method features an electro-thermal ink transfer printing system and one-directional ink ribbon feeding at a constant speed. The image quality problems which were found in a preliminary experiment have been solved by using a newly developed ribbon and controlling the drive current pulse.
Adenosine A<sub>2A</sub>Receptor Stimulation Reduces Inflammation and Neointimal Growth in a Murine Carotid Ligation Model (2001)

Endothelial activation and leukocyte recruitment are early events in atherosclerosis and the vascular response to injury. Adenosine has anti-inflammatory effects on leukocytes and endothelial cells mediated through its A(2A) receptor. We tested the hypothesis that A(2A) activation would reduce inflammation and neointimal formation in a murine carotid ligation model. Before injury, mice were randomized to a 7-day subcutaneous infusion of a specific A(2A) receptor agonist (ATL-146e, 0.004 microg/kg per minute), vehicle control, ATL-146e plus ZM241385 (a selective A(2A) antagonist), or ZM241385 alone. Leukocyte recruitment and adhesion molecule expression were assessed at early time points, and the neointimal area was measured at 14 and 28 days after injury. Compared with control mice, ATL-146e-treated mice had significantly less neutrophil and macrophage recruitment and vascular cell adhesion molecule-1, intercellular adhesion molecule-1, and P-selectin expression in the first 7 days after injury. Neointimal area was markedly and persistently reduced by 80% at 14 and 28 days, despite termination of ATL infusion at 7 days. ATL-146e+ZM241385-treated and ZM241385-treated animals had neointimal areas similar to those of control animals, confirming that the observed effects of ATL-146e were mediated specifically by the A(2A) receptor. These data demonstrate that novel stimulation of adenosine A(2A) receptors can inhibit early inflammatory processes that are important in neointimal formation after vascular injury.
Hermite functions and regularized deconvolution in sonar waveform design and processing (2002)

A special type of comb waveform based on the Hermite function space is described. This family of waveforms is well-suited for providing simultaneous range and Doppler resolution, is relatively efficient in its use of sonar projector power, and is especially amenable to the use of constrained regularized deconvolution methods to robustly reduce sidelobes and retain intrinsic range and Doppler resolution.
Changing Patterns of Gene Expression Identify Multiple Steps During Regression of Rat Prostate in Vivo (1998)

The rat ventral prostate is an androgen-dependent organ that undergoes dramatic cell death upon removal of testosterone by surgical castration. Several well characterized criteria, such as nuclear condensation, organelle blebbing, and DNA fragmentation, have been used to demonstrate that most of this cell loss is due to programmed cell death, or apoptosis, of the secretory epithelial cells. In addition to changes in morphology, it is well known that cells undergoing apoptosis show alterations in gene expression, and it is widely assumed that many of these genes are directly involved in the mechanism of programmed cell death. Using poly A+ RNA derived from normal rat prostate as well as from the regressing prostates of castrated rats, we have used a PCR-based subtractive hybridization approach to generate complementary DNA (cDNA) libraries greatly enriched in cDNAs strongly regulated during rat prostate regression. Several hundred of the genes represented in these libraries appear to be strongly regulated during prostate regression and most of these are prostate specific. Sequence analysis indicates that up to 30% of these clones are similar or identical to genes of known function, approximately 20% are similar to expressed sequence tags (ESTs), and as many as 50% of these clones have not been characterized previously. Analysis of selected clones using in situ hybridization indicates that they are expressed specifically in prostate epithelial cells, and that certain of these clones are regulated temporally in a pattern consistent with apoptosis. The patterns of gene expression include: 1) genes whose expression decreases uniformly after removal of androgen, indicative of androgen sensitive genes; 2) genes whose expression increases in apoptotic prostate cells and in other tissues, suggesting a class of genes generally involved in apoptosis; 3) and genes whose expression increases in individual regressing prostate epithelial cells, suggesting a class of prostate specific genes associated with apoptosis.
Mid-IR room temperature quantum cascade lasers (1997)

The high power operation of mid-infrared quantum cascade lasers at temperatures up to T equals 320 K is reported. Gain at high temperature is optimized by a design combining low doping, a funnel injector and a three well vertical transition active region. A molecular beam epitaxy grown InP top cladding layer is also used to optimize heat dissipation. Peak pulsed optical power of 200 mW and average power of 6 mW are obtained at 300 K and at a wavelength (lambda) equals 5.2 micrometers . At (lambda) equals 8.5 micrometers , the pulsed optical power is 10 mW.
Angled facet waveguide quantum cascade laser for external cavity system (2018)

We describe the use of an angled facet to achieve low reflectance of one facet of a quantum cascade laser. A bent waveguide allows one facet to be angled with respect to the waveguide and still use the natural cleavage plane of the crystal. The application of such structures is external-cavity wavelength tunable quantum cascade lasers. The reflectance is studied as a function of angle with an angle of 11.2° reducing the reflectance from 28% to 3.5%. When combined with a dielectric anti-reflection coating, better external-cavity laser performance is possible.
Cold Matter Assembled Atom-by-Atom (2016)

The realization of large-scale fully controllable quantum systems is an exciting frontier in modern physical science. We use atom-by-atom assembly to implement a novel platform for the deterministic preparation of regular arrays of individually controlled cold atoms. In our approach, a measurement and feedback procedure eliminates the entropy associated with probabilistic trap occupation and results in defect-free arrays of over 50 atoms in less than 400 ms. The technique is based on fast, real-time control of 100 optical tweezers, which we use to arrange atoms in desired geometric patterns and to maintain these configurations by replacing lost atoms with surplus atoms from a reservoir. This bottom-up approach enables controlled engineering of scalable many-body systems for quantum information processing, quantum simulations, and precision measurements.
Gain in Statistical Remultiplexing of MPEG-2 Transport Streams (1999)

1.0 Abstract In this paper, we study the effect of statistical remultiplex­ ing on improving bandwidth utilization of multiplexed MPEG signals . The study is done through simulation results of 2 and 12 channels of compressed bit stream feeds into a real-time rate remultiplexing systems with optimal combination of transcoding and buffering strate­ gies. Our results indicates that larger number of channels, when rate remultiplexed together, results in reduced need for transcoding and improved overall video quality preser­ vation. 2.0 Overview Statistical multiplexing of MPEG-2 transport streams has been widely recognized as the effective way to optimize the quality of compressed video signals under the con­ straint of a fixed total transmission bandwidth. The result­ ing improvement can be described in terms of the so called ' statistical gain', which can be measured in several ways . It can be measured either in terms of the improvement of subjective visual quality of the decoded video, or in terms of the objective average reduction in quantization value, or in terms of the reduction of the quantization value variabil­ ity (statistical variance), etc. Statistical remultiplexing, also called statistical rate remul­ tiplexing, is a process which performs statistical multi­ plexing of signals already in compressed format. Statistical remultiplexing allows the operators to re-allo­ cate the bit budgets among different video channels by performing transcoding on the pre-compressed signals . Statistical remultiplexing systems are used as a way to remove the dependency of the transmission channel on real-time encoding. When used in video-on-demand sys­ tems, digital cable headend systems and digital advertise­ ment insertion systems, statistical remultiplexing can improve the overall system efficiency, resulting in better bandwidth utilization and reduced transmission cost. In this paper, we study the overall bandwidth reduction due to statistical remultiplexing. We will study the bit­ streams and their associated bit rate distributions to under­ stand the effect of statistical remultiplexing on the quality of the video signals. We will also consider issues on the amount of transcoding as it related to the bit rate and the number of bit streams at the input of the statistical remulti­ plexer. The simulation results are presented to show that statistical remultiplexing gain can be greatly affected by several important factors including input bit rates, number of inputs, and the amount of transcoding allowed.
A DNA Vaccine for Venezuelan Equine Encephalitis Virus Delivered by Intramuscular Electroporation Elicits High Levels of Neutralizing Antibodies in Multiple Animal Models and Provides Protective Immunity to Mice and Nonhuman Primates (2011)

We evaluated the immunogenicity and protective efficacy of a DNA vaccine expressing codon-optimized envelope glycoprotein genes of Venezuelan equine encephalitis virus (VEEV) when delivered by intramuscular electroporation. Mice vaccinated with the DNA vaccine developed robust VEEV-neutralizing antibody responses that were comparable to those observed after administration of the live-attenuated VEEV vaccine TC-83 and were completely protected from a lethal aerosol VEEV challenge. The DNA vaccine also elicited strong neutralizing antibody responses in rabbits that persisted at high levels for at least 6 months and could be boosted by a single additional electroporation administration of the DNA performed approximately 6 months after the initial vaccinations. Cynomolgus macaques that received the vaccine by intramuscular electroporation developed substantial neutralizing antibody responses and after an aerosol challenge had no detectable serum viremia and had reduced febrile reactions, lymphopenia, and clinical signs of disease compared to those of negative-control macaques. Taken together, our results demonstrate that this DNA vaccine provides a potent means of protecting against VEEV infections and represents an attractive candidate for further development.
Cloud thermodynamic phase detection with a 3-channel shortwave infrared polarimeter (2018)

Knowing the thermodynamic phase of a cloud–whether it is composed of spherical water droplets or polyhedral ice crystals–is critical in remote sensing applications and in climate studies. We recently showed that we can determine cloud phase with visible-wavelength sky polarimetry, and in this presentation we extend that method to shortwave infrared wavelength bands near 1.6 microns. We describe the instrument, a passive, three-channel polarimeter with spectral bands at 1550 nm, 1640 nm, and 1700 nm with approximate width of 40 nm and how we are using it in experiments to discriminate between liquid-water and ice clouds. This portable polarimeter measures scattered sunlight using polarizers orientated at 0° , 45‡ , and 90° with respect to the solar vertical scattering plane. It has a 4.9° field-of-view and a motorized, computer-controlled pan-and-tilt mount that controls the positioning of the polarimeter so that it can measure any point in the sky.
Computational Identification of Antisense Oligonucleotides That Rapidly Hybridize to RNA (2004)

The ability of a computational model to determine the relative rate of hybridization between anti-sense oligonucleotides and RNA was tested using HIV-1 tat mRNA. The model, which was based on the assumptions that hybridization is a second-order reaction and that early in the hybridization reaction the concentrations of intermediates are approximately constant (steady-state), allows calculation of a rate factor that is proportional to the reaction constant. Formation of oligodeoxynucleotide (ODN)-RNA hybrid, detected by RNase H-dependent cleavage, increased nearly linearly during an initial incubation period, consistent with the steady-state approximation. The initial hybridization rate increased linearly with substrate RNA concentration and with ODN concentration, indicating a second-order reaction. The logarithm of the second-order reaction constant, determined from the initial rate for hybridization between tat mRNA and 16 ODNs targeted to various sites, was linearly related to the logarithm of the calculated rate factor (r = 0.83, p < 0.001). Thus, the rate factor can be used to identify rapidly hybridizing antisense sequences using target nucleotide sequence information.
Human papillomavirus type 28 (HPV-28), an HPV-3-related type associated with skin warts (1989)

The cloning and partial characterization of the genome of human papillomavirus type 28 (HPV-28) is presented. The virus is a distinct type and by hybridization analyses is most closely related to HPV-3 and HPV-10.