gebhart/patrepeval huggingface dataset:
<title>Spectroscopy And Photochemistry In Cryogenic Solutions</title> (1978)

Ultraviolet and infrared spectra are presented for CO<sub>2</sub>, CH<sub>2</sub>O, CD<sub>2</sub>O, CC1<sub>2</sub>F<sub>2</sub>, C<sub>2</sub>H<sub>3</sub>C1, CH<sub>3</sub>OH, and 0s0<sub>4</sub> dissolved in liquified Xe, Kr, Ar, or air, and SeF<sub>6</sub> dissolved in solid Xe. The infrared absorption features in the liquid solutions are narrower than the corresponding gas phase vibrational bands but broader than rotational lines. Absorption bands in the solids are narrower than in the liquids. Absorption bands in SeF<sub>6</sub> exhibit the Se-isotope splitting. The frequencies of the absorption features are observed to shift with solvent, temperature, and isotopic composition. High solute densities (10<sup>17</sup> to 10<sup>19</sup> molecules/cm<sup>3</sup>) are obtainable. Some unstable compounds, such as CH<sub>2</sub>O monomer at 10<sup>18</sup> molecules/cm<sup>3</sup>, form stable cryogenic solutions. Cryogenic solutions are shown to be useful for spectroscopic detection of parts per million to parts per billion impurities in gases and for photochemically induced isotope separation.
All-optical 2R regeneration based on a compact self-seeded fabry-Pe/spl acute/rot laser diode with an embedded fiber Bragg grating (2006)

A cost-effective method, based on the injection-locking technique of a compact self-seeded Fabry-Peacuterot laser diode with a 10-mm-long embedded fiber Bragg grating cavity, is proposed and experimentally compared with the two-mode injection-locked scheme for all-optical 2R regeneration at 10 Gb/s. Placing the presented all-optical 2R regenerator after a 50-km fiber significantly improves the transmission performance of a signal over 50- and 100-km fiber links. The power penalties at BER=10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> are similar to those of the two-mode injection-locked scheme
The Amazon rain forest plant Uncaria tomentosa (cat’s claw) and its specific proanthocyanidin constituents are potent inhibitors and reducers of both brain plaques and tangles (2019)

Brain aging and Alzheimer's disease both demonstrate the accumulation of beta-amyloid protein containing "plaques" and tau protein containing "tangles" that contribute to accelerated memory loss and cognitive decline. In the present investigation we identified a specific plant extract and its constituents as a potential alternative natural solution for preventing and reducing both brain "plaques and tangles". PTI-00703 cat's claw (Uncaria tomentosa from a specific Peruvian source), a specific and natural plant extract from the Amazon rain forest, was identified as a potent inhibitor and reducer of both beta-amyloid fibrils (the main component of "plaques") and tau protein paired helical filaments/fibrils (the main component of "tangles"). PTI-00703 cat's claw demonstrated both the ability to prevent formation/aggregation and disaggregate preformed Aβ fibrils (1-42 and 1-40) and tau protein tangles/filaments. The disaggregation/dissolution of Aβ fibrils occurred nearly instantly when PTI-00703 cat's claw and Aβ fibrils were mixed together as shown by a variety of methods including Thioflavin T fluorometry, Congo red staining, Thioflavin S fluorescence and electron microscopy. Sophisticated structural elucidation studies identified the major fractions and specific constituents within PTI-00703 cat's claw responsible for both the observed "plaque" and "tangle" inhibitory and reducing activity. Specific proanthocyanidins (i.e. epicatechin dimers and variants thereof) are newly identified polyphenolic components within Uncaria tomentosa that possess both "plaque and tangle" reducing and inhibitory activity. One major identified specific polyphenol within PTI-00703 cat's claw was epicatechin-4β-8-epicatechin (i.e. an epicatechin dimer known as proanthocyanidin B2) that markedly reduced brain plaque load and improved short-term memory in younger and older APP "plaque-producing" (TASD-41) transgenic mice (bearing London and Swedish mutations). Proanthocyanidin B2 was also a potent inhibitor of brain inflammation as shown by reduction in astrocytosis and gliosis in TASD-41 transgenic mice. Blood-brain-barrier studies in Sprague-Dawley rats and CD-1 mice indicated that the major components of PTI-00703 cat's claw crossed the blood-brain-barrier and entered the brain parenchyma within 2 minutes of being in the blood. The discovery of a natural plant extract from the Amazon rain forest plant (i.e. Uncaria tomentosa or cat's claw) as both a potent "plaque and tangle" inhibitor and disaggregator is postulated to represent a potential breakthrough for the natural treatment of both normal brain aging and Alzheimer's disease.
Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues (2019)

Abstract Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols. Here we present a multi-immersion open-top light-sheet microscope that enables simple mounting of multiple specimens processed with a variety of protocols, which will facilitate wider adoption by preclinical researchers and clinical laboratories. One Sentence Summary Glaser et al. describe a multi-immersion open-top light-sheet microscope that enables simple and high-throughput imaging of large numbers of preclinical and clinical specimens prepared with a variety of clearing protocols.
“First AID” for T cell adoptive transfer: TCR affinity maturation by somatic hypermutation (2013)

Meeting abstracts Adoptive cell transfer (ACT) of tumor specific T lymphocytes, after host immunodepletion, was shown to mediate objective cancer regression of metastatic melanoma. Effective T cell activation depends, among other factors, on the functional avidity of the peptide-MHC complex (pMHC)
A Novel Rolling Circle Amplification-Based Detection of SARS-CoV-2 with Multi-Region Padlock Hybridization (2022)

SARS-CoV-2 has remained a global health burden, primarily due to the continuous evolution of different mutant strains. These mutations present challenges to the detection of the virus, as the target genes of qPCR, the standard diagnostic method, may possess sequence alterations. In this study, we develop an isothermal one-step detection method using rolling circle amplification (RCA) for SARS-CoV-2. This novel strategy utilizes a multi-padlock (MP-RCA) approach to detect viral-RNA via a simplified procedure with the reliable detection of mutated strains over other procedures. We designed 40 padlock-based probes to target different sequences across the SARS-CoV-2 genome. We established an optimal one-step isothermal reaction protocol utilizing a fluorescent output detected via a plate reader to test a variety of padlock combinations. This method was tested on RNA samples collected from nasal swabs and validated via PCR. S-gene target failure (SGTF)-mutated strains of SARS-CoV-2 were included. We demonstrated that the sensitivity of our assay was linearly proportional to the number of padlock probes used. With the 40-padlock combination the MP-RCA assay was able to correctly detect 45 out 55 positive samples (81.8% efficiency). This included 10 samples with SGTF mutations which we were able to detect as positive with 100% efficiency. We found that the MP-RCA approach improves the sensitivity of the MP-RCA assay, and critically, allows for the detection of SARS-CoV-2 variants with SGTF. Our method offers the simplicity of the reaction and requires basic equipment compared to standard qPCR. This method provides an alternative approach to overcome the challenges of detecting SARS-CoV-2 and other rapidly mutating viruses.
EFFECTS OF FIVE DIVERSE LIGNOCELLULOSIC DIETS ON DIGESTIVE ENZYME BIOCHEMISTRY IN THE TERMITE <i>Reticulitermes flavipes</i> (2015)

Termites have recently drawn much attention as models for biomass processing, mainly due to their lignocellulose digestion capabilities and mutualisms with cellulolytic gut symbionts. This research used the lower termite Reticulitermes flavipes to investigate gut enzyme activity changes in response to feeding on five diverse lignocellulosic diets (cellulose filter paper [FP], pine wood [PW], beech wood xylan [X], corn stover [CS], and soybean residue [SB]). Our objectives were to compare whole-gut digestive enzyme activity and host versus symbiont contributions to enzyme activity after feeding on these diets. Our hypothesis was that enzyme activities would vary among diets as an adaptive mechanism enabling termites and symbiota to optimally utilize variable resources. Results support our "diet-adaptation" hypothesis and further indicate that, in most cases, host contributions are greater than those of symbionts with respect to the enzymes and activities studied. The results obtained thus provide indications as to which types of transcriptomic resources, termite or symbiont, are most relevant for developing recombinant enzyme cocktails tailored to specific feedstocks. With regard to the agricultural feedstocks tested (CS and SB), our results suggest endoglucanase and exoglucanase (cellobiohydrolase) activities are most relevant for CS breakdown; whereas endoglucanase and xylosidase activities are relevant for SB breakdown. However, other unexplored activities than those tested may also be important for breakdown of these two feedstocks. These findings provide new protein-level insights into diet adaptation by termites, and also complement host-symbiont metatranscriptomic studies that have been completed for R. flavipes after FP, PW, CS, and SB feeding.
Simultaneous blue- and red-shift of light-hole and heavy-hole band in a novel variable-strain quantum well heterostructure (1995)

We have designed and studied a new type of strained semiconductor quantum well structure, variable-strain quantum well. The strain within the quantum well is graded from compressive to tensile in order to obtain mutually opposing slopes for the heavy- and light-hole band edges, causing the heavy and light holes to experience opposite fields created by the same strain. A unique bias controlled crossover with a simultaneous red and blue quantum confined Stark shift for the heavy- and light-hole transitions, respectively, has been observed by electroreflectance spectra. This results in a bias controlled change of the polarization properties and the transition energies suitable for polarization controllable photonic devices.
Molecular cloning and characterization of Mustang, a novel nuclear protein expressed during skeletal development and regeneration (2004)

Bone regeneration occurs as a series of events that requires temporal and spatial orchestration of numerous cell types guided by the transcriptional activity of thousands of genes, as recently demonstrated by our laboratory. Using the rat femoral fracture model, bioinformatics, cloning, expression assays, fusion proteins, and transfection, we report on the identification and characterization of one such differentially expressed gene, termed Mustang (musculoskeletal temporally activated novel gene). Mustang encodes for an 82 amino acid nuclear protein with no homology to any known protein family. However, other species homologues (mouse, human, cow) were identified within EST (expressed sequence tag) databases. Nuclear localization was confirmed using a GFP-Mustang fusion protein. Using in situ hybridization, Mustang expression was localized to differentiating periosteal osteogenic cells, proliferating chondrocytes, and osteoblasts of the fracture callus. Unlike adult tissues, developing embryos abundantly express Mustang, especially in mesenchymal condensations of limbs, vertebral perichondrium, and mesenchymal cells of the intervertebral discs. Although the precise function of Mustang is unknown, its unique pattern of expression during bone development and regeneration, absence in adult tissues (except skeletal muscle and tendon), and nuclear localization suggest that Mustang is involved in the development and regeneration of the mammalian musculoskeletal system.
The omni microstrip antenna: a new small antenna (1979)

The omni microstrip antenna is a microstrip-shorted quarter-wave resonator that is wrapped around a cylinder. It is an electrically short antenna, and it can be made to radiate an omnidirectional pattern normal to the axis of the cylinder. Equations governing the design of the antenna are given along with a method of excitation. An example of a design at 41.4 MHz is given, and experimental results are reported.
Two Cellobiohydrolase-Encoding Genes from <i>Aspergillus niger</i> Require <scp>d</scp> -Xylose and the Xylanolytic Transcriptional Activator XlnR for Their Expression (1999)

Two cellobiohydrolase-encoding genes, cbhA and cbhB, have been isolated from the filamentous fungus Aspergillus niger. The deduced amino acid sequence shows that CbhB has a modular structure consisting of a fungus-type cellulose-binding domain (CBD) and a catalytic domain separated by a Pro/Ser/Thr-rich linker peptide. CbhA consists only of a catalytic domain and lacks a CBD and linker peptide. Both proteins are homologous to fungal cellobiohydrolases in family 7 of the glycosyl hydrolases. Northern blot analysis showed that the transcription of the cbhA and cbhB genes is induced by D-xylose but not by sophorose and, in addition, requires the xylanolytic transcriptional activator XlnR.
Therapeutic CMP-Nonulosonates against Multidrug-Resistant <i>Neisseria gonorrhoeae</i> (2020)

<i>Neisseria gonorrhoeae</i> deploys a unique immune evasion strategy wherein the lacto-<i>N</i>-neotetraose termini of lipooligosaccharide (LOS) are "capped" by a surface LOS sialyltransferase (Lst), using extracellular host-derived CMP-sialic acid (CMP-Neu5Ac in humans). LOS sialylation enhances complement resistance by recruiting factor H (FH; alternative complement pathway inhibitor) and also by limiting classical pathway activation. Sialylated LOS also engages inhibitory Siglecs on host leukocytes, dampening innate immunity. Previously, we showed that analogues of CMP-sialic acids (CMP-nonulosonates [CMP-NulOs]), such as CMP-Leg5,7Ac<sub>2</sub> and CMP-Neu5Ac9N<sub>3</sub>, are also substrates for Lst. Incorporation of Leg5,7Ac<sub>2</sub> and Neu5Ac9N<sub>3</sub> into LOS results in <i>N. gonorrhoeae</i> being fully serum sensitive. Importantly, intravaginal administration of CMP-Leg5,7Ac<sub>2</sub> attenuated <i>N. gonorrhoeae</i> colonization of mouse vaginas. In this study, we characterize and develop additional candidate therapeutic CMP-NulOs. CMP-ketodeoxynonulosonate (CMP-Kdn) and CMP-Kdn7N<sub>3</sub>, but not CMP-Neu4,5Ac<sub>2</sub>, were substrates for Lst, further elucidating gonococcal Lst specificity. Lacto-<i>N</i>-neotetraose LOS capped with Kdn and Kdn7N<sub>3</sub> bound FH to levels ∼60% of that seen with Neu5Ac and enabled gonococci to resist low (3.3%) but not higher (10%) concentrations of human complement. CMP-Kdn, CMP-Neu5Ac9N<sub>3</sub>, and CMP-Leg5,7Ac<sub>2</sub> administered intravaginally (10 μg/d) to <i>N. gonorrhoeae</i>-colonized mice were equally efficacious. Of the three CMP-NulOs above, CMP-Leg5,7Ac<sub>2</sub> was the most pH and temperature stable. In addition, Leg5,7Ac<sub>2</sub>-fed human cells did not display this NulO on their surface. Moreover, CMP-Leg5,7Ac<sub>2</sub> was efficacious against several multidrug-resistant gonococci in mice with a humanized sialome (<i>Cmah<sup>-/-</sup></i> mice) or humanized complement system (FH/C4b-binding protein transgenic mice). CMP-Leg5,7Ac<sub>2</sub> and CMP-Kdn remain viable leads as topical preventive/therapeutic agents against the global threat of multidrug-resistant <i>N. gonorrhoeae</i>.
Alternating Copolymerization of 3,4-Epoxy-1-Butene and Derivatives with Maleic Anhydride (1997)

Abstract 3,4-Epoxy-1-butene (I), prepared by the selective oxidation of butadiene, is an unusual difunctional monomer containing polymerizable vinyl and epoxy groups. As expected, free radical homopolymerization of I and its cyclic ketal derivatives was found to be very sluggish, as expected, for the allylic monomer structures. However, I was found to form alternating copolymers with maleic anhydride with both 1,2- and 1,5- enchainment observed. The structures of the alternating copolymers were observed to be solvent dependent with the in situ formation of cyclic ketals and their incorporation into the copolymers in polymerizations done in ketone solvents. Various cyclic ketal monomers derived from I readily formed alternating copoymers with maleic anhydride. Thermally activated self-crosslinking of these resins was observed.
Improved Quality and Yield of Islets Isolated from Human Pancreata Using a Two-Step Digestion Method (2000)

A new approach, involving a two-step digestion process and Los Angeles preservation solution #1 (LAP-1), a cold storage solution, was developed for isolation of high-quality islets from human pancreata for transplantation. This approach markedly improves the islet yield, purity and viability, and the isolation success rate. In this method, the pancreas was digested first in warm collagenase solution for up to 20 minutes. After decanting the enzyme solution, partially digested tissue was dissociated by gentle agitation in cold LAP-1 solution without additional collagenase. The digested tissues were stored in cold LAP-1 solution until islet purification on Euro-Ficoll. Forty-six islet isolations were performed consecutively by the new method (group 1). These results were compared to those obtained earlier with 46 consecutive isolations, using our previous method that had been used before development of the new method (group 2). Our old method was a modification of Ricordi's method involving only warm collagenase digestion and the storage of digested tissues in cold Hanks balanced salt solution. All pancreata were partial, containing the body and tail. There were no significant differences in both groups with regard to the donor age, cold ischemic time, harvesting conditions, and pancreatic weight. Pancreas digestion was completed in approximately 1 hour in both groups. The isolation success rate as determined by viable islets after 2 days in culture was 93.5% (43 of 46 cases) in group 1, and 56.5% (26 of the 46) in group 2. Immediately after isolation, the new method yielded a total of 335,739 +/- 36,244 islets equivalent to 150 microm (IEQ) and 6,233 +/- 681 IEQ/g of pancreas with 83 +/- 2.5% purity, whereas the old method yielded a total of 195,587 +/- 25,242 IEQ and 3,763 +/- 5,509 IEQ/g with 69.2 +/- 4.7% purity. Isolated islets in group 1 maintained a good three-dimensional structure, displayed normal insulin release to high glucose stimulation in vitro, and restored euglycemia after transplantation into streptozotocin-diabetic athymic mice. The two-step digestion method provides a sufficient number of islets for transplantation from a single pancreas.
High Speed Imaging of Bubble Clouds Generated in Pulsed Ultrasound Cavitational Therapy - Histotripsy (2007)

Our recent studies have demonstrated that mechanical fractionation of tissue structure with sharply demarcated boundaries can be achieved using short (< 20 micros), high intensity ultrasound pulses delivered at low duty cycles. We have called this technique histotripsy. Histotripsy has potential clinical applications where noninvasive tissue fractionation and/or tissue removal are desired. The primary mechanism of histotripsy is thought to be acoustic cavitation, which is supported by a temporally changing acoustic backscatter observed during the histotripsy process. In this paper, a fast-gated digital camera was used to image the hypothesized cavitating bubble cloud generated by histotripsy pulses. The bubble cloud was produced at a tissue-water interface and inside an optically transparent gelatin phantom which mimics bulk tissue. The imaging shows the following: (1) Initiation of a temporally changing acoustic backscatter was due to the formation of a bubble cloud; (2) The pressure threshold to generate a bubble cloud was lower at a tissue-fluid interface than inside bulk tissue; and (3) at higher pulse pressure, the bubble cloud lasted longer and grew larger. The results add further support to the hypothesis that the histotripsy process is due to a cavitating bubble cloud and may provide insight into the sharp boundaries of histotripsy lesions.
Generation of Bright Isolated Attosecond Soft X-Ray Pulses Driven by Multi-Cycle Mid-Infrared Lasers (2014)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. -. Chen, C. Mancuso, C. Hernández-García, F. Dollar, B. Galloway, D. Popmintchev, B. Langdon, A. Auger, P. -. Huang, B. C. Walker, L. Plaja, A. Jaron-Becker, A. Becker, M. M. Murnane, H. C. Kapteyn, and T. Popmintchev, "Generation of Bright Isolated Attosecond Soft X-Ray Pulses Driven by Multi-Cycle Mid-Infrared Lasers," in 19th International Conference on Ultrafast Phenomena, OSA Technical Digest (online) (Optica Publishing Group, 2014), paper 07.Mon.A.2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Human CD4 <sup>+</sup> T Cell Responses to an Attenuated Tetravalent Dengue Vaccine Parallel Those Induced by Natural Infection in Magnitude, HLA Restriction, and Antigen Specificity (2017)

Dengue virus (DENV) is responsible for growing numbers of infections worldwide and has proven to be a significant challenge for vaccine development. We previously demonstrated that CD8<sup>+</sup> T cell responses elicited by a dengue live attenuated virus (DLAV) vaccine resemble those observed after natural infection. In this study, we screened peripheral blood mononuclear cells (PBMCs) from donors vaccinated with a tetravalent DLAV vaccine (TV005) with pools of dengue virus-derived predicted major histocompatibility complex (MHC) class II binding peptides. The definition of CD4<sup>+</sup> T cell responses after live vaccination is important because CD4<sup>+</sup> T cells are known contributors to host immunity, including cytokine production, help for CD8<sup>+</sup> T and B cells, and direct cytotoxicity against infected cells. While responses to all antigens were observed, DENV-specific CD4<sup>+</sup> T cells were focused predominantly on the capsid and nonstructural NS3 and NS5 antigens. Importantly, CD4<sup>+</sup> T cell responses in vaccinees were similar in magnitude and breadth to those after natural infection, recognized the same antigen hierarchy, and had similar profiles of HLA restriction. We conclude that TV005 vaccination has the capacity to elicit CD4<sup>+</sup> cell responses closely mirroring those observed in a population associated with natural immunity.<b>IMPORTANCE</b> The development of effective vaccination strategies against dengue virus infection is of high global public health interest. Here we study the CD4 T cell responses elicited by a tetravalent live attenuated dengue vaccine and show that they resemble responses seen in humans naturally exposed to dengue virus. This is an important issue, since it is likely that optimal immunity induced by a vaccine requires induction of CD4<sup>+</sup> responses against the same antigens as those recognized as dominant in natural infection. Detailed knowledge of the T cell response may further contribute to the identification of robust correlates of protection against dengue virus.