gebhart/patrepeval huggingface dataset:
Techniques and tactics used in determining the structure of the trimericebolavirusglycoprotein (2009)

The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008), Nature (London), 454, 177-182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glycoprotein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the proper sequence register was confirmed by building alternate sequences using N-linked glycan sites as anchors and secondary-structural predictions.
Comparison of wide-field scatter methods for surface weighted imaging: active illumination versus high spatial frequency imaging (Conference Presentation) (2020)

Surface weighted imaging in a wide-field manner is useful for many biomedical applications such as margin status determination in breast conserving surgery. One technique that has shown promise for this application is modulated imaging at high spatial frequency. A new technique to provide similar information in a more compact manner with the ability to customize based on desired depth penetration was developed. This technique involves quickly scanning a point source over the tissue surface and selective removing diffuse photons in image processing. These two techniques were compared using custom made depth phantoms of tissue equivalent material.
Potassium tert-Butoxide Promoted Intramolecular Arylation via a Radical Pathway (2011)

Potassium tert-butoxide mediated intramolecular cyclization of aryl ethers, amines, and amides was efficiently performed under microwave irradiation to provide the corresponding products in high regioisomeric ratios. The reaction proceeds via single-electron transfer to initiate the formation of an aryl radical, followed by a kinetically favored 5-exo-trig and subsequent ring expansion.
The Doubled-Suture Nice Knot (2016)

The authors describe a novel suture fixation technique that combines a doubled suture with a sliding knot. The knot can be tied in both open and arthroscopic surgery to fix torn tendons/ligaments and fractured/osteotomized bones. The advantages of the doubled-suture Nice knot include strength, adjustability, simplicity, and versatility. This technique, which has proven useful in the authors' practice for the past 10 years, has replaced metallic wires and cables for bone fixation. The doubled-suture Nice knot can also be tied over a double-button and has been used for ankle syndesmosis, acromioclavicular joint separation repair, and coracoid bone block fixation. [Orthopedics. 2017; 40(2):e382-e386.].
Six ‘Must-Have’ Minerals for Life’s Emergence: Olivine, Pyrrhotite, Bridgmanite, Serpentine, Fougerite and Mackinawite (2020)

Life cannot emerge on a planet or moon without the appropriate electrochemical disequilibria and the minerals that mediate energy-dissipative processes. Here, it is argued that four minerals, olivine ([Mg>Fe]<sub>2</sub>SiO<sub>4</sub>), bridgmanite ([Mg,Fe]SiO<sub>3</sub>), serpentine ([Mg,Fe,]<sub>2-3</sub>Si<sub>2</sub>O<sub>5</sub>[OH)]<sub>4</sub>), and pyrrhotite (Fe<sub>(1-x)</sub>S), are an essential requirement in planetary bodies to produce such disequilibria and, thereby, life. Yet only two minerals, fougerite ([Fe<sup>2+</sup><sub>6x</sub>Fe<sup>3+</sup><sub>6(x-1)</sub>O<sub>12</sub>H<sub>2(7-3x)</sub>]<sup>2+</sup>·[(CO<sup>2-</sup>)·3H<sub>2</sub>O]<sup>2-</sup>) and mackinawite (Fe[Ni]S), are vital-comprising precipitate membranes-as initial "free energy" conductors and converters of such disequilibria, i.e., as the initiators of a CO<sub>2</sub>-reducing metabolism. The fact that wet and rocky bodies in the solar system much smaller than Earth or Venus do not reach the internal pressure (≥23 GPa) requirements in their mantles sufficient for producing bridgmanite and, therefore, are too reduced to stabilize and emit CO<sub>2</sub>-the staple of life-may explain the apparent absence or negligible concentrations of that gas on these bodies, and thereby serves as a constraint in the search for extraterrestrial life. The astrobiological challenge then is to search for worlds that (i) are large enough to generate internal pressures such as to produce bridgmanite or (ii) boast electron acceptors, including imported CO<sub>2</sub>, from extraterrestrial sources in their hydrospheres.
Conventional Microscope-Integrated Intraoperative OCT Versus Digitally Enabled Intraoperative OCT in Vitreoretinal Surgery in the DISCOVER Study (2020)

Feasibility and utility of iOCT were similar in both groups. Digitally enabled iOCT datastream enabled increased attention on the surgical field during OCT review. [Ophthalmic Surg Lasers Imaging Retina. 2020;51:S37-S43.].
The CENP-A homolog CaCse4p in the pathogenic yeastCandida albicansis a centromere protein essential for chromosome transmission (2002)

The gene encoding CaCse4p, a homolog of the evolutionarily conserved histone H3-like kinetochore protein CENP-A, has been cloned from the human pathogenic diploid yeast Candida albicans. To study the phenotype of C. albicans diploid cells depleted of CaCse4p, we deleted one copy of CaCSE4 and brought the other copy under control of a regulated PCK1 promoter (repressed by glucose and induced by succinate). Inability of this strain to grow on glucose medium indicates that CaCse4p is essential for cell viability. Shutdown of CaCSE4 expression resulted in a sharp decline of CaCse4p levels with concomitant loss of cell viability. Examination of these CaCse4p-depleted cells revealed a mitosis-specific arrest phenotype with accumulation of large-budded cells containing single G(2) nuclei at or near the bud neck along with short mitotic spindles. Subcellular localization of CaCse4p by anti-CaCse4p antibodies in both budding and filamentous C. albicans cells revealed an intense dot-like signal always colocalized with 4',6-diamidino-2-phenylindole-stained nuclei. Unlike higher eukaryotes but similar to the budding yeast Saccharomyces cerevisiae, centromere separation in the budding yeast form of C. albicans occurs before anaphase, at a very early stage of the cell cycle. In the filamentous mode of cell division, however, centromere separation appears to occur in early anaphase. Coimmunostaining with anti-CaCse4p and antitubulin antibodies shows that CaCse4p localizes near spindle pole bodies, analogous to the localization pattern observed for kinetochore proteins in S. cerevisiae. CaCse4p promises to be a highly useful reagent for the study of centromere/kinetochore structure in C. albicans.
Simple calibration of non-overlapping cameras with a mirror (2008)

Calibrating a network of cameras with non-overlapping views is an important and challenging problem in computer vision. In this paper, we present a novel technique for camera calibration using a planar mirror. We overcome the need for all cameras to see a common calibration object directly by allowing them to see it through a mirror. We use the fact that the mirrored views generate a family of mirrored camera poses that uniquely describe the real camera pose. Our method consists of the following two steps: (1) using standard calibration methods to find the internal and external parameters of a set of mirrored camera poses, (2) estimating the external parameters of the real cameras from their mirrored poses by formulating constraints between them. We demonstrate our method on real and synthetic data for camera clusters with small overlap between the views and non-overlapping views.
Abstract 10306: Identification and Characterization of Orally Bioavailable Small Molecule Protease Proprotein Convertase Subtilisin-like Kexin Type 9 Inhibitors (Best of Basic Science Abstract) (2015)

Intervention with drugs to reduce low density lipoprotein-cholesterol (LDL-C) has proven to decrease mortality and morbidity. Here, we report the development of small molecules that lower LDL-C by targeting the LDL-receptor (LDLR) degradation pathway, which is modulated by the protease proprotein convertase subtilisin-like kexin type 9 (PCSK9). PCSK9 is synthesized as a 72-kDa zymogen that undergoes autocatalytic processing between the prodomain and catalytic domain, an important step that is absolutely required for secretion of PCSK9 and its function. Secreted PCSK9 binds to the LDLR and enhances its degradation. We have identified inhibitors of the autocatalytic processing by virtual docking of millions of commercial compounds into the atomic structure of the PCSK9 active site. Top scoring compounds that showed the best fit in the active site were selected for screening. These compounds were tested for their ability to inhibit the autocatalytic processing/secretion of PCSK9. The most potent compounds exhibited a concentration-dependent inhibition of the PCSK9 processing/secretion with IC50’s in the nanomolar range. These compounds were tested for selectivity against other PCSK’s. The data demonstrated that these compounds were selective in that they inhibit PCSK9 processing/secretion without affecting the secretion of other related PCSK’s. Furthermore, these compounds exhibited a 5- to 10-fold LDLR upregulation at 1.6 μM in two recombinant cell-based assays as well as exhibited an increase in the fluorescently labeled DiI-LDL uptake in situ in the nanomolar range. In animal studies, intraperitoneal (IP) injection of these compounds administered alone resulted in more than 20% reduction in LDL-C in mice fed a high fat/high cholesterol diet and over 40% reduction in LDL-C if administered in combination with atorvastatin. In vivo pharmacokinetic (PK) and pharmacodynamic (PD) evaluation of these compounds demonstrated that they are orally efficacious, with one compound exhibiting 43% oral bioavailability. Thus, identifying small molecule, orally active PCSK9 modulators represents a significant advance and opportunityfor drug development.
A Low Power Embedded SRAM for Wireless Applications (2006)

This paper introduces a novel ultra low power SRAM. A large power reduction is obtained by the use of four new techniques that allow for a wider and better trade-off between area, delay and active and passive energy consumption for low power embedded SRAMs. The design targets wireless applications that require a moderate performance and an ultra low power consumption. The implemented design techniques consist of a more efficient memory databus, the exploitation of the dynamic read stability of SRAM cells, a new low swing write technique and a distributed decoder. An 8 KByte 5T SRAM was fabricated in a 0.18mum technology. The measurement results confirm the feasibility and the usefulness of the proposed techniques. A reduction of active power consumption with a factor of 2 is reported as compared to the current state of the art. The results are generalized towards a 32 KByte SRAM
Metal‐Insulator Transition in ALD VO2 Ultrathin Films and Nanoparticles: Morphological Control (2014)

Nanoscale morphology of vanadium dioxide (VO 2 ) films can be controlled to realize smooth ultrathin (&lt;10 nm) crystalline films or nanoparticles with atomic layer deposition, opening doors to practical VO 2 metal‐insulator transition (MIT) nanoelectronics. The precursor combination, the valence of V, and the density for as‐deposited VO 2 films, as well as the postdeposition crystallization annealing conditions determine whether a continuous thin film or nanoparticle morphology is obtained. It is demonstrated that the films and particles possess both a structural and an electronic transition. The resistivity of ultrathin films changes by more than two orders of magnitude across the MIT, demonstrating their high quality.
Observation of Atom Images by Means of Field Emission STEM (1977)

Journal Article Observation of Atom Images by Means of Field Emission STEM Get access Hideo TODOKORO, Hideo TODOKORO Central Research Laboratory, Hitachi, Ltd.Kokubunji, Tokyo, 185 Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Setsuo NOMURA, Setsuo NOMURA Central Research Laboratory, Hitachi, Ltd.Kokubunji, Tokyo, 185 Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Tsutomu KOMODA Tsutomu KOMODA Central Research Laboratory, Hitachi, Ltd.Kokubunji, Tokyo, 185 Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Electron Microscopy, Volume 26, Issue 3, 1977, Pages 213–214, https://doi.org/10.1093/oxfordjournals.jmicro.a050068 Published: 01 January 1977 Article history Published: 01 January 1977 Received: 10 May 1977 Accepted: 03 June 1977
Dynamic nuclear polarization in a charged quantum dot induced by the AC Stark effect (2019)

The energy levels of an optically active quantum system can be shifted via the AC Stark effect by applying a strong, far-detuned laser. In addition to achieving a spin-selective AC Stark shift larger than 20 GHz, we observe a small Overhauser shift of approximately 1 GHz in a single negatively charged InGaAs quantum dot. We attribute this small shift to dynamic nuclear polarization via electron spin pumping induced by the high power, although far-detuned AC Stark laser. Low power scans reveal two regimes: high power where the frequency shift is linear in AC Stark laser power, and low power where the behavior is non-linear. Linewidth analysis provides a method to quantify the effect of the AC Stark laser on the nuclear spin environment, which in turn affects the quantum dot transitions.
Hepatitus B virus: specific binding and internalization of small HBsAg by human hepatocytes (1995)

Previously, we identified human liver endonexin II (EII) present on human hepatocyte plasma membrane as a specific hepatitis B surface antigen (HBsAg) binding protein. We also showed the spontaneous development of anti-idiotypic (anti-HBsAg) antibodies in rabbits immunized with EII and in chicken immunized with the F(ab')2 fragment of rabbit anti-EII IgG. These findings suggest the existence of a receptor-ligand relationship between EII and HBsAg. In the present study, we demonstrate that small HBsAg conjugated to 10 nm colloidal gold also binds specifically to human hepatocytes. Invagination of the coated pit region at the HBsAg binding sites on the human hepatocyte plasma membrane results in the internalization of the HBsAg-gold particles. The binding and consequently the internalization of HBsAg is inhibited by anti-EII or anti-idiotypic (anti-HBsAg) antibodies. These findings indicate that EII is directly involved in the binding and uptake of hepatitis B envelope proteins.
Effect of osmolarity on the zero-stress state and mechanical properties of aorta (2007)

Some pathological conditions may affect osmolarity, which can impact cell, tissue, and organ volume. The hypothesis of this study is that changes in osmolarity affect the zero-stress state and mechanical properties of the aorta. To test this hypothesis, a segment of mouse abdominal aorta was cannulated in vivo and mechanically distended by perfusion of physiological salt (NaCl) solutions with graded osmolarities from 145 to 562 mosM. The mechanical (circumferential stress, strain, and elastic modulus) and morphological (wall thickness and wall area) parameters in the loaded state were determined. To determine the osmolarity-induced changes of zero-stress state, the opening angle was observed by immersion of the sectors of mouse, rat, and pig thoracic aorta in NaCl solution with different osmolarities. Wall volume and tissue water content of the rings were also recorded at different osmolarities. Our results show that acute aortic swelling due to low osmolarity leads to an increase in wall thickness and area, a change in the stress-strain relationship, and an increase in the elastic modulus (stiffness) in mouse aorta. The opening angle, wall volume, and water content decreased significantly with increase in osmolarity. These findings suggest that acute aortic swelling and shrinking result in immediate mechanical changes in the aorta. Osmotic pressure-induced changes in the zero-stress state may serve to regulate mechanical homeostasis.
Supplementary Figures 1-6 from Intravesical Delivery of Small Activating RNA Formulated into Lipid Nanoparticles Inhibits Orthotopic Bladder Tumor Growth (2023)

&lt;p&gt;PDF file - 687K, Figure S1. dsP21-322 triggers changes in cell morphology associated with growth inhibition. Figure S2. Anti-growth activities of LNP-dsP21-322-2'F and its non-formulated derivatives. Figure S3. Duplex stability in water and detection of nucleic acid background signal in urine. Figure S4. Uptake of LNP-formulated dsP21-322-2'F-FITC by bladder urothelium. Figure S5. GFP signature of orthotopic tumors in excised mouse bladders. Figure S6. Muscle invasive bladder tumor and metastatic bladder tumor in the kidney&lt;/p&gt;
TP73 Is an Amyotrophic Lateral Sclerosis Candidate Risk Gene (S25.006) (2018)

To better understand amyotrophic lateral sclerosis (ALS) pathogenesis by identifying novel ALS candidate risk genes.
Cross-language multimedia information retrieval (2000)

Simple measures can achieve high-accuracy cross-language retrieval in carefully chosen applications. Image retrieval is one of those applications, with results ranging from 68% of human translator performance for German, to 100% for French.
Multimodal augmentation of surfaces using conductive 3D printing (2016)

Accessible tactile pictures (ATPs) consist of tactile representations that convey different kinds of messages and present information through the sense of touch. Traditional approaches use contours and patterns, which create a distinct and recognizable shape and enables separate objects to be identified. The success rate for recognizing pictures by touch is much lower than it would be for vision. Besides that, some pictures are more frequently recognized than others. Finally, there is also some variation from individual to individual: while some blind people recognize many images, others recognize few. Auditory support can improve the points listed before, even eliminating the need for sighted assistance.
Cord Blood Transplantation for Long Term Management or Possible Cure of HIV Infection (2012)

The most important mechanism for natural protection against HIV transmission is a mutation in the CCR5 gene leading to a 32-base-pair deletion (CCR5-delta32) and a non-functional CCR5 protein. Prior to 2001, Chow et al pioneered the concept to screen allogeneic stem cell donors for those homozygous for CCR5-delta32 to transplant HIV infected patients (U.S. patent 2003/0099621 A1), as acknowledged by Hutter et al recently (TheScientificWorld Journal, 2011;11:1068-1076). Hutter et al (NEJM 2009;360:692-698) performed a bone marrow transplant in a patient with acute leukemia who was infected with HIV using a donor homozygous for the CCR5-delta32 deletion. More than 4 years later the patient does not require antiretrovial therapy and no viral load or proviral DNA can be detected. However, this procedure cannot be generalized using adult donors because the variant allele is quite unusual (<1% of Caucasians, and much lower in other ethnic groups) and a very close HLA match is required between adult donors and patients. Cord blood HCT requires HLA matching of only 4 of 6 alleles. Therefore, our hypothesis is that an inventory of cord blood units homozygous for the CCR5-delta32 allele will provide an improved probability of finding an appropriately HLA-matched donor for a patient with HIV infection in need of a HCT. CCR5 genotype analysis is performed on DNA extracted from cord blood using a PCR based assay. Biomathematicians at the NMDP developed estimates regarding the probability of providing an adequately HLA matched cord blood unit. We have tested about 10,000 cryopreserved cord blood units and have identified 81 homozygous CCR5-delta32 units. Testing an additional 25,000 cord blood units from Caucasians is expected to increase the special inventory to about 300 units which is projected to provide for Caucasians an adequately HLA matched cord blood unit with an adequate cell dose for 73.61% of pediatric patients and 27.92% of adults. The initial population for transplantation is patients in need of a HCT for a hematologic malignancy or other indication, and who are also infected with HIV, although some selected patients with AIDS who have no other illness may also ultimately be considered for transplantation. Cord blood transplantation has a unique role in providing for long term control or possible cure of HIV infection.
Growth of As overlayers on vicinal Si(100) surfaces (1991)

First-principles total-energy calculations are used to study the structure of As overlayers deposited on a stepped Si(100) surface. It is predicted that deposition of As at low substrate temperatures allows the As to grow directly on top of the Si surface, while growth at high temperatures results in a rearrangement of the surface as if the As replaced the original top Si layer. This result explains the sublattice orientation dilemma in GaAs-on-Si epitaxy.