gebhart/patrepeval huggingface dataset:
Exploring Brain Connectivity with Two-Dimensional Neural Maps (2011)

We introduce two-dimensional neural maps for exploring connectivity in the brain. For this, we create standard streamtube models from diffusion-weighted brain imaging data sets along with neural paths hierarchically projected into the plane. These planar neural maps combine desirable properties of low-dimensional representations, such as visual clarity and ease of tract-of-interest selection, with the anatomical familiarity of 3D brain models and planar sectional views. We distribute this type of visualization both in a traditional stand-alone interactive application and as a novel, lightweight web-accessible system. The web interface integrates precomputed neural-path representations into a geographical digital-maps framework with associated labels, metrics, statistics, and linkouts. Anecdotal and quantitative comparisons of the present method with a recently proposed 2D point representation suggest that our representation is more intuitive and easier to use and learn. Similarly, users are faster and more accurate in selecting bundles using the 2D path representation than the 2D point representation. Finally, expert feedback on the web interface suggests that it can be useful for collaboration as well as quick exploration of data.
Construction of Chimerical Fungal Phytase and its Resistance to Proteolysis (2008)

Chimera Ⅰ,Ⅱ and Ⅲ were created by stepwise substitutions of DNA fragments encoding region 1-47,178-237 and 338-381 from Aspergillus niger NRRL 3135 phytase(Anp) gene for their counterparts in Aspergillus fumigatus phytase(Afp) gene,expressed in Pichia pastoris,and then purified.All chimera and parent phytases resisted to pepsin.Afp and all chimeras lost 13%～23% phytase activities at m(trypsin)/m(phytase)ratio of 0.1,while Anp was thoroughly inactivated.However,SDS-PAGE of trypsin digestion results suggested serious proteolysis of Chimera Ⅱ and Ⅲ.But nondenaturing PAGE analysis showed they still kept structural intact in nature state after trypsin treatment.Chimera phtases also possessed novel pH profiles and thermo stability different from Anp and Afp.These results demonstrated the feasibility of improving fungal phytase via gene fragment repalcement.
Decamethylcucurbit[5]uril (1992)

Patience is a virtue in chemistry too! This is demonstrated once again by the synthesis of the title compound 1 from dimethylglycoluril and formaldehyde in boiling nitric acid, and the structural investigation of this new molecular receptor. The crystallization of 1 from dilute nitric acid took twelve months!
Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence. (2022)

Amid the pandemic of 2019 novel coronavirus disease (COVID-19) infected by SARS-CoV-2, a vast amount of drug research for prevention and treatment has been quickly conducted, but these efforts have been unsuccessful thus far. Our objective is to prioritize repurposable drugs using a drug repurposing pipeline that systematically integrates multiple SARS-CoV-2 and drug interactions, deep graph neural networks, and in-vitro/population-based validations. We first collected all the available drugs (n= 3,635) involved in COVID-19 patient treatment through CTDbase. We built a SARS-CoV-2 knowledge graph based on the interactions among virus baits, host genes, pathways, drugs, and phenotypes. A deep graph neural network approach was used to derive the candidate representation based on the biological interactions. We prioritized the candidate drugs using clinical trial history, and then validated them with their genetic profiles, in vitro experimental efficacy, and electronic health records. We highlight the top 22 drugs including Azithromycin, Atorvastatin, Aspirin, Acetaminophen, and Albuterol. We further pinpointed drug combinations that may synergistically target COVID-19. In summary, we demonstrated that the integration of extensive interactions, deep neural networks, and rigorous validation can facilitate the rapid identification of candidate drugs for COVID-19 treatment. This is a post-peer-review, pre-copyedit version of an article published in Scientific Reports The final authenticated version is available online at: https://www.nature.com/articles/s41598-021-02353-5.
Development of an actively adaptable in-pipe robot (2009)

This paper proposes an in-pipe robot adaptable to pipe diameter change. The robot can adapt to 400 to 700 mm diameter piping. A pantograph mechanism provides the adaptability and the robot drives using tracks. One track module consists of front and rear tracks connected by an active joint with structural compliance. Its passive foldable characteristics provide information of the frontal space and help keeping contact with the surface on which it travels. This paper also suggests two control algorithms. One is a method to keeping proper normal force without pressure sensors. The other is a posture control to move in curved pipe by pantograph angle detection. These algorithms are verified by experiment.
Analytical Method for Pattern Generation in Five-Level Cascaded H-Bridge Inverter Using Selective Harmonic Elimination (2014)

This paper proposes an analytical procedure for computation of all pairs of valid switching angles used in pattern generation in five-level H-bridge cascaded inverters. The proposed procedure eliminates harmonic components from inverter output voltage and, for each harmonic, returns the exact boundaries of all valid modulation index intervals. Due to its simple mathematical formulation, it can be easily implemented in real time using a digital signal processor or a field-programmable gate array. In this paper, after a detailed description of the method, simulation and experimental results demonstrate the high quality of achievable results.
Formal syntax and semantics of programming languages (1994)

This text developed out of our experiences teaching courses covering the formal semantics of programming languages.
Porous silicon as the carrier matrix in microstructured enzyme reactors yielding high enzyme activities (1997)

Miniaturization and silicon integration of micro enzyme reactors for applications in micro total analysis systems (µTASs) require new methods to achieve structures with a large surface area onto which the enzyme can be coupled. This paper describes a method to accomplish a highly efficient silicon microstructured enzyme reactor utilizing porous silicon as the carrier matrix. The enzyme activity of microreactors with a porous layer was recorded and compared with a microreactor without the porous layer.
Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications (2018)

The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogram human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy. However, fundamental questions have been raised regarding the molecular mechanism of iPSCs generation, a process still poorly understood by scientists. The efficiency of reprogramming of iPSCs remains low due to the effect of various barriers to reprogramming. There is also the risk of chromosomal instability and oncogenic transformation associated with the use of viral vectors, such as retrovirus and lentivirus, which deliver the reprogramming transcription factors by integration in the host cell genome. These challenges can hinder the therapeutic prospects and promise of iPSCs and their clinical applications. Consequently, extensive studies have been done to elucidate the molecular mechanism of reprogramming and novel strategies have been identified which help to improve the efficiency of reprogramming methods and overcome the safety concerns linked with iPSC generation. Distinct barriers and enhancers of reprogramming have been elucidated, and non-integrating reprogramming methods have been reported. Here, we summarize the progress and the recent advances that have been made over the last 10 years in the iPSC field, with emphasis on the molecular mechanism of reprogramming, strategies to improve the efficiency of reprogramming, characteristics and limitations of iPSCs, and the progress made in the applications of iPSCs in the field of disease modelling, drug discovery and regenerative medicine. Additionally, this study appraises the role of genomic editing technology in the generation of healthy iPSCs.
A Recombinant fusion toxin targeted to the granulocyte-Macrophage colony-Stimulating factor receptor (1997)

Human granulocyte-macrophage colony stimulating factor (GMCSF) and its high affinity receptor function to regulate the proliferation and differentiation of myeloid lineage hematopoietic cells, and may participate in the pathogenesis of many malignant myeloid diseases. We have used genetic engineering based on the elucidated molecular structures of human granulocyte-macrophage colony-stimulating factor and diphtheria toxin (DT) to produce a recombinant fusion toxin, DTctGMCSF, that targets diphtheria toxin to high affinity GMCSF receptors expressed on the surface of blast cells from a large fraction of patients with acute myeloid leukemia (AML). DTctGMCSF was specifically immunoreactive with antidiphtheria toxin and anti-GMCSF antiseras, and exhibited the characteristic catalytic activity of diphtheria toxin, catalyzing the in vitro ADP-ribosylation of purified elongation factor 2. The cytotoxic effects of DTctGMCSF were examined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-tetrazolium (MTT) bromide assay of cell viability and in vivo assays of protein synthesis inhibition. DTctGMCSF were specifically cytotoxic to human leukemia cell lines bearing high affinity receptors for human GMCSF with IC50 of 10(-9) to 10(-11) M. It was not toxic to mammalian hematopoietic cell lines lacking human GMCSF (hGMCSF) receptors. In receptor positive cells, cytotoxicity can be specifically blocked by a large excess of hGMCSF, confirming that its cytotoxicity is mediated through the hGMCSF receptor. THough DTctGMCSF inhibited granulocyte-macrophage colony formation by committed myeloid progenitor cells (CFU-GM), it did not significantly affect erythroid burst formation by committed erythroid progenitor cells (BFU-E), or mixed granulocyte-erythroid-macrophage-megakaryocyte colony formation by pluripotent multilineage progenitor cells (CFU-GEMM). DTctGMCSF holds promise for the treatment of myeloid lineage malignancies, and is a useful reagent to study hematopoiesis.
Students of factors affecting career decision level and career preparation behavior -Centering on students studying Dental Technology Daegu·Gyeongbuk area- (2012)

Selecting one's career is one of the most important decisions for individuals because it will have a strong influence on his/her life. Especially for college students who are in the process of getting ready to step into the society after the graduation, career decision making becomes one of the most difficult tasks, and a real one. The purpose of this study was to analyze decision making styles and career decision making progress of Dental Laboratory Technology college students, and to test hypotheses which are related to the effects of counseling programs on students' decision making styles.
Statistics of macromolecular solutions trapped in small pores (1977)

We analyse the theoretical behaviour of macromolecular chains dissolved in a good solvent, and confined into tubes (or slits) of diameter D comparable to the coil radius. The repulsive interactions between monomers are taken into account by a scaling method which goes beyond the usual Flory Huggins approach. For the slit problem, we find five different regimes (depending on the concentration C and on the diameter D) with smooth cross-overs at all boundaries. For the tube problem, one of these regimes disappears and two cross-over lines merge, giving rise to a line of stronger discontinuity. This is related to the fact that, when D decreases down to the monomer size, different coils cannot overlap each other at all. For all regimes that thermodynamic properties, the local correlations and the overall chain size are estimated. The scaling arguments, however, predict only the power laws (in C and D) for all these quantities, and do not give precise numerical coefficients.
Reconfigurable optical wireless (2003)

We propose a natural step in freespace optical communications that is wireless. Namely, we propose the use of inertialess optical scanners as the agile free space light routing method within a multi-user free-space optical wireless network to realize all-optical advanced wireless networking. For instance, optical intersatellite links can use the highly accurate and fast beam pointing capabilities of the scanner to enhance the tradeoff between link distance and data rates.
Isolation and characterisation of collagen from the ribbon jellyfish (<i><scp>C</scp>hrysaora</i> sp.) (2013)

Summary Pepsin‐solubilised collagen from the ribbon jellyfish ( C hrysaora sp., morphotype 1) umbrella ( JPSC ) was isolated and characterised. The yield of collagen varied (9–19%, based on ash‐free dry weight) depending on the amount of pepsin used. Type II collagen was the major component of extracted collagen. The peptide map of JPSC differed from that of standard collagen type II , which indicates their different primary structures. FTIR spectra of JPSC , however, did not differ significantly from those of type II collagen. The T max of JPSC was 37.38 °C, which is higher than that of other marine collagens. Glycine was the main amino acid in JPSC (320 residues per 1000 residues), followed by glutamic acid, alanine, proline, aspartic acid and hydroxyproline. The isoelectric point of JPSC was 6.64. These results indicate that this jellyfish species has the potential to be a marine source of type II collagen that can be used in place of land‐based sources.
Polarization behavior in multiply perturbed single-mode fibers (1982)

A general theory is presented for polarization evolution characteristics in anisotropic single-mode optical fibers to which plural perturbations of different kinds are applied simultaneously. This treatment is based on modified coupled-mode theory. Polarization performance in the system can be described by a simple projection rule when the birefringence caused by individual perturbation is known. Several examples of applications are classified according to their mode coupling properties in fused silica fibers.
Additive Manufacturing Utilizing Stock Ultraviolet Curable Silicone (2017)

Extrude and Cure Additive Manufacturing (ECAM) is a method that enables 3D printing (3DP) of common thermoset materials. Ultraviolet (UV)-curable silicone is an example of a thermoset material with a large number of industrial and medical applications. 3D printed silicone prototype parts are obtained using a custom high pressure ram, valve, and UV exposure system. This paper will address issues with printing stock UV curable silicone such as electrostatic repulsion, in-nozzle curing, and extrudate slumping. One solution that addresses two issues is adding carbon black (CB) to the mixture to reduce electrostatic repulsion while also inhibiting UV cure depth, hence preventing material from curing in the nozzle. Evidence shows that too much carbon black can be detrimental to the structural stiffness of the resulting part.
In Search of the Function of the Peripheral‐Type Benzodiazepine Receptor (2004)

The peripheral-type benzodiazepine receptor (PBR) is a mitochondrial protein, involved in the regulation of cholesterol transport from the outer to the inner mitochondrial membrane, the rate-determining step in steroid hormone biosynthesis. Molecular modeling of PBR suggested that it might function as a channel for cholesterol. Indeed, cholesterol uptake and transport by bacteria cells was induced upon PBR expression. Amino acid deletion, site-directed mutagenesis, and structural studies identified a cholesterol recognition/interaction amino acid consensus sequence in the cytoplasmic carboxy-terminus of the receptor. In vitro reconstitution experiments demonstrated that the 18 kDa PBR protein binds with high affinity both drug ligands and cholesterol. In situ and in vitro studies indicated that in steroidogenic cells the StAR-induced cholesterol import into mitochondria was mediated by the outer mitochondrial membrane PBR. In search of the tissue specificity of PBR expression it was shown that the high levels of PBR expression in steroidogenic cells are due, at least in part, to the expression of Sp1/Sp3 transcription factors. Moreover, PBR's function in cholesterol transport was found to be conserved across kingdoms because a PBR-homologous Arabidopsis sequence when expressed in bacteria protoplasts caused a ligand-induced uptake of cholesterol suggesting that the Arabidopsis PBR homologue is involved in steroid import in plant mitochondria. In conclusion, these studies suggest that PBR's ability to bind and transport cholesterol is a well-conserved function of this ubiquitous protein. Expression of specific transcription factors results in the overexpression of PBR and increased cholesterol transport into mitochondria associated with a specialized function (steroidogenesis). In other tissues, PBR expression might be part of the mitochondrial membrane biogenesis process involved in increased cell proliferation (cancer, gliosis) and tissue repair (nerve damage and ischemia-reperfusion injury).
Wild-Type Measles Virus Interferes with Short-Term Engraftment of Human CD34 <sup>+</sup> Hematopoietic Progenitor Cells (2011)

Transient lymphopenia is a hallmark of measles virus (MV)-induced immunosuppression. To address to what extent replenishment of the peripheral lymphocyte compartment from bone marrow (BM) progenitor/stem cells might be affected, we analyzed the interaction of wild-type MV with hematopoietic stem and progenitor cells (HS/PCs) and stroma cells in vitro. Infection of human CD34(+) HS/PCs or stroma cells with wild-type MV is highly inefficient yet noncytolytic. It occurs independently of CD150 in stroma cells but also in HS/PCs, where infection is established in CD34(+) CD150(-) and CD34(+) CD150(+) (in humans representing HS/PC oligopotent precursors) subsets. Stroma cells and HS/PCs can mutually transmit MV and may thereby create a possible niche for continuous viral exchange in the BM. Infected lymphocytes homing to this compartment may serve as sources for HS/PC or stroma cell infection, as reflected by highly efficient transmission of MV from both populations in cocultures with MV-infected B or T cells. Though MV exposure does not detectably affect the viability, expansion, and colony-forming activity of either CD150(+) or CD150(-) HS/PCs in vitro, it efficiently interferes with short- but not long-term hematopoietic reconstitution in NOD/SCID mice. Altogether, these findings support the hypothesis that MV accession of the BM compartment by infected lymphocytes may contribute to peripheral blood mononuclear cell lymphopenia at the level of BM suppression.
Accelerating Convolutional Neural Networks for Mobile Applications (2016)

Convolutional neural networks (CNNs) have achieved remarkable performance in a wide range of computer vision tasks, typically at the cost of massive computational complexity. The low speed of these networks may hinder real-time applications especially when computational resources are limited. In this paper, an efficient and effective approach is proposed to accelerate the test-phase computation of CNNs based on low-rank and group sparse tensor decomposition. Specifically, for each convolutional layer, the kernel tensor is decomposed into the sum of a small number of low multilinear rank tensors. Then we replace the original kernel tensors in all layers with the approximate tensors and fine-tune the whole net with respect to the final classification task using standard backpropagation. \\ Comprehensive experiments on ILSVRC-12 demonstrate significant reduction in computational complexity, at the cost of negligible loss in accuracy. For the widely used VGG-16 model, our approach obtains a 6.6$\times$ speed-up on PC and 5.91$\times$ speed-up on mobile device of the whole network with less than 1\% increase on top-5 error.
Two working models for the SN2 mechanism (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTwo working models for the SN2 mechanismMartin M. Anderson Cite this: J. Chem. Educ. 1987, 64, 12, 1023Publication Date (Print):December 1, 1987Publication History Received3 August 2009Published online1 December 1987Published inissue 1 December 1987https://doi.org/10.1021/ed064p1023RIGHTS & PERMISSIONSArticle Views347Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Coherent Control of Retinal Isomerization in Bacteriorhodopsin (2006)

Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.