gebhart/patrepeval huggingface dataset:
Photoablation of plasma polymerized polyacetylene films (1987)

Polyacetylenes are the simplest organic polymers which readily undergo photoablation. We describe and justify the use of a less well-known technique for synthesizing polyacetylenes and characterize the films so formed. This is of interest because polyacetylenes are organic semiconductors. Glow discharge polymerization yields layers around 1 μm thick. Efficient ablative decomposition of polyacetylene films requires multishot exposures. The role of conjugation in the chains and efficiency of the process as opposed to thermal decomposition is discussed. Because the polymer contains only carbon and hydrogen, ablation in vacuum yields readily identifiable products.
Near‐Surface Spectrally Stable Nitrogen Vacancy Centres Engineered in Single Crystal Diamond (2012)

A method for engineering thin (<100 nm) layers of homoepitaxial diamond containing high quality, spectrally stable, isolated nitrogen-vacancy (NV) centres is reported. The photoluminescence excitation linewidth of the engineered NVs are as low as 140 MHz, at temperatures below 12 K, while the spin properties are at a level suitable for quantum memory and spin register applications. This methodology of NV fabrication is an important step toward scalable and practical diamond based photonic devices suitable for quantum information processing.
Mechanistic Aspects of Alkylchlorosilane Coupling Reactions (1997)

Toluene solutions of monochlorosilane and trichlorosilane coupling agents are shown to react differently with hydrated and dry silicon surfaces. For typical hydrated surfaces produced by piranha (H2O2 + H2SO4) etching, the saturation coverages of octadecyldimethylchlorosilane (ODMS) (one reactive Si−O bond) are approximately a third that of octadecyltrichlorosilane (ODTS) (three reactive Si−O bonds). In contrast, for samples vacuum baked at 400 °C, the saturation coverages of ODTS and ODMS are comparable. These data are consistent with coupling reactions limited to the surface hydroxyl groups. The ODTS saturation coverage on vacuum-fired silicon samples can be increased by soaking in water followed by a second ODTS exposure. From X-ray photoelectron spectra (XPS) and secondary ion mass spectra (SIMS) obtained as a function of solution exposure time, saturation coverage is shown to take at least 2 h and to be limited by the concentration of surface hydroxyl groups; a direct correlation is seen in SIMS between the exposure dependent gain in the surface alkyl signal and the loss of the SiOH signal. The coefficient of friction of silicon (piranha etched) is reduced by an order of magnitude by saturation coverages of ODTS, but continued rubbing for over 50 cycles at a normal loading of 245 mN results in decay of the friction coefficient to the value appropriate for uncoated silicon. These results as well as others from the literature are discussed in this paper in terms of a mechanism for the reaction of alkylchlorosilanes with silicon.
Molecular obesity, potency and other addictions in drug discovery (2011)

Molecular Obesity is the tendency for lead optimisation to yield candidate molecules that are unfit for their continued survival towards becoming a drug. Reasons for this and other issues are discussed.
Review of Alterations in Perlecan-Associated Vascular Risk Factors in Dementia (2020)

Perlecan is a heparan sulfate proteoglycan protein in the extracellular matrix that structurally and biochemically supports the cerebrovasculature by dynamically responding to changes in cerebral blood flow. These changes in perlecan expression seem to be contradictory, ranging from neuroprotective and angiogenic to thrombotic and linked to lipid retention. This review investigates perlecan's influence on risk factors such as diabetes, hypertension, and amyloid that effect Vascular contributions to Cognitive Impairment and Dementia (VCID). VCID, a comorbidity with diverse etiology in sporadic Alzheimer's disease (AD), is thought to be a major factor that drives the overall clinical burden of dementia. Accordingly, changes in perlecan expression and distribution in response to VCID appears to be injury, risk factor, location, sex, age, and perlecan domain dependent. While great effort has been made to understand the role of perlecan in VCID, additional studies are needed to increase our understanding of perlecan's role in health and in cerebrovascular disease.
A highly selective agonist for the metabotropic glutamate receptor mGluR2 (2011)

The three conformationally restricted cyclopropyl glutamate analogues (3, 4, 5) were synthesised and their affinity for ionotropic and activity at metabotropic glutamate receptors were probed. Compound 4 turned out to be a highly selective agonist at the metabotropic glutamate receptor mGluR2 with at least two orders of magnitude selectivity in potency compared to the very homologous mGluR3 as well as mGluR1, 4, 5, 7. We also tried to synthesise the two epimers of 6, but the two compounds underwent fast epimerisation in H2O. Furthermore, two cyclopropyl arginine analogues (7, 8) were synthesised and characterised pharmacologically at GPRC6A.
Modular Assembly of Purine-like Bisphosphonates as Inhibitors of HIV-1 Reverse Transcriptase (2014)

Bisphosphonates can mimic the pyrophosphate leaving group of the nucleotidyl transfer reaction and effectively inhibit RNA/DNA polymerases. In a search of HIV-1 reverse transcriptase (RT) inhibitors, a new chemotype of nonhydrolyzable purine diphosphate mimic was synthesized. A modular synthetic protocol was developed, utilizing 2-amino-6-(methylthio)-4-(trimethylsilyl)nicotinonitrile as the key synthon in the preparation of highly substituted 2-aminonicotinonitriles. These building blocks were subsequently elaborated to the pyrido[2,3-d]pyrimidine bisphosphonates (PYPY-BPs). Biochemical screening identified analogs of PYPY-BPs that inhibit HIV-1 RT-catalyzed DNA synthesis.
Next-Generation data storage: Transistor and DNA (2018)

With the generation of diverse data growing at exponential rates, investigating better digital storage media is inevitable. Currently, one solution is the utilization of solid-state based memory devices, which offer several desirable characteristics, including very fast write/read operations, scalability, and reduced fabrication costs. However, with the increased need for long term and large storage space, their data retention capabilities drastically decline. Another emerging storage technology on the horizon is the biotechnological based DNA storage, which renders a phenomenal storage capacities. In this paper, basics of these two promising storage technologies are reviewed and their potential future trends are discussed.
Chemoselectivity in Chemical Biology: Acyl Transfer Reactions with Sulfur and Selenium (2011)

A critical source of insight into biological function is derived from the chemist's ability to create new covalent bonds between molecules, whether they are endogenous or exogenous to a biological system. A daunting impediment to selective bond formation, however, is the myriad of reactive functionalities present in biological milieu. The high reactivity of the most abundant molecule in biology, water, makes the challenges all the more difficult. We have met these challenges by exploiting the reactivity of sulfur and selenium in acyl transfer reactions. The reactivity of both sulfur and selenium is high compared with that of their chalcogen congener, oxygen. In this Account, we highlight recent developments in this arena, emphasizing contributions from our laboratory. One focus of our research is furthering the chemistry of native chemical ligation (NCL) and expressed protein ligation (EPL), two related processes that enable the synthesis and semisynthesis of proteins. These techniques exploit the lower pK(a) of thiols and selenols relative to alcohols. Although a deprotonated hydroxyl group in the side chain of a serine residue is exceedingly rare in a biological context, the pK(a) values of the thiol in cysteine (8.5) and of the selenol in selenocysteine (5.7) often render these side chains anionic under physiological conditions. NCL and EPL take advantage of the high nucleophilicity of the thiolate as well as its utility as a leaving group, and we have expanded the scope of these methods to include selenocysteine. Although the genetic code limits the components of natural proteins to 20 or so α-amino acids, NCL and EPL enable the semisynthetic incorporation of a limitless variety of nonnatural modules into proteins. These modules are enabling chemical biologists to interrogate protein structure and function with unprecedented precision. We are also pursuing the further development of the traceless Staudinger ligation, through which a phosphinothioester and azide form an amide. We first reported this chemical ligation method, which leaves no residual atoms in the product, in 2000. Our progress in effecting the reaction in water, without an organic cosolvent, was an important step in the expansion of its utility. Moreover, we have developed the traceless Staudinger reaction as a means for immobilizing proteins on a solid support, providing a general method of fabricating microarrays that display proteins in a uniform orientation. Along with NCL and EPL, the traceless Staudinger ligation has made proteins more readily accessible targets for chemical synthesis and semisynthesis. The underlying acyl transfer reactions with sulfur and selenium provide an efficient means to synthesize, remodel, and immobilize proteins, and they have enabled us to interrogate biological systems.
The Hemostatic State in Cancer Patients: The Relationship between Hypercoagulable Markers and Cancer Prognostic Markers. (2004)

Abstract Background: The most common abnormalities described in cancer patients are the elevation of the clotting factors V, VIII, IX, and XI; increased fibrinogen/fibrin degradation products; hyperfibrinogenemia; and thrombocytosis. We performed a prospective study to evaluate the relationship between changes in hemostatic parameters and cancer prognostic markers. Methods: We enrolled patients who were diagnosed as having different types of nonhematological, solid organ tumor. The most important natural inhibitors of abnormal coagulation (protein C, protein S, and antithrombin) and D-dimer and prothrombin activation peptide F 1 + 2 as markers of the status of coagulation system were studied in these groups of patients prior to any form of therapy. These markers were repeatedly measured with each treatment course and their results were correlated with other markers of tumor prognosis. These parameters were also studied before and after any surgical intervention for the tumor. The main aim of the study was to assess the changes in hemostatic parameters and to see if these changes can be used as markers for tumor prognosis. Results: Fifty-two patients were enrolled in this study. Two patients had esophageal adenocarcinoma, 6 had gastric cancer, 16 had colorectal cancer, 4 had exocrine pancreatic carcinoma, 2 had adenocarcinoma of gallbladder, 6 had adenocarcinomatous type of non-small cell lung cancer, 2 had small cell lung cancer, 12 had infiltrating breast carcinoma, and 2 had ovarian cancer. In all cases, the elevation of the levels of hypercoaguable markers was directly correlated with tumor stage, tumor markers, and radiological findings of cancer state. Additionally, the level of naturally occurring coagulation inhibitors were all decreased with progression of tumor. These hypercoaguable parameters were also raised after surgical resection of these tumors. Conclusions: Based on our findings, determination of D-dimer, F1 + 2, protein C, protein S, and antithrombin levels can be used as markers to assess the tumor prognosis.
Bounds on MIMO channel estimation and equalization with side information (2002)

We present constrained Cramer-Rao bounds for multi-input multi-output (MIMO) channel and source estimation. We find the MIMO Fisher information matrix (FIM) and consider its properties, including the maximum rank of the unconstrained FIM, and develop necessary conditions for the FIM to achieve full rank. Equality constraints provide a means to study the potential value of side information, such as training (semi-blind case), constant modulus (CM) sources, or source non-Gaussianity. Non-redundant constraints may be combined in an arbitrary fashion, so that side information may be different for different sources. The bounds are useful for evaluating various MIMO source and channel estimation algorithms. We present an example using the constant modulus blind equalization algorithm.
Semantic Consistency Guided Instance Feature Alignment for 2D Image-Based 3D Shape Retrieval (2020)

2D image-based 3D shape retrieval (2D-to-3D) investigates the problem of matching the relevant 3D shapes from gallery dataset when given a query image. Recently, adversarial training and environmental style transfer learning have been successful applied to this task and achieved state-of-the-art performance. However, there still exist two problems. First, previous works only concentrate on the connection between the label and representation, where the unique visual characteristics of each instance are paid less attention. Second, the confused features or the transformed images can only cheat the discriminator but can not guarantee the semantic consistency. In another words, features of 2D desk may be mapped nearby the features of 3D chair. In this paper, we propose a novel semantic consistency guided instance feature alignment network (SC-IFA) to address these limitations. SC-IFA mainly consists of two parts, instance visual feature extraction and cross-domain instance feature adaptation. For the first module, unlike previous methods, which merely employ 2D CNN to extract the feature, we additionally maximize the mutual information between the input and feature to enhance the capability of feature representation for each instance. For the second module, we first introduce the margin disparity discrepancy model to mix up the cross-domain features in an adversarial training way. Then, we design two feature translators to transform the feature from one domain to another domain, and impose the translation loss and correlation loss on the transformed features to preserve the semantic consistency. Extensive experimental results on two benchmarks, MI3DOR and MI3DOR-2, verify SC-IFA is superior to the state-of-the-art methods.
Editorial (2008)

The Journal of Biomechanical Engineering reports the results of original research involving the application of mechanical engineering knowledge, skills, and principles to the analysis, design, development, and function of native and engineered biological systems across all dimensional scales. Subject areas include: native and artificial organs, prostheses, bioinstrumentation and measurements, bioheat transfer, biomaterials, tissue biomechanics, bioprocess engineering, cellular and biomolecular mechanics, design and control of biological and physiological systems. The journal presents full length original research articles, technical briefs, announcements, calls for papers, calendar of events, and letters to the Editor.Along with the Associate editors and the BED, I have a mission to make JBME a premier biomedical engineering journal. For this year, several changes are in the works, including cover art. More importantly, in collaboration with the New Directions and the Executive Committees, I submitted a letter outlining changes needed to allow JBME to become internationally competitive and designated a one-year timeframe for implementation. This letter was well received by ASME and I have already engaged in discussions with Phillip DiVietro, Managing Director, ASME Publishing, to make these very necessary changes to the journal publication procedures. Immediate changes include:11. JBME, which is currently published bi-monthly, will begin monthly publication beginning with the January 2009 issue.22. The annual page budget, currently at 1,100 published pages, will be increased immediately to 1,500 published pages.33. ASME has approved the journal revenue sharing funds to support the publication of Special Issues, which will be published above and beyond the monthly issues. This will allow us to publish high-impact special issues without interfering with normal issue publication.Changes planned to be implemented include:11. Modify the ASME Journal Production process so that once a manuscript is accepted, it will be sent immediately to production and the proof generated. Once the corrected proof is returned by the authors, it will be placed immediately on-line for public access and the citation submitted to MEDLINE. The on-line version will be swapped with the actual published version once the assigned issue is published.22. Establishment of a “Legacy” JBME paper award for high-impact papers published a minimum of five years ago. It was proposed that this award be named after a major figure in Biomechanics.33. Building an endowment for JBME's Skalak best paper award.Finally, I am pleased to announce that I am appointing several new Associate Editors to start in January 2009 to help ease the load and improve review times. Announcement of the new Associate Editors will be made once the ASME Publications Committee has approved them. I look forward to reporting more good news in the very near future.
Low levels of interleukin‐4 and high levels of transforming growth factor β in rheumatoid synovitis (1990)

Since interleukin-4 (IL-4) displays agonistic effects on both T and B cells, we studied whether this lymphokine is involved in rheumatoid synovitis, a disease characterized by intense T cell infiltration and B cell stimulation. Rheumatoid arthritis synovial fluids (RA SF) contained no (less than 15 pg/ml) or very low amounts (less than 25 pg/ml) of IL-4, as measured by a sensitive and specific enzyme-linked immunosorbent assay. No IL-4 was produced by unstimulated rheumatoid synovial membrane. RA SF were found to inhibit phorbol myristate acetate (PMA)-dependent proliferation of normal peripheral blood lymphocytes (PBL). An inhibitory fraction with an apparent molecular weight of 150 kd was isolated by gel filtration. The inhibitory fraction strongly blocked the proliferation of PBL induced by PMA, PMA + IL-2, or PMA + IL-4. However, this fraction was less effective in blocking the proliferation of PBL induced by PMA + IL-2 + IL-4. High levels of transforming growth factor beta (TGF beta) were found in these RA SF, and an anti-TGF beta antibody was able to partially reduce the inhibitory activity. RA SF were found to inhibit phytohemagglutinin-induced IL-4 production by PBL. These data indicate that IL-4, similar to other T cell lymphokines, cannot be detected in RA SF and that RA SF contains an inhibitory activity, related in part to TGF beta, which blocks mitogen-induced proliferation of PBL, at least in part through an inhibition of T cell-derived lymphokine release.
Noncholinergic Penile Erection in Mice Lacking the Gene for Endothelial Nitric Oxide Synthase (2002)

With the current understanding that nitric oxide (NO) mediates penile erection, the endothelial isoform of NO synthase (eNOS) has been implicated in this function. We undertook this study applying transgenic mice with targeted deletion of the eNOS gene (eNOS-/- mice) as an experimental approach to evaluate the importance of eNOS in cholinergically stimulated erectile function in vivo. Combined pharmacostimulation with intracavernosal carbachol (3 ng) administration and submaximal cavernous nerve (CN) electrical stimulation (16 Hz, 5 millisecond, 1 V) simultaneous with intracavernosal pressure (ICP) monitoring, and both biochemical assay of NO synthase activity and Western blot analysis of eNOS protein content in penile tissue, were performed on eNOS-/- mice and wild-type controls. Combined intracavernosal carbachol administration and submaximal CN electrical stimulation raised the recorded ICP, elicited by CN electrical stimulation alone in wild-type mice (from 35.7 +/- 2.7 to 48.1 +/- 5.5 mm Hg, P < .05) but not in eNOS-/ - mice (from 54.9 +/- 6.3 to 51.0 +/- 9.5 mm Hg, not significant [NS]). Pretreatment with the nonselective nitric oxide synthase inhibitor nitro-L-arginine methyl ester (L-NAME; 100 mg intracavernosally) blocked electrically stimulated ICP responses in eNOS-/- mice to baseline levels (37.8 +/- 4.4 vs 12.7 +/- 4.0 mm Hg, P < .05). In penes of eNOS-/- mice, approximately 60% NO synthase activity of wild-type penis levels was retained (NS), and eNOS protein was absent. We concluded that eNOS-/- mice preserve erectile function on the basis of a noncholinergic but NO-dependent mechanism and that eNOS physiologically mediates penile erection under cholinergic stimulation.
Laparoscopic Surgical Simulator and Port Placement Study (2000)

We have developed a virtual laparoscopic surgical simulator and gathered data during student trial runs. The students performed simulated surgical dissections from 3 pairs of port positions with angles between the cutting and grasping instruments set to 60, 90, and 120 degrees. Preliminary data indicates improved performance at the 90 degree angle. Study updates can be found at http:¿www.hitl.washington.edu/research/lss
GaN nanostructure design for optimal dislocation filtering (2010)

The effect of image forces in GaN pyramidal nanorod structures is investigated to develop dislocation-free light emitting diodes (LEDs). A model based on the eigenstrain method and nonlocal stress is developed to demonstrate that the pyramidal nanorod efficiently ejects dislocations out of the structure. Two possible regimes of filtering behavior are found: (1) cap-dominated and (2) base-dominated. The cap-dominated regime is shown to be the more effective filtering mechanism. Optimal ranges of fabrication parameters that favor a dislocation-free LED are predicted and corroborated by resorting to available experimental evidence. The filtering probability is summarized as a function of practical processing parameters: the nanorod radius and height. The results suggest an optimal nanorod geometry with a radius of ∼50b (26 nm) and a height of ∼125b (65 nm), in which b is the magnitude of the Burgers vector for the GaN system studied. A filtering probability of greater than 95% is predicted for the optimal geometry.
Dynamin-Like Protein B of Dictyostelium Contributes to Cytokinesis Cooperatively with Other Dynamins (2019)

Dynamin is a large GTPase responsible for diverse cellular processes, such as endocytosis, division of organelles, and cytokinesis. The social amoebozoan, <i>Dictyostelium discoideum</i>, has five dynamin-like proteins: dymA, dymB, dlpA, dlpB, and dlpC. DymA, dlpA, or dlpB-deficient cells exhibited defects in cytokinesis. DlpA and dlpB were found to colocalize at cleavage furrows from the early phase, and dymA localized at the intercellular bridge connecting the two daughter cells, indicating that these dynamins contribute to cytokinesis at distinct dividing stages. Total internal reflection fluorescence microscopy revealed that dlpA and dlpB colocalized at individual dots at the furrow cortex. However, dlpA and dlpB did not colocalize with clathrin, suggesting that they are not involved in clathrin-mediated endocytosis. The fact that dlpA did not localize at the furrow in dlpB null cells and vice versa, as well as other several lines of evidence, suggests that hetero-oligomerization of dlpA and dlpB is required for them to bind to the furrow. The hetero-oligomers directly or indirectly associate with actin filaments, stabilizing them in the contractile rings. Interestingly, dlpA, but not dlpB, accumulated at the phagocytic cups independently of dlpB. Our results suggest that the hetero-oligomers of dlpA and dlpB contribute to cytokinesis cooperatively with dymA.