gebhart/patrepeval huggingface dataset:
SCREAM I: A single mask, single-crystal silicon process for microelectromechanical structures (2002)

A process outline for a one-mask version of the single-crystal silicon reactive etch and metal (SCREAM) process called SCREAM-I, for fabricating silicon microelectromechanical (MEM) devices, is presented. The process defines single-crystal silicon (SCS) high-aspect ratio beams using submicron optical lithography. The process defines MEM devices with a single mask, including contact pads, interconnects, released beams, and lateral capacitors. SCREAM 1 is a self-aligned, low-temperature (<300 degrees C) process that can be completed in approximately=6-8 hr. All fabrication steps rely on industry standard, high-throughput fabrication tools. Beam elements 0.5 mu m to 5 mu m in width can be fabricated with aspect ratios of greater than 10 to 1.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of the Influence of Compound Structure on Stacked-Dimer Formation in the DNA Minor Groove (2001)

The Human Genome Project as well as sequencing of the genomes of other organisms offers a wealth of DNA targets for both therapeutic and diagnostic applications, and it is important to develop additional DNA binding motifs to fully exploit the potential of this new information. We have recently found that an aromatic dication, DB293, with an amidine-phenyl-furan-benzimidazole-amidine structure can recognize specific sequences of DNA by binding in the minor groove as a dimer [Wang, L., Bailly, C., Kumar, A., Ding, D., Bajic, M., Boykin, D. W., and Wilson, W. D. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 12-16]. The dimer binding is strong, highly cooperative and, in contrast to many closely related heterocyclic dications, has both GC and AT base pairs in the minor groove binding site. The aromatic heterocycle stacked dimer is quite different in structure from the polyamide-lexitropsin type compounds, and it is a dication while all lexitropsin dimers are monocations. The heterocyclic dimer represents only the second small molecule class that can recognize mixed sequences of DNA. To test the structural limits on the new type of complex, it is important to probe the influence of compound charge, chemical groups, and structural features. The effects of these compound molecular variations on DNA complex formation with several DNA sequences were evaluated by DNase I footprinting, CD and UV spectroscopy, thermal melting, and quantitative analysis with surface plasmon resonance biosensor methods. Conversion of the amidines to guanidinium groups does permit the cooperative dimer to form but removal of one amidine or addition of an alkyl group to the amidine strongly inhibited dimer formation. Changing the phenyl of DB293 to a benzimidazole or the benzimidazole to a phenyl or benzofuran also inhibited dimer formation. The results show that formation of the minor groove stacked-dimer complex is very sensitive to compound structure. The discovery of the aromatic dimer mode offers new opportunities to enhance the specificity and expand the range of applications of the compounds that target DNA.
The dynamic relationship between COVID-19 cases and SARS-CoV-2 wastewater concentrations across time and space: considerations for model training data sets (2022)

Abstract During the COVID-19 pandemic, wastewater-based surveillance has been used alongside diagnostic testing to monitor infection rates. With the decline in cases reported to public health departments due to at-home testing, wastewater data may serve as the primary input for epidemiological models, but training these models is not straightforward. We explored factors affecting noise and bias in the ratio between wastewater and case data collected in 26 sewersheds in California from October 2020 to March 2022. The strength of the relationship between wastewater and case data appeared dependent on sampling frequency and population size, but was not increased by wastewater normalization to flow rate or case count normalization to testing rates. Additionally, the lead and lag times between wastewater and case data varied over time and space, and the ratio of log-transformed individual cases to wastewater concentrations changed over time. This ratio increased sequentially in the Epsilon/Alpha, Delta, and Omicron BA.1 variant surges of COVID-19 and was also related to the diagnostic testing rate. Based on this analysis, we present a framework of scenarios describing the dynamics of the case to wastewater ratio to aid in data handling decisions for ongoing modeling efforts.
Biomedical Research Programs at Present and Future High-Energy Particle Accelerators (2020)

Biomedical applications at high-energy particle accelerators have always been an important section of the applied nuclear physics research. Several new facilities are now under constructions or undergoing major upgrades. While the main goal of these facilities is often basic research in nuclear physics, they acknowledge the importance of including biomedical research programs and of interacting with other medical accelerator facilities providing patient treatments. To harmonize the programs, avoid duplications, and foster collaboration and synergism, the International Biophysics Collaboration is providing a platform to several accelerator centers with interest in biomedical research. In this paper, we summarize the programs of various facilities in the running, upgrade, or construction phase.
Radiation-force-based estimation of acoustic attenuation using harmonic motion imaging (HMI) in phantoms andin vitrolivers before and after HIFU ablation (2015)

Acoustic attenuation represents the energy loss of the propagating wave through biological tissues and plays a significant role in both therapeutic and diagnostic ultrasound applications. Estimation of acoustic attenuation remains challenging but critical for tissue characterization. In this study, an attenuation estimation approach was developed using the radiation-force-based method of harmonic motion imaging (HMI). 2D tissue displacement maps were acquired by moving the transducer in a raster-scan format. A linear regression model was applied on the logarithm of the HMI displacements at different depths in order to estimate the acoustic attenuation. Commercially available phantoms with known attenuations (n = 5) and in vitro canine livers (n = 3) were tested, as well as HIFU lesions in in vitro canine livers (n = 5). Results demonstrated that attenuations obtained from the phantoms showed a good correlation (R² = 0.976) with the independently obtained values reported by the manufacturer with an estimation error (compared to the values independently measured) varying within the range of 15-35%. The estimated attenuation in the in vitro canine livers was equal to 0.32 ± 0.03 dB cm(-1) MHz(-1), which is in good agreement with the existing literature. The attenuation in HIFU lesions was found to be higher (0.58 ± 0.06 dB cm(-1) MHz(-1)) than that in normal tissues, also in agreement with the results from previous publications. Future potential applications of the proposed method include estimation of attenuation in pathological tissues before and after thermal ablation.
Reply (2008)

Retina: October 2008 - Volume 28 - Issue 9 - p 1372-1373 doi: 10.1097/IAE.0b013e3181846650
Quick, efficient and effective patient-specific intensity-modulated radiation therapy quality assurance using log file and electronic portal imaging device (2017)

The methodology demonstrated can be used for establishing the accuracy of trajectory log data and for independent routine IMRT QA by generating single number like gamma index to indicate pass or fail of an IMRT treatment plan. The QA indices such as numbers of occurrences of ≥2 mm error in LPS are found more than 5% of total number of occurrences; the dosimetric review of planned treatment is advisable.
Magnetic domains in magnetostrictive Fe–Ga alloys (2008)

Lorentz microscopy was applied to the observation of magnetic domains in iron-gallium (Fe–Ga) alloys. Results did not show any link between the magnetic domains and the magnetostriction enhancement by Ga addition, but did reveal that the drastic decrease in magnetostriction for Fe–31.2 at. % Ga was due to the presence of large scale precipitates. Magnetic domain features did not change in the alloys of A2, D03, A2+D03, A2+B2+D03, and A2+fine scale precipitates. Large scale precipitates within the slow-cooled Fe–31.2 at. % Ga affected both the distribution and wall motion of magnetic domains.
Bilirubin Can Induce Tolerance to Islet Allografts (2005)

Induction of heme oxygenase-1 (HO-1) expression in recipients of allogeneic islets can lead to long-term survival (>100 d) of those islets. We tested whether administration of bilirubin would substitute for the beneficial effects of HO-1 expression in islet transplantation. Administering bilirubin to the recipient (B6AF1) or incubating islets in a bilirubin-containing solution ex vivo led to long-term survival of allogeneic islets in a significant percentage of cases. In addition, administering bilirubin to only the donor frequently led to long-term survival of DBA/2 islets in B6AF1 recipients and significantly prolonged graft survival of BALB/c islets in C57BL/6 recipients. Donor treatment with bilirubin up-regulated mRNA expression of protective genes such as HO-1 and bcl-2 and suppressed proinflammatory and proapoptotic genes including monocyte chemoattractant protein-1 and caspase-3 and -8 in the islet grafts before transplantation. Furthermore, treatment of only the donor suppressed the expression of proinflammatory cytokines including TNF-alpha, inducible nitric oxide synthase, monocyte chemoattractant protein-1, and other proapoptotic and proinflammatory genes normally seen in the islets after transplantation. Donor treatment also reduced the number of macrophages that infiltrated the islet grafts in the recipients. Preincubation of betaTC3 cells with bilirubin also protected the cells from lipid peroxidation. Our data suggests that the potent antioxidant and antiinflammatory actions of bilirubin may contribute to islet survival.
Enhanced transport bindings for efficient SOAP messaging (2005)

Within the past years the Web service technology emerged into more and more fields of application. In some cases the classical approach of using HTTP as a transport binding for SOAP seems no longer adequate. As a full scale application protocol HTTP causes a high amount of protocol overhead and is too inflexible for many Web Service scenarios. In this paper we initially give an in-depth review of existing transport bindings with a strong focus on data rate efficiency. Then we introduce an advanced UDP binding called PURE that significantly reduces the protocol overhead and enables interesting additional features such as point-to-multipoint communication via IP multicast and broadcast.
Chlamydia1 Infections, a Worldwide Problem (1981)

George Williams Hooper Foundation and the Francis 1. Proctor Foundation, University of California, San Francisco, California
A GaAs pressure sensor with frequency output based on resonant tunneling diodes (1999)

We present a novel bulk semiconductor pressure sensor based on an Al/sub x/Ga/sub 1-x/As/GaAs resonant tunneling diode (RTD) with a frequency output. A relaxation oscillator is obtained with the RTD biased in the negative differential resistance (NDR) region. Pressure applied to the RTD changes the frequency of oscillation due to the shift in current-voltage characteristics. Frequency measurements have been performed on [001]-oriented RTD's with [110]-compressive uniaxial pressure. Sensitivities of up to 0.8 kHz/MPa at 113 kHz have been measured. The main feature of this sensor type is the direct frequency output obtained by using only a maximum of three components including the RTD. Using a simplified differential equation of the oscillator circuit, the pressure-dependent effects of the RTD current-voltage characteristics on the sensor output have been investigated.
Scanning tunneling microscopy of mercapto-hexyl-oligonucleotides attached to gold (1996)

6-mercapto hexyl-oligonucleotides bind to a gold surface strongly enough to permit imaging by a scanning tunneling microscope (STM). STM images showed worm-like chains that were approximately 12-(A-wide for single-stranded DNA and 20-(A-wide for double-stranded DNA. The chain lengths corresponded to 3.4 +/- 0.4 A per basepair for double-stranded DNA and 2.2 +/- 0.4 A per base for single-stranded DNA. This unexpectedly short length for single-stranded DNA was confirmed using oligomers with both single- and double-stranded regions. When the attachment of the samples was weakened (by imaging in water or scraping with the STM tip) the images changed to pairs of "blobs," apparently reflecting the attachment points of the molecules to the gold surface. Given this interpretation, images of DNA containing a five-base bulge imply that the bulge bends the oligomer by 90 degrees +/- 20 degrees.
Collaborative integration of ultrafine Fe2P nanocrystals into Fe, N, P-codoped carbon nanoshells for highly-efficient oxygen reduction (2023)

The rational design and facile synthesis of cost-effective and high-performance carbon-based catalysts for oxygen reduction reaction (ORR) is of great significance but remain challenging. Herein, we report the crafting of a robust Fe,N,P-codoped, ultrafine Fe2P nanocrystals decorated, highly hierarchical porous carbon nanoshells (denoted Fe,N,P-CNSs/Fe2P) via a simple yet robust one-step synergetic phosphorization and pyrolysis approach for highly-efficient ORR. Specifically, well-defined polypyrrole-co-polyaniline hollow nanospheres with a shell thickness of ≈ 43 nm (PPy-co-PANI-HNs) are first elaborately synthesized via a facile soft-templating (Triton X-100 micelles) copolymerization of pyrrole and aniline monomers. Subsequent one-step synergetic phosphorization and pyrolysis of PPy-co-PANI-HNs pre-impregnated with NaH2PO2·H2O and FeCl3 (H2PO2-,Fe3+@PPy-co-PANI-HNs) yields Fe,N,P-CNSs/Fe2P with a well-crafted ultrathin nanoshell (shell thickness of ≈13 nm) architecture containing abundant hierarchical porosity. Remarkably, an alkaline electrolyte capitalizing on the resulting Fe,N,P-CNSs/Fe2P manifests excellent ORR performance with the half-wave and onset potentials (E1/2 of 0.854 V and Eonset of 0.955 V) comparable to Pt/C, diffusion limited current density (JL of −5.98 mA cm−2) higher than Pt/C, and long-time durability and methanol resistance better than Pt/C, demonstrating great potential as air cathode in zinc-air batteries (maximum power density of 170 mW cm−2 and specific capacity of 824.5 mA h g−1). Combined experimental and theoretical studies reveal that the impressive ORR performance of Fe,N,P-CNSs/Fe2P originates from simultaneous compositional (i.e., Fe,N,P-codoping and ultrafine Fe2P nanocrystals decorating) and structural (i.e., hierarchically porous ultrathin nanoshell architecture) tailoring enabled by the judicious one-step synergetic phosphorization and pyrolysis.
Isolation and 1H and 13C NMR of Ammiol and Khellol Glucosides (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsolation and 1H and 13C NMR of Ammiol and Khellol GlucosidesLarry W. Tjarks, Gayland F. Spencer, and Eric P. SeestCite this: J. Nat. Prod. 1989, 52, 3, 655–656Publication Date (Print):May 1, 1989Publication History Published online1 July 2004Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/np50063a033https://doi.org/10.1021/np50063a033research-articleACS PublicationsRequest reuse permissionsArticle Views96Altmetric-Citations4LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Suppression of Vaccine Immunity by Inflammatory Monocytes (2012)

Vaccine adjuvant-induced inflammation augments vaccine immunity in part by recruiting APCs to vaccine draining lymph nodes (LNs). However, the role of one APC subtype, inflammatory monocytes, in regulating vaccine immunity in healthy animals has not been fully examined in detail. Therefore, vaccine-mediated monocyte recruitment and subsequent immune responses were investigated using murine vaccination models and in vitro assays. Recruitment of inflammatory monocytes to vaccine draining LNs was rapid and mediated primarily by local production of MCP-1, as revealed by studies in MCP-1(-/-) mice. Interrupting monocyte recruitment to LNs by either transient monocyte depletion or monocyte migration blockade led to marked amplification of both cellular and humoral immune responses to vaccination. These results were most consistent with the idea that rapidly mobilized inflammatory monocytes were actually suppressing vaccine responses. The suppressive nature of vaccine-elicited monocytes was confirmed using in vitro cocultures of murine monocytes and T cells. Furthermore, it was determined that inflammatory monocytes suppressed T cell responses by sequestering cysteine, as cysteine supplementation in vitro and in vivo appreciably augmented vaccine responses. These findings indicated, therefore, that vaccination-elicited inflammation, although necessary for effective immunity, also generated potent counter-regulatory immune responses that were mediated primarily by inflammatory monocytes. Therefore, interrupting monocyte-mediated vaccine counterregulatory responses may serve as an effective new strategy for broadly amplifying vaccine immunity.
Cell‐specific targeting of extracellular vesicles through engineering the glycocalyx (2022)

Extracellular vesicles (EVs) are promising carriers for the delivery of a variety of chemical and biological drugs. However, their efficacy is limited by the lack of cellular specificity. Available methods to improve the tissue specificity of EVs predominantly rely on surface display of proteins and peptides, largely overlooking the dense glycocalyx that constitutes the outermost layer of EVs. In the present study, we report a reconfigurable glycoengineering strategy that can endogenously display glycans of interest on EV surface. Briefly, EV producer cells are genetically engineered to co-express a glycosylation domain (GD) inserted into the large extracellular loop of CD63 (a well-studied EV scaffold protein) and fucosyltransferase VII (FUT7) or IX (FUT9), so that the engineered EVs display the glycan of interest. Through this strategy, we showcase surface display of two types of glycan ligands, sialyl Lewis X (sLeX) and Lewis X, on EVs and achieve high specificity towards activated endothelial cells and dendritic cells, respectively. Moreover, the endothelial cell-targeting properties of sLeX-EVs were combined with the intrinsic therapeutic effects of mesenchymal stem cells (MSCs), leading to enhanced attenuation of endothelial damage. In summary, this study presents a reconfigurable glycoengineering strategy to produce EVs with strong cellular specificity and highlights the glycocalyx as an exploitable trait for engineering EVs.
Antibiotics-induced monodominance of a novel gut bacterial order (2019)

The bloom of <sup>U</sup><i>B. ceftriaxensis</i> and a subsequent one of <i>Parabacteroides distasonis</i> demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.
The Anti-inflammatory Effects of Methylsulfonylmethane on Lipopolysaccharide-Induced Inflammatory Responses in Murine Macrophages (2009)

Methylsulfonylmethane (MSM), also known as dimethyl sulfone and methyl sulfone, is an organic sulfur-containing compound that occurs naturally in a variety of fruits, vegetables, grains, and animals, including humans. In the present study, we demonstrated the anti-inflammatory effects of MSM in lipopolysaccharide (LPS)-stimulated murine macrophages, RAW264.7 cells. MSM significantly inhibited the release of nitric oxide and prostaglandin E(2) by alleviating the expression of inducible nitric oxide synthase and cyclooxygenase-2 in LPS-stimulated RAW264.7 cells. Furthermore, the levels of interleukin-6 and tumor necrosis factor-alpha were decreased by MSM treatment in cell culture supernatants. Further study indicated that the translocation of the p65 subunit of nuclear factor (NF)-kappaB to the nucleus was inhibited by MSM treatment in LPS-stimulated RAW264.7 cells, in which it helped block degradation of inhibitor of NF-kappaB. In addition, in vivo studies demonstrated that topical administration of MSM at 500-1250 microg/ear resulted in similar inhibitory activities in 12-O-tetradecanoylphorbol 13-acetate-induced mouse ear edema. Collectively, theses results indicate that MSM inhibits LPS-induced release of pro-inflammatory mediators in murine macrophages through downregulation of NF-kappaB signaling.
Energy-Based Modeling and Control of a Piezotube Actuated Optical Fiber (2022)

This article presents an energy-based modeling and control design method for a piezotube actuated optical fiber. A nonlinear infinite dimensional port Hamiltonian (pH) formulation of the 3-D flexible optical fiber is derived from the Cosserat rod dynamical equations. Then, the proposed infinite dimensional model is discretized using a pH structure and passivity preserving discretization method for the simulation and control design. This model is then validated against experimental data obtained using a built-in experimental setup equipped with a MEMS Analyzer. A complete pH formulation of the piezotube actuated optical fiber is proposed, combining the Cosserat rod model and actuator dynamics. This model is used for the end-point path control design using an interconnection and damping assignment passivity based control (IDA-PBC) method. Both the proposed pH model of the overall system and the controller are validated in simulation and against experimental results.
Hypertension Detection and Follow-up Program Study of Serum Retinol, Retinol-Binding Protein, Total Carotenoids, and Cancer Risk: A Summary<xref ref-type="fn" rid="FN1">1</xref><xref ref-type="fn" rid="FN2">2</xref> (1984)

In a recently reported study by us, no significant associations were found between retinol, retinol-binding protein (RBP), and total carotenoid levels in prediagnositic serum and the incidence of cancer at all sites combined. Inasmuch as other investigators, in addition to us, have not been able to confirm the two original reports of an inverse association between serum retinol and overall cancer incidence, the relationship, if it exists at all, is probably complex and limited to certain population subgroups. Such subgroups may be defined by extreme values of serum retinol, certain levels of other nutrients, or specific types of cancer. In the present study an inverse association was observed between serum retinol levels and cancer among subjects with low serum selenium levels and for subjects with gastrointestinal cancer. In addition, the risk of cancer was elevated for those individuals with the combination of low serum retinol and high RBP. However, since significant associations will arise by chance alone when many subgroups are examined, these findings are difficult to interpret. Additional studies will be needed to determine whether they are reproducible or are simply the results of chance.