gebhart/patrepeval huggingface dataset:
How Low Can You Go? Low Densities of Poly(ethylene glycol) Surfactants Attract Stealth Proteins (2018)

It is now well-established that the surface chemistry and "stealth" surface functionalities such as poly(ethylene glycol) (PEG) chains of nanocarriers play an important role to decrease unspecific protein adsorption of opsonizing proteins, to increase the enrichment of specific stealth proteins, and to prolong the circulation times of the nanocarriers. At the same time, PEG chains are used to provide colloidal stability for the nanoparticles. However, it is not clear how the chain length and density influence the unspecific and specific protein adsorption keeping at the same time the stability of the nanoparticles in a biological environment. Therefore, this study aims at characterizing the protein adsorption patterns depending on PEG chain length and density to define limits for the amount of PEG needed for a stealth effect by selective protein adsorption as well as colloidal stability during cell experiments. PEG chains are introduced using the PEGylated Lutensol AT surfactants, which allow easy modification of the nanoparticle surface. These findings indicate that a specific enrichment of stealth proteins already occurs at low PEG concentrations; for the decrease of unspecific protein adsorption and finally the colloidal stability a full surface coverage is advised.
Resonance Raman Structural Evidence that the Cis-to-Trans Isomerization in Rhodopsin Occurs in Femtoseconds (2001)

Picosecond time-resolved resonance Raman spectroscopy is used to probe the structural changes of rhodopsin's retinal chromophore as the cis-to-trans isomerization reaction occurs that initiates vision. Room-temperature resonance Raman spectra of rhodopsin's photoproduct with time delays from -0.7 to 20.8 ps are measured using 2.2 ps, 480 nm pump and 1.5 ps, 600 nm probe pulses. Hydrogen-out-of-plane (HOOP) modes at 852, 871, and 919 cm(-1), fingerprint peaks at 1272, 1236, 1211, and 1166 cm(-1), and a broad red-shifted ethylenic band at 1530 cm(-1) are present at the earliest positive pump-probe time delay of 0.8 ps, indicating that the chromophore is already in a strained, all-trans configuration. Kinetic analyses of both the HOOP and ethylenic regions of the photoproduct spectra reveal that these features grow in with fast ( approximately 200 fs) and slow ( approximately 2-3 ps) components. These data provide the first structural evidence that photorhodopsin has a thermally unrelaxed, torsionally strained all-trans chromophore within approximately 1 ps, and possibly within 200 fs, of photon absorption. Following this ultrafast product formation, the all-trans chromophore cools and conformationally relaxes within a few picoseconds to form bathorhodopsin. This cooling process is revealed as an ethylenic frequency blue-shift of 6 cm(-1) (tau approximately 3.5 ps) as well as an ethylenic width narrowing (tau approximately 2 ps). The ultrafast production of photorhodopsin is likely accompanied by an impulsively driven, localized protein response. More delocalized protein modes are unable to relax on this ultrafast time scale enabling the chromophore-protein complex to store the large amounts of photon energy (30-35 kcal/mol) that are subsequently used to drive activating protein conformational changes.
Design and Construction of New Potentiometric Sensors for Determination of Copper(II) Ion Based on Copper Oxide Nanoparticles (2015)

New chemically modified carbon paste (CPEs) and screen-printed electrodes (SPEs) were fabricated incorborating copper oxide nanoparticles (CuO NPs) as a neutral ionophore and explored as Cu(II) selective electrodes. The electrodes were found to display Nernstian response over Cu(II) concentration of 5.3×10’7 to 1x10-2 and 6.1x10-8 to 1x10’2 mol L’⁎ 1. The detection limits were found to be 5.3x10’7 and 6.1x10’8 mol L’1 for modified carbon paste (MCPEs; electrodes I and II) and screen- printed electrodes (MSPEs; electrodes III and IV), respectively. The MCPEs with dibutylphthalate (DBP) (electrode I) and tricresylphosphate (TCP) (electrode II) as plasticizers were found to have slope values of 29.65±0.30 and 28.99±0.60 mV decade’1, respectively. Also, the MSPEs with DBP (electrode III) and TCP (electrode IV) plasticizers showed Nernstian slopes of 30.01±0.20 and 29.35±0.40 mV decade’1, respectively. The electrodes have fast response time (8, 10, 5 and 7s for electrodes I, II, III and IV, respectively) and good selectivity with respect to different interfering ions. The fabricated electrodes were satisfactory applied to determine Cu(II) ion in pure solutions and different real spiked water samples using the proposed potentiometric method. The results obtained applying MCPEs and MSPEs agree well with the inductively coupled plasma atomic emission spectrometry (ICP’AES).
Fiber Optic Sensor Programs At The University Of Washington (1990)

Fiber optics provide a technology which may be readily applied to chemical sensing. This application is the main thrust of fiber optic sensor development at the University of Washington. Researchers from a number of academic departments are investigating fiber optic based chemical sensors for applications in industrial, environmental, and biomedical monitoring. A brief overview is given with several examples of current sensor projects.
DOPAMINE β-HYDROXYLASE INHIBITOR PRODUCED BY GLOEOPHYLLUM STRIATUM AND ITS IDENTITY WITH OOSPONOL (1972)

A dopamine β-hydroxylase inhibitor produced by Gloeophyllum striatum was isolated and found to be identical with oosponol. The inhibition is competitive with tyramine and noncompetitve with ascorbic acid. This inhibitor showed a hypotensive effect.
A 100 Gbps flexible optoelectronic interconnection with multi-mode optical waveguide circuits (2007)

We developed a 100 Gbps bandwidth (12.5 Gbps/ch × 8 ch) flexible optoelectronic interconnection with electrical circuits and 40 um core multi-mode optical waveguide circuits. The electrical circuits work for not only electrical interconnections but also electrodes for wiring the optical devices and buffer ICs. (2 pages)
In search of a combined brucellosis and tuberculosis vaccine for cattle (2021)

Bovine brucellosis is caused by Brucella abortus. The bacterial pathogen causes economic losses because it induces abortion in cattle. Vaccination of calves with live B. abortus strain 19 induces a certain level of protection but induces persistent antibodies against cell envelope lipopolysaccharide that make it difficult to Distinguish Infected from Vaccinated Animals (DIVA). Live vaccine B. abortus strain RB51 was developed to eliminate such interfering antibodies and therefore, facilitate the differentiation of infected from vaccinated animals and help in the eradication of the disease. Vaccination with strain RB51 induces levels of protection similar to strain 19 but neither of the two vaccines give complete protection. We have been working to enhance protection induced by strain RB51 vaccine. Protective Brucella antigens can be over-expressed in strain RB51 by introducing a plasmid containing the leuB gene and the genes encoding such antigens. To avoid the expression of antibiotic resistance genes, we produced a leuB deficient strain RB51 and introduced a plasmid containing the leuB gene and the genes to be over-expressed. This new strain maintains the plasmid and has induced significantly high protection levels in mice. In addition, it allowed the construction of an RB51 vaccine strain able to express Mycobacterium bovis protective antigens so that the vaccine could protect against brucellosis and tuberculosis simultaneously.
Molecular-Clinical Correlation in Pediatric Medulloblastoma: A Cohort Series Study of 52 Cases in Taiwan (2020)

In 2016, a project was initiated in Taiwan to adopt molecular diagnosis of childhood medulloblastoma (MB). In this study, we aimed to identify a molecular-clinical correlation and somatic mutation for exploring risk-adapted treatment, drug targets, and potential genetic predisposition. In total, 52 frozen tumor tissues of childhood MBs were collected. RNA sequencing (RNA-Seq) and DNA methylation array data were generated. Molecular subgrouping and clinical correlation analysis were performed. An adjusted Heidelberg risk stratification scheme was defined for updated clinical risk stratification. We selected 51 genes for somatic variant calling using RNA-Seq data. Relevant clinical findings were defined. Potential drug targets and genetic predispositions were explored. Four core molecular subgroups (WNT, SHH, Group 3, and Group 4) were identified. Genetic backgrounds of metastasis at diagnosis and extent of tumor resection were observed. The adjusted Heidelberg scheme showed its applicability. Potential drug targets were detected in the pathways of DNA damage response. Among the 10 patients with SHH MBs analyzed using whole exome sequencing studies, five patients exhibited potential genetic predispositions and four patients had relevant germline mutations. The findings of this study provide valuable information for updated risk adapted treatment and personalized care of childhood MBs in our cohort series and in Taiwan.
The Influence of Arm and Shoulder Position on the Bear-Hug, Belly-Press, and Lift-Off Tests (2011)

Clinicians may feel comfortable in using any of the 3 tests, depending on the patient, to isolate the function of the subscapularis as a single muscle. Furthermore, clinicians should not solely focus on a patient's arm position when administering an examination but also compare the affected arm to the contralateral shoulder when appropriate.
BLM-dependent Break-Induced Replication handles DSBs in transcribed chromatin upon impaired RNA:DNA hybrids dissolution (2020)

Abstract Transcriptionally active loci are particularly prone to breakage and mounting evidence suggest that DNA Double-Strand Breaks arising in genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loops accumulation and dissolution. Here, we uncovered a critical function of the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in a R-loop dissolution-deficient background BLM switches from promoting Homologous Recombination to promoting Break-Induced Replication (BIR), which strongly impairs cell viability. Altogether our work unveils a role for BLM in BIR at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at these transcription-associated DSBs.
ChemInform Abstract: α‐Ketocyclopropane Ring‐Opening Reactions via O‐Stannyl Ketyls. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Human anti-IgE monoclonal antibody blocks passive sensitization of human and rhesus monkey bladder. (1997)

IgE antibodies may play an important role in noninfectious urinary inflammation, including interstitial cystitis (IC). In this study, urinary bladder strips were passively sensitized for 20 hours with serum from a ragweed-sensitive patient in the absence or presence of an anti-human IgE monoclonal antibody (MaE11) at 0, 1-, or 5-fold IgE concentration. The urinary bladder strips then were suspended in a superfusion apparatus for measurement of contraction and histamine release in response to antigen E (AgE) challenge. Non-sensitized tissues did not react to AgE challenge, whereas AgE challenge of passively-sensitized tissues resulted in time-dependent bladder contraction and histamine release. MaE11 abolished AgE-induced contraction and histamine release in a concentration-dependent manner. The safety of MaE11 was confirmed by its failure to contract or release histamine from passively-sensitized bladder tissues. The results of this study suggest that MaE11 may have immunotherapeutic benefit for amelioration of IgE-mediated diseases of the urinary system.
Combining Neural Networks and Tree Search for Task and Motion Planning in Challenging Environments (2017)

We consider task and motion planning in complex dynamic environments for problems expressed in terms of a set of Linear Temporal Logic (LTL) constraints, and a reward function. We propose a methodology based on reinforcement learning that employs deep neural networks to learn low-level control policies as well as task-level option policies. A major challenge in this setting, both for neural network approaches and classical planning, is the need to explore future worlds of a complex and interactive environment. To this end, we integrate Monte Carlo Tree Search with hierarchical neural net control policies trained on expressive LTL specifications. This paper investigates the ability of neural networks to learn both LTL constraints and control policies in order to generate task plans in complex environments. We demonstrate our approach in a simulated autonomous driving setting, where a vehicle must drive down a road in traffic, avoid collisions, and navigate an intersection, all while obeying given rules of the road.
New horizon on successful management for a woman with repeated implantation failure due to unresponsive thin endometrium: Use of extended estrogen supplementation (2013)

An adequate thickness and pattern of the pre-ovulatory endometrium is considered one of the essential requirements for a successful pregnancy. Although various methods for increasing endometrial thickness have been proposed, the real value of these interventions remains controversial. Here, we present a case of successful administration of extended estrogen supplementation before conventional controlled ovarian hyperstimulation in a woman who had experienced repeated implantation failure because of an unresponsive thin endometrium. After the estrogen supplement was administrated for an extended period, the in vitro fertilization/embryo transfer in this patient led to an uneventful twin pregnancy and delivery at term.
Supplementary Figures 1-8 from HS1-Associated Protein X-1 Regulates Carcinoma Cell Migration and Invasion via Clathrin-Mediated Endocytosis of Integrin α<sub>v</sub>β<sub>6</sub> (2023)

Supplementary Figures 1-8 from HS1-Associated Protein X-1 Regulates Carcinoma Cell Migration and Invasion via Clathrin-Mediated Endocytosis of Integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;
Data from Phase Ib Study of Buparlisib plus Trastuzumab in Patients with HER2-Positive Advanced or Metastatic Breast Cancer That Has Progressed on Trastuzumab-Based Therapy (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Phosphoinositide 3-kinase (PI3K)/AKT/mTOR pathway activation in patients with HER2-positive (HER2&lt;sup&gt;+&lt;/sup&gt;) breast cancer has been implicated in &lt;i&gt;de novo&lt;/i&gt; and acquired trastuzumab resistance. The purpose of this study was to determine the clinical activity of the PI3K inhibitor buparlisib (BKM120) in patients with HER2&lt;sup&gt;+&lt;/sup&gt; advanced/metastatic breast cancer resistant to trastuzumab-based therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; In the dose-escalation portion of this phase I/II study, patients with trastuzumab-resistant locally advanced or metastatic HER2&lt;sup&gt;+&lt;/sup&gt; breast cancer were treated with daily oral doses of buparlisib and weekly intravenous trastuzumab (2 mg/kg). Dose escalation was guided by a Bayesian logistic regression model with overdose control.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Of 18 enrolled patients, 17 received buparlisib. One dose-limiting toxicity of grade 3 general weakness was reported at the 100-mg/day dose level (the single-agent maximum tolerated dose) and this dose level was declared the recommended phase II dose (RP2D) of buparlisib in combination with trastuzumab. Common (&gt;25%) adverse events included rash (39%), hyperglycemia (33%), and diarrhea (28%). The pharmacokinetic profile of buparlisib was not affected by its combination with trastuzumab. At the RP2D, there were two (17%) partial responses, 7 (58%) patients had stable disease (≥6 weeks), and the disease control rate was 75%. Pharmacodynamic studies showed inhibition of the PI3K/AKT/mTOR and RAS/MEK/ERK pathways.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; In this patient population, the combination of buparlisib and trastuzumab was well tolerated, and preliminary signs of clinical activity were observed. The phase II portion of this study will further explore the safety and efficacy of this combination at the RP2D. &lt;i&gt;Clin Cancer Res; 20(7); 1935–45. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Formation And Properties Of Optical Waveguides In Strontium Barium Niobate (Sbn:60) (1987)

Single mode channel and planar waveguides have been formed in strontium barium niobate Sr<sub>0.6</sub> Ba<sub>0.4</sub>Nb<sub>2</sub>0<sub>6</sub> (SBN:60) by sulfur indiffusion.1 The vapor diffusion is performed in a sealed ampule and is followed by oxidation in an open tube. Present channel waveguide losses are high: approximately 15-20 dB/cm for the TM mode and 27-32 dB/cm for the TE mode in Z-cut substrates. After poling of the substrate, electro-optic modulation was observed. The effective electro-optic coefficient was determined experimentally as 3.3 ± 0.2 x 10<sup>-10 </sup>m/V (over the frequency range 100 Hz-1 MHz) which is about 15 times greater than for the commonly used integrated optical materials, LiNbO<sub>3</sub> and LiTaO<sub>3</sub>. Diffusions were conducted with the S35 radio-isotope in order to determine the sulfur distribution within the SBN. The atomic sulfur concentration was estimated to be approximately 4 x 10<sup>17</sup> cm<sup>-3</sup> in the region from the surface to a 2.5 tim depth and there was still a significant concentration (approximately an order of magnitude smaller) at depths of &gt; 20 &mu;m.
Parametric instability in coupled nonlinear microcavities (2020)

We report the observation of a parametric instability in the out-of-equilibrium steady state of two coupled Kerr microresonators coherently driven by a laser. Using a resonant excitation, we drive the system into an unstable regime, where we observe the appearance of intense and well-resolved sideband modes in the emission spectrum. This feature is a characteristic signature of self-sustained oscillations of the intracavity field. We comprehensively model our findings using semiclassical Langevin equations for the cavity field dynamics combined with a linear stability analysis. The inherent scalability of our semiconductor platform, enriched with a strong Kerr nonlinearity, is promising for the realization of integrated optical parametric oscillator networks.
Silicon-germanium BiCMOS technology and a CAD environment for 2-40 GHz VLSI mixed-signal ICs (2002)

SiGe BiCMOS technology provides a stable, ultra-high performance, semiconductor technology capable of supporting large mixed-signal VLSI circuit designs for a variety of emerging communications applications. This technology has been wedded to a CAD system that supports a variety of high-performance circuit designs, mixed-signal circuit block re-use, and the ability to accurately predict circuit performance at the highest frequencies. This paper will summarize the progress this technology has made in recent years in moving from the research laboratory into a production environment.
Sub-kHz linewidth lasers using integrated Si 3 N 4 ring resonators (2015)

Frequency discriminators are attractive devices for reducing integrated laser linewidths for coherent communication systems and high purity microwave photonic systems. Standard diode lasers have MHz level linewidths, with recent integrated delay line lasers showing a 50 kHz [1]. Typical on chip devices allow for a few cm of delay in a Mach Zehnder (MZI) configuration, but larger delays are needed for integrated devices. Here, we show a fully integrated Si3N4 ring resonator used as an optical discriminator with a sensitivity better than a 10 meter delay line interferometer. We utilize the Pound-Drever-Hall (PDH) technique to characterize the resonator bandwidth and improve the linewidth of a state of the art commercial laser by locking to the waveguide coupled resonator.
Revealing temperature-dependent polymer aggregation in solution with small-angle X-ray scattering (2022)

Small-angle X-ray scattering is used to probe the solution behavior of two similar electron donor polymers. Differences in aggregate crystallinity are observed upon cooling for the two polymers which is then correlated with the film morphology.
A Simple, Cost-Effective Method to Improve Cell Viability in Microniche Culture Systems (2010)

Microfluidic networks are increasingly used to generate custom microenvironmental niches for cell culture and assays of cellular behavior. Perfusion systems are typically required to overcome diffusive limitations associated with culturing cells longer than a few hours when nutrient delivery, oxygen delivery and metabolic waste removal are required to maintain cell viability. In addition to the added complexity of experimental methods, perfusion systems can result in nonuniform nutrient delivery and subject cells to shear stresses, which may alter cell behavior and possibly cause cell death. In particular, when culturing cells within hydrogel scaffold-filled networks, as may be done in micro-tissue engineering, the need for perfusion culture also increases the likelihood of a destructive bubble entering the network. Moreover, analysis of micro-cultures frequently entails labelling with antibodies and/or fluorescent probes, which again requires controlled perfusion of the various reagents through the network. We have developed a simple technique to preserve cell viability and simplify labeling within microscale cultures without the need for perfusion. Instead of bonding a microfluidic network to glass, PDMS, or another impermeable substrate, the network is bonded to a semi-permeable microdialysis membrane, which allows free exchange of oxygen, proteins, nutrients, and waste between the microfluidic channels and culture media in static culture plates.
Expanding the Cationic Polycarbonate Platform: Attachment of Sulfonium Moieties by Postpolymerization Ring Opening of Epoxides (2016)

Postpolymerization modification is a critical strategy for the development of functional polycarbonate scaffolds for medicinal applications. To expand the scope of available postpolymerization functionalization methods, polycarbonates containing pendant thioether groups were synthesized by organocatalyzed ring-opening polymerization. The thioether group allowed for the postpolymerization ring-opening of functional epoxides, affording a wide variety of sulfonium-functionalized A-B diblock and A-B-A triblock polycarbonate copolymers. The pendant thioether groups were found to be compatible with previously developed postsynthesis functionalization methods allowing for selective and orthogonal modifications of the polycarbonates.
MR elastography of the lung with hyperpolarized 3He (2007)

MR elastography (MRE) is a phase contrast-based technique for spatially mapping the mechanical properties of tissue-like materials. While hyperpolarized noble gases such as helium-3 ((3)He) have proven to be an ideal contrast mechanism for imaging of the lung using conventional MR techniques, their applicability for lung MRE is unknown, due to the fact that gases do not support shear. In this study, we report on the application of MRE to an ex vivo porcine lung specimen inflated with a hyperpolarized noble gas. Unlike proton MRE, shear wave propagation is encoded into the gas entrapped within the alveolar spaces rather than the parenchyma itself. These data provide first evidence of the technical feasibility of MRE of the lung using hyperpolarized noble gases.