gebhart/patrepeval huggingface dataset:
Development of separation technology for the removal of radium-223 from decayed thorium-227 in drug formulations. Material screening and method development (2015)

Targeted thorium conjugates are currently being investigated as a new class of alpha-radiopharmaceuticals. The natural decay of thorium-227 ((227)Th) results in the ingrowth of radium-223 ((223)Ra). Consideration must, therefore, be given to define acceptable limits of (223)Ra in the drug product at the time of dose administration. By effective sequestration of (223)Ra, we aim to improve the radiochemical purity and extend the effective user window of drug products containing (227)Th. (223)Ra is the first progeny of (227)Th and the only one with a long half-life (days). We have, therefore, focused on the removal of this specific species since the progenies of (223)Ra will have a very limited lifetime in the formulation once (223)Ra is removed. In this study, we investigated a multitude of materials for their ability to reduce the (223)Ra level by: (1) passive diffusion or (2) by cartridge filtration on gravity columns. In addition, we probe the compatibility of these materials in the presence of antibody trastuzumab to assess the level of protein binding and estimate the quenching of radiolysis by binding of radionuclides. A screening matrix of organic and inorganic materials was established, i.e. strontium and calcium alginate gel beads, distearoyl phosphatidylglycerol (DSPG) liposomes, ceramic hydroxyapatite, Zeolite UOP type 4A and cation exchange resins AG50W-X8 and SOURCE 30S. First, passive diffusional uptake of (223)Ra by suspended materials present in the formulation was measured as a decrease in sample radioactivity after separation. Second, selected materials were packed on gravity columns in order to evaluate the efficiency of column separation versus diffusional adsorption. The retention of (223)Ra and (227)Th were characterized by measuring the radioactivity in the eluate and on the columns. Finally, the compatibility between trastuzumab, as a selected model antibody, and suspensions of the binding materials was analyzed during storage of the drug product in the presence of adsorbent. The formation of H2O2 was evaluated to measure the influence of radionuclide binding material on radiolysis in the formulation. All the materials bound (223)Ra by passive diffusional uptake ranging from 31% to 95% with DSPG liposomes demonstrating superiority at 95% efficiency. All materials suitable for assessment by gravity column filtration bound (223)Ra almost quantitatively (∼100%) and with minimal variation (relative standard deviation <1%). The uptake was significantly higher compared to passive diffusional uptake. Alginate gel beads, ceramic hydroxyapatite and SOURCE 30S reduced the antibody concentration in solution to 40-50% while the Zeolite UOP type 4A, AG50W-X8 resin and DSPG liposomes showed ≤10% reduction of antibody concentration. Ceramic hydroxyapatite significantly reduced H2O2 formed by radionuclide initiated radiolysis.
An initial step towards improving the accuracy of the oscillometric blood pressure measurement (2013)

We conceived a set of physical model-based techniques to compute blood pressure (BP) from a standard oscillometric cuff pressure measurement. First, the cuff pressure measurement is represented with a physical model. Then, the model unknowns are determined from the measurement via a parametric, non-parametric or hybrid technique. Finally, the entire BP waveform is computed from the determined model. For an initial assessment, we compared the accuracy of these techniques with the conventional fixed-ratio technique for computing systolic and diastolic pressures using cuff pressure measurements simulated with an established oscillometric model over a wide parameter range. The new techniques afforded much greater accuracy than the conventional technique. Our future efforts will focus on experimental validation.
Expression analysis of microRNA as prognostic biomarkers in colorectal cancer (2016)

microRNA (miRNA) based biomarkers have unique advantages due to their critical regulatory function, superior stability, and relatively small number compared to mRNAs. A number of miRNAs play key roles in colon cancer stem cell chemoresistance and have clinical potential as prognostic biomarkers. The purpose of this study is to systematically validate the prognostic potential of miRNAs in colorectal cancer. In this study, we validated the prognostic potential of a panel of miRNAs using 205 stage II, III, and IV colorectal cancer specimens by qRT-PCR analysis. We cross validated our results using The Cancer Genome Atlas (TCGA) database. Many of the miRNAs we investigated have been functionally validated to be important in contributing to chemoresistance to 5-fluorouracil (5-FU) based chemotherapy. We determined that miR-16 is the most consistent miRNA for expression normalization in colorectal cancer. We have validated several miRNAs (miR-15b, miR-215, miR-145, miR-192, let-7g) that are significantly associated with progression free survival (PFS) and/or overall survival (OS) of colorectal cancer patients independent of tumor stage and age at diagnosis. These 5 miRNAs are significantly associated with OS of colorectal cancer even after tumor location (left side vs. right side) is adjusted for. Furthermore, the prognostic value of let-7g for overall survival was independently validated using the RNA-Seq results from TCGA colorectal cancer database. These results, taken together, establish a solid foundation towards miRNA based precision management of colorectal cancer.
Protocol for Direct Counterfactual Quantum Communication (2013)

It has long been assumed in physics that for information to travel between two parties in empty space, "Alice" and "Bob," physical particles have to travel between them. Here, using the "chained" quantum Zeno effect, we show how, in the ideal asymptotic limit, information can be transferred between Alice and Bob without any physical particles traveling between them.
Trade-Off between Parasitic Deposition and SiC Homoepitaxial Growth Rate Using Halogenated Si-Precursors (2013)

We discuss the use of halogenated Si-X precursors, compared to the traditional silane precursor, to increase the growth rate of thick, high quality SiC homoepitaxial layers by chemical vapor deposition for power electronics applications. These precursors reduce gas phase nucleation and parasitic deposition to increase the availability of reactive Si-species at the SiC growth front due to their less reactive nature compared to silane. While less reactive Si-X species are expected to provide lower activity of Si-species at the growth front, the reduced parasitic deposition and precursor depletion from the gas delivery system leads to an effective increase in overall growth rate. This trade-off is explored in the context of parasitic deposition-induced particulate formation that degrades SiC epilayer morphology, while introducing structural defects. It is difficult to effectively compare different precursors used by various researchers, as there is no standard set of reported epilayer crystal quality parameters that takes into account various precursor/epilayer related benefits/tradeoffs. We propose a set of reactor-independent metrics that may enable realistic comparison across the various Si-X precursor chemistries. Results at the authors' laboratory indicate that tetrafluorosilane precursor shows great promise in breaking the growth-rate/parasitic deposition trade-offs inherent in SiC growth, critical for widespread commercial adoption of SiC technology.
<i>Superior</i>: A Novel Repetitive DNA Element Dispersed in the Rye Genome (2009)

A new class of rye-specific repetitive DNA elements designated Superior has been identified. The rye genome library was constructed by cleavage with EcoO109I, the recognition sites of which consisted of 5'-PuGGNCCPy-3' multi-sequences and were present with high frequency in the rye repetitive families. A novel 495-bp segment enriched in the rye genome was successfully identified. Southern blot hybridization and fluorescence in situ hybridization using the repetitive element showed a dispersed array through all 7 chromosomes of rye. The repetitive DNA element did not share identity with known class I or class II transposable elements or known repetitive elements. Only several DNA segments in BACs and ESTs of barley showed partial similarity to the repetitive DNA element in all DNA databases of living species. The new class of dispersed repetitive elements was designated Superior. The entire structure of Superior was determined by using a rye genomic library of lambda FIXII screened by the 495-bp probe. The Superior family consisted of 1,292-bp, 1,324-bp, and 1,432-bp elements in which the 5' regions had been destroyed, indicating the presence of considerable structural diversity. Superior might be a useful tool for studying genomic organization and differentiation.
Type I and Type II Interferon Receptors (1984)

Binding site competition studies of 125I-interferon (IFN)-gamma were performed with homogeneous preparations of IFNs alpha 2, beta, and gamma. It was found that only IFN-gamma could compete for the specific binding site of 125I-IFN-gamma in both WISH and FS11 cells. Thus, a clear distinction between the receptor of IFN- alpha and beta on one hand, and the receptor of IFN-gamma on the other hand, was obtained. This result is unambiguous because all IFN preparations which were used were purified to homogeneity by specific monoclonal antibody immunoaffinity chromatography. We propose to assign the names "Type I" for the receptor of IFN-alpha and IFN-beta, and "Type II" for the specific receptor of IFN-gamma.
An interpenetrating polymer network hydrogel with biodegradability through controlling self-assembling peptide behavior with hydrolyzable cross-linking networks (2021)

Hydrogels are used as cell culture scaffolds for tissue engineering and regeneration. These hydrogel designs are inevitably complicated because favorable scaffolds should have stiffness to sustain alignment of the cells and mimic the structure of the extracellular matrix (ECM) in the targeted tissue. However, the incorporation of biodegradability, which is an essential property for practical applications, into complex hydrogels is not easily attained. Herein, we established a new concept for constructing biodegradable hydrogels with an interpenetrating polymer network (IPN) structure, composed of a covalent cross-linked network and peptide self-assembling networks, to solve this dilemma of selecting between the complicated structure and facile biodegradability. Assuming that the diffusion of the self-assembled peptides out of the IPN hydrogel would be facilitated by the disappearance of the covalent cross-linked networks, we designed an IPN hydrogel with chitosan cross-linked with poly(ethylene glycol)-block-poly(dl-lactide)-block-poly(ethylene glycol) as the covalent cross-linked networks with hydrolysis properties and RADA16 peptides as the self-assembling networks. This IPN hydrogel showed overall degradation, based on hydrolysis of the poly(dl-lactide) domain, and was more effective as a scaffold for culturing chondrocytes to form articular cartilage tissues compared with the IPN hydrogel without the poly(dl-lactide) domain, likely owing to the promotion of ECM deposition. These results verified our strategy of constructing a hydrogel with a complicated, but biodegradable, structure.
Low-Power 16 x 10 Gb/s Bi-Directional Single Chip CMOS Optical Transceivers Operating at ≪ 5 mW/Gb/s/link (2009)

We report here on a parallel optical transceiver based on a single 0.13 mum CMOS amplifier chip with 16 transmitter and 16 receiver channels. The transceiver is designed to support very low-power, chip-to-chip optical data buses on printed circuit boards at data rates up to 10 Gb/s/channel. Optical interfaces to the chip are provided by 16-channel photodiode (PD) and VCSEL arrays directly flip-chip soldered to the CMOS IC. The resulting complete transceivers, or optochips, are low-cost, low-profile highly-integrated chip-scale components. The packaging approach, dense hybrid-integration of optical devices with CMOS, facilitates further scaling to even larger 2-D arrays for future massively parallel optical data buses. Comparison with a previously reported high-speed transceiver Optochip is provided to provide insight into the design space of dense CMOS-based parallel optical transceivers.
Cover Picture: An Organic Light‐Emitting Diode with Field‐Effect Electron Transport (Adv. Funct. Mater. 1/2008) (2008)

Abstract The cover shows an organic light‐emitting diode with remote metallic cathode, reported by Sarah Schols and co‐workers on p. 136. The metallic cathode is displaced from the light‐emission zone by one to several micrometers. The injected electrons accumulate at an organic heterojunction and are transported to the light‐emission zone by field‐effect. The achieved charge‐carrier mobility and in combination with reduced optical absorption losses because of the remoteness of the cathode may lead to applications as waveguide OLEDs and possibly a laser structure. (The result was obtained in the EU‐funded project “OLAS” IST‐ FP6‐015034.) We describe an organic light‐emitting diode (OLED) using field‐effect to transport electrons. The device is a hybrid between a diode and a field‐effect transistor. Compared to conventional OLEDs, the metallic cathode is displaced by one to several micrometers from the light‐emitting zone. This micrometer‐sized distance can be bridged by electrons with enhanced field‐effect mobility. The device is fabricated using poly(triarylamine) (PTAA) as the hole‐transport material, tris(8‐hydroxyquinoline) aluminum (Alq 3 ) doped with 4‐(dicyanomethylene)‐2‐methyl‐6‐(julolindin‐4‐yl‐vinyl)‐4H‐pyran (DCM 2 ) as the active light‐emitting layer, and N , N ′‐ditridecylperylene‐3,4,9,10‐tetracarboxylic diimide (PTCDI‐C 13 H 27 ), as the electron‐transport material. The obtained external quantum efficiencies are as high as for conventional OLEDs comprising the same materials. The quantum efficiencies of the new devices are remarkably independent of the current, up to current densities of more than 10 A cm –2 . In addition, the absence of a metallic cathode covering the light‐emission zone permits top‐emission and could reduce optical absorption losses in waveguide structures. These properties may be useful in the future for the fabrication of solid‐state high‐brightness organic light sources.
3D-microdevice for the in vivo capture of cancer-associated circulating cells. (2017)

e579 Background: Circulating tumor cells (CTCs) are cancer cells that have detached from a tumor and have entered into the blood circulation at a very low concentration (D. Shook, Mech. Dev., Nov 2003). CTCs have a strong prognostic value, as their number has been correlated to overall survival in different metastatic cancers (J. S. de Bono, Clin. Cancer Res., Oct 2008). Considering the rareness of CTCs in blood, capturing them in vitro is very challenging. CTCs being mainly larger and less deformable than most of blood cells, ISET was the first system exploiting their physical traits using a filtration membrane to enrich 10mL blood samples (G. Vona, Am. J. Pathol., Jan 2000). However, placing the trapping system directly within the bloodstream would increase the amount of blood screened and ensure no sampling bias. To our knowledge, the only system developed for in vivo capture of CTCs relies on an immunologic detection targeting CTCs with specific epithelial-cell adhesion molecules (N. Saucedo-Zeni, Int. J. Oncol., Oct 2012). The major drawback of this technique is the selection bias induced, given the strong heterogeneity of antigen expression profiles in CTC population as confirmed by several studies. Methods: Our device combines the advantages of in vivo capture and physical trapping of CTCs. A polymeric 3D net-like microdevice is fabricated using a Direct Laser Writing technique (Nanoscribe) and integrated onto a Nitinol guidewire to be introduced into the basilic vein through a routine 20G catheter. To optimize the design, we conducted simulation studies and in vitro assays using a fluidic platform reproducing in vivo conditions. Results: We succeeded in capturing PC3 human prostate cancer cells from 20 mL healthy donor blood spiked with 1,000 PC3 cells in 2 minutes, demonstrating the capability to capture CTCs in conditions close to those found in vivo, in terms of pressure and flow rate and without any additional treatment or dilution of the blood. Conclusions: This device could facilitate treatment personalization and follow-up. Its versatility should render it transposable to the capture of single or clustered CTCs, derived from all types of cancer and, by extension, to other circulating cellular and molecular biomarkers.
Patternable Solvent-Processed Thermoplastic Graphite Electrodes (2017)

Since their invention in the 1950s, composite carbon electrodes have been employed in a wide variety of applications, ranging from batteries and fuel cells to chemical sensors, because they are easy to make and pattern at millimeter scales. Despite their widespread use, traditional carbon composite electrodes have substandard electrochemistry relative to metallic and glassy carbon electrodes. As a result, there is a critical need for new composite carbon electrodes that are highly electrochemically active, have universal and easy fabrication into complex geometries, are highly conductive, and are low cost. Herein, a new solvent-based method is presented for making low-cost composite graphite electrodes containing a thermoplastic binder. The electrodes, which are termed thermoplastic electrodes (TPEs), are easy to fabricate and pattern, give excellent electrochemical performance, and have high conductivity (700 S m–1). The thermoplastic binder enables the electrodes to be hot embossed, molded, templated, and/or cut with a CO2 laser into a variety of intricate patterns. Crucially, these electrodes show a marked improvement in peak current, peak separation, and resistance to charge transfer over traditional carbon electrodes. The impact of electrode composition, surface treatment (sanding, polishing, plasma treatment), and graphite source were found to significantly impact fabrication, patterning, conductivity, and electrochemical performance. Under optimized conditions, electrodes generated responses similar to more expensive and difficult to fabricate graphene and highly oriented pyrolytic graphite electrodes. The TPE electrode system reported here provides a new approach for fabricating high performance carbon electrodes with utility in applications ranging from sensing to batteries.
WebWave: globally load balanced fully distributed caching of hot published documents (2002)

Document publication service over such a large network as the Internet challenges us to harness available server and network resources to meet fast growing demand. We show that large scale dynamic caching can be employed to globally minimize server idle time, and hence maximize the aggregate server throughput of the whole service. To be efficient, scalable and robust, a successful caching mechanism must have three properties: (1) maximize the global throughput of the system; (2) find cache copies without recourse to a directory service, or to a discovery protocol; and (3) be completely distributed in the sense of operating only on the basis of local information. We develop a precise definition, which we call tree load balance (TLB), of what it means for a mechanism to satisfy these three goals. We present an algorithm that computes TLB offline, and a distributed protocol that induces a load distribution that converges quickly to a TLB one. Both algorithms place cache copies of immutable documents on the routing tree that connects the cached document's home server to its clients, thus enabling requests to stumble on cache copies en route to the home server.
Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran (2004)

Renewable lignocellulosic materials are attractive low-cost feedstocks for bioethanol production. Furfural and 5-hydroxymethylfurfural (HMF) are among the most potent inhibitory compounds generated from acid hydrolysis of lignocelluloses to simple sugars for fermentation. In Saccharomyces cerevisiae ATCC 211239 and NRRL Y-12632 and Pichia stipitis NRRL Y-7124, furfural and HMF inhibition were determined to be dose-dependent at concentrations from 10 to 120 mM. The yeast strains were more sensitive to inhibition by furfural than HMF at the same concentration, while combined treatment of furfural and HMF synergistically suppressed cell growth. A metabolite transformed from HMF by strain NRRL Y-12632 was isolated from the culture supernatant, and conclusively identified as 2,5-bis-hydroxymethylfuran, a previously postulated HMF alcohol, with a composition of C6H8O3 and a molecular weight of 128. It is proposed that, in the presence of HMF, the yeast reduces the aldehyde group on the furan ring of HMF into an alcohol, in a similar manner as for furfural. The accumulation of this biotransformed metabolite may be less toxic to yeast cultures than HMF, as evidenced by the rapid yeast fermentation and growth rates associated with HMF conversion. The ability of yeasts to adapt to and transform furfural and HMF offers the potential for in situ detoxification of these inhibitors and suggests a genetic basis for further development of highly tolerant strains for biofuel production.
Ultra-High-Resolution Ion Mobility Separations Over Extended Path Lengths and Mobility Ranges Achieved using a Multilevel Structures for Lossless Ion Manipulations Module (2020)

Over the past few years, structures for lossless ion manipulations (SLIM) have used traveling waves (TWs) to move ions over long serpentine paths that can be further lengthened by routing the ions through multiple passages of the same path. Such SLIM "multipass" separations provide unprecedentedly high ion mobility resolving powers but are ultimately limited in their ion mobility range because of the range of mobilities spanned in a single pass; that is, higher mobility ions ultimately "overtake" and "lap" lower mobility ions that have experienced fewer passes, convoluting their arrival time distribution at the detector. To achieve ultrahigh resolution separations over broader mobility ranges, we have developed a new multilevel SLIM possessing multiple stacked serpentine paths. Ions are transferred between SLIM levels through apertures (or ion escalators) in the SLIM surfaces. The initial multilevel SLIM module incorporates four levels and three interlevel ion escalator passages, providing a total path length of 43.2 m. Using the full path length and helium buffer gas, high resolution separations were achieved for Agilent tuning mixture phosphazene ions over a broad mobility range (<i>K</i><sub>0</sub> ≈ 3.0 to 1.2 cm<sup>2</sup>/(V*s)). High sensitivity was achieved using "in-SLIM" ion accumulation over an extended trapping region of the first SLIM level. High transmission efficiency of ions over a broad mobility range (e.g., <i>K</i><sub>0</sub> ≈ 3.0 to 1.67 cm<sup>2</sup>/(V*s)) was achieved, with transmission efficiency rolling off for the lower mobility ions (e.g., <i>K</i><sub>0</sub> ≈ 1.2 cm<sup>2</sup>/(V*s)). Resolving powers of up to ∼560 were achieved using all four ion levels to separate reverse peptides (SDGRG<sup>1+</sup> and GRGDS<sup>1+</sup>). A complex mixture of phosphopeptides showed similar coverage could be achieved using one or all four SLIM levels, and doubly charged phosphosite isomers not significantly separated using one SLIM level were well resolved when four levels were used. The new multilevel SLIM technology thus enables wider mobility range ultrahigh-resolution ion mobility separations and expands on the ability of SLIM to obtain improved separations of complex mixtures with high sensitivity.