gebhart/patrepeval huggingface dataset:
Highly Selective Photothermal Therapy by a Phenoxylated‐Dextran‐Functionalized Smart Carbon Nanotube Platform (2016)

Near-infrared (NIR) photothermal therapy using biocompatible single-walled carbon nanotubes (SWNTs) is advantageous because as-produced SWNTs, without additional size control, both efficiently absorb NIR light and demonstrate high photothermal conversion efficiency. In addition, covalent attachment of receptor molecules to SWNTs can be used to specifically target infected cells. However, this technique interrupts SWNT optical properties and inevitably lowers photothermal conversion efficiency and thus remains major hurdle for SWNT applications. This paper presents a smart-targeting photothermal therapy platform for inflammatory disease using newly developed phenoxylated-dextran-functionalized SWNTs. Phenoxylated dextran is biocompatible and efficiently suspends SWNTs by noncovalent π-π stacking, thereby minimizing SWNT bundle formations and maintaining original SWNT optical properties. Furthermore, it selectively targets inflammatory macrophages by scavenger-receptor binding without any additional receptor molecules; therefore, its preparation is a simple one-step process. Herein, it is experimentally demonstrated that phenoxylated dextran-SWNTs (pD-SWNTs) are also biocompatible, selectively penetrate inflammatory macrophages over normal cells, and exhibit high photothermal conversion efficiency. Consequently, NIR laser-triggered macrophage treatment can be achieved with high accuracy by pD-SWNT without damaging receptor-free cells. These smart targeting materials can be a novel photothermal agent candidate for inflammatory disease.
Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules (1999)

In common multidimensional NMR experiments for studies of biological macromolecules in solution, magnetization transfers via spin-spin couplings [insensitive nuclei enhanced by polarization transfer (INEPT)] are key elements of the pulse schemes. For molecular weights beyond 100,000, transverse relaxation during the transfer time may become a limiting factor. This paper presents a transfer technique for work with big molecules, cross relaxation-enhanced polarization transfer (CRINEPT), which largely reduces the size limitation of INEPT transfers with the use of cross-correlated relaxation-induced polarization transfer. The rate of polarization transfer by cross-correlated relaxation is proportional to the rotational correlation time, so that it becomes a highly efficient transfer mechanism for solution NMR with very high molecular weights. As a first implementation, [15N,1H]-correlation experiments were designed that make use of cross-correlation between dipole-dipole coupling and chemical shift anisotropy of the 15N---1H-moieties for both CRINEPT and transverse relaxation-optimized spectroscopy (TROSY). When compared with INEPT-based [15N,1H]-TROSY, these experiments yielded up to 3-fold signal enhancement for amide groups of a 110,000-Da protein in aqueous solution at 4 degrees C. CRINEPT opens avenues for solution NMR with supramolecular structures such as membrane proteins solubilized in micelles or lipid vesicles, proteins attached to nucleic acid fragments, or oligomeric proteins.
A Stable Vanadium Redox‐Flow Battery with High Energy Density for Large‐Scale Energy Storage (2011)

Abstract The all‐vanadium redox flow battery is a promising technology for large‐scale renewable and grid energy storage, but is limited by the low energy density and poor stability of the vanadium electrolyte solutions. A new vanadium redox flow battery with a significant improvement over the current technology is reported in this paper. This battery uses sulfate‐chloride mixed electrolytes, which are capable of dissolving 2.5 M vanadium, representing about a 70% increase in energy capacity over the current sulfate system. More importantly, the new electrolyte remains stable over a wide temperature range of −5 to 50 °C, potentially eliminating the need for electrolyte temperature control in practical applications. This development would lead to a significant reduction in the cost of energy storage, thus accelerating its market penetration.
Rotational Doppler-effect due to selective excitation of vector-vortex field in optical fiber (2011)

Experimental demonstration of rotational Doppler-effect due to direct and simultaneous excitation of orthogonal elliptically-polarized fundamental and vortex modes in a two-mode optical fiber is presented here. The rotation frequency and the trajectory of the zero-intensity point in the two-mode fiber output beam measured as a function of analyzer rotation matches with the S-contour of polarization singularity in the beam, identified via Stokes parameter measurement. The characteristics of the S-contour around the C-point in the output beam is also measured as a function of rotating Dove prism and half-wave plate - Dove prism combination to highlight the role of polarization modifying components on the observed rotational Doppler-effect of vector-vortex beams.
Diversity of Ubiquitin and ISG15 Specificity among Nairoviruses' Viral Ovarian Tumor Domain Proteases (2013)

Nairoviruses are responsible for numerous diseases that affect both humans and animal. Recent work has implicated the viral ovarian tumor domain (vOTU) as a possible nairovirus virulence factor due to its ability to edit ubiquitin (Ub) bound to cellular proteins and, at least in the case of Crimean-Congo hemorrhagic fever virus (CCHFV), to cleave the Ub-like protein interferon-stimulated gene 15 (ISG15), a protein involved in the regulation of host immunity. The prospective roles of vOTUs in immune evasion have generated several questions concerning whether vOTUs act through a preserved specificity for Ub- and ISG15-conjugated proteins and where that specificity may originate. To gain insight into the substrate specificity of vOTUs, enzymological studies were conducted on vOTUs from Dugbe, CCHFV, and Erve nairoviruses. These studies revealed that vOTUs originating from different nairoviruses display a significant divergence in their preference toward Ub and ISG15. In addition, a recently identified vOTU from turnip yellow mosaic tymovirus was evaluated to elucidate any possible similarities between vOTUs originating from different viral families. Although possessing a similar preference for certain polymeric Ub moieties, its activity toward Ub in general was significantly less then those of nairoviruses. Lastly, the X-ray crystallographic structure of the vOTU from the Dugbe nairovirus was obtained in complex with Ub to reveal structural commonalities of vOTUs originating from nairoviruses. The structure suggests that divergences between nairovirus vOTUs specificity originate at the primary structural level. Comparison of this structure to that originating from CCHFV identified key residues that infer the substrate specificity of vOTUs.
Anti-CmεX monoclonal antibodies potentially applicable for targeting mIgE-expressing B cells (140.20) (2009)

Abstract On B lymphocytes, membrane-bound IgE (mIgE) is part of BCR and essential for generating isotype-specific IgE response. On mIgE+ B cells in man, the membrane-bound ε chain (mε) exists predominantly in the long form (mεL), containing 52-a.a. CεmX domain between CH4 and the C-terminal membrane-anchoring segment; the conventional form of mε (mεS) exists in minor proportions. CεmX thus provides an attractive site for immunological targeting of mIgE+ cells. Here we have shown that 9 newly prepared CεmX-specific monoclonal antibodies (mAbs), as well as previously reported a20, can bind to mIgE.FcL-expressing CHO cells, while only 4B12 and 26H2 can bind to mIgE.FcL-expressing B cell line Ramos cells. In epitope mapping studies using synthetic peptides representing different parts of CεmX, 4B12 was shown to bind to the N-terminal part, 26H2 the middle part, and all others the C-terminal part of CεmX. These results suggest that the C-terminal part of CεmX is sterically hindered for mAb binding by associated components in the BCR. The chimerized mAbs c4B12 and c26H2, when cross-linked by secondary antibodies, could lyse mIgE.FcL-expressing Ramos cells by apoptosis through a BCR-dependent caspase pathway. Using PBMCs as the source of effector cells, c4B12 and c26H2 could cause ADCC against mIgE.FcL-expressing Ramos cells in a does-dependent fashion. These results indicate that anti-CεmX mAbs, 4B12 and 26H2, can bind to native mIgE on B cells and are potentially useful for targeting mIgE+ B cells for controlling IgE production.
The Role of Alpha-Hemoglobin Stabilizing Protein in Redox Chemistry, Denaturation, and Hemoglobin Assembly (2009)

Hemoglobin biosynthesis in erythrocyte precursors involves several steps. The correct ratios and concentrations of normal alpha (alpha) and beta (beta) globin proteins must be expressed; apoproteins must be folded correctly; heme must be synthesized and incorporated into these globins rapidly; and the individual alpha and beta subunits must be rapidly and correctly assembled into heterotetramers. These events occur on a large scale in vivo, and dysregulation causes serious clinical disorders such as thalassemia syndromes. Recent work has implicated a conserved erythroid protein known as Alpha-Hemoglobin Stabilizing Protein (AHSP) as a participant in these events. Current evidence suggests that AHSP enhances alpha subunit stability and diminishes its participation in harmful redox chemistry. There is also evidence that AHSP facilitates one or more early-stage post-translational hemoglobin biosynthetic events. In this review, recent experimental results are discussed in light of several current models describing globin subunit folding, heme uptake, assembly, and denaturation during hemoglobin synthesis. Particular attention is devoted to molecular interactions with AHSP that relate to alpha chain oxidation and the ability of alpha chains to associate with partner beta chains.
Biomimetic finger control by filtering of distributed forelimb pressures (2001)

A linear filter was developed for decoding finger commands from volitional pressures distributed within the residual forelimb. Filter parameters were based on dynamic pressures recorded from the residual limb within its socket, during specific finger commands. A matrix of signal features was derived from eight-dimensional (8-D) pressure vectors, and its pseudoinverse comprised the filter parameters. Results with amputees showed that the filter could discriminate specific finger flexion commands, suggesting that pressure vector decoding (PVD) can provide them with biomimetic finger control.
Identification of an activation site in Bak and mitochondrial Bax triggered by antibodies (2016)

During apoptosis, Bak and Bax are activated by BH3-only proteins binding to the α2-α5 hydrophobic groove; Bax is also activated via a rear pocket. Here we report that antibodies can directly activate Bak and mitochondrial Bax by binding to the α1-α2 loop. A monoclonal antibody (clone 7D10) binds close to α1 in non-activated Bak to induce conformational change, oligomerization, and cytochrome c release. Anti-FLAG antibodies also activate Bak containing a FLAG epitope close to α1. An antibody (clone 3C10) to the Bax α1-α2 loop activates mitochondrial Bax, but blocks translocation of cytosolic Bax. Tethers within Bak show that 7D10 binding directly extricates α1; a structural model of the 7D10 Fab bound to Bak reveals the formation of a cavity under α1. Our identification of the α1-α2 loop as an activation site in Bak paves the way to develop intrabodies or small molecules that directly and selectively regulate these proteins.
Longwave infrared (LWIR) coded aperture dispersive spectrometer (2007)

We describe a static aperture-coded, dispersive longwave infrared (LWIR) spectrometer that uses a microbolometer array at the detector plane. The two-dimensional aperture code is based on a row-doubled Hadamard mask with transmissive and opaque openings. The independent column code nature of the matrix makes for a mathematically well-defined pattern that spatially and spectrally maps the source information to the detector plane. Post-processing techniques on the data provide spectral estimates of the source. Comparative experimental results between a slit and coded aperture for emission spectroscopy from a CO(2) laser are demonstrated.
Identification of a 14 kb deletion involving the promoter region of BRCA1 in a breast cancer family (1997)

BRCA1 is a breast and ovarian cancer susceptibility gene. An inferred germline regulatory mutation was previously reported in the BRCA1-linked kindred K2035, based on the absence of transcripts from the BRCA1 allele associated with the cancer susceptibility haplotype. In this study, the promoter region of BRCA1 was examined in individuals from K2035 for evidence of a mutation which could halt transcription. Evaluation of a polymorphism located within intron 2 of BRCA1 gave results consistent with the presence of a large deletion in K2035 mutation carriers. Southern blot analysis identified unique restriction fragments which occurred as a result of a 14 kb deletion that removed both of BRCA1's transcription start sites (exons 1a and 1b) as well as exon 2. Sequencing indicated that unequal crossover between Alu repeats was the likely cause of the deletion. Similar deletions may be responsible for other reported inferred regulatory mutations, as well as unidentified mutations in families linked to BRCA1.
Mining time-dependent patient outcomes from hospital patient records. (2002)

We describe REMIND, a data mining framework that accurately infers missing clinical information by reasoning over the entire patient record. Hospitals collect computerized patient records (CPR's) in structured (database tables) and unstructured (free text) formats. Structured clinical data in the CPR's is often poorly recorded, and information may be missing about key outcomes and processes. For instance, for a population of 344 colon cancer patients, important clinical outcomes, such as disease state and its evolution, are stored only as unstructured data (doctors' dictations) in the CPR. Raw evidence (extracted directly from the CPR) is not a good predictor of disease state. Yet by combining this evidence in a principled fashion (using methods from uncertain and temporal reasoning), REMIND accurately infers disease state sequences for recurrence, a complex time-varying outcome, for these patients. These outcomes can now be added back into the CPR in structured form.
Unicondylar Knee Replacement (1976)

Unicompartmental knee arthroplasty was conceived for the treatment of osteoarthritic knees with deterioration of either the medial or lateral compartment of the knee. The Unicondylar prosthesis was used in 19 medial and 5 lateral compartment arthroplasties. A two to 4 year follow-up evaluation of these patients was somewhat disappointing as only 5 knees could be rated excellent and 6 rated a good result. The best results were seen in the lateral compartment arthroplasties. Such deformities may be the only future indication for the use of this operation as these knees do not do well when treated by tibial osteotomy. However, when only the medial compartment is involved, osteotomy may still remain the treatment of choice.
8T single-ended sub-threshold SRAM with cross-point data-aware write operation (2011)

This paper presents a new 8T SRAM cell with data-aware cross-point Write operation and series connected Read buffer for low power and low voltage operation. The cell features a shared footer device to control the VGND for cell pass-gate (Write) transistors and the Read buffer. The row-based VGND control and the column-based data-aware Write Word-Line form a cross-point Write structure, thus eliminating Write Half-Select Disturb to facilitate bit-interleaving architecture. Replica based timing tracking circuit is used to control the pulse width of Word-Line Enable (WLE) signal to overcome the large timing variation at low voltage and to reduce the Word-Line active power consumption. A 4Kbit SRAM test chip implemented in 90nm HVT CMOS technology operates at 120MHz at 0.6V and 6MHz at 0.38V with measured power consumption of 2.99uW at 6MHz, 0.38V.
Packaging of viral RNAs in virions of adenoviruses (2009)

Earlier, we detected viral RNAs packaged in the porcine adenovirus (PAdV) -3 virions. Using Southern blot analysis, we further demonstrated that the viral RNAs were predominantly packaged in CsCl purified mature capsids (containing viral genome) than empty/intermediate capsids. Some of the packaged viral RNAs appear to be polyadenylated. Real-time reverse transcription (RT)-PCR analysis indicated that the copy number of the tested viral mRNAs encoding E1Bsmall and fiber proteins was less than one per full capsid. Moreover, detection of viral RNA packaged in CsCl purified human adenovirus (HAdV) -5 virions indicates that the viral RNA packaging might be a common phenomenon in members of Adenoviridae family. Further quantitative analysis of viral protein, DNA, and RNA in CsCl purified mature and empty/intermediate capsids of recombinant HAdV-5 expressing enhanced green fluorescent protein indicated that the traceable viral RNA detected in empty/intermediate capsids seems associated with the presence of traceable viral genomic DNA. Taken together, our data suggest that the viral RNAs may be passively packaged in adenovirus virion during encapsidation of viral genomic DNA in cell nuclei. Thus, viral RNA packaging may be a characteristic feature of adenoviral genomic DNA encapsidation.
Large-Scale Geospatial Planning of Wireless Backhaul Links (2020)

In telecommunication networks, microwave backhaul links are often used as wireless connections between towers. They are used in places where deploying optical fibers is impossible or too expensive. The relatively high frequency of microwaves increases their ability to transfer information at a high rate, but it also makes them susceptible to obstructions and interference. When deploying microwave links, there should be a clear line of sight between every pair of receiver and transmitter, and a buffer around the line of sight defined by the first Fresnel zone should be clear of obstacles. In this paper we discuss the geospatial aspects of microwave backhaul planning and the challenges in developing a system for large scale planning, with the following requirements: (1) the need to cover all of the USA, (2) distance of up to 80 kilometers between towers, and (3) computing batches of thousands of pairs within a few minutes.
Pseudosubstrate regulation of the SCF <sup>β-TrCP</sup> ubiquitin ligase by hnRNP-U (2002)

beta-TrCP/E3RS (E3RS) is the F-box protein that functions as the receptor subunit of the SCF(beta-TrCP) ubiquitin ligase (E3). Surprisingly, although its two recognized substrates, IkappaB(alpha) and beta-catenin, are present in the cytoplasm, we have found that E3RS is located predominantly in the nucleus. Here we report the isolation of the major E3RS-associated protein, hnRNP-U, an abundant nuclear phosphoprotein. This protein occupies E3RS in a specific and stoichiometric manner, stabilizes the E3 component, and is likely responsible for its nuclear localization. hnRNP-U binding was abolished by competition with a pIkappaB(alpha) peptide, or by a specific point mutation in the E3RS WD region, indicating an E3-substrate-type interaction. However, unlike pI(kappa)Balpha, which is targeted by SCF(beta-TrCP) for degradation, the E3-bound hnRNP-U is stable and is, therefore, a pseudosubstrate. Consequently, hnRNP-U engages a highly neddylated active SCF(beta-TrCP), which dissociates in the presence of a high-affinity substrate, resulting in ubiquitination of the latter. Our study points to a novel regulatory mechanism, which secures the localization, stability, substrate binding threshold, and efficacy of a specific protein-ubiquitin ligase.
Analysis of Salmonella enterica Serotype Paratyphi A Gene Expression in the Blood of Bacteremic Patients in Bangladesh (2010)

To our knowledge, we describe the first microarray-based transcriptional analysis of a pathogen in the blood of naturally infected humans.
Template‐Directed Assembly of Zeolite‐like Metal–Organic Frameworks (ZMOFs): A usf‐ZMOF with an Unprecedented Zeolite Topology (2008)

Zeolith mit Indium: Molekulare Bausteine (MBBs) mit achtfach koordinierten Indiumzentren und 4,5-Imidazoldicarboxylat(Himdc)-Liganden bauen in Gegenwart eines strukturgebenden Agens ein vierfach verknüpftes Zeolith-artiges metall-organisches Netzwerk (ZMOF) mit neuartiger Zeolithtopologie auf (med-Topologie, siehe Bild; In grün, C grau, N blau, O rot; die Netzwerktopologie von usf-ZMOF ist durch grüne Tetraeder veranschaulicht).
32 × 10 Gb/s WDM transmission over 640 km using broad band, gain-flattened erbium-doped silica fiber amplifiers (1997)

Dense wavelength division multiplexed (DWDM) optical fiber communications systems with 20 Gb/s capacity (8 channels each with 2.5 Gb/s) are now widely deployed and sixteen channel commercial systems are not far behind.
Control of an Omni-directional Power-assisted Cart (2003)

This paper describes an easy-to-operate, omni-directional cart. This cart includes power assist technology that acts for both the longitudinal and rotational motions of the cart. Two objectives are set for this development. The first objective is to overcome the difficulty of shifting the cart laterally. Therefore, the equation for calculating the cart turning speed is modified so that the moment, which is driven by the operating force in the right/left direction, is offset. As a result, it becomes possible to stabilize the balance between the operating force in the right/left direction and the operating moment, and improve the operating performance. The second objective is to overcome the other difficulty whereby, during the one-hand pull-operation, the cart tended to run off course to the right/left. To solve this problem, we add a positional control in the right/left direction. As a result, we reduce the lateral deviation of the cart, and improve the operating performance.
Electrochemical measuring cell. [exhaust gas oxygen meter] (1980)

An electrochemical measuring cell for determining the oxygen content in exhaust gases from internal-combustion engines and combustions is described having an ion-conducting solid electrolyte with a measuring electrode as a first layer on the solid electrolyte and a reference electrode as a second layer on the solid electrolyte. A third layer coats the first layer measuring electrode and contains a material with a high partial oxygen pressure to obtain a characteristic U f( Lambda ) which has a small slope in the range of the air number of about 1; a material with a medium partial oxygen pressure to obtain a characteristic with a medium slope; and a material with low partial oxygen pressure to obtain a characteristic with a steep slope.
Mutant Metabolic Enzymes Are at the Origin of Gliomas (2009)

Mutations of the isocitrate dehydrogenase (IDH) metabolic enzymes IDH1 and IDH2 have been found to be frequent and early genetic alterations in astrocytomas and oligodendrogliomas. All mutations identified to date affect a single amino acid located within the isocitrate binding site (R132 of IDH1 and the analogous R172 residue of IDH2). IDH1 and IDH2 mutations define a specific subtype of gliomas and may have significant utility for the diagnosis, prognosis, and treatment of patients with these tumors.
An Improved Process for the Production of Rivastigmine Tartrate, a Cholinesterase Inhibitor (2010)

An improved and scalable process for the production of rivastigmine tartrate is reported. The improved process provides rivastigmine tartrate at considerably lower cost and allows the omission of hazardous chemicals. The overall yield is increased from 4.66% (reported process) to 17% with the improved process. Keywords: Rivastigmine tartrate, a cholinesterase inhibitor, alzheimer's disease, improved process, impurities