gebhart/patrepeval huggingface dataset:
An Activatable siRNA Probe: Trigger‐RNA‐Dependent Activation of RNAi Function (2009)

Catch and release: A hairpin-shaped sense strand (red)/antisense strand (blue) siRNA probe was designed to be activated by a trigger RNA molecule. In the presence of the trigger RNA, clear OFF-to-ON switching of RNAi activity was observed with high sequence dependency (see schematic illustration). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Compliance and Force Control for Computer Controlled Manipulators (1981)

Compliant motion of a manipulator occurs when the manipulator position is constrained by the task geometry. Compliant motion may be produced either by a passive mechanical compliance built in to the manipulator, or by an active compliance implemented in the control servo loop. The second method, called force control, is the subject of this paper. In particular a theory of force control based on formal models of the manipulator and the task geometry is presented. The ideal effector is used to model the manipulator, the ideal surface is used to model the task geometry, and the goal trajectory is used to model the desired behavior of the manipulator. Models are also defined for position control and force control, providing a precise semantics for compliant motion primitives in manipulation programming languages. The formalism serves as a simple interface between the manipulator and the programmer, isolating the programmer from the fundamental complexity of low-level manipulator control. A method of automatically synthesizing a restricted class of manipulator programs based on the formal models of task and goal trajectory is also provided by the formalism.
Prognostic value of epidermal growth factor receptor in patients with glioblastoma multiforme. (2003)

Glioblastoma multiforme (GBM) frequently involves amplification and alteration of the epidermal growth factor receptor (EGFR) gene, resulting in overexpression of varied mutations, including the most common mutation, EGFRvIII, as well as wild-type EGFR (EGFRwt). To test the prognostic value of EGFR, we retrospectively analyzed the relationship between treatment outcomes and the EGFR gene in 87 newly diagnosed adult patients with supratentorial GBM enrolled in clinical trials. The EGFR gene status was assessed by Southern blots and EGFR expression by immunohistochemistry using three monoclonal antibodies (EGFR.25 for EGFR, EGFR.113 for EGFRwt, and DH8.3 for EGFRvIII). EGFR amplification was detected in 40 (46%) of the 87 GBM patients; in 39 (97.5%) of these, EGFR was overexpressed. On the other hand, in 46 of 47 patients without EGFR amplification (97.9%), no EGFR overexpression was present. There was a close correlation between EGFR amplification and EGFR overexpression (P < 0.0001). EGFRwt was overexpressed in 27 of the 40 (67.5%) patients with, and in none without, EGFR amplification (P < 0.0001). Similarly, EGFRvIII was overexpressed in 18 (45.0%) of 40 patients with and in 4 (8.5%) of 47 patients without EGFR amplification (P < 0.0001). The finding that 8 (20%) of the patients with EGFR amplification/EGFR overexpression manifested overexpression of neither EGFRwt nor EGFRvIII indicates that they overexpressed other types of EGFR. Multivariate analysis demonstrated that EGFR amplification was an independent, significant, unfavorable predictor for overall survival (OS) in all patients (P = 0.038, HR = 1.67). With respect to the relationship of age to EGFR prognostication, the EGFR gene status was a more significant prognosticator in younger patients, particularly in those <60 years (P = 0.0003, HR = 3.15), whereas not so in older patients. EGFRvIII overexpression, on the other hand, was not predictive for OS. However, in patients with EGFR amplification, multivariate analysis revealed that EGFRvIII overexpression was an independent, significant, poor prognostic factor for OS (P = 0.0044, HR = 2.71). This finding indicates that EGFRvIII overexpression in the presence of EGFR amplification is the strongest indicator of a poor survival prognosis. In GBM patients, EGFR is of significant prognostic value for predicting survival, and the overexpression of EGFRvIII with amplification plays an important role in enhanced tumorigenicity.
Treatment of cutaneous T-cell lymphoma with chimeric anti-CD4 monoclonal antibody (1996)

Chimeric anti-CD4 monoclonal antibody was administered intravenously as a single dose to eight patients with mycosis fungoides. The dose was escalated throughout the study between patients groups, and individual patients received 50, 100, or 200 mg per dose. Seven of eight patients responded to treatment with an average freedom from progression of 25 weeks (range, 6 to 52 weeks). The treatment was well tolerated, and there was no clinical evidence of immunosuppression. Following treatment, there was significant suppression of peripheral blood CD4 counts in all patients for 1 to 22+ weeks. Only one patient made a very low titer human antichimeric antibody response. All but two patients made primary antibody and T-cell proliferative responses to a foreign antigen administered 24 hours after antibody infusion. However, there was generally marked, but temporary suppression of T-cell proliferative responses in vitro to phytohemagglutinin (PHA), tetanus toxoid, and normal donor lymphocytes. We conclude that at the dose levels studied, this antibody (1) had clinical efficacy against mycosis fungoides; (2) was well tolerated; (3) had a low level of immunogenicity; (4) decreased T-cell proliferative responses in vitro, and (5) did not induce tolerance to a foreign antigen.
Effect of Bardoxolone Methyl on Kidney Function in Patients with T2D and Stage 3b–4 CKD (2011)

&lt;i&gt;Background/Aims:&lt;/i&gt; Bardoxolone methyl, a novel synthetic triterpenoid, induces Nrf2, a transcription factor known to play a key role in decreasing oxidative stress and the production of pro-inflammatory molecules. &lt;i&gt;Methods:&lt;/i&gt; This exploratory multi-center, open-label study assessed the clinical activity and safety of bardoxolone methyl in 20 patients with moderate to severe chronic kidney disease and type 2 diabetes. Patients received 25 mg of bardoxolone methyl daily for 28 days, followed by 75 mg daily for another 28 days. &lt;i&gt;Results:&lt;/i&gt; The study achieved its primary efficacy endpoint, as demonstrated by a significant increase from baseline in estimated glomerular filtration rate (eGFR) of 7.2 ml/min/1.73 m&lt;sup&gt;2&lt;/sup&gt; (p &lt; 0.001). Improvements were seen in approximately 90% of patients and showed a dose- and time-dependent increase in eGFR. The eGFR change paralleled a significant reduction in serum creatinine (–0.3 mg/dl) and blood urea nitrogen (–4.9 mg/dl), along with an increase in creatinine clearance (+14.6 ml/min/1.73 m&lt;sup&gt;2&lt;/sup&gt;), without a change in the 24-hour creatinine excretion rate. Markers of vascular injury and inflammation were improved by treatment with bardoxolone. No life-threatening adverse events or drug-related serious adverse events were reported. &lt;i&gt;Conclusions:&lt;/i&gt; The results describe an apparent increase in kidney function following relatively short-term treatment with bardoxolone methyl, a promising new agent that warrants placebo-controlled studies to define its long-term effects on renal function.
A separate editing exonuclease for DNA replication: the epsilon subunit of Escherichia coli DNA polymerase III holoenzyme. (1984)

DNA polymerase III (polIII) holoenzyme of Escherichia coli has 3'----5' exonuclease ("editing") activity in addition to its polymerase activity, a property shared by other prokaryotic DNA polymerases. The polymerization activity is carried by the large alpha subunit, the product of the dnaE gene. Mutations affecting the fidelity of DNA replication in vivo and the activity of 3'----5' exonuclease assayed in vitro are found in the dnaQ gene, which specifies the epsilon subunit. To determine whether epsilon carries the 3'----5' exonuclease activity, we have used an overproduction protocol to purify epsilon separately from the other subunits of polIII holoenzyme. We find that epsilon has 3'----5' exonuclease activity indistinguishable from that of polIII core, the subassembly of polIII holoenzyme consisting of the alpha, epsilon, and theta subunits. We conclude that the editing and polymerization activities of polIII holoenzyme reside on distinct subunits, in contrast to DNA polymerase I of E. coli and DNA polymerase of phage T4. This functional separation may provide for regulation of exonucleolytic editing independently of polymerization, allowing cellular control of replication fidelity.
New Opportunities for an Ancient Material (2010)

Spiders and silkworms generate silk protein fibers that embody strength and beauty. Orb webs are fascinating feats of bioengineering in nature, displaying magnificent architectures while providing essential survival utility for spiders. The unusual combination of high strength and extensibility is a characteristic unavailable to date in synthetic materials yet is attained in nature with a relatively simple protein processed from water. This biological template suggests new directions to emulate in the pursuit of new high-performance, multifunctional materials generated with a green chemistry and processing approach. These bio-inspired and high-technology materials can lead to multifunctional material platforms that integrate with living systems for medical materials and a host of other applications.
The Helminth-Derived Immunomodulator AvCystatin Reduces Virus Enhanced Inflammation by Induction of Regulatory IL-10+ T Cells (2016)

Respiratory Syncytial Virus (RSV) is a major pathogen causing low respiratory tract disease (bronchiolitis), primarily in infants. Helminthic infections may alter host immune responses to both helminths and to unrelated immune triggers. For example, we have previously shown that filarial cystatin (AvCystatin/Av17) ameliorates allergic airway inflammation. However, helminthic immunomodulators have so far not been tested in virus-induced disease. We now report that AvCystatin prevents Th2-based immunopathology in vaccine-enhanced RSV lung inflammation, a murine model for bronchiolitis. AvCystatin ablated eosinophil influx, reducing both weight loss and neutrophil recruitment without impairing anti-viral immune responses. AvCystatin also protected mice from excessive inflammation following primary RSV infection, significantly reducing neutrophil influx and cytokine production in the airways. Interestingly, we found that AvCystatin induced an influx of CD4+ FoxP3+ interleukin-10-producing T cells in the airway and lungs, correlating with immunoprotection, and the corresponding cells could also be induced by adoptive transfer of AvCystatin-primed F4/80+ macrophages. Thus, AvCystatin ameliorates enhanced RSV pathology without increasing susceptibility to, or persistence of, viral infection and warrants further investigation as a possible therapy for virus-induced airway disease.
Evidence of Reperfusion Injury, Exacerbated by Thrombolytic Therapy, in Human Focal Brain Ischemia Using a Novel Imaging Marker of Early Blood–Brain Barrier Disruption (2004)

Loss of integrity of the blood-brain barrier (BBB) resulting from ischemia and reperfusion is a hypothesized precursor to hemorrhagic transformation (HT) and worse clinical outcome than would be expected from the beneficial effects of reperfusion. We used a novel magnetic resonance imaging marker to characterize early BBB disruption in acute focal brain ischemia and tested associations with reperfusion, HT, and poor outcome (modified Rankin score >2). The BBB disruption was evident as delayed gadolinium enhancement of cerebrospinal fluid space on fluid-attenuated inversion recovery (FLAIR) images and, for convenience, has been termed hyperintense acute reperfusion marker (HARM). HARM was found in 47 of 144 (33%) ischemic stroke patients. Reperfusion was found to be the strongest independent predictor of early BBB disruption (P=0.018) in multivariate analysis. HARM was associated with HT and worse clinical outcome (after adjustment for initial severity). It was also associated with more severe strokes at onset and greater age. Because the timing of the disruption was early enough (median estimate 3.8 hours from onset) to make it relevant to acute thrombolytic therapy, early BBB disruption as defined by HARM may be a promising target for adjunctive therapy to reduce the complications associated with thrombolytic therapy, broaden the therapeutic window, and improve clinical outcome.
Highly Stable Cp*−Ir(III) Complexes with N-Heterocyclic Carbene Ligands as C−H Activation Catalysts for the Deuteration of Organic Molecules (2006)

The preparation of a series of complexes of the type CpIrX2(NHC) provides effective catalysts for the H/D exchange of a wide range of organic molecules in methanol-d4. The reaction proceeds with higher yields under milder reaction conditions than previous CpIr systems reported thus far. For comparative purposes, we also studied the catalytic activity of CpIrCl2(PMe3) under the same reaction conditions. The molecular structures of two of the new CpIr(NHC) complexes are described.
The implications of condensed tannins on the nutritive value of temperate forages fed to ruminants (1999)

New methodology for measuring forage condensed tannin (CT) content is described and the effects of CT upon forage feeding and nutritive value for ruminant animals are reviewed. CT react with forage proteins in a pH-reversible manner, with reactivity determined by the concentration, structure and molecular mass of the CT. Increasing concentrations of CT in Lotus corniculatus and Lotus pedunculatus reduce the rates of solubilization and degradation of fraction 1 leaf protein in the rumen and increase duodenal non-NH3 N flow. Action of medium concentrations of total CT in Lotus corniculatus (30-40 g/kg DM) increased the absorption of essential amino acids from the small intestine and increased wool growth, milk secretion and reproductive rate in grazing sheep without affecting voluntary feed intake, thus improving the efficiency of food conversion. High concentrations of CT in Lotus pedunculatus (75-100 g/kg DM) depressed voluntary feed intake and rumen carbohydrate digestion and depressed rates of body and wool growth in grazing sheep. The minimum concentration of CT to prevent rumen frothy bloat in cattle is defined as 5 g/kg DM and sheep grazing CT-containing legumes were shown to better tolerate internal parasite infections than sheep grazing non CT-containing forages. It was concluded that defined concentrations of forage CT can be used to increase the efficiencies of protein digestion and animal productivity in forage-fed ruminants and to develop more ecologically sustainable systems of controlling some diseases under grazing.
Profiling Cys34 Adducts of Human Serum Albumin by Fixed-Step Selected Reaction Monitoring (2010)

A method is described for profiling putative adducts (or other unknown covalent modifications) at the Cys34 locus of human serum albumin (HSA), which represents the preferred reaction site for small electrophilic species in human serum. By comparing profiles of putative HSA-Cys34 adducts across populations of interest it is theoretically possible to explore environmental causes of degenerative diseases and cancer caused by both exogenous and endogenous chemicals. We report a novel application of selected-reaction-monitoring (SRM) mass spectrometry, termed fixed-step SRM (FS-SRM), that allows detection of essentially all HSA-Cys34 modifications over a specified range of mass increases (added masses). After tryptic digestion, HSA-Cys34 adducts are contained in the third largest peptide (T3), which contains 21 amino acids and an average mass of 2433.87 Da. The FS-SRM method does not require that exact masses of T3 adducts be known in advance but rather uses a theoretical list of T3-adduct m/z values separated by a fixed increment of 1.5. In terms of added masses, each triply charged parent ion represents a bin of ±2.3 Da between 9.1 Da and 351.1 Da. Synthetic T3 adducts were used to optimize FS-SRM and to establish screening rules based upon selected b- and y-series fragment ions. An isotopically labeled T3 adduct is added to protein digests to facilitate quantification of putative adducts. We used FS-SRM to generate putative adduct profiles from six archived specimens of HSA that had been pooled by gender, race, and smoking status. An average of 66 putative adduct hits (out of a possible 77) were detected in these samples. Putative adducts covered a wide range of concentrations, were most abundant in the mass range below 100 Da, and were more abundant in smokers than in nonsmokers. With minor modifications, the FS-SRM methodology can be applied to other nucleophilic sites and proteins.
Biological Functionalization of Drug Delivery Carriers To Bypass Size Restrictions of Receptor-Mediated Endocytosis Independently from Receptor Targeting (2013)

Targeting of drug carriers to cell-surface receptors involved in endocytosis is commonly used for intracellular drug delivery. However, most endocytic receptors mediate uptake via clathrin or caveolar pathways associated with ≤200-nm vesicles, restricting carrier design. We recently showed that endocytosis mediated by intercellular adhesion molecule 1 (ICAM-1), which differs from clathrin- and caveolae-mediated pathways, allows uptake of nano- and microcarriers in cell culture and in vivo due to recruitment of cellular sphingomyelinases to the plasmalemma. This leads to ceramide generation at carrier binding sites and formation of actin stress-fibers, enabling engulfment and uptake of a wide size-range of carriers. Here we adapted this paradigm to enhance uptake of drug carriers targeted to receptors associated with size-restricted pathways. We coated sphingomyelinase onto model (polystyrene) submicro- and microcarriers targeted to clathrin-associated mannose-6-phosphate receptor. In endothelial cells, this provided ceramide enrichment at the cell surface and actin stress-fiber formation, modifying the uptake pathway and enhancing carrier endocytosis without affecting targeting, endosomal transport, cell-associated degradation, or cell viability. This improvement depended on the carrier size and enzyme dose, and similar results were observed for other receptors (transferrin receptor) and cell types (epithelial cells). This phenomenon also enhanced tissue accumulation of carriers after intravenous injection in mice. Hence, it is possible to maintain targeting toward a selected receptor while bypassing natural size restrictions of its associated endocytic route by functionalization of drug carriers with biological elements mimicking the ICAM-1 pathway. This strategy holds considerable promise to enhance flexibility of design of targeted drug delivery systems.
Deterministic Remote Entanglement of Superconducting Circuits through Microwave Two-Photon Transitions (2018)

Large-scale quantum information processing networks will most probably require the entanglement of distant systems that do not interact directly. This can be done by performing entangling gates between standing information carriers, used as memories or local computational resources, and flying ones, acting as quantum buses. We report the deterministic entanglement of two remote transmon qubits by Raman stimulated emission and absorption of a traveling photon wave packet. We achieve a Bell state fidelity of 73%, well explained by losses in the transmission line and decoherence of each qubit.
Structural Basis of Immune Recognition of Influenza Virus Hemagglutinin (1990)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Possibility of Superconductive-Type Enhanced Conductivity in DNA at Room Temperature (1969)

Applying Little's formalism to investigate the possibility of superconductive regions at room temperature in organic polymers, we have calculated the Coulomb and effective attractive terms for the polycytosine homopolynucloetide. Little's original idea that the effective interaction between the mobile electrons of the spine is due to the polarization of the side-chain electrons has been extended to take into account the polarization of the $\ensuremath{\sigma}$ electrons of the same systems which provide the mobile electrons. According to the results obtained for many intraband and interband scattering processes, the absolute value of the attractive term is larger than, or about the same as, that of the Coulomb term. Therefore, we cannot exclude the possibility of superconductive-type enhanced conductivity in some regions of DNA. Finally, the effects of the finite dimensions of a cytosine molecule are discussed from the point of view of screening and thermodynamic fluctuations.
Development and performance analysis of an intra-body communication device (2004)

Personal area networks would benefit from a wireless communication system in which a variety of information could be exchanged through wearable electronic devices and sensors. Intra-body communication using the human body as the transmission medium enables wireless communication without transmitting radio waves through the air. A human arm phantom is designed and used to reduce uncertainty in experiments with the human body. The phantom exhibits transmission characteristics similar to those of the human body at frequencies between 1 MHz and 10 MHz. A 10.7 MHz frequency modulation (FM) intra-body transmitter and receiver are developed which allow transmission of analog sine waves even in the presence of external noise. Digital data transmission at 9600 bps was also achieved using newly fabricated 10.7 MHz frequency shift keying (FSK) transmitter and receiver devices. The carrier frequency of 10.7 MHz, which is the intermediate frequency in FM radio receivers, means that a wide selection of commercial radio frequency (RF) devices is available.
Direct evidence for a protein recognized by a monoclonal antibody against oxidatively modified LDL in atherosclerotic lesions from a Watanabe heritable hyperlipidemic rabbit. (1989)

Low density lipoproteins (LDL) that have been oxidatively modified have been implicated in the pathogenesis of atherosclerosis. Monoclonal antibodies were generated against oxidatively modified human low density lipoproteins (OxLDL); these antibodies reacted with OxLDL, but did not react with native LDL, either in an enzyme-linked immunosorbent assay (ELISA) or a Western blot analysis. The anti-OxLDL antibodies did react with other modified forms of LDL (eg, acetylated LDL, malondialdehyde-modified LDL, and cell-modified LDL) that were recognized by the scavenger receptor on macrophages. Single- and double-label immunofluorescence of atheromatous lesions from a Watanabe heritable hyperlipidemic (WHHL) rabbit demonstrated some colocalization of proteins detected by anti-LDL and anti-OxLDL antibodies. However, clearly there were also areas stained by the anti-OxLDL antibodies that did not stain with anti-LDL. Staining of the lesion by the anti-OxLDL antibody was abolished by adsorption of the antibody with OxLDL, but not by adsorption with LDL or bovine serum albumin. Arterial tissue from a control New Zealand White rabbit did not show staining with anti-LDL or anti-OxLDL antibodies. These observations suggest that OxLDL (or possibly other proteins recognized by the anti-OxLDL antibody) is present in atheromatous lesions of WHHL rabbits, and are consistent with oxidatively modified lipoproteins having a role in atherogenesis.