gebhart/patrepeval huggingface dataset:
Intracellular Labeling with Extrinsic Probes: Delivery Strategies and Applications (2020)

Extrinsic probes have outstanding properties for intracellular labeling to visualize dynamic processes in and of living cells, both in vitro and in vivo. Since extrinsic probes are in many cases cell-impermeable, different biochemical, and physical approaches have been used to break the cell membrane barrier for direct delivery into the cytoplasm. In this Review, these intracellular delivery strategies are discussed, briefly explaining the mechanisms and how they are used for live-cell labeling applications. Methods that are discussed include three biochemical agents that are used for this purpose-purpose-different nanocarriers, cell penetrating peptides and the pore-foraming bacterial toxin streptolysin O. Most successful intracellular label delivery methods are, however, based on physical principles to permeabilize the membrane and include electroporation, laser-induced photoporation, micro- and nanoinjection, nanoneedles or nanostraws, microfluidics, and nanomachines. The strengths and weaknesses of each strategy are discussed with a systematic comparison provided. Finally, the extrinsic probes that are reported for intracellular labeling so-far are summarized, together with the delivery strategies that are used and their performance. This combined information should provide for a useful guide for choosing the most suitable delivery method for the desired probes.
A Randomized Clinical Trial Comparing Open and Arthroscopic Stabilization for Recurrent Traumatic Anterior Shoulder Instability (2014)

Background: The literature comparing open and arthroscopic repair for glenohumeral instability is conflicting. We performed a prospective, expertise-based, randomized clinical trial to compare open shoulder stabilization with arthroscopic shoulder stabilization by measuring quality-of-life outcomes and recurrence rates at two years among patients treated for traumatic anterior shoulder instability. Methods: Computer-generated, variable-block-size, concealed randomization allocated 196 patients to either the open-repair group (n = 98) or the arthroscopic-repair group (n = 98). An expertise-based randomization design was employed to avoid a differential bias in terms of physician experience. Outcomes were measured at baseline, at three and six months postoperatively, and at one and two years postoperatively with use of the Western Ontario Shoulder Instability Index (WOSI) and the American Shoulder and Elbow Surgeons (ASES) functional outcome scale. Recurrent instability was also analyzed. Results: There were no significant differences in outcome scores at baseline. At two years, seventy-nine patients in the open group and eighty-three patients in the arthroscopic group were available for follow-up. There was no significant difference in mean WOSI scores between the groups; the mean WOSI score (and standard deviation) for the open group was 85.2 ± 20.4 (95% confidence interval [CI] = 80.5 to 89.8), and for the arthroscopic group, 81.9 ± 19.8 (95% CI = 77.4 to 86.4); p = 0.31. There was also no significant difference in mean ASES scores: 91.4 ± 12.7 (95% CI = 88.5 to 94.4) for the open group and 88.2 ± 15.9 (95% CI = 84.6 to 91.8) for the arthroscopic group; p = 0.17. Recurrence rates at two years were significantly different: 11% in the open group and 23% in the arthroscopic group (p = 0.05). Recurrent instability was more likely in patients with a preoperative Hill-Sachs lesion and in male patients who were twenty-five years old and younger. There was no significant difference in shoulder motion between the groups at two years. Conclusions: There was no difference between open and arthroscopic repair in terms of patient quality of life. Open repair resulted in a significantly lower risk of recurrence. Secondary outcome data from this trial suggest that open surgical repair may be recommended to reduce the risk of recurrent instability in younger male patients with a Hill-Sachs lesion. Level of Evidence: Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.
Identification of PTCSC3 as a Novel Locus for Large‐Vessel Ischemic Stroke: A Genome‐Wide Association Study (2016)

Our data provide strong support for future studies on the role of PTCSC3 in the pathogenesis of LAA stroke and the association between LAA stroke development and thyroid function. In addition, these findings provide insights into the genetic basis of LAA stroke and identify a novel pathway that might be applicable for future therapeutic intervention.
Roles of Na-K-2Cl and Na-Cl cotransporters and ROMK potassium channels in urinary concentrating mechanism (1998)

The cloning of the apical transport proteins involved in NaCl absorption in the thick ascending limb of Henle and the distal convoluted tubule has ushered in a new era that promises to provide molecular details of the urinary concentrating and diluting processes. We now have at hand tools to examine the regulation of these proteins that can affect the concentrating and diluting capacity.
Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue (2015)

A novel technique of virion-enrichment from plasma has allowed to identify two host proteins that have prognostic value for classifying patients with acute dengue who are more likely to develop a severe dengue. The impact of these host proteins on pathogenicity and disease outcome are discussed.
Recent Results from Gas Loaded Nanoparticle-Type Cluster Power Units (2013)

This research was done is support of the development of modular 5 kW co-generation power cells by LENUCO LLC. The aim of this research was to determine the dependence of particle composition and initial temperature on peak power and total heat output. Three particle compositions, composing of various amounts of nickel, palladium and zirconium, have been studied. The effects of initial temperature are also discussed. Excess heat generation is seen and is theorized to be attributed to Low Energy Nuclear Reactions(LENR).
Interleukin 4 inhibits stimulation of hepatic lipogenesis by tumor necrosis factor, interleukin 1, and interleukin 6 but not by interferon-alpha. (1991)

Multiple cytokines stimulate hepatic lipogenesis in rodents. We have previously shown that lipogenic cytokines can be divided into 2 classes by their mechanism of action and their synergistic interactions. We now report the effects of interleukin 4, a cytokine known to inhibit the synthesis and action of other cytokines. Interleukin 4 by itself did not alter hepatic lipogenesis. However, interleukin 4 inhibited the characteristic stimulation of hepatic lipogenesis that is seen with tumor necrosis factor, interleukin 1, and interleukin 6. These 3 cytokines stimulate hepatic lipogenesis by the same mechanism, increasing hepatic levels of citrate, a key allosteric activator of acetyl CoA carboxylase, the rate-limiting enzyme of fatty acid synthesis. Interleukin 4 blocks the ability of tumor necrosis factor to increase hepatic citrate. In contrast, interleukin 4 does not block the stimulation of hepatic lipogenesis by interferon-alpha, a cytokine that increases hepatic lipogenesis by a mechanism other than increasing hepatic citrate levels. These results demonstrate that interleukin 4 can inhibit the metabolic action of selected cytokines, which provides strong support for our proposal that lipogenic cytokines operate through 2 distinct mechanisms of action and can therefore be divided into 2 separate classes based on their interactions. These results also emphasize the multiple relationships between the immune response and lipid metabolism.
Enhancement of the StreptoTag method for isolation of endogenously expressed proteins with complex RNA binding targets (2006)

StreptoTag is a novel affinity chromatography-based method for the isolation of high- and low-affinity RNA binding proteins. Originally it was shown possible to isolate recombinant protein from yeast or bacterial extracts using small, specific, well-characterised RNA binding targets. Here we show that using an enhanced aptamer it is not only possible to efficiently immobilise large, highly structured RNA binding targets onto the streptomycin columns but also that the StreptoTag method can be used for the isolation and purification of endogenously expressed regulatory proteins, with relatively low abundance, from eukaryotic extracts. As an example for this we uncover the identity of a karyophilic cellular protein which specifically binds to an area within the large, highly folded structure that characterises the mRNA from the unique 3' region (U3) of the mouse mammary tumour virus (MMTV) long terminal repeat (LTR). Hence, this method is now suitable for the quick and efficient isolation and identification of novel RNA binding proteins such as regulatory factors.
On the Robustness of an Analog VLSI Implementation of a Time Encoding Machine (2005)

Time encoding is a mechanism for representing the information contained in a continuous time, bandlimited, analog signal as the zero-crossings of a binary signal. Time decoding algorithms have been developed that make a perfect recovery of time encoded bandlimited signals possible. We consider a simple one-opamp active RC implementation of the time encoder and investigate the robustness in performance of the time decoder when the former is subject to non-idealities of the analog VLSI realization. We show that up to a constant scaling factor, delay and offset the input signal can be accurately reconstructed even if the opamp has a finite DC gain and finite bandwidth and the circuit exhibits parameter offsets. We develop an experimental upper bound for the reconstruction error that can be used in the design of the encoder. The analytical results are verified with numerical simulations.
Conventional Choices in Outcome Measures Influence Meta-Analytic Results (2022)

Abstract It is a plausible speculation that conventional choices in outcome measures might influence the results of meta-analyses. We test that speculation by simulating data from trials on antidepressants. We vary real drug effectiveness while modulating conventional values for outcome measures. We had previously shown that one conventional choice used in meta-analyses of antidepressants falls in a narrow range of values that maximize estimates of effectiveness. Our present analysis investigates why this phenomenon occurs. Moreover, our results suggest the superiority of absolute outcome measures over relative measures. This research program can be extended to test numerous other aspects of clinical research.
ChemInform Abstract: COMPLEX CHEMISTRY OF REACTIVE ORGANIC COMPOUNDS, XX. HALOBENZOCYMANTRENES (1978)

Abstract Die nach Hochvakuumsublimation hellgelben Feststoffe (III) sind sowohl in Substanz, als auch in Lösung ziemlich luftbeständig.
Distinct differences in the nanoscale behaviors of the twist-bend liquid crystal phase of a flexible linear trimer and homologous dimer (2017)

We synthesized the liquid crystal dimer and trimer members of a series of flexible linear oligomers and characterized their microscopic and nanoscopic properties using resonant soft x-ray scattering and a number of other experimental techniques. On the microscopic scale, the twist-bend phases of the dimer and trimer appear essentially identical. However, while the liquid crystal dimer exhibits a temperature-dependent variation of its twist-bend helical pitch varying from 100 - 170 Å on heating, the trimer exhibits an essentially temperature-independent pitch of 66 Å, significantly shorter than those reported for other twist-bend forming materials in the literature. We attribute this to a specific combination of intrinsic conformational bend of the trimer molecules and a sterically favorable intercalation of the trimers over a commensurate fraction (two-thirds) of the molecular length. We develop a geometric model of the twist-bend phase for these materials with the molecules arranging into helical chain structures, and we fully determine their respective geometric parameters.
Bidirectional Crosstalk and Back-Reflection Free WDM Active Optical Interconnects (2013)

In this letter, we present an integrated solution for bidirectional WDM optical interconnection based on semiconductor optical amplifiers and nonreciprocal micro-ring resonators in Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> /Ce:YIG. The circuit performance has been numerically evaluated, demonstrating a reduction of crosstalk and back-reflection of for a 10-channel 100-GHz-spaced WDM bidirectional active optical interconnect. Although a silicon-nitride platform has been considered, the proposed solution can be effective also on a silicon platform, where back-scattering induced by the waveguide roughness is much stronger.
Organic and Polymeric Semiconductors Enhanced by Noncovalent Conformational Locks (2017)

Constructing highly planar, extended π-electron systems is an important strategy for achieving high-mobility organic semiconductors. In general, there are two synthetic strategies for achieving π-conjugated systems with high planarity. The conventional strategy connects neighboring aromatic rings through covalent bonds to restrict the rotation about single bonds. However, this usually requires a complex sequence of synthetic steps to achieve this target, which can be costly and labor-intensive. More recently, noncovalent through-space intramolecular interactions, which are defined here as noncovalent conformational locks, have been employed with great success to increase the planarity and rigidity of extended π-electron systems; this has become a well-known and important strategy to design and synthesize highly planar π-conjugated systems for organic electronics. This review offers a comprehensive and general summary of conjugated systems with such noncovalent conformational locks, including O···S, N···S, X···S (where X = Cl, Br, F), and H···S through-space interactions, together with analysis by density functional theory computation, X-ray diffraction, and microstructural characterization, as well as by evaluation of charge transport in organic thin-film transistors and solar cells.
The Human Pathogen Streptococcus pyogenes Releases Lipoproteins as Lipoprotein-rich Membrane Vesicles (2015)

Bacterial lipoproteins are attractive vaccine candidates because they represent a major class of cell surface-exposed proteins in many bacteria and are considered as potential pathogen-associated molecular patterns sensed by Toll-like receptors with built-in adjuvanticity. Although Gram-negative lipoproteins have been extensively characterized, little is known about Gram-positive lipoproteins. We isolated from Streptococcus pyogenes a large amount of lipoproteins organized in vesicles. These vesicles were obtained by weakening the bacterial cell wall with a sublethal concentration of penicillin. Lipid and proteomic analysis of the vesicles revealed that they were enriched in phosphatidylglycerol and almost exclusively composed of lipoproteins. In association with lipoproteins, a few hypothetical proteins, penicillin-binding proteins, and several members of the ExPortal, a membrane microdomain responsible for the maturation of secreted proteins, were identified. The typical lipidic moiety was apparently not necessary for lipoprotein insertion in the vesicle bilayer because they were also recovered from the isogenic diacylglyceryl transferase deletion mutant. The vesicles were not able to activate specific Toll-like receptor 2, indicating that lipoproteins organized in these vesicular structures do not act as pathogen-associated molecular patterns. In light of these findings, we propose to name these new structures Lipoprotein-rich Membrane Vesicles.
On-chip cell labelling and washing by capture and release using microfluidic trap arrays (2017)

Flow cytometry analysis requires a large amount of isolated, labelled, and purified cells for accurate results. To address the demand for a large quantity of cells prepared in a timely manner, we describe a novel microfluidic trap structure array for on-chip cell labelling, such as intracellular and extracellular labelling, and subsequent washing and release of cells. Each device contains [Formula: see text] trap structures, which made the preparation of large numbers of cells [Formula: see text] possible. The structure has a streamlined shape, which minimizes clogging of cells in capture and release steps. The trap structure arrays are built and tested using leukocytes, with different load flow speeds, incubation times, and release flow speeds. ∼85% of cells are captured independent of the input flow speed. The release efficiency depends on the incubation time, with over ∼80% of captured cells released for up to 20 min incubation, and on-chip labelling and washing with STYO13 are demonstrated. Qualitative models are developed as guidance for designing the proposed trap structure and to explain the increased performance over previous approaches.
Biologically inspired technologies in NASA's morphing project (2003)

For centuries, biology has provided fertile ground for hypothesis, discovery, and inspiration. Time-tested methods used in nature are being used as a basis for several research studies conducted at the NASA Langley Research Center as a part of Morphing Project, which develops and assesses breakthrough vehicle technologies. These studies range from low drag airfoil design guided by marine and avian morphologies to soaring techniques inspired by birds and the study of small flexible wing vehicles. Biology often suggests unconventional yet effective approaches such as non-planar wings, dynamic soaring, exploiting aeroelastic effects, collaborative control, flapping, and fibrous active materials. These approaches and other novel technologies for future flight vehicles are being studied in NASA's Morphing Project. This paper will discuss recent findings in the aeronautics-based, biologically-inspired research in the project.
Enhancement of retroviral infectionin vitroby anti-LeyIgG: reversal by humanization of monoclonal mouse antibody (1993)

Monoclonal mouse IgG3 antibody (ABL 364) against the carbohydrate Ley antigen enhanced infection in vitro with HTLV-1 and with HIV-1 when propagated in both transformed and normal lymphocytes. Enhancement was independent of complement, occurred with both lymphocytes and monocytes as target cells, and did not use either Ley epitopes on target cells for cross-linkage of virus to the cell or the Fc part of the antibody as a ligand for any cellular receptor. For enhancement to occur, binding of anti-Ley antibody to virus was required to take place before virus binding to its specific receptor with no indication of any alternative pathway of infection, as evidenced by abrogation of enhancement by anti-CD4 MAb or soluble recombinant CD4, and also the inability of anti-Ley MAb to mediate HIV infection of HSB-2 cells in which HTLV-1/HIV pseudovirus infection was enhanced. While F(ab)2 fragments of ABL 364 also enhanced infection, a human/mouse chimeric antibody and a fully humanized antibody had no enhancing effect on free virus infection. We suggest that binding of anti-Ley ABL 364 or its F(ab)2 fragment induced a conformational change in the gp120 oligomers facilitating the process of infection, and that this function was abrogated by the IgG1 Fc of the chimeric and the humanized antibodies. The observations indicate that the non-paratope domains of antiviral antibodies can influence their function as neutralizing or enhancing for infection.
LOW LOSS SINGLE MODE FIBER SPLICES USING ULTRAVIOLET CURABLE CEMENT (1983)

Sensitivity of splice loss to alignment errors and low losses typical of single mode fibers make splicing a much more critical element for the FT4E single mode system than for the FT3 multimode system.
Building memory with concept learning capabilities from large-scale knowledge base (2015)

We present a new perspective on neural knowledge base (KB) embeddings, from which we build a framework that can model symbolic knowledge in the KB together with its learning process. We show that this framework well regularizes previous neural KB embedding model for superior performance in reasoning tasks, while having the capabilities of dealing with unseen entities, that is, to learn their embeddings from natural language descriptions, which is very like human's behavior of learning semantic concepts.
Observation of Recombination-Enhanced Defect Reactions in Semiconductors (1974)

Recombination-enhanced annealing of defects in semiconductors has been observed directly for the first time. The defects were produced in GaAs by 1-MeV electron irradiation and observed by transient-junction-capacitance techniques. The data clearly relate the enhanced defect annealing rate to electron-hole recombination processes at the defect.
Analysis of parallel mixed-mode simulation algorithms (2002)

This paper presents a performance analysis of several parallel algorithms for the mixed-mode simulation of digital systems. The performance model is an architectural simulation of the parallel algorithms running on a hypercube multiprocessor. Workload data is collected from a uniprocessor-based mixed-mode simulator on several benchmark circuits, and two distinct circuit partitioning algorithms are considered. The results indicate that the performance of the parallel simulations is highly circuit dependent, in some cases performing worse than a uniprocessor and in others approaching optimal performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Putative Calcium Channels CchA and MidA Play the Important Roles in Conidiation, Hyphal Polarity and Cell Wall Components in Aspergillus nidulans (2012)

Although the high affinity Ca(2+) channel, Cch1, and its subunit Mid1 have been investigated and evaluated in yeast and some of filamentous fungi, little is known about the function of their homologs in the Aspergilli. Here, we have functionally characterized the yeast homologs, CchA and MidA, in Aspergillus nidulans using conditional and null deletion mutants. CchA and MidA not only have functional benefits of fast growth, which is consistent with Cch1 and Mid1 in yeast, but also have unique and complex roles in regulating conidiation, hyphal polarity and cell wall components in low-calcium environments. The defect of CchA or MidA resulted in a sharp reduction in the number of conidiospores, accompanied by abnormal metulae, and undeveloped-phialides at a higher density of inoculum. Most interestingly, these conidiation defects in mutants can, remarkably, be rescued either by extra-cellular Ca(2+) in a calcineurin-dependent way or by osmotic stress in a calcineurin-independent way. Moreover, the fact that the phenotypic defects are not exacerbated by the presence of the double deletion, together with the Y2H assay, indicates that CchA and MidA may form a complex to function together. Our findings suggest that the high-affinity Ca(2+) channel may represent a viable and completely unexplored avenue to reduce conidiation in the Aspergilli.