gebhart/patrepeval huggingface dataset:
Multiplexed Affinity-Based Separation of Proteins and Cells Using Inertial Microfluidics (2016)

Isolation of low abundance proteins or rare cells from complex mixtures, such as blood, is required for many diagnostic, therapeutic and research applications. Current affinity-based protein or cell separation methods use binary 'bind-elute' separations and are inefficient when applied to the isolation of multiple low-abundance proteins or cell types. We present a method for rapid and multiplexed, yet inexpensive, affinity-based isolation of both proteins and cells, using a size-coded mixture of multiple affinity-capture microbeads and an inertial microfluidic particle sorter device. In a single binding step, different targets-cells or proteins-bind to beads of different sizes, which are then sorted by flowing them through a spiral microfluidic channel. This technique performs continuous-flow, high throughput affinity-separation of milligram-scale protein samples or millions of cells in minutes after binding. We demonstrate the simultaneous isolation of multiple antibodies from serum and multiple cell types from peripheral blood mononuclear cells or whole blood. We use the technique to isolate low abundance antibodies specific to different HIV antigens and rare HIV-specific cells from blood obtained from HIV+ patients.
Digital Camera with Spiral Odd-Symmetry Phase Grating Supports Full-Resolution Computational Refocussing (2013)

Novel odd-symmetry phase gratings produce spatially varying depth-dependent point-spread functions on an imager’s sensor plane. The severely blurred sensed image can be inverted computationally to refocus and estimate target distances.
Catabolism of tissue-type plasminogen activator by the human hepatoma cell line Hep G2 (1989)

Catalytic activity of tissue-type plasminogen activator (t-PA) in plasma is regulated in part by formation of complexes with specific inhibitors as well as by hepatic clearance. Potential interaction of these two regulatory mechanisms was examined in the human hepatoma cell line Hep G2. These cells secrete plasminogen activator inhibitor type-1 (PAI-1) and initiate catabolism of exogenous t-PA by receptor-mediated endocytosis. Specific binding of 125I-t-PA to cells at 4 degrees C results in dose-dependent formation of a 95-kDa species recognized by monospecific anti-PAI-1 and anti-t-PA antibodies and stable in the presence of low (0.2%) concentrations of sodium dodecyl sulfate (SDS). Specific binding of 125I-t-PA and formation of the 95-kDa SDS-stable species are inhibited in a concentration-dependent manner following preincubation of cells with anti-PAI-1 antibodies. High and low molecular weight forms of urokinase plasminogen activator (u-PA) capable of forming specific complexes with PAI-1 complete for 125I-t-PA binding sites. However, the proenzyme form of u-PA (scu-PA), incapable of forming complexes with PAI-1, does not compete for 125I-t-PA binding sites. The role of the serine protease active site of t-PA in mediating both interaction with PAI-1 and specific binding was examined using 125I-t-PA that had been functionally inactivated with D-phenylalanyl-L-propyl-L-arginyl-chloromethyl ketone (PPACK). 125I-t-PA-PPACK, despite a 6-fold lower affinity than active 125I-t-PA, exhibited specific binding to cells without detectable formation of SDS-stable complexes with PAI-1. Both surface-bound 125I-t-PA and 125I-t-PA-PPACK are internalized and degraded by cells at 37 degrees C. 125I-t-PA is internalized as a stable complex with PAI-1, whereas 125I-t-PA-PPACK is internalized with similar kinetics but without the presence of an SDS-stable complex. Thus, PAI-1 appears capable of modulating t-PA catabolism in the human hepatocyte.
<title>Heat generation of magneto-rheological fluid dampers</title> (2000)

This study presents a theoretical analysis of heat generation and dissipation of field-controllable magneto-rheological fluid (MRF) shock absorbers. Since MRF dampers are energy- dissipating devices, the issues of heat generation and dissipation are important in predicting their performance. A theoretical model is developed based on Bingham plastic model to estimate temperature history of the MRF dampers. The governing equation includes the MRF viscosity as a function of the temperature. The numerical solutions are compared with experimental results in order to validate the accuracy of the model, and excellent agreements are obtained.
P3‐161: Tau autoproteolytic activity is induced by tau oligomerization (2011)

tau self-assembly into oligomers, fibrils and higher order structures, such as neurofibrillary tangles, is a pathological process in Alzheimer's disease (AD) and related tauopathies (Gendron T.F. and Petrucelli L. 2009 Mol Neurodegener. 4:13). The oligomeric forms of tau appear to be the aggregates most closely associated with neuronal loss and memory impairment in mouse models of tauopathy (Berger Z. et al., 2007 J Neurosci. 27:3650-62; Yoshiyama Y. et al., Neuron. 2007 53:337-51), and granular tau oligomers are also increased in AD brain (Maeda S. et al., Neurosci Res. 2006 54:197-201). Furthermore, extracellular oligomeric tau has been shown to inhibit LTP and formation of associative fear memory in mice (Fá M. et al., 2010, submitted for publication). tau is a microtubule binding protein that normally functions in axons to maintain microtubule structure but is hyperphosphorylated in AD facilitating its dissociation from microtubules and accumulation in the somatodendritic compartment where it can aggregate (Iqbal K. et al., 2010 Curr Alzheimer Res. 7:656-64). The loss of tau function caused by hyperphosphorylation can be restored by dephosphorylation (Tanimukai H. et al., Psychogeriatrics. 2009 9:103-9). However, irreversible loss of function can be caused by tau truncation which at the same time forms tau fragments with a higher propensity to aggregate (Hanger DP, Wray S. Biochem Soc Trans. 2010 38:1016-20; Kovacech B. and Novak M. 2010 Curr Alzheimer Res. 7:708-16). Here, we present the observation that tau oligomerization induces autoproteolytic cleavage. Recombinant tau protein was highly purified and incubated to form oligomers. The non-reactive monomer and disulfide-mediated tau dimer and trimer oligomeric species were purified and incubated. The oligomeric tau species formed cleavage products, whereas the tau monomer was stable. The association between tau oligomerization and the formation of these cleavage products was observed multiple times. Tau aggregation schematic. Tauf = free tau (not bound microtubules); ↑[Tauf] = intracellular accumulation of tauf; Taudimer = Tau self interaction (monomer-monomer); Taudsm-dimer = Disulfide mediated dimmer; N+1Taudsm-oligomer = Disulfide mediated dimmer (3R Tau), disulfide mediated dimmer, trimer, tetramer, etc (4R Tau, and 3R/4R tau); tTau = truncated and full length 3R and 4R tau.
The application of perfluoroheteroaromatic reagents in the preparation of modified peptide systems (2017)

The perfluoroheteroaromatic reagent pentafluoropyridine has proved to be a highly reactive electrophile, undergoing S<sub>N</sub>Ar arylation reactions in the presence of a range of nucleophilic peptide side chains (i.e. cysteine, tyrosine, serine and lysine) under mild conditions. Moreover, we have shown how one-step peptide-modification using perfluoroheteroaromatics can deliver enhanced proteolytic stability in pharmaceutically-relevant peptides such as oxytocin.
A Graphical Model for Simultaneous Partitioning and Labeling. (2005)

In this work we develop a graphical model for describing probability distributions over labeled partitions of an undirected graph which are conditioned on observed data. We show how to efficiently perform exact inference in these models, by exploiting the structure of the graph and adapting the sum-product and max-product algorithms. We demonstrate our approach on the task of segmenting and labeling hand-drawn ink fragments, and show that a significant performance increase is obtained by labeling and partitioning simultaneously. 1
Sulforhodamine B and exogenous surfactant effects on alveolar surface tension under acute respiratory distress syndrome conditions (2020)

Abstract In the acute respiratory distress syndrome (ARDS), alveolar surface tension, T , may be elevated. Elevated T should increase ventilation-induced lung injury. Exogenous surfactant therapy, intended to lower T , has not reduced mortality. Sulforhodamine B (SRB) might, alternatively, be employed to lower T . We test whether substances suspected of elevating T in ARDS raise T in the lungs and test the abilities of exogenous surfactant and SRB to reduce T . In isolated rat lungs, we micropuncture a surface alveolus and instill a solution of a purported T- raising substance: control saline, cell debris, secretory phospholipase A 2 (sPLA 2 ), acid or mucins. We test each substance alone; with albumin, to model proteinaceous edema liquid; with albumin and exogenous surfactant; or with albumin and SRB. We determine T in situ in the lungs by combining servo-nulling pressure measurement with confocal microscopy, and applying the Laplace relation. With control saline, albumin does not alter T , additional surfactant raises T and additional SRB lowers T . The experimental substances, without or with albumin, raise T . Excepting under aspiration conditions, addition of surfactant or SRB lowers T . Exogenous surfactant activity is concentration and ventilation dependent. Sulforhodamine B, which could be delivered intravascularly, holds promise as an alternative therapeutic. New and Noteworthy In the acute respiratory distress syndrome (ARDS), lowering surface tension, T , should reduce ventilation injury yet exogenous surfactant has not reduced mortality. We show with direct T -determination in isolated lungs that substances suggested to elevate T in ARDS indeed raise T , and exogenous surfactant reduces T . Further, we extend our previous finding that sulforhodamine B (SRB) reduces T below normal in healthy lungs and show that SRB, too, reduces T under ARDS conditions.
GridBatch: Cloud Computing for Large-Scale Data-Intensive Batch Applications (2008)

To be competitive, enterprises are collecting and analyzing increasingly large amount of data in order to derive business insights. However, there are at least two challenges to meet the increasing demand. First, the growth in the amount of data far outpaces the computation power growth of a uniprocessor. The growing gap between the supply and demand of computation power forces Enterprises to parallelize their application code. Unfortunately, parallel programming is both time-consuming and error-prone. Second, the emerging Cloud Computing paradigm imposes constraints on the underlying infrastructure, which forces enterprises to rethink their application architecture. We propose the GridBatch system, which aims at solving large-scale data-intensive batch problems under the Cloud infrastructure constraints. GridBatch is a programming model and associated library that hides the complexity of parallel programming, yet it gives the users complete control on how data are partitioned and how computation is distributed so that applications can have the highest performance possible. Through a real client example, we show that GridBatch achieves high performance in Amazon's EC2 computing Cloud.
Electrochemical detection of arsenic via a microfluidic sensor and mobile interface towards affordable, rapid, and point-of-use water monitoring (2013)

Arsenic contamination of groundwater presents a major obstacle to the development of water infrastructure in developing countries, with severe long-term health consequences. Current solutions for arsenic testing range from simple colorimetric assays to sophisticated laboratory tests. Colorimetric kits are simple and low-cost, yet these types of tests generally suffer from a lack of precision and use toxic chemicals as test reagents while laboratory-based techniques, such as mass spectrometry, are accurate but considerably more expensive, requiring off-site analysis of samples. Electrochemical detection in a microfluidic platform offers many advantages, such as portability, minimal use of instrumentation, and ready integration with electronics. Toward a solution to water quality interventions, we have demonstrated an electrochemical sensor combined with mobile interface that detects arsenic suitable for rapid, affordable, and point-of-care water monitoring. Using this platform, we successfully demonstrate the detection of arsenic and the automatic interpretation and mapping of the detection results via a mobile application. We expect such a platform for diagnostics via mobile phone with automated test interpretation and mapping to provide an indispensable tool, especially in rural areas where the needs are the greatest, but the lack of laboratory facilities and trained personnel is a real obstacle.
Bufalin-Loaded PEGylated Liposomes: Antitumor Efficacy, Acute Toxicity, and Tissue Distribution (2019)

Bufalin, derived from Venenum Bufonis, exerts antitumor effects but has low bioavailability and adverse effects when administered as a single agent. The purpose of this study was to evaluate the physical and chemical properties, antitumor efficacy, general pharmacology, acute toxicity, and tissue distribution profile of bufalin-loaded PEGylated liposomes (BF/PEG-LP), which were prepared in a previous study. To evaluate the safety of the preparation, a red blood cell hemolysis test was performed, which indicated that the hemolysis rate of BF/PEG-LP was significantly lower than that of bufalin alone. Cell viability assay revealed that the blank liposomes were nontoxic. In an in vitro experiment, BF/PEG-LP dose-dependently induced the apoptosis of HepG2, HCT116, A549, and U251 cancer cells, with half-maximal inhibitory concentration (IC<sub>50</sub>) values of 21.40 ± 2.39, 21.00 ± 3.34, 43.39 ± 6.43, and 31.14 ± 2.58 ng/mL, respectively, at 24 h. Tumor xenograft experiments in nude mice showed that BF/PEG-LP significantly inhibited the growth of U251 cells. Pharmacological evaluation revealed that BF/PEG-LP impacted the general behavior, independent activities, and coordination of mice after a week of administration compared with those of mice in the control group. In an acute toxicity test, the median lethal concentration (LD<sub>50</sub>) of BF and BF/PEG-LP in mice was 0.156 and 3.03 mg/kg, respectively. Tissue distribution profiles showed that the BF concentration in brain tissue was 20% higher, whereas that in heart tissue was 30% lower when BF/PEG-LP was administered to mice compared with BF. Thus, BF/PEG-LP exhibited lower hemolysis and cytotoxicity and improved pharmacokinetic and antitumor properties compared with bufalin alone, indicating its potential for future pharmacological application, particularly for glioma treatment.
Primary amines enhance triplet energy transfer from both the band edge and trap state from CdSe nanocrystals (2019)

In this study, the role that primary amines play during triplet energy transfer from photoexcited CdSe nanocrystals (NCs) was examined. Colloidally synthesized CdSe NCs were placed in varying concentrations of 1-propyl- or 1-octylamine, with and without 2-anthracenecarboxylic acid transmitter ligands attached. This primary amine increases upconversion quantum yield approximately 5-fold. Further addition of amine does not improve photon upconversion, as CdSe NC photoluminescence (PL) increases at the expense of triplet energy transfer. Transient absorption measurements show that the amine plays three key roles. Primary amines enhance NC PL by decreasing the nonradiative decay rate, increase the rate of triplet energy transfer, and enable the broad trap state in these CdSe NCs to participate in triplet photosensitization.
Design, synthesis, and a novel application of quorum-sensing agonists as potential drug-delivery vehicles (2010)

Surface adhered bacterial colonies or biofilms are an important problem in medical and food industries. Bacteria use a chemical language to monitor their quorum and to express virulence factors, which eventually help them in colonization and manifestation of an infection. The LasR-LasI and RhlR-RhlI quorum-sensing (QS) systems of Pseudomonas aeruginosa control expression of virulence factors in a population density-dependent fashion. In this study we investigated the role of synthetic analogs to RhlR-RhlI system of P. aeruginosa strains (PAO-1; wild-type and mutants JP-1, PDO-100, and JP-2) responsible for production of acyl-homoserine lactones-2; butanol homoserine lactone (AHL-2; C(4)-HSL). We synthesized double (QS1207) and single (QS0108) sulfur analogs against (C(4)-HSL; AHL-2), an autoinducer of Pseudomonas QS system. Extensive biological investigation of these analogs suggested a growth promoting activity for these analogs in Pseudomonas controlling biofilm production and exo-protease secretion. We hypothesized that these thiolactone analogs could be potentially utilized as potent drug-delivery vehicles against biofilm-producing pathogens. As a proof of principle we conjugated the single sulfur analog QS0108 with the broad-spectrum antibiotic, ciprofloxacin (QS0108-Cip). The QS analog-antibiotic conjugate was significantly more effective at disrupting both the nascent and mature biofilms of P. aeruginosa than the free antibiotic.
CoREST in Peace: Dual Action Inhibitors of Histone Deacetylase and Lysine Specific Demethylase (2015)

Histone deacetylases (HDACs) have been shown to act broadly on thousands of protein lysine acetylation sites to regulate cell growth and gene expression. The class I enzymes HDAC1 and HDAC2 can be found in various corepressor complexes in cells, including the CoREST complex, that also incorporates histone demethylase LSD1. Various combinations of HDAC inhibitors and LSD1 inhibitors have been reported previously to show additive or synergistic effects as anti‐tumor agents. In this study, we prepared several dual action HDAC/LSD1 inhibitors that integrate established pharmacophores targeting the active sites of these enzymes. We showed that several of these hybrid compounds can potently inhibit HDAC and LSD1 activity while maintaining the selectivity associated with the parent molecules. One of these compounds, 2‐68, derived from HDAC inhibitor MS‐275 (entinostat) and LSD1 inhibitor bizine, induced potent and predicted increases in histone H3 K9 acetylation and H3 K4 methylation. Interestingly, MS‐275 and 2‐68 showed anti‐proliferative effects across a panel of melanoma lines, but 2‐68 did not inhibit the proliferation of primary human melanocytes whereas MS‐275 did. Furthermore, we showed that, compared to the parent compounds, 2‐68 was superior in suppressing the function of regulatory T cells, suggesting that dual action CoREST inhibitors may offer advantages in enhancing tumor immune surveillance.
Bulk superconductivity above 20 K in Nb&lt;inf&gt;3&lt;/inf&gt;Ge (1975)

The superconducting properties of bulk films(0.02- 0.06 mm thick) of Nb 3 Ge deposited on Cu substrates by chemical vapor deposition have been studied along with physical parameters characterizing these deposits. Results of susceptibility measurements showing superconducting onsets greater than 21 K and resistivity measurements showing onset greater than 22 K are presented along with heat capacity measurements. Data are also presented defining a relationship between superconducting transition temperature and lattice spacing throughout the range of 4 - 21 K. In addition, the effects of substrate temperature and substrate material, as well as mechanical properties such as substrate adherence are described.
Maintenance of genetic integrity in frozen and freeze-dried mouse spermatozoa (2001)

Chromosome stability was maintained in mouse spermatozoa after freeze-drying or freezing without cryoprotection in a simple Tris.HCl buffer containing EGTA (50 mM) and NaCl (50 mM). The ability of spermatozoa to activate oocytes spontaneously was not destroyed by freeze-drying or freezing without cryoprotection in this solution. Embryos derived after injecting oocytes with sperm heads from rehydrated freeze-dried and from thawed spermatozoa developed normally. Provided the DNA integrity of the sperm nucleus is maintained, embryos can be generated by the intracytoplasmic sperm injection technique (ICSI) from severely damaged spermatozoa that are no longer capable of normal physiological activity. This procedure was effective for preserving spermatozoa from strains (C57BL/6J, 129/SvJ, and BALB/c) in which the fertility of spermatozoa frozen conventionally is extremely poor. The technique provides an effective means of storing mouse spermatozoa from many different inbred, mutant, and transgenic strains for biomedical research.
A cell-permeant peptide corresponding to the cUBP domain of USP5 reverses inflammatory and neuropathic pain (2016)

Our findings reveal a crucial region in the cUBP domain of USP5 that is important for substrate recognition and binding to the III-IV linker of Cav3.2 channels. Targeting the interaction of this region with the Cav3.2 channel can be exploited as the basis for therapeutic intervention into inflammatory and neuropathic pain.
Optoelectronic tweezers with patterned photoconductive layer for selecting, moving and storing particles and cells (2019)

In this work, we introduce a new type of optical micromanipulation platform that we call patterned optoelectronic tweezers (p-OET). In p-OET devices, the photoconductive layer (that is contiguous in a conventional OET device) is patterned, forming regions in which the electrode layer is locally exposed. We demonstrate that the micro-patterns in the photoconductive layer are useful for repelling unwanted particles/cells, and also for keeping selected particles/cells in place after turning off the light source. We propose that the new technique may be useful for myriad applications in the rapidly growing area of optical micromanipulation.
Correction for local flare effects approximated with double Gaussian profile in ArF lithography (2003)

A method has been developed for correcting line width variations due to midrange flare with a scattering range of over a few tens of micrometers (which we call local flare). It is shown that the conventional single Gaussian point spread function (PSF) is not sufficient and that a double Gaussian point spread function is needed to explain the line width variation caused by local flare. The remaining errors after correction are discussed under the assumptions that the mask correction is linear with respect to local flare intensity and is independent of pattern layout considering the order of the local flare correction (LFC) and optical proximity correction (OPC). This simple sizing method can reduce the critical dimension (CD) variation regardless of whether LFC is done before or after OPC. The LFC performance was evaluated using actual 90-nm-node LSI data. A much faster correction time than that of OPC was achieved by introducing the area density map method. The CD variation due to local flare was reduced from 22 to 5 nm.
Full-Color Two-Dimensional Optical Coherence Tomography (2004)

A technique is described to obtain two-dimensional OCT images with full natural color representation. The interference image is acquired using a color camera and the three color channels are processed separately, recomposing the final image.