gebhart/patrepeval huggingface dataset:
Tumor Necrosis Factor Receptor-1 Can Function through a Gαq/11-β-Arrestin-1 Signaling Complex (2007)

Tumor necrosis factor-alpha (TNFalpha) is a proinflammatory cytokine secreted from macrophages and adipocytes. It is well known that chronic TNFalpha exposure can lead to insulin resistance both in vitro and in vivo and that elevated blood levels of TNFalpha are observed in obese and/or diabetic individuals. TNFalpha has many acute biologic effects, mediated by a complex intracellular signaling pathway. In these studies we have identified new G-protein signaling components to this pathway in 3T3-L1 adipocytes. We found that beta-arrestin-1 is associated with TRAF2 (TNF receptor-associated factor 2), an adaptor protein of TNF receptors, and that TNFalpha acutely stimulates tyrosine phosphorylation of G alpha(q/11) with an increase in G alpha(q/11) activity. Small interfering RNA-mediated knockdown of beta-arrestin-1 inhibits TNFalpha-induced tyrosine phosphorylation of G alpha(q/11) by interruption of Src kinase activation. TNFalpha stimulates lipolysis in 3T3-L1 adipocytes, and beta-arrestin-1 knockdown blocks the effects of TNFalpha to stimulate ERK activation and glycerol release. TNFalpha also led to activation of JNK with increased expression of the proinflammatory gene, monocyte chemoattractant protein-1 and matrix metalloproteinase 3, and beta-arrestin-1 knockdown inhibited both of these effects. Taken together these results reveal novel elements of TNFalpha action; 1) the trimeric G-protein component G alpha(q/11) and the adapter protein beta-arrestin-1 can function as signaling molecules in the TNFalpha action cascade; 2) beta-arrestin-1 can couple TNFalpha stimulation to ERK activation and lipolysis; 3) beta-arrestin-1 and G alpha(q/11) can mediate TNFalpha-induced phosphatidylinositol 3-kinase activation and inflammatory gene expression.
Supplementary Table 2 from MicroRNA Microarray Identifies <i>Let-7i</i> as a Novel Biomarker and Therapeutic Target in Human Epithelial Ovarian Cancer (2023)

Supplementary Table 2 from MicroRNA Microarray Identifies &lt;i&gt;Let-7i&lt;/i&gt; as a Novel Biomarker and Therapeutic Target in Human Epithelial Ovarian Cancer
Is SARS‐CoV‐2 viral clearance in nasopharyngeal swabs an appropriate surrogate marker for clinical efficacy of neutralising antibody‐based therapeutics? (2021)

Viral clearance is likely the best way to assess the efficacy of antibody-based therapies. Although antibodies can mediate a variety of effects that include modulation of inflammation, the demonstration of viral clearance provides an accessible and measurable parameter that can be used to evaluate efficacy and determine dosing. Therefore, it is important to ascertain the ability of monoclonal antibodies and convalescent plasma to effect viral clearance. For COVID-19, which is caused by the respiratory virus SARS-CoV-2, the most common assay to assess viral clearance is via a nasopharyngeal swab (NPS). However, assessment of antibody efficacy by sampling this site may be misleading because it may not be as accessible to serum antibodies as respiratory secretions or circulating blood. Adding to the complexity of assessing the efficacy of administered antibody, particularly in randomised controlled trials (RCTs) that enroled patients at different times after the onset of COVID-19 symptoms, viral clearance may also be mediated by endogenous antibody. In this article we critically review available data on viral clearance in RCTs, matched control studies, case series and case reports of antibody therapies in an attempt to identify variables that contribute to antibody efficacy and suggest optimal strategies for future studies.
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES (2022)

Supplementary data are available at Bioinformatics online.
ChemInform Abstract: Chemoselective Modification of Proteins: Hitting the Target (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Efficiency Improvement and Analysis of Changes in Microstructure Associated to a Uniform Pressure Actuator (2006)

During the 1st international Conference on HIGH SPEED FORMING held in Dortmund in 2004 a new forming coil giving significant advantages was presented in the framework of ongoing R&amp;D programs at OSU (The Ohio State University). It established the improvement provided by the return path for currents induced in the workpiece. To quantify the mentioned improvement, Labein has performed classical cone forming experiments with both configurations and analyzed energetic efficiency using well known alloys, more precisely AA 6016 and 1050. Both deformation mechanisms and contour analysis of the specimens were studied. General purpose multi-turn coils provide pressure distributions not extended to the whole forming area, resulting in zones undergoing significant delay as die the deformation sequence is referred. As a result, varied deformation patterns can be found along the contour of a cone specimen formed in such way. Firstly, a macroscopic survey of the specimens shows that uniform pressure distributes deformation over the entire formed area during the deformation process. Secondly, the effect on efficiency provided by this new coil concept is focuses not only on the ability for distributing deformation, but on the energy required to create such deformation. Finally, to validate the whole simulation, the predicted strain level, shape, and internal energy of the workpiece are compared with the experimental specimens. A key point in the validation process is checking the internal energy. It is known that the ratio of stored energy to deformation energy ranges in the order of 30 %. The procedure for the experiments follows this methodology.
Graph Unrolling Networks: Interpretable Neural Networks for Graph Signal Denoising (2021)

We propose an interpretable graph neural network framework to denoise single or multiple noisy graph signals. The proposed graph unrolling networks expand algorithm unrolling to the graph domain and provide an interpretation of the architecture design from a signal processing perspective. We unroll an iterative denoising algorithm by mapping each iteration into a single network layer where the feed-forward process is equivalent to iteratively denoising graph signals. We train the graph unrolling networks through unsupervised learning, where the input noisy graph signals are used to supervise the networks. By leveraging the learning ability of neural networks, we adaptively capture appropriate priors from input noisy graph signals. A core component of graph unrolling networks is the edge-weight-sharing graph convolution operation, which parameterizes each edge weight by a trainable kernel function whose trainable parameters are shared by all the edges. The proposed convolution is permutation-equivariant and can flexibly adjust the edge weights to various graph signals. We further consider two special cases of this class of networks, graph unrolling sparse coding (GUSC) and graph unrolling trend filtering (GUTF), by unrolling sparse coding and trend filtering, respectively. To validate the proposed methods, we conduct extensive experiments on both real-world datasets and simulated datasets, and demonstrate that our methods have smaller denoising errors than conventional denoising algorithms and state-of-the-art graph neural networks. For denoising a single smooth graph signal, the normalized mean square error of the proposed networks is around 40% and 60% lower than that of graph Laplacian denoising and graph wavelets, respectively.
Range 7 Scanner Integration with PaR Robot Scanning System (2011)

An interface bracket and coordinate transformation matrices were designed to allow the Range 7 scanner to be mounted on the PaR Robot detector arm for scanning the heat shield or other object placed in the test cell. A process was designed for using Rapid Form XOR to stitch data from multiple scans together to provide an accurate 3D model of the object scanned. An accurate model was required for the design and verification of an existing heat shield. The large physical size and complex shape of the heat shield does not allow for direct measurement of certain features in relation to other features. Any imaging devices capable of imaging the entire heat shield in its entirety suffers a reduced resolution and cannot image sections that are blocked from view. Prior methods involved tools such as commercial measurement arms, taking images with cameras, then performing manual measurements. These prior methods were tedious and could not provide a 3D model of the object being scanned, and were typically limited to a few tens of measurement points at prominent locations. Integration of the scanner with the robot allows for large complex objects to be scanned at high resolution, and for 3D Computer Aided Design (CAD) models to be generated for verification of items to the original design, and to generate models of previously undocumented items. The main components are the mounting bracket for the scanner to the robot and the coordinate transformation matrices used for stitching the scanner data into a 3D model. The steps involve mounting the interface bracket to the robot's detector arm, mounting the scanner to the bracket, and then scanning sections of the object and recording the location of the tool tip (in this case the center of the scanner's focal point). A novel feature is the ability to stitch images together by coordinates instead of requiring each scan data set to have overlapping identifiable features. This setup allows models of complex objects to be developed even if the object is large and featureless, or has sections that don't have visibility to other parts of the object for use as a reference. In addition, millions of points can be used for creation of an accurate model [i.e. within 0.03 in. (=0.8 mm) over a span of 250 in. (=635 mm)].
Processing and Characterization of Carbon Nanotube Composites (2014)

Recent advances in the synthesis of large-scale quantities of carbon nanotubes (CNT) have provided the opportunity to study the mechanical properties of polymer matrix composites using these novel materials as reinforcement. Nanocomp Technologies, Inc. currently supplies large sheets with dimensions up to 122 cm x 244 cm containing both single-wall and few-wall CNTs. The tubes are approximately 1 mm in length with diameters ranging from 8 to 12 nm. In the present study being conducted at NASA Langley Research Center (LaRC), single and multiple layers of CNT sheets were infused or coated with various polymer solutions that included commercial toughened-epoxies and bismaleimides, as well as a LaRC developed polyimide. The resulting CNT composites were tested in tension using a modified version of ASTM D882-12 to determine their strength and modulus values. The effects of solvent treatment and mechanical elongation/alignment of the CNT sheets on the tensile performance of the composite were determined. Thin composites (around 50 wt% CNT) fabricated from acetone condensed and elongated CNT sheets with either a BMI or polyimide resin solution exhibited specific tensile moduli approaching that of toughened epoxy/ IM7 carbon fiber unidirectional composites.
Abdominal Injuries in Frontal Crashes: Influence of Occupant Age and Seating Position (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Objective: This study investigated the incidence of abdominal injuries in frontal crashes by occupant age and seating position. It determined the risk for abdominal injury (AIS 2+) by organ and injury source.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Methods: 1997-2015 NASS-CDS was analyzed to estimate the occurrence of abdominal injuries in non-ejected, belted occupants involved in frontal crashes. Vehicles were included with 1997+ model year (MY). The annual incidence and rate for different types of abdominal injury were estimated with standard errors. The sources for abdominal injury were determined.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Results: 77.8% of occupants were drivers, 16.7% were right-front passengers and 5.4% were rear passengers. Rear passengers accounted for 77.1% of 8-11 year old (yo) and 17.2% of 12-17 yo group. The risk for moderate abdominal injury (MAIS 2 + abdo) was 0.30% ± 0.053% in drivers, 0.32% ± 0.086% in right-front passengers and 0.38% ± 0.063% in rear occupants. The risk of MAIS 2 + abdo was highest at 0.76% ± 0.30% in the 60-84 yo group for right-front passengers and in the 85+ yo group and 8-11 yo children for rear passengers. The liver and spleen had the highest abdominal injury risk in drivers, the spleen in right-front passengers and the digestive system in rear passengers. The leading source for injury was the seatbelt at 38.6% in the drivers, 73.9% in right-front passenger and 96.2% in rear passengers. The NASS-CDS case review identified lap-belt loading on the abdomen and improper seatbelt use as injury mechanisms for rear seated children.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Conclusions: The risk of abdominal injury was high in lap-shoulder belted 8-11 yo children and 60+ yo adults in the rear in frontal crashes. There was an association between abdominal injury and the seatbelt.&lt;/div&gt;&lt;/div&gt;
TCP Performance in Wireless Systems with Opportunistic Scheduling (2002)

Abstract — Recent research on opportunistic schedulers for wireless data transmission has shown that link utilization is greatly improved by exploiting the independent variations in the wireless channels of users. The trade-off between spectral efficiency and fairness among users at the link level has been well studied in the literature. The focus of this paper is the impact of the variable rate and delay jitter induced by opportunistic scheduling on the congestion control and avoidance mechanisms of TCP. We use extensive simulations to expose the linkage between scheduling at the medium access (MAC) layer and TCP performance. The results in this paper underscore the need for careful design of opportunistic scheduling mechanisms in order to ensure that gains in MAC layer are also realized by TCP.
Development of a Topically Active Imiquimod Formulation (1999)

ABSTRACTThe purpose of this work was to develop a topical formulation of imiquimod, a novel immune response modifier, to induce local cytokine production for the treatment of external genital and perianal warts. A pH-solubility profile and titration data were used to calculate a pKa of 7.3, indicative of a weak base. Solubility experiments were conducted to identify a solvent that dissolves imiquimod to achieve a 5% formulation concentration. Studies to select surfactants, preservatives, and viscosity-enhancing excipients to formulate an oil-in-water cream indicated that fatty acids were the preferred solvent for topical imiquimod formulations, and isostearic acid (ISA) was selected. A relationship existed between the fatty acid composition of four commercially available ISA sources and the solubility of imiquimod. A combination of polysorbate 60, sorbitan monostearate, and xanthan gum was used to produce a physically stable cream. The preservative system included parabens and benzyl alcohol to meet the USP criteria for preservative activity. An in vitro method was developed to demonstrate that imiquimod was released from the formulation. Topical application of the formulation induced local cytokine activity in mice.KEY WORDS: : CytokinesEmulsionImiquimodIsostearic acidSolubility
Generation and validation of a PITX2–EGFP reporter line of human induced pluripotent stem cells enables isolation of periocular mesenchymal cells (2020)

PITX2 (Paired-like homeodomain transcription factor 2) plays important roles in asymmetric development of the internal organs and symmetric development of eye tissues. During eye development, cranial neural crest cells migrate from the neural tube and form the periocular mesenchyme (POM). POM cells differentiate into several ocular cell types, such as corneal endothelial cells, keratocytes, and some ocular mesenchymal cells. In this study, we used transcription activator-like effector nuclease technology to establish a human induced pluripotent stem cell (hiPSC) line expressing a fluorescent reporter gene from the <i>PITX2</i> promoter. Using homologous recombination, we heterozygously inserted a PITX2-IRES2-EGFP sequence downstream of the stop codon in exon 8 of <i>PITX2</i> Cellular pluripotency was monitored with alkaline phosphatase and immunofluorescence staining of pluripotency markers, and the hiPSC line formed normal self-formed ectodermal autonomous multizones. Using a combination of previously reported methods, we induced PITX2 in the hiPSC line and observed simultaneous EGFP and PITX2 expression, as indicated by immunoblotting and immunofluorescence staining. <i>PITX2</i> mRNA levels were increased in EGFP-positive cells, which were collected by cell sorting, and marker gene expression analysis of EGFP-positive cells induced in self-formed ectodermal autonomous multizones revealed that they were genuine POM cells. Moreover, after 2 days of culture, EGFP-positive cells expressed the PITX2 protein, which co-localized with forkhead box C1 (FOXC1) protein in the nucleus. We anticipate that the PITX2-EGFP hiPSC reporter cell line established and validated here can be utilized to isolate POM cells and to analyze PITX2 expression during POM cell induction.
Pseudo-differential signaling scheme based on 4b/6b multiwire code (2008)

The majority of todaypsilas memory interfaces use single-ended signaling instead of differential signaling. Extending the performance of single-ended systems beyond a few Gb/s is a very challenging task mainly due to crosstalk and SSO noise. This paper presents a pseudo-differential signaling scheme based on an encoding technique which maps 4 bits of data to six coded bits with balanced numbers of 0s and 1s. The proposed scheme successfully removes the impact of SSO and VREF noise. The simulation results based on graphics memory channels show significant improvements in performance over the non-coded case.
Laser ReSeal – Combination of Accelerometer and Gyroscope Sensors in a Single MEMS Chip Silicon Wafer Processing Technology for Six Degrees of Freedom in Inertial Sensors (2020)

"Laser ReSeal", a novel innovative combination of laser and semiconductor technology for Micro Electro Mechanical Systems (MEMS) allows the cost efficient fabrication of small, high performance and low power inertial measurement units (combined accelerometers and gyroscopes). The new process solves the intrinsic challenge since these two sensor types require two different operating pressures within one wafer. The laser hermetically seals the sensor cavity of the gyroscope, thus enabling a precise subsequent adjustment of the optimum operating pressure.
A novel output voltage regulation strategy for primary side of flyback converter (2011)

It is often required in the robot and battery charging systems that the primary side of the input power source and secondary side of the load should be isolated by the transformer and that the output voltage should be regulated in the primary side. This paper presents a novel output voltage regulation strategy in the primary side of flyback converters. Also, the nonlinear control is useful to perform the high degree of output voltage regulation when the input voltage and the load change largely. The insights of the nonlinear control and over-voltage/current protection method are obtained analytically.
Effekt der Mycophenolsäure auf die Aktivität der Inosinmonophosphatdehydrogenase (IMPDH) bei Lebertransplantierten (2018)

Die Mycophenolsäure (MPS) ist nicht-kompetitiver Inhibitor der Inosinmonophosphatdehydrogenase (IMPDH) und zur Abstoßungsprophylaxe nach Herz-, Nieren- und Lebertransplantation (LTx) zugelassen. Die Messung der IMPDH-Aktivität als pharmakodynamischer Surrogatmarker der MPS-induzierten Immunsuppression könnte zur besseren Beurteilung selbiger führen und so MPS-vermittelte Toxizität begrenzen. Ziel war es, das Ausmaß der IMPDH-Inhibition bei Lebertransplantierten und deren Einfluss auf Infektionen, Gallenwegskomplikationen, Abstoßungen und Überleben zu bestimmen.
Hearing and Vision Screening Program for newborns in Italy. (2021)

HEARING SCREENING. Overall 427,365 newborns out of 448,386 (95.3%) received the hearing screening test (first level) in 391 out of the 409 maternity hospitals (95.5%), with a national mean referral rate of 3.63% (SD ± 4.58). A statistically significant increase (p<0.034) of newborns sent to audiological examination was found in maternity hospitals with Neonatal Intensive Care Unit (NICU) with "TEOAE only" protocol (9.32% SD ± 7.57), compared to those with "TEOAE/AABR" (3.0% SD ± 3.29). VISION SCREENING. Overall 335,262 newborns out of 448,386 (74.7%) received vision screening (Red Reflex test) for vision impairment in 302 out of 409 maternity hospitals (73.8%), before nursery discharge. The mean referral rate, recorded in only 22 maternity hospitals out of 302 (7.2%), was 0.48% with a rate of lost to follow up of 0.75 %.
Characterization of a Thermoacidophilic l -Arabinose Isomerase from Alicyclobacillus acidocaldarius : Role of Lys-269 in pH Optimum (2005)

The araA gene encoding L-arabinose isomerase (AI) from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius was cloned, sequenced, and expressed in Escherichia coli. Analysis of the sequence revealed that the open reading frame of the araA gene consists of 1,491 bp that encodes a protein of 497 amino acid residues with a calculated molecular mass of 56,043 Da. Comparison of the deduced amino acid sequence of A. acidocaldarius AI (AAAI) with other AIs demonstrated that AAAI has 97% and 66% identities (99% and 83% similarities) to Geobacillus stearothermophilus AI (GSAI) and Bacillus halodurans AI (BHAI), respectively. The recombinant AAAI was purified to homogeneity by heat treatment, ion-exchange chromatography, and gel filtration. The purified enzyme showed maximal activity at pH 6.0 to 6.5 and 65 degrees C under the assay conditions used, and it required divalent cations such as Mn2+, Co2+, and Mg2+ for its activity. The isoelectric point (pI) of the enzyme was about 5.0 (calculated pI of 5.5). The apparent Km values of the recombinant AAAI for L-arabinose and D-galactose were 48.0 mM (Vmax, 35.5 U/mg) and 129 mM (Vmax, 7.5 U/mg), respectively, at pH 6 and 65 degrees C. Interestingly, although the biochemical properties of AAAI are quite similar to those of GSAI and BHAI, the three AIs from A. acidocaldarius (pH 6), G. stearothermophilus (pH 7), and B. halodurans (pH 8) exhibited different pH activity profiles. Based on alignment of the amino acid sequences of these homologous AIs, we propose that the Lys-269 residue of AAAI may be responsible for the ability of the enzyme to act at low pH. To verify the role of Lys-269, we prepared the mutants AAAI-K269E and BHAI-E268K by site-directed mutagenesis and compared their kinetic parameters with those of wild-type AIs at various pHs. The pH optima of both AAAI-K269E and BHAI-E268K were rendered by 1.0 units (pH 6 to 7 and 8 to 7, respectively) compared to the wild-type enzymes. In addition, the catalytic efficiency (kcat/Km) of each mutant at different pHs was significantly affected by an increase or decrease in Vmax. From these results, we propose that the position corresponding to the Lys-269 residue of AAAI could play an important role in the determination of the pH optima of homologous AIs.