gebhart/patrepeval huggingface dataset:
Supplementary Methods from <i>Neuropilin-1</i> Stimulates Tumor Growth by Increasing Fibronectin Fibril Assembly in the Tumor Microenvironment (2023)

&lt;p&gt;PDF file - 50K, Supplementary Methods includes Confocal immunofluorescence microscopy, Western Blot analysis and c-Abl kinase assays, Retrovirus generation and transduction, and supplemental references&lt;/p&gt;
Novel Fabrication and Enhanced Photosensitivity of Selenium Filament Arrays by Optical-Fiber Thermal Drawing (2009)

We report break-up of cylindrical shell into well-ordered filament arrays by optical-fiber thermal drawing. Enhanced photosensitivity of centimeter-long crystalline-Se nano-filaments is observed and the mechanism is discussed. This work paves a way to in-fiber nanodevices.
Supplementary Table 1 from The OPCML Tumor Suppressor Functions as a Cell Surface Repressor–Adaptor, Negatively Regulating Receptor Tyrosine Kinases in Epithelial Ovarian Cancer (2023)

&lt;p&gt;PDF file - 76K&lt;/p&gt;
Sensing Hand Tremor in a Vitreoretinal Microsurgical Instrument (2018)

An instrument for intraoperative sensing of surgeons’ hand tremor during vitreoretinal microsurgery has been developed. Real-time monitoring of tremor is useful to surgeons for purposes of training, adjustment of technique, monitoring of fatigue, and deciding when or whether to perform certain procedures. The instrument incorporates six inertial sensors (three accelerometers and three rate gyros), mounted at the back end of the handle, to detect translation and rotation in six degrees of freedom. The accelerometer data are integrated to obtain translational velocity, and the gyro data are integrated to determine the time-varying rotation matrix needed to transform the instrument motion to a fixed frame of reference. Instrument tip velocity in three dimensions is computed using this information. The displacement amplitude of the tremor is then approximated analytically from the velocity data, approximating it as a sinusoid. Four preliminary tests are presented: 1-dof translation (no rotation); 1-dof translation with amplitude modulation; 3-dof translation (no rotation); 6-dof motion (translation and rotation). The instrument presently estimates oscillations at physiological tremor frequencies with less than 7% error.
Quantitative impact of immunomodulation versus oncolysis with cytokine-expressing virus therapeutics (2015)

The past century's description of oncolytic virotherapy as a cancer treatment involving specially-engineered viruses that exploit immune deficiencies to selectively lyse cancer cells is no longer adequate. Some of the most promising therapeutic candidates are now being engineered to produce immunostimulatory factors, such as cytokines and co-stimulatory molecules, which, in addition to viral oncolysis, initiate a cytotoxic immune attack against the tumor. This study addresses the combined effects of viral oncolysis and T-cell-mediated oncolysis. We employ a mathematical model of virotherapy that induces release of cytokine IL-12 and co-stimulatory molecule 4-1BB ligand. We found that the model closely matches previously published data, and while viral oncolysis is fundamental in reducing tumor burden, increased stimulation of cytotoxic T cells leads to a short-term reduction in tumor size, but a faster relapse. In addition, we found that combinations of specialist viruses that express either IL-12 or 4-1BBL might initially act more potently against tumors than a generalist virus that simultaneously expresses both, but the advantage is likely not large enough to replace treatment using the generalist virus. Finally, according to our model and its current assumptions, virotherapy appears to be optimizable through targeted design and treatment combinations to substantially improve therapeutic outcomes.
A Regularization Workflow for the Processing of Cross-spread COV Data (2009)

Data regularization is critical for the suppression of Kirchhoff migration noise and the production of a clean migration image. We introduce a workflow utilizing Fourier reconstruction in two spatial dimensions to fully regularize cross-spread COV data i
Compact, Physics-Based Modeling of Nanoscale Limits of Double-Gate MOSFETs (2004)

Compact, physics-based models of subthreshold swing and threshold voltage are presented for double-gate (DG) MOSFETs in symmetric, asymmetric, and ground-plane modes. Applying these device models, threshold voltage variations in DG MOSFETs are comprehensively and exhaustively investigated using a unique, scale-length based methodology. Quantum mechanical effects and fringe-induced barrier lowering effect on threshold voltage, caused by ultra-thin silicon film and potential use of high-permittivity gate dielectrics, respectively, have been analytically modeled giving close agreement to numerical simulations. Scaling limits projections indicate that individual DG MOSFETs with good turn-off behavior are feasible at 10 nm scale; however, practical exploitation of these devices toward gigascale integrated systems requires development of novel technologies for significant improvement in process control.
324 Naturalistic Characterization of Sleep in Chronic Insomnia Using a Non-Contact Sleep Measurement Device (2021)

Abstract Introduction Individuals with insomnia report poor sleep quality and non-restorative sleep, and often exhibit irregular sleep patterns over days and weeks. First night effects and logistical challenges make it difficult to measure these sleep characteristics in the laboratory. Also, sensitivity to sleep disruption from obtrusive measurement devices confounds sleep measurements in people with insomnia in their naturalistic setting. Non-contact sleep measurement devices have the potential to address these issues and enable ecologically valid, longitudinal characterization of sleep in individuals with insomnia. Here we use a non-contact device – the SleepScore Max (SleepScore Labs) – to assess the sleep of individuals with chronic insomnia, compared to healthy sleeper controls, in their home setting. Methods As part of a larger study, 13 individuals with chronic insomnia (ages 25-60y, 7 males) and 8 healthy sleeper controls (ages 21-46y, 6 females) participated in an at-home sleep monitoring study. Enrollment criteria included an age range of 18-65y and, for the insomnia group, ICSD-3 criteria for chronic insomnia with no other clinically relevant illness. Participants used the non-contact sleep measurement device to record their sleep periods each night for 8 weeks. Sleep measurements were analyzed for group differences in both means (characterizing sleep overall) and within-subject standard deviations (characterizing sleep variability across nights), using mixed-effects regression controlling for systematic between-subject differences. Results Based on the non-contact sleep measurements, individuals with chronic insomnia exhibited greater variability in bedtime, time in bed, total sleep time, sleep latency, total wake time across time in bed, wakefulness after sleep onset, sleep interruptions, and estimated light sleep, compared to healthy sleeper controls (all F&amp;gt;5.7, P&amp;lt;0.05). No significant differences were found for group averages and for variability in estimated deep and REM sleep. Conclusion In this group of individuals with chronic insomnia, a non-contact device used to characterize sleep naturalistically captured enhanced variability across nights in multiple aspects of sleep stereotypical of sleep disturbances in chronic insomnia, differentiating the sample statistically significantly from healthy sleeper controls. Support (if any) NIH grant KL2TR002317; research devices provided by SleepScore Labs.
Can Paraffin Wax Deposit Above Wax Appearance Temperature? A Detailed Experimental Study (2020)

Abstract Shale producers in North America continue to face challenges with paraffin wax deposition in well bores, production tubing and flowlines as production declines and artificial lift methods such as gas lift are applied. Preventative measures are often based on traditional screening and assessment methods which rely on crude’s wax appearance temperature (WAT). Recent studies have shown that operators are increasingly turning to costly remediation program and stimulation jobs to maintain production rates as oil wells decline at faster rates than anticipated. It appears in many cases that these declines can be exacerbated by downhole organic fouling and wax deposition that surprisingly may have occurred above the original WAT. This paper aims to conduct a root cause analysis to identify the key internal and external factors impacting an oil’s WAT. Four crude oils and field wax deposits from Gulf of Mexico, South Texas and West Texas areas were used for this study. Due to the unique composition of the field deposits and depleted crude sample available for analysis, a novel strategy for lab screening was adopted. Crude oil samples were examined "as received" and after reconditioning via the addition of solvents and/or field deposits. Further measurements were performed to identify and quantify the effects of the addition of production chemicals particularly hydrate inhibitors. A series of dispersion and deposition tests were then conducted in order to demonstrate the potential impacts of incompatible chemistries. Fractionation based on solubility revealed a dynamic behavior for the WAT of crudes that corelated to their paraffin content and distribution. Samples containing C45+ paraffin chains demonstrated significant WAT changes upon reconditioning. The addition of methanol and MEG typically used as hydrate inhibitors, impacted the WATs of the crudes as measured by DSC showing increases in the WATs compared to unconditioned samples. An additional suite of dispersion and deposition testing conducted on the same samples supported the findings of the DSC studies. A nonlinear correlation was found between increasing WAT and paraffin deposition rate. The approach outlined in this paper provides a more accurate field condition simulation leading to more effective inhibitor selection and ultimately improved flow assurance management in more complex production systems. The methodology of mimicking hydrocarbon fluid behavior was the key factor identified by the root cause analysis and correlated to the series of past failures attributed to organic fouling. WAT was found to be a parameter that can vary for a crude oil over the life of a production system. With the current evolution of shale oil production in North America and around the world, we expect these findings will also be relevant to unconventional production and will aid the oil industry to anticipate and manage previously unforeseen problematic paraffins in production systems.
Elimination of BMP7 from the developing limb mesenchyme leads to articular cartilage degeneration and synovial inflammation with increased age (2015)

While osteo- and chondro-inductive activities of recombinant human bone morphogenetic protein 7 are well established, evaluation of the role of endogenous BMP7 in skeletal homeostasis has been hampered by perinatal lethality in BMP7 knockout mice. Here, we examined physiological roles of endogenous BMP7 in joint homeostasis and showed that proteoglycan contents in articular cartilage were significantly reduced in the absence of BMP7. Loss of BMP7 did not affect survival of articular cartilage cells, but resulted in reduced expression of aggrecan and enhanced expression of matrix metalloproteinase 13. We also found extensive synovial hyperplasia and enhanced expression of Activin A. These findings suggest that locally produced BMP7 is prerequisite for postnatal synovial joint homeostasis and may be involved in osteoarthritic changes in adults.
Micelle Formation from Amphiphilic “Cylindrical Brush”—Coil Block Copolymers Prepared by Metallocene Catalysis (2004)

Giant rod–coil amphiphilic block copolymers were prepared by metallocene-catalyzed polymerization. The hydrophilic coiled block consists of polymethacrylic acid and the rod component of a hydrophobic cylindrical brush polymer. The high solubility of the stiff block results in the micelles being formed with the stiff block forming the solubilizing corona. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z53259_s.pdf or from the author. 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.
Coordinated morphogenesis of epithelia during development of the Caenorhabditis elegans uterine-vulval connection. (1996)

Development of the nematode egg-laying system requires the formation of a connection between the uterine lumen and the developing vulval lumen, thus allowing a passage for eggs and sperm. This relatively simple process serves as a model for certain aspects of organogenesis. Such a connection demands that cells in both tissues become specialized to participate in the connection, and that the specialized cells are brought in register. A single cell, the anchor cell, acts to induce and to organize specialization of the epidermal and uterine epithelia, and registrates these tissues. The inductions act via evolutionarily conserved intercellular signaling pathways. The anchor cell induces the vulva from ventral epithelial cells via the LIN-3 growth factor and LET-23 transmembrane tyrosine kinase. It then induces surrounding uterine intermediate precursors via the receptor LIN-12, a founding member of the Notch family of receptors. Both signaling pathways are used multiple times during development of Caenorhabditis elegans. The outcome of the signaling is context-dependent. Both inductions are reciprocated. After the anchor cell has induced the vulva, it stretches toward the induced vulval cells. After the anchor cell has induced specialized uterine intermediate precursor cells, it fuses with a subset of their progeny.
Any-Shot GIN: Generalizing Implicit Networks for Reconstructing Novel Classes (2022)

We address the task of estimating the 3D shapes of novel shape classes from a single RGB image. Prior works are either limited to reconstructing known training classes or are unable to reconstruct high-quality shapes. To solve those issues, we propose Generalizing Implicit Networks (GIN) which decomposes 3D reconstruction into 1.) front-back depth estimation followed by differentiable depth voxelization, and 2.) implicit shape completion with 3D features. The key insight is that the depth estimation network learns local class-agnostic shape priors, allowing us to generalize to novel classes, while our implicit shape completion network is able to predict accurate shapes with rich details by learning implicit surfaces in 3D voxel space. We conduct extensive experiments on a large-scale benchmark using 55 classes of ShapeNet and real images of Pix3D. We qualitatively and quantitatively show that the proposed GIN significantly outperforms the state of the art on both seen and novel shape classes for single-image 3D reconstruction. We also illustrate that our GIN can be further improved by using only few-shot depth supervision from novel classes.
Performance of thin-film ferroelectric capacitors for EMC decoupling (2008)

This paper studied the effects of thin-film ferroelectrics as decoupling capacitors for electromagnetic compatibility applications. The impedance and insertion loss of PZT capacitors were measured and compared with the results from commercial off-the-shelf capacitors. An equivalent circuit model was extracted from the experimental results, and a considerable series resistance was found to exist in ferroelectric capacitors. This resistance gives rise to the observed performance difference around series resonance between ferroelectric PZT capacitors and normal capacitors. Measurements on paraelectric (Ba,Sr)TiO(3)-based integrated varactors do not show this significant resistance. Some analyses were made to investigate the mechanisms, and it was found that it can be due to the hysteresis in the ferroelectric thin films.
Location of the Antidepressant Binding Site in the Serotonin Transporter (2009)

The serotonin transporter (SERT) regulates extracellular levels of serotonin (5-hydroxytryptamine, 5HT) in the brain by transporting 5HT into neurons and glial cells. The human SERT (hSERT) is the primary target for drugs used in the treatment of emotional disorders, including depression. hSERT belongs to the solute carrier 6 family that includes a bacterial leucine transporter (LeuT), for which a high resolution crystal structure has become available. LeuT has proved to be an excellent model for human transporters and has advanced the understanding of solute carrier 6 transporter structure-function relationships. However, the precise structural mechanism by which antidepressants inhibit hSERT and the location of their binding pockets are still elusive. We have identified a residue (Ser-438) located within the 5HT-binding pocket in hSERT to be a critical determinant for the potency of several antidepressants, including the selective serotonin reuptake inhibitor citalopram and the tricyclic antidepressants imipramine, clomipramine, and amitriptyline. A conservative mutation of Ser-438 to threonine (S438T) selectively increased the K(i) values for these antidepressants up to 175-fold. The effects of introducing a protein methyl group into the 5HT-binding pocket by S438T were absent or reduced for analogs of these antidepressants lacking a single methyl group. This suggests that these antidepressants interact directly with Ser-438 during binding to hSERT, implying an overlapping localization of substrate- and inhibitor-binding sites in hSERT suggesting that antidepressants function by a mechanism that involves direct occlusion of the 5HT-binding site.
Re-expression of RAG-1 and RAG-2 genes and evidence for secondary rearrangements in human germinal center B lymphocytes (1998)

V(D)J recombination occurs in immature B cells within primary lymphoid organs. However, recent evidence demonstrated that the recombination activating genes RAG-1 and RAG-2 can also be expressed in murine germinal centers (GC) where they can mediate secondary rearrangements. This finding raises a number of interesting questions, the most important of which is what is the physiological role, if any, of secondary immunoglobulin (Ig) gene rearrangements. In the present report, we provide evidence that human GC B cells that have lost surface immunoglobulin re-express RAG-1 and RAG-2, suggesting that they may be able to undergo Ig rearrangement. Furthermore, we describe two mature B cell clones in which secondary rearrangements have possibly occurred, resulting in light chain replacement. The two clones carry both kappa and lambda light chains productively rearranged, but fail to express the x chain on the cell surface due to a stop codon acquired by somatic mutation. Interestingly, the analysis of the extent of somatic mutations accumulated by the two light chains might suggest that the lambda chain could have been acquired through a secondary rearrangement. Taken together, these data suggest that secondary Ig gene rearrangements leading to replacement may occur in human GC and may contribute to the peripheral B cell repertoire.
ChemInform Abstract: Isotopic Exchange Reactions Occurring in the Hydrogenation of (1,5‐Cyclooctadiene)dialkylplatinum(II) Complexes Over Platinum Black. (1988)

Abstract The extent of deuterium incorporation into cyclooctane during reduction of (cod)Pt(RD)2 complexes (RD: deuterium‐labeled alkyl groups) with H 2 over Pt black is determined as a function of the structure of the alkyl group and the position of the D label in it.
Sensitivity Evaluation for Reflection Phase Measurements of Resonant Microwave Near-Field Sensors with Artificial Transmission Lines (2018)

In this contribution, we present a design process to increase the dielectric sensitivity of resonant microwave near-field sensors based on artificial transmission lines to detect small relative permittivity variations down to approximately 0.1 ppm with reflection phase measurements. To support the theory and to achieve an applicable sensor design, circuit and three-dimensional electromagnetic field simulations with AWR and CST Microwave Studio are performed. Moreover, measurements of a realized prototype sensor, that operates at multiple frequencies in the range of 5 to 6 GHz, confirm the design process. In addition, measurements inside a pressure chamber, that produces small pressure and thus midget permittivity variations, state the excellent sensitivity of the sensor.
Supplemental Table S1 from Advances in the Classification and Treatment of Mastocytosis: Current Status and Outlook toward the Future (2023)

&lt;p&gt;Supplemental Table S1&lt;/p&gt;
Preparation of Poly(phenylene sulfide)s: Polymerization of Aromatic Disulfides with Lewis Acids (1989)

Abstract Poly(p-phenylene sulfide) is prepared through the polymerization of diphenyl disulfide with various Lewis acids, such as AlCl3 and SbCl5. Thiophenol also yield poly(p-phenylene sulfide) through its oxidation to diphenyl disulfide in the presence of an oxidizing agent or electrolysis during polymerization. Alkyl-substituted diphenyl disulfides are polymerized with a Lewis acid to efficiently yield alkyl-substituted poly(p-phenylene sulfide)s such as poly(2-methyl-, 2,6-dimethyl-, and 2,6-diethylphenylene sulfide)s, with high molecular weight and solubility in common solvents.
Simulation of laser beam cladding by powder injection (2003)

Summary form only given. Laser beam cladding is successfully applied to the deposition of wear and corrosion protective coatings and the repair of wear damaged parts. Simulating the cladding process on a virtual machine may facilitate the estimation of process windows and save cost in manufacturing. The presented model predicts the results of processing within a few minutes by simulating the powder preheating by the laser beam, the powder resorption in the melt pool, and the heat transfer in the work piece, taking into account the influences of surface tension, gravity forces, and Marangoni flow on bead shape, temperature field, metallurgical structure, and dilution.
The regulatory mechanisms of human immunodeficiency virus replication predict multiple expression rates. (1990)

The qualitative nature of human immunodeficiency virus replication dynamics is examined by using the known action of regulatory proteins. The combination of activation of transcription by the Tat protein and the influence of the Rev protein on processing of RNA leads to a regulatory loop that can have multiple expression rates. In the lower state, the regulatory loop leads to low, or no, production of virus, which corresponds to its quiescent state. Conversely, when the regulatory loop is in the upper state, active production of virus is maintained over time. These features of the kinetic model have implications for both human immunodeficiency virus-related illness and therapeutics and predict testable experimental results in vitro.
Response to Drs. Luzza et al. and Furuta et al. (1998)

Rudi, Jochen MD*; Zuna, Ivan PhD; Stremmel, Wolfgang MD; Raedsch, Richard MD Author Information
Challenge problems in spectrum engineering and waveform diversity (2013)

We describe and discuss some of the current challenges facing radar that result from continued spectral encroachment, which necessitating enhanced robustness to interference, agile waveform-diverse operation, and greater synergy between the signal processing and the physical radar/environment. Subsequently, specific research topics are suggested in which spectrum engineering and waveform diversity may yield viable solutions. In so doing, this paper also provides an introduction to the special session on radar spectrum engineering and waveform diversity affiliated with NATO Task Groups SET-182 and SET-179, respectively.