gebhart/patrepeval huggingface dataset:
IMPS-29REFUTING BRAIN IMMUNE PRIVILEGE: LONGITUDINAL MULTIPHOTON IMAGING THROUGH SKULL WINDOWS REVEALS THE IMMUNE SURVEILLANCE OF BRAIN METASTASES AND ITS REGULATION BY FRACTALKINE (2015)

INTRODUCTION: The has conventionally been considered to be immune-privileged, which has detracted from the pursuit of immunotherapies for tumors. However, whether malignancies remain insulated from the immune system is unclear. T cell migration in tissues is regulated in part by chemokines often in an organ-specific manner. We hypothesized that tumors are accessible to T cell surveillance, and that this process is regulated by a chemokine called fractalkine, which is highly expressed in the brain. METHODS: Cranial windows for intravital multiphoton microscopy were established in novel transgenic murine models in which T cells, macrophages, microglia, and dendritic cells were distinctly gene-labeled with fluorescent tags. For comparison, multicolor reporter mice deficient in fractalkine receptor (CX3CR1gfp/gfp-KO) were used. Brain metastases (BM) were induced via carotid artery injection of fluorescent MCA fibrosarcoma cells and the immune dynamics at tumor lesions was imaged longitudinally. RESULTS: BM regressed after initial progression in wild-type (WT) mice, but were lethal in Rag1-KO mice, and importantly also lethal in CX3CR1-KO mice. Intravital microscopy in WT reporter mice revealed hotspots of T cell migration at BM foci followed by tumor fragmentation. In striking contrast, T cells were reduced in BM in CX3CR1-KO reporter mice and exhibited increased meandering and decreased engagement with cancer cells. CONCLUSION: With live imaging, we directly show the existence of robust and effective immune surveillance within the contrary to the concept of brain immune privilege. Furthermore, we identify the fractalkine/CX3CR1 chemokine-receptor axis as a key regulator of T cell immune surveillance in the malignant brain.
Evaluation of Neurosecretome from Mesenchymal Stem Cells Encapsulated in Silk Fibroin Hydrogels (2019)

Physical and cognitive disabilities are hallmarks of a variety of neurological diseases. Stem cell-based therapies are promising solutions to neuroprotect and repair the injured brain and overcome the limited capacity of the central nervous system to recover from damage. It is widely accepted that most benefits of different exogenously transplanted stem cells rely on the secretion of different factors and biomolecules that modulate inflammation, cell death and repair processes in the damaged host tissue. However, few cells survive in cerebral tissue after transplantation, diminishing the therapeutic efficacy. As general rule, cell encapsulation in natural and artificial polymers increases the in vivo engraftment of the transplanted cells. However, we have ignored the consequences of such encapsulation on the secretory activity of these cells. In this study, we investigated the biological compatibility between silk fibroin hydrogels and stem cells of mesenchymal origin, a cell population that has gained increasing attention and popularity in regenerative medicine. Although the survival of mesenchymal stem cells was not affected inside hydrogels, this biomaterial format caused adhesion and proliferation deficits and impaired secretion of several angiogenic, chemoattractant and neurogenic factors while concurrently potentiating the anti-inflammatory capacity of this cell population through a massive release of TGF-Beta-1. Our results set a milestone for the exploration of engineering polymers to modulate the secretory activity of stem cell-based therapies for neurological disorders.
Analysis of Natural Graphite, Synthetic Graphite, and Thermosetting Resin Candidates for Use in Fuel Compact Matrix (2011)

The AGR-1 and AGR-2 compacting process involved overcoating TRISO particles and compacting them in a steel die. The overcoating step is the process of applying matrix to the OPyC layer of TRISO particles in a rotating drum in order to build up an overcoat layer of desired thickness. The matrix used in overcoating is a mixture of natural graphite, synthetic graphite, and thermosetting resin in the ratio, by weight, of 64:16:20. A wet mixing process was used for AGR-1 and AGR-2, in that the graphites and resin were mixed in the presence of ethyl alcohol. The goal of the wet mixing process was to 'resinate' the graphite particles, or coat each individual graphite particle with a thin layer of resin. This matrix production process was similar to the German, Chinese, Japanese, and South African methods, which also use various amount of solvent during mixing. See Appendix 1 for information on these countries matrix production techniques. The resin used for AGR-1 and AGR-2 was provided by Hexion, specifically Hexion grade Durite SC1008. Durite SC1008 is a solvated (liquid) resole phenolic resin. A resole resin does not typically have a hardening agent added. The major constituent of SC1008 is phenol, with minor amounts of formaldehyde. Durite SC1008 is high viscosity, so additional ethyl alcohol was added during matrix production in order to reduce its viscosity and enhance graphite particle resination. The current compacting scale up plan departs from a wet mixing process. The matrix production method specified in the scale up plan is a co-grinding jet mill process where powdered phenolic resin and graphite are all fed into a jet mill at the same time. Because of the change in matrix production style, SC1008 cannot be used in the jet milling process because it is a liquid. The jet milling/mixing process requires that a suite of solid or powdered resins be investigated. The synthetic graphite used in AGR-1 and AGR-2 was provided by SGL Carbon, grade KRB2000. KRB2000 is a graphitized petroleum coke. The availability of KRB2000 is perhaps in question, so a replacement synthetic graphite may need to be identified. This report presents data on potential replacements for KRB2000.
1621: Pre-Treatment Semen Parameters in Men with Cancer (2006)

You have accessJournal of UrologyModerated Poster, Wednesday, May 24, 2006, 1:00 - 3:00 pm1 Apr 20061621: Pre-Treatment Semen Parameters in Men with Cancer Daniel H. Williams, Edward Karpman, James C. Sander, and Larry I. Lipshultz Daniel H. WilliamsDaniel H. Williams More articles by this author , Edward KarpmanEdward Karpman More articles by this author , James C. SanderJames C. Sander More articles by this author , and Larry I. LipshultzLarry I. Lipshultz More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)33813-8AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1621: Pre-Treatment Semen Parameters in Men with Cancer." The Journal of Urology, 175(4S), p. 522 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 4SApril 2006Page: 522 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Daniel H. Williams More articles by this author Edward Karpman More articles by this author James C. Sander More articles by this author Larry I. Lipshultz More articles by this author Expand All Advertisement Loading ...
Mapping the Maze of Minimally Invasive Surgery Simulators (2011)

No simulator yet provides the ability to train the entire set of required psychomotor skills or procedures for MIS. A multiyear training program combining various simulators for multiple-level training, including team training, should be constructed.
Effects of Topical Corticosteroids and Nonsteroidal Anti-Inflammatory Drugs on Prostaglandin E<sub>2</sub>-Induced Aqueous Flare Elevation in Pigmented Rabbits (2003)

We evaluated the effects of anti-inflammatory potency of corticosteroids and nonsteroidal anti-inflammatory drugs on prostaglandin E2 (PGE2)-induced aqueous flare elevation in pigmented rabbits. Transcorneal diffusion of PGE2, 25 microg/ml (7.09 x 10(-2) mmol/l), with the use of a glass cylinder was achieved to produce aqueous flare elevation. Anti-inflammatory drugs were topically administered once before PGE2 application. Aqueous flare was measured with a laser flare-cell meter. Topical single instillation of dexamethasone sodium metasulfobenzoate 0.1%, dexamethasone sodium phosphate 0.1%, and fluorometholone 0.1% 6 h before PGE2 application inhibited 56, 59, and 43% of flare elevation, respectively. Topical single instillation of bromfenac sodium 0.1% and pranoprofen 0.1% 1 h before PGE2 application inhibited 33 and 15% of flare elevation, respectively. Indomethacin 0.5% did not inhibit flare elevation. Corticosteroid eyedrops needed several hours from topical instillation to exhibit inhibition of flare elevation. Most nonsteroidal anti-inflammatory drug eyedrops inhibited aqueous flare elevation when instilled 1 h before PGE2 application.
A high-throughput path metric for multi-hop wireless routing (2003)

This paper presents the expected transmission count metric (ETX), which finds high-throughput paths on multi-hop wireless networks. ETX minimizes the expected total number of packet transmissions (including retransmissions) required to successfully deliver a packet to the ultimate destination. The ETX metric incorporates the effects of link loss ratios, asymmetry in the loss ratios between the two directions of each link, and interference among the successive links of a path. In contrast, the minimum hop-count metric chooses arbitrarily among the different paths of the same minimum length, regardless of the often large differences in throughput among those paths, and ignoring the possibility that a longer path might offer higher throughput.This paper describes the design and implementation of ETX as a metric for the DSDV and DSR routing protocols, as well as modifications to DSDV and DSR which allow them to use ETX. Measurements taken from a 29-node 802.11b test-bed demonstrate the poor performance of minimum hop-count, illustrate the causes of that poor performance, and confirm that ETX improves performance. For long paths the throughput improvement is often a factor of two or more, suggesting that ETX will become more useful as networks grow larger and paths become longer.
A rigid, stand‐off hybrid dipole, and birdcage coil array for 7 T body imaging (2017)

The constructed coil array is easy to handle, safe, and patient friendly, allowing further development of abdominal imaging at 7 T. Quantitative MRI in the abdomen is possible with Plug-and-Play MRF using the designed coil array. Magn Reson Med 80:822-832, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Review of conformation-specific affinity purification methods for plasma vitamin K-dependent proteins (1996)

There are seven known vitamin K-dependent proteins in blood. These proteins require calcium ion for expressing their full biological activities. Calcium ion also induces conformational changes in this class of proteins. Taking advantage of the ligand induced conformational changes, a number of unique approaches of affinity chromatography have been developed. These methodologies have been very useful tools for both the purification and for understanding the structure-function relationships of this class of proteins. One method is the use of metal ion dependent immunoaffinity chromatography. The antigen can be dissociated from the antibodies with either the removal or addition of calcium ion under physiological conditions. The other method is pseudoaffinity chromatography. This method uses conventional ion-exchange or hydrophobic resin and manipulates the mobilities of the proteins on these resins by the presence or absence of calcium ions. Researchers working with other calcium binding proteins or other proteins that are known to undergo ligand induced conformational changes may benefit from the experience of these unique conformation-specific affinity chromatography approaches.
Clinical Outcome in a Randomized 1-Year Trial of Clozapine Versus Treatment as Usual for Patients With Treatment-Resistant Illness and a History of Mania (2003)

Objective: Case series and follow-up studies suggest that clozapine may have mood-stabilizing properties in addition to antipsychotic action in patients with schizoaffective disorder, bipolar type, and bipolar I disorder, but the generalizability of these findings is limited. This article describes a randomized, open study of clozapine add-on therapy versus treatment as usual for patients with treatment-resistant illness and a history of mania. Method: Thirty-eight patients meeting the DSM-IV criteria for schizoaffective or bipolar disorder that was deemed treatment-resistant were randomly assigned to clozapine add-on treatment (N=19) or treatment as usual (no clozapine) (N=19) and followed up for 1 year. Patients received monthly ratings on the Brief Psychiatric Rating Scale, Clinical Global Impression scale, Bech-Rafaelsen Mania Scale, Hamilton Depression Rating Scale, Scale for the Assessment of Positive Symptoms, Scale for the Assessment of Negative Symptoms, Abnormal Involuntary Movement Scale, and a 40-item side effect checklist. Differences between treatment groups were assessed according to a pattern-mix random-regression model. An additional analysis compared group differences in rating scale scores against relative time in the study. Results: Significant between-group differences were found in scores on all rating scales except the Hamilton depression scale. Total medication use over 1 year significantly decreased in the clozapine group. No significant differences between groups in somatic complaints were noted. The subjects with nonpsychotic bipolar I disorder who received clozapine showed a degree of improvement similar to that of the entire clozapine-treated group. Clozapine dose was significantly higher for the patients with schizoaffective illness than for those with bipolar disorder. Conclusions: The results of this study support clozapine’s independent mood-stabilizing property. They demonstrate that clozapine use was associated with significant clinical improvement relative to treatment as usual.
Lift-off process for achieving fine-line metallization (1983)

A trilevel lift-off process using a soluble polyimide as the base layer is described. Al–Cu–Si metallizations are obtained with good pattern fidelity over 1 μm high structures with the use of substrate metallization temperatures of up to 325 °C. The process routinely produces metallizations 1 μm thick with linewidths less than 1.5 μm and pitch less than 2.5 μm.
Reliable Spanners for Metric Spaces (2022)

A spanner is reliable if it can withstand large, catastrophic failures in the network. More precisely, any failure of some nodes can only cause a small damage in the remaining graph in terms of the dilation. In other words, the spanner property is maintained for almost all nodes in the residual graph. Constructions of reliable spanners of near linear size are known in the low-dimensional Euclidean settings. Here, we present new constructions of reliable spanners for planar graphs, trees, and (general) metric spaces.
High-Quality 0.5mm Isotropic fMRI: Random Matrix Theory Meets Physics-Driven Deep Learning (2023)

Submillimeter fMRI plays a vital role in studying the brain function at the mesoscale level, allowing investigation of functional activity in small cortical structures. However, such resolutions require extreme trade-offs between SNR, spatio-temporal resolution and coverage leading to numerous challenges. Therefore, interpretable locally low-rank denoising methods based on random matrix theory have been proposed and built into fMRI pipelines, but they require well-characterized noise distributions on reconstructed images, which hinders the use of emerging physics-driven deep learning reconstructions. In this work, we re-envision the conventional fMRI computational imaging pipeline to an alternative where denoising is performed prior to reconstruction. This allows for a synergistic combination of random matrix theory based thermal noise suppression and physics-driven deep learning re-construction, enabling high-quality 0.5mm isotropic functional MRI. Our results show that the proposed strategy improves on denoising or physics-driven deep learning reconstruction alone, with better delineation of brain structures, higher tSNR particularly in mid-brain areas and the largest expected extent of activation in GLM-derived t-maps.
Giant Dielectric Permittivities in Functionalized Carbon‐Nanotube/ Electroactive‐Polymer Nanocomposites (2007)

Trifluorophenyl-functionalized multi-walled-carbon-nanotube/poly(vinylidene fluoride) (TFP-MWNT/PVDF) nanocomposites are fabricated by employing a wet-chemistry route. The modified MWNTs are observed to form a well-dispersed, structurally random nanophase within the polymer matrix (see figure). The TFP-MWNT/PVDF nanocomposite exhibits enhanced dielectric permittivity when the content of TFP-MWNT is close to the percolation threshold.
Genetic dissection of the secretory route followed by a fungal extracellular glycosyl hydrolase (2018)

Hyphal tip cells of Aspergillus nidulans are > 100 µm-long, which challenges intracellular traffic. In spite of the basic and applied interest of the secretory pathway of filamentous fungi, only recently has it been investigated in detail. We used InuA, an inducible and highly glycosylated inulinase, and mutations affecting different intracellular membranous compartments, to investigate the route by which the enzyme traffics to the extracellular medium. InuA is core-N-glycosylated in the ER and hyperglycosylated during transit across the Golgi. Hyperglycosylation was prevented by ts mutations in sarA<sup>SAR1</sup> impeding ER exit, and in sedV<sup>SED5</sup> and rabO<sup>RAB1</sup> dissipating the early Golgi, but not by mutations in the TGN regulators hypA<sup>TRS120</sup> and hypB<sup>SEC7</sup> , implicating the early Golgi in cargo glycosylation. podB1<sup>ts</sup> (cog2<sup>ts</sup> ) affecting the COG complex also prevents glycosylation, without disassembling early Golgi cisternae. That InuA exocytosis is prevented by inactivation of any of the above genes shows that it follows a conventional secretory pathway. However, ablation of RabB<sup>RAB5</sup> regulating early endosomes (EEs), but not of RabS<sup>RAB7</sup> , its equivalent in late endosomes, also prevents InuA accumulation in the medium, indicating that EEs are specifically required for InuA exocytosis. This work provides a framework to understand the secretion of enzyme cargoes by industrial filamentous fungi.
Les anticorps anti-VIH-1 et la transmission virale de cellule à cellule (2014)

International audience
Rapid selection of sperm with high DNA integrity (2014)

Sperm selection is essential to assisted reproductive technology (ART), influencing treatment outcomes and the health of offspring. The fundamental challenge of sperm selection is dictated by biology: a heterogeneous population of ~10(8) sperm per milliliter with a short lifetime in vitro. However, conventional sperm selection approaches result in less than 50% improvement in DNA integrity. Here, a clinically applicable microfluidic device is presented that selects sperm based on the progressive motility in 500 parallel microchannels. The result is a one-step procedure for semen purification and high DNA integrity sperm selection from 1 mL of raw semen in under 20 minutes. Experiments with bull sperm indicate more than 89% improvement in selected sperm vitality. Clinical tests with human sperm show more than 80% improvement in human DNA integrity, significantly outperforming the best current practices. These results demonstrate the presence of a sub-population of sperm with nearly intact chromatin and DNA integrity, and a simple clinically-applicable lab-on-a-chip method to select this population.
License tracing in free, open, and proprietary software (2003)

The freedom to view a program's source code is preserved by licensing this program with a free source license. Free and open software licenses often contain clauses that cause them to be incompatible with other software licenses. Thus, if a program is created from sources licensed under a variety of software licenses, it is important to identify the entire set of licenses applicable to this program, so that this set of licenses may be examined for conflicts. This paper describes a software tool that examines a program and the sources from which this program was built and produces the full set of software licenses applicable to this program. The tool also flags missing and potentially conflicting licenses. The intent of this tool is to promote an awareness of the sources from which a program is built and the software licenses applicable to this program. This tool is not warranted in any way. In particular, it cannot make determinations as to the legality of any combination of software licenses for any program.
Joint inversion of time-lapse crosswell electromagnetic, seismic, and production data for reservoir monitoring and characterization (2012)

We present a quantitative approach for the joint interpretation of time-lapse crosswell electromagnetic, time-lapse crosswell seismic, and production data. Because the time-lapse electromagnetic data are sensitive to saturation changes and the time-lapse seismic data are sensitive to both saturation and pressure changes, conditioning the reservoir model to these data can impose additional constraints to the inverse problem, and the resulting reservoir model will honor the saturation and pressure changes due to the recovery process. The reservoir simulator is a key component of the workflow being used to model the recovery process and to compute the time-dependent production data for the wells as well as the temporal and spatial distributions of fluid properties such as saturation, salt concentration, phase density, and pore pressure in the reservoir. These fluid properties together with rock properties can be transformed into the electrical and acoustic properties using prescribed rock physics relations. Three-dimensional finite-difference electromagnetic solver and acoustic solver are then used to calculate electromagnetic and full-waveform seismic responses. We use a multiplicative-regularized Gauss-Newton algorithm to iteratively update the reservoir model to simultaneously minimize data misfits between observed and simulated time-lapse electromagnetic, seismic, and production data. A synthetic cross-well case is employed to demonstrate that the proposed approach can significantly improve the permeability estimation as well as the fluid-front movement monitoring.
A high dynamic range pulse counting detection system for mass spectrometry (2013)

A new high dynamic range pulse counting system has been developed demonstrating the ability to operate at up to 2e8 cps on a triple quadrupole mass spectrometer. This provides an upward extension of the detector's linear dynamic range by about two orders of magnitude over previous pulse counting systems.