gebhart/patrepeval huggingface dataset:
Aging of deep venous thrombosis using polarization sensitive optical coherence tomography (2022)

Deep venous thrombosis is a global health problem with significant complications and high recurrence. Supporting the search for more effective therapies, polarization-sensitive optical coherence tomography (PS-OCT) may offer diagnostic imaging to determine the age of thrombus and personalize treatment. To assess sensitivity to thrombus aging, the IVC of two rat cohorts were imaged in-vivo at 24 hours (acute) or 28 days (chronic) after thrombus creation. The PS-OCT metrics were capable of differentiating acute and chronic thrombi with 98.2% total accuracy. These results demonstrate that PS-OCT is sensitive to structural changes in thrombi and could help guide advanced thrombolytic therapies.
Thoracic Idiopathic Scoliosis Severity Is Highly Correlated with 3D Measures of Thoracic Kyphosis (2017)

The findings of this study suggest that 3D assessment is critical for adequate characterization of the multiplanar deformity of idiopathic scoliosis and deformity in the sagittal plane is linked to deformity in the coronal plane. Increasing severity of coronal plane curvature is associated with a progressive loss of thoracic kyphosis that should be anticipated so that the appropriate intraoperative techniques for correction of idiopathic scoliosis can be applied in all 3 planes.
Noninvasive murine glioma detection improved following photobleaching of skin PpIX fluorescence (2008)

Aminolevulinic Acid (ALA) is a prodrug which can be administered to cells, animals or patients after which it is transformed via the Heme synthesis pathway into the fluorescent molecule Protoporphyrin IX (PpIX). PpIX has been shown to be useful as both a photosensitizer for photodynamic therapy (PDT) and as a fluorescence imaging contrast agent. The ALA-PpIX system not only provides contrast for fluorescence imaging but also gives information about the metabolic activity of the imaged tissue and thus could be useful for monitoring cancer therapy. In the current study skin photobleaching was examined to determine if PpIX fluorescence contrast in malignant brain tumors could be better visualized noninvasively. Red light photobleaching decreased skin PpIX fluorescence and increased the ability to noninvasively quantify PpIX fluorescence in murine gliomas, as in vivo measurements of mean PpIX fluorescence more closely matched ex vivo quantification following skin photobleaching. Three doses of blue light photobleaching (4 J/cm2, 8 J/cm2 and 12 J/cm2) were tested and determined to give similar levels of skin photobleaching as well as a similar window of decreased skin PpIX fluorescence for noninvasive fluorescence imaging following the photobleaching dose administration.
A Priori Shape Information in Image Segmentation (2004)

Prior knowledge is an essential component of the human vision system, allowing us to be more selective and effective in a visual recognition task. In computer vision, this need for including prior knowledge about the task to be realised is increasingly recognised. In this talk, we will show how shape information can be considered in a computer vision problem. Active contours, and especially geodesic active contours, provide an efficient formalism for including this kind of information in the segmentation process. We will show two approaches to tackle this. The first one uses an image template, described by an analytical decomposition using Matching Pursuit, to represent the typical object to be segmented. A multi-scale affine invariant decomposition of the target image using the template decomposition as a model allows to drive geodesic active contours towards the objects with the desired shape. In a second approach, the shape information is directly included in the evolution equations of a geodesic active contour. In this approach, the shape information is represented by a statistical representation (e.g a PCA) of example objects, described by their Signed Distance Functions, in a level set formalism. Examples on synthetic and real images will be shown.
InfoSphere Streams architecture (2014)

In this chapter, we switch the focus from a conceptual description of the SPS architecture to the specifics of one such system, InfoSphere Streams. The concepts, entities, services, and interfaces described in Chapter 7 will now be made concrete by studying the engineering foundations of Streams. We start with a brief recount of Streams' research roots and historical context in Section 8.2. In Section 8.3 we discuss user interaction with Streams’ application runtime environment.
[Preclinical and clinical studies on a tumor marker, galactosyltransferase associated with tumor (GAT), in ovarian cancer (second report)--clinical significance of GAT and comparison with other tumor markers]. (1993)

Galactosyltransferase Associated with Tumor (GAT) was clinically studied in cases of ovarian cancer. When two cut-off levels of GAT were compared, the cut-off level of 16 U/ml (which corresponds to mean + 2SD among healthy females) was found to be more suitable than the cut-off level of 14 U/ml (the level maximizing the diagnostic efficiency between malignant and benign ovarian tumors). When the GAT positive rate was examined for gynecologic tumors, the rate was 5.7% for benign ovarian cyst, 6.6% for endometriosis, 20.5% for cervical cancer, 19.5% for endometrial cancer, and 52.9% for ovarian cancer. The GAT positive rate for different histologic types of ovarian carcinoma was relatively high for each type, e.g., 55.0% for clear cell adenocarcinoma and 66.7% for endometrioid adenocarcinoma. The GAT positive rate increased gradually with the stage of ovarian cancer. In patients with benign diseases, in particular endometriosis, the GAT positive rate was lower than the positive rate with any other simultaneously determined marker (CA602, CA125, CA54/61, CA72-4, STN, and SLX). The GAT level most weakly correlated with the level of any of the other markers assessed. An assay combining GAT with CA602 or CA54/61 resulted in a higher positive rate and a higher diagnostic efficiency, when compared with the assay for GAT alone. The lower positive rate of GAT in endometriosis, when compared with the positive rate of other markers, suggests the usefulness of GAT in distinguishing malignant ovarian tumors from benign ovarian tumors. The use of GAT in a combination assay is expected to overcome the disadvantages of CA602 or CA125.
Morphogenesis of poliovirus. IV. existence of particles sedimenting at 150S and having the properties of provirion (1977)

An apparent precursor to the poliovirion that cosediments with the virion at 150S was identified by its content of VP-0. It has properties previously associated with the provirion, a structure that sedimented at 125S, and it may be an alternate form of provirion. Like virions, the 150S precursor binds to and elutes from cells, after which it sediments at about 125S.
Combination of Artesunate and WNT974 Induces KRAS Protein Degradation by Upregulating E3 Ligase ANACP2 and β-TrCP in the Ubiquitin–proteasome Pathway (2021)

Abstract Background KRAS mutation is one of the dominant gene mutations in colorectal cancer (CRC). Up to present, targeting KRAS for CRC treatment remains a clinical challenge. WNT974 (LGK974) is a porcupine inhibitor that interferes Wnt signaling pathway. Artesunate (ART) is a water-soluble semi-synthetic derivative of artemisinin. Methods The synergistic effect of ART and WNT974 combination in reducing CRC cell viability was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. RT-PCR was utilized for the mRNA levels of KRAS, CUL7, ANAPC2, UBE2M, RNF123, SYVN1, or β-TrCP. Western blot assay was utilized for the protein levels of KRAS, ANAPC2, β-TrCP, or GSK-3β. Xenograft mouse model assay was performed for the anti-CRC effect of combination of ART and WNT974 in vivo . IHC assay was utilized for the levels of KRAS, β-TrCP, or GSK-3β in tumor tissues. Results Our study shows that the combination of WNT974 and ART exhibits synergistic effect in reducing CRC growth. The combination treatment significantly reduces KRAS protein level and activity in CRC cells. Interestingly, the combination treatment increases E3 ligases ANAPC2 expression. Our data show that overexpression of ANAPC2 significantly reduces KRAS protein levels, which is reversed by MG132. Knockdown of ANAPC2 in CRC abolishes the combination treatment-reduce KRAS expression. Besides, the treatment also increases the expressions of GSK-3β and E3 ligase β-TrCP that is known to degrade GSK-3β-phosphorylated KRAS protein. Knockdown of β-TrCP- and inhibition of GSK-3β abolish the combination treatment-induce KRAS ubiquitination and reduction in expression. Conclusions Our data clearly show that the combination treatment significantly enhances KRAS protein degradation via the ubiquitination ubiquitin–proteasome pathway, which is also demonstrated in xenograft mouse model. The study provides strong scientific evidence for the development of the combination of WNT974 and ART as KRAS-targeting therapeutics for CRC treatment.
Adaptation of the Iosipescu In-plane Shear Test Method for High Strength Textile Composites (2001)

In order to use the Iosipescu V-notch beam test for determining the in-plane shear strength of high strength 2D 2 × 2 biaxial braided composites, two modifications were made to the specimen geometry. First, they were tabbed to prevent buckling at the gage section and pinching of the specimen at grip sections. Tabbed specimens having gage sections of 0.50″, 0.35″, 0.188″ were studied. Also, to reduce the load required for failure, the shear area was decreased by deepening the V-notch. Failure modes of specimens having notch widths of 0.425″, 0.350″, 0.325″, and 0.300″ were examined. In this investigation, high toughness PR520 epoxy resin was selected to make panels by resin transfer molding (RTM). An initial study was conducted to find the best possible specimen geometry using ±45° braid. Then, both ±45° and ±60° braid angles were studied for the selected geometry. In order to investigate the cut direction effects on the ±60° braid in-plane shear modulus and the strength, the specimens were cut in both 0° and 90° directions of the panel. Tabbed specimens with a gage length of 0.188″ demonstrated the highest average shear strength. The notch width of 0.325″ produced acceptable failures. Thus, it was selected as the minimum notch width. Then, both ±45° and ±60° specimens having gage section of 0.188″ and notch width of 0.325″ were tested for shear properties. The tabs minimized the bending loads due to buckling and pinching of the specimens across the gage section. Modifications increased the in-plane shear strength by about 33–55% for ±45°. The 0° cut-direction specimens, which had ±30° fibers with respect to the loading path, had lower strength and modulus values than that of the 90° cut-direction specimens. Modulus results for ±60° specimens were close to analytical predictions regardless of the cut direction.
L2ight: Enabling On-Chip Learning for Optical Neural Networks via\n Efficient in-situ Subspace Optimization (2021)

Silicon-photonics-based optical neural network (ONN) is a promising hardware\nplatform that could represent a paradigm shift in efficient AI with its\nCMOS-compatibility, flexibility, ultra-low execution latency, and high energy\nefficiency. In-situ training on the online programmable photonic chips is\nappealing but still encounters challenging issues in on-chip implementability,\nscalability, and efficiency. In this work, we propose a closed-loop ONN on-chip\nlearning framework L2ight to enable scalable ONN mapping and efficient in-situ\nlearning. L2ight adopts a three-stage learning flow that first calibrates the\ncomplicated photonic circuit states under challenging physical constraints,\nthen performs photonic core mapping via combined analytical solving and\nzeroth-order optimization. A subspace learning procedure with multi-level\nsparsity is integrated into L2ight to enable in-situ gradient evaluation and\nfast adaptation, unleashing the power of optics for real on-chip intelligence.\nExtensive experiments demonstrate our proposed L2ight outperforms prior ONN\ntraining protocols with 3-order-of-magnitude higher scalability and over 30X\nbetter efficiency, when benchmarked on various models and learning tasks. This\nsynergistic framework is the first scalable on-chip learning solution that\npushes this emerging field from intractable to scalable and further to\nefficient for next-generation self-learnable photonic neural chips. From a\nco-design perspective, L2ight also provides essential insights for\nhardware-restricted unitary subspace optimization and efficient sparse\ntraining. We open-source our framework at\nhttps://github.com/JeremieMelo/L2ight.\n
Models of multilayer antenna radomes with anisotropic materials (2006)

A modified Paris' model (Paris, 1970) for computed-aided radome analysis is presented, which takes into account the dielectric material anisotropy of the radome layers. The analytical model is combined with a practically realized two-resonator method for characterization of the normal and parallel to the surface dielectric parameters of the radome layers. Finally, several examples are given, which illustrate the steps for introduction of appropriate radome models of reinforced and composite radome structures with anisotropy, which accurate represent all the layers formed in the practical radome construction - cores, skins, irregular epoxy glue fillets, protective coatings, etc.
Capture of di-protonated [2.2.2]cryptand in the cavity of two p-sulfonated calixarenes as part of 2-D bi-layer lanthanide coordination polymers (2002)

Treating p-sulfonatocalix[4]arene with lanthanide ions, Ln3+ (Ln = Ce, Nd, Sm and Eu), in the presence of [2.2.2]cryptand results in a 2-D bi-layer coordination polymer with axially elongated diprotonated cryptand in the cavity of two p-sulfonatocalix[4]arenes.
Quasi-solid aqueous electrolytes based on bio-derived polymers (2017)

In recent years, with the idea of creating efficient, safe, and low-cost DSSCs, the research moved the attention towards alternative solvent-based electrolytes. Above all, DSSCs with water-based electrolytes have been proposed as one of the possible solution providing reduced costs, non-flammability and environmental compatibility. Recently we demonstrated that stability issues can be properly addressed by choosing the appropriate dye. Moreover, the possibility of gelling the liquid solvent into a polymeric matrix can reduce the electrolyte leakage outside the device, increasing the long-term stability. In this contribution, the investigation on a series of iodine and cobalt-based 100% aqueous electrolytes is presented. Thanks to our previous experience and to a multivariate approach (Design of Experiment), the effects of the change in redox mediator concentrations and in photoanode preparation on DSSCs performances have been evaluated. Finally, the gelation of the best aqueous electrolytes with bio-derived polymers has been performed. Photovoltaic performances and stabilities will be discussed by comparing liquid and gel electrolytes. In lab-scale solar cells interesting photovoltaic performances superior to 4% were achieved.
Synthesis of Acid-Degradable Poly(amidoamine)s (2007)

A new class of acid-degradable polymers with poly(amidoamine) backbones was synthesized. Reaction of N-(2-hydroxyethyl)phthalimide (1) with acetal 2a or ketal 2b provided intermediate 3, which was deprotected with NaOH and further reacted with acryloyl chloride (4) to afford monomer 5. Michael addition of piperazine monomer (6) to 5 provided the desired poly(amidoamine)s 7, which were characterized by NMR spectroscopy and GPC. The hydrolysis rate constants and half-lives of the polymers were also obtained from the hydrolysis kinetic studies. The data suggested the potential usefulness of polymer 7 in the field of polymer therapeutics and drug delivery.
Multiparameter brain tissue monitoring - Correlation between parameters and identification of CPP thresholds (2000)

Continuous monitoring of brain interstitial gas concentrations allows direct regional evaluation of the pathophysiology of cerebral tissues. We have incorporated the Paratrend 7 (P7) multiparameter sensor into our established multimodal monitoring of head injured patients, to investigate the relationship between brain and arterial pO2, pCO2, and pH, as well as defining thresholds for cerebral perfusion pressure (CPP). A P7 sensor was inserted into the brain tissue of 40 adult head injured patients via a modified Camino bolt or triple lumen bolt. A second sensor was placed in the femoral artery for continuous monitoring of blood gases. Data signals from 19 monitored parameters were collected onto computer at the bedside for up to 14 days. No complications were seen. For individual patients the changes in brain tissue parameters showed large variations over 24 hours and the relationship between parameters varied considerably both between patients and during the period of monitoring any one individual. Changes related to periods of arterial desaturation, cerebral hypoperfusion and therapeutic manoeuvres could be seen. Good correlation was seen between brain pCO2 and arterial pCO2 (r = 0.58). Poor correlation was seen between CPP and brain pO2, and between brain pO2 and ICP. However, by grouping values for intracranial pressure (ICP) and CPP, thresholds for brain tissue pO2 were identified in 16 patients where CPP fell below 60 mmHg. No patients where CPP was always > 60 mmHg showed a significant threshold for a drop in brain pO2 (n = 16). In conclusion, the P7 shows potential as a monitor of regional brain oxygenation and for detection of potentially damaging secondary insults. The results must be interpreted whilst considering catheter position, autoregulation and systemic arterial changes for each individual.
Magnetoresistance of a weakly disordered III-V semiconductor quantum well in a magnetic field parallel to interfaces (1997)

We have investigated the weak-localization effects on the magnetoresistance of a two-dimensional electron gas in a quantum well of a semiconductor with a zinc-blende crystal structure under a sufficiently weak magnetic field $H$ applied parallel to interfaces, so it interacts only with the electron spins due to the Zeeman term in the Hamiltonian. We found a positive magnetoresistance, which depends strongly on the crystal orientation of the well, and varies with the direction of the field depending on the relative strengths of the Rashba and Dresselhaus terms in the spin-orbit coupling. For a [001]-oriented well we found that the magnetic field destroys antilocalization when the Zeeman energy $g\ensuremath{\mu}H$ is larger than $({\ensuremath{\tau}}_{\ensuremath{\varphi}}{\ensuremath{\tau}}_{\mathrm{so}}{)}^{\ensuremath{-}1/2}$, where ${\ensuremath{\tau}}_{\ensuremath{\varphi}}$ is the inelastic dephasing time and ${\ensuremath{\tau}}_{\mathrm{so}}$ the spin-orbit relaxation time. On the other hand, in a symmetric [011]-oriented quantum well, the Zeeman interaction leads to a weak localization of electrons.
Ochratoxin A induced early hepatotoxicity: new mechanistic insights from microRNA, mRNA and proteomic profiling studies (2014)

Abstract The mycotoxin ochratoxin A (OTA) is found widely in agricultural commodities. OTA can induce various toxicities. In this study, rats were gavaged with OTA for different weeks. Then, the expression of microRNAs, mRNAs and proteins were measured in the rat livers treated with OTA for 13 weeks. Our sequencing data suggests that the medial and the high doses of OTA exert different effects on livers. Five distinctive pathways were induced after OTA treatment as collectively demonstrated at miRNA, mRNA and protein levels. Two (primary bile acid biosynthesis and metabolism of xenobiotics by cytochrome P450) are directly associated with liver damage, whereas the remaining pathways (arginine and proline metabolism, cysteine and methionine metabolism and PPAR signaling pathway) cause metabolic disease. This study reveals OTA-induced early hepatotoxicity for the first time by combining multi-omics methods. The novel metabolic pathways may contribute to the pathogenesis of metabolic diseases later in life.
Experimental Analysis of Potentials for Tire Friction Estimation in Low-Slip Operating Mode (2006)

&lt;div class="htmlview paragraph"&gt;This paper presents a detailed experimental analysis of potentials for road condition estimation based on the tire static curve gradient in the low-slip region, and the damping of the 40 Hz tire vibration mode. An experimental vehicle equipped with four standard ABS sensors (44 pulses/rev), two special high-resolution wheel speed sensors (512 pulses/rev), and a halfshaft torque sensor was utilized for collecting the experimental data. The test data were recorded on a test track characterized by different road conditions such as dry concrete, wet and dry ice, and wet and dry snow.&lt;/div&gt;
Figure S1 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs (2023)

&lt;p&gt;Figure S1. Summary of kinome screen.&lt;/p&gt;
Mechanism underlying the DNA-binding preferences of the Vibrio cholerae and vibriophage VP882 VqmA quorum-sensing receptors (2021)

Quorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. In the global pathogen Vibrio cholerae, one quorum-sensing receptor and transcription factor, called VqmA (VqmAVc), activates expression of the vqmR gene encoding the small regulatory RNA VqmR, which represses genes involved in virulence and biofilm formation. Vibriophage VP882 encodes a VqmA homolog called VqmAPhage that activates transcription of the phage gene qtip, and Qtip launches the phage lytic program. Curiously, VqmAPhage can activate vqmR expression but VqmAVc cannot activate expression of qtip. Here, we investigate the mechanism underlying this asymmetry. We find that promoter selectivity is driven by each VqmA DNA-binding domain and key DNA sequences in the vqmR and qtip promoters are required to maintain specificity. A protein sequence-guided mutagenesis approach revealed that the residue E194 of VqmAPhage and A192, the equivalent residue in VqmAVc, in the helix-turn-helix motifs contribute to promoter-binding specificity. A genetic screen to identify VqmAPhage mutants that are incapable of binding the qtip promoter but maintain binding to the vqmR promoter delivered additional VqmAPhage residues located immediately C-terminal to the helix-turn-helix motif as required for binding the qtip promoter. Surprisingly, these residues are conserved between VqmAPhage and VqmAVc. A second, targeted genetic screen revealed a region located in the VqmAVc DNA-binding domain that is necessary to prevent VqmAVc from binding the qtip promoter, thus restricting DNA binding to the vqmR promoter. We propose that the VqmAVc helix-turn-helix motif and the C-terminal flanking residues function together to prohibit VqmAVc from binding the qtip promoter.