gebhart/patrepeval huggingface dataset:
Vector flow imaging using a deep neural network (2019)

Vector flow imaging (VFI) estimates blood flow velocities in both azimuth and axial dimensions. VFI has promising applications in the characterization of complex flow patterns, including cardiac flow and abdominal flow imaging. Conventional VFI relies on the use of multiple angles in transmit or receive, or speckle tracking. They are computationally intensive and estimate quality may be sacrificed to improve computational speed. In this work, we report a vector flow estimation technique using a deep neural network. The network extracts feature from high-pass filtered beamsummed RF data of two consecutive Doppler packets. For each packet, the RF data have azimuth and axial dimensions. It then performs estimation of vector flow in the feature space, and maps the estimate back to the spatial domain. The total computation time is 0.11 s for a pair of Doppler frames of 1024 × 128 samples. The performance of the method is characterized using Field II simulation studies, flow phantom studies, and an in vivo liver study with a Verasonics Vantage 256 scanner. The simulation and flow phantom studies show good agreement between the estimates and the ground truth. The in vivo studies demonstrate that the method is capable of characterizing complex flow patterns in human liver vessels.
Abstract 2949: YK-4-279 is a small molecule inhibitor of ETV1 and inhibits metastasis in a mouse model (2014)

Abstract The erythroblastosis virus E26 transforming sequences (ETS) family of transcription factors consists of a highly conserved group of genes that play important roles in cellular proliferation, differentiation, migration and invasion. Chromosomal translocations fusing ETS factors to promoters of androgen responsive genes have been found in a majority of prostate cancers, including the most clinically aggressive forms. ERG and ETV1 are the most commonly translocated ETS proteins. Over-expression of these proteins in prostate cancer cells results in a more invasive phenotype. The high prevalence of these rearrangements, and their biological significance represents a novel therapeutic target for the treatment of prostate cancer. We recently demonstrated that the small molecule YK-4-279 inhibits ERG and ETV1 biological activity in fusion-positive prostate cancer cells leading to decreased motility and invasion in-vitro. Here, we present our findings in an in-vivo mouse xenograft model. SCID-beige mice were subcutaneously implanted with fusion-positive LNCaP and fusion-negative PC-3 tumors. Animals were treated with YK-4-279 and its effect on tumor size, lung metastasis and survival were observed. YK-4-279 treatment resulted in decreased tumor size in the LNCaP cohort only. A reduction in tumor metastasis to the lungs was observed in compound treated LNCaP animals with comparable tumor sizes. YK-4-279 also increased survival in LNCaP mice. Expression of ETV1 target genes MMP7, FKBP10 and GLYATL2 was reduced as well. ETS fusion-negative PC-3 xenografts were unresponsive to the compound. YK-4-279 is a chiral molecule that exists as a racemic mixture of R and S enantiomers. As part of this study, we also established that (S) -YK-4-279 is the active enantiomer in prostate cancer cells. (S) -YK-4-279 binds to ETV1 with comparable kinetics as the racemic mixture and inhibits ETV1 activity. (R) -YK-4-279 does not demonstrate ETV1 binding or inhibition. Our results demonstrate that YK-4-279 is a potent inhibitor of ETV1 and should be further evaluated for its clinical applications in prostate cancer. Citation Format: Said Rahim, Sarah Justvig, Sung-Hyeok Hong, Perrer Tosso, Haydar Celik, Yasemin Sayedigar-Kont, Milton Brown, Colm Morrissey, Jeffrey Toretsky, Aykut Üren. YK-4-279 is a small molecule inhibitor of ETV1 and inhibits metastasis in a mouse model. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2949. doi:10.1158/1538-7445.AM2014-2949
Local Heating in the Galactic Center Western Arc (2003)

We present arcsecond resolution, 10.8, 11.7, and 18.2 lm images of the central few parsecs of the Galaxy. These images show for the rst time the clumpiness of the dust in the western arc. The 11.7 and 18.2 lm images of part of the western arc were used to evaluate the dust temperature and optical depth distribution of this region. We see several mid-infrared emission peaks that coincide with dust temperature peaks and regions of low optical depth, and we infer the presence of embedded sources in the western arc. Minimum luminosity estimates for two of these sources (5 104L and 2 10 4L) suggest that the circumnuclear ring is being locally heated by relatively young stars.
An in-silico quality assurance study of contouring target volumes in thoracic tumors within a cooperative group setting (2019)

High degree of inter-observer variation was noted for all target volume except for GTV_P, unveiling potentials for protocol modification for subsequent clinically meaningful improvement in target definition. Various similarity indices exist that can be used to guide multi-institutional radiotherapy delineation QA credentialing.
Online simulation‐based process control for injection molding (2009)

Abstract An online numerical simulation is presented that is capable of predicting state variables such as flow rate, melt temperature, shear rate, and melt viscosity by using real time data from a nozzle pressure sensor. The simulation solves the non‐Newtonian nonisothermal polymer flow into multicavity tools while executing rapidly enough for real time process control. Numerical accuracy and stability were first validated offline by comparing the online simulation to results obtained from a commercial mold filling simulation. Simulation‐based process control was then demonstrated by transferring a molding machine from fill to pack‐based on the predicted flow front position. The simulation‐based controller dynamically determined the appropriate transfer position for each part and transferred the machine at the correct time, thereby eliminating flash. The simulation, however, did increase process variability slightly due to delay times associated with the controller‐machine interface. A full factorial design of experiments (DOE) was performed varying injection velocity, mold temperature, and melt temperature. Results show that while the simulation dynamically adjusted the process on a part‐by‐part basis, it did not fully account for the process changes. Accuracy could potentially be improved by incorporating data from additional process sensors, by developing adaptive viscosity models, and by accounting for the melt compressibility. POLYM. ENG. SCI., 2009. © 2009 Society of Plastics Engineers
The Poxvirus p28 Virulence Factor Is an E3 Ubiquitin Ligase (2004)

A majority of the orthopoxviruses, including the variola virus that causes the dreaded smallpox disease, encode a highly conserved 28-kDa protein with a classic RING finger sequence motif (C(3)HC(4)) at their carboxyl-terminal domains. The RING domain of p28 has been shown to be a critical determinant of viral virulence for the ectromelia virus (mousepox virus) in a murine infection model (Senkevich, T. G., Koonin, E. V., and Buller, R. M. (1994) Virology 198, 118-128). Here, we demonstrate that the p28 proteins encoded by the ectromelia virus and the variola virus possess E3 ubiquitin ligase activity in biochemical assays as well as in cultured mammalian cells. Point mutations disrupting the RING finger domain of p28 completely abolish its E3 ligase activity. In addition, p28 functions cooperatively with Ubc4 and UbcH5c, the E2 conjugating enzymes involved in 26 S proteasome degradation of protein targets. Moreover, p28 catalyzes the formation of Lys-63-linked polyubiquitin chains in the presence of Ubc13/Uev1A, a heterodimeric E2 conjugating enzyme, indicating that p28 may regulate the biological activity of its cognate viral and/or host cell target(s) by Lys-63-linked ubiquitin multimers. We thus conclude that the poxvirus p28 virulence factor is a new member of the RING finger E3 ubiquitin ligase family and has a unique polyubiquitylation activity. We propose that the E3 ligase activity of the p28 virulence factor may be targeted for therapeutic intervention against infections by the variola virus and other poxviruses.
Nanoscale Conducting Oxide Writing: Nanoscale Writing of Transparent Conducting Oxide Features with a Focused Ion Beam (Adv. Mater. 6/2009) (2009)

A conductive atomic force microscopy tip probes an embedded, optically transparent, electrically conducting oxide nanowire that was patterned on an indium oxide substrate using focused ion beam implantation. The nanowire is 160 nm wide, 7 nm deep, and theoretically limitless in length, connectivity, and shape. Nanowires of this type have potential application as interconnects in transparent electronics. Further details can be found in the article by Tobin Marks, Mark Hersam and co-workers on p.721.
Supplemental Figure 3 from Notch1 Mutations Are Drivers of Oral Tumorigenesis (2023)

&lt;p&gt;Supplemental Figure 3. A. Association between tumor stage of OSCC patients and NOTCH1 mutation-status. B. Table demonstrates differences in smoking and alcohol consumption rates between the OSCC and leukoplakia patients. C. Table demonstrates differences in smoking and alcohol consumption rates between the OSCC and leukoplakia lesions with mutated NOTCH1. D. The pattern of NOTCH1 base-pair mutations resulting from exposure to tobacco in OSCC and leukoplakia patients (in blue, base-pair mutations that found in both, smokers and non-smokers).&lt;/p&gt;
To Grow or Not to Grow: Isolation and Cultivation Procedures in the Genomic Age (2013)

This chapter contains sections titled: Isolation, Growth, and Cultivation Changes in a Changing World
HEAD-NECK BIOMECHANICS IN SIMULATED REAR IMPACT (1998)

The first objective of this study is to present an overview of the human cadaver studies aimed to determine the biomechanics of the head-neck in a simulated rear crash. The need for kinematic studies to better understand the mechanisms of load transfer to the human head-neck complex is emphasized. Based on this need, a methodology is developed to delineate the dynamic kinematics of the human head-neck complex. Intact human cadaver head-neck complexes were subjected to postero-anterior impact using a mini-sled pendulum device. The integrity of the soft tissues including the musculature and skin were maintained. The kinematic data were recorded using high-speed photography coupled with retroreflective targets placed at various regions of the human head-neck complex. The overall and segmental kinematics of the entire head-neck complex, and the localized facet joint motions were determined. During the initial stages of loading, a transient decoupling of the head occurred with respect to the neck exhibiting a lag of the cranium. The upper cervical spine-head undergoes local flexion concomitant with a lag of the head while the lower cervical spinal column is in local extension. This establishes a reverse curvature to the cervical head-neck complex. With continued loading, head motion ensues and approximately at the end of the loading phase, the entire head-neck complex is under the extension mode with a single curvature. In contrast, the lower cervical spine facet joint kinematics show varying compression and sliding. While both the anterior and posterior-most regions of the facet joint slide, the posterior-most region (mean: 2.84 mm) of the joint compresses more than the anterior-most (mean: 2.02 mm) region. These varying kinematics at the ends of the facet joint result in a pinching mechanism. These biomechanical kinematic findings may be correlated to the presence of headaches and neck pain (Lord, Bogduk et al. 1992; Barnsley, Lord et al. 1995), based on the unique human head-neck anatomy at the upper cervical spine region and the associated facet joint characteristics, and clinical studies.
Iridium/Monodentate Phosphoramidite Catalyzed Asymmetric Hydrogenation ofN-Aryl Imines (2009)

Asymmetric hydrogenation of N-aryl acetophenone imines using iridium/PipPhos leads to very high enantioselectivities up to >99% depending on the presence of electron-donating substituents in the 2-, 3-, and 5-position of the aryl ring. If the substituent is 2-methoxy, the resultant secondary amines are easily oxidatively deprotected using trichloroisocyanuric acid to give the primary amines in good yield with full retention of enantioselectivity.
Supplementary Table 2 from Integrated Next-Generation Sequencing and Avatar Mouse Models for Personalized Cancer Treatment (2023)

&lt;p&gt;PDF file - 57KB, Avatar treatment results.&lt;/p&gt;
Annotation of glycolysis, gluconeogenesis, and trehaloneogenesis pathways provide insight into carbohydrate metabolism in the Asian citrus psyllid (2021)

Abstract Citrus greening disease is caused by the pathogen Candidatus Liberibacter asiaticus, which is transmitted by the Asian citrus psyllid, Diaphorina citri . There is no curative treatment or significant prevention mechanism for this detrimental disease that causes continued economic losses from reduced citrus production. A high quality genome of D. citri is being manually annotated to provide accurate gene models required to identify novel control targets and increase understanding of this pest. Here, we annotated genes involved in glycolysis, gluconeogenesis, and trehaloneogenesis in the D. citri genome, as these are core metabolic pathways and suppression could reduce this pest. Specifically, twenty-five genes were identified and annotated in the glycolysis and gluconeogenesis pathways and seven genes for the trehaloneogenesis pathway. Comparative analysis showed that the glycolysis genes in D. citri are highly conserved compared to orthologs in other insect systems, but copy numbers vary in D. citri . Expression levels of the annotated gene models were analyzed and several enzymes in the glycolysis pathway showed high expression in the thorax. This is consistent with the primary use of glucose by flight muscles located in the thorax. A few of the genes annotated in D. citri have been targeted for gene knockdown as a proof of concept, for RNAi therapeutics. Thus, manual annotation of these core metabolic pathways provides accurate genomic foundations for developing gene-targeting therapeutics to reduce D. citri .
An automatic user study demo in indoor environments and its privacy implications (2009)

User studies usually involve much organization and manual labor. Even when performed correctly, a common problem of the studies is user bias. This occurs when participating users' knowledge of the study influences their actions. Another problem is the willingness of the users to participate at all. Finally, participants will always have privacy concerns. We have developed a framework to help with anonymized user studies, trying to solve the aforementioned problems. We have prepared a demo to show the effectiveness of our system.
Terpenoids from Bovista sp. 96042. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Partially Isolated Multiport Converter With Automatic Current Balancing Interleaved PWM Converter and Improved Transformer Utilization for EV Batteries (2022)

Multiport converters (MPCs) that can regulate multiple input/output ports have been proposed to reduce the converter count in electric vehicle battery systems consisting of multiple batteries (12-V, 48-V, and high-voltage batteries). Conventional MPCs consist of an interleaved PWM converter and DAB converter, and an active current balancing control is indispensable for the interleaved converter. Furthermore, the transformer utilization unavoidably decreases because switches are driven with a nominal duty cycle of 0.75 for 48-/12-V batteries. This article proposes a novel MPC with an automatic current balancing capability and improved transformer utilization. A flying capacitor (FC) is added to the interleaved PWM converter to automatically balance inductor currents. The added FC also allows operations with a nominal duty cycle of 0.5 for 48-/12-V batteries, improving the transformer utilization. The experimental verification tests using a 1-kW prototype demonstrated the automatic current balancing capability, improved transformer utilization, and flexible power exchange among three batteries.
Reinforcement Learning with General Value Function Approximation: Provably Efficient Approach via Bounded Eluder Dimension (2020)

Value function approximation has demonstrated phenomenal empirical success in reinforcement learning (RL). Nevertheless, despite a handful of recent progress on developing theory for RL with linear function approximation, the understanding of general function approximation schemes largely remains missing. In this paper, we establish a provably efficient RL algorithm with general value function approximation. We show that if the value functions admit an approximation with a function class $\mathcal{F}$, our algorithm achieves a regret bound of $\widetilde{O}(\mathrm{poly}(dH)\sqrt{T})$ where $d$ is a complexity measure of $\mathcal{F}$ that depends on the eluder dimension [Russo and Van Roy, 2013] and log-covering numbers, $H$ is the planning horizon, and $T$ is the number interactions with the environment. Our theory generalizes recent progress on RL with linear value function approximation and does not make explicit assumptions on the model of the environment. Moreover, our algorithm is model-free and provides a framework to justify the effectiveness of algorithms used in practice.
Phenotypic Diversity of Peripheral Blood Plasma Cells in Primary Sjögren’s Syndrome (2010)

Production of autoantibodies is one of the main features of primary Sjögren's syndrome (pSS). Long-lived plasma cells (PC) can produce autoantibodies for prolonged period of times without being affected by immunosuppressive therapies. As of today, little is known about the long-lived PC subset and their contribution to autoimmunity. We have characterized the phenotypic and migratory properties of peripheral blood PC isolated from pSS patients (grouped by focus score, FS) and compared them to PC from rheumatoid arthritis (RA) patients and normal non-autoimmune subjects. We observed two populations of PC in all study groups, CD19+ PC and CD19- PC. Interestingly, the CD19- PC subset was most prominent in autoimmune patients (pSS and RA) compared to normal controls. Further investigation of the PC phenotype revealed that a high percentage of both CD19+ and CD19- PC isolated from pSS and RA patients did not express the CD27 marker, which is normally highly expressed on all types of PC. Differences in the expression of markers such as IgM, IgG, CD95 and CXCR3 in the group with high FS compared to FS = 1, underscore the heterogeneity of pSS patient group and demonstrate that phenotypic pattern of circulating PC associates with the severity of inflammation in the salivary glands of these patients. Our migration experiments show that addition of CXCL12 to PC in vitro, do not alter the migration potential of PC in any group tested. However, we observed an overall higher spontaneous migration of PC from pSS compared to both RA and normal controls.
Thermodesulfovibrio aggregans sp. nov. and Thermodesulfovibrio thiophilus sp. nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus Thermodesulfovibrio (2008)

Four obligately anaerobic, thermophilic, sulfate-reducing bacterial strains, designated TGE-P1T, TDVT, TGL-LS1 and TSL-P1, were isolated from thermophilic (operated at 55 °C) methanogenic sludges from waste and wastewater treatment. The optimum temperature for growth of all the strains was in the range 55–60 °C. The four strains grew by reduction of sulfate with a limited range of electron donors, such as hydrogen, formate, pyruvate and lactate. In co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus ΔHT, strains TGE-P1T, TGL-LS1 and TSL-P1 were able to utilize lactate syntrophically for growth. The DNA G+C contents of all the strains were in the range 34–35 mol%. The major cellular fatty acids of the strains were iso-C17 : 0, iso-C16 : 0, C16 : 0 and anteiso-C15 : 0. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belong to the Thermodesulfovibrio clade of the phylum ‘Nitrospirae’. On the basis of their physiological, chemotaxonomic and genetic properties, strains TGL-LS1 (=JCM 13214) and TSL-P1 (=JCM 13215) were classified as strains of Thermodesulfovibrio islandicus. Two novel species of the genus Thermodesulfovibrio are proposed to accommodate the other two isolates: Thermodesulfovibrio aggregans sp. nov. (type strain TGE-P1T =JCM 13213T =DSM 17283T) and Thermodesulfovibrio thiophilus sp. nov. (type strain TDVT =JCM 13216T =DSM 17215T). To examine the ecological aspects of Thermodesulfovibrio-type cells in the sludge from which the strains were originally isolated, an oligonucleotide probe targeting 16S rRNA of all Thermodesulfovibrio species was designed and applied to thin sections of thermophilic sludge granules. Fluorescence in situ hybridization using the probe revealed rod- or vibrio-shaped cells as a significant population within the sludge, indicating their important role in the original ecosystem.
Mechanism of S2 chemiluminescence in the reaction of hydrogen atoms with hydrogen sulphide (1969)

Ground-state sulphur atoms were generated in a discharge flow system by the rapid reaction between H and H2S: H + H2S = H2+ HS (1), H + HS = H2+ S (2) The resulting chemiluminescence by the B3Σ–u state of S2 is shown to arise (a) by two-body combination of S atoms into level v′= 10; (b) by three-body recombination into lower levels: S(3P)+ S(3P)+ M = S*2(B3Σ–uv′⩽9)+ M (3), S*2= S2(X3Σ–g)+hv(4), S*2+ M = S2+ M (5) with k3=(1.0 ± 0.2)× 1015 cm6 mole–2 sec–1 and k4/k5= 2.0 × 10–7 mole cm–3 for M = Ar at 298°K; also D(S—S)= 101.7 ± 0.4 kcal/mole. The mechanism of the sulphur-catalyzed heterogeneous recombination of hydrogen atoms is studied and discussed.
Protection against β‐amyloid neurotoxicity by a non‐toxic endogenous N‐terminal β‐amyloid fragment and its active hexapeptide core sequence (2017)

High levels (μM) of beta amyloid (Aβ) oligomers are known to trigger neurotoxic effects, leading to synaptic impairment, behavioral deficits, and apoptotic cell death. The hydrophobic C-terminal domain of Aβ, together with sequences critical for oligomer formation, is essential for this neurotoxicity. However, Aβ at low levels (pM-nM) has been shown to function as a positive neuromodulator and this activity resides in the hydrophilic N-terminal domain of Aβ. An N-terminal Aβ fragment (1-15/16), found in cerebrospinal fluid, was also shown to be a highly active neuromodulator and to reverse Aβ-induced impairments of long-term potentiation. Here, we show the impact of this N-terminal Aβ fragment and a shorter hexapeptide core sequence in the Aβ fragment (Aβcore: 10-15) to protect or reverse Aβ-induced neuronal toxicity, fear memory deficits and apoptotic death. The neuroprotective effects of the N-terminal Aβ fragment and Aβcore on Aβ-induced changes in mitochondrial function, oxidative stress, and apoptotic neuronal death were demonstrated via mitochondrial membrane potential, live reactive oxygen species, DNA fragmentation and cell survival assays using a model neuroblastoma cell line (differentiated NG108-15) and mouse hippocampal neuron cultures. The protective action of the N-terminal Aβ fragment and Aβcore against spatial memory processing deficits in amyloid precursor protein/PSEN1 (5XFAD) mice was demonstrated in contextual fear conditioning. Stabilized derivatives of the N-terminal Aβcore were also shown to be fully protective against Aβ-triggered oxidative stress. Together, these findings indicate an endogenous neuroprotective role for the N-terminal Aβ fragment, while active stabilized N-terminal Aβcore derivatives offer the potential for therapeutic application.