gebhart/patrepeval huggingface dataset:
Targeting survival and cell trafficking in multiple myeloma and Waldenstrom macroglobulinemia using pan‐class I PI3K inhibitor, buparlisib (2014)

The phosphatidylinositol-3 kinase (PI3K) pathway is activated in multiple myeloma (MM) and Waldenstrom Macroglobulenima (WM), and plays a crucial role in tumor progression and drug resistance. In this study, we characterized the role of pan-class I PI3K inhibition on cell trafficking and survival of MM and WM cells. We tested the effect of pan-class I PI3K inhibition by siRNA silencing or pharmacologic inhibition with buparlisib on MM cell survival, apoptosis and cell cycle in vitro and tumor growth and mobilization of MM cells in vivo. We then evaluated buparlisib-dependent mechanisms of induced MM cell mobilization. Moreover, the effect of buparlisib on cell survival, apoptosis, and adhesion of WM cells to bone marrow stromal cells (BMSCs) has been evaluated. We showed that buparlisib induced toxicity in MM cells, supported by induction of apoptosis and cell cycle arrest. Buparlisib was also found to reduce tumor progression in vivo. Importantly, buparlisib enhanced MM cell mobilization in vivo which was driven by decreased adhesion of MM cells to BMSCs and increased chemotaxis via up-regulation of CXCR4 expression. Similar to its effects on MM cells, buparlisib also induced cell survival and apoptosis, and decreased adhesion in WM cells. These data highlight the critical contribution of class I PI3K signaling to the regulation of survival and cell dissemination in B-cell malignancies.
Distributed electrode Mach-Zehnder modulator with double-pass phase shifters and integrated inductors (2015)

A novel high-speed Mach-Zehnder modulator (MZM) fully integrated into a 90 nm CMOS process is presented. The MZM features 'double-pass' optical phase shifter segments, and the first use of integrated inductors in a 'velocity-matched' distributed-electrode configuration.
The fully human anti-CD30 antibody 5F11 activates NF-κB and sensitizes lymphoma cells to bortezomib-induced apoptosis (2005)

5F11, a fully human monoclonal antibody directed against CD30, effectively induces killing of CD30-expressing lymphoma cell lines in vitro and in animal models. A recently conducted phase 1/2 study shows that 5F11 is well tolerated in heavily pretreated patients with relapsed and refractory CD30(+) lymphoma and has some clinical activity. In the present study, we demonstrate that 5F11 activates nuclear factor kappaB (NF-kappaB) and the anti-apoptotic protein cellular FLICE (Fas-associating protein with death domain-like interleukin-1beta-converting enzyme) inhibitory protein (c-flip) in Hodgkin lymphoma (HD)-derived cell lines, which might cause apoptosis resistance, thus limiting the clinical use of 5F11. To overcome this resistance, we combined 5F11 with the proteasome inhibitor bortezomib, which has been shown to suppress NF-kappaB activity. This combination revealed a synergistic cytotoxic effect in vitro and in a human HD xenograft model provided that 5F11 precedes bortezomib treatment. We conclude that initial 5F11-mediated NF-kappaB signaling sensitizes the tumor cells to bortezomib-induced cell death. These data suggest a therapeutic value of this combination for HD patients.
G150021 Tactile Sense Evaluation based on Vibration Information obtained during Active Touch (2012)

This paper presents a novel tactile sense measurement method. Tactile sense has not been measured quantitatively which is an important manufacture evaluation factor though. The authors constructed the tactile sense measurement system using vibration information during the active touch. First knowing what factors are related to touch feeling, sensory evaluation about the several samples' tactile sense is carried out. From factor analysis of the sensory evaluation result, three factors are obtained that related to softness, roughness, stickiness. Next, the measurement system imitating human active touch is constructed. The samples which will be evaluated is fixed on a sample table and rotated with constant speed. Then a piezoelectric element touches the object surface with constant normal force. The piezoelectric element measures the vibration information during active touch. Additionally, evaluation values related to tactile factors are defined using the vibration information obtained in experiments. Comparing the evaluation values with the sensory evaluation results, the paper shows effectiveness of this method.
Neurology ® Genetics Acknowledgment to Reviewers (2022)

We wish to acknowledge the individuals who have completed reviews for the journal over the course of 2021. Your thoughtful comments and insights are tremendously helpful, highly appreciated, and imperative for excellence in the field of neurogenetics. We are also grateful for your cooperation in returning reviews in a timely manner. Please find the guidelines for reviewing articles on the Neurology: Genetics website at [ng.neurology.org/][1]. This page provides information on expectations of reviewers regarding confidentiality, timeliness, and reviewer conflicts of interest; it also provides instructions for formatting the comments to editors and authors to enable the most effective communication with authors. [1]: http://ng.neurology.org/
Involvement of Lipogenic Pathway In 5-Azacytidine-Induced Cytotoxicity In Waldenstrom's Macroglobulinemia (2010)

Abstract Abstract 2991 5-azacitidine and 5-aza-2`-deoxycytidine are demethylation agents used for the treatment of myelodysplastic syndrome (MDS). Despite a putative role for the reactivation of epigenetically silenced tumor-suppressor genes, the mechanism of action for these agents remains to be clarified. Recent studies suggest that 5-azacitidine may also act at the post-transcriptional level by insertion into RNA transcripts. As part of these efforts, we investigated the therapeutic potential of these agents in Waldenstrom's Macroglobulinemia (WM), and characterized molecular changes associated with treatment. We observed that 5-azacitidine was more potent than 5-aza-2`-deoxycytidine in inducing dose-dependent cytotoxicity against BCWM.1 WM cells and primary WM lymphoplasmacytic cells. 5-azacitidine-induced cell cycle arrest at G1 was accompanied by up-regulation of the cyclin-dependent kinase inhibitor p21 (Cip1/WAF1) through a p53-independent pathway. Activation of caspase-3, 7, 8, and 9, and PARP was also observed indicating involvement of both mitochondrial and death receptor pathways for 5-azacitidine-induced apoptosis. The BH3 domain proteins Bim and Puma were increased in WM cells treated with 5-azacitidine, and siRNA-mediated knockdown of Bim and Puma provided moderate protection from 5-azacitidine-induced apoptosis. In contrast, PI3K/AKT/mTOR and NF- B activities were not significantly altered by 5-azacitidine. To further characterize the molecular changes with 5-azacitidine, we profiled mRNA expression in the WM cells associated with 5-azacitidine treatment. The most strikingly down-regulated genes by 5-azacitidine include FASN and SCD1, which encode enzymes essential for lipogenesis. Importantly, by quantitative RT-PCR, FASN mRNA expression levels were significantly higher in WM patients versus healthy donors (p=0.001). WM patients who expressed higher levels of FASN mRNA showed greater bone marrow involvement (p=0.003). Importantly, siRNA-mediated knockdown of FASN or SCD1 induced significant growth arrest and apoptosis in WM cells. siRNA-mediated knockdown of the sterol regulatory element binding protein 1 (SREBP-1), a transcriptional activator for FASN and SCD1 was associated with reduced transcription of FASN and SCD1, along with increased cytotoxicity in WM cells. Inhibition of FASN activity by Cerulenin also induced significant apoptosis, and the combination of 5-azacitidine and Cerulenin resulted in a synergistic induction of apoptosis in WM cells. In conclusion, the results of this study support an important role for the lipogenic genes in the 5-azacitidine-induced cytotoxicity in WM cells, and highlight a novel mechanistic pathway for this agent, as well as novel targets for drug therapy in WM. Disclosures: Off Label Use: Role of 5-azacytidine in Waldenstrom's macroglobulinemia.
Precision measurement of the Λc+, Ξc+, and Ξc0 baryon lifetimes (2019)

Precision measurement of the + c , + c , and 0 c baryon lifetimes
Generation and Analysis of an Artificial Gene Dosage Series in Tomato to Study the Mechanisms by Which the Cloned Quantitative Trait Locus fw2.2 Controls Fruit Size (2003)

It has been proposed that fw2.2 encodes a negative fruit-growth regulator that underlies natural fruit-size variation in tomato (Lycopersicon spp.) via heterochronic allelic variation of fw2.2 expression, rather than by variation in the structural protein itself. To further test the negative regulator and the transcriptional control hypotheses, a gene dosage series was constructed, which produced a wider range of fw2.2 transcript accumulation than can be found in natural tomato populations. Fruit developmental analyses revealed that fw2.2 transcript levels were highly correlated (negatively) with fruit mass, supporting the negative regulator and transcriptional regulation hypotheses. Further, the effect of fw2.2 on fruit mass was mediated by repressing three- and two-dimensional cell division in placental and pericarp tissues, respectively. Finally, fw2.2 had little effect on fertility and seed size/number, indicating that fruit size effects of fw2.2 are due largely to expression in the maternal tissues of developing fruit and not mediated through fertility or seed-setting-related processes.
Porphyrin-lipid stabilized paclitaxel nanoemulsion for combined photodynamic therapy and chemotherapy (2021)

PLNE-PTX combining PDT and chemotherapy in a single platform enables superior anti-tumor effects and holds potential to reduce side effects associated with monotherapy chemotherapy. The inherent imaging modality of PLNE-PTX enables real-time tracking and permits spatial and temporal regulation to improve cancer treatment.
Understanding Thickness-Dependent Transport Kinetics in Nanosheet-Based Battery Electrodes (2020)

There is a growing need for thicker electrode designs to achieve high energy/power for ever-increasing power needs by electronic devices and electric automobiles. Though great efforts, such as structure optimization, have been devoted on fabricating thick electrodes, understanding of performance-limiting factors essential to electrode architecture design, has not been well established. In this study, the dependence of electrochemical behavior on electrode mass loading is comprehensively investigated in nanosheet-based electrodes. In particular, the effects of electrical conductivity and porosity are illustrated. In drop-casted electrodes, where nanosheets are highly stacked, ionic diffusion in the electrolyte has been determined to be the controlling step in electrodes with high thickness. To overcome the limitation of such sluggish ionic transport, a facile ice-templating strategy was employed to create vertically aligned channels, offering fast-diffusion pathways for the Li ion in the electrolyte. Impressively, the ice-templated electrodes exhibit a specific capacity of 144 mA h g–1 at 0.2 C and retain 83 mA h g–1 at 10 C with high mass loading ∼10 mg cm–2. The enhanced ion transport kinetics was verified by various electrochemical and structural characterizations. This work demonstrates the thickness scaling effect of nanosheet-based electrodes and highlights the importance of promoting ionic transport and electrolyte access for designing thick electrodes.
Measurements of Path Characteristics in PlanetLab (2009)

We discuss findings from Internet measurements conducted within the global PlanetLab overlay network. Our study comprises results from two traceroute round-trip measurements, covering more than 250 nodes, as well as one-way packet dynamics measurements for another 20 selected nodes worldwide. For that purpose we devised a PCAP-based active probing framework with packet replay capabilites, using fixed-sized, Poisson sampled UDP probe packets. We combine our results with geotargeting information, and from that derive distance and Hop-Count dependent path characteristics, such as Delay, Delay Variation and Packet Loss. Based on assumptions provided by ITU G.114, packet delays are found to be averagely induced by one third within router queues and by two third due to signal propagation times. Spatial properties and routing behaviour within PlanetLab, including observed routing anomalies are treated as well. In order to assess measuring accuracy on PlanetLab nodes, we then examine the Linux timer system, show the impact of clock ”noise” on the Poisson sampling process, and point out simple enhancements of the Linux kernel, that significantly improve timing accuracy. We show the impact of clock skew and provide theoretical background to encounter such uncertainties. Then real-world application performance is also adressed by utilizing Voice over IP measurements on particular Internet2 paths, finding jitter not a limiting factor on voice quality.
Evolution of influenza A virus in intensive and free-range swine farms in Spain (2021)

Swine harbor genetically diverse influenza A viruses (IAVs) with the capacity to host-switch to humans, causing global pandemics. Spain is the largest swine producer in Europe and has a mixed production system that includes 'white coat' pigs raised intensively in modern buildings and free-range Iberian pigs that interface differently with humans, wildlife, and other swine. Through active longitudinal IAV surveillance in nine Spanish provinces during 2015-9, we generated forty-seven complete or near-complete genome sequences from IAVs collected from swine in both systems. Genetically diverse IAVs were identified in intensively raised white pigs and free-range Iberian pigs, including new H3N1 reassortants. Both systems are dynamic environments for IAV evolution, but driven by different processes. IAVs in white pigs were genetically related to viruses found in swine raised intensively in other European countries, reflecting high rates of viral introduction following European trade routes. In contrast, IAVs in Iberian pigs have a genetic makeup shaped by frequent introductions of human IAVs, reflecting rearing practices with high rates of human contact. Transmission between white and Iberian pigs also occurred. In conclusion, Iberian swine with high rates of human contact harbor genetically diverse IAVs and potentially serve as intermediary hosts between white pigs and humans, presenting an understudied zoonotic risk that requires further investigation.
Polymers with hydro-responsive topography identified using high throughput AFM of an acrylate microarray (2011)

Atomic force microscopy has been applied to an acrylate polymer microarray to achieve a full topographic characterisation. This process discovered a small number of hydro-responsive materials created from monomers with disparate hydrophilicities that show reversibility between pitted and protruding nanoscale topographies.
Heterolysis of Re2O7: Generation and Stabilization of the Cation [ReO3]+ (1993)

No side products and no change in the oxidation state of the metal are observed in the cleavage of Re2O7 into [ReO3]+ and [ReO4]−, if the cation is generated and stabilized by open-chain or cyclic tridentate donor ligands (XNH, NCH3, S in 1). The heterolysis, which is driven by coordination chemistry factors, is set up by an unsymmetric solvation of Re2O7 in donor solvents like THE.
A history-taking system that uses continuous speech recognition. (1992)

Q-MED is an automated history-taking system that uses speaker-independent continuous speech as its main interface modality. Q-MED is designed to allow a patient to enter her basic symptoms by engaging in a dialog with the program. Error-recovery mechanisms help to eliminate findings resulting from misrecognitions or incorrect parses. An evaluation of the natural language parser that Q-MED uses to map user utterances to findings showed an overall semantic accuracy of 87 percent; Q-MED asks more specific questions to capture findings that were not volunteered, or that were unable to be parsed in their initial, open-ended form.
Primary optics for efficient high-brightness LED color mixing (2012)

ESR1 mutations contribute to endocrine resistance and occur in a high percentage of hormone-receptor-positive (HR+) metastatic breast cancer (mBC) cases. Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) changed the treatment landscape of HR+ mBC, as they are able to overcome estrogen resistance. The present retrospective study investigates the clinical benefit of CDK4/6i in ESR1 mutant HR+ mBC patients treated with a CDK4/6i as first- or second-line therapy. Plasma was collected at baseline prior to CDK4/6i plus hormone therapy as a first- or second-line treatment. Circulating free DNA (cfDNA) was extracted from plasma, and ESR1 mutation analysis was performed on a ddPCR. Statistical analyses were performed to investigate the predictive power of ESR1 mutations and any association with clinical factors. A total of 42 patients with mBC treated with CDK4/6i plus endocrine therapy as first- (<i>n</i> = 35) or second-line (<i>n</i> = 7) were enrolled. Twenty-eight patients received hormonal therapy (AI or tamoxifen) in the adjuvant setting. ESR1 mutation status in blood was associated with shorter median disease-free survival (DFS) (30 vs. 110 months; <i>p</i> = 0.006). Multivariate analysis confirmed ESR1 mutations as independent factors of resistance in adjuvant hormone therapy. On the contrary, no difference in progression-free survival (PFS) was observed in the presence or absence of an ESR1 mutation in patients treated with CDK4/6i as first-line treatment (<i>p</i> = 0.29). No statistically significant correlation between the best response to CDK4/6i and ESR1 mutation was found (<i>p</i> = 0.46). This study indicates that the ESR1 mutation detected in cfDNA is an independent predictive factor of clinical recurrence in the adjuvant setting and that CDK4/6i can overcome ESR1-dependent resistance.
The Uridine Diphosphate Glucuronosyltransferase 2B15 D85Y and 2B17 Deletion Polymorphisms Predict the Glucuronidation Pattern of Androgens and Fat Mass in Men (2007)

The UGT2B15 D85Y and the UGT2B17 deletion polymorphisms are both predictors of the glucuronidation pattern of androgens/androgen metabolites. Our findings indicate that UGT2B17 is involved in 17-glucuronidation of mainly T but also of DHT and androstanediol and that UGT2B15 is involved in the 17-glucuronidation of androstanediol. Furthermore, these two polymorphisms are predictors of fat mass in men.
Federated Edge Learning with Misaligned Over-The-Air Computation (2021)

Over-the-air computation (OAC) is a promising technique to realize fast model aggregation in the uplink of federated edge learning. OAC, however, hinges on accurate channel-gain precoding and strict synchronization among the edge devices, which are challenging in practice. As such, how to design the maximum likelihood (ML) estimator in the presence of residual channel-gain mismatch and asynchronies is an open problem. To fill this gap, this paper formulates the problem of misaligned OAC for federated edge learning and puts forth a whitened matched filtering and sampling scheme to obtain oversampled, but independent, samples from the misaligned and overlapped signals. Given the whitened samples, a sum-product ML estimator and an aligned-sample estimator are devised to estimate the arithmetic sum of the transmitted symbols. In particular, the computational complexity of our sum-product ML estimator is linear in the packet length and hence is significantly lower than the conventional ML estimator. Extensive simulations on the test accuracy versus the average received energy per symbol to noise power spectral density ratio (EsN0) yield two main results: 1) In the low EsN0 regime, the aligned-sample estimator can achieve superior test accuracy provided that the phase misalignment is non-severe. In contrast, the ML estimator does not work well due to the error propagation and noise enhancement in the estimation process. 2) In the high EsN0 regime, the ML estimator attains the optimal learning performance regardless of the severity of phase misalignment. On the other hand, the aligned-sample estimator suffers from a test-accuracy loss caused by phase misalignment.
Analytical computation of IPMSM air gap magnetic flux density and Electrical parameters considering space harmonics (2009)

International audience
DCLK1-Isoform2 Alternative Splice Variant Promotes Pancreatic Tumor Immunosuppressive M2-Macrophage Polarization (2020)

Tumor-associated M2-macrophages are one of the most abundant immunosuppressive cell types in the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME). However, the molecular mechanisms responsible for the generation of M2-macrophages are unclear. Here, we demonstrated that overexpression of DCLK1-isoform2 in AsPC1 and MIA PaCa2 cells resulted in the polarization of M1-macrophages toward an M2 phenotype via secreted chemokines/cytokines. These M2-macrophages enhanced parental PDAC cell migration, invasion, and self-renewal, and this was associated with increased expression of Snail and Slug. We observed distinct expression of Dclk-isoform2, marked infiltration of M2-macrophages, and a marginal increase of CD8<sup>+</sup> T cells in 20-week-old KPCY mice pancreas compared with 5 weeks old. Utilizing an autochthonous mouse model of pancreatic adenocarcinoma, we observed distinct immunoreactive Dclk1 and arginase1 in tissues where CD8<sup>+</sup> T-cell infiltration was low and observed a paucity of DCLK1 and arginase1 staining where CD8<sup>+</sup> T-cell infiltration was high. Finally, we found that DCLK1-isoform2 tumor-educated M2-macrophages inhibit CD8<sup>+</sup> T-cell proliferation and granzyme-B activation. Inhibition of DCLK1 in an organoid coculture system enhanced CD8<sup>+</sup> T-cell activation and associated organoid death. We conclude that DCLK1-isoform2 is a novel initiator of alternate macrophage activation that contributes to the immunosuppression observed in the PDAC TME. These data suggest that tumor DCLK1-isoform2 may be an attractive target for PDAC therapy, either alone or in conjunction with immunotherapeutic strategies.
Measurement of acoustic properties of materials at low frequencies in a water-filled tube (1995)

Two of the traditional methods for measuring the complex reflection coefficient of a material, the standing-wave tube method and the pulse tube method, each have shortcomings when the measurements are to be made in a water-filled tube at low frequencies. An acoustic impedance tube has been designed to overcome these shortcomings. The design uses a transient incident signal as opposed to a cw signal in order to minimize the problem of vibrations in the tube wall. It also uses a dual sensor system [D. Guicking and K. Karcher, Trans. ASME: J. Vib. Acoust. Stress Reliability Design 106, 393–396 (1984)] to separate the incident signal from the reflected signal without them being temporally separated. Active impedance control at the end of the tube opposite from the samples reduces the reflection from that end. The tube has been designed so that ambient pressure and temperature can be controlled during measurements to simulate an ocean environment. The analytic design of the tube and preliminary experimental results will be presented. [Work supported by ONR and NSF.]