gebhart/patrepeval huggingface dataset:
Molecular Alterations in Pediatric Sarcomas: Potential Targets for Immunotherapy (1998)

Purpose/results/discussion. Recurrent chromosomal translocations are common features of many human malignancies. While such translocations often serve as diagnostic markers, molecular analysis of these breakpoint regions and the characterization of the affected genes is leading to a greater understanding of the causal role such translocations play in malignant transformation. A common theme that is emerging from the study of tumor-associated translocations is the generation of chimeric genes that, when expressed, frequently retain many of the functional properties of the wild-type genes from which they originated. Sarcomas, in particular, harbor chimeric genes that are often derived from transcription factors, suggesting that the resulting chimeric transcription factors contribute to tumorigenesis. The tumor-specific expression of the fusion proteins make them likely candidates for tumor-associated antigens (TAA) and are thus of interest in the development of new therapies. The focus of this review will be on the translocation events associated with Ewing's sarcomas/PNETs (ES), alveolar rhabdomyosarcoma (ARMS), malignant melanoma of soft parts (MMSP) (clear cell sarcoma), desmoplastic small round cell tumor (DSRCT), synovial sarcoma (SS), and liposarcoma (LS), and the potential for targeting the resulting chimeric proteins in novel immunotherapies.
Uro-Science (2023)

No AccessJournal of UrologyUrological Survey1 Sep 2023Uro-Science Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003575AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Uro-Science." The Journal of Urology, 210(3), p. 559 © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 210 Issue 3 September 2023 Page: 559-559 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.Metrics Author Information Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...
An Overlay File System for cloud-assisted mobile applications (2016)

With cloud assistance, a mobile application can offload its resource-demanding computation tasks to the cloud (public cloud, cloudlet, or personal cloud, etc). This leads to a scenario where computation tasks in the same application run concurrently on both the mobile device and the cloud. These tasks need to save, read, and write files on both the mobile device and the cloud. An important challenge is to ensure that the tasks are able to access and share the files in a manner that is efficient, consistent, and transparent to locations. The paper addresses this issue by designing an application-level file system called Overlay File System (OFS). To improve efficiency, OFS maintains and buffers local copies of data sets on both the cloud and the mobile device. OFS ensures consistency and guarantees that all the reads get the latest data. It combines write-invalidate and write-update policies to effectively reduce the network traffic incurred by invalidating/updating stale data copies and to reduce the application delay when the latest data cannot be accessed locally. To guarantee location transparency, OFS creates an unified view of the data that is location independent and is accessible as local storage. Our experiments show that OFS can effectively support task offloading and efficient execution of offloaded tasks by significantly decreasing both file access latency and network traffic incurred by file accesses.
A sulfated metabolite produced bystf3negatively regulates the virulence ofMycobacteriumtuberculosis (2006)

Sulfated molecules have been shown to modulate isotypic interactions between cells of metazoans and heterotypic interactions between bacterial pathogens or symbionts and their eukaryotic host cells. Mycobacterium tuberculosis, the causative agent of tuberculosis, produces sulfated molecules that have eluded functional characterization for decades. We demonstrate here that a previously uncharacterized sulfated molecule, termed S881, is localized to the outer envelope of M. tuberculosis and negatively regulates the virulence of the organism in two mouse infection models. Furthermore, we show that the biosynthesis of S881 relies on the universal sulfate donor 3'-phosphoadenosine-5'-phosphosulfate and a previously uncharacterized sulfotransferase, stf3. These findings extend the known functions of sulfated molecules as general modulators of cell-cell interactions to include those between a bacterium and a human host.
Regiocontrolled synthesis of poly(3‐alkylthiophene)s by Grignard metathesis (2004)

Abstract Poly(3‐octadecylthiophene)s (P3OTs) were prepared via Grignard metathesis polymerization of 2,5‐dibromo‐3‐octadecylthiophene in the presence of palladium and nickel catalysts. The effect of catalyst structure and reaction temperature on the regioregularity of P3OTs was investigated. Nickel catalysts provided P3OTs with higher regioregularity, while palladium catalysts gave lower regioregularity. Surprisingly, the regioregularity of P3OTs increased when the polymerization was conducted at higher temperature. The catalyst and temperature dependence of the regioregularity is consistent with two competing mechanisms. Polymerizations at higher temperature with nickel catalysts occur primarily via chain‐growth reactions, while polymerizations at lower temperature with palladium catalysts have competing step‐growth and chain growth reactions. P3OTs with higher regioregularity have longer wavelength visible absorptions, while P3OTs with lower regioregularity have shorter wavelength absorptions. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5538–5547, 2004
Data from Targeting Cancer Stem Cells in Castration-Resistant Prostate Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Clinical evidence suggests increased cancer stem cells (CSCs) in a tumor mass may contribute to the failure of conventional therapies because CSCs seem to be more resistant than differentiated tumor cells. Thus, unveiling the mechanism regulating CSCs and candidate target molecules will provide new strategy to cure the patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental design:&lt;/b&gt; The stem-like cell properties were determined by a prostasphere assay and dye exclusion assay. To find critical stem cell marker and reveal regulation mechanism, basic biochemical and molecular biologic methods, such as quantitative real-time PCR, Western blot, reporter gene assay, and chromatin immunoprecipitation assay, were used. In addition, to determine the effect of combination therapy targeting both CSCs and its progeny, &lt;i&gt;in vitro&lt;/i&gt; MTT assay and &lt;i&gt;in vivo&lt;/i&gt; xenograft model was used.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We demonstrate immortalized normal human prostate epithelial cells, appeared nontumorigenic &lt;i&gt;in vivo&lt;/i&gt;, become tumorigenic, and acquire stem cell phenotype after knocking down a tumor suppressor gene. Also, those stem-like cells increase chemoresistance to conventional anticancer reagent. Mechanistically, we unveil that Wnt signaling is a key pathway regulating well-known stem cell marker CD44 by directly interacting to the promoter. Thus, by targeting CSCs using Wnt inhibitors synergistically enhances the efficacy of conventional drugs. Furthermore, the &lt;i&gt;in vivo&lt;/i&gt; mouse model bearing xenografts showed a robust inhibition of tumor growth after combination therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Overall, this study provides strong evidence of CSC in castration-resistant prostate cancer. This new combination therapy strategy targeting CSC could significantly enhance therapeutic efficacy of current chemotherapy regimen only targeting non-CSC cells. &lt;i&gt;Clin Cancer Res; 22(3); 670–9. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
1306. Real-World Experience of Cefiderocol in Treating Bacterial Infection in US Hospitals (Jan 2020-June 2021) (2022)

Abstract Background Cefiderocol (CFDC) is a Gram-negative antibiotic (GNA) with a unique mode of cell entry against carbapenem resistance. This study described the initial use of CFDC in US hospitals since its approval in November 2019. Methods This was a retrospective study of patients treated with CFDC consecutively for ≥3 days in US hospitals, as captured in Premier Healthcare Data from January 2020 to June 2021. This study described the clinical characteristics, CFDC usage, and Post-CFDC initiation 14-day and 28-day in-hospital all-cause mortality (IH-ACM). For patients with microbiology results, the pathogen, susceptibility and culture site associated with CFDC use were described. Index culture was the culture(s) taken on the day closest to CFDC initiation. Results Among 313 of 360 in-patients who received ≥3 days CFDC, the median age was 58 years (range: 17 - 89 years), and 91% were hospitalized via emergency room, trauma, or urgent admission. The most common conditions were severe sepsis with septic shock, palliative care, and multi-drug resistant infection. Also 34% had a ‘do not resuscitate order’. About 64% of patients received mechanical ventilation and 79% had ICU stay. Median length of hospital stay was 27 days (range: 3-310 days). Median days on CFDC was 8 days (range: 3 - 66 days). Over 58% received ≥2 other GNAs within 14-days of initiating CFDC. Among 187 patients with microbiology results, 75% had index cultures with one pathogen, and 73% had confirmed carbapenem resistant pathogens. The most common pathogens were Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Klebsiella pneumoniae and Acinetobacter baumannii. The most common index culture site was respiratory. The 14-day and 28-day crude IH-ACM from CFDC initiation was 16.3% (95%CI: 12.2%-20.4%) and 23.6% (95%CI: 18.9 – 28.4%), respectively. Among those with microbiology results, 14-day and 28-day IH-ACM was 17.1% (95%CI: 11.7% - 22.5%) and 23.5% (95%CI: 17.4-29.6%), respectively. Among patients who died, 83% had severe sepsis with septic shock, 76% were in palliative care, 71% had a ‘do not resuscitate order’, and 44% had COVID-19. Conclusion CFDC was used most frequently in critically ill patients. IH-ACM was comparable with other studies. Disclosures Bin Cai, MD, PhD, Shionogi: Shionogi employee Yun Zhou, MS, Shionogi: Employee of CRO hired by Shionogi Andrew Cooper, PhD, Shionogi: Shionogi employee Stephen Marcella, MD, MPH, Shionogi: Shionogi employee|Shionogi, Inc: Employee.
Decoupled stochastic parallel gradient descent optimization for adaptive optics: integrated approach for wave-front sensor information fusion (2002)

A new adaptive wave-front control technique and system architectures that offer fast adaptation convergence even for high-resolution adaptive optics is described. This technique is referred to as decoupled stochastic parallel gradient descent (D-SPGD). D-SPGD is based on stochastic parallel gradient descent optimization of performance metrics that depend on wave-front sensor data. The fast convergence rate is achieved through partial decoupling of the adaptive system's control channels by incorporating spatially distributed information from a wave-front sensor into the model-free optimization technique. D-SPGD wave-front phase control can be applied to a general class of adaptive optical systems. The efficiency of this approach is analyzed numerically by considering compensation of atmospheric-turbulence-induced phase distortions with use of both low-resolution (127 control channels) and high-resolution (256 x 256 control channels) adaptive systems. Results demonstrate that phase distortion compensation can be achieved during only 10-20 iterations. The efficiency of adaptive wave-front correction with D-SPGD is practically independent of system resolution.
GPGPU Accelerated Deep Object Classification on a Heterogeneous Mobile Platform (2016)

Deep convolutional neural networks achieve state-of-the-art performance in image classification. The computational and memory requirements of such networks are however huge, and that is an issue on embedded devices due to their constraints. Most of this complexity derives from the convolutional layers and in particular from the matrix multiplications they entail. This paper proposes a complete approach to image classification providing common layers used in neural networks. Namely, the proposed approach relies on a heterogeneous CPU-GPU scheme for performing convolutions in the transform domain. The Compute Unified Device Architecture(CUDA)-based implementation of the proposed approach is evaluated over three different image classification networks on a Tegra K1 CPU-GPU mobile processor. Experiments show that the presented heterogeneous scheme boasts a 50× speedup over the CPU-only reference and outperforms a GPU-based reference by 2×, while slashing the power consumption by nearly 30%.
Hepcidin quantification: methods and utility in diagnosis (2014)

Hepcidin is a 25-amino acid peptide hormone that is produced and secreted predominantly by hepatocytes, circulates in the bloodstream, and is excreted by the kidneys. Since the discovery of hepcidin and the elucidation of its important role in iron homeostasis, hepcidin has been suggested as a promising diagnostic marker for iron-related disorders. In this regard, a number of analytical methods have been developed in order to assess hepcidin concentration in different biological fluids, particularly serum and urine. In this critical review we have tried to address the issues still pending in accurate determination of this peptide by evaluating the available analytical methodologies. Among them, the use of ELISA strategies (in competitive or sandwich formats) and molecular mass spectrometry (MS) including MALDI and/or LC-MS has been critically compared. The use of elemental mass spectrometry (ICP-MS) has also been included as a possible complementary tool to the previous ones. In addition, this manuscript has revised the existing and potentially emerging clinical applications of hepcidin testing for diagnosis. These include the iron disorders such as iron deficiency anemia (IDA, low hepcidin), anemia of chronic disease (ACD, high hepcidin) and the combined state of ACD and IDA or hemochromatosis. Other applications such as using hepcidin in assessing the response to existing therapies in cancer have also been revised in the manuscript.
283 COMPARATIVE CHARACTERIZATIONS OF PORCINE MESENCHYMAL STEM CELLS AND SKIN-DERIVED CELLS (2008)

Mesenchymal stem cells (MSC) have high potential in regenerative medicine such as skin substitute for a burn healing. The present study compared the characterizations of porcine MSCs (pMSC) derived from bone marrow to the same porcine adult ear and different porcine fetal skin derived cells on morphology of cell growth, alkaline phosphatase (AP) activity, cell surface (CD) markers (CD 29, 45, 90 and 105) and cell cycle by flow cytometer and protein and mRNA expression of Oct3/4, Nanog and Sox2 by immunocytochemistry and RT-PCR (Carlin et al. 2006 Reprod. Biol. Endocrinol. 4, 8) in 1–3 passage. The pMSC were isolated with Ficoll–Paque Plus (Amersham Science, USA) and skin-derived cells were separated with trypsin-EDTA solution treatment of tissue. Basal medium used for culture of pMSC and skin-derived cells was advanced-DMEM supplemented with 10% FBS and 1% penicillin–streptomycin (10 000 IU and 10 000 µg mL–1, Gibco) and culture medium was exchanged every 3 days. Skin-derived cells were observed similar patterns of colony formation and AP expression by AP chromogen kit (BCIP/NBT) (Abcam Inc., MA, USA) to pMSC on plating culture. pMSC and skin-derived cells were found to have a stronger reaction of CD 45– (St. Louis, MO, USA), CD 29+ (BD Bioscience, US), and CD 90+ (BD Bioscience, US). However, CD 105+ (abD Serotec, UK) weakly expressed in pMSC and skin-derived cells were almost negative. The population of cells at S-phase of the cycle in pMSC was significantly (P &amp;lt; 0.05) greater than those in adult ear and fetal-derived skin cells (30.4 ± 5.3 v. 19.1 ± 3.6 and 21.3 ± 1.7, respectively; mean ± SD). Protein of Oct3/4 (goat polyclonal IgG, Santa Cruz, CA, USA), Nanog (goat polyclonal IgG, Santa Cruz, CA, USA) and Sox2 (rabbit polyclonal IgG, Santa Cruz, CA, USA) were observed at both nucleus and cytoplasm in all cell types. However, the pattern of mRNA expression was different among cell types. Nanog and Sox2 expression was the greatest in pMSC and fetal skin cells, respectively. Oct 4 expression should read extremely low in pMSC compared with skin-derived cells, contrary to expectation. Taken together, pMSC and skin-derived cells revealed similar characterization, indicating that pMSC can expect a role of skin substitute. This work was supported by grant from Biogreen21 (20070301034040), Ministry of Agriculture and Forestry, Republic of Korea.
An OFDM Signal Identification Method for Wireless Communications Systems (2015)

Distinction of orthogonal frequency-division multiplexing (OFDM) signals from single-carrier signals is highly important for adaptive receiver algorithms and signal identification applications. OFDM signals exhibit Gaussian characteristics in the time domain, and fourth-order cumulants of Gaussian distributed signals vanish, in contrast to the cumulants of other signals. Thus, fourth-order cumulants can be utilized for OFDM signal identification. In this paper, first, formulations of the estimates of the fourth-order cumulants for OFDM signals are provided. Then, it is shown that these estimates are significantly affected by wireless channel impairments, frequency offset, phase offset, and sampling mismatch. To overcome these problems, a general chi-square constant false-alarm rate Gaussianity test, which employs estimates of cumulants and their covariances, is adapted to the specific case of wireless OFDM signals. Estimation of the covariance matrix of the fourth-order cumulants is greatly simplified, peculiar to the OFDM signals. A measurement setup is developed to analyze the performance of the identification method and for comparison purposes. A parametric measurement analysis is provided, depending on modulation order, signal-to-noise ratio, number of symbols, and degree of freedom of the underlying test. The proposed method outperforms statistical tests that are based on fixed thresholds or empirical values, whereas the a priori information requirement and complexity of the proposed method are lower than the coherent identification techniques.
The Evolution of the Polarization Calculii (2008)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text R. A. Chipman, "The Evolution of the Polarization Calculii," in Frontiers in Optics 2008/Laser Science XXIV/Plasmonics and Metamaterials/Optical Fabrication and Testing, OSA Technical Digest (CD) (Optica Publishing Group, 2008), paper SWB3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
PhD forum: Heterogeneous interconnection of ICs using stitch-chips (2017)

In this paper, a heterogeneous interconnect stitching technology (HIST) is presented. Stitch chips with high-density fine pitch wires are used to connect active dice of various functions in a manner that mimics system-on-chip (SoC) like performance. Microbumps and compressible microinterconnects (CMIs) are used to provide die-to-die and die-to-package interconnection. A testbed containing two dummy dice and one stitch chip is fabricated and tested. The average measured post-assembly resistance of the microbumps and the CMIs is 116.5 μΩ and 195.9 mμ, respectively. Using an electrical model for HIST signal channels, a 50%-50% delay as small as 140 ps with an energy efficiency of 0.24 pJ/bit may be achieved for a 1mm channel. In addition, some power delivery challenges and opportunities of HIST are highlighted through simulations. The results show that compared to interposer based 2.5-D integration, HIST may reduce the IRdrop by approximately 18.4%.
Trench shielded planar gate IGBT (TSPG-IGBT) for low loss and robust short-circuit capalibity (2013)

A trench shielded planar gate IGBT is proposed in this paper. The unique 3D top cell structure, combining high density trench and low channel density, offers an excellent conduction vs. switching loss trade-off and a significantly better Short-circuit SOA compared to trench IEGTs. Measurements on fabricated devices show a 0.1V lower V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CESAT</sub> for the same E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> , and a 2x improvement in short circuit SOA.
Asymptotically optimal delay-aware scheduling in wireless networks (2018)

In this paper, we investigate a channel allocation problem in networks taking into account the queues of users. Typically, there are less available channels than users, and at each slot the channels are allocated to users in such a way to minimize the total average queues in the network. We show that the problem falls in the framework of Restless Bandit Problems (RBP), for which obtaining the optimal solution is out of reach. This problem is analyzed in this paper using Whittle index approach. First, using the Lagrangian relaxation method, we provide a relaxed problem and show that it can be decomposed into simpler one-dimensional subproblems for which the optimal solution is a threshold-based policy. This allows us to characterize Whittle's indices for these one-dimensional systems and to develop an index-based heuristic policy for the original scheduling problem. We prove that this heuristic is asymptotically optimal in the infinitely many users regime and provide numerical results that illustrate its remarkably good performance.
Lack of β-methylamino-l-alanine in brain from controls, AD, or Chamorros with PDC (2005)

High levels of beta-methylamino-l-alanine (BMAA), a putative neurotoxin, have been reported in brain samples from Chamorros and patients with Alzheimer disease (AD) from western Canada. The authors assayed free BMAA in the brains of five control subjects and five patients with AD from the US Pacific Northwest as well as Chamorros with and without Parkinson-dementia complex. In contrast to others, they detected no free BMAA in any of these samples.
Ethernet OAM Overview: Making Ethernet Manageable. (2008)

This paper provides an overview of three important tools for Ethernet Operations, Administration, and Maintenance (OAM): Link-layer Ethernet OAM, Ethernet-Local Management Interface (E-LMI), and Service Layer Ethernet OAM – commonly referred to as “Connectivity Fault Management”.