gebhart/patrepeval huggingface dataset:
Stereoselective Synthesis of N‐Glycosyl Amino Acids by Traceless Staudinger Ligation of Unprotected Glycosyl Azides (2009)

Abstract The stereoconservative Staudinger ligation of unprotectedα‐ and β‐glycosyl azides with 2‐(diphenylphosphanyl)‐4‐fluorophenyl esters to afford α‐ and β‐ N ‐glycosyl amino acids is described. The ligation method works reliably well for unprotected β‐azides of the gluco , galacto and fuco series. Lower yields (ca. 50 %) were obtained with a β‐glucosyl‐ N ‐acetyl azide. The reaction of an α‐glucosyl azide also led to major improvements compared with the use of non‐fluorinated phosphanes. All the N ‐glycosyl amino acid products can be isolated and byproducts removed from the crude reaction mixtures by simple water extraction.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
The Expanding Therapeutic Armamentarium for Inflammatory Bowel Disease: How to Choose the Right Drug[s] for Our Patients? (2017)

The therapeutic landscape for inflammatory bowel disease [IBD] is rapidly evolving. Two new biologic drugs, vedolizumab and ustekinumab, have recently entered the marketplace, the first biosimilars have been introduced, and several other agents are at an advanced stage of clinical development. In parallel, therapeutic goals have shifted from symptom control towards mucosal healing and prevention of bowel damage. In the coming years, gastroenterologists will be faced with unprecedented choices when selecting the best treatment for their patients with IBD. In this article, we review existing data on the mechanisms of action, efficacy, and safety of recently approved and late-stage pipeline therapies, and use this information to speculate on the positioning of these drugs, alone or in combination, in therapeutic algorithms for Crohn's disease and ulcerative colitis.
Integer-pel Motion Estimation specific instructions and their hardware architecture for ASIP (2011)

This paper proposes Integer-pel Motion Estimation (IME) specific instructions and their hardware architecture for Application Specific Instruction-set Processor (ASIP). With parallel SAD Processing Elements (PEs) using pattern information, the proposed IME instruction supports not only the full search algorithm but also various fast search algorithms. Moreover, the revisiting prevention technique enables that the proposed ASIP can efficiently perform the fast search operations. The gate count is 43K gates for each Processing Element Group (PEG) which has 256 SAD PEs. The proposed ASIP with eight PEGs runs at 160MHz and can handle 1080p@30 frames in real-time.
Modeling, Simulation and Control Strategy Optimization of Fuel Cell Hybrid Electric Vehicle (2023)

This work represents the development of a Fuel Cell Hybrid Electric Vehicle (FCHEV) model, its validation, and the comparison of different control strategies based on the Toyota Mirai (1st generation) vehicle and its subsystems. The main investigated parameters are hydrogen consumption, and the variation of the state of charge, current, and voltage of the battery. The FCHEV model, which is made up of multiple subsystems, is developed and simulated in MATLAB® Simulink environment using a rule-based control strategy derived from the real system. The results of the model were validated using the experimental data obtained from the open-source Argonne National Laboratory (ANL) database. In the second part, the equivalent consumption minimization strategy is implemented into the controller logic to optimize the existing control strategy and investigate the difference in hydrogen consumption. It was found that the ECMS control strategy outperforms the rule-based one in all drive cycles by 0.4–15.6%. On the other hand, when compared to the real controller, ECMS performs worse for certain considered driving cycles and outperforms others.
Genomic Flexibility of Human Endogenous Retrovirus Type K (2014)

ABSTRACT Human endogenous retrovirus type K (HERV-K) proviruses are scattered throughout the human genome, but as no infectious HERV-K virus has been detected to date, the mechanism by which these viruses replicated and populated the genome remains unresolved. Here, we provide evidence that, in addition to the RNA genomes that canonical retroviruses package, modern HERV-K viruses can contain reverse-transcribed DNA (RT-DNA) genomes. Indeed, reverse transcription of genomic HERV-K RNA into the DNA form is able to occur in three distinct times and locations: (i) in the virus-producing cell prior to viral release, yielding a DNA-containing extracellular virus particle similar to the spumaviruses; (ii) within the extracellular virus particle itself, transitioning from an RNA-containing particle to a DNA-containing particle; and (iii) after entry of the RNA-containing virus into the target cell, similar to canonical retroviruses, such as murine leukemia virus and HIV. Moreover, using a resuscitated HERV-K virus construct, we show that both viruses with RNA genomes and viruses with DNA genomes are capable of infecting target cells. This high level of genomic flexibility historically could have permitted these viruses to replicate in various host cell environments, potentially assisting in their many integration events and resulting in their high prevalence in the human genome. Moreover, the ability of modern HERV-K viruses to proceed through reverse transcription and package RT-DNA genomes suggests a higher level of replication competency than was previously understood, and it may be relevant in HERV-K-associated human diseases. IMPORTANCE Retroviral elements comprise at least 8% of the human genome. Of all the endogenous retroviruses, HERV-K viruses are the most intact and biologically active. While a modern infectious HERV-K has yet to be found, HERV-K activation has been associated with cancers, autoimmune diseases, and HIV-1 infection. Thus, determining how this virus family became such a prevalent member of our genome and what it is capable of in its current form are of the utmost importance. Here, we provide evidence that HERV-K viruses currently found in the human genome are able to proceed through reverse transcription and historically utilized a life cycle with a surprising degree of genomic flexibility in which both RNA- and DNA-containing viruses were capable of mediating infection.
Integrated-Phased-Array-Based Visible-Light Near-Eye Holographic Projector (2019)

An integrated-phased-array-based visible-light holographic projector is proposed as a scalable solution towards the next generation of augmented-reality head-mounted displays. A passive pixel-based architecture is developed and projection of a wire-frame cube is experimentally demonstrated © 2019 The Author(s)
Data from Identification and Characterization of Tyrosine Kinase Nonreceptor 2 Mutations in Leukemia through Integration of Kinase Inhibitor Screening and Genomic Analysis (2023)

&lt;div&gt;Abstract&lt;p&gt;The amount of genomic information about leukemia cells currently far exceeds our overall understanding of the precise genetic events that ultimately drive disease development and progression. Effective implementation of personalized medicine will require tools to distinguish actionable genetic alterations within the complex genetic landscape of leukemia. In this study, we performed kinase inhibitor screens to predict functional gene targets in primary specimens from patients with acute myeloid leukemia and chronic myelomonocytic leukemia. Deep sequencing of the same patient specimens identified genetic alterations that were then integrated with the functionally important targets using the HitWalker algorithm to prioritize the mutant genes that most likely explain the observed drug sensitivity patterns. Through this process, we identified tyrosine kinase nonreceptor 2 (TNK2) point mutations that exhibited oncogenic capacity. Importantly, the integration of functional and genomic data using HitWalker allowed for prioritization of rare oncogenic mutations that may have been missed through genomic analysis alone. These mutations were sensitive to the multikinase inhibitor dasatinib, which antagonizes TNK2 kinase activity, as well as novel TNK2 inhibitors, XMD8-87 and XMD16-5, with greater target specificity. We also identified activating truncation mutations in other tumor types that were sensitive to XMD8-87 and XMD16-5, exemplifying the potential utility of these compounds across tumor types dependent on TNK2. Collectively, our findings highlight a more sensitive approach for identifying actionable genomic lesions that may be infrequently mutated or overlooked and provide a new method for the prioritization of candidate genetic mutations. &lt;i&gt;Cancer Res; 76(1); 127–38. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Spiral Air-Coupled Ultrasonic Phased Array for High Resolution 3D Imaging (2020)

Spiral-shaped phased arrays are widely used for sound source localization and are trending in other fields, e.g. 3D medical ultrasound imaging. The non-uniform element geometry allows grating lobe free beamforming without an inter-element spacing of half wavelength. We demonstrate the 3D imaging capabilities of an air-coupled ultrasonic 40-kHz phased array based on 64 Murata MA40S4S transducers, spirally arranged on a 200 mm aperture. The 3D image is generated by sequentially transmitting beamformed pulses in discrete directions and capturing the corresponding echo signals, using all transducers. The GPU accelerated array signal processing consists of matched filtering, conventional beamforming and envelope extraction. The origins of the echos are visualized in B-Scans and 3D-Scans using OpenGL. We characterize the far-field transmit and receive directivity patterns, as well as the angular resolution in an anechoic chamber. The main lobe widths and maximum side lobe levels of the transmit (2.6°, -11.5 dB), the receive (2.6°, -11.6 dB) and the ideal model directivity patterns (2.4°, -13.4 dB) are in good agreement. Two laterally positioned rods (Ø10 mm) are separately detectable with an angular resolution of 2.3 °. The localization of multiple scatterers at the same range (2 m) is demonstrated by a test pattern of corner reflectors. Overall, the spiral array allows highly directional sound beam steering and localization, making it ideal for imaging and other in-air applications.
Computational and Experimental Evidence of Through‐Space NMR Spectroscopic J Coupling of Hydrogen Atoms (2011)

J coupling in NMR spectroscopy is conventionally associated with covalent bonds. A noncovalent contribution often called through-space coupling (TSC) has been observed for heavy atoms. In this study, the TSC was detected and analyzed for the more common (1)H-(1)H coupling as well. In synthesized model molecules the hydrogen positions could be well controlled. For several coupling constants the through-space mechanism was even found to be the predominant factor. The nature and magnitude of the phenomenon were also analyzed by density functional computations. Calculated carbon- and hydrogen-coupling maps and perturbed electronic densities suggest that the aromatic system strongly participates in the noncovalent contribution. Unlike covalent coupling, which is usually governed by the Fermi contact, TSC is dominated by the diamagnetic term comprising interactions of nuclei with the electron orbital angular momentum. The computations further revealed a strong distance and conformational dependence of TSC. This suggests that the through-space coupling can be explored in molecular structural studies in the same way as the covalent one.
Data from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;Histopathologic analysis through biopsy has been one of the most useful methods for the assessment of malignant neoplasms. However, some aspects of the analysis such as invasiveness, evaluation range, and turnaround time from biopsy to report could be improved. Here, we report a novel method for visualizing human cervical tissue three-dimensionally, without biopsy, fixation, or staining, and with sufficient quality for histologic diagnosis. Near-infrared excitation and nonlinear optics were employed to visualize unstained human epithelial tissues of the cervix uteri by constructing images with third-harmonic generation (THG) and second-harmonic generation (SHG). THG images enabled evaluation of nuclear morphology in a quantitative manner with six parameters after image analysis using deep learning. It was also possible to quantitatively assess intraepithelial fibrotic changes based on SHG images and another deep learning analysis. Using each analytical procedure alone, normal and cancerous tissue were classified quantitatively with an AUC ≥0.92. Moreover, a combinatory analysis of THG and SHG images with a machine learning algorithm allowed accurate classification of three-dimensional image files of normal tissue, intraepithelial neoplasia, and invasive carcinoma with a weighted kappa coefficient of 0.86. Our method enables real-time noninvasive diagnosis of cervical lesions, thus constituting a potential tool to dramatically change early detection.&lt;/p&gt;Significance:&lt;p&gt;This study proposes a novel method for diagnosing cancer using nonlinear optics, which enables visualization of histologic features of living tissues without the need for any biopsy or staining dye.&lt;/p&gt;&lt;/div&gt;
Wytyczne ESC dotyczące stymulacji serca i terapii resynchronizującej w 2013 roku (2013)

Rady ESC: Cardiology Practice Niniejsze wytyczne Europejskiego Towarzystwa Kardiologicznego (ESC) opublikowano wyłącznie do użytku prywatnego w celach edukacyjnych.Nie zezwala się na ich wykorzystywanie w celach komercyjnych.Żadna część wytycznych ESC nie może być przetłumaczona ani kopiowana w żadnej postaci bez wcześniejszej pisemnej
Transplantation Tolerance (2004)

Organ transplantation is now firmly established as the therapy of choice for end-stage organ failure. Specific immunological tolerance of transplant recipients towards their foreign organ or tissue grafts is a goal that has been sought by transplant biologists for almost 50 years following the original description of the phenomenon in experimental animals by Medawar and colleagues. Since that time, a wealth of experimental data has accumulated relating to strategies for extending allograft survival and function. Recent studies have shed new light on the molecular and cellular basis of transplant rejection and have better defined the mechanisms of allograft tolerance with particular emphasis on a role for regulatory T cells. Still, the question remains of how near we are to the day when long-term tolerance of engrafted organs or tissues will be a clinical reality. Recently, clinical trials to explore pilot tolerance protocols in humans have been initiated under the auspices of the Immune Tolerance Network (www.immunetolerance.org). In this review we will highlight the promise and challenges of making transplantation tolerance a clinical reality.
Genomic and transcriptomic characterisation of undifferentiated pleomorphic sarcoma of bone (2018)

Abstract Undifferentiated pleomorphic sarcoma of bone (UPSb) is a rare primary bone sarcoma that lacks a specific line of differentiation. There is very little information about the genetic alterations leading to tumourigenesis or malignant transformation. Distinguishing between UPSb and other malignant bone sarcomas, including dedifferentiated chondrosarcoma and osteosarcoma, can be challenging due to overlapping features. To explore the genomic and transcriptomic landscape of UPSb tumours, whole‐exome sequencing (WES) and RNA sequencing (RNA‐Seq) were performed on UPSb tumours. All tumours lacked hotspot mutations in IDH1/2 132 or 172 codons, thereby excluding the diagnosis of dedifferentiated chondrosarcoma. Recurrent somatic mutations in TP53 were identified in four of 14 samples (29%). Moreover, recurrent mutations in histone chromatin remodelling genes, including H3F3A , ATRX and DOT1L , were identified in five of 14 samples (36%), highlighting the potential role of deregulated chromatin remodelling pathways in UPSb tumourigenesis. The majority of recurrent mutations in chromatin remodelling genes identified here are reported in COSMIC, including the H3F3A G34 and K36 hotspot residues. Copy number alteration analysis identified gains and losses in genes that have been previously altered in UPSb or UPS of soft tissue. Eight somatic gene fusions were identified by RNA‐Seq, two of which, CLTC‐VMP1 and FARP1‐STK24 , were reported previously in multiple cancers. Five gene fusions were genomically characterised. Hierarchical clustering analysis, using RNA‐Seq data, distinctly clustered UPSb tumours from osteosarcoma and other sarcomas, thus molecularly distinguishing UPSb from other sarcomas. RNA‐Seq expression profiling analysis and quantitative reverse transcription‐polymerase chain reaction showed an elevated expression in FGF23 , which can be a potential molecular biomarker for UPSb. To our knowledge, this study represents the first comprehensive WES and RNA‐Seq analysis of UPSb tumours revealing novel protein‐coding recurrent gene mutations, gene fusions and identifying a potential UPSb molecular biomarker, thereby broadening the understanding of the pathogenic mechanisms and highlighting the possibility of developing novel targeted therapeutics. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.
Exciton Dynamics in (6,5) Carbon Nanotubes (2008)

Relaxation dynamics in carbon nanotubes, measured by transient absorption spectroscopy, are shown to exhibit stretched exponential behavior. The power dependence of the zero time delay signal is shown to behave as a two level system.
Abstract 130: Discovery and characterization of small molecules targeting the DNA-binding ETS domain of ERG in prostate cancer (2017)

Abstract Genomic alterations involving translocations of the ETS-related gene ERG occur in approximately half of prostate cancer cases. These alterations result in aberrant, androgen-regulated production of ERG protein variants that directly contribute to disease development and progression. This study describes the discovery and characterization of a new class of small molecule ERG antagonists identified through rational in silico methods. These antagonists are designed to sterically block DNA binding by the ETS domain of ERG and thereby disrupt transcriptional activity. We confirmed the direct binding of a lead compound, VPC-18005, with the ERG-ETS domain using biophysical approaches. We then demonstrated VPC-18005 reduced migration and invasion rates of ERG expressing prostate cancer cells, and reduced metastasis in a zebrafish xenograft model. These results demonstrate proof-of-principal that small molecule targeting of the ERG ETS domain can suppress transcriptional activity and reverse transformed characteristics of prostate cancers aberrantly expressing ERG. Clinical advancement of the developed small molecule inhibitors may provide new therapeutic agents for use as alternatives to, or in combination with, current therapies for men with ERG-expressing metastatic castration-resistant prostate cancer. Citation Format: Miriam S. Butler, Mani Roshan-Moniri, Michael Hsing, Desmond Lau, Ari Kim, Paul Yen, Marta Mroczek, Mannan Nouri, Scott Lien, Peter Axerio-Cilies, Kush Dalal, Clement Yau, Fariba Ghaidi, Yubin Guo, Takeshi Yamazaki, Sam Lawn, Martin Gleave, Cheryl Y. Gregory-Evans, Lawrence P. McIntosh, Paul S. Rennie, Artem Cherkasov, Michael E. Cox. Discovery and characterization of small molecules targeting the DNA-binding ETS domain of ERG in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 130. doi:10.1158/1538-7445.AM2017-130
ThrottleBot - Performance without Insight (2017)

Large scale applications are increasingly built by composing sets of microservices. In this model the functionality for a single application might be split across 100s or 1000s of microservices. Resource provisioning for these applications is complex, requiring administrators to understand both the functioning of each microservice, and dependencies between microservices in an application. In this paper we present ThrottleBot, a system that automates the process of determining what resource when allocated to which microservice is likely to have the greatest impact on application performance. We demonstrate the efficacy of our approach by applying ThrottleBot to both synthetic and real world applications. We believe that ThrottleBot when combined with existing microservice orchestrators, e.g., Kubernetes, enables push-button deployment of web scale applications.
Monolithically integrated quantum dot optical modulator with semiconductor optical amplifier for thousand and original band optical communication (2016)

Abstract A monolithically integrated quantum dot (QD) optical gain modulator (OGM) with a QD semiconductor optical amplifier (SOA) was successfully developed with T-band (1.0 µm waveband) and O-band (1.3 µm waveband) QD optical gain materials for Gbps-order, high-speed optical data generation. The insertion loss due to coupling between the device and the optical fiber was effectively compensated for by the SOA section. It was also confirmed that the monolithic QD-OGM/SOA device enabled &gt;4.8 Gbps optical data generation with a clear eye opening in the T-band. Furthermore, we successfully demonstrated error-free 4.8 Gbps optical data transmissions in each of the six wavelength channels over a 10-km-long photonic crystal fiber using the monolithic QD-OGM/SOA device in multiple O-band wavelength channels, which were generated by the single QD gain chip. These results suggest that the monolithic QD-OGM/SOA device will be advantageous in ultra-broadband optical frequency systems that utilize the T+O-band for short- and medium-range optical communications.
Bioluminescent Monitoring of Islet Graft Survival after Transplantation (2004)

Islet transplantation offers a potential therapy to restore glucose homeostasis in type 1 diabetes patients. A method to image transplanted islets noninvasively and repeatedly would greatly assist studies of islet transplantation. Using recombinant adenovirus, we show that isolated rodent and human islets can be genetically engineered to express luciferase and then imaged after implantation into NOD-scid mice using a cooled charge-coupled device. The magnitude of the signal was dependent on the islet dose. Adenovirus-directed luciferase expression, however, rapidly attenuated. We next tested lentivirus vectors that should direct the long-term expression of reporter genes in transduced islets. Transplanted lentivirus-transduced islets restored euglycemia long term in streptozotocin-treated NOD-scid mice. The signal from implanted lentivirus-transduced islets was related directly to the implanted islet mass, and the signal did not attenuate over the observation period. Viral transduction, luciferase expression, and repeated imaging had no apparent long-term deleterious effects on islet function after implantation. These data demonstrate that the introduction of reporter genes into an isolated tissue allows the long-term monitoring of its survival following implantation. Such imaging technologies may allow earlier detection of graft rejection and the adjustment of therapies to prolong graft survival posttransplantation.
SRAF를 적용한 극자외선 노광기술용 위상 변위 마스크의 반사도에 따른 이미징 특성 연구 (2015)

이 논문은 한국 정부 (MSIP)에서 후원하는 한국연구재단 (National Research Foundation of Korea,NRF) 의 기초연구 사업 (Grant No.2011-0028570) 및 KLA-Tencor사의 PROLITHTM에 의하여 지원되었음.