gebhart/patrepeval huggingface dataset:
OC-066 The Cancer Research UK (Cruk) Funded ICGC Oesophageal Adenocarcinoma Project: MRC Research Centre and Cruk Cambridge Research Institute (2013)

Introduction Esophageal adenocarcinoma (EAC) has one of the fastest rising incidences of any cancer in the western world. With a 5-year survival below 10% it is one of the most common causes of cancer death in US and UK. Currently little is understood about the genetic alterations that drive the development of OAC. Better understanding of these alterations may allow the development of novel therepeutic approaches Methods We have performed whole genome sequencing on 22 cases. Targeted amplicon resequencing of 27 recurrently mutated genes was performed on a validation cohort of 100 further oesophageal adenocarcinomas. Results In the discover set of 22 OACs we identified recurrent mutations (>3 tumours) in 31 genes including several implicated in tumorigenesis; TP53, CDKN2A, ARID1A. Strikingly in the validation cohort we observed that > 30% of EAC samples harbour mutation of one or both of the SWI/SNF complex members ARID1A and SMARCA4. In addition we identified highly recurrent mutations in several additional genes including TRIM58, SSTR4 and MYO18B. Conclusion Whole genome sequencing provides an unbiased screen of mutational architecture of OAC. This has allowed the identification of several recurrently mutated genes not previously implicated in this disease providing a unique insight to it’s pathogenesis Disclosure of Interest None Declared
Joint compensation of IQ imbalance and phase noise (2004)

Today a lot of effort is spent on developing inexpensive OFDM receivers. Especially, zero-IF receivers are very appealing, because they avoid costly IF filters. However, zero-IF front-ends introduce more front-end distortion such as IQ imbalance and phase noise. Unfortunately, OFDM is very sensitive to these receiver non-idealities. Therefore, we developed a new estimation/compensation scheme to jointly combat the IQ imbalance and phase noise at baseband, taking channel estimation into account. In this paper, we describe the algorithms and present the performance results. Our compensation scheme eliminates IQ imbalance based on one OFDM symbol and performs well in the presence of phase noise, the overall system performance is within 0.6 dB of the optimal case. As such, our estimation/compensation scheme greatly relaxes the mismatch specifications and enables low-cost zero-IF receivers.
Compact reversed field pinch (CRFP) reactor concept (1980)

The feasibility of a small 100 MWe reverse-field pinch reactor is discussed. Typical design parameters are described along with possible cost benefits. (MOW)
Binding of Dopamine D1 Receptor and Noradrenaline Transporter in Individuals with Autism Spectrum Disorder: A PET Study (2020)

Although previous studies have suggested the involvement of dopamine (DA) and noradrenaline (NA) neurotransmissions in the autism spectrum disorder (ASD) pathophysiology, few studies have examined these neurotransmissions in individuals with ASD in vivo. Here, we investigated DA D1 receptor (D1R) and noradrenaline transporter (NAT) binding in adults with ASD (n = 18) and neurotypical controls (n = 20) by utilizing two different PET radioligands, [11C]SCH23390 and (S,S)-[18F]FMeNER-D2, respectively. We found no significant group differences in DA D1R (striatum, anterior cingulate cortex, and temporal cortex) or NAT (thalamus and pons) binding. However, in the ASD group, there were significant negative correlations between DA D1R binding (striatum, anterior cingulate cortex and temporal cortex) and the "attention to detail" subscale score of the Autism Spectrum Quotient. Further, there was a significant positive correlation between DA D1R binding (temporal cortex) and emotion perception ability assessed by the neurocognitive battery. Associations of NAT binding with empathic abilities and executive function were found in controls, but were absent in the ASD group. Although a lack of significant group differences in binding might be partly due to the heterogeneity of ASD, our results indicate that central DA and NA function might play certain roles in the clinical characteristics of ASD.
Optimized pulsed write schemes improve linearity and write speed for low-power organic neuromorphic devices (2018)

Neuromorphic devices are becoming increasingly appealing as efficient emulators of neural networks used to model real world problems. However, no hardware to date has demonstrated the necessary high accuracy and energy efficiency gain over CMOS in both (1) training via backpropagation and (2) in read via vector matrix multiplication. Such shortcomings are due to device non-idealities, particularly asymmetric conductance tuning in response to uniform voltage pulse inputs. Here, by formulating a general circuit model for capacitive ion-exchange neuromorphic devices, we show that asymmetric nonlinearity in organic electrochemical neuromorphic devices (ENODes) can be suppressed by an appropriately chosen write scheme. Simulations based upon our model suggest that a nonlinear write-selector could reduce the switching voltage and energy, enabling analog tuning via a continuous set of resistance states (100 states) with extremely low switching energy (~170 fJ m -2 ). This work clarifies the pathway to neural algorithm accelerators capable of parallelism during both read and write operations.
Tissue‐Engineered Grafts for Bone and Meniscus Regeneration and Their Assessment Using MRI (2017)

Magnetic resonance imaging (MRI) is a noninvasive imaging modality with potential to visualize tissue injury, repair, replacement, and regeneration. In this chapter, we describe some of the technical advances of MRI used in tissue regeneration, with bone and meniscus as model systems. Development in MRI technologies has poised to improve imaging quality of hard and soft tissues, even for the information about macromolecules such as collagen and proteoglycans. Quantitative MRI is being developed with improved modalities for planning and outcomes of preclinical and clinical studies. The application of magnetic resonance (MR) images in the 3D modeling of bone and meniscus and relative prototype manufacturing is another important section of this chapter. The image data files of MRI can be extracted and used for computerized 3D anatomical modeling and prototyping. Tissue engineering has achieved prospective progress in both bone and meniscus regenerations. MRI as an imaging modality may enable preclinical evaluation; anatomical and medical modeling for surgical planning, preoperative planning and intraoperative planning; and postoperative tracking and evaluation.
Manufacturing Polarisation in Contemporary India: The Case of Identity Politics in Post-Left Bengal (2019)

This article explores ethnographically the manufacturing of religious polarisation and violence in West Bengal, India. Since 2014, India has experienced a rise in religion-based identity conflict. Although West Bengal experienced riots during the partition of India, it remained unaffected during the subsequent three decades of Left rule. More recently, however, secular democratic forces have been marginalised and riot-like conflicts have emerged. We argue that identity consolidation in West Bengal is part of an increasing trend of religious polarisation in the country. To bridge the gap between scholarly discussions on the concepts of secularism and communalisation, the paper presents micro-narratives illuminating the background of religious polarisation and violence. We provide ethnographic details of the mechanisms by which religious identities are consolidated. With a case-based approach, this article unearths the mechanisms of identity-based polarisation, and its politicisation in a region which has not experienced this level of violence for several decades.
Experimental validation of more realistic computer models for stent‐graft repair of abdominal aortic aneurysms, including pre‐load assessment (2016)

Although the endovascular repair of abdominal aortic aneurysms is a less invasive alternative than classic open surgery, complications such as endoleak and kinking still need to be addressed. Numerical simulation of endovascular repair is becoming a valuable tool in stent-graft (SG) optimization, patient selection and surgical planning. The experimental and numerical forces required to produce SG deformations were compared in a range of in vivo conditions in the present study. The deformation modes investigated were: bending as well as axial, transversal and radial compressions. In particular, an original method was developed to efficiently account for radial pre-load because of the pre-compression of stents to match the graft dimensions during manufacturing. This is important in order to compute the radial force exerted on the vessel after deployment more accurately. Variations of displacement between the experimental and numerical results ranged from 1.39% for simple leg bending to 5.93% for three-point body bending. Finally, radial pre-load was modeled by increasing Young's modulus of each stent. On average, it was found that Young's modulus had to be augmented by a factor of 2. Copyright © 2016 John Wiley & Sons, Ltd.
Dynamic Defense against Adaptive and Persistent Adversaries (2018)

This talk will cover two topics, namely, modeling and design of Moving Target Defense (MTD), and DIFT games for modeling Advanced Persistent Threats (APTs). We will first present a game-theoretic approach to characterizing the trade-off between resource efficiency and defense effectiveness in decoy- and randomization-based MTD. We will then address the game formulation for APTs. APTs are mounted by intelligent and resourceful adversaries who gain access to a targeted system and gather information over an extended period of time. APTs consist of multiple stages, including initial system compromise, privilege escalation, and data exfiltration, each of which involves strategic interaction between the APT and the targeted system. While this interaction can be viewed as a game, the stealthiness, adaptiveness, and unpredictability of APTs imply that the information structure of the game and the strategies of the APT are not readily available. Our approach to modeling APTs is based on the insight that the persistent nature of APTs creates information flows in the system that can be monitored. One monitoring mechanism is Dynamic Information Flow Tracking (DIFT), which taints and tracks malicious information flows through a system and inspects the flows at designated traps. Since tainting all flows in the system will incur significant memory and storage overhead, efficient tagging policies are needed to maximize the probability of detecting the APT while minimizing resource costs. In this work, we develop a multi-stage stochastic game framework for modeling the interaction between an APT and a DIFT, as well as designing an efficient DIFT-based defense. Our model is grounded on APT data gathered using the Refinable Attack Investigation (RAIN) flow-tracking framework. We present the current state of our formulation, insights that it provides on designing effective defenses against APTs, and directions for future work.
A virtualization architecture for wireless network cards (2006)

This doctoral dissertation describes the design and applications of a new virtualization architecture for wireless network cards, called MultiNet. MultiNet virtualizes a single wireless card to appear as multiple virtual wireless cards to the user. Each virtual card can then be configured separately on a physically different network. The goal of MultiNet is to provide a user-level illusion of simultaneous connectivity on all virtual cards although the network card is on a single network at any instant. MultiNet achieves this transparency using intelligent buffering and switching algorithms. The switching and buffering mechanisms are implemented as a kernel driver, while the policies are implemented as a user-level service. The MultiNet system has been implemented over Windows XP and has been operational for over two years. It is agnostic of the upper layer protocols, and works well over popular IEEE 802.11 wireless LAN cards. Further, MultiNet enables a new class of applications, which were earlier only possible with multiple wireless cards in the device. This dissertation describes two such applications: Slotted Seeded Channel Hopping (SSCH) and Client Conduit. 
SSCH is a new channel hopping protocol that works over MultiNet, and utilizes frequency diversity to increase the capacity of IEEE 802.11 wireless networks. Each node using SSCH switches across channels in such a manner that nodes desiring to communicate overlap, while disjoint communications do not overlap, and hence do not interfere with each other. To achieve this, SSCH uses a novel scheme for distributed rendezvous and synchronization. Simulation results show that SSCH significantly increases network capacity in several multihop and single hop wireless networking scenarios. 
Client Conduit is a novel technique for providing connectivity to disconnected wireless clients with the help of nearby connected clients. It is based on MultiNet and takes advantage of the beaconing and probing mechanisms of IEEE 802.11 to ensure that connected clients do not pay unnecessary overheads while helping disconnected clients. Client Conduit has been implemented over Windows XP as part of an architecture for diagnosing faults in wireless networks.
Abstract LB-1: Discovery and optimization of orally bioavailable, selective and potent ATP-independent Akt inhibitors (2012)

Abstract Herein we describe the implementation of a biochemical and biophysical screening strategy to discover small molecules that inhibit Akt through a mechanism distinct from ATP-competitive inhibitors. A series of novel derivatives of the core scaffold 3H-imidazo[4,5-b]pyridine were identified and optimized. These Akt inhibitors demonstrated potent inhibition of intracellular Akt and downstream targets including PRAS40 activation in vitro. Pharmacodynamic and pharmacokinetic studies in vivo demonstrated the effectiveness of the series at inhibiting the activation of Akt and an additional downstream effector (p70S6) following oral dosing in mice. Co-crystallization studies with un-phosphorylated Akt1 revealed that as a consequence of binding these novel, potent and selective, ATP-independent inhibitors the ATP binding cleft is occupied by non-polar residues which are associated as tight clusters. The cleft is closed with a ‘hydrophobic lock’ which may function to sterically exclude the binding of both ATP and ATP-competitive inhibitors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-1. doi:1538-7445.AM2012-LB-1
Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study (2017)

HSV-2 dual-strain infection was detected in 3.7% of paired samples from individual participants, and was more frequent among people with HIV infection. Simulations suggest that the true prevalence of dual-strain infection is 7%. Our data indicate that naturally occurring immunity to HSV-2 may be protective against infection with a second strain. This study is limited by the inability to determine the timing of acquisition of the second strain.
On compression with two-way head machines (2002)

Motivated by the study of various kinds of machines as recognizers of formal languages, the authors compare the encoding and decoding power of finite state sequential machines and extensions thereof. They show that, with a forward moving head, the best compression achievable for a given sequence, to be decoded by a finite state decoder, is the same as the best ratio attainable for that sequence when encoded by a finite state information lossless encoder. They cannot gain in compression by allowing a finite state encoder to move its head back and forth on an input sequence, even if the decoder has unrestricted power. However, better compression can be achieved for specific infinite sequences using an unrestricted encoder and a two-way finite state decoder.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Komplexchemie reaktiver organischer Verbindungen, XXIV. Fünfgliedrige Cobaltacyclen durch Carben‐Addition an Dicarbonyl‐(η 5 ‐cyclopentadienyl)cobalt (1979)

Durch Photolyse der Diazomalonsäure-dialkylester 2a–g in Gegenwart von Dicarbonyl-(η5-cyclopentadienyl)cobalt (1) in Tetrahydrofuran sind die Cobaltacyclen 3a–g zugänglich. Die Bildung der neuen, am Beispiel von 3c auch röntgenstrukturanalytisch gesicherten Verbindungen ist formal das Ergebnis einer [2 + 3]-Cycloaddition der von den Diazo-Vorstufen 2a–g abgeleiteten Carbene an das Organometall-Substrat 1. Unter Öffnung des metallacyclischen Strukturelements sind die cyclischen Cobalt-Derivate 3a–g bei thermischer Umsetzung mit 1 in die zweikernigen μ-Methylen-Cobalt-Komplexe 4a–g überführbar. Complex Chemistry of Reactive Organic Compounds, XXIV. Five-Membered Cobalta Cycles from Carbene Addition to Dicarbonyl (η5-cyclopentadienyl)cobalt Photolysis of the dialkyl diazomalonates 2a–g in the presence of dicarbonyl(η5-cyclopentadienyl)cobalt (1) in tetrahydrofuran yields the cobalta cycles 3a–g. The formation of the new compounds, established by X-ray structural determination on the case of 3c, can be explained formally as a result of a [2 + 3]-cycloaddition of the carbenes derived from the diazo precursors 2a–g to the organometallic substrate 1. The cyclic cobalt compounds 3a–g are converted by a thermal reaction with 1 through opening of the metalla cyclic structural element into the dinuclear μ-methylene cobalt compounds 4a–g.
Studies of the 6.7 family of dispersed genomic fragments within the MHC class I Region. (1997)

Searches for MHC-encoded disease susceptibility genes have led to considerable knowledge of the content of the class I region. In an effort to further understand the nature of the five 6.7 family members previously mapped to this region of the genome, we have further analyzed the cross-reactive members of the family and have observed additional genomic instability within the HLA-A subregion. Such genomic variation may underscore the slower evolutionary rates of the HLA-A allelic family and the extended linkage disequilibrium of markers distal to this locus. Moreover, one of the largest genes associated with a member of the 6.7 family, the 3.8-1 gene found proximal to HLA-B, was found to demonstrate limited, composite similarity to RAG2 and complement C4a gene sequences. A pancreas-specific transcript embedded in a 6.7 cross-reactive fragment was found distal to HLA-H and suggests that the fragments have remained linked to transcriptionally active chromatin comprised of both a major class I gene and a second novel coding sequence since the time of their dispersal. The absence of a 6.7 fragment in the HLA-B subregions of higher nonhuman primates lends credence to the possibility that the great apes have suffered a recent deletion event within this region following the emergence of Homo sapiens.
4.2.3 - H2S-Dosimeter mit einstellbarer Schaltschwelle auf Basis von Kupferoxid Halbleiterschichten (2016)

von Kupferoxid Halbleiterschichten Christoph Seitz1, Giuliana Beck1, Jorg Hennemann1, Christian Kandzia2, Philipp Hering2, Angelika Polity2, Andrej Paul3, Thorsten Wagner3, Stefanie Russ4 und Bernd Smarsly1 1Justus-Liebig-Universitat Giesen, Physikalisch Chemisches Institut, Heinrich-Buff-Ring 17, 35392 Giesen, Tel.: 0049-641-34590, E-Mail: Bernd.Smarsly@phys.chemie.uni-giessen.de 2Justus-Liebig-Universitat Giesen, Institut fur Angewandte Physik, Heinrich-Buff-Ring 16, 35392 Giesen 3Universitat Paderborn, Naturwissenschaftliche Fakultat, Department Chemie, Warburger Strase 100, 33098 Paderborn 4Freie Universitat Berlin, Fachbereich Physik, Arnimallee 14, 14195 Berlin
Reduction of Matrix Metallopeptidase 13 and Promotion of Chondrogenesis by Zeel T in Primary Human Osteoarthritic Chondrocytes (2021)

<b>Objectives:</b> Zeel T (Ze14) is a multicomponent medicinal product. Initial preclinical data suggested a preventive effect on cartilage degradation. Clinical observational studies demonstrated that Ze14 reduced symptoms of osteoarthritis (OA), including stiffness and pain. This study aimed to explore these effects further to better understand the mode of action of Ze14 on human OA chondrocytes <i>in vitro</i>. <b>Methods:</b> Primary chondrocytes were obtained from the knees of 19 OA patients and cultured either as monolayers or in alginate beads. The cultures were treated with 20% or 10% (v/v) Ze14 or placebo. For RNA-seq, reads were generated with Illumina NextSeq5000 sequencer and aligned to the human reference genome (UCSC hg19). Differential expression analysis between Ze14 and placebo was performed in R using the DESeq2 package. Protein quantification by ELISA was performed on selected genes from the culture medium and/or the cellular fractions of primary human OA chondrocyte cultures. <b>Results:</b> In monolayer cultures, Ze14 20% (v/v) significantly modified the expression of 13 genes in OA chondrocytes by at least 10% with an adjusted <i>p</i>-value < 0.05: EGR1, FOS, NR4A1, DUSP1, ZFP36, ZFP36L1, NFKBIZ, and CCN1 were upregulated and ATF7IP, TXNIP, DEPP1, CLEC3A, and MMP13 were downregulated after 24 h Ze14 treatment. Ze14 significantly increased (mean 2.3-fold after 24 h, <i>p</i> = 0.0444 and 72 h, <i>p</i> = 0.0239) the CCN1 protein production in human OA chondrocytes. After 72 h, Ze14 significantly increased type II collagen pro-peptide production by mean 27% (<i>p</i> = 0.0147). For both time points CCN1 production by OA chondrocytes was correlated with aggrecan (r = 0.66, <i>p</i> = 0.0004) and type II collagen pro-peptide (r = 0.64, <i>p</i> = 0.0008) production. In alginate beads cultures, pro-MMP-13 was decreased by Ze14 from day 7-14 (from -16 to -25%, p < 0.05) and from day 17-21 (-22%, <i>p</i> = 0.0331) in comparison to controls. <b>Conclusion:</b> Ze14 significantly modified the expression of DUSP1, DEPP1, ZFP36/ZFP36L1, and CLEC3A, which may reduce MMP13 expression and activation. Protein analysis confirmed that Ze14 significantly reduced the production of pro-MMP-13. As MMP-13 is involved in type II collagen degradation, Ze14 may limit cartilage degradation. Ze14 also promoted extracellular matrix formation arguably through CCN1 production, a growth factor well correlated with type II collagen and aggrecan production.
Reversible helical electromagnetic launchers for time acceleration waveform replication (2014)

A 750 mm barrel length × 40 mm bore diameter hollow projectile, reversible helical electromagnetic launcher (RHEML) is evaluated for its ability to produce a negative acceleration (i.e., a “jerk”). The RHEML projectile and payload weighs approximately 750 grams and will travel with velocity up to 100 m/s. A 450 kJ multiple-module capacitive pulse forming network (PFN) with the ability to provide both positive and negative voltage and current is used to power the RHEML launcher. Special precautions must be taken when designing this type of PFN and RHEML. Theoretical and practical design guidelines for this type of PFN are presented and discussed. The results of the systematic experimental approach taken to generate and evaluate the transient current waveforms is presented and analyzed. Results show the reversible HEML is able to produce a negative jerk and travel in the opposite direction.