gebhart/patrepeval huggingface dataset:
14 The presence of diabetes as a comorbidity adversely affects the phenotypic expression of hypertrophic cardiomyopathy (2021)

<h3>Background</h3> Type 2 diabetes mellitus (DM) is associated with worsened clinical outcomes in hypertrophic cardiomyopathy (HCM) patients, although the mechanisms of this association are incompletely understood. <h3>Objectives</h3> Utilizing <sup>31</sup>Phosphorus magnetic resonance spectroscopy (<sup>31</sup>P-MRS) and cardiovascular magnetic resonance (CMR) in a prospective observational study of groups of patients with concomitant HCM and DM (HCM-DM), isolated HCM, isolated DM and healthy volunteers (HV), we tested the hypotheses that the collective impact of HCM and DM on the myocardium aggravates myocardial energetic impairment, contractile dysfunction, and fibrosis, and impairs coronary microvascular function. <h3>Methods</h3> Seventy-five age- and sex-matched participants were recruited (20 HCM-DM, 20 HCM, 20 DM and 15 HV). HCM groups were matched for HCM phenotype. DM groups were matched for diabetes treatment, duration and HbA1c. <h3>Results</h3> ESC sudden cardiac death risk scores were comparable between the HCM groups (HCM:2.2±1.5%, HCM-DM:1.9±1.2%; p=NS) and sarcomeric mutations were equally common. HCM-DM had the highest NT-proBNP levels (HV:42 ng/L[IQR:35–66 ng/L], DM:118 ng/L[IQR:53–187 ng/L], HCM:298 ng/L[IQR:157–837 ng/L], HCM-DM:726 ng/L[IQR:213–8695 ng/L]; p&lt;0.0001). Left-ventricular ejection fraction, mass and wall thickness were similar between the HCM groups. HCM-DM displayed a greater degree of fibrosis burden with higher extracellular volume fraction and scar percentage, more significant reductions in global longitudinal strain and left atrial function compared to the isolated HCM. PCr/ATP was similarly decreased in the HCM-DM and DM (HV:2.17±0.49, DM:1.58±0.27, HCM:1.93±0.38, HCM-DM:1.54±0.27; p=0.0002). HCM-DM had the lowest stress myocardial blood flow (HV:2.06±0.42 ml/min/g, DM:1.95±0.41 ml/min/g, HCM:1.74±0.44 ml/min/g, HCM-DM:1.39±0.42 ml/min/g; p=0.0017). <h3>Conclusions</h3> Comorbid diabetes adversely affects the HCM phenotype with greater reductions in myocardial energetics, perfusion, strain, increased scar burden and higher NT-proBNP levels compared to isolated HCM. Our findings suggest that specific, targeted therapeutic approaches may be useful in hypertrophic cardiomyopathy patients with diabetes comorbidity to improve clinical outcomes.
FK506-binding protein-like and FK506-binding protein 8 regulate dual leucine zipper kinase degradation and neuronal responses to axon injury (2022)

The dual leucine zipper kinase (DLK) is a key regulator of axon regeneration and degeneration in response to neuronal injury; however, regulatory mechanisms of the DLK function via its interacting proteins are largely unknown. To better understand the molecular mechanism of DLK function, we performed yeast two-hybrid screening analysis and identified FK506-binding protein-like (FKBPL, also known as WAF-1/CIP1 stabilizing protein 39) as a DLK-binding protein. FKBPL binds to the kinase domain of DLK and inhibits its kinase activity. In addition, FKBPL induces DLK protein degradation through ubiquitin-dependent pathways. We further assessed other members in the FKBP protein family and found that FK506-binding protein 8 (FKBP8) also induced DLK degradation. We identified the lysine 271 residue in the kinase domain as a major site of DLK ubiquitination and SUMO3 conjugation and was thus responsible for regulating FKBP8-mediated proteasomal degradation that was inhibited by the substitution of the lysine 271 to arginine. FKBP8-mediated degradation of DLK is mediated by autophagy pathway because knockdown of Atg5 inhibited DLK destabilization. We show that in vivo overexpression of FKBP8 delayed the progression of axon degeneration and suppressed neuronal death after axotomy in sciatic and optic nerves. Taken together, this study identified FKBPL and FKBP8 as novel DLK-interacting proteins that regulate DLK stability via the ubiquitin-proteasome and lysosomal protein degradation pathways.
CCDC 840800: Experimental Crystal Structure Determination (2012)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Solving Infeasibility Problems in Computerized Test Assembly (1998)

Linear programming techniques have been used successfully in a variety of test assembly problems. It is, however, possible that no test can be found meeting all the constraints in the linear programming model. The problem of diagnosing and repairing infeasible linear programming models is discussed. It is demonstrated that it is possible to localize the causes of infeasibility.
Atypical Protein Kinase C Regulates Primary Dendrite Specification of Cerebellar Purkinje Cells by Localizing Golgi Apparatus (2010)

Neurons have highly polarized structures that determine what parts of the soma elaborate the axon and dendrites. However, little is known about the mechanisms that establish neuronal polarity in vivo. Cerebellar Purkinje cells extend a single primary dendrite from the soma that ramifies into a highly branched dendritic arbor. We used the zebrafish cerebellum to investigate the mechanisms by which Purkinje cells acquire these characteristics. To examine dendritic morphogenesis in individual Purkinje cells, we marked the cell membrane using a Purkinje cell-specific promoter to drive membrane-targeted fluorescent proteins. We found that zebrafish Purkinje cells initially extend multiple neurites from the soma and subsequently retract all but one, which becomes the primary dendrite. In addition, the Golgi apparatus specifically locates to the root of the primary dendrite, and its localization is already established in immature Purkinje cells that have multiple neurites. Inhibiting secretory trafficking through the Golgi apparatus reduces dendritic growth, suggesting that the Golgi apparatus is involved in the dendritic morphogenesis. We also demonstrated that in a mutant of an atypical protein kinase C (aPKC), Prkci, Purkinje cells retain multiple primary dendrites and show disrupted localization of the Golgi apparatus. Furthermore, a mosaic inhibition of Prkci in Purkinje cells recapitulates the aPKC mutant phenotype. These results suggest that the aPKC cell autonomously controls the Golgi localization and thereby regulates the specification of the primary dendrite of Purkinje cells.
Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food (2012)

These data provide important knowledge for the identification and computational prediction of functional motifs related to programmed cell death. Potential implications of these findings include the use of engineered probiotic interventions in food or use of a natural probiotic cocktail with specificity for controlling targeted foodborne pathogens.
Threading DNA through nanopores for biosensing applications (2015)

This review outlines the recent achievements in the field of nanopore research. Nanopores are typically used in single-molecule experiments and are believed to have a high potential to realize an ultra-fast and very cheap genome sequencer. Here, the various types of nanopore materials, ranging from biological to 2D nanopores are discussed together with their advantages and disadvantages. These nanopores can utilize different protocols to read out the DNA nucleobases. Although, the first nanopore devices have reached the market, many still have issues which do not allow a full realization of a nanopore sequencer able to sequence the human genome in about a day. Ways to control the DNA, its dynamics and speed as the biomolecule translocates the nanopore in order to increase the signal-to-noise ratio in the reading-out process are examined in this review. Finally, the advantages, as well as the drawbacks in distinguishing the DNA nucleotides, i.e., the genetic information, are presented in view of their importance in the field of nanopore sequencing.
Multi-tenancy in Cloud Computing (2014)

As Cloud Computing becomes the trend of information technology computational model, the Cloud security is becoming a major issue in adopting the Cloud where security is considered one of the most critical concerns for the large customers of Cloud (i.e. governments and enterprises). Such valid concern is mainly driven by the Multi-Tenancy situation which refers to resource sharing in Cloud Computing and its associated risks where confidentiality and/or integrity could be violated. As a result, security concerns may harness the advancement of Cloud Computing in the market. So, in order to propose effective security solutions and strategies a good knowledge of the current Cloud implementations and practices, especially the public Clouds, must be understood by professionals. Such understanding is needed in order to recognize attack vectors and attack surfaces. In this paper we will propose an attack model based on a threat model designed to take advantage of Multi-Tenancy situation only. Before that, a clear understanding of Multi-Tenancy, its origin and its benefits will be demonstrated. Also, a novel way on how to approach Multi-Tenancy will be illustrated. Finally, we will try to sense any suspicious behavior that may indicate to a possible attack where we will try to recognize the proposed attack model empirically from Google trace logs. Google trace logs are a 29-day worth of data released by Google. The data set was utilized in reliability and power consumption studies, but not been utilized in any security study to the extent of our knowledge.
Fully quantified spectral imaging revealsin vivomembrane protein interactions (2016)

Here we introduce the fully quantified spectral imaging (FSI) method as a new tool to probe the stoichiometry and stability of protein complexes in biological membranes. The FSI method yields two dimensional membrane concentrations and FRET efficiencies in native plasma membranes. It can be used to characterize the association of membrane proteins: to differentiate between monomers, dimers, or oligomers, to produce binding (association) curves, and to measure the free energies of association in the membrane. We use the FSI method to study the lateral interactions of Vascular Endothelial Growth Factor Receptor 2 (VEGFR2), a member of the receptor tyrosine kinase (RTK) superfamily, in plasma membranes, in vivo. The knowledge gained through the use of the new method challenges the current understanding of VEGFR2 signaling.
Sustaining an Industry Obsession (2002)

Device scaling has long been an acceptedmantra,even an obsession, in the semiconductor industry, and if recent predictions are true, the march of deep-submicron (DSM)devicesinto the nanoscale era will continue.Process anddevice engineers will somehow find a way toovercome the looming technical challenges, justlike they always have from the earliest MOS technology days. Long-range planning, such as thatreflected in the International TechnologyRoadmap for Semiconductors, has only accelerated this trend. However,device scaling has a fundamental business purpose:either a cost advantage or a performance--and, therefore, price--advantage.At some point, the migrationof process technology nodes becomes a returnon investment (ROI)issue with direct consequences for the rest of the microelectronicsindustry.For design and test engineers, application developers, and system builders, maintaining the historic ROI for the semiconductorindustry often means doing more with less.
On the Security of Ultrasound as Out-of-band Channel (2007)

Ultrasound has been proposed as out-of-band channel for authentication of peer devices in wireless ad hoc networks. Ultrasound can implicitly contribute to secure communication based on inherent limitations in signal propagation, and can additionally be used explicitly by peers to measure and verify their relative positions. In this paper we analyse potential attacks on an ultrasonic communication channel and peer-to-peer ultrasonic sensing, and investigate how potential attacks translate to application-level threats for peers seeking to establish a secure wireless link. Based on our analysis we propose a novel method for authentic communication of short messages over an ultrasonic channel.
Proceedings of the 2002 ACM SIGMOD international conference on Management of data (2002)

The 2002 ACM SIGMOD International Conference on Management of Data, was held June 4-6, 2002 at the spectacular Frank Lloyd Wright-designed Monona Terrace conference center in Madison, Wisconsin. The SIGMOD conference has long held its status a leading forum for database researchers, practitioners, developers, and users to explore cutting-edge ideas and to exchange techniques, tools, and experiences. This year we are pleased to have a particularly strong program, including significant representation from both industry and academia and contributions from around the world. The SIGMOD conference is sponsored by the Association for Computing Machinery (ACM) and its Special Interest Group on Management of Data (SIGMOD). As has become customary, two days of the conference were overlapped with the Symposium on Principles of Database Systems (PODS). In addition, there were a number of important events co-located with SIGMOD this year, including the 5th International Workshop on the Web and Databases (WebDB), the Workshop on Research Issues in Data Mining and Knowledge Discovery (DMKD), and the New Database Faculty Symposium.As with previous years, acceptance into the conference proceedings was extremely competitive. From the 240 research program submissions, the program committee selected 42 papers for presentation and inclusion in the proceedings. These papers span the range of traditional database topics as well as issues of emerging interest such as data streaming, middle-tier data management, and integration with web services and the WWW. The: program committee worked hard to select these papers through a detailed review process and active discussion both electronically and at the program committee meeting held in January at Berkeley. We are deeply indebted to Surajit Chaudhuri and Jonathan Simon for their efforts in developing and hosting the Conference Management Tool at Microsoft. We used the CMT to run the entire submissions and review process for research papers, including the program committee meeting. We would also like to thank Umesh Dayal, who took on extra work to help manage the review process.In addition to the research track, we had 41 submissions to the Demonstrations track, of which 21 projects were invited to present. The Demonstrations track has become a key venue for the early dissemination of cutting-edge prototype and systems development experience. Paul Aoki chaired the demos program committee, which put together a diverse and exciting program. The Industrial program committee, chaired by Mike Carey took an active role in soliciting quality submissions and have put together a program that is a key component of this year's conference. Likewise, Donald Kossmann and Peter Scheuermann and the tutorial committee organized an excellent slate of Panels and Tutorials to round out the program.
Protein Arginine Methyltransferase 3 Enhances Chemoresistance in Pancreatic Cancer by Methylating hnRNPA1 to Increase ABCG2 Expression (2018)

Pancreatic cancer is poorly responsive to chemotherapy due to intrinsic or acquired resistance. Our previous study showed that epigenetic modifying enzymes including protein arginine methyltransferase 3 (PRMT3) are dysregulated in gemcitabine (GEM)-resistant pancreatic cancer cells. Here, we attempt to elucidate the role of PRMT3 in chemoresistance. Overexpression of PRMT3 led to increased resistance to GEM in pancreatic cancer cells, whereas reduction of PRMT3 restored GEM sensitivity in resistant cells. We identified a novel PRMT3 target, ATP-binding cassette subfamily G member 2 (ABCG2), which is known to play a critical role in drug resistance. PRMT3 overexpression upregulated ABCG2 expression by increasing its mRNA stability. Mass spectrometric analysis identified hnRNPA1 as a PRMT3 interacting protein, and methylation of hnRNPA1 at R31 by PRMT3 in vivo and in vitro. The expression of methylation-deficient hnRNPA1-R31K mutant reduced the RNA binding activity of hnRNPA1 and the expression of ABCG2 mRNA. Taken together, this provides the first evidence that PRMT3 methylates the RNA recognition motif (RRM) of hnRNPA1 and promotes the binding between hnRNPA1 and ABCG2 to enhance drug resistance. Inhibition of PRMT3 could be a novel strategy for the treatment of GEM-resistant pancreatic cancer.
Linearity of p MOS radiation dosimeters operated at zero bias (1985)

A new mode of operation of pMOS radiation dosimeters is explored, using zero applied oxide field. Over a certain dose range, a linear dependence of response against dose was found. Charge pumping currents and threshold voltages were measured as a function of dose.
Scene Segmentation With Dual Relation-Aware Attention Network (2020)

In this article, we propose a Dual Relation-aware Attention Network (DRANet) to handle the task of scene segmentation. How to efficiently exploit context is essential for pixel-level recognition. To address the issue, we adaptively capture contextual information based on the relation-aware attention mechanism. Especially, we append two types of attention modules on the top of the dilated fully convolutional network (FCN), which model the contextual dependencies in spatial and channel dimensions, respectively. In the attention modules, we adopt a self-attention mechanism to model semantic associations between any two pixels or channels. Each pixel or channel can adaptively aggregate context from all pixels or channels according to their correlations. To reduce the high cost of computation and memory caused by the abovementioned pairwise association computation, we further design two types of compact attention modules. In the compact attention modules, each pixel or channel is built into association only with a few numbers of gathering centers and obtains corresponding context aggregation over these gathering centers. Meanwhile, we add a cross-level gating decoder to selectively enhance spatial details that boost the performance of the network. We conduct extensive experiments to validate the effectiveness of our network and achieve new state-of-the-art segmentation performance on four challenging scene segmentation data sets, i.e., Cityscapes, ADE20K, PASCAL Context, and COCO Stuff data sets. In particular, a Mean IoU score of 82.9% on the Cityscapes test set is achieved without using extra coarse annotated data.
A cached WORM file system (1991)

Abstract This paper describes a general‐purpose file system that uses a write‐once‐read‐many (WORM) optical disk accessed via a magnetic disk cache. The cache enables blocks to be modified a number of times before they are written to the WORM and increases performance. Snapshots of the file system can be made at any time without limiting the users' access to files. These snapshots reside entirely on the WORM, are accessible to the user via a second read‐only file system, do not contain multiple copies of unchanged data, and can be used to rebuild the file system in the event that the disk cache is destroyed. The file system has been implemented as part of Plan 9, an experimental operating system under development at AT&amp;T Bell Laboratories.
TCP-aware scheduling in LTE networks (2014)

Designing scheduling algorithms that work in synergy with TCP is a challenging problem in wireless networks. Extensive research on scheduling algorithms has focused on inelastic traffic, where there is no correlation between traffic dynamics and scheduling decisions. In this work, we study the performance of several scheduling algorithms in LTE networks, where the scheduling decisions are intertwined with wireless channel fluctuations to improve the system throughput. We use ns-3 simulations to study the performance of several scheduling algorithms with a specific focus on Max Weight (MW) schedulers with both UDP and TCP traffic, while considering the detailed behavior of OFDMA-based resource allocation in LTE networks. We show that, contrary to its performance with inelastic traffic, MW schedulers may not perform well in LTE networks in the presence of TCP traffic, as they are agnostic to the TCP congestion control mechanism. We then design a new scheduler called “Queue MW” (Q-MW) which is tailored specifically to TCP dynamics by giving higher priority to TCP flows whose queue at the base station is very small in order to encourage them to send more data at a faster rate. We have implemented Q-MW in ns-3 and studied its performance in a wide range of network scenarios in terms of queue size at the base station and round-trip delay. Our simulation results show that Q-MW achieves peak and average throughput gains of 37% and 10% compared to MW schedulers if tuned properly.
Emergence of Slow-Switching Assemblies in Structured Neuronal Networks (2015)

Unraveling the interplay between connectivity and spatio-temporal dynamics in neuronal networks is a key step to advance our understanding of neuronal information processing. Here we investigate how particular features of network connectivity underpin the propensity of neural networks to generate slow-switching assembly (SSA) dynamics, i.e., sustained epochs of increased firing within assemblies of neurons which transition slowly between different assemblies throughout the network. We show that the emergence of SSA activity is linked to spectral properties of the asymmetric synaptic weight matrix. In particular, the leading eigenvalues that dictate the slow dynamics exhibit a gap with respect to the bulk of the spectrum, and the associated Schur vectors exhibit a measure of block-localization on groups of neurons, thus resulting in coherent dynamical activity on those groups. Through simple rate models, we gain analytical understanding of the origin and importance of the spectral gap, and use these insights to develop new network topologies with alternative connectivity paradigms which also display SSA activity. Specifically, SSA dynamics involving excitatory and inhibitory neurons can be achieved by modifying the connectivity patterns between both types of neurons. We also show that SSA activity can occur at multiple timescales reflecting a hierarchy in the connectivity, and demonstrate the emergence of SSA in small-world like networks. Our work provides a step towards understanding how network structure (uncovered through advancements in neuroanatomy and connectomics) can impact on spatio-temporal neural activity and constrain the resulting dynamics.
No-Contact Penetrating Radar for Cultural Heritage Applications: a Case Study in Palazzo Vecchio (Firenze) (2004)

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