gebhart/patrepeval huggingface dataset:
Identifying Controlling Nodes in Neuronal Networks in Different Scales (2012)

Recent studies have detected hubs in neuronal networks using degree, betweenness centrality, motif and synchronization and revealed the importance of hubs in their structural and functional roles. In addition, the analysis of complex networks in different scales are widely used in physics community. This can provide detailed insights into the intrinsic properties of networks. In this study, we focus on the identification of controlling regions in cortical networks of cats' brain in microscopic, mesoscopic and macroscopic scales, based on single-objective evolutionary computation methods. The problem is investigated by considering two measures of controllability separately. The impact of the number of driver nodes on controllability is revealed and the properties of controlling nodes are shown in a statistical way. Our results show that the statistical properties of the controlling nodes display a concave or convex shape with an increase of the allowed number of controlling nodes, revealing a transition in choosing driver nodes from the areas with a large degree to the areas with a low degree. Interestingly, the community Auditory in cats' brain, which has sparse connections with other communities, plays an important role in controlling the neuronal networks.
Tuning wettability and getting superhydrophobic surface by controlling surface roughness with well-designed microstructrures (2005)

We proposed a method to tune the wettability of a solid surface by changing its roughness. With specific designed micro square-pillar arrays, the apparent contact angle of a hydrophobic surface can be continuously adjusted from the intrinsic contact angle above. The samples were fabricated by combining silicon micromachining and self-assembled monolayer modification. The experimental results were closer to Cassie's theoretical predictions on the super-hydrophobic surfaces than that by Wenzel's. With the same contact angle (CA, 110/spl deg/) on the flat surface, the apparent CAs can be tuned from 110/spl deg/ to nearly 180/spl deg/. The largest apparent CA can be up to 173/spl deg/, with pillars of 9.08/spl mu/m /spl times/ 9.08/spl mu/m /spl times/ 16/spl mu/m ( width /spl times/ width /spl times/ height ) and the spacing of 31.61/spl mu/m.
Semicustom Design of Zigzag Power-Gated Circuits in Standard Cell Elements (2009)

Zigzag power gating (ZPG) can overcome the long wake-up delay of standard power gating, but its requirement for both nMOS and pMOS current switches, in a zigzag pattern, requires complicated power networks, limiting application to custom designs. We propose a design framework for cell-based semicustom design of ZPG circuits, using a new power network architecture that allows the unmodified conventional logic cells to be combined with custom circuitry such as ZPG flip-flops, input forcing circuits, and current switches. The design flow, from register transfer level description to layout, is described and applied to a 32-b microprocessor design using a 1.2-V 65-nm triple-well bulk CMOS process. The use of a sleep vector in ZPG requires additional switching power when entering standby mode and returning to active mode. The switching power should be minimized so that is does not outweigh the leakage saved by employing ZPG scheme. We formulate the selection of a sleep vector as a multiobjective optimization problem, minimizing both the transition energy and the total wirelength of a design. We solve the problem by employing multiobjective genetic-based algorithm. Experimental results show an average saving of 39% in transition energy and 8% in total wirelength for several benchmark circuits in 65-nm technology.
Sharoes: A Data Sharing Platform for Outsourced Enterprise Storage Environments (2008)

With fast paced growth of digital data and exploding storage management costs, enterprises are looking for new ways to effectively manage their data. One such cost-effective paradigm is the storage-as-a-service model, in which enterprises outsource their storage to a storage service provider (SSP) by storing data at a remote SSP-managed site and accessing it over a high speed network. Often for a variety of reasons, enterprises find it unacceptable to fully trust the SSP and prefer to store data in an encrypted form. This typically limits collaboration and data sharing among enterprise users due to complex key management and access control challenges. In this paper, we propose a platform called SHAROES that provides data sharing capability over such outsourced storage environments. SHAROES provide rich *nix-like data sharing semantics over SSP stored data, without trusting the SSP for data confidentiality or access control. SHAROES is unique in its ability in reducing user involvement during setup and operation through the use of in-band key management and allows a near-seamless transition of existing storage environments to the new model. It is also superior in performance by minimizing the use of expensive public-key cryptography in metadata management. We present the architecture and implementation of various SHAROES components and our experiments demonstrate performance superior to other proposals by over 40% on a number of benchmarks.
Scheduling Hadoop Jobs to Meet Deadlines (2010)

User constraints such as deadlines are important requirements that are not considered by existing cloud-based data processing environments such as Hadoop. In the current implementation, jobs are scheduled in FIFO order by default with options for other priority based schedulers. In this paper, we extend real time cluster scheduling approach to account for the two-phase computation style of MapReduce. We develop criteria for scheduling jobs based on user specified deadline constraints and discuss our implementation and preliminary evaluation of a Deadline Constraint Scheduler for Hadoop which ensures that only jobs whose deadlines can be met are scheduled for execution.
The Calcium-Dependent Switch Helix of L-Plastin Regulates Actin Bundling (2017)

L-plastin is a calcium-regulated actin-bundling protein that is expressed in cells of hematopoietic origin and in most metastatic cancer cells. These cell types are mobile and require the constant remodeling of their actin cytoskeleton, where L-plastin bundles filamentous actin. The calcium-dependent regulation of the actin-bundling activity of L-plastin is not well understood. We have used NMR spectroscopy to determine the solution structure of the EF-hand calcium-sensor headpiece domain. Unexpectedly, this domain does not bind directly to the four CH-domains of L-plastin. A novel switch helix is present immediately after the calcium-binding region and it binds tightly to the EF-hand motifs in the presence of calcium. We demonstrate that this switch helix plays a major role during actin-bundling. Moreover a peptide that competitively inhibits the association between the EF-hand motifs and the switch helix was shown to deregulate the actin-bundling activity of L-plastin. Overall, these findings may help to develop new drugs that target the L-plastin headpiece and interfere in the metastatic activity of cancer cells.
Multifunctional, Tunable Metal–Organic Framework Materials Platform for Bioimaging Applications (2017)

Herein, we describe a novel multifunctional metal-organic framework (MOF) materials platform that displays both porosity and tunable emission properties as a function of the metal identity (Eu, Nd, and tuned compositions of Nd/Yb). Their emission collectively spans the deep red to near-infrared (NIR) spectral region (∼614-1350 nm), which is highly relevant for in vivo bioimaging. These new materials meet important prerequisites as relevant to biological processes: they are minimally toxic to living cells and retain structural integrity in water and phosphate-buffered saline. To assess their viability as optical bioimaging agents, we successfully synthesized the nanoscale Eu analog as a proof-of-concept system in this series. In vitro studies show that it is cell-permeable in individual RAW 264.7 mouse macrophage and HeLa human cervical cancer tissue culture cells. The efficient discrimination between the Eu emission and cell autofluorescence was achieved with hyperspectral confocal fluorescence microscopy, used here for the first time to characterize MOF materials. Importantly, this is the first report that documents the long-term conservation of the intrinsic emission in live cells of a fluorophore-based MOF to date (up to 48 h). This finding, in conjunction with the materials' very low toxicity, validates the biocompatibility in these systems and qualifies them as promising for use in long-term tracking and biodistribution studies.
Interphase and Metaphase Resolution of Different Distances Within the Human Dystrophin Gene (1990)

Fluorescence in situ hybridization makes possible direct visualization of single sequences not only on chromosomes, but within decondensed interphase nuclei, providing a potentially powerful approach for high-resolution (1 Mb and below) gene mapping and the analysis of nuclear organization. Interphase mapping was able to extend the ability to resolve and order sequences up to two orders of magnitude beyond localization on banded or unbanded chromosomes. Sequences within the human dystrophin gene separated by less than 100 kb to 1 Mb were visually resolved at interphase by means of standard microscopy. In contrast, distances in the 1-Mb range could not be ordered on the metaphase chromosome length. Analysis of sequences 100 kb to 1 Mb apart indicates a strong correlation between interphase distance and linear DNA distance, which could facilitate a variety of gene-mapping efforts. Results estimate chromatin condensation up to 1 Mb and indicate a comparable condensation for different cell types prepared by different techniques.
Gene Conversion Within Regulatory Sequences Generates Maize <i>r</i> Alleles With Altered Gene Expression (2001)

The maize r locus encodes a transcription factor that regulates the developmental expression of the plant pigment anthocyanin. In an unusual example of gene regulatory diversity, the R-sc (Sc, strong seed color) and the R-p (P, plant color) alleles of r have nonoverlapping tissue specificity and nonhomologous 5' flanking sequences. Heterozygotes between wild-type P and Sc mutants with Ds6 transposable element inserts (r-sc:m::Ds6 or sc:m) produce colored seed derivatives (Sc+) during meiotic recombination. The sc:m alleles with Ds6 insertion in 3' regions of r produce crossover Sc+ derivatives. sc:m alleles with Ds6 elements inserted in 5' regions produce rare Sc+ derivatives borne on nonrecombinant chromosomes. Among 52 such noncrossover Sc+ derivatives, 18 are indistinguishable from the Sc progenitor in phenotype and DNA sequence [Scp(+) alleles]. The remaining 34 derivatives have strong Sc+ expression, including darkly pigmented aleurone, scutellum, coleoptile, and scutellar node [Scp(e) alleles]. The coleoptile and scutellar node phenotypes are unique from either progenitor but are similar to those of some naturally occurring r alleles. Both classes of Sc+ derivatives are explained by gene conversion between the promoter region of Sc:124 and a homologous region located proximal to P. The recombinational intermediate formed between sc:m alleles and P results in deletion of the Ds6 element alone or both Ds6 and a nearby unrelated transposable element-like sequence.
Compact modeling for the negative tone development processes (2017)

When the negative tone development (NTD) process was introduced into photolithography, it brought fidelity improvement with it. However, the NTD process behaves in a manner that is not readily comprehended by the computational techniques used to create high-speed photolithography models for use in the Optical Proximity Correction (OPC) process. These effects are mechanical in nature and are not governed by the diffraction phenomena used to create high speed process models. This study will discuss an attempt to utilize the high speed OPC model methods to deliver an accurate representation of the NTD process. This paper will discuss a compact modeling flow for NTD processes. The flow works to emulate first principle modeling techniques for NTD in an OPC model. This is accomplished through a combination of the new mechanical methods and traditional Dill’s parameters. It also reduces the data volume required to generate the OPC model. The models generated using this method accurately represent NTD SEM image contours. The results will be demonstrated and discussed.
Sense-Through-Wall Channel Modeling Using UWB Noise Radar (2009)

Sensing-through-wall will benefit various applications such as emergence rescues and military operations. In order to add more signal processing functionality, it is vital to understand the characterization of sense-through-wall channel. In this paper, we propose a statistical channel model on a basis of real experimental data using UWB noise radar. We employ CLEAN algorithm to obtain the multipath channel impulse response (CIR) and observe that the channel amplitude at each path can be accurately characterized as T location-scale distribution. We also analyze that the multipath contributions arrive at the receiver are grouped into clusters. The time of arrival of clusters can be modeled as a Poisson arrival process, while within each cluster, subsequent multipath contributions or rays also arrive according to a Poisson process. However, these arrival rates are much smaller than those of indoor UWB channels.
A Neural Network-Based Harmonic Suppression Algorithm for Medium-to-High Resolution ADCs (2021)

This paper proposes a novel high-precision ADC digital calibration algorithm based on neural network (NN). The algorithm is to suppress the harmonic distortion caused by the non-ideal factors in ADC. As a result, regardless of the non-ideal types, it can be universally used as a back-end calibration black box in various ADC structures. A 14-bit ADC with trained NN reaches more than 12.3-bit of ENOB in behavioral simulation. We also applied the NN to a practical 12-bit sigma-delta ADC and achieved a significant improvement of more than 1-bit of ENOB.
Preliminary results of a data acquisition subsystem for distributed, digital, computational, APD-based, dual-modality PET/CT architecture for small animal imaging (2005)

A new highly integrated data acquisition (DAQ) system for a combined, APD-based, dual-modality PET/CT scanner, implementing both analog and digital electronics on the same board, has been fabricated and tested. The DAQ system was designed to achieve high-precision (<1 ns) coincidence detection in PET and high-rate event counting in CT imaging using the same detectors and electronics. One DAQ board holds 64 parallel detector channels that can be sampled directly at the output of the charge-sensitive preamplifiers (CSP) at a rate of 100 MHz with free-running analog-to-digital converters (ADC) from Maxim. Digital signal processing is performed in field programmable gate arrays (FPGAs) from Xilinx. Independent 500 V voltage regulators are mounted on board for optimum biasing of individual APDs coupled to phoswich detectors. The DAQ board has been fabricated on a 12 copper layers printed circuit board (PCB). The low-noise analog front-end is directly interfaced on board through differential CSP outputs to the high-speed digital circuits for optimum coupling and noise immunity. The board shows excellent electrical characteristics with all circuitry powered up, featuring a mean signal to noise and distortion ratio (SINAD) of 47.7 dB over all 64 channels when supplied with a 10 MHz sine waveform at its input. Initial performance characteristics with BGO/LSO phoswich detectors are reported.
Cardiotoxicity of Anticancer Drugs: The Need for Cardio-Oncology and Cardio-Oncological Prevention (2009)

Due to the aging of the populations of developed countries and a common occurrence of risk factors, it is increasingly probable that a patient may have both cancer and cardiovascular disease. In addition, cytotoxic agents and targeted therapies used to treat cancer, including classic chemotherapeutic agents, monoclonal antibodies that target tyrosine kinase receptors, small molecule tyrosine kinase inhibitors, and even antiangiogenic drugs and chemoprevention agents such as cyclooxygenase-2 inhibitors, all affect the cardiovascular system. One of the reasons is that many agents reach targets in the microenvironment and do not affect only the tumor. Combination therapy often amplifies cardiotoxicity, and radiotherapy can also cause heart problems, particularly when combined with chemotherapy. In the past, cardiotoxic risk was less evident, but it is increasingly an issue, particularly with combination therapy and adjuvant therapy. Today's oncologists must be fully aware of cardiovascular risks to avoid or prevent adverse cardiovascular effects, and cardiologists must now be ready to assist oncologists by performing evaluations relevant to the choice of therapy. There is a need for cooperation between these two areas and for the development of a novel discipline, which could be termed cardio-oncology or onco-cardiology. Here, we summarize the potential cardiovascular toxicities for a range of cancer chemotherapeutic and chemopreventive agents and emphasize the importance of evaluating cardiovascular risk when patients enter into trials and the need to develop guidelines that include collateral effects on the cardiovascular system. We also discuss mechanistic pathways and describe several potential protective agents that could be administered to patients with occult or overt risk for cardiovascular complications.
Storageless value prediction using prior register values (1999)

This paper presents a technique called register value prediction (RVP) which uses a type of locality called register-value reuse. By predicting that an instruction will produce the value that is already stored in the destination register, we eliminate the need for large value buffers to enable value prediction. Even without the large buffers, register-value prediction can be made as or more effective than last-value prediction, particularly with the aid of compiler management of values in the register file.Both static and dynamic register value prediction techniques are demonstrated to exploit register-value reuse, the former requiring minimal instruction set architecture changes and the latter requiring a set of small confidence counters. We show an average gain of 12% with dynamic RVP and moderate compiler assistance on a next generation processor, and 15% on a 16-wide processor.
A torque-measuring micromotor provides operator independent measurements marking four different density areas in maxillae (2015)

The implant motor demonstrated to be a helpful tool to properly plan implant placement and loading irrespective of the operator using it.
Cleavage of RNA Hairpins Mediated by a Developmentally Regulated CCCH Zinc Finger Protein (1996)

Control of RNA turnover is a major, but poorly understood, aspect of gene regulation. In multicellular organisms, progress toward dissecting RNA turnover pathways has been made by defining some cis-acting sequences that function as either regulatory or cleavage targets (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993). However, the identification of genes encoding proteins that regulate or cleave target RNAs has been elusive (C. A. Beelman and R. Parker, Cell 81:79-183, 1995); this gap in knowledge has made it difficult to identify additional components of RNA turnover pathways. We have utilized a modified expression cloning strategy to identify a developmentally regulated gene from Drosophila melanogaster that encodes a RNase that we refer to as Clipper (CLP). Significant sequence matches to open reading frames encoding unknown functions identified from the Caenorhabditis elegans and Saccharomyces cerevisiae genome sequencing projects suggest that all three proteins are members of a new protein family conserved from lower eukaryotes to invertebrates. We demonstrate that a member of this new protein family specifically cleaves RNA hairpins and that this activity resides in a region containing five copies of a previously uncharacterized CCCH zinc finger motif. CLP's endoribonucleolytic activity is distinct from that associated with RNase A (P. Blackburn and S. Moore, p. 317-433, in P. D. Boyer, ed., The Enzymes, vol. XV, part B, 1982) and is unrelated to RNase III processing of rRNAs and tRNAs (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993, and S. A. Elela, H. Igel, and M. Ares, Cell 85:115-124, 1995). Our results suggest that CLP may function directly in RNA metabolism.
Sound transmission through the human body with digital weaver modulation (DWM) method (2014)

An innovative sound transmission system which transmits sound wirelessly to ears without making any other noise outside is suggested. The system utilizes the human body as a sound transmission medium. The human body is a nonlinear medium and the nonlinear characteristic is the basis of the theorem for the system. When two ultrasonic waves with different frequencies are transmitted into the body, the difference frequency signal between the two original ultrasonic waves is generated during the propagation process and audible to a user. In this paper, single sideband amplitude modulation (SSB AM) method is used as a modulation scheme. SSB AM method can minimize the noise which occurs in the process of generating audible sound. To make a SSB AM modulator with a higher degree of accuracy, digital weaver modulation (DWM) method is adopted. DWM method enables a sharp cutoff filter to be implemented without increasing computational complexity in the DSP. An Equalizer filter which compensates the distortions in the ultrasonic transducer is also designed. The developed system was evaluated with a loaf of beef instead of the human body, and generation of full-bandwidth music sound in the beef was demonstrated. If the proposed system is applied to the human body, sound transmission may be possible without cable line required in conventional earphones.
Galectin-1: A Jack-of-All-Trades in the Resolution of Acute and Chronic Inflammation (2017)

Regulatory signals provide negative input to immunological networks promoting resolution of acute and chronic inflammation. Galectin-1 (Gal-1), a member of a family of evolutionarily conserved glycan-binding proteins, displays broad anti-inflammatory and proresolving activities by targeting multiple immune cell types. Within the innate immune compartment, Gal-1 acts as a resolution-associated molecular pattern by counteracting the synthesis of proinflammatory cytokines, inhibiting neutrophil trafficking, targeting eosinophil migration and survival, and suppressing mast cell degranulation. Likewise, this lectin controls T cell and B cell compartments by modulating receptor clustering and signaling, thus serving as a negative-regulatory checkpoint that reprograms cellular activation, differentiation, and survival. In this review, we discuss the central role of Gal-1 in regulatory programs operating during acute inflammation, autoimmune diseases, allergic inflammation, pregnancy, cancer, and infection. Therapeutic strategies aimed at targeting Gal-1-glycan interactions will contribute to overcome cancer immunosuppression and reinforce antimicrobial immunity, whereas stimulation of Gal-1-driven immunoregulatory circuits will help to mitigate exuberant inflammation.