gebhart/patrepeval huggingface dataset:
Sequence and expression analysis of gaps in human chromosome 20 (2012)

The finished human genome-assemblies comprise&#13;\nseveral hundred un-sequenced euchromatic gaps,&#13;\nwhich may be rich in long polypurine/polypyrimidine&#13;\nstretches. Human chromosome 20 (chr 20) currently&#13;\nhas three unfinished gaps remaining on its q-arm.&#13;\nAll three gaps are within gene-dense regions and/or&#13;\noverlap disease-associated loci, including the&#13;\nDLGAP4 locus. In this study, we sequenced ~99%&#13;\nof all three unfinished gaps on human chr 20,&#13;\ndetermined their complete genomic sizes and&#13;\nassessed epigenetic profiles using a combination&#13;\nof Sanger sequencing, mate pair paired-end&#13;\nhigh-throughput sequencing and chromatin, methylation&#13;\nand expression analyses. We found histone 3&#13;\ntrimethylated at Lysine 27 to be distributed across&#13;\nall three gaps in immortalized B-lymphocytes. In one&#13;\ngap, five novel CpG islands were predominantly&#13;\nhypermethylated in genomic DNA from peripheral&#13;\nblood lymphocytes and human cerebellum. One of&#13;\nthese CpG islands was differentially methylated and&#13;\npaternally hypermethylated. We found all chr 20&#13;\ngaps to comprise structured non-coding RNAs&#13;\n(ncRNAs) and to be conserved in primates. We&#13;\nverified expression for 13 candidate ncRNAs, some&#13;\nof which showed tissue specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated&#13;\nexpression in the human brain. Our data suggest&#13;\nthat unfinished human genome gaps are likely to&#13;\ncomprise numerous functional elements.
Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage (2015)

Living organisms have adapted to atmospheric dioxygen by exploiting its oxidizing power while protecting themselves against toxic side effects. Reactive oxygen and nitrogen species formed during oxidative stress, as well as high-potential reactive intermediates formed during enzymatic catalysis, could rapidly and irreversibly damage polypeptides were protective mechanisms not available. Chains of redox-active tyrosine and tryptophan residues can transport potentially damaging oxidizing equivalents (holes) away from fragile active sites and toward protein surfaces where they can be scavenged by cellular reductants. Precise positioning of these chains is required to provide effective protection without inhibiting normal function. A search of the structural database reveals that about one third of all proteins contain Tyr/Trp chains composed of three or more residues. Although these chains are distributed among all enzyme classes, they appear with greatest frequency in the oxidoreductases and hydrolases. Consistent with a redox-protective role, approximately half of the dioxygen-using oxidoreductases have Tyr/Trp chain lengths ≥3 residues. Among the hydrolases, long Tyr/Trp chains appear almost exclusively in the glycoside hydrolases. These chains likely are important for substrate binding and positioning, but a secondary redox role also is a possibility.
NC-Audit: Auditing for network coding storage (2012)

Network coding-based storage has recently received a lot of attention in the network coding community. Independently, another body of work has proposed integrity checking schemes for cloud storage, none of which, however, is customized for network coding storage or can efficiently support repair. In this work, we bridge the gap between these currently disconnected bodies of work, and we focus on the (novel) advantage of network coding for integrity checking. We propose NC-Audit - a remote data integrity checking scheme, designed specifically for network coding-based storage cloud. NC-Audit provides a unique combination of desired properties: (i) efficient checking of data integrity (ii) efficient support for repairing failed nodes (iii) full support for modification of outsourced data and (iv) protection against information leakage when checking is performed by a third party. The key ingredient of the design of NC-Audit is a novel combination of SpaceMac, a homomorphic MAC scheme for network coding, and NCrypt, a novel CPA-secure encryption scheme that is compatible with SpaceMac. Our evaluation of a Java implementation of NC-Audit shows that an audit costs the storage node and the auditor only a few milliseconds of computation time, and lower bandwidth than prior work.
Biological Properties of IDN5174, a New Synthetic Camptothecin with the Open Lactone Ring (2006)

A series of water-soluble camptothecins obtained by linking a spermidine moiety to the 21-position of the open form through an amidic bond have been tested for their biochemical and biological activities. Growth inhibition assay on the human non-small cell lung cancer carcinoma NCI-H460 cell line revealed that the camptothecin analogues were less potent than topotecan and SN38 after 1 hour of treatment. The potency increased after 72 hours of exposure, being similar to that of reference camptothecins. The analysis of topoisomerase I-mediated DNA cleavage using the purified enzyme indicated that the novel camptothecin analogues retained ability to poison topoisomerase I and displayed the same cleavage pattern of SN38. Persistence of the DNA cleavage was comparable with that of SN38. Stabilization of the cleavable complex was not the result of hydrolysis of the N-C bond between polyamine and the drug because no free camptothecin was recovered at the end of DNA cleavage in presence of IDN5174, the analogue selected for detailed studies. IDN5174 exhibited an antitumor activity comparable with that of topotecan and irinotecan against NCI-H460 tumor xenograft. The pharmacokinetics in mice showed a favorable disposition in tumor tissue with low amount of camptothecin detectable in plasma and tumor (around 5-10%), thus supporting the efficacy of intact IDN5174. In conclusion, we found that IDN5174 maintained the biological and antitumor properties, in spite of lack of the closed E ring. The available results support the interpretation that the polyamine linked at the 21-position may allow a favorable drug interaction in the ternary complex.
Compact Design of an Electrically Tunable and Rotatable Polarizer Based on a Liquid Crystal Photonic Bandgap Fiber (2009)

In this letter, a compact electrically controlled broadband liquid crystal (LC) photonic bandgap fiber polarizer is designed and fabricated. A good fiber coupling quality between two single-mode fibers and one 10-mm-long LC-filled photonic crystal fiber is obtained and protected by using SU-8 fiber fixing structures during the device assembly. The total insertion loss of this all-in-fiber device is 2.7 dB. An electrically tunable polarization extinction ratio of 21.3 dB is achieved with 45deg rotatable transmission axis as well as switched on and off in the wavelength range of 1300-1600 nm.
Influence of the Kerr-Nonlinearity in MDM Transmission Systems Scaling with the Number of Modes in Dependence of the Core Radius (2018)

Scaling the radius of graded-index multimode fibers, while keeping the refractive index difference between the core and the cladding constant, is a promising approach to adjust the number of modes in multimode fibers. With an increasing number of modes, more modes are involved in the nonlinear coupling induced by the Kerr-nonlinearity. This potentially increases the nonlinear impairments. However, the nonlinear coefficient g decreases at the same time due to increasing effective areas. We investigate by numerical simulations which one of the two effects is dominating and clarify if the nonlinear impairments are increased or even reduced with an increasing capacity.
Wafer-surface flattening control using a wafer deforming chuck driven by piezoelectric actuators. (1989)

A wafer-surface flattening technique has been developed to improve patterning accuracy of VLSI fabrication systems. The technique is especially applicable to X-ray exposure systems. This paper presents the wafer-surface flattening method, including a wafer deforming chuck and its operating system, as well as an evaluation of the system accuracy. The wafer deforming chuck is designed so that a wafer held onto an elastically deformable plate by vacuum suction is flattened by controlling the heights of piezoelectric actuators underneath the deformable plate based on flatness error measured by an electrostatic displacement detector. A unique open loop voltage control method to improve wafer flattening accuracy by eliminating the displacement error due to hysteresis in the piezoelectric actuators is also discussed. The experimental results show this method is capable of flattening a wafer-surface to within ±0.5 μm of a perfect plane, independent of wafer size.
Microbial Ligninolysis: Toward a Bottom-Up Approach for Lignin Upgrading (2018)

Lignin, an underutilized source of biomass, is a challenging target for decomposition by both biological and nonbiological approaches. As lignin accounts for 15-40% of the dry weight of lignocellulose, its conversion to valued chemicals is considered promising. Although depolymerization of the complicated lignin structures is still not fully understood, biochemical reactions for various lignin-derived compounds, especially dimeric and monomeric aromatics, have been characterized in some fungi and bacteria known as natural lignin degraders. Synthetic biology, as a useful tool for exploring and engineering biosystems, could be used for protein design and constructing biosynthetic pathways for lignin utilization and upgrading. Understanding mechanisms of ligninolysis will facilitate synthetic biology implementation. In this Perspective, fungal and bacterial biochemical mechanisms for breaking lignin linkages, degrading monomers, and cleaving aromatic rings are examined, whereas enabling valued chemical biosynthesis from lignin-derived compounds via synthetic biology approaches is emphasized. On the basis of the advances in enzyme discovery and metabolic reconstruction, we propose a bottom-up approach to developing microbial platforms for producing valued chemicals from lignin sources.
Method for deploying and recovering a wave energy converter (2023)

A system for transporting a buoy and a heave plate. The system includes a buoy and a heave plate. An outer surface of the buoy has a first geometrical shape. A surface of the heave plate has a geometrical shape complementary to the first geometrical shape of the buoy. The complementary shapes of the buoy and the heave plate facilitate coupling of the heave plate to the outer surface of the buoy in a transport mode.
CDNF and MANF regulate ER stress in a tissue-specific manner (2022)

Cerebral dopamine neurotrophic factor (CDNF) and mesencephalic astrocyte-derived neurotrophic factor (MANF) display cytoprotective effects in animal models of neurodegenerative diseases. These endoplasmic reticulum (ER)-resident proteins belong to the same protein family and function as ER stress regulators. The relationship between CDNF and MANF function, as well as their capability for functional compensation, is unknown. We aimed to investigate these questions by generating mice lacking both CDNF and MANF. Results showed that CDNF-deficient Manf<sup>-/-</sup> mice presented the same phenotypes of growth defect and diabetes as Manf<sup>-/-</sup> mice. In the muscle, CDNF deficiency resulted in increased activation of unfolded protein response (UPR), which was aggravated when MANF was ablated. In the brain, the combined loss of CDNF and MANF did not exacerbate UPR activation caused by the loss of MANF alone. Consequently, CDNF and MANF deficiency in the brain did not cause degeneration of dopamine neurons. In conclusion, CDNF and MANF present functional redundancy in the muscle, but not in the other tissues examined here. Thus, they regulate the UPR in a tissue-specific manner.
Design and analysis of network codes (2005)

The information theoretic aspects of large networks with many terminals present several interesting and non-intuitive phenomena. One such crucial phenomenon was first explored in a detailed manner in the excellent work [1]. It compared two paradigms for operating a network one in which interior nodes were restricted to only copying and forwarding incoming messages on outgoing links, and another in which internal nodes were allowed to perform non-trivial arithmetic operations on incoming links to generate information on outgoing links. It showed that the latter approach could substantially improve throughput compared to the more traditional scenario. Further work by various authors showed how to design codes (called network codes ) to transmit under this new paradigm and also demonstrated exciting new properties of these codes such as distributed design, increased security, and robustness against network failures. 
In this work, we consider the low-complexity design and analysis of network codes, with a focus on codes for multicasting information. We examine both centralized and decentralized design of such codes, and also both randomized and deterministic design algorithms. We compare different notions of linearity and show the interplay between these notions in the design of linear network codes. We determine bounds on complexity of network codes. We also consider the problem of error-correction and secrecy for network codes when a malicious adversary controls some subset of the network resources.
Optical distortion correction using radial basis function interpolation (2012)

Optical distortion is often not corrected in compact optical systems prompting the need for post-processing distortion correction. We propose a distortion correction algorithm using radial basis functions and demonstrate real-time distortion correction.
Cell environment shapes TDP-43 function with implications in neuronal and muscle disease (2022)

TDP-43 (TAR DNA-binding protein 43) aggregation and redistribution are recognised as a hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. As TDP-43 inclusions have recently been described in the muscle of inclusion body myositis patients, this highlights the need to understand the role of TDP-43 beyond the central nervous system. Using RNA-seq, we directly compare TDP-43-mediated RNA processing in muscle (C2C12) and neuronal (NSC34) mouse cells. TDP-43 displays a cell-type-characteristic behaviour targeting unique transcripts in each cell-type, which is due to characteristic expression of RNA-binding proteins, that influence TDP-43's performance and define cell-type specific splicing. Among splicing events commonly dysregulated in both cell lines, we identify some that are TDP-43-dependent also in human cells. Inclusion levels of these alternative exons are altered in tissues of patients suffering from FTLD and IBM. We therefore propose that TDP-43 dysfunction contributes to disease development either in a common or a tissue-specific manner.
Transition States for Oxidative Addition to Three-Coordinate Ir(I): H-H, C-H, C-C, and C-F Bond Activation Processes (1999)

We have examined elementary oxidative addition reactions involving the Ir(PH3)2X (X = Cl, H, Li, BH2, NH2, F, Ph) system and small substrates such as dihydrogen (H2), methane (CH4) and fluoromethanes (CH3F, CHF3, CF4), and ethane (C2H6). Electronic structure calculations employed the B3LYP hybrid density functional, an effective core potential on the metal atom, and basis sets of valence double-zeta or better quality. H-H and, in some cases, C-H bond activation occurs with no apparent or only modest activation energy barriers. The cleavage of C-F bonds, in contrast, requires surmounting a sometimes substantial activation energy barrier as does C-C cleavage, even though these addition reactions are also thermodynamically favorable. A substituent effect study shows that π-donation from the ancillary ligand X favors the addition reaction, whereas σ-donation from X is unfavorable.
Synthetic approaches to cationic silylene-, germylene-, and stannylene-transition metal complexes via halide ion abstraction (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic approaches to cationic silylene-, germylene-, and stannylene-transition metal complexes via halide ion abstractionTobin J. Marks and Afif M. SeyamCite this: Inorg. Chem. 1974, 13, 7, 1624–1627Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://pubs.acs.org/doi/10.1021/ic50137a016https://doi.org/10.1021/ic50137a016research-articleACS PublicationsRequest reuse permissionsArticle Views266Altmetric-Citations34LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Injection locked oscillator based RF transmitters (2006)

In this paper a new concept of RF transmitter dedicated to low-power low-voltage applications using injection locked oscillator is described. A 2-GHz injection locked oscillator was implemented in a 0.35 mum BiCMOS STMicroelectronics technology in order to validate the theoretical results of the GMSK modulation of such oscillators
Membrane vesicles from multidrug-resistant human carcinoma cells contain a specific 150,000-170,000 dalton protein detected by photoaffinity labeling (1986)

The authors have selected multidrug-resistant human KB carcinoma cells in high levels of colchicine (KB-C4) or vinblastine (KB-V1) which are cross-resistant to many other structurally unrelated chemotheraputic agents. To determine the mechanism of reduced drug accumulation, they measured /sup 3/H-vinblastine (/sup 3/H-VBL) association with membrane vesicles made from parental drug sensitive, drug-resistant and revertant cells. Membrane vesicles from highly multidrug resistant cells exhibited increased specific and saturable binding of vinblastine, (Kd = 1 ..mu..M) that was temperature dependent and trypsin sensitive. To identify the molecules which bind vinblastine, membrane vesicles were exposed to two photo-activatable analogs of vinblastine, (N-P-(azido-3,5,-(/sup 3/H)-benzoyl)-N'-..beta..-aminoethylvindisine (/sup 3/H-NAB) and N-P-(azido-3-(/sup 125/I)-solicyl)-N'-..beta..-aminoethylvindesine (/sup 125/I-NASV). The specific labeling of a 150,000-170,000 dalton protein in membrane vesicles from multidrug-resistant KB-C4 and KB-V1 cells was found. /sup 125/I-NASV labeling was inhibited by vinblastine, vincrinstine and verapamil but not by colchicine or dexamethasone. The 150,000-170,000 dalton protein may have an important role in the multidrug resistance phenotype.
GRIN lens design through the use of surrogate models based on Zernike aberrations (2016)

In this paper, we present a computational method for rapidly designing GRadient-INdex (GRIN) lenses by employing a surrogate model that relates input lens parameters to output Zernike aberrations. This approach also provides a path forward for the designer to identify which lens parameters have the largest impact on specific aberrations. Through the use of orthogonal Latin Hypercube Sampling (LHS) and multivariate polynomial regressions, a surrogate model is trained to approximate the ray trace evaluations. Finally, a plano-convex GRIN lens based on Silicon-Germanium mixing is optimized using both full ray trace and surrogate model evaluations. A ~40× speed improvement is realized with the surrogate-assisted optimization while achieving similar optical performance.
Failure of Differentiation into Mature Myotubes by Muscle Precursor Cells with the Side-Population Phenotype after Injection into Irreversibly Damaged Striated Urethral Sphincter (2005)

We previously showed that the injection of a heterogeneous population of muscle precursor cells (MPCs) into striated urethral sphincter irreversibly damaged by electrocoagulation results in the formation of functional myotubes. To gain further insights into the role played by the different types of MPCs, we elected to sort the MPCs by Hoechst 33342 staining/fluorescence-activated cell-sorter analysis before injection. We found that the side population (SP) cells (muscle stem cells) injected in isolation survived, whereas the main population (MP) cells did not. However, the SP cells failed to differentiate into mature myotubes, as observed previously with unfractionated MPCs containing both SP and MP cells. This result suggests that interactions between SP and MP cells are required for the formation of myotubes in a nonregenerating muscle. In the setting of sphincter insufficiency, injection of MPCs at different stages of maturation may be a better option than purified muscle stem cells.
Efficient simulation of multicarrier digital communication systems in nonlinear channel environments (1993)

When simulating multicarrier digital communication systems operating over nonlinear channels, the required high sampling rate contributes significantly to long execution times. A new method that reduces the sampling rate of simulations of such systems is developed. The partial rate of products (ParSOP) method reduces the sampling rate by generating only the intermodulation products that lie in a frequency band of interest. The ParSOP method requires that the bandpass nonlinearity be represented by memoryless operations on the complex envelope of the signal and that the subcarriers constituting the frequency-division multiplexed signal are sufficiently separated to prevent significant adjacent channel interference. Simulation results for such systems show that an order of magnitude reduction in the sampling rate is possible while producing only minimal error in the bit error rate estimate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Guest Editorial Communication-Efficient Distributed Learning Over Networks (2023)

Distributed machine learning is envisioned as the bedrock of future intelligent networks, where agents exchange information with each other to train models collaboratively without uploading data to a central processor. Despite its broad applicability, a downside of distributed learning is the need for iterative information exchange between agents, which may lead to high communication overhead unaffordable in many practical systems with limited communication resources. To resolve this communication bottleneck, we need to devise communication-efficient distributed learning algorithms and protocols that can reduce the communication cost and simultaneously achieve satisfactory learning/optimization performance. Accomplishing this goal necessitates synergistic techniques from a diverse set of fields, including optimization, machine learning, wireless communications, game theory, and network/graph theory. This Special Issue is dedicated to communication-efficient distributed learning from multiple perspectives, including fundamental theories, algorithm design and analysis, and practical considerations.