gebhart/patrepeval huggingface dataset:
A Solid State <sup>13</sup>C NMR, Crystallographic, and Quantum Chemical Investigation of Phenylalanine and Tyrosine Residues in Dipeptides and Proteins (2007)

We report the results of a solid-state NMR and quantum chemical investigation of the 13C gamma NMR chemical shifts in phenylalanine and tyrosine in dipeptides and proteins. Accurate computation of the experimental shifts is shown to require a good description of local electrostatic field effects, and we find the best results (R2=0.94, rmsd=1.6 ppm, range = 17.1 ppm, N=14) by using a self-consistent reaction field continuum model. There are no obvious correlations with phi, psi, chi 1, or chi2 torsion angles, unlike the results seen with other amino acids. There is, however, a linear relation between computed C gamma atomic charges and shifts for the 14 peptide as well as 18 protein residues investigated. This result is similar to the correlation reported in the 1960s between pi-electron density and 13C shifts for classical 4n + 2 (n=0, 1, 2) pi-electron aromatic species, such as cyclopentadienide and the tropylium cation, and in fact, we found that the shielding/atomic charge correlation seen in the peptides and proteins is virtually identical to that seen with a broad range of aromatic carbocations/carbanions. These results suggest the dominance of an electrostatic field polarization model in which increasing pi electron density results in an increase in C gamma atomic charge and increased shielding (of sigma 11 and sigma 22, perpendicular to the pi orbital) in Phe and Tyr, as well as in the other aromatic species. These results are of general interest since they demonstrate the importance of electrostatic field effects on Phe and Tyr C gamma chemical shifts in peptides and proteins and imply that inclusion of these effects will be necessary in order to interpret the shifts of other aromatic species, such as drug molecules, bound to proteins.
Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family (2006)

Arabidopsis thaliana has nine genes that constitute a family of putative carotenoid cleavage dioxygenases (CCDs). While five members of the family are believed to be involved in synthesis of the phytohormone abscisic acid, the functions of the other four enzymes are less clear. Recently two of the enzymes, CCD7/MAX3 and CCD8/MAX4, have been implicated in synthesis of a novel apocarotenoid hormone that controls lateral shoot growth. Here, we report on the molecular and genetic interactions between CCD1, CCD7/MAX3 and CCD8/MAX4. CCD1 distinguishes itself from other reported CCDs as being the only member not targeted to the plastid. Unlike ccd7/max3 and ccd8/max4, both characterized as having highly branched phenotypes, ccd1 loss-of-function mutants are indistinguishable from wild-type plants. Thus, even though CCD1 has similar enzymatic activity to CCD7/MAX3, it does not have a role in synthesis of the lateral shoot growth inhibitor. Rather, it may have a role in synthesis of apocarotenoid flavor and aroma volatiles, especially in maturing seeds where loss of function leads to significantly higher carotenoid levels.
Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021 (2021)

We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).
Near-field imaging of coupled photonic-crystal microcavities (2009)

We report by means of near-field microscopy on the coupling between two adjacent photonic crystal microcavities. Clear-cut experimental evidence of the spatial delocalization of coupled-cavity optical modes is obtained by imaging the electromagnetic local density of states. We also demonstrate that it is possible to design photonic structures with selective coupling between different modes having orthogonal spatial extensions
The Three-Phase Common-Mode Inductor: Modeling and Design Issues (2010)

This paper presents a comprehensive physical characterization and modeling of the three-phase common-mode (CM) inductors along with the equivalent circuits that are relevant for their design. Modeling issues that are treated sparsely in previous literature are explained in this paper, and novel insightful aspects are presented. The calculation of the leakage inductance is reviewed, along with the magnetic core saturation issues, and a new expression for the leakage flux path is derived. The influence of the core material characteristics on the performance of the component is discussed, and a new method for the selection of the material for the minimized volume CM inductors is proposed in order to simplify the design procedure. Experimental results which validate the model are presented.
When Less is More: Relevance Feedback Falls Short and Term Expansion Succeeds at HARD 2005 (2006)

We used clarification forms to study passage term feedback. When compared against pseudo-relevance feedback with an extremely large external corpus, we found that passage feedback resulted in a reduction in performance while term feedback significantly improved recall. 1. OVERVIEW UMass tested several new techniques in the HARD track this year. First, we developed a new baseline pseudo-relevance feedback technique based on expanding from a large, external corpus [6]. Our results indicate that externally expanding a query can result in improvements over passage feedback. Second, we present a new feedback technique which incorporates both relevance and non-relevance information. Our results indicate that this regularization-based technique can improve performance when used in conjunction with traditional feedback techniques. Third, we present two successful term feedback techniques. Our most successful technique exploits a structured query language in order to significantly improve recall. 2. BASELINE ALGORITHMS We used the Indri retrieval engine for retrieval experiments [7]. We did not submit any runs which did not perform pseudo-relevance feedback. We experimented with a mixture of relevance models for our baseline ranking algorithm (also introduced in our Robust runs this year) [6]. Readers should consult the refered work for a more thorough description of parameters. Mixture parameters were set to P (aquaint) = 1 for MASSbaseTRM3 and P (bignews) = 1 for MASSbaseTEE3. No dependence models were used in our baselines. 3. CLARIFICATION FORMS Our clarification form consisted of several pages of dialog with the searcher. This dialog followed three phases. In the first phase, the searcher was presented with passages from which to judge document relevance. The second phase consisted of term-based feedback; searchers were asked to judge the expected frequency of terms in relevant documents. 3.1 Passage Presentation In previous years, we found that passages acted as suitable surrogates for documents when being judged for relevance [1]. We divided each of the top 5 documents in the MASSbaseEE3 run into 150-word, half-overlapping passages. We
Secondary Radar (1987)

SSR, also known in the USA as beacon radar, has a number of similarities with primary surveillance radar. Both use a ground-based rotating antenna, with a pulse transmitter and receiver. Like its primary counterpart, the signals from an SSR normally undergo plot extraction at the radar site, followed by transmission by landline to an ATC or operations centre. Secondary radar antennas are often mounted above primary antennas (see figure 1.2), saving the cost of separate drive motors and gearboxes, and ensuring azimuthal alignment. Plot extraction may include correlation of primary and secondary radar signals, giving increased confidence about the position and identity of wanted targets.
Observation of large positive magneto-resistance in bubble decorated graphene oxide films derived from shellac biopolymer: a new carbon source and facile method for morphology-controlled properties (2015)

We report a large positive magneto-resistance (MR) in bubble decorated graphene oxide films that are derived from shellac biopolymer as a carbon source. These films were produced on a quartz substrate by heating the biopolymer coated substrate at 900 °C in an argon atmosphere. The characterization data of the films using Raman, X-ray photoelectron spectroscopy, field emission scanning electron microscopy and transmission electron microscopy reveal that shellac can be used as a new carbon source to produce transparent bubble decorated graphene oxide films. The magneto-resistance results show a 130% change in the resistance of the films at 3 K under a perpendicular magnetic field of 15 T, and the value decreases exponentially up to 50 K. The observed MR properties of the bubble decorated graphene oxide films are explained using a weak anti-localization and quantum interference model in the low magnetic field region, while the Lorentz force accounts for the MR properties well in the high magnetic field region.
Corticotropin-releasing factor antagonists in affective disorders (1999)

Following a search lasting nearly three decades, corticotropin-releasing factor (CRF), a 41 amino acid-containing peptide, was isolated and characterised in 1981. In the preceding 18 years, a concatenation was developed that appears to show that CRF integrates not only the endocrine, but also the autonomic, immunologic and behavioural responses of mammalian organisms to stress. Direct CNS administration of CRF to laboratory animals produces actions similar to those observed after exposure to stress. Moreover, CNS administration of peptidergic CRF antagonists blocks many of the behavioural responses to stress. Since both early untoward life events as well as recently experienced stress have been implicated in the pathophysiology of affective disorders, and because there is substantial evidence for CRF neuronal hyperactivity in patients with affective disorders, small molecule, lipophilic CRF antagonists have been hypothesised to possess antidepressant and/or anxiolytic activity. Within the last few years, a number of pharmaceutical companies have developed selective, small molecule CRF(1) receptor antagonists. These compounds block the effects of CRF both in vitro and in vivo. There is also evidence that these agents possess anxiolytic and antidepressant activity in animal behavioural models. Compounds that act upon the CRF system have been hypothesised to be of value not only for certain psychiatric disorders, but also in neurodegenerative and inflammatory disorders. Some of these CRF(1) receptor antagonists are currently undergoing clinical trials to determine their efficacy and tolerability in patients with mood and anxiety disorders.
Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM (2013)

A major hurdle to evolutionary engineering approaches for multigenic phenotypes is the ability to simultaneously modify multiple genes rapidly and selectively. Here, we describe a method for in vivo-targeted mutagenesis in yeast, targeting glycosylases to embedded arrays for mutagenesis (TaGTEAM). By fusing the yeast 3-methyladenine DNA glycosylase MAG1 to a tetR DNA-binding domain, we are able to elevate mutation rates >800 fold in a specific ∼20-kb region of the genome or on a plasmid that contains an array of tetO sites. A wide spectrum of transitions, transversions and single base deletions are observed. We provide evidence that TaGTEAM generated point mutations occur through error-prone homologous recombination (HR) and depend on resectioning and the error-prone polymerase Pol ζ. We show that HR is error-prone in this context because of DNA damage checkpoint activation and base pair lesions and use this knowledge to shift the primary mutagenic outcome of targeted endonuclease breaks from HR-independent rearrangements to HR-dependent point mutations. The ability to switch repair in this way opens up the possibility of using targeted endonucleases in diverse organisms for in vivo-targeted mutagenesis.
El ejército romano según el "Breve tratado de términos militares", de Modesto ("Modesti libellus de vocabulis rei militaris ad Tacitum Augustum"). Traducción (2003)

The present work is a continuation of our previous microscopic, spectroscopic and microcalorimetric measurements of liposomes and poly(ribo)nucleotides and their ternary complexes with inorganic cations as an alternative formulation employing zwitterionic phospholipids instead of cytotoxic cationic lipids. Current report describes Fourier transform infrared spectrometric study as employed to follow structural transitions of newly proposed ternary solid neutral lipid-Mg(2+)-DNA complexes as promising gene delivery formulation. Spectra of the unbound components are compared with those obtained after their complexation as binary and ternary mixtures. Results are described at the levels of carbonyl, phosphate, choline and CH groups and discussed as effects of nucleic acid and phosphatidylcholine moiety on each other in the absence and in the presence of Mg(2+). The infrared spectra of DNA-lipid phases are dominated by the lipid specific absorption bands, with a very little contribution of DNA. Data suggest that upon recognition of DNA with lipids, the DNA undergoes helical transition. Mg(2+) effects are interpreted as dehydrations of phosphates and H-bonding inducing effects on carbonyl groups. The role of residual and surface water on these associations, as well as on chain packing is also discussed followed by possible implications of the ternary complex formation for further gene transfer designs.
Agent-based Extensions for the UML Profile and Metamodel for Service-oriented Architectures (2008)

Service-oriented architectures are today's favorite answer to solve interoperability issues. As various kinds of systems can be used to implement service-oriented architectures, the recent trend is to apply principles of model-driven development by (i) modeling the service-oriented architecture in an abstract manner and (ii) providing model transformations between this abstract specification and the underlying platform specific systems. As such, multiagent systems became very popular as both, service-oriented architectures and multiagent systems, share several commonalities. In this paper, we compare the core building blocks of multiagent systems and the emerging UPMS (UML profile and metamodel) standard for service-oriented architectures from the Object Management Group (OMG). The major objective of this investigation is to identify if SOA-Pro-the current submission under review--offers functionalities to allow modeling of multiagent systems adequately and if not to identify what kind of functionality is missing and how this functionality can be achieved to provide model transformations between service-oriented architectures and multiagent systems.
Potential benefits of hierarchical modes of the DVB-T specification (1999)

Many engineers and broadcasters are very familiar with the concept of digital terrestrial television (DTT), and hopefully will all have seen live reception of the signals at some time. However a number of those people will not have encountered the idea of hierarchical modulation, which is a part of the ETSI standard-the definition of the RF transmission standard for DVB-T signals. This paper introduces the ideas behind the hierarchical modes, and shows one of the ways in which they could be used at some time in the future, or perhaps by countries still in the process of planning their DTT services at the moment. This paper is not intended to suggest that the existing UK DTT services should be replaced by hierarchical services, but instead it points out a potential way in which the DTT system could be used, if additional frequencies become available in the future.
Efficient Test of Dynamic Read Destructive Faults in SRAM Memories (2005)

This paper presents an analysis of the electrical origins of dynamic Read Destructive Faults (dRDFs) that affects the SRAM memories. This fault is the consequence of resistive-open defects in the refreshment loop of the SRAM core-cells. The consequence of this fault is that multiple consecutive read operations on a cell may induce the faulty swap of the stored value. In a recent paper, we have considered only two of the four possible dRDF fault primitives. Here, we complete this study by evaluating the effectiveness of all fault primitives. We also show that read or write operations on a cell involve a stress on the other cells of the same word line. This stress, called Read Equivalent Stress (RES), has the same effect as an actual read operation for the dRDF sensitization. On this basis, we demonstrate that RESs can replace actual read operations in the dRDF fault primitives making them more efficient. 1.
Biocontrol of postharvest diseases of apple using<i>Bacillus</i>spp. isolated from stored apples (1995)

Ninety-five bacterial isolates were recovered from 38 of 77 apples that had been stored at 1 °C for 6–7 months. The highest number of bacteria were recovered in nutrient, dextrose, and V8 juice broths, respectively. The bacteria were screened as biocontrol agents on cultivar Red Delicious apples primarily for control of blue mold caused by Penicillium expansum. Three bacteria effective against P. expansum were also tested against Botrytis cinerea for control of gray mold. Ten, four, and five isolates significantly reduced blue mold decay when apples were stored at 5, 10, and 20 °C. Two isolates tested against gray mold decay significantly reduced decay at 5 and 10 °C and one isolate was effective at 20 °C. Thirty-six isolates that had been selected for identification by the Biolog Microstation™ System were Gram positive and contained endospores, and 30 of these were positively identified as Bacillus spp. Further testing of 15 isolates that were effective biocontrol agents identified 7 as Bacillus subtilis on the basis of 15 microbiological tests used for determining species within the genus Bacillus.Key words: endophytic, bacteria, biocontrol, postharvest.
The Cerebral Cortex is Bisectionally Segregated into Two Fundamentally Different Functional Units of Gyri and Sulci (2018)

The human cerebral cortex is highly folded into diverse gyri and sulci. Accumulating evidences suggest that gyri and sulci exhibit anatomical, morphological, and connectional differences. Inspired by these evidences, we performed a series of experiments to explore the frequency-specific differences between gyral and sulcal neural activities from resting-state and task-based functional magnetic resonance imaging (fMRI) data. Specifically, we designed a convolutional neural network (CNN) based classifier, which can differentiate gyral and sulcal fMRI signals with reasonable accuracies. Further investigations of learned CNN models imply that sulcal fMRI signals are more diverse and more high frequency than gyral signals, suggesting that gyri and sulci truly play different functional roles. These differences are significantly associated with axonal fiber wiring and cortical thickness patterns, suggesting that these differences might be deeply rooted in their structural and cellular underpinnings. Further wavelet entropy analyses demonstrated the validity of CNN-based findings. In general, our collective observations support a new concept that the cerebral cortex is bisectionally segregated into 2 functionally different units of gyri and sulci.
Electrochemical Fabrication of Titanium Oxide Film from an Aqueous Solution Containing Titanium Ion and Hydroxylamine (2011)

TiO2 films with poly crystal were electrodeposited on conductive substrate (NESA glass, Approximately 10Ω/□, Asahi glass Co. Ltd.) from the titanium potassium oxalate dehydrate aqueous solution containing hydroxylamine adjusted pH 9 with KOH aq. at 333k. The peak corresponded to Ti3+ion into these TiO2 film was not observed by using X-ray photoelectron spectroscopy (XPS). The photocatalysis of TiO2 film increased with a decrease of cathodic potential. In particular, TiO2 film obtained at cathodic potential of -1.3V, had the higher photocatalysis than that of other potential.
Organic complementary-like inverters employing methanofullerene-based ambipolar field-effect transistors (2004)

We demonstrate a complementary-like inverter comprised of two identical ambipolar field-effect transistors based on the solution processable methanofullerene [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). The transistors are capable of operating in both the p- and n-channel regimes depending upon the bias conditions. However, in the p-channel regime transistor operation is severely contact limited. We attribute this to the presence of a large injection barrier for holes at the Au∕PCBM interface. Despite this barrier the inverter operates in both the first and third quadrant of the voltage output versus voltage input plot exhibiting a maximum gain in the order of 20. Since the inverter represents the basic building block of most logic circuits we anticipate that other complementary-like circuits can be realized by this approach.
Pulse shaping for 112 Gbit/s polarization multiplexed 16-QAM signals using a 21 GSa/s DAC (2011)

The implications of increasing the symbol rate for a given digital-to-analog converter (DAC) sampling rate are investigated by considering the generation of 112 Gbit/s PM 16-QAM signals (14 Gsym/s) using a 21 GSa/s DAC with 6-bit resolution.
Characterization of an intronic enhancer that regulates myelin proteolipid protein (Plp) gene expression in oligodendrocytes (2005)

The myelin proteolipid protein (Plp) gene is expressed in oligodendrocytes and encodes the most abundant protein (approximately 50%) present in mature myelin from the central nervous system (CNS). Plp gene activity is low to nonexistent early in development but sharply increases, concurrently with the active myelination period of CNS development. Work from our laboratory suggests that the temporal regulation of Plp gene expression in mice is mediated by a positive regulatory element located within Plp intron 1 DNA. We have termed this regulatory element/region ASE (for antisilencer/enhancer). The ASE is situated approximately 1 kb downstream of exon 1 DNA and encompasses nearly 100 bp. To understand the mechanisms by which the ASE augments Plp gene expression in oligodendrocytes, Plp-lacZ constructs were generated and transfected into a mouse oligodendroglial cell line (N20.1). Results presented here demonstrate that upstream regulatory elements in the Plp promoter/5'-flanking DNA are not required for ASE activity; the ASE worked perfectly well when the thymidine kinase (TK) promoter was substituted for the Plp promoter. However, the relative location of the ASE appears to be important. When placed upstream of 2.4 kb of Plp 5'-flanking DNA, or downstream of the lacZ expression cassette, the ASE was no longer effective. Thus, the ASE might have to be in the context of the intron in order to function. To begin to identify the crucial nucleotides within the ASE, orthologous sequences from rat, human, cow, and pig Plp genes were swapped for the mouse sequence. Results presented here demonstrate that the orthologous sequence from rat can substitute for the mouse ASE, unlike those from human, cow, or pig.