gebhart/patrepeval huggingface dataset:
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets (2013)

Massively parallel sequencing technologies have made the generation of genomic data sets a routine component of many biological investigations. For example, Chromatin immunoprecipitation followed by sequence assays detect genomic regions bound (directly or indirectly) by specific factors, and DNase-seq identifies regions of open chromatin. A major bottleneck in the interpretation of these data is the identification of the underlying DNA sequence code that defines, and ultimately facilitates prediction of, these transcription factor (TF) bound or open chromatin regions. We have recently developed a novel computational methodology, which uses a support vector machine (SVM) with kmer sequence features (kmer-SVM) to identify predictive combinations of short transcription factor-binding sites, which determine the tissue specificity of these genomic assays (Lee, Karchin and Beer, Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011; 21:2167-80). This regulatory information can (i) give confidence in genomic experiments by recovering previously known binding sites, and (ii) reveal novel sequence features for subsequent experimental testing of cooperative mechanisms. Here, we describe the development and implementation of a web server to allow the broader research community to independently apply our kmer-SVM to analyze and interpret their genomic datasets. We analyze five recently published data sets and demonstrate how this tool identifies accessory factors and repressive sequence elements. kmer-SVM is available at http://kmersvm.beerlab.org.
Addition of Phosphates, Proteins, and Gums to Reduced‐Salt Frankfurter Batters (1984)

ABSTRACT Reducing the added salt levels in frankfurter batters from 2.5 to 1.5% decreased water binding aoilities. Gel strength was less affected and fat release least affected. Tripolyphosphate and pyrophosphate were very effective at levels of 0.1% in restoring the water binding and gel strength. The effectiveness of these phosphates was nearly identical although they have opposing effects on batter pH. Soy isolate and rennet‐treated, calcium‐reduced dried skim milk improved the batters when added at 1 and 3%. Additions of alginate or especially xanthan gums (0.1‐0.3%) improved the water binding but were very detrimental to the gel strength.
A 1V CMOS PLL designed in high-leakage CMOS process operating at 10-700MHz (2005)

A PLL is fabricated in a 0.13 /spl mu/m logic process where leakage currents are high. The loop capacitor is implemented by a structure of poly and 9 metal layers. The VCO is implemented with common-mode feedback to compensate for leakage currents. Maximum VCO frequency is 1400 MHz. Typical power is 7 mW at 200 MHz. RMS jitter is 25.4 ps at 360 MHz.
Performance analysis of shared-buffered banyan networks under arbitrary traffic patterns (2002)

The performance of multistage banyan networks with a shared buffer in each switching element is studied. Two different internal protocols are considered for the transfer of packets from stage to stage based on the presence or absence of interstage backpressure signals to signal the occurrence of buffer saturation conditions. As far as the offered traffic is concerned, two kinds of traffic patterns have been studied, a burst and an unbalanced traffic pattern. For both of them an analytical model is developed based on the iterative solution of state equations in order to compute the main traffic performance of the network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modulation-Doped Multi-Quantum Well (MD-MQW) Lasers. II. Experiment (1990)

Detailed experimental results on p-type modulation-doped multi-quantum well (MD-MQW) lasers are discussed. The GaAs/GaAlAs MD-MQW laser was grown by low temperature (600°C) molecular beam epitaxy using Be as the p-type dopant. The realization of the p-type MD-MQW structure was fully confirmed by high resolution secondary ion mass spectroscopy, transmission electron microscopy, and photoluminescence measurement. An ultrahigh relaxation oscillation frequency of up to 30 GHz was realized, which is 2.5 times that of undoped MQW lasers and also 5 times that of double heterostructure lasers. In addition, the spectral chirping width of p-type MD-MQW lasers was experimentally confirmed to be 1/5 that of undoped MQW lasers. These improvements result from the enhancement of the differential gain due to the modulation doping effect in addition to the quantum size effect. These results are in good agreement with the theoretical analyis.
Hempel revisited (1984)

Journal Article Hempel revisited Get access A. J. Dale A. J. Dale The UniversityHull HU6 7RX Search for other works by this author on: Oxford Academic Google Scholar Analysis, Volume 44, Issue 2, March 1984, Pages 90–92, https://doi.org/10.1093/analys/44.2.90 Published: 01 March 1984
Kinetics and Mechanism of Copper Dissolution in Aqueous Ammonia (1963)

Abstract The dissolution of copper in aqueous solutions of ammonia is a corrosion process in which the cathodic reaction is the reduction of oxygen at the surface of the metal according to: and the anodic reaction is the oxidation of copper according to: Superimposed with these reactions is the cuprous‐cupric equilibrium: A theoretical derivation of the velocity equation of the dissolution process has been obtained, which describes quantitatively the experimental facts. The equation is as follows: where k 1 , k 2 , k 3 and f are constants, A is the surface area of the metal in contact with the aqueous phase and [O 2 ], [NH 3 ] and [Cu 2+ ] are oxygen, ammonia and cupric ion concentrations respectively.
Synthesis and Characterization of Lithium, Zirconium, and Hafnium Derivatives of <i>N</i>-Isopropyl-2-(isopropylamino)troponiminate (1996)

The reaction of N-isopropyl-2-(isopropylamino)troponimine, [(i-Pr)2ATI]H, with n-BuLi in Et2O−THF gave [(i-Pr)2ATI]Li(THF)2 in excellent yield. The [(i-Pr)2ATI]2ZrCl2 and [(i-Pr)2ATI]2HfCl2 complexes were prepared by treating the respective metal tetrachlorides with 2 equiv of the lithium adduct. These metal complexes were characterized by NMR spectroscopy and X-ray crystallography. X-ray crystallographic data of the lithium, zirconium, and hafnium complexes show monomeric structures in the solid state. The lithium complex has a tetrahedral lithium ion and a slightly twisted C7N2Li framework. The zirconium and hafnium metal centers in [(i-Pr)2ATI]2ZrCl2 and [(i-Pr)2ATI]2HfCl2 show pseudooctahedral geometry with chlorides occupying the cis positions. The dialkyl derivative [(i-Pr)2ATI]2Zr(CH2SiMe3)2 was prepared by treating Zr(CH2SiMe3)4 with 2 equiv of the free ligand [(i-Pr)2ATI]H. Crystal data with Mo Kα (λ = 0.710 73 Å) at 193 K: [(i-Pr)2ATI]Li(THF)2, C21H35LiN2O2, a = 9.2318(8) Å, b = 14.624(2) Å, c = 16.071(2) Å, β = 94.954(5)°, V = 2661.3(5) Å3, monoclinic, space group P21/n, Z = 4, R = 0.0607; [(i-Pr)2ATI]2ZrCl2, C26H38Cl2N4Zr, a = 9.569(3) Å, b = 15.877(4) Å, c = 18.241(6) Å, β = 94.480(10)°, V = 2763.0(14) Å3, monoclinic, space group P21/n, Z = 4, R = 0.0401; [(i-Pr)2ATI]2HfCl2, C26H38Cl2HfN4, a = 9.540(1) Å, b = 15.813(2) Å, c = 18.118(3) Å, β = 94.546(11)°, V = 2724.8(7) Å3, monoclinic, space group P21/n, Z = 4, R = 0.0313.
Some improvements in the implementation of multithreshold and multivalued I<sup>2</sup>.L circuits (1989)

After a brief analysis of some problems that arise in the implementation of multi-threshold and multivalued I2L circuits, a global solution for these problems is proposed based on a proper dimensioning of the current mirrors. This solution implies an adequate design of the circuit layout, but the manufacturing process can be the same as for the binary I2L circuits. The problems posed and its practical solutions are checked by simulation with SPICE2 of two circuits: a comparator circuit to detect three current thresholds, and a new 4-bits adder with lookahead carry.
Understanding the backward slices of performance degrading instructions (2000)

For many applications, branch mispredictions and cache misses limit a processor's performance to a level well below its peak instruction throughput. A small fraction of static instructions, whose behavior cannot be anticipated using current branch predictors and caches, contribute a large fraction of such performance degrading events. This paper analyzes the dynamic instruction stream leading up to these performance degrading instructions to identify the operations necessary to execute them early. The backward slice (the subset of the program that relates to the instruction) of these performance degrading instructions, if small compared to the whole dynamic instruction stream, can be pre-executed to hide the instruction's latency. To overcome conservative dependance assumptions that result in large slices, speculation can be used, resulting in speculative slices. This paper provides an initial characterization of the backward slices of L2 data cache misses and branch mispredictions, and shows the effectiveness of techniques, including memory dependence prediction and control independence, for reducing the size of these slices. Through the use of these techniques, many slices can be reduced to less than one tenth of the full dynamic instruction stream when considering the 512 instructions before the performance degrading instruction.
Tripolitania, Hadd Hajar (1972)

Mr. Peter Holmes was able to return to photograph the wall in the Gebel south-west of Asabaa, called Hadd Hajar , mentioned in the Society's Second Annual Report , 1970–1, p. 11. Pl. VIII shows one of his photographs. In the foreground is Ras at-Tays al-Abyad, and the main wall below, which runs for 6 km. to Ras Sa'id. A small quantity of pottery found by the watch-tower was clearly Roman, and included an amphora rim and small pieces of late Roman lamp. 2½ km. south of Hadd Hajar near its south-west end another watch-tower was found on Ras at-Tays al-Aswad.
Challenges and Strategies in the Synthesis of Mesoporous Alumina Powders and Hierarchical Alumina Monoliths (2012)

A new rapid, very simple and one-step sol-gel strategy for the large-scale preparation of highly porous γ-Al₂O₃ is presented. The resulting mesoporous alumina materials feature high surface areas (400 m² g<sup>-1</sup>), large pore volumes (0.8 mL g<sup>-1</sup>) and the γ-Al₂O₃ phase is obtained at low temperature (500 °C). The main advantages and drawbacks of different preparations of mesoporous alumina materials exhibiting high specific surface areas and large pore volumes such as surfactant-nanostructured alumina, sol-gel methods and hierarchically macro-/mesoporous alumina monoliths have been analyzed and compared. The most reproducible synthesis of mesoporous alumina are given. Evaporation-Induced Self-Assembly (EISA) is the sole method to lead to nanostructured mesoporous alumina by direct templating, but it is a difficult method to scale-up. Alumina featuring macro- and mesoporosity in monolithic shape is a very promising material for in flow applications; an optimized synthesis is described.
Zur Kenntnis des S<sub>π</sub> (1962)

Abstract Mit Hilfe einer auf dem nukleophilen Angriff der Schwefel‐Schwefel‐Bindung durch Triphenylphosphin beruhenden jodometrischen Methode wurden S π und S λ in Schwefel‐Kohlenstofflösungen nebeneinander quantitativ bestimmt. Durch Vergleich der so erhaltenen Werte mit den durch Eindunsten der Lösungen und Extraktion der Rückstande mit CS 2 für den entstandenen S μ erhaltenen Werten, ergibt sich, daß Sx mit einer Umwandlungsausbeute von 55%in S μ übergeht. Dies steht in Übereinstimmung mit früheren Befunden, in denen wir auf Grund von kryoskopischen Bestimmungen in CS 2 für S, eine Molekelgröße von S π gefunden und zur Deutung der Schmelzpunktsanomalie des monoklinen Schwefels eine etwa 60proz. Umwandlung des S π in S μ angenommen hatten.
Challenges for the Development of Ribonucleoside Analogues as Inducers of Error Catastrophe (2004)

RNA viruses are responsible for numerous human diseases; some of these viruses are also potential agents of bioterrorism. In general, the replication of RNA viruses results in the incorporation of at least one mutation per round of replication, leading to a heterogeneous population, termed a quasispecies. The antiviral nucleoside ribavirin has been shown to cause an increase in the mutation frequency of RNA viruses. This increase in mutation frequency leads to a loss of viability due to error catastrophe. In this article, we review lethal mutagenesis as an antiviral strategy, emphasizing the challenges remaining for the development of lethal mutagenesis into a practical clinical approach.
Isoprostanes (2008)

The isoprostanes (IsoPs) are a unique series of prostaglandin-like compounds formed in vivo via a nonenzymatic mechanism involving the free radical-initiated peroxidation of arachidonic acid. This article summarizes our current knowledge of these compounds. Herein, a historical account of their discovery and the mechanism of their formation are described. A specific class of IsoPs, the F2-IsoPs, are stable, robust molecules that can be measured as indices of endogenous oxidant stress. The utility of these molecules as biomarkers and methods by which these compounds can be quantified are discussed. In addition to the F2-IsoPs, isoprostanes with other prostane ring structures as well as oxidation products with furan and dioxolane rings can be generated from arachidonic acid. And, in more recent years, isoprostane-like compounds have been shown to be formed from polyunsaturated fatty acids including eicosapentaenoic acid [C20:5, omega-3], docosahexaenoic acid [C22:6, omega-3], and adrenic acid [C22:4, omega-6]. These findings will be summarized as well.
Enhanced casein kinase II activity in human tumour cell cultures (1984)

Casein kinase II (CKII) activity is enhanced as much as 2-3 fold in established and 4-5-fold in transformed human cell lines when compared to that of fibroblasts and primary human tumour cell cultures where CKII activity never exceeded a basic level. The high activity of CKII in transformed cells and in established cell lines was reduced to about the same basic level after treatment with heparin, a highly specific inhibitor of CKII activity. The activity of the cAMP-dependent protein kinase was virtually the same in fibroblasts and various human tumour cell lines investigated.
<i>Arabidopsis</i> EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action and promote growth by directing EIN3 degradation (2004)

Ubiquitination of various intracellular proteins by ubiquitin-protein ligases (or E3s) plays an essential role in eukaryotic cell regulation primarily through its ability to selectively target proteins for degradation by the 26S proteasome. Skp1, Cullin, F-box (SCF) complexes are one influential E3 class that use F-box proteins to deliver targets to a core ligase activity provided by the Skp1, Cullin, and Rbx1 subunits. Almost 700 F-box proteins can be found in Arabidopsis, indicating that SCF E3s likely play a pervasive role in plant physiology and development. Here, we describe the reverse genetic analysis of two F-box proteins, EBF1 and -2, that work coordinately in SCF complexes to repress ethylene action. Mutations in either gene cause hypersensitivity to exogenous ethylene and its precursor 1-aminocyclopropane-1-carboxylic acid. EBF1 and -2 interact directly with ethylene insensitive 3 (EIN3), a transcriptional regulator important for ethylene signaling. Levels of EIN3 are increased in mutants affecting either EBF1 or -2, suggesting that the corresponding SCF complexes work together in EIN3 breakdown. Surprisingly, double ebf1 ebf2 mutants display a substantial arrest of seedling growth and have elevated EIN3 levels, even in the absence of exogenous ethylene. Collectively, our results show that the SCF(EBF1/EBF2)-dependent ubiquitination and subsequent removal of EIN3 is critical not only for proper ethylene signaling but also for growth in plants.
A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease (2019)

Analyzing 5770 all-cause cirrhosis cases and 572,850 controls from seven cohorts, we identify a missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene ( MARC1 p.A165T) that associates with protection from all-cause cirrhosis (OR 0.88, p=2.1*10 −8 ). This same variant also associates with lower levels of hepatic fat on computed tomographic imaging and lower odds of physician-diagnosed fatty liver as well as lower blood levels of alanine transaminase (−0.012 SD, 1.4*10 −8 ), alkaline phosphatase (−0.019 SD, 6.6*10 −9 ), total cholesterol (−0.037 SD, p=1*10 −18 ) and LDL cholesterol (−0.035 SD, p=7.3*10 −16 ). Carriers of rare protein-truncating variants in MARC1 had lower liver enzyme levels, cholesterol levels, and reduced odds of liver disease (OR 0.19, p= 0.04) suggesting that deficiency of the MARC1 enzyme protects against cirrhosis.
<title>Microscanner actuated by double PZT thin film</title> (2001)

Lead zirconate titanate (PZT) has been used in microsystems because of its high piezoelectric properties. We have succeeded in developing a beam and mirror scanner actuated by sol-gel deposited PZT ([Pb(Zr,Ti)O<SUB>3</SUB>] thin films as in our previous work. However, the problem of residual stress, which was observed in all fabricated devices, has not been solved yet. In this study, we developed a scanner actuated by double layered PZT to compensate for the residual stress and gain greater actuation force. The PZT layer was prepared by the sol-gel technique. The crystal orientation of the PZT films showed a strong (111)texture, which was reported to have good dielectric and ferroelectric properties in our previous work. The devices were fabricated through thin film depositions, lithography, dry plasma etching, and ICP releasing processes. By comparing with the conventional single layer PZT structure, the residual stress can be reduced in the double layered PZT structure. For a one dimensional bimorph beam scanner, an optical scanning angle of approximately 45- degree was obtained at a resonant frequency of 4.25 kHz, which is much larger than the one actuated by a single layered PZT unimorph beam scanner.
A Quadrupole Mass Analyzer Combined with a BA-Gauge (2005)

A new total pressure measurement method in a quadrupole mass analyzer is described. A needle collector inserted in the grid functions as an ion collector of a Bayard-Alpert gauge when the needle collector is biased at ground potential via an electrometer. The sensitivity factor is about 0.016 Pa-1 with 2 mA emission current. The ion current via the needle collector is linear between 10-9 Pa and 10-1 Pa. When the needle collector is biased at gird potential, the peak height of spectrum increased by a factor of 19. Thus, once the multiplied value of a secondary electron multiplier is confirmed for the total pressure values with the needle collector at around 10-8 Pa, we are able to measure the total pressure of 10-11 Pa with the new RGA as well as the partial pressure quantitatively.
Strong Segregation Theory of Bicontinuous Phases in Block Copolymers (1998)

We compute phase diagrams for AnBm starblock copolymers in the strong-segregation regime as a function of volume fraction φ, including bicontinuous phases related to minimal surfaces (G, D, and P surfaces) as candidate structures. We present the details of a general method to compute free energies in the strong segregation limit and demonstrate that the gyroid G phase is the most nearly stable among the bicontinuous phases considered. We explore some effects of conformational asymmetry on the topology of the phase diagram.
IS THE EXTRACT FROM THE PLANT CATMINT (NEPETA CATARIA) REPELLENT TO MOSQUITOES IN AUSTRALIA? (2007)

The repellency of Nepeta cataria (catmint or catnip) was tested against Aedes aegypti, Ae. vigilax, Culex annulirostris, and Cx. quinquefasciatus, and compared with a blend of natural plant extracts and N,N-diethyl-3-methylbenzamide (deet) on human skin. The catmint and natural plant extract blend did not provide the same level of protection from biting mosquitoes as deet. There were significant differences in the level of protection provided by catmint to the 4 species of mosquito, with mean protection times ranging from 0 min for Ae. aegypti up to 240 +/- 60 min for Cx. quinquefasciatus. Significant differences in the mean landing rates of the 4 mosquito species on untreated forearms highlighted the difficulties in comparing laboratory tests of repellents between species.
Proline Editing: A General and Practical Approach to the Synthesis of Functionally and Structurally Diverse Peptides. Analysis of Steric versus Stereoelectronic Effects of 4-Substituted Prolines on Conformation within Peptides (2013)

Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.
Synthesis of Novel Thin-Film Materials by Pulsed Laser Deposition (1996)

Pulsed laser deposition (PLD) is a conceptually and experimentally simple yet highly versatile tool for thin-film and multilayer research. Its advantages for the film growth of oxides and other chemically complex materials include stoichiometric transfer, growth from an energetic beam, reactive deposition, and inherent simplicity for the growth of multilayered structures. With the use of PLD, artificially layered materials and metastable phases have been created and their properties varied by control of the layer thicknesses. In situ monitoring techniques have provided information about the role of energetic species in the formation of ultrahard phases and in the doping of semiconductors. Cluster-assembled nanocrystalline and composite films offer opportunities to control and produce new combinations of properties with PLD.