bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes
Authors: Feng Yi , Neme Rafik , Beh Leslie Y , Chen Xiao , Braun Jasper , Lu Michael W , Landweber Laura F
Published: November 2022

Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila, and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate O. trifallax. We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha’s: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.
Nucleotide-level linkage of transcriptional elongation and polyadenylation
Authors: Geisberg Joseph V , Moqtaderi Zarmik , Fong Nova , Erickson Benjamin , Bentley David L , Struhl Kevin
Published: November 2022

Alternative polyadenylation yields many mRNA isoforms whose 3’ termini occur disproportionately in clusters within 3’ untranslated regions. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et al., 2020). Pol II derivatives with slow elongation rates confer an upstream-shifted poly(A) profile, whereas fast Pol II strains confer a downstream-shifted poly(A) profile. Within yeast isoform clusters, these shifts occur steadily from one isoform to the next across nucleotide distances. In contrast, the shift between clusters – from the last isoform of one cluster to the first isoform of the next – is much less pronounced, even over large distances. GC content in a region 13–30 nt downstream from isoform clusters correlates with their sensitivity to Pol II elongation rate. In human cells, the upstream shift caused by a slow Pol II mutant also occurs continuously at single nucleotide resolution within clusters but not between them. Pol II occupancy increases just downstream of poly(A) sites, suggesting a linkage between reduced elongation rate and cluster formation. These observations suggest that (1) Pol II elongation speed affects the nucleotide-level dwell time allowing polyadenylation to occur, (2) poly(A) site clusters are linked to the local elongation rate, and hence do not arise simply by intrinsically imprecise cleavage and polyadenylation of the RNA substrate, (3) DNA sequence elements can affect Pol II elongation and poly(A) profiles, and (4) the cleavage/polyadenylation and Pol II elongation complexes are spatially, and perhaps physically, coupled so that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast
Authors: Varier Radhika A , Sideri Theodora , Capitanchik Charlotte , Manova Zornitsa , Calvani Enrica , Rossi Alice , Edupuganti Raghu R , Ensinck Imke , Chan Vincent WC , Patel Harshil , Kirkpatrick Joanna , Faull Peter , Snijders Ambrosius P , Vermeulen Michiel , Ralser Markus , Ule Jernej , Luscombe Nicholas M , van Werven Folkert J
Published: November 2022

N6- methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.
Calculation of the Single-Walled Carbon Nanotubes' Elastic Modulus by Using the Asymptotic Homogenization Method
Authors: Ferdosi Sima Besharat , Porbashiri Meisam
Published: November 2022

This article uses the asymptotic homogenization method to investigate the mechanical characteristics of single-walled carbon nanotubes. The asymptotic homogenization method has been used to derive the equations for the homogenized elastic properties matrix. Then, MATLAB is used to model nanotubes and implement the finite element simulation. Two types of chiralities, including armchair and zigzag, are taken into account in this regard. Young's modulus and shear modulus have been estimated for both armchair and zigzag nanotubes in accordance with the relationships between the derived coefficients and molecular mechanical characteristics. Investigations have been done into how diameter and orientation affect the mechanical characteristics of carbon nanotubes. The research's findings are corroborated and generally consistent with those found in other articles.
Moderating role of Negative Career Thoughts in the Relationship between Motivation and Burnout in Portuguese Dual Career Athletes
Authors: Faria Liliana , Vieira Paulo Nuno
Published: November 2022

The purpose of this study was to examine the relationship between motivation and burnout among Portuguese dual career athletes, and moderating role of negative career thoughts in the relationship between both. A total of 187 student-athletes, playing various sports, participated in the study and completed questionnaires on motivation, burnout and negative thoughts about their careers. Moderation effects were tested using linear regression models. The results indicated that there was a negative association between motivation and burnout and a moderating effect of anxiety and decision insecurity on the relationship between motivation and burnout. Understanding these variables is essential for the development of career intervention programs suitable for dual career of student-athletes.
Possible involvement of the 440 kDa isoform of ankyrinB in neuritogenesis in human neuroblastoma NB‐1 cells
Authors: Kunimoto Manabu
Published: July 2002

Two isoforms of brain ankyrin, 440 kDa and 220 kDa ankyrinB, which are products of alternatively spliced pre‐mRNA encoded by a single gene, are both expressed in human neuroblastoma NB‐1 cells. Expression of the polypeptide and mRNA of the larger isoform increased upon induction of neurite outgrowth in NB‐1 cells by dibutyryl cAMP, while those of the smaller isoform were unaffected. The expressed 440 kDa ankyrinB was concentrated at the tip of growing neurites and was partly co‐localized with GAP‐43. These results suggest that 440 kDa ankyrinB is one of the neuronal growth‐associated proteins and provides an interesting example of gene regulation by alternative splicing in neuronal cells.
Cadherin‐dependent cell aggregation is affected by decapeptide derived from rat extracellular super‐oxide dismutase
Authors: Willems Jean , Bruyneel Erik , Noë Veerle , Slegers Herman , Zwijsen An , Mège René-Marc , Mareel Marc
Published: July 2002

A synthetic HAV‐containing decapeptide homologous to the amino acid sequence 44R‐Q53 in rat extracellular superoxide dismutase B affects cadherin‐dependent cell aggregation. Cell lines, some of them transfected, expressing different types of cadherins were tested using in vitro cell aggregation and cell dissociation assays. A concentration‐dependent inhibition of aggregation by the EC‐SOD‐derived HAV‐containing peptide was detected only in N‐cadherin expressing cells. These results suggest the localisation and possible protective role of EC‐SOD B for cells expressing N‐cadherin.
Threading analysis suggests that the obese gene product may be a helical cytokine
Authors: Madej Thomas , Boguski Mark S. , Bryant Stephen H.
Published: July 2002

The ob gene encodes a protein that, in mutant form, is associated with obesity and type II diabetes in mice. Sequence analysis has revealed no similarities to other proteins, however, and no clues as to possible functions. The possibility nonetheless remains that ob is functionally or ancestrally related to other proteins, whose sequences are divergent to the point that only a comparison of three‐dimensional structures might detect relationship. To explore this possibility, we conduct a ‘threading’ search of a 3‐dimensional structure database, to determine whether the ob protein might adopt a fold similar to any known structure. This search reveals that the ob sequence is compatible, at a significance level of P < 0.05, with structures from the family of helical cytokines that includes interleukin‐2 and growth hormone. A structural model of ob based upon these results is physically and biologically plausible and leads to testable predictions, including the prediction that ob may activate the JAK‐STAT pathway, via binding to a receptor resembling those of the cytokine family.
Expression, purification and kinetic behaviour of fission yeast low Mr protein‐tyrosine phosphatase
Authors: Modesti Alessandra , Cirri Paolo , Raugei Giovanni , Carraresi Laura , Magherini Francesca , Manao Giampaolo , Camici Guido , Ramponi Giampietro
Published: July 2002

A gene named stp1
+, coding for a 17.5‐kDa protein, that rescues cdc25‐22 when overexpressed, has been previously isolated from fission yeast. Here we describe the expression and purification of Stp1 protein as a fusion with the glutathione S‐transferase in E. coli and its kinetic characterisation. Stp1 deduced protein sequence shows an high homology to members of a class of cytosolic low M

r
protein phosphatase previously known to exist only in mammalian species. Stp1 has a kinetic behaviour that appears to be intermediate with respect to the two isoenzymatic forms of low M

r
protein tyrosine phosphatases present in mammalian tissues. These differing kinetic characteristics are mainly due to the sequence 45–56 that is spatially close to the active site pocket.
The C‐terminal tetrapeptide HWFW of theChlorellaHUP1 hexose/H+‐symporter is essential for full activity and an α‐helical structure of the C‐terminus
Authors: Graßl Renate , Robl Ingrid , Opekarovà Miroslava , Tanner Widmar
Published: July 2002

C‐terminal tails of plant hexose/H+‐symporters of the major facilitator superfamily contain a highly conserved motif of four amino acids: HWFW. A deletion of these four amino acids in theChlorellaHUP1 protein leads to a decrease in transport activity by a factor of 3–4. The mutated tail is highly sensitive to trypsin; it does not show α‐helical conformation in contrast to the wild type C‐terminal peptide with an α‐helical content of at least 15%. The production of monoclonal antibody 416B8 recognizing an epitope within the central loop of HUP1 protein has been a prerequisite for the experiments described.
PrrC fromRhodobacter sphaeroides, a homologue of eukaryotic Sco proteins, is a copper‐binding protein and may have a thiol‐disulfide oxidoreductase activity
Authors: McEwan Alastair G , Lewin Allison , Davy Sharon L , Boetzel Ruth , Leech Andrew , Walker Daniel , Wood Tania , Moore Geoffrey R
Published: July 2002

PrrC fromRhodobacter sphaeroidesprovides the signal input to a two‐component signal transduction system that senses changes in oxygen tension and regulates expression of genes involved in photosynthesis (Eraso, J.M. and Kaplan, S. (2000) Biochemistry 39, 2052‐2062; Oh, J.‐I. and Kaplan, S. (2000) EMBO J. 19, 4237‐4247). It is also a homologue of eukaryotic Sco proteins and each has a C‐x‐x‐x‐C‐P sequence. In mitochondrial Sco proteins these cysteines appear to be essential for the biogenesis of the CuAcentre of respiratory cytochrome oxidase. Overexpression and purification of a water‐soluble and monomeric form of PrrC has provided sufficient material for a chemical and spectroscopic study of the properties of the four cysteine residues of PrrC, and its ability to bind divalent cations, including copper. PrrC expressed in the cytoplasm ofEscherichia colibinds Ni2+tightly and the data are consistent with a mononuclear metal site. Following removal of Ni2+and formation of renatured metal‐free rPrrC (apo‐PrrC), Cu2+could be loaded into the reduced form of PrrC to generate a protein with a distinctive UV‐visible spectrum, having absorbance with aλmaxof 360 nm. The copper:PrrC ratio is consistent with the presence of a mononuclear metal centre. The cysteines of metal‐free PrrC oxidise in the presence of air to form two intramolecular disulfide bonds, with one pair being extremely reactive. The cysteine thiols with extreme O2sensitivity are involved in copper binding in reduced PrrC since the same copper‐loaded protein could not be generated using oxidised PrrC. Thus, it appears that PrrC, and probably Sco proteins in general, could have both a thiol‐disulfide oxidoreductase function and a copper‐binding role.
The determinants of the oligomeric structure in Hsp16.5 are encoded in the α‐crystallin domain
Authors: Koteiche Hanane A , Mchaourab Hassane S
Published: July 2002

The determinants of the oligomeric assembly of Hsp16.5, a small heat‐shock protein (sHSP) from Methanococcus jannaschii, were explored via site‐directed truncation and site‐directed spin labeling. For this purpose, subunit contacts around the two‐, three‐ and four‐fold symmetry axes were fingerprinted using patterns of proximities between nitroxide spin labels introduced at selected sites. The lack of change in this fingerprint in an N‐terminal truncation of the protein demonstrates that the interactions are encoded in the α‐crystallin domain. In contrast, the truncation of the N‐terminal domain of Mycobacterium tuberculosis Hsp16.3, a bacterial sHSP with an equally short N‐terminal region, results in the dissociation of the oligomer to a trimer. These results, in conjunction with those from previous truncation studies in mammalian sHSP, suggest that as the α‐crystallin domain evolved to encode a smaller basic unit than the overall oligomer, the control of the assembly and dynamics of the oligomeric structure became encoded in the N‐terminal domain.
Axonal sprouting regulates myelin basic protein gene expression in denervated mouse hippocampus
Authors: Jensen Michael B. , Poulsen Frantz R. , Finsen Bente
Published: July 2002

The regulation of oligodendrocyte gene expression and myelination in vivo in the normal and injured adult CNS is still poorly understood. We have analyzed the effects of axotomy‐induced axonal sprouting and microglial activation, on oligodendrocyte myelin basic protein (MBP) gene expression from 2 to 35 days after transection of the entorhino‐hippocampal perforant path axonal projection. In situ hybridization analysis showed that anterograde axonal and terminal degeneration lead to upregulated oligodendrocyte MBP mRNA expression starting between day 2 and day 4, in (1) the deep part of stratum radiatum of CA3 and the dentate hilus, which display axonal sprouting but no degenerative changes or microglial activation, and (2) the outer part of the molecular layer of the fascia dentata, and in stratum moleculare of CA3 and stratum lacunosum‐moleculare of CA1, areas that display dense anterograde axonal and terminal degeneration, myelin degenerative changes, microglial activation and axotomi‐induced axonal sprouting. Oligodendrocyte MBP mRNA expression reached maximum in both these areas at day 7. MBP gene transcription remained constant in stratum radiatum, stratum pyramidale and stratum oriens of CA1, areas that were unaffected by perforant path transection. These results provide strong evidence that oligodendrocyte MBP gene expression can be regulated by axonal sprouting independently of microglial activation in the injured adult CNS.
Conversion of Fumaric Acid to l‐Malic by Sol‐Gel Immobilized Saccharomyces cerevisiae in a Supported Liquid Membrane Bioreactor
Authors: Bressler Eyal , Pines Ophry , Goldberg Israel , Braun Sergei
Published: July 2002

Conversion of fumaric acid (FA) to l‐malic acid (LMA) was carried out in a bioreactor divided by two supported liquid membranes (SLMs) into three compartments: Feed, Reaction, and Product. The Feed/Reaction SLM, made of tri‐ n‐octylphosphine oxide (vol 10%) in ethyl acetate, was selective toward the substrate, fumaric acid ( SFA/LMA = 10). The Reaction/Product SLM, made of di(2‐ethylhexyl) phosphate (vol 10%) in dichloromethane, was selective toward the product, l‐malic acid ( SLMA/FA = 680). Immobilized yeast engineered to overproduce the enzyme fumarase [E.C. 4.2.1.2] was placed in the Reaction compartment and served as the catalyst. The yeast was immobilized in small glasslike beads of alginate‐silicate sol‐gel matrix. The construction of the bioreactor ensured unidirectional flow of the substrate from the Feed to the Reaction and of the product from the Reaction to the Product compartments, with the inorganic counterion traveling in the opposite direction. The conversion of almost 100%, above the equilibrium value of ca. 84% and higher than that for the industrial process, 70%, was achieved. In contrast to the existing industrial biocatalytic process resulting in l‐malic acid salts, direct production of the free acid is described.
Skin‐prick test findings in students from moisture‐ and mould‐damaged schools: A 3‐year follow‐up study
Authors: Immonen Johanna , Meklin Teija , Taskinen Taina , Nevalainen Aino , Korppi Matti
Published: July 2002

Dampness and moisture problems in a building may cause growth of moulds, leading to sensitization and symptoms in the inhabitants. The mechanism by which sensitization to moulds takes place has remained obscure; in particular, the role of atopy is not clear. In 1996, 622 pupils (7–13 years of age) attending a school with a moisture problem (index school; 414 pupils) and a control school (208 pupils) were screened using a questionnaire. Two‐hundred and twelve children had doctor‐diagnosed asthma, parental‐reported wheezing or prolonged cough, and they participated in a clinical study, which included skin prick tests (SPT) to 12 moulds. An identical, follow‐up study was performed 3 years later in 1999. In the follow‐up study, 144 of the original 212 students participated. They were now attending four different schools: the index primary school had been renovated and the control school remained unchanged, but the two secondary schools had moisture and mould problems. The purpose of the study was to evaluate the occurence of mould allergy in children of school age and to compare sensitization to moulds in relation to age, exposure, asthma, and atopy. In 1999, SPT responses to moulds were demonstrated in 17 (12%) of the 144 children. Six children had SPT reactions ≥ 3 mm and all but one were older than 14 years. During the 3‐year follow‐up period, mould allergy developed in five children and disappeared in two children. Five of the six children with reactions ≥ 3 mm to moulds had positive responses to other allergens, five had clinical atopy but only two had asthma. Likewise, all six children had been exposed to moisture and dampness in the school buildings. In conclusion, mould allergy diagnosed by SPTs was rare in students. Most reactions to moulds were in students older than 14 years with multiple SPT reactions to common allergens, and there was no significant association with asthma.
Reactive sulphur species: an in vitro investigation of the oxidation properties of disulphide S-oxides
Authors: GILES Gregory I. , TASKER Karen M. , COLLINS Catriona , GILES Niroshini M. , O'ROURKE Elizabeth , JACOB Claus
Published: July 2002

We have recently proposed that disulphide S-monoxides (thiosulphinates) and disulphide S-dioxides (thiosulphonates) are formed from their parent disulphides and ‘reactive oxygen species’ during oxidative stress. These ‘reactive sulphur species’ are themselves strong oxidizing agents that preferably attack the thiol functionality. We now show that under conditions where disulphides show little effect, disulphide S-oxides rapidly modify metallothionein, alcohol and glyceraldehyde 3-phosphate dehydrogenases and a zinc finger-protein fragment in vitro. The known antioxidants ascorbate, NADH, trolox and melatonin are unable to inhibit this oxidation pathway and only an excess of the cellular redox-buffer glutathione quenches the disulphide S-oxide activity. These results suggest that, under conditions of oxidative stress, despite the presence of high concentrations of antioxidants, reactive sulphur species formation may occur and inhibit the function of thiol-dependent proteins. Such a characterization of the disulphide S-oxide-oxidation pathway might also account for some previously observed anomalies in protein oxidation.
Comparative demography of two giant caulescent rosettes (Espeletia timotensis and E. spicata) from the high tropical Andes
Authors: Silva Juan F. , Trevisan Maria Cristina , Estrada Carlos A. , Monasterio Maximina
Published: July 2002

Using field data from previous studies we built matrix models for two populations of giant rosettes, Espeletia timotensis Cuatrec. and E. spicata Sch. Bip. Wedd., from the Andes Cordillera in Mérida, Venezuela. We analysed the models and calculated population growth rate (λ), sensitivities, elasticities and the sensitivity of the elasticities to changes in the vital rates. The analysis showed that the two species behave alike in general demographic terms. In both models, population growth rate is positive and sensitivities of λ to changes in vital rates decrease markedly in this order: plant establishment, progression of juvenile–adult, germination and survival. The relative contributions of vital rates to λ (elasticities) are very similar to those of other woody plant species: a higher contribution of survival and a very low contribution of fecundity. Transition from seedling to juvenile is most important and the younger established stages (juveniles and young adults) play a predominant demographic role in both populations. Seed banks and older adults are playing a relatively minor role in the dynamics of both populations. However, they may be important in relation to unpredictable, favourable or detrimental events. Perturbation analysis of elasticities showed that increasing the rate of plant establishment will decrease the relative importance of stasis. We conclude that both species are demographically very close, and similar to other long‐lived woody plant species. However, the two species differ in the role of the seed bank, which seems more important in the demography of E. spicata than in E. timotensis.
Accommodative error, adaptation and myopia
Authors: Rosenfield Mark , Gilmartin Bernard
Published: July 2002

Accommodative adaptation, resulting from the sustained output of slow blur‐driven accommodation during the course of a sustained near‐vision task, has generally been assessed under open‐loop conditions. This study examined whether adaptation influences closed‐loop accommodation during the course of a sustained near‐vision task. Accommodative adaptation was assessed in 18 fully‐corrected subjects by comparing pre‐ and post‐task values of dark accommodation recorded objectively with an infra‐red optometer. Subjects performed a continuous 10 min binocular near‐vision task at a viewing distance of 33 cm, with the within‐task accommodative response being assessed at 1 min intervals during this period. Subjects were categorized into adaptors (N=11) and non‐adaptors (N=7) on the basis of whether their initial 10 sec post‐task adaptation exceeded +0.30D. The adapting group exhibited a significant decline in the lag of accommodation during the first 3  min of the near‐task, whereas no significant change in the within‐task response over time was observed in the non‐adapting group. These results indicate that accommodative adaptation increases the accuracy of the within‐task, closed‐loop accommodative response. Furthermore, we speculate that a deficit in accommodative adaptation, being accompanied by increased retinal defocus during near fixation, may contribute to the development of nearwork‐induced myopia.
Buried double waveguide by ion implantation in quartz
Authors: Chandler P. J. , Lama F. L. , Townsend P. D. , Zhang L.
Published: July 2002

Ion implantation may be used to produce barrier-confined optical waveguides in many crystalline materials by decreasing the refractive index in the nuclear stopping region at the end of the ion’s track. In quartz this is particularly effective as the nuclear damage soon saturates at ∼5%, and also practically no index change occurs along the initial part of the track, thus enabling multiple-energy implants to produce broad, flat barriers. We report the use of this technique in the construction of a device with two such barriers at different depths, thus producing a pair of overlayed waveguides. The profile of this composite system could not be determined by any conventional mode analysis method, and so we have extended our dark mode reflectivity technique to cope with multiple barriers. It has proved a very powerful tool for this application, able to probe at sufficient depth below the surface to supply accurate information about the entire double profile.
Schottky barrier and contact resistance at a niobium/silicon interface
Authors: Heslinga D. R. , Klapwijk T. M.
Published: July 2002

Electrical transport properties of niobium-silicon contacts are reported over a wide doping range. It is found that a short low-energy argon plasma sputtering of the silicon surface prior to metal deposition lowers the Schottky barrier height by 0.12 eV, without degrading diode ideality. This result is interpreted as a partial explanation for the dependence of the superconducting proximity effect in semiconductors on sputter cleaning.
High-speed absorption recovery in quantum well diodes by diffusive electrical conduction
Authors: Livescu G. , Miller D. A. B. , Sizer T. , Burrows D. J. , Cunningham J. E. , Gossard A. C. , English J. H.
Published: July 2002

We present here picosecond time-resolved electroabsorption measurements in GaAs quantum well p-i-n diode structures. While the dynamics of the vertical transport is not completely understood at present, our data reveal the importance of the ‘‘lateral’’ propagation of the photoexcited voltage pulse over the area of the doped regions. We propose a two-dimensional ‘‘diffusive conduction’’ mechanism, which predicts a fast relaxation of the electrical pulse, with time constants ranging from 50 fs to 500 ps, determined by the size of the exciting spot, the resistivity of the doped regions, and the capacitance of the intrinsic region.
Tetragonal and monoclinic forms of GexSi1−x epitaxial layers
Authors: Eaglesham D. J. , Maher D. M. , Fraser H. L. , Humphreys C. J. , Bean J. C.
Published: July 2002

The effect of strains on the local crystallographic symmetry and structure of a Si/GexSi1−x model heterostructure grown on a (100) silicon substate was studied using convergent beam electron diffraction techniques and a cross-sectional specimen geometry. The alloy layers are seen to distort into relaxed tetragonal and monoclinic structures which are dependent on position and/or alloy composition. These observations can be explained in terms of strain relaxation in a thin-film specimen and deviations of the substrate from a perfect (100) orientation. The results have implications not only for the use of cross-sectioned specimens in the characterization of strained-layer heterostructures, but also for the band engineering of Si/GexSi1−x strained-layer superlattices and other materials which are grown on vicinal (100) and other low-symmetry substrate orientations. In particular relaxed tetragonal and monoclinic structures may be quite relevant to the emerging science of strain-induced lateral confinement of carriers in quantum well semiconductors.
Fabrication and structure of epitaxial Er silicide films on (111) Si
Authors: d’Avitaya F. Arnaud , Perio A. , Oberlin J.-C. , Campidelli Y. , Chroboczek J. A.
Published: July 2002

We prepared Er silicide films on (111) Si by (1) deposition of Er and contact reaction at 380 °C or (2) vacuum codeposition of Er and Si maintaining the flux ratio close to 1:2. Subsequent annealing at temperatures up to 900 °C yielded monocrystalline, continuous layers, whose properties were examined by means of low-energy electron diffraction, Auger spectroscopy (in situ) and (ex situ), x-ray and high-energy electron diffraction, and Rutherford backscattering. Method 2 was shown to give better results. The films had a hexagonal AlB2 structure with Si deficiency up to 20%, which is consistent with formerly published results on Si vacancy formation. We showed that the film structure had an additional periodicity of 15 Å along the 〈110〉 orientations of Si and of 6 Å along the 〈112〉 orientations of Si. We demonstrated a feasibility of Si reepitaxy on Er silicide deposited on (111) Si, thus fabricating a novel semiconductor/metal/semiconductor epitaxial heterostructure.
Extremely low resistivity erbium ohmic contacts to n-type silicon
Authors: Janega P. L. , McCaffrey J. , Landheer D.
Published: July 2002

Employing structures consisting of Pt, Si, and Er layers on Si, contacts to nSi with resistivities as low as 3.7×10−8 Ω cm2 were obtained and a low-leakage high-breakdown voltage Schottky diode on pSi was realized. Measured contact resistivities are lowest among the known contacts to nSi. Extended transmission line method measurements were made to determine contact resistivities for contacts to n-type silicon doped in the range 1018 –1020 cm−3 . The data are consistent with a barrier height of ∼0.37 eV. The metallurgy of the contacts was studied using transmission electron microscopy.
Epitaxial explosive crystallization of amorphous silicon
Authors: Polman A. , Mous D. J. W. , Stolk P. A. , Sinke W. C. , Bulle-Lieuwma C. W. T. , Vandenhoudt D. E. W.
Published: July 2002

It is shown that amorphous silicon can be transformed to monocrystalline silicon via an explosive epitaxial crystallization process induced by pulsed laser irradiation. 370-nm-thick amorphous Si layers, buried beneath a 130-nm-thick crystalline surface layer, were irradiated with a 32 ns ruby laser pulse. Real-time reflectivity measurements indicate that internal melting can be initiated at the amorphous-crystalline interface, immediately followed by explosive crystallization of the buried amorphous Si layer. Channeling and cross-sectional transmission electron microscopy reveal that explosive crystallization proceeds epitaxially with formation of twins extending into the sample. The crystal growth velocity is determined to be 16.2±1.2 m/s, close to the fundamental limit for crystalline ordering at a liquid Si/Si(100) interface.
Effects of frequency spreads on beam breakup instabilities in linear accelerators
Authors: Colombant D. G. , Lau Y. Y.
Published: July 2002

Structure mode frequency spreads are shown to have a rather different influence on beam breakup growths than betatron frequency spreads. The present analytic and numerical studies show that a finite spread in the breakup mode frequency leads to an algebraic decay of the beam breakup instabilities even if the quality factor Q→∞. Effects of stagger tuning are examined.
Coherent operation of an array of diode lasers using a spatial filter in a Talbot cavity
Authors: D’Amato F. X. , Siebert E. T. , Roychoudhuri C.
Published: July 2002

Coherent operation of an array of AlGaAs diode lasers was obtained by placing the array in an external cavity which made use of the Talbot self-imaging effect to couple the laser diodes together. A spatial filter was required to suppress oscillation of the highest order mode of the array. This filter introduced no significant loss to the cavity mode, and the mode was observed to be stable up to the maximum rated drive current for the device.
High-power and high-speed 1.3 μm V-grooved inner-stripe lasers with new semi-insulating current confinement structures on p-InP substrates
Authors: Wada H. , Horikawa H. , Matsui Y. , Ogawa Y. , Kawai Y.
Published: July 2002

A significant improvement in the maximum output power of a 1.3 μm GaInAsP/InP laser with a semi-insulating current confinement structure is reported. The improvement has been achieved by interposing an n-type InP layer between a p-InP substrate and an Fe-doped InP layer. A maximum cw output power of 180 mW and a modulation bandwidth of 8.5 GHz have been obtained.
Magnetosonic wave generation by super-Alfvénic ion ring propagation in plasma
Authors: Schamiloglu E. , Greenly J. B. , Hammer D. A.
Published: July 2002

A weakly diamagnetic rotating proton beam propagating at about four times the Alfvén speed along a magnetized hydrogen plasma column generated magnetosonic waves when the beam rise time was less than about three radial Alfvén transit times. The waves were collisionally damped and the damping increased as the induced cross-field plasma current became stronger. Our beam and plasma conditions suggest that the damping is due to an enhanced collision frequency resulting from a modified two-stream instability.
Magnetic microstructure of the (0001) surface of hcp cobalt
Authors: Unguris J. , Scheinfein M. R. , Celotta R. J. , Pierce D. T.
Published: July 2002

The magnetic domain structure of the (0001) surface of a hcp cobalt crystal was investigated using scanning electron microscopy with polarization analysis (SEMPA). This is the first observation by SEMPA of both out-of-plane and in-plane magnetization components. The perpendicular magnetization imaged with SEMPA showed a branched structure very similar to that previously observed by magneto-optic Kerr microscopy. In addition, a previously unobserved in-plane magnetic substructure was measured. The in-plane magnetization is divided into well-defined submicron domains that appear to reflect the sixfold symmetry of the crystal surface.
Depolarization field and ionic effects on the bistability of surface-stabilized ferroelectric liquid-crystal devices
Authors: Yang K. H. , Chieu T. C. , Osofsky S.
Published: July 2002

Based on a collective switching model coupled to a simplified continuity equation for impurity ions, the internal electric field and light transmission of a surface-stabilized (SS), layer-tilted ferroelectric liquid-crystal (FLC) cell with insulating alignment layers have been calculated as a function of time, under bipolar voltage pulses. The polarization and ionic charges, accumulated on the interfaces between the FLC medium and alignment layers, tend to partially screen the external on-field and generate a depolarization field to reverse the spontaneous polarization when the external field is off. When the thickness of the alignment layer is greater than 1000 Å, it is difficult to achieve bistability using FLC mixtures with a spontaneous polarization larger than approximately 20 nC/cm2. For bistability to occur in a SSFLC cell with high spontaneous polarization, thin insulating or conducting alignment layers are preferred. We also found that the existence of impurity ions in a SSFLC cell is always detrimental to bistability in spite of their low mobilities (≂10−7 cm2/V s).
Kinetics aspects of TiSi2 deposition without silicon consumption
Authors: Bensahel D. , Regolini J. L. , Mercier J.
Published: July 2002

Selectively deposited layers of TiSi2 have been obtained without Si substrate consumption using the TiCl4/SiH4 system diluted in H2 at 800 °C. For a given set of parameters, we show that TiSi2 formation uses Si coming from the substrate or from the gas phase, the principal parameters being the TiCl4/SiH4 ratio, the carrier gas, and gas mass transfer as the limiting mechanism of the reactions.
Electron cyclotron resonance plasma etching of InP in CH4/H2/Ar
Authors: Pearton S. J. , Chakrabarti U. K. , Kinsella A. P. , Johnson D. , Constantine C.
Published: July 2002

Plasma etching of InP in a microwave (2.45 GHz) electron cyclotron resonance (ECR) CH4/H2/Ar discharge has been investigated as a function of additional radio frequency (rf, 13.56 MHz) self-biasing of the sample. The etch rate of InP in a 1 mTorr, 250 W CH4/H2/Ar (5/15/7) ECR discharge increases linearly with applied rf bias, from 50 Å min−1 at 0 V to 350 Å min−1 at 200 V. Etching under ECR conditions alone yields smooth surface morphologies, while additional rf biasing of the discharge leads to In droplets remaining on the surface. This appears to be a result of preferential removal of P by the high atomic hydrogen density in the discharge. The room-temperature photoluminescence intensity from InP is reduced by approximately an order of magnitude after ECR etching, but is restored after removal of ∼20 Å from the surface by wet chemical etching. Gold Schottky contacts on InP samples etched under ECR conditions only yield barrier heights of 0.48 eV and ideality factors of 1.1, essentially identical to those on wet-etched control samples. ECR etching performed with an additional 100 V rf bias yields diodes with barrier heights of 0.44 eV and ideality factors of 1.6. Removal of ∼20 Å of the surface on these samples restores the values to those obtained on the control material.
High-speed laser direct writing of tungsten conductors from W(CO)6
Authors: Nambu Y. , Morishige Y. , Kishida S.
Published: July 2002

High-speed laser direct writing of tungsten conductors using tungsten-hexacarbonyl [W(CO)6] is demonstrated. Tungsten lines were constructed on the Si-LSI substrate at a writing speed as high as 300 μm/s with laser-induced low-pressure chemical vapor deposition. This speed is more than two orders of magnitude higher than the previously reported value for this material. Experiments are analyzed within the conventional three-dimensional diffusion theory for the reactant. It has been found that the deposition rate limiting factor is the transport rate for the reactant into the reaction zone. The upper limit of the writing speed is predicted to be of the order of mm/s for the present material.
Highly efficient and stable nonlinear optical polymers via chemical cross-linking under electric field
Authors: Jungbauer D. , Reck B. , Twieg R. , Yoon D. Y. , Willson C. G. , Swalen J. D.
Published: July 2002

Extending the novel method of Eich et al. [J. Appl. Phys. 66, 3241 (1989)] to prepare highly stable second-order nonlinear optical (NLO) polymers via chemical cross-linking under electric field, we have obtained a new polymer exhibiting large and stable second-order optical nonlinearities after relaxation at 80 °C. This was achieved by forming a network polymer from two NLO-active monomers, bifunctional N,N-(diglycidyl)-4-nitroaniline and trifunctional N-(2-aminophenyl)-4-nitroaniline. Here, every NLO moiety is connected to the network by a single covalent bond. After full cure under corona poling at 120 °C, the sample exhibited at ambient conditions d33≂50 pm/V and d31≂16 pm/V at 1064 nm fundamental wavelength, as estimated from the Maker fringe data. Upon heating to 80 °C, the nonlinearities decreased somewhat initially, but leveled off and remained stable at 80 °C. This stable sample gave d33≂42 pm/V and d31≂14 pm/V at ambient conditions. Furthermore, the linear electro-optical coefficient of this sample, measured with a Mach–Zehnder interferometer, was r13≂6.5 pm/V at 530.9 nm. From this r13 coefficient one estimates d31≂11 pm/V at 1064 nm, in good agreement with the Maker fringe value.
Fabrication and investigation of asymmetric current-voltage characteristics of a metal/Langmuir–Blodgett monolayer/metal structure
Authors: Geddes N. J. , Sambles J. R. , Jarvis D. J. , Parker W. G. , Sandman D. J.
Published: July 2002

Metal/Langmuir–Blodgett monolayer/metal devices, where the monolayer consists of the dodecyloxyphenylcarbamate of 2-bromo, 5(2′-hydroxyethoxy) tetracyanoquinodimethan, a donor-σ-acceptor molecular system, have been constructed, and dc current-voltage (I-V) characteristics of these devices were recorded at room temperature. For biases of ±20 mV, the I-V characteristics are linear, changing to a nonlinear form for higher voltages. This nonlinear characteristic exhibited a ln(I)∝V1/4 dependence for both positive and negative voltages up to ±1 V. For positive voltages >+2.0 V for as-prepared devices and >+1.5 V for annealed devices, a ln(I)∝V3 dependence was observed, revealing a very large increase in current for small voltage changes. Such behavior was not observed for corresponding negative voltages, indicating rectification across a distance approximated by the length of an individual molecule.
Polymer-dispersed chiral liquid crystal color display
Authors: Crooker P. P. , Yang D. K.
Published: July 2002

We describe a new type of color display consisting of polymer-dispersed droplets of chiral liquid crystal having negative dielectric anisotropy. In the field-off state, the droplets scatter light randomly. In the field-on state the droplets selectively reflect a bright color. Measurements of reflectivities and switching times are presented and we discuss possible applications.
GaAs/GaInP multiquantum well long-wavelength infrared detector using bound-to-continuum state absorption
Authors: Gunapala S. D. , Levine B. F. , Logan R. A. , Tanbun-Ek T. , Humphrey D. A.
Published: July 2002

We demonstrate an 8 μm superlattice infrared detector which utilizes bound-to-continuum state intersubband absorption in lattice-matched GaAs/Ga0.5In0.5P multiquantum well structures grown by atmospheric pressure metalorganic vapor phase epitaxy. The band offsets of the GaAs/Ga0.5In0.5P heterosystem are obtained by comparing the theoretical absorption spectrum and the measured responsivity spectrum. The values determined for ΔEc and ΔEv are 221 and 262 meV, respectively.
Heteroepitaxial ultrafine wire-like growth of InAs on GaAs substrates
Authors: Yazawa M. , Koguchi M. , Hiruma K.
Published: July 2002

We demonstrate heteroepitaxial ultrafine wire-like growth of InAs. Ultrafine InAs whiskers with diameters less than 20 nm are grown selectively on SiO2-patterned GaAs substrates using metalorganic vapor phase epitaxy. These InAs nanowhiskers grow epitaxially with a growth axis parallel to the 〈111〉As dangling bond direction of the GaAs substrate surface irrespective of substrate orientation.
Current quenching in the pseudospark
Authors: Hartmann W. , Kirkman G. F. , Gundersen M. A.
Published: July 2002

A study of current quenching in the pseudospark is presented. Current quenching during the conductive phase limits peak conduction current in certain thyratron switches. The quenching phenomenon also occurs in the pseudospark. However, a remarkable feature is that current quenching is observed only below currents of ≊ 2–3 kA, near the onset of superemissive behavior, and thus in the pseudospark is not an upper limit to high current operation. A mechanism involving an instability caused by ion depletion at the plasma boundary is discussed.
Excitons and light-induced degradation of amorphous hydrogenated silicon
Authors: Brandt Martin S. , Stutzmann Martin
Published: July 2002

Excitonic states involved in electronic transport of undoped amorphous hydrogenated silicon (a-Si:H) are observed using spin-dependent photoconductivity (SDPC). Upon light soaking the excitonic signal decreases with regard to the SDPC signal due to recombination via dangling bonds. It has been suggested that excitonic tail-to-tail recombination leads to metastable defect creation in a-Si:H. Our experimental results are shown to be consistent with this model.
Multichannel slab discharge for CO2 laser excitation
Authors: Yelden E. F. , Seguin H. J. J. , Capjack C. E. , Nikumb S. K.
Published: July 2002

Experimental results on a unique multichannel slab-type CO2 discharge system are presented. The interdigital discharge geometry incorporates both large-area and multibeam laser array concepts into a single, compact package. Small signal gain and saturation intensity values indicate that this structure is well suited for use in a CO2 laser.
Measurement of aluminum concentration in epitaxial layers of AlxGa1−xAs on GaAs by double axis x-ray diffractometry
Authors: Tanner B. K. , Turnbull A. G. , Stanley C. R. , Kean A. H. , McElhinney M.
Published: July 2002

The composition of a series of AlxGa1−xAs layers grown epitaxially by molecular beam epitaxy (MBE) on GaAs has been measured independently by double axis x-ray diffractometry and reflection high-energy electron diffraction. From a quadratic fit to the data, we deduce the lattice parameter mismatch between AlAs and GaAs and the Poisson ratio of AlAs. Asymmetric reflection rocking curves and synchrotron x-ray topography have been used to show that the anomalously low substrate-layer peak splitting for the 1-μm-thick AlAs layer results from relaxation, which is asymmetric. Use of the AlAs rocking curve peak splitting corrected for relaxation yields a mismatch of 1600 ppm (±1%) between AlAs and GaAs, and 0.28±0.01 for the Poisson ratio of AlAs.
Blue light generation by frequency doubling of AlGaAs broad area amplifier emission
Authors: Goldberg L. , Busse L. , Mehuys D.
Published: July 2002

The diffraction limited emission of a traveling wave single pass 600-μm wide SQW GaAlAs amplifier injected by a Ti:Sapphire laser was frequency doubled in KNbO3 to generate 400 mW peak power 5 μs long pulses of 431 nm light. A maximum single pass frequency conversion efficiency of 6.3% was observed.
Plating-free metal ion implantation utilizing the cathodic vacuum arc as an ion source
Authors: Sroda T. , Meassick S. , Chan C.
Published: July 2002

A plating-free ion-implantation system utilizing the cathodic vacuum arc as a pulsed source of metal ions has been demonstrated. This process incorporates a dc target bias and an electromagnetic ion-separation mechanism to produce a fully ionized ion beam that is free of neutrals and macroparticles. Analysis of aluminum ions implanted into silicon using energy dispersive analysis indicates that the total implanted-ion dose increases linearly with the number of pulses reaching a dose of 3×1014/cm2 for 650 000 pulses. An alternate analysis, utilizing a bevel-and-stain technique, also indicates an implanted dose that increases linearly with the number of pulses.