bluuebunny/crossref_metadata_2025 huggingface dataset:
Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data
Authors: Noureen Nighat , Ye Zhenqing , Chen Yidong , Wang Xiaojing , Zheng Siyuan
Published: February 2022

Quantifying the activity of gene expression signatures is common in analyses of single-cell RNA sequencing data. Methods originally developed for bulk samples are often used for this purpose without accounting for contextual differences between bulk and single-cell data. More broadly, few attempts have been made to benchmark these methods. Here, we benchmark five such methods, including single sample gene set enrichment analysis (ssGSEA), Gene Set Variation Analysis (GSVA), AUCell, Single Cell Signature Explorer (SCSE), and a new method we developed, Jointly Assessing Signature Mean and Inferring Enrichment (JASMINE). Using cancer as an example, we show cancer cells consistently express more genes than normal cells. This imbalance leads to bias in performance by bulk-sample-based ssGSEA in gold standard tests and down sampling experiments. In contrast, single-cell-based methods are less susceptible. Our results suggest caution should be exercised when using bulk-sample-based methods in single-cell data analyses, and cellular contexts should be taken into consideration when designing benchmarking strategies.
Sonographic Assessment of Fetal Cephalic Index in a Sampled Nigerian Population
Authors: Erim Akwa E. , Ijever Wueseter A. , Efanga Itoro S. , Udoh Benjamin E.
Published: February 2022

Objectives: The study aimed to determine fetal cephalic index among fetuses in Cross River State, Nigeria. Materials and Method: Transabdominal ultrasound was carried out on 220 women attending obstetric sonography in their second and third trimesters between September and December, 2020 in Cross River State, Nigeria. Each patient was scanned in a supine position, Bi-parietal diameter (BPD) measurements were taken from the outer edge of the closer temporoparietal bone to the inner edge of the farther temporoparietal bone. The occipito-frontal (OF) measurements were taken from the occipital bone to the frontal bone, and the cephalic index determined using the formula CI = BPD/OF *100. Results: Mean values of cephalic index and standard deviation was calculated for the fetuses at different gestational ages. The results showed that the mean cephalic index was 76.48±11.87. Male fetuses had cephalic index of 78.18±4.11 while female had cephalic index of 74.34±16.52. There was significant difference in the cephalic index between male and female fetuses (p0.002). Conclusion: The present study shows the cephalic index of fetuses of cross river state population remained mesaticephalic from 13 weeks of gestation to full term. This may be attributed to the ethnicity and race of this group of people.
COVID-19 Drugs and Glucose-6-phosphate Dehydrogenase Deficiency: A Matter of Life Threatening And Public Health
Authors: Ioscoa Carmela , Eason Verity , Gueyec Ibrahima , Leavy Renee
Published: February 2022

Background: The current COVID-19 pandemic has created significant health consequences for the world population. Therapies and drugs are being continuously developed in an effort to implement the most effective treatment. G6PD deficiency is the most prevalent human enzymatic defect, affecting more than 500 million people worldwide, but is infrequently taken into consideration in healthcare practice. Purpose: The aim of this review is collecting and assembling the most relevant information about safety of current drugs and nutraceuticals, proposed or already used for COVID-19 treatment, with regard to G6PD deficient people, in order to know possible drug-induced adverse effects. Methods: An extensive literature search was performed through scientific papers, unsafe drug lists, drug datasheets, drug databases, National Public Health institutional websites. Results: Methylene blue, ozone, chloroquine and hydroxychloroquine administration should be avoided in G6PD deficient patients. The other reviewed drugs should be administered at therapeutic doses under medical supervision. Conclusion: The list of drugs and nutraceuticals for use in COVID-19 here provided, usefully brought to Healthcare personnel’s and patients’ awareness before any drug administration, may allow you to avoid or at least manage any possible drug-associated symptoms - particularly hemolytic crisis, which is a potentially fatal risk for G6PD deficient patients.
Identification and Validation of a Prognostic Biomarker for Septic Arthritis: A Hypothesis
Authors: Adusumalli Ravi , Sreenivasa Swamy
Published: February 2022

Inflammation is a hallmark of many diseases including septic arthritis (SA) or infectious arthritis (IA). The bacteria Staphylococcus aureus is the most common cause of septic arthritis in humans. The statistical incident rate for SA is 2-10 per 100,000 patients years in the USA and Western Europe. Currently, there is no ideal diagnostic or prognostic biomarker for SA at the moment. By virtue of their lack of specificity and accuracy, traditional inflammatory biomarkers are often ineffective in distinguishing SA from infectious joint disease. The present hypothesis wishes to explore the discriminatory power of unique inflammatory biomarkers in liquid biopsy samples of bacteria induced mice and SA patient samples by means of genome wide analysis in which includes epigenetic, genomics and transcriptome expression pattern. Investigation on gene expression by RNA sequencing and DNA methylation studies provides the best possible target genes of differentially expressed both RNA and DNA marker genes. The aim is to find a meaningful positive or negative association between gene expression in RNA sequencing data and DNA methylation status. Validation of differentially expressed genes and differentially methylated genes by functional mechanistic studies to determine the best predictive and prognostic marker for SA for regular therapeutic use by comparison with established reference genes. With respect to bacterial mediated mice vs SA patient gene contrast, the predicted results clarifies the in-depth understanding of pathophysiology, disease development, and SA status.
From entangled membranes to eclectic morphologies: cubic membranes as subcellular space organizers
Authors: Landh Tomas
Published: July 2002

The identification of evolutionary conserved membrane morphologies whose architecture is governed by cubic symmetry — cubic membranes — adds a new dimension to cell membrane functions and, perspicuously, to their role in subcellular space organization. Through analysis of electron micrographs, three families of cubic membranes have been unequivocally identified in which one or more (parallel) membranes, described by periodic cubic surfaces, partition space into two or more independent, albeit convoluted, subspaces of membrane potential determined dimensions. The choice of a particular cubic symmetry is suggested to be due to its activity. Here the architecture and function of multiple (≥ 3) subspace organization in classical membrane bound organelles is addressed. As it can be precisely determined with cubic membranes suggests that they can be employed as a reference morphology.
Molecular characterization of two forms of nontoxic‐nonhemagglutinin components of Clostridium botulinum type A progenitor toxins
Authors: Fujita Ryuji , Fujinaga Yukako , Inoue Kaoru , Nakajima Hiroshi , Kumon Hiromi , Oguma Keiji
Published: July 2002

The entire sequences of the type A nontoxic‐nonhemagglutinin gene and an adjacent open reading frame designated as orf 22‐a, which are located between the neurotoxin and the HA‐35 genes were determined. SDS‐PAGE and N‐terminal amino acid sequence analyses of the purified type A progenitor toxins (12S, 16S and 19S) indicate that the nontoxic‐nonhemagglutinins of 16S and 19S are single peptides of approximately 120k, but that of 12S has a cleavage at the site between Pro‐144 and Phe‐145 of this protein.
γ‐Amido‐ATP stabilizes a high‐fluorescence state of myosin subfragment 1
Authors: Wray John , Jahn Werner
Published: July 2002

On binding to myosin subfragment 1 (S1), the γ‐amido derivative of ATP (ATPγNH2), an isomer of adenosine 5′‐[β,γ‐imido]‐triphosphate (AMPPNP), induces a larger increase in the intrinsic (tryptophan) fluorescence than is seen with ATP. A binding constant of 1.7×107 M−1 was measured for ATPγNH2, compared to 2.1–2.4×107 M−1 for AMPPNP. ATPγNH2 was hydrolyzed only very slowly by S1. ATPγNH2 appears to stabilize the ‘closed’ conformation of S1, and does so without cleavage of the β–γ phosphate bond. The dissociation of actin‐S1 by ATPγNH2 and that of S1.ATPγNH2 by actin are both strikingly slow.
A Recombinant Lipoprotein Antigen against Lyme Disease Expressed in E.coli: Fermentor Operating Strategies for Improved Yield
Authors: Madurawe Rapti D. , Chase Terry E. , Tsao Eric I. , Bentley William E.
Published: July 2002

Decorin‐binding lipoprotein, lpp‐DBP, a bacterial surface adhesin, shows promise as a vaccine against Lyme disease. It is expressed in recombinant E. coli as an undesirable 20.5 KDa apoprotein that is subsequently lipidated in vivo to the desired 22 KDa lpp‐DBP form. This study defines fermentation conditions for maximizing lpp‐DBP yield. Super broth medium, a low post‐induction temperature (30 °C), and a glucose feed based on dissolved oxygen resulted in high lpp‐DBP yield and minimized apoprotein formation. Since cells lysed within 2−3 h after induction, the cell yield was maximized by growing cells to high cell density prior to induction. Compared to a glucose feed based on maintaining a constant fermentor glucose concentration (Glucose‐Stat), feeding based on maintaining a constant dissolved oxygen level (DO‐Stat) improved yields. Also, a dissolved oxygen level of 60% (air saturation) was best, as no product degradation was detected by Western blotting and SDS‐PAGE. Acetic acid levels under both modes of glucose feed were sufficiently low, and no adverse growth effects were observed.
Stress Survival of a Genetically Engineered Pseudomonas in Soil Slurries: Cytochrome P‐450cam‐Catalyzed Dehalogenation of Chlorinated Hydrocarbons
Authors: Rattan Kavita , Shanker Rishi , Khanna Purushottam , Atkins William M.
Published: July 2002

Biological treatment of hazardous chemical wastes has potential as an effective, practical, and economically viable process in above the ground treatment systems that consist of both genetically engineered microorganisms (GEMs) and bioreactors with process control instruments to create ideal conditions for biodegradation. A strain of Pseudomonas putida coexpressing cytochrome P‐450cam and luciferase (lux) that provides both the reductive detoxification potential of the hemoprotein and a mechanism for its reduction in the absence of “normal” P‐450 redox partners was evaluated for its ability to survive and remain metabolically competent under nutrient stress in soil slurry microcosms. More than 74% of the cells of engineered Pseudomonas were culturable after 7 days of multiple nutrient (C,N,P) starvation. The diagnostic luminescence and carbon monoxide‐difference spectra for the two engineered traits could be detected in a significant fraction of the surviving population. The GEM could be revived after repeated desiccation and starvation using Luria broth, benzoate, or citrate as nutrients. Soil slurries inoculated with the GEM transformed hexachloroethane (HCE) to tetrachloroethylene (tetraCE) 8–10‐fold faster than uninoculated slurries. The GEM also transformed the insecticide, γ‐HCH (γ‐3,4,5,6‐hexachlorocyclhexene), to γ‐3,4,5,6‐tetrachlorocyclohexene (γtetraCH) in soil slurries under subatmospheric conditions. These results indicate that GEMs can be constructed with broad substrate range detoxification catalysts such as cytochrome P‐450 for remediation.
Studies on analogs of a peptide derived from alpha‐fetoprotein having antigrowth properties
Authors: Eisele L.E. , Vakharia D.D. , MacColl R. , Mizejewski G.J. , Mesfin F.B. , Bennett J.A. , Andersen T.T. , Jacobson H.I.
Published: July 2002

Abstract: A 34‐amino acid portion of the third domain of alpha‐fetoprotein possesses antigrowth and anticancer activities. Three analogs of this sequence were chemically synthesized, in which the two cysteines of the original sequence were replaced by alanines, glycines or serines. The original cysteine and alanine peptides formed trimers at 0.20 g/L in pH 7.4 phosphate buffer, and the glycine and serine peptides formed dimers. Trimer preparations were more potent in inhibiting estrogen‐induced growth in the mouse uterine assays than the two dimeric oligomers. Of salient importance is that the alanine peptide retained its trimeric form in solution much longer than the cysteine peptide. Antigrowth assays were performed starting with stock solutions at a peptide concentration of 0.20 g/L, because at very high peptide concentration (8.0 g/L) the peptides aggregated extensively. All the peptides, although differing in biological activity, had almost identical secondary structures. Unlike alpha‐fetoprotein, the three peptides have low amounts of α‐helix. Trifluoroethanol has the ability to convert peptides into a helical conformation when they have a propensity for that structure. At trifluoroethanol concentrations of 20% and higher, the alanine and glycine peptides were changed into highly helical structures.
Global form perception: interactions between luminance and texture information
Authors: Van Der Zwan Rick , Badcock David R , Parkin Brent
Published: July 2002

Purpose: This experiment reports the independence of first‐ and second‐order processing mechanisms in form perception.

Methods: Symmetrical dot patterns were created using either luminance‐increment dots (luminance above background), or texture‐defined dots (average luminance equal to background). The proportion of luminance increment or texture dots defining each pattern was varied among fields of noise dots of the same type to determine symmetry detection thresholds.

Results: Differences in detection thresholds were found between luminance‐ and texture‐defined patterns. Further, symmetry detection thresholds for luminance‐increment dot patterns were resistant to noise defined by dots of opposite contrast polarity (luminance‐decrement dots) or texture, while texture‐defined patterns were resistant to neither texture nor luminance‐decrement noise.

Conclusions: These data suggest that symmetry perception, along with other types of form perception, use both first‐ and second‐order processing mechanisms. The data are compatible with a second‐order system that includes a negative half‐wave rectifying non‐linearity.
URINARY ALBUMIN IS A POWERFUL INDICATOR OF POOR HEALTH AND RISK FOR PREMATURE DEATH AMONG ABORIGINES (A)
Authors: We Hoy , Z Wang , P Baker , S McDonald , Jd Mathews , P. Van Buynder
Published: July 2002

Background: Adult death rates of A in the NT are increased 3‐6‐fold. Albuminuria (high albumin/creatinine ratio, ACR, gm/mol) is also pervasive & progressive. In a study of one community, ACR correlated with indices of poor health, including early malnutrition, increasing BP, glycemia and dyslipidemia, heavy drinking, & infections, and it predicts not only renal failure, but natural death (McDonald et al CEPP 1999). We further develop this last association and discuss its implications.

Methods: 763 adults (20+ yr)were screened & followed for 1‐8 yr (mean 4.3) yr, until death, renal failure, start of treatment or close‐out in April ‘98.

Results: Twelve people started dialysis: all had ACR 100+ at baseline. There were 61 natural deaths; 21 were cardiovascular (CV), 40 others were due to lung disease, infections, liver disease, amyloidosis, cancer etc. Death rates (CV and nonCV) correlated with increasing baseline ACR over a continuum in nondiabetics and diabetics. People with baseline ACR < 3.4 had a death rate of 4.7./1000 person yr, the referent group, while hazard ratios for natural death of persons with baseline ACRs of 3.4‐33, 34‐99 and 100+ were 2.3 (95% CI 0.98‐5.3), 3.2 (1.3‐7.9) and 5.1(2.1‐12.8) respectively (p = .0029) after accounting for age and sex. The population attributable risk for natural death or dialysis marked by ACR 3.4+ was 0.67 (CI .37‐.83), and for natural death alone was 0.59 (.22‐.79) after accounting for age, sex, diabetes & hyper‐tension. The excess CV mortality of diabetics was entirely represented by their higher baseline ACRs.

Conclusion:.
Much of the excess mortality in this group is predicted by albumin‐uria. Thus the kidney, whose maturation is very sensitive to early environment, and has vast vascular networks, high blood flow, high metabolic rate, and concentrating, phagocytic & endocrine functions, seems an exquisite marker of general health in A people. The ACR is a simple, reproducible, cheap test, which has wide potential application in definition of community health profiles and trends, and in defining diagnosis and prognosis. Initiation and titration of treatment might be guided by the ACR, and arrest of its progression results in dramatic reductions in natural deaths and renal failure.(Hoy et al, ANZSN '99).
TRANSGENIC MOUSE MODELS OF CHARCOT‐MARIE‐TOOTH 1b
Authors: Feltri M.L. , Quattrini A. , D'antonio M. , Imperiale D. , Dati G. , Previtali S. , Canal N. , Messing A. , Wrabetz L.
Published: July 2002

We are creating transgenic mouse models of hereditary motor and sensory neuropathy to address pathogenethic questions. First, we are testing the hypothesis that some Po mutations act through gain of function, by expressing a CMT1b mutation, delSer34, in addition to two normal copies of Po. We have shown previously that overexpression of wild type Po causes dysmyelination in a dose‐dependent fashion. Less than 50% overexpression of Po protein produces no effect, whereas higher overexpression causes severe dysmyelination. We have produced 5 lines of delSer34 transgenic mice that express the transgene at different levels, ranging from 5% to 300% of wild type Po. Lines that express Po delSer34 below the 50% threshold show abnormal myelin sheaths containing metachromatic material in semithin sections. Lines that express above the 50% threshold show positive signs characteristic of CMT1b, like “onion bulbs,” together with signs typical of wildtype Po overexpression. These myelin sheath abnormalities and onion bulbs are specific to mutant Po, as they were never observed in mice overexpressing wildtype Po. These preliminary results suggest that CMT1b mutations may have their effect through a dominant negative or toxic mechanism. In one line, mutant Po expression is roughly 50% of wildtype Po, a level comparable with one normal Mpz allele. This line was crossed with heterozygous Po knock out mice to obtain a genotype (Po wt/−/PodelSer34) similar to that of a CMT1b patient. These mice represent a potential model of CMT1b.
Therapeutic Pancreatic Endoscopy
Authors: Kozarek R. A.
Published: July 2002

Therapeutic endoscopy in pancreatitis has included biliary or pancreatic sphincterotomy, or both, for microlithiasis and sphincter dysfunction. Alternatively, endoscopic treatment has been used to treat ductal disruption, including external or internal fistulas (high amylase effusions, pancreatic ascites, pancreaticoenteric communications, or pseudocysts). Finally, endoscopy has been used to treat obstructive disease, including both stones and strictures. This article reviews the state of the art in this field over the past year. Unfortunately, this is an area in which the appropriate approaches are still poorly defined, and prospective studies randomly assigning patients to endoscopic treatment in comparison with medical or surgical therapy remain few and far between.
Universal resputtering curve
Authors: Morgan W. L.
Published: July 2002

The process of resputtering of material being sputter deposited onto a substrate is investigated via Monte Carlo simulations and simple analytical models. This resputtering comprises contributions from self-sputtering and from neutralized ions reflected from the target being sputtered. The results of these models are in reasonable agreement with recent measurements over a wide variety of gases and metal targets. When plotted versus a dimensionless mass parameter, the intrinsic resputtered fraction lies on a seemingly universal curve. The reason for this becomes clear through the development of the simple analytical models.
Interferometric detection of forward scattered light from small particles
Authors: Batchelder J. S. , Taubenblatt M. A.
Published: July 2002

The detection of subtenth micron paticles in processing fluids is a critical and growing need in the semiconductor industry. In this letter, we show that a small dielectric particle in a focused monochromatic light beam produces a scattered wave (Rayleigh scattering) in phase quadrature with the far-field incident beam, therefore causing a phase shift in this beam. Thus, the forward scattered field due to the particle may be detected using a bright field interferometer. This allows detection which is near Shott noise limited even for very small particles, and measures the sign of the scattered field as well, such that particles may be distinguished from bubbles. We describe an appropriate interferometer design based on Nomarski optics, which we have used to verify our calculation, measuring scattering in water from single polystyrene spheres as small as 0.038 μm in diameter.
Lattice contraction due to carbon doping of GaAs grown by metalorganic molecular beam epitaxy
Authors: de Lyon T. J. , Woodall J. M. , Goorsky M. S. , Kirchner P. D.
Published: July 2002

Epitaxial layers of GaAs have been grown by metalorganic molecular beam epitaxy (MOMBE) with atomic carbon concentrations ranging from 4×1017 to 3.5×1020 cm−3. The dependences of GaAs lattice parameter and hole concentration on atomic carbon concentration have been determined from x-ray diffraction, Hall effect, and secondary-ion mass spectrometry measurements. For atomic carbon concentrations in excess of 1×1019 cm−3, the hole concentrations are less than the corresponding atomic carbon concentrations. Lattice parameter shifts as large as 0.2% are observed for carbon concentrations in excess of 1×1020 cm−3, which results in misfit dislocation generation in some cases due to the lattice mismatch between the C-doped epilayer and undoped substrate. Over the entire range of carbon concentrations investigated, Vegard’s law accurately predicts the observed lattice contraction.
Refractive switch for two-dimensional electrons
Authors: Spector J. , Stormer H. L. , Baldwin K. W. , Pfeiffer L. N. , West K. W.
Published: July 2002

A refractive electrostatic prism is used to switch a beam of ballistic electrons between different collectors in the two-dimensional electron gas of an AlGaAs-GaAs heterostructure. This represents a new concept in electronic switching which utilizes the electrostatically controlled refraction of ballistic electrons in high-mobility two-dimensional systems.
Solid immersion microscope
Authors: Mansfield S. M. , Kino G. S.
Published: July 2002

A new type of real-time optical microscope has been developed that operates on the same principle as a liquid immersion microscope, with the liquid replaced by a solid lens of high refractive index material. Using a lens with an index n=2 and 436 nm illumination, this microscope has resolved 100 nm lines and spaces and has demonstrated a factor of two improvement in the edge response over a confocal microscope.
Soft x-ray (97-eV) phase retardation using transmission multilayers
Authors: Kortright J. B. , Kimura H. , Nikitin V. , Mayama K. , Yamamoto M. , Yanagihara M.
Published: July 2002

Phase retardation as a function of incidence angle of 97-eV soft x rays from a laser plasma source on transmission through a free-standing molybdenum/silicon multilayer was measured using a multilayer polarizer and a polarization analyzer. The maximum retardation of 49° between σ and π components is over 2/3 that calculated for an ideal structure. At maximum retardation the transmittance ratio of σ- to π-amplitudes was 0.66 and the intensity transmittance, averaged for both components, was 20%. These multilayer structures will be useful in soft x-ray polarization applications.
Epitaxial growth of LiNbO3 thin films by excimer laser ablation method and their surface acoustic wave properties
Authors: Shibata Yoshihiko , Kaya Kiyoshi , Akashi Kageyasu , Kanai Masaki , Kawai Tomoji , Kawai Shichio
Published: July 2002

We have formed epitaxial LiNbO3 thin films of high quality on sapphire substrates (001) using an excimer-laser ablation technique and evaluated the surface acoustic wave (SAW) properties of these films. It is demonstrated that the LiNbO3 thin films on the sapphire are the candidates for a high frequency SAW filter because of their high velocities of propagation (5300–6600 m/s) and good temperature coefficients (−34 to −80 ppm/ °C).
Femtosecond carrier kinetics in low-temperature-grown GaAs
Authors: Zhou X. Q. , van Driel H. M. , Rühle W. W. , Gogolak Z. , Ploog K.
Published: July 2002

The carrier energy distribution and recombination kinetics in low-temperature-grown and annealed GaAs (with 1% excess arsenic occurring as microclusters/point defects) have been time resolved at 295 K through luminescence upconversion and correlation spectroscopy using an 80 fs, 720 nm Ti:sapphire laser. We infer that the radiative recombination coefficient is the same in GaAs:As as in normal GaAs and that both electron and hole trapping times are about 1 ps. Luminescence is detected at energies as much as 300 meV below the band gap and is identified with delocalized states induced by excess As. We observe that the presence of excess As gives photoexcited carriers a higher initial temperature than in GaAs. Finally, since the carrier density decays faster than the emitted optical phonons, energy relaxation is inhibited more effectively than in normal GaAs.
Contact resistance measurements on p-type 6H-SiC
Authors: Crofton J. , Barnes P. A. , Williams J. R. , Edmond J. A.
Published: July 2002

Specific contact resistance measurements are reported for Al-Ti ohmic contacts to epitaxial p-type 6H-SiC as a function of epitaxial doping. The circular transmission line method was used to measure the specific contact resistance including the sheet resistance of the epitaxial layer and the modified sheet resistance under the contact. Epitaxial layers with Al doping between 5.5×1015 and 2×1019 cm−3 yielded specific contact resistances between 2.9×10−2 and 1.5×10−5 Ω cm2. A good theoretical fit to the contact resistance data was obtained by assuming the metal-6H-SiC barrier height to equal 0.37 eV.
Magnetotransport in lateral periodic potentials formed by surface-layer-induced modulation in InAs-AlSb quantum wells
Authors: Nguyen Chanh , Brar Berinder , Jayaraman Vijay , Lorke Axel , Kroemer Herbert
Published: July 2002

We report the realization of strong lateral superlattice potentials in not-intentionally doped InAs-AlSb quantum wells. By spatially alternating the surface layer between thin layers of InAs and GaSb, which shift the pinning position of the Fermi level at the surface, we induce a lateral density modulation of 4×1011 cm−2, equivalent to a potential modulation of 30 meV inside quantum wells 20 nm away from the surface. Both one- and two-dimensional lateral potentials were fabricated and studied by magnetotransport measurements. Strong commensurability oscillations are observed.
Soliton versus nonsoliton operation of fiber ring lasers
Authors: Tamura K. , Nelson L. E. , Haus H. A , Ippen E. P.
Published: July 2002

To date most passively mode-locked erbium-doped fiber laser systems have employed solitons for short pulse generation, and ultrashort high energy pulses have been difficult to achieve. We show that by reducing the system nonlinearity via pulse stretching and employing net positive dispersion cavities, pulses of sub-100-fs duration and ≳100 pJ energy are readily generated. Data are presented for varying net dispersion in a fiber ring.
Room-temperature violet stimulated emission from optically pumped AlGaN/GaInN double heterostructure
Authors: Amano H. , Tanaka T. , Kunii Y. , Kato K. , Kim S. T. , Akasaki I.
Published: July 2002

An AlGaN/GaInN heterostructure has been fabricated by metalorganic vapor phase epitaxy. We observed room-temperature (RT) violet stimulated emission from an optically pumped double heterostructure (DH) using GaInN as an active layer. The peak wavelength of the stimulated emission at RT from Al0.17Ga0.83N/Ga0.91In0.09N DH is 402.5 nm, and the threshold of excitation power density is about 0.13 MW/cm2.
Scanning tunneling microscopy based lithography of octadecanethiol on Au and GaAs
Authors: Lercel M. J. , Redinbo G. F. , Craighead H. G. , Sheen C. W. , Allara D. L.
Published: July 2002

We have demonstrated that low energy electron beams (≤10 eV) from a scanning tunneling microscope (STM) can be used to modify a surface of self-assembled monolayers of octadecanethiol [ODT, CH3(CH2)17SH] on gold and GaAs. STM modification in air was used to produce grating patterns up to 140 μm in total size. Line sizes as small as 15 nm were produced in ODT on GaAs at a bias of 10 V, and slightly larger sizes were produced on the gold substrate. Biases of greater than 4 V are necessary for the fabrication of these raised lines, as observed with an atomic force microscope (AFM). The patterns in ODT on gold were successfully transferred into the gold layer with a wet chemical etch demonstrating that the monolayer performs as a positive electron beam resist.
Temperature activated conductance in GaN/AlGaN heterostructure field effect transistors operating at temperatures up to 300 °C
Authors: Khan M. Asif , Shur Michael S. , Kuznia John N. , Chen Q. , Burm Jin , Schaff William
Published: July 2002

We report on the dc characteristics and microwave performance of AlGaN/GaN heterostructure field effect transistors in the temperature range from 25 to 300 °C. At temperatures above 200 °C, we observe the temperature activated shunt conductance which is independent of the gate voltage (the activation energy is 0.505 eV). The cutoff frequency and the maximum frequency of oscillations vary from 22 and 70 GHz at 25 °C to 5 and 4 GHz at 300 °C, respectively. The gate leakage current in the range of gate biases from −4 to +1 V is small and nearly proportional to the gate voltage even at 300 °C. At temperatures above 200 °C, the gate leakage current is temperature activated (the activation energy is 0.88 eV). These results show that deep traps strongly affect the AlGaN/GaN characteristics at elevated temperatures.
Polarized neutron reflectometer: A new instrument to measure magnetic depth profiles
Authors: Felcher G. P. , Hilleke R. O. , Crawford R. K. , Haumann J. , Kleb R. , Ostrowski G.
Published: July 2002

A description is given of the prototype polarized neutron reflectometer installed at the intense pulsed neutron source. This instrument is designed for determining the magnetic depth profiles near the surfaces of ferromagnets and superconductors, by measuring the spin-dependent reflectivities of a well-collimated (0.01°) beam of cold neutrons from surfaces of a few cm2. Magnetic profiles can be determined with the spatial resolution of 40 Å, over thicknesses up to 5000 Å. Variations of the magnetic flux of the order of 10−5 G cm2 can be detected.
Force microscopy with a bidirectional capacitance sensor
Authors: Neubauer Gabi , Cohen Sidney R. , McClelland Gary M. , Horne Don , Mate C. Mathew
Published: July 2002

A new method for sensing cantilever deflection in the atomic force microscope (AFM), based on capacitance measurement, is described. Parameters governing the design of such an instrument are considered in detail. Two different geometries are compared, wire on plate and an integrated flat plate sensor. The electronic circuitry, providing 6×10−19 F noise in a 0.01–1000 Hz bandwidth, is also described. Implementation of the design ideas into a working AFM in ultrahigh vacuum is demonstrated. This AFM allows simultaneous measurement of cantilever deflection in two orthogonal directions, necessary for our nanotribology studies. The theoretical sensitivity of 5×10−7 F/m is not achieved due to roughness. The bidirectional sensing and imaging capabilities are demonstrated for an Ir tip on cleaved graphite, and a diamond tip on diamond films. The capacitance detection technique is compared and contrasted with other AFM sensors.
H− temperature dependences in a Penning surface-plasma source
Authors: Smith H. Vernon , Sherman Joseph D. , Geisik Carl , Allison Paul
Published: July 2002

Simple analysis of the nearly Maxwellian angular distributions of the ribbon H− ion beams extracted from a long, narrow slit on the 8X source yields the H− temperature, kTH−. The derived kTH− are 0.1–0.3 eV for a 2-A dc discharge and 0.7–1.3 eV for a 400-A pulsed discharge. Because this diagnostic method relies on simple electronic techniques, it allows rapid study of the dependences of kTH− on the source parameters, such as gas flow and discharge current. These variations of kTH− in the 8X source are qualitatively similar to those observed for the H-atom temperature, kTH0, in the 4X source, another Penning surface-plasma source.
Preparation of homogeneous Cu(InGa)Se2 films by selenization of metal precursors in H2Se atmosphere
Authors: Marudachalam M. , Hichri H. , Klenk R. , Birkmire R. W. , Shafarman W. N. , Schultz J. M.
Published: July 2002

Homogeneous single phase Cu(InGa)Se2 films with Ga/(In+Ga)=0.25–0.75 were formed by reacting Cu–Ga–In precursor films in H2Se followed by an anneal in Ar. X-ray diffraction and Auger analysis show that the metal precursors reacted only in H2Se were multiphase films having a layered CuInSe2/CuGaSe2 structure. Solar cells made with the multiphase films have properties similar to CuInSe2 devices. Cells made with the annealed single phase films behave like Cu(InGa)Se2 devices with the band gap expected for the precursor composition.
Ultrahigh impedance capacitively coupled heart imaging array
Authors: Clippingdale A. J. , Prance R. J. , Clark T. D. , Watkins C.
Published: July 2002

We describe a prototype electrocardiographic (ECG) array system comprising 25 ultrahigh impedance sensors, which does not require ohmic electrical contact with the body.
Frequency dependence of metal-particle/insulating oil electrorheological fluids
Authors: Wen Weijia , Lu Kunquan
Published: July 2002

The frequency dependence of the shear stress of metal-particle/insulating oil electrorheological (ER) fluids under an ac electric field has been studied. The results show that the shear stress of the metal-particle ER fluid under a fixed electric field increases with increasing frequency and then tends to a saturated value at higher frequency. The shear stress at 103 Hz is much larger than that under a dc field. The transition of the shear stress shifts to higher frequency when the conductivity of the fluid is larger. The measurements are consistent with the theoretical model proposed by Davis [J. Appl. Phys. 73, 680 (1993)].
Ultrafast far-infrared GaAs/AlGaAs photon drag detector in microwave transmission line topology
Authors: Sigg H. , Kwakernaak M. H. , Margotte B. , Erni D. , van Son P. , Köhler K.
Published: July 2002

A novel room temperature GaAs/AlGaAs multiquantum-well photon drag detector operating in the 10 μm wavelength range and designed as a microstrip transmission line has been developed. Total-reflection angle incoupling, using a Ge prism, provides velocity matching between the optical and electrical pulses. Signal transients with 10 ps rise and fall time have been measured using 2 ps pulses from a free electron laser. From the wavelength dependence of the photon drag signal the room temperature momentum relaxation times in the first and second electron subband can be determined.
0.4 μm spatial resolution with 1 GHz (λ=30 cm) evanescent microwave probe
Authors: Tabib-Azar M. , Su D.-P. , Pohar A. , LeClair S. R. , Ponchak G.
Published: July 2002

In this article we describe evanescent field imaging of material nonuniformities with a record resolution of 0.4 μm at 1 GHz (λg/750 000), using a resonant stripline scanning microwave probe. A chemically etched tip is used as a point-like evanescent field emitter and a probe–sample distance modulation is employed to improve the signal-to-noise ratio. Images obtained by evanescent microwave probe, by optical microscope, and by scanning tunneling microscope are presented for comparison. Probe was calibrated to perform quantitative conductivity measurements. The principal factors affecting the ultimate resolution of evanescent microwave probe are also discussed.
Detection of surface-plasmon evanescent fields using a metallic probe tip covered with fluorescence
Authors: Wakamatsu T. , Nakano T. , Shinbo K. , Kato K. , Kaneko F.
Published: July 2002

A new experimental system has been constructed to detect evanescent fields of metal surface plasmons (SPs) using a metallic probe tip covered with fluorescence cadmium sulfide (CdS). The evanescent fields of the SPs sensitive to the metal interfaces were observed as fluorescent light from CdS on the tip. No additional lock-in detection technique with a vibrating probe tip is necessary in the system, in spite of the scattered light enhanced by SP due to the surface roughness. The fluorescent light measured for the Al film sample shows exponential decay with distance from the sample surface, indicating that the SP evanescent fields are detected with our apparatus.
Open-core screw dislocations in GaN epilayers observed by scanning force microscopy and high-resolution transmission electron microscopy
Authors: Qian W. , Rohrer G. S. , Skowronski M. , Doverspike K. , Rowland L. B. , Gaskill D. K.
Published: July 2002

Structural investigations of organometallic vapor phase epitaxy grown α-GaN films using high-resolution transmission electron microscopy and scanning force microscopy have revealed the presence of tunnel-like defects with 35–500 Å radii that are aligned along the growth direction of the crystal and penetrate the entire epilayer. These defects, which are termed ‘‘nanopipes,’’ terminate on the free surface of the film at the centers of hexagonal growth hillocks and form craters with 600–1000 Å radii. Either one or two pairs of monolayer-height spiral steps were observed to emerge from the surface craters which allowed us to conclude that nanopipes are the open cores of screw dislocations. The measured dimensions of the defects are compared to Frank’s theory for the open-core dislocation.
Hopping conduction in SiO2 films containing C, Si, and Ge clusters
Authors: Fujii Minoru , Inoue Yoku , Hayashi Shinji , Yamamoto Keiichi
Published: July 2002

Temperature dependence of electrical characteristics of SiO2 films doped with C, Si, and Ge were studied. The conductivity σ was found to vary with the temperature as lnσ∝T−1/4 over a wide temperature range, indicative of the conduction by the variable range hopping (VRH) mechanism. Since the previous optical studies for the same films indicate the existence of clusters in the films, it is very likely that the VRH through localized states associated with clusters dominates the conduction process, irrespective of the kind of group IV elements.
Laser ablation of dielectrics with pulse durations between 20 fs and 3 ps
Authors: Kautek Wolfgang , Krüger Jörg , Lenzner Matthias , Sartania Sasa , Spielmann Christian , Krausz Ferenc
Published: July 2002

Laser-induced ablation has been extended down to a pulse duration of 20 fs generated by a Ti sapphire laser system at a wavelength of 780 nm. Barium aluminum borosilicate glass with an extremely high glass transformation temperature (∼600 °C) served as target material. The most significant observation was a substantial decrease of the ablation threshold fluence at pulse durations below 100 fs. All results indicate a dominant role of multiphoton absorption in addition to collisional ionization in this time domain.
Phase-contrast microtomography with coherent high-energy synchrotron x rays
Authors: Raven C. , Snigirev A. , Snigireva I. , Spanne P. , Souvorov A. , Kohn V.
Published: July 2002

Cross-sectional information on low electron density materials can be obtained by probing a sample with a 60 keV coherent synchrotron x-ray beam in an in-line holography setup. Such objects are practically transparent to high energy x rays and create a phase shift of the wave front only. Images of a 100 μm diameter boron fiber were recorded in the extreme near field region, where contrast occurs only at interfaces between regions with different decrements of refractive index. Theoretical simulations are in good agreement with the measured intensities. In a tomographic reconstruction the 15 μm diameter core of the fiber is clearly visible, demonstrating the possibility of reconstructing three dimensional interfaces between low density materials.
Shock-induced chemical reactions in a Ni/Al powder mixture
Authors: Yang Y. , Gould R. D. , Horie Y. , Iyer K. R.
Published: July 2002

A new 50 mm powder gun was used to reproduce and to extend the real-time observations of ultra-fast exothermic reactions in a Ni/Al powder mixture at the shock front. Shock profiles measured by a manganin gauge show that (1) the threshold pressure for reaction is about 14 GPa; (2) the initiation criteria based either on shock energy or melting are in contradiction with experimental evidence.
Self-assembled-monolayer film islands as a self-patterned-mask for SiO2 thickness measurement with atomic force microscopy
Authors: Komeda T. , Namba K. , Nishioka Y.
Published: July 2002

A novel method for measuring ultrathin (2–12 nm) SiO2 film thickness is discussed. The process consists of: (1) formation of octadecyltrichlorosilane (OTS) self-assembled-monolayer (SAM) islands on SiO2 of which thickness to be measured, (2) removal of the SiO2 layers not covered by the OTS-SAM islands, and (3) measurement of the height difference between the etched and nonetched areas by atomic-force-microscopy. The OTS film is good resist against HF and its islands can be regarded as self-patterned-mask. Practical usefulness is demonstrated not only by the compatibility of the measured values but also by the short measurement period resulting from the directness of the method.
Observation of multiple defect states at silicon–silicon nitride interfaces fabricated by low-frequency plasma-enhanced chemical vapor deposition
Authors: Schmidt Jan , Schuurmans Frank M. , Sinke Wim C. , Glunz Stefan W. , Aberle Armin G.
Published: July 2002

Silicon nitride films are deposited onto monocrystalline p- and n-type silicon wafers by low-frequency plasma-enhanced chemical vapor deposition. Using small-pulse deep-level transient spectroscopy, three different types of defects are identified at the silicon–silicon nitride interface. All defects are located in the lower half of the silicon band gap and show a very broad Gaussian-like distribution of the state density. For all three defects, the capture cross sections for electrons, σn, and holes, σp, decrease strongly towards the conduction and valence band edge, respectively, while the capture cross-section ratio σn/σp at midgap, and hence the resulting recombination rate, is very different for each defect type.
Characterization of intra-cavity reflections by Fourier transforming spectral data of optically pumped InGaN lasers
Authors: Hofstetter Daniel , Romano Linda T. , Thornton Robert L. , Bour David P. , Johnson N. M.
Published: July 2002

Fourier analysis of laser emission spectra just above threshold is used to evaluate the impact of structural defects on the emission from optically pumped InGaN lasers. By dry etching a 300-nm-deep groove into the surface of a laser bar, we have modified the emission spectrum of such a device in a controlled manner. The occurrence of sharp features in the Fourier transformed spectrum allowed the identification of the mode spacing corresponding to the full cavity length, as well as to fractions of the full cavity length due to the etched groove. This enables us to identify additional features in the transform spectrum as being due to scattering centers within the waveguide. Identification of the density and strength of such centers is an important capability for the fabrication of blue diode lasers in the gallium–nitride material system.
Quantum mechanical effects in the silicon quantum dot in a single-electron transistor
Authors: Ishikuro Hiroki , Hiramoto Toshiro
Published: July 2002

The quantum mechanical effects in silicon single-electron transistors have been investigated. The devices have been fabricated in the form of point contact metal–oxide–semiconductor field-effect transistors with various channel widths using electron beam lithography and the anisotropic etching technique on silicon-on-insulator substrates. The device with an extremely narrow channel shows Coulomb blockade oscillations at room temperature. At low temperatures, negative differential conductances and fine structures are superposed on the device characteristics, which are attributed to the quantum mechanical effects in the silicon quantum dot in the channel. The energy spectrum of the dot is extracted from the experimental results.
High power KrF laser with a phase-unifying unstable cavity
Authors: De Nunzio G. , Perrone M. R. , Panzera C. , Flori D. , Piegari A. , Scaglione S.
Published: July 2002

The performance of a 0.45 J KrF excimer laser with an unstable cavity using a phase-unifying mirror as an output coupler is described. The output beam having a cross section of 2.4×1.2 cm2 exhibits a smooth far field profile with 86.5% of the total near field energy contained within a far-field full angle θ⩽0.05 mrad. The measurements for determining the beam quality factor M2 and the beam angular stability are also reported.
Enhanced sensitivity near-field scanning optical microscopy at high spatial resolution
Authors: Hamann H. F. , Gallagher A. , Nesbitt D. J.
Published: July 2002

An apertureless near-field optical-imaging method is presented that achieves high spatial resolution as well as a ∼4000-fold increase in detection sensitivity, by exploiting the highly localized enhanced near-field interactions between the sample (e.g., Au nanospheres) and a sharp atomic force microscope tip under evanescent laser field illumination. This represents a general method for optical imaging at ⩽2 nm spatial resolution, and is applicable to both resonant (i.e., scattering) as well as nonresonant (i.e., fluorescence, Raman, etc.) spectroscopic methods.
Effect of surface layer on optical properties of GaN and InxGa1−xN upon thermal annealing
Authors: Oh Eunsoon , Kim Bongjin , Park Hyeongsoo , Park Yongjo
Published: July 2002

We investigated the effect of rapid thermal annealing (RTA) on the optical properties of GaN and InxGa1−xN. It was found that some of the changes in the photoluminescence spectra of GaN upon annealing were associated with the properties of the surface layer. For example, a new low-temperature photoluminescence line associated with donor–acceptor pair (DAP) recombination appeared at around 3.40 eV upon annealing, but disappeared after etching off the surface layer. This indicates that the acceptors responsible for the DAP emission were created only near the surface. After the RTA process, the near-band-edge emission was blueshifted, and the relative intensity of yellow luminescence with respect to the near-band-edge emission was increased, which were also attributed to the influence of the surface layer. The thermal annealing effect of an InxGa1−xN multiple quantum well structure is also discussed.