cssi/SciSciGPT-SciSciNet huggingface dataset:
Quantitative Raman Spectroscopy of Homogeneous Molecular Profiles in Optical Waveguides via Direct Measurement

Quantitative measurements of Raman scattering from three-layer asymmetric slab dielectric waveguides made of organic macromolecular materials have been obtained from homogeneous distributions of scatterers as a function of mode by direct measurement of all mode-dependent quantities. For low-order modes, precision of the Raman intensity is limited to ∼5% by uncertainty in the measurement of the coupling coefficient, γ; while for high-order modes, precision was limited at the same level by uncertainty in the integrated electric field due to film-thickness variations. Observation of Raman instead of Rayleigh scatter vs. distance in the waveguide allowed measurement of the optical loss function, α, to be made down to 0.2 dB/cm with less than 1% uncertainty, so it is never the limiting factor.
Joint Commission on Accreditation of Healthcare Organizations requirements for sedation.

Abstract [Sklar DP: Joint Commission on Accreditation of Healthcare Organizations requirements for sedation. Ann Emerg Med April 1996;27:412-413.]
Transition metal dithiolene complexes as near-IR dyes for liquid crystal device applications

Both commercial and military applications (e.g., free-space IR communications and sensor protection) exist for guest-host liquid crystal (LC) devices operating in the near- to mid-IR region. Progress in this area has been hindered by the severe lack of near-IR dyes with good solubility in the LC host, low impact on the inherent order of the LC phase, good thermal and chemical stability, and a large absorbance maximum tunable by structural modification over a broad range of the near-IR region. Transition metal complexes based on nickel, palladium, or platinum dithiolene cores show substantial promise in meeting these requirements. These new dye complexes are extraordinarily stable, possess liquid crystalline phases in their own right with the proper terminal functional groups, and can have melting points below room temperature. The latter property is especially significant for producing liquid crystal/dye mixtures with both high dye concentration and good resistance to phase separation. Because they are zerovalent, they can exhibit high solubility in LC hosts (up to 10 wt%). The λ max in these materials can range from 600 nm to 1600 nm, depending on structure. With enantiomerically enriched terminal substituents, nickel dithiolenes can induce a chiral mesophase in a nonchiral nematic host. This finding opens the possibility of generating novel LC mixtures with two degrees of tunability : an electronic absorbance band tunable by synthesis, and a selective reflection band tunable by temperature or applied electric field. Such a materials system would be particularly advantageous in sensor protection for dealing with frequency-agile laser threats.
Haloperidol-induced supersensitivity to the discrimination of apomorphine

Abstract Rats were trained to discriminate between the stimulus properties of intraperitoneal 0.16 mg/kg apomorphine and saline in a two-lever, food-motivated operant task. Once trained, the rats were tested with the ED50 of apomorphine (0.02 mg/kg) or saline before and 1–22 days after a ten-day regiment of daily 2.0 mg/kg administrations of haloperidol. Chronic haloperidol treatment produced increased discrimination of, and lever selection perseverance to, the low dose of apomorphine when rats were tested at 12 days after the withdrawal of holoperidol and this increased discrimination returned to pre-haloperidol levels by the sixteenth day. The results suggest the development of supersensitivity by prolonged pharmacologic blockade of central dopaminergic receptors with haloperidol and indicate the peak and duration of this effect.
Orphan receptors, proto-oncogenes and other nuclear factors regulate P450C17 gene transcription.

Concerted, regulated expression of the rat P450c 17 gene relies on the combined participation of multiple DNA regions and factors that bind to these sequences. SF-1 binds to at least two different regions, and has activities dependent upon the DNA context. COUP-TF, NGF-IB, together with SF-1, bind to overlapping regions, and the interaction among these factors increases or decreases transcription. A newly identified factor, the proto-oncogene SET, binds to a portion of the COUP-TF site, and strongly activates P450c 17 transcription. SET mRNA is highly expressed early during development, and its expression decreases thereafter. P450c17 expression is not restricted to steroidogenic tissues, but rather is highly expressed in specific locations in the central (CNS) and peripheral nervous systems (PNS) during development, where its steroidal products may regulate neuronal maturation. We have shown that physiologic concentrations of steroids derived from P450c 17 activity, DHEA and DHEAS, have direct and distin...
Taxonomy and Habits of the Charrs, Salvelinus Malma and Salvelinus Alpinus, of the Karluk Drainage System

Abstract In the course of a study of the importance of charrs as predators on the red salmon of the Karluk watershed on Kodiak Island, Alaska, during the summers of 1939 to 1941, it became apparent that two distinct species of charrs were present. Results of tagging experiments, of stomach examinations of thousands of charrs, and of the analysis of comprehensive morphometric and meristic data made it easy to separate the dolly varden charrs from the red lake or alpine charrs at Karluk. These species have often been confused with each other, and may show intergradation in other parts of the world. At Karluk, however, the dolly varden charr, Salvelinus malma (Walbaum), is typically anadromous, spawns in streams, and has fewer than 20 gill rakers and fewer than 35 pyloric caeca. The red lake or alpine charr, Salvelinus alpinus (Linnaeus), of the same region is not anadromous, spawns in the lake, and has more than 20 gill rakers and more than 35 pyloric caeca.
DNA methylation changes in the postmortem dorsolateral prefrontal cortex of patients with schizophrenia.

Background: Schizophrenia is a complex psychiatric disorder with a lifetime morbidity rate of 0.5 ―1.0%. The pathophysiology of schizophrenia still remains obscure. Accumulating evidence indicates that DNA methylation, which is the addition of a methyl group to the cytosine in a CpG dinucleotide, might play an important role in the pathogenesis of schizophrenia. Methods: To gain further insight into the molecular mechanisms underlying schizophrenia, a genome-wide DNA methylation profiling (27,578 CpG dinucleotides spanning 14,495 genes) of the human dorsolateral prefrontal cortex (DLPFC) was conducted in a large cohort (n = 216) of well characterized specimens from individuals with schizophrenia and non-psychiatric controls, combined with an analysis of genetic variance at ~880,000 SNPs. Results: Aberrant DNA methylation in schizophrenia was identified at 107 CpG sites at 5% Bonferroni correction (p < 1.99 x 10-6). Of these significantly altered sites, hyper-DNA methylation was observed at 79 sites (73.8%), mostly in the CpG islands (CGIs) and in the regions flanking CGIs (CGI: 31 sites; CGI shore: 35 sites; CGI shelf: 3 sites). Furthermore, a large number of cis- methylation quantitative trait loci (mQTL) were identified, including associations with risk SNPs implicated in schizophrenia. Conclusions: These results suggest that altered DNA methylation might be involved in the pathophysiology and/or treatment of schizophrenia, and that a combination of epigenetic and genetic approaches will be useful to understanding the molecular mechanism of this complex disorder.
Endplate current fluctuations reveal only one channel type at frog neuromuscular junction

SIGNAL transduction between nerve and muscle is mediated by a chemical process at the neuromuscular junction. In the nerve ending electrical activity causes the release of acetylcholine (ACh) into the synaptic cleft separating the nerve and muscle cells. ACh can bind to specific chemical receptors in the postjunctional muscle membrane; these receptors control a gating mechanism that can increase membrane conductance locally. Normal nervous activity triggers an action potential and contraction in twitch muscle fibres. At constant membrane potential the membrane conductance change induces a current that is carried largely by Na+ and K+ in frog1, moving through ACh-gated membrane channels. There has been a controversy regarding the nature of the chemically gated endplate channels; are there kinetically-independent channels for Na+ and K+ , or are these ions transported by the same channel? Maeno2 initially proposed separate endplate channels, arguing that the two component decay of endplate potentials in procaine-treated cells resulted from a selective effect on Na+ channel kinetics. Kordas3,4 and Magleby and Stevens5 argued that Maeno's two-channel hypothesis could not account for the unique reversal potential observed or the monotonic voltage dependence of endplate current (EPC) decay. The analysis below of iontophoretically-induced EPC fluctuations in procaine-treated and untreated preparations indicates that the ions which constitute the EPC are not carried by kinetically distinguishable endplate channels.
Metabolic Response in Arenicola marina to Limiting Oxygen as Reflected in the 1H‐NMR Oxymyoglobin Signal

Many intertidal animals can endure prolonged periods of environmental stress and have developed strategies to preserve a functioning energy state in the cell. Recent 1H/31P-NMR techniques have allowed investigators to monitor directly mammalian tissue metabolism in vivo. In particular, the signals of myoglobin (Mb) offer a unique opportunity to explore the intracellular oxygen-partial-pressure [p(O2)] interaction in Arenicolu marina, a standard model to study hypoxia tolerance in invertebrates. The present study reveals that the 1H-NMR MbO, signal at -2.9 ppm is detectable in tissue and reflects directly the oxygenated state. As the p (02) declines, MbO2, saturation and oxygen consumption decrease. However, phosphotaurocyamine concentration remains unaltered until the MbO2, saturation falls below 33%. The extracellular to intracellular p (O2) gradient appears substantial. The study establishes the 1H-NMR technique as an approach to measure the intracellular p (O2) with an oxygenated state marker and presents the interrelationship between oxygen and the metabolic adaptation during hypoxic stress.
Kinematics, motion planning and design of a free-floating dual-arm planar manipulator

Abstract Dual-arm free-floating robots will play an important role in space robotics and industrial handling over large factory work floors. This paper deals with analytical studies of a free-floating dual-arm planar manipulator which is currently under construction at Ohio University. The robot floats on a flat table using air bearings. In the absence of externally applied forces in the plane of operation and couples normal to this plane, the linear momentum in the plane and angular momentum normal to this plane are conserved. These conservation principles are not applicable to structurally similar fixed-based manipulators. As a result, kinematics, motion planning, and design of dual-arm free-floating planar manipulators are different from structurally similar fixed-base manipulators. In this paper, we address the following topics for dual-arm free-floating planar robots: (1) development of a forward kinematic model and a procedure for computation of the inverse kinematic solutions, (2) motion planning using position inverse kinematics and (3) design guidelines for dual-arm free-floating planar robots.
Synthesis, Characterization, and One-Electron Reduction of Mixed-Cyclopentadienyl/Aryloxide Titanium Dichlorides

The synthesis and characterization of a series of titanium dichloride derivatives containing both cyclopentadienyl and various substituted aryloxide ligands, [CpTi(OAr)Cl2] 10−18 and [Cp*Ti(OAr)Cl2] 19, 20, have been investigated. Compounds 10−18 are formed from the reaction of [CpTiCl3] with either 1 equiv of the substituted parent phenol in the presence of excess pyridine or with 1 equiv of the corresponding lithium salt of the substituted parent phenoxide in hydrocarbon solvents. Compounds 13, 14, 16, and 17 are chiral molecules (a nonresolved racemic pair) as a result of the presence of either ortho-(1-naphthyl) or ortho-(1-tetrahydronaphthyl) substituents on the phenoxide ligands. Titanium dichloride compounds 19 and 20 are formed in the reaction of [Cp*TiCl3] with the corresponding lithium salts of the substituted parent phenoxides in hydrocarbon solvents. The compounds 11, 13, 14, 15, 16, 18, 19, and 20 have been subjected to single-crystal X-ray diffraction analysis, and each was shown to possess ...
2-D Array Photonic Crystal Sensing Motif

We have developed the first high-diffraction-efficiency two-dimensional (2-D) photonic crystals for molecular recognition and chemical sensing applications. We prepared close-packed 2-D polystyrene particle arrays by self-assembly of spreading particle monolayers on mercury surfaces. The 2-D particle arrays amazingly diffract 80% of the incident light. When a 2-D array was transferred onto a hydrogel thin film showing a hydrogel volume change in response to a specific analyte, the array spacing was altered, shifting the 2-D array diffraction wavelength. These 2-D array photonic crystals exhibit ultrahigh diffraction efficiencies that enable them to be used for visual determination of analyte concentrations.
Drug Use and Intimate Partner Violence Among College Students: An In-Depth Exploration:

College students experience an extremely high level of violence among intimate partners during their college careers, with prevalence rates ranging between 20% and 50%. Because intimate partner violence (IPV) among college students is such a widespread problem, it is important to understand the factors that contribute to this type of abuse. Studies using a variety of samples demonstrate that drug use is one such factor. However, research to date fails to identify specific types of drugs linked to college students' use of violence against intimates. In an attempt to fill this void, this exploratory study uses data from the Relationship Characteristics Study, which was conducted in 2001 and includes a sample of 1,938 college students, to provide a more comprehensive understanding of the relationship between college students' drug use and IPV perpetration than the current literature allows.
Driven exercise among treatment-seeking youth with eating disorders.

Purpose This study evaluated the prevalence and clinical significance of driven exercise (DE) in treatment-seeking youth.
Silicide Formation using Laser and Electron Beams

The reaction of thin metal films with single crystal or amorphous silicon to form silicide compounds has been successfully undertaken using both scanned-cw and pulsed beam processing. Similar to the case for beam annealing of ion-implanted semiconductors, both the basic mechanisms and the experimental results are found to depend on whether pulsed or scanned beams are used to promote the reactions. For both cases the experimental results are often found to differ sharply from those obtained with standard furnace processing. For the pulsed beam reaction, melting and rapid resolidification occurs in the metal silicon films. The principal result is that the reacted film is frozen in a mixed phase compound which can consist of several silicide compounds including silicon and metal precipitation. Compositions inaccessible by conventional furnace annealing can also be formed by this process. In contrast to the pulsed beam results, scanned-cw beam processing of metal silicon films is found to result in the formation of large area uniform silicide phases with essentially no silicon or metal precipitation. These films are generally found to be homogeneous with well defined silicon/silicide interfaces.
Invasion of the Nucleotide Snatchers: Structural Insights into the Mechanism of G Protein GEFs

Although the mechanics differ, GEFs appear to deform their substrates in similar ways. In all cases, switch I is pulled away from switch II and the P loop, exposing the active site; dislocation of switch I also displaces a Mg2+-binding residue, but this in itself should have little affect on GDP affinity. GEFs also restructure and displace the amino terminus of switch II and consequently dismantle the γ-phosphate-binding site, at the same time moving a conserved aspartate residue that serves as a water-mediated Mg2+ ligand. Residues, either from the GEF or the G protein, are positioned to occupy and block the phosphate- and Mg2+-binding sites. To varying extents, the P loop is altered and a conserved lysine residue is extracted from the phosphate-binding site. While structural changes in the P loop may occur as a response to the evacuation of the nucleotide-binding site, it appears, especially in the case of EF-Ts, that it is GEF mediated. These rearrangements, however, leave the purine-binding site relatively undisturbed and easily accessed. Hence, incoming nucleotide can gain some purchase onto the GTP-binding site and complete the exchange reaction. Although the dissociation constants for G·GTP, G·GDP, and G·GEF are subnanomolar, that of the ternary complex with either nucleotide (GEF·G protein·GXP) is micromolar (Klebe et al. 1995xKlebe, C., Prinz, H., Wittinghofer, A., and Goody, R.S. Biochemistry. 1995; 34: 12543–12552Crossref | PubMedSee all ReferencesKlebe et al. 1995). The ternary complex is therefore a viable, yet transient intermediate in the pathway of nucleotide exchange in vivo. The delicate energetic balance between binary and ternary complexes is perhaps controlled by the relative concentrations of the two nucleotides. Clearly, structural changes, which have yet to be characterized, must attend the formation of the ternary complex. It is possible that other GEFs, in particular heterotrimeric G protein receptors, employ exchange mechanisms that differ substantially from those discussed here. Nevertheless, there is sufficient diversity among these to offer new insights into both common and unique properties of GEFs, each of which appears to have arisen independently in evolution, and each of which must catalyze nucleotide exchange in a different functional context.
History of Clinical Transplantation

The emergence of transplantation has seen the development of increasingly potent immunosuppressive agents, progressively better methods of tissue and organ preservation, refinements in histocompatibility matching, and numerous innovations in surgical techniques. Such efforts in combination ultimately made it possible to successfully engraft all of the organs and bone marrow cells in humans. At a more fundamental level, however, the transplantation enterprise hinged on two seminal turning points. The first was the recognition by Billingham, Brent, and Medawar in 1953 that it was possible to induce chimerism-associated neonatal tolerance deliberately. This discovery escalated over the next 15 years to the first successful bone marrow transplantations in humans in 1968. The second turning point was the demonstration during the early 1960s that canine and human organ allografts could self-induce tolerance with the aid of immunosuppression. By the end of 1962, however, it had been incorrectly concluded that turning points one and two involved different immune mechanisms. The error was not corrected until well into the 1990s. In this historical account, the vast literature that sprang up during the intervening 30 years has been summarized. Although admirably documenting empiric progress in clinical transplantation, its failure to explain organ allograft acceptance predestined organ recipients to lifetime immunosuppression and precluded fundamental changes in the treatment policies. After it was discovered in 1992 that long-surviving organ transplant recipients had persistent microchimerism, it was possible to see the mechanistic commonality of organ and bone marrow transplantation. A clarifying central principle of immunology could then be synthesized with which to guide efforts to induce tolerance systematically to human tissues and perhaps ultimately to xenografts.
Genetic aspects of vulvar lichen sclerosus

Thirteen instances of familial lichen sclerosus have been recorded in the literature. This report documents the disease in two additional families and adds genetic data on their HLA characteristics. The relationship of these factors to a possible autoimmune mechanism for the disease is discussed.
Transport processes in steam generator crevices. II. A simplified method for estimating impurity accumulation rates

An approximate, yet accurate method for calculating average volume concentrations of impurities and corrosion products in Pressurized Water Reactor (PWR) Steam Generator (SG) tube/tube support plate crevices has been developed. The method is based on the assumption that the real concentration profiles can be approximated by ideal step functions. The method yields analytical expressions for such important parameters as the rate of accumulation of impurities, corrosion current density, liquid velocity, saturation, transition time, and wetted length. It is shown that, under normal operating conditions of a PWR SG, we can estimate the corrosion rate even when only meager information is available for the physical parameters of the system. The method also permits prediction of the accumulation of impurities in crevices for long times, if the corresponding experimental measurements are available only for short times. Long-term predictions from the model describe the experimental data with great accuracy.
DEVELOPMENT OF VERBAL CONTROL OVER BIZARRE GESTURES OF RETARDATES THROUGH IMITATIVE AND NONIMITATIVE REINFORCEMENT PROCEDURES1

Two retardates, manifesting hand gestures and minimal instructional control, were trained by imitative reinforcement procedures to imitate a response that was in contrast to gesturing. Next, with the contrast response continuing to be imitatively reinforced, gesturing was reduced by nonimitative reinforcement procedures; while providing facial and gesture cues, the adult said, “Do not do this”. Imitative and nonimitative procedures were found to have the same effects on the contrast response as on the gesturing response, such that imitative procedures increased both responses, whereas nonimitative procedures decreased both. Nonperformance of gesturing was further maintained when (1) explicit verbal directions for nongesturing were superimposed upon the demonstrational-facial-verbal cues as these collective stimuli were faded out and (2) food reinforcers for nongesturing were gradually removed while social consequences continued to be administered.
Pharmaceutical Equivalence by Design for Generic Drugs: Modified-Release Products

The Office of Generic Drugs has ensured the high quality of generic products based upon two requirements: pharmaceutical equivalence and bioequivalence to the reference listed drug (RLD). This paradigm has been used with success toward ensuring quality generic drug products that provide the same therapeutic benefit as the RLD. Drug products have increased in design complexity; as a result, approaches to ensure therapeutic equivalence must evolve to provide assurance of quality generic drug products. The Food and Drug Administration quality by design initiative (QbD) provides an enhanced evaluation approach by introducing the concept of a quality target product profile (QTPP). The QTPP introduces, within the context of the current regulatory framework, the quality concept of “pharmaceutical equivalence by design.” This article illustrates through several examples how this QbD element in the evaluation of modified-release drug products enhances the current framework to ensure generic drug product equivalence. It achieves this by complementing the traditional paradigm, “equivalence by testing,” where product equivalence is based upon inferences from a limited bioequivalence study, to one that also considers whether the drug product was developed to be an equivalent to the RLD, using appropriate quality surrogates that target “pharmaceutical equivalence by design.”
Microstructure of amorphous and microcrystalline Si and SiGe alloys using X-rays and neutrons

This review describes recent experimental applications of small-angle X-ray (SAXS) and neutron scattering, as well as X-ray diffraction (XRD), for the determination of the microstructure of relevant solar cell thin film materials based on hydrogenated amorphous Si and SiGe alloys. Due to the recent trend toward use of amorphous Si and SiGe materials prepared near the onset of microcrystallinity, this review also describes the use of XRD to detect and determine the role of medium-range order and partial microcrystallinity in solar cell behavior. Some recent results from SAXS and XRD applied to microcrystalline Si are also summarized.
Long‐term Exposure to the Anti‐inflammatory Agent Phenylbutazone Induces Kidney Tumors in Rats and Liver Tumors in Mice

Long-term toxicity and carcinogenicity of phenylbutazone, a nonsteroidal anti-inflammatory drug, were evaluated in F344/N rats and B6C3F1 mice. In 2-year studies, phenylbutazone was given in corn oil by gavage 5 days per week to groups of 50 rats of each sex at doses of 0, 50, or 100 mg/kg body weight, and to groups of 50 mice at doses of 0, 150, or 300 mg/kg body weight. Body weights and survival were similar among groups. Major target organs are kidneys in rats, and liver in mice. Kidney: inflammation, papillary necrosis, and mineralization in both sexes of rats, and hyperplasia and dilatation of the pelvis epithelium, and cysts in female rats. Uncommon tubular cell tumors of the kidney were found in 13 exposed rats: 5 in the 50 mg group and 4 in the 100 mg group of males; 4 in dosed female rats; none in controls. In female rats, dose-related increases in hyperplasia of the pelvis transitional epithelium, and 2 carcinomas were discovered. Urinary bladder: papillomas of the transitional epithelium were seen in 2 low-dose male and in 1 low-dose female rats. Forestomach: ulcers in rats, with acanthosis, hyperkeratosis, and basal cell hyperplasia in female rats; however, no neoplasms were associated with these lesions. Liver: primarily in male mice exposed to. phenylbutazone, hemorrhage, centrilobular cytomegaly and karyomegaly, fatty metamorphosis, cellular degeneration, and coagulative necrosis were seen; clear cell foci were observed in male mice. In summary, under the conditions of these 2-year oral intubation studies, phenylbutazone is associated with renal carcinogenicity in rats, as evidenced by increases in tubular cell neoplasms in both sexes. Evidence of carcinogenicity for male mice was shown by increased incidences and multiplicity of liver tumors. No carcinogenic activity was found for female mice.
Cross-cultural comparison of perianesthesia nursing: Challenges encountered in the PACU ☆

Nurses often consider caring for the pediatric patient in the PACU stressful. This stress may be compounded when providing this care in a foreign country. This article compares and contrasts the challenges experienced by one nurse when working in both Russia and China as a PACU nurse for the volunteer group, Operation Smile. Topics discussed in this article include the physical setup of the PACU; safety issues within the PACU; and the importance of communication, pain management, and parents within the PACU. The author elaborates on how to provide safe, competent, and culturally sensitive care to children within the PACU setting.
The Development of a Measure of Correlates of Child Sexual Abuse: The Traumatic Sexualization Survey

The present research developed an instrument which assesses cognitive and behavioral factors purportedly associated with child sexual abuse histories. Finkelhor and Browne's construct of traumatic sexualization served as a guide for item selection. The study resulted in a 38-item reliable measure consisting of four subscales: Avoidance and Fear of Sexual and Physical Intimacy, Thoughts About Sex, Role of Sex in Relationships, and Attraction/Interest and Sexuality. Construct validity was established using a variety of self-report instruments associated with the dimensions of traumatic sexualization. Sexually abused women scored higher than nonabused women on three TSS factors. Physically abused women differed from nonabused women on only one factor. Sexually abused women did not score significantly higher than physically abused women on any factors.
Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

We discuss the identification of features that are associated with an outcome in RNA-Sequencing (RNA-Seq) and other sequencing-based comparative genomic experiments. RNA-Seq data takes the form of counts, so models based on the normal distribution are generally unsuitable. The problem is especially challenging because different sequencing experiments may generate quite different total numbers of reads, or 'sequencing depths'. Existing methods for this problem are based on Poisson or negative binomial models: they are useful but can be heavily influenced by 'outliers' in the data. We introduce a simple, non-parametric method with resampling to account for the different sequencing depths. The new method is more robust than parametric methods. It can be applied to data with quantitative, survival, two-class or multiple-class outcomes. We compare our proposed method to Poisson and negative binomial-based methods in simulated and real data sets, and find that our method discovers more consistent patterns than competing methods.
ENDOR Spectroscopy Reveals Light Induced Movement of the H-Bond from Ser-L223 upon Forming the Semiquinone (QB -¥ ) in Reaction Centers from Rhodobacter sphaeroides †

Proton ENDOR spectroscopy was used to monitor local conformational changes in bacterial reaction centers (RC) associated with the electron-transfer reaction DQB → D+•QB-• using mutant RCs capable of photoreducing QB at cryogenic temperatures. The charge separated state D+•QB-• was studied in mutant RCs formed by either (i) illuminating at low temperature (77 K) a sample frozen in the dark (ground state protein conformation) or (ii) illuminating at room temperature prior to and during freezing (charge separated state protein conformation). The charge recombination rates from the two states differed greatly (>106 fold) as shown previously, indicating a structural change (Paddock et al. (2006) Biochemistry 45, 14032−14042). ENDOR spectra of QB-• from both samples (35 GHz, 77 K) showed several H-bond hyperfine couplings that were similar to those for QB-• in native RCs indicating that in all RCs, QB-• was located at the proximal position near the metal site. In contrast, one set of hyperfine couplings were no...
The Mcm Complex: Unwinding the Mechanism of a Replicative Helicase

Summary: The Mcm2-7 complex serves as the eukaryotic replicative helicase, the molecular motor that both unwinds duplex DNA and powers fork progression during DNA replication. Consistent with its central role in this process, much prior work has illustrated that Mcm2-7 loading and activation are landmark events in the regulation of DNA replication. Unlike any other hexameric helicase, Mcm2-7 is composed of six unique and essential subunits. Although the unusual oligomeric nature of this complex has long hampered biochemical investigations, recent advances with both the eukaryotic as well as the simpler archaeal Mcm complexes provide mechanistic insight into their function. In contrast to better-studied homohexameric helicases, evidence suggests that the six Mcm2-7 complex ATPase active sites are functionally distinct and are likely specialized to accommodate the regulatory constraints of the eukaryotic process.
Embedded MPLS architecture

This paper presents a hardware architecture for multiprotocol label switching (MPLS). MPLS is a protocol used primarily to prioritize Internet traffic and improve bandwidth utilization. Furthermore it increases the performance of Internet applications and overall efficiency. However, most existing MPLS solutions are entirely software based. MPLS performance can be enhanced by executing core tasks (i.e. label stack modification) in hardware while allowing other tasks to be executed in software to guard against performance degradation. This paper proposes a hardware/software design of MPLS on an FPGA for increased performance and efficiency. Greatest emphasis is placed on the hardware components.
ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank

© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. MOTIVATION: Studies of the biochemical functions and activities of uncultivated microorganisms in the environment require analysis of DNA sequences for phylogenetic characterization and for the development of sequence-based assays for the detection of microorganisms. The numbers of sequences for genes that are indicators of environmentally important functions such as nitrogen (N2) fixation have been rapidly growing over the past few decades. Obtaining these sequences from the National Center for Biotechnology Information's GenBank database is problematic because of annotation errors, nomenclature variation and paralogues; moreover, GenBank's structure and tools are not conducive to searching solely by function. For some genes, such as the nifH gene commonly used to assess community potential for N2 fixation, manual collection and curation are becoming intractable because of the large number of sequences in GenBank and the large number of highly similar paralogues. If analysis is to keep pace with sequence discovery, an automated retrieval and curation system is necessary. RESULTS: ARBitrator uses a two-step process composed of a broad collection of potential homologues followed by screening with a best hit strategy to conserved domains. 34 420 nifH sequences were identified in GenBank as of November 20, 2012. The false-positive rate is ∼0.033%. ARBitrator rapidly updates a public nifH sequence database, and we show that it can be adapted for other genes. AVAILABILITY AND IMPLEMENTATION: Java source and executable code are freely available to non-commercial users at http://pmc.ucsc.edu/∼wwwzehr/research/database/. CONTACT: zehrj@ucsc.edu SUPPLEMENTARY INFORMATION: SUPPLEMENTARY INFORMATION is available at Bioinformatics online.
High Lateral Resolution Auger Electron Spectroscopic (AES) Measurements for Sn Whiskers on Brass

We report high lateral resolution Auger electron spectroscopic (AES) measurements on high aspect ratio Sn whiskers. The whiskers were grown from compressively stressed thin films (~ 6000 Å) of Sn on brass using a magnetron sputtering system. The Auger spectra show that, after sputter cleaning, the whisker is nearly 100% Sn at all locations along the whisker shaft, at the growing blunt end of the shaft, and with depth (~ 1000 Å) into the side of the whisker. The “as received” Sn whisker surface shows the expected ~ 200 Å of native Sn oxide at all locations and the O signal nearly disappeared (~ 3 atom%) after 200 Å of sputter cleaning. There was no evidence of high amounts of oxygen within the bulk of the whisker. That brass is not observed in the whisker shaft supports the notion that whisker formation is accompanied by material mass transport through interfaces and grain boundaries which causes stress (usually compressive) relief. This is supported by the most remarkable aspect of the whisker growth; namely, that high aspect ratio Sn whiskers ~ 100-500 μm in length containing no brass can be grown from a ~ 0.6 μm thin film of Sn.
Recovery during concurrent on-line testing of identical circuits

We show that a concurrent online testing scheme based on output comparison of identical circuits can also identify situations where the circuit recovers from a permanent fault, i.e., functional operation can continue temporarily in spite of the presence of a fault. We show that the ability to recover from a fault is circuit-dependent, and that some circuits are better than others at allowing recovery. We also discuss the possibility of false recovery in the presence of multiple faults and its implications.
An Early-Reply Based Framework: Reliable Concurrency that Is Verifiable

Despite its widespread use, concurrent programming is still plagued by reliability problems, such as race conditions and deadlock, not found in sequential programs. We present a concurrency framework to help developers avoid these error conditions, and make it possible to verify their absence through static analysis.
Effects of a Research-Infused Botanical Curriculum on Undergraduates’ Content Knowledge, STEM Competencies, and Attitudes toward Plant Sciences

In response to the American Association for the Advancement of Science's Vision and Change in Undergraduate Biology Education initiative, we infused authentic, plant-based research into majors’ courses at a public liberal arts university. Faculty members designed a financially sustainable pedagogical approach, utilizing vertically integrated curricular modules based on undergraduate researchers’ field and laboratory projects. Our goals were to 1) teach botanical concepts, from cells to ecosystems; 2) strengthen competencies in statistical analysis and scientific writing; 3) pique plant science interest; and 4) allow all undergraduates to contribute to genuine research. Our series of inquiry-centered exercises mitigated potential faculty barriers to adopting research-rich curricula, facilitating teaching/research balance by gathering publishable scholarly data during laboratory class periods. Student competencies were assessed with pre- and postcourse quizzes and rubric-graded papers, and attitudes were evaluated with pre- and postcourse surveys. Our revised curriculum increased students’ knowledge and awareness of plant science topics, improved scientific writing, enhanced statistical knowledge, and boosted interest in conducting research. More than 300 classroom students have participated in our program, and data generated from these modules’ assessment allowed faculty and students to present 28 contributed talks or posters and publish three papers in 4 yr. Future steps include analyzing the effects of repeated module exposure on student learning and creating a regional consortium to increase our project's pedagogical impact.
Immune hemolytic anemia—selected topics

Autoimmune hemolytic anemia (AIHA) is most often idiopathic. However, in recent years, AIHA has been noted with increased incidence in patients receiving purine nucleoside analogues for hematologic malignancies; it has also been described as a complication of blood transfusion in patients who have also had alloimmunization. As the technology of hematopoietic stem cell transplantation has become more widespread, immune hemolysis in the recipients of ABO-mismatched products has become better recognized. The syndrome is caused by passenger lymphocytes transferred from the donor and, although transient, can be quite severe. A similar syndrome has been observed in recipients of solid organ transplants when there is ABO-incompatibility between donor and recipient. Venous thromboembolism is a little-recognized, though likely common, complication of AIHA, and may in some instances be related to coexistent antiphospholipid antibodies. While AIHA is a well-documented complication of malignant lymphoproliferative disorders, lymphoproliferative disorders may also paradoxically appear as a consequence of AIHA. A number of newer options are available for treatment of AIHA in patients refractory to corticosteroids and splenectomy. Newer immunosuppressives such as mycophenolate mofetil may have a role in such cases. Considerable experience has been accumulating in the last few years with monoclonal antibody therapy, mainly rituximab, in difficult AIHA cases; it appears to be a safe and effective option.
Sub-graph routing: a generalized fault-tolerant strategy for link failures in WDM optical networks

Single- and multiple-link failure resilience are of critical importance in survivable wavelength division multiplexed (WDM) optical network design. Networks are not made up simply of logical links, but also of links that are physically routed together or share a common node. Links that share a common physical duct are known in literature as shared risk link groups (SRLGs), and their impact on network design is widely studied. This paper presents a complete survivability approach for WDM optical network design known as sub-graph fault tolerance. Sub-graphs are created by removing any combination of components in the network to accommodate specific fault scenarios. Connections in the network are accepted if they can be routed in all predetermined sub-graphs. In this manner, protection against 100% of all multiple- and single-link failure scenarios designated by the designer is achieved, and heuristic best-effort protection is provided against subsequent or simultaneous link failures for which the network is not specifically designed. for which the network has not explicitly provisioned for, is also performed.
An Ethnoarchaeological Perspective on the Material and Chemical Residues of Communal Feasting at El Coyote, Northwest Honduras

This paper examines artifact distributions and chemical analysis of anthropogenic sediments by ICP-AES spectroscopy from the main civic-ceremonial plaza at the Late Classic (ca. AD 700-900) site of El Coyote in northwestern Honduras. Based on ethnoarchaeological comparisons drawn from a phosphate study of plaza soils in the nearby modern-day town of Petoa, spatial aspects of the organization of communal feasting are inferred for El Coyote.
Algorithm for optimizing energy use and path resilience in sensor networks

Sensor networks will change the way computers interface with our world and with each other. This transformation will be shaped by the network centric paradigm demonstrated in sensor networks. Sensor networks also require a data-centric communication paradigm to efficiently and effectively share data. Directed diffusion is a data-centric communication paradigm that forms a foundation of this paper. Energy efficient routing algorithms have been developed for directed diffusion; however, we have developed improved algorithms, which are described in this paper. We also present computer simulation results, which verify the effectiveness of previously established routing algorithms and compare them to our new and improved routing algorithms. The results show significant increase in energy efficiency and resilience. Finally, the paper incorporates effective techniques for modeling of sensor networks to demonstrate the usefulness of the new algorithms.
Release of endothelin from cultured bovine endothelial cells.

Abstract Recently discovered endothelin is a powerful vasoconstrictor of vascular smooth muscle in vitro, which also profoundly affects the mechanical function of the heart [1, 2]. An increased level of plasma endothelin in patients with acute myocardial infarction suggests the enhanced release of endothelin from vascular endothelium under pathophysiological conditions of the heart [3]. The reperfusion of ischemic myocardium is associated with the activation of polymorphonuclear leukocytes (PMN) generating oxygen-derived free radicals (OFR), as well as, enhanced responsiveness of myocardial α1-adrenergic receptors [4,5]. Both OFR and catecholamines are implicated in the modulation of release of endothelium-derived peptides [6].
Ets-1, a functional cofactor of T-bet, is essential for Th1 inflammatory responses

To mount an effective type 1 immune response, type 1 T helper (Th1) cells must produce inflammatory cytokines and simultaneously suppress the expression of antiinflammatory cytokines. How these two processes are coordinately regulated at the molecular level is still unclear. In this paper, we show that the proto-oncogene E26 transformation–specific-1 (Ets-1) is necessary for T-bet to promote interferon-γ production and that Ets-1 is essential for mounting effective Th1 inflammatory responses in vivo. In addition, Ets-1–deficient Th1 cells also produce a very high level of interleukin 10. Thus, Ets-1 plays a crucial and unique role in the reciprocal regulation of inflammatory and antiinflammatory Th responses.
Geodynamic Information in Peridotite Petrology

Systematic differences are observed in the petrology and major element geochemistry of natural peridotite samples from the sea floor near oceanic ridges and subduction zones, the mantle section of ophiolites, massif peridotites, and xenoliths of cratonic mantle in kimberlite. Some of these differences reflect variable temperature and pressure conditions of melt extraction, and these have been calibrated by a parameterization of experimental data on fertile mantle peridotite. Abyssal peridotites are examples of cold residues produced at oceanic ridges. High-MgO peridotites from the Ronda massif are examples of hot residues produced in a plume. Most peridotites from subduction zones and ophiolites are too enriched in SiO2 and too depleted in Al2O3 to be residues, and were produced by melt–rock reaction of a precursor protolith. Peridotite xenoliths from the Japan, Cascades and Chile–Patagonian back-arcs are possible examples of arc precursors, and they have the characteristics of hot residues. Opx-rich cratonic mantle is similar to subduction zone peridotites, but there are important differences in FeOT. Opx-poor xenoliths of cratonic mantle were hot residues of primary magmas with 16–20% MgO, and they may have formed in either ancient plumes or hot ridges. Cratonic mantle was not produced as a residue of Archean komatiites.
Ambient ozone exposure and children’s acute asthma in New York City: a case-crossover analysis

Background Childhood asthma morbidity has been associated with ambient ozone in case-crossover studies. Varying effects of ozone by child age and sex, however, have been less explored.
Postformal (Mis)Communications

Postformal capacities should be employed on everything from poverty to war to planetary survival, yet, there are inherent, unrecognized problems to resolve before they are likely to succeed. Ironically, the very benefits of postformal thought are what make it hard to operationalize those benefits. Postformal thought-leaders need to re-learn and strategically use their earlier ways of thinking and speaking. “Translations” of words using hierarchical complexity's different languages illustrate why. Additional inquiry and dialogic interactions can improve communications and benefit work on our pressing planetary futures.
Travel distance and sociodemographic correlates of potentially avoidable emergency department visits in California, 2006–2010: an observational study

Introduction Use of the hospital emergency department (ED) for medical conditions not likely to require immediate treatment is a controversial topic. It has been faulted for ED overcrowding, increased expenditures, and decreased quality of care. On the other hand, such avoidable ED utilization may be a manifestation of barriers to primary care access.