cssi/SciSciGPT-SciSciNet huggingface dataset:
Gene expression in the deep biosphere

Gene expression of microbes in anaerobic sediment from the Peru Margin at depths up to 159 metres below the sea floor is analysed: anaerobic metabolism of amino acids, carbohydrates and lipids are seen to be the dominant metabolic processes, and genes associated with cell division are found to be correlated with microbial cell concentration, suggesting that ongoing cell division contributes to biomass turnover. Microbial metabolism in the marine subsurface environment is an important factor in various global biogeochemical cycles, yet our understanding of the types of metabolism occurring is limited. This study uses metatranscriptomics to investigate gene expression in sediments up to 159 metres below the seafloor off the coast of Peru. Anaerobic metabolism of amino acids, carbohydrates and lipids are the predominant metabolic processes in this 'deep biosphere' environment, and the distribution of transcripts associated with cell division suggests that microbial cell division is occurring, not just biomass turnover without division. Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles1,2,3, but deep biosphere activities are not well understood1. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles1. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations1 and models4 of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.
Rapid cytopathic changes and transformation in human foreskin cell cultures infected with simian virus 40

Abstract Human foreskin cells exposed to SV40 exhibited characteristic cytopathic changes as early as 2 days after infection. The changes, occurring much sooner than in other reported human cells, included enlargement of nuclei and nucleoli, formation of multiple eosinophilic nuclear inclusions, and basophilic RNA-containing bodies in the cytoplasm. The nuclei showed bright fluorescence of various patterns with the indirect Coons' method. During the following days cell destruction occurred simultaneously with increased cell proliferation. Foci of rapidly dividing transformed cells appeared 3–4 weeks after infection. The transformed cells also differed from untransformed cells in morphology and growth pattern, showing many abnormal mitoses, and were more easily suspended by trypsinization. Virus was released, but in decreasing amounts, with serial passage of the transformed cell cultures. Occasional cells with typical cytopathic nuclear changes and specific nuclear immunofluorescence were present in the seventh passage after transformation. The demonstration of the SV40 complement-fixing tumor antigen in the transformed cells confirmed the specificity of the transformation. Electron microscope evidence for the early intranuclear multiplication of the virus and preliminary observations of the ultrastructure of the transformed cells are presented.
Longitudinal variability of the mesopause SAO

A longitudinal variation in the mesopause semi-annual oscillation (SAO) is documented from wind observations made by the High Resolution Doppler Imager satellite instrument. The asymmetry is dominated by a wavenumber 1 pattern with a variable phase. During the easterly phase of the mesopause SAO (equinoxes), maximum tropical easterlies occur over eastern South America and the Atlantic Ocean in the longitude band 300°-360°. During the westerly phase (solstices), the westerly winds descend more rapidly and are larger below ∼80 km in this same (Atlantic) longitude band. To the best that can be determined with sparse data, the longitudinal asymmetries near the stratopause are weak and are in phase with those in the mesosphere.
Skills-Enhancement Training Program for Home Care Providers: Implications for Redefining Quality Care

This study reports on a skills-enhancement training series for direct care workers providing personal assistance under a waiver for Medicaid home care services. Designed to increase professionalism...
Impact of management on nutrients, carbon, and energy in aboveground biomass components of mid-rotation loblolly pine ( Pinus taeda L.) plantations

To sustainably manage loblolly pine plantations for bioenergy and carbon sequestration, accurate information is required on the relationships between management regimes and energy, carbon, and nutrient export. The effects of cultural intensity and planting density were investigated with respect to energy, carbon, and essential nutrients in aboveground biomass of mid-rotation loblolly pine plantations, and the effects of harvesting scenarios on export of nutrients were tested. Destructive biomass sampling of a 12 years-old loblolly pine culture/density experiment, and analysis of variance were used to assess the effects of cultural intensity (operational vs. intensive) and six planting densities ranging from 741 to 4,448 trees ha−1. Two harvesting scenarios (stem-only vs. whole-tree harvesting) were assessed in terms of energy, carbon, and nutrient export. The concentrations of energy, carbon, and nutrients varied significantly among stem wood, bark, branch, and foliage components. Cultural intensity and planting density did not significantly affect these concentrations. Differences in energy, carbon and nutrient contents among treatments were mainly mediated by changes in total biomass. Nutrient contents were affected by either cultural intensity or planting density, or both. Stem-only harvesting removed 71–79 % of aboveground energy and carbon, 29–45 % of N, 28–44 % of P, 44–57 % of K, 51–65 % of Ca, and 50–61 % of Mg. Stem-only harvesting would be preferred to whole-tree harvesting, from a site nutrient conservation perspective.
Polyethylene implants in head and face surgery

Abstract Surgical implants of pure polyethylene for restoration of parts of the head and face have the advantage of maximum tissue tolerance, lightness of weight, flexibility, radiolucency, low thermal conductivity, and resistance to fracture and indentation. Polyethylene is particularly useful because of its ease of manipulation and carving qualities which permit easy and rapid adjustment in the operating room. The technique for processing the implants is described.
Effects of methylphenidate on the persistence of ADHD boys following failure experiences.

We examined the effects of methylphenidate on the task persistence of 21 boys with attention-deficit hyperactivity disorder (ADHD), after they had been exposed to both solvable and insolvable problems. The boys attempted to solve 10 different find-a-word puzzles on each of 4 days, involving the crossing of medication (placebo vs. 0.3 mg/kg) and prior task difficulty (solvable vs. insolvable). The results revealed that medication prevented the decrement in performance following the insolvable problems that was evident with the placebo days. In addition, on medication compared with placebo, the boys were more likely to make external attributions for failure and internal attributions for success. The results are discussed in terms of the impact of medication on ADHD boys' performance as medicated by cognitivemotivational state mechanisms.
OPEN GRID BRIDGE NOISE FROM GRID AND TIRE VIBRATIONS

The noise generated during the passage of vehicles on open grid bridge decks has a strong tonal component, which can be a source of annoyance to nearby residents. Potential sources of noise are the vibrations of the grid and the vibrations of the tire. In this paper, the relative contributions from the grid and the tire are investigated by using analytic modelling and field and laboratory measurements. It is shown that the contribution to the overall noise level measured at the curb from the vibrations of the grid is small compared to that from the vibrations of the tire. This is attributed to the fact that the grid has a poor acoustic radiation efficiency because of the large percentage of open area, and the individual grid elements are also very inefficient acoustic radiators in the frequency range of interest. Based on an estimate of the interaction force between the tire and the grid, the radiated noise from the tire alone accounts for the field measured noise level at the curb. To verify that the tire is the dominant source of noise, sound pressure level measurements were performed on a simulated track with the contribution from the grid vibrations removed. The measured sound pressure levels were similar to those measured at the curb. The significance of this result is that mitigation procedures that only reduce the vibration of the grid will not significantly reduce the overall radiated noise, and alternative mitigation procedures must be considered that attempt to reduce the excitation of the tire.
SMAD3 augments FoxO3-induced MuRF-1 promoter activity in a DNA-binding-dependent manner

Muscle-specific RING finger-1 (MuRF-1), a ubiquitin ligase and key regulator of proteasome-dependent protein degradation, is highly expressed during skeletal muscle atrophy. The transcription factor forkhead box O3 (FoxO3) induces MuRF-1 expression, but the direct role of other major atrophy-related transcription factors, such as SMAD3, is largely unknown. The goal of this study was to determine whether SMAD3 individually regulates, or with FoxO3 coordinately regulates, MuRF-1 expression. In cultured myotubes or human embryonic kidney cells, MuRF-1 mRNA content and promoter activity were increased by FoxO3 but not by SMAD3 overexpression. However, FoxO3 and SMAD3 coexpression synergistically increased MuRF-1 mRNA and promoter activity. Mutation of the SMAD-binding element (SBE) in the proximal MuRF-1 promoter or overexpression of a SMAD3 DNA-binding mutant attenuated FoxO3-dependent MuRF-1 promoter activation, showing that SMAD binding to DNA is required for optimal activation of FoxO3-induced transcription of MuRF-1. Using chromatin immunoprecipitation, SMAD3 DNA binding increased FoxO3 abundance and SBE mutation reduced FoxO3 abundance on the MuRF-1 promoter. Furthermore, SMAD3 overexpression dose-dependently increased FoxO3 protein content, and coexpression of FoxO3 and SMAD3 synergistically increased FoxO-dependent gene transcription [assessed with a FoxO response element (FRE)-driven reporter]. Collectively, these results show that SMAD3 regulates transcription of MuRF-1 by increasing FoxO3 binding at a conserved FRE-SBE motif within the proximal promoter region, and by increasing FoxO3 protein content and transcriptional activity. These data are the first to indicate that two major transcription factors regulating protein degradation, FoxO3 and SMAD3, converge to coordinately and directly regulate transcription of MuRF-1.
An iterative FDM/BEM method for the conjugate heat transfer problem — parallel plate channel with constant outside temperature

An iterative method for the solution of the conjugate heat transfer problem is presented. Convection heat transfer in a channel is solved using an FDM, and conduction heat transfer in the channel wall is solved using a BEM. The FDM and BEM are coupled to iteratively solve the conjugate problem. Numerical results are in good agreement with experimental data. The influences of the conductivity ratio of solid on fluid, solid wall thickness, channel aspect ratio, and of the input velocity on the interfacial temperature and Nusselt number distribution are studied.
Origins of Stereoselectivity in Diels−Alder Cycloadditions Catalyzed by Chiral Imidazolidinones

B3LYP/6-31G(d) density functional theory has been used to study Diels-Alder reactions of cyclopentadiene with alpha,beta-unsaturated aldehydes and ketones organocatalyzed by MacMillan's chiral imidazolidinones. Preferred conformations of transition structures and reaction intermediates have been located. The dramatically different reactivities and enantioselectivities exhibited by two similar chiral imidazolidinones are rationalized.
Roles of mechano-sensitive ion channels, cytoskeleton, and contractile activity in stretch-induced immediate-early gene expression and hypertrophy of cardiac myocytes

Mechanical loading of cardiac and skeletal muscles in vivo and in vitro causes rapid activation of a number of immediate-early (IE) genes and hypertrophy of muscle cells. However, little is known as to how muscle cells sense mechanical load and transduce it into intracellular signals of gene regulation. We examined roles of putative cellular mechanotransducers, mechanosensitive ion channels, the cytoskeleton, and contractile activity in stretch-induced hypertrophy of cardiac myocytes grown on a deformable silicone sheet. Using the patch-clamp technique, we found a single class of stretch-activated cation channel that was completely blocked by gadolinium (Gd3+). Inhibition of this channel by Gd3+ did not affect either the stretch-induced expression of IE genes or the increase in protein synthesis. Neither disruption of microtubules with colchicine nor that of actin microfilaments by cytochalasin D prevented the stretch-induced IE gene expression and increase in protein synthesis. Arresting contractile activity of myocytes by high K+, tetrodotoxin, or Ba2+ did not affect the stretch-induced IE gene expression. Tetrodotoxin-arrested myocytes could increase protein synthesis in response to stretch. These results suggest that Gd(3+)-sensitive ion channels, microtubules, microfilaments, and contractile activity may not be necessary for transduction of mechanical stretch into the IE gene expression and hypertrophy. The stimulus of membrane stretch may be transmitted to the cell nucleus through some mechanisms other than electrical or direct mechanical transduction in cardiac myocytes.
Clinical pharmacology of ceftriaxone in patients with neoplastic disease.

Pharmacological studies of ceftriaxone, a new semisynthetic cephalosporin, were conducted in 35 cancer patients. This antibiotic was administered in a variety of doses and schedules with no observed toxicity. Intramuscular administration of 500 mg of ceftriaxone to seven patients produced mean peak serum concentrations of 32.9 μg/ml 2.0 h after administration. The terminal serum half-life was 10.9 h. Intravenous infusion of 500 mg of ceftriaxone over 5 min to the same group of seven patients produced a mean peak concentration of the drug in serum of 83 μg/ml at the end of administration which decreased to 16.8 μg/ml at 8 h. A dose of 1 g of ceftriaxone given in identical fashion to the same group of seven patients produced mean peak concentrations in serum of 130 μg/ml at the end of administration and 17.3 μg/ml at 12 h. The mean percentages of drug recovered in urine 12 h after single intravenous doses of 500 mg and 1 g were 30 and 20%, respectively. A 1-g dose of ceftriaxone was administered every 8 h to 10 patients, and a 2-g dose was administered every 12 hours to 9 patients. Drug concentrations in serum were measured for each patient after drug administration on day 1, day 3 or 4, and day 7 or 8. The 1-g dose produced an observed mean peak concentration of 154 μg/ml and a mean terminal-phase half-life of 5.6 h on day 3 or 4. The 2-g dose produced a mean peak concentration in serum of 262 μg/ml and a terminal-phase serum half-life of 6.3 h on day 3 or 4. Continuous infusion studies were performed in nine neutropenic patients for up to 8 days by using a loading dose of 1 g over 30 min, followed by 2 g every 8 h. Mean concentrations in serum were maintained at about 135 μg/ml during the infusion period. Images
Direct numerical determination of the stress field in a thin elastic disk

Die gebrauchlichen Methoden der numerischen Spannungsbestimung in zwei- oder dreidimensionalen elastischen Kontinua haben indirekten und kinematischen Charakter. Das Verschiebungsfeld wird durch eine Linearkombination lokalisierter Verschiebungsfelder angenahert, deren Intensitaten nach dem Prinzip der minimalen potentiellen Energie bestimmt werden. Angenaherte Spannungen werden dann erhalten durch Anwendung des Hookeschen Gesetzes auf die Verformungen des angenaherten Verschiebungsfelds. Im Gegensatz zu diesem Vorgehen entwickelt die vorliegende Arbeit eine statische Methode zur unmittelbaren Bestimmung der Spannungen in einer dunnen elastischen Scheibe. Das Spannungsfeld wird durch eine Linearkombination von lokalisierten Feldern stuckweise konstanter Spannung angenahert, in denen nur die zur Trennungslinie benachbarter Felder konstanter Spannung parallele Normalspannung unstetig ist. Die Intensitaten dieser lokalisierten Spannungsfelder werden nach dem Prinzip der minimalen Erganzungsarbeit bestimmt. Die sich ergebenden linearen Gleichungen fur diese Intensitaten werden besprochen und durch numerische Beispiele illustriert.
Abnormal cathepsin B activity in Batten disease

Fibroblasts cultured from patients with various forms of neuronal ceroid-lipofuscinosis (NCL; Batten disease) showed variably decreasing cathepsin B activity with increasing passage number and months in culture in the presence of fetal calf serum. Cathepsin H activity and that of a wide range of lysosomal hydrolases was unaffected by these conditions. Cathepsin B activity was assayed either colorimetrically (N alpha-benzoyl-DL-Arg-beta-naphthylamide; BANA), fluorimetrically (Z-Arg-Arg-methylcoumarin), or autoradiographically, following NaDodSO4-12.5% polyacrylamide gel electrophoresis ([125]Tyr-Ala-Lys-Arg-CH2Cl) and was found to be lysosomal in localization. Fractionation of disrupted fibroblasts on a Percoll gradient showed evidence of abnormally buoyant lysosomes in some NCL patients, and these tended to be low in cathepsin B but rich in other lysosomal hydrolases. Our data do not support a primary defect in cathepsin B as the basic defect in NCL. However, a possible explanation for various studies implicating a protease defect in NCL is that cathepsin B was highly sensitive to inactivation by peroxides and aldehydes. Thus hydrogen peroxide (0.3 mM) or 4-hydroxynonenal (1 nM) inactivated cathepsin B without inhibiting cathepsin H or lysosomal hydrolases such as alpha-L-fucosidase. Since peroxides and 4-hydroxynonenal have been shown to accumulate in NCL tissue (despite apparently normal peroxidase activity), we tested the possibility of a defect in the removal of peroxidized lipids from phospholipids as the primary defect in NCL. The nociceptive peptide bradykinin (BK) normally initiates a cascade involving receptor-mediated phospholipase C activation and release of arachidonate and prostanoids from cultured skin fibroblasts. Release of [3H]arachidonate by BK was deficient in NCL fibroblasts, suggesting that the primary defect in NCL could involve the deficiency of a specific phospholipase A2 activity.
Phonological context in speech perception

Speech perception can be viewed in terms of the listener’s integration of two sources of information: the acoustic features transduced by the auditory receptor system and the context of the linguistic message. The present research asked how these sources were evaluated and integrated in the identification of synthetic speech. A speech continuum between the glide-vowel syllables /ri/ and /li/ was generated by varying the onset frequency of the third formant. Each sound along the continuum was placed in a consonant-cluster vowel syllable after an initial consonant /p/, /t/, /s/, and /v/. In English, both /r/ and /l/ are phonologically admissible following /p/ but are not admissible following /v/. Only /l/ is admissible following /s/ and only /r/ is admissible following /t/. A third experiment used synthetic consonant-cluster vowel syllables in which the first consonant varied between /b/ and /d and the second consonant varied between /l/ and /r/. Identification of synthetic speech varying in both acoustic featural information and phonological context allowed quantitative tests of various models of how these two sources of information are evaluated and integrated in speech perception.
Critical Role of Specific Ions for Ligand-Induced Changes Regulating Pyruvate Dehydrogenase Kinase Isoform 2†

In the complete absence of K+ and phosphate (Pi), pyruvate dehydrogenase kinase isoform 2 (PDHK2) was catalytically very active but with an elevated Km for ATP, and this activity is insensitive to effector regulation. We find that K+ or 5-fold lower levels of NH4+ markedly enhanced quenching of Trp383 fluorescence of PDHK2 by ADP and ATP. K+ binding caused an ∼40-fold decrease in the equilibrium dissociation constants (Kd) for ATP from ∼120 to 3.0 μM and an ∼25-fold decrease in Kd for ADP from ∼950 to 38 μM. Linked reductions in Kd of PDHK2 for K+ were from ∼30 to ∼0.75 mM with ATP bound and from ∼40 to ∼1.7 mM with ADP bound. Without K+, there was little effect of ADP on pyruvate binding, but with 100 mM K+ and 100 μM ADP, the L0.5 of PDHK2 for pyruvate was reduced by ∼14 fold. In the absence of K+, Pi had small effects on ligand binding. With 100 mM K+, 20 mM Pi modestly enhanced binding of ADP and hindered pyruvate binding but markedly enhanced the binding of pyruvate with ADP; the L0.5 for pyruvate wa...
Oceanographic control of diatom abundances and species distributions in surface sediments of the tropical and southeast Atlantic

Abstract This paper is a descriptive account of the diatomaceous component of pelagic sediments from the tropical and southeast Atlantic Ocean. Geographic patterns of diatom abundances (whole and fragment forms) per gram, major species relative abundances and diatom assemblages (resolved by Q-mode factor analysis) are presented. Comparisons drawn to sea-surface temperature, salinity and productivity distributions suggest that: (i) diatom abundances primarily reflect surface productivity with no apparent dissolution effects due to water depth; (ii) relative abundances of major species vary in their ecologic dependence but do reflect major oceanographic features of the surface waters; and (iii) of the five diatom assemblages resolved, four finely delineate the complexity of the low-latitude oceanography. These assemblages, in decreasing order of statistical importance, are associated with: (1) warm waters of moderate to high primary productivity; (2) the oceanward margin of the Benguela Current, a region of high primary production with a maximum in austral summer; (3) low-salinity waters off the mouths of the Zaire and Niger rivers; and (4) subtropical to tropical waters of lower productivity, mostly in the western equatorial Atlantic. The fifth factor represents the equatorward advection of Subantarctic to Antarctic diatoms by deep-ocean currents.
Assessing the distribution patterns of wildfire sizes in Mississippi, USA

Wildland fires can produce dramatic ecological and economic impacts. The objective of this study was to analyse the temporal and spatial distribution patterns of wildland fires using 64 474 fire records in Mississippi, collected between 1991 and 2007. The methodology employed was descriptive statistics and extreme value statistics. The analyses were conducted for all the fires combined, and also by year, period, ecoregion and cause separately. Wildland fires occurred most frequently between February and May, with more than half of all the fires occurring in that period. The ecoregion of outer coastal plain mixed-forest province had more fire occurrences and the ecoregion of south-eastern mixed-forestry province had more catastrophic fires. By fire cause, debris and incendiary fires combined were responsible for 89.6% of the area burned. The top 10% of the largest fires burned 58.8% of the total area. The extreme value statistics revealed that wildfires in Mississippi displayed a generalised Pareto distribution. Based on predictions from the peaks-over-threshold models, the largest wildland fire in Mississippi within the next 10 years could burn 2171 ha. These outcomes can help landowners and government agencies make better decisions related to forest investments, fire suppression and budget planning.
Shedding light on immunotherapy for cancer.

There are two experimental approaches to treat cancer through tweaking the immune system; both depend on T lymphocytes' having access to tumor. A recent study involving a mouse model demonstrates t...
Touching art: Intimacy, embodiment, and the somatosensory system

Viewers have a way of using their somatosensory system to create temporary boundary changes that bring them into intimate relationships with art objects. Spectators experience this imaginary fusion when simultaneously attending to their own somatosensory sensations, which occur inside the body, and to qualities of the artwork, which exist in the external world. At such moments viewers reinterpret their somatosensory sensations as a quality of the artwork. When inside and outside are reinterpreted, viewers cross the conventional boundary between self and object. This effect can be illustrated in first person reports and supported by current research in the neurosciences and the humanities.
The effect of resection on satellite cell activity in rabbit extraocular muscle.

Skeletal muscle is a complex tissue composed of thousands of individual multinucleated myofibers. It is considered postmitotic, in that the myonuclei residing within these myofibers do not divide in adult muscle.1,2 Residing outside the sarcolemma but within the basal lamina of individual myofibers is a population of cells that are responsible for muscle repair and regeneration, the satellite cells.3 When a muscle is injured, this specialized cell population becomes activated, divides, and either repairs damaged fibers or forms new myofibers. There are a number of factors that initiate myofiber remodeling in adult skeletal muscles. Among these are hypertrophy induced by synergist ablation,4 low-frequency stimulation,5 and eccentric exercise.6 These manipulations result in satellite cell activation and proliferation, which in turn are responsible for muscle repair and regeneration. Irradiation treatment, which eliminates satellite cells from these muscles, prevents the compensatory hypertrophy in these types of experiments.4 Another stimulus that activates satellite cells is stretching of the muscle.7–9 In fact, passive stretching alone can activate limb muscle satellite cells.10 Even more compelling is a recent study that subjected individual quiescent satellite cells isolated from adult limb muscle to stretching in vitro, and showed that direct stretching of the satellite cells themselves results in activation and bromodeoxyuridine (BrdU) incorporation.11 In a similar study, stretching was shown to activate satellite cells on individually isolated myofibers in vitro that had been prepared by using a method that maintains satellite cell quiescence.12 In animal models that induce significant amounts of stretching, particularly limb lengthening procedures that result in distraction-induced muscle stretching, muscle growth is a critical factor in the success of these procedures clinically.13,14 Strabismus surgery is a common procedure used to restore binocular alignment. One procedure typically used for an underacting muscle is surgical resection of the affected extraocular muscle (EOM). Resection procedures do not significantly alter the axial position of the globe in the orbit. Instead, resection rotates the eye in the direction of the resected muscle around a relatively fixed axis of rotation. This increases the resting tension and therefore stretching of both the resected muscle and its antagonist. In a previous study, resection of an extraocular rectus muscle induced fiber hypertrophy—presumably a response to the increased load created by the surgery.15 However, the mechanism of fiber hypertrophy in resected EOM is unknown and cannot be inferred directly from limb muscle studies because of significant differences known to exist between limb muscle and the EOMs.16 The effect of resection of the EOMs on satellite cell activation, myonuclear addition, and myosin heavy chain (MyHC) isoform expression has not been examined. This study was designed to determine the effects of this common strabismus treatment on the EOM of adult rabbits.
Bacteriophage-directed association of DNA polymerase I with host membrane: A dispensable function

After infection of Escherichia coli by bacteriophages T4, T7, or lambda, DNA polymerase I was observed to become transiently associated with the host membrane. This phenomenon was found to be controlled by both host and phage genes, as it was not observed in a pol A mutant of E. coli or after infection of pol A + cells by mutants of phage T7 from which the dispensable leftmost region of the T7 genome had been deleted. This region specifies the synthesis of several class I phage proteins. Ghosts of phage T4 also did not show this phenomenon. Chloramphenicol inhibited the membrane association of DNA polymerase when added at 0 min, or inhibited its further increase when added at 2.5 min or 5 min after infection. This indicated that continued phage-directed protein synthesis was essential for maximal membrane-DNA polymerase binding. Genetic and biochemical evidence suggested that the binding was not mediated by phage-induced endonucleolytic attack of membrane-bound DNA nor by nonspecific trapping of the cytoplasmic enzyme in vesicles formed during preparation of the membranes.
We're All in This Together: Library Faculty and Staff and Their Reporting of Electronic Resource Problems.

Libraries continue to shift budgets toward obtaining more electronic resources. Electronic resources can develop problems at any time when a library offers access. Staff collaboration is vital in ensuring availability to those resources. Partnering with areas in the library that work most closely with patrons can help share the load of the technical services staff that maintain such resources. At Milner Library, the authors observed anecdotally that faculty and staff had varying opinions toward reporting problems with electronic resources. The authors polled Milner's faculty and staff to identify factors that lead them to report problems.
Unification scheme for 3D surface reconstruction using physically based models

We propose a unification framework for three-dimensional shape reconstruction using physically based models. A variety of 3D shape reconstruction techniques have been developed in the past two decades, such as shape from stereopsis, from shading, from texture gradient, and from structured lighting. However, the lack of a general theory that unifies these shape reconstruction techniques into one framework hinders the effort of a synergistical image interpretation scheme using multiple sensors/information sources. Most shape-from-X techniques use an “observable” (e.g., the stereo disparity, intensity, or texture gradient) and a model, which is based on specific domain knowledge (e.g., the triangulation principle, reflectance function, or texture distortion equation) to predict the observable, in 3D shape reconstruction. We show that all these “observable–prediction-model” types of techniques can be incorporated into our framework of energy constraint on a flexible, deformable image frame. In our algorithm, if the observable does not confirm to the predictions obtained using the corresponding model, a large “error” potential results. The error potential gradient forces the flexible image frame to deform in space. The deformation brings the flexible image frame to “wrap” onto the surface of the imaged 3D object. Surface reconstruction is thus achieved through a “package wrapping” or a “shape deformation” process by minimizing the discrepancy in the observable and the model prediction. The dynamics of such a wrapping process are governed by the least action principle which is physically correct. A physically based model is essential in this general shape reconstruction framework because of its capability to recover the desired 3D shape, to provide an animation sequence of the reconstruction, and to include the regularization principle into the theory of surface reconstruction.
Visualization of Crushing Evolution in Granular Materials under Compression using DEM

Granular materials forming part of natural slopes, embankments, subgrades of foundations, and pavement structures are subjected to both static and dynamic loads during their engineering lives. As a result of these loads, particle crushing may occur. The present study demonstrates that the discrete-element method (DEM) can be used to visualize the evolution of this breakage process. In particular, the evolution of crushing in a simulated granular material subjected to uniaxial compression is presented. Even though DEM does not normally consider particle breakage, it is possible to simulate crushing by replacing one particle that has failed in tension with a combination of many particles of different sizes. The results from the simulation indicate that crushing does not develop uniformly throughout the sample, but rather concentrates in certain regions. These observations agree with experimental results of uniaxial tests conducted on sand. Other results from the simulation satisfactorily agree with experimental results previously reported by other researchers. In this way, by using a simplified failure criterion, DEM can be used to visualize and understand the evolution of granular crushing. This is something that is very difficult to do with laboratory tests alone.
Upregulation of amyloid precursor protein gene promoter in rat primary hippocampal neurons by phorbol ester, IL-1 and retinoic acid, but not by reactive oxygen species

Abstract The APP gene promoter has multiple regulatory sequences, some of which may contribute to the neuropathology of Alzheimer's disease (AD). In this study, we investigated the effects of phorbol ester (PMA), IL-1, retinoic acid and reactive oxygen species on APP promoter activity in primary hippocampal neurons. We transfected neurons with either of two APP promoter constructs, a −2.8 kb and a shorter −488 bp upstream fragment fused to the chloramphenicol transferase (CAT) reporter gene. We demonstrated that phorbol 12-myristate-13 acetate (PMA), retinoic acid and IL-1 all stimulated both APP promoter constructs in hippocampal neurons after 24 h treatment. PMA and IL-1 treatments led to 2-fold increases of APP promoter activity. Retinoic acid induced a 3-fold increase. In addition, the magnitude of APP promoter responses to PMA and IL-1 treatment was similar between APP −2.8 kb and −488 bp plasmid transfected neurons. This suggests that the AP-1 sequence at −350 to −344 in the APP promoter may mediate the stimulatory effects of PMA and IL-1, as previously observed in endothelial and HeLa cells. In contrast, hydrogen peroxide, which was shown to activate NF-κB in primary neurons, failed to stimulate APP promoter activity, suggesting that the regulatory elements in the APP promoter may not respond to reactive oxygen species. Overall, these data indicate that APP expression in primary neurons can be modulated by PMA, IL-1 and retinoic acid. However, the contribution of reactive oxygen to Alzheimer's disease may not be directly related to the activation of the APP gene promoter but instead to neuronal damage associated with oxidative stress. Since elevated levels of IL-1 have been observed in AD brain, IL-1 could contribute to development of Alzheimer's disease by stimulating APP synthesis in primary neurons.
Material failure modes, part III: A brief tutorial on corrosion-related material failure modes

This article is the final installment of a three-part series on material failure modes recently published in the MaterialEASE section of AMPTIAC Quarterly. Part One introduced the concept of material failure modes and covered fracture, ductile failure, elastic deformation, creep, and fatigue. Part Two continued the discussion with brief descriptions of impact, spalling, wear, brinelling, thermal shock, and radiation damage. This article completes the series on material failure modes, covering uniform, galvanic, crevice, pitting, intergranular, and erosion corrosion; selective leaching/dealloying; hydrogen damage; stress-corrosion cracking; and corrosion fatigue. The three articles taken together make a valuable desk reference for any professional making material selection and design decisions.
COMPETITION AND FACILITATION BETWEEN EUCALYPTUS AND NITROGEN-FIXING FALCATARIA IN RELATION TO SOIL FERTILITY

The balance between tree competition and facilitation may shift in relation to gradients in soil resource supplies, thereby determining patterns in overall stand-level production and community structure. We tested for variation in the nature and intensity of interactions between Eucalyptus saligna and nitrogen-fixing Falcataria mollucana along a gradient of soil nitrogen and phosphorus supply in Hawaii, USA. Neighborhood indexes were used to describe competitive and facilitative interactions between trees, and spatially explicit models of individual tree growth and survival were developed to look at the effects of soil nutrient supply on those interactions. The dynamics between neighboring trees depended strongly on soil nutrient supply. Large trees generally grew faster than smaller trees, but this pattern was moderated by interactions between nutrient availability and the intensity of competition and facilitation. Falcataria survival decreased by up to 30% with increasing Eucalyptus on low-nitrogen soils, but increased by nearly 70% on soils with higher nitrogen levels. Intraspecific interactions reduced Falcataria growth by up to 100% on high-phosphorus soils, yet facilitated the growth of focal trees growing on low-phosphorus soils by up to 60%. The effect of Falcataria neighbors on Eucalyptus growth also depended on phosphorus supply: increased Falcataria reduced predicted growth of the focal tree by 20% on low-phosphorus soils, but increased growth by 8% on high-phosphorus soils. Relationships between species were more dynamic at the scale of individual trees than previously indicated by stand-level assessments. The important role of soil nutrient supply in moderating both the intensity and nature of tree interactions implies that competition and facilitation studies need to consider a wide range of soil conditions to be generalizable.
Competitive Pricing of Farmer Mac's Mortgage-Backed Securities and Its Future Viability: A Contingent Claims Analysis Approach

A continuous-time contingent claims pricing model is used to price Farmer Mac mortgage-backed securities. The required investor yields are then compared with mortgage rates from various financial institutions to determine the competitiveness of loan rates needed for the Farmer Mac market. Our results indicate that Farmer Mac
Effect of Light on Human Circadian Physiology.

The circadian system in animals and humans, being near but not exactly 24 hours in cycle length, must be reset on a daily basis to remain in synchrony with external environmental time. This process of entrainment is achieved in most mammals through regular exposure to light and darkness. In this article, we review the results of studies over the past 25 years conducted in our laboratory and in those of others investigating the effects of light on the human circadian timing system. These studies have revealed how the timing, intensity, duration, and wavelength of light affect the human biologic clock. Our most recent studies also demonstrate that much is yet to be learned about the effects of light on the human circadian timing system.
The Beginning of the End of AIDS

We are at a moment of great optimism in the response to HIV, thanks to breakthroughs in chemoprophylaxis, a possible vaccine, and the benefits of early treatment. What will it take to achieve what Secretary of State Hillary Clinton has called an AIDS-free generation?
Thermal extraction-two-dimensional gas chromatography-mass spectrometry with heart-cutting for nitrogen heterocyclics in biomass burning aerosols

A thermal extraction-two-dimensional gas chromatography-mass spectrometry (TE-GC-GC-MS) method with heart-cutting is developed for quantitatively assessing nitrogen (N)-bearing organic species (e.g., pyrrole, pyridine, nitriles, and amines) in aerosols emitted from agricultural fires. Pyrolysis of the constituents in the crop residue is a likely formation pathway for these compounds. An evaluation of the TE-GC-GC-MS method proficiency for them confirms low carryover (<1%), adequate recovery (84-100%), high reproducibility (<9% RSD), picogram method detection limits, and a linear dynamic range spanning four orders of magnitude. The 14 substances for which quantitative results are available are primarily heterocyclic aromatic N compounds that comprise 0.7% (w/w) of the total fine aerosol mass. The benefits of TE-GC-GC-MS versus conventional GC-MS methods for organic N species in aerosols may depend on the matrix and the target N analyte concentration in that matrix; for the biomass burning aerosol examined in this study, the former approach reduces the unresolved complex mixture and detects organic N species not seen with GC-MS. We show another advantage of TE-GC-GC-MS is that it adequately resolves the anhydro-sugar (e.g., levoglucosan), alkanoic acid, and substituted phenol molecules in the biomass burning aerosol without the use of methylation or trimethyl-silyl derivatizing agents.
Potential energy surfaces and dynamical properties of three low-lying states of silylene

Abstract Two-dimensional MCSCF 6-31G ∗∗ potential energy surfaces of the lowest three states, 1A1, 3B1, and 1B1, of silylene are reported. The seam between the two-dimensional potential energy surfaces of the 1A1 and 3B1 states is found to be in the neighborhood of the 3B1 minimum. This suggests that fast radiationless transitions may occur from the 3B1 state to the 1A1 state. The transition dipole length and velocity connecting the 1A1 and 1B1 states strongly depend on the normal coordinates. The vibrational structure of the absorption spectrum from the 1A1 state to the 1B1 state calculated by using the dipole length as a simple function of the normal coordinates is similar to that obtained within the Franck-Condon approximation.
Aminopyridinecarboxamide-based inhaled IKK-2 inhibitors for asthma and COPD: Structure-activity relationship

Installation of sites for metabolism in the lead compound PHA-767408 was the key focus of the IKK-2 inhaled program. This paper reports our efforts to identify a novel series of aminopyridinecarboxamide-based IKK-2 inhibitors, which display low nanomolar potency against IKK-2 with long duration of action (DOA), and metabolically labile to phase I and/or phase II metabolizing enzymes with potential capability for multiple routes of clearance. Several compounds have demonstrated their potential usefulness in the treatment of asthma and chronic obstructive pulmonary disease (COPD).
Flow Cytometric Immunophenotyping of the Blood and CSF of Patients with Multiple Sclerosis (P02.081)

Objective: To monitor intrathecal immune responses and to investigate their role in pathogenesis of multiple sclerosis (MS). Background Immune cells in the cerebrospinal fluid (CSF) better reflect intrathecal inflammation than peripheral blood. However, low cellularity and susceptibility to apoptosis makes immunophenotyping of CSF challenging. Design/Methods: CSF and concomitant peripheral blood was collected in prospective manner in untreated patients (N=36) who presented for the diagnostic work-up of neuroimmunological disorder. Cells were isolated from 10-15cc of CSF within 15 min of collection. An optimized 12 color flow cytometric immunophenotyping (FCI) protocol was used to identify immune subpopulations (CD4, CD8 T cells, B cells, CD56bright- and CD56dim NK cells, monocytes, myeloid and plasmacytoid dendritic cells (DCs)) and their activation markers. FCI results were analyzed in an unbiased manner with the absolute cell count in blood and CSF and with the diagnosis established by the clinicians. Results: Upon unblinding, our cohort consisted of clinically isolated syndrome (CIS, N=2), relapsing-remitting MS (RR-MS, N=18), primary progressive MS (PP-MS, N=4), secondary progressive MS (SP-MS, N=4), non-inflammatory neurological diseases (NIND, N=4) and other inflammatory neurological diseases (OIND, N=5) controls. CSF was enriched for T cells, HLA-DR+ (i.e. activated) T cells and CD56bright NK cells in comparison to blood. We observed positive correlations between blood and CSF B cells, and blood and CSF HLA-DR+ T cells and terminally-differentiated double negative T cells, suggesting a link between systemic and intrathecal immune activation. Intrathecal differences between MS patients and controls consisted of elevated B cell to monocyte ratio (p=0.0004) and elevated CD4/CD8 T cell ratio (p=0.0007). Conclusions: The CSF immunophenotyping has been adapted to all NIB clinical protocols, including interventional trials, so updated results will be presented. We expect that with expanded cohort and longitudinal data, CSF immunophenotyping will provide essential information about intrathecal immune responses in neuroimmunological diseases. Supported by: NIH Intramural Research Program. Disclosure: Dr. Han has nothing to disclose. Dr. Salgado has nothing to disclose. Dr. Alfahad has nothing to disclose. Dr. Bielekova has received royalty payments from NIH.
Corneal ulcers in corneal transplants

Twenty-nine eyes, representing an infection rate of 4.9%, developed corneal ulcers following corneal transplant surgery; 26 with available data are presented. All occurred in the graft or at the wound margin. The median postoperative time to ulcer development was 5.5 months. All eyes were on topical steroids when the ulcer developed. Other associated factors were: loose sutures, bandage lenses and eyes grafted for herpes simplex keratitis. Ninety percent of the ulcers had one or more of these factors. Positive cultures for organisms were obtained in 75% and positive gram stain in 68% of the ulcers. Nine genera of bacteria were cultured; S. epidermidis, S. pneumoniae, P. aeruginosa and Corynebacterium were the most common organisms. Ninety-five percent of the bacteria tested were sensitive to gentamicin. Visual reduction occurred in 46% of the cases overall; herpetic corneas had an 88% incidence of visual loss.
A Caenorhabditis elegans homologue of hunchback is required for late stages of development but not early embryonic patterning.

Abstract We have cloned a Caenorhabditis elegans homologue of the Drosophila gap gene hunchback ( hb ) and have designated it hbl-1 ( h unch b ack- l ike). hbl-1 encodes a predicted 982-amino-acid protein, containing two putative zinc-finger domains similar to those of Drosophila Hunchback. The gene is transcribed embryonically, but unlike the maternally expressed Drosophila hb, its mRNA is not detected in C. elegans oocytes. A hbl-1::gfp reporter is expressed primarily in ectodermal cells during embryonic and larval development. Double-stranded RNA-interference (RNAi) was used to indicate hbl-1 loss-of-function phenotypes. Progeny of hbl-1(RNAi) hermaphrodites exhibit a range of defects; the most severely affected progeny arrest as partially elongated embryos or as hatching, misshapen L1 larvae. Animals that survive to adulthood exhibit variably dumpy (Dpy), uncoordinated (Unc), and egg-laying defective (Egl) phenotypes, as well as defects in vulval morphology (Pvl). Abnormal organization of hypodermal cells and expression of a hypodermal marker in hbl-1(RNAi) animals suggests that most of the phenotypes observed could be due to improper specification of hypodermal cells. The pattern of hbl-1 expression is similar to that reported for the leech hunchback homologue Lzf-2, suggesting that these proteins may have similar biological functions in diverse species with cellular embryos.