cssi/SciSciGPT-SciSciNet huggingface dataset:
Were there any “misassignments” among iron–sulfur clusters N4, N5 and N6b in NADH-quinone oxidoreductase (complex I)?

Abstract NADH-quinone oxidoreductase (complex I) in bovine heart mitochondria has a molecular weight of approximately 1 million Da composed of 45 distinct subunits. It is the largest energy transducing complex so far known. Bacterial complex I is simpler and smaller, but the essential redox components and the basic mechanisms of electron and proton translocation are the same. Over the past three decades, Ohnishi et al. have pursued extensive EPR studies near liquid helium temperatures and characterized most of the iron–sulfur clusters in complex I. Recently, Yakovlev et al. [G. Yakovlev, T. Reda, J. Hirst, Reevaluating the relationship between EPR spectra and enzyme structure for the iron-sulfur clusters in NADH:quinone oxidoreductase, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 12720–12725] challenged Ohnishi's group by claiming that there were EPR “misassignments” among clusters N4, N5 and N6b (in order to prevent confusion, we used current consensus nomenclature, as the nickname). They claimed that we misassigned EPR signals arising from cluster N5 to cluster N4, and signals from cluster N6b to cluster N4. They also proposed that cluster N5 has (4Cys)-ligands. Based on the accumulated historical data and recent results of our site-specific mutagenesis experiments, we confirmed that cluster N5 has (1His + 3Cys)-ligands as we had predicted. We revealed that E. coli cluster N5 signals could be clearly detected at the sample temperature around 3 K with microwave power higher than 5 mW. Thus Hirst's group could not detect N5 signals under any of their EPR conditions, reported in their PNAS paper. It seems that they misassigned the signals from cluster N4 to N5. As to the claim of “misassignment” between clusters N4 and N6b, that was not a possibility because our mutagenesis systems did not contain cluster N6b. Therefore, we believe that we have not made any “misassignment” in our work.
Overview and status of the Lunar Laser Communications Demonstration

The Lunar Laser Communications Demonstration (LLCD), a project being undertaken by MIT Lincoln Laboratory, NASA's Goddard Space Flight Center, and the Jet Propulsion Laboratory, will be NASA's first attempt to demonstrate optical communications between a lunar orbiting spacecraft and Earth-based ground receivers. The LLCD space terminal will be flown on the Lunar Atmosphere and Dust Environment Explorer (LADEE) spacecraft, presently scheduled to launch in 2013. LLCD will demonstrate downlink optical communications at rates up to 620 Mbps, uplink optical communications at rates up to 20 Mbps, and two-way time-of-flight measurements with the potential to perform ranging with sub-centimeter accuracy.
Born model calculation of defect energies in CaF2

A general formulation of the Born model as applied to the calculation of the energies to form point defects in ionic crystals is given, and then specialized to vacancies and interstitials of both kinds in CaF2. After examination of the effects produced by several factors in the calculation, ‘best’ values are chosen for the formation energies. These are used to compute the energies to form anion Frenkel pairs (2·7 ± 0·4 eVpair), cation Frenkel pairs (7·5 ± 0.8 eVpair) and Schottky trois (5·1 ± 0·7 eVtrio). The results are in reasonable agreement with Ure's experimental results, which indicate that anion Frenkel pairs are the equilibrium defects in CaF2, with a formation energy of 2·8 eV.
Redox state of Earth's upper mantle from kimberlitic ilmenites

Temperatures and oxygen fugacities are reported on discrete ilmenite nodules in kimberlites from West Africa which demonstrate that the source region in the upper mantle is moderately oxidized, consistent with other nodule suites in kimberlites from southern Africa and the United States. A model is presented for a variety of tectonic settings, proposing that the upper mantle is profiled in redox potential, oxidized in the fertile asthenosphere but reduced in the depleted lithosphere.
A Method for Photoinitating Protein Folding in a Nondenaturing Environment

The early kinetic events of protein folding are an important part of the folding pathway, yet our understanding towards the process is limited. Information from the study of these early events can allow us to distinguish between the various models that have been proposed to describe the folding of a protein in real time. Unlike “typical” chemical kinetics with well-defined initial and final states, the initial state of a denatured protein is relatively ill-defined. This uncertainty introduces ambiguity in the interpretation of the experimental data on the early events in protein folding. Toward developing a unified theory of protein folding, it is necessary to begin the observation of the refolding process from a well-defined initial state, trigger folding as rapidly as possible, and to follow the protein in real time as it samples its conformational space over its highly complex free-energy landscape.
Xanthine nucleotide-specific G-protein α-subunits: a novel approach for the analysis of G-protein-mediated signal transduction

Pro- and eukaryotic cells express multiple GTP-binding proteins that play crucial roles in signal transduction. GTP-binding proteins possess a highly conserved NKX D motif critically involved in guanine binding. In order to selectively activate a defined GTP-binding protein, base-specificity can be switched from guanine to xanthine by mutating the conserved aspartate into asparagine (D/N-mutation). This approach was very successful at elucidating the function of structurally diverse GTP-binding proteins in complex systems. However, attempts to generate functional xanthine nucleotide-specific alpha-subunits of heterotrimeric GTP-binding proteins (G-proteins) met more difficulties. Recent studies have shown that a sufficiently high GDP-affinity is critical for functional expression of xanthine nucleotide-selective G-protein mutants. Moreover, xanthosine 5'-[gamma-thio]triphosphate and xanthosine 5'-[gamma, beta-imido]triphosphate are not functionally equivalent activators of D/N-G-protein mutants. We are now in the position to exploit xanthine nucleotide-specific G-proteins to dissect signaling pathways activated by a given G-protein in complex systems.
1223 HIGH EXTRACELLULAR PHOSPHATE (Pi) IN VITRO REVERSES THE INHIBITION OF 1,25(OH) 2 D 3 (1,25D) SYNTHESIS IN CHRONIC METABOLIC ACIDOSIS (CMA)

1223 HIGH EXTRACELLULAR PHOSPHATE (Pi) IN VITRO REVERSES THE INHIBITION OF 1,25(OH) 2 D 3 (1,25D) SYNTHESIS IN CHRONIC METABOLIC ACIDOSIS (CMA)
Osteocalcin production in primary osteoblast cultures derived from normal and Hyp mice.

Rickets and osteomalacia are characteristic features of the Hyp mouse model of human X-linked hypophosphatemia. Hyp mice demonstrate elevated circulating osteocalcin levels, as well as altered regulation of osteocalcin by 1,25(OH)2D3. Whether this osteocalcin abnormality is intrinsic to the osteoblast, or mediated by the in vivo milieu, has not been established. We therefore characterized osteocalcin production and its regulation by 1,25(OH)2D3 in primary cultures of murine osteoblasts and examined osteocalcin and its messenger RNA in response to 1,25(OH)2D3 in cultures of Hyp mouse-derived osteoblasts. Cell viability and osteocalcin production are optimal when murine cells are harvested within 36 h of age. Murine primary osteoblast cultures mineralize and produce osteocalcin in a maturation-dependent fashion (as demonstrated in other species), and continuous exposure to 1,25(OH)2D3, beginning at day 9 of culture, inhibits osteoblast differentiation and osteocalcin production and prevents mineralization o...
Clinical Case Conference—An Alliteration

Alliteration is the repetition of the same letter at the beginning of words. It has a long history, and many excellent examples are to be found in the works of William Shakespeare (e.g., “Whereat with blade, with bloody blameful blade, He bravely broach'd his boiling bloody breast”). Shifting forward to more recent times, toxicologists may find the very lengthy alliteration on alcohol by the Rev. James Nelson Hulme, MD, sobering reading. It was published in 1882 and is titled ALLITERATION. An alliterated ALLOCUTION by the Letter A against Alcohol and all alcoholic admixtures, agencies and appliances; and also advocating all ATTEMPERANCE; as addressed at ABECEDARY ALHAMBRA, afore all …. The verse is 500 lines …
Risk Assessment of Enteric Virus Disease Transmission by Shellfish Consumption

Densely populated coastal regions of the world generate large quantities of domestic sewage and sludge which is often disposed into the marine environment. Present in these wastes are human pathogenic viruses which are capable of surviving for prolonged periods of time in the marine environment and transmitting disease to humans. Hepatitis A virus and Norwalk virus outbreaks associated with shellfish consumption continue to occur in the United States. Three separate epidemiological studies have also shown an epidemiological association between shellfish consumption and increased risk of hepatitis A infection in consumers. An epidemiological association between non-A and non-B hepatitis has also been demonstrated. A review of the risks of infection, clinical illness and mortality associated with enteroviruses suggest that the present of these viruses in shellfish presents a significant risk to the consumer.
Virtual reality training for carotid intervention.

Virtual reality simulation has a growing role in teaching physicians to perform high-risk, complex or technically demanding procedures. In this Training Matters article, David Dawson discusses the benefits of using this approach for training in carotid artery stenting.
Persistent binding of MgADP to the E187A mutant of Escherichia coli phosphofructokinase in the absence of allosteric effects.

MgADP binding to the allosteric site enhances the affinity of Escherichia coli phosphofructokinase (PFK) for fructose 6-phosphate (Fru-6-P). X-ray crystallographic data indicate that MgADP interacts with the conserved glutamate at position 187 within the allosteric site through an octahedrally coordinated Mg(2+) ion [Shirakihara, Y., and Evans, P. R. (1988) J. Mol. Biol. 204, 973-994]. Lau and Fersht reported that substituting an alanine for this glutamate within the allosteric site of PFK (i.e., mutant E187A) causes MgADP to lose its allosteric effect upon Fru-6-P binding [Lau, F. T.-K., and Fersht, A. R. (1987) Nature 326, 811-812]. However, these authors later reported that MgADP inhibits Fru-6-P binding in the E187A mutant. The inhibition presumably occurs by preferential binding to the inactive (T) state complex of the Monod-Wyman-Changeux two-state model [Lau, F. T.-K., and Fersht, A. R. (1989) Biochemistry 28, 6841-6847]. The present study provides an alternative explanation of the role of MgADP in the E187A mutant. Using enzyme kinetics, steady-state fluorescence emission, and anisotropy, we performed a systematic linkage analysis of the three-ligand interaction between MgADP, Fru-6-P, and MgATP. We found that MgADP at low concentrations did not enhance or inhibit substrate binding. Anisotropy shows that MgADP binding at the allosteric site occurred even when MgADP produced no allosteric effect. However, as in the wild-type enzyme, the binding of MgADP to the active site in the mutant competitively inhibited MgATP binding and noncompetitively inhibited Fru-6-P binding. These results clarified the mechanism of a three-ligand interaction and offered a nontraditional perspective on allosteric mechanism.
Pharmacotherapy for Alcohol-Related Disorders: What Clinicians Should Know

Alcohol-related disorders are a major public health problem in the United States. Alcohol interacts with several neurotransmitter systems causing both acute and chronic effects in the brain. While the mainstay of treatment of alcohol-related disorders, with the exception of alcohol withdrawal, has historically been psychosocial, pharmacotherapy is increasingly being investigated and incorporated into standard clinical practice. Patients with alcohol use disorders and comorbid psychiatric conditions, most commonly depressive and anxiety disorders, can benefit from symptom-targeted pharmacotherapy, even if the patient fails to achieve abstinence from alcohol. Although benzodiazepines remain the treatment of choice to treat alcohol withdrawal, a variety of other agents is being investigated, particularly in the outpatient setting. Further randomized clinical trials of alcohol-related disorder pharmacotherapy, particularly of comorbid subpopulations, are needed to better inform clinical decision making. The routine exclusion of alcohol-dependent patients from pharmacotherapy trials of psychiatric disorders presents a barrier to gathering more data. Recommendations for future research are discussed.
Results of the treatment of children with recurrent gliomas with lomustine and vincristine.

Gliomas comprise over 50% of all childhood brain tumors. Treatment of recurrent childhood gliomas has been disappointing and the effectiveness of therapy has been difficult to judge because of the variable natural history of the disease. Information gathered recently has suggested that treatment with [1-(2-chloroethyl)-3-cyclohexyl-I-nitrosourea)J (CCNU) and vincristine (VCR) after radiotherapy is effective in prolonging survival in children with newly diagnosed anaplastic gliomas. The authors have used these same drugs-CCNU (100 mg/m2) and VCR (1.5 mg/m2 up to a maximum dose of 2 mg)- in 6-week cycles for a maximum of eight cycles in children with recurrent gliomas. To date, 15 patients have been treated; five patients had malignant gliomas and ten low-grade gliomas. Three children showed improvement, five had stable disease, and seven had progressive disease. Of the five patients with malignant gliomas, four progressed within two cycles of treatment and one had stable disease for 7 months on treatment and then relapsed. Seven of ten children with low-grade gliomas benefitted from treatment and six remain in continuous remission a median of 16 months after initiation of therapy. Three of these children are off all therapy 21.30, and 30 months after treatment, respectively. Therapy was well tolerated and toxicity consisted primarily of reversible bone marrow suppression. The authors conclude that CCNU and VCR chemotherapy is effective in children with recurrent low-grade gliomas and can result in relatively long-term disease stabilization. In limited experience of the authors, it is not of benefit in children with recurrent anaplastic lesions. Cuncer 619396-902, 1988. HEMOTHERAPY of recurrent gliomas in childhood C is difficult to evaluate because of the small numbers of patients in individually reported series and the variable natural history of this disease. Regardless, results to date have been disappointing. Recent reviews of the efficacy of chemotherapy for adults and children with recurrent gliomas have suggested that drugs are of limited, if any, efficacy and those studies purporting beneficial responses to treatment have not documented this stringently.'-6 Also, almost all studies have dealt with recurrent malignant gliomas, primarily in adults, and there has been little evaluation of the utility of chemotherapy in patients with low-grade gliomas. Over
Soil organic carbon quality in forested mineral wetlands at different mean annual temperature

Forested mineral soil wetlands (FMSW) store large stocks of soil organic carbon (SOC), but little is known on: (i) whether the quality of SOC stored in these soils (proportion of active versus more resistant SOC compounds) differs from SOC in upland soils; (ii) how the quality of SOC in FMSW varies with mean annual temperature (MAT); and (iii) whether SOC decomposition rates in these environments respond to warming and drying more strongly than those observed in upland soils. To address this substantial knowledge gap, we identified nine FMSW and fifteen paired upland forest sites across three bioregions in North America (sub-alpine in Colorado; north-temperate in Minnesota; and south-temperate in South Carolina) to test the following three hypotheses. First, FMSW store a higher proportion of active SOC compared with upland systems because long anaerobic periods favor the accumulation of labile substrates. Second, in FMSW, SOC quality decreases from cold to warm bioregions because high quality detritus accumulates preferentially at cool sites where decomposition is slow. Finally, decomposition of SOC in FMSW will respond more strongly to warming under aerobic conditions than SOC from upland forest soils because of higher accumulation of active SOC in FMSW. To test these hypotheses, we incu- bated FMSW and upland forest soils at two constant temperatures (10 and 30 � C) for 525-d under aerobic conditions and constant moisture. In contrast to our first hypothesis, we observed similarly rapid depletion of active SOC compounds at initial stages of incubation across FMSW and upland sites, and across the 525-d incubations we observed overall lower SOC decomposition rates in our FMSW soils. In line with our second hypothesis, and across FMWS and upland soils, we found greater SOC loss in the sub-alpine bioregion than both temperate regions. In contrast to our last hypothesis, we found no difference in the temperature sensitivity (Q10) of SOC decomposition in FMSW and upland forest soils. Critically, total SOC loss (g SOC per g soil) was larger in FMSW because of the large amount of SOC stored in these ecosystems, indicating that despite a lack of difference between FMSW and upland responses, the total release of C from FMSW that could result from global warming may be large.
Altered patterns of keratin synthesis in human epidermal keratinocytes transformed by SV40

Transformation of human epidermal keratinocytes by the oncogenic virus SV40 is a stage-specific process in which normal patterns of differentiation are progressively altered over time following infection. Within the context of this scheme, we examined the keratins produced by the infected cells. Immunofluorescence studies indicated that viral infection led to the formation of variant cells visibly lacking the normal keratin cytoskeleton after about 10-15 serial passages (60-90 cell generations) post infection. Analyses of variant cell formation in clonal populations grown on palladium islands revealed that the variants were derived within 2-3 cell divisions from cells containing an apparently normal keratin cytoskeleton, but that variant formation depended upon cell density. Immunoprecipitation of 35S-methionine labelled keratins from the infected keratinocytes revealed a gradual loss of the normal 46, 50, 56 and 58Kd keratin species over a period of many months after infection. The loss of the normal keratins was accompanied by the appearance of at least two species in the 48-52Kd size range not present in uninfected cells and the enhancement of a third, 40Kd, protein quite early after infection. Analysis of the altered keratin patterns on two-dimensional acrylamide gels using either isoelectric focusing (IEF) or non-equilibrium pH gradient electrophoresis (NEPHG) along the first dimension showed that the infected cells produced basic keratins which increased in relative abundance as cells became more transformed with serial passage including at least five isoelectric forms not seen in uninfected cells. Translation of poly A+ RNAs from the infected cells indicated that the altered keratin synthesis probably reflects changes in the translatable mRNA pool.
Survival of intracellular freezing, lipid coalescence and osmotic fragility in fat body cells of the freeze-tolerant gall fly Eurosta solidaginis

Abstract Although it is generally believed that under natural conditions, freeze-tolerant organisms can survive only if ice formation is restricted to the extracellular space, in 1959 R. W. Salt reported that fat body cells of the freeze-tolerant gall fly, Eurosta solidaginis (Diptera: Tephritidae), survive intracellular freezing. Using cryomicroscopy, intracellular freezing was observed at −4.6±0.1°C for cells in Grace's media. Freezing was apparently caused by inoculative freezing from outside the cell, since fat body cells in oil cooled to below −15°C without internal ice formation. Viability of cells was assessed using fluorescent vital dyes immediately following freezing for 24 h at temperatures between −5 and −80°C. At −25°C or lower few cells survived freezing in Grace's medium alone. At −25 and −80°C, cells frozen in Grace's media supplemented with 1 M glycerol exhibited rates of survival similar to those in whole larvae. No larvae (n = 20) survived freezing to −80°C, but more than 60% of the fat body cells survived this treatment. Most fat body cells survived osmotic concentrations from 0.25 to 2 times that of the normal concentration of Grace's media (340 mOsm) for 24 h at 4°C. More than 60% of the cells survived 5 M glycerol in Grace's media under these conditions. An unusual response of these cells to freezing is the coalescence of intracellular lipid droplets upon thawing. The magnitude of coalescence increases with decreasing temperature and increasing duration of exposure, but decreases with the addition of glycerol to the media. Coalescence in itself is not indicative of injury, since larvae frozen under conditions that cause extensive coalescence readily survived to complete their development and emerge as adults.
Electronic structure of highly dispersed supported transition metal clusters

Results are reported here of a systematic study of the electronic structure of very small transition metal molecular clusters [Os3(CO)12, Os6(CO)18, Ru3(CO)12 and Ir4(CO)12] on solid surfaces as a function of both the condensed and the decomposed states in terms of cluster size, composition, and surface coverage. The probe technique used is primarily UPS and XPS photoelectron spectroscopy. Electron beam decomposition of the adsorbed molecular clusters at low temperatures on carefully prepared ordered or amorphous substrates made it possible to prepare layers characterized by a narrow size distribution of small, stable aggregates of well-defined composition and size. A primary objective of this work was to investigate the decomposition mechanisms of condensed clusters both in their initial state and in terms of the resulting rearrangement of the metal aggregates and ligands upon decomposition with reference to the nature of the substrate, their electronic properties, and chemical reactivity.
Unusual particles in a case of carcinomatous neuronal disease

Unusual particles are present in neurons and some astrocytes of a patient whose death was caused by the combined effects of oat-cell carcinoma and neuronal degeneration. The possibility of virus infection is discussed.
Dynamics of Dynamics within a Single Data Acquisition Session: Variation in Neocortical Alpha Oscillations in Human MEG

Background: Behavioral paradigms applied during human recordings in electro- and magneto- encephalography (EEG and MEG) typically require 1–2 hours of data collection. Over this time scale, the natural fluctuations in brain state or rapid learning effects could impact measured signals, but are seldom analyzed. Methods and Findings: We investigated within-session dynamics of neocortical alpha (7–14 Hz) rhythms and their allocation with cued-attention using MEG recorded from primary somatosensory neocortex (SI) in humans. We found that there were significant and systematic changes across a single ,1 hour recording session in several dimensions, including increased alpha power, increased differentiation in attention-induced alpha allocation, increased distinction in immediate time-locked post-cue evoked responses in SI to different visual cues, and enhanced power in the immediate cue-locked alpha band frequency response. Further, comparison of two commonly used baseline methods showed that conclusions on the evolution of alpha dynamics across a session were dependent on the normalization method used. Conclusions: These findings are important not only as they relate to studies of oscillations in SI, they also provide a robust example of the type of dynamic changes in brain measures within a single session that are overlooked in most human brain imaging/recording studies.
Effects of land use change on North American climate: impact of surface datasets and model biogeophysics

This study examines the impact of historical land-cover change on North American surface climate, focusing on the robustness of the climate signal with respect to representation of sub-grid heterogeneity and land biogeophysics within a climate model. We performed four paired climate simulations with the Community Atmosphere Model using two contrasting land models and two different representations of land-cover change. One representation used a biome classification without subgrid-scale heterogeneity while the other used high-resolution satellite data to prescribe multiple vegetation types within a grid cell. Present-day and natural vegetation datasets were created for both representations. All four sets of climate simulations showed that present-day vegetation has cooled the summer climate in regions of North America compared to natural vegetation. The simulated magnitude and spatial extent of summer cooling due to land-cover change was reduced when the biome-derived land-cover change datasets were replaced by the satellite-derived datasets. The diminished cooling is partly due to reduced intensity of agriculture in the satellite-derived datasets. Comparison of the two land-surface models showed that the use of a comparatively warmer and drier land model in conjunction with satellite-derived datasets further reduced the simulated magnitude of summer cooling. These results suggest that the cooling signal associated with North American land-cover change is robust but the magnitude and therefore detection of the signal depends on the realism of the datasets used to represent land-cover change and the parametrisation of land biogeophysics.
Inservice Teachers Mentoring Aspiring Teachers

This qualitative study examined the impact of mentoring relationships upon preservice and inservice teachers' literacy instruction. Twenty-two undergraduate students seeking teacher certification were assigned in pairs to tutor primary school students in a university reading clinic. Eleven classroom teachers seeking reading specialist certification conducted ten mentoring sessions with each pair of preservice teachers. Purposeful sampling was used to select three of the mentoring teams for data analysis. In two out of three teams, results indicated that preservice teachers expanded their instructional strategies as a result of three components of the mentoring relationship: selection of strategies, organization, and non-judgmental support. All inservice teachers reported increased reflection on and adaptation to their instructional strategies. Findings support the conclusion that early mentoring experiences foster growth for both preservice and inservice teachers.
Home Total Parenteral Nutrition During Pregnancy: A Case Report

A 26-year-old female was given total parenteral nutrition without complications during the last 2 months of her pregnancy. A partial small bowel obstruction caused by Crohn's disease prevented oral alimentation, necessitating parenteral nutrition. A term, female infant weighing 2680 grams was delivered vaginally without complications. At birth and 11 months of age, the infant's physical and developmental assessments were normal. This case report demonstrates that total parenteral nutrition can be administered during the last trimester of pregnancy to improve maternal nutrition so as to promote fetal growth.
EFFECTS OF NEONATAL AND ADULT ENUCLEATION ON THE SYNAPTIC ORGANIZATION OF THE SEROTONINERGIC PROJECTION TO THE SUPERFICIAL GRAY LAYER OF THE HAMSTER'S SUPERIOR COLLICULUS

Previous experiments from this laboratory have demonstrated that either neonatal or adult enucleation results in a marked increase in the density of the serotoninergic (5-HT) projection to the superficial layers of the hamster's superior colliculus (SC). The present study was undertaken to determine whether this alteration in the density of the 5-HT projections to SC in hamsters that sustained eye removals was associated with any change in the synaptic organization of this pathway. In normal adult hamsters, only 4.0% of 500 5-HT-immunoreactive profiles made synaptic contacts in the stratum griseum superficiale (SGS). Of these, 65% were axoaxonic, 30% were axodendritic, and 5% were axosomatic. In contrast, 22% of 400 5-HT-positive profiles in the neonatally enucleated hamsters and 17.5% of 400 such profiles in hamsters that sustained eye removals in adulthood made synaptic contacts. In the neonatal enucleates, 66% of the contacts were axoaxonic, 33% were axodendritic, and 1% were axosomatic. In the adult enucleates, 73% of the contacts were axoaxonic, 26% were axodendritic, and 1% were axosomatic. Thus, both neonatal and adult enucleation increase the percentage of 5-HT-positive profiles that make synaptic contacts in SC, but neither manipulation significantly changes the distribution of these contacts among different types of postsynaptic targets.
Coarse woody type: A new method for analyzing coarse woody debris and forest change

The species composition of both standing live and down dead trees has been used separately to determine forest stand dynamics in large-scale forest ecosystem assessments. The species composition of standing live trees has been used to indicate forest stand diversity while the species composition of down dead trees has been used to indicate wildlife habitat. To assess the ability of combined species information of standing live and down dead trees to indicate forest stand dynamics (i.e., successional trends), the species compositions of standing live trees and coarse woody debris (CWD) were compared using data from forest inventory plots across large-scales. Distinct differences were found between the species composition of standing live trees and that of CWD for nearly half of all study observations. However, there was no predictable shift in species composition along a defined forest succession trajectory with species composition shifts appearing to be successionally forward and backward depending on unique forest stand histories, CWD decay rates, stand structure, species composition, and site attributes. Suggested as a methodology complementary to other techniques such as historical stand reconstruction, differences in species composition of standing live and down dead trees may help indicate historical mortality patterns and successional directions of forest stands.
Spatial and temporal variation in lead and cadmium in the Laughing Gull, Larus atricilla

Abstract Lead and cadmium concentrations were measured in eggs and in bone, kidney, liver and stomach contents of downy young, prefledgling, and adult Laughing Gulls collected from Matagorda Bay and Galveston Bay, Texas. Matagorda Bay drains a rural, moderately industrialized region while the Galveston Bay area is heavily urbanized and industrialized. Lead levels were lower in birds from Matagorda Bay and decreased in birds from Galveston Bay between 1977 and 1980. Cadmium levels were also lower in birds from Matagorda Bay but increased over the three-year period in those from Galveston Bay. The temporal decrease in lead may be associated with such environmental control efforts as reduced point source emissions and substitution of unleaded gasoline.
Unveiling the mechanism of uptake and sub-cellular distribution of cerium oxide nanoparticles

Cerium oxide nanoparticles (CNPs) have been recently studied for their potent superoxide scavenging properties in both cell and animal model systems. Data from these model systems have shown that exposure of cells to CNPs results in the protection against reactive oxygen species (ROS). Despite these exciting findings, very little is known regarding the uptake or subcellular distribution of these nanomaterials inside cells. In this study we utilized fluorophore (carboxyfluorescein) conjugated cerium oxide NPs (CCNPs) to study the mechanism of uptake and to elucidate the subcellular localization of CNPs using a keratinocyte model system. We observed rapid uptake (within 3 h) of CCNPs that was governed by energy-dependent, clathrin-mediated and caveolae-mediated endocytic pathways. We found CCNPs co-localized with mitochondria, lysosomes and endoplasmic reticulum as well as being abundant in the cytoplasm and the nucleus. Given the radical scavenging properties of cerium oxide and the widespread cellular disposition we observed, CNPs likely act as cellular antioxidants in multiple compartments of the cell imparting protection against a variety of oxidant injuries.
Buddhist Universities in the United States of America

This article is written with a purpose to initiate a public discussion of Buddhist-based universities in the united states of America. These universities provide education in liberal arts and professional fields, while employing the time-tested methods of traditional Buddhist pedagogy. Because these universities are generally unknown to the public, I have provided information about their history, academic programs, and the educational success created on their campuses. These universities, in my view, serve as a model of higher education which is successful on many different levels and produces satisfactory results for both those who provide and those who receive the higher education. Buddhist Dharma has spread in the United States of America in many different ways. One important way in which it has successfully permeated the consciousness of the broader public is through educational institutions. This is consistent with the nature of Buddhism itself. In each country to which it historically spread, it created schools, universities, and various centers for learning, meditation, and moral practicea. In the USA, a great variety of Buddhistbased institutions of learning were created during the last half of the 20th century. These include, but are not limited to kindergartens, elementary and secondary schools, institutes for vocational training, and universities granting professional degrees. In this article, we will investigate one particular type of Buddhist educational institution, which we refer to as a “Buddhist University.”
Geometric partial differential equations and image analysis

1. Basic mathematical background 2. Geometric curve and surface evolution 3. Geodesic curves and minimal surfaces 4. Geometric diffusion of scalar images 5. Geometric diffusion of vector valued images 6. Diffusion on non-flat manifolds 7. Contrast enhancement 8. Additional theories and applications.
Fire-Related Sedimentation Events on Alluvial Fans, Yellowstone National Park, U.S.A.

ABSTRACT We document initiation and flow processes, deposit facies, and geomorphic effects of forest-fire-related sedimentation on small alluvial fans in Yellowstone National Park. Brief, intense convective-storm precipitation on steep basins burned in the 1988 fires produced sedimentation events involving a variety of depositional processes on fans. Over the course of all documented events, flows on fans progressed from higher to lower sediment concentration. Events were often dominated by either debris flows or relatively sediment-poor streamflow processes; in some events, however, flows ranging a over wide spectrum of sediment concentration produced significant fan deposits. Debris flows were generated by progressive sediment bulking involving pervasive surface runoff and rill erosion on st ep upper basin slopes, followed by deep incision as flows progressed down channels. Debris-flow deposits show a marked decline in thickness and coarse gravel content downfan, often with extensive distal gravel-poor facies. We recognized a relatively minor percentage of noncohesive debris-flow and hyperconcentrated-flow facies, with sorting and stratification intermediate between muddy debris-flow and streamflow facies; these were deposited where dilute flows bulked with coarse sediment by eroding channel alluvium or earlier deposits of the event. Below incised fan channels, streamflows expanded as sheetfloods, which prograded lower fans with distally fining deposits. Basins > 3 km2 typically produced streamflow events on fans, but sediment texture and availability on slopes and in channels are primary factors determining flow processes on fans of smaller basins. Burned soil surfaces provided abundant silt and clay for debris-flow generation, but because soil surface sediment was stripped and/or compacted over time, the lack of available fines resulted in dominance of streamflow processes in later events.
Deconstructing fragment-based inhibitor discovery

Fragment-based screens test multiple low-molecular weight molecules for binding to a target. Fragments often bind with low affinities but typically have better ligand efficiencies (DeltaG(bind)/heavy atom count) than traditional screening hits. This efficiency, combined with accompanying atomic-resolution structures, has made fragments popular starting points for drug discovery programs. Fragment-based design adopts a constructive strategy: affinity is enhanced either by cycles of functional-group addition or by joining two independent fragments together. The final inhibitor is expected to adopt the same geometry as the original fragment hit. Here we consider whether the inverse, deconstructive logic also applies--can one always parse a higher-affinity inhibitor into fragments that recapitulate the binding geometry of the larger molecule? Cocrystal structures of fragments deconstructed from a known beta-lactamase inhibitor suggest that this is not always the case.
The Problem of Wet Poultry House Litter: Influence of Total Dietary Protein and Soybean Meal Content on Water Intake and Urinary and Fecal Water Elimination in Growing Chickens

Abstract IT WOULD appear logical that urinary and fecal water elimination are major factors leading to the accumulation of moisture in poultry house litter. A solution of the problem of “wet litter” would thus involve determination of those factors responsible for the elimination of excessive amounts of water via the renal and alimentary routes. One of these causal factors is diet. In a recent note (James and Wheeler, 1949), we reported that the amount of water consumed, as well as the amount of excreta voided by growing chickens varied almost directly with the protein level of the diet. It is interesting that although the birds on the higher protein levels eliminated more urinary and fecal water (by virtue of greater volume of droppings), the moisture content of the excreta was not elevated, nor was feed consumption affected. In this work the varying protein levels were obtained by changing the amounts of . . .
Cost of allergy immunotherapy: sublingual vs subcutaneous administration

Background: Allergy immunotherapy is an effective way to manage the allergic patient and may be administered either through the subcutaneous route (SCIT) or the sublingual route (SLIT). Both have been proven efficacious; however, SLIT is currently not covered by insurance companies and is an out-of-pocket expense. The goal of the current study is to compare the costs of SCIT to SLIT. Methods: For SCIT, a total of 9 different insurance groups were studied including 8 preferred provider organizations (PPOs) and Medicare. Costs were broken down according to the percentage of coverage for the injections, serum vial fees, weekly co-pay, and deductibles. Total yearly cost for SCIT was calculated for the varying insurance plans and compared to the yearly cost of SLIT. Results: PPO plans covered between 60% and 100% of allergy immunotherapy treatment with a range of weekly co-pay between $0 and $50. Deductibles ranged between $0 and $7000. Medicare had a flat rate of 80% coverage costing the insurer $807.20 for the year of therapy. None of the above costs include loss of work productivity and travel expense. The cost of SLIT ranged from $500 to $2100 depending on the allergy practice and number on antigens treated. Conclusion: The cost of SCIT varies dramatically according to insurance plan whereas the cost of SLIT varies between practices. When loss of productivity and travel expense are added into the cost of SCIT, SLIT might be comparable in cost and more convenient for the patient. Although the lack of insurance coverage for SLIT currently makes it more expensive than SCIT, we have found that the financial gap is much smaller than initially thought, especially when indirect costs and plans with less than 80% coverage or high weekly co-pay are factored into the equation.
Bottleneck-free separable affine image warping

This paper presents a decomposition of the affine transformation matrix into three matrix operations consisting of only skew and scaling in a single dimension. This decomposition allows the presentation of a new algorithm for separable affine image warping. The algorithm is a three-pass approach incorporating only scaling, translation, and skew in a single dimension in each pass. The three-pass approach prevents the problem of decreased image resolution in intermediate images. The result is an algorithm with improved resulting image quality in conjunction with higher performance.
Multidimensional divide-and-conquer

Most results in the field of algorithm design are single algorithms that solve single problems. In this paper we discuss multidimensional divide-and-conquer, an algorithmic paradigm that can be instantiated in many different ways to yield a number of algorithms and data structures for multidimensional problems. We use this paradigm to give best-known solutions to such problems as the ECDF, maxima, range searching, closest pair, and all nearest neighbor problems. The contributions of the paper are on two levels. On the first level are the particular algorithms and data structures given by applying the paradigm. On the second level is the more novel contribution of this paper: a detailed study of an algorithmic paradigm that is specific enough to be described precisely yet general enough to solve a wide variety of problems.
An avidin-based assay for histone debiotinylase activity in human cell nuclei

The covalent binding of biotin to histones participates in heterochromatin formation, cell cycle progression and cellular response to DNA breaks. Biotinylation of histones appears to be a reversible process, but the identity of enzymes that remove biotin marks is largely unknown. Our long-term goal is to identify histone debiotinylases in human cells. Here we developed an avidin-based plate assay to quantify histone debiotinylase activities in nuclear extracts. This assay is an essential first step in purifying and identifying histone debiotinylases from human cells. Using this assay, we demonstrated that debiotinylation of histones depends on temperature and pH, consistent with enzyme catalysis. Experiments with purified histones, proteases and protease inhibitors provide evidence that removal of biotin marks from histones is mediated by debiotinylases rather than by proteases. Activities of histone debiotinylases varied among human tissues: colon=lung>placenta=liver>lymphoid cells. This assay proved useful in monitoring activities of putative histone debiotinylases during their partial purification from cells. Collectively, this assay is a useful tool for investigating histone debiotinylases in human tissues.
Physiological and behavioral effects of social introduction on adult male rhesus macaques

Pair housing of laboratory macaques is widely considered to lead to positive changes in well-being, yet the process of introduction is viewed as potentially stressful and risk-prone. Behavioral and physiological data were collected on eight adult male rhesus macaques before, during, and after the process of introduction, in order to measure the initial stress of introduction as well as long-term changes in well-being. Socially experienced subjects, all implanted with biotelemetry devices, were studied in five successive phases: baseline (singly housed), 1 day each of protected contact and full contact introduction, post-introduction (1–3 weeks after introduction), and settled pairs (≥20 weeks after introduction). One hundred and seventy-six hours of behavioral data and 672 hr of heart rate data were analyzed. Fecal cortisol was also measured for the baseline, post-introduction, and settled pair phases. All introductions were successful and subjects showed no physiological or behavioral signs of stress, such as increased heart rate, abnormal behavior, or psychological indices of distress (depressive/anxiety-related behavior). Agonism was minimal throughout the introduction process and over the subsequent months; only one wound was incurred over the course of the study. Levels of abnormal behaviors, psychological indices of distress, locomotion, inactivity, and affiliation showed improvements within several weeks after introduction; these changes were still present 5–9 months later for the latter two categories. Heart rates during introduction fell significantly in the settled pair phase, and also varied predictably with time of day. Fecal cortisol levels were lower in settled pairs than in single housing. The fact that reductions in abnormal behavior did not persist over the long term may have been confounded by increasing duration of time spent caged. The results of this study may be of practical use for designing and monitoring social introductions and suggest that managers should not dismiss the feasibility of successful pairing of adult male rhesus macaques.
Dissolving the Nematocyst Capsule Wall and Identifying its Protein Component(s)

Since the properties of the nematocyst capsule and thread undoubtedly play a significant role in the mechanism of nematocyst discharge, solubilization of these structures facilitates the chemical and physical analyses of some of their components. Analyses show that nematocysts contain a collagenlike protein (Lenhoff et al, 1957) linked by disulfide bonds (Blanquet and Lenhoff, 1966).
A Map-Reduce Framework for Clustering Metagenomes

The past few years has seen an explosion in the use of sequence technologies for met genomics i.e., determination of the collective genome of microorganisms co-existing within several environments. In parallel, there has been rapid development of computational tools for the quantification of abundance, diversity and functionality of different species within these communities. Several clustering algorithms (also called binning algorithms) have been developed to categorize similar met genome sequence reads for efficient post-processing and analysis. In this paper we present a distributed algorithm for clustering met genome sequence reads. The algorithm is implemented within the Map-Reduce based Hadoop platform, and approximates the computation of pair wise sequence similarity with a minwise hashing approach. The algorithm is capable of performing agglomerative hierarchical clustering or a greedy clustering approach and is referred to as MrMC-MinH. The key advantage of MrMC-MinH is it's ability to handle large volumes of sequence reads obtained from targeted 16S metagenomic or whole metagenomic data. We evaluate the performance of our algorithm on several real and simulated metagenome benchmarks and demonstrate that our approach is computationally efficient, and produces accurate clustering results when evaluated using external ground truth. The source code for MrMC-MinH will be made available at the supplementary website.