cssi/SciSciGPT-SciSciNet huggingface dataset:
Teaching NeuroImages: Colchicine-induced vacuolar myopathy

An 86-year-old man presented with 1 year of insidiously progressive weakness that started around 2 weeks after colchicine initiation for gout. Examination noted proximal more than distal weakness with diffuse hyporeflexia. Creatine kinase was 3,172 U/mL and electrodiagnostic study was consistent with a myopathic process. Muscle biopsy (figure) showed necrotizing myopathy with vacuoles, as well as mild chronic denervation/reinnervation. Weakness improved after cessation of colchicine.
SWear: Sensing Using WEARables. Generalized Human Crowdsensing on Smartwatches

In this work, we present SWear, a generalized human crowdsensing platform to collect human behavior data on smartwatches. It uses the stand-alone capabilities of smartwatches to collect data without being connected to smartphones. SWear collects both sensor data (e.g. GPS and audio) and self-reported survey data through micro surveys administered on the watch. SWear has been validated in multiple studies to understand the relationship between humans and their context.
Early Screening of African Americans (45-50 Years Old) in a Fecal Immunochemical Test-Based Colorectal Cancer Screening Program

Abstract: Background & Aims Some guidelines recommend starting colorectal cancer (CRC) screening before age 50 years for African Americans, but there are few data on screening uptake and yield in this population. Methods We performed a prospective study of fecal immunochemical test (FIT) screening among African American members of the Kaiser Permanente Northern California health plan. We compared data from African American members screened when they were 45–50 years old (early screening group) in 2018 with data from previously unscreened African American, white, Hispanic, and Asian/Pacific Islander health plan members, 51–56 years old. Screening outreach was performed with mailed FIT kits. Logistic regression models, adjusted for sex, were used to evaluate differences among groups in screening uptake, colonoscopy follow up of abnormal test results, and test yield. Results Among 10,232 African Americans in the early screening group who were mailed a FIT, screening was completed by 33.1%. Among the 4% with positive test results, 85.3% completed a follow-up colonoscopy: 57.8% had any adenoma, 33.6% had an advanced adenoma (adenoma with advanced histology or polyp ≥10 mm), and 2.6% were diagnosed with CRC. African Americans in the early screening group were modestly more likely to have completed screening than previously unscreened African Americans, whites, and Hispanics 51–56 years old. The groups did not differ significantly in positive results from the FIT (range, 3.8%–4.6%) and more than 74% received a follow-up colonoscopy after a positive test result. The test yields for any adenoma (range, 56.7%–70.7%), advanced adenoma (range, 20.0%–33.6%), and CRC (range, 0 to 7.1%) were similar. Conclusions Proportions of African Americans who participated in early (ages 45–50 years) FIT screening, and test yield, were comparable to those of previously unscreened African Americans, whites, Hispanics, and Asian/Pacific islanders who were 51–56 years old.
Exploring Interdisciplinary Pedagogy with “Data in Social Context”

This feature brings together three current and former instructors teaching as part of the Data in Social Context (DiSC) program at Virginia Tech. The DiSC program teaches students to use humanities skills, such as close reading, contextual interpretation, ethical reasoning, and empathy to understand data as a representation of human experience and understanding. The current and former instructors for the “Introduction to Data in Social Context” course discuss pedagogical strategies, interdisciplinary education, and the opportunities and challenges in exploring what it means to be human when so many elements of daily lives are measured by numbers, managed by algorithms, and classified as data.
Cross-sectional analysis of plasma and CSF metabolomic markers in Huntington's disease for participants of varying functional disability: a pilot study.

Huntington’s Disease (HD) is a progressive, fatal neurodegenerative condition. While generally considered for its devastating neurological phenotype, disturbances in other organ systems and metabolic pathways outside the brain have attracted attention for possible relevance to HD pathology, potential as therapeutic targets, or use as biomarkers of progression. In addition, it is not established how metabolic changes in the HD brain correlate to progression across the full spectrum of early to late-stage disease. In this pilot study, we sought to explore the metabolic profile across manifest HD from early to advanced clinical staging through metabolomic analysis by mass spectrometry in plasma and cerebrospinal fluid (CSF). With disease progression, we observed nominally significant increases in plasma arginine, citrulline, and glycine, with decreases in total and d-serine, cholesterol esters, diacylglycerides, triacylglycerides, phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins. In CSF, worsening disease was associated with nominally significant increases in NAD+, arginine, saturated long chain free fatty acids, diacylglycerides, triacylglycerides, and sphingomyelins. Notably, diacylglycerides and triacylglyceride species associated with clinical progression were different between plasma and CSF, suggesting different metabolic preferences for these compartments. Increasing NAD+ levels strongly correlating with disease progression was an unexpected finding. Our data suggest that defects in the urea cycle, glycine, and serine metabolism may be underrecognized in the progression HD pathology, and merit further study for possible therapeutic relevance.
The Tweet Heard Round the World: Daryl Morey, the NBA, China, and Attribution of Responsibility:

Following Houston Rockets General Manager Daryl Morey’s social media post advocating for Hong Kong independence, a 2 (NBA, Houston Rockets) × 3 (attacking the accuser, justification, apology) exper...
Dioxin-induced transcriptional regulation of CYP1A1 and CYP1B1 by the aryl hydrocarbon receptor complex

875 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced activation of cytochrome P450 1A1 (CYP1A1) and cytochrome P450 1B1 (CYP1B1) is mediated by the Aryl Hydrocarbon Receptor complex (AHRC). The AHRC consists of a heterodimer formed between the Aryl Hydrocarbon Receptor (AHR) and the Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT). The aim of this study was to investigate the kinetics of AHR and coactivator recruitment to two AHRC target genes CYP1A1 and CYP1B1 by TCDD in the human breast carcinoma cell line MCF-7. We also seek to identify coactivator proteins that are essential for CYP1A1 and/ or CYP1B1 induction. We hypothesize that the differences in TCDD-induction of CYP1A1 and CYP1B1 in these cells are based on the differences in promoter/enhancer structure of the two genes and the coactivator proteins that are recruited to each gene. The chromatin immunoprecipitation assay was employed to determine the kinetics of TCDD-induced protein recruitment to the CYP1A1 and CYP1B1 promoter and enhancer regions. We found that TCDD treatment leads to rapid recruitment of AHR to the enhancer region of both genes. As opposed to other published reports, we observed no “cycling” of the AHR on and off of the enhancer region of either gene up to 105 minutes of TCDD treatment. Nor did we observe binding of the AHR to the promoter region of either gene. Conversely, RNA polymerase II is recruited to the promoter region of both genes and not to the enhancer. RNA interference was utilized to identify coactivator proteins that are essential for cytochrome P450 induction by TCDD. We found the coactivator proteins p300 and Steroid Receptor Interacting Protein-2 (SRC-2) to be essential for both CYP1A1 and CYP1B1 maximal TCDD-induction. While the nucleosome remodeling factors Brahma/SWI2 Related Gene 1 (BRG-1) and Brahma (BRM) appear to be required for CYP1A1 induction and not CYP1B1. These results indicate that the promoter regions of CYP1A1 and CYP1B1 require a different set of transcriptional coactivators and thus may explain their different induction levels in these MCF-7 breast carcinomas.
Evaluation and Management of Patients with Leg Swelling: Therapeutic Options for Venous Disease and Lymphedema

Lower extremity swelling is a common condition which has a variety of etiologies and can be challenging to diagnose and manage. Swelling is usually the result of the accumulation of interstitial fluid in the subcutaneous tissues. Common etiologies include systemic, superficial, and deep venous, and lymphatic disorders. Leg swelling can occur bilaterally or unilaterally, with venous disorders being one of the most common causes of unilateral lower extremity edema.
Automated photonic tuning of silicon microring resonators using a 3D-printed microfluidic mixer

We demonstrate a method to automate the tuning of microring resonators using 3D-printed microfluidic control capable of resonance wavelength shifts of 4 nm. We use a custom 3D-printer that can fabricate microfluidic devices with sub-10 μm features and that perform automatic pumping, mixing, and dilution operations.
Budesonide/Glycopyrrolate/Formoterol Fumarate Co-suspension Metered Dose Inhaler: A Triple Therapy for the Treatment of Chronic Obstructive Pulmonary Disease:

Objective:To review current evidence on the use of a fixed-dose combination (FDC) of budesonide/glycopyrrolate/formoterol fumarate (BGFF) triple therapy delivered via metered dose inhaler (MDI) in ...
Air-coupled ultrasonic transducer application on icing load on-line monitoring system

Ultrasound has found application in many different sectors, especially the evaluation industry to investigate component structural integrity, including the icing load on transmission line. In many cases, a liquid coupling medium is used to efficiently transfer energy between the transducer and the sample under investigation. There are some materials which are not suitable for liquid coupling, either through material properties or the complexity of the environmental condition. The alternative of using an air-coupled approach is inherently challenging due to a large acoustic impedance mismatch between the transducer and air, resulting in low system signal-to-noise ratio (SNR). A segmented annular array system has been designed for non-contact inspection applications, which provides control of the depth focussing with beam steering on the central axis. Assessment of the inspection capability of the developed array system was undertaken through manual scans of icing defect structures with a reasonable quality images have been acquired.
Flow, form and force: methods and frameworks for field studies of macroalgal biomechanics.

Macroalgae are ecologically important organisms that often inhabit locations with physically challenging water motion. The biomechanical traits that permit their survival in these conditions have been of interest to biologists and engineers alike, but logistical and technical challenges of conducting investigations in macroalgal habitats have often prevented optimal study of these traits. Here, we review field methods for quantifying three major components of macroalgal biomechanics in moving water: fluid flow, macroalgal form, and hydrodynamic force. The implementation of some methodologies is limited due to the current state and accessibility of technology, but many of these limitations can be remedied by custom-built devices, borrowing techniques from other systems, or shifting lab-based approaches to the field. We also describe several frameworks for integrating flow, form, and force data that can facilitate comparisons of macroalgal biomechanics in field settings to predictions from theory and lab-based experiments, or comparisons between flow conditions, habitats, and species. These methods and frameworks, when used on scales that are relevant to the examined processes, can reveal mechanistic information about the functional traits that permit macroalgae to withstand physically challenging water motion in their habitats, using the actual fluid flows, macroalgal forms, and physical forces that occur in nature.
The Protein as a Glass

A spin glass-like model of protein conformational structure is described. Proteins such as myoglobin may be examples of “intrinsically complex” systems in the computational sense. Consequences for both thermodynamic and dynamic properties will be discussed.
The Environmental Impact Issues in Energy Development in the United States

Possibly the most interesting policy confrontations of recent years could be found in those areas where environmental and energy choices clash (or appear to) head on. Both areas are of the nature of political sacred cows to some constituency or other, and both have been preferred to the general public as being in “crisis.” It is in situations such as these, where problematical and emotionally charged issues meet, that the more interesting and difficult policy analyses lie. In this paper we shall, in a general fashion, catalog the environmental aspects of the energy problem from the point of view of one observer in the U.S. Department of Energy. Of necessity, both because of limited perspective and information, the viewpoint is flawed. However, the opinion of the evolution of environmental/energy analyses gets more accurate toward the present, as my own experience is greater. Nonetheless, I hope the reader will permit me a minimum of philosophy.
Studies on the Reconstitution of Bovine Erythrocyte Superoxide Dismutase: IV. PREPARATION AND SOME PROPERTIES OF THE ENZYME IN WHICH CO(II) IS SUBSTITUTED FOR ZN(II)

Abstract Two metal derivatives of superoxide dismutase have been prepared and partially characterized by optical, circular dichroic (CD), and EPR spectroscopies. Only 2 Co(II) ions will bind to apo superoxide dismutase and evidence is presented that these occupy the zinc-binding sites of the protein molecule. This derivative, referred to as 2Co protein, has an absorption maximum at 583 nm with each ion having a molar absorbance of ∼370. The CD spectrum possesses at least two weak negative bands near 585 nm and 530 nm. The EPR spectrum below 100°K shows g⊥ = 4 and g|| = 2.16 resonances. Addition of 2 meq of Cu(II) ions to the 2Co protein over a period of 1 to 24 hours results in the formation of a complex in which Cu(II) appears to be bound in its native position. This derivative, referred to as 2Co2Cu protein, has an absorption maximum near 680 nm with each Cu(II) having an absorbance index of ∼150 liters per mole cm. The Co(II) in this derivative has absorption maxima at 568 nm and 598 nm, the latter having an absorbance index per mole of Co(II) of 370. Evidence is presented that the optical and CD spectra of the 2Co2Cu protein are not the sum of the appropriate spectra of 2Co and native proteins; thus, the spectral properties of each ion depend on the presence of the other. Only 20 to 30% of the Cu(II) in the 2Co2Cu protein can be detected by EPR spectroscopy. Similarly, only a portion of the Co(II) is observed by EPR at helium temperatures. However, on reduction of the Cu(II) an EPR signal appears which has an intensity and parameters similar to that of the 2Co protein. Thus, the Co(II) and Cu(II) ions must be quite close to one another in this derivative. By analogy, this supports our previous contention that the zinc and copper ions are bound as two copper-zinc pairs in the native protein (Fee, J. A., and Gaber, B. P. (1972) J. Biol. Chem. 247, 60).
The Origin of Energetic Outflows in Young Stellar Objects

The observational evidence for an association between energetic bipolar outflows in Young Stellar Objects and circumstellar accretion disks is summarized, and arguments are presented in favor of a model in which this apparent connection is attributed to the winds being centrifugally driven outflows that act as the main angular momentum transport mechanism in the disks. In this picture, the wind is accelerated by interstellar magnetic field lines that thread the differentially rotating disk. The kinematic and thermal properties of the winds are discussed and are shown to account naturally for many of the distinctive radiative properties of these objects. The implications of these results to jets in active galactic nuclei are also briefly considered.
Estimating Acute Air Pollution Health EFFects from Cohort Study Data

Summary Traditional studies of short-term air pollution health effects use time series data, while cohort studies generally focus on long-term effects. There is increasing interest in exploiting individual level cohort data to assess short-term health effects in order to understand the mechanisms and time scales of action. We extend semiparametric regression methods used to adjust for unmeasured confounding in time series studies to the cohort setting. Time series methods are not directly applicable since cohort data are typically collected over a prespecified time period and include exposure measurements on days without health observations. Therefore, long-time asymptotics are not appropriate, and it is possible to improve efficiency by exploiting the additional exposure data. We show that flexibility of the semiparametric adjustment model should match the complexity of the trend in the health outcome, in contrast to the time series setting where it suffices to match temporal structure in the exposure. We also demonstrate that pre-adjusting exposures concurrent with the health endpoints using trends in the complete exposure time series results in unbiased health effect estimation and can improve efficiency without additional confounding adjustment. A recently published article found evidence of an association between short-term exposure to ambient fine particulate matter (PM2.5) and retinal arteriolar diameter as measured by retinal photography in the Multi-Ethnic Study of Atherosclerosis (MESA). We reanalyze the data from this article in order to compare the methods described here, and we evaluate our methods in a simulation study based on the MESA data.
College Students’ Personal Financial Literacy: Economic Impact and Public Policy Implications

This study analyzes the level of financial literacy among college students in Lynchburg VA area as well as the factors that impact the students’ competency in the field. Furthermore, it examines how the level of financial knowledge influences students’ opinions and decisions on personal finance matters. Past research indicates that non-business majors, women, students under age 30, with lower class ranks, and with little work experience have lower levels of financial knowledge. A major focus of this study is to test these hypotheses by administering a survey to college students in Lynchburg VA area and make inferences based on the collected data about the economic implications of the students’ financial literacy levels on the local and neighboring regions’ economies. This article is available in Undergraduate Economic Review: http://digitalcommons.iwu.edu/uer/vol4/iss1/1 Undergraduate Economic Review A publication of Illinois Wesleyan University Vol. IV – 2007 2008 Title “College Students’ Personal Financial Literacy: Economic Impact and Public Policy Implications” Author Florentina Furtuna Affiliation Randolph-Macon Woman’s College Abstract This study analyzes the level of financial literacy among college students in Lynchburg VA area as well as the factors that impact the students’ competency in the field. Furthermore, it examines how the level of financial knowledge influences students’ opinions and decisions on personal finance matters. Past research indicates that non-business majors, women, students under age 30, with lower class ranks, and with little work experience have lower levels of financial knowledge. A major focus of this study is to test these hypotheses by administering a survey to college students in Lynchburg VA area and make inferences based on the collected data about the economic implications of the students’ financial literacy levels on the local and neighboring regions’ economies. 1 Furtuna: College Students’ Personal Financial Literacy: Economic Impact an Published by Digital Commons @ IWU, 2008
Time trends in the association of ESRD incidence with area-level poverty in the US population

The objective of this study was to examine the temporal trends of the association between area-level poverty status and end-stage renal disease (ESRD) incidence. We hypothesized that the association between area-level poverty status and ESRD incidence has increased significantly over time. Patient data from the United States Renal Data System were linked with data from the 2000 and 2010 US census. Area-level poverty was defined as living in a zip code-defined area with ≥20% of households living below the federal poverty line. Negative binomial regression models were created to examine the association between area-level poverty status and ESRD incidence by time period in the US adult population while simultaneously adjusting for the distribution of age, sex, and race/ethnicity within a zip code. Time was categorized as January 1, 1995 through December 31, 2004 (Period 1) and January 1, 2005 through December 31, 2010 (Period 2). The percentage of adults initiating dialysis with area-level poverty increased from 27.4% during Period 1 to 34.0% in Period 2. After accounting for the distribution of age, sex, and race/ethnicity within a zip code, area-level poverty status was associated with a 1.24 (95% confidence interval [CI] 1.22, 1.25)-fold higher ESRD incidence. However, this association differed by time period with 1.04-fold (95% CI 1.02, 1.05) higher ESRD incidence associated with poverty status for Period 2 compared with the association between ESRD and poverty status in Period 1. Area-level poverty and its association with ESRD incidence is not static over time.
Concerning the superconducting gap symmetry in YBa₂Cu₃O₇- δ, YBa₂Cu₄O, and La₂ - xSrxCuO₄ determined from muon spin rotation in mixed states of crystals and powders.

Muon spin rotation (?+SR) measurements of square-root second moments of local magnetic fields ? in superconducting mixed states, as published for oriented crystals and powder samples of YBa2Cu3O7 ? ? (??0.05), YBa2Cu4O8 and La2 ? xSrxCuO4 (x ~ 0.15?0.17), are subjected to comparative analysis for superconducting gap symmetry. For oriented crystals it is shown that anomalous dependences of ? on temperature T and applied field H, as-measured and extracted a-?and b-axial components, are attributable to fluxon depinning and disorder that obscure the intrinsic character of the superconducting penetration depth. Random averages derived from oriented crystal data differ markedly from corresponding non-oriented powders, owing to the weaker influence of pinning in high-quality crystals. Related indicators for pinning perturbations, such as non-monotonic H dependence of ?, irreproducible data and strong H dependence of apparent transition temperatures, are also evident. Strong intrinsic pinning suppresses thermal anomalies in c-axis components of ?, which reflect nodeless gap symmetries in YBa2Cu3O7 ? ? and YBa2Cu4O8. For YBa2Cu3O7 ? ?, the crystal (a?b components, corrected for depinning) and powder data all reflect a nodeless gap (however, a?b symmetries remain unresolved for crystalline YBa2Cu4O8 and La1.83Sr0.17CuO4). Inconsistencies contained in multiple and noded gap interpretations of crystal data, and observed differences between bulk ?+SR and surface-sensitive measurements are discussed.
Plasma amino acids in patients with the carcinoid syndrome.

Plasma tryptophan (Trp) is reported to be decreased in some patients with the carcinoid syndrome. To determine if the plasma levels of other amino acids are also altered in the carcinoid syndrome, we used a gas-liquid chromatographic method to determine the plasma amino acid concentration of nine patients with the carcinoid syndrome and nine age-matched healthy control subjects. In comparison to the control subjects, the patients with the carcinoid syndrome had decreased plasma concentrations of valine (Val), isoleucine (Ile), lysine (Lys), and ornithine (Orn), and an increased plasma concentration of methionine (Met). With the exception of a decrease in urinary excretion of proline (Pro) and hydroxyproline (Hyp), the patients with the carcinoid syndrome had normal quantities of amino acids in their urine. Plasma Met returned to normal when serotonin production by the tumor was reduced 60% by parachlorophenylalanine (PCPA); the other amino acid abnormalities persisted. Further studies are needed to determine the significance of these amino acid abnormalities.
Mechanisms of limb patterning

The development of the vertebrate limb requires the coordinated action of multiple signals to achieve the proper arrangement of adult tissues. Recently, several molecules have been identified which play central roles in patterning of the limb bud. Sonic hedgehog, a homolog of the Drosophila segment polarity gene hedgehog, is likely to regulate anterior/posterior pattern formation. FGF-2 and FGF-4, members of the fibroblast growth factor family, have been shown to provide important signals for limb bud outgrowth and to indirectly regulate proximal/distal patterning. Some candidate effectors of the activity of Sonic hedgehog and of FGFs are known, including members of the clustered Hox genes.
DNA sequence based typing of swine leukocyte antigens in Yucatan miniature pigs.

: Background: We have established a breeding program to develop additional lines of swine leukocyte antigens (SLA) homozygous miniature pigs derived from the Yucatan Miniature Pig. Yucatan pigs have been used extensively in biomedical research since the 1970s and are known for their docile nature and small size. The breed has no consanguinity with the Hormel or Pittman-Moore breeds used to produce the NIH Miniature Pigs, the only other SLA homozygous miniature pigs in the USA. Methods: SLA typing was initially done by restriction fragment length polymorphism. Then a cDNA library was constructed using spleen cells from these pigs, from which we cloned and sequenced nearly all alleles for the SLA-1, 3, 2, 6, DRB1, DQA and DQB1 loci. Results: Four SLA homozygous lines were established with haplotypes that we have designated ‘w, x, y and z’. An SLA class I/II crossover haplotype, designated ‘q’, with the SLA class I alleles of ‘w’ and the SLA class II alleles of ‘z’ was discovered and used to establish a fifth line. The cDNA sequences were used to develop locus specific primers for each locus and an reverse transcription-polymerase chain reaction sequence based typing (SBT) method. We have used this method to perform SBT on SLA homozygous Yucatan pigs with these haplotypes and on the NIH pig ‘a, c and d’ haplotypes. Conclusions: These pig lines represent a new resource for transplantation research and the methods we describe can be used to SLA type any herd of pigs.
A Model Study of the Stably Stratified Planetary Boundary Layer

Abstract A second-order turbulence model is used to study the stable boundary layer (SBL). Over a horizontal surface, a constant surface cooling rate drives the SBL to a steady state within a few hours. Parameterizations are developed for eddy diffusivities, the kinetic energy dissipation rate and the geostrophic drag law in this idealized case. Over a sloped surface, a constant cooling rate produces a quasi-steady-state SBL in which some flow properties continue to vary but h(|f|/u*L)½ becomes constant; however, this constant is a function of the wind direction relative to the slope and the baroclinity, as measured by the cooling rate times the slope. Calculated eddy diffusivity profiles in the baroclinic (sloping terrain) case compare well with recent data from Antarctica. If a surface energy budget is used rather than a constant cooling rate, the SBL does not reach a steady state even over a horizontal surface; the nondimensional height slowly decays. We conclude that equilibrium models of the SBL are ...
Autologous Apoptotic Cell Engulfment Stimulates Chemokine Secretion by Vascular Smooth Muscle Cells

Apoptosis of vascular smooth muscle cells (VSMCs) occurs in vivo under both physiological and pathological settings. The clearance of apoptotic cells may be accomplished in part by the surrounding normal VSMCs. However, the fate of internalized apoptotic cells, the rate of intracellular degradation, and the consequences of these processes to VSMC biology are unknown. Electron microscopy and confocal fluorescence imaging showed that rat VSMCs effectively bound and internalized autologous apoptotic VSMCs in vitro. Within 2 hours, the internalized apoptotic cells were delivered to lysosomes, and the majority of these internalized cells and their proteins were efficiently degraded by 24 hours. After degradation was completed, the phagocytic VSMCs remained viable with normal rates of proliferation. Clearance of apoptotic cells by VSMCs did not induce the release of vascular wall matrix proteases but was associated with a 1.6-fold increase in transforming growth factor-β1 release. Interestingly, clearance of apoptotic cells stimulated VSMCs to secrete monocyte-chemoattractant protein-1 and cytokine-induced neutrophil chemoattractant. The coordinated release of transforming growth factor-β1 and chemokines suggests that autologous apoptotic cell clearance stimulates VSMCs to release molecules that specifically recruit professional phagocytes while simultaneously dampening the inflammatory response and preventing vascular injury.
Use of γ-hexachlorocyclohexane as a terminal electron acceptor by an anaerobic enrichment culture.

Abstract The use of γ-hexachlorocyclohexane (HCH) as a terminal electron acceptor via organohalide respiration was demonstrated for the first time with an enrichment culture grown in a sulfate-free HEPES-buffered anaerobic mineral salts medium. The enrichment culture was initially developed with soil and groundwater from an industrial site contaminated with HCH isomers, chlorinated benzenes, and chlorinated ethenes. When hydrogen served as the electron donor, 79–90% of the electron equivalents from hydrogen were used by the enrichment culture for reductive dechlorination of the γ-HCH, which was provided at a saturation concentration of approximately 10 mg/L. Benzene and chlorobenzene were the only volatile transformation products detected, accounting for 25% and 75% of the γ-HCH consumed (on a molar basis), respectively. The enrichment culture remained active with only hydrogen as the electron donor and γ-HCH as the electron acceptor through several transfers to fresh mineral salts medium for more than one year. Addition of vancomycin to the culture significantly slowed the rate of γ-HCH dechlorination, suggesting that a Gram-positive organism is responsible for the reduction of γ-HCH. Analysis of the γ-HCH dechlorinating enrichment culture did not detect any known chlororespiring genera, including Dehalobacter . In bicarbonate-buffered medium, reductive dechlorination of γ-HCH was accompanied by significant levels of acetogenesis as well as methanogenesis.
Effects of thymidine analogs on Syrian hamster melanoma cells: phenotypes arising from selection for analog resistance.

In order to compare the biological effects of different thymidine (dT) analogs, two unusual cell lines (B-4 and HAB) previously isolated from a Syrian hamster melanoma line by selection with 5-bromodeoxyuridine (BrdU) were analyzed for their response to other analogs. B-4 cells require high concentrations of BrdU for optimal growth, and it was seen that the requirement for BrdU could be satisfied partially by 5-chlorodeoxyuridine (CldU) but not by the other dT analogs tested. HAB cells are able to grow with all the dT residues in nuclear DNA replaced by BrdU, and it was found that they could also grow with essentially all the dT residues in nuclear DNA replaced by CldU but not by other analogs. New cell lines resistant to 100 μM concentrations of CldU, 5-iododeoxyuridine (IdU), and 5-hydroxymethyldeoxyuridine (HMdU) were isolated from the melanoma line and tested for cross-resistance to the other dT analogs. A high level of cross-resistance was observed only with BrdU and CldU. The ability of the cell lines resistant to BrdU, CldU, and IdU to incorporate these analogs into nuclear DNA also was determined. BrdU and CldU were incorporated efficiently by all of the lines tested, but the IdU-resistant cells seemed to preferentially exclude IdU.
Refinement of the Citrus Tristeza Virus Resistance Gene ( Ctv ) Positional Map in Poncirus trifoliata and Generation of Transgenic Grapefruit ( Citrus paradisi ) Plant Lines with Candidate Resistance Genes in this Region

Citrus tristeza virus (CTV) is a major pathogen of Citrus. A single dominant gene Ctv present in the trifoliate relative of Citrus, Poncirus trifoliata confers broad spectrum resistance against CTV. Refinement of genetic maps has delimited this gene to a 121 kb region, comprising of ten candidate Ctv resistance genes. The ten candidate genes were individually cloned in Agrobacterium based binary vector and transformed into three CTV susceptible grapefruit varieties. Two of the candidate R-genes, R-2 and R-3 are exclusively expressed in transgenic plants and in Poncirus trifoliata, while five other genes are also expressed in non-transformed Citrus controls. Northern blotting with a CTV derived probe for assessment of infection in virus inoculated plants over a span of three growth periods, each comprising of six to eight weeks, indicates either an absence of initiation of infection or it's slow spread in R-2 plant lines or an initial appearance of infection and it's subsequent obliteration in some R-1 and R-4 plant lines. Limited genome walk up- and downstream form R-1 gene, based on it's 100% sequence identity between Poncirus and Citrus, indicates promoter identity of 92% between the two varieties. Further upstream and downstream sequencing indicates the presence of an O-methyl transferase and a Copia like gene respectively in Citrus instead of the amino acid transporter like gene upstream and a sugar transporter like gene downstream in Poncirus. The possibility of recombinations in the resistance locus of Citrus and the need for consistent monitoring for virus infection and gene expression in the transgenic Citrus trees is discussed.
Intrapleural instillation of urokinase in the treatment of loculated pleural effusions in children

The authors report on the use of intrapleural instillation of urokinase in the treatment of loculated pleural effusions in two pediatric patients. Urokinase helps to lyse fibrin by converting plasminogen to plasmin. The intrapleural instillation of urokinase is safe and effective for promoting drainage of loculated intrapleural effusions, and it proved a useful option in the treatment of persistent loculations.
Event building at multi-kHz rates: lessons learned from the PHENIX event builder

The PHENIX experiment is one of four located at BNL's Relativistic Heavy Ion Collider (RHIC). It is a high rate, large data volume detector, consisting of 14 detector subsystems. The PHENIX DAQ is a highly-pipelined parallel system. Central to the DAQ back-end is the PHENIX Event Builder (EvB). Since the start of RHIC in 2000, the EvB has undergone steady evolution towards the goal of archiving at multiple kHz event rates. The most recent major development towards the goal of 5 kHz archiving rate for Run5 was the migration of the Event Builder from Win32 to Linux. The current status of the PHENIX Event builder is presented with a focus on the lessons learned in the process. The transition to Linux is discussed, comparing the issues and performance to the previous implementation on Win32
Problems of persons with HIV/AIDS hospitalized for Pneumocystis carinii pneumonia

The authors of this prospective study describe the problems of persons living with HIV/AIDS hospitalized for Pneumocystis carinii pneumonia (PCP) ( N =90) and examine how the problems change over time. Data were obtained from four sources and were classified into major problem categories. The largest mean number of problems were reported in the category of PCP. Specific psychosocial problems were more likely to be reported in the patient and nurse interviews than in the chart and intershift report. The study findings validate the physical symptoms addressed in the published care plans and guidelines for caring for patients with PCP. The study identified the limitation of using the patient record as the only data source in determining nursing care needs and emphasized the importance of the patient perspective.
The Philosophy of William James: An Introduction

This 2004 book is an accessible introduction to the full range of the philosophy of William James. It portrays that philosophy as containing a deep division between a Promethean type of pragmatism and a passive mysticism. The pragmatist James conceives of truth and meaning as a means to control nature and make it do our bidding. The mystic James eschews the use of concepts in order to penetrate to the inner conscious core of all being, including nature at large. Richard Gale attempts to harmonize these pragmatic and mystical perspectives. This introduction is drawn from and complements the author's much more comprehensive and systematic study The Divided Self of William James, a volume that has received the highest critical praise. With its briefer compass and non-technical style this introduction should help to disseminate the key elements of one of the great modern philosophies to an even wider readership.
Kinetic Buffering of Cross Talk between Bacterial Two-Component Sensors

Two-component systems are a class of sensors that enable bacteria to respond to environmental and cell-state signals. The canonical system consists of a membrane-bound sensor histidine kinase that autophosphorylates in response to a signal and transfers the phosphate to an intracellular response regulator. Bacteria typically have dozens of two-component systems. The key questions are whether these systems are linear and, if they are, how cross talk between systems is buffered. In this work, we studied the EnvZ/OmpR and CpxA/CpxR systems from Escherichia coli, which have been shown previously to exhibit slow cross talk in vitro. Using in vitro radiolabeling and a rapid quenched-flow apparatus, we experimentally measured 10 biochemical parameters capturing the cognate and non-cognate phosphotransfer reactions between the systems. These data were used to parameterize a mathematical model that was used to predict how cross talk is affected as different genes are knocked out. It was predicted that significant cross talk between EnvZ and CpxR only occurs for the triple mutant ΔompR ΔcpxA ΔactA-pta. All seven combinations of these knockouts were made to test this prediction and only the triple mutant demonstrated significant cross talk, where the cpxP promoter was induced 280-fold upon the activation of EnvZ. Furthermore, the behavior of the other knockouts agrees with the model predictions. These results support a kinetic model of buffering where both the cognate bifunctional phosphatase activity and the competition between regulator proteins for phosphate prevent cross talk in vivo.
Product quality inspection in Bernoulli lines: analysis, bottlenecks, and design

This paper is devoted to serial production lines consisting of producing and inspection machines that obey the Bernoulli reliability and Bernoulli quality models. Such production lines are encountered in automotive assembly and painting operations where the downtime is relatively short and the defects are due to uncorrelated random events. For these systems, this paper develops analytical methods for performance analysis, bottleneck identification, and design. In addition, insights into the nature of bottlenecks in such systems are provided, and an empirical rule for placing an inspection machine that maximises the production rate of non-defectives is formulated.
Energy and structure of (001) twist interphase boundaries in the Ag/Ni system

Abstract Computer calculations of coincidence (001) Ag/Ni twist interphase boundaries were performed with the Embedded Atom Method (EAM). The results show the variation of interfacial energy with azimuthal misorientation in the range 0–45°. Relative minima in the energy-misorientation curve are predicted; the lowest minimum is at 26.56°. Predicted low-energy boundaries at 4.4 and 26.56° are confirmed experimentally by the rotating crystallite method. The rotations of Ag crystallites on the (001) surface of a Ni thin film are determined by transmission electron microscopy with special use of double diffraction.
Stress-responsive regulation of mitochondria through the ER unfolded protein response

The endoplasmic reticulum (ER) and mitochondria form physical interactions involved in the regulation of biologic functions including mitochondrial bioenergetics and apoptotic signaling. To coordinate these functions during stress, cells must coregulate ER and mitochondria through stress-responsive signaling pathways such as the ER unfolded protein response (UPR). Although the UPR is traditionally viewed as a signaling pathway responsible for regulating ER proteostasis, it is becoming increasingly clear that the protein kinase RNA (PKR)-like endoplasmic reticulum kinase (PERK) signaling pathway within the UPR can also regulate mitochondria proteostasis and function in response to pathologic insults that induce ER stress. Here, we discuss the contributions of PERK in coordinating ER–mitochondrial activities and describe the mechanisms by which PERK adapts mitochondrial proteostasis and function in response to ER stress.
Reproductive characteristics of female sea otters

: Several important aspects of reproduction in the female sea otter, such as gestation, pupping frequency, period of pup dependency, and annual pupping rate, were unclear when this study was begun. We present data from 75 tagged adult females that indicate gestation is variable, but on average is about 6 months, the length of pup dependency is 6 mo, thus the pupping interval is usually 12–13 mo. Most females breed for the first time in their fifth year of life. About 85–90% of adult females pup in a given year.
Practical methods of electron depth-dose measurement compared to use of the NACP design chamber in water

Central axis relative dose versus depth measurements were performed using two different small volume thimble ionization chambers and a p‐type silicon diode in a water phantom and with two parallel‐plate ionization chambers,thermoluminescent dosimeters, and radiographic film in a popular clear polystyrene phantom. Values obtained were compared to the results of similar measurements in a water phantom performed with a plane‐parallel ionization chamber designed and optimized for use in electron beams by the Nordic Association of Clinical Physicists (NACP). The NACP chamber is expected to minimally perturb the electron fluence and be least prone to point of measurement uncertainties. Its use in a water phantom closely approximates the spirit of recent international protocols. Data were obtained for the foil scatteredelectron beamsgenerated by two different accelerators for field sizes from 6 cm × 6 cm to 25 cm × 25 cm and energies between 6 and 20 MeV. Easily identifiable effective points of measurements were defined for each measurement device and standard corrections were applied to the raw data to obtain depth‐dose curves. The degree of agreement between the various techniques and the NACP‐water standard was quantitatively analyzed through comparison of the resulting depths of 50% dose and practical range. All methods were found to yield reasonable results when carefully implemented, with average differences of less than 1 mm being easily achievable. Measurements with p‐type silicon diode detectors were found to be particularly useful, as they are pointlike and appear from all practical considerations to directly represent relative dose, thus requiring little or no correction to raw readings.
Modeling of Interconnect Dielectric Lifetime Under Stress Conditions and New Extrapolation Methodologies for Time-Dependent Dielectric Breakdown

Advanced microelectronics interconnect systems can have metal leads several hundred meters long with minimum metal to metal spacing of <100nm. The low-k dielectric between adjacent metal lines has a lower dielectric breakdown strength compared to gate oxides. Accelerated testing of the interconnect time-dependent dielectrics breakdown (TDDB) is required during the development of new technology nodes, to ensure the reliability of these systems. This paper presents simulations that show how actual line-to-line spacing variations influence test results such that they can predict too low product lifetime. In fact, it is argued here that one can adhere to a conservative model for the lifetime dependence on the electric field (such as the is-model) and still pass stringent reliability requirements if the accelerated breakdown test results distributions are interpreted correctly.
Somatomedin C in Treated Acromegaly: Poor Correlation with Growth Hormone and Clinical Response

To determine the usefulness of commercially available somatomedin C levels in the evaluation of the treatment of acromegaly, 15 patients were tested at 0.25-15.4 yr after onset of therapy. Clinical response, as determined by a numerical scoring system, was compared with RIA of GH and somatomedin C. Symptomatic response was poorly correlated with somatomedin C (r = 0.033) as well as with GH (r = 0.24). The correlation of GH and somatomedin C was also poor (r = 0.46, P greater than 0.05). Eighty-three percent of patients with clinical improvement had GH less than or equal to 10 ng/ml, 50% had GH less than or equal to 5 ng/ml, while 42% had somatomedin C less than or equal to 3.0 U/ml. All patients who were evaluated at 1 yr or less after therapy had elevated somatomedin C levels with normal or near normal GH values. In contrast only 2 of 11 patients evaluated at more than 1 yr after therapy had a mild persistence of somatomedin C elevation with normal GH levels. Determination of somatomedin c costs more than GH determinations and appears to offer no apparent advantage over GH in following patients treated for acromegaly.
Heuristic considerations pertaining to hailstone size distributions in the plain of Friuli-Venezia Giulia

Abstract In this work, the hailstone size distributions at the ground in the plain of Friuli-Venezia Giulia are presented, as revealed through a network of polystyrene pads (hailpads), managed by volunteers, which has been active since 1988. The aim of this work is to highlight possible differences in the diurnal and seasonal behavior of hail at the ground, both from Friuli-Venezia Giulia and other countries, in order to improve the knowledge of this meteorological phenomenon. In the comparison between different countries, differences are found between the yearly size distributions of Friuli-Venezia Giulia and those of North-East Colorado, measured during the National Hail Research Experiment (NHRE). The size distributions obtained in South West France and in Friuli-Venezia Giulia are quite similar and they are slightly different from those of the Grossversuch experiment. In the comparison between different periods of the year, relevant differences are found between April and May and the other months. In particular, thunderstorms are less efficient in producing big hailstones during the former months. The most prolific month in producing hailstones is June, followed by September. This feature is interpreted as due to a form of synergy between the frequency of the synoptic forcing of storms and the amount of available energy at the ground. Analyzing the size distributions at different times of the day, the greatest differences are found in the intervals [00–06] and [06–12] in local time (respectively, [22–04] and [04–10] in UTC). These differences cannot be ascribed to the melting of the hailstones during their fall.