cssi/SciSciGPT-SciSciNet huggingface dataset:
The role of cysteine proteases in hypoxia-induced rat renal proximal tubular injury

Abstract The role of the lysosomal proteases cathepsins B and L and the calcium-dependent cytosolic protease calpain in hypoxia-induced renal proximal tubular injury was investigated. As compared to normoxic tubules, cathepsin B and L activity, evaluated by the specific fluorescent substrate benzyloxycarbonyl-L-phenylalanyl-L-arginine-7-amido-4-methylcoumarin, was not increased in hypoxic tubules or the medium used for incubation of hypoxic tubules in spite of high lactate dehydrogenase (LDH) release into the medium during hypoxia. These data in rat proximal tubules suggest that cathepsins are not released from lysosomes and do not gain access to the medium during hypoxia. An assay for calpain activity in isolated proximal tubules using the fluorescent substrate N-succinyl-Leu-Tyr-7-amido-4-methylcoumarin was developed. The calcium ionophore ionomycin induced a dose-dependent increase in calpain activity. This increase in calpain activity occurred prior to cell membrane damage as assessed by LDH release. Tubular calpain activity increased significantly by 7.5 min of hypoxia, before there was significant LDH release, and further increased during 20 min of hypoxia. The cysteine protease inhibitor N-benzyloxycarbonyl-Val-Phe methyl ester (CBZ) markedly decreased LDH release after 20 min of hypoxia and completely prevented the increase in calpain activity during hypoxia. The increase in calpain activity during hypoxia and the inhibitor studies with CBZ therefore supported a role for calpain as a mediator of hypoxia-induced proximal tubular injury.
Methylene blue for distributive shock: a potential new use of an old antidote.

Methylene blue is used primarily in the treatment of patients with methemoglobinemia. Most recently, methylene blue has been used as a treatment for refractory distributive shock from a variety of causes such as sepsis and anaphylaxis. Many studies suggest that the nitric oxide–cyclic guanosine monophosphate (NO–cGMP) pathway plays a significant role in the pathophysiology of distributive shock. There are some experimental and clinical experiences with the use of methylene blue as a selective inhibitor of the NO–cGMP pathway. Methylene blue may play a role in the treatment of distributive shock when standard treatment fails.
A model for information processing with reference to vision.

Abstract A model for some aspects of visual information processing is proposed, based on a random array of overlapping test figures, analogous to receptive fields. It is shown, on the basis of the model, how quantities like length, area, and curvature can be obtained, and how it is possible to center an image and to detect boundaries and movement. Optical illusions can be simulated by suitable test figure geometries. The value of the model lies in establishing possible ways in which visual processes might operate.
Sir Moses Finley

Finley was an instructor and assistant professor in the history department at Rutgers-Newark from 1948 to 1952. He then went on to Cambridge University for a brilliant career as a classics scholar until his death in 1986. What makes his tenure at Rutgers significant is that he was dismissed by the Board of Trustees in 1952 because he refused to answer questions before the U. S. Senate Internal Security Committee on grounds of the Fifth Amendment. As a suspected communist, he was fired, deemed unfit to teach by the Board of Trustees. It was one of the most famous cases of attacks on academic freedom during the McCarthy era. This article is an edited version of an address given by McCormick (who had defended Finley before the Trustees) at Finley’s memorial service in the Kirkpatrick Chapel on November 8, 1986.
An Electron Microscopic Immunogold Analysis of Developmental Up-Regulation of the Blood—Brain Barrier GLUT1 Glucose Transporter

Electron microscopy was used to quantitate blood-brain barrier (BBB) glucose transporters in newborn, 14-day-old suckling, 28-day-old weanling, and adult rabbits. A rabbit polyclonal antiserum to a synthetic peptide encoding the 13 C-terminal amino acids of the human erythrocyte glucose transporter (GLUT1) was labeled with 10-nm gold particle-secondary antibody conjugates and localized immunoreactive GLUT1 molecules in rabbit brain capillary endothelia. Three distinct populations of brain capillary profiles were identified in newborn rabbits: prepatent capillary buds, partially patent capillaries with highly amplified luminal membranes, and patent capillaries. Immunogold analyses indicated that the GLUT1 transporter abundance positively correlated with capillary developmental status. The mean number of gold particles per capillary profile increased at each developmental age examined, suggesting that developmental up-regulation of the BBB glucose transporter occurred in rabbits. GLUT1 immunoreactivity was three- to fourfold greater on the abluminal than luminal capillary membranes among all ages examined. Changes in the proportions of GLUT1 transporter were also seen, and possible reasons for the postnatal decrease in the percentage of cytoplasmic GLUT1 transporter are discussed. The numbers of cytoplasmic and membrane-associated immunogold particles increased with age. We conclude that regulatory modulations of BB glucose transport may be characterized by increases in BBB glucose transporter density with age and state of development. In addition, modulation of glucose transporter activity may be reflected by minor postnatal shifts of GLUT1 from cytoplasmic to membrane compartments, which can be demonstrated with quantitative immunogold electron microscopy.
Numerical mass balance for soil-moisture transport problems

Abstract The Galerkin finite element method coupled with the Crank-Nicolson time advance procedure is often used as a numerical analog for unsaturated soil-moisture transport problems. The Crank-Nicolson procedure leads to numerical mass balance problems which results in instability. A new temporal and spatial integration procedure is proposed that exactly satisfies mass balance for the approximating function used. This is accomplished by fitting polynomials continuously throughout the time and space domain and integrating the governing differential equations. To reduce computational effort, the resulting higher order polynomials are reduced to quadratic and linear piece-wise continuous polynomial approximation functions analogous to the finite element approach. Results indicate a substantial improvement in accuracy over the combined Galerkin and Crank-Nicolson methods when comparing to simplified problems where analytical solutions are available.
"What Fermented in Me for Years": Cantor's discovery of transfinite numbers

Transfinite (ordinal) numbers were a crucial step in the development of Cantor's set theory. The new concept depended in various ways on previous problems and results, and especially on two questions that were at the center of Cantor's attention in September 1882, when he was about to make his discovery. First, the proof of the Cantor-Bendixson theorem motivated the introduction of transfinite numbers, and at the same time suggested the “principle of limitation,” which is the key to the connection between transfinite numbers and infinite powers. Second, Dedekind's ideas, which Cantor discussed in September 1882, seem to have played an important heuristic role in his decision to consider the “symbols of infinity” that he had been using as true numbers, i.e., as autonomous objects; to this end Cantor introduced in his work, for the first time, ideas on (well) ordered sets.
Acute Kidney Injury in the Neonate

Critically ill neonates are at risk for acute kidney injury (AKI). AKI has been associated with increased risk of morbidity and mortality in adult and pediatric patients, and increasing evidence suggests a similar association in the neonatal population. This article describes the current AKI definitions (including their limitations), work on novel biomarkers to define AKI, diagnosis and management strategies, long-term outcomes after AKI, and future directions for much-needed research in this important area.
Guided Ultrasonic Wave Imaging for Immersed Plates Based on Wavelet Transform and Probabilistic Analysis

We propose a nondestructive evaluation method for immersed structures based on the propagation of ultrasonic waves induced by means of laser pulses and detected with an array of immersion transducers. In the study presented in this article, a laser operating at 532 nm is employed to excite leaky guided waves on an aluminum plate immersed in water. An array of immersion transducers is used to record the waves radiating from the laser-illuminated point. The detected signals are processed with an imaging algorithm based on continuous wavelet transform and probabilistic analysis to localize the presence of artificial defects machined in the plate. With respect to the existing imaging methods for plates, the proposed algorithm is pseudo baseline free, because it does not require data recorded from a pristine plate, but it requires that only a portion of the plate is free from defects. We find that the proposed algorithm enables the detection of surface cracks. Advantages and limitations of the algorithm for th...
Cost-effectiveness of targeted versus tailored interventions to promote mammography screening among women military veterans in the United States.

Abstract Objective We conducted an economic evaluation of mammography promotion interventions in a population-based, nationally representative sample of 5500 women veterans. Methods Women 52 years and older were randomly selected from the National Registry of Women Veterans and randomly assigned to a survey-only control group and two intervention groups that varied in the extent of personalization (tailored vs. targeted). Effectiveness measures were the prevalence of at least one self-reported post-intervention mammogram and two post-intervention mammograms 6–15 months apart. Incremental cost-effectiveness ratios (ICERs) were the incremental cost per additional person screened. Uncertainty was examined with sensitivity analysis and bootstrap simulation. Results The targeted intervention cost $25 per person compared to $52 per person for the tailored intervention. About 27% of the cost was incurred in identifying and recruiting the eligible population. The percent of women reporting at least one mammogram were .447 in the control group, .469 in the targeted group, and .460 in the tailored group. The ICER was $1116 comparing the targeted group to the control group (95% confidence interval (CI) = $493 to dominated). The tailored intervention was dominated (more costly and less effective) by the targeted intervention. Conclusion Decision-makers should consider effectiveness evidence and the full recruitment and patient time costs associated with the implementation of screening interventions when making investments in mammography screening promotion programs. Identification and recruitment of eligible participants add substantial costs to outreach screening promotion interventions. Tailoring adds substantial cost to the targeted mammography promotion strategy without a commensurate increase in effectiveness. Although cost-effectiveness has been reported to be higher for some in-reach screening promotion interventions, a recent meta-analysis revealed significant heterogeneity in the effect sizes of published health-plan based intervention studies for repeat mammography (i.e., some studies reported null effects compared with control groups).
Perturbation theory and the single sextupole

Perturbation theory is applied to the problem of the single thin sextupole in one degree of freedom in order to see whether the first few low order terms model the system's behavior reasonably well within a phase space region of interest. It is found that perturbation enables calculation of the position and shape of the stability boundary. (LEW)
Warm ischemic damage to the epiphyseal growth plate: A rabbit model

Warm ischemic growth plate damage was produced in the hindlimbs of 33 New Zealand white rabbits, who were 7 weeks old, by isolating the knee joint on a popliteal vascular pedicle. Zero, 3, 7, and 12 hours of warm ischemia were produced by pedicle occlusion. The 0- and 3-hour ischemic groups showed mild growth disturbances related to the surgical model and were not statistically different at 90 days postoperatively. The 7- and 12-hour ischemia groups showed severe growth disturbances and were statistically different from the 0- and 3-hour groups at all periods measured ( p
Lack of physiological plasticity in the early chicken embryo exposed to acute hypoxia.

By exposing chicken embryos to hypoxia (10%) acutely (2, 4, and 6 hr) during early development (2, 3, and 4 days) we tested the hypothesis that hypoxia has an impact on embryonic growth and impairs cardiac development at the time cardiac morphogenesis is taking place. After the hypoxic perturbation, the embryos were allowed to develop until day 9, when embryo mass, heart mass, and rate of oxygen consumption were recorded. Four-day-old embryos exposed to 6 hr of hypoxia showed an increased mortality (38.9% versus 18% for controls), indicating the immediate effect of hypoxia on survivability. While only 8% of the controls displayed morphological abnormalities, 3- and 4-day-old embryos exposed for 6 hr showed more frequent developmental abnormalities (25% and 30% respectively). No significant differences in embryo or heart mass were found except in 4-day-old embryos exposed for 2 hr. Mass-specific oxygen consumption was not different between controls and embryos exposed to hypoxia at 2 or 3 days of development, but it was increased in 4-day-old embryos exposed for 4 hr (P < 0.05). These results suggest that an acute hypoxic episode does not have an impact when occurring very early in development (days 2 or 3). However, when the hypoxic episode occurs on day 4, survivability is largely decreased. Considering the lack of permanent effects on the surviving embryos, we suggest that the early embryo resorts to a simple strategy of death or survival, and the individual capacity for survival must be based on interindividual differences rather than the existence of compensatory mechanisms. J. Exp. Zool. 286:450-456, 2000.
Theoretical analysis of conjugate localization in two-step cancer chemotherapy.

Considerable research has been aimed at improving the efficacy of chemotherapeutic agents for cancer therapy. A promising two-step approach that is designed to minimize systemic drug toxicity while maximizing activity in tumors employs monoclonal antibody-enzyme conjugates for the activation of anti-cancer prodrugs. A mathematical model based on the biology of human 3677 melanoma xenografts in nude mice is presented, analyzed, and numerically simulated to study the biodistribution, pharmacokinetics, and intratumoral localization properties of L49-β-lactamase fusion proteins in solid tumor masses. The model predictions were compared with published experimental data and an excellent correlation was found to exist. Analytic expressions for the total concentration of conjugate in the tumor, the time at which the concentration is maximal, and the half life of conjugate in the tissue were derived. From these results, key parameters were isolated; and the effects of the tumor vasculature, binding kinetics, and administration schedule were investigated. The antibody-antigen dissociation ratio, the conjugate permeability, and the inter-capillary half distance within the tumor mass were found to strongly influence localization and retention in the tumor. The model was used to examine various dosing strategies in an attempt to determine which regimen would provide the best biodistribution results. The results of administering a uniform dose of conjugate via bolus injection, multiple injections, and continuous infusion were compared. The model predicts that when saturation of binding sites does not occur, dosing strategy has little effect on the amount of conjugate that localizes in the tumor.
Anticoagulant activity in salivary glands of the insect vector Culicoides variipennis sonorensis by an inhibitor of factor Xa.

Blood feeding by the insect vector Culicoides variipennis sonorensis involves laceration of superficial host tissues, an injury that would be expected to trigger the coagulation cascade. Accordingly, the salivary glands of C.v. sonorensis were examined for the presence of an antihemostatic that prevents blood coagulation. Assays using salivary gland extracts showed a delay in the recalcification time of plasma devoid of platelets, indicating the presence of anticoagulant activity. Retardation in the formation of a fibrin clot was also observed after the addition of tissue factor to plasma that was preincubated with salivary gland extracts. Similarly, an inhibitory effect by salivary gland extracts was detected in assays that included factors of the intrinsic pathway. Inhibition of the catalytic activity of purified factor Xa toward its chromogenic substrate suggested that it was the target of the salivary anticoagulant of C.v. sonorensis. This was corroborated by the coincidence of anticoagulant and anti-FXa activities obtained by reverse-phase HPLC. The depletion of anti-FXa activity from salivary glands during blood feeding suggests that the FXa inhibitor functions as anticoagulant. Molecular sieving HPLC yielded an apparent molecular mass of 28 kDa for the salivary FXa inhibitor of C.v. sonorensis. Preventing the formation of thrombin through the inhibition of FXa likely facilitates blood feeding by maintaining the pool of blood fluid at the feeding site. The salivary FXa inhibitor of C.v. sonorensis could impair the network of host-defense mechanisms in the skin microenvironment by avoiding blood coagulation at the site of feeding.
Searching for new heavy fermion materials in cerium intermetallic compounds

Abstract We report the results of the heat capacity and magnetic susceptibility measurements on several cerium intermetallic compounds. No heavy fermion behavior was found in these compounds. CePtGa3 has a broad anomaly in its heat capacity near 2 K and whose origin is not well understood. CeCd11 has an unusual temperature dependence of its heat capacity which is due to a crystalline electric field effect which occurs at an exceptionally low temperature. CeCd2 and CeCd3 are magnetically ordered at low temperatures. The low-temperature behavior of these and other cerium intermetallic compounds are discussed.
A novel method for determining the solubility of small molecules in aqueous media and polymer solvent systems using solution calorimetry.

Purpose To explore the application of solution calorimetry for measuring drug solubility in experimentally challenging situations while providing additional information on the physical properties of the solute material.
Role of ion valence in the submillisecond collapse and folding of a small RNA domain.

Following the addition of ions to trigger folding, RNA molecules undergo a transition from rigid, extended states to a compact ensemble. Determining the time scale for this collapse provides important insights into electrostatic contributions to RNA folding; however, it can be challenging to isolate the effects of purely nonspecific collapse, e.g., relaxation due to backbone charge compensation, from the concurrent formation of some tertiary contacts. To solve this problem, we decoupled nonspecific collapse from tertiary folding using a single-point mutation to eliminate tertiary contacts in the small RNA subdomain known as tP5abc. Microfluidic mixing with microsecond time resolution and Forster resonance energy transfer detection provides insight into the ionic strength-dependent transition from extended to compact ensembles. Differences in reaction rates are detected when folding is initiated by monovalent or divalent ions, consistent with equilibrium measurements illustrating the enhanced screening of ...
The Response of Terrestrial C Storage to Climate Change: Modeling C Dynamics at Varying Temporal and Spatial Scales

The response of terrestrial C storage to GCM derived climate change scenarios was investigated over a range of temporal and spatial scales. The potential changes in the global distribution of major ecosystem complexes were examined by combining changes in land cover and corresponding soil type with C storage estimates for each of the ecosystem types. All scenarios consistently showed an overall increase in global carbon storage. On a more regional basis, the potential impacts of climate change on the structure, composition and biomass dynamics of major forest types within the North American Boreal zone were investigated using individual based stand models. Biomass fluxes were found to be dependent on the tree species, site and GCM parameters. A method to simulate corresponding changes in intra- and interannual patterns of CO2 flux by combining a gap model with an ecosystem model which incorporates photosynthesis, respiration (both canopy and decomposer) and transpiration is demonstrated.
On some decidable properties of finite state translations

In this paper we present algorithms to decide: 1) single-valuedness of nondeterministic finite transducers, 2) equivalence of single-valued transducers, and 3) whether a given nondeterministic finite transduction can be realized by a deterministic transducer. When such a deterministic realization is possible our proof gives an effective construction of the deterministic transducer. The decidability of single-valuedness and equivalence for a-transducers has been obtained independently by Blattner and Head [3]. Our results introduce different characterizations for decidability and use a different proof that is interesting on its own. We began this research by generalizing the results about decoding automata presented in [5]. A report of these results with a heavy emphasis placed on applications to crytography appears in [6]. This paper presents results applicable in the more general area of finite state translations.
Phylogeography across a continent: the evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor).

Abstract Most phylogeographic studies examine organisms that do not have transcontinental distributions and therefore the genetic and temporal effects of barriers across an entire continent cannot be assessed with respect to a single species. We examined the phylogeographic structure, lineage age, and historical demography using sequences from the mtDNA cytochrome b gene of the widespread North American racer (Coluber constrictor), one of the few abundant transcontinental snakes that occurs throughout many diverse biomes. Our results indicate that this complex is comprised of six lineages differing greatly in geographic extent, with the largest (a central US clade) being ∼26 times greater than the smallest (a lineage restricted to the Florida Panhandle and nearby portions of adjacent States). Most of the six lineages appear to be separated at previously identified genetic barriers for several vertebrates with similar ranges. Lineage diversification in this species began in the late Miocene, separating populations in the Florida Peninsula from the remainder of the US. Diversification of lineages continued throughout the Pliocene and early Pleistocene. Four of the six lineages occur east of the Mississippi River, with only two distinctly young (∼1.5 mya) lineages found west of the Mississippi River (one occurs west of Continental Divide). All methods of demographic inference, including the mismatch distribution, Fu and Li’s D∗ and Tajima’s D∗, and Bayesian skyline plots revealed population expansion occurring in the mid-to-late Pleistocene for every lineage, regardless of size or proximity to formerly glaciated areas. Population expansion for lineages found east of the Mississippi River occurred earlier and was much greater than those found west of the River.
Polyethylene and polypropylene nanocomposites based upon an oligomerically modified clay

Montmorillonite clay was modified with an oligomeric surfactant, which was then melt blended with polyethylene and polypropylene in a Brabender mixer. The morphology was characterized by X-ray diffraction and transmission electron microscopy, while thermal stability was evaluated from thermogravimetric analysis and the fire properties by cone calorimetry. The nanocomposites are best described as mixed immiscible/intercalated/delaminated systems and the reduction in peak heat release rate is about 40% at 5% inorganic clay loading.
Mycotic Coronary Artery Aneurysm From Fungal Prosthetic Valve Endocarditis

Two cases of mycotic aneurysms of the left anterior descending coronary artery in patients with fungal prosthetic valve endocarditis are reported. One was managed with exclusion and interposition graft, and the other was managed by aneurysm excision, wide debridement, and distal bypass. The current literature and management strategies are reviewed.
Dust mobilization studies in the TDMX facility

Abstract The Toroidal Dust Mobilization eXperiment (TDMX) system is designed to experimentally simulate flow features and dust mobilization mechanisms in tokamak fusion reactor loss of vacuum accidents. A transparent toroidal chamber with several flow and aerosol mass diagnostics comprises the experiment system. Scoping tests have demonstrated the ability to generate conditions resulting in dust re-suspension and deposition in a toroidal geometry and explore effective methods of monitoring the distribution of re-deposited dust. This paper introduces TDMX by providing a description of the TDMX preliminary design, a summary of results from initial scoping tests, and a discussion of experiment improvements and future directions of the research.
Low-temperature formation of hydrocarbon gases in San Francisco Bay sediment (California, U.S.A.)

Abstract To understand the processes responsible for the presence of low-molecular-weight hydrocarbons (C 1 -C 4 ) in anoxic environments, we studied sediments collected from an anaerobic estuarine mudflat. In these sediments methane (C 1 ) was several orders of magnitude more abundant than all other C 2 -C 4 hydrocarbons; the C 1 ( C 2 + C 3 ) ratio was ∼ 13,000. Mean ethane/ethene and propane/propene ratios were 0.4 and 0.7, respectively. Production of C 1 -C 4 hydrocarbons was monitored during prolonged incubation (7 months) of sediments at 27° and 4°C. Samples stored at 27°C generated significant quantities of C 1 -C 4 hydrocarbon gases. Incubation at 4°C inhibited production of these gases. Several bactericides were tested with respect to their ability to inhibit formation of gaseous hydrocarbons. Sodium azide, chloroform, and 2-bromoethanesulfonic acid effectively inhibited methane formation, but not ethene formation in dilute continuously-shaken sediment slurries. Zephiran chloride only caused partial inhibition of methanogenesis (46%) and ethene generation (34%) in these slurries. In experiments with more concentrated unshaken sediment slurries, however, zephiran chloride and sodium azide did not block formation of methane, ethane, or propane. Only storage at −10°C prevented production of these gases. These results indicate that C 1 -C 4 hydrocarbons can be formed by low-temperature reactions, possibly mediated by microorganisms.
WHAT ARE VALIDATION EXPERIMENTS

ASCI has brought to the fore many important issues related to the ability of computational simulations to predict the response of a wide variety of complex engineered systems. The building blocks of our confidence assessment are verification of computer codes and validation of computational models. We contend that a new type of experiment, a validation experiment, is needed so that more quantifiable statements of level of agreement between computational results and experimental data can be made. Only with experimentalists and computational analysts working closely together can we better understand the limits of computational models and improve our experimental capabilities. We must also improve our understanding of how validation evidence for our computational models can be used to quantify our assessment of prediction accuracy.
Postoperative Hemostasis Monitoring and Management

Although postoperative hemorrhage is an understood sequela, surgery also elicits an inflammatory response that may result in a hypercoagulable state and risk for venous or arterial thromboembolism. Postoperative venous thromboembolism is well documented in humans and is multifactorial in nature; however, evidence for its presence in veterinary medicine remains sparse. There is no consensus on the ideal type, dose, and duration of thromboprophylactic therapy in the perioperative period. Regardless, coagulation perturbations secondary to surgical stress are important considerations for the perioperative patient to reduce the possible fatal risks of hemorrhage or thrombosis.
Antedependence models for nonstationary categorical longitudinal data with ignorable missingness: likelihood-based inference.

Time index-ordered random variables are said to be antedependent (AD) of order (p1 ,p2 , … ,pn ) if the kth variable, conditioned on the pk immediately preceding variables, is independent of all further preceding variables. Inferential methods associated with AD models are well developed for continuous (primarily normal) longitudinal data, but not for categorical longitudinal data. In this article, we develop likelihood-based inferential procedures for unstructured AD models for categorical longitudinal data. Specifically, we derive maximum likelihood estimators (MLEs) of model parameters; penalized likelihood criteria and likelihood ratio tests for determining the order of antedependence; and likelihood ratio tests for homogeneity across groups, time invariance of transition probabilities, and strict stationarity. We give closed-form expressions for MLEs and test statistics, which allow for the possibility of empty cells and monotone missing data, for all cases save strict stationarity. For data with an arbitrary missingness pattern, we derive an efficient restricted expectation-maximization algorithm for obtaining MLEs. We evaluate the performance of the tests by simulation. We apply the methods to longitudinal studies of toenail infection severity (measured on a binary scale) and Alzheimer's disease severity (measured on an ordinal scale). The analysis of the toenail infection severity data reveals interesting nonstationary behavior of the transition probabilities and indicates that an unstructured first-order AD model is superior to stationary and other structured first-order AD models that have previously been fit to these data. The analysis of the Alzheimer's severity data indicates that the antedependence is second order with time-invariant transition probabilities, suggesting the use of a second-order autoregressive cumulative logit model.
DMSO resolves certain compressions and signal dropouts in fluorescent dye labeled primer-based DNA sequencing reactions

Automated base calling algorithms are more sensitive to the quality of the DNA sequencing data than are the labor intensive visual methods of base calling. To improve this quality, data from DNA sequencing reactions have been compared in order to determine the effects of the inclusion of dimethyl sulfoxide (DMSO). Inclusion of 10% DMSO into the reaction cocktail resolves at least one type of sequence compression. This compression may be due to the lack of ability in T7 DNA polymerase to read through certain sequences correctly. The poor quality of these data is seen as radioactive bands or fluorescent signal peaks that have an abnormal alignment, either in the wrong order or as single bands/peaks. The inclusion of DMSO also resolves sequences where the peak signal is absent or severely diminished, leading to a “gap” in the chromatogram profile. DMSO is better than deaza-dITP for resolving certain compressions. Addition of DMSO is a cheaper and more efficient method for high-throughput DNA sequencing than ...
Using Voice Transformations to Create Additional Training Talkers for Word Spotting

Speech recognizers provide good performance for most users but the error rate often increases dramatically for a small percentage of talkers who are "different" from those talkers used for training. One expensive solution to this problem is to gather more training data in an attempt to sample these outlier users. A second solution, explored in this paper, is to artificially enlarge the number of training talkers by transforming the speech of existing training talkers. This approach is similar to enlarging the training set for OCR digit recognition by warping the training digit images, but is more difficult because continuous speech has a much larger number of dimensions (e.g. linguistic, phonetic, style, temporal, spectral) that differ across talkers. We explored the use of simple linear spectral warping to enlarge a 48-talker training data base used for word spotting. The average detection rate overall was increased by 2.9 percentage points (from 68.3% to 71.2%) for male speakers and 2.5 percentage points (from 64.8% to 67.3%) for female speakers. This increase is small but similar to that obtained by doubling the amount of training data.
Statistical evaluation of remotely sensed snow-cover products with constraints from streamflow and SNOTEL measurements

Using streamflow and Snowpack Telemetry (SNOTEL) measurements as constraints, the evaluation of the Moderate Resolution Imaging Spectroradiometer (MODIS) daily and 8-day snow-cover products is carried out using the Upper Rio Grande River Basin as a test site. A time series of the snow areal extent (SAE) of the Upper Rio Grande Basin is retrieved from the MODIS tile h09v05 covering the time period from February 2000 to June 2004 using an automatic Geographic Information System (GIS)-based algorithm developed for this study. Statistical analysis between the streamflow at Otowi (NM) station and the SAE retrieved from the two MODIS snow-cover products shows that there is a statistically significant correlation between the streamflow and SAE for both products. This relationship can be disturbed by heavy rainstorms in the later springtime, especially in May. Correlation analyses show that the MODIS 8-day product has a better correlation (r=� 0.404) with streamflow and has less percentage of spurious snowmelt events in wintertime than the MODIS daily product (r=� 0.300). Intercomparison of these two products, with the SNOTEL data sets as the ground truth, shows that (1) the MODIS 8-day product has higher classification accuracy for both snow and land; (2) the omission error of misclassifying snow as land is similar for both products, both are low; (3) the MODIS 8-day product has a slightly higher commission error of misclassifying land as snow than the MODIS daily product; and (4) the MODIS daily product has higher omission errors of misclassifying both snow and land as clouds. Clouds are the major cause for reduction of the overall accuracy of the MODIS daily product. Improvement in suppressing clouds in the 8-day product is obvious from this comparison study. The sacrifice is the temporal resolution that is reduced from 1 to 8 days. The significance of the results is that the 8-day product will be more useful in evaluating the streamflow response to the snow-cover extent changes, especially from the long-term point of view considering its lower temporal resolution than the daily product. For clear days, the MODIS daily algorithm works quite well or even better than the MODIS 8-day algorithm. D 2004 Elsevier Inc. All rights reserved.
Pronounced climatic variations in Alaska during the last two millennia.

Paired oxygen-isotopic analyses of abiotic carbonate and benthic-ostracode shells from lake sediments provide a continuous quantitative record of growing-season temperature for the past 2000 years in the northwestern foothills of the Alaska Range. This record reveals three time intervals of comparable warmth: anno Domini (A.D.) 0–300, 850-1200, and post-1800, the latter two of which correspond to the Medieval Climatic Anomaly and climatic amelioration after the end of the Little Ice Age. The Little Ice Age culminated at A.D. 1700, when the climate was ≈1.7°C colder than at present. A marked climatic cooling also occurred around A.D. 600, coinciding with extensive glacial advances in Alaska. Comparisons of this temperature record with ostracode trace-element ratios (Mg/Ca, Sr/Ca) further suggest that colder periods were wetter and vice versa during the past 2000 years.
IDENTIFICATION AND ENUMERATION OF CULTURED AND WILD PSEUDO‐NITZSCHIA (BACILLARIOPHYCEAE) USING SPECIES‐SPECIFIC LSU rRNA‐TARGETED FLUORESCENT PROBES AND FILTER‐BASED WHOLE CELL HYBRIDIZATION

Efforts to understand the ecologic and environmental parameters that govern harmful algal blooms (HABs) require rapid and specific identification of causative species. Traditional methods of species identification using light and electron microscopy are useful in this regard but are also time consuming, making routine analysis of a large number of samples difficult. Techniques that speed and ease the detection of HAB species as they occur in natural populations are therefore desirable. In this paper, we continue efforts to develop species-specific large subunit ribosomal RNA (LSU rRNA)-targeted fluorescent DNA probes for a variety of Pseudo-nitzschia H. Peragallo species, a group of marine pennate diatoms that includes representatives linked to production of domoic acid and amnesic shellfish poisoning (ASP). A custom filter tube and filtration manifold that has utility for both whole cell (in situ) hybridization as well as preparing samples for scanning electron microscopy (SEM) is described. Filter-based whole cell hybridization was used to identify a variety of newly isolated Pseudo-nitzschia clones, and probe results were confirmed using SEM. Some isolates of P. pungens (Grunow) Hasle exhibited variable (intraclonal) reactivity toward the P. pungens-specific probe. Three isolates of P. subpacifica (Hasle) Hasle were found to cross-react with probes designed for P. fraudulenta (Cleve) Hasle and P. heimii Manguin. Four isolates did not react with any species-specific probes; this group comprised three distinct morphotypes whose fine-scale morphologic features did not agree with published descriptions of Pseudo-nitzschia species. Evaluation of the filter method using cultured cells added to natural (whole water) samples indicated quantitative recovery of target species. Confirming results of probe assays using SEM was difficult when the target species was less than 10 4 cells·L 21 in the presence of greater than 106 cells·L 21 of other nontarget diatom species. A variety of Pseudo-nitzschia, including P. australis Frenguelli, P. fraudulenta, P. heimii, P. pseudodelicatissima (Hasle) Hasle, P. pungens, P. multiseries (Hasle) Hasle, and Nitzschia americana Hasle, were identified using whole cell hybridization in a variety of field samples containing mixed assemblages of plankton, and these results were confirmed using SEM. The filter tube method of applying probes was used onboard ship for near real-time identification and enumeration of a variety of Pseudonitzschia species.
Near-zone expansions for the vector potential of the traveling-wave current loop antenna

This paper presents exact representations for the near-zone vector potential integrals corresponding to a thin circular loop antenna with a traveling-wave current distribution. These expansions are derived by employing an exact integration procedure for vector potentials of thin circular loops with arbitrary current distributions.
Gonadotropin-releasing hormone neurosecretion in the human hypothalamus: in vitro regulation by dopamine.

An in vitro perifusion system was used to investigate GnRH release from adult human hypothalami in response to dopamine (DA) and the DA receptor antagonist haloperidol (HAL). Administration of a 1-µM pulse of DA consistently elicited a mean ± SE 218 ± 59%increase(P < 0.05; n = 5) in GnRH release, whereas 1 µM HAL had no effect. Administration of 1 µM DA during three perifusions in which 1 µM HAL was added to the medium failedto alter basal GnRH release. Incontrast, DA did evoke an acute 98 ± 39% increase (P < 0.06) in GnRH release during threematching perifusions with medium containing the α-adrenergic antagonist phentolamine. These studies demonstrate that DA can stimulate in vitro release of GnRH from the adult human hypothalamus by a DA receptormediated mechanism.
Cell cycle– and swelling-induced activation of a Caenorhabditis elegans ClC channel is mediated by CeGLC-7α/β phosphatases

ClC voltage-gated anion channels have been identified in bacteria, yeast, plants, and animals. The biophysical and structural properties of ClCs have been studied extensively, but relatively little is known about their precise physiological functions. Furthermore, virtually nothing is known about the signaling pathways and molecular mechanisms that regulate channel activity. The nematode Caenorhabditis elegans provides significant experimental advantages for characterizing ion channel function and regulation. We have shown previously that the ClC Cl− channel homologue CLH-3 is expressed in C. elegans oocytes, and that it is activated during meiotic maturation and by cell swelling. We demonstrate here that depletion of intracellular ATP or removal of Mg2+, experimental maneuvers that inhibit kinase function, constitutively activate CLH-3. Maturation- and swelling-induced channel activation are inhibited by type 1 serine/threonine phosphatase inhibitors. RNA interference studies demonstrated that the type 1 protein phosphatases CeGLC-7α and β, both of which play essential regulatory roles in mitotic and meiotic cell cycle events, mediate CLH-3 activation. We have suggested previously that CLH-3 and mammalian ClC-2 are orthologues that play important roles in heterologous cell–cell interactions, intercellular communication, and regulation of cell cycle–dependent physiological processes. Consistent with this hypothesis, we show that heterologously expressed rat ClC-2 is also activated by serine/threonine dephosphorylation, suggesting that the two channels have common regulatory mechanisms.
Acute coronary syndromes: from bench to bedside–the Twenty-first annual Arnold O. Beckman Conference in Clinical Chemistry

The 1998 Arnold O. Beckman Conference continued the tradition of focusing on the interface between clinical medicine and the clinical laboratory. Because this year marks the 50th anniversary of the founding of the American Association for Clinical Chemistry (AACC), the association’s governing body has deemed appropriate the historical review of all its sponsored events. Therefore, this introduction has two parts: a historical summary of the A.O. Beckman Conference and a summary of the current conference. Generous donations from the Arnold and Mabel Beckman Foundation support this series of conferences and their proceedings. I introduced this year’s conference by reviewing both Dr. Beckman’s history and the conference history. Dr. Beckman’s life story is more fully described on a page of the Beckman Coulter web site (1). Arnold O. Beckman was born in Cullom, Illinois, on April 10, 1900, to a farming family. Chemistry interested the young Beckman, and he pursued this interest for his higher education. He obtained a bachelor degree in chemical engineering from the University of Illinois in 1922 and a doctor of philosophy degree in photochemistry from the California Institute of Technology in 1928. Although he started his career in academics, Dr. Beckman excelled in the area of scientific instrument invention. His seminal invention of the “acidimeter” would lead, in 1935, to the founding of a …
Bis(2‐propanolato)[(1,2‐η)‐1‐propene]titanium

[169123-69-7] C9H20O2Ti (MW 208.12) InChI = 1S/2C3H7O.C3H6.Ti/c2*1-3(2)4;1-3-2;/h2*3H,1-2H3;3H,1H2,2H3;/q2*-1;;+2 InChIKey = PPVJQIIELFTSDE-UHFFFAOYSA-N (reagent used for cyclopropanol and cyclopropylamine synthesis, intramolecular nucleophilic acylsubstitution reactions, synthesis of allyl and allenyl organometallics, coupling of alkenes and alkynes, and formation of alkenyl vicinal dianions) Alternate Name: Kulinkovich reagent. Solubility: reactions employing the title reagent are typically performed in diethyl ether. THF can also be used for many reactions, although it has been noted to give capricious results. Form Supplied in: not commercially available. Preparative Methods: the title reagent is readily prepared by reaction of titanium tetraisopropoxide and an isopropylmagnesium halide (e.g., isopropylmagnesium chloride) and is used in situ. Other titanium sources ‘e.g., chlorotitanium tris(isopropoxide)’ have been employed for some reactions. Handling, Storage, and Precautions: reactions should be performed under an inert atmosphere, with the exclusion of moisture.
SOX Costs: Auditor Attestation under Section 404

This study examines the cost of the new internal control audit required by the Sarbanes-Oxley Act of 2002 (SOX) for a sample of Fortune 1000 companies. The average audit fee increase from 2003 to 2004 of $2.3 million is significant and is primarily attributable to the new SOX audit. SOX audit costs appear to be based on company size, asset growth, and the effectiveness of internal controls in addition to the 2003 financial statement audit rate. Specifically, the SOX audit costs increase with size, but the SOX audit unit costs vary inversely with size. This inverse relationship is consistent with larger companies benefiting from returns to scale and smaller companies spending fewer resources on internal controls and being more likely to have material weaknesses in internal controls. The positive relationship between SOX audit costs and asset growth supports the notion that rapidly growing firms may not be able to update their internal control systems in a timely manner and, therefore, may be more likely to experience internal control weaknesses. Firms that reported ineffective internal controls experienced higher SOX audit costs than those that reported effective internal controls. We also find evidence that financial services firms paid significantly lower SOX audit rates and electronic equipment and electronics firms paid significantly higher SOX audit rates than firms in other industries.
Current Status of Developments and Applications of Micro-CT

Use of microscopic computed-tomography (micro-CT) scanning continues to grow in biomedical research. Laboratory-based micro-CT scanners, laboratory-based nano-CT scanners, and integrated micro-CT/SPECT and micro-CT/PET scanners are now manufactured for "turn-key" operation by a number of commercial vendors. In recent years a number of technical developments in X-ray sources and X-ray imaging arrays have broadened the utility of micro-CT. Of particular interest are photon-counting and energy-resolving detector arrays. These are being explored to maximize micro-CT image grayscale dynamic range and to further increase image contrast by utilizing the unique spectral attenuation characteristics of individual chemical elements. X-ray phase-shift images may increase contrast resolution and reduce radiation exposure. Although radiation exposure is becoming a concern with the drive for increased spatial and temporal resolution, especially for longitudinal studies, gated scans and limited scan-data-set reconstruction algorithms show great potential for keeping radiation exposure to a minimum.