cssi/SciSciGPT-SciSciNet huggingface dataset:
Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014).
Idioms of logical modelling

Most modeling languages embody a particular idiom: the state/invariant/operations idiom for VDM and Z; the variable-update/temporal-logic idiom for SMV and Murphi; the imperative-programming idiom for Promela and Zing; and so on. Fixing an idiom makes tools easier to build, and helps novice modellers. But it also makes the language less flexible.
NAD(P)+ Binding to Dehydrogenases

Each NAD-dependent dehydrogenase binds its coenzyme in a unique manner. Virtually all possess a highly conserved binding domain called the Rossmann fold that is involved in this interaction and dictates the specificity of hydride transfer. Keywords: NAD+; NADP+; dehydrogenases; rossmann fold; coenzyme; redox reactions
ROCKY MOUNTAIN SPOTTED FEVER WITHOUT A RASH Report of a Case Treated with Chloramphenicol

An unusually severe case of Rocky Mountain spotted fever that failed to develop a rash by the eighth day of fever in spite of the delay in beginning specific chloramphenicol therapy until that time is reported. Due to the absence of a rash the diagnosis was of necessity only presumptive when chloramphenicol therapy was begun. It was not definitely established until later, when the agglutination and complement fixation tests became positive. Chloramphenicol effected a recovery within 48 hours of its initiation. This is the first reported case of severe tick fever to survive eight days of symptoms without specific therapy and yet fail to develop a rash.
Physician-scientists--endangered and essential.

If the country9s medical research enterprise is to make the contributions it is poised to deliver, the progressive, dangerous decline in the number of physician-scientists must be reversed. This decline--most pronounced among trainees and young investigators--has resulted from: societal pressures toward careers in primary care; economic disincentives, a shift in funding priorities; and the growth of managed care. Because physician-scientists are indispensable participants in the bi-directional flow of information from bedside to laboratory, and because no single agency can correct this problem alone, a major national effort--catalyzed by federal legislation-is recommended: to establish a climate in academia conducive to creating physician-scientists; to set up a network of clinical research units; to enlist the support of foundations, biopharmaceutical companies and managed care entities, as well as government and academia; and to set up a national database of physicians scientists.
Reasoning by Plausible Inference

The PI (Plausible Inference) system has been implemented with the ability to reason in both directions, unlike previous AI systems for inexact reasoning. This is combined with truth-maintenance, dependency-directed backtracking, and time-varying contexts to permit modelling dynamic situations. Four rules of inference are employed in PI, Modus Ponens, Modus Tollens, Confirmation, and Denial. Each of these causes credibility as well as truth value to be propagated in a semantic network of assertions. Applications are foreseen in ‘guessing’ the answers to problems in formal deduction so that search trees may be pruned, and in the flexible selection of strategies for planning, as well as diagnostic or trouble-shooting models involving less-than-certain assertions.
Analytic Functions of a Complex Variable

The MAA is pleased to re-issue the early Carus Mathematical Monographs in ebook and print-on-demand formats. Readers with an interest in the history of the undergraduate curriculum or the history of a particular field will be rewarded by study of these very clear and approachable little volumes. The theory of functions of a complex variable has been developed by the efforts of thousands of workers through the last hundred years. To give even the briefest account of the present state of that theory in all its branches would be impossible within the limits of this book. What is attempted here is a presentation of fundamental principles with sufficient details of proof and discussion to avoid the style of a mere summary or synopsis. In various places there are indications of directions in which special portions of the subject branch off from the main stem. The reader is assumed to have an acquaintance with elementary differential and integral calculus. Without such knowledge one may, however, obtain some idea of the scope and purposes of the theory of functions from this monograph. Those should profit most who are familiar with more than the elements of the calculus.
The impaired response of spinal cord injured individuals to repeated surface pressure loads

Abstract Three cyclic pressure loads (10 minutes "on" and 5 minutes "off") of 30 or 75mmHg were applied to the flat anterior surface of the tibia on 11 able bodied (AB) and nine spinal cord injured (SCI) subjects. Transcutaneous PO 2 (TcPO 2 ) and PCO 2 (TcPCO 2 ), laser Doppler (LD) skin blood flow, velocity, and volume, and the depth of leg indentation (LI) were recorded. In the AB subjects the mean TcPO 2 decreased from 31.5 to 27.2mmHg with the 30mmHg load, In contrast for the SCI subjects TcPO 2 decreased from 32.3 to 7.3mmHg (significantly different from AB group at p p p p 2 , LD volume, and LI data support the hypothesis that the SCI subjects have a reduced vascular response to loading and thus may be more susceptible to develop pressure sores for physiological reasons. The greatest difference is in the 30mmHg load range where autoregulation can be observed.
Studies on Human β-d-N-Acetylhexosaminidases I. PURIFICATION AND PROPERTIES

Abstract β-d-N-Acetylhexosaminidase A and B were purified from human placenta. In the initial steps of purification, namely, extraction, ammonium sulfate precipitation, lyophilization, Sephadex G-200 filtration, and DEAE-cellulose column chromatography hexosaminidase A and hexosaminidase B were purified together. Hexosaminidase A was further purified by a second DEAE-cellulose column chromatography followed by ECTEOLA-cellulose column chromatography, Sephadex G-200 filtration, electrofocusing, and a third Sephadex G-200 filtration. Hexosaminidase B was further purified by CM-cellulose column chromatography, electrofocusing, and Sephadex-G-200 filtration. After the first Sephadex G-200 filtration hexosaminidase A and B were also purified by a second method. This method involved calcium phosphate gel, DEAE-Sephadex, ECTEOLA-cellulose, CM-Sephadex and CM-cellulose column chromatography, and preparative polyacrylamide disc electrophoresis. Purified hexosaminidase A and hexosaminidase B moved on polyacrylamide disc electrophoresis as single protein bands with virtually all of the enzyme activity. Hexosaminidase A and B in 10 mm phosphate buffer containing 0.1 m (NH4)2SO4 were stable at 4° for at least 4 months. The isoelectric points of hexosaminidase A and hexosaminidase B were found to be pH 5.4 and 7.9, respectively. Placental hexosaminidases were found to differ electrophoretically and antigenically from the liver and fibroblast enzymes. In contrast to the reports of others neuraminidase failed to convert heat-labile hexosaminidase A to a heatstable form of enzyme resembling hexosaminidase B.
A Theoretical Foundation and a Method for Document Table Structure Extraction and Decompositon

The algorithm described in this paper is designed to detect potential table regions in the document, to decide whether a potential table region is, in fact, a table, and, when it is, to analyze the table structure. The decision and analysis phases of the algorithm and the resulting system are based primarily on a precise definition of table, and it is such a definition that is discussed in this paper. An adequate definition need not be complete in the sense of encompassing all possible structures that might be deemed to be tables, but it should encompass most such structures, it should include essential features of tables, and it should exclude features never or very rarely possessed by tables.
A Comparison of RSA and the Naccache-Stern Public-Key Cryptosystem

In September 1995, David Naccache and Jacques Stern proposed a new public key cryptosystem. We give an analysis of this cryptosystem and we make a comparison with the well-known RSA system.
Implications of multi-image for concept acquisition

This study explored a number of questions related to multi-image presentation of information and acquisition of a concept — in this case, classifying plants in the subphylum Pteropsida. Of particular interest was whether redundancy (i.e., additional positive examples of plants in the classes) and an opportunity to view nonexamples as well as examples of classes would be helpful to the seventhgrade subjects.
Improved Gold Chloride Procedure for Nerve Staining in Whole Mounts of Rat Corneas

The purpose of this study was to modify the gold chloride procedure for studies of total innervation in corneal whole mounts to provide a decrease in nonspecific background staining and to eliminate the progressively deteriorating stain quality of standard gold chloride techniques. Modifications included use of cryoprotective agents, mechanical removal of Descemet's membrane-endothelium complex prior to fixation, treatment with alpha amylase, and halting the reduction of gold chloride to metallic gold using Kodak rapid fixer with hardener. Rat corneas were stored at -70 C in O.C.T. compound. The Descemet's membrane-endothelium complex was removed after thawing, and corneas were fixed in 4% NaPO4-buffered paraformaldehyde with 8% sucrose. Fixed corneas were incubated in NaPO4-buffered saline containing alpha amylase, placed in 100% lemon juice, then in 1% gold chloride solution, transferred to glacial acidic acid, placed in rapid fixer, rinsed in NaPO4-buffered saline, and dehydrated in graded alcohols. Flat mounts of whole corneas were examined using contralateral corneas as controls. Freezing corneas in O.C.T. compound, removal of the Descemet's membrane-endothelium complex, and treatment with alpha amylase reduced non-specific background staining compared to controls. Treatment with Kodak rapid fixer prevented the deterioration of staining quality for at least 8 months. These improvements allow the gold chloride technique to be used with immunohistochemical procedures where the reaction products would be obscured by background staining.
A Role For Protein Phosphorylation In Fusion Pore Opening And Transmitter Release

Activity-dependent regulation of protein kinase A (PKA) and protein kinase C (PKC), is essential for modulation of neurosecretion. To study the role of protein phosphorylation in the dynamics of the fusion pore opening and transmitter release, carbon fiber amperometry and cell-attached capacitance measurements were performed in bovine chromaffin cells. In cells treated with the PKC inhibitor, bisindolylmaleimide I (100nM, 10Ki), release frequency was significantly reduced to 5.0±1.2events/min (from control 17.1±2.0events/min). Amperometric spikes also showed increased half width of 22.3±2.0ms (from 11.5±0.9ms control) and smaller amperometric spike amplitude of 21.9±3.7pA (from 56.2±9.4pA control). In the cells treated with PKA inhibitor, KT 5720 (500nM, 10Ki), the duration of foot signals of amperometric events was prolonged to 14.4±1.6ms (from 9.0±1.0 ms control), consistent with prolonged fusion pore duration in cell-attached capacitance measurements of 27.7±6.8ms (from 11.8±1.4ms control). In contrast to PKC inhibitor, KT 5720 did not affect the release frequency.These results indicate that PKC affects the rate of fusion pore formation and release after full fusion but not early fusion pore expansion, while PKA specifically affects the expansion of the early fusion pore as well as release after full fusion.View Large Image | View Hi-Res Image | Download PowerPoint Slide
Studies on the biosynthesis of the oogoniols

In feeding experiments withAchlya heterosexualis, [3-3H] fucosterol was efficiently incorporated into oogoniols possessing an unsaturated side chain as well as those with a saturated side chain (clionasterol skeleton). [23,25-3H]-29-Hydroxyfucosterol was also efficiently incorporated into the oogoniols and its role as an intermediate in the biosynthesis was confirmed by a trapping experiment. This indicated the presence of a small pool of endogenous 29-hydroxyfucosterol in the mycelium. [23, 25-3H]-29-Oxofucosterol was also well incorporated into the oogoniols and it is probably an intermediate in the biosynthesis. It was found to be converted to 29-hydroxyfucosterol in a trapping experiment. Reduction of the C-24(28) double bond make take place after all the functional groups have been introduced, at C7, C-11 and C-15, in the tetracyclic structure.
Non-traumatic CSF fistulae: Clinical history and management

Non-traumatic 'spontaneous' CSF fistulae are uncommon. The clinical features of 23 patients treated for non-traumatic CSF fistulae are presented. Twenty of these patients had normal CSF pressure and six developed meningitis. Surgical repair of these fistulae is recommended in order to reduce the risk of meningitis. For this their localization is essential.
Utilization of mining and mineral processing wastes in the United States

Huge quantities of solid wastes are generated as a result of mining and mineral processing activities in the United States. Over the years, the majority of these by-products have been disposed of in unsightly dumping areas which are aesthetically unattractive and often degrading to the environment. However, many of these wastes, because of their similarity to conventional soils and aggregates, represent potentially useful sources of material for a variety of applications.
Malignant obstructive jaundice: Treatment with external-beam and intracavitary radiotherapy

Eleven patients with obstructive jaundice from unresectable cholangiocarcinoma, metastatic porta hepatis adenopathy, or direct compression from a pancreatic malignancy were treated at the Stanford University Medical Center from 1978-1983 with an external drainage procedure followed by high-dose external-beam radiotherapy and by an intracavitary boost to the site of obstruction with Iridium192 (Ir192). A median dose of 5000 cGy was delivered with 4-6 Mv photons to the tumor bed and regional lymphatics in 9 patients, 1 patient received 2100 cGy to the liver in accelerated fractions because of extensive intrahepatic disease, and 1 patient received 7000 "equivalent" cGy to his pancreatic tumor bed and regional lymphatics with neon heavy particles. An Ir192 wire source later delivered a 3100-10,647 cGy boost to the site of biliary obstruction in each patient, for a mean combined dose of 10,202 cGy to a point 5 mm from the line source. Few acute complications were noted, but 3/11 patients (27%) subsequently developed upper gastrointestinal bleeding from duodenitis or frank duodenal ulceration 4 weeks, 4 months, and 7.5 months following treatment. Eight patients died--5 with local recurrence +/- distant metastasis, 2 with sepsis, and 1 with widespread systemic metastasis. Autopsies revealed no evidence of biliary tree obstruction in 3/3 patients. Mean survival time from initial laparotomy and bypass was 16.1 months, and from radiotherapy completion was 8.3 months. Evolution of radiation treatment techniques for biliary obstruction in the literature is reviewed. High-dose external-beam therapy followed by high-dose Ir192 intracavitary boost is well tolerated and provides significant palliation. Survival of these aggressively managed patients approaches that of patients with primarily resectable tumors.
Domains of regularity of a harmonic function determined by the coefficients of its power series

Theorems are proved which give a sufficient condition on the coefficients of a harmonic function in order that the function be regular in the domain {(x, y, z) | x < A } and is singular at the point (A, 0, 0).
The decline of a model? Challenge and response in the Italian industrial districts

The article presents an extensive critical review of recent debates on the restructuring of Italian industrial districts in the 1990s. It shows that, despite consensus on the empirical 'facts' of district restructuring, there remains extensive disagreement over appropriate public policies. This debate fundamentally turns on analysts' interpretations of how, or indeed whether, strong institutions and localized subcultures allow territorial networks of small firms to compete successfully with larger and more highly capitalized multinational corporations. But perhaps the most crucial and contentious issues are questions about the past adequacy of the districts' regulatory and service institutions in overcoming structural difficulties of the model, and, more importantly, about further innovations that may be required given recent changes in the external economic context.
Police: Professionals or craftsmen? An empirical assessment of professionalism and craftsmanship among eight municipal police agencies

Abstract Researchers on police attitudes frequently have assessed the degree to which police exhibit values reflecting professionalism. The present research, conducted on eight municipal police agencies in Illinois, examined the extent to which police exhibit values more characteristic of craftsmanship. Based on Wilson's (1968) discussion of styles of municipal policing, four craftsmanship constructs—apprenticeship, a holistic work-ethic, lack of deference to authority, and oral traditions—were measured using a 30-item craftsmanship inventory. Factor-analytic strategies were used to develop eight composite measures of craftsmanship. A comparison of responses to craftsmanship and professionalism composite scales suggested that the world view of police is more accurately characterized in terms of professionalism than craftsmanship. The conclusions discuss changes in policing in the two decades following Wilson's research that are consistent with notions of professionalism.
Mixed-Integer Approach for Obtaining Unique Solutions in Source Inversion of Water Networks

This paper addresses the problem of contamination source determination in municipal drinking water networks. In previous work, the authors introduced a large-scale nonlinear programming approach for identifying both the time and location of contamination sources given concentration information from a limited number of sensors. Due to the sparseness of the sensor grid, this problem inherently has nonunique solutions. The problem was therefore regularized, and the regularized solution provided an approximate linear combination of possible injection scenarios. In this paper, a mixed-integer quadratic program is presented to refine the solution provided by the nonlinear programming formulation. We introduce a two-phase approach. In the n-phase, the number of likely injection locations is estimated. Using this information, the e-phase is performed to extract the likely injection scenarios from the family of nonunique solutions. This two-phase approach is tested on a realistic municipal water network model with approximately 400 nodes, simulating five different injection scenarios. In all five examples, the approach was able to determine the correct number of injection locations and identify a set of possible injection scenarios containing the actual simulated injections.
The economic determinants of specialty choice by medical residents.

Abstract This paper analyzes how economic factors (relative expected earnings, relative expected hours worked, and relative length of training period) affect the distribution of medical residents across specialties. The results show that the percent of residents in a given specialty changes more than proportionately when relative hours change (hours elasticities averaged between - 1.2 and - 2.0) and less than proportionately when relative earnings change (earnings elasticities averaged between 0.3 and 0.6). Residents appear to be quite unresponsive to changes in the length of training period.
Further Observations on Penicillin-Treated Cardiovascular Syphilis

One hundred and eleven cases of cardiovascular syphilis were treated with penicillin and, of these, 13 were in congestive heart failure, eight suffered from angina pectoris, and three had a history of coronary occlusion. Except for mild fever in a few instances therapeutic shock was not observed in any of the patients and therapeutic paradox, although sought for, was also not observed. There is evidence to suggest that penicillin has a favorable influence upon cardiovascular syphilis; angina pectoris and congestive heart failure do not contraindicate the use of penicillin in cardiovascular syphilis.
Back navigation shortcuts for screen reader users

When screen reader users need to back track pages to re-find previously visited content, they are forced to listen to some portion of each unwanted page to recognize it. This makes aural back navigation inefficient, especially on large websites. To address this problem, we introduce topic- and list-based back: two navigation strategies that provide back browsing shortcuts by leveraging the conceptual structure of content-rich websites. Both are manifested in Webtime, an accessible website on the history of the Web. A controlled study (N=10) conducted at the Indiana School for the Blind and Visually Impaired compared topic- and list-based back to traditional back mechanisms while participants completed fact-finding tasks. Topic- and list-based back significantly decreased time-on-task and number of backtracked pages; the navigation shortcuts were also associated with positive improvements in perceived cognitive effort and navigation experience. The proposed strategies can operate as a supplement to current back mechanisms in information-rich websites.
Enhancement of bacterial porphyrin biosynthesis by exogenous aminolevulinic acid and isomer specificity of the products

Abstract 5-Aminolevulinic acid (ALA) added to cultures of Pseodomonas leads to enhanced biosynthesis of porphyrins whereby metabolites are secreted directly into the medium. The total amount of secreted porphyrins increases with increasing ALA concentration up to ca. 2 mM, beyond which ALA becomes toxic to the cells. At 2 mM ALA, the predominant product secreted is uroporphyrin. Other porphyrins can be isolated including coproporphyrin and the decarboxylation metabolites in between uroporphyrin and coproporphyrin, as well as variable amounts of the zinc and copper chelates of these. After conversion to methyl ester derivatives and purification by HPLC, uroporphyrin. coproporphyrin, and esters of some of the intermediates were examined by NMR. In six strains examined, it was found that the majority of secreted uroporphyrin was the type I isomer. The coproporphyrin on the other hand ranged from pure coproporphyrin III in some strains to variable mixtures of the I and III isomers in others.
Temporal change in forest fragmentation at multiple scales

Previous studies of temporal changes in fragmentation have focused almost exclusively on patch and edge statistics, which might not detect changes in the spatial scale at which forest occurs in or dominates the landscape. We used temporal land-cover data for the Chesapeake Bay region and the state of New Jersey to compare patch-based and area–density scaling measures of fragmentation for detecting changes in the spatial scale of forest that may result from forest loss. For the patch-based analysis, we examined changes in the cumulative distribution of patch sizes. For area–density scaling, we used moving windows to examine changes in dominant forest. We defined dominant forest as a forest parcel (pixel) surrounded by a neighborhood in which forest occupied the majority of pixels. We used >50% and ≥60% as thresholds to define majority. Moving window sizes ranged from 2.25 to 5,314.41 hectares (ha). Patch size cumulative distributions changed very little over time, providing no indication that forest loss was changing the spatial scale of forest. Area–density scaling showed that dominant forest was sensitive to forest loss, and the sensitivity increased nonlinearly as the spatial scale increased. The ratio of dominant forest loss to forest loss increased nonlinearly from 1.4 to 1.8 at the smallest spatial scale to 8.3 to 11.5 at the largest spatial scale. The nonlinear relationship between dominant forest loss and forest loss in these regions suggests that continued forest loss will cause abrupt transitions in the scale at which forest dominates the landscape. In comparison to the Chesapeake Bay region, dominant forest loss in New Jersey was less sensitive to forest loss, which may be attributable the protected status of the New Jersey Pine Barrens.
Identification of the interaction sites of Inhibitor-3 for protein phosphatase-1.

Abstract Inhibitor-3 is a potent inhibitor of protein phosphatase-1, with an IC 50 in the nanomolar range for the inhibition of the dephosphorylation of phosphorylase a . Human Inhibitor-3 possesses a putative protein phosphatase-1 binding motif, 39 KKVEW 43 . We provide direct evidence that this sequence is involved in PP1 interaction by examining the effects of site-directed mutations of Inhibitor-3 on its ability to inhibit protein phosphatase-1. A second interaction site whose deletion led to loss of inhibitory potency was identified between residues 65 and 77. The existence of two interaction sites is consistent with the high inhibitory potency of Inhibitor-3, and with current models for other inhibitor and targeting proteins that interact with protein phosphatase-1 with high affinity.
Difficulties in Ferrous Iron Mordant Hematoxylin Staining and Some Hematoxylin Substitutes

A gradual deterioration of intensity of sequence ferrous sulfate hematoxylin staining was traced, after elimination of hematoxylin quality as a cause, to a deterioration of the metal salt, associated with caking of the crystals. Fresh samples were also partly caked and ineffective. Ferrous ammonium sulfate was found also subject to the same deterioration. Ferrous chloride freshly prepared as a 1 M solution from iron wire under anaerobic conditions at biweekly intervals proved to be satisfactory as a mordant source. Of several other mordant dyes tested: gallein, brazilin and chromoxane pure blue B were the best, but none was equal to good hematoxylin.
LES and RANS Simulation of Turbulent Airflow and Tracer Gas Injection in a Generic Aircraft Cabin Model

This study is a continuation of a previous research in numerical simulation of a turbulent airflow in a generic aircraft cabin model. Specifically, the primary objective of this project is to use Computational Fluid Dynamics (CFD) to simulate transport of a tracer gas injected into the generic aircraft cabin. The research work reported herein is composed of three parts. First, both Large Eddy Simulation (LES) and Reynolds averaged Navier Stokes (RANS) methods are used to simulate airflow from a full-height nozzle and corresponding airflow characteristics within the mockup aircraft cabin. The computational results are validated by comparing them with Particle Image Velocity (PIV) data and published CFD predictions available in the literature. Through these comparisons, the potential for using the CFD methods to predict unsteady as well as time-averaged velocity for a generic aircraft cabin model is examined. Second, airflow characteristics are studied by reducing the inlet nozzle height to one-half of its original size but keeping the total volumetric airflow rate the same as that of the full-height nozzle. Accuracy of the LES approach in predicting airflow in the half-height nozzle is evaluated by comparing prediction results with the PIV measurement data for the mockup cabin. Third, simulation of a tracer gas injection through the injecting tube placed in different locations in the half-height nozzle cabin is investigated. In this part, carbon dioxide (CO2 ) is chosen as the tracer gas. The LES method is used to solve the equations of motion and the unsteady species transport equation for tracer gas concentration. The predictions are compared with the average measurement data for CO2 -concentration in various locations in the cabin.Copyright © 2010 by ASME
The Crystal Structure of Recombinant Human Neutrophil-activating Peptide-2 (M6L) at 1.9-Å Resolution

Neutrophil-activating peptide-2 (NAP-2) is a 70-residue carboxyl-terminal fragment of platelet basic protein, which is found in the α-granules of human platelets. NAP-2, which belongs to the CXC family of chemokines that includes interleukin-8 and platelet factor 4, binds to the interleukin-8 type II receptor and induces a rise in cytosolic calcium, chemotaxis of neutrophils, and exocytosis. Crystals of recombinant NAP-2 in which the single methionine at position 6 was replaced by leucine to facilitate expression belong to space group P1 (unit cell parameters a = 40.8, b = 43.8, and c = 44.7 A and α = 98.4°, β = 120.3°, and γ = 92.8°), with 4 molecules of NAP-2 (Mr = 7600) in the asymmetric unit. The molecular replacement solution calculated with bovine platelet factor 4 as the starting model was refined using rigid body refinement, manual fitting in solvent-leveled electron density maps, simulated annealing, and restrained least squares to an R-factor of 0.188 for 2 σ data between 7.0- and 1.9-A resolution. The final refined crystal structure includes 265 solvent molecules. The overall tertiary structure, which is similar to that of platelet factor 4 and interleukin-8, includes an extended amino-terminal loop, three strands of antiparallel β-sheet arranged in a Greek key fold, and one α-helix at the carboxyl terminus. The Glu-Leu-Arg sequence that is critical for receptor binding is fully defined by electron density and exhibits multiple conformations.
Mechanistic scaling of ecosystem function and dynamics in space and time: Ecosystem Demography model version 2

[1] Insights into how terrestrial ecosystems affect the Earth’s response to changes in climate and rising atmospheric CO2 levels rely heavily on the predictions of terrestrial biosphere models (TBMs). These models contain detailed mechanistic representations of biological processes affecting terrestrial ecosystems; however, their ability to simultaneously predict field-based measurements of terrestrial vegetation dynamics and carbon fluxes has remained largely untested. In this study, we address this issue by developing a constrained implementation of a new structured TBM, the Ecosystem Demography model version 2 (ED2), which explicitly tracks the dynamics of fine-scale ecosystem structure and function. Carbon and water flux measurements from an eddy-flux tower are used in conjunction with forest inventory measurements of tree growth and mortality at Harvard Forest (42.5N, 72.1W) to estimate a number of important but weakly constrained model parameters. Evaluation against a decade of tower flux and forest dynamics measurements shows that the constrained ED2 model yields greatly improved predictions of annual net ecosystem productivity, carbon partitioning, and growth and mortality dynamics of both hardwood and conifer trees. The generality of the model formulation is then evaluated by comparing the model’s predictions against measurements from two other eddy-flux towers and forest inventories of the northeastern United States and Quebec. Despite the markedly different composition throughout this region, the optimized model realistically predicts observed patterns of carbon fluxes and tree growth. These results demonstrate how TBMs parameterized with field-based measurements can provide quantitative insight into the underlying biological processes governing ecosystem composition, structure, and function at larger scales.
Relationships between depression and causal attributions about stressful life events

Cognitive hypotheses about depression derived from the reformulated learned helplessness theory were tested in students' attributional analyses of the causes of their own recent stressful life events. Results supported the hypothesis that depression as measured by the Beck Depression Inventory is associated with certain causal cognitions, and these cognitions were predictive of the intensity, chronicity, and generality of depression 2 months after the initial testing. Cognitions especially related to depression emphasized perceived low control over causes of events and globality of the causes. Attribution theory-based predictions that internal locus of causality and stability would be related to naturally occurring depression were not supported. In addition, there were no sex differences in attributions. While the results support the possible role of cognitive mediators between life events and depressive reactions, they also suggest that depression-related causal analyses may vary across situations and populations.
The Development of Underdevelopment in China: An Afterword

When I submitted my article on "The Development of Underdevelopment in China" to Modern China, I welcomed its use as the basis for a symposium, for I believed the historical and theoretical issues involved to be of such importance and complexity that only the clash of contending perspectives could serve to reveal them fully. For the most part, I believe that the symposium which resulted (Modern China, Vol. 4 No. 3, July 1978) served this purpose well. It seems to me, however, that a number of important ambiguities remain to be cleared up, and it is to pursue this purpose that I would like to present this research note. In "The Development of Underdevelopment in China," I argued that underdevelopment in nineteenthand twentiethcentury China could not simply have meant "not yet developed," because historically, in the Song period (960-1279) for example, China was incontestably the most advanced civilization in the world. Thus, modern underdevelopment could have emerged only as the result of a historical process, the development of underdevelopment. After an admittedly cursory look at some of the important changes between the Song and modern periods,
A dynamic family practice information system for enhanced financial management

The definition of the fiscal unit/family structure has enabled users of the FMIS, or family practices in Colorado and Wyoming, to maintain accurate, ongoing financial information on their patients. In turn, this structure has been a major incentive for maintaining accurate family information, and a distinct benefit to FMIS users. This article has presented the rationale, design, and method of implementation of the fiscal unit structure, with the intention of presenting this concept to others for use in other information systems used in maintaining family-oriented financial and medical information for medical practices.
Epidemiological Correlates of Diabetic Neuropathy: Report From Pittsburgh Epidemiology of Diabetes Complications Study

The natural history of diabetic neuropathy and its risk factors are not well understood, apart from the recognition that prevalence increases with duration and, in many studies, degree of glycemia. The role of potential risk factors was therefore evaluated in a cross-sectional analysis from the baseline examination of the Pittsburgh Epidemiology of Diabetes Complications Study. We present results from the first 400 subjects seen at baseline examination. Neuropathy was determined by a trained internist with a standardized examination and was defined as the presence of at least two of three criteria: abnormal sensory or motor signs, symptoms consistent with neuropathy, and decreased tendon reflexes. The prevalence of neuropathy in this cohort was 34% (18%, 18-29 yr old, 58% greater than or equal to 30 yr old) with no difference by sex. By focusing on subjects greater than or equal to 18 yr old, all significant univariate variables (e.g., duration, glycosylated hemoglobin [HbA1]) were analyzed in 3 multiple logistic regression models: all subjects greater than or equal to 18 yr old and separating the same subjects into two groups based on age (18-29 and greater than or equal to 30 yr). Duration, HbA1, smoking status, and high-density lipoprotein cholesterol were found to be associated with neuropathy in the models for the greater than or equal to 18-yr-old group and the greater than or equal to 30-yr-old group. In the 18- to 29-yr-old group, duration, HbA1, and hypertension status were found to be significantly associated with neuropathy.(ABSTRACT TRUNCATED AT 250 WORDS)
Bisection of equine embryos

Summary Three experiments were designed to evaluate methods of bisecting equine embryos. Viability of demi-embryos was compared to whole embryos in vitro and in vivo. In Experiment 1, Day 6 embryos were bisected either using a standard micromanipulation technique or a manual split of embryos that were adhered to a petri dish. Viability was assessed by culture in vitro. Bisected embryos in both groups increased in size during culture and developed normally. In general, manual bisection was accomplished with less difficulty and time than the micromanipulation method. Eleven additional embryos were bisected manually and both halves transferred surgically into the same recipient (Experiment 2). More pregnancies were obtained from transfer of twin whole embryos (16/22) compared to bisected, demi-embryos (5/22). In Experiment 3, 30 embryos were bisected manually; 15 were encapsulated in agar chip. Both halves were transferred non-surgically to each recipient. Fifteen whole embryos were transferred non-surgically to recipients as controls. The number of vesicles per original embryo was greater for whole embryos than for demi-embryos in agar chips.
Integrated Pump Sharing Modules for Amplifier Systems

A novel optoelectronic pump-sharing module for conversion of high-power multimode lasers to an array of high-power single-mode pumps is proposed. 1x4 modules are designed and fabricated through the sol-gel process.
Reduced complexity acquisition of GPS signals for software embedded applications

Location technologies have many possible applications in wireless communications, surveillance, military equipment, gaming industry, tracking and safety applications to name a few. Wireless operators expect annual revenues to be tens of billions from potential location-based services. The paper focuses on the positioning in cellular wireless networks using Assisted Global Positioning System (A-GPS) technology. State-of-the-art A-GPS receivers are implemented using hardware correlators, as the computational complexity is very high. Positioning receivers are operated in many operational modes depending on the environment, provided assistance, internally available data and measurements. Hardware implementations constrain the performance of A-GPS receivers and as a result their operation is not robust indoors and in urban canyons. Highly reconfigurable receivers can accommodate all the possible modes of operation, and receivers implemented in 'software' are the most promising and flexible ones. To implement A-GPS receivers in 'software', one should drastically reduce the complexity of algorithms. The authors suggest a novel fast Fourier transform (FFT)-based correlator which is good for software implementations. As the focus is on A-GPS, the assistance information from aiding sources reduces the operational range of the correlator and this approach combines gains due to FFT processing and aiding. The complexity is further reduced by employing a search in frequency in FFT domain which is called the shifting replica method. Extensive simulations on several platforms confirm the validity of the proposed method.
Upstream stimulatory factors, USF1 and USF2, bind to the human haem oxygenase-1 proximal promoter in vivo and regulate its transcription.

The human HO-1 (haem oxygenase-1) gene encodes a microsomal enzyme responsible for the breakdown of haem, and is also cytoprotective in response to various cellular insults. HO-1 transcription is induced by a vast array of compounds including, but certainly not limited to, haem and heavy metals such as cadmium. In the present study, we show that upstream stimulatory factors, USF1 and USF2, ubiquitous proteins belonging to the basic helix–loop–helix-leucine zipper family of transcription factors, constitutively bind to the class B E-box located in the proximal promoter of the human HO-1 gene and are responsible for the enhancement of HO-1 gene transcription in human renal proximal tubular epithelial cells. Dimethylsulphate in vivo footprinting studies have identified three protected guanine residues in the E-box of the HO-1 proximal promoter. One of these guanine contact points is essential for USF binding, and when mutated mimics a deletion mutation of the entire E-box palindrome sequence encompassing all three guanine contact points. Binding of USF1 and USF2 to the HO-1 E-box was confirmed by chromatin immunoprecipitation and gel-shift assays. Furthermore, we show that overexpression of USF1 or USF2 enhances the basal expression of HO-1 and that expression of a USF dominant negative form reduces its expression. These results demonstrate for the first time that USF proteins bind to the human HO-1 promoter in vivo and are required for high-level expression of HO-1 by haem and cadmium in human renal epithelial cells.
Use of Albumin as a Predictor of Mortality in Community- Dwelling and Institutionalized Elderly Populations

This study was undertaken to identify variables that could explain the association between low albumin and a 9- to 12-year mortality follow-up among 287 community-dwelling and 176 institutionalized people aged 60 years and over. A wide array of nutrition assessment variables was simultaneously examined in this population to identify confounders of the association. The results show that the risk of mortality for subjects with albumin values of 40 g/liter and over was 0.46 of the risk for those with albumin values below 40 g/liter, after controlling for the confounders age, blood urea nitrogen, triglyceride, history of diseases, and inability to shop owing to medical conditions. Similarly, albumin was also inversely associated with mortality among institutionalized subjects even after controlling for the confounders age, sex, blood urea nitrogen, transferrin, and history of stroke. However, the association was no longer significant among the institutionalized population once the deaths that occurred within the first 3 years after study participation were eliminated. The results indicate that albumin is a long-term predictor of mortality among noninstitutionalized subjects and increased mortality is not only a result of age, history of chronic diseases, medication use, or protein intake. Among institutionalized subjects, albumin appeared to be a short-term predictor of mortality.
Activation of the double‐stranded RNA‐dependent eIF‐2α kinase by cellular RNA from 3T3‐F442A cells

The interferon induced double-stranded-RNA-dependent eIF-2α kinase has an established role in mediating part of interferons anti-viral effects. Several studies have suggested that it may have additional functions in cells not infected with virus. The mechanism of activation of the kinase and the consequences of its activity in uninfected cells remain to be determined. Our previous results have indicated that the activation (phosphorylation) of this kinase may be an important regulatory signal to the arrest of growth of mouse 3T3-F442A fibroblasts and their subsequent differentiation to adipocytes. We have found that the phosphorylation of the kinase occurred in vivo in the absence of viral infection and in vitro without the addition of dsRNA. We demonstrate here that total cytoplasmic RNA from 3T3-F442A cells contains a regulatory RNA(s) capable of activating dsRNA-dependent eIF-2α kinase. Fractionation of the cytoplasmic RNA by oligo(dT)-cellulose indicated that the regulatory RNA eluted with the poly(A)-rich RNA fraction. It bound tightly to the dsRNA-dependent eIF-2α kinase and was immune-precipitated with its antibodies as a complex of regulatory RNA and dsRNA-dependent eIF-2α kinase. The regulatory RNA activity was further purified by phenol extraction of immune precipitates containing this complex. These findings indicated that the regulatory RNA forms a specific complex with the dsRNA-dependent eIF-2α kinase. The activity of the regulatory RNA was sensitive to the dsRNA-specific RNase VI but not to proteinase K, DNase I or ssRNA-specific RNase T1. The activation of the dsRNA-dependent eIF-2α kinase by regulatory RNA was prevented by addition of a high concentration of poly(I) · poly(C). The regulatory RNA was also shown to activate partially purified dsRNA-dependent eIF-2α kinase prepared from rabbit reticulocyte lysates and to inhibit protein synthesis in reticulocyte lysates. Our findings, that cellular RNAs can specifically activate the dsRNA-dependent eIF-2α kinase, are consistent with a physiological role for the dsRNA-dependent eIF-2α kinase and interferon during cell growth and differentiation. The relationship of the regulatory RNA activity to growth and differentiation of 3T3-F442A cells is discussed.
Evaluation of Aedes albopictus tissue culture for use in association with arbovirus isolation.

The susceptibility and sensitivity of Aedes albopictus cell cultures to five different primary and four different low-passage arboviruses were tested. Yellow fever, West Nile, Ilesha, eastern equine encephalitis, and Flanders viruses replicated in A albopictus tissue cultures. Replication was determined by the ability of selected tissue culture fluids to infect suckling mice, and by recovery from tissue culture fluid of progressively increasing amounts of complementfixing (CF) antigen with time. Virus persistence was demonstrated with Nodamura, western equine encephalitis, and Mayaro viruses, but multiplication was not proven; neither persistence nor multiplication was demonstrated with a Kemerovo group virus. When yellow fever and Ilesha viruses were simultaneously inoculated into A albopictus culture, CF antigen for each was consistently detected. In a more detailed comparative study of field specimens, 12 unpassaged strains of yellow fever virus were tested for infectivity in A albopictus tissue culture, Vero cells, and baby mice. Higher titers of virus were detected (0.8–2.3 log ID50 per ml) in Vero cell culture than in A albopictus tissue culture or baby mouse systems. These results suggest the feasibility of using A albopictus cells in association with the primary isolation of arboviruses.