cssi/SciSciGPT-SciSciNet huggingface dataset:
Scarecrow: A Framework for Scrutinizing Machine Text.

Modern neural text generation systems can produce remarkably fluent and grammatical texts. While earlier language models suffered from repetition and syntactic errors, the errors made by contemporary models are often semantic, narrative, or discourse failures. To facilitate research of these complex error types, we introduce a new structured, crowdsourced error annotation schema called Scarecrow. The error categories used in Scarecrow -- such as redundancy, commonsense errors, and incoherence -- were identified by combining expert analysis with several pilot rounds of ontology-free crowd annotation to arrive at a schema which covers the error phenomena found in real machine generated text. We use Scarecrow to collect 13k annotations of 1.3k human and machine generate paragraphs of English language news text, amounting to over 41k spans each labeled with its error category, severity, a natural language explanation, and antecedent span (where relevant). We collect annotations for text generated by state-of-the-art systems with varying known performance levels, from GPT-2 Small through the largest GPT-3. We isolate several factors for detailed analysis, including parameter count, training data, and decoding technique. Our results show both expected and surprising differences across these settings. These findings demonstrate the value of Scarecrow annotations in the assessment of current and future text generation systems. We release our complete annotation toolkit and dataset at this https URL.
Abstract 1254: Preclinical studies with TGN-1062, a selective and reversible small molecule inhibitor of CDK7

Purpose: Cancer causing mutations promote unchecked cell cycle progression and altered gene expression to drive tumor growth. Cyclin-dependent Kinase 7 (CDK7) is a critical player in tumorigenesis not only due to its role in cell cycle regulation through the phosphorylation of other CDKs, but also as part of the TFIIH complex where it stimulates transcription via phosphorylation of RNA Polymerase II. It is also known to be associated with Super Enhancers (SEs). When tumor cells acquire SEs at oncogenic driver genes, such as BCL2, GFI1, and MYC, it can lead to the activation of their expression as well as induce transcriptional reprogramming. When CDK7 is overexpressed, it is associated with poor clinical outcomes (AML, breast, ovarian, pancreatic, SCLC, etc.). Inhibition of CDK7 is a promising strategy for abating uncontrolled expression of these oncogenic genes. We have developed TGN-1062, designed to competitively bind the CDK7 catalytic ATP pocket. TGN-1062 is a potent, selective, and reversible inhibitor of CDK7 with desirable drug-like properties. Here, we have further validated our candidate TGN-1062 as a potent inhibitor of CDK7 with efficacy in multiple murine in vivo models. Methods: In vivo efficacy studies were conducted in nude mice engrafted with A2780, HCT116, or MV4-11 tumor cells and treatment with TGN-1062. Tumors were measured to determine tumor growth inhibition (TGI) and correlating drug accumulation were measured in both tumors and plasma using mass spectrometry. Immunohistochemistry (IHC) was performed on tumors to determine changes in cleaved Caspase, cMYC, Ki67, and RNA Pol II. NanoBRET assay was used to demonstrate inhibition of CDK7 activity in living cells. Changes in MCL-1, MYC, cleaved PARP, and RNA Pol II phosphorylation was demonstrated by Western blotting from TGN-1062 treated A2780 and MV4-11 cellular lysates. Drug combinations with TGN-1062 were performed in multiple cancer cell lines. Results: TGN-1062 inhibits CDK7 in the NanoBRET cellular assay with low nanomolar potency ( Conclusion: TGN-1062 is a novel, selective, and reversible inhibitor of CDK7 and has significant antitumor activity in vivo. TGN-1062 is a potent CDK7 inhibitor with potential for clinical development. Citation Format: Ryan L. Rodriguez del Villar, Trason G. Thode, Alexis Weston, Serina Ng, Raffaella Soldi, Mohan Kaadige, Srinivas Kasibhatla, Vincent Chung, Joseph Chao, Daniel D. Von Hoff, Sunil Sharma. Preclinical studies with TGN-1062, a selective and reversible small molecule inhibitor of CDK7 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1254.
Motion/direction-sensitive thalamic neurons project extensively to the middle layers of primary visual cortex

Abstract The motion/direction-sensitive and location-sensitive neurons are two major functional types in mouse visual thalamus that project to the primary visual cortex (V1). It has been proposed that the motion/direction-sensitive neurons mainly target the superficial layers in V1, in contrast to the location-sensitive neurons which mainly target the middle layers. Here, by imaging calcium activities of motion/direction-sensitive and location-sensitive axons in V1, we find no evidence for these cell-type specific laminar biases at population level. Furthermore, using a novel approach to reconstruct single-axon structures with identified in vivo response types, we show that, at single-axon level, the motion/direction-sensitive axons have middle layer preferences and project more densely to the middle layers than the location-sensitive axons. Overall, our results demonstrate that Motion/direction-sensitive thalamic neurons project extensively to the middle layers of V1, challenging the current view of the thalamocortical organizations in the mouse visual system.
Tasking framework for adaptive speculative parallel mesh generation

Handling the ever-increasing complexity of mesh generation codes along with the intricacies of newer hardware often results in codes that are both difficult to comprehend and maintain. Different facets of codes such as thread management and load balancing are often intertwined, resulting in efficient but highly complex software. In this work, we present a framework which aids in establishing a core principle, deemed separation of concerns, where functionality is separated from performance aspects of various mesh operations. In particular, thread management and scheduling decisions are elevated into a generic and reusable tasking framework. The results indicate that our approach can successfully abstract the load balancing aspects of two case studies, while providing access to a plethora of different execution back-ends. One would expect, this new flexibility to lead to some additional cost. However, for the configurations studied in this work, we observed up to $$13\%$$ speedup for some meshing operations and up to $$5.8\%$$ speedup over the entire application runtime compared to hand-optimized code. Moreover, we show that by using different task creation strategies, the overhead compared to straight-forward task execution models can be improved dramatically by as much as $$1200\%$$ without compromises in portability and functionality.
Analysis of a Prototype Electric Retractor, a Seat Belt Pre-Tensioning Device and Dummy Lateral Motion Prior to Vehicle Rollover

Vehicle motion prior to a rollover can influence an occupant's position in the vehicle. Lateral deceleration prior to a tripped rollover may cause the occupant to move outboard. This outboard motion may have several effects on the occupant such as, repositioning the occupant with relation to the seat and seat restraint, and allowing the occupant's head to travel further into the side curtain deployment zone. To reduce occupant lateral motion, the effectiveness of applying tension to the seatbelt was evaluated. The evaluation consisted of two test conditions simulating vehicle lateral motion prior to a trip using a Deceleration Rollover Sled [1]. The test conditions were designed to ensure a vehicle experiences a period of pure lateral motion before the onset of a lateral trip. A standard seat belt combined with various means of applying tension and activated at different times during the test were evaluated. The conclusions were based on analyzing the dummy lateral motion, belt loads, and dummy head and chest acceleration from these tests.
Materials And Corrosion History With Labarge Madison Production: A 20 Year Story Of Success.

The LaBarge operation produces sour gas from the Madison Formation with a total acid gas content of 70 %; elemental sulfur is produced in most well bores and is expected to increase as the reservoir depletes. The field is situated in the Bridger Teton National Forest, an area of outstanding environmental interest, and has an expected production life of 50 years. Production therefore poses unique challenges in terms of corrosivity, environmental protection and asset preservation. This paper presents design characteristics of the facilities, materials and corrosion requirements and outlines the research work undertaken in support of the design. Of particular interest are the highly reliable corrosion inhibition program and the design features which allowed this high level of reliability.
Transient Simulation and Experimental Verification of Gas-Steam and Liquid-Steam, Shell, and Tube Type Heat Exchangers

The condensing steam heaters dynamically modeled in this work are shell and tube type heat exchangers with the condensing steam on the shell side. Two variations of the model are developed, one for heating a gas stream where the thermal mass of the gas is very small, and one for heating a liquid stream where the thermal mass of the heated fluid is appreciable. Predictions from the gas heater model compare excellently with data collected from transient experiments on two industrial heat exchangers at the General Electric Coal Gasification Process Evaluation Facility. These two heat exchangers differ widely in their design and operating conditions. Consequently, the good agreement that was found between the model predictions and experimental data show the wide applicability of the model.
Market-Aware Agents for a Multiagent World

A computational market is any collection of software agents interacting through a price system. Markets can provide effective allocation of resources for a variety of distributed environments, and economic analysis is a powerful design tool for interaction mechanisms. The spread of computational markets puts a premium on market-aware agents, and presents a case for market awareness on the part of agent developers and AI researchers as well. © 1998 Elsevier Science B.V. All rights reserved.
Fabrication Of Graded Germanium-Doped CH Shells

One of the current capsule designs for achieving ignition on the National Ignition Facility (NIF) is a 2 mm diameter graded Ge-doped CH shell that has a 160 {micro}m thick wall. The Ge doping is not uniform, but rather is in radial steps. This graded Ge-doped design allows rougher surface finish than the original undoped CH design thus has a less stringent new surface standard. We selected quality mandrel mandrels by coating dozens of mandrel batches to {approx}70 {micro}m thickness to amplify sub-micrometer defects on the mandrels and successively removed inferior batches. The Ge-doping layers are made by introducing (CH{sub 3}){sub 4}Ge to the gas stream. The doping concentrations were determined by performing tryout runs and characterized by X-ray fluorescence analyses and quantitative radiograph calculations, with good agreement between the methods being demonstrated. The precise layer thickness and Ge concentrations were determined by a non-destructive quantitative contact radiograph. The as-coated shell has an inner 10 {micro}m undoped CH layer, followed by a 48 {micro}m thick 0.83 at.% Ge-doped CH, 10 {micro}m thick 0.38 at.% Ge-doped CH and then 90 {micro}m of undoped CH. The shell meets nearly all the NIF design thickness specifications and Ge concentrations. The atomic force microscope power spectrum of the shell meets the new NIF standard. The shells has a root-mean-square surface roughness of {approx}24 nm (modes 100-1000). A few surface flaws are isolated domes of 1 {micro}m tall and 20 {micro}m in diameter. Mandrel was successfully removed by pyrolysis at 305 C for 10-20 h. After pyrolysis, the diameter and wall shrink 0.4% and 5.7%, respectively. The shell's inner surface has root-mean-square roughness ranging from 1.1-6.5 nm by WYKO interferometer measurement.
Capital Allocation and Timely Accounting Recognition of Economic Losses

Abstract: This paper explores direct relations between corporate investment behavior and the timeliness of accounting recognition of economic losses (TLR) reflected in a country's accounting regime. We explicitly investigate the extent to which TLR influences investment decisions of firm managers. Given the asymmetric emphasis on negative outcomes inherent in TLR, we hypothesize that TLR will most strongly influence investment behavior when managers face deteriorating investment environments. We conjecture that TLR will have an asymmetric impact on investment behavior whereby TLR impacts firms’ investment decisions in the face of declining investment opportunities, but not in the face of increasing in investment opportunities. Using firm-level investment decisions spanning twenty five countries, we find that investment responses to declining opportunities increases with TLR, while we find no evidence that TLR influences the sensitivity of investment to increasing investment opportunities. Our results are robust to alternative estimates of TLR, alternative estimates of investment responses to changing investment opportunities, and to controls for important country-level, industry-level, and firm-level variables that may impact firms’ investment decisions.
Associations between genetic variants in folate and drug metabolizing pathways and relapse risk in pediatric acute lymphoid leukemia on CCG-1952

Genetic variation in drug detoxification pathways may influence outcomes in pediatric acute lymphoblastic leukemia (ALL). We evaluated relapse risk and 24 variants in 17 genes in 714 patients in CCG-1961. Three TPMT and 1 MTR variant were associated with increased risks of relapse (rs4712327, OR 3.3, 95%CI 1.2-8.6; rs2842947, OR 2.7, 95%CI 1.1-6.8; rs2842935, OR 2.5, 95%CI 1.1-5.0; rs10925235, OR 4.9, 95%CI 1.1-25.1). One variant in SLC19A1 showed a protective effect (rs4819128, OR 0.5, 95%CI 0.3-0.9). Our study provides data that relapse risk in pediatric ALL is associated with germline variations in TPMT, MTR and SLC19A1.
Katharine Bement Davis (1860-1935)

Abstract Katharine Bement Davis is a significant figure in American criminology, homosexuality studies, penology, and several social movements, including women's suffrage, African Americans' civil rights, and the social settlement. Although Davis was a widely recognized criminologist for almost three decades, her life and career are acknowledged rarely in the annals of the profession. To address this serious omission in the history of criminology, I introduce her biography, analyze her theory and practice, and locate her in a historical context of powerful women who changed American life and politics.
Effect of exercise on mRNA expression of select adrenal medullary catecholamine biosynthetic enzymes

The effect of submaximal endurance training (SET) on sympathoadrenal activity is not clear. We tested the hypothesis that SET (90 min/day, 5 days/wk, for 12 wk) elevates mRNA expression of catechol...
X-ray guided three-dimensional diffuse optical tomography: in vivo study of osteoarthritis in the finger joints

Osteoarthritis (OA), characterized by the damage of the articular cartilage, is the most common joint problem worldwide. In the effort of developing new clinical tools with the potential to alter the natural history of OA, near-infrared diffuse optical tomography (DOT) has received much attention due to its unique advantages. For optical imaging in highly heterogeneous media such as the finger joints, prior information could improve the quality of optical imaging. We report a hybrid imaging system for early detection of OA in the finger joints by imposing the geometry information obtained by X-ray on three-dimensional near-infrared DOT. X-ray tomosynthesis was employed to recover the three-dimensional structure of the two bones based on 16 X-ray projections generated with a mini C-arm system at different directions within a range of 180 degrees. The interface was carefully designed to guarantee an accurate co-registration of the optical and x-ray modalities. The prior structural information of bones was incorporated into our multi-modality imaging reconstruction algorithm to enhance the recovery of the optical properties of joint tissues. Several healthy and OA finger joints were examined. The initial clinical results showed that this hybrid imaging system had the ability to provide much enhanced image resolution and contrast than DOT alone for OA detection.
Preoperative thrombolysis and venoplasty affords no benefit in patency following first rib resection and scalenectomy for subacute and chronic subclavian vein thrombosis

Background Axillosubclavian vein thrombosis, also known as Paget-Schroetter syndrome, is a rare presentation of thoracic outlet syndrome (TOS) representing approximately 5% of all cases. Conventional management consists of routine anticoagulation, operative decompression via first rib resection and scalenectomy (FRRS), and, recently, thrombolysis. The purpose of our study was to retrospectively review our experience with this condition and compare the effectiveness of preoperative endovascular intervention with thrombolysis and venoplasty to anticoagulation alone in those undergoing FRRS to preserve subclavian vein patency. Methods A retrospective review was conducted for all venous TOS patients from July 2003 to May 2009 from a prospectively maintained database. Preoperative clinic notes were reviewed to allow stratification into two groups. One group consisted of patients undergoing preoperative endovascular intervention with thrombolysis and venoplasty, while the other group consisted of patients managed medically with anticoagulation alone prior to FRSS. Operative notes, postoperative venograms, and postoperative duplex imaging results were reviewed for presence of recanalization, chronic nonocclusive thrombus, or continued occlusion. Results One hundred three patients had 110 FRRS for subclavian vein thrombosis (53 men, 50 women), seven of which had contralateral FRRS for thrombosis. The cohort averaged 31 years of age (range, 16-54 years) with an overall, mean follow-up time of 16 months (range, 1-52 months). Of the 110 veins evaluated, 45 underwent endovascular intervention (thombolysis, with or without venoplasty) prior to FRRS, and at 1 year, 41 (91%) were patent with improvement of symptoms. In the 65 veins on anticoagulation alone, 59 (91%) ultimately were patent, with symptomatic improvement in all. Overall, 91% (100/110) of subclavian veins were patent in patients completing follow-up, were asymptomatic, and back to their previous active lifestyle. Conclusions Preoperative endovascular intervention offered no benefit over simple anticoagulation prior to FRRS, since the use of thrombolysis prior to FRRS, regardless of need for postoperative venoplasty, had little impact on overall rates of patency. The optimal treatment algorithm may merely be routine anticoagulation for all effort thrombosis patients prior to FRRS followed by venography with venoplasty if needed. The role of thrombolysis for Paget-Schroetter syndrome should be further investigated in randomized trials.
Noise Considerations for PET Quantification Using Maximum and Peak Standardized Uptake Value

In tumor response monitoring studies with 18F-FDG PET, maximum standardized uptake value (SUVmax) is commonly applied as a quantitative metric. Although it has several advantages due to its simplicity of determination, concerns about the influence of image noise on single-pixel SUVmax persist. In this study, we measured aspects of bias and reproducibility associated with SUVmax and the closely related peak SUV (SUVpeak) using real patient data to provide a realistic noise context. Methods: List-mode 3-dimensional PET data were acquired for 15 min over a single bed position in twenty 18F-FDG oncology patients. For each patient, data were sorted so as to form 2 sets of images: respiration-gated images such that each image had statistical quality comparable to a 3 min/bed position scan, and 5 statistically independent (ungated) images of different durations (1, 2, 3, 4, and 5 min). Tumor SUVmax and SUVpeak (12-mm-diameter spheric region of interest positioned so as to maximize the enclosed average) were analyzed in terms of reproducibility and bias. The component of reproducibility due to statistical noise (independent of physiologic and other variables) was measured using paired SUVs from 2 comparable respiration-gated images. Bias was measured as a function of scan duration. Results: Replicate tumor SUV measurements had a within-patient SD of 5.6% ± 0.9% for SUVmax and 2.5% ± 0.4% for SUVpeak. SUVmax had average positive biases of 30%, 18%, 12%, 4%, and 5% for the 1-, 2-, 3-, 4-, and 5-min images, respectively. SUVpeak was also biased but to a lesser extent: 11%, 8%, 5%, 1%, and 4% for the 1-, 2-, 3-, 4-, and 5-min images, respectively. Conclusion: The advantages of SUVmax are best exploited when PET images have a high statistical quality. For images with noise properties typically associated with clinical whole-body studies, SUVpeak provides a slightly more robust alternative for assessing the most metabolically active region of tumor.
Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models

High-throughput techniques for measuring protein interactions have enabled the systematic study of complex protein networks. Comparing the networks of different organisms and identifying their common substructures can lead to a better understanding of the regulatory mechanisms underlying various cellular functions. To facilitate such comparisons, we present an efficient framework based on hidden Markov models (HMMs) that can be used for finding homologous pathways in a network of interest. Given a query path, our method identifies the top k matching paths in the network, which may contain any number of consecutive insertions and deletions. We demonstrate that our method is able to identify biologically significant pathways in protein interaction networks obtained from the DIP database, and the retrieved paths are closer to the curated pathways in the KEGG database when compared to the results from previous approaches. Unlike most existing algorithms that suffer from exponential time complexity, our algorithm has a polynomial complexity that grows linearly with the query size. This enables the search for very long paths with more than 10 proteins within a few minutes on a desktop computer. A software program implementing the algorithm is available upon request from the authors.
Synthesis of the mitomycin and FR900482 ring systems via dimethyldioxirane oxidation.

Dimethyldioxirane oxidizes a 2,3-dihydo-1H-pyrrolo[1,2-a]indole unsubstituted at the C-9 position stereoselectively to form a hydroxy ketone with all the basic elements of the mitomycin ring system. On the other hand, a 2,3-dihydo-1H-pyrrolo[1,2-a]indole derivative substituted with an alkyl group at C-9 undergoes an oxidative ring expansion in the presence of dimethyldioxirane to give an FR900482 analogue.
Derivation of strong and weak forces from magnetic interactions in quantum electrodynamics (QED)

The principles of magnetic interactions between stable particles are outlined and a simple theory of matter is discussed based on absolutely stable particles proton, electron and neutrino as constituents. Experimental tests are proposed.
The MDL principle, universal coding, and modeling

In this talk we establish an equivalence between the MDL principle and a maximum unconditional likelihood principle, which thereby links statistical modeling in an inextricable manner with universal coding. Generalizing the Shannon information, defined for a single distribution, we define the Stochastic Complexity of a string of data, relative to a parametric family of distributions, to be the greatest lower bound for the number of binary digits with which the observed data can be encoded. This bound also sets the greatest lower bound for the prediction errors that result when the data are predicted. A recently derived approximation to stochastic complexity for regression problems has been extended to a new model selection criterion for the ARMA models.
The clinical significance of caspase regulation in acute leukemia.

Disruptions of pathways of programmed cell death, or apoptosis, are increasingly found in malignant cells of both solid and hematologic neoplasms. Caspases belong to a family of cysteine proteases and have emerged as central regulators of the apoptotic cascade. Despite many and diverse signals that can trigger apoptosis, the execution of apoptosis appears to be uniformly mediated through activation of caspase enzymes. Inapproriate expression of cas-pases or malfunctions in their regulation through other pathways may also be an important step in the pathogenesis of acute leukemias. Recent studies have shown that overexpression of the inactive forms of caspases CPP32 (caspase 3) and ICH-1 (caspase 2) is frequently observed in the blasts of patients with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Many other enzymes involved in apoptosis are expressed at high levels in patients with acute leukemia. Whether this signals the capacity of leukemic cells to rapid induction of apoptosis wi...
A Two-Hybrid Assay to Study Protein Interactions within the Secretory Pathway

Interactions of transcriptional activators are difficult to study using transcription-based two-hybrid assays due to potent activation resulting in false positives. Here we report the development of the Golgi two-hybrid (G2H), a method that interrogates protein interactions within the Golgi, where transcriptional activators can be assayed with negligible background. The G2H relies on cell surface glycosylation to report extracellularly on protein-protein interactions occurring within the secretory pathway. In the G2H, protein pairs are fused to modular domains of the reporter glycosyltransferase, Och1p, and proper cell wall formation due to Och1p activity is observed only when a pair of proteins interacts. Cells containing interacting protein pairs are identified by selectable phenotypes associated with Och1p activity and proper cell wall formation: cells that have interacting proteins grow under selective conditions and display weak wheat germ agglutinin (WGA) binding by flow cytometry, whereas cells that lack interacting proteins display stunted growth and strong WGA binding. Using this assay, we detected the interaction between transcription factor MyoD and its binding partner Id2. Interfering mutations along the MyoD:Id2 interaction interface ablated signal in the G2H assay. Furthermore, we used the G2H to detect interactions of the activation domain of Gal4p with a variety of binding partners. Finally, selective conditions were used to enrich for cells encoding interacting partners. The G2H detects protein-protein interactions that cannot be identified via traditional two-hybrid methods and should be broadly useful for probing previously inaccessible subsets of the interactome, including transcriptional activators and proteins that traffic through the secretory pathway.
A Comparison of Majority-race Children With and Without a Minority-race Friend

Majority-race (black or white)1 elementary school children with and without a minority friend (black or white) in their classroom were compared on measures of social, behavioral, and affective characteristics. Analyses focused on 260 4th through 6th grade students who were racial majorities in their classrooms and had at least one reciprocated friendship in the classroom-based peer group. Overall, the results were consistent with the scenario that majority children with minority friends are high status, prosocial, and socially satisfied members of the peer group, compared to majority children without a cross-race friendship, although race and gender differences were observed. In contrast, class-level characteristics (e.g. class size, the proportion of participating children in each classroom of the majority race, and the number of minority-race children in the classroom) were not predictive of whether a majority child had a cross-race friendship or not. Implications for the current status of black– white relations among our youth were discussed.
Modulation of the low-calcium response in Yersinia pestis via plasmid-plasmid interaction.

Virulent cells of Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica are known to exhibit a low-calcium response in vitro characterized by restriction of growth and induction of V antigen at 37 °C in Ca2+-deficient media (Lcr+). A shared Lcr plasmid mediates these properties and encodes yersiniae outer membrane peptides (Yops) that are expressed in Lcr+Y. pseudotuberculosis and Y. enterocolitica but not Y. pestis. We present direct evidence here verifying that synthesis of major Yops in the former two species is, like V, repressed by Ca2+ and that these structures are located primarily in the outer membrane. We also verified that rabbits infected with live Lcr+Y. pestis can raise antibodies against V and Yops. Similar antisera, however, were recovered after immunization with sterile extracts of Ca2+-starved Lcr+ cells of Y. pestis. Results of immunoblots obtained with these antisera showed that restricted Y. pestis produced Yops of about 46 kDa (YopB) and 44 kDa (YopC) after shiftup by addition of Ca2+ at 37 °C or reduction of temperature to 26 °C. It is established that virulent cells of Y. pestis also possess a unique plasmid known to mediate pesticinogeny (Pst+). Restricted Lcr+, Pst−Y. pestis expressed YopB and YopC plus additional 76 kDa (YopF), 48 kDa (YopH), 36 kDa (YopD), 32.5 kDa (YopJ), and 27 kDa (YopE) outer membrane structures at concentrations comparable to those in Ca2+-starved Y. pseudotuberculosis and Y. enterocolitica. These findings indicate that carriage of the Pst plasmid prevents expression of the Lcr plasmid-mediated Yops in wild type Y. pestis.
Time interval photoelectron statistics of non-gaussian scattered light

Abstract Time interval distributions are evaluated for coherent light scattered by a small collection of independent, but polydispensive, particles. Two situations are considered: when the number of scatterers within the scattering volume, N , is fixed, and when N is allowed to fluctuate randomly with a Poisson distribution.
Convergence analysis of Davidchack and Lai's algorithm for finding periodic orbits

Abstract We rigorously study a recent algorithm due to Davidchack and Lai (DL) [Davidchack RL, Lai Y-C. Phys Rev E 1999;60(5):6172–5] for efficiently locating complete sets of hyperbolic periodic orbits for chaotic maps. We give theorems concerning sufficient conditions on convergence and also describing variable sized basins of attraction of initial seeds, thus pointing out a particularly attractive feature of the DL-algorithm. We also point out the true role of involutary matrices which is different from that implied by Schmelcher and Diakonos [Schmelcher P, Diakonos FK. Phys Rev E 1998;57(3):2739–46] and propagated by Davidchack and Lai.
Molecular Dynamics Simulations of Flexible Polymer Chains Wrapping Single-Walled Carbon Nanotubes

The goal of this study is to explore the interface between single-walled carbon nanotubes (SWCNTs) and polymer chains with flexible backbones in vacuo via molecular dynamics (MD) simulations. These...
Studies in Synthetic Validity. I. An exploratory investigation of clerical jobs

Summary This research has undertaken the task of attempting to establish test standards when accepted validation procedures are inapplicable. An elemental approach to job analysis has been used, test requirements for the elements have been established, and a procedure for their use is proposed.
Laser-Induced Photo-Cross-Linking of Cisplatin-Modified DNA to HMG-Domain Proteins †

Laser-induced photo-cross-linking was investigated for DNA, modified with cisplatin at specific sites, bound to structure-specific recognition domains of proteins in the high-mobility group (HMG) class. The efficiency of photo-cross-linking depends on the wavelength and power of the laser, the nature of the protein domain, and the oligodeoxyribonucleotide sequences flanking the platinated site. Introduction of 5-iodouridine at thymine sites of the oligodeoxyribonucleotide as an additional photoreactive group did not increase the photo-cross-linking yield. Formation of platinum-mediated DNA-DNA interstrand cross-linking observed previously upon irradiation with 302 nm light [Kane, S. A., and Lippard, S. J. (1996) Biochemistry 35, 2180-2188] was significantly reduced with laser irradiation. HMG1 domain B is superior to domain A for platinum-mediated photo-cross-linking, a result attributed to the different positioning of the proteins with respect to the platinum adduct and the greater ability of domain B to access photolabilized platinum in the major groove. Studies with proteins containing specifically mutated amino acids, and with DNA probes in which the sequences flanking the platinum cross-link site were varied, suggest that the most effective photo-cross-linking occurs for protein domains bound symmetrically and flexibly to cisplatin-modified DNA. The thermodynamic equilibrium between the protein-platinated DNA complex and its components, revealed in gel electrophoretic mobility shift assays (EMSAs), is significantly shifted to the right upon irreversible photo-cross-linking. Thus, only upon photo-cross-linking can the interaction of cisplatin-DNA 1,3-intrastrand d(GpTpG) or interstrand cross-links with HMG1 domain B protein be detected. Photo-cross-linking is thus an effective tool for investigating the interaction of cisplatin-modified DNA with damage-recognition proteins under heterogeneous conditions such those in cell extracts or living cells.
The Effects of Thrombocytopenia on Vessel Stasis and Macromolecular Leakage after Photodynamic Therapy Using Photofrin

Several studies have reported thrombus formation and/or the release of specific vasoactive eicosanoids, suggesting that platelet activation or damage after photodynamic therapy (PDT) may contribute to blood flow stasis. The role of circulating platelets on blood flow stasis and vascular leakage of macromolecules during and after PDT was assessed in an intravital animal model. Sprague-Dawley rats bearing chondrosarcoma on the right hind limb were injected intravenously (i.v.) with 25 mg/kg Photofrin 24 h before light treatment of 135 J/cm2 at 630 nm. Thrombocytopenia was induced in animals by administration of 3.75 mg/kg of rabbit anti-rat platelet antibody i.v. 30 min before the initiation of the light treatment. This regimen reduced circulating platelet levels from 300,000/mm3 to 20,000/mm3. Reductions in the luminal diameter of the microvasculature in normal muscle and tumor were observed in control animals given Photofrin and light. Venule leakage of macromolecules was noted shortly after the start of light treatment and continued throughout the period of observation. Animals made thrombocytopenic showed none of these changes after PDT in either normal tissues or tumor. The lack of vessel response correlated with the absence of thromboxane release in blood during PDT. These data suggest that platelets and eicosanoid release are necessary for vessel constriction and blood flow stasis after PDT using Photofrin.
An Acidic Ring in the Palm Domain of ASIC1a Facilitates Pore opening

Acid-sensing ion channels (ASICs) are neuronal cation selective proton-gated ion channels that contribute to nociception, mechanosensation, synaptic plasticity, learning and memory, and fear conditioning. ASIC subunits have two transmembrane helices, intracellular N- and C- termini, and a large extracellular region organized in discrete domains named the thumb, finger, palm, beta-ball and knuckle. The palm domain is directly connected to the pore-forming transmembrane helices. We combined site-directed mutagenesis and electrophysiology to examine the contribution of residues Glu79 and Glu416 to ASIC1a proton-gating and desensitization. These acidic residues are located in the core of the palm domain forming a ring-like structure. Individual substitution at these positions to Cys, Lys or Gln shifted the apparent proton affinity of ASIC1a approximately one pH unit toward more acidic values. A similar shift in apparent proton affinity was observed in channels bearing substitutions at both positions, indicating that Glu79 and Glu416 cooperatively contribute to proton-gating. E79C and E416C mutants were modified by MTSET in the closed, but not in the desensitized state. MTSET-modification of E79C increased the magnitude of the response to protons by approximately six-fold and slowed desensitization by ten-fold, while MTSET-modification of E416C only reduced the response to protons nearly 50 percent. Ala mutagenesis at neighboring positions of Glu79 indicates that the covalently modified side chain of Cys at position 79 became closer to residues in the thumb and palm domains during channel gating. Our results suggest that Glu79 and Glu416 facilitate pore opening, and that the palm domain experiences a rotation during proton-dependent activation and desensitization.
Teacher Characteristics, Classroom Instruction, and Student Literacy and Language Outcomes in Bilingual Kindergartners.

Abstract This study investigated the relation of teacher characteristics, including ratings of teacher quality, to classroom instructional variables and to bilingual students’ literacy and oral language outcomes at the end of the kindergarten year. Teacher characteristics included observational measures of oral language proficiency, quality, and classroom activity structure, as well as surveys of knowledge of reading‐related skills. Student outcomes in both languages included letter naming, word reading, and phonological awareness and oral language composites. The study involved 141 teachers from a multisite project who were observed up to 3 times at the beginning, middle, and end of the year during their reading/language arts block while teaching English language learners to read in their primary language (Spanish) and/or in English. Teacher quality, but not teacher knowledge, was related positively to student engagement and negatively to time spent in noninstructional activities. Initial student and cla...
Pleiotropic effects of mutations that alter the Sinorhizobium meliloti cytochrome c respiratory system.

Using transposon mutagenesis, mutations have been isolated in several genes (ccdA, cycM, ccmC, ccmB and senC) that play a role in Sinorhizobium meliloti cytochrome metabolism. As in other bacteria, mutations in the S. meliloti ccdA, ccmB and ccmC genes resulted in the absence of all c-type cytochromes. However, the S. meliloti ccdA mutant also lacked cytochrome oxidase aa 3, a defect that does not appear to have been reported for other bacteria. The aa 3-type cytochromes were also missing from a mutant strain with an insertion into the gene encoding the haem-containing subunit (SU)I of aa 3 cytochrome c oxidase, but not in mutants unable to make SUII or SUIII, indicating that CcdA probably plays a role in assembling SUI. The cytochrome-deficient mutants also had other free-living phenotypes, including a significant decrease in growth rate on rich media and increased motility on minimal media. A senC mutant also had significantly decreased motility, but the motility and growth properties of the cycM mutant were unchanged. Unlike similar mutants in Bradyrhizobium japonicum and Rhizobium leguminosarum, an S. meliloti Rm1021 cycM mutant contained cytochrome oxidase aa 3. Cytochrome maturation in strain Rm1021 appeared to be similar to maturation in other rhizobia, but there were some differences in the cytochrome composition of the strain, and respiration chain function and assembly.
Kremlin: like gprof, but for parallelization

This paper overviews Kremlin, a software profiling tool designed to assist the parallelization of serial programs. Kremlin accepts a serial source code, profiles it, and provides a list of regions that should be considered in parallelization. Unlike a typical profiler, Kremlin profiles not only work but also parallelism, which is accomplished via a novel technique called hierarchical critical path analysis. Our evaluation demonstrates that Kremlin is highly effective, resulting in a parallelized program whose performance sometimes outperforms, and is mostly comparable to, manual parallelization. At the same time, Kremlin would require that the user parallelize significantly fewer regions of the program. Finally, a user study suggests Kremlin is effective in improving the productivity of programmers.
Interoperability between DEVS simulators using service oriented architecture and DEVS namespace

DEVS Modeling and Simulation (M&S) has various implementations with various computer languages such as JAVA, C++, and C#. To enhance model reusability with different implementation, we need interoperable systems such as CORBA, HLA, and SOA, and an interoperable mechanism for simulation of heterogeneous DEVS models. As an infrastructure of an interoperable system, SOA is applicable because it provides platform and language independence. In this paper, we apply DEVS/SOA system to embody interoperability between heterogeneous DEVS models. Also, we define common DEVS simulator interface required to simulate DEVS models. To expose simulators' ports information described in XML schema type, the interface has additional description operations. The XML schema type is registered into DEVS namespace which is common place to look up the schema type for ports when heterogeneous DEVS models are integrated through DEVS simulation service integration/execution which we propose. We will illustrate the example of DEVS simulator interoperability with DEVSJAVA and ADEVS models which is implemented with JAVA and C++, respectively
A Bayesian model of plan recognition

Abstract We argue that the problem of plan recognition, inferring an agent's plan from observations, is largely a problem of inference under conditions of uncertainty. We present an approach to the plan recognition problem that is based on Bayesian probability theory. In attempting to solve a plan recognition problem we first retrieve candidate explanations. These explanations (sometimes only the most promising ones) are assembled into a plan recognition Bayesian network , which is a representation of a probability distribution over the set of possible explanations. We perform Bayesian updating to choose the most likely interpretation for the set of observed actions. This approach has been implemented in the Wimp3 system for natural language story understanding.
Nonlinear Rayleigh-Taylor Evolution of a Three-Dimensional Multimode Perturbation

The ablation front Rayleigh-Taylor evolution of a well-characterized 3D multimode surface perturbation was measured on a foil accelerated with an x-ray drive as it progressed into the weakly nonlinear regime. The perturbation pattern was locally random and consisted of modes within the first ten harmonics of a 300 {mu}m square. The pattern evolved into bubbles separated by narrow, interconnecting spike sheets, unambiguously indicating entry into the nonlinear regime. Nonlinear effects occurred when mode amplitudes were relatively small: {eta}{sub n}{lt}{lambda}{sub n}/10 . Experimental results are in quantitative agreement with results of our numerical simulations. {copyright} {ital 1998} {ital The American Physical Society}
Nonthyroidal action of propylthiouracil in euthyroid, hypothyroid and hyperthyroid man.

The nonthyroidal action of 6-n-propylthiouracil (6-PTU) on the metabolism of 131I-labeled thyroxine was investigated in patients with and without thyroid disease. Nineteen studies were performed in 15 hospitalized patients. Thyroidal radioiodine uptake was blocked with potassium perchlorate. 131I-labeled T4 was injected iv and its rate of disappearance was established by repeated determinations of PB131I over 7.5 days on average. PTU was then administered and the studies were continued. Other parameters of thyroid function and metabolic status were also examined serially. The rate of T4 degradation decreased in all 5 patients with active thyrotoxicosis. One patient with euthyroid Graves' disease, studied twice, and 2 hypothyroid patients also had decreases in thyroxine disappearance rates. There were no effects on the other tudy patients. Three control subjects, 2 with thyrotoxicosis, were included to define the specificity of these findings. It is concluded that 6-PTU has a nonthyroidal action in man whi...
Overview of IBM zEnterprise 196 I/O subsystem with focus on new PCI express infrastructure

IBM zEnterprise® 196 introduces a new input/output (I/O) s5ubsystem, including a new I/O drawer that is largely based on a greatly expanded exploitation of industry-standard high-volume PCI Express® (PCIe®) links and switches. The System z® qualities of reliability, availability, and serviceability (RAS) are preserved and enhanced by combining the PCIe RAS capabilities with new System z capabilities. PCIe ports connecting the processor book to the I/O drawer are provided by a new IBM-designed PCIe fan-out card. This fan-out card and its firmware (Licensed Internal Code) support both traditional System z I/O and new I/O paradigms. In the new PCIe I/O drawer, PCIe switches provide fan-out and the well-established System z I/O failover function referred to as redundant I/O interconnect. This is the third generation of the I/O drawer/cage to be used in System z platforms. The PCIe I/O drawer design is extremely compact and provides enhanced I/O port granularity and density. It has been designed to provide performance extendibility for future I/O advancements. Traditional I/O such as FICONA, Fibre Channel Protocol, and Ethernet are provided with enhanced functionality and are packaged in this new PCIe I/O drawer. The advent of this new infrastructure opens up the possibility of attaching native PCIe adapters while allowing them to be controlled by system firmware or by the operating systems directly.
Unsteady Heat Flow between Solids with Partially Contacting Interface

The problem of the transient thermal response of two semi-infinite solids not making perfect contact, is treated analytically by modeling the interface to be a series of equally spaced strips making perfect contact. The remaining area is assumed to perfectly insulated, and a criterion is established for the validity of this assumption, taking radiation into consideration. The mixed interface conditions present a considerable difficulty and a long-time perturbation scheme is therefore used to obtain approximate expressions for the transient temperature distributions, average heat flux and the thermal contact resistance. The method is applicable to a large class of problems with mixed boundary conditions for which the existing techniques give exact solutions only for the steady state.
Nuclear magnetic resonance relaxation of lithium ions in water solutions in porous materials

Abstract Nuclear magnetic resonance (NMR) longitudinal relaxation times ( T 1 's) of lithium nuclei were measured in porous porcelain media containing solutions of lithium chloride in water. For constant salt concentration, 1/ T 1 for 7 Li was found to be proportional to the specific surface area of the media. For constant specific surface area, T 1 ( 7 Li) decreased with increase in concentration within the range studied, while T 1 ( 6 Li) did not vary significantly with concentration. The results are discussed in terms of chemical exchange between bulk phase ions and ions in electrical double layers near the solid surface.