cssi/SciSciGPT-SciSciNet huggingface dataset:
An Examination of the Effects of Feedback Accuracy on Academic Task Acquisition in Analogue Settings

Performance feedback is a common procedure used in a variety of settings to change behavior. Although reviews of the literature have identified a number of characteristics of performance feedback that are predictive of effectiveness, little research has examined the influence of feedback accuracy on behavior. The purpose of the present study was to examine both the short-term and long-term effects of inaccurate feedback on the acquisition of match-to-sample tasks. The first study adopted a translational, human operant paradigm to evaluate the effects under highly controlled conditions. Undergraduate students were presented an arbitrary match-to-sample task on a computer. Feedback accuracy was manipulated in an initial phase followed by a condition where only accurate feedback was provided. The second study extended these findings to a more applied setting and population. The results of both studies demonstrated that exposure to inaccurate feedback generally resulted in the failure to acquire the tasks. Of even greater importance, for most participants a carryover effect was obtained, represented by a delay to acquisition following the improvement of feedback accuracy. The patterns of responding obtained suggested both a reinforcement function and rule-governance. Further inquiries into the function of feedback may facilitate an interpretation of feedback accuracy within the context of procedural fidelity. These findings may have implications for organizational and educational settings where circumstances lead individuals to be exposed to conflicting sources of feedback.
Carbonate rocks in the Mojave Desert as an analogue for Martian carbonates

Carbonate rocks in the Mojave Desert are presented as potential analogues for the carbonates on Mars. Rocks collected from the Little Red Hill site contain iron oxide-bearing coatings that greatly suppress the spectral features due to carbonate of the underlying material and impart a spectral slope. The Mojave Desert was formerly a lush pedogenic soil environment that, over time, transformed into the current arid climate with abundant rock varnish. One niche for microbes in the current desolate environment is inside and underneath the rocks where the microbes profit from solar protection by the iron oxide rock coatings. Carbonates were long predicted to be present on Mars and have recently been detected by instruments on Phoenix and MER and using hyperspectral orbiters such as the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM), the Planetary Fourier Spectrometer (PFS) and the Thermal Emission Spectrometer (TES). We describe here the results of a study of carbonate rocks from the Little Red Hill site of the Mojave Desert that includes X-ray diffraction (XRD), chemistry and visible-infrared reflectance spectroscopy. Coatings on the carbonate rocks greatly reduced the strength of the carbonate bands and caused changes in the shape of some bands. We compare these data with a carbonate outcrop at Nili Fossae, Mars. If microbes once inhabited Mars, similar carbonate rocks with iron oxide coatings could have provided a UV-protected niche there as well. Thus, analysis of carbonate-bearing regions on Mars by future landers would be useful sites to search for biosignatures.
The Parting of Being: On Creation and Sharing in Nancy’s Political Ontology

I expose facets of Nancy’s notion of being singular plural. Nancy’s political ontology overcomes the metaphysical dualism of theory and practice by thinking the space of the between as primary. Nancy’s treatment of the event of creation and the presence of the divine rethink meta-physical notions of origin and God in a way that emphasizes the parting of unity and the plurality of the world. Nancy thinks the everyday and the existential together by affirming the importance of curiosity and wonder in the face of what is. Nancy offers an ontology of space (being-with) that uncovers what it means to be in touch as a way of being.
A critical evaluation of the research methodology employed in the investigation of causative factors of child abuse and neglect

The present assessment of the literature pertaining to the causative factors of child abuse was conducted to determine the scientific merits of the existing literature in this field. The reviewing process entailed randomly assigning those articles that presented original data to four reviewers. Each reviewer then evaluated the studies independently using a standard evaluation procedure that addressed quality of methodological design, clarity of exposition, reliability and validity of data source and appropriateness of analysis. It was discovered that the quality of this scientific inquiry was variable and often not satisfying the basic requirements of sound experimental design. In fact, the majority of the papers reviewed presented no original data to support their positions. Those studies incorporating empirical evidence were frequently plagued with methodological and statistical problems. The specific problems discussed were the following: inappropriate comparison group, lack of a priori predictions, insufficient documentation pertaining to the reliability and validity of data sources, lack of adequate demographic descriptors to provide a context and enable future analyses to be performed, omission of informed consent, and illogically derived conclusions. Concrete recommendations were then addressed to each area.
Effect of the Wingate test on mechanomyography and electromyography.

Rana, S.R. Effect of the Wingate test on mechanomyography and electromyography. J. Strength Cond. Res. 20(2): 292-297. 2006.-The purpose of this investigation was to examine mechanomyographic (MMG) and electromyographic (EMG) amplitude responses of the superficial quadriceps femoris muscles during the Wingate Anaerobic Test (WAnT). Ten healthy adults (age 21 ± 1.2 years) volunteered to perform the WAnT on a calibrated Monark 894E cycle ergometer while the EMG and MMG signals were recorded. The EMG and MMG amplitude and power output (W) values per 5-second segments of the test were averaged and normalized to the highest value found during the test, respectively. The statistical analysis indicated that EMG amplitude did not change significantly over the 30-second test, but W and MMG amplitude decreased significantly. There is dissociation between EMG and MMG amplitude over the 30-second anaerobic test, providing evidence that MMG amplitude could be used as a monitor of W during such a task. MMG amplitude could potentially be used as a direct monitor of mechanical activity, which could be of benefit to those who train athletes when a direct assessment of mechanical contribution from a given muscle to a fatiguing activity is desired (such as when monitoring an injury), but it must be studied under various conditions, such as the current study, before such applications are made
Discrete Model Analysis of Optimal Columns

Keller has determined in [2] the shape of the strongest hinged-hinged column. This was the stepping stone in the solution of the long standing Lagrange problem of finding the shape of the strongest column in the clamped-free configuration. We consider here the discrete link-spring model of column which is hinged on one side and spring supported on the other side that maximizes the buckling load. It is shown that for certain rigidity of the supporting spring the solution is not unique. For the other range of rigidity the shape of the strongest column is invariant of the spring constant.Copyright © 2008 by ASME
Simulated complex dynamics of glycolysis in the protozoan parasite Trypanosoma brucei

Glycolysis in Trypanosoma brucei was modeled using a reaction transport simulator and tested for possible complex dynamics. The glycolytic model is multi-compartmentalized and accounts for the exchange of metabolites between the glycosomes, cytosol, mitochondrion and the host medium. The model is used to examine the effects of a range of culture medium concentrations of oxygen on the glycolysis of T. brucei. Our results are in good agreement with steady-state experiments. We also find that under aerobic conditions, increasing the activity of glycerol-3-phosphate dehydrogenase induces complex dynamics in the system. We report the presence of three distinct types of these dynamics. Varying the oxygen concentration in the medium can induce the transition between these dynamics.
760. Overcoming Rhesus Macaque Endogenous Restriction Factors during HIV-1 Vector Transduction

Top of pageAbstract The ability to deliver genes into hematopoietic stem cells via HIV-1 derived vectors holds promise to investigate the pathobiology and therapeutic applications for infectious diseases. In vivo HIV-1 infection models are limited. The NOD/SCID-hu mouse has been an excellent model to study thymic function and HIV-1 thymic depletion. However, to better understand HIV-1 pathogenesis in humans, non-human primate models must be used. The rhesus macaque simian immunodeficiency virus (SIV) model recapitulates aspects of the pathology seen in human HIV-1 infection. Our laboratory has designed and previously described a CCR5 intrabody HIV-1 vector that efficiently prevents R5-tropic HIV-1 entry and provides transduced CD4+ T cells with a selective advantage during a dendritic cell-mediated infection. Unfortunately, transduction with a HIV-1 derived vector undergoes a post-entry restriction when introduced into rhesus macaque cells. The target for rhesus macaque endogenous restriction factors lies within the HIV-1 capsid protein, and may be due to rhesus macaque Cyclophilin A (CypA) incorporation and TRIM-5|[alpha]| capsid interactions. To increase transduction efficacy in both non-human primate and human hematopoietic cells we have assessed a naturally occurring HIV-1 capsid motif (V86P/H87Q/I91V/M96I), which evades both CypA- dependence in human cells and TRIM-5|[alpha]|-CypA restriction in owl monkey kidney cells during HIV-1 infection (Chatterji, et al. JBC, 2005). The V86P/H87Q/I91V/M96I capsid mutation within the CypA binding loop also rendered VSV-G pseudotyped HIV-1 vectors independent of CypA incorporation during human and non-human primate cell transduction. Interestingly, HIV-1 vectors with the V86P/H87Q/I91V/M96I capsid mutation were able to efficiently transduce non-human primate Vero and sMAGI cell lines and yielded a 1.4-fold increase in transduction efficiency in primary human CD4+ T cells. However, the V86P/H87Q/I91V/M96I HIV-1 vector did not efficiently transduce primary rhesus macaque CD4+ T cells. We are now in the process of evaluating novel HIV-1 capsid mutations that lie within and around the CypA binding loop in our HIV-1 vector system, such as H87Q and Q50Y/T54Q. Some of these capsid mutations in HIV-1 are required to efficiently infect primary rhesus macaque macrophages. We will present our findings on HIV-1 capsid mutations that allow HIV-1 vector entry into primary rhesus macaque CD4+ T cells.
Qualitative inquiry: a method for validating patient perceptions of palliative care while enrolled on a cancer clinical trial

Palliative care is a vital component of patient-centered care. It has increasingly become central to the management and care of seriously ill patients by integrating physical, psychosocial, and spiritual supportive services. Through qualitative inquiry, this paper examines cancer patients’ perceptions of the process and outcomes of the pain and palliative care consultative services they received while enrolled in a clinical trial. A qualitative analysis of open-ended questions was conducted from a sub-sample of patients (n = 34) with advanced cancers enrolled in a randomized controlled trial exploring the efficacy of a palliative care consult service. Two open-ended questions focused on patient perceptions of continued participation on their primary cancer clinical trials and their perceptions of interdisciplinary communication. Three overarching themes emerged when asked whether receiving pain and palliative care services made them more likely to remain enrolled in their primary cancer clinical trial: patients’ past experiences with care, self-identified personal characteristics and reasons for participation, and the quality of the partnership. Four themes emerged related to interdisciplinary communication including: the importance of developing relationships, facilitating open communication, having quality communication, and uncertainty about communication between the cancer clinical trial and palliative care teams. Our findings suggest the importance of qualitative inquiry methods to explore patient perceptions regarding the efficacy of palliative care services for cancer patients enrolled in a cancer clinical trial. Validation of patient perceptions through qualitative inquiry regarding their pain and palliative care needs can provide insight into areas for future implementation research. NIH Office of Human Subjects Research Protection OHSRP5443 and University of Pennsylvania 813365
Computer-Based Patient Reported Outcomes in Outpatient Palliative Care: Feasibility

the severity of disease and ultimately fatal prognosis the treating team felt that prolonged ventilation was not in his best interests. The parents, however, refused extubation on cultural and religious grounds, but agreed to a nonescalation of life-support technologies with a focus on comfort and quality of life. He was transferred intubated and ventilated to the medical ward where he was cared for by his parents for 3 months. After 8 months of intubation, his parents asked for him to be extubated and allowed to die. III. Conclusion. Although not a first choice, when needed, an endotracheal tube can be kept in place longer than is commonly thought without deterioration of the tube. This case also highlights several ethical issues surrounding decision-making and conflict between parents and the treating team.
Effective Nissen fundoplication length and bougie diameter size in young children undergoing laparoscopic Nissen fundoplication.

Abstract Background/Purpose: Laparoscopic Nissen fundoplication (LNF) is utilized in the management of symptomatic gastroesophageal reflux disease (GERD) in children. An effective length of fundoplication and bougie size has never been established in infants and children requiring LNF for GERD. To determine this effective fundoplication length and appropriate bougie size, we analyzed all patients less than 15 kg undergoing LNF for GERD over a 2-year period. Methods: Data recovered retrospectively included age, weight, gender, need for gastrostomy, length of postoperative hospitalization, operating time, bougie size, and fundoplication length. Results: One hundred patients weighed less than 15 kg (mean, 7.23 kg). Mean operating time was 95 minutes (range, 31 minutes to 159 minutes). Gastrostomies were placed in 32 patients. Postoperative hospitalization averaged 1.8 days for elective LNF. Fundoplication length was measured in each patient and averaged 2.06 cm. Bougie size varied from 22F to 42F, and the size utilized was based on the patient's weight. There were no instances of dysphagia or the need for esophageal dilatation postoperatively. Two patients have been seen for recurrent symptoms. One patient has required a second LNF, and the other has a normal upper gastrointestinal study and pH study. Conclusion: This study of LNF in small children has shown that resolution of GERD symptoms in most patients can be accomplished with an average fundoplication length of approximately 2 cm and a graduated bougie size relative to the patient's weight. J Pediatr Surg 37:1664-1666. Copyright 2002, Elsevier Science (USA). All rights reserved.
A visual syntax-directed editor for the Descartes specification language

The front end of the software life cycle is an important phase in the development of quality software systems. Due to the interactive nature of the requirements specification phase, automated tools assist in capturing user concepts and conveying these concepts to the developers. This paper presents a syntax-directed editor developed for the Descartes software specification language. The editor helps in constructing the specifications by detecting and preventing syntactic and static semantic errors. The editor uses the visual notation of Nassi–Shneiderman charts for the external representation of Descartes specifications. The specifications are edited in their visual form directly within the editor. Use of a syntax-directed editor for the construction of Descartes specifications is expected to reduce specification errors, enhance constructibility, and in turn increase productivity. © 1997 John Wiley & Sons, Ltd.
Sub-Doppler Excited Molecule Energy Transfer' Spectroscopy

A sub-Doppler spectroscopic technique involving the detection of vibrational energy transfer in excited molecules with selected velocity components at a microphone diaphragm is demonstrated. The technique is applied to the investigation of thev 3 R(16) transition in HCN and the results compared with a previously derived theoretical model.
Monitoring land use and cover around parks: A conceptual approach

Many of the habitats and resources which influence ecological functioning within National Parks, and protected areas in general, are located outside of their borders in unprotected areas. Hence, land use and land cover changes in surrounding areas may substantially influence the natural resources within parks. The US National Park Service has recognized these threats and incorporated land use and land cover monitoring into its Inventory and Monitoring Program. The purpose of this paper is to provide a framework based on a conceptual approach for planning and implementing monitoring within this Program. We present a conceptual model, based on ecological theory, which illustrates how land use and land cover change impact park resources, and helps to identify monitoring indicators that will measure relevant attributes of land use and land cover change. We also discuss potential sources of data for quantifying indicators of land use and land cover change over time, including remote sensing data and ancillary spatial datasets. Finally, we describe steps for analyzing monitoring data so that the intensity and direction of changes in land use and land cover over time are quantified, as well as trends in the status of important park resources impacted by these changes. Integration of land use and land cover monitoring data and park resource data will allow for analysis of change from past to present, and can be used to project trends into the future to provide knowledge about potential land use and land cover change scenarios and ecological impacts. We illustrate our monitoring approach with an example from the Inventory and Monitoring Program's Greater Yellowstone Network.
Health system reform. A different approach.

Early in his administration, President Clinton placed health system reform at the top of the nation's domestic policy agenda. Since then proposals from all parts of the political spectrum have proliferated. Many of these proposals are embodied in specific legislation now under consideration by Congress. Unfortunately, none of the proposed plans will finance coverage efficiently and equitably and slow the rate of growth of health care spending while providing the flexibility, freedom of choice, and improvement in quality that is desirable and feasible. In my judgment, a different approach is needed to achieve these objectives. I believe we must develop a national financial plan to cover basic care for all, accelerate the present trend toward integrated health care systems, attack directly the major causes of increased health care spending, and completely change the nation's policy regarding malpractice. The approach outlined herein consists of five interrelated components. A Value-Added Tax Earmarked
Uniqueness of solutions of parabolic semilinear nonlocal-boundary problems

Abstract The purpose of the paper is to give two theorems about the uniqueness of solutions of parabolic semilinear nonlocal-boundary problems. The paper is a continuation of previous papers by Byszewski and the generalization of some results from [ R. Rabczuk, “Introduction to Differential Inequalities,” PWN, Warsaw, 1976 [Polish]; J. Chabrowski, On nonlocal problems for parabolic equations, Nagoya Math. J. 93 (1984), 109–131 ], The theorems obtained in this paper can be applied in the theories of diffusion and heat conduction with better effects than the analogous theorems about parabolic initial-boundary problems and than the analogous theorems about parabolic periodic-boundary problems.
A multicentre evaluation of the effectiveness and safety of high-dose daptomycin for the treatment of infective endocarditis

Objectives Despite significant medical advances, infective endocarditis (IE) remains an infection associated with high morbidity and mortality. The objective was to assess the safety and efficacy of high-dose daptomycin, defined as ≥8 mg/kg/day, in patients with confirmed or suspected staphylococcal and/or enterococcal IE.
PATHOGENIC FACTORS IN VASCULAR LESIONS OF EXPERIMENTAL SERUM SICKNESS

The present studies suggest that polymorphonuclear leukocytes (PMN's) are essential for the development of cardiovascular lesions in serum sickness. In the absence of PMN's, necrotic vascular lesions were never seen and endothelial proliferation in arteries was inhibited. Zones of fibrinoid deposits did not occur. By contrast, at least two-thirds of the control animals exhibited endothelial proliferation, and half had necrosis of arterial walls, usually with fibrinoid deposits. In arterial lesions that involved the intima and media, the internal elastic lamina was disrupted. This was associated with accumulations of PMN's and was prevented when PMN's were depleted. The observations suggested that the elastic lamina acts as a barrier to the outward spread of inflammation in arteries and that it is an important substrate of PMN action. Although glomerulitis and proteinuria developed in PMN-depleted animals, no conclusions could be drawn concerning the pathogenic role of PMN's in renal lesions, since PMN depletion could not be effected before the onset of immune elimination without influencing the immune response itself. Host complement (s1C-globulin) was localized along with the antigen and rabbit gamma globulin in glomeruli and arteries showing lesions. In the glomeruli these deposits formed a granular lining along the area of the basement membrane. In arteries the fluorescent amorphous particles were in the intima and media of inflamed vessels. The immune response to BSA and the incidence and severity of cardiovascular and renal lesions were enhanced by the intravenous administration of pooled rabbit antiserum to BSA given 18 hours before BSA antigen and by injecting endotoxin along with the BSA. These additions to the usual procedure of inducing serum sickness did not appear to change the quality of the disease. In normal rabbits, the peak incidence of cardiovascular lesions was early in immune elimination of antigen, at a time when levels of circulating complexes was maximal. Conversely, the severest renal injury was noted several days later, at the completion of immune elimination.
Effects of Poultry Manure Application on Phosphorus in Soil and Tile Drain Water Under a Corn-Soybean Rotation

Long-term application of manure can lead to phosphorus accumulation in the soil and increase the risk of P delivery to tile drainage waters. A long-term study (1998–2009) was conducted on eight tile-drained field plots, ranging in size from 0.19 to 0.47 ha, to investigate the effects of long-term surface application of poultry manure on soil phosphorus dynamics and PO4-P loss in tile drainage in Iowa under a corn-soybean rotation system. The experimental treatments included two poultry manure treatments, applied on an N basis at target rates of 168 kg N ha−1 (PM) and 336 kg N ha−1 (PM2), each with three replications, and one chemical fertilizer treatment of urea ammonium nitrate (UAN) at a rate of 168 kg N ha−1 with two replications. Actual manure application rates and estimated plant available N (PAN) varied annually. Bray1-P methods were used to analyze deep core soil samples at five depths (0–15, 15–30, 30–60, 60–90, and 90–120 cm), which were collected in the spring and fall on the half of each plot planted to corn. Tile drainage samples were collected from each actively draining plot equipped throughout the spring and fall drainage season each year, and PO4-P concentrations were analyzed. The results of this study indicated PM2 and PM resulted in a statistically significant increase in topsoil P at 0–30 cm, with no significant movement of P to deeper soil depths. Although an increase in topsoil P levels was observed with poultry manure application, average annual tile drainage P concentrations were not statistically different throughout the study with average PO4-P concentrations of 0.019 ppm with PM2 application and 0.011 and 0.012 ppm for PM and UAN, respectively. Poultry manure application at agronomical recommended application rates may be an environmentally sound fertilizer option for tile drained fine-loamy, calcareous soils under a corn-soybean rotation. However, surface runoff was not evaluated in this study, and high P levels in topsoil could contribute to elevated PO4-P runoff losses.
Track and Intensity Forecasting of Hurricanes: Impact of Convection-Permitting Resolution and Global Ensemble Kalman Filter Analysis on 2010 Atlantic Season Forecasts

AbstractTwice-daily 48-h tropical cyclone (TC) forecasts were produced for the fall 2010 Atlantic hurricane season using the Advanced Research core of the Weather Research and Forecasting (WRF-ARW) model on a large 4-km grid covering much of the northern Atlantic. WRF forecasts initialized from operational Global Forecast System (GFS) analyses based on the gridpoint statistical interpolation (GSI) three-dimensional variational data assimilation (3DVAR) system and from experimental global ensemble Kalman filter (EnKF) analyses, and corresponding global GFS forecasts were intercompared. For the track, WRF forecasts show improvement over GFS forecasts using either set of initial conditions (ICs). The EnKF-initialized GFS and WRF are also better than the corresponding GSI-initialized forecasts, but the difference is not always statistically significant. At all lead times, the WRF track errors are comparable to or smaller than the National Hurricane Center (NHC) official track forecast error, with those of the...
Method for Widespread microRNA-155 Inhibition Prolongs Survival in ALS-Model Mice

microRNAs (miRNAs) are dysregulated in a variety of disease states, suggesting that this newly discovered class of gene expression repressors may be viable therapeutic targets. A microarray of miRNA changes in ALS-model superoxide dismutase 1 (SOD1)G93A rodents identified 12 miRNAs as significantly changed. Six miRNAs tested in human ALS tissues were confirmed increased. Specifically, miR-155 was increased 5-fold in mice and 2-fold in human spinal cords. To test miRNA inhibition in the central nervous system (CNS) as a potential novel therapeutic, we developed oligonucleotide-based miRNA inhibitors (anti-miRs) that could inhibit miRNAs throughout the CNS and in the periphery. Anti-miR-155 caused global derepression of targets in peritoneal macrophages and, following intraventricular delivery, demonstrated widespread functional distribution in the brain and spinal cord. After treating SOD1G93A mice with anti-miR-155, we significantly extended survival by 10 days and disease duration by 15 days (38%) while a scrambled control anti-miR did not significantly improve survival or disease duration. Therefore, antisense oligonucleotides may be used to successfully inhibit miRNAs throughout the brain and spinal cord, and miR-155 is a promising new therapeutic target for human ALS.
The National Vegetation Classification Standard applied to the remote sensing classification of two semiarid environments

The National Vegetation Classification Standard (NVCS) was implemented at two US National Park Service (NPS) sites in Texas, the Padre Island National Seashore (PINS) and the Lake Meredith National Recreation Area (LMNRA), to provide information for NPS oil and gas management plans. Because NVCS landcover classifications did not exist for these two areas prior to this study, we created landcover classes, through intensive ground and aerial reconnaissance, that characterized the general landscape features and at the same time complied with NVCS guidelines. The created landcover classes were useful for the resource management and were conducive to classification with optical remote sensing systems, such as the Landsat Thematic Mapper (TM). In the LMNRA, topographic elevation data were added to the TM data to reduce confusion between cliff, high plains, and forest classes. Classification accuracies (kappa statistics) of 89.9% (0.89) and 88.2% (0.87) in PINS and LMNRA, respectively, verified that the two NPS landholdings were adequately mapped with TM data. Improved sensor systems with higher spectral and spatial resolutions will ultimately refine the broad classes defined in this classification; however, the landcover classifications created in this study have already provided valuable information for the management of both NPS lands. Habitat information provided by the classifications has aided in the placement of inventory and monitoring plots, has assisted oil and gas operators by providing information on sensitive habitats, and has allowed park managers to better use resources when fighting wildland fires and in protecting visitors and the infrastructure of NPS lands.
'Not by the chair of my hinny hin hin': some general properties of slips of the tongue in young children.

Young children's slips of the tongue are a rich source of information about developing language processing and storage mechanisms. This paper presents an analysis of 907 slips from 32 children, ages 1;4-6;0, collected in naturalistic settings. It is found that these children make most of the same types and proportions of slips as adults: phonological errors outnumber lexical, which exceed phrasal. In phonological errors, anticipations are most common, followed by perseverations and exchanges; children make more completed anticipations and exchanges than adults, probably due to less mature self-monitoring. Like adults, children make more substitutions than additions or omissions. Children's slips support a theory of speech planning in which propositional, syntactic, intonational, content word, function word and phonological levels have somewhat independent status; however, there is little evidence for a derivational morphology level at this age.
Influence of oxygen on the repair of direct radiation damage to DNA by thiols in model systems

Here the reactions of thiols with DNA primary radical intermediates formed after γ-irradiation of frozen (77 K) anoxic and oxic solutions of DNA/thiol mixtures are investigated. Through analysis of the experimental composite spectra at each annealing temperature, the relative concentrations of individual radicals present are estimated and reaction sequences inferred. In all samples the primary DNA radical anions and cations (DNA*+ and DNA*−) are suggested to be the predominant radicals at low temperatures. In anoxic samples, TH* (5,6-dihydrothym-5-yl radical), RSSR*− and, in glutathione samples, *GSH [γ-glu-NHC(CH2SH)CO-gly] radicals are observed as the temperature is increased. The presence of oxygen efficiently suppresses the formation of RSSR*− and *GSH; instead, in oxic samples, O*−2, DNAOO*, RSOO* and RSO* are observed at higher temperatures. The photolytic conversion of RSOO* to RSO*2 is used to verify the presence of RSOO* in γ-irradiated DNA/thiol systems and confirm that the computer analysis emp...
'Where Have all the Slaves Gone?' Emancipation and Post-Emancipation in Lamu, Kenya

The legal emancipation of slaves in Zanzibar and on the Swahili coast of Kenya was enacted in 1907, but the measure was not enforced on Lamu Island until 1910. The slave-owners of Lamu were already in dire straits from the decline of their plantations on the mainland and from the changes accompanying colonial rule which, by contrast with Mombasa, left Lamu Island as an economic backwater. They were little inclined to co-operate with the provisions of the legislation and were actively abetted in this by some their slaves. Emancipation was therefore a more protracted process than in those parts of the coast where alternative opportunities had opened up for ex-slaves and for landowners. Those who were gradually liberated either emigrated elsewhere or entered into new forms of dependent relationships with the Afro-Arab aristrocracy. Meanwhile, slavery lingered on under the noses of British officials.
Metadata standard and data exchange specifications to describe, model, and integrate complex and diverse high-throughput screening data from the library of integrated network-based cellular signatures (LINCS)

The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available.
Guaranteed convergence in a class of Hopfield networks

A class of symmetric Hopfield networks with nonpositive synapses and zero threshold is analyzed in detail. It is shown that all stationary points have a one-to-one correspondence with the minimal vertex covers of certain undirected graphs, that the sequential Hopfield algorithm as applied to this class of networks converges in at most 2n steps (n being the number of neurons), and that the parallel Hopfield algorithm either converges in one step or enters a two-cycle in one step. The necessary and sufficient condition on the initial iterate for the parallel algorithm to converge in one step are given. A modified parallel algorithm which is guaranteed to converge in (3n/2) steps ((x) being the integer part of x) for an n-neuron network of this particular class is also given. By way of application, it is shown that this class naturally solves the vertex cover problem. Simulations confirm that the solution provided by this method is better than those provided by other known methods. >
Social network analysis of wild chimpanzees provides insights for predicting infectious disease risk

1. Heterogeneity in host association patterns can alter pathogen transmission and strategies for control. Great apes are highly social and endangered animals that have experienced substantial population declines from directly transmitted pathogens; as such, network approaches to quantify contact heterogeneity could be crucially important for predicting infection probability and outbreak size following pathogen introduction, especially owing to challenges in collecting real-time infection data for endangered wildlife. 2. We present here the first study using network analysis to quantify contact heterogeneity in wild apes, with applications for predicting community-wide infectious disease risk. Specifically, within a wild chimpanzee community, we ask how associations between individuals vary over time, and we identify traits of highly connected individuals that might contribute disproportionately to pathogen spread. 3. We used field observations of behavioural encounters in a habituated wild chimpanzee community in Kibale National Park, Uganda to construct monthly party level (i.e. subgroup) and close-contact (i.e. ≤ 5 m) association networks over a 9-month period. 4. Network analysis revealed that networks were highly dynamic over time. In particular, oestrous events significantly increased pairwise party associations, suggesting that community-wide disease outbreaks should be more likely to occur when many females are in oestrus. 5. Bayesian models and permutation tests identified traits of chimpanzees that were highly connected within the network. Individuals with large families (i.e. mothers and their juveniles) that range in the core of the community territory and to a lesser extent high-ranking males were central to association networks, and thus represent the most important individuals to target for disease intervention strategies. 6. Overall, we show striking temporal variation in network structure and traits that predict association patterns in a wild chimpanzee community. These empirically-derived networks can inform dynamic models of pathogen transmission and have practical applications for infectious disease management of endangered wildlife species.
Conformational changes of macromolecules in transient elongational flow

Calculations are reported which describe the elongation of flexible macromolecules in a pulse-like elongational How. The polymer molecules are modeled as FENE (finitely extendable nonlinear elastic) dumbbells. The results are in qualitative agreement with experimental results on dilute solutions of polyisobutylene in decalin (10) which form a two parameter family of extension versus position curves. The two parameters-in the FENE model that are used to fit the data are λH, a time constant and b, which is related to the maximum extension that can be achieved by the molecules. Quantitative comparisons are frustrated by difficulty in estimating the model parameter, b. It is suggested, based on this work, that internal self entanglements in the polymers must be considered in the determination of b.
A Bayesian network approach to root cause diagnosis of process variations

This paper addresses the challenges inherent in root cause diagnosis of process variations in a production machining environment. We develop and present a process monitoring and diagnosis approach based on a Bayesian belief network for incorporating multiple process metrics from multiple sensor sources in sequential machining operations to identify the root cause of process variations and provide a probabilistic confidence level of the diagnosis. The vast majority of previous work in machining process monitoring has focused on single-operation tool wear monitoring. The focus of the present work is to develop a methodology for diagnosing the root cause of process variations that are often confounded in process monitoring systems, namely workpiece hardness, stock size, and tool wear variations. To achieve this goal, multiple sensor metrics have been identified with statistical correlations to the process faults of interest. Data from multiple sensors on sequential machining operations are then combined through a causal belief network framework to provide a probabilistic diagnosis of the root cause of the process variation.
Structural Basis for Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease

Maturation of human immunodeficiency virus (HIV) depends on the processing of Gag and Pol polyproteins by the viral protease, making this enzyme a prime target for anti-HIV therapy. Among the protease substrates, the nucleocapsid-p1 (NC-p1) sequence is the least homologous, and its cleavage is the rate-determining step in viral maturation. In the other substrates of HIV-1 protease, P1 is usually either a hydrophobic or an aromatic residue, and P2 is usually a branched residue. NC-p1, however, contains Asn at P1 and Ala at P2. In response to the V82A drug-resistant protease mutation, the P2 alanine of NC-p1 mutates to valine (AP2V). To provide a structural rationale for HIV-1 protease binding to the NC-p1 cleavage site, we solved the crystal structures of inactive (D25N) WT and V82A HIV-1 proteases in complex with their respective WT and AP2V mutant NC-p1 substrates. Overall, the WT NC-p1 peptide binds HIV-1 protease less optimally than the AP2V mutant, as indicated by the presence of fewer hydrogen bonds and fewer van der Waals contacts. AlaP2 does not fill the P2 pocket completely; PheP1′ makes van der Waals interactions with Val82 that are lost with the V82A protease mutation. This loss is compensated by the AP2V mutation, which reorients the peptide to a conformation more similar to that observed in other substrate-protease complexes. Thus, the mutant substrate not only binds the mutant protease more optimally but also reveals the interdependency between the P1′ and P2 substrate sites. This structural interdependency results from coevolution of the substrate with the viral protease.
MHD channel flow control in 2D: Mixing enhancement by boundary feedback

A nonlinear Lyapunov-based boundary feedback control law is proposed for mixing enhancement in a 2D magnetohydrodynamic (MHD) channel flow, also known as Hartmann flow, which is electrically conducting, incompressible, and subject to an external transverse magnetic field. The MHD model is a combination of the Navier-Stokes PDE and the Magnetic Induction PDE, which is derived from the Maxwell equations. Pressure sensors, magnetic field sensors, and micro-jets embedded into the walls of the flow domain are employed for mixing enhancement feedback. The proposed control law, designed using passivity ideas, is optimal in the sense that it maximizes a measure related to mixing (which incorporates stretching and folding of material elements), while at the same time minimizing the control and sensing efforts. A DNS code is developed, based on a hybrid Fourier pseudospectral-finite difference discretization and the fractional step technique, to numerically assess the controller.
Systematic control of nonlinear optical processes using optimally shaped femtosecond pulses

This article reviews experimental efforts to control multiphoton transitions using shaped femtosecond laser pulses, and it lays out the systematic study being followed by us for elucidating the effect of phase on nonlinear optical laser–molecule interactions. Starting with a brief review of nonlinear optics and how nonlinear optical processes depend on the electric field inducing them, a number of conclusions can be drawn directly from analytical solutions of the equations. From a Taylor expansion of the phase in the frequency domain, we learn that nonlinear optical processes are affected only by the second- and higher-order terms. This simple result has significant implications on how pulse-shaping experiments are to be designed. If the phase is allowed to vary arbitrarily as a continuous function, then an infinite redundancy that arises from the addition of a linear phase function across the spectrum with arbitrary offset and slope could prevent us from carrying out a closed-loop optimization experiment. The early results illustrate how the outcome of a nonlinear optical transition depends on the cooperative action of all frequencies in the bandwidth of a laser pulse. Maximum constructive or destructive interference can be achieved by programming the phase using only two phase values, 0 and p. This assertion has been confirmed experimentally, where binary phase shaping (BPS) was shown to outperform other alternative functions, sometimes by at least on order of magnitude, in controlling multiphoton processes. Here we discuss the solution of a number of nonlinear problems that range from narrowing the second harmonic spectrum of a laser pulse to optimizing the competition between two- and three-photon transitions. This Review explores some present and future applications of pulse shaping and coherent control.
Informatics in Radiology: Automated Structured Reporting of Imaging Findings Using the AIM Standard and XML

Quantitative and descriptive imaging data are a vital component of the radiology report and are frequently of paramount importance to the ordering physician. Unfortunately, current methods of recording these data in the report are both inefficient and error prone. In addition, the free-text, unstructured format of a radiology report makes aggregate analysis of data from multiple reports difficult or even impossible without manual intervention. A structured reporting work flow has been developed that allows quantitative data created at an advanced imaging workstation to be seamlessly integrated into the radiology report with minimal radiologist intervention. As an intermediary step between the workstation and the reporting software, quantitative and descriptive data are converted into an extensible markup language (XML) file in a standardized format specified by the Annotation and Image Markup (AIM) project of the National Institutes of Health Cancer Biomedical Informatics Grid. The AIM standard was created to allow image annotation data to be stored in a uniform machine-readable format. These XML files containing imaging data can also be stored on a local database for data mining and analysis. This structured work flow solution has the potential to improve radiologist efficiency, reduce errors, and facilitate storage of quantitative and descriptive imaging data for research.
Asymptotic Geometry of the Mapping Class Group and Teichmuller Space

In this work, we study the asymptotic geometry of the mapping class group and Teichmuller space. We introduce tools for analyzing the geometry of “projection” maps from these spaces to curve complexes of subsurfaces; from this we obtain information concerning the topology of their asymptotic cones. We deduce several applications of this analysis. One of which is that the asymptotic cone of the mapping class group.
Alteration of Enamel Proteins in Hypomaturation Amelogenesis Imperfecta

Amelogenesis imperfecta (AI) is a diverse group of disorders that affects primarily the enamel of teeth through a number of developmental processes. The purpose of this study was to characterize the enamel proteins in normal enamel and in hypomaturation AI enamel. Impacted teeth, which were at similar stages of development, were obtained for analysis from an individual with Al and from normal healthy controls. Evaluation of the amino acid profile and quantity of organic material collected showed that there was an excess of enamel protein material that had an amelogenin-like amino acid profile in mature hypomaturation AI enamel. The AI enamel protein content was 5%, while the control enamel had 0.1% protein (by weight). These findings indicate that the maturation process had been altered in this type of AI, and that maturation did not progress beyond the initial stages of secondary mineralization. Since this disorder is inherited as an autosomal recessive condition, it seems likely that the primary defect ...
Correlation between adherence rates measured by MEMS and self-reported questionnaires: a meta-analysis

Purpose It is vital to understand the associations between the medication event monitoring systems (MEMS) and self-reported questionnaires (SRQs) because both are often used to measure medication adherence and can produce different results. In addition, the economic implication of using alternative measures is important as the cost of electronic monitoring devices is not covered by insurance, while self-reports are the most practical and cost-effective method in the clinical settings. This meta-analysis examined the correlations of two measurements of medication adherence: MEMS and SRQs.