cssi/SciSciGPT-SciSciNet huggingface dataset:
Low-Cost, Large-Scale Production of the Anti-viral Lectin Griffithsin

Griffithsin, a broad-spectrum antiviral lectin, has potential to prevent and treat numerous viruses including HIV, HCV, HSV, SARS-CoV, and SARS-CoV-2. For these indications, the annual demand for Griffithsin could reach billions of doses and affordability is paramount. We report the lab-scale validation of a bioprocess that supports production volumes of >20 tons per year at a cost of goods sold below $3,500/kg. Recombinant expression in engineered E. coli enables Griffithsin titers ∼2.5 g/L. A single rapid precipitation step provides > 90% yield with 2-, 3-, and 4-log reductions in host cell proteins, endotoxin, and nucleic acids, respectively. Two polishing chromatography steps remove residual contaminants leading to pure, active Griffithsin. Compared to a conventional one this process shows lower costs and improved economies of scale. These results support the potential of biologics in very large-scale, cost-sensitive applications such as antivirals, and highlight the importance of bioprocess innovations in enabling these applications.
Biosynthesis and characterization of deuterated chitosan in filamentous fungus and yeast.

Deuterated chitosan was produced from the filamentous fungus Rhizopus oryzae, cultivated with deuterated glucose in H2O medium, without the need for conventional chemical deacetylation. After extraction and purification, the chemical composition and structure were determined by Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and small-angle neutron scattering (SANS). 13C NMR experiments provided additional information about the position of the deuterons in the glucoseamine backbone. The NMR spectra indicated that the deuterium incorporation at the non-exchangeable hydrogen positions of the aminoglucopyranosyl ring in the C3 - C5 positions was at least 60-80 %. However, the C2 position was deuterated at a much lower level (6%). Also, SANS showed that the structure of deuterated chitosan was very similar compared to the non-deuterated counterpart. The most abundant radii of the protiated and deuterated chitosan fibers were 54 A and 60 A, respectively, but there is a broader distribution of fiber radii in the protiated chitosan sample. The highly deuterated, soluble fungal chitosan described here can be used as a model material for studying chitosan-enzyme complexes for future neutron scattering studies. Because the physical behavior of non-deuterated fungal chitosan mimicked that of shrimp shell chitosan, the methods presented here represent a new approach to producing a high quality deuterated non-animal-derived aminopolysaccharide for studying the structure-function association of biocomposite materials in drug delivery, tissue engineering and other bioactive chitosan-based composites.
Teaching the Amistad

This brief essay discusses the use of a slavery case, the Amistad, in teaching a first-year Property Law course. It argues that teaching about slavery in the first year of law school not only emphasizes the significance of race issues in American legal history, but also helps students to connect broader philosophical ideas to the rules at hand. The essay reviews the facts underlying the Amistad case, including reference to the movie about the case and to intellectual property issues that arose in the making of the movie. The essay then traces the deployment in the Amistad case of the standard property themes of possession and title. The essay closes with suggestions about how to connect the discussion of the Amistad to broader themes in property law.
Nonverbal Behavioral Patterns Predict Social Rejection Elicited Aggression

Peer-based aggression following social rejection is a costly and prevalent problem for which existing treatments have had little success. This may be because aggression is a complex process influenced by current states of attention and arousal, which are difficult to measure on a moment to moment basis via self report. It is therefore crucial to identify nonverbal behavioral indices of attention and arousal that predict subsequent aggression. We used Support Vector Machines (SVMs) and eye gaze duration and pupillary response features, measured during positive and negative peer-based social interactions, to predict subsequent aggressive behavior towards those same peers. We found that eye gaze and pupillary reactivity not only predicted aggressive behavior, but performed better than models that included information about the participant’s exposure to harsh parenting or trait aggression. Eye gaze and pupillary reactivity models also performed equally as well as those that included information about peer reputation (e.g. whether the peer was rejecting or accepting). This is the first study to decode nonverbal eye behavior during social interaction to predict social rejection-elicited aggression.
Stochastic Cutting Planes for Data-Driven Optimization

We introduce a stochastic version of the cutting-plane method for a large class of data-driven Mixed-Integer Nonlinear Optimization (MINLO) problems. We show that under very weak assumptions the stochastic algorithm is able to converge to an $\epsilon$-optimal solution with high probability. Numerical experiments on several problems show that stochastic cutting planes is able to deliver a multiple order-of-magnitude speedup compared to the standard cutting-plane method. We further experimentally explore the lower limits of sampling for stochastic cutting planes and show that for many problems, a sampling size of $O(\sqrt[3]{n})$ appears to be sufficient for high quality solutions.
Large Scale GPU Based Simulations of Turbulent Bubbly Flow in a Square Duct

In this paper, we present the results of a numerical study of air-water turbulent bubbly flow in a periodic vertical square duct. The study is conducted using a novel numerical technique which leverages Volume of Fluid method for interface capturing and Sharp Surface Force method for accurate representation of the surface tension forces. A three-dimensional geometry construction method is employed during solution of interface equation which gives absolute conservation of mass and sharp interface between gas and liquid phases. The entire algorithm has been implemented on a data parallel mode on multiple graphics processing units (GPU) taking advantage of the large number of available cores. We have studied the dynamics of a swarm of spherical bubbles co-flowing with the upward turbulent flow and compared results with an unladen turbulent flow. The frictional Reynolds number of the unladen $Re_{\tau}$ is 360, which is sufficient to sustain a turbulent flow. We observe the turbulence-driven secondary flows in the mean flow, with complex instantaneous turbulent vortical structures. The interaction of these secondary flows with the upwards rising bubbles is very complex and leads to significant changes in the instantaneous and time-averaged flow field. We present the results of mean void fraction distribution, mean velocities, longitudinal and transverse turbulence intensities along the wall, corner bisector, and wall bisector. A peak in the void fraction distribution near the walls is observed representing the migration of bubbles to a preferred section of the duct. The effects of turbulence-driven secondary flows and instantaneous large eddies on preferential concentration of the bubbles are discussed. The dispersed bubbles are seen to break the long elongated turbulent structures commonly observed in the unladen turbulent flow.
Characterizing therapist delivery of evidence-based intervention strategies in publicly funded mental health services for children with autism spectrum disorder: Differentiating practice patterns in usual care and AIM HI delivery.

This study identified patterns of therapist delivery of evidence-based intervention strategies with children with autism spectrum disorder within publicly funded mental health services and compared...
Failure to Launch: Stranded Geographies in Italy and the Dizionario di geografia (1797)

Italy’s woes as a maligned and misrepresented nation in the French-language encyclopedias of the eighteenth century inspired Italian encyclopedists to respond. In 1783 the Encyclopedie methodique de Padoue, a revised edition of Panckoucke’s Encyclopedie methodique (1782–1832), was published by a group of Italian encyclopedists in Padua. They corrected the articles about Italian culture, politics, and trade for a European audience, which is why the publishing house, the Seminario di Padova, published in French, aiming to become the purveyors of French-language content for nobles, educated merchants, and the bourgeoisie throughout Europe. However, the lower socio-economic classes needed encyclopedic compilations written in Italian. This chapter studies one such endeavor, the Dizionario di geografia moderna composto per l’Enciclopedica metodica (1797). The Dizionario was presented as an Italian translation of the geographic volumes of the French Encyclopedie methodique. However, upon examination, they differ not only in format, but in content as well. Donato examines the criteria for translating and adapting the geographical content for a more popular Italian audience, analyzing the Dizionario’s legacy in the evolution of encyclopedic print culture in Italy and Europe. The stranded status of the Dizionario, as well as other Italian-language compilations produced in eighteenth-century Italy, is also discussed.
Abstract 415: Effect of aerobic and resistance exercise on the mitochondrial peptide MOTSc in Hispanic and non-Hispanic breast cancer survivors

Background MOTS-c is a mitochondrial derived peptide with exercise mimetic activity that elicits beneficial effects on metabolism and exercise capacity. MOTS-c stimulates glucose utilization, fat-oxidization, reduces inflammation, and protects against experimental models of metabolic disease. Furthermore, MOTS-c effects in humans are affected by race, potentially via ethnic-specific mtDNA variations. Women treated for breast cancer are at an increased risk for risk for cardiovascular disease, diabetes and obesity, due to side effects of cancer-treatments. Exercise mitigates many of these side effects, but the role of MOTS-c regulation by exercise among breast cancer survivors (BCS) of varying ethnicities is unknown. We examined the effects of a 16-week aerobic and resistance exercise intervention on MOTS-c in Hispanic and Non-Hispanic BCS. Methods BCS (Stage I-III) were randomized to exercise (n=50) or standard care (n=50). The intervention promoted supervised, progressive moderate-vigorous aerobic and resistance exercise thrice weekly for 16 weeks. Aerobic exercise was performed at 65-85% maximum heart rate. Resistance exercise was performed in circuit-fashion with 3 sets of 10-15 repetitions including upper and lower body exercises at 65-70% 1-repetition maximum. Fasting blood draws were obtained at baseline and post-intervention (4 months). Body composition was assessed by dual energy x-ray absorptiometry. MOTS-c was analyzed in plasma using an in-house ELISA. Within and between group differences were assessed by paired t-test and repeated measures ANOVA. Pearson9s correlation was computed to assess the association between MOTS-c and metabolic biomarkers. ResultsTwenty-five Hispanic BCS and 24 non-Hispanic BCS (age 53.5±10.4 years) and BMI of 33.5±5.5 kg/m2 were included. Hispanic BCS were younger, of greater adiposity, had higher stage cancers, and had worse metabolic profiles at baseline compared to non-Hispanic BCS (p 0.05). Conclusions A 16-week aerobic and resistance intervention increased MOTS-c levels among non-Hispanic BCS but not Hispanic BCS. Non-Hispanic BCS who experience exercise-induced improvements in MOTS-c may also experience improved insulin sensitivity thereby reducing the risk for comorbid conditions. Despite poorer metabolic profiles, Hispanic BCS may not experience exercise-induced benefits on MOTS-c. Future trials should aim for reducing potential ethnic differences in cardiometabolic health. Citation Format: Christina M. Dieli-Conwright, Nathalie Sami, Mary K. Norris, Junxiang Wan, Hiroshi Kumagai, Pinchas Cohen. Effect of aerobic and resistance exercise on the mitochondrial peptide MOTSc in Hispanic and non-Hispanic breast cancer survivors [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 415.
Spatiotemporality in the Anthropocene: Deleuzoguattarian philosophy, quantum physics, and the German Netflix series dark

Crises alter our perception of time. For medical personnel faced with treating unprecedented numbers of critically ill patients under conditions of personal threat, COVID-19 has most recently accelerated the subjective perception of time. For millions of others, social isolation has decelerated our lives. For all of us, at least in the short term, the future has become more uncertain. Theoretical physicists tell us, however, that under any conditions, the human perception of the flowing of time is only a result of our blurred, limited, macroscopic vision. As the quantum physicist Carlo Rovelli writes, therefore, “[t]o understand ourselves is to reflect on time” (2018: 179). Potentially caused by humans’ failed interactions with wild animals, the contemporary global pandemic, as well as previous outbreaks such as SARS (Severe Acute Respiratory Syndrome-related coronavirus) or the bird flu, has led to calls to reevaluate humans’ relationships with nonhuman life, with the natural environment that includes us, in the epoch that may soon be named for our very failure – the Anthropocene. In an era in which our usual, day-to-day certainties and desire for human control have been upended, not only by the current medical crisis but also by the continuing existential threat to terrestrial life that is climate change, a rethinking of the category of the human, a new conceptualization of the entangled (human and nonhuman) material relationships on our planet and beyond, requires reflecting on time. This article engages in such reflection through a conversation with the philosophical writings of Gilles Deleuze and Felix Guattari. © Koninklijke Brill NV, Leiden, 2021
How NSF S-STEM Scholarship Students Experience College during COVID-19: Lessons to Improve STEM Education

Everett Community College (EvCC) made numerous changes to retain and support students enrolled in science, technology, engineering, and mathematics (STEM) education during the coronavirus pandemic....
Effect of process parameters on tensile properties of SS 316 prepared by directional energy deposition

Abstract Directed energy deposition (DED) recently have become the most used and popular metal additive manufacturing (AM) process and has extensive applications in repair, overhauling and rapid prototyping. Most of the AM processes are likely to have pre-programmed and fixed optimized process parameters for materials whereas DED machines comes with flexibility. The process parameters, such as laser power, scanning speed, energy density and layer height, play a great deal in controlling and affecting the properties of DED fabricated parts. Therefore, it is required to identify the beneficial process parameters and their effects on the print quality for a particular output and material in DED process. In this study, the effects of the process parameters on the tensile behaviours of the 316 stainless steel parts fabricated by DED process is exhibited using a machine learning algorithm called XGBoost based on F score.
Food Acquisition and Daily Life for U.S. Families with 4-to 8-Year-Old Children during COVID-19: Findings from a Nationally Representative Survey

Evidence of short-term impacts of the coronavirus disease 2019 (COVID-19) pandemic on family life is emerging. Continued research can shed light on potential longer-term impacts. An online survey of U.S. parents with 4- to 8-year-old children (n = 1000) was administered in October 2020. The survey examined parent-reported impacts of COVID-19 on lifestyle (e.g., work, child-care, grocery shopping), as well as current family food acquisition and eating behaviors (e.g., cooking, restaurant use). Descriptive statistics were calculated, incorporating sampling weights based on sociodemographics. In terms of COVID-19 impacts, parents reported increases in working from home, decreased work hours, and increased child care and instruction, with most children attending school or receiving care at home. Parents reported increased home cooking and online grocery shopping; only 33% reported increased take-out or delivery from restaurants. About half of parents reported that their child dined at restaurants, 62% reported getting take-out, and 57% reported delivery from restaurants at least 2-3 times per month. About half viewed dining at restaurants as safe, while take-out and delivery were seen as safe by around three-quarters. Approximately two-thirds reported recent food insecurity. These nationally-representative results illustrate possible longer-lasting shifts in family life, with the potential to impact health and well-being. Sociodemographic differences and research and policy implications are discussed.
Buckling of Open Cylindrical Shells

The buckling of cylindrical shells with free longitudinal edges subjected to uniform axial compression is examined. The solutions are based on the simplified elastic equations of the small deflection theory known as the Donnell's equations. Results obtained were presented in a number of charts. It was found that in the practical range of thin shell structures, the critical buckling stress of a cylindrical shell may be 1/10, 1/100, or 1/1000 of the buckling value of a corresponding cylindrical tube with the same radius, R , thickness, t , and length L , as the ratio of t/R decreases and the ratio of L/R increases. Although the small deflection theory may give buckling stresses higher than the actual buckling values, it will serve the purpose of establishing the upper bounds of the buckling loads. The study of shells with free longitudinal edges and subjected to uniform axial compression may be regarded as an initial step for studying shell roofs with edge beams and subjected to longitudinal membrane stresses varying from compression to tension.
Design and Real Time Implementation of an Intelligent Bioreactor Control Scheme

Effective bioprocessing is often hindered by a lack of detailed knowledge about system dynamics and by the lack of appropriate sensors. The design and implementation of control strategies for bioreactors requires that all available information about the process be considered. When knowledge about process dynamics is incomplete, additional useful information is available from past data trends, expert process operators and the research literature. In this work, an expert system based bioreactor control scheme is developed and evaluated. The expert system supervisor utilizes on-line real-time data as well as archived data, facts and heuristic information to analyze the process checking for data consistency, equipment failure and realization of process goals. The results of an analysis are then used to suggest and implement an acceptable control procedure to help achieve a desired goal. The behavior and performance of some aspects of a real-time implementation of the expert system controller to Clostridium acetobutylicum will be presented and discussed.
Diversity in Academic Biomedicine: An Evaluation of Education and Career Outcomes with Implications for Policy

Currently, the U.S. population is undergoing major racial and ethnic demographic shifts that could affect the pool of individuals interested in pursuing a career in biomedical research. To achieve its mission of improving health, the National Institutes of Health must recruit and train outstanding individuals for the biomedical workforce. In this study, we examined the educational transition rates in the biomedical sciences by gender, race, and ethnicity, from high school to academic career outcomes. Using a number of educational databases, we investigated gender and racial/ethnic representation at typical educational and career milestones en route to faculty careers in biomedicine. We then employed multivariate regression methods to examine faculty career outcomes, using the National Science Foundation’s Survey of Doctorate Recipients. We find that while transitions between milestones are distinctive by gender and race/ethnicity, the transitions between high school and college and between college and graduate school are critical points at which underrepresented minorities are lost from the biomedical pipeline, suggesting some specific targets for policy intervention.
Limitations of Segmented Wavefront Control Devices in Emulating Optical Turbulence

Using a device to act as a surrogate for atmospheric turbulence in a laboratory is necessary to build and test optical systems for imaging, lidar, laser weapons, and laser communications. Liquid-crystal spatial light modulators (LC SLMs) and segmented micro-electro-mechanical-system (MEMS) deformable mirrors (DMs) are common devices for altering wavefronts to simulate a portion of atmospheric turbulence. The limitations of pixelation effects on a segmented wavefront control device were investigated theoretically. The results of this analysis were then verified by simulation. It was found that while LC SLMs with fine pixel resolution have almost no adverse effects from pixelation, segmented MEMS DMs have limitations related to the number of mirror segments on a DM. The performance capabilities of several available commercial devices are better understood as a result of this research.
55. The role of the liver in E. coli-induced memory impairments in aged rats

Aged rats show a particular vulnerability to long-term memory impairments following a peripheral immune challenge. We have previously shown that aged rats infected with E. coli exhibit a long lasting hippocampal-dependent memory impairment, and an accompanying exaggerated cytokine response in the hippocampus. Interestingly, cytokines were not exaggeratedly elevated in serum or spleen samples. The lack of a long-lasting cytokine response in these peripheral samples suggested that the signal potentiating hippocampal cytokines was being generated from within the brain, and not coming from the periphery. Evidence from the present study however, suggests that the liver may be of significant importance because we show that pro-inflammatory cytokines in this peripheral organ are indeed potentiated in only aged and infected subjects. Young infected rats do not show this potentiation. Here, we examine the role of the liver in signaling the hippocampus following an immune challenge using both in vivo and ex vivo manipulations. Finally, we examine the directionality of that signal by blocking cytokine action in the brain with IL-1 receptor antagonist, or by blocking cytokine action in the liver by depleting liver macrophages with clodronate-encapsulated liposomes either before, or shortly after infection.
Structural roles of subunit cysteines in the folding and assembly of the DNA packaging machine (portal) of bacteriophage P22.

The DNA packaging machine (portal assembly) of bacteriophage P22 is constructed from 12 copies of a multidomain 725-residue subunit comprising a complex alpha/beta fold. The portal subunit contains four cysteines (Cys 153, Cys 173, Cys 283, and Cys 516), which produce distinctive Raman markers in the spectral interval 2500-2600 cm(-1) originating from S-H bond-stretching vibrations diagnostic of S-H...X hydrogen-bonding interactions. The Raman spectrum is unique in the capability to characterize cysteine sulfhydryl interactions in proteins and shows that portal cysteine environments are significantly altered by assembly (Rodriguez-Casado et al. (2001) Biochemistry 40, 13583-13591). We have employed site-directed mutagenesis, size-exclusion chromatography, and Raman difference spectroscopy to characterize the roles of portal cysteines in subunit folding and dodecamer assembly. The stability of the portal monomer is severely reduced by a Cys --> Ser point mutation introduced at either residue 173 or 516. In the case of C516S, the destabilized monomer still forms portal rings, as visualized by negative-stain electron microscopy, whereas portal ring formation cannot be detected for C173S, which forms aberrant aggregates. The C283S mutant is a hyperstable monomer that is defective in portal ring formation. Interestingly, Cys 283 is suggested by secondary structure homology with the phi29 portal to be within a domain involved in DNA translocation. Conversely, the phenotype of the C153S mutant is close to that of the wild-type protein, implying that the sulfhydryl moiety of Cys 153 is not essential to formation of the native subunit fold and productive assembly dynamics. The present results demonstrate that cysteines of the P22 portal protein span a wide range of sulfhydryl hydrogen-bonding strengths in the wild-type assembly, that three of the four sulfhydryls play key roles in portal protein stability and assembly kinetics, and that substitution of a mutant seryl interaction (O-H...X) for a wild-type cysteinyl interaction (S-H...X) can either stabilize or destabilize the native fold depending upon sequence context.
The Need to Compromise Existence. Nation and Decolonization in the Bolivian Cinema of the Neoliberal Era

The aim of this essay is twofold: to analyze post-dictatorial Bolivian filmic discourse on the thematic of the nation vis-a-vis processes of decolonization, and to observe the effect that this relation had in the formation of subjectivities during the so called “neoliberal” era . Toward this end, I examine three films that reflect on the colonial condition of the nation through cinematographic language: Mi socio (Paolo Agazzi, 1982), La nacion clandestina (Jorge Sanjines, 1989), and American Visa (Juan Carlos Valdivia, 2005).
Adventures in attonewton force detection

We report detection of forces as small as 1.4 × 10-18 N in a 1 Hz bandwidth using ultrathin silicon cantilevers operating at liquid helium temperatures. Cantilever fabrication, the importance of surface cleanliness and various measurement issues are discussed. Tip–surface interactions are described, including the detection of single electron trapping–untrapping events. Applications of attonewton force detection for single spin magnetic resonance force microscopy (MRFM) and ultrasensitive magnetometry are discussed.
Apical control, gravitropic signaling, and the growth of lateral roots in Arabidopsis

Most research on gravity responses in plants has focused on primary roots and shoots, which typically grow in a vertical orientation. However, the patterns of lateral organ growth, which generally have large effects on overall plant architecture, are such that the organs are typically not vertical. In lateral roots of Arabidopsis, growth is initially in a nearly horizontal orientation but changes to a near-vertical orientation as the lateral root develops. Although the non-vertical lateral roots are gravitropically competent, following gravitropic reorientation of seedlings, the lateral roots on the upper flank of the primary root have different growth patterns from those on the lower side of the primary root. The differences are in part dependent on reorientation of the primary root, suggesting that gravitropic signaling from the primary root also contributes to the control of lateral root growth. The hormone auxin appears to play a role in this signaling between the primary and lateral roots, as auxin transport inhibitors applied to the primary root affect lateral root growth. Also, lateral roots of pin3 mutants, which are impaired in polar auxin transport, have altered lateral root orientations. However, other signals from the primary root tip also play an important role in regulating lateral root growth.
Can Changes in Differential Dropout Rates Reduce Adverse Impact? A Computer Simulation Study of a Multi‐wave Selection System

A simulation was used to explore the effects of variations in the rate at which applicants drop out of selection processes on racial differences in selection outcomes. Archival data was used to simulate a realistic range of selection scenarios in which test score differences between groups and selection ratios varied. The basis for dropping out was manipulated in two separate studies. Study 1 simulated dropout decisions that occurred at random within racial subgroups; in this study, dropout rates of minority versus White candidates were varied. Study 2 examined dropout decisions that occurred as a function of test scores. Results from both studies showed that mean test score differences between White and minority applicants have the largest influence on adverse impact. Interventions designed to reduce the tendency of minority applicants to withdraw from selection are likely to have, at best, small effects on the adverse impact of selection tests.
Teaching Fisher's Theory of Interest in a Simple Auction Setting

Theories of the interest rate begin with either the supply and demand of loanable funds or the stock of investment opportunities and their rates of return. Fisher's (1930) two-period model has an undifferentiated stock of investment opportunity. Teaching the standard Fisher theory of interest to undergraduates is generally difficult and not very successful. The graphical version with its double tangency solution to the production-consumption problem is only convincing to undergraduate economics or finance majors with unusual mathematical sophistication. Moreover that treatment, found in Hirschleifer (1970) and in Fama and Miller (1972) as well as in later treatments like Howe and Gronewoller (1990), has no capital goods and no explicit capital market. The model I propose requires no graphs and puts students in the position of being present at the auction for credit to see how simple maximizing behavior determines the rate of interest and how outside factors raise and lower it.
Optimized laser beam parameters for communications in space environments in the presence of pointing errors

We investigate the behavior of spatially partially coherent beams (PCBs) in the presence of pointing errors in the space communication environment. Closed form expressions for the optimal coherence length for minimizing outage probability and maximizing average signal-to-noise ratio (SNR) are derived. In the case of outage probablity, we observe that the optimal coherence parameter does not depend on the pointing error statistics. For average SNR results, PCBs can improve performance when large fixed beam offsets are present. We also provide BER performance analysis results for a convolutionally coded system and demonstrate significant performance improvement using PCBs with optimized parameters.
Stimulation of DNA synthesis by adenosine diphosphoribosylation of HeLa nuclear proteins during the cell cycle

Abstract The inhibition of DNA synthesis by ADP-ribosylation of nuclear proteins noted in rat liver nuclei, does not occur during various phases of the cell cycle of HeLa cells. In contrast, a significant enhancement of template activity is noted for either endogenous or microbial DNA polymerases due to this nuclear modification. The greatest stimulation was noted with G2 HeLa nuclei. The stimulation is specific for the generation of the poly-ADPR polymer and transcription is essentially not affected by this modification during the cell cycle.
Estimates of Carrington-class solar particle event radiation exposures as a function of altitude in the atmosphere of Mars☆

Abstract Radiation exposure estimates for crew members on the surface of Mars may vary widely because of the large variations in terrain altitude. The maximum altitude difference between the highest (top of Olympus Mons) and the lowest (bottom of the Hellas impact basin) points on Mars is about 32 km. In this work estimates of radiation exposures as a function of altitude, from the Hellas impact basin to Olympus Mons, are made for a solar particle event proton radiation environment comparable to the Carrington event of 1859. We assume that the proton energy distribution for this Carrington-type event is similar to that of the Band Function fit of the February 1956 event. In this work we use the HZETRN 2010 radiation transport code, originally developed at NASA Langley Research Center, and the Computerized Anatomical Male and Female human geometry models to estimate exposures for aluminum shield areal densities similar to those provided by a spacesuit, surface lander, and permanent habitat as a function of altitude in the Mars atmosphere. Comparisons of the predicted organ exposures with current NASA Permissible Exposure Limits (PELs) are made.
Genetic response to environmental heterogeneity.

ONE of the major problems of contemporary population genetics is how to account for the large amount of genetic variation occurring in natural populations. Considerable controversy exists between those people proposing that the variation is adaptively neutral, and those arguing that most of the variation is maintained by balancing selection. One of the processes of balancing selection postulated, is based on the idea that different genetic variants are favoured in different environmental niches. We report results from an experiment designed to test this hypothesis in which populations of Drosophila were exposed to experimental environments of various degrees of heterogeneity. The rationale is simple—if genetic variation is adaptively neutral, all populations should maintain about the same amount of genetic variation; if the ‘environmental heterogeneity’ hypothesis is correct, the degree of genetic variation in a population should be correlated with the degree of heterogeneity of its environment.
Higher neutrophil infiltration mediated by osteopontin is a likely contributing factor to the increased susceptibility of females to alcoholic liver disease

Alcoholic liver disease (ALD) is a major public health problem in the United States and women are known to be more susceptible to ALD. However, the precise mechanism for increased susceptibility of females to ALD is not completely understood. The present study is based on the hypothesis that induction of osteopontin (OPN), a matricellular protein, is the likely contributing factor for higher neutrophil recruitment in females during alcoholic steatohepatitis (ASH). ASH was induced in male and female Sprague-Dawley rats by feeding them a Lieber-DeCarli diet containing ethanol (EtOH) for 6 weeks, followed by a single injection of lipopolysaccharide (LPS, 10 mg/kg, ip). Liver injury, measured by plasma transaminase elevations and confirmed by haematoxylin and eosin-stained liver sections, revealed approximately 25-fold higher liver injury in the female ASH model compared with the males. Although steatosis, necrosis, and neutrophil infiltration were evident in both male and female rats, hepatic neutrophilic necrotic foci were noted as early as 2 h after LPS injection in the EtOH-treated female rats. Hepatic neutrophil infiltration correlated with higher expression of cleaved (cOPN) and uncleaved OPN in the EtOH + LPS-treated female rats compared with the males. OPN secretion was localized predominantly in the biliary epithelium and females had significantly higher OPN mRNA than their male counterparts in the ASH model. The ability of OPN to attract neutrophils was further confirmed in vivo, in a peritonitis rat model, and by neutralizing OPN (nOPN) antibody experiments. Hepatic neutrophil infiltration was largely inhibited ( approximately 50%) by nOPN antibody. Flow cytometry experiments revealed OPN-mediated up-regulation of the CD11b neutrophil adhesion molecule. In conclusion, these data suggest that higher hepatic expression of OPN is the likely reason for higher and early hepatic neutrophil infiltration making females more susceptible to ALD during ASH.
Charges in Hydrophobic Environments in Proteins

Ionizable groups buried in the hydrophobic interior of proteins play central roles in a wide variety of essential biochemical processes. Owing to the inherent differences in the dielectric properties of water and of protein, buried ionizable groups usually titrate with anomalous pKa values shifted relative to normal pKa values in water in the direction that favors the neutral state. The determinants of these unusual pKa values are being examined systematically with a family of variants of staphylococcal nuclease with Lys, Arg, His, Asp and Glu in 25 internal positions. Some of these ionizable groups titrate with normal pKa values, but the majority of them have anomalous pKa values, some shifted by as many as 6 units relative to the normal values. Dozens of crystal structures confirm that the ionizable groups are buried, at least when they are in the neutral state, often in complex with water molecules never before observed at internal locations in SNase. The structures show that the microenvironments of the ionizable groups range between the fully hydrophobic to the highly polar, but they do not fully explain the unusual properties of these groups. NMR spectroscopy has been used to examine the range of structural reorganization that can be coupled to the ionization of the internal ionizable. While the ionization of some residues is not easily detected in HSQC spectra, in most cases there is clear evidence of modest charge-induced changes in local structure or increased conformational fluctuations. Interactions between internal groups and polar groups, surface charges, and other internal groups have also been measured. These data constitute an extensive, quantitative description of origins of the apparent dielectric properties of proteins. They also show that proteins tolerate internal charges without the need for any special structural adaptations.
Dynamic Decision Support in the Advanced Tactical Architecture for Combat Knowledge System

As modern military systems demand faster reactions and become more mobile, the difference between planning and execution will fade until the planning process appears to merge with the battle management process. Continuous planning systems must be fast, intuitive, and accurate. In particular, the amount of information will be overwhelming and the number of options unmanageable for many future tactical environments. The Advanced Tactical Architecture for Combat Knowledge System (ATACKS) has been designed to incorporate both visualization tools and intelligent algorithms to allow for rapid visualization and decision making in these military environments. The work presented in this paper demonstrates how an external, intelligent system, in this case a system based on the Discrete Event System Specification (DEVS) framework, was adapted and successfully integrated with ATACKS to produce dynamic decision support for battlefield visualization in a distributed environment. The DEVS decision support application was designed to provide recommendations on the feasibility of proposed courses of action enacted in ATACKS. By querying the appropriate unit models, it derives the state of the current battle. Subsequently, DEVS uses its wargaming rules to formulate a Go or No-Go decision, which is communicated back to the commander working with ATACKS.
Synthesis of Actively Adjustable Springs by Antagonistic Redundant Actuation

A methodology for active spring generation is presented based on antagonistic redundant actuation. Antagonistic properties are characterized using an effective system stiffness. 'Antagonistic stiffness' is generated by preloading a closed-chain (parallel) linkage system. Internal load distribution is investigated along with the necessary conditions for spring synthesis. The performance and stability of a proposed active spring are shown by simulation, and applications are discussed.
Exact Solution of the Dirac Equation in the Field of a 't Hooft-Polyakov Monopole

This paper presents an exact solution of the Dirac equation for an $I=\frac{1}{2}$ fermion in the field of a 't Hooft-Polyakov magnetic monopole (in the Prasad-Sommerfield limit), which is analytic at $\mathcal{r}=0$. Helicity conservation restricts the $J=0$ $S$ matrix to be pure charge exchange. Because of the long-range interaction, the scattering amplitude is enhanced at long wavelengths $\ensuremath{\lambda}\ensuremath{\gg}\frac{1}{M}$ (the monopole structure size). The relevance of the present results for the question of proton decay catalysis is briefly discussed.
Real-time ambient occlusion for dynamic character skins

We present a single-pass hardware accelerated method to reconstruct compressed ambient occlusion values in real-time on dynamic character skins. This method is designed to work with meshes that are deforming based on a low-dimensional set of parameters, as in character animation. The inputs to our method are rendered ambient occlusion values at the vertices of a mesh deformed into various poses, along with the corresponding degrees of freedom of those poses. The algorithm uses k-means clustering to group the degrees of freedom into a small number of pose clusters. Because the pose variation in a cluster is small, our method can define a low-dimensional pose representation using principal component analysis. Within each cluster, we approximate ambient occlusion as a linear function in the reduced-dimensional representation. When drawing the character, our method uses moving least squares to blend the reconstructed ambient occlusion values from a small number of pose clusters. This technique offers significant memory savings over storing uncompressed values, and can generate plausible ambient occlusion values for poses not seen in training. Because we are using linear functions our output is smooth, fast to evaluate, and easy to implement in a vertex or fragment shader.
Attributable Fractions for Sufficient Cause Interactions

A number of results concerning attributable fractions for sufficient cause interactions are given. Results are given both for etiologic fractions (i.e. the proportion of the disease due to a particular sufficient cause) and for excess fractions (i.e. the proportion of disease that could be eliminated by removing a particular sufficient cause). Results are given both with and without assumptions of monotonicity. Under monotonicity assumptions, exact formulas can be given for the excess fraction. When etiologic fractions are of interest or when monotonicity assumptions do not hold for excess fractions then only lower bounds can be given. The interpretation of the results in this paper and in a proposal by Hoffmann et al. (2006) are discussed and compared. A method is described to estimate the lower bounds on attributable fractions using marginal structural models. Identification is discussed in settings in which time-dependent confounding may be present.
Lower functional gastrointestinal disorders: evidence of abnormal colonic transit in a 287 patient cohort.

BACKGROUND Abnormalities of colonic motility were reported in relatively small studies of patients with lower functional gastrointestinal disorders (FGID) including irritable bowel syndrome (IBS). The influence of gender and body mass on the observed motor pathophysiology is unclear. We sought to compare colonic transit in patients within different lower FGID subgroups and healthy controls, controlling for gender and BMI, and to determine whether BMI independently influences colonic motility. METHODS We evaluated a scintigraphic gastrointestinal and colonic transit database of 287 lower FGID patients associated with constipation (IBS-C, or functional constipation, n = 118), diarrhoea (IBS-D or functional diarrhoea, n = 139) or mixed bowel function (IBS-M, n = 30) and 170 healthy controls. We measured colon filling at 6 h (CF 6 h), and overall colonic transit at 8, 24 and 48 h. KEY RESULTS Colon filling at 6 h did not differentiate health from FGID. Colonic transit was abnormal at 24 h (GC24 of 3.86) in 29.7% of all lower FGID patients. There was a significant overall association between colonic transit and subject group (healthy controls and FGID subgroups) at 8 (P = 0.01), 24 (P < 0.001) and 48 h (P < 0.001) in particular for those with diarrhoea or constipation at 24 and 48 h (P < 0.05), even after adjusting for age, gender and BMI. In addition, BMI was associated with colonic transit after adjusting for age, gender and subject group. CONCLUSIONS & INFERENCES Abnormal transit is documented non-invasively with scintigraphy in 30% of lower FGID patients; transit measurement may help document pathophysiology and inform selection of therapy in lower FGID.
Rapid thermal chemical vapor deposition of germanium on silicon and silicon dioxide and new applications of Ge in ULSI technologies

In this study, low pressure chemical vapor deposition of pure germanium on silicon and silicon dioxide has been considered for new applications in future ultra large scale integration (ULSI) technologies. Germanium depositions were performed in a lamp heated cold-wall rapid thermal processor using thermal decomposition of GeH4. It is shown that Ge deposition on Si can be characterized by two different regions: a) at temperatures below approximately 450° C, the deposition is controlled by the rate of surface reactions resulting in an activation energy of 41.7 kcal/mole. b) Above this temperature, mass transport effects become dominant. The deposition rate at the transition temperature is approximately 800 A/min. It is shown that Ge deposition on SiO2 does not occur, even at temperatures as high as 600° C, resulting in a highly selective deposition process. Selectivity, combined with low deposition temperature makes the process very attractive for a number of applications. In this work, it is shown for the first time that selective Ge deposition can be used to eliminate silicon consumption below the gate level during the silicidation of the shallow source and drain junctions of deep submicron MOSFETs. In addition, a new in situ technique has been developed which allows polycrystalline germanium (poly-Ge) deposition on SiO2. In this work poly-Ge has been considered as a low temperature alternative to polycrystalline silicon (poly-Si) in the formation of gate electrodes in single-wafer manufacturing where low-thermal budget processes are most desirable.