cssi/SciSciGPT-SciSciNet huggingface dataset:
DNA base flipping by both members of the PspGI restriction-modification system.

The PspGI restriction–modification system recognizes the sequence CCWGG. R.PspGI cuts DNA before the first C in the cognate sequence and M.PspGI is thought to methylate N4 of one of the cytosines in the sequence. M.PspGI enhances fluorescence of 2-aminopurine in DNA if it replaces the second C in the sequence, while R.PspGI enhances fluorescence when the fluorophore replaces adenine in the central base pair. This strongly suggests that the methyltransferase flips the second C in the recognition sequence, while the endonuclease flips both bases in the central base pair out of the duplex. M.PspGI is the first N4-cytosine MTase for which biochemical evidence for base flipping has been presented. It is also the first type IIP methyltransferase whose catalytic activity is strongly stimulated by divalent metal ions. However, divalent metal ions are not required for its base-flipping activity. In contrast, these ions are required for both base flipping and catalysis by the endonuclease. The two enzymes have similar temperature profiles for base flipping and optimal flipping occurs at temperatures substantially below the growth temperature of the source organism for PspGI and for the catalytic activity of endonuclease. We discuss the implications of these results for DNA binding by these enzymes and their evolutionary origin.
Loss of the ETR1 ethylene receptor reduces the inhibitory effect of far-red light and darkness on seed germination of Arabidopsis thaliana

When exposed to far-red light followed by darkness, wild-type Arabidopsis thaliana seeds fail to germinate or germinate very poorly. We have previously shown that the ethylene receptor ETR1 (ETHYLENE RESPONSE1) inhibits and ETR2 stimulates seed germination of Arabidopsis during salt stress. This function of ETR1 requires the full-length receptor. These roles are independent of ethylene levels and sensitivity and are mainly mediated by a change in abscisic acid (ABA) sensitivity. In the current study we find that etr1-6 and etr1-7 loss-of-function mutant seeds germinate better than wild-type seeds after illumination with far-red light or when germinated in the dark indicating an inhibitory role for ETR1. Surprisingly, this function of ETR1 does not require the receiver domain. No differences between these mutants and wild-type are seen when germination proceeds after treatment with white, blue, green, or red light. Loss of any of the other four ethylene receptor isoforms has no measurable effect on germination after far-red light treatment. An analysis of the transcript abundance for genes encoding ABA and gibberellic acid (GA) metabolic enzymes indicates that etr1-6 mutants may produce more GA and less ABA than wild-type seeds after illumination with far-red light which correlates with the better germination of the mutants. Epistasis analysis suggests that ETR1 may genetically interact with the phytochromes (phy), PHYA and PHYB to control germination and growth. This study shows that of the five ethylene receptor isoforms in Arabidopsis, ETR1 has a unique role in modulating the effects of red and far-red light on plant growth and development.
Deficient post-translational processing of Rap 1A in variant HL-60 cells

Variant HL-60 cells resistant to differentiation induced by nitroprusside and cGMP analogs have normal guanylate cyclase and cGMP-dependent protein kinase (G-kinase) activity (J. Biol. Chem. 269, 32155–32161, 1994). We found decreased phosphorylation of a low molecular weight protein (pp23) in the variant cells and by co-migration on two-dimensional polyacrylamide gels, phosphopeptide mapping, immunoprecipitation and immunoblotting, we showed that pp23 was one of three post-translationally modified forms of Rap 1A expressed in HL-60 cells. Using an in vitro transcription/translation system, we studied each of the post-translational processing steps of Rap 1A and we showed that pp23 represented fully processed Rap 1A. By immunoprecipitation, immunoblotting and 35S-methionine/cysteine incorporation, we showed that the variant cells were deficient in pp23, and thus in fully processed Rap 1A, but that these cells did express normal amounts of completely unprocessed Rap 1A and geranylgeranylated Rap 1A; the lack of Rap 1A processing beyond geranylgeranylation in the variant cells was not secondary to a change in Rap 1A's amino acid sequence. The variant cells had normal carboxyl methyltransferase activity suggesting they are deficient in proteolytic cleavage of Rap 1A. The deficient post-translational processing of Rap 1A had no effect on Rap 1A's subcellular distribution and we found no evidence for altered post-translational processing of H-Ras.
Immunofluorescence and Subsequent Confocal Microscopy of Intracellular TNF in Human Neutrophils

Immunofluorescence is an important technique required to observe expression, localization and colocalization of proteins within the cell. Here we describe the immunofluorescence and subsequent confocal microscopy technique of tumor necrosis factor-α (TNF) in human neutrophils (polymorphonuclear leukocytes; PMN). The qualitative technique can be used to observe the expression pattern changes from resting to stimulated leukocytes. Colocalization with other cytokines, proteins, or organelles can be observed. This immunofluorescence technique can be done in 1-2 days.
PWE-402 The impact of surgeon laparoscopic training on conversion during laparoscopic colorectal surgery

Introduction Laparoscopic colorectal resections are currently the focus of colorectal training programs. Conversion rates are similar between inexperienced fellowship-trained surgeons and those with more experience. This study aimed to determine if primarily open or laparoscopoic surgical training influences type of colorectal operations performed and rates of conversion. Method Following IRB approval, review of a prospectively maintained database was performed for all patients with a colorectal resection performed by 6 surgeons for all diagnoses from 2010–2014. Surgeons were designated as laparoscopic- or open-trained based on self-declared exposure to laparoscopy during training. Procedures were categorised by type and included if the procedure was performed both open and laparoscopic. Operative technique was recorded as laparoscopic, open, or converted; conversion was re-categorised as preemptive or reactive. Univariate analyses were performed using Chi-squared test for categorical variables. Multivariable logistic regression was performed to adjust for confounding and identify the role of variables on predicting SSI outcome. Results 573 patients were included [mean age 57 (±17) years; 49.3% male]. Patients in the laparoscopic-trained group were older (59.8 vs. 55.9 years; p = 0.017). All other demographic variables were equivalent between groups. Laparoscopic-trained surgeons were less likely to perform proctectomy or resections involving anastomosis (p Conclusion There is a difference in the types of procedures performed by surgeons who are laparoscopic-trained compared to their open-trained colleagues given that they are earlier in their career. There was no difference in conversion rates between open and laparoscopic-trained surgeons, despite an experiential difference. Larger multi-institutional studies will strengthen our findings. Disclosure of interest None Declared.
Misreporting of contraceptive hormone use in clinical research participants.

Abstract Objective Researchers traditionally rely on participant self-report for contraceptive use. We hypothesized that self-reported contraceptive use by clinical research participants may disagree with objectively measured hormonal status. Study design We enrolled women in Harare, Zimbabwe, aged 18–34, who by self-report had not used hormonal or intrauterine contraception for >30 days, or depot medroxyprogesterone acetate for >10 months, into a study designed to assess biologic changes with contraceptive initiation and use. Blood samples obtained at enrollment and each follow-up visit (N=1630 from 447 participants) were evaluated by mass spectrometry for exogenous hormones. We individually interviewed a subset of participants (n=20) with discrepant self-reported and measured serum hormones to better understand nondisclosure of contraceptive use. Results Discrepant with self-reported nonuse of hormonal contraception, synthetic progestogens were detectable in 120/447 (27%, 95% confidence interval 23%–31%) enrolled women. Measured exogenous hormones consistent with use of contraceptive pills (n=102), injectables (n=20) and implants (n=3) were detected at enrollment, with 7 women likely using >1 contraceptive. In-depth interviews revealed that participants understood the requirement to be hormone free at enrollment (100%). Most (85%) cited partner noncooperation with condoms/withdrawal and/or pregnancy concerns as major reasons for nondisclosed contraceptive use. All interviewed women (100%) cited access to health care as a primary motivation for study participation. Of participants who accurately reported nonuse of hormonal contraception at enrollment, 41/327 (12.5%) had objective evidence of nonstudy progestin use at follow-up that disagreed with self-reported nonuse. Conclusions Women joining contraceptive research studies may misrepresent their use of nonstudy contraceptive hormones at baseline and follow-up. Objective measures of hormone use are needed to ensure that study population exposures are accurately categorized. Implications statement Among Zimbabwean women participating in a contraceptive research study, 27% had objective evidence of use of nonstudy contraceptives at enrollment that disagreed with self-report. Studies that rely on self-report to identify contraceptive hormone exposure could suffer from significant misclassification.
Ultrafast Strain Dynamics at a Ferroelectric/Ferromagnetic Oxide Interface

We investigated ultrafast strain dynamics at the BiFeO3 (BFO) / La0.3Sr0.7MnO3 (LSMO) interface using time resolved second harmonic generation (trSHG). The dynamics are driven by the strain in a small boundary layer at the interface.
Cell Dynamics in the Wound Healing Process in Tumor Environment After Treatments

Although the failure of cancers treatments has been mostly linked with the existence of resistant cells or cancer stem cells, new findings show a significant correlation between circulating inflammatory biomarkers and treatment failures. Most cancer treatments cause necrotic cell deaths in the tumor environment. Necrotic cells send signals to the immune cells to start the wound healing process in the tissue. Therefore, we assume after stopping treatments there is a wound that needs to be healed. The stochastic simulations of epithelial cell dynamics after a treatment, which only kills cells without changing the tumor9s inflammatory environment, show that higher fitness of cancer cells causes earlier relapses. Moreover, the tumor returns even if a single cancer cell with high fitness remains in the wound9s boundary after such treatments. Although the involvement of cancer cells in the wound healing after treatments leads to the fast relapse, the cancer cells outside of the wound can also cause a slow recurrence of the tumor. Therefore, the absence of relapse after such treatments implies a slow-developing tumor that might not reach an observable size in the patient9s lifetime. Conversely, a large solid tumor in a young patient suggests the presence of high fitness cancer cells and therefore a high likelihood of relapse after conventional therapies. Additionally, the location of remaining cancer cells after treatments is a very important factor in the recurrence time. The fastest recurrence happens when a high fitness cancer cell is located in the middle of the wound. However, the longest time to recurrence corresponds to cancer cells located outside of the wound9s boundary.
Multidrug resistant Pseudomonas aeruginosa causing prosthetic valve endocarditis: A genetic-based chronicle of evolving antibiotic resistance

Background. Successful treatment of infections caused by multidrug-resistant (MDR) Pseudomonas aeruginosa is thwarted by the emergence of antibiotic resistance and biofilm formation on prosthetic devices. Our aims were to decipher the molecular basis of resistance in a unique case of prosthetic valve endocarditis (PVE) caused by MDR P. aeruginosa. Methods. Five sequential MDR P. aeruginosa blood isolates collected during a 7-month period were recovered from a patient suffering from PVE previously exposed to β-lactam antibiotics. Minimum inhibitory concentrations (MICs) of several classes of antibiotics were used to indicate clinical resistance characteristics; relatedness of the isolates was determined using multilocus sequence typing and repetitive sequence-based polymerase chain reaction. Amplification and sequencing of regulatory and resistance genes was performed. Results. All isolates belonged to ST 298, possessed blaPDC-16, and were resistant to fluoroquinolones and carbapenems. In the course of therapy, we observed a >2-fold increase in cephalosporin resistance (4 µg/mL to >16 µg/mL). Sequencing of the AmpC regulator, ampR, revealed a D135N point mutation in cephalosporin-resistant isolates. Common carbapenemase genes were not identified. All isolates demonstrated a premature stop codon at amino acid 79 of the outer membrane protein OprD and mutations in the quinolone resistance-determining regions of gyrA and parC. Point mutations in nalC, an efflux pump regulator, were also observed. Conclusions. In this analysis, we chart the molecular evolution of β-lactam resistance in a case of PVE. We show that mutations in regulatory genes controlling efflux and cephalosporinase production contributed to the MDR phenotype.
Movement patterns in women at risk for perinatal depression: use of a mood-monitoring mobile application in pregnancy.

Objectives To examine, using a smartphone application, whether mood is related to daily movement patterns in pregnant women at risk for perinatal depression. Materials and Methods Thirty-six women with elevated depression symptoms (PHQ-9 ≥ 5) in pregnancy used the application for 8 weeks. Mood was reported using application-administered surveys daily (2 questions) and weekly (PHQ-9 and GAD-7). The application measured daily mobility (distance travelled on foot) and travel radius. Generalized linear mixed-effects regression models estimated the association between mood and movement. Results Women with milder depression symptoms had a larger daily radius of travel (2.7 miles) than women with more severe symptoms (1.9 miles), P = .04. There was no difference in mobility. A worsening of mood from the prior day was associated with a contracted radius of travel, as was being in the group with more severe symptoms. No significant relationships were found between anxiety and either mobility or radius. Discussion We found that the association of mood with radius of travel was more pronounced than its association with mobility. Our study also demonstrated that a change in mood from the prior day was significantly associated with radius but not mood on the same day that mobility and radius were measured. Conclusion This study lays the groundwork for future research on how smartphone mood-monitoring applications can combine actively and passively collected data to better understand the relationship between the symptoms of perinatal depression and physical activity that could lead to improved monitoring and novel interventions.
Volunteering and Psychological Well-Being: Assessing Variations by Gender and Social Context

A well-developed literature suggests that people who volunteer more often tend to enjoy better physical and mental health. The current study contributes to this work in three potentially important ways. First, the authors assess whether volunteering in religious settings is more strongly associated with well-being than volunteering in secular contexts. Second, they examine whether women volunteer more frequently than men. Third, they evaluate whether the relationship between volunteering in religious settings and well-being is stronger among women than among men. The data are from a nationally representative online survey (N = 1075). The findings suggest that more frequent volunteering in the church as well as more frequent volunteering in secular settings is associated with a greater sense of well-being. However, the difference between the two was not statistically significant. Second women volunteer at church more often than men, but significant gender differences in the rate of volunteering in secular settings did not emerge from the data. Third, volunteering at church was associated with a greater sense of well-being among women, but not among men.
Locke’s ‘Dubia circa Philosophiam Orientalem’ and the Reception of Kabbala Denudata in England During the Seventeenth Century

‘Dubia circa Philosophiam Orientalem’ is a manuscript containing John Locke’s critical thoughts on a brief work entitled Adumbratio Kabbalae Christianae. It is composed in Latin and written in his hand. The text and a translation of it follow this introduction.
Limited-Knowledge Economic Dispatch Prediction using Bayesian Averaging of Single-Node Models

A great deal of literature examines economic dispatch from the perspective of a grid operator, assuming full knowledge of generating unit costs and constraints, network topology, line capacities, etc. But others without access to the complete, data-intensive model may also wish to predict unit dispatch under various scenarios. This paper develops a Bayesian approach to predicting future economic dispatch, which relies only on historical dispatch observations, as well as general assumptions of operating costs. The approach uses a Markov-chain Monte Carlo method to create an ensemble of network-free models, which capture fundamental properties of economic dispatch (like merit order and marginal generator behavior) under particular “regimes” of grid operation (a particular range of load, set of congested lines, set of committed units, etc.). It then uses Bayesian averaging over many of these simple models to create an ensemble model, which approximates economic dispatch under general operating conditions. A case study using data from New York is used to verify the ensemble model.
Differential developmental changes in cortical representations of auditory-vocal stimuli in songbirds

Motor skill learning entails changes in selectivity for behaviorally relevant stimuli across cortical regions, yet the neural representation of these stimuli remains understudied. We investigated h...
A Logical Path From Neural Ensemble Formation to Cognition With Mind-Light-Matter Unification: The Eternal Dao Can Be Told (Survey)

Based on a geometrical and logical unification of mind, light, and matter, a revision of Laozi is proposed and a logical path is identified from neural ensemble formation to cognition. Mind-matter or mind-body unification has been a longstanding impasse in philosophy and science hindering the advancement of biophysics, quantum biology, neuroscience, human level AI, and cognitive informatics. However, this article shows that such a unification can be reached logically. To achieve the goal, the eternal Dao is told as the Being of revealing with a formal YinYang logic. It is illustrated with computer simulation that neural ensembles can form a causal network for cognition with information conservation. It is suggested that if the theory is confirmed, the search for mind-body unification will reach a major milestone on the eternal Dao toward a better understanding of the nature of human intelligence and mental health. This work leads to a number of predictions in science philosophy.
First Experiments on Measuring Light Pressure II (Ernest Fox Nichols and Gordon Ferrie Hull)

This chapter contains an essay of Elsa Garmire about Nichols (1869–1924) and Hull’s (1870–1956) results on measurements of light pressure in 1901 and later and their comparison with Lebedev’s results (Sect. 13.1). It also contains a reprint of the paper of Nichols and Hull of 1901 in which their first results were reported (Sect. 13.2).
Reproductive factors associated with breast cancer risk in Li-Fraumeni syndrome.

Abstract Li–Fraumeni syndrome (LFS) is a rare autosomal dominant cancer predisposition syndrome with exceptionally high lifetime cancer risks, caused primarily by germline TP53 variants. Early-onset breast cancer is the most common cancer in women with LFS. Associations between female reproductive factors and breast cancer risk have been widely studied in the general population and BRCA1/2 mutation carriers but not in LFS. We evaluated whether reproductive factors are associated with breast cancer in LFS. Questionnaire data were collected for 152 women with confirmed germline TP53 variants enrolled in the National Cancer Institute's LFS study (NCT01443468); of which, 85 had breast cancer, confirmed by pathology/medical reports. Fisher's exact test and Cox proportional hazards were used to calculate the effect of reproductive factors on breast cancer risk. Lifetime breastfeeding for at least 7 months was associated with lower breast cancer risk (hazard ratio [HR] 0.57, p = 0.05). Parity did not independently change breast cancer risk (HR 1.08, p = 0.8) but suggested an increased risk with older age at first live birth (HR 2.14, p = 0.05). Age at menarche (HR 1.09, p = 0.24) and use of oral contraceptives (HR 0.88; p = 0.7) did not significantly affect breast cancer risk. In this first study of reproductive factors and breast cancer in women with LFS, breastfeeding was observed to be protective against breast cancer risk, especially with at least 7 months of lifetime breastfeeding. Older age at first live birth was suggested to slightly increase breast cancer risk. Larger prospective studies of reproductive factors are warranted in women with LFS before making definitive clinical recommendations.
Current Status of the Use of Machine Learning and Magnetic Resonance Imaging in the Field of Neuro-Radiomics

Brain tumors exhibit heterogeneous profile with anomalous hemodynamics. In spite of significant advances at diagnostic and therapeutic fronts in the past couple of decades, the prognosis still remains poor. Magnetic resonance imaging (MRI), which provides information about the structural and functional aspects of the tumor in a noninvasive manner, has gained a lot of popularity for evaluating brain tumors. Several studies have been proposed in the recent past that focused on quantifying the characteristics of brain tumors as seen on MRI scans in terms of various descriptors, such as shape/morphology, texture, signal strength, and temporal dynamics, and then integrating these quantitative descriptors into various diagnostic and prognostic indices. This article first presents an overview of various MRI imaging sequences, such as contrast-enhanced, dynamic susceptibility contrast, diffusion tensor imaging, and conventional MRI, used in routine clinical settings. Later, it provides a detailed overview of the current status of the use of machine learning on MRI scans, with focus on clinical applications of these imaging sequences in brain tumors, including grading, assessment of the treatment response, prediction of prognosis, and identification of molecular markers. The article also highlights current challenges and future research directions.
Simple, Low-Hysteresis, Foldable, Fabric Pneumatic Artificial Muscle

Soft robots offer advantages over rigid robots in adaptability, robustness to uncertainty, and human safety. However, realizing soft actuators for these robots is still a challenge. We present a simple, highly conformable pneumatic artificial muscle made of a thin, single layer of woven, bias-cut fabric. The airtight fabric is adhered together with a flexible adhesive, negating the need for a bladder or sewing. Thus, it is foldable when depressurized and behaves like a McKibben muscle when pressurized, but without the friction of a bladder or braided sheath. Experiments show that the muscle exhibits repeatable, near-linear behavior with less than 1% hysteresis, over an order of magnitude less than that of McKibben muscles. Dynamic testing shows that the muscle responds quickly, even at lengths over 60 cm, contracting in 0.03 s, an order of magnitude quicker than series pouch motors. A fatigue test shows that its life exceeds 100,000 cycles. We also demonstrate that the muscle is well suited for steering tip-extending robots, and actuating folding, deployable structures. Our muscle offers improvements over various existing pneumatic artificial muscles, providing a simple new option for soft robotic actuation that has potential to advance the field.
Does Fiscal Monitoring Make Better Governments? Evidence from US Municipalities

I study the effect of state fiscal monitoring on municipal governance. I focus on governance outcomes related to financial reporting quality, local corruption, political entrenchment, and the financial soundness of municipalities. I exploit the staggered adoption of fiscal monitoring policies, which entail a regular review of municipal financial reporting for signs of fiscal distress. I find that the introduction of monitoring policies is associated with an increase in proxies for reporting quality, a decrease in corruption convictions, and a reduced likelihood of reelection of incumbent politicians. Consistent with the intended purpose of state monitoring, I find evidence consistent with the financial health of municipalities improving following the initiation of state monitoring, as measured with financial statement-based ratios. Collectively, my results are consistent with state fiscal monitoring improving several important aspects of municipal governance.
Behind the eight ball: the effects of race and number of infractions on the severity of exclusionary discipline sanctions issued in secondary school

African American and Hispanic students receive more punitive school discipline than White students even when students of color commit similar infractions as Whites. Similarly, students with a disab...
Transcriptomic profiling of fetal membranes of mice deficient in biglycan and decorin as a model of preterm birth

Approximately, 25% of all preterm births are due to preterm premature rupture of membranes. Mice deficient in proteoglycans biglycan (Bgn) and decorin (Dcn) display abnormal fetal membranes and increased incidence of preterm birth. We conducted RNA-Seq to profile fetal membranes and identify molecular pathways that may lead to preterm birth in double knockout (DKO) mice (Bgn–/–; Dcn–/–) compared to wild-type (WT) at two different gestational stages, E12 and E18 (n = 3 in each group). 3264 transcripts were differentially regulated in E18 DKO vs. WT fetal membranes, and 96 transcripts differentially regulated in E12 DKO vs. WT fetal membranes (FDR 10) for transcription factor binding sites for Nr2f1 at E18. We propose that in DKO mice, cell cycle arrest results in lack of cell proliferation in fetal membranes, inability to contain the growing fetus, and preterm birth.Summary sentenceWe have conducted transcriptomic profiling of fetal membranes from mice deficient in biglycan and decorin and identified molecular pathways of interest.
A comparative analysis of freeway crash incident clearance time using random parameter and latent class hazard-based duration model.

Abstract The effects of freeway incident clearance times on the flow of traffic have recently increased interests in understanding what factors influence incident durations. This has particularly become topical due to the financial and economic implications of traffic gridlocks caused by freeway incidents on industries and personal mobility. This paper presents two advanced econometric modeling methods, random parameters duration modeling and latent class duration modeling in understanding the factors that impact freeway incident clearance times in the State of Alabama. These two modeling approaches were further compared to identify which of them provides the best fit for the data with respect to accounting for unobserved heterogeneity. A total of 2206 freeway crash incident data from January 1 to December 31, 2018 were examined in developing the models. The study was based on a unique dataset that involved merging and matching Traffic Incident Management response data from the Alabama Department of Transportation (ALDOT) Traffic Management Center (TMC), freeway crash data from the Center for Advanced Public Safety (CAPS) at the University of Alabama, Alabama Service and Assistance Patrol (ASAP) data from ALDOT and traffic volume from ALDOT’s Highway Performance Management System (HPMS). The model estimation results reveal that a total of nineteen variables were found statistically significant with five random variables (on-road, nighttime, rain, AADT, and ASAP existing coverage area) and fourteen fixed effects variables for the random parameters model. For latent class model, a total of eighteen variables were observed statistically significant within two distinct latent classes (Latent Class 1 with class membership probability of 0.23 and Latent Class 2 with class membership probability of 0.77) at a 0.05 significance level. A comparison of the two models reveals that the latent class model provides the better fit for the incident duration data. The findings of this study are expected to contribute to the body of knowledge on incident duration by employing two advanced econometric modeling methods and to inform statewide efforts in significantly reducing the duration of freeway incident clearance time. Moreover, this is to ensure that policy decisions that may arise from the findings of the study are sound and based on data-driven evidence.
Do Trade Agreements Actually Reduce Trade Volatility

A frequently stated objective of regional and multilateral trade agreements is to stabilize trade and reduce volatility in trade flows. We examine whether trade agreements accomplish this goal. Using a structural gravity approach we identify two potential channels through which international trade institutions may influence the volatility of bilateral trade flows: by affecting the variance of trade barriers and by affecting the covariance of economic outcomes between the trading partners. We then use a panel of bilateral industry-level trade data to empirically examine the effects of regional trade agreements and GATT/WTO membership on export earnings volatility. We find some evidence that joining a multilateral trade agreement such as the GATT does make export earnings less volatile. However, regional trade agreements increase measured volatility in bilateral exports, and this rise in volatility increases as the agreement becomes deeper and more integrated.
Distinctive non-methanogen archaeal populations in anaerobic digestion

Methanogens define the archaeal communities involved in anaerobic digestion. Recently, non-methanogen archaeal populations have been unexpectedly identified in anaerobic digestion processes. To gain insight into the ecophysiology of these uncharacterized archaeal populations, for the first time, a phylogenetic analysis was performed on a collection of non-methanogen archaeal 16S rRNA gene sequences from anaerobic digesters of broad geographic distribution, revealing a distinct clade formed by these sequences in subgroup 6 of the Miscellaneous Crenarchaeotal Group in the newly proposed archaeal phylum Bathyarchaeota. This exclusive phylogenetic assemblage enabled the development of a real-time quantitative PCR (qPCR) assay specifically targeting these non-methanogen archaeal populations in anaerobic digestion. Application of the qPCR assay in continuous anaerobic digesters indicated that these archaeal populations were minor constituents of the archaeal communities, and the abundance of these populations remained relatively constant irrespective of process perturbations. Analysis of the archaeal populations in methanogenic communities further revealed the co-occurrence of these non-methanogen archaea with acetoclastic methanogens. Nevertheless, the low abundance of non-methanogen archaea as compared with acetoclastic methanogens suggests that the non-methanogen archaeal populations were not major players in animal waste-fed methanogenic processes investigated in this study and the functions of these archaeal populations remain to be identified.
Better Logging through Formality

We rely on programs that consume audit logs to do so successfully (a robustness issue) and form the correct interpretations of the input (a semantic issue). The vendor's documentation of the log format is an important part of the specification for any log consumer. As a specification, it is subject to improvement using formal specification techniques. This work presents a methodology for formalizing and refining the description of an audit log to improve robustness and semantic accuracy of programs that use the log. Ideally applied during design of a new format, the methodology is also profitably applied to existing log formats. Its application to Solaris BSM (an existing, commercial format) demonstrated utility by detecting ambiguities or errors of several types in the documentation or implementation of BSM logging, and identifying opportunities to improve the content of the logs. The products of this work are the methodology itself for use in refining other log formats and their consumers, and an annotated, machine-readable grammar for Solaris BSM that can be used by the community to quickly construct applications that consume BSM logs.
A Biological Approach to the Development of Computer Autoimmune Systems

Experiencing repeated computer virus attacks over the last decade has led to a number of intriguing technological challenges. The study of human immunology may help to solve these challenges and aid in the understanding of how and why computer viruses propagate. Current techniques employ heuristic systems to ferret the viral attacks and annihilate them. This technology is more suited for addressing known viruses and has been relatively successful. However, there remains a challenge as to how to deal with the virus problems of the near future, albeit unknown viral code. Ultimately, this paper will stimulate new innovations in anti-virus technology. This paper explores current research in the area of protection from computer viruses and suggests a possible framework for virus detection in such an autoimmune system. Hence, this paper exposes the mechanics of virus detection in the human immune system. Then it suggests techniques that could be used to identify or detect unknown viruses by distinguishing between "self" and foreigner.
Image quality assessment of MUGA SPECT using enhanced acquisition and reconstruction

1658 Objectives New hardware and software developments have promised reduced scan time (ST) or injected activity (IA) while maintaining equivalent image quality in nuclear cardiac imaging. Our aim was to compare the effects of decreased ST and/or IA on image quality between Siemens’ IQ-SPECT (SMARTZOOM collimator Flash 3D OSEM), standard LEHR collimator SPECT with either Flash 3D or FBP processing, and routine planar imaging, when applied to gated blood pool (MUGA) studies. Methods An anthropomorphic torso phantom with a cardiac LV insert and filled with Tc-99m water was imaged in gated mode (16 bins) on a Siemens dual-head Symbia T6 SPECT/CT scanner using: a) IQ-SPECT, b) SPECT and c) LEHR Planar. IQ-SPECT and SPECT data were acquired into 128x128 matrix (4.8 mm/pixel) using a non-circular orbit (208° & 180°, respectively); 17 & 32 views/head; and total acquisition time equivalent to our 26-min, two-view planar MUGA. The total activity in the various phantom chambers when all 16 bins were summed corresponded to that in one bin of a 100% ST or IA MUGA scan. ST or IA of 100, 69, 50, and 38% were then simulated by summing 16, 11, 8 and 6 bins, and reconstructed using Flash 3D (SMARTZOOM and LEHR) and FBP (LEHR) using manufacturer recommended parameters. No attenuation correction was applied since it is not supported in gated IQ-SPECT. Image quality was assessed visually and by measuring contrast and %σ in a LV volume of interest. Results Visual inspection showed that IQ-SPECT had the lowest noise content. Quantitative evaluation however showed that SPECT+Flash 3D had slightly higher contrast than IQ-SPECT and SPECT+FBP, but the difference decreased with increasing ST/IA. The %σ was 0.32, 0.31, 0.29 for SPECT+Flash 3D, IQ-SPECT, and SPECT+FBP respectively. Contrast in SPECT+Flash 3D, IQ-SPECT, and SPECT+FBP at 38% ST/IA was higher than planar by 5.1, 4.7 and 4.6 times, respectively. Conclusions IQ-SPECT imaging improves MUGA image quality even at 38% ST/IA when compared to planar. This improvement however is diminished when compared to standard SPECT. Supporting patient data will also be presented.
Economic burden associated with Parkinson's disease on elderly Medicare beneficiaries.

We evaluated medical utilization and economic burden of self-reported Parkinson's disease (PD) on patients and society. Using the 1992–2000 Medicare Current Beneficiary Survey, we compared health care utilization and expenditures (in 2002 U.S. dollars) of Medicare subscribers with and without PD, adjusting for sociodemographic characteristics and comorbidities. PD patients used significantly more health care services of all categories and paid significantly more out of pocket for their medical services than other elderly (mean ± SE, $5,532 ± $329 vs. $2,187 ± $38; P < 0.001). After adjusting for other factors, PD patients had higher annual health care expenses than beneficiaries without PD ($18,528 vs. $10,818; P < 0.001). PD patients were more likely to use medical care (OR = 3.77; 95% CI = 1.44–9.88), in particular for long-term care (OR = 3.80; 95% CI = 3.02–4.79) and home health care (OR = 2.08; 95% CI = 1.76–2.46). PD is associated with a significant economic burden to patients and society. Although more research is needed to understand the relationship between PD and medical expenditures and utilization, these findings have important implications for health care providers and payers that serve PD populations. © 2005 Movement Disorder Society
Molecular Basis of the Biological Function of Molybdenum EFFECT OF TUNGSTEN ON XANTHINE OXIDASE AND SULFITE OXIDASE IN THE RAT

Administration of tungsten to rats at levels of 1 to 100 ppm in the drinking water resulted in proportionate decreases in xanthine oxidase and sulfite oxidase activities and the native molybdenum electron paramagnetic resonance signal of the latter as well as total liver molybdenum. The time course of loss of the two enzyme activities fitted first order kinetics in all tissues studied. The t1/2 for sulfite oxidase activity was longer than that for xanthine oxidase in both liver and kidney, while both activities disappeared rapidly from intestinal tissue. The quantitative aspects of the biphasic loss of hepatic molybdenum revealed the existence of an unidentified and relatively unstable pool of molybdenum. This pool appeared to be replaced by tungsten early in the course of administration of the metal at 100 ppm. The simultaneous presence of 1 ppm of molybdenum almost completely superseded the effect of 100 ppm of tungsten. The results have been interpreted to indicate inhibition of molybdenum utilization by dietary tungsten. The tungsten effect was also observed when the metal was administered intraperitoneally. Injection of molybdenum into rats depleted of hepatic sulfite oxidase and xanthine oxidase activities by tungsten treatment resulted in significant restoration of both activities in 5½ hours. The use of cycloheximide and puromycin showed that the reactivation was independent of new protein synthesis. The inability to effect such reactivation in vitro points to the requirement for activation or modification of molybdate as a prerequisite for prosthetic attachment to the enzymes. Unlike tungsten, vanadium was incapable of generating experimental molybdenum deficiency in the rat.
Evaluating the state of a section under bending using the location of neutral axis

Neutral axis of a composite section under loading is a line in the cross-section along which the section experiences zero strain. When a structure is under no axial load, the location of the neutral axis passes through the centroid of stiffness of the cross-section, which can be calculated based on geometric and stiffness properties of the cross-section. When the structure experiences damage, the location of the centroid of stiffness as well as the neutral axis shift in position, a phenomenon that can be used as an indication of damage. According to literature, damage in a cross-section of the concrete deck of a composite concrete-steel structure causes the neutral axis to move down. This paper attempts to explain an observation from field data that the neutral axis could move up in the presence of damage in the concrete deck of a composite structure. Preliminary results show that the use finite element model has potential to produce results that help explain the observation.
Population recovery in New Orleans after Hurricane Katrina: exploring the potential role of stage migration in migration systems

In this research brief, we explore how places affected by natural disasters recover their populations through indirect, or "stage," migration. Specifically, we consider the idea that post-disaster impediments (e.g., housing and property damage) in disaster-affected areas spawn migration flows toward and, over time, to disaster-affected areas through intermediary destinations. Taking as our case Orleans Parish over a five-year period after Hurricane Katrina, we show that stage migration accounted for up to about one-fourth of population recovery. We close by discussing the implications, limitations, and potential extensions of our work.
Modeling the Pathways and Mean Dynamics of River Plume Dispersal in the New York Bight

Abstract This study investigates the dispersal of the Hudson River outflow across the New York Bight and the adjacent inner- through midshelf region. Regional Ocean Modeling System (ROMS) simulations were used to examine the mean momentum dynamics; the freshwater dispersal pathways relevant to local biogeochemical processes; and the contribution from wind, remotely forced along-shelf current, tides, and the topographic control of the Hudson River shelf valley. The modeled surface currents showed many similarities to the surface currents measured by high-frequency radar [the Coastal Ocean Dynamics Applications Radar (CODAR)]. Analysis shows that geostrophic balance and Ekman transport dominate the mean surface momentum balance, with most of the geostrophic flow resulting from the large-scale shelf circulation and the rest being locally generated. Subsurface circulation is driven principally by the remotely forced along-shelf current, with the exception of a riverward water intrusion in the Hudson River she...
Recovery of close Frenkel pairs produced by low energy recoils in SiC

Simulations of displacement cascades in silicon carbide (SiC) indicate that most defects created are point defects, where interstitials are displaced only a small distance from the nearest vacancies. Of the interstitial defects produced in SiC, about 40% survive as freely migrating interstitials that can contribute to microstructural evolution during irradiation of SiC. The stable defect configurations in this study were created with low-energy recoils using molecular dynamics (MD) simulation. These stable Frenkel pairs have been annealed at different temperatures, using MD methods, to determine the time required for interstitials to recombine with vacancies. The MD data have been analyzed using an Arrhenius relation, and the activation energies for defect recombination processes range from 0.22 to 1.6 eV for C Frenkel pairs and from 0.28 to 0.9 eV for Si Frenkel pairs. These low activation energies for spontaneous recovery of Frenkel pairs in SiC are qualitatively consistent with the recovery processes o...
Thermionic emission from giant fullerenes

Large even-numbered carbon clusters in the size range from 100 to 600 atoms (giant fullerenes) were generated by laser vaporization and directly injected as positive ions via a supersonic beam into the magnetic trap of an ion cyclotron resonance apparatus. Intense laser excitation of the magnetically levitated fullerenes at 4.0 eV was found to result in production of multiply charged fragments in the trap. Details of the time scale and size dependence of this process suggest it is due to thermionic emission from the superheated gas phase clusters.
Excitation of zero-frequency magnetic field-aligned currents by ionospheric heating

Time-dependent, three-dimensional numerical simulations of the reduced MHD model describing shear Alfven waves in the magnetosphere provide an interesting prediction superficially similar to results of several ionospheric heating experiments conducted at high altitudes. In these experiments, heating of the ionospheric F-region with a constant/zero-frequency beam of HF waves causes luminous structures in the ionosphere in the form of a ring or a solid spot with a characteristic size comparable to the size of the heated spot. Simulations suggest that spots/rings or similar optical appearance might be associated with a magnetic field-aligned current system produced by the ionospheric heating. Two of the most interesting features of this current system are (1) strong localization across the ambient magnetic field and (2) distinctive non-symmetrical luminous signatures (ring/spot) in magnetically conjugate locations in the ionosphere.
Ranking economic liberty across countries

We have constructed a number of summary indexes of economic liberty based on principal component and hedonic weighting techniques. While overall these indexes are related to each other in a statistical sense, there are sufficient differences among them to impact the rankings of the individual countries. Because the liberty indicators currently available for use are fairly coarse, the differences that these weighting techniques yield in the summary liberty indexes are understated. As research on liberty yields finer measures of the liberty indicators, the choice of the weighting technique will become more crucial in defining an overall measure of economic liberty. As Table 3 indicates, the simple overall ranking index we created summarizes the information content of all the other indexes (based on hedonic, data variance, etc. rationale) and appears to be very robust with respect to all of them. In addition, all the rankings indicate that economic growth and RGDP are positively correlated with the level of economic liberty within a nation.
A memorable drive through calculus

ABSTRACT In a project involving a short car trip, students experience an early opportunity to work in teams and think about mathematics. Students gather and analyze speed and distance data, and then produce a report on their findings. A typical student-authored solution is provided.
Analytical applications of laser moding caused by intracavity absorption

Abstract A continuous CO2 laser with a reflecting mirror can operate at several wavelengths simultaneously. If an organic vapor is introduced into a separate cavity in the laser optical path, the laser will sometimes mode rapidly causing some lasing lines to diminish to zero and others to become enhanced; this has been observed even for very low amounts (10-5 g) of organic gases. Laser intercavity absorption spectroscopy depends on overlap of a vibrational—rotational line of a sample with a laser transition line. The absorption by the sample greatly affects the laser wavetrain at that particular wavelength and interferes with the lasing action. The technique is not based on Beer's law, and the detection limits observed are orders of magnitude better than those of conventional infrared absorption spectroscopy. Two laser systems were used and various organic gases were studied. When a totally reflecting mirror which permitted free moding was used, the detection limits found were 0.14 μg, 0.95 μg and 0.60 μg for vinyl chloride, propylene, and ethylene, respectively. When a grating was used as the rear cavity optics restricting the wavelengths of the laser lines, the detection limits were 140 μg, 94 μg, 63 μg and 0.26 μg for vinyl chloride, propylene. ethylene and ethyl chloride, respectively.