cssi/SciSciGPT-SciSciNet huggingface dataset:
A New Approach to River Management: Action for a Sustainable Coastal Landscape

On June 1, 2006 at the beginning of the first hurricane season after Hurricanes Katrina and Rita, a group of 35 experts in geology, ecology, coastal geomorphology, oceanography, engineering, and economics from across the United States and from as far away as Italy, the Netherlands, the United Kingdom, Egypt, Russia, and Australia delivered this message to the Governor of the State of Louisiana (http:// www.futureofthegulfcoast.org/files/finalreport. pdf). Brought together to consider the future of the Louisiana coast after the hurricanes of 2005, for a week in April 2006 the Technical Group of the Envisioning the Future of the Gulf Coast (TGEFGC) conference toured the coast, heard about its problems, shared their perspectives, and then developed their recommendations. This paper considers those recommendations and the progress, or lack thereof, toward their implementation in the post-Katrina management of the Louisiana coast.
Effects of Domestic Violence on Perinatal and Early-Childhood Mortality: Evidence From North India

Objective. We examined the effect of physical violence during pregnancy on perinatal and early-childhood mortality.Methods. We estimated the prevalence of domestic violence during pregnancy among a population-based sample of 2199 women in Uttar Pradesh, India. We used a survival regression model to examine the risks for perinatal, neonatal, postneonatal, and early-childhood (aged 1–3 years) mortality by mother’s exposure to domestic violence, after we controlled for other sociodemographic and maternal health behavior risk factors.Results. Eighteen percent of the women in our study experienced domestic violence during their last pregnancy. After we adjusted for other risk factors, births among mothers who had experienced domestic violence had risks for perinatal and neonatal mortality that were 2.59 (95% confidence interval [CI]=1.35, 4.95) and 2.37 (95% CI=1.21, 4.62) times higher, respectively, than births among mothers who had not experienced violence. We found no significant associations between domest...
Marine-derived omega-3 fatty acids: fishing for clues for cancer prevention

Omega-3 fatty acids (FA) are polyunsaturated essential FA with anti-inflammatory properties. The most potent are the marine-derived eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which counteract the pro-inflammatory omega-6 FA. Americans take in an average of only 100 mg of EPA plus DHA per day resulting in a low omega-3:omega-6 intake ratio of 1:10 favoring inflammation. Cohort and/or case control studies suggest EPA and DHA are promising for breast, colon, and prostate cancer risk reduction. Mechanistic studies largely in preclinical models suggest EPA and DHA reduce synthesis of prostaglandin E2 and other inflammatory cytokines, decrease aromatase activity and proliferation, promote differentiation and apoptosis, and enhance insulin sensitivity. Animal models using 7% to 20% omega-3 added to chow are promising; however, this amount of omega-3 in a diet is unlikely to be acceptable to humans. The optimal EPA:DHA ratio or the lowest effective dose of EPA and DHA for cancer prevention is unclear, but it is likely to be more than 600 mg/day, which is six times the average American intake. Most phase II prevention trials use 1 to 3.3 g of EPA and DHA, which is safe and well tolerated. Two grams of EPA was associated with fewer polyps in individuals with familial adenomatous polyposis in a randomized, placebo-controlled trial. Identification of serum risk biomarkers modulated by EPA and DHA in healthy humans has remained elusive, but phase II prevention trials with tissue obtained for risk and response biomarkers are ongoing.
Might Fundamental Tax Reform Increase Criminal Activity

Fundamental tax reform, replacing the income tax with a sales tax, is commonly thought to reduce levels of criminal and other ‘underground’ economic activity by implicitly taxing their returns. This paper finds instead that the impact of tax reform depends on the relative labour intensity of production in the legitimate and illegitimate sectors of the economy. In the likely event that illegitimate output is produced by using more labour-intensive techniques than is legitimate output, then replacing an income tax with a sales tax reduces the cost of criminal and other underground activity, thereby stimulating its growth.
Needs of Parents of Young Children with Developmental Delay: Implications for Social Work Practice

Recent legislation (P.L. 99–457, Part H) requires that parental needs be addressed in the service delivery to families of infants and toddlers with a developmental delay. The author reviews the his...
Bounds for the chromatic number of graphs with partial information

We obtain bounds for the chromatic and clique numbers of a simple graph, first in terms of the number of vertices and edges it contains, and then in terms of its vertex degrees. In every case, we examine the tightness of the bounds we obtain. We also briefly discuss lower bounds for the independence number of a graph in terms of the same parameters.
Yin and Yang of an endothelial cell: from normal to the extreme in growth, secretion, and transdifferentiation capabilities

Jacques Hadamard, the brilliant French mathematician, wrote that, to study a phenomenon, one should look at it not only from up close but also from afar, not only for its main features but also for extremes.1 Application of this conceptual approach to the subject of our interest, pulmonary vascular endothelium, can potentially generate new ideas regarding endothelial cell (EC) functions. Though well studied with regard to its “traditional” roles in controlling vascular tone, coagulation, permeability and inflammation, less is known about more “extreme” capabilities of EC, such as disordered proliferation, control of smooth muscle cell (SMC) phenotype, and transdifferentiation into mesenchymal cells. By not regarding these extreme EC capabilities as rare or improbable, but rather by studying their regulatory mechanisms, we might gain better insight into the potential contribution of endothelium to the pathogenesis of pulmonary vascular diseases. The vascular endothelium is no longer believed to be a homogeneous population of cells as it might appear from the picture of a morphologically homogeneous EC culture (Figure 1A). It is, in fact, a highly heterogeneous tissue, with differences between cells in different vascular beds along the longitudinal axis of a single vessel and even at the same vascular site.2−6 Heterogeneity of endothelium
Inference and minimization of hidden Markov chains

A hidden Markov chain (hmc) is a finite ergodic Markov chain in which each of the states is labelled 0 or 1. As the Markov chain moves through a random trajectory, the hmc emits a 0 or a 1 at each times step according to the label of the state just entered.The inference problem is to construct a mechanism which will emit 0's and 1's and which is equivalent to a given hmc in the sense of having identical long-term behavior. We define the inference problem in a learning setting in which an algorithm can query an oracle for the long-term probability of any binary string. We prove that inference is hard: any algorithm for inference must make exponentially many oracle calls. Our method is information-theoretic and does not depend on separation assumptions for any complexity classes. We show that the related discrimination problem is also hard, but that on a nontrivial subclass of hmc's there is a randomized algorithm for discrimination. Finally, we give a polynomial-time algorithm for reducing a hidden Markov chain to its minimal form, and from this there follows a new algorithm for equivalence of hmc's.
Review of Self-Report Depression and Anxiety Measures:

Although there are numerous self-report depression and anxiety measures, the correlation between self-report and interview methods is only moderate. Self-report instruments, however, have a definite place in psychiatric research. In this paper, commonly used self-report scales of depression and anxiety symptom severity are reviewed and critiqued, paying special attention to issues of treatment sensitivity in psychiatric efficacy studies. The validity and reliability of the following instruments are summarized: Beck Depression Inventory (BDI), Carroll Rating Scale for Depression (CRS), Zung Self-Rating Depression Scale (SDS), single item and multiple item Visual Analogue Scales (VAS), Symptom Checklist (SCL-90), Profile of Mood States (POMS), and State Trait Anxiety Inventory (STAI). Although self-report scales cannot substitute for interview methods, they are a useful adjunct approach in psychiatric outcome studies.
Learning conditional frequencies in a probability learning task

Abstract The study was prompted by a theoretical discussion of probability learning by Estes (1976). In three separate experiments, subjects were presented with frequency information in the form of wins and losses among 3 teams, and later predicted future wins and losses. Frequencies were devised so that conditional win frequencies for a pair of teams were either inconsistent or consistent with marginal win frequencies for each team. In experiment 1, when subjects predicted future events on the basis of known past frequencies, predictions were generally based on conditional frequencies. In experiment 2 six blocks of observations were presented, with predictions following each block. What little learning did occur was in the direction of the conditional frequencies. Subjects in experiment 3 were able to learn conditional frequencies when given explicit instructions to do so. Results were discussed in terms of a two-stage hypothesis generation model that might operate within the framework of an associative theory of probability learning.
THE HEDJAZ METEORITE

The Hedjaz meteorite has been studied in detail and on a chemical basis, with 22.1% total Fe, 9% metallic Fe, 1.3% Ni and constant olivine composition (Fa23–24), can be classified as an L-group chondrite. However, petrographically Hedjaz is quite hoterogeneous and contains features characteristic of types 3, 4, 5, and 6, observations that refute a petrographic type classification. Indeed, Hedjaz, as a complex breccia, exhibits no evidence of metamorphic equilibration after accretion and supports the contention that type 4 (also 5 and 6) chondrites are not derivatives of type 3 material, and that types 5 and 6 are not necessarily more “metamorphosed,” only better crystallized.
The pentose cycle in the liver. Estimation under conditions of gluconeogenesis

Abstract 1. 1. Two simplified models were developed representing the interaction of the pentose cycle and the gluconeogenic pathway in the liver. 2. 2. Under conditions of gluconeogenesis, the stoichiometry of the pentose cycle becomes 1 glucose 6-P → 6 CO2, rather than 1 glucose 6-P → 1 triose P + 3CO2 as in glycolytic tissues. 3. 3. The first model to estimate pentose cycle uses the relative 14C yields in 14CO2 and glucose from [1-14C] galactose, together with an estimation of the rate of glucose 6-phosphatase, obtained from analytical data on the rate of glucose formation, together with isotopic data on the rate of glucose phosphorylation when glucose is initially present. 4. 4. The second model involves determination of the randomization of 14C in glucose formed from substrates which introduce 14C into C-3 (or C-2) of glucose 6-P. 5. 5. Preliminary degradation data, obtained in experiments with liver cells from starved-refed rats in which lipogenesis was high, are in accord with the classical formulation of the pentose cycle.
Detrimental effects of repeated administration of the tryptophan-load test for vitamin B-6 status on deficient and pair-fed control rats

Abstract The tryptophan (trp)-load test is a commonly used test of vitamin B-6 status, in which urinary xanthurenic acid (XA) is measured following a dose of trp. Repeated trp-loads were administered to twelve week old, female Long-Evans rats and several physiologic variables were compared to those in non-loaded rats. Trp-loaded rats (n=7–8) were fed a purified diet devoid of pyridoxine HCl (DEF), or a control diet (AIN-76A) ad libitum (AL-CON) or pair-fed (PF-CON) to DEF for 17 weeks. Rats were injected i.p. with 5 mg trp/100 g body weight weekly for 11 weeks, then again at week 18. Another three groups (n=9–12) were fed similarly, but were never given a trp-load. XA excretion was elevated (P
Growth hormone-releasing hormone is produced by rat Leydig cell in culture and acts as a positive regulator of Leydig cell function

Rat GH-releasing hormone (GHRH), mainly contained in hypothalamic neurons, has also been identified in several extraneural tissues, including the gastrointestinal tract, placenta, ovary, and testis. In the testis, GHRH mRNA is ontogenically regulated, and GHRH immunoreactivity can be observed in interstitial cells and tubules, suggesting an intratesticular role for the peptide. Leydig cells in culture are able to produce hypothalamic releasing hormones, i.e. CRH, which acts as an autocrine negative regulator of Leydig cell function. In this study we investigated whether GHRH is present in Leydig cells and evaluated the role of the peptide in Leydig cell function. Adult Leydig cells in culture produced considerable amounts of immunoreactive GHRH [23.9 +/- 2.1 (+/- SE) pg/10(6) cells.30 min], and the release of the peptide was acutely stimulated by hCG. HPLC analysis of GHRH in media from basal and hCG-treated cultures showed the presence of a single peak eluting at the same retention time as that of hypoth...
Changes in myocardial repolarization in patients undergoing balloon valvuloplasty for congenital pulmonary stenosis: evidence for contraction-excitation feedback in humans.

Alterations in ventricular loading conditions lead to changes in action potential duration and arrhythmias via contraction-excitation feedback; a decrease in load leads to prolongation of repolarization. To determine whether changes in right ventricular load alter ventricular repolarization in man, the corrected QT interval, a measure of overall ventricular repolarization, was measured in 32 patients before and after valvuloplasty for pulmonary stenosis. Right ventricular systolic pressure decreased (82.5 +/- 30.7 to 40.5 +/- 9.5 mm Hg, p less than .001) and the QTc increased concurrently (409.1 +/- 24.3 to 440.7 +/- 28.0 msec, p less than .001) after successful valvuloplasty. The increase in QTc was most marked for those patients with a greater than 30 mm Hg decrease in right ventricular pressure (40.0 +/- 23.3 vs 16.3 +/- 21.3 msec, p = .006). In a subset of seven patients in whom monophasic action potentials were recorded, monophasic action potential duration, a measure of local repolarization, was prolonged (230.0 +/- 24.3 vs 216.9 +/- 21.9, p less than .001) after successful valvuloplasty, confirming that the QTc prolongation reflected changes in local ventricular repolarization. In addition, during nine acute right ventricular outflow tract occlusions in a subset of six patients, monophasic action potential duration shortened (206.6 +/- 17.6 vs 221.7 +/- 20.9 msec, p less than .01) and early afterdepolarizations developed consistent with contraction-excitation feedback. These data suggest that, in humans, changes in mechanical load are associated with changes in ventricular repolarization consistent with contraction-excitation feedback.
Anticoagulant heparan sulfate: structural specificity and biosynthesis

Heparan sulfate (HS) is present on the surface of endothelial and surrounding tissues in large quantities. It plays important roles in regulating numerous functions of the blood vessel wall, including blood coagulation, inflammation response, and cell differentiation. HS is a highly sulfated polysaccharide containing glucosamine and glucuronic/iduronic acid repeating disaccharide units. The unique sulfated saccharide sequences of HS determine its specific functions. Heparin, an analog of HS, is the most commonly used anticoagulant drug. Because of its wide range of biological functions, HS has become an interesting molecule to biochemists, medicinal chemists, and developmental biologists. In this review, we summarize recent progress toward understanding the interaction between HS and blood-coagulating factors, the biosynthesis of anticoagulant HS and the mechanism of action of HS biosynthetic enzymes. Furthermore, knowledge of the biosynthesis of HS facilitates the development of novel enzymatic approaches to synthesize HS from bacterial capsular polysaccharides and to produce polysaccharide end products with high specificity for the biological target. These advancements provide the foundation for the development of polysaccharide-based therapeutic agents.
Interpretation of floodplain pollen in alluvial sediments from an Arid Region

Pollen was collected from modern alluvium and from the atmosphere to document the nature and amount of paleoenvironmental information reflected by alluvial pollen chronologies. Results indicate that pollen in alluvium is a homogeneous mixture derived almost entirely from the floodplain itself. The few pollen grains derived from nonfloodplain plant communities and preserved in alluvial sediments are so well mixed that their frequencies no longer reflect the geographic distribution of the specific plant communities in which they originated. In contrast, the abundance of alluvial pollen grains, derived from the major floodplain taxa (Chenopodiineae, Ambrosia type), varies with summer and winter climate. This annual variation is preserved in alluvial pollen assemblages through a combination of processes within sedimentation basins involving discontinuous deposition events and mechanical pollen degradation. The high-frequency, wide-amplitude pollen variance in alluvial pollen assemblages contrasts with the low-frequency, narrow-amplitude pollen variance in sediments of lakes and ponds. The slight geographic variance in alluvial pollen assemblages, in contrast to the large variance in soil pollen, allows use of alluvial pollen to infer climate throughout the watershed in which pollen is sampled.
Toward synthetic tubes for NO2/N2O4: design, synthesis, and host-guest chemistry.

Design of molecular nanotubes is proposed for entrapment and conversion of NO2/N2O4 gases. Synthesis of 1,3-alternate bis-calix[4]arene tube 3 of 5 × 11 A internal dimensions is presented, and its reversible reactions with NO2/N2O4 in solution are studied. Exposure of 3 to NO2/N2O4 in chlorinated solvents results in the rapid encapsulation of nitrosonium (NO+) cations within its interior. Mono- and dinitrosonium complexes 4 and 5, respectively, were isolated and characterized by UV−vis, FTIR, and 1H NMR spectroscopies, and also molecular modeling. The NO+ entrapment process is reversible, and addition of water quickly recovered starting tube 3. Encapsulated within the tube NO+ species act as nitrosating agents for secondary amides. These findings open wider perspectives toward NO2/NOx storing and converting materials and also offer a promise for further development of supramolecular chemistry of synthetic nanotubes.
Ventral tegmental lesions impair sexual receptivity in female hamsters.

Abstract The ventral mesencephalon appears to be one of the sites of progesterone action in the control of sexual receptivity in female hamsters. The behavioral response to systemic progesterone was assessed in female hamsters following electrolytic lesions of portions of the ventral mesencephalon. Adult female hamsters were ovariectomized and pretested for sexual receptivity, then were given bilateral lesions aimed at the region of the ventral mesencephalon where progesterone implants have been shown to facilitate receptivity. Lesions were produced by stereotaxically lowering an electrode and applying anodal direct current of 1–2 mA for 5–20 seconds. One week later the hamsters were injected with estrogen followed 44 h later by progesterone. They were then tested for sexual receptivity. After this test, their brains were removed and histologically prepared. Lesion location was determined and lesion size was quantified with a digitizing pad. Lesions which were centered in and destroyed much of the ventral tegmental area produced the greatest lordosis impairments. Mesencephalic lesions which did not bilaterally damage the ventral tegmental area had little effect. These results support the hypothesis that the ventral mesencephalon. particularly the ventral tegmental area, is an important site for the facilitative action of progesterone on sexual receptivity in estrogen-primed female hamsters.
Attitudes about infertility interventions among fertile and infertile couples.

BACKGROUND. There has been marked progress in the development of infertility interventions. This paper reports attitudes about 11 interventions for infertility. METHODS. Face-to-face interviews were conducted with each member of 185 infertile and 90 presumed fertile couples in southeastern Michigan. RESULTS. Seven of these interventions were generally viewed favorably and four were generally viewed negatively, regardless of the couple's fertility status. Infertile couples viewed all interventions, except for adoption, more favorably than did fertile couples. Multidimensional scaling was used to cluster the interventions according to similarity in endorsement. These clusters form a continuum from interventions that allow only one member of the couple to be a biological parent to the most noninvasive techniques. All clusters remain roughly equidistant from adoption, in which neither member of the couple is a biological parent. CONCLUSIONS. Interventions that produce a child who is biologically related to on...
Analgesia following microinjection of phosphodiesterase inhibitors at brainstem sites

Abstract Microinjection of RO 20-1724 (0.60 μg) at sites in the caudal reticular formation of the rat brainstem resulted an analgesia in the tail flick, paw pinch and hot plate tests. Microinjection of theophylline (0.45 μg) at sites in the caudal reticular formation also produced analgesia in the tail flick and hot plate tests, but not in the paw pinch test. Since these agents inhibit phosphodiesterase and elevate cyclic nucleotides in rat brain homogenates, these data suggest that cyclic nucleotides have a functional role in brainstem structures involved in modulation of nociceptive threshold.
Transcatheter arterial chemoembolization with drug eluting beads in the setting of portal vein thrombosis: Single center evaluation of survival

Purpose To evaluate the short- and long-term survival outcomes of drug-eluting bead transcatheter arterial chemoembolization (DEB-TACE) in patients with portal vein tumor thrombus (PVTT). Materials and Methods Between November 2007 and June 2012, 1019 DEB-TACE procedures were performed with doxorubicin loaded 100-300 LC Beads (Biocompatibles, United Kingdom) in 626 consecutive patients with hepatocellular carcinoma (HCC). Retrospective analysis of the medical record revealed a cohort of 35 patients that had PVTT with no prior treatment. 30-day mortality, overall survival, and treatment response to DEB-TACE on follow-up imaging, as determined by mRECIST criteria, was compared in patients with main PVTT to those with branch PVTT. No patients had PVTT extending into the superior mesenteric vein or splenic vein. Results Mean overall survival was significantly shorter in patients with main PVTT compared to those with branch PVTT (105 ± 68 days vs. 283 ± 257 days, p=0.05). Mortality at 30 days was 22% and 8% in the main PVTT and branch PVTT groups respectively, not significantly different (p=0.27). Disease progression on initial follow-up imaging was 22% and 15% in the main PVTT and branch PVTT groups respectively, not significantly different (p=0.60). Conclusion Extent of PVTT has important prognostic value, with main PVTT associated with significantly shorter overall survival compared to patients with branch PVTT. Main PVTT was not associated with a significantly higher 30-day mortality.
Cloning of the marmoset herpesvirus thymidine kinase gene and analyses of the boundaries of the coding region.

Abstract In order to delimit the approximate boundaries of the marmoset herpesvirus (MarHV) thymidine kinase (TK) gene, Hind III and Bam HI digests of MarHV DNA were cloned in plasmid pBR322. Several recombinant plasmids which transformed E. coli K12 strain RR1 to ampicillin resistance were isolated. The MarHV DNA inserts in these plasmids accounted for about half of the MarHV genome. One of the plasmids, pMAR4, contained a 9.1-kbp fragment of MarHV DNA ( Hind III-G), transformed LM(TK − ) cells to TK + , and hybridized to the Bam HI-I fragment of MarHV DNA, which had previously been shown to have TK-transforming activity. pMAR4 DNA had little or no homology to the 2-kbp Puv II fragment of HSV-1 DNA, which contains the HSV-1 TK gene. Cleavage with Pvu II, Sac I, Sma I, and Kpn I inactivated the TK-transforming activity of pMAR4, but cleavage with Hind III, Pst I, Eco RI, Xho I, Xba I, and Bam HI did not. Deletion mutants pMAR401 and pMAR420, which lacked the 2.6-kbp Kpn I and the 2.75-kbp Eco RI fragments, respectively, of pMAR4, lost transforming activity, whereas pMAR410, which lacked a 2.9kbp Xho I fragment of pMAR4 did not. Recombinant plasmid pMAR430, which contained a 3-kbp Pst I fragment of pMAR4, also transformed LM(TK − ) cells to TK + . The results strongly suggest that the coding region of the MarHV TK gene was within a 2.4-kbp pMAR4 sequence extending from the Pst I (0.33 kbp) to the Eco RI (2.7 kbp) cleavage sites.
Effect of pharmacological purging on natural killer cell number and activity in human bone marrow

Abstract We assayed natural killer (NK) cell activity and phenotype from human bone marrow (BM) following “purge” with 4-hydroperoxycyclophosphamide (4HC) at 60 μg/ml for 30 min in vitro. In all cases studied, lytic activity against the K562 cell line was either significantly decreased or abolished following 4HC purge. Although NK activity was significantly affected by 4HC treatment, no major differences in the phenotype between the purged and unpurged population were seen. Further, while in vitro culture of BM with IL2 resulted in a significant increment of NK activity, no IL-2 responsive cells were found in the 4HC purged BM after 14 days of culture. This study demonstrates that pharmacological purging of bone marrow results in a persistent functional decline of NK cell activity and may serve as a useful model for the study of the ontogeny of NK cells.
Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP•Mg2+ and 5′-OH oligonucleotide and a product complex with GDP•Mg2+ and 5′-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition

Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor. Here we report the crystal structures of CthPnk-D38N in a Michaelis complex with GTP•Mg(2+) and a 5'-OH oligonucleotide and a product complex with GDP•Mg(2+) and a 5'-PO4 oligonucleotide. The O5' nucleophile is situated 3.0 A from the GTP γ phosphorus in the Michaelis complex, where it is coordinated by Asn38 and is apical to the bridging β phosphate oxygen of the GDP leaving group. In the product complex, the transferred phosphate has undergone stereochemical inversion and Asn38 coordinates the 5'-bridging phosphate oxygen of the oligonucleotide. The D38N enzyme is poised for catalysis, but cannot execute because it lacks Asp38-hereby implicated as the essential general base catalyst that abstracts a proton from the 5'-OH during the kinase reaction. Asp38 serves as a general acid catalyst during the 'reverse kinase' reaction by donating a proton to the O5' leaving group of the 5'-PO4 strand. The acceptor strand binding mode of CthPnk is distinct from that of bacteriophage T4 Pnk.
Baker’s yeast (Saccharomyces cerevisiae) mediated transformations of C-aryl-N-phenylnitrones

Abstract C -Aryl- N -phenylnitrones are transformed to a mixture of azoxybenzene and aryl aldehydes when treated with a mixture of Baker’s yeast and sucrose in pH = 6.0 phosphate buffer medium at 32 °C.
Phylogeography: retrospect and prospect

Phylogeography has grown explosively in the two decades since the word was coined and the discipline was outlined in 1987. Here I summarize the many achievements and novel perspectives that phylogeography has brought to population genetics, phylogenetic biology and biogeography. I also address future directions for the field. From the introduction of mitochondrial DNA assays in the late 1970s, to the key distinction between gene trees and species phylogenies, to the ongoing era of multi-locus coalescent theory, phylogeographic perspectives have consistently challenged conventional genetic and evolutionary paradigms, and they have forged empirical and conceptual bridges between the formerly separate disciplines of population genetics (microevolutionary analysis) and phylogenetic biology (in macroevolution).
Impact of intraoperative dexmedetomidine on postoperative analgesia following gynecologic surgery

AbstractObjective:To assess the impact of intraoperative dexmedetomidine infusion on postoperative analgesia in women undergoing major open and laparoscopic gynecologic surgery under general anesthesia.Research design and methods:A retrospective analysis of patients who underwent major open and laparoscopic gynecologic surgery under general anesthesia from January 2007 to October 2008. Patients who received intraoperative opioids with a dexmedetomidine infusion were compared to those who received opioids alone. Patients who received regional anesthesia, remifentanil, or other analgesic adjuncts were excluded. Data were collected in the postanesthesia care unit (PACU) for all patients, and for 24 hours in the open group.Results:A total of 580 women were included in the analysis (293 open surgery [103 dexmedetomidine, 190 controls] and 287 laparoscopic surgery [101 dexmedetomidine, 186 controls]). In the open group, patients who received dexmedetomidine required less opioids intraoperatively and in PACU. Ho...
Gas Mixtures For X-Ray Proportional Counters

Results are presented which detail the performance of proportional counters when filled with a wide variety of argon- and xenon-based gas mixtures. It is shown that alternative gas mixtures can offer considerable advantages in the counters. The mixtures of argon plus 10 percent propane and xenon plus 10 percent propylene look particularly attractive in terms of operating voltage and energy resolution. The quench gas CO2 returns the poorest results in all areas except aging.
Absolute absorption measurements in polymer films using photothermal deflection spectroscopy

The weak absorption of waveguide materials can be measured by Photothermal Deflection Spectroscopy (PDS) with two orders of magnitude or higher sensitivity than conventional UV-VIS absorption spectroscopy. While it is easy to obtain relative absorption spectra for thin polymer films with PDS, extracting absolute absorption coefficients is more involved. The PDS measured signals depend on both thermal and optical absorption properties of materials. Knowledge of thermal properties is necessary to extract absorption coefficients. We report a methodology to obtain from PDS independently the thermal properties and absolute absorption coefficients.
Solar Wind Speed Structure in the Inner Corona at 3-12 Ro

Estimates of solar wind speed obtained by Armstrong et al. [1986] based on 1983 VLA multiple-station intensity scintillation measurements inside 12 R(sub o) have been correlated with the electron density structure observed in white-light coronagraph measurements. The observed large- scale and apparently systematic speed variations are found to depend primarily on changes in heliographic latitude and longitude, which leads to the first results on large-scale speed structure in the acceleration region of the solar wind. Over an equatorial hole, solar wind speed is relatively steady, with peak-to-peak variations of 50 km/s and an average of 230 km/s. In contrast, the near-Sun flow speed across the streamer belt shows regular large-scale variations in the range of 100-300 km/s. Based on four groups of data, the gradient is 36 km/s per degree in heliocentric coordinates (corresponding to a rise of 260 km/s over a spatial distance on the Sun of two arcmin) with a standard deviation of 2.4 km/s per degree. The lowest speeds most likely coincide with the stalks of coronal streamers observed in white-light measurements. The detection of significant wind shear over the streamer belt is consistent with in situ and scintillation measurements showing that the density spectrum has a power-law form characteristic of fully developed turbulence over a much broader range of scales than in neighboring regions.
Functional flexibility in T cells: independent regulation of CD4+ T cell proliferation and effector function in vivo.

Abstract Proliferation and differentiation of CD4 + T cells are often correlated, but it is not clear whether they are mechanistically linked. When antigen-specific T cells are present at high frequency in vivo, they all respond to antigenic peptide stimulation by expressing activation markers, but only a subset begins to proliferate. However, noncycling cells may synthesize the effector cytokine IFNγ even though their cell cycle is blocked in G1. These data show that proliferation and effector function are not rigidly linked in T cells. Instead, CD4 + T cells have the flexibility to engage in or bypass clonal expansion based on the integration of multiple signals, including the frequency of other responding T cells.
RELIABILITY THEORY APPLIED TO ACCOUNTING INTERNAL CONTROL: A FIELD STUDY

Abstract Reliability modeling of accounting internal control structures has appeared in professional accounting literature but has not resulted in application in practice. Reasons for this include the lack of a prototype for application, the lack of expertise in the accounting discipline, computational complexities, and the resistance of the accounting profession to quantitative methods. The increased power and portability of computers and the need of the accounting profession for more interdisciplinary approaches to the evaluation and design of such systems have generated the need to reconsider the potential of the reliability approach. This paper presents a prototype for application and reports on a field study using this prototype.
Identifying New Methylated Arginines via Granular Decision Fusion with SVM Modeling

Traditional methods of discovering new methylated arginines in proteins involve conducting delicate experiments to examine every arginine in the primary sequence. Such process is labor-intensive and time-consuming. To speed up this process, one popular way is using machine learning method to model the underlying mechanism of protein methylation based on known methylated proteins and then suggesting candidate positions on unknown proteins. In this paper, we first collect several proteins methylated by different families of PRMTs, and then use granular computing methods to build a granular decision fusion method based on SVM modeling. Such decision fusion method can produce high prediction accuracy. More importantly, we use this method to successfully discover several highly possible methylation sites on some unknown proteins, biological experiments have verified our results.
Cell-based therapeutic products: potency assay development and application

Potency is a critical quality attribute of biological products, defined by the US FDA as the specific ability or capacity of the product, as indicated by appropriate laboratory tests or by adequately controlled clinical data obtained through the administration of the product in the manner intended, to effect a given result. Ideally, a potency assay will leverage the product’s mechanism of action. Alternatively, the assay may focus on a therapeutically relevant biological activity. The absence of rigorous mechanistic data for the majority of cell-based therapeutics currently in the process research pipeline has impeded efforts to design and validate indices of product potency. Development of a systematic battery of parallel functional assays that, taken together, can address all potential mechanisms of action believed to be relevant for the product platform is recommended. Such an approach is especially important during preclinical development. Here, we summarize the principal and unique challenges facing ...
Nucleic Acids for Computation

Nucleic acids have many features that are ideal for molecular computation. Using nucleic acids, we have constructed a full set of molecular logic gates, with modular stem-loop-controlled deoxyribozymes as switches and single-stranded oligonucleotides as inputs and outputs. These gates have been combined to form basic computational circuits, including a half- and a full-adder, and can also be assembled into automata to perform complex computational tasks such as game playing. Our most advanced automaton to-date integrates more than 100 nucleic acid logic gates to play a complete game of tic-tac-toe encompassing 76 possible game plays. Inputs and outputs can also be coupled with upstream and downstream components, such as aptamers, sensors, secondary gate activation, and small-molecule release, indicating the potential for nucleic acid computation in the engineering of autonomous therapeutic and diagnostic molecular devices.
Effect of regional anesthesia on pain sensitization after surgery: New concepts

Severe postoperative pain and wound hyperalgesia, a clinical sign of central sensitization, are risk factors for the development of chronic postsurgical pain. This article describes the neuronal changes that surgical pain and possibly high opioid doses cause in the central nervous system. It also relates how regional anesthesia might oppose these changes and block both the pain sensitization and the pain chronification following surgery.
Cell-Surface display of heterologous proteins: From high-throughput screening to environmental applications.

A variety of expression systems for the display of either short peptides or fully folded proteins on E.coli and, to a lesser extent, on Gram-positive bacteria have been developed. The expression of proteins on the surface of microbial cells has proved extremely important for numerous applications ranging from combinatorial library screening and protein engineering, to whole cell biocatalysts and adsorbants for bioremediation purposes.
Preliminary Long-Term Follow-up of Mindfulness-Based Cognitive Therapy-Induced Remission of Depression

Major depressive disorder is often chronic and characterized by relapse and recurrence despite successful treatments to induce remission. Mindfulness-based cognitive therapy (MBCT) was developed as a means of preventing relapse for individuals in remission using cognitive interventions. In addition, MBCT has preliminarily been found to be useful in treating active depression. This current investigation is unique in evaluating the long-term outcome of individuals with active depression who achieved remission with MBCT. Eighteen participants who achieved remission after an 8-week MBCT group were seen for evaluation at a mean follow-up interval of 48.7 months (SD = 10.2) after completing treatment. The current study shows that in these participants, the gains achieved after the initial treatment including remission of depression, decreased rumination, decreased anxiety, and increased mindfulness continued for up to 58.9 months of follow-up. The data suggest that all levels of depression from less recurrent and mild to more recurrent and severe were responsive to MBCT. The average number of minutes per week of continued practice in our cohort was 210, but the number of minutes of practice did not correlate with depression outcomes. MBCT's effects may be more related to regularity of practice than specific quantity. This study provides a preliminary exploration of MBCT's long-term effects, which can aid in future research with a typically chronic illness.
Radiocarbon in organic compound classes in particulate organic matter and sediment in the deep northeast Pacific Ocean

Radiocarbon (Δ14C) and stable carbon isotopes (δ13C) were measured for total amino acids, carbohydrates, lipids and acid-insoluble organic fractions separated from sinking particulate organic matter (POMsink), detrital aggregates, sediment floe and sediments collected from the deep Northeast Pacific Ocean. The results show distinct Δ14C signatures among these organic compound classes. Bomb 14C, produced 3–4 decades ago in the atmosphere, was present in all organic fractions in the POMsink in the deep sea. Δ14C values decrease with depth, from the sediment trap POMsink (3450 m) to the sediment (4100 m), with rapid changes occurring at the sediment-water interface. Total lipid had much ‘older’ Δ14C values than those of amino acid and carbohydrate fractions in detrital aggregates, sediment floe and sediments. These data demonstrate that two processes may be occurring: 1) preferential decomposition of organic matter at the sediment-water interface, and 2) incorporation of ‘old’ organic carbon into POM and sediment. The alteration of carbon found in these organic compound classes suggests that differences in decomposition and chemical behavior exist for each of these compound classes in the deep ocean.
The Structure and Effects of Moral Predispositions in Contemporary American Politics

Moral values are frequently invoked in election campaigns. Some past studies have taken into account the effect of moral traditionalism on voting. However, a related moral predisposition—moral judgment—may have greater effects, and not taking moral judgment into account may lead to underestimation of the importance of moral values in affecting people's attitudes. Two statewide surveys are analyzed to determine the added effect of moral judgment. Moral judgment is found to have a greater impact that moral traditionalism on abortion views, some other cultural issues, and attitudes toward the Clinton impeachment.
Real-time estimation and control of particle size in semi-batch emulsion polymerization

The control of the relative particle growth of a bidisperse emulsion polymerization is investigated in an automated reactor control facility capable of online density and online particle size measurements. Final diameter ratio values are controlled by manipulating the monomer feed rate to the reactor using a control scheme comprised of a parameter adaptive Kalman filter with steady state gains and a nonlinear model predictive controller. One of the main features of the implemented controller is the connection of the prediction horizon to the criterion that the overall conversion equal 90% at the end of the batch. Feedback is incorporated into the algorithm at each sampling time by starting the model prediction calculation at the current estimated values of the model states. The controller performs well to meet a challenging diameter ratio set point at the end of the batch. The robustness of the controller to reject an induced initial initiator concentration disturbance is demonstrated.
A comparison of teacher checklists used over 15 days and a one-day antecedent analysis to conduct a medication trial

A one-day antecedent analysis and an extended school-based double-blind medication trial were used to assess the effects of Ritalin on the disruptive behavior of a child diagnosed with ADHD. The evaluations took place in an outpatient clinic and in the child's general education classroom. The results of both evaluations indicated that the medication had a positive effect on reducing disruptive behaviors. The investigation suggests that the one-day antecedent analysis procedure could be used as an initial evaluation of the use of Ritalin. More importantly, the one-day trial provided results similar to the outcomes obtained during the school-based evaluation. © 2004 Wiley Periodicals, Inc. Psychol Schs 41: 235–240, 2004.
MOCVD Growth of InNxAs1—x on GaAs Using Dimethylhydrazine

InNAs/GaAs multiple-quantum-well samples were grown by MOCVD on (100) n + -GaAs substrates at 500 °C and 60 Torr using uncracked dimethylhydrazine (DMHy). Quantum well layers were grown using trimethylindium, tertiarybutylarsine, and 95-97.5% of DMHy in the vapor phase, while GaAs buffer, barrier, and cap layers were grown using trimethylgallium and arsine. The crystalline quality and solid phase composition were evaluated using high-resolution X-ray diffraction analysis. The nitrogen content in InNAs wells was determined to be 18%. Surface morphology was investigated by atomic force microscopy (AFM) and field emission microscopy (FEM). Photoluminescence measurements confirm that the bandgap energy of InNAs is significantly lower than that of InAs. The peak emission wavelength of ∼6.5 μm at 10 K is the longest reported so far for dilute nitride semiconductors.
Implementation and evaluation of various demons deformable image registration algorithms on a GPU

Online adaptive radiation therapy (ART) promises the ability to deliver an optimal treatment in response to daily patient anatomic variation. A major technical barrier for the clinical implementation of online ART is the requirement of rapid image segmentation. Deformable image registration (DIR) has been used as an automated segmentation method to transfer tumor/organ contours from the planning image to daily images. However, the current computational time of DIR is insufficient for online ART. In this work, this issue is addressed by using computer graphics processing units (GPUs). A gray-scale-based DIR algorithm called demons and five of its variants were implemented on GPUs using the compute unified device architecture (CUDA) programming environment. The spatial accuracy of these algorithms was evaluated over five sets of pulmonary 4D CT images with an average size of 256 × 256 × 100 and more than 1100 expert-determined landmark point pairs each. For all the testing scenarios presented in this paper, the GPU-based DIR computation required around 7 to 11 s to yield an average 3D error ranging from 1.5 to 1.8 mm. It is interesting to find out that the original passive force demons algorithms outperform subsequently proposed variants based on the combination of accuracy, efficiency and ease of implementation.
The Hematopoietic Transcription Factor AML1 (RUNX1) Is Negatively Regulated by the Cell Cycle Protein Cyclin D3

The family of cyclin D proteins plays a crucial role in the early events of the mammalian cell cycle. Recent studies have revealed the involvement of AML1 transactivation activity in promoting cell cycle progression through the induction of cyclin D proteins. This information in combination with our previous observation that a region in AML1 between amino acids 213 and 289 is important for its function led us to investigate prospective proteins associating with this region. We identified cyclin D3 by a yeast two-hybrid screen and detected AML1 interaction with the cyclin D family by both in vitro pull-down and in vivo coimmunoprecipitation assays. Furthermore, we demonstrate that cyclin D3 negatively regulates the transactivation activity of AML1 in a dose-dependent manner by competing with CBFbeta for AML1 association, leading to a decreased binding affinity of AML1 for its target DNA sequence. AML1 and its fusion protein AML1-ETO have been shown to shorten and prolong the mammalian cell cycle, respectively. In addition, AML1 promotes myeloid cell differentiation. Thus, our observations suggest that the direct association of cyclin D3 with AML1 functions as a putative feedback mechanism to regulate cell cycle progression and differentiation.