cssi/SciSciGPT-SciSciNet huggingface dataset:
Boolean analysis of high-throughput biological datasets

Advances in DNA microarray technology that enable the simultaneous measurement of thousands of genes in a single experiment has revolutionized current molecular biology. The 21st century is witnessing an explosion in the amount of biological information on normal and disease biological processes. Scalable approaches for the analysis and the organization of this vast amount of information into usable forms is needed. We introduce StepMiner, a tool for the analysis of timecourse microarray data that discovers stepwise changes in the timecourse. StepMiner groups genes whose expressions change at the same direction and at the same time. In addition, we present the use of Boolean implication relationships for mining massive amounts of publicly available gene-expression microarray datasets. The Boolean analysis results are easily understandable and directly interpretable from visual and computational inspection of the heatmap and the scatter plots. We demonstrate how Boolean analysis is used to understand gene regulation, gene function and various human diseases. We have experimentally validated new biological hypothesis that were generated using our Boolean implication network. In particular, we applied our Boolean network toward the identification of genes related to B cell development. We validated these genes by measuring their expression levels on different stages of the mouse B cell development. Two prognostic markers of B cell lymphoma appeared in our prediction that relates clinical information to the biology of B cell development.
Chapter 1 Molecular Simulations of pH-Mediated Biological Processes

Publisher Summary This chapter discusses the recent development of a pH-coupled molecular dynamics technique, called “continuous constant pH molecular dynamics” (CPHMD), and its applications to first principles pKa calculations and pH-coupled biological phenomena. Conformational dynamics and acid–base equilibria are microscopically coupled. However, traditional molecular dynamics simulations are performed with fixed protonation states. The development of CPHMD has improved the physical realism in molecular simulations. It has enabled, for the first time, quantitative pKa prediction for biological macromolecules on a first-principles level, thereby eliminating the need for ad hoc assignment of a protein dielectric constant and for a high-resolution structure as in the traditional Poisson–Boltzmann based approaches. Despite this success, the accuracy of the CPHMD method can be further improved through the continuing development of the underlying generalized Born (GB) implicit solvent model and its parameterization. The underestimation of pKa shifts for deeply buried residues may be reduced by using a molecular surface that accounts for the solvent excluded volume.
3-Hydroxy-3-Methylglutaryl-CoA Lyase (HMG-CoA Lyase)

This article has no abstract. Keywords: 3-hydroxy-3-methylglutaryl-CoA lyase (HMG-CoA lyase)
Hand detection in American Sign Language depth data using domain-driven random forest regression

In Automatic Sign Language Recognition (ASLR), robust hand tracking and detection is key to good recognition accuracy. We introduce a new dataset of depth data from continuously signed American Sign Language (ASL) sentences. We present analysis showing numerous errors of the Microsoft Kinect Skeleton Tracker (MKST) in cases where hands are close to the body, close to each other, or when the arms cross. We also propose a method based on domain-driven random forest regression, which predicts real world 3D hand locations using features generated from depth images. We show that our hand detector (DDRFR) has >20% improvement over the MKST within a margin of error of 5 cm from the ground truth.
IL-1β and IL-6 in mouse parotid acinar cells: characterization of synthesis, storage, and release

Synthesis, storage, and secretion of the proinflammatory cytokine interleukin-1β (IL-1β) and the anti-inflammatory cytokine IL-6 have not been established in normal exocrine gland secretory cells. ...
TAPping into mRNA Export

There seem to be numerous pathways for exporting mRNAs from the nucleus to the cytoplasm. But working out which set of export adaptors and receptors transport individual mRNAs has been very difficult. In a Perspective, [Moore and Rosbash][1] discuss a new strategy using cell-penetrating peptide inhibitors for unraveling the routes of mRNA export in living cells ([Gallouzi and Steitz][2]). [1]: http://www.sciencemag.org/cgi/content/full/294/5548/1841 [2]: http://www.sciencemag.org/cgi/content/short/294/5548/1895
Key issues in essential tremor genetics research: Where are we now and how can we move forward?

Genetics research is an avenue towards understanding essential tremor (ET). Advances have been made in genetic linkage and association: there are three reported ET susceptibility loci, and mixed but growing data on risk associations. However, causal mutations have not been forthcoming. This disappointing lack of progress has opened productive discussions on challenges in ET genetics research, including fundamental assumptions in the field. This article reviews the ET genetics literature, results to date, the open questions in ET genetics and the current challenges in addressing them. Several inherent ET features complicate genetic linkage and association studies: high potential phenocopy rates, inaccurate tremor self-reporting, and ET misdiagnoses are examples. Increasing use of direct exam data for subjects, family members and controls is one current response. Smaller moves towards expanding ET phenotype research concepts into non-tremor features, clinically disputed ET subsets, and testing phenotype features instead of clinical diagnosis against genetic data are gradually occurring. The field has already moved to considering complex trait mechanisms requiring detection of combinations of rare genetic variants. Hypotheses may move further to consider novel mechanisms of inheritance, such as epigenetic. It is an exciting time in ET genetics as investigators start moving past assumptions underlying both phenotype and genetics experimental contributions, overcoming challenges to collaboration, and engaging the ET community. Multicenter collaborative efforts comprising rich longitudinal prospective phenotype data and neuropathologic analysis combined with the latest in genetics experimental design and technology will be the next wave in the field.
Differences in methotrexate and 7-hydroxymethotrexate inhibition of folate-dependent enzymes of purine nucleotide biosynthesis

7-Hydroxymethotrexate (7-OH-MTX) is the major and, frequently the only, pteridine metabolite found in bone-marrow aspirates of patients chronically treated with low-dose oral methotrexate (MTX) [Sonneveld, Schultz, Nooter and Hahlen (1986) Cancer Chemother. Pharmacol. 18, 111-116]. The Ki values for MTX and 7-OH-MTX for avian liver 5-amino-imidazole-4-carboxamide ribonucleotide transformylase differ by 4.5-fold in favour of 7-OH-MTX as the better inhibitor, while Ki values for avian liver glycinamide ribonucleotide transformylase differ by 1.9-fold favouring MTX as the better inhibitor. Thus 7-OH-MTX possesses a different enzyme-inhibiting repertoire from its parent drug and this information may be useful in explaining the mechanism of action of low-dose MTX therapies used to treat autoimmune disease.
Modeling of plastic yielding at a crack tip by inclined slip planes

This paper is concerned with the problem of inclined slip planes as a model of the plastic yielding region at a crack tip under conditions of plane strain. Some of the disagreements in the literature are discussed and comparisons are made with the results in the present study. To characterize the location of the plastic zones, an ad hoc criterion is used to choose an angle of inclination for the slip bands.
Energy Tradeoffs in Automotive Use of Steel, Fiber-Reinforced Plastics and Aluminum

Etude comparative de l'energie emmagasinee, des poids et de l'energie necessaire a la marche (besoins en carburant) pour le choix des materiaux en construction automobile, afin de determiner les economies totales d'energie resultant de la substitution des materiaux
Treatment of acute gouty arthritis with intramuscular ketorolac tromethamine

Nine consecutive patients presenting with acute gouty arthritis were treated with ketorolac 60 mg intramuscularly (IM). The average age was 58. Seven were male, and six were black. Pain was quantified in 6 of the patients using a 10-cm visual analog scale that the patients completed before and 30, 60, and 90 minutes after ketorolac administration. The mean pain score (+/- standard error of the mean) dropped from 6.43 (+/- 1.25), out of a possible 10, to 1.01 (+/- 35) (P < .01). There were no side effects of the medication. All of the patients were able to leave the treatment area satisfied with their treatment. None of the patients required crutches at discharge.
What Makes a Prion Infectious

Prions are unconventional infectious agents that cause fatal neurological illnesses such as Creutzfeldt-Jakob disease, bovine spongiform encephalopathy, and scrapie. Many hypotheses have been advanced to explain the chemical composition of infectious prions and the mechanism of their formation in the neurons of infected hosts, but none has yet been proven. Perhaps the most provocative proposal has been the “protein-only” hypothesis, which posits that the infectious agent is composed exclusively of a misfolded, host-encoded protein called the prion protein (PrP). However, three decades of investigation have yielded no direct experimental proof for this stringent hypothesis. Moreover, various biochemical studies have suggested that nonproteinaceous cofactors may be required to produce infectious prions, possibly by forming physical complexes with PrP ( 1 1– 4 ). On page 1132 of this issue, Wang et al. demonstrate the importance of cofactors for producing recombinant infectious prions in vitro ( 5 ). Another study by Li et al. suggests that endogenous cofactors may also influence the strain properties of prions in cells ( 6 ).
Analysis of large versus small pheochromocytomas: operative approaches and patient outcomes.

Background. Laparoscopic adrenalectomy for small pheochromocytomas, although challenging, is widely accepted. However, its application to pheochromocytomas larger than 6 cm is questioned due to concerns of malignancy and case complexity. Our aim was to examine the impact of pheochromocytoma tumor size (≥6 cm vs <6 cm) on operative approach and postoperative patient outcomes. Methods. A retrospective review of adrenalectomies performed at 3 university hospitals over 1 decade was analyzed. All pheochromocytomas were identified and then divided based on size into large (≥6 cm) and small (< 6 cm) groups. We examined patient and tumor demographics, pathologic diagnosis, operative approach (laparoscopic vs open), postoperative complications, and biochemical cure rates. Data were analyzed using the Student t test and Fisher exact test with a P value <.05 considered significant. Results. From 1995 to 2005, 65 pheochromocytomas were resected. Of the total, 38% (n = 25) tumors were ≥6 cm and 62% (n = 40) were <6 cm. For the large tumors, 1 out of 25 (4%) was malignant, whereas no small tumors were malignant. There was no statistically significant increased risk of malignancy in tumors ≥6 cm in size (P =.31). Initial operative approach was based on surgeon preference. Of the adrenalectomies performed, 88% were laparoscopic, with 3 of 25 (12%) large tumors requiring conversion from laparoscopic to open for intraoperative bleeding. None of the small tumors required conversion. No major postoperative complications (eg, stroke or myocardial infarction) occurred in either group. Minor complications (eg, wound infections and hematomas) were noted in 16% of large tumors and 12.5% of small tumors (P =.45). A total of 96% (24 of 25) patients with large tumors and 100% with small tumors showed postoperative biochemical cure. Tumor recurrence was noted in 1 patient with a tumor <6 cm. Conclusions. Pheochromocytomas ≥6 cm pose a challenge for laparoscopic resection, and concerns have been raised about the validity of this operative approach. This study demonstrates that there is no significant difference in the rate of malignancy for pheochromocytomas ≥6 cm versus <6 cm. There also were no significant differences identified in complication rates, postoperative biochemical cures, or tumor recurrence rates between these groups. Laparoscopic resection of pheochromocytomas can be safely accomplished regardless of size in centers with surgeons experienced in these procedures.
Bench to Bedside and Back Again: Molecular Mechanisms of α-Catenin Function and Roles in Tumorigenesis

The cadherin/catenin complex, comprised of E-cadherin, β-catenin and α-catenin, is essential for initiating cell-cell adhesion, establishing cellular polarity and maintaining tissue organization. Disruption or loss of the cadherin/catenin complex is common in cancer. As the primary cell-cell adhesion protein in epithelial cells, E-cadherin has long been studied in cancer progression. Similarly, additional roles for β-catenin in the Wnt signaling pathway has led to many studies of the role of β-catenin in cancer. Alpha-catenin, in contrast, has received less attention. However, recent data demonstrate novel functions for α-catenin in regulating the actin cytoskeleton and cell-cell adhesion, which when perturbed could contribute to cancer progression. In this review, we use cancer data to evaluate molecular models of α-catenin function, from the canonical role of α-catenin in cell-cell adhesion to non-canonical roles identified following conditional α-catenin deletion. This analysis identifies α-catenin as a prognostic factor in cancer progression.
Consumer Characteristics Associated with Dealing: An Empirical Example

The targeting of consumer deals, as well as our understanding of consumer behavior, would be enhanced by knowledge of what consumer characteristics relate systematically to deal purchasing activities in a product market. This study examines possible relationships between a housewife's dealing activity in a product class (dentifrice) and certain of her social-psychological and purchasing characteristics. Nearly one billion dollars was spent for coupons distributed by direct mail, magazines, and newspapers, in 1960 [5]. To this must be added the cost of price-off labels, premium packs, and other consumer deals. Yet in spite of its economic significance, there has been little study of market response to dealing. Notable exceptions are [2, 3, 6]. Two previous studies of dealing are relevant to this one. Webster [6] analyzed the relationship between a family's deal proneness index and 11 socioeconomic and 34 purchasing characteristics. The deal proneness index reflected a family's propensity to deal more or less than expected in a product class. He found brand loyalty (proportion of purchases concentrated on the favorite brand) to be negatively related to deal proneness. Of the socioeconomic variables, only age of housewife related significantly to deal proneness. Similarly, Massy and Frank [3], in distributed lag regressions of weekly price and dealing on a brand's market share, found that brand loyal consumers were less responsive to dealing than were nonloyal consumers. The picture that emerges from the limited empirical work to date is that brand loyalty and dealing tend to be inversely related and that most traditional socioeconomic measures are not useful predictors of dealing activity. THE VARIABLES
Expression of a set of head-specific genes during Drosophila development.

Abstract The expression of 20 cloned DNA sequences, selected on the basis of the prevalence of their transcripts in Drosophila adult head, was examined during Drosophila development. The amount of polyadenylated RNA complementary to these clones was measured in the cytoplasm of 0- to 20-hr embryos and on the polysomes of third instar larvae and 5- to 7-hr pupae. Four patterns of developmental expression were observed among the 20 clones, including 6 clones whose transcripts are prevalent only on polysomes of the adult head. Multiple genes closely clustered within the DNA of individual clones were shown to be expressed coordinately during development in some cases and differentially in others.
901-83 Troponin T and Perioperative Ischemia in Noncardiac Surgery

To evaluate troponin T (TnT) as a marker for perioperative ischemia, we prospectively studied 1028 patients (PTS) undergoing major noncardiac procedures. Clinical data included preoperative examinations, daily clinical follow-up, and serial electrocardiograms, CK/CK-MB, and TnT levels. Major cardiac complications (COMPS) were classified by reviewers blinded to TnT data in 29 (3%) of PTS, including acute myocardial infarction (AMI). pulmonary edema, cardiac arrest, complete heart block, and sustained ventricular tachycardia or fibrillation. AMI was diagnosed using CK-MB criteria in 14 (1.4%) PTS, for whom peak TnT levels were g 0.1 mcg/l in 86% and g 0.2 mcg/l in 62%. No postoperative clinical complications occurred to the two PTS with CK-MB criteria for AMI but normal TnT levels. Among the 1014 PTS without CK-MB criteria for AMI, COMPS occurred in 5 (0.6%) of 855 PTS with TnT ≤ 0.1 mcg/l versus 10 (6%) of 159 with higher peak TnT levels (p l 0.0001). This table shows the distribution of peak TnT levels by procedure type: Procedure TnT l 0.1 0.1-0.2 g 0.2 Abdom. Aortic Aneur. 39 (66%) 13 (22%) 7 (12%) Other vascular 160 (79%) 20 (10%) 23 (11%) Thoracic 75 (64%) 30 (26%) 12( 10%) Abdominal 99 (89%) 8 (7%) 4 (4%) Orthopedic 304 (92%) 16 (5%) 12 (4%) Other 180 (87%) 16 (8%) 10 (5%) We conclude that Tnt correlates with rates of COMP after major noncardiac surgery even among PTS without AMI by CK-MB criteria. In this cohort, elevated TnT levels were more common with procedures generally associated with a higher risk of COMPS. Long term follow-up is needed to determine whether elevated TnT levels in patients without COMPS were false positive results or subclinical ischemic events.
Prostate cancer: beta control your hormones.

Differentiation status influences the prognosis for localized prostate cancer. In this issue of Cancer Cell , Mak and coworkers describe a signaling pathway involving estrogen receptor β (ERβ) that governs whether prostate carcinoma cells maintain an epithelial phenotype or undergo epithelial-mesenchymal transition, suggesting that ERβ would have prognostic or therapeutic value.
Polymorphisms in TRPV1 and TAS2Rs associate with sensations from sampled ethanol.

Background Genetic variation in chemosensory genes can explain variability in individual's perception of and preference for many foods and beverages. To gain insight into variable preference and intake of alcoholic beverages, we explored individual variability in the responses to sampled ethanol (EtOH). In humans, EtOH elicits sweet, bitter, and burning sensations. Here, we explore the relationship between variation in EtOH sensations and polymorphisms in genes encoding bitter taste receptors (TAS2Rs) and a polymodal nociceptor (TRPV1). Methods Caucasian participants (n = 93) were genotyped for 16 single nucleotide polymorphisms (SNPs) in TRPV1, 3 SNPs in TAS2R38, and 1 SNP in TAS2R13. Participants rated sampled EtOH on a generalized Labeled Magnitude Scale. Two stimuli were presented: a 16% EtOH whole-mouth sip-and-spit solution with a single time-point rating of overall intensity and a cotton swab saturated with 50% EtOH on the circumvallate papillae (CV) with ratings of multiple qualities over 3 minutes. Area-under-the-curve (AUC) was calculated for the time-intensity data. Results The EtOH whole-mouth solution had overall intensity ratings near “very strong.” Burning/stinging had the highest mean AUC values, followed by bitterness and sweetness. Whole-mouth intensity ratings were significantly associated with burning/stinging and bitterness AUC values on the CV. Three TRPV1 SNPs (rs224547, rs4780521, rs161364) were associated with EtOH sensations on the CV, with 2 (rs224547 and rs4780521) exhibiting strong linkage disequilibrium. Additionally, the TAS2R38 SNPs rs713598, rs1726866, and rs10246939 formed a haplotype, and were associated with bitterness on the CV. Last, overall intensity for whole-mouth EtOH associated with the TAS2R13 SNP rs1015443. Conclusions These data suggest genetic variation in TRPV1 and TAS2Rs influence sensations from sampled EtOH and may potentially influence how individuals initially respond to alcoholic beverages.
HORMONAL RESPONSES TO EXTERNAL STIMULI IN BIRDS

Summary. 1 Within the breeding seasons regulated by annual changes in environmental conditions, there exist detailed changes in the pattern of hormone secretion from stage to stage within the season, which are in part responsible for the successive changes in behaviour during the season. 2 In many species of birds the general environmental variables induce greater development in the male reproductive system than in the female, so that males arriving at the breeding grounds in spring are usually more advanced toward full spermatogenesis than are the females toward ovulation. Experimentally, additional illumination alone is capable of bringing about full testicular development, but not full ovarian development. 3 Stimuli arising from courtship behaviour induce the secretion of follicle-stimulating hormone by the pituitary gland of the female in many species of birds. 4 The presence of nesting material and of the nest, and/or participation in nest-building behaviour, further contribute to the advancement of the reproductive cycle, probably contributing to the stimulation of luteinizing hormone secretion by the pituitary. 5 Stimuli provided by the eggs appear to be able to induce prolactin secretion, and to inhibit the secretion of FSH. The prolactin secretion so stimulated probably, in turn, contributes to the maintenance of incubation, and of the brood patch. 6 Stimuli provided by the young are capable of inhibiting or delaying the onset of a new laying cycle, although the physiological basis of this is rather obscure. 7 Recently discovered details of the physiological and anatomical relationships between the brain and the pituitary gland provide insight into the anatomical and physiological mechanisms by means of which external stimuli can reflexly cause changes in hormone secretion. 8 The synchronization of the behaviour of the members of a mated pair, necessary for effective reproduction, is probably in part effected by the effects upon their endocrine glands of stimuli which they provide to each other, and which they receive from the eggs and young. 9 These processes of neuro-endocrine and “psycho-endocrine” regulation provide a link, in certain areas, between the work of physiologists, ethologists, ecologists, and animal psychologists.
A Child With Pneumomediastinum

An infant (<12months)presentedwith a several-day history of fevers, malaise, and progressive respiratory distress associated with a worsening cough and subjective wheezing. His caretakers reported that he had previously been evaluated formild reactive airway disease initially noted several months prior that had failed to respondtosymptomatic treatmentwithanalbuterolnebulizer.Over the several daysprecedingpresentation, his baselinewheezingand workofbreathinghadacutely increased.Ofnote, a twin sibling also had symptoms of an upper respiratory illness. His birth historywas uneventful, and no further pertinent data were elicited during the initial evaluation. At the timeofpresentation, thechildwas inmild respiratorydistress with oxygen saturation levels between 90% and 92%. His examination was significant for crepitus in the anterior side of the neck, increased work of breathing with accessory muscle use, diffuse rales, and rhonchi throughout his lung fieldswith amildly prolongedexpiratoryphase.Hewasadmitted for furtherevaluationand symptomatic treatment. A viral panel was positive for human respiratory syncytial virus (RSV) typeB. The initial chest radiograph is shown inFigure, A. Progression of radiographic findings and further respiratory decompensation prompted a computed tomographic (CT) scan of the patient’s chest (Figure, B-D). Following the CT scan of his chest, he continued to slowly decompensate and develop further respiratory distress. What is your diagnosis? A
The rate of morphological evolution in mammals from the standpoint of the neutral expectation

A comparison of the evolutionary rates of cranial morphology in mammals with the neutral expectation suggests that stabilizing selection is a predominant evolutionary force keeping the long-term diversification of lineages well below its potential. The rate of morphological divergence of almost all lineages, including the great apes, is substantially below the minimum neutral expectation. The divergence of the modern races of man is slightly above the minimum neutral rate but well below the maximum rate. Therefore, there is no need to invoke extraordinary mutational mechanisms, such as regulatory gene evolution, to explain what has been perceived as rapid morphological evolution in mammals. Nor does it appear that behavioral drive needs to be invoked to explain rapid morphological evolution in hominoids. Outside of man, the long-term rate of phenotypic evolution in the great apes is actually lower than that for other mammals. The data suggest that, immediately after reproductive isolation, most lineages d...
The labor of mimesis

This article is a preliminary examination of the conception of mimesis as it unfolds in Rey Chow's work. Focusing on Chow's work on film, the article shows how Chow rejects a certain iconophobic imperative with which anti-orientalist critiques come laden, with all of the assumptions about surface/depth, misrepresentation/truth, and myth/reality that attend such iconophobia. Since there is no Archimedean point outside of the “fabulation” of the world, the labor of critique must work at two simultaneous levels that are not related to each other as surface and depth, but rather as an extension of the surface of critique itself: analyze the cultural work done by the image itself; and, by means of this analysis, gain insight into the “condition of possibility for what becomes visible”. The notion of mimesis that one gleans from Chow's work is informed by a Heideggerian ontology, but modulated by a Benjaminian materialism. In this light, both the objects of Chow's study and her own reading practices form a cont...
Complex refractive index in the infrared for NaCl, NaNO 3 , and NaHCO 3 in water*

Relative specular reflectances of individual 0.5M aqueous solutions of NaNO3, NaHCO3, NaCl, and of 0.25M NaCl were measured in the 500–5000 cm−1(2–20 μm) region of the infrared for linearly polarized radiant flux having the electric field vector perpendicular to the plane of incidence. Distilled water was the reflectance standard. The angle of incidence was 70.03° ± 0.23°. Kramers-Kronig analysis of the relative reflectance spectra provided phase-difference spectra for the aqueous solutions and a tabulation of spectral values for the complex refractive index n + ik. The strengths of selected infrared active vibrational bands of the molecular anions NO3− and HCO3− were determined by integrating values for their molecular extinction coefficients over spectral regions of the bands.
Direct simulation of turbulent flow and heat transfer in a channel. Part II: A Green's function technique for wavy walls

The possibility of improving heat transfer rates by the imposition of a wavy boundary led to this extension of direct simulation of heat transfer in turbulent flow in a channel. This part of the paper shows how a pattern of micro-riblets on the surface and parallel to the flow is incorporated into the solution of the Navier-Stokes and temperature equations. The channel is two-dimensional with walls at different but uniform temperatures, and the fluid properties are constant. The presence of the patterns presents a considerable computational problem that can be largely overcome by the use of a discrete Green function technique. The method is illustrated by making short-time calculations of the velocity and temperature fields for a Prandtl number of 0.72, a Reynolds number based on channel half-width and bulk velocity of 2800, and a sinusoidal pattern with a height of 5 wall units.
Effects of NH4+ on the growth and K+ (86Rb) uptake of various ectomycorrhizal fungi in pure culture

As a result of considerable deposition of ammonium sulphate on vegetation and soil the NH4/K ratios in the soil water extracts of pine forests in the Netherlands are increasing. Increasing the NH4/K ratios from 1 to 40 in the solid nutrient medium of isolated ectomycorrhizal fungi will in general result in a 60 to 80% inhibition of the lateral growth. On increasing the NH4/K ratio the biomass of most of the fungi examined shows a maximum at ratios of approximately 10 to 20, although the colony diameter at those ratios remains rather small. NH4 +also exerts a pronounced + effect on the uptake rate of Rb+ in Rhizopogon luteolus. At low Rb concentrations the inhibitory effect of NH4 is maximal, whereas on increasing the Rb+ concentration the inhibitory effect of NH4 +is abolished. This means that NH4+ competitively inhibits the Rb+uptake in R. luteolus.
Major surgical trauma induces proteolysis of insulin-like growth factor binding protein-3 in transgenic mice and is associated with a rapid increase in circulating levels of matrix metalloproteinase-9

The authors previously demonstrated a significant decrease in plasma levels of intact insulin-like growth factor binding protein-3 (IGFBP-3) after major open but not after laparoscopic-assisted surgery in humans. They postulated that this decrease may have an effect on postoperative tumor growth. It also has been shown that plasma levels of matrix metalloproteinase-9 (MMP-9), a protease capable of degrading IGFBP-3, are transiently increased after open colectomy in humans. The authors aimed to develop an animal model that would allow further study of the effect that surgical trauma has on plasma levels IGFBP-3 and MMP-9. In addition, they set out to assess the concentration of MMP-9 in circulating monocytes before and after surgery. The 30 mice included in this study were divided into three groups: sham laparotomy, carbon dioxide (CO2) pneumoperitoneum, and anesthesia control. All mice were IGFBP-3 transgenics (overexpressing human IGFBP-3) on a CD1 background. The mice were anesthetized using ketamine and xylazine. Blood was drawn retroorbitally 48 h before the procedure. The duration of the procedure was 30 min. The animals were killed 24 h postoperatively and blood was drawn. Intact IGFBP-3 levels were measured using a combination of Western blot analysis and enzyme-linked immunoassay (ELISA) at the two time points: before and after the operation. Plasma and peripheral blood mononuclear cell levels of MMP-9 were measured at each time point using zymography. Mononuclear cell lysates were used to determine intracellular MMP-9 levels. Plasma levels of intact IGFBP-3 were significantly lower than preoperative levels after sham laparotomy. A mean decrease of 76.6% was noted (p 0.05). The anesthesia control group did not demonstrate a significant change in either circulating intact IGFBP-3 levels or MMP-9 levels. Mononuclear intracellular levels of MMP-9 were significantly lower after laparotomy than the preoperative levels (3 vs 37 RU). The postprocedure intracellular levels of MMP-9 were not significantly decreased in the pneumoperitoneum or anesthesia control group. Plasma levels of intact IGFBP-3, a cell growth regulating factor, were found to be decreased significantly after laparotomy. This decrease was not seen after pneumoperitoneum. Depletion of intact IGFBP-3 after laparotomy correlated with a rapid release of MMP-9 from mononuclear cells and an increase in circulating plasma MMP-9 levels. Matrix metalloproteinase-9 may play an important role in IGFBP-3 proteolysis after surgical trauma. Furthermore, circulating mononuclear cells are one source of MMP-9 after surgery. Finally, the model used reproduces events in humans after surgery, and thus should permit further study on the mechanism of IGFBP-3 proteolysis after surgical trauma.
Disturbance localization using a multifunctional antenna-buoy sensor network

This work examines the integration of a spherical inverted-F antenna (SIFA) and a spherical buoy structure. The resulting multifunctional antenna system includes an inertial measurement unit (IMU), microcontroller (MCU), rechargeable battery, and wireless radio. The IMU collects motion-dynamic information from the structure and relays this information in a star network configuration to a central node for processing. This information was used with numerically-derived shallow ocean wave propagation data as basis functions in a modified MUSIC algorithm to determine the wave fronts' point of origin. Results for the SIFA-buoy and network are included.
Comparative surface analysis of intraocular lenses

Abstract In 1977 a study using scanning electron microscopy (SEM) to examine intraocular lenses found several undesirable lens surface characteristics. In early 1980, an apparent increase in patient complications with one lens style spurred a new study of 39 lenses from nine manufacturers. Most of these lenses appeared to have improved surface finishes when compared to the 1977 lenses. Both groups of lenses were compared to a series of 19 explanted lenses; similar surfaces were found on lenses of similar design. Some explanted lens styles which had not previously been examined exhibited characteristics considered undesirable in 1977. Typical results of the three studies are shown.
Urban Watershed Management: Sustainability, One Stream at a Time

(2006). Urban Watershed Management: Sustainability, One Stream at a Time. Environment: Science and Policy for Sustainable Development: Vol. 48, No. 4, pp. 26-42.
Chlamydial infection in vitamin D receptor knockout mice is more intense and prolonged than in wild-type mice

Vitamin D hormone (1,25-dihydroxyvitamin D) is involved in innate immunity and induces host defense peptides in epithelial cells, suggesting its involvement in mucosal defense against infections. Chlamydia trachomatis is a major cause of bacterial sexually transmitted disease worldwide. We tested the hypothesis that the vitamin D endocrine system would attenuate chlamydial infection. Vitamin D receptor knock-out mice (VDR(-/-)) and wild-type mice (VDR(+/+)) were infected with 10(3) inclusion forming units of Chlamydia muridarum and cervical epithelial cells (HeLa cells) were infected with C. muridarum at multiplicity of infection 5:1 in the presence and absence of 1,25-dihydroxyvitamin D3. VDR(-/-) mice exhibited significantly higher bacterial loading than wild-type VDR(+/+) mice (P<0.01) and cleared the chlamydial infection in 39 days, compared with 18 days for VDR(+/+) mice. Monocytes and neutrophils were more numerous in the uterus and oviduct of VDR(-/-) mice than in VDR(+/+) mice (P<0.05) at d 45 after infection. Pre-treatment of HeLa cells with 10nM or 100nM 1,25-dihydroxyvitamin D3 decreased the infectivity of C. muridarum (P<0.001). Several differentially expressed protein spots were detected by proteomic analysis of chlamydial-infected HeLa cells pre-treated with 1,25-dihydroxyvitamin D3. Leukocyte elastase inhibitor (LEI), an anti-inflammatory protein, was up-regulated. Expression of LEI in the ovary and oviduct of infected VDR(+/+) mice was greater than that of infected VDR(-/-) mice. We conclude that the vitamin D endocrine system reduces the risk for prolonged chlamydial infections through regulation of several proteins and that LEI is involved in its anti-inflammatory activity.
Nearctic species of the new genus Tigrosa (Araneae: Lycosidae)

The new genus Tigrosa is established for five Nearctic species originally described in the genus Lycosa Latreille 1804. Four of the species are transferred from Hogna Simon 1885: H. annexa (Chamberlin & Ivie 1944), H. aspersa, (Hentz 1844), H. grandis (Banks 1894) and H. helluo (Walckenaer 1837). The remaining species, Allocosa georgicola (Walckenaer 1837) is transferred from Allocosa Banks 1900. The presumed synapomorphy that supports Tigrosa is the color pattern on the dorsum of the cephalothorax, which is described and illustrated. In addition to their distinct color pattern, Tigrosa species are very similar in characteristics of the male palpus and epigynum, details of the eye arrangement, leg length in relation to body dimensions, as well as foraging habits. Comparisons made between Hogna, as defined by the type species H. radiata, Latreille 1817, and Tigrosa, as defined in this paper, demonstrate distinct differences in dorsal color pattern, structure of the epigynum, dimensions of the eye rows, color pattern of the venter and habitat preferences.
The absorption and fluorescence spectra of bivalent europium ion in crystals

Abstract Although bivalent europium ion (Eu++) and trivalent gadolinium ion (Gd+++) are isoelectronic, there is no resemblance in their spectra either as regards intensity or structure. Instead of the sharp spectrum of Gd+++ even at room temperature, the spectrum of Eu++ consists, both in absorption and in fluorescence, of broad bands which show signs of an underlying discreteness at liquid air temperatures and at the temperature of liquid hydrogen become resolved into lines in some regions. The spectrum of Eu++ in crystals is perhaps one hundred to one thousand times as intense as the spectrum of the gadolinium ion. To obtain transmission, the bivalent salts were greatly diluted to form mixed crystals with the corresponding colorless strontium salt. In contrast with the spectra of Gd+++, the spectra of Eu++ are rich in vibrational structure, with an interval 215 cm−1 as especially prominent, in the anhydrous chloride. The spectra of Eu++ are also exceptional in their strong dependence on the crystalline environment about the europium ions. That is, different salts of bivalent europium differ widely in the character of their spectra in contrast with the typical behavior of rare earths. The chief feature many of the salts have in common is a strong fluorescence in the ultraviolet. The character of the spectrum is ascribed principally to transitions between a sharp basic level 8 S 7 2 with the seven “optical” electrons in the 4f shell and activated states having one of these electrons in a 5d, 6s, 6p, etc., or the lattice. There are possibilities here that some of the sharp activated states which correspond to those in Gd+++ have nearly the same energy as those which have one electron in the outer shells of the ion or in the lattice and thus resonance arises between the “inner” and “outer” states. Some evidence is offered for such radiationless transitions and for transitions to the lattice.
Preliminary chemical and nutritional characterization of liver from longnose skates (Raja rhina)

Abstract Skates ( Raja rhina ) have recently become a small commercial fishery in Alaska and along the western United States coast. Most of the skate byproduct is discarded or made into meal; therefore, there is opportunity to enhance the utilization for skate byproducts. The objective of this research project was to chemically characterize longnose skate livers. Livers from five long nose skates, caught off the coast of Kodiak, Alaska, were obtained immediately after the fins (called “wings”) had been removed by a commercial processor. Each liver was subjected to the following analysis: proximate composition, minerals, amino acids, α-tocopherol, protein gel electrophoresis, fatty acid profiles, thiobarbituric acid reactive substances (TBARS) and biogenic amines (BA). Livers were composed of lipid (49.6%), moisture (41.0%), protein (10.9%) and ash (0.8%). High levels of α-tocopherol were found in the livers (142 μg/g oil). Fatty acid profile indicated that the lipids extracted from livers contained high concentrations of eicosapentaenoic acid (16.0%) and docosahexaenoic acid (17.7%). Average TBARS values were low at 1.5 μg malondialdehyde/g oil, indicating low levels of lipid oxidation. The lysine content as percent of total amino acids on a weight basis was 6.1% and methionine content was 2.8%. Analysis of BA found putrescine (31 mg/kg liver) and spermine (85 mg/kg liver) present. Preliminary results suggest long nose skate livers as an abundant source of n-3 fatty acids and amino acids.
Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation

Genome-wide association studies (GWAS) have in recent years discovered thousands of associated markers for hundreds of phenotypes. However, associated loci often only explain a relatively small fraction of heritability and the link between association and causality has yet to be uncovered for most loci. Rare causal variants have been suggested as one scenario that may partially explain these shortcomings. Specifically, Dickson et al. recently reported simulations of rare causal variants that lead to association signals of common, tag single nucleotide polymorphisms, dubbed “synthetic associations”. However, an open question is what practical implications synthetic associations have for GWAS. Here, we explore the signatures exhibited by such “synthetic associations” and their implications based on patterns of genetic variation observed in human populations, thus accounting for human evolutionary history –a force disregarded in previous simulation studies. This is made possible by human population genetic data from HapMap 3 consisting of both resequencing and array-based genotyping data for the same set of individuals from multiple populations. We report that synthetic associations tend to be further away from the underlying risk alleles compared to “natural associations” (i.e. associations due to underlying common causal variants), but to a much lesser extent than previously predicted, with both the age and the effect size of the risk allele playing a part in this phenomenon. We find that while a synthetic association has a lower probability of capturing causal variants within its linkage disequilibrium block, sequencing around the associated variant need not extend substantially to have a high probability of capturing at least one causal variant. We also show that the minor allele frequency of synthetic associations is lower than of natural associations for most, but not all, loci that we explored. Finally, we find the variance in associated allele frequency to be a potential indicator of synthetic associations.
Streamflow simulation using a water-balance model with annually-resolved inputs

Summary Availability of long-term information on the variability of water resources in a given area is particularly important for sustainable resource management. Developing watershed simulation models that can be run using annually-resolved proxy climate data provides a way to improve reconstructions of hydrological parameters over multi-century time scales. Through the addition of a snowmelt modeling component, we enhanced a simple water-balance model to simulate streamflow at seasonal resolution. The model was calibrated to the upper Meadow Valley Wash, Nevada, USA, using USGS gage number 09417500 streamflow records. PRISM data at 2.5 arc-min resolution were used to reconstruct streamflow at the seasonal timescale (October through May) from 1896 to 2008, with and without a temperature-index snowmelt component. Best-fit model simulations had an R 2 of 0.81 against stream gage observations. Average predicted seasonal streamflow during calibration was 0.81 cm with a standard deviation of 0.35 cm, compared to the observed average seasonal streamflow of 0.76 cm and standard deviation of 0.48 cm. Despite some shortcomings for this watershed, the model approach has promise for providing scenario-based estimates of hydrologic variability in semi-arid mountain environments.
Specification and composition of network services in future internet architectures

The inadequacies of the current Internet data and control planes to adapt to changes have given rise to several new proposed Internet architectures. In many cases, these new architectures enable a variety of "services" in the network that can be used to customize network functionality and to add new features after deployment. One key challenge to such network services is that they need to be composed from various networking resources at runtime. Therefore, it is critical to develop methods for accurately specifying the semantics of network services and composing them dynamically. In this article, we propose a service description semantic, discuss how to formalize the service composition problem and use the formalization in conjunction with a logic planner to provide an efficient solution.
Atomic structure and chemistry of dense nano-precipitates in MgB2 ceramic

Ceramic MgB2 superconductor has great potential for applications in the devices. Doping MgB2 with carbon or SiC has been successful in improving critical current density Jc, the upper critical field Hc2 and flux-pinning. However, the presence of nano-precipitates, and their microstructure and chemistry, upon alloying/doping MgB2 grains are largely unexplored. In this paper, the atomic structure and chemistry of 5–10 nm dense nano-precipitates were discovered in purified MgB2 pellets by removing B2O3. The nano-precipitates are platelet-shaped and fully coherent with the MgB2 grains and having the longer axis of the plate perpendicular to the c-axis of MgB2 grains. Systematic conventional and analytical Transmission Electron Microscopy (TEM) was carried out to study the atomic structure and chemistry of those nano-precipitates. The practical experimental approach of optimizing the composition and synthesis heat treatment of MgB2 to induce dense uniformly distributed nano-precipitates is also discussed.
Peptide-Mass Profiles of Polyvinylidene Difluoride-Bound Proteins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in the Presence of Nonionic Detergents

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), in conjunction with enzymatic digestion of proteins and molecular weight search of peptide-mass database is a powerful technique for peptide/protein identification. Ideally, peptide mixtures should be compatible with both MALDI-TOF and microsequencing. In our laboratory, enzymatic digestion and extraction of peptides from polyvinylidene difluoride (PVDF)-bound proteins is performed in the presence of nonionic detergents. However, nonionic detergents have been shown to cause signal suppression in MALDI-TOF analysis. This study demonstrates that by using a modified matrix solution, peptide-mass fingerprinting of PVDF-bound proteins by MALDI-TOF can be obtained in the presence of nonionic detergents such as hydrogenated Triton X-100 (RTX-100), octylglucopyranoside, and Tween 20.