cssi/SciSciGPT-SciSciNet huggingface dataset:
Effects of stocking different fractions of size graded juvenile prawns on production and population structure during a temperature-limited growout period

Abstract Size grading of juvenile prawns prior to pond stocking is used to disrupt negative social interactions. Animals graded off the upper end of the size range can outperform ungraded animals by 20–50%. However, reports differ on the performance of the lower grade fraction. Some studies indicate that lower grade prawns can out perform ungraded populations within a 120–140-day growing season while other studies indicate that >140 growing days are required. The objective of this study was to compare the growth of this lower grade fraction with the upper grade fraction and an ungraded fraction of the same population within a temperature-constrained growing season of 100–120 days. Prawn juveniles that had been nursed 60 days were separated into three groups. Approximately 50% of the population was maintained ungraded with the full range of size variation. The other 50% was separated into two fractions (large=upper grade; small=lower grade) using a #13 bar grader (0.5-cm spacing). Ponds were randomly assigned to receive one of the three treatments (ungraded controls, upper grade, and lower grade) with average stocking weights of 0.5±0.3, 0.8±0.4, and 0.2±0.1 g ( x ±S.D.), respectively. There were three replicate 0.04-ha ponds per treatment. All ponds were stocked at 59,280 ha −1 . Artificial substrate was added to ponds at a rate to increase available surface area by 50%. After 104 days, there was no significant difference ( P >0.05) in survival of prawns from the three fractions (overall average 88%). Total production, marketable production (>20, >30 g) and average individual weight was significantly greater ( P P >0.05) in total production or average individual weight of prawns stocked from the ungraded or lower graded fractions. Impacts of grading procedures on population structures were much more pronounced in females than in males with upper graded animals having a significantly higher ( P ≤0.05) percentage of sexually mature reproductive females. Compared to ungraded juveniles, projected net returns were lower for lower graded prawns, higher for upper graded, and higher for combined lower and upper under all model farm scenarios. In summary, stocking of the upper graded fraction increased total production, average weights, and marketable production. There was no difference in lower graded and ungraded animal production variables.
A model in dermatology for long-distance mentoring

INTRODUCTION Mentorship is an important element for a successful career in any field. Physicians who have had mentors report having more career satisfaction and believe that the relationship has positively affected their job experience and promotions in their field. However, multiple studies have documented that a significant number of young physicians report not having a mentor through training and their early stage of career. Within the field of dermatology, mentorship has recently been emphasized in many training programs through assigned mentors with a high degree of resident satisfaction. Once past residency, however, early career physicians may have fewer opportunities for mentorship, while they also may be expected to become mentors themselves. In 2005, the American Academy of Dermatology established an Academic Dermatology Leadership Program (ADLP). This program has been well received, with consistently positive formal and informal evaluations. Moreover, participants report very high retention rates in full-time academic practice ([75%).* An important component of the ADLP is the matching of participants, who are early in their career as academic dermatologists, with a mentor— often located at a distant geographic locations—as a way to help them succeed in the field and advance as leaders. In most cases, mentorship is conducted primarily via phone calls with only a few in-person meetings. While this approach can pose unique challenges, it has great potential, particularly in a field like dermatology. Most academic departments in dermatology are small, and the opportunity to be matched with a mentor from
Molecular characterization of hasB from an operon required for hyaluronic acid synthesis in group A streptococci. Demonstration of UDP-glucose dehydrogenase activity

The membrane-associated hyaluronate synthase produces capsular hyaluronate in group A streptococci by the alternate addition of UDP-N-acetylglucosamine and UDP-glucuronic acid. Previous studies identified a locus required for hyaluronate synthase activity and suggested that a gene involved in the production of UDP-glucuronic acid (UDP-glucose dehydrogenase) also mapped to the locus. In the present study the putative UDP-glucose dehydrogenase gene (hasB) was cloned and the DNA sequence determined. The hasB gene product was shown to have global similarity with AlgD, a dehydrogenase, which catalyzes the production of GDP-mannuronic acid for the alginate capsule of Pseudomonas aeruginosa. Regions of local homology have been identified which apparently correspond to the NAD-binding and enzyme active sites of HasB and AlgD. In order to show that hasB expression correlated with UDP-glucose dehydrogenase activity, the hasB gene was cloned under control of the T7 promoter. Hyperexpression of hasB resulted in a protein of approximately 47 kDa and high levels of UDP-glucose dehydrogenase activity were observed. These data demonstrate that hasB encodes the UDP-glucose dehydrogenase of group A streptococci.
Direct Comparison of Aspirin Plus Hirudin, Aspirin Plus Heparin, and Aspirin Alone Among 12,000 Patients with Acute Myocardial Infarction Not Receiving Thrombolysis: Rationale and Design of the First American Study of Infarct Survival (ASIS-1).

While antithrombotic therapy of acute myocardial infarction is clearly beneficial, substantial controversy exists regarding the optimal regimen. In particular, while aspirin alone has proven highly effective in reducing rates of reinfarction, stroke, and death following acute coronary occlusion, heparin has not clearly been shown to have additional benefit when added to aspirin but is associated with increased rates of hemorrhagic stroke and major bleeding. At the same time, available data for newer specific thrombin inhibitors such as hirudin suggest greater benefits than aspirin alone or aspirin plus heparin in terms of maintaining coronary flow, but possibly higher risks of hemorrhagic stroke and major bleeding. Since no completed or ongoing large-scale clinical trial has directly compared aspirin plus hirudin, aspirin plus heparin, and aspirin alone, it is not currently possible to decide which of these three antithrombotic regimens provides the optimal bmefit-to-risk ratio. The First American Study of Infarct Survival (ASIS-1) is directly comparing aspirin alone, aspirin plus heparin, and aspirin plus hirudin among 12,000 patients presenting with signs and symptoms of acute myocardial infarction who are not felt by their responsible physicians to be appropriate candidates for thrombolytic therapy. Such patients comprise almost two thirds of all U.S. subjects presenting with acute myocardial infarction and are a group at substantial risk of death, reinfarction, and stroke. Thus, the ASIS-I trial will provide importantly relevant data regarding the optimal antithrombotic regimen for the majority of patients presenting with acute myocardial infarction. In this manuscript we provide the rationale and design for the First American Study of Infarct Survival (ASIS-1), a randomized, double-blind, placebo-controlled trial directly comparing aspirin alone, aspirin plus intravenous heparin, and aspirin plus intravenous hirudin in the treatment of acute myocardial infarction patients not receiving thrombolytic therapy.
Temperature dependence of the probabilities of VV energy exchange between H2 and DCl

Abstract The temperature dependence of the removal of the vibrational energy of H 2 by DCl in H 2 (1) + DCl(0) has been investigated over the range of 300–3000 K. The energy transfer probability of H 2 (1) + DCl(0) → H 2 (0) + DCl(1), where the vibrational energy of H 2 (1) is removed by both the vibrational and rotational motions of DCl(0), is found to be strongly temperature dependent and increases with temperature closely following the relation log P α T 1/3 . Over the temperature range it changes by two orders of magnitude. The probability of the near-resonant process H 2 (1) + DCl(O) → H 2 (0) + DCl(2) is very close to that of the former at 300 K, but it increases only slightly as the temperature is raised to 3000 K. The sum of the probabilities of these two processes at 300 K is 3.4 × 10 −5 , which agrees with the experimental value of 3.95 × 10 −5 .
The influence of gender and aortic aneurysm size on eligibility for endovascular abdominal aortic aneurysm repair

Objectives The purpose of this study was to compare the eligibility of men and women with infrarenal abdominal aortic aneurysms (AAAs) for on-label endovascular aneurysm repair (EVAR) as part of the clinician-Food & Drug Administration (FDA) collaborative effort, the Characterization of Human Aortic Anatomy Project (CHAP). Methods Computed tomography (CT) scans with 3D reconstruction from a single institution obtained between July 1996 and December 2009, including standardized measurements by a blinded third-party (M2S, West Lebanon, NH) were examined. For inclusion, abdominal aortic aneurysm (AAA) had to be infrarenal, unrepaired, and >5 cm, or 4 cm to 5 cm if the orthogonal sac diameter was more than twice the aortic diameter at the renal level. Scans were included regardless of subsequent EVAR, open repair, or lack of treatment. One thousand sixty-three unique, unrepaired AAAs were analyzed. Results Neck length, diameter, and angulation differ for women (P 6 mm. Logistic regression modeling shows that older patient age (odds ratio [OR], 0.84 per decade), increased aneurysm diameter (OR, 0.70 per cm), and female gender (OR, 0.4) are each independently associated with decreased odds of meeting all device IFU neck criterion (P Conclusion Women are significantly less likely to meet device IFU criterion for EVAR. Aortic neck criteria and iliac access are important for men and women, but more women than men fail to meet IFU criterion. Devices that accommodate shorter infrarenal AAA neck length will have the greatest impact on expanding on-label EVAR regardless of gender. Lower profile devices and those that accommodate higher neck angulation are expected to expand EVAR eligibility further for women. EVAR eligibility is unlikely to be lost as AAAs enlarge to 5.5 cm in women and 6.5 cm in men. Observation of small AAAs until they reach the standard threshold size for repair should not compromise EVAR eligibility.
Neoantigens associated with halothane hepatitis.

(1989). Neoantigens Associated with Halothane Hepatitis. Drug Metabolism Reviews: Vol. 20, No. 2-4, pp. 203-217.
Dielectric properties of polymers based on hexafluoropropylene

Dielectric measurements have been made at frequencies from 10 Hz to 100 kHz and temperatures from 4 K to at least 300 K on a number of polymers containing units of hexafluoropropylene (HFP). These included copolymers of tetrafluoroethylene (TFE) and HFP, the homopolymer of HFP, elastomeric copolymers of HFP and vinylidene fluoride, and alternating copolymers of methyl vinyl ether with TFE and HFP. The effect of an ether linkage between the CF3 group and the chain was also considered. Most of these polymers exhibited a main chain local mode relaxation near 228 K and a side group relaxation near 93 K.
Cheating: The illusory edge

Abstract This experiment studied the relationships among cheating, overall test performance, and the relatedness of materials available and unavailable to the cheater. Subjects learned a free-recall list and were then tested for recall either when cheating was impossible or when half of the list had been left “carelessly” exposed. For half of the cheat subjects the exposed and the unexposed words belonged to different categories, while for the remaining halves the items belonged to the same categories. Recall was scored for both exposed and unexposed words. The results indicate that significant cheating did occur, that cheating did not improve overall performance, and that while cheating elevated the numbers of recorded exposed words it depressed recall of stored unexposed items (for both related and unrelated sets). This associated cost effect is discussed in connection with category retrieval, output interference, attention, and arousal.
Does preferential use of endovascular interventions by vascular surgeons improve limb salvage, control of symptoms, and survival of patients with critical limb ischemia?

Abstract Background Our approach to patients with critical limb ischemia (CLI) underwent a rapid evolution from open surgery to preferential use of endovascular procedures. The goal of the current report was to evaluate the impact of this change on patients with CLI. Methods Consecutive patients with CLI were compared between 3 periods: June 2001 to October 2002 (I) versus November 2002 to October 2003 (II) versus November 2003 to June 2005 (III). Results A total of 275 patients (301 limbs, mean age 70 ± 11) underwent revascularization or primary major amputation (PA) for CLI (81 in I, 76 in II, 144 in III). PA decreased from 14.8%, 10.5%, and 3.5% ( P P = .001), and 71%, 77%, and 88% following LS attempt ( P = .017), with no difference in survival. Length of stay (LOS) decreased from 10.7 ± 12.1 (I) to 5.2 ± 6.2 days (III) ( P = .001). Conclusions Preferential use of endovascular interventions in patients presenting with CLI resulted in decreased number of PA, improved LS, and decreased LOS, without a difference in survival.
Case report: clinical findings and successful resection of melanoma metastatic to the right atrium.

(1994). Case Report: Clinical Findings and Successful Resection of Melanoma Metastatic to the Right Atrium. Cancer Investigation: Vol. 12, No. 4, pp. 409-413.
Spectral relaxation of the benzophenone negative ion in alcohol glasses: Evidence for solvent reorientation

Abstract The kinetics of spectral relaxation of the benzophenone anion (Bp· - ) in ethanol and methanol glasses were studied in the temperature range 4–77 K. The pronounced blue shift observable in both glasses at 77 K is essentially stopped in ethanol and substantially slowed in methanol by lowering the temperature to 4 K. In contrast, electron transfer involving Bp· - as a donor proceeds unhindered in ethanol glass at 4 K, indicating that two different mechanisms are responsible for the spectral relaxation and electron transfer. Both processes are independent of the concentration of neutral benzophenone, precluding a hopping mechanism. The data are consistent with solvent reorientation as the mechanism of the spectral shifts and long range tunneling as the mechanism of electron transfer. For trapped electrons (e - t ) in ethanol glass, the kinetics of spectral shifts and of electron transfer to acceptors are similar to those of Bp· and are affected similarly by temperature. The data clearly rule out the unified hopping mechanism for spectral shifts and electron transfer processes of e - t . The similarities to Bp· - suggest that hopping has no significant role in either process.
Toward haptic/aural touchscreen display of graphical mathematics for the education of blind students

We propose the use of a haptic touchscreen to convey graphical and mathematical concepts through aural and/or vibratory tactile feedback. We hypothesize that an important application of such a display will be in teaching visually impaired students concepts that are traditionally learned almost entirely visually. This paper describes initial feasibility studies using a commercially available haptic touchscreen to display grids, points, lines, and shapes - some of the first visual graphical entities students encounter in K-12 mathematics education, and from which more complex lessons can be constructed. We conducted user studies designed to evaluate perception of these objects through haptic feedback alone, auditory feedback alone, and combinations of the two. Our results indicate that both sensory channels can be valuable in user perception.
The G Protein β5 Subunit Interacts Selectively with the Gq α Subunit

The diversity in the heterotrimeric G protein α, β, and γ subunits may allow selective protein-protein interactions and provide specificity for signaling pathways. We examined the ability of five α subunits (αi1, αi2, αo, αs, and αq) to associate with three β subunits (β1, β2, and β5) dimerized to a γ2 subunit containing an amino-terminal hexahistidine-FLAG affinity tag (γ2HF). Sf9 insect cells were used to overexpress the recombinant proteins. The hexahistidine-FLAG sequence does not hinder the function of the β1γ2HF dimer as it can be specifically eluted from an αi1-agarose column with GDP and AlF4−, and purified β1γ2HF dimer stimulates type II adenylyl cyclase. The β1γ2HF and β2γ2HF dimers immobilized on an anti-FLAG affinity column bound all five α subunits tested, whereas the β5γ2HF dimer bound only αq. The ability of other α subunits to compete with the αqsubunit for binding to the β5γ2HF dimer was tested. Addition of increasing amounts of purified, recombinant αi1 to the αq in a Sf9 cell extract did not decrease the amount of αq bound to the β5γ2HF column. When G proteins in an extract of brain membranes were activated with GDP and AlF4− and deactivated in the presence of equal amounts of the β1γ2HF or β5γ2HF dimers, only αq bound to the β5γ2HF dimer. The αq-β5γ2HF interaction on the column was functional as GDP, and AlF4−specifically eluted αq from the column. These results indicate that although the β1 and β2 subunits interact with α subunits from the αi, αs, and αq families, the structurally divergent β5 subunit only interacts with αq.
Adaptive stress signaling in targeted cancer therapy resistance

The identification of specific genetic alterations that drive the initiation and progression of cancer and the development of targeted drugs that act against these driver alterations has revolutionized the treatment of many human cancers. Although substantial progress has been achieved with the use of such targeted cancer therapies, resistance remains a major challenge that limits the overall clinical impact. Hence, despite progress, new strategies are needed to enhance response and eliminate resistance to targeted cancer therapies in order to achieve durable or curative responses in patients. To date, efforts to characterize mechanisms of resistance have primarily focused on molecular events that mediate primary or secondary resistance in patients. Less is known about the initial molecular response and adaptation that may occur in tumor cells early upon exposure to a targeted agent. Although understudied, emerging evidence indicates that the early adaptive changes by which tumor cells respond to the stress of a targeted therapy may be crucial for tumo r cell survival during treatment and the development of resistance. Here we review recent data illuminating the molecular architecture underlying adaptive stress signaling in tumor cells. We highlight how leveraging this knowledge could catalyze novel strategies to minimize or eliminate targeted therapy resistance, thereby unleashing the full potential of targeted therapies to transform many cancers from lethal to chronic or curable conditions.
Overexpression of the CstF-64 and CPSF-160 polyadenylation protein messenger RNAs in mouse male germ cells.

Messenger RNAs for several components of the transcriptional apparatus are greatly overexpressed in postmeiotic male germ cells in rodents (Schmidt and Schibler, Development 1995; 121: 2373‐2383). Because of the tight coupling of polyadenylation and transcription, we examined expression in germ cells of mRNAs for key polyadenylation factors. The mRNA for the 64 000 Mr subunit of the cleavage stimulation factor (CstF-64) was expressed at least 250-fold greater in mouse testicular RNA than in liver RNA. RNA blot analysis showed that the mRNA for the 160 000 Mr subunit of the cleavage and polyadenylation specificity factor was similarly overexpressed, as was the mRNA for the large subunit of RNA polymerase II. General transcription factors, such as the TATA-binding protein and transcription factor IIH, and splicing factors, such as components of the small nuclear ribonucleoproteins, were also expressed in meiotic and postmeiotic germ cells. The X-linked CstF-64 protein is expressed before and after but not during meiosis in the mouse (Wallace et al., Proc Natl Acad Sc iUSA 1999; 96:6763‐6768), which suggests that overexpression of mRNA transcription and processing factors plays an essential role in postmeiotic germ cell mRNA metabolism. gametogenesis, gene regulation, meiosis, spermatogenesis, testis
An explicit cloud microphysics/LES model designed to simulate the Twomey effect

A three dimensional model for simulating the effect of enhanced cloud condensation nucleus (CCN) concentrations on stratocumulus clouds is presented. The model is a largeeddy simulation version of the Regional Atmospheric Modeling System (RAMS) with explicit representation of the CCN spectrum and cloud droplet spectrum. Results of two dimensional tests of the model are presented. A new droplet activation scheme based on a bi-modal size-distribution of CCN is presented. Microphysical sensitivity to a five-fold increase in initial CCN concentrations is examined. Results show that droplet concentrations increase about three-fold, effective radii decrease by 40%, and liquid water contents show less significant variations. These results are consistent with both observations and expectations. We have identified numerically-produced anomalies in the cloud microstructure at the sharp cloud-top boundaries which we believe are associated with the advection scheme. Because the focus of the research is on examining the effects of increasing CCN on cloud albedo, these numerical artifacts need to be addressed.
The seamless approach to reconciling communication and locality in distributed memory parallel systems

With recent improvements in single CPU performance, several issues become more important in multiprocessor design. Two of these are interprocessor communication and locality. In parallel systems with fast CPUs, locality is vital to performance. However, traditional parallel programming models such as shared memory or message passing do not naturally lead to programs that exhibit locality. In the paper, the Seamless model for interprocessor communication is presented which is based on locality and that allows the programmer to explicitly manipulate a program's locality to optimize performance. Additionally, this model can support latency tolerance with proper hardware support. Extensions to the C programming language that support this model are also presented. Finally, a parallel program utilizing this model is provided to illustrate the paradigm. >
Solving the Ecological Problems of Capitalism: Capitalist and Socialist Possibilities:

In this article, the author identifies three ecological problems of capitalism—growth, technology, and consumption—that must be solved to develop a sustainable society. Consistent with previous work, especially in the Marxist ecology tradition, the author argues that overcoming the growth problem requires an alternative to capitalism. This is necessary, though not sufficient: ecological sustainability also depends on overcoming the problems of technology and consumption, which requires an ongoing reform but of a sort only minimally attainable under capitalism. Yet, as the historical record demonstrates, there are no guarantees that socialist alternatives to capitalism will be ecologically sustainable. For socialism to be ecologically sustainable, it must (a) represent a revolutionary break from capitalist approaches toward growth and (b) involve the ongoing reform of technology and consumption, beyond what is possible in capitalism. Examples from the Soviet Union and Cuba illustrate the argument.
H-2 Dd transgene suppresses Theiler's virus-induced demyelination in susceptible strains of mice

Theiler's murine encephalomyelitis virus is a picornavirus which induces chronic immune-mediated central nervous system demyelination and virus persistence in susceptible strains of mice. Using murine strains with congeneic recombinant haplotypes, the H-2D region within the class I major histocompatibility complex has been shown to be important in determining susceptibility/resistance to chronic Theiler's murine encephalomyelitis virus infection. We examined the role of H-2D in demyelinating disease with the use of transgenic D8 mice (H-2Dd, resistant haplotype) crossed to susceptible B10.Q (H-2q) and B10.S (H-2s) mice. Expression of the H-2Dd transgene dramatically suppressed demyelination and reduced the number of virus-antigen positive cells in the spinal cord 45 days following infection. More complete protection was observed in transgenic B10.Q (D8+) mice than in transgenic B10.S (D8+) mice. These experiments support the hypothesis that the immunologic basis of resistance by H-2D is determined by effective antigen presentation which prevents virus persistence and subsequent demyelination.
An ecological evaluation of Eagleson's optimality hypotheses

Summary 1. The pioneering work of Peter Eagleson has been proposed as a theoretical basis for ecohydrology. Central to the theory are three ‘ecological optimality hypotheses’ which represent ecologically important aspects of atmosphere‐soil‐vegetation interactions. 2. The model and its underlying assumptions have never been evaluated in an explicitly ecological context. We examine each of the three optimality hypotheses in turn and test the ability of the model to make ecologically relevant predictions using climate, soil and vegetation data from a semi-arid woodland site in central New Mexico, USA. 3. We find that all three of the optimality hypotheses are ecologically flawed. While we could qualitatively reproduce previously published results, model behaviour under novel conditions was highly variable and frequently unrealistic. 4. The poor performance of the model was probably due to the inadequate treatment of water-limited transpiration in its original derivation. The theory thus requires redevelopment for ecological application, and we suggest several strands of research that could contribute to its improvement.
Explosive trace detection with FBAR-based sensor

This paper describes explosive trace detection through mass sensing with film bulk acoustic resonator (FBAR) coated with antibodies. Mass sensing for a specific explosive is done with the use of antibody made specifically for the targeted explosive. Antibodies were immobilized on the backside of FBAR mass sensors using an antibody immobilization protocol. When the specific explosive is exposed to the sensor, it binds to the antibody on the sensor, causing a shift in the resonant frequency of the FBAR sensor. This sensing technique has been shown to selectively detect vapor traces of TNT (trinitrotoluene, a common explosive) and RDX (cyclotrimethylenetrinitramine which has one of the lowest vapor pressures among various explosives) without any pre-concentrator.
Pamidronate treatment and posttreatment bone density in children with spastic quadriplegic cerebral palsy.

Abstract Little is known about the long-term effects of a course of pamidronate treatment on bone mineral density (BMD) of children with spastic quadriplegic cerebral palsy (SQCP). Nine patients with SQCP who had low bone density and/or history of previous fracture(s) were studied during treatment and more than 1 yr after cyclic pamidronate treatment ended. Over the 12 mo of treatment, spine BMD increases raised average Z-score from −4.0 to −2.8. In the distal femoral metaphysis, BMD increase raised average Z-score from −3.6 to −1.7. Observations posttreatment ranged from 12 to 49 mo. Changes in BMD were variable among individuals. Group spine Z-score an average of 34 mo posttreatment approached pretreatment value. Six of eight patients had final distal femur posttreatment Z-scores the same or better than pretreatment baseline an average of 27.1 mo later. While most but not all gains in BMD were lost over the first 2 yr after treatment, no patient sustained fracture during or after treatment for a cumulative follow-up of more than 27 patient-yr.
ORCA's oceanographic sensor suite

The Mapping, Charting and Geodesy Branch of the Naval Research Laboratory (NRL) at Stennis Space Center, MS, is conducting a multi-year program for the development of unmanned, untethered sensor systems for the collection of tactical oceanographic data in littoral regions. This paper reviews the sensor systems, program progress to date and the future plans for a comprehensive oceanographic survey system. The prototype platform currently in use for this project is the ORCA semi-submersible. The ORCA is an air-breathing vessel which travels just below the water surface. The vessel utilizes a direct radio link for real-time data and control communications, as well as a DGPS system for precise platform positioning. The primary sensor installed on ORCA is the Simrad EM950 system which collects bathymetry and collocated acoustic imagery in water up to 300 meters in depth. With realtime data telemetry to the ORCA host vessel and the NRL developed HMPS bathymetry post-processing software, the system is capable of same-day chart production. In contrast to a full size survey vessel, ORCA is able to collect bathymetric data of the same quantity and quality, but will have one fortieth the life-cycle costs. Other sensors being integrated into ORCA include an acoustic sediment classification system, an acoustic Doppler current profiler, and obstacle avoidance systems.
Jurassic volcanic glass from the Stonyford volcanic complex, Franciscan assemblage, northern California Coast Ranges

Hyaloclastite breccias that occur near the top of the Stonyford volcanic complex contain abundant volcanic glass and rare basaltic clasts that have not been altered significantly by hydrothermal processes or by subsequent metamorphism. They resemble hyaloclastites observed in the summit regions of young Pacific seamounts, and appear to have formed by submarine fire fountains, during which globules of the erupting lava were fragmented by thermal shock from contact with seawater. These breccias contain the first-reported occurrence of unaltered olivine (Fo 86 ) and plagioclase (An 63-80 ) in volcanic rocks of the Franciscan complex. The glasses are rich in K 2 O, Nb, Zr, Rb, and Sr relative to both normal and enriched mid-ocean ridge basalt (MORB), and low in Y, V, and Sc. Pillow lavas intercalated with the hyaloclastites and a crystalline basalt clast have similar compositional characteristics. These magmas are similar to alkalic and transitional basalts that are common in intraplate seamounts and along oceanic spreading centers associated with large ion lithophile element (LILE)-enriched mantle plumes. Other volcanic rocks of the Stonyford complex are LILE-rich tholeiitic basalts and ferrobasalts characteristic of intraplate seamounts. A heterogeneous source region that has at least two distinct end members is suggested by the Zr-Nb systematics: depleted suboceanic asthenosphere (normal MORB-type source) and enriched asthenosphere.
A Multi-Host Approach for the Systematic Analysis of Virulence Factors in Cryptococcus neoformans

A multi-host approach was followed to screen a library of 1201 signature-tagged deletion strains of Cryptococcus neoformans mutants to identify previously unknown virulence factors. The primary screen was performed using a Caenorhabditis elegans-C. neoformans infection assay. The hits among these strains were reconfirmed as less virulent than the wild type in the insect Galleria mellonella-C. neoformans infection assay. After this 2-stage screen, and to prioritize hits, we performed serial evaluations of the selected strains, using the C. elegans model. All hit strains identified through these studies were validated in a murine model of systemic cryptococcosis. Twelve strains were identified through a stepwise screening assay. Among them, 4 (CSN1201, SRE1, RDI1, and YLR243W) were previously discovered, providing proof of principle for this approach, while the role of the remaining 8 genes (CKS101, CNC5600, YOL003C, CND1850, MLH3, HAP502, MSL5, and CNA2580) were not previously described in cryptococcal virulence. The multi-host approach is an efficient method of studying the pathogenesis of C. neoformans. We used diverse model hosts, C. elegans, G. mellonella, and mice, with physiological differences and identified 12 genes associated with mammalian infection. Our approach may be suitable for large pathogenesis screens.
Altering Glypican-1 levels modulates canonical Wnt signaling during trigeminal placode development

Glypicans are conserved cell surface heparan sulfate proteoglycans expressed in a spatiotemporally regulated manner in many developing tissues including the nervous system. Here, we show that Glypican-1 (GPC1) is expressed by trigeminal placode cells as they ingress and contribute to trigeminal sensory neurons in the chick embryo. Either expression of full-length or truncated GPC1 in vivo causes defects in trigeminal gangliogenesis in a manner that requires heparan sulfate side chains. This leads to either abnormal placodal differentiation or organization, respectively, with near complete loss of the ophthalmic (OpV) trigeminal ganglion in the most severe cases after over-expression of full-length GPC1. Interestingly, modulating GPC1 alters levels of endogenous Wnt signaling activity in the forming trigeminal ganglion, as indicated by Wnt-reporter expression. Accordingly, GPC1 over-expression phenocopies Wnt inhibition in causing loss of OpV placodal neurons. Furthermore, increased Wnt activity rescues the effects of GPC1 over-expression. Taken together, these results suggest that appropriate levels of GPC1 are essential for proper regulation of canonical Wnt signaling during differentiation and organization of trigeminal placodal cells into ganglia.
The influence of coherent structures and microfronts on scaling laws using global and local transforms

This study examines the influence of coherent structures and attendant microfronts on scaling laws. Toward this goal, we analyse atmospheric observations of turbulence collected 45 m above a flat surface during the Lammefjord Experiment in Denmark. These observations represent more than 40 hours of nearly stationary strong wind conditions and include more than 1600 samples of the main coherent structures. These samples occupy about 40% of the total record and explain the majority of the Reynolds stress.To study the dependence of the scaling laws on the choice of basis set, the time series of velocity fluctuations are decomposed into Fourier modes, the local Haar basis set and eigenvectors of the lagged covariance matrix. The three decompositions are compared by formulating joint projections. The decompositions are first applied to the samples of phased-locked coherent structures centred about eddy microfronts. The eigenvector decomposition is able to partially separate the small-scale variances due to the coherent eddy microfronts from that due to the small-scale structure with random phase. In the Fourier spectrum, both of these contributions to the variance appear together at the higher wavenumbers and their individual contributions cannot be separated. This effect is relatively minor for the scale distribution of energy but exerts an important influence on higher-moment statistics. Deviations from the − scaling are observed to be slight and depend on choice of basis set.The microfronts strongly influence the higher-order statistics such as the sixth-order structure function traditionally used to estimate the energy transfer variance. The intermittency of fine-scale structure, energy transfer variance and dissipation are not completely characterized by random phase, as often assumed, but are partly associated with microfronts characterized by systematic phase with respect to the main transporting eddies. These conclusions are supported by both the higher-order structure function and the higher-order Haar transform.The Fourier and Haar spectra are also computed for the entire record. The peak of the Haar energy spectrum occurs at smaller scales than those of the Fourier spectrum. The Haar transform is local and emphasizes the width of the events. The Fourier spectrum peaks at the scale of the main periodicity, if it exists, which includes the spacing between the events.
Distribution of COL8A2 and COL8A1 gene variants in Caucasian primary open angle glaucoma patients with thin central corneal thickness

Purpose: One approach to identify genes that contribute to common complex ocular disorders such as primary open angle glaucoma (POAG) is to study the genetic determinates of endophenotypes that are defined by underlying pre-disposing heritable quantitative traits such as central corneal thickness (CCT). Collagen VIII is a major component of Descemet’s membrane and studies in mice have indicated that targeted inactivation of the genes encoding the collagen type 8 alpha1 (Col8a1) and collagen type 8 alpha2 (Col8a2) subunits (COL8A1 and COL8A2) results in thinning of the corneal stroma and of Descemet’s membrane. The purpose of this study is to evaluate COL8A1 and COL8A2 as candidate genes for thin CCT in human POAG patients. Methods: 100 Caucasian POAG patients were enrolled in this study. The entire COL8A1 and COL8A2 coding sequence was determined in 8 patients with CCT 586 µm (one standard deviation above the mean). Selected COL8A2 exons containing variants of interest were sequenced in the full POAG cohort. Association and quantitative trait analyses were performed. Results: Three patients with CCT less than 513 µm and advanced POAG were found to have missense changes in COL8A2; two patients had a previously identified mutation, R155Q and one had a novel change, P678L (p=0.0035, Fisher’s exact test). Missense changes were not found in any of the patients with CCT>513 µm and missense changes in the COL8A1 gene were not found in any patient. One common COL8A2 SNP, rs274754 was also statistically associated with CCT (p=0.018). Conclusions: In this study we have identified COL8A2 missense changes in a group of Caucasian patients with very thin CCT and advanced POAG. These results suggest that DNA sequence variants in the COL8A2 gene may be associated with thin corneas in some glaucoma patients. Further study of COL8A2 variants in other patient populations, especially those with thinner CCT such as African-Americans would provide further support for a role of COL8A2 in corneal thickness and in glaucoma.
Identification of two post-translational modifications via tandem mass spectrometry

Post-Translational Modifications (PTMs) play most important roles in the accomplishment of biological processes and molecular functions. It is challenging to identify two PTMs for a tandem mass spectrum. In this paper, we proposed a new algorithm to detect two PTMs with unknown types. First, we constructed a Pair of Peak Set (PPS) which is composed of pairs of peaks that have the highest sum of intensities. Second, we revealed the relationship between PPS and the whole experimental spectrum. Third, a series of logic conditions was proposed to detect PTMs from a MS/MS spectrum. Finally, we used a scoring function to rank the candidate hits. We applied the method to a large MS/MS data set and the experimental results demonstrated that the proposed method achieved better performance of identifying any types of PTMs in a blind mode than current existing methods.
Mining audit data to build intrusion detection models

In this paper we discuss a data mining framework for constructing intrusion detection models. The key ideas are to mine system audit data for consistent and useful patterns of program and user behavior, and use the set of relevant system features presented in the patterns to compute (inductively learned) classifiers that can recognize anomalies and known intrusions. Our past experiments showed that classifiers can be used to detect intrusions, provided that sufficient audit data is available for training and the right set of system features are selected. We propose to use the association rules and frequent episodes computed from audit data as the basis for guiding the audit data gathering and feature selection processes. We modify these two basic algorithms to use axis attribute(s) as a form of item constraints to compute only the relevant ("useful") patterns, and an iterative level-wise approximate mining procedure to uncover the low frequency (but important) patterns. We report our experiments in using these algorithms on real-world audit data.
Biomarkers of TGF-β signaling pathway and prognosis of pancreatic cancer.

Background Transforming growth factor (TGF)-β signaling pathway, may act both as a tumor suppressor and as a tumor promoter in pancreatic cancer, depending on tumor stage and cellular context. TGF-β pathway has been under intensive investigation as a potential therapeutic target in the treatment of cancer. We hypothesized a correlation between TGF-βR2/SMAD4 expression in the tumor, plasma TGF-β1 ligand level, genetic variation in TGF-B pathway and prognosis of pancreatic cancer. Method We examined TGF-βR2 and SMAD4 protein expression in biopsy or surgical samples from 91 patients with pancreatic ductal adenocarcinoma (PDAC) using immunohistochemistry. Plasma level of TGF-β1 was measured in 644 patients with PDAC using ELISA. Twenty-eight single nucleotide polymorphisms (SNP) of the TGF-β1, TGF-β2, TGF-β3, TGF-βR1, TGF-βR2, and SMAD4 genes were determined in 1636 patients with PDAC using the Sequenom method. Correlation between protein expression in the tumor, plasma TGF-β1 level, and genotypes with overall survival (OS) was evaluated with Cox proportional regression models. Results The expression level of TGF-βR2 and SMAD4 as an independent marker was not associated with OS. However, patients with both low nuclear staining of TGF-βR2 and high nuclear staining of SMAD4 may have better survival (P = 0.06). The mean and median level of TGF-β1 was 15.44 (SD: 10.99) and 12.61 (interquartile range: 8.31 to 19.04) ng/ml respectively. Patients with advanced disease and in the upper quartile range of TGF-β1 level had significantly reduced survival than those with low levels (P = 0.02). A significant association of SMAD4 SNP rs113545983 with overall survival was observed (P<0.0001). Conclusion Our data provides valuable baseline information regarding the TGF-β pathway in pancreatic cancer, which can be utilized in targeted therapy clinical trials. High TGF-β1 plasma level, SMAD4 SNP or TGF-βR2/SMAD4 tumor protein expression may suggest a dependence on this pathway in patients with advanced pancreatic cancer.
Distributed supply chain simulation using a generic job running framework

For supply chain performance simulation that involves aggregating results from multiple runs of the same underlying model, simulation iterations can be distributed to networked computing resources to achieve significant speedup. We present a generic distributed job running framework that facilitates such high performance supply chain simulation. We first introduce a supply chain modeling and simulation tool developed by IBM Research, and summarize the strategy to enhance it. A closer look is then taken at a generic job running framework we designed and how it was used to bring the distributed simulation capability to the tool.
Ultrafiltration for Volume Control in Decompensated Heart Failure

Although ultrafiltration is currently reserved in most centers for the patient who has not responded to standard intravenous diuretic therapy with advanced congestion, its implementation earlier in the hospitalization may have definite advantages. This approach, however, will require further investigation with specific emphasis on safety and costs.
Power-Aware 3D Computer Graphics Rendering

Real-time 3D Graphics rendering consumes significant power because of its very high computation and memory access rate. Due to variation in workload and perceptual tolerance, power-awareness can optimize this power consumption significantly, thus facilitating migration to future power-constrained devices such as personal digital assistants (PDAs), tablets, wearables, phones etc. This work proposes such a low power system based on Approximate Graphics Rendering (AGR). The AGR system supports various algorithms and incremental changes to the computational mechanism based on certain pre-specified parameters. The knowledge available apriori about the signal and noise models of graphic images and Human Visual Perception (HVP) are used to select the configuration that meets the quality needs at the lowest power consumption. The power savings using the AGR system are examined for two power hungry stages of the 3D graphics rendering system, namely shading and texture mapping. Besides supporting various algorithms, two novel parameterizable computation schemes are proposed. First, iterative COordinate Rotation DIgital Computer (CORDIC) algorithm based units are incorporated for certain computations. Second, a scheme for dynamically enhancing the perceived image spatial correlation for reduced computations is presented. A hardware synthesis and estimation methodology based on realistic graphics content from the well-known 3D graphics benchmarks and the game Quake2 [1] is used for estimation of power savings. Significant power savings of 75.1%, 73.8% and 72% are demonstrated in the shading, texture mapping function blocks and CORDIC based 3D vector interpolator respectively.
Inactivation of bacteriophage ØX174 by sublethal nitrous acid — Produced lesions

Abstract Nitrous acid (HNO 2 ) treated whole OX174 bacteriophage particles, but not treated OX174 DNA, were found to lose viability while being stored at 5°–8°C at pH 8.0. Thus, although the DNA moiety of the virus was the target for HNO 2 inactivation when infectivity was measured immediately after treatment, the protein moiety was implicated in loss of infectivity during storage following HNO 2 treatment. The viability of HNO 2 treated OX174 DNA depended on the age of the spheroplast culture used for the bioassay. Survival curves of treated DNA showed slower inactivation on newly prepared spheroplasts than on “old” ones. Some HNO 2 lesions which are normally sublethal are apparently lethal in older spheroplasts.
Geographic information system (GIS) analysis of ecosystem invasion: Exotic mussels in Lake Erie

Geographic information system (GIS) analysis with bathymetric, substrate, and side scan sonar (SSS) data was used to assess both spatial and temporal expansion of exotic dreissenid mussels onto sedimentary habitats in Lake Erie. These data were used for developing multiple regression models with substrate types and SSS data to interpret the expansion of Dreissena assemblages across the central and western basins of Lake Erie from 1994 to 1998. The 1994‐1996 GIS model predicted the 1997 SSS measurements of Dreissena coverage correctly in 84% of the cases (n 5 50). Similarly, the 1994‐1997 GIS model predicted the 1998 SSS measurements of Dreissena coverage correctly in 80% of the cases (n 5 20). These models indicated that Dreissena coverage ranged from ,1% on muds in 1994 to 67% on sands and gravels in 1997. Based on all of the substrates, the 1994‐1997 model indicates that Dreissena beds have been expanding since 1994 at 1,000 6 6k m 2 yr 21 and presently occupy 5,484 6 32 km 2 of the 25,734 km 2 sedimentary bottom of Lake Erie. Our observations indicate that expanding Dreissena beds are altering soft-substrate habitats and influencing the ecosystem dynamics throughout Lake Erie. Furthermore, this study demonstrates that the distribution, abundance, and ecosystem impacts of invasive species in other watersheds can be accurately described and interpreted over diverse spatial and temporal scales using GIS models.