cssi/SciSciGPT-SciSciNet huggingface dataset:
A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps

Although many electron density maps have been produced into the medium resolutions, it is still challenging to derive the atomic structure from such volumetric data. Current methods primarily rely on the availability of an existing atomic structure for fitting or a homologous template structure for modeling. In the process of developing a template-free, de novo, method, the topology of the secondary structure elements need to be resolved first. In this paper, we extend our previous algorithm of finding the optimal solution in the constraint graph problem. We illustrate an approach to obtain the top-K topologies by combining a dynamic programming algorithm with the K-shortest path algorithm. The effectiveness of the algorithms is demonstrated from the test using three datasets of different nature. The algorithm improves the accuracy, space and time of an existing method.
Medical treatment for men who have sex with men and are living with HIV/AIDS.

This study focuses on a sample of men who have sex with men (MSM) living with HIV/AIDS in a south Florida community. The study uses a mixed-method, quantitative, and qualitative research design. Th...
Vitamin D Regulation of Immune Function: Implications for Bone Loss During Inflammation

Although the best known actions of vitamin D involve its regulation of bone mineral homeostasis, actions critical for a healthy skeleton, vitamin D exerts its influence on many physiologic processes. One of these processes is the immune system. Both the adaptive and innate immune systems are impacted by the active metabolite of vitamin D, 1,25(OH)2D3. In turn, the immune system is now recognized as having a major impact on the skeleton. In this review, I will examine the regulation by 1,25(OH)2D3 of immune function, then examine the evidence for such regulation as potential means of ameliorating the bone loss that accompanies the inflammatory state.
Destabilization of mouse liver lysosomes by vitamin A compounds and analogues.

Abstract In an investigation of the basis for toxicity of vitamin A, 13 vitamin A compounds and analogues were evaluated for destabilization of lysosomes. Those most effective for the release of liver acid phosphatase were, in decreasing order, retinol. N , N -diethylretinamide, N -ethylretinamide, retinyl acetate. 9- cis -retinal, retinoic acid, retinal, 13- cis -retinal, 13- cis -retinoic acid. For the release of liver β-glucuronidase, deoxyribonuclease and N -acetyl-β-D-glucosaminidase, these compounds were about equally active. The differential release of acid phosphatase, compared to the other enzymes, and a differential stabilization by chloroquine and 3',5'-cyclic AMP of the retinol-induced release of the four enzymes were consistent with the idea that a heterogeneous population of lysosomes exists within liver cells. Chloroquine. which prevented the release of some lysosomal enzymes, did not reverse the toxicity of retinyl acetate to mice; and the release of β-glucuronidase form mouse L-929 fibroblast lysosomes correlated poorly with toxicity of the vitamin A compounds to these cells in culture. The results indicate that the toxicity of vitamin A compounds is not due solely to destabilization of lysosomes.
Humeans aren't out of their minds

Humeanism is “the thesis that the whole truth about a world like ours supervenes on the spatiotemporal distribution of local qualities.” (Lewis, 1994, 473) Since the whole truth about our world contains truths about causation, causation must be located in the mosaic of local qualities that the Humean says constitute the whole truth about the world. The most natural ways to do this involve causation being in some sense extrinsic. To take the simplest possible Humean analysis, we might say that c causes e iff throughout the mosaic events of the same type as c are usually followed by events of type e. For short, the causal relation is the constant conjunction relation. Whether this obtains is determined by the mosaic, so this is a Humean theory, but it isn’t determined just by c and e themselves, so whether c causes e is extrinsic to the pair. Now this is obviously a bad theory of causation, but the fact that causation is extrinsic is retained even by good Humean theories of causation. John Hawthorne (2004) objects to this feature of Humeanism. I’m going to argue that his arguments don’t work, but first we need to clear up three preliminaries about causation and intrinsicness. First, my wording so far has been cagey because I haven’t wanted to say that Humeans typically take causation to be an extrinsic relation. That’s because the greatest Humean of them all, David Lewis, denies that causation is a relation at all, and hence that it is an extrinsic relation (Lewis, 2004b). We can go some way to avoiding this complication by talking, as Hawthorne does, about properties of regions, and asking the property of containing a duplicate of c that causes a duplicate of e is intrinsic or extrinsic.1 Humeans typically take causation to be extrinsic in this sense. Second, nothing in Humeanism requires that causation is extrinsic in that sense. If one analysed causation as that intrinsic relation that actually most tightly correlates with the constant conjunction relation, then one would have guaranteed that causation was an intrinsic relation. Moreover, one would have a perfectly Humean theory of causation. (A perfectly awful theory, to be sure, but still a Humean one.) Peter Menzies (1996, 1999) develops a more sophisticated version of such a theory, and though Menzies describes his view as anti-Humean, one can locate the relation we’ve defined here in the Humean mosaic, so such an approach might be consistent with Humeanism in the intended sense. Third, there is good reason, independent of Humeanism, to accept that causation is extrinsic. As Ned Hall (2004) argues, it is very hard to square the intrinsicness of causation with the possibility of causation by omission. Given the choice between
Juvenile Hormone Regulates Vitellogenin Gene Expression through Insulin-like Peptide Signaling Pathway in the Red Flour Beetle, Tribolium castaneum

Our recent studies identified juvenile hormone (JH) and nutrition as the two key signals that regulate vitellogenin (Vg) gene expression in the red flour beetle, Tribolium castaneum. Juvenile hormone regulation of Vg synthesis has been known for a long time in several insects, but the mechanism of JH action is not known. Experiments were conducted to determine the mechanism of action of these two signals in regulation of Vg gene expression. Injection of bovine insulin or FOXO double-stranded RNA into the previtellogenic, starved, or JH-deficient female adults increased Vg mRNA and protein levels, thereby implicating the pivotal role for insulin-like peptide signaling in the regulation of Vg gene expression and possible cross-talk between JH and insulin-like peptide signaling pathways. Reduction in JH synthesis or its action by RNAi-mediated silencing of genes coding for acid methyltransferase or methoprene-tolerant decreased expression of genes coding for insulin-like peptides (ILPs) and influenced FOXO subcellular localization, resulting in the down-regulation of Vg gene expression. Furthermore, JH application to previtellogenic female beetles induced the expression of genes coding for ILP2 and ILP3, and induced Vg gene expression. FOXO protein expressed in baculovirus system binds to FOXO response element present in the Vg gene promoter. These data suggest that JH functions through insulin-like peptide signaling pathway to regulate Vg gene expression.
Seeking the ‘Lord with a Club’: Locating Lakulīśa in the Early History of Pāśupata Śaivism (sixth to ninth century CE)

As the emblem of Pāśupata identity, representations of the deified teacher called Lakulīśa (the ‘Lord with a Club’) became a prominent feature of the expanding Śaiva religious landscape in early medieval northwest India. This study works to recover some of Lakulīśa’s historical contingency by reading his appearance in both text and image as a reflection of or response to particular concerns of the developing Śaiva religious community. The significance of Lakulīśa’s literary debut in the Nepalese recension of the early Skandapurāṇa is examined first. I then explore the visual representations of this figure by considering patterns in Lakulīśa’s iconography and the place of his images within sanctified spaces. Since temples were vital loci of interaction across a wide spectrum of social groups and religious communities, even ostensibly Śaiva centres would have accommodated a range of deities, religious practitioners, and devotional repertoires. Given the multivocality of these sanctified spaces, I propose th...
Potassium removal with peritoneal dialysis

Peritoneal dialysis is often performed in patients with hyperkalemia with a goal of removing potassium (K) rapidly from the extracellular fluid space (ECF). Increased plasma clearances of urea, creatinine and calcium have been demonstrated during hypertonic peritoneal dialysis (HPD) using 7% (682 mOsm/kg H20), as compared to the less hypertonic 1.5% (374 mOsm/kg H20) dextrose dialysis solutions [1—5]. The following studies demonstrate that only modest increases in K clearances are achieved with HPD and K diffusion from ECF accounts for the majority of K removal during peritoneal dialysis. Like sodium (Na), K does not proportionately accompany the bulk flow of extracellular water during HPD in the absence of a concentration gradient for net diffusion [2, 6]. Methods. Study exchanges (fifty-two 1.5% dextrose and thirty-four 7% dextrose) were performed during 19 separate peritoneal dialysis in 10 uremic patients. No patient manifested any clinical or electrocardiographic manifestations of hyperkalemia and the highest serum K (PK) value observed before or during these studies was 6.8 mEq/Iiter. All dialysis solutions were prewarmed to body temperature prior to instillation. Two liter exchanges were instilled by gravity into the peritoneal cavity over a 10 mm period, allowed to dwell for 30 mm, and drained by gravity over another 30 mm to assure as complete a drainage as possible. After good mechanical drainage was established, a series of study exchanges was started which consisted of a 1.5% dextrose exchange followed by one to three 7 % dextrose exchanges. Studies were performed both early and late in dialysis. All instillation volumes were measured by marking the fluid level in each bottle prior to instillation and measuring the volume of water required to fill to that level following instillation. Total drainage volume was measured in a
A hypercircle method of frame analysis—II. Practice

Abstract The hypercircle method of structural analysis, the theory of which was developed in Part I, is shown to have certain advantages, in terms of computer time required, over conventional methods of analysis for very large rigid-jointed planar frames. This efficiency is achieved by the systematic use of “superelements” based on the four-node rectangular finite clement.
Biosynthesis and structure of lipopolysaccharide in an outer membrane-defective mutant of Escherichia coli J5.

Abstract Membrane-defective mutants of Escherichia coli J5 were isolated on the basis of supersensitivity to the antibiotic novobiocin. These mutants display an increased sensitivity to a wide range of antibiotics and to several dyes and detergents. In addition, several mutants leak the periplasmic enzymes, alkaline phosphatase and ribonuclease. This evidence indicates an outer membrane defect in these mutants. The inner and outer membranes of one mutant were separated and subjected to compositional analysis. A deficiency in galactose-containing lipopolysaccharide in the outer membrane of the mutant was observed. Two possible causes of this deficiency were examined and discounted: defective galactose uptake into the cell, and defective translocation of lipopolysaccharide from the inner membrane. Extraction and chemical analysis of mutant and wild type lipopolysaccharides suggests that the mutant is defective in the enzyme which transfers glucose to the growing lipopolysaccharide core, UDPglucose transferase. Thus, the mutant's deficiency in galactose-containing lipopolysaccharide can be ascribed to the fact that addition of glucose to the lipopolysaccharide core is a prerequisite for galactose addition. The physiological implications of this alteration are discussed.
A Smoothest Path algorithm and its visualization tool

In this paper we present an extension of the Shortest Path Problem: the Smoothest Path. A Smoothest Path algorithm optimizes both distance and slope to produce the least rigorous path available. Useful in simulated and real-world path finding, a smoothest path algorithm can provide useful data for a variety of applications. While smooth path algorithms exist, the notion of a smoothest path is fairly new. Simulated visualizations of algorithms have become a popular and effective learning tool. In the past, algorithms have been taught through exhaustive chalkboard drawings and pseudo-code guidelines. Visualization tools are therefore an attractive learning essential for instructors and students alike. Increased performance in languages such as Java along with robust graphical interfacing libraries such as Swing and JOGL make this a conquerable problem. In this paper, we also present a tool to visualize our smoothest path algorithm. Our goal is to simplify the algorithm into a series of visual steps that can be understood by elementary computer science students.
The Thermodynamic Significance of Order Parameters During Glass Relaxation

The thermodynamic state of a glass is often described in terms of a number of order parameters, each of which evolves toward its equilibrium value during glass relaxation. The problem comes in identifying these order parameters and determining their physical significance. The authors argue that the order parameters in a glass can be defined in terms of a set of configurational temperatures, each corresponding to a particular mode of energy storage. The evolution of glass properties can then be calculated using a coupled set of rate equations describing the relaxation of the configurational temperatures toward their equilibrium values, viz., the reservoir temperature. The authors illustrate the concept of configurational temperatures by considering the free energy of mixing in alkali borate and silicate glasses.
Multiple Enzyme Layers on Carbon Nanotubes for Electrochemical Detection Down to 80 DNA Copies

Signal amplification using enzyme multilayers on carbon nanotube (CNT) templates is shown to yield a remarkably sensitive electrochemical detection of proteins and nucleic acids. The electrostatic layer-by-layer (LBL) self-assembly onto CNT carriers maximizes the ratio of enzyme tags per binding event to offer the greatest amplification factor reported to date. Absorption spectroscopy, TEM, and electrochemical characterization confirm the formation of LBL enzyme nanostructures on individual CNT carriers. The enzymatic activity is found to increase with the number of enzyme layers. The new protocol is illustrated for monitoring sandwich hybridization and antibody−antigen interactions in connection with alkaline phosphatase tracers. Factors affecting the enzyme loading and the analytical performance have been optimized. Such amplified bioelectronic assays allow detection of DNA and proteins down to 80 copies (5.4 aM) and 2000 protein molecules (67 aM), respectively. Given the enormous amplification afforded...
Improving High-Performance Sparse Libraries Using Compiler-Assisted Specialization: A PETSc Case Study

Scientific libraries are written in a general way in anticipation of a variety of use cases that reduce optimization opportunities. Significant performance gains can be achieved by specializing library code to its execution context: the application in which it is invoked, the input data set used, the architectural platform and its backend compiler. Such specialization is not typically done because it is time consuming, leads to nonportable code and requires performance-tuning expertise that application scientists may not have. Tool support for library specialization in the above context could potentially reduce the extensive understanding required while significantly improving performance, code reuse and portability. In this work, we study the performance gains achieved by specializing the single processor sparse linear algebra functions in PETSc (Portable, Extensible Toolkit for Scientific Computation) in the context of three scalable scientific applications on the Hopper Cray XE6 Supercomputer at NERSC. We use CHiLL (Compos able High-Level Loop Transformation Framework) to apply source level transformations tailored to the special needs of sparse computations and automatically generate highly optimized PETSc functions. We demonstrate significant performance improvements of more than 1.8X on the library functions and overall gains of 9 to 24% on three scalable applications that use PETSc's sparse matrix capabilities.
Biocorrosion investigation of two shape memory nickel based alloys: Ni-Mn-Ga and thin film NiTi.

Thin film nitinol and single crystal Ni-Mn-Ga represent two new shape memory materials with potential to be used as percutaneously placed implant devices. However, the biocompatibility of these materials has not been adequately assessed. Immersion tests were conducted on both thin film nitinol and single crystal Ni-Mn-Ga in Hank's balanced salt solution at 37°C and pH 7.4. After 12 h, large pits were found on the Ni-Mn-Ga samples while thin film nitinol displayed no signs of corrosion. Further electrochemical tests on thin film nitinol samples revealed breakdown potentials superior to a mechanically polished nitinol disc. These results suggest that passivation or electropolishing of thin film nitinol maybe unnecessary to promote corrosion resistance. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Invariant *‐product quantization of the one‐dimensional Kepler problem

It is shown that, with proper interpretation, phase space trajectories for the one‐dimensional Kepler problem retain their significance after quantization. The classical and quantum theories are both entirely conventional; only the Wigner correspondence (Weyl quantization rule) is not. The usual quantum theory may be obtained by so(2,1) ‐invariant *‐product quantization (generalized Moyal mechanics). [The analog in three dimensions is so(4,2) invariant *‐quantization; it is believed that this should encounter no new difficulties of principle.] New results concerning invariant *‐products on polynomials, in the case of so(2,1), are presented. The Kepler problem is the first known example of a nonanalytic *‐representation. Piecewise analytic *‐representations are defined and are shown to provide a general framework for invariant quantization on singular orbits of semisimple groups. When piecewise analytic *‐representations are allowed, then the specification of an invariant *‐product on polynomials is no longer sufficient to determine a unique quantum theory.
KIT oncogenic signaling mechanisms in imatinib-resistant gastrointestinal stromal tumor: PI3-kinase/AKT is a crucial survival pathway

Most gastrointestinal stromal tumor (GIST) patients respond to KIT inhibition with imatinib, yet will eventually exhibit resistance. Imatinib-resistance mechanisms are heterogeneous, and little is known about KIT functional roles in imatinib-resistant GIST. Biological consequences of biochemical inhibition of KIT, phosphatidyl-inositol-3-kinase (PI3-K), PLCgamma, MAPK/ERK kinase/mitogen-activated protein kinase (MEK/MAPK), mammalian target of rapamycin (mTOR) and JAK were determined by immunoblotting for protein activation, and by cell proliferation and apoptosis assays in GIST cell lines from imatinib-sensitive GIST (GIST882), imatinib-resistant GISTs (GIST430 and GIST48) and KIT-negative GIST (GIST62). KIT activation was 3- to 6-fold higher in GIST430 and GIST48 than in GIST882, whereas total KIT expression was comparable in these three GIST lines. In addition to the higher set point for KIT activation, GIST430 and GIST48 had intrinsic imatinib resistance. After treatment with 1 muM imatinib, residual KIT activation was 6- and 2.8-fold higher in GIST430 and GIST48, respectively, compared to GIST882. In all GIST lines, cell growth arrest resulted from PI3-K inhibition, and - to a lesser extent - from MEK/MAPK and mTOR inhibition. Inhibition of JAK/STAT or PLCgamma did not affect cell proliferation. Similarly, only PI3-K inhibition resulted in substantial apoptosis in the imatinib-resistant GISTs. We conclude that GIST secondary KIT mutations can be associated with KIT hyperactivation and imatinib resistance. Targeting critical downstream signaling proteins, such as PI3-K, is a promising therapeutic strategy in imatinib-resistant GISTs.
A four-parameter model of the glottis and vocal fold contact area

Abstract Articulatory models of speech production are generally controlled by kinematic parameters that govern the position and movement of tissue and air. A four parameter model of the glottis is described with similar kinematic parameters to complement this approach. Parameters are nondimensional zed quotients that control the static and dynamic shape of the glottis. The model can stimulate glottal flow, glottal area, and vocal contact area simultaneously which identical parameters. Specific features of these waveforms are discussed in terms of the glottal configuration that was used to produce them. In particular, a detailed description of the contact area waveshape is included. The model is expected to be applied to vocal fold imaging techniques that rely on signals gathered noninvasively on the surface of the body. For synthesis, the model provides an alternative to flow pulse modeling because it can include some source-system interactions with relatively little computational overhead.
The Role of Genetics in Host Responses to Mucosal and Invasive Candidiasis

The development of mucosal and invasive candidiasis depends upon a variety of innate and acquired risk factors. The number of genes known to be important for immunity against candidiasis has been increasing. Studies of variants of these genes are facilitating our knowledge of host predisposition to infection. Insights gleaned from genetic variants identified in patients with primary immunodeficiency syndromes such as chronic mucocutaneous candidiasis have further aided in this process. This article reviews data from genomic association studies in patients with such syndromes and in broader patient populations. These studies are placed within the framework of our current understanding of antifungal host defenses.
Cks1 proteasomal degradation is induced by inhibiting Hsp90-mediated chaperoning in cancer cells.

Purpose Cks1, a conformationally heterogenous 9 kDa protein, is markedly overexpressed in cancer cells and contributes to tumor development. Cks1 is an essential component of the SCF-Skp2 ubiquitin ligase complex that targets the Cdk inhibitors p27Kip1 and p21Cip1. Cks1 is known to interact with the Hsp90-Cdc37 chaperone machinery, although whether this facilitates its conformational maturation and stability is not known. To test whether abrogating the chaperone function of Hsp90 could destabilize Cks1, we examined the effects of treating different cancer cell lines with the benzoquinone ansamycin 17-allylamino geldanamycin (17-AAG), a compound that selectively binds Hsp90 and potently inhibits its ATP-dependent chaperone activity.
The Cell Cycle–Regulated Genes of Schizosaccharomyces pombe

Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 wave included many genes involved in ribosome biogenesis, possibly explaining the cell cycle oscillation in protein synthesis in S. pombe. The G2/M wave included at least three distinctly regulated clusters of genes: one large cluster including mitosis, mitotic exit, and cell separation functions, one small cluster dedicated to DNA replication, and another small cluster dedicated to cytokinesis and division. S. pombe cell cycle genes have relatively long, complex promoters containing groups of multiple DNA sequence motifs, often of two, three, or more different kinds. Many of the genes, transcription factors, and regulatory mechanisms are conserved between S. pombe and S. cerevisiae. Finally, we found preliminary evidence for a nearly genome-wide oscillation in gene expression: 2,000 or more genes undergo slight oscillations in expression as a function of the cell cycle, although whether this is adaptive, or incidental to other events in the cell, such as chromatin condensation, we do not know.
Surgery for Lumbar Spinal Stenosis: Informed Patient Preferences Should Weigh Heavily

In this issue, Delitto and colleagues examined surgical versus nonsurgical treatment options for lumbar spinal stenosis. The editorialist discusses the strengths of the trial, notes similar studies...
The isolation, cloning and identification of a vegetative catalase gene from Bacillus subtilis.

Abstract A Bacillus subtilis library of Tn917∷lacZ insertions was screened for mutants that were unable to grow in the presence of normally sublethal concentrations of hydrogen peroxide. The identification and subsequent analysis of one mutant strain, YB2003, which carried the mutation designated kat-19, revealed that this strain was deficient in the expression of a vegetative catalase. Regions of the chromosome both 5′ and 3′ to the site of the Tn917 insertion, as well as the gene without the insertion (kat-19+) were cloned. The presence of the functional kat-19+ gene on a high-copy plasmid restored catalase activity to the kat-19∷Tn917 strain as well as to strains of B. subtilis that carried the katA1 mutation. While the katA+ locus is believed to represent the structural gene for the vegetative catalase of B. subtilis [Loewen and Switala, J. Bacteriol. 169 (1987) 5848–5851], the sequence analysis of the cloned kat-19+ DNA fragments revealed an open reading frame that showed significant homology between the deduced amino acid sequence of this gene product and that of known eukaryotic catalases.
Bringing the Question of Chinese IPR Enforcement to the WTO Under TRIPS: An Effective Strategy or a Meaningless and Overused Tactic by the U.S.?

China has had a long history of high levels of piracy and counterfeiting. Leaders of China’s Food and Drug Administration have confessed that their pharmaceutical market is immersed in fake and deadly drugs. 1 In addition, DVD’s and VCD’s 2 containing pirated versions of Chinese and foreign films or television series are easily found in China’s major cities. 3 Since China is the world’s fastest growing economy and the contributor of the largest trade deficit to the United States (U.S.) (U.S. $268 billion in 2008), 4 it is no surprise that the issue of Intellectual Property Right (IPR) counterfeiting and piracy are of national interest to the U.S..
Analysis of cyclic variability in spark-assisted HCCI combustion using a double Wiebe function

A heuristic algorithm based on a double Wiebe function is proposed for estimating the relative importance of distinct combustion modes (propagating flame and compression ignition) occurring within individual combustion cycles as an engine is transitioned from conventional spark-ignited (SI) combustion to homogeneous charge compression ignition (HCCI). The proposed algorithm automates the analysis and categorization of pressure measurements from large numbers of individual cycles, providing new insight into the unstable combustion processes occurring during mode transition. Similar techniques could potentially be utilized for on-line diagnostics and control of the balance between SI and HCCI combustion in spark-assisted HCCI.
Vertex potentials evoked during auditory signal detection - Relation to decision criteria

Vertex potentials were recorded from eight subjects performing in an auditory threshold detection task with rating scale responses. The amplitudes and latencies of both the N1 and the late positive (P3) components were found to vary systematically with the criterion level of the decision. These changes in the waveshape of the N1 component were comparable to those produced by varying the signal intensity in a passive condition, but the late positive component in the active task was not similarly related to the passively evoked P2 component. It was suggested that the N1 and P3 components represent distinctive aspects of the decision process, with N1 signifying the quantity of signal information received and P3 reflecting the certainty of the decision based upon that information.
Custody Evaluations: Ethics in Training Evaluators

Little has been written addressing ethical considerations in the training of custody evaluators and mediators. This article summarizes the ethical principles involved in training new evaluators and in providing ongoing training to experienced evaluators. Model programs for both types of training are presented.
PAN-1, a P-granule component important for C. elegans fertility, has dual roles in the germline and soma

In Caenorhabditis elegans, P granules are germline-specific, RNA-containing granules that segregate into the germline precursor cell during early embryogenesis. In this short report, PAN-1, which previously has been found by others in screens for genes causing larval molting defects, is identified here as a novel P-granule component and a binding partner of GLH-1 (Germline RNA Helicase-1), a constitutive, germline-specific, P-granule protein. The PAN-1 predicted protein contains multiple leucine-rich repeats (LRRs) and regions with similarities to F-box proteins. Antibodies raised against PAN-1 reveal it is present both in the soma and the germline. In the germline, PAN-1 uniquely localizes to P granules from the first larval stage onward and is unusual for a P-granule component in lacking recognizable RNA binding motifs. Homozygous pan-1(gk142) deletion worms arrest as larvae that are unable to molt and this phenotype is also seen with pan-1(RNAi) into wild type worms. pan-1(RNAi) into the somatic RNAi-defective strain rrf-1(pk1417) bypasses the larval arrest and allows an assessment of PAN-1 function in the germline. We find pan-1(RNAi) is variably effective in knocking down PAN-1 protein and results in adult progeny that display multiple germline defects. These phenocopies range from under-proliferation of the germline, as also seen with loss of GLH-1, to the induction of endomitotic replication in oocytes, both defects that result in sterility, to fertile animals with significantly reduced progeny numbers. Thus, while loss of PAN-1 in the soma inhibits molting, this report demonstrates that PAN-1 is also a P-granule component that is essential for fertility.
Pharmacokinetics and effect of intravenous meloxicam in weaned Holstein calves following scoop dehorning without local anesthesia

Dehorning is a common practice involving calves on dairy operations in the United States. However, less than 20% of producers report using analgesics or anesthetics during dehorning. Administration of a systemic analgesic drug at the time of dehorning may be attractive to dairy producers since cornual nerve blocks require 10 – 15 min to take effect and only provide pain relief for a few hours. The primary objectives of this trial were to (1) describe the compartmental pharmacokinetics of meloxicam in calves after IV administration at 0.5 mg/kg and (2) to determine the effect of meloxicam (n = 6) or placebo (n = 6) treatment on serum cortisol response, plasma substance P (SP) concentrations, heart rate (HR), activity and weight gain in calves after scoop dehorning and thermocautery without local anesthesia. Plasma meloxicam concentrations were detectable for 50 h post-administration and fit a 2-compartment model with a rapid distribution phase (mean T½α = 0.22 ± 0.087 h) and a slower elimination phase (mean T½β = 21.86 ± 3.03 h). Dehorning caused a significant increase in serum cortisol concentrations and HR (P < 0.05). HR was significantly lower in the meloxicam-treated calves compared with placebo-treated calves at 8 h (P = 0.039) and 10 h (P = 0.044) after dehorning. Mean plasma SP concentrations were lower in meloxicam treated calves (71.36 ± 20.84 pg/mL) compared with control calves (114.70 ± 20.84 pg/mL) (P = 0.038). Furthermore, the change in plasma SP from baseline was inversely proportional to corresponding plasma meloxicam concentrations (P = 0.008). The effect of dehorning on lying behavior was less significant in meloxicam-treated calves (p = 0.40) compared to the placebo-treated calves (P < 0.01). Calves receiving meloxicam prior to dehorning gained on average 1.05 ± 0.13 kg bodyweight/day over 10 days post-dehorning compared with 0.40 ± 0.25 kg bodyweight/day in the placebo-treated calves (p = 0.042). To our knowledge, this is the first published report examining the effects of meloxicam without local anesthesia on SP, activity and performance of calves post-dehorning. These findings suggest that administration of meloxicam alone immediately prior to dehorning does not mitigate signs of acute distress but may have long term physiological, behavior and performance effects.
Warfarin Versus New Agents: Interpreting the Data

Stroke prevention in atrial fibrillation (AF) is a rapidly expanding indication for lifelong oral anticoagulation. The vitamin K antagonists (VKAs) effectively prevent stroke, but are notoriously difficult to manage and are associated with frequent adverse events. These factors account for the widespread underuse of warfarin for patients with AF who are qualified candidates for therapy. New oral anticoagulants with different mechanisms of action are beginning to exit phase III trials and may replace the VKAs for a number of indications, especially AF. The oral direct thrombin and Xa inhibitors are furthest along in development. Dabigatran etexilate, a thrombin inhibitor, has recently shown excellent outcomes in the prevention of stroke in patients with AF. The oral Xa inhibitors are still in phase III trials for stroke prevention in AF, but results from trials for other indications look promising. These short-acting, short-duration, unmonitored drugs are not without limitations and potential adverse effects. The perceived drawbacks of the VKAs may actually be assets in the management of patients with AF, and the pros and cons of each class of drug must be taken into account as physicians consider or patients request transition to a new class of oral anticoagulants.
Fracture densities and fracture azimuths evident in the azimuthal amplitudes from the top of a fractured carbonate oil reservoir

Summary A high-fold full-azimuth full-offset 3D P-P reflection survey was acquired and processed for the purpose of characterizing a naturally fractured carbonate reservoir. The reservoir is a thick carbonate, overlain by a shale, which will flow oil with a sufficient fracture network. The calibration data for the natural fractures are: 1) a loggingwhile-drilling (LWD) Star Trak™ resistivity image log in a horizontal borehole, and 2) micro-seismic (m-s) data. The 3D P-P reflection data were processed through azimuthal prestack depth migration (PSDM), and the azimuthal traveltimes were quantified in a non-sectored analysis and then removed into attribute volumes, leaving flat common image gathers (CIGs). A companion paper presents the minimum horizontal stress (taken as the Instantaneous Shut In Pressure gradients) correlation with the azimuthal interval velocity slow. After the offset vector tile (OVT) PSDM, four azimuth sectors (0-180 degrees), each with four angle stacks, enabled the AVOaz computation for Top/Reservoir, as well as the computations for the azimuthal variation of each angle of incidence. Inversions, both azimuthally-isotropic as well as azimuthally (only VS was allowed to change azimuthally), gave estimates of rock properties. The azimuthal amplitudes themselves gave insight into the natural fractures network. The results presented in this paper are: 1) The azimuthal variation of the near-offset amplitudes (7 o ) best matched the calibration data of the Star Trak image log and microseismic (m-s) data; the AVOaz results were acceptable, but did not match as well as the 7° angle of incidence azimuthal amplitudes; 2) the m-s events for most of the frac stages studied showed the NE-SW spatial distribution indicating a NE-SW maximum horizontal stress orientation, consistent with the NE-SW azimuth of VINTfast; 3) at several frac stage centers, the m-s events showed detailed spatial patterns that track the azimuth and density of the natural fractures as interpreted from azimuthal amplitudes, specifically, the 7° angle of incidence azimuthal amplitudes. 4) To explain the m-s data, knowledge of the in-situ stress (azimuthal VINT) and the natural fractures (azimuthal amplitudes) must be used.
Differential Regulation of Telencephalic Pallial–Subpallial Boundary Patterning by Pax6 and Gsh2

In the embryonic telencephalon, the pallial–subpallial boundary (PSB) separates the dorsal Pax6+ pallium from the ventral Gsh2+ subpallium. Previous studies have revealed that this region is a source of cells that will populate both the olfactory bulb and basal telencephalic limbic system. However, the level of progenitor cell heterogeneity and developmental genetic regulation of this progenitor region remains to be fully elucidated. In this study we carried out a comprehensive analysis of gene expression patterns at the PSB, in addition to an examination of the combinatorial function of Pax6 and Gsh2 in the specification of the PSB. First, we reveal that the PSB is comprised of a complex mix of molecularly distinct progenitor pools. In addition, by analysis of single Sey, Gsh2, and Sey/Gsh2 double mutant mice, we demonstrate that both Pax6 and Gsh2 are directly required for major aspects of PSB progenitor specification. Our analysis also reveals that the establishment of the epidermal growth factor receptor positive lateral cortical stream migratory route to the basal telencephalon is Pax6 dependent. Thus, in addition to their well-characterized cross-repressive roles in dorsal/ventral patterning our analyses reveal important novel functions of Gsh2 and Pax6 in the regulation of PSB progenitor pool specification and patterning.
A 16-year record of eolian dust in Southern Nevada and California, USA: Controls on dust generation and accumulation

An ongoing project monitors modern dust accumulation in the arid southwestern United States to (1) determine the rate and composition of dust inputs to soils and (2) relate dust accumulation to weather patterns to help predict the effects of climate change on dust production and accumulation. The 16-year records of 35 dust-trap sites in the eastern Mojave Desert and southern Great Basin reveal how generation and accumulation of dust, including the silt-clay, carbonate, and soluble-salt fractions, is affected by the amount and seasonal distribution of rainfall and the behavior of different source types (alluvium, dry playas, and wet playas). Accumulation rates (fluxes) of the silt-clay fraction of dust, including carbonates, range from about 2–20 g/m 2 /yr. Average rates are higher in the southern part of the study area (south of latitude 36.51N) and annually fluctuate over a larger range than rates in the northern part of the area. Sites throughout the study area show peaks in dust flux in the 1984–1985 sampling period and again in 1997–1999; northern sites also show increased flux in 1987–1988 and southern sites in 1989–1991. These peaks of dust flux correspond with both La Nina (dry) conditions and with strong El Nino (wet) periods. The accumulation rates of different components of mineral dusts fluctuate differently. For example, soluble-salt flux increases in 1987–1988, coincident with a moderate El Nino event, and increases very strongly in 1997–1999, overlapping with a strong El Nino event. Both of these highrainfall winters were preceded and accompanied by strong summer rains. In contrast, little or no change in soluble-salt flux occurred during other periods of high winter rainfall but little summer rain, e.g. 1992–1995. The differences between northern vs. southern sites and between sites with playa dust sources vs. alluvial dust sources indicate that regional differences in the response of precipitation and vegetation growth to ENSO influence and differences in the response of source types control dust production and accumulation.
Native communities determine the identity of exotic invaders even at scales at which communities are unsaturated.

Aim To determine why some communities are more invasible than others and how this depends on spatial scale. Our previous work in serpentine ecosystems showed that native and exotic diversity are negatively correlated at small scales, but became positively correlated at larger scales. We hypothesized that this pattern was the result of classic niche partitioning at small scales where the environment is homogeneous, and a shift to the dominance of coexistence mechanisms that depend on spatial heterogeneity in the environment at large scales. Location Serpentine ecosystem, Northern California. Methods We test the above hypotheses using the phylogenetic relatedness of natives and exotics. We hypothesized that (1) at small scales, native and exotic species should be more distantly related than expected from a random assemblage model because with biotic resistance, successful invaders should have niches that are different from those of the natives present and (2) at large scales, native and exotic species should not be more distantly related than expected. Result We find strong support for the first hypothesis providing further evidence of biotic resistance at small scales. However, at large scales, native and exotic species were also more distantly related than expected. Importantly, however, natives and exotics were more distantly related at small scales than they were at large scales, suggesting that in the transition from small to large scales, biotic resistance is relaxed but still present. Communities at large scales were not saturated in the sense that more species could enter the community, increasing species richness. However, species did not invade indiscriminately. Exotic species closely related to species already established the community were excluded. Main conclusions Native communities determine the identity of exotic invaders even at large spatial scales where communities are unsaturated. These results hold promise for predicting which species will invade a community given the species present.
On load latency in low-power caches

Many of the recently proposed techniques to reduce power consumption in caches introduce an additional level of non-determinism in cache access latency. Due to this additional latency, instructions speculatively issued and dependent on a non-deterministic load must be re-executed. Our experiments show that there is a large performance degradation and associated energy wastage due to these effects of instruction re-execution. To address this problem, we propose an early cache set resolution scheme. It is based on the observation that the displacement values used for address generation are generally small. Our experimental evaluation shows that this technique is quite effective in mitigating this problem.
Reliable transient transformation of intact maize leaf cells for functional genomics and experimental study

Maize (Zea mays) transformation routinely produces stable transgenic lines essential for functional genomics; however, transient expression of target proteins in maize cells is not yet routine. Such techniques are critical for rapid testing of transgene constructs and for experimental studies. Here, we report bombardment methods that depend on leaf developmental stage and result in successful expression with broad applications. Fluorescent marker genes were constructed and bombarded into five developmental regions in a growing maize leaf. Expression efficiency was highest in the basal-most 3 cm above the ligule of an approximately 50-cm growing adult leaf. Straightforward dissection procedures provide access to the receptive leaf regions, increasing efficiency from less than one transformant per cm2 to over 21 transformants per cm2. Successful expression was routine for proteins from full genomic sequences driven by native regulatory regions and from complementary DNA sequences driven by the constitutive maize polyubiquitin promoter and a heterologous terminator. Four tested fusion proteins, maize PROTEIN DISULFIDE ISOMERASE-Yellow Fluorescent Protein, GLOSSY8a-monomeric Red Fluorescent Protein and maize XYLOSYLTRANSFERASE, and maize Rho-of-Plants7-monomeric Teal Fluorescent Protein, localized as predicted in the endoplasmic reticulum, Golgi, and plasma membrane, respectively. Localization patterns were similar between transient and stable modes of expression, and cotransformation was equally successful. Coexpression was also demonstrated by transiently transforming cells in a stable line expressing a second marker protein, thus increasing the utility of a single stable transformant. Given the ease of dissection procedures, this method replaces heterologous expression assays with a more direct, native, and informative system, and the techniques will be useful for localization, colocalization, and functional studies.
Regulation of ROMK (Kir1.1) channels: new mechanisms and aspects

This brief review attempts to provide an overview regarding recent developments in the regulation of ROMK channels. Studies performed in ROMK null mice suggest that ROMK cannot only form hometetramers such as the small-conductance (30-pS) K channels but also construct heterotetramers such as the 70-pS K channel in the thick ascending limb (TAL). The expression of ROMK channels in the plasma membrane is regulated by protein tyrosine kinase (PTK), serum and glucorticoid-induced kinase (SGK), and with-no-lysine-kinase 4. PTK is involved in mediating the effect of low K intake on ROMK channel activity. Increases in superoxide anions induced by low dietary K intake are responsible for the stimulation of PTK expression and tyrosine phosphorylation of ROMK channels. Finally, a recent study indicated that ROMK channels can be monoubiquitinated and monoubiquitination regulates the surface expression of ROMK channels.
EMPLOYMENT CLOTHING PRACTICES AND ATTITUDES OF WHITE-COLLAR FEMALE WORKERS '

The business clothing practices and attitude toward clothing of 313 white-collar female workers in a large state organization were investigated. The purposes of the present study were to investigate whether (1) there were significant differences in types of clothing chosen for work by managerial and nonmanagerial women, (2) there were correlations among types of clothing chosen and the attitudes toward employment clothing, career commitment, and apparel evaluative criteria, and (3) the factors contributed to the prediction of type of clothing chosen and clothing expenditures. Analysis yielded significant differences in the types of clothing chosen for work by those two groups and significant correlations between those types of clothing and clothing attitudes, and the apparel evaluative criteria. The multiple regression results indicated that the attitudes about clothing, price, career commitment, perceived new clothing needs, and age contributed to the prediction of employment clothing practices and expen...