cssi/SciSciGPT-SciSciNet huggingface dataset:
Deep learning-based MSMS spectra reduction in support of running multiple protein search engines on cloud

The diversity of the available protein search engines with respect to the utilized matching algorithms, the low overlap ratios among their results and the disparity of their coverage encourage the community of proteomics to utilize ensemble solutions of different search engines. The advancing in cloud computing technology and the availability of distributed processing clusters can also provide support to this task. However, data transferring and results' combining, in this case, could be the major bottleneck. The flood of billions of observed mass spectra, hundreds of Gigabytes or potentially Terabytes of data, could easily cause the congestions, increase the risk of failure, poor performance, add more computations' cost, and waste available resources. Therefore, in this study, we propose a deep learning model in order to mitigate the traffic over cloud network and, thus reduce the cost of cloud computing. The model, which depends on the top 50 intensities and their m/z values of each spectrum, removes any spectrum which is predicted not to pass the majority voting of the participated search engines. Our results using three search engines namely: pFind, Comet and X!Tandem, and four different datasets are promising and promote the investment in deep learning to solve such type of Big data problems.
Heuristics for planning with rare catastrophic events

High-dimensional Markov decision processes are often solved using online sampling-based methods such as Monte Carlo tree search. Problems that involve rare catastrophic events with large negative rewards can be very challenging for such approaches. The difficulty arises because the common policies for expanding a search tree are not able to handle rare large negative rewards appropriately, leading to high variance estimates of value. This paper studies the impact of reward structure with rare catastrophic events on the performance of common algorithms and proposes enhanced tree policy strategies for Monte Carlo tree search. Numerical experiments suggest that our proposed methods can significantly improve performance on a variety of problem domains ranging from stochastic multi-armed bandits to aircraft rerouting problems.
Clear Cell Carcinoma of Salivary Glands Is Frequently p16 Positive: A Pitfall in the Interpretation of Oropharyngeal Biopsies.

Clear cell carcinoma (CCC) is a low-grade malignancy that commonly arises in minor salivary glands of the oropharynx and other sites. EWSR1-ATF1 gene fusions seem to be specific for this salivary neoplasm. Testing for EWSR1-ATF1 has expanded the histologic spectrum of CCC. As one important example,
Automatic detection of idiomatic clauses

We describe several experiments whose goal is to automatically identify idiomatic expressions in written text. We explore two approaches for the task: 1) idiom recognition as outlier detection; and 2) supervised classification of sentences. We apply principal component analysis for outlier detection. Detecting idioms as lexical outliers does not exploit class label information. So, in the following experiments, we use linear discriminant analysis to obtain a discriminant subspace and later use the three nearest neighbor classifier to obtain accuracy. We discuss pros and cons of each approach. All the approaches are more general than the previous algorithms for idiom detection --- neither do they rely on target idiom types, lexicons, or large manually annotated corpora, nor do they limit the search space by a particular type of linguistic construction.
Parkin is a disease modifier in the mutant SOD1 mouse model of ALS

Abstract Mutant Cu/Zn superoxide dismutase (SOD1) causes mitochondrial alterations that contribute to motor neuron demise in amyotrophic lateral sclerosis (ALS). When mitochondria are damaged, cells activate mitochondria quality control (MQC) mechanisms leading to mitophagy. Here, we show that in the spinal cord of G93A mutant SOD1 transgenic mice (SOD1‐G93A mice), the autophagy receptor p62 is recruited to mitochondria and mitophagy is activated. Furthermore, the mitochondrial ubiquitin ligase Parkin and mitochondrial dynamics proteins, such as Miro1, and Mfn2, which are ubiquitinated by Parkin, and the mitochondrial biogenesis regulator PGC1α are depleted. Unexpectedly, Parkin genetic ablation delays disease progression and prolongs survival in SOD1‐G93A mice, as it slows down motor neuron loss and muscle denervation and attenuates the depletion of mitochondrial dynamics proteins and PGC1α. Our results indicate that Parkin is a disease modifier in ALS, because chronic Parkin‐mediated MQC activation depletes mitochondrial dynamics‐related proteins, inhibits mitochondrial biogenesis, and worsens mitochondrial dysfunction.
MeV photon imaging with robotic sample positioning at a research reactor

This paper summarizes the development and demonstration of an X-ray and gamma-ray radiography capability using a TRIGA MARK-II reactor. Photons are a combination of Bremsstrahlung X-rays and gamma rays from fission and radioactive decay. The energy spectrum of the facility was analyzed with a NaI(Tl) scintillator detector. A digital X-ray camera for use with MeV-range photons images a duplex wire-type penetrameter to analyze unsharpness and spatial resolution. An industrial manipulator precisely positions the sample, which allows objects to have larger dimensions than the detector’s field-of-view. Future work includes performing computed tomography to create 3-dimensional representations of objects.
Green's Functions in Lossy Multi-Layer Dielectrics for 3D IC/Packaging Applications

Green's function in lossy multi-layer dielectrics is presented using DCIM method for 3D IC/packaging in this paper. Loss effects in layered medium are analysed through the components extracted from DCIM. The proposed layered Green's function can be used for 3D IC and packaging applications.
Synthetic cannabinoid use among a sample of individuals enrolled in community-based recovery programs: Are synthetic cannabinoids actually preferred to other drugs?

AbstractBackground: Over the past decade, availability and use of novel psychoactive substances such as synthetic cannabinoid receptor agonists (SCRA) have proliferated globally. However, the preva...
Counterfactual Randomization: Rescuing Experimental Studies from Obscured Confounding

Randomized clinical trials (RCTs) like those conducted by the FDA provide medical practitioners with average effects of treatments, and are generally more desirable than observational studies due to their control of unobserved confounders (UCs), viz., latent factors that influence both treatment and recovery. However, recent results from causal inference have shown that randomization results in a subsequent loss of information about the UCs, which may impede treatment efficacy if left uncontrolled in practice (Bareinboim, Forney, and Pearl 2015). Our paper presents a novel experimental design that can be noninvasively layered atop past and future RCTs to not only expose the presence of UCs in a system, but also reveal patient- and practitioner-specific treatment effects in order to improve decision-making. Applications are given to personalized medicine, second opinions in diagnosis, and employing offline results in online recommender systems.
Radiosensitizers and Thymine Base Damage

The use of radiosensitizers in the therapy of cancer in conjunction with radiation has been of considerable interest. The mechanism by which they act, however, is not clear. Because these compounds have an electron affinity similar to oxygen and/or are free radicals, it was postulated that their presence might have an effect on the formation of DNA base damage induced by radiation. The effect of three sensitizers, misonidazole, p-nitroacetophenone and 4-hydroxy-2,2,6,6-tetramethylpiperidino-1-oxy (TMPN), on formation of thymine damage of the 5,6-dihydroxydihydrothymine type by irradiation with gamma rays was characterized in HeLa cells. The three sensitizers have different electron affinities, or, in the case of TMPN, are a stable free radical. The formation of thymine base damage was measured in the presence of increasing concentrations of each of the three sensitizers with and without 500 Gy of cobalt-60 gamma rays, at ice temperature. Each sensitizer gave a different result. Increasing concentrations of misonidazole suppressed the formation of base damage in air but had no apparent effect under hypoxia. In the presence of p-nitroacetophenone, similar amounts of base damage were formed under both aerobic and hypoxic conditions. TMPN, on the other hand, resulted in a complex pattern, with suppression at higher concentrations (60 mM). The overall conclusion is that the sensitizers do not result in increased base damage but, if anything, suppress its formation. Therefore, the mechanism by which they sensitize under hypoxic conditions, such as found in solid tumors, is not by an increase in thymine base damage.
2D Materials for Field-Effect Transistor–Based Biosensors

Abstract Transition metal dichalcogenides (TMDs), an emerging 2D analogy of graphene, with their captivating physiochemical properties find applications in advanced point-of-care diagnosis of various health related issues. Specially, multidimensional structures of TMDs and its structure dependent electronic, optical and electrocatalytic properties are apt for the design of different types (electrochemical, photoluminescence and colorimetric) of biosensing devices. This chapter outlines the field-effect transistor–based biosensing applications of TMDs and its recent developments.
Obesity, physical activity, and sedentary behaviors in adolescents with autism spectrum disorder compared with typically developing peers:

Decreased engagement in beneficial physical activity and increased levels of sedentary behavior and unhealthy weight are a continued public health concern in adolescents. Adolescents with autism sp...
GROUP R$sub 4$ IN ATOMIC-STRUCTURE THEORY: THE HYDROGENIC R$sub 4$ VERSUS THE MATHEMATICAL R$sub 4$ AND THE COULOMB INTERACTION IN 2s/sup m/2p/sup n/ AND 3s/sup m/ 3p/sup n/3d/sup r/ CONFIGURATIONS.

The rotation group in four dimensions ${R}_{4}$ is applied to the study of the $2{s}^{m}2{p}^{n}$ configurations of atoms. This Lie group is used in both the mathematical sense, describing the transformation properties of the angular parts of the $2s$ and $2p$ electrons, and in the more physical sense of an approximate symmetry group for the first-row atoms. The various states of each configuration are classified by means of ${R}_{4}$. By expressing the Coulomb interaction in terms of tensors, transforming according to irreducible representations of ${R}_{4}$, Coulomb and exchange integrals are evaluated group theoretically. The method is extended to $3{s}^{m}3{p}^{n}3{d}^{\mathcal{r}}$ configurations. The states are classified by means of ${R}_{4}$ and Coulomb and exchange integrals are approximately evaluated.
A monocyte-keratinocyte-derived co-culture assay accurately identifies efficacies of BET inhibitors as therapeutic candidates for psoriasiform dermatitis.

Abstract Background Bromodomain and extra-terminal (BET) proteins perform key roles in epigenetic control of gene expression that is involved in inflammatory conditions, including psoriasiform dermatitis (PsD). Predicting which (of many potential available BET inhibitors) will be effective in vivo is challenging. Objective We determine if a novel in vitro assay that includes two critical cell types involved in human psoriasis can predict the therapeutic potential of specific BET inhibitors in vivo. Methods An in vitro model consisting of U-937 and HaCaT cell co-culture was created to screen small molecule BET antagonists for inhibition of cutaneous inflammatory genes. Efficacious BET inhibitors were tested in a mouse imiquimod (IMQ)-induced PsD model. Results In the co-culture system, HaCaT cells exhibited a marked increase in the secretion of a characteristic set of proinflammatory and Th17-associated cytokines. Of the ten commercially-available small molecules targeting BET proteins assayed, most compounds exhibited inhibitory functions at 1 μM against inflammatory activation, but responded variably at lower concentrations. OTX015, a typical representative for most of the compounds, barely inhibited the inflammatory reactions at 0.1 μM. By contrast, ABBV075 was effective in concentrations as low as 0.01 μM. While oral administration OTX015 in IMQ-treated mice reduced disease severity, ABBV075 equally decreased the symptoms and molecular and cellular severity markers at one-tenth of the minimal dosing required for OTX015. Conclusion In vitro screening system combined with an in vivo animal model, can serve as a convenient pre-clinical screening tool for the selection of BET inhibitors (and possibly other drugs) that may have clinical potential in psoriasis therapy.
Emerging systemic therapies for atopic dermatitis: oral small molecules and targeted topical agents.

Background Until recently, treatment of atopic dermatitis has been limited to topical corticosteroids, calcineurin inhibitors, phototherapy, and systemic immunomodulatory agents. With improved understanding of the pathogenesis underlying atopic dermatitis, targeted oral small molecules and topical agents are being developed. Objective Discuss efficacy and safety profiles of emerging oral small molecules and targeted topical agents in phase 2 and 3 clinical trials. Methods A systemic literature review was conducted to identify results of randomized, placebo-controlled trials of oral small molecules and topical Janus kinase inhibitors up to March 1 2020 for the treatment of atopic dermatitis. Results Three novel oral small molecules, abrocitinib, upadacitinib, and baricitinib, demonstrated improvement of clinical severity, pruritus, and quality of life with acceptable safety profiles. Apremilast, a phosphodiesterase inhibitor, was less efficacious with use limited by adverse effects. Two novel topical agents, ruxolitinib and delgocitinib, were effective and well-tolerated. Conclusions Targeted therapeutics including oral small molecules and topical agents show promise for the treatment of atopic dermatitis. The use of validated core measures is necessary for future trials in order to adequately compare agents and progress evidence-based medicine.
Crypto-Governance: The Ethical Implications of Blockchain in Public Service

Blockchain systems are positioned to revolutionize many aspects of governance and public service. This paper explores the ethical implications of blockchain for government ethics leaders implementi...
Follicular dendritic cell dysfunction contributes to impaired antigen-specific humoral responses in sepsis-surviving mice

Sepsis survivors exhibit impaired responsiveness to antigen (Ag) challenge associated with increased mortality from infection. The contribution of follicular dendritic cells (FDCs) in the impaired humoral response in sepsis-surviving mice is investigated in this study. We demonstrated that mice subjected to sepsis from cecal ligation and puncture (CLP mice) have reduced NP-specific high-affinity class-switched Ig antibodies (Abs) compared with sham-operated control mice following immunization with the T cell-dependent Ag, NP-CGG. NP-specific germinal center (GC) B cells in CLP mice exhibited reduced TNF-α and AID mRNA expression compared with sham-operated mice. CLP mice showed a reduction in FDC clusters, a reduced binding of immune complexes on FDCs, and reduced mRNA expression of CR2, ICAM-1, VCAM-1, FcγRIIB, TNFR1, IKK2, and LTβR compared with sham-operated mice. Adoptive transfer studies showed that there was no B cell-intrinsic defect. In summary, our data suggest that the reduced Ag-specific Ab response in CLP mice is secondary to a disruption in FDC and GC B cell function.
Robotic Resection of Deep Infiltrating Pelvic Sidewall Endometriosis and Concomitant Nephrectomy

Study Objective To demonstrate a surgical video wherein deep infiltrating endometriosis (DIE) was resected off the left pelvic sidewall. Design Step-by-step video demonstration of DIE resection from the external iliac vessels and the ureter. Setting Academic tertiary referral center. Patients or Participants 41-year-old female with history of endometriosis, presented with pelvic pain and left lower extremity swelling. Abdominal and pelvic imaging revealed extensive left pelvic sidewall fibrosis, resulting in compression of the external iliac vein, hydroureter and renal atrophy. Further urologic workup showed minimal to no residual function of the left kidney. Interventions Patient was taken to the operating room for resection of sidewall endometriosis and concomitant nephrectomy. Exploration of the peritoneal cavity showed that endometriosis was confined to the pelvis, heavily involving the left pelvic sidewall. The left retroperitoneum was entered and avascular spaces were elaborated. The left hydroureter and IP ligament were identified above the pelvic brim, as well as the common iliac vessels. Once proximal and distal access to the external iliac vessels were obtained, the majority of DIE was resected off the vessels. Complete resection of sidewall DIE would have led to vascular injury; therefore, the decision was made to proceed with debulking of fibrosis off the vessel surface and the remainder of the lesions inferior to the external iliac vessels. Given inability to salvage distal left ureter and non-functional kidney, concomitant left nephrectomy was performed. Measurements and Main Results The procedure and post-operative course were uncomplicated. There was significant improvement in patient's pelvic pain and lower extremity swelling. One month after surgery, she underwent balloon angioplasty and stenting of left external iliac vein to attain complete patency of the vein. Conclusion Long-standing DIE can lead to vascular compression and unsalvageable renal obstruction, which requires a multidisciplinary team approach in order to address this multisystem disease.
Efficacy of immunotherapy in hepatocholangiocarcinoma (HCC-CC): Proof of concept.

e16194Background: Hepatocholangiocarcinoma (HCC-CC) is a rare form of cancer with a poor prognosis. Of all primary liver cancers, the incidence of HCC-CC ranges from 0.4 to 14.2%. HCC-CC is a mixed...
Oxidizing intermediates in P450 catalysis: a case for multiple oxidants.

Cytochrome P450 (P450 or CYP) catalysis involves the oxygenation of organic compounds via a series of catalytic intermediates, namely, the ferric-peroxo, ferric-hydroperoxo, Compound I (Cpd I) and FeIII−(H2O2) intermediates. Now that the structures of P450 enzymes have been well established, a major focus of current research in the P450 area has been unraveling the intimate details and activities of these reactive intermediates. The general consensus is that the Cpd I intermediate is the most reactive species in the reaction cycle, especially when the reaction involves hydrocarbon hydroxylation. Cpd I has recently been characterized experimentally. Other than Cpd I, there is a multitude of evidence, both experimental as well as theoretical, supporting the involvement of other intermediates in various types of oxidation reactions. The involvement of these multiple oxidants has been experimentally demonstrated using P450 active-site mutants in epoxidation, heteroatom oxidation and dealkylation reactions. In this chapter, we will review the P450 reaction cycle and each of the reactive intermediates to discuss their role in oxidation reactions.
An Informal Occasion with Robert Hass

RH: I haven't arrived for myself at any very satisfactory formulation of what a prose poem is. Certainly it has something to do with condensation. If it's narrative in form and gets to a certain length, it's probably a story; if it's very short and in a book by a fiction writer, it's a sudden fiction; if it's in a book by a poet, it's a prose poem; and if it gets to a certain length, it's an essay, or a sketch, or something like that. So I suppose condensation has something to do with it. I don't know how to define it in terms of genre, and when I was work ing, I guess I just stopped trying to think about that. What I did think about was what the conventions of the prose poem were. At the time that I was starting to write them, the prose poem, as it had been revived in America, was used almost entirely for a kind of wacky surrealist work, and I think that nervousness about using prose was that then you had to put a lot of what people thought was poetic ?that is to say, wildness and imagination and free association ?into it to make sure that it was poetry, because if it got too near the conventions and sentence sounds of exposi tory prose or narrative prose or something like that, then it really wasn't poetry. So almost as soon as I started working, I got interested in those boundaries: what the prose poem wasn't supposed to sound like. I think I came on it in the first place from writing prose. When I was writing essays, I found that there would be a passage where I wanted to give an example, or tell a short anecdote to make a point, and that I would find myself laboring over the making of that paragraph with the kind of pleasure I get from working on a poem. So that was in my mind with "Museum" ? the prose poem about the young man and woman handing their baby back and forth in the restaurant. It was very hard to ... I had seen it and I was very moved by it, but I couldn't find a rhythm for it. Each time I got into it there was some prosodie problem with the business of people handing each other the baby, back and forth. If I wrote it sort of
The Continuing Violation Theory and the Concept of Jurisdiction in Title VII Suits

When confronted with a title VII plaintiff who has failed to make a timely filing of his charge with the EEOC, courts have reached inconsistent results. In this article Messrs. Jackson and Matheson analyze the most recent Supreme Court decisions in this area and present a coherent approach to the problem. They conclude that under the continuing violation theory courts should entertain an action based on an existing policy of discrimination even if the specific act alleged occurred in the remote past. In addition, the authors conclude that the title VII filing requirement is not a jurisdictional absolute, but should instead be treated like a statute of limitations.
Retiree Health Benefit Trends Among the Medicare-Eligible Population

This paper examines the prevalence of retiree health benefits among Medicare-eligible retirees. It discusses the percentage of retirees with employment-based retiree health benefits over the 1994-2008 period. It also examines the trend for individually purchased coverage as a supplement to Medicare. Perhaps the single most-important factor that has affected the availability of health benefits for retirees through former private-sector employers was a 1990 accounting rule. FAS 106 required companies to record and disclose retiree health benefit liabilities on their financial statements and triggered many of the changes to retiree health benefits, most notably the sharp decline in the benefits being offered. GASB Statements No. 43 and 45, which impose new accounting standards on public-sector sponsors of retiree health benefits, are similar to FAS 106 and will have a similar, if not greater, impact on the financial statements of public-sector entities. As a result of FAS 106 and the rising cost of providing retiree health benefits, most U.S. private-sector workers will never become eligible for health insurance in retirement through a former employer. Fewer employers are offering health benefits to future retirees; when those benefits are offered, eligibility criteria are becoming harder to meet; and employer subsidies are disappearing. In 2008, 26 percent of 65-69-year-olds had retiree health benefits, down from 32 percent in 1994, and the numbers are lower for older retirees. It is possible that the decline in coverage would have been even larger had it not been for changes in the work status of individuals eligible for Medicare. In 1995, 59 percent of individuals ages 65-69 considered themselves retired, and that fell to 53.6 percent in 2008, while those saying they were working increased from 28 percent in 1995 to 35 percent in 2008.The PDF for the above title, published in the January 2010 issue of EBRI Notes, also contains the full text of another January 2010 EBRI Notes article abstracted on SSRN: “Employee Tenure, 2008.”
The negative effect of an accounting standard on employee welfare

Investigates the negative effect on employee welfare caused by economic decisions taken by corporate managements which they attribute to the adoption of an accounting standard, focusing on the case of McDonnell Douglas Corporation, which ended health‐care benefits for non‐union employees as a result of adopting the Financial Accounting Standards Board′s Statement 106 (FASB 106). It is estimated that the adoption of FASB 106 caused $148 billion in charges to earnings to be recorded by companies in the Standard & Poor′s 500 Index. Despite the large negative effect on earnings, FASB 106 had little or no impact on the economic condition of the affected firms. Nevertheless, managements have taken economic actions that have negatively affected employee welfare, and these actions have been attributed to FASB 106. Some of the hardest hit are employees at older industrial companies with mature workforces hired during the 1950s and 1960s. Some companies ended retirement health plans abruptly, while others required ...
Curtailment of Early Election Predictions: Can We Predict the Outcome?

This note analyzes the constitutional ramifications of legislative attempts to restrict early election predictions. First, specific congressional proposals and state legislative enactments will be examined. Secondly, the various standards of review the Supreme Court applies when government regulation threatens to infringe upon first amendment free speech will be examined. Lastly, this paper will examine the competing interests involved in early election predictions and will conclude that limitations on this process would be an unconstitutional impairment of the public's first amendment rights.
Abstract 3588: Reactivation of dormant estrogen-dependent breast cancer micrometastases by bone marrow stromal injury in anin vitromodel of dormancy

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Estrogen-dependent (ER+) breast cancer can remain dormant in the bone marrow for more than a decade and continues to recur in a stochastic pattern at continuous, low rates. Mechanisms of dormancy in the bone marrow are mostly uncharacterized but data suggest that dormancy depends on close interactions of micrometastases with stromal elements and on effects by structural and soluble proteins. We have developed an extensive and well characterized in vitro model incorporating relevant elements of the bone marrow niche. We have demonstrated that FGF-2, abundantly deposited on bone marrow stroma, induces a partial re-differentiation of ER+ human breast cancer cell lines, manifested in part by cell cycle arrest in G1 and re-expression of integrins lost with dedifferentiation. Ligation of integrin α5β1 by incubation of cells on fibronectin completes the model. It specifically induces a dormant epithelial phenotype with RhoA inactivation through the Rho Gap GRAF, cortical actin rearrangement, omnidirectional focal complex activation and adhesion and activation of survival signaling. The signaling is dually initiated through FGF-2 receptors and fibronectin ligation, which activate PI3K/Akt, Erk and p38. The model is recapitulated on both human and murine bone stromal monolayer coincubations of human ER+ breast cancer cell lines, with the FGF-2 and fibronectin provided by the stroma. Mechanisms of breast cancer recurrence are also not understood, but data in other systems suggest that inflammatory cytokines can stimulate proliferation of breast cancer cells. We hypothesized that injury to bone marrow stroma can be the source of such cytokines. Towards this end, we injured human and murine bone marrow stromal monolayers by oxidation and hypoxia through one hour exposures to variable concentrations of H2O2 and a cyanide-containing analog, respectively, and by estrogen deprivation. These interventions induced secretion of IL-6 and IL-8, and induced activation TGFβ and TNFα under variable conditions. Incubation of human recombinant IL-6, IL-8 and TGFβ with dormant colonies in fibronectin culture induced dormant clones to proliferate into growing colonies. These data suggest a potential mechanism for reactivation of dormant breast cancer micrometastases and identify potential targets for suppression of the effect. Citation Format: Samir Tivari, Haiyan Lu, Tanya Dasgupta, Robert Wieder. Reactivation of dormant estrogen-dependent breast cancer micrometastases by bone marrow stromal injury in an in vitro model of dormancy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3588. doi:10.1158/1538-7445.AM2014-3588
The intracellular localization of calcium within the mature human placental barrier.

Abstract Tissue samples were taken from term human placentas and fixed in a saturated pyroantimoniate solution in order to complex the calcium in the form of granular deposits that can be readily observed. These tissues were processed for electron microscopy and observed for the intracellular locations of calcium within the cells of the placental barrier. Granular deposits were observed associated with granular endoplasmic reticulum in the form of vesicles within the periphery of the cells and in the form of fine granules or larger, more dense granules within the mitochondria of these cells. The granule-laden mitochondria were most frequently and most abundantly observed within the endothelium of the fetal capillaries. It was concluded that these granular deposits represent the locations of calcium as it is being actively transported across the placental barrier within the cells.
Genetics, Synergists, and Age Affect Insecticide Sensitivity of the Honey Bee, Apis mellifera

The number of honey bee colonies in the United States has declined to half of its peak level in the 1940s, and colonies lost over the winter have reached levels that are becoming economically unstable. While the causes of these losses are numerous and the interaction between them is very complex, the role of insecticides has garnered much attention. As a result, there is a need to better understand the risk of insecticides to bees, leading to more studies on both toxicity and exposure. While much research has been conducted on insecticides and bees, there have been very limited studies to elucidate the role that bee genotype and age has on the toxicity of these insecticides. The goal of this study was to determine if there are differences in insecticide sensitivity between honey bees of different genetic backgrounds (Carniolan, Italian, and Russian stocks) and assess if insecticide sensitivity varies with age. We found that Italian bees were the most sensitive of these stocks to insecticides, but variation was largely dependent on the class of insecticide tested. There were almost no differences in organophosphate bioassays between honey bee stocks (<1-fold), moderate differences in pyrethroid bioassays (1.5 to 3-fold), and dramatic differences in neonicotinoid bioassays (3.4 to 33.3-fold). Synergism bioassays with piperonyl butoxide, amitraz, and coumaphos showed increased phenothrin sensitivity in all stocks and also demonstrated further physiological differences between stocks. In addition, as bees aged, the sensitivity to phenothrin significantly decreased, but the sensitivity to naled significantly increased. These results demonstrate the variation arising from the genetic background and physiological transitions in honey bees as they age. This information can be used to determine risk assessment, as well as establishing baseline data for future comparisons to explain the variation in toxicity differences for honey bees reported in the literature.
Design patterns for sorting

Drawing on Merritt's divide-and-conquer sorting taxonomy [1], we model comparison-based sorting as an abstract class with a template method to perform the sort by relegating the splitting and joining of arrays to its concrete subclasses. Comparison on objects is carried out via an abstract ordering strategy. This reduces code complexity and simplifies the analyses of the various concrete sorting algorithms. Performance measurements and visualizations can be added without modifying any code by utilizing the decorator design pattern. This object-oriented design not only provides the student a concrete way of unifying seemingly disparate sorting algorithms but also help him/her differentiate them at the proper level of abstraction.
Conformation and shear stability of xanthan gum in solution

Xanthan gum, the extracellular polysacchuride produced by the microorganism Xanthomonas campestris has unique rheological properties and as a result found many industrial uses. The primary structure o xanthan consists of a cellulose backbone substituted on alternate residues with charged trisaccharide side chains. The polymer undergoes an ordered ⇄ disordered conformation transformation, Very recently determinations of the secondary and tertiary structures have shown that the ordered conformation is helical. The two conformations have different solution properties. Rheological evidence indicates that xanthan conformation is critically dependent on the presence or absence of-salt. In this work we show that the polymer shear degrades to a larger extent in the disordered conformation than in the ordered conformation. That is, the ordered conformation is more shear stable.
pH dependence of antibody: hapten association.

Abstract Monoclonal antibody NC6.8 is specific for the superpotent sweetener, N-(p-cyanophenyl)-N′-(diphenylmethyl)-guanidiniumacetic acid. The three-dimensional structure of the complex shows the close proximity of complementary charged residues on the antibody and groups of the hapten. As a result, association is dependent on the pH, dielectric, and ionic strength of the medium. Continuum electrostatics methods are used to calculate the pH-dependent association energetics of NC6.8 with the superpotent sweetener. In addition to providing a titration profile, the calculations quantitatively assess the relative influence of charged groups on the energetics of association. Models of site directed mutants are constructed to probe the influence of each charged interface residue on the pH-dependent energetics of association. Examination of electrostatic contribution to free energy of association in mutant complexes, where the key acidic residues on the antibody are neutralized, shows that charge complementarity at the combining site is an important requirement for hapten binding. Also, based on the pKa values of several combining site tyrosine residues, aromatic π-stacking and van der Waal’s contacts between the antibody and hapten contribute to the specificity of the complex.
Turbulence Model Assessment for Conjugate Heat Transfer in a High Pressure Turbine Vane Model

An assessment of steady state Reynolds Averaged Navier-Stokes (RANS) models has been undertaken for conjugate heat transfer of an internally cooled high-pressure turbine vane with and without film cooling. The assessment includes near wall treatment and different 2-equation Eddy Viscosity Models (EVM) and 6-equation Reynolds Stress Models (RSM) models. The present study was conducted using CFX v11.0 with unstructured tetrahedral meshes with near wall prism layers. The validation cases are the 1983 NASA C3X internally cooled vane and the 1988 NASA C3X internally and film cooled vane. Internal cooling for both cases is achieved with ten radial cooling channels of constant cross-sectional area. Film cooling is achieved for the same airfoil geometry but with three separately fed upstream plenums feeding various rows of film cooling holes. Predictions obtained with the different modeling strategies are compared to documented metal surface pressures and temperatures and the differences are discussed. A conjugate heat transfer assessment is made using the vane Biot number. In general good agreement with experimental data is obtained for wall integration meshes with the k-ω and SST turbulence models.Copyright © 2008 by ASME
Cloning and characterization of Planctomyces limnophilus rpoN: complementation of a Salmonella typhimurium rpoN mutant strain

Abstract The rpoN gene, which encodes the alternative sigma factor σ54, was cloned from the budding, peptidoglycan-less bacterium Planctomyces limnophilus. P. limnophilus rpoN complemented the Ntr− phenotype of a Salmonella typhimurium rpoN mutant strain. The P. limnophilus rpoN gene encoded a predicted polypeptide that was 495 residues in length and shared a significant homology with other members of the σ54 family. The protein sequence displayed all of the characteristic motifs found in members of this family, including the C-terminal helix–turn–helix motif and the well-conserved RpoN box. A potential σ54-dependent activator was also identified in P. limnophilus. These findings extend the range of phylogenetic groups within the Domain Bacteria that are known to contain σ54.
Bivalve hemocyanins--a comparison with other molluscan hemocyanins.

Abstract 1. 1. The hemocyanins of the protobranch bivalves Yoldia thraciaeformis, Yoldia limatula and Acila castrensis have absorption spectra similar to other hemocyanins. 2. 2. Hemocyanins from all three bivalves appear as six-tiered cylinders in the electron microscope (30–32 nm in diameter by 34–38 nm in height). Yoldia thraciaeformis and A. castrensis hemocyanins tend to dissociate to three-tiered half molecules with polar images and also to associate into long tubular polymers. 3. 3. Yoldia thraciaeformis and A. castrensis hemocyanins chromatograph on Sepharose 4B gel close to gastropod hemocyanin (M r = 9 × 10 6 ) rather than chiton hemocyanin (M r = 4 × 10 6 ). 4. 4. Hemocyanins from all three bivalves have subunits with electrophoretic mobilities similar to gastropod and polyplacophoran hemocyanin subunits and slower than octopodan hemocyanin subunits. 5. 5. These similarities between bivalve and gastropod hemocyanins are consistent with the hypothesis that bivalves and gastropods have shared a common ancestor.
An online learning approach to throughput optimization in wireless networks under dynamic and unknown interference conditions

In this paper, we consider a multi-user communication system with dynamically varying interference on block fading channels. We focus on a multi-antenna receiver, single-antenna transmitters, and the case in which the receiver has no knowledge of the channel state information, interference dynamics, and the variance of the additive noise. Pilot-assisted transmission techniques are employed to enable channel estimation at the receiver. For a given channel coherence length, increasing the number of pilots improves the estimation accuracy, with the tradeoff of reduction in data throughput. Thus, we propose to optimize the pilot content within the data frame to maximize the average data throughput. We employ well-known cross-validation techniques from the machine learning literature to simultaneously improve the estimation accuracy as well as the average throughput. Simulation results with the proposed approach suggest that even when the average number of active interferers is larger than the number of degrees of freedom, at least 85% of the ideal throughput can be achieved with the optimum pilot overhead.
Multiple Flow Equilibria in the Atmosphere and Blocking

Abstract A barotropic channel model is used to study the planetary-scale motions of an atmosphere whose zonal flow is externally driven. Perturbations are induced by topography and by d barotropic analogue of thermal driving. The use of highly truncated spectral expansions shows that there may exist a multiplicity of equilibrium states for a given driving, of which two or more may be stable. In the case of topographical forcing, two stable equilibrium states of very different character may be produced by the same forcing: one is a “low-index” flow with a strong wave component and a relatively weaker zonal component which is locked close to linear resonance; the other is a “high-index” flow with a weak wave component and a relatively stronger zonal component which is much farther from linear resonance. It is suggested that the phenomenon of blocking is a metastable equilibrium state of the low-index near-resonant character. The existence of the two types of equilibria has been confirmed by numerical integr...
Long-term mechanical ventricular assistance toward myocardial recovery.

As discussed in the preceding chapters, most devices are placed in anticipation of acute ventricular recovery (bridge to recovery, BTR), or as a stabilizing measure until cardiac transplantation can be undertaken (bridge to transplant, BTT). Recently, attention has been directed toward using ventricular assist devices (VADs) for permanent cardiac replacement, or destination therapy. This alternative to transplantation is necessary because of the limited number of available organs and the large number of heart failure patients who are not candidates for transplantation. Another recent development is the removal of long-term ventricular assist devices (VADs) in patients who have exhibited ventricular recovery after a prolonged period of ventricular unloading. Patients for VAD weaning and explantation should be identified preoperatively, because this may influence device selection and method of cannulation. Of the many different available designs, VAD selection depends on patient body size and which ventricles need support (Table 1). The anticipated length of support is a critical factor in determining which device is used, and this is most dependent upon the anticipated outcome after device implantation. When recovery of ventricular function is expected acutely, or where the waiting time for transplantation is expected to be brief, a short-term or intermediate-term device may be appropriate. However, long-term devices are usually required when transplantation or recovery is expected to be significantly delayed. Recovery of ventricular function after a period of mechanical support in an acute setting is not a new concept. The first use of a VAD was to support a patient in postoperative cardiogenic shock [1], and only later were these devices used as a BTT [2]. VADs continue to be used as a BTR in patients with acute cardiac decompensation who are expected to have rapid recovery of ventricular function. Using VADs as BTR for chronic heart failure is gaining acceptance as more reports describe successful explantation of long-term devices. Despite this expanding role for VADs in heart failure, the patient selection criteria for VAD insertion must be maintained to minimize the risk of having a nontransplantable patient supported by a device that cannot be weaned. This scenario will become less important as VADs gain acceptance as destination devices.
Dipole moment functions for a 3II and A 1II carbon monoxide

Author Institution: Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin
Exploitative competition between invasive herbivores benefits a native host plant.

Although biological invasions are of considerable concern to ecologists, relatively little attention has been paid to the potential for and consequences of indirect interactions between invasive species. Such interactions are generally thought to enhance invasives' spread and impact (i.e., the ''invasional meltdown'' hypothesis); however, exotic species might also act indirectly to slow the spread or blunt the impact of other invasives. On the east coast of the United States, the invasive hemlock woolly adelgid (Adelges tsugae, HWA) and elongate hemlock scale (Fiorinia externa, EHS) both feed on eastern hemlock (Tsuga canadensis). Of the two insects, HWA is considered far more damaging and disproportionately responsible for hemlock mortality. We describe research assessing the interaction between HWA and EHS, and the consequences of this interaction for eastern hemlock. We conducted an experiment in which uninfested hemlock branches were experimentally infested with herbivores in a 2 3 2 factorial design (either, both, or neither herbivore species). Over the 2.5-year course of the experiment, each herbivore's density was ;30% lower in mixed- vs. single-species treatments. Intriguingly, however, interspecific competition weakened rather than enhanced plant damage: growth was lower in the HWA- only treatment than in the HWA þ EHS, EHS-only, or control treatments. Our results suggest that, for HWA-infested hemlocks, the benefit of co-occurring EHS infestations (reduced HWA density) may outweigh the cost (increased resource depletion).
Springs in time: fish fauna and habitat changes in springs over a 20‐year interval

1. Despite the range of threats to springs and the number of spring-endemic species, studies of temporal changes in the fauna of springs have rarely been reported. Changes in the fish of 22 Oklahoma (USA) springs were compared among surveys in 1981, 1982, and 2001. 2. Twenty-year assemblage differences were correlated with physical alteration of specific springs and stocking of native fish, which was made possible by past habitat changes that produced pools. Physical alteration of springs is a major ongoing threat to Oklahoma springs. 3. Variation in spring fish assemblages among the three surveys was apparently affected by fish movement in and out of springs, and the greater rain-induced connectivity between springs and streams during one year. 4. Although flow reduction is a commonly cited threat to springs, there was little evidence of flow reduction impacts in this study because Oklahoma springs may have been affected prior to 1981 and high-flow springs, which most often contain fish, were in areas with low groundwater water use. Copyright © 2008 John Wiley & Sons, Ltd.
Distribution of insects in soybean fields.

A 3-year study of spatial distribution patterns of insect pests in soybean fields revealed that the Poisson series described the distribution of most species. These species were: green cloverworms, Plathypena scabra (Fabricius); velvetbean caterpillars, Anticarsia gemmatalis Hubner; loopers Trichoplusia ni (Hubner), Pseudoplusia includens (Walker), and Heliothis spp. The Poisson with zeros distribution was second in characterizing the spatial patterns of many of the species. Field counts of Mexican bean beetles, Epilachna varivestis Mulsant, fitted the Neyman’s type A and negative binomial distributions most often.
Nanocrystal development during primary crystallization of amorphous alloys

Abstract During primary crystallization of multicomponent amorphous alloys a high density of nanocrystals can develop at levels up to 1023 m−3 and volume fractions >0.30. For Al-base amorphous alloys at high Al nanocrystal densities, diffusion field impingement develops quickly above the glass transition and provides for a kinetic stabilization. A kinetics analysis has been developed to account for nanocrystal growth with diffusion field impingement and unequal component diffusivities. The analysis together with a thermodynamic model of the f.c.c.-liquid phase equilibria for Al–Y–Fe was applied to model DSC exotherms corresponding to primary f.c.c. nanocrystal formation. From the kinetics analysis an estimate of the diffusion coefficient of yttrium in the liquid is obtained above the glass transition as 1.4×10−17 m2/s. New alloying strategies are discussed based upon the implications of the kinetics analysis.