cssi/SciSciGPT-SciSciNet huggingface dataset:
Hobby-Eberly Telescope: LRS-J HAWAII-1 detector electronics

The first second-generation instrument for the Hobby-Eberly telescope is a novel J band camera (LRS-J) which mates to the existing low resolution spectrograph (LRS). This camera uses the existing LRS longslit and mutltiobject units as well as the LRS five element collimator but uses its own J optimized volume holographic grisms, f/1 cryogenically cooled camera, and readout electronics built around a Rockwell HAWAII-1 array. We minimized the development time of the controller by reusing as much of the existing framework as possible. The modular design of the existing LRS CCD controller allows us to modify only the clock-driver and penthouse (pre-amplifier) modules. Furthermore, we were able to use existing multilayer circuit boards already fabricated for these two modules. Thus, the LRS-J controller required only the substitution of components on two modules and the design of a new header (dewar) board to fit the HAWAII-1 socket. With these modifications, based on its perfomance with CCDs, we predict a noise and crosstalk performance at the most competitive level.
Analysis/synthesis techniques for subband image coding

Analysis/synthesis systems designed for low bit rate image coding, their impact on overall system quality, and their computational complexity are discussed. The investigation focuses on the design of analysis/synthesis systems for image coding and the perceptual impact of these systems at low bit rates. Two objectives are emphasized in developing these systems: confining the total size of the subband images to be equal to the original image size, and designing the filters so that perceptual distortion is not introduced by the analysis/synthesis system. Methods based on circular convolution and symmetric extensions are developed and discussed in detail. The theory, design, and implementation of both recursive and nonrecursive filtering systems are discussed. Methods are introduced which display advantages over conventional quadrature mirror filter based approaches. >
The Sterility of Platelet and Granulocyte Concentrates Collected by Discontinuous Flow Centrifugation

Platelet concentrates prepared by a discontinuous flow centrifugal technique (Haemonetics) were examined for evidence of bacterial contamination and subsequent growth from 3 to 11 days after collection. Of the 126 platelet concentrates examined, 4 revealed bacterial growth. However, the growth patterns indicated contamination during the microbiologic manipulations rather than contamination of the units during preparation. These studies indicate that platelet concentrates prepared using the Haemonetics Blood Processor can be safely transfused for up to three days after collection if stored at 4 to 6 C.
Natural killer cell receptors: The offs and ons of NK cell recognition

David H. Raulet and Werner Held Department of Molecular and Cell Biology and Cancer Research Laboratory University of California Berkeley, California 94720 Natural killer (NK) cells constitute a distinct lineage of lym- phocytes that kill a variety of target cells, including tumor cells, cells infected with some viruses or bacteria, and some normal cell types. NK cells resemble cytotoxic T lymphocytes (CTLs) in some respects, including cytokine production and the use of the perforin-dependent cytolytic machinery. Significantly, however, NK cells do not ex- press T cell receptors or immunoglobulins, and they are apparently unaffected by defects in the V-D-J recombina- tion machinery. Furthermore, early efforts to define dis- crete patterns of recognition by NK cells met with failure, leading to the notion that NK recognition is "primitive." However, recent results suggest that target cell lysis by NK cells is regulated by a balance between specific activating and inhibitory receptors. A major component of recogni- tion involves receptors specific for class I major histocom- patibility complex (MHC) molecules on target cells, en- gagement of which inhibits N K lysis. Thus, cells exhibiting abnormal or reduced amounts of class I molecules, which are therefore invisible to CTLs, are killed by NK cells. The recent characterization of several novel recognition struc- tures on NK cells has added a wealth of new information, but at the same time has generated a number of fascinat- ing puzzles. Recognition of Class I MHC Molecules by NK Cells The role of NK ceils in bone marrow allograft rejection was the initial hint that they recognize MHC molecules (for review see Yu et al., 1992). Then it was discovered that the sensitivity of many tumor cells to lysis by NK cells in vitro is inversely related to the levels of MHC class I molecules on the tumor cells (for review see Ljunggren and Karre, 1990), a finding later extended to nontransformed lymphoblasts from class I-deficient mice (Liao et al., 1991). Class I molecules on target cells somehow prevent NK cell-mediated lysis. The situation proved more complex when it was appreci- ated that NK cells can discriminate class I alleles. Human NK clones were shown to lyse allogeneic T cell blasts, and the target cell genes controlling susceptibility to lysis were mapped to the MHC (Ciccone et al., 1992). In the murine system, an NK cell subset defined by expression of the Ly49A moleculewas shown to discriminate between tumor target cells expressing different MHC haplotypes (Karl- hofer et al., 1992). Class I Expression by Target Cells Inhibits NK Cells and Activates T Cells Fragments of intracellular protein antigens are presented by MHC class I molecules on the cell surface. Hence, class I molecules allow specific recognition and lysis of infected
Femtosecond observation of benzyne intermediates in a molecular beam: Bergman rearrangement in the isolated molecule.

In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules (p-, m-, and o-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-level ab initio calculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of the three isomers on the femtosecond time scale.
Highly spin-polarized room-temperature tunnel injector for semiconductor spintronics using MgO(100).

The spin polarization of current injected into GaAs from a $\mathrm{C}\mathrm{o}\mathrm{F}\mathrm{e}/\mathrm{M}\mathrm{g}\mathrm{O}(100)$ tunnel injector is inferred from the electroluminescence polarization from $\mathrm{G}\mathrm{a}\mathrm{A}\mathrm{s}/\mathrm{A}\mathrm{l}\mathrm{G}\mathrm{a}\mathrm{A}\mathrm{s}$ quantum well detectors. The polarization reaches 57% at 100 K and 47% at 290 K in a 5 T perpendicular magnetic field. Taking into account the field dependence of the luminescence polarization, the spin injection efficiency is at least 52% at 100 K, and 32% at 290 K. We find a nonmonotonic temperature dependence of the polarization which can be attributed to spin relaxation in the quantum well detectors.
Tertiary hyperparathyroidism attributable to long-term oral phosphate therapy.

Objective: To report a rare case of tertiary hyperparathyroidism (HPT) as a result of long-term oral phosphate therapy. Methods: We present a case report, with a focus on clinical manifestations and biochemical findings during the course of tertiary HPT, and discuss the pathophysiologic features of this disorder and the therapeutic strategies. Results: A 35-year-old woman, 22 years after the initial diagnosis of familial hypophosphatemic rickets and initiation of treatment with phosphate and vitamin D, underwent assessment for recurrent symptomatic kidney stones, bone pain, and fatigue. Laboratory studies performed 10 months before this presentation showed findings consistent with secondary HPT. Examination was notable for short stature, and pertinent laboratory results were as follows: intact parathyroid hormone 602 pg/mL, calcium 10.9 mg/dL, and phosphorus 3.6 mg/dL. Tertiary HPT was diagnosed, and she underwent subtotal parathyroidectomy and transcervical thymectomy. Postoperatively, she had hypocalcem...
Structure−Reactivity Relationships for Graphene Nanoribbons

The first structure−reactivity relationships for electron-transfer reactions of graphene nanoribbons (GNR) have been derived. These relationships are represented as relative reaction rate constants calculated by considering different electronic structure approximations of GNR and the Gerischer−Marcus (GM) or Marcus theories of electron transfer. The reactivity of GNR is observed to directly depend on the ribbon width and the orientations of carbon atoms at their edges. A comparison of relative rate constants for the more accurate GM electron-transfer theory and tight-binding approximations predicts that armchair and zigzag GNR have opposite trends in reactivity with the former increasing with width and the latter decreasing. For zigzag ribbons, the major reactivity contribution comes from their edge states, and hence, ribbons of small widths are predicted to be the most reactive among all ribbons including armchair ribbons. The reactivity trend for zigzag GNR is reversed, however, when recent first-princi...
Genius is not immune to persistent misconceptions: conceptual difficulties impeding Isaac Newton and contemporary physics students

Recent research has shown that serious misconceptions1 frequently survive high school and university instruction in mechanics. It is interesting to inquire whether Newton himself encountered conceptual difficulties before he wrote the Principia: (a) Did he have serious difficulties? (b) If so, were they difficult to overcome? We shall present evidence from Newton's writings of affirmative answers to both questions. Newton's development of his system of mechanics was hampered by a persistent belief in ‘the force of a [moving] body’ from 1664 to 1685. His belief in centrifugal force was an additional restraining factor that remained intact until Hooke's intervention in 1679 and weakened only gradually over the next two years. Three additional years passed before the resulting successes weakened his commitment to impetus sufficiently to permit conceptualization of mass as an inert surrogate. This paper will compare Newton's pre‐Principia beliefs with those of contemporary students in the areas of impetus for...
Identification of pneumonia and influenza deaths using the death certificate pipeline

Death records are a rich source of data, which can be used to assist with public surveillance and/or decision support. However, to use this type of data for such purposes it has to be transformed into a coded format to make it computable. Because the cause of death in the certificates is reported as free text, encoding the data is currently the single largest barrier of using death certificates for surveillance. Therefore, the purpose of this study was to demonstrate the feasibility of using a pipeline, composed of a detection rule and a natural language processor, for the real time encoding of death certificates using the identification of pneumonia and influenza cases as an example and demonstrating that its accuracy is comparable to existing methods. A Death Certificates Pipeline (DCP) was developed to automatically code death certificates and identify pneumonia and influenza cases. The pipeline used MetaMap to code death certificates from the Utah Department of Health for the year 2008. The output of MetaMap was then accessed by detection rules which flagged pneumonia and influenza cases based on the Centers of Disease and Control and Prevention (CDC) case definition. The output from the DCP was compared with the current method used by the CDC and with a keyword search. Recall, precision, positive predictive value and F-measure with respect to the CDC method were calculated for the two other methods considered here. The two different techniques compared here with the CDC method showed the following recall/ precision results: DCP: 0.998/0.98 and keyword searching: 0.96/0.96. The F-measure were 0.99 and 0.96 respectively (DCP and keyword searching). Both the keyword and the DCP can run in interactive form with modest computer resources, but DCP showed superior performance. The pipeline proposed here for coding death certificates and the detection of cases is feasible and can be extended to other conditions. This method provides an alternative that allows for coding free-text death certificates in real time that may increase its utilization not only in the public health domain but also for biomedical researchers and developers. This study did not involved any clinical trials.
The Cumulative Electrostatic Effect of Aromatic Stacking Interactions and the Negative Electrostatic Environment of the Flavin Mononucleotide Binding Site Is a Major Determinant of the Reduction Potential for the Flavodoxin from Desulfovibrio vulgaris [Hildenborough]†

Flavodoxins are typified by the very low one-electron reduction potential for the semiquinone/hydroquinone couple (Esq/hq) of the flavin mononucleotide (FMN) cofactor. In the Desulfovibrio vulgaris flavodoxin, the elimination of the side chain of Tyr98, which flanks the outer or si face of the flavin, through the Y98A mutation results in a substantial increase in Esq/hq of 139 mV, representing about one-half of the total shift in Esq/hq in this flavodoxin [Swenson, R. P., & Krey, G. D. (1994) Biochemistry 33, 8505-8514]. The extent to which this large effect was the result of the elimination of unfavorable coplanar aromatic stacking interactions or to the greater solvent exposure of the flavin ring was not known. The significance of the latter effect was heightened by the characterization of the Fld+6 mutant which demonstrated that the unfavorable interaction between the negative electrostatic environment provided by the asymmetric clustering of acidic residues surrounding the cofactor and the FMN hydroquinone anion is responsible for about one-third of the total decrease in Esq/hq in this flavodoxin [Zhou, Z., & Swenson, R. P. (1995) Biochemistry 34, 3183-3192]. In this study, a flavodoxin mutant was generated in which an alanine was substituted for Tyr98 while at the same time the negative electrostatic surface was partially neutralized by the substitution of the six acidic amino acid residues with their amide equivalents. The Esq/hq value of this mutant was found to have increased by 221 mV relative to wild type, which accounts for 70-80% of the total shift in Esq/hq in this flavodoxin. This increase is very similar to the sum of the individual changes in Esq/hq introduced independently in the Y98A and Fld+6 mutants. The similarity in the magnitude of the effect of the neutralization of the six acidic residues in the context of an alanine residue at position 98 (Y98A) relative to an aromatic tyrosine residue (wild type) suggests that the increase in Esq/hq observed for the Y98A mutant is more likely due to the elimination of unfavorable pi-pi interactions between Tyr98 and the FMN hydroquinone rather than to the increased solvent exposure of the flavin. This study provides further support for the concept that the cumulative effect of the unfavorable electrostatic interactions introduced by coplanar aromatic or pi-pi stacking interactions and the negative electrostatic environment of the FMN binding site is a major determinant of the low one-electron reduction potential of the flavodoxin.
Disorders of hemostatic function in patients with systemic lupus erythematosus

Abstract A wide spectrum of hemostatic abnormalities is found in patients with SLE. Thrombocytopenia and qualitative platelet disorder (impaired aggregation to collagen) are probably both due to antiplatelet antibodies, which can be found in most patients with the disease. About 10% of patients with SLE have a circulating anticoagulant . These circulating anticoagulants are broadly heterogeneous. Although most reported cases act at the level of the prothrombin converting complex, 15 of the 74 cases here reviewed had other points of action. The anticoagulants are probably all antibodies; they differ (with rare exceptions) from other naturally occurring circulating anticoagulants in having an immediate rather than a progressive effect, and in acting, not against pre-existing procoagulants, but against unstable complexes. An anticoagulant of the type found in SLE is only rarely observed in the absence of SLE; its presence in a patient is thus of some diagnostic importance. Hypoprothrombinemia is a common second lesion in patients with circulating anticoagulants. Its pathogenesis is obscure. Two patients with acquired von Willebrand's disease have been observed. All the hemostatic abnormalities found in SLE probably have immunologic bases; all respond to glucocorticoid treatment.
The impact of metropolitan opportunity structure on the economic status of Blacks and Hispanics in Newark.

In this paper, the utility of the opportunity structure model as a framework for explaining patterns of minority residence and concentrated poverty is assessed. The primary goals of the research are ( I ) to analyze the effects of economic restructuring and demographic transformations on minority poverty, (2) to assess the impact of these changes for central city and suburban minority populations, and (3) to examine the links between residential location and poverty. In order to test the propositions of the model, we utilize data for the Newark metropolitan area. Our findings underscore the continuing importance of racial and ethnic factors in determining the economic mobility of households. Regardless of residential location, blacks and Hispanics in Newark experience higher rates of economic distress. Continued segregation exacerbates their precarious status. The one factor most likely to adversely affect the economic status of minority households is the growth of single-parent households. The findings s...
Transient Noise Amplification and Gene Expression Synchronization in a Bistable Mammalian Cell-Fate Switch

Summary Progenitor cells within a clonal population show variable proclivity toward lineage commitment and differentiation. This cell-to-cell variability has been attributed to transcriptome-wide gene expression noise generated by fluctuations in the amount of cellular machinery and stochasticity in the biochemical reactions involved in protein synthesis. It therefore remains unclear how a signaling network, in the presence of such noise, can execute unequivocal cell-fate decisions from external cues. Here, we use mathematical modeling and model-guided experiments to reveal functional interplay between instructive signaling and noise in erythropoiesis. We present evidence that positive transcriptional feedback loops in a lineage-specific receptor signaling pathway can generate ligand-induced memory to engender robust, switch-like responses. These same feedback loops can also transiently amplify gene expression noise in the signaling network, suggesting that external cues can actually bias seemingly stochastic decisions during cell-fate specification. Gene expression levels among key effectors in the signaling pathway are uncorrelated in the initial population of progenitor cells but become synchronized after addition of ligand, which activates the transcriptional feedback loops. Finally, we show that this transient noise amplification and gene expression synchronization induced by ligand can directly influence cell survival and differentiation kinetics within the population.
Criteria for release of genetically-improved phytoseiids: an examination of the risks associated with release of biological control agents

Biological control of agricultural pests by phytoseiid predators has been achieved through classical introductions, conservation of indigenous and established foreign species, and augmentation of both introduced and indigenous species. Laboratory selection of phytoseiids has produced several strains that have been mass reared and released for pest management programs in glasshouses and agricultural cropping systems. Concerns over risks of classical biological control have developed recently. The development of recombinant DNA (rDNA) techniques for the genetic manipulation of crops and microorganisms also has inaugurated a debate on the safety of releasing transgenic organisms into the environment. This debate will extend to the release of phytoseiids that have been manipulated with rDNA techniques. Risks associated with releasing phytoseiids for augmentation or classical biological control programs are minimal and the benefits are great. Research initiated to answer questions about the risks of releasing transgenic phytoseiids into the environment provides opportunities to expand our understanding of the ecological impact of phytoseiids in agricultural and natural environments and could lead to improved pest management tactics.
Simple traffic light controller: A digital systems design project

In the past few years, laboratory exercises for our Digital Systems course were typically self contained. The lack of integration prevented students from fully realizing a complete digital system during the course of the class. The simple traffic light controller design project was introduced to alleviate this shortcoming and to ensure students gain experience in solving implementation and interfacing problems of a modern digital system. Students implement a fully functional traffic signal controller for a four-way intersection. The intersection is complete with sensors to detect the presence of vehicles waiting at or approaching the intersection. The project incorporates many concepts and components that are discussed in detail throughout the course. These include FPGAs, VHDL for modeling and synthesis, finite state machines, embedded microprocessors, memory interfaces, serial communication, and signal synchronization. A bottom-up with a partially specified design methodology is used to encourage students to use their breadth of knowledge and creativity. By the end of the project, students will have gained a better understanding of digital system design methodologies through hands-on experience.
Development of a dynamic pharmacokinetic model to estimate bioconcentration of xenobiotics in earthworms.

A simple and dynamic pharmacokinetic model was developed to predict bioconcentration of organic contaminants in earthworms. The model was parameterized experimentally by placing Lumbricus terrestris in soil contaminated with 200 µg/cm2 of malathion. The toxicokinetics of malathion uptake, depuration, and degradation in soil is measured. After parameterization, the model was able to accurately predict the bioconcentration factor of malathion at steady state. Sensitivity analyses were performed and the rate of absorption was determined to be the most sensitive parameter. Varying the rate of malathion elimination from earthworm tissues, malathion degradation, and the amount of malathion applied to the soil by 25-fold did not result in the bioconcentration of malathion. An increase in the rate of malathion absorption into earthworm tissues by 25-fold did result in bioconcentration. Previously published pharmacokinetic studies on xenobiotics with log Kow values ranging up to 8.05 were used to test the predictive capacity of the model. The model was able to predict from 83% to 105% of the experimentally derived bioconcentration factors.
Effects of tumor promoters, genotoxic carcinogens and hepatocytotoxins on mouse hepatocyte intercellular communication.

Intercellular communication via gap junctions may be an important mechanism of cellular growth control. Tumor promoters can inhibit intercellular communication between cultured cells, while genotoxic carcinogens apparently lack this capability. The inhibition of intercellular communication by tumor promoters may be an essential mechanism by which tumor promotion occurs in vivo. In this study, the liver tumor promoters phenobarbital, lindane (1,2,3,4,5,6-hexachlorocyclohexane, γ-isomer), DDT (1,1-Bis[4-chlorophenyl],-2,2,2-trichloroethane), Aroclor 1254 (a polychlorinated biphenyl mixture) and dieldrin inhibited intercellular communication between male B6C3F1 mouse hepatocytes in primary culture. Intercellular communication was detected as the passage of [5-3H]uridine nucleotides from pre-labelled donor hepatocytes to non-labelled recipient heptocytes. Mouse hepatocyte intercellular communication was also inhibited by the skin tumor promoter TPA (12-0-tetradecanoyl phorbol-13-acetate), but not by the bladder tumor promoter saccharin. The genotoxic hepatocarcinogens dimethylnitrosamine, diethylnitrosamine, benzo[a]pyrene and 2-acetylaminofluorene, and the hepatocytotoxins bromobenzene, acetaminophen, carbon tetrachloride, chloroform and methotrexate had no effect on mouse hepatocyte intercellular communication at non-cytotoxic levels. These results suggest that the ability to inhibit mouse hepatocyte intercellular communication is an effect specific to tumor promoters.
WE-G-110-04: Finding the Optimal Thickness of Large Area Thin-Film CdTe Detector under Diagnostic X-Ray Beams

Purpose: Recent developments in large area photovoltaic applications of have moved cadmium telluride (CdTe) to the frontiers of thin‐film manufacturing, making the photoconductor a promising candidate for large‐area flat panel digital x‐ray detectors. We model thin‐film CdTedetector in direct detection configuration to find its intrinsic imagingcharacteristics, such as MTF(modulation transfer function), NPS (noise power spectrum), and DQE (detective quantum efficiency), as well as its electronic properties with the objective of determining the optimal thickness of CdTe.Material and Methods: The intrinsic imagingcharacteristics of thin‐film CdTedetector under diagnostic spectra were modeled with Monte Carlo simulation package, MCNP5. They were compared to those of other two photoconductors used in direct detectionimaging, a‐Se and HgI2. The electronic properties of CdTe were studied with SCAPS simulation software, routinely used for photovoltaic device modeling. Results: While MTF decreases with increasing film thickness, the resultant DQE(f) increased with the thickness. The optimal thickness of CdTe under diagnostic x‐ray beams was found to be around 300&#956;m, taking into account the resolution and detection efficiency factors. Although a‐Se shows better MTF under 80kVp, the DQE(f) of thin‐film CdTe is superior to that of a‐Se because of its much higher absorption efficiency. Electronic properties' study demonstrated that thin‐film CdTe device can provide adequate output under diagnostic x‐ray beams. We also found that increasing CdTe thickness beyond 300&#956;m does not improve the output signal significantly. Conclusion: Our results show that the detectorsystem based on thin‐film CdTe is capable of achieving high resolution as well as high quantum efficiency in diagnostic imaging applications. It also provides easily measurable signal output under this energy range. The optimal thickness of thin film CdTe for diagnostic x‐ray imaging is determined to be around 300&#956;m.
The effect of progesterone in vivo on the subcellular distribution and properties of progesterone receptors in guinea pig uterus.

Abstract The distribution of progesterone receptors between cytosol and nuclear fractions of guinea-pig uterus was determined after the injection of 1 mg/kg and 10 mg/kg progesterone. After the lower dose, the concentration of cytoplasmic receptors decreased to approx. 2 3 of the preinjection level within 30–60 min and then gradually increased to almost the control value by 24 h. The nuclear receptors increased by an equivalent amount within 30–60 min and were retained at a slightly lower concentration for 4 h. Nuclear receptors decreased to the control level within 8 h and were not changed further. After 10 mg/kg, the cytoplasmic receptors decreased to approx. 1 2 the control value within 30 min and thereafter continued to decrease gradually. The nuclear receptors increased correspondingly to a maximum after 30 min and remained at somewhat less than the maximum concentration for 4 h. By 8 h the concentration of nuclear receptors had decreased to the control level. The properties of the cytoplasmic receptor (sedimentation coefficient of 7S (unactivated) and 5.5S (activated); K D 6–9 nM) were not changed after the administration of progesterone. However, the properties of the nuclear receptor changed in some respects. When exchange with [ 3 H]-R5020 was carried out on nuclei suspended in 5 mM phosphate buffer, at least 80% of the specifically bound 3 H was found in the supernatant. The tritium was not absorbed by dextran-coated charcoal and on sucrose density gradient centrifugation, a binding peak with a sedimentation coefficient of 3.5S was seen. Binding was temperature sensitive and was suppressed by unlabeled steroids in the following order: progesterone > 5α-pregnanedione testosterone cortisol. The nuclear receptor, extracted by 0.3–0.5 M KCl, also had a sedimentation coefficient of 3.5S on sucrose gradients in 5 mM phosphate. Competition by unlabeled steroids was similar to that seen with the receptor soluble in 5 mM phosphate.
Associations of Cocaine Use and HIV Infection With the Intestinal Microbiota, Microbial Translocation, and Inflammation

Objective:HIV and illicit drug use have been associated with altered nutrition, immune function, and metabolism. We hypothesized that altered composition and decreased diversity of the intestinal microbiota, along with microbial translocation, contribute to nutritional compromise in HIV-infected drug users.Method:We enrolled 26 men and 6 women, 15 HIV infected and 17 HIV uninfected, in this exploratory, cross-sectional study; 7 HIV-infected and 7 HIV-uninfected participants had used cocaine within the previous month. We examined the independent effects of cocaine use and HIV infection on the composition and diversity of the intestinal microbiota, determined by 16S rRNA gene pyrosequencing. Using dietary records, anthropometrics, and dual x-ray absorptiometry, we examined the additional effects of nutritional indices on the intestinal microbiota. We compared markers of inflammation and microbial translocation between groups.Results:Cocaine users had a higher relative abundance of Bacteroidetes (M ± SD = 57...
Relativity: Testing times in space

We take for granted that physical 'constants', such as the speed of light, are fixed values. But they might not be, and experiments in space may allow us to investigate this possibility.
Disk scheduling revisited: can O(n2) algorithms compete?

A simple O(n2) disk scheduling algorithm is suggested, and its performance on a real system, an Intel P6-based system running Linux 2.0.18, is compared with that of standard O(n) scheduling algorithms, with the aim of determining whether the large disparity between processor speeds and disk speeds might now allow for improved disk scheduling under heavy loads. The simple O(n2) algorithm is seen to provide some modest performance improvements over the best linear algorithms. The study also identifies several areas where potentially large additional performance improvements may be found by extending the framework suggested here.
The determination of groups of functionally integrated industries in the United States using a 1967 interindustry flow table

A two-stage standardization and grouping algorithm is applied to a 75×75 submatrix of the 86×86 1967 United States interindustry transaction table. The rows and columns of the submatrix are first adjusted so that they all have uniform sums. Entries of the adjusted table are maximum entropy estimates of flows in an idealized economy, in which all industries produce and consume an equal value of goods. Industries are then aggregated according to whether or not they are connected by chains of links with values equal to adjusted entries, all of which are greater than a given threshold level. Variation of the threshold yields a hierarchical aggregation scheme. Groups of functionally integrated industries can be identified through the examination of a tree diagram (dendrogram) which shows the aggregation results.
On the vorticity of long gravity waves in water of variable depth

Abstract Yoon and Liu's analysis of long gravity waves in water of slowly varying depth is modified to allow for conservation of potential vorticity in place of their (incorrect) conservation at conventional vorticity.
A Simple Bound for Stable Non-linear Systems with Input

ABSTRACT A simple bound for the system [xdot] = Ax + G(x, t)x + u(t) is given, when A is a stability matrix. Only knowledge of the eigenvectors and eigenvalues of A is needed. The bound is shown to be the post possible of its typo for second-order systems.
Technology insight: brain MRI and cardiac surgery--detection of postoperative brain ischemia

Annually, an estimated 1 million patients undergo heart surgery worldwide. Unfortunately, stroke continues to be a frequent complication of cardiac surgery, with the specific cerebrovascular risk depending upon the particular surgical procedure performed. Neuroimaging has an integral role in the initial evaluation and management of patients who present with acute stroke symptoms following cardiac surgery. The aim of this paper is to review the role brain MRI has in detecting postoperative brain ischemia in these patients. Multimodal MRI--using diffusion-weighted MRI (DWI), perfusion-weighted MRI, and gradient-recalled echo imaging--has an excellent capacity to identify and delineate the size and location of acute ischemic strokes as well as intracerebral hemorrhages. This differentiation is critical in making appropriate treatment decisions in the acute setting, such as determining patient eligibility for thrombolytic or hemodynamic therapies. At present, DWI offers prognostic value in patients with strokes following cardiac surgery. Additionally, DWI could be a valuable tool for evaluating stroke preventive measures as well as therapeutic interventions in patients undergoing CABG surgery.
Reactivity of biologically important reduced pyridines V. Relative importance of electron versus proton loss in ferricyanide-mediated oxidation of dihydronicotinamides

Abstract Kinetics of ferricyanide-mediated oxidation of various 1-(4-substituted phenyl)-1,4-dihydronicotinamides were studied assuming either a rate determining initial electron loss or a rate determining proton loss following a rapid pre-equilibrium step. Values obtained using both methods were similar. In addition, vertical ionization potentials generated using the AM1 molecular orbital approximation were found to be highly correlated with log(oxidation rates) while calculation on the proton loss from the dihydropyridine radical cations showed much less dependence. Measured kinetic deuterium isotope effects were small. These data suggest that the initial electron loss from the dihydronicotinamides is the most important event determining the reaction rates.
Phase-modulated pupil for achromatic imaging of faint companions

Abstract Planets outside our solar system may harbour life but their faint images are lost in the bright diffraction haloes of their parent stars. Here we show with a simple example that it is possible to suppress the star haloes without substantially weakening the planet signal if starlight, entering a telescope pupil, is phase-modulated in a prescribed pattern. The modulation remains effective throughout the entire visible light band and for a wide range of view angles. Furthermore, “phase only” modulation over the pupil suggests an attractive possibility of using a single optical element (deformable mirror) for simultaneously removing diffraction haloes and correcting phase errors.
Annual Primary Production in Narragansett Bay with no Bay-Wide Winter-Spring Phytoplankton Bloom

Abstract Primary production was estimated over the annual cycle from 14C incubations conducted in 5 m deep enclosures and modeled for 16 stations in Narragansett Bay with data from biweekly surveys in which light, chlorophyll, attenuation coefficients and other parameters were measured. Annual values ranged from 160 g C m−2 y−1 in the lower West Passage to 619 g C m−2 y−1 at the mouth of the Providence River. The annual bay-wide, area mean fell near the middle of this range at 323 g C m−2 y−1 and was not apparently different from previous surveys. In the 1998 warm, El Nino winter, no bay-wide winter–spring phytoplankton flowered. Bloom limitation was correlated with warm temperatures which may have stimulated grazing rates. The lack of a bloom did not change annual levels of primary production but this alteration in carbon flow may impact macrofauna in the benthic infauna community.
Interleukin-10 Inhibits Gram-Negative-Microbe-Specific Human Receptor Activator of NF-κB Ligand-Positive CD4+-Th1-Cell- Associated Alveolar Bone Loss In Vivo

To study anti-inflammatory cytokine effects on RANKL+-T-cell-mediated osteoclastogenesis in vivo, we injected human interleukin-10 (hIL-10) into pathogen-infected HuPBL-NOD/SCID mice. The results show significantly decreased RANKL+ Th1-associated alveolar bone loss and coexpression of human gamma interferon (hIFN-γ) and human macrophage colony-stimulating factor, but not hIL-4, in RANKL+ Th cells compatible with those from successfully treated aggressive periodontitis subjects. Thus, there are critical cytokine interactions linking hIFN-γ+ Th1 cells to RANKL-RANK/OPG signaling for periodontal osteoclastogenesis in vivo.
Patterns of morphological variation amongst semifossorial shrews in the highlands of Guatemala, with the description of a new species (Mammalia, Soricomorpha, Soricidae)

Members of the Cryptotis goldmani group of small-eared shrews (Mammalia, Soricomorpha, Soricidae) represent a clade within the genus that is characterized by modifications of the forelimb that include broadened forefeet, elongated and broadened foreclaws, and massive humeri with enlarged processes. These modifications are consistent with greater adaptation to their semifossorial habits than other members of the genus. The species in this group occur discontinuously in temperate highlands from southern Tamaulipas, Mexico, to Honduras. In Guatemala, there are three species: the relatively widespread Cryptotis goodwini and two species (Cryptotis lacertosus, Cryptotis mam) endemic to highland forests in the Sierra de los Cuchumatanes of western Guatemala. Ongoing studies focusing on the relationships of variation in cranial and postcranial skeletal morphology have revealed a fourth species from remnant cloud forest in the Sierra de Yalijux, central Guatemala. In this paper, I describe this new species and characterize its morphology relative to other species in the C. goldmani group and to other species of Cryptotis in Guatemala. In addition, I summarize available details of its habitat and ecology.
Progenitor cell therapy for traumatic brain injury: effect of serum osmolarity on cell viability and cytokine production

Introduction: The potential translation of mesenchymal stem cell (MSC) therapy into a multimodal protocol for traumatic brain injury requires evaluation of viability and cytokine production in a hyperosmolar environment. Optimization of MSC therapy requires delivery to the target area without significant loss of cellular function or viability. No model evaluating the potential efficacy of MSC therapy at varying osmolarities currently exists. Methods: Rat MSCs were characterized with flow cytometric immunophenotyping. MSCs (passage 3) were placed in culture with multipotent adult progenitor cell media at varying osmolarities (250, 270, 290, 310, 330, 350 and 370 mOsm) potentially found with hypertonic saline infusion. After culture for 24 h, cellular viability was measured using flow cytometry (n = 6). Next, brain tissue supernatant was harvested from both normal rat brains and injured brains 6 h after cortical injury. Subsequently, MSCs were placed in culture with multipotent adult progenitor cell media ±...
Model-free data screening and cleaning

Categories of data screening and cleaning issues are reviewed and discussed. Bivariate model-free approaches, specialized model-free regression techniques, together with order statistic-based (OSB) approaches are illustrated and shown to be of particular value for a variety of data screening and cleaning applications. It is shown how a combination of curve estimation with OSB approaches can help screen a progression to AIDS data set. WIREs Comp Stat 2011 3 168–176 DOI: 10.1002/wics.140 For further resources related to this article, please visit the WIREs website.
CD44 is prognostic for overall survival in the NCI randomized trial on breast conservation with 25 year follow-up

CD44 is a transmembrane glycoprotein involved in numerous cellular functions, including cell adhesion and extracellular matrix interactions. It is known to be functionally diverse, with alternative splice variants increasingly implicated as a marker for tumor-initiating stem cells associated with poor prognosis. Here, we evaluate CD44 as a potential marker of long-term breast cancer outcomes. Tissue specimens from patients treated on the National Cancer Institute 79-C-0111 randomized trial of breast conservation versus mastectomy between 1979 and 1987 were collected, and immunohistochemistry was performed using the standard isoform of CD44. Specimens were correlated with patient characteristics and outcomes. Survival analysis was performed using the log rank test. Fifty-one patients had evaluable tumor sections and available long-term clinical follow up data at a median follow up of 25.7 years. Significant predictors of OS were tumor size (median OFS 25.4 years for ≤2 cm vs. 7.5 years for >2 cm, p = 0.001), nodal status (median OS 17.2 years for node-negative patients vs. 6.7 years for node positive patients, p = 0.017), and CD44 expression (median OS 18.9 years for CD44 positive patients vs. 8.6 years for CD44 negative patients, p = 0.049). There was a trend toward increased PFS for patients with CD44 positive tumors (median PFS 17.9 vs. 4.3 years, p = 0.17), but this did not reach statistical significance. These findings illustrate the potential utility of CD44 as a prognostic marker for early stage breast cancer. Subgroup analysis in patients with lymph node involvement revealed CD44 positivity to be most strongly associated with increased survival, suggesting a potential role of CD44 in decision making for axillary management. As there is increasing interest in CD44 as a therapeutic target in ongoing clinical trials, the results of this study suggest additional investigation regarding the role CD44 in breast cancer is warranted.
A Method for Simulating Burr Type III and Type XII Distributions through -Moments and -Correlations

This paper derives the Burr Type III and Type XII family of distributions in the contexts of univariate -moments and the -correlations. Included is the development of a procedure for specifying nonnormal distributions with controlled degrees of -skew, -kurtosis, and -correlations. The procedure can be applied in a variety of settings such as statistical modeling (e.g., forestry, fracture roughness, life testing, operational risk, etc.) and Monte Carlo or simulation studies. Numerical examples are provided to demonstrate that -moment-based Burr distributions are superior to their conventional moment-based analogs in terms of estimation and distribution fitting. Evaluation of the proposed procedure also demonstrates that the estimates of -skew, -kurtosis, and -correlation are substantially superior to their conventional product moment-based counterparts of skew, kurtosis, and Pearson correlations in terms of relative bias and relative efficiency—most notably when heavy-tailed distributions are of concern.
Thermomechanical Characterization Of Flip Chip Solder Bumps For Multichip Module Applications

In this paper, the responses of a self-stretching flip chip solder joint under thermal fatigue crack propagation have been study. Emphasis is placed on the determination of the J-integral and stress intensity factor around the crack tips of the solder joint by the finite element method. A 5th order polynomial has been used to best fit the J-integral and stress intensity factor as a function of the crack length in the solder joint. Thermal fatigue life of the solder joint was then estimated based on the calculated stress intensity factor, Paris' law, and fatigue crack growth rate data on solders. Furthermore, a correlation between the analytical and experimental results has also been made.
The effects of spatial attention on motion processing in deaf signers, hearing signers, and hearing nonsigners.

Visual abilities in deaf individuals may be altered as a result of auditory deprivation and/or because the deaf rely heavily on a sign language (American Sign Language, or ASL). In this study, we asked whether attentional abilities of deaf subjects are altered. Using a direction of motion discrimination task in the periphery, we investigated three aspects of spatial attention: orienting of attention, divided attention, and selective attention. To separate influences of auditory deprivation and sign language experience, we compared three subject groups: deaf and hearing native signers of ASL and hearing nonsigners. To investigate the ability to orient attention, we compared motion thresholds obtained with and without a valid spatial precue, with the notion that subjects orient to the stimulus prior to its appearance when a precue is presented. Results suggest a slight advantage for deaf subjects in the ability to orient spatial attention. To investigate divided attention, we compared motion thresholds obtained when a single motion target was presented to thresholds obtained when the motion target was presented among confusable distractors. The effect of adding distractors was found to be identical across subject groups, suggesting that attentional capacity is not altered in deaf subjects. Finally, to investigate selective attention, we compared performance for a single, cued motion target with that of a cued motion target presented among distractors. Here, deaf, but not hearing, subjects performed better when the motion target was presented among distractors than when it was presented alone, suggesting that deaf subjects are more affected by the presence of distractors. In sum, our results suggest that attentional orienting and selective attention are altered in the deaf and that these effects are most likely due to auditory deprivation as opposed to sign language experience.