cssi/SciSciGPT-SciSciNet huggingface dataset:
Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers

Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2–4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair. We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75–100% of genes involved in MMR and HR are present in 0–2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3–8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes. The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids.
Two-site regional oxygen saturation and capnography monitoring during resuscitation after cardiac arrest in a swine pediatric ventricular fibrillatory arrest model

To investigate the use of two-site regional oxygen saturations (rSO2) and end tidal carbon dioxide (EtCO2) to assess the effectiveness of resuscitation and return of spontaneous circulation (ROSC). Eight mechanically ventilated juvenile swine underwent 28 ventricular fibrillatory arrests with open cardiac massage. Cardiac massage was administered to achieve target pulmonary blood flow (PBF) as a percentage of pre-cardiac arrest baseline. Non-invasive data, including, EtCO2, cerebral rSO2 (C-rSO2) and renal rSO2 (R-rSO2) were collected continuously. Our data demonstrate the ability to measure both rSO2 and EtCO2 during CPR and after ROSC. During resuscitation EtCO2 had a strong correlation with goal CO with r = 0.83 (p < 0.001) 95% CI [0.67–0.92]. Both C-rSO2 and R-rSO2 had moderate and statistically significant correlation with CO with r = 0.52 (p = 0.003) 95% CI (0.19–0.74) and 0.50 (p = 0.004) 95% CI [0.16–0.73]. The AUCs for sudden increase of EtCO2, C-rSO2, and R-rSO2 at ROSC were 0.86 [95% CI, 0.77–0.94], 0.87 [95% CI, 0.8–0.94], and 0.98 [95% CI, 0.96–1.00] respectively. Measurement of continuous EtCO2 and rSO2 may be used during CPR to ensure effective chest compressions. Moreover, both rSO2 and EtCO2 may be used to detect ROSC in a swine pediatric ventricular fibrillatory arrest model.
NOTCH3 expression in metastatic TNBC cells.

e12123Background: Onset of metastases involves a complex multistep biological process termed the invasion-metastasis cascade, which include dissemination of cancer cells from the primary tumor to s...
Momentum and Forces

In the second chapter, we introduce the concepts of force, traction, and stress developing in a fluid consisting of a single chemical species. By invoking Newton’s second law of motion for a material fluid parcel, we derive the Cauchy equation of motion for a compressible or incompressible fluid. By combining the equation of motion with the Reynolds transport equation, we derive a momentum balance and associated equation of momentum transport over a control volume in a way that is rigorous, intuitive, and free of ad-hoc stipulations.
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity.

Motivation Vast majority of human genetic disorders are associated with mutations that affect protein-protein interactions by altering wild-type binding affinity. Therefore, it is extremely important to assess the effect of mutations on protein-protein binding free energy to assist the development of therapeutic solutions. Currently, the most popular approaches use structural information to deliver the predictions, which precludes them to be applicable on genome-scale investigations. Indeed, with the progress of genomic sequencing, researchers are frequently dealing with assessing effect of mutations for which there is no structure available. Results Here, we report a Gradient Boosting Decision Tree machine learning algorithm, the SAAMBE-SEQ, which is completely sequence-based and does not require structural information at all. SAAMBE-SEQ utilizes 80 features representing evolutionary information, sequence-based features and change of physical properties upon mutation at the mutation site. The approach is shown to achieve Pearson correlation coefficient (PCC) of 0.83 in 5-fold cross validation in a benchmarking test against experimentally determined binding free energy change (ΔΔG). Further, a blind test (no-STRUC) is compiled collecting experimental ΔΔG upon mutation for protein complexes for which structure is not available and used to benchmark SAAMBE-SEQ resulting in PCC in the range of 0.37-0.46. The accuracy of SAAMBE-SEQ method is found to be either better or comparable to most advanced structure-based methods. SAAMBE-SEQ is very fast, available as webserver and stand-alone code, and indeed utilizes only sequence information, and thus it is applicable for genome-scale investigations to study the effect of mutations on protein-protein interactions. Availability and implementation SAAMBE-SEQ is available at http://compbio.clemson.edu/saambe_webserver/indexSEQ.php#started. Supplementary information Supplementary data are available at Bioinformatics online.
Reconfigurable Assembly of Chiral Metamaterials on Solid Substrates

We report an all-optical approach to build colloids into active chiral nanostructures on a solid substrate, where the chiroptical response can be tailored on-demand.
Interstellar Medium Sculpting of the HD 32297 Debris Disk

We detect the HD 32297 debris disk in scattered light at 1.6 and 2.05 {mu}m. We use these new observations together with a previous scattered light image of the disk at 1.1 {mu}m to examine the structure and scattering efficiency of the disk as a function of wavelength. In addition to surface brightness asymmetries and a warped morphology beyond {approx}1.''5 for one lobe of the disk, we find that there exists an asymmetry in the spectral features of the grains between the northeastern and southwestern lobes. The mostly neutral color of the disk lobes implies roughly 1 {mu}m-sized grains are responsible for the scattering. We find that the asymmetries in color and morphology can plausibly be explained by HD 32297's motion into a dense interstellar medium cloud at a relative velocity of 15 km s{sup -1}. We model the interaction of dust grains with H I gas in the cloud. We argue that supersonic ballistic drag can explain the morphology of the debris disks of HD 32297, HD 15115, and HD 61005.
Locating Early Modern Women’s Participation in the Public Sphere of Botany: Agnes Block (1629-1704) and Networks in Print

Although we are frequently confronted with an image of early modern Dutch women as existing primarily, if not exclusively, within the realm of household management, the reality was far more nuanced. A case study of Agnes Block (1629-1704) shows that by focusing on relationships, she succeeded in participating in the creation and dissemination of knowledge of botany in the public sphere and achieved recognition in that sphere, notwithstanding the institutional limits imposed upon her due to her gender. By adapting our methodological and analytical frameworks, in this case by looking to social networks and the power of print media, we can recover the stories of early modern women that are otherwise obscured in the archives and write them into history.
Association Between Iron and Cholesterol in Neuroblastomas.

Background/aim Neuroblastoma is the most common childhood extracranial solid malignancy. Although cancer cells need iron and lipids for active cell division, possible links between iron and lipid metabolism in neuroblastomas have not been studied. Materials and methods We evaluated the levels and association between iron and cholesterol on in vitro neuroblastoma cancer models. Results We found that the levels of iron and cholesterol are diverse among neuroblastoma cell lines. There is a bi-directional association between iron and cholesterol in drug-resistant neuroblastoma SK-N-AS cells. In drug-resistant neuroblastoma cells, low concentration of an iron chelator did not have an impact on iron levels, but on cellular cholesterol levels. Furthermore, a cholesterol decreasing agent, simvastatin, influenced both iron and cholesterol levels in drug-resistant neuroblastoma cells. Conclusion Cholesterol decreasing agents may be more effective than iron chelators for drug-resistant neuroblastoma treatment.
Low-loss Non-volatile Phase-change Integrated Photonics at 1550nm and 750nm

The phase shifting effect and low loss of Sb 2 S 3 are verified experimentally for the first time on SOI and SiN integrated photonics platform using microring resonators at the telecom C-band and near visible wavelengths.
Diurnal variations in midluteal serum progesterone measurements

The utility of a single midluteal phase progesterone (P) value has been questioned by studies that document pulsatile P secretion. In this study, fluctuations of P values during clinical sampling times were investigated. Significant differences were found between morning and afternoon mean P values and in the timed occurrence of clinically relevant P values. Despite reported pulsatile secretion, the impact of clinically significant fluctuations may be minimized by the use of timed sampling.
Bearing-Type Bolted Hybrid Joints

The results of an analytical study of hybrid steel bolted joints of A36, A440, and A514 steel are presented. The joints were fastened by either A325 or A490 bolts. The studies were designed to determine the effect of variables on the joint strength. The major variables studied were joint length and the ratio of the net plate area, A n , to the total fastener shear area, A s . The studies indicated that the average shear strength of hybrid joints was equal or greater than the average shear strength of homogeneous joints. Hybrid joints behaved similarly to homogeneous joints in that as the joint length was increased, the average shear strength decreased. Also, a decrease in A n /A s ratio in hybrid joints was accompanied by the decrease in average shear strength experienced with homogeneous joints. Currently used (1966) design stresses were examined and it was demonstrated that increasing allowable stresses in both A325 and A490 bolts would have little effect on the minimum factor of safety in bearing-type connection.
A Benefits System for the Information Age

The veterans benefits system that we have today is, with modest changes, the same one that was created in 1917 for the veterans of World War I. We have advanced since then, however, from the Industrial Age to today’s Information Age, which has ushered in huge changes for the fields of law, medicine, government, and information technology. Nevertheless, the veterans benefits system remains trapped at the start of the previous century. Today’s challenge for the system is two-fold. First, we must recognize the many ways in which the system is outdated. Second, we must make conscious, strategic decisions as to how to structure the system among all the new possibilities. There is no definitive way in which a modern veterans benefits system must be structured. However, the current out-dated process is certainly not the solution that best handles today’s challenges and opportunities.
Active Sensing Capabilities of the Rat Whisker System

The rat whisker system may be a good model for approaching the design of robust robotic active sensing and exploratory systems. Here we examine how rats use their whiskers (vibrissae) during free exploratory behavior and during a texture discrimination task. Results show that during free exploration, the rat rhythmically moves its head to place its small (micro) vibrissae on the surfaces it is exploring. These periodic “microvibrissal placements” are temporally synchronized with the whisking movements of the large (macro) vibrissae. The periodic microvibrissal placements occurred even during a texture discrimination task, in which a smooth, continuous movement might have been equally effective at extracting the required information. Finally, it was found that rats may sometimes use their micro and macro vibrissae i>consecutively, instead of simultaneously. This suggests that, like humans, rats' exploration consists of a series of movement sequences in which increasingly refined information is gathered about an object. Some implications of these results for the design of artificial exploratory systems are discussed.
Information Technology Ethics - The Future of Our Jesuit Education

Address given at the dedication of the College of Computer & Information Science at Regis University on September 16, 2014.
Hybrid Theranostic Platform for Second Near-IR Window Light Triggered Selective Two-Photon Imaging and Photothermal Killing of Targeted Melanoma Cells.

Despite advances in the medical field, even in the 21st century cancer is one of the leading causes of death for men and women in the world. Since the second near-infrared (NIR) biological window light between 950 and 1350 nm offers highly efficient tissue penetration, the current article reports the development of hybrid theranostic platform using anti-GD2 antibody attached gold nanoparticle (GNP) conjugated, single-wall carbon nanotube (SWCNT) for second near-IR light triggered selective imaging and efficient photothermal therapy of human melanoma cancer cell. Reported results demonstrate that due to strong plasmon-coupling, two-photon luminescence (TPL) intensity from theranostic GNP attached SWCNT materials is 6 orders of magnitude higher than GNP or SWCNT alone. Experimental and FDTD simulation data indicate that the huge enhancement of TPL intensity is mainly due to strong resonance enhancement coupled with the stronger electric field enhancement. Due to plasmon coupling, the theranostic material se...
Topography of the multifocal electroretinogram.

The functional topography of the human retina was characterized using the multifocal electroretinogram (ERG), with particular attention to the form of the decline in response with retinal eccentricity. Population response variability was examined and compared to standard full field ERG variability. Burian-Allen contact lens electrodes were used to record the cone multifocal ERG from 50 young eyes (28.3 years ± 5.9 years). Responses were recorded in 8 min from 103 retinal locations within the central ± 22°. The spatial distribution of local responses showed an exponential fall-off with eccentricity. The exponential slope parameter was highly similar across individuals. Excluding responses to the central element, the fall off with eccentricity approximated a power function with an exponent of -0.6, which compares to the -0.74 exponent for the human cone density profile. The inter-individual variance in response density is greatest at the central fovea, reducing towards more peripheral locations. The logarithm of response density, however, shows approximately equal variance across eccentricity, making log density a more appropriate way to view response topography. The population range (± 2 S.D.) of response density is 0.42 log unit, similar to that of standardized ganzfeld electroretinography. The response exponential decay provides a potentially useful addition to element-by-element comparison, in deciding whether an eye's response is within normal limits.
Software Model Checking Improving Security of a Billion Computers

I will present a form of software model checking that has improved the security of a billion computers (and has saved Microsoft millions of dollars). This form of software model checking is dubbed whitebox fuzz testing, and builds upon recent advances in systematic dynamic test generation (also known as DART) and constraint solving. Starting with a well-formed input, whitebox fuzzing symbolically executes the sequential program under test dynamically, and gathers constraints on inputs from conditional statements encountered along the execution. The collected constraints are negated systematically one-by-one and solved with a constraint solver, yielding new inputs that exercise different execution paths in the program. This process is repeated using novel state-space exploration techniques that attempt to sweep through all (in practice, many) feasible execution paths of the program while checking simultaneously many properties. This approach thus combines program analysis, testing, model checking and automated theorem proving (constraint solving). Whitebox fuzzing has been implemented in the tool SAGE, which is optimized for long symbolic executions at the x86 binary level. Over the past 18 months, SAGE has been running on hundreds of machines and has discovered many new expensive security-critical bugs in large shipped Windows applications, including image processors, media players and file decoders, that are deployed on more than a billion computers worldwide. SAGE is so effective in finding bugs missed by other techniques like static analysis or blackbox random fuzzing that it is now used daily in various Microsoft groups. This is joint work with Michael Levin (Microsoft CSE) and other contributors.
What Good Is Gratitude

If gratitude is indeed worthy of study in positive psychology, then research should demonstrate that gratitude is important to the good life. If gratitude amplifies the good, then gratitude should enhance well-being. In this chapter I explore this issue by investigating the relationships between gratitude in three areas of well-being: emotional, social, and physical. Both correlation and experimental studies provide solid support for the theory that gratitude enhances emotional and social well-being. Furthermore, preliminary research offers promising results that gratitude supports various aspects of physical health as well. Taken together, research suggests that gratitude is one of the most important aspects of human flourishing.
DISTRIBUTION AND CHARACTERISTICS OF THE CATALASES OF LACTOBACILLACEAE.

Johnston, M. A. (Cornell University, Ithaca, N.Y.), and E. A. Delwiche. Distribution and characteristics of the catalases of Lactobacillaceae. J. Bacteriol. 90:347-351. 1965.-Certain strains of lactobacilli and pediococci incorporated hematin during growth, with the concomitant formation of cyanide- and azide-sensitive catalase. Three of five strains of lactobacilli and five of 25 strains of pediococci were capable of this biosynthesis. The pediococci required the heme component of blood, whereas the lactobacilli could incorporate the heme component in the form of purified and solubilized hemin or from blood. In all cases where inhibitor-sensitive enzyme was produced, it was accompanied by the production of inhibitor-insensitive enzyme. In the absence of hematin, only insensitive enzyme was obtained. Two catalase-positive strains of Streptococcus faecalis were found incapable of the synthesis of a heme-type enzyme, as was one member of the genus Leuconostoc. Iron and manganese in the growth medium stimulated the production of the insensitive catalase, but significant quantities of these metals could not be found in a purified enzyme preparation obtained from Lactobacillus plantarum. Aeration had little or no effect on growth, but it consistently doubled the amount of cyanide- and azide-resistant catalase. By means of conventional enzyme fractionation techniques, it was possible to separate the two different enzymes present in the cell-free extract of a strain of Pediococcus homari which had been grown in the presence of blood.
Algebraic Proof II- Fermat's Last Theorem

In 1995, A, Wiles announced, using cyclic groups, a proof of Fermat's Last Theorem, which is stated as follows: If \(\pi\) is an odd prime and \(x, y, z\) are relatively prime positive integers, then \(z^\pi\not=x^\pi+y^\pi.\) In this note, a proof of this theorem is offered, using elementary Algebra. It is proved that if \(\pi\) is an odd prime and \(x, y, z\) are positive inyegera satisfying \(z^\pi=x^\pi+y^\pi\), then \(x, y,\) and $z$ are each divisible by \(\pi\).
Varieties of Verticicladiella wageneri.

Ninety-eight strains of Verticicladiella wageneri Kendr., cause of black stain root disease on conifers, were isolated from species of Pinus, Pseudotsuga, and Tsuga across the known range of the pathogen in western North America. Examination of these strains (45 of which were examined in detail) resulted in recognition of three apparently host-specialized morphological variants. Mycelial pigmentation, presence or absence of a hyaline margin on advancing mycelia, growth rate at 25 C, capacity for conidiophore production, and presence or absence of a swelling at the apex of conidiophore stipes were used to delineate the variants. The variant isolated primarily from hard pines (Pinus ponderosa, P. jeffreyi and P. contorta) is described as V. wageneri var. ponderosa var. nov. The variants from pinyons (Pinus monophylla and P. edulis) and Douglas-fir (Pseudotsuga menziesii) are not consistently distinguishable from each other and are retained in V. wageneri var. wageneri.
PERSPECTIVE: Ten Years Of Experience Teaching A Multi-Disciplinary Product Development Course⋆⋆

Abstract Integrated Design for Marketability and Manufacturing (IDMM at Stanford) is an Integrated Product Development course (IPD at Michigan) that is distinguished by hands-on manufacture of customer-ready prototypes executed by cross-disciplinary teams of students (MBAs and graduate Engineering and Design students) in a simulated economic competition against benchmark products and against each other. The course design is such that teams can succeed only by performing well in each of the marketing, manufacturing, engineering, and design dimensions. Student failure modes include adopting the wrong product strategy, failure to execute a sound strategy of producing a product that meets market needs, failure to drive costs down, poor product positioning and/or communication, poor forecasting and inventory management, and poor team dynamics. Instructors adopting this course model will face challenges that derive from its definitively cross-functional nature. The course involves faculty from Business, Engineering, and Design in a world where teaching load, compensation and infrastructural support is most often tallied on a unit-specific basis. The course requires faculty with broad interests in a world in which narrow academic depth is often more highly valued. Other challenges the course presents include maintaining a sense of fairness in the final product competition, so that students can move beyond the anger of a potential failure to learn from their experience. Also, in its current manifestations on the Stanford and Michigan campuses the course requires expensive general-purpose machine tools and instruction for students to build fully functional (customer-ready) product prototypes. We provide our current resolutions to these challenges, and the rewards for making the effort. In the end, the course’s survivability can be traced to the benefits it provides to all stakeholders: students, faculty, and administrators. These benefits include a course that integrates disciplines in a way that students believe will increase their integrative skills and marketability, a course that faculty can embrace as a vehicle for their own development in teaching and research, and that administrators find sufficiently novel and engaging to attract the attention of outside constituencies and the press.
Mismatch Errors in Microwave Power Measurements

Expressions are derived for error due to mismatch when a UHF or microwave power meter is calibrated by comparison with a standard power meter. Three different methods are considered: (a) alternate connection to a stable power source, (b) the use of a microwave junction which simultaneously supplies power to the uncalibrated power meter and the standard power meter in a known ratio, (c) alternate connection to a microwave junction. The relative merits of the methods are discussed. Expressions are derived for error due to mismatch when using a calibrated power meter in the following situations: (a) direct connection of power meter to power source, (b) reduction of power into the power meter by means of an attenuator, (c) reduction of power into the power meter by means of a directional coupler.
Time-Domain Holographic Digital Memory

An optical storage technique based on time-domain holography for the rapid recording and readout of page-formatted digital data is demonstrated. Storage of 356 kilobits of data was achieved at a single spatial location in a rare-earth–doped crystal. The digital data were recorded and accurately retrieved at a peak rate of 300 megabits per second without the use of error-correcting codes. The system's raw bit error rate is about 10− 7. This low bit error rate was achieved by a detection scheme for extraction of binary data. These results have implications for dynamic optical memory.
Effects of Selective Logging on Breeding Bird Communities in Bottomland Hardwood Forests in Louisiana

Abstract Bottomland hardwood forests of the southeastern United States support a rich avifauna, including >20 species of conservation concern; understanding the impact of land use practices on these communities is critical to their conservation. Selective timber harvesting is a common management practice in southern bottomland hardwood forests, but little research has examined impacts >5 years after harvesting. We studied breeding bird communities in selectively harvested bottomland forests in northeastern Louisiana during 2003–2004. We conducted point counts in recently harvested stands (1–5 yr postharvest) and older harvests (12–18 yr postharvest); we paired each with a reference stand that had not been harvested for >30 years. Of 35 species with sufficient detections for analysis, we found evidence that abundances of 17 species differed among treatments. Three species were sensitive to creation of canopy openings by timber harvests, including 2 species of concern in the Mississippi Alluvial Valley, USA...
Sucrose Exclusion and Inclusion in a Lipid-Water System

Sugars are known to strongly affect lipid-water phase behavior and often serve as protectants against cold, heat, and dehydration. However, a detailed picture of how sugars interact with lipids remains an active question. We have determined the phase diagram of the lipid SOPE (1-stearoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) as a function of sucrose concentration by means of DSC and laser-light scattering. Using thermodynamic arguments, our data can be used to determine the interfacial concentration of sucrose in lipid-water-sucrose mixtures. Our preliminary results are consistent with a model of sucrose being excluded in a thin layer of water immediately in front of the lipid head groups, but partially included in the gaps between lipid head groups in the fluid lamellar phase and in the core of the inverted hexagonal phase.
“Doing well by doing good” garners broad appeal for Academy of Management Conference

Purpose – The purpose of this paper is to report on the 67th Annual Academy of Management Conference held 3‐8 August 2007, in Philadelphia, Pennsylvania, USA.Design/methodology/approach – Conference highlights are categorized into five themes: justice and equality, ethics and social responsibility, power and privilege, harassment and discrimination and diversity and inclusion. A sampling of papers and symposia deemed exemplars for each theme were included in the report.Findings – The conference theme, “doing well by doing good”, generated theme‐related submissions which are of interest to the EOI readership.Originality/value – The report offers insights on various themes from authors from different theoretical perspectives and varied research methodologies.
On the complexity of measuring software complexity

The term software complexity (program quality, program complexity,...) has been used by software engineering researchers to denote the testability, maintainability, readability, and/or comprehensibility of a program. Curtis points out a common bond that unites all these concepts: a program's complexity determines how difficult it is for programmers to work with.
Two-photon spectroscopy of aligned acetaldehyde

Abstract We reinvestigate the two-photon absorption of the (3s-n) transition in acetaldehyde and its implications for the observation of collision-induced alignment. The two-photon spectroscopy of an aligned ensemble of acetaldehyde produced in collisions with He provides clear evidence for the quantum interference of tensors of different rank. The observed polarization effect can be understood in terms of the non-vanishing tensor components Z 0 (0) =1.0, Z 0 (2) =0.4±0.1 and | Z ±2 (2) |=0.3±0.1. For a collision energy of 916 cm −1 , the alignment is largely consistent with the predictions of the kinematic apse model.
Numerical strategies in the construction of amplitudes satisfying unitarity, analyticity and crossing symmetry. I

Abstract Numerical strategies for the construction of amplitudes satisfying Mandelstam unsubtracted analyticity, crossing, elastic unitarity exactly and preserving inelastic unitarity bounds are studied. A slightly modified set of equations are considered in this paper. The various strategies are compared and the number of iterations required to yield a converging solution established. Further numerical simplifications are proposed.
Rare event statistics in reaction-diffusion systems.

We present an efficient method to calculate probabilities of large deviations from the typical behavior (rare events) in reaction-diffusion systems. This method is based on a semiclassical treatment of an underlying ``quantum'' Hamiltonian, encoding the system's evolution. To this end, we formulate the corresponding canonical dynamical system and investigate its phase portrait. This method is presented for a number of pedagogical examples.
The determination of the potential of zero charge on solid metals

Abstract An attempt has been made to evaluate several experimental methods by which the potentials of zero charge (pzc) of metals could be concordantly measured. The methods chosen involved measurements of the adsorption in the double layer of a neutral organic compound as a function of the concentration of the supporting electrolyte; double-layer capacitance as a function of potential; and static friction between surfaces in solution. The pzc for Pt containing a negligible amount of H is Eq=0 = 0·56 (±0·07) − 0·067 pH (3 methods). For Au, Eq=0 = 0·15 ± 0·02 (2 methods). For Ag, Eq=0 = −0·44 ± 0·02 (2 methods). For Ni, Eq=0 = −0·26 ± 0·06 (3 methods). Introduction of H into Pt shifts the pzc in the negative direction. Anodic and cathodic pulsing of Au and Ag electrodes produced surfaces which gave pzc values 0·2 and 0·4 V respectively more positive than those for unpulsed electrodes. Results reported earlier for Pt are for Pt containing dissolved H. The dissolved proton concentration, abnormally high near the surface, contributes significantly to the surface potential. The results obtained oil pulsing of silver and gold are for dermasorbed surfaces. The most satisfactory methods for the determination of the pzc are the capacitance, static friction, immersion, and tension vibration methods.
Single-strand interactions of mouse satellite DNA

Abstract Interactions of the complementary strands of mouse satellite DNA were investigated in the presence of polyribonucleotides, at high ionic strengths, and at different molar ratios of the two strands. Polyribonucleotide binding demonstrated the presence of T-rich and (A,C)-rich or C-rich sequences on the heavy strand. Ribopolymers bound to one strand of mouse satellite DNA were displaced by addition of the complementary DNA strand. However, the formation of mouse satellite DNA · DNA hybrids is essentially irreversible. High ionic strengths and formaldehyde were used to investigate the two steps, nucleation and rewinding, which comprise the reassociation of mouse satellite DNA. Compared with procaryotic DNA's, the complementary strands of mouse satellite DNA nucleate rapidly. The rewinding of nucleated complementary strands of mouse satellite DNA is inhibited at high ionic strengths and low temperatures. The effects of rapid nucleation of mismatched strands on the reassociation of animal satellite DNA's are discussed.
Amiloride-sensitive regulation of intracellular pH in B-cells: Activation by glucose

Abstract Alterations in intracellular pH (pH i ) generated by metabolism of glucose has been proposed to be a transduction device for controlling changes in K + conductance in the plasma membrane of the B-cell leading to depolarization and cyclic variations in the membrane potential associated with spike activity. The influence of permeable weak acids or bases and amiloride inhibition of H + extrusion by a Na:H exchanger on glucose-induced electrical activity has suggested that the electrical events are pH-sensitive. In order to document that these conditions alter pH i , we determined the influence of glucose, propionic acid, and NH 4 Cl, in the presence or absence of amiloride on pH i of rat islets using [ 14 C] DMO. Glucose, 2.8 mmol/L decreased pH i by .09 unit compared to the absence of glucose (pH i = 7.08 ± .01, M ± SEM) and 16.7 mmol/L glucose reduced pH i by .19 unit. The glucose dose-related decrease in pH i yielded a half-maximal response at 4 mmol/L. The addition of 0.1 mmol/L amiloride had no influence on pH i without glucose and decreased pH i in the presence of 2.8 mmol/L glucose by .14 unit. The addition of 20 mmol/L propionic acid to 2.8 mmol/L glucose reduced pH i to 6.85 ± .05, whereas 20 mmol/L NH 4 Cl increased pH i to 7.27 ± .07. The addition of amiloride did not further lower the reduction in pH i elicited by 20 mmol/L propionic acid or 16.7 mmol/L glucose. These results suggest that the amiloride-sensitive Na:H exchanger plays a major role in regulation of pH i , but another modality for pH i regulation exists to compensate for inhibition of Na:H exchange under conditions of an acid load.
Neo-industrial Tokyo: Urban Development and Globalisation in Japan's State-centred Developmental Capitalism

This paper analyses the relation between Tokyo and globalisation in the framework of regulation theory and attempts to draw theoretical implications for Tokyo's current urban development. Regulation theorists contend that globalisation, particularly global capital and finance mobility, has led to the crisis of regulatory institutions that sustained the post-war Fordist growth regime and that the new finance-market-centred growth regime emerging out of the crisis in the UK and the US is now challenging other capitalist societies. Tokyo's urban experience in the past decade conforms to and yet deviates from regulation theory. The paper argues that, although local and national politics have played the most important role in reshaping Tokyo's urban development, it is Japan's state-centred developmental, capitalist system that has enabled Tokyo to resist the new Anglo-American growth regime. Tokyo's growth strategy in the 1990s has instead re-emphasised manufacturing technology. The impact of the new finance-m...
Tissue-specific and cell type–specific RNA interference in vivo

RNA interference (RNAi) is an efficient method for silencing genes in cultured cells. Here we describe a simple RNAi approach for silencing genes in a cell type-specific and tissue-specific way in vivo. The approach, which mimics the means by which naturally occurring 'microRNA's are generated, uses a tissue-specific polymerase II promoter to drive the expression of a short hairpin RNA (shRNA) directed against the gene target. The shRNA is cleaved by ubiquitously expressed endonucleases to form an active small interfering RNA of about 22 nt. As a proof of principle, it has been shown that expression of a shRNA directed against the transcription factor Wilms tumor 1 in transgenic mice reduces that protein specifically in nurse cells in the testis. Our transgenic RNAi approach offers a cost-effective means of rapidly (within months) addressing the function(s) of genes of interest in a wide variety of specific cell types and tissues in mice in vivo.
News as nonfiction theater: How dispositions toward the public cast of characters affect reactions

Affective dispositions toward public persons and groups were ascertained and related to enjoyment reactions to news reports featuring these parties as recipients of bad or good fortune. Consistent with predictions derived from drama theory, favorable dispositions heightened enjoyment reactions to good‐fortune reports, and they suppressed such reactions to bad‐fortune reports. Unfavorable dispositions, in contrast, heightened enjoyment reactions to bad‐fortune reports and suppressed such reactions to good‐fortune reports. Regarding the revelation of bad fortunes, the effects were limited to reports of comparatively minor misfortunes. Reports of grievous harm to target persons were essentially unaffected by dispositional variations.
Speculations on the maturity of infrared technologies

Infrared imaging is at a transition where the market, product development and even research and development are driven by cost and applications rather than increased performance. The technology and industry are maturing and transitioning from a purely military and scientific to a predominant commercial thrust. Recent trends in infrared imaging are compared to academic technology development theories and similar past trends in other industries to draw conclusions regarding the level of technological maturization. The relationship of infrared technology to technology life cycles is discussed.
The “Death of God, ” American Style

It has been argued that a kenotic theology leads to and demands a willing of the death of God. Yet the passage in Philippians that serves as the source of this notion says nothing about the death of God or the total incarnation of God in Jesus Christ. Rather it emphasizes the distinction between Christ and God by asserting that Christ did not seize equality with God and by concluding that at last all men will confess Christ as Lord "to the glory of God the Father" (2:5-11). We are also referred to Nietzsche, Blake, and Hegel, whose powerful intimations of the death of God seem persuasive and supportive of contemporary forms of God's "demise." Yet the characteristic American cultural and religious ethos has seldom, if ever, been deeply influenced by these authors. The very complexity and abstract profundity of their speculations are not likely at this late date to do more than complement the views of those already convinced on other grounds. These classical figures do not speak to the experience of the many who are necessary to the development and success of the "death of God" as a movement. Or again, we find that modern secular man experiences the "death of God" in the alienation in which his social crises and technological culture have placed him. But we have difficulty, not only in identifying this stock figure of "pop" theology in living form, but also in assessing why in other periods, when social turmoil was high and in relative terms technological progress seemed prodigiously rapid, men did not succumb to a "death-of-God" outlook but often clung more desperately to some form of theistic faith. It must be that cultural ferment is not a sufficient reason for denying God's existence, since it has as often driven men to take refuge in God as it has driven them to deny his existence. Finally, analytical philosophy has been counted as a decisive instrument in expressing another phase of the "death of God." This approach, it is claimed, has shut off the possibility of meaningful, linguistic references to a transcendent realm. But it is equally clear that philosophical analysis can be a tool in the hands of a believer in deity as well as an unbeliever.
Immune cross-reactivity of penicillin and cephalothin.

WE recently described positive direct Coombs tests in patients receiving sodium cephalothin1. Because most normal sera caused the in vitro agglutination of red cells coated with cephalothin, we concluded that some of the positive direct Coombs tests must be related to non-immune binding of a serum protein–cephalothin complex to the red cell surface. We also suggested the possibility that some of these test sera contained anti-penicillin agglutinins.
Information of varying cardinality

Abstract We study adaptive information of varying cardinality for linear problems defined on a separable Banach space. It is known that for linear problems adaptive information of fixed cardinality does not help in the worst case setting. It does not help also in the average case setting with Gaussian measures. We prove that in the worst case setting a similar result holds for information of varying cardinality . In the average case setting with Gaussian measures, information of varying cardinality can be more powerful than information of fixed cardinality. However, optimal information has a structure which is almost as simple as nonadaptive information of fixed cardinality. We also give a condition under which varying cardinality does not help. These results are useful for deriving tight bounds on complexity, which is also studied in this paper.
Computational Strategies for Multivariate Linear Mixed-Effects Models With Missing Values

This article presents new computational techniques for multivariate longitudinal or clustered data with missing values. Current methodology for linear mixed-effects models can accommodate imbalance or missing data in a single response variable, but it cannot handle missing values in multiple responses or additional covariates. Applying a multivariate extension of a popular linear mixed-effects model, we create multiple imputations of missing values for subsequent analyses by a straightforward and effective Markov chain Monte Carlo procedure. We also derive and implement a new EM algorithm for parameter estimation which converges more rapidly than traditional EM algorithms because it does not treat the random effects as “missing data,” but integrates them out of the likelihood function analytically. These techniques are illustrated on models for adolescent alcohol use in a large school-based prevention trial.
Beekeeping In the Gambia An Update

In June 2011 Bee World published an article on the work of Africa BEECause and its journey in supporting sustainable beekeeping development in The Gambia. Just over a year later Africa BEECause has gained further perspective through time spent with African bees and the beekeepers of The Gambia. With this perspective Africa BEECause hopes to further rural beekeeping knowledge through its observations and comprehensive trainings that it carries out all over the country.
Md+Qm Calculations Explore the Origins of Differences amongst the Red Fluorescent Proteins

We present a number of theoretical results concerning the properties of and differences amongst several red fluorescent proteins (RFPs). RFPs are an extraordinarily useful group of fluorescent proteins that fluoresce at red-shifted wavelengths compared to GFP, thereby extending the color palette of fluorescent proteins for use in applications like FRET and multi-channel imaging. This redder fluorescence is caused by the extension of the pi-conjugated chain through oxidation of a second backbone bond of either Phenylalanine or Isoleucine, depending on the particular RFP. Our work has focused on the RFPs mCherry, mPlum, and DsRed, which share a common chromophore. Since these RFPs share a chromophore, differences in their photophysical properties must be due to differences in their chromophore environments. We performed a series of 100 ns molecular dynamics simulations followed by ZINDO semi-empirical quantum mechanical calculations in an effort to explore variables such as excitation wavelength, quantum yield, and photostability in these RFPs. The ZINDO calculations were performed on MD simulation frames at 1 ps resolution. This fine resolution allowed for the observation of rare conformational states that suggest reasons for the known differences in quantum yield amongst the proteins. Notably, the electric field contributions from every non-chromophore protein atom and ion, and the ∼14,000 simulation cell water molecules, were used as a perturbation in the ZINDO calculations, which allowed us to query the electrostatic environmental influence on the chromophore.
Advanced X-ray Optics Metrology

The International Bureau of Weights and Measures defines metrology as “the science of measurement, embracing both experimental and theoretical determinations at any level of uncertainty in any field of science and technology…. Measurement science is not, however, purely the preserve of scientists. It is something of vital importance to us all. The intricate but invisible network of services, suppliers, and communications upon which we are all dependent relies on metrology for its efficient and reliable operation….”
On the Neural Mechanisms Underlying Developmental and Individual Differences in Visual Fixation in Infancy: Two Hypotheses

Abstract Both developmental and individual differences in fixation duration during the first year of life suggest that the duration of visual fixations is correlated with the rapidity of visual encoding: fixation durations decrease significantly over the first year, and individual differences in infant fixation duration within ages are reliable characteristics that correlate with measures of cognitive performance in infancy and in later childhood. The mechanism(s) responsible for these apparent individual and developmental differences in fixation (and thus, visual encoding) has yet to be determined. This review presents hypotheses concerning two specific CNS systems and how they might contribute to such individual and developmental differences in infancy. One system is the "transient" and "sustained" pathways of visual processing within the primary geniculostriate visual system (the magnocellular and parvocellular layers of the lateral geneculate). The other system is a "posterior attentional system" that has been identified with the engagement and disengagement of visuospatial orienting. Evidence is reviewed regarding how each subsystem might account for developmental and individual differences in infant visual fixation.