cssi/SciSciGPT-SciSciNet huggingface dataset:
A Comprehensive Evaluation of Methods for Mendelian Randomization Using Realistic Simulations of Genome-wide Association Studies

Mendelian randomization (MR) has provided major opportunities for understanding the causal relationship among complex traits. Previous studies have often evaluated MR methods based on simulations that do not adequately reflect the data-generating mechanism in GWAS and thus there is often discrepancies in performance of MR methods in simulation studies and in real datasets. We use a simulation framework that generates data on full GWAS for two traits under realistic model for effect-size distribution coherent with heritability, co-heritability and polygenicity typically observed for complex traits. We select instruments based on SNPs which reach genome-wide significance in the underlying study of one of the traits the causal effect of which to be tested on the other. Results show that the weighted mode method and MRMix are the only two methods which maintain correct type I error rate in a diverse set of scenarios. Between the two methods, MRMix tends to be more powerful for larger GWAS while the opposite being true for smaller sample sizes. Among other methods, random effect based IVW analysis, MR analyses based on robust loss function (MR-Robust) and robust profile-scores (MR-RAPS) tend to perform best in terms of maintaining low MSE when the InSIDE assumption is satisfied. However, when the InSIDE assumption is violated, all methods except weighted mode and MRMix can produce large bias and correspondingly large mean squared errors (MSE). In conclusion, the results show that relative performance of different methods depends heavily on sample sizes of underlying GWAS, proportion of valid instruments and validity of the InSIDE assumption.
Insights from machine learning of carbon electrodes for electric double layer capacitors

Abstract Recent years have witnessed the broad use of carbon electrodes for electric double layer capacitors (EDLCs) because of large surface area, high porosity and low cost. Whereas experimental investigations are mostly focused on the device performance, computational studies have been rarely concerned with electrochemical properties at conditions remote from equilibrium, limiting their direct applications to materials design. Through a comprehensive analysis of extensive experimental data with various machine-learning methods, we report herein quantitative correlations between the structural features of carbon electrodes and the in-operando behavior of EDLCs including energy and power density. Machine learning allows us to identify important characteristics of activated carbons useful to optimize their efficiency in energy storage.
The turn to dignity

‘To think seriously about Martin Luther King, Jr as a political philosopher’, Paul Taylor writes in To Shape a New World, ‘is to engage in multiple acts of heresy’ (35). Tommie Shelby and Brandon T...
Noninvasive Tracking of Implanted Cells: Superparamagnetic Iron Oxide Nanoparticles as a Long-Term, Multimodal Imaging Label

Superparamagnetic iron oxide (SPIO) nanoparticles can function as specific, long-term multimodal contrast agents for noninvasive imaging studies. Here we describe how to achieve high-resolution, long-term, serial images of single-label transplanted cells through two complementary imaging techniques: magnetic resonance imaging (MRI) and microcomputed tomography (μCT).
Data Consistency Assessment Function (DCAF)

Abstract A Data Consistency Assessment Function (DCAF) is developed to check the consistency of a measurement or set of measurements to all of the data in the entire data set. The inconsistent data can be precisely spotted and identified, which are recognized as the poorly measured data and can also be modified to be consistent with the rest of the data with an expansion process. The data can be either mode shapes, dynamic time response, frequency response functions or strain fields. Depending on the particular situation, three forms of the data expansion approach can be selected to implement the DCAF: System Equivalent Reduction Expansion Process (SEREP) with finite element model, SEREP with experimental mode shapes, and polynomial expansion. Some academic and industrial structures are used as examples to study the application of DCAF. Experimental data are used to validate the technique.
Cardiac Output Measurement With Echocardiography and Pressure Recording Analytical Method in Pediatric Patients Admitted to the Cardiac Intensive Care Unit: A Retrospective Assessment of Bias Between the Two Methods.

Objectives This study aimed to compare, in a cohort of critically ill children with biventricular anatomy and no cardiovascular shunt, cardiac output (CO) and cardiac index (CI) assessed by echocardiography and a continuous pulse-contour method, MostCareUP, to measure the differences between these techniques (biasCO and biasCI), and their association with clinical variables. Design Retrospective study. Setting Tertiary pediatric cardiac intensive care unit. Participants Children admitted to the pediatric cardiac intensive care unit who underwent echocardiography with CO measurement. Interventions None. Measurements and Main Results Thirty-five patients were included. BiasCO was –0.02 (0.26) L/min (percentage error 36%). BiasCI was 0.07 (0.34) L/min/m2 (percentage error 18%). Biases and percentage errors were higher in 24 nonsupervised echocardiographies. A negative biasCO (overestimation by MostCareUP) was associated with post-surgical status (v cardiomyopathy), higher systolic arterial pressure, and spontaneous breathing (v intubation). When only absolute values were considered, biasCONONEG correlated with age, weight, arterial pressure, and heart rate, whereas biasCINONEG was associated with a femoral arterial cannula, no use of inotropes, and the absence of mechanical ventilation. After adjustment, biasCONONEG remained independently associated with patients’ body weight(p = 0.0001). BiasCINONEG showed a nonlinear relationship with weight below 20 kg and above 40 kg. Conclusions Children with extreme low or high weights, those who are extubated, and those with a femoral cannula carry the highest bias. When younger patients are considered, CI should be evaluated instead of CO, because biases are better highlighted by indexing data on body surface area. In children, both echocardiography and MostCareUP may be responsible of inaccurate CO/CI assessment.
When Geneology Matters: Intercountry Adoption, International Human Rights, and Global Neoliberalism

This Article traces the genealogies of intercountry adoption, human rights, and neoliberalism and explains how they converge. Part I examines adoption genealogies, noting that “stranger” adoption erases genealogy, eliminating the legal and social consequences of an illegitimate birth and giving the child a new legal identity. This Part then describes the globalization of adoption after World War II, including the paradox of “saving” children by sending them away, and the futility of erasing genealogy when it is as plain as the nose on a child’s face, or the shape of her eyes, or the color of her skin. Part II sets out the genealogies of the human rights which should govern adoption and explains why, for the most part, they don’t. There are multiple human rights instruments and multiple human rights movements, and they overlap and build on each other in complicated ways. These include a rich genealogy of children’s rights as well as the story of a “world made new” after World War II. The entire array of human rights has been challenged, however, their intricate networks sliced through in favor of a new pop-up conception of human rights that emerged “seemingly out of nowhere” in the 1970s. Part III zooms out from the intimate scale of intercountry adoption, and the broader but still insistently human scale of human rights, to situate the preceding genealogies within the massive project of globalized neoliberalism. It tracks the genealogy of neoliberalism, from its intellectual origins, through the Washington Consensus, up through the global recession and the shaky recovery. Part IV explains when, and why, genealogy matters in these contexts. Genealogy matters, for example, when the Haitian orphans “rescued” after the earthquake turned out not to be orphans at all. It matters when the affluence of the industrialized West is conflated with “human rights” to which all must aspire. It matters in this time of unprecedented inequality, when, as Thomas Piketty has shown, birth predicts wealth as certainly as it did during the Gilded Age. This Part concludes that genealogy matters now because it reminds us where we come from and how we got here, exposing “what currently remains hidden in plain sight;” that is, the runaway train of global capitalism, which commodifies everything in its path, including babies and human rights.
Critical Infrastructure Security

What if a cyber-attack could result in explosions, large scale blackouts, intentional flooding, a nuclear meltdown or nuclear war? Hollywood has provided us with many examples of how hackers could intentionally or unintentionally cause catastrophic failures of critical infrastructure. In 1983’s Wargames, a hacker connects to a top-secret computer which is tied into the United States’ nuclear arsenal (IMDb, 2020). The 2007 movie Live Free or Die Hard, depicts hackers systematically shutting down the United States Stock Market, disrupting communications and traffic safety, and tampering with other critical infrastructure (IMDb, 2020). Lastly, the 2016 movie Zero Days details an attack on a foreign government’s nuclear enrichment facilities and other critical infrastructure (IMDb, 2020). All these examples may seem like farfetched Hollywood fantasies; yet the last example is a documentary of the United States’ collaboration with Israel to attack Iranian nuclear enrichment facilities and critical infrastructure. As demonstrated by these examples, the line between fiction and reality is being erased. Initially, this paper will analyze the concept of critical infrastructure by defining the term, briefly describing the sectors related to critical infrastructure, and describing why these sectors are critical. Next, this paper will analyze the United States’ preparedness to protect critical infrastructure and recommended best practices for fortifying these critical resources. Finally, this paper will conduct a comparison between the United States Cyber Security readiness to that of Germany.
Development and Validation of the Career Crafting Assessment (CCA)

This research introduces career crafting to describe a set of lifelong career behaviors that individuals engage in when developing their meaningful career paths. The Career Crafting Assessment (CCA...
A High Step-Up Z-Source DC-DC Converter for Integration of Photovoltaic Panels into DC Microgrid

This paper presents a Z-source-based high step-up DC-DC converter that benefits from high voltage gain, low voltage stress on the semiconductor devices and the capacitors. The switched-capacitor cells are integrated with the conventional Z-source impedance network resulting in a new high step-up DC-DC converter. The proposed converter is suitable for photovoltaic (PV) applications where PV panels are linked to a 400 V DC bus in a DC microgrid. The proposed converter reduces the voltage stress on the diodes and the power switch to less than half the output voltage and achieves a high-voltage gain without imposing a limitation on the duty cycle and requiring a large number of components. The operating principles, the steady-state analysis, and a comparison with other similar high step-up DC-DC converters are presented. The simulation and experimental results validate the performance and the applicability of the proposed converter.
Case 1: Now What Will You Do?

You are in Northern Zambia. You are the sole anesthesiologist for the next 3 months in a mission hospital. This is your first day. Your own anesthetic equipment has not yet arrived and is not expected for another 2 weeks.
Nuclear magnetic resonance spectrum of 2,7,8-trioxa-1-phosphabicyclo [3.2.1] octane

Abstract The PMR spectrum of 2,7,8-trioxa-1-phosphabicylo[3.2.1]octane (I) has been fully analysed by the first order assumption and a preferred conformation of the molecule was determined on the basis of the coupling constants. Many 4 J (long-range coupling through four bonds) were observed both in the coplaner and non-coplaner systems. An unexpected 5 J was observed, which can be considered as a “ through-space ” long-range coupling. Attention has been directed also to the angular dependency of J POCH and J POCCH .
Reaction list for charged-particle-induced nuclear reactions: Part I: Z=1 to Z=98 (H to Cf), July 1970–June 1971 Part II: Coulomb Excitation, 1956–June 1971

PART I of this reaction list for charged-particle-induced nuclear reactions has been prepared from the journal literature for the period from July 1970 through June 1971. Each published experimental paper is listed under the target nucleus in the nuclear reaction with a brief statement of the type of data in the paper. The nuclear reaction is denoted by A(a,b)B, where Ma≥ (one-nucleon mass). There is no restriction on energy. Nuclear reactions involving mesons in the outgoing channel are not included. Beginning with this supplement, theoretical papers which treat directly with the analysis of nuclear reaction data and results are included in the reaction list. In PART II is presented a reaction list for the Coulomb excitation reaction which has been prepared from the journal literature for the period from 1956 through June 1971.
Prokaryotic Regulation of Epithelial Responses by Inhibition of IκB-α Ubiquitination

Epithelia of the vertebrate intestinal tract characteristically maintain an inflammatory hyporesponsiveness toward the lumenal prokaryotic microflora. We report the identification of enteric organisms (nonvirulent Salmonella strains) whose direct interaction with model human epithelia attenuate synthesis of inflammatory effector molecules elicited by diverse proinflammatory stimuli. This immunosuppressive effect involves inhibition of the inhibitor kappaB/nuclear factor kappaB (IkappaB/NF-kappaB) pathway by blockade of IkappaB-alpha degradation, which prevents subsequent nuclear translocation of active NF-kappaB dimer. Although phosphorylation of IkappaB-alpha occurs, subsequent polyubiquitination necessary for regulated IkappaB-alpha degradation is completely abrogated. These data suggest that prokaryotic determinants could be responsible for the unique tolerance of the gastrointestinal mucosa to proinflammatory stimuli.
Vibrational predissociation and electronic quenching dynamics of OHN2 (A 2Σ

Abstract The vibrational predissociation and electronic quenching dynamics of weekly bound OH  N 2 ( A 2 Σ + ) complexes have been examined using laser-induced fluorescence and dispersed fluorescence. We find that predissociation occurs on a ⩽1 ps timescale for complexes prepared in levels correlating with OH A 2 Σ + (ν′=1) + N 2 X 1 Σ + (ν″=0) . Furthermore, we suggest a simple kinetic analysis which describes the removal of population and lack of fluorescence from OHN 2 levels bound by the OH A 2 Σ + (ν′=0) + N 2 X 1 Σ(ν″=0) potential energy surface. This mechanism implies that nonadiabatic decay, i.e. quenching, may be important for these complexes.
Addition of a UL5 helicase-primase subunit point mutation eliminates bursal-thymic atrophy of Marek's disease virus ∆Meq recombinant virus but reduces vaccinal protection.

Marek's disease virus (MDV) is an oncogenic alphaherpesvirus and the causative agent of Marek's disease (MD), characterized by immunosuppression, paralysis, nerve enlargement and induction of T-cell lymphomas in chickens. Despite widespread usage of vaccines since the 1970s to control MD, more virulent field strains of MDV have emerged that overcome vaccinal protection, necessitating the development of new and more protective MD vaccines. The ∆Meq virus, a recombinant Md5 strain MDV lacking the viral oncogene Meq, is one candidate MD vaccine with great potential but unfortunately it also causes bursal–thymic atrophy (BTA) in maternal antibody negative chickens, raising concerns that impede commercial use as a vaccine. Previously, we identified a point mutation within UL5 that reduced in vivo replication in attenuated viruses. We proposed that introduction of the UL5 point mutation into the ∆Meq virus would reduce in vivo replication and eliminate BTA yet potentially retain high protective abilities. In bi...
Ultrasound and MR identification of ectopic gallstones as a complication of laparoscopic cholecystectomy

Abstract A 23 year old female underwent laparoscopic cholecystectomy complicated by gallstone and biliary spillage into the peritoneal cavity. Six years after surgery, ectopic gallstones were identified in the pelvis on sonography and MR imaging. Identification of ectopic gallstones is imperative for the expeditious diagnosis of the etiology and cause of the patient's symptoms prior to the development of more severe complications. Clinical sequelae of dropped gallstones include abscess formation, empyema, intra-abdominal adhesions, and draining sinus formation. Delay in diagnosis and treatment is often due to lack of awareness of intraoperative events and potential complications, unusual presentation of symptoms, and unexpected site of infection.
Pushing Back: Wound Mechanotransduction in Repair and Regeneration

Human skin is a highly specialized mechanoresponsive interface separating our bodies from the external environment. It must constantly adapt to dynamic physical cues ranging from rapid expansion during embryonic and early postnatal development to ubiquitous external forces throughout life. Despite the suspected role of the physical environment in cutaneous processes, the fundamental molecular mechanisms responsible for how skin responds to force remain unclear. Intracellular pathways convert mechanical cues into biochemical responses (in a process known as mechanotransduction) via complex mechanoresponsive elements that often blur the distinction between physical and chemical signaling. For example, cellular focal adhesion components exhibit dual biochemical and scaffolding functions that are critically modulated by force. Moreover, the extracellular matrix itself is increasingly recognized to mechanically regulate the spatiotemporal distribution of soluble and matrix-bound ligands, underscoring the importance of bidirectional crosstalk between cells and their physical environment. It seems likely that a structural hierarchy exists to maintain both cells and matrix in mechanical homeostasis and that dysregulation of this architectural integrity may underlie or contribute to various skin disorders. An improved understanding of these interactions will facilitate the development of novel biophysical materials and mechanomodulatory approaches to augment wound repair and regeneration.
Methyl bromide exposure and cancer risk in the Agricultural Health Study

Purpose Methyl bromide is a genotoxic soil fumigant with high acute toxicity, but unknown human carcinogenicity. Although many countries have reduced methyl bromide use because of its ozone depleting properties, some uses remain in the United States and other countries, warranting further investigation of human health effects.
Book Review: Why music gets the brain excited

Music does some remarkably strange things to people's brains. Frances H. Rauscher looks at a neurologist's valiant attempt to make sense of it all
IT-17ONO-AE3-208 INHIBITS MYELOID-DERIVED SUPPRESSOR CELLS AND GLIOMA GROWTH

Myeloid-Derived Suppressor Cells (MDSCs) heavily infiltrate in a variety of solid tumors and suppress anti-tumor T-cell activity. Our recent studies have demonstrated the ability of monocytic, Ly6C+ MDSCs to promote glioma growth through the activation of cyclooxygenase (COX)-2 pathway, which is responsible for plostaglandin-synthesis. ONO-AE3-208 is an antagonist of the prostaglandin E (EP)-4 receptor, which is an important positive feedback regulator of the COX-2 pathway. We thus examined the ability of ONO-AE3-208 to suppress MDSC activity in gliomas. ONO-AE3-208 treatment in mice bearing established GL261-quad glioma in the brain resulted in complete and persistent rejection of the tumors. Flow cytometric analysis revealed that gliomas in the ONO-AE3-208-treated mice were infiltrated by fewer numbers of Ly6C+ MDSCs compared with non-treated animals. We subsequently isolated glioma-infiltrating Ly6C+ MDSCs by flow-sorting to address their functions. RT-PCR analysis revealed that the Ly6C+ MDSCs derived from ONO-AE3-208 treated mice expressed lower levels of the Arg1 and Cox2 expression compared to control animals. Consistently, brain infiltrating leukocytes in ONO-AE3-208 treated tumor-bearing mice demonstrated enhanced Ifng expression compared with control mice, suggestive of enhanced T-cell activity. Importantly, ONO-AE3-208 inhibited glioma growth and promoted immune activity in 2 additional murine glioma models: the Sleeping Beauty de novo glioma model and the SB28 glioma cell line model. Our data demonstrate that ONO-AE3-208 may be useful in the treatment of glioma patients to suppress Ly6C+ MDSCs and promote anti-tumor immunity.
Measurement of replacement factors for a parallel-plate chamber.

We have measured the replacement correction factors ({ital P}{sub repl}) for a PTW/Markus parallel plate chamber at mean incident electron energies of 3.1, 4.4, 8.9, 13.0, 16.3, and 18.8 MeV. The factors are significantly different from unity at low energies.
STIMULATION OF STEROID C-21 HYDROXYLASE ACTIVITY IN ADRENAL MICROSOMES BY SERUM PROTEIN.

Abstract : The ability of rat serum to stimulate corticosteroidogenesis in surviving rat-adrenal tissue and in adrenal homogenates has been described. The active material was present in serum of normal, adrenalectomized, and hypophysectomized rats, was firmly associated with the serum proteins, and appeared to be distinct from other known stimulators of adrenocortical activity. Addition of small ammounts of rat serum to adrenal homogenates (0.I ml/100 mg adrenal tissue) markedly enhanched the conversion of progesterone to II-deoxycorticosterone and corticosterone and suppressed the formation of II bets-hydroxyproggsterone. (Author)
Proteinase K decreases Pseudomonas aeruginosa adhesion to wounded cornea.

The present study was designed to obtain further information regarding the molecular nature of the corneal receptor(s) facilitating Pseudomonas aeruginosa adhesion to cornea. Scarified adult mouse corneas in organ culture were treated for 10 or 60 min with a panel of lipase-free proteases [each at 20 μg ml−1 or 0·22 Units (U) ml−1, activity] including trypsin, chymotrypsin, V8 protease, elastase, subtilisin A, pronase protease and proteinase K. All of these, except proteinase K treatment (20 μg ml−1 for 60 min), either significantly elevated or had no effect (proteinase K 20 μg ml−1 for 10 min) on subsequent bacterial adhesion at 60 min following topical application of the inoculum to the scarified corneal surface. Enzyme treatment times of 10, 30 or 60 min at a higher concentration (50 μg ml−1) of proteinase K, significantly decreased binding at 60 min after bacterial application for each enzyme treatment time. The combined effects of proteases and lipase on bacterial binding also was examined. Eyes treated with proteinase K (20 μg ml−1 for 1 hr) or protease-free lipase (50 000 U ml−1 for 1 hr) alone or in combination, all reduced bacterial binding, but the effect was not additive. Trypsin or lipase alone significantly enhanced or decreased binding, respectively. In contrast, trypsin (20 μg ml−1 for 1 hr) followed by lipase treatment (50 000 U ml−1 for 1 hr) resulted in binding which was not significantly different than phosphate-buffered saline (PBS) control binding, indicating that the trypsin exposed receptor was lipase sensitive. Lastly, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of corneal epithelium obtained from trypsin versus proteinase K-treated scarified corneas, revealed that trypsin treatment (20 μg ml−1 for 10 min) generally enhanced corneal epithelial proteins, while similar treatment with proteinase K, but for 30 min, generally decreased corneal epithelial proteins. These findings provide evidence that the binding of P. aeruginosa to the wounded adult ocular surface involves interaction of bacterial adhesins with corneal epithelial host receptor proteins as well as lipids.
Delineating Sea Level Rise Inundation Using a Graph Traversal Algorithm

The rate of sea level rise will roughly double over the next century with a conservative projection of 0.18–0.59 m by 2100 (IPCC 2007). Inundation caused by sea level rise will likely disrupt the physical, economic, and social systems in coastal regions worldwide. All existing methods to assess the potential impacts of sea level rise could only delineate the inundation by a specific sea level rise. In addition to providing another inundation method based on the cost distance GIS function, this research developed an innovative method that calculated the minimum sea level rise needed to inundate each cell in a Digital Elevation Model (DEM). Both methods considered water connectivity and performed better than the simple “bathtub” approach, especially with sea level rises below 1 m. Implementation data structures significantly affected the efficiency of the new method. Several data structures were proposed and compared. Our results indicated the combination of a binary heap and hash table data structure was t...
Issues in the development of a theory of interpersonal competence in the intercultural context

Abstract A brie/review of competence relevant literature in intercultural communication reveals several problems. Specifically, the research on intercultural communication competence tends to suffer from a lack of theoretical integration and serious problems in measurement development and validation. The thesis of this analysis is that progress is most likely to occur when cross-cultural models and theories of communication are refined in the inercultural context. Toward this end, a speculative attempt is made to sketch the outline of such a model.
A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli. Evaluation of some molecular parameters of translation in vivo.

Abstract The efficiency of missense and nonsense suppressors is affected in different ways in Escherichia coli strains carrying different kinds of ribosomal mutations: see Gorini's review (1970). This led Gorini (1971) to postulate a “ribosomal screen” able to distinguish between normal and mutant tRNAs. Here we examine the alternative hypothesis, that the results on suppression can be accounted for by minor changes in the kinetics of polypeptide chain elongation in mutant ribosomes. A general kinetic scheme for the attachment of tRNA to the A site of ribosomes is described. It is postulated that the tRNA first makes a “loose” bond with the codon. A second event is required to stabilize binding and to allow transpeptidation. The probability that the second event occurs is related to the time that the tRNA sticks to the codon in the loose binding state. Ribosomal mutations would make the transition from loose to tight binding more probable (ram) or less probable (strA), per collision. A method of analysis is developed that enables one to relate directly the experimental measurements on suppression to molecular parameters. By numerical fitting, it is shown that the following set of conditions can account for the behaviour of the various ribosomal mutants. 1. (a) In the wild-type cell, when a codon becomes associated with its cognate tRNA or release factor, the probability of ensuing chain elongation or termination is very close to unity. The probability of elongation decreases to about one-half in strA1 strains. 2. (b) Loaded nonsense suppressor tRNAs su1, su2 and su3 are present in such amounts that they collide with UAG about as often as the release factor does, but their binding is such that peptide bond formation is not very efficient. 3. (c) In contrast, the low efficiency of two missense suppressors appears related to a relatively low frequency of codon-loaded suppressor collisions, while the association itself may be either stronger (su58) or much weaker (su78) than that of the corresponding normal codon-tRNA association.
Assessing the effect of sequencing depth and sample size in population genetics inferences.

Next-Generation Sequencing (NGS) technologies have dramatically revolutionised research in many fields of genetics. The ability to sequence many individuals from one or multiple populations at a genomic scale has greatly enhanced population genetics studies and made it a data-driven discipline. Recently, researchers have proposed statistical modelling to address genotyping uncertainty associated with NGS data. However, an ongoing debate is whether it is more beneficial to increase the number of sequenced individuals or the per-sample sequencing depth for estimating genetic variation. Through extensive simulations, I assessed the accuracy of estimating nucleotide diversity, detecting polymorphic sites, and predicting population structure under different experimental scenarios. Results show that the greatest accuracy for estimating population genetics parameters is achieved by employing a large sample size, despite single individuals being sequenced at low depth. Under some circumstances, the minimum sequencing depth for obtaining accurate estimates of allele frequencies and to identify polymorphic sites is , where both alleles are more likely to have been sequenced. On the other hand, inferences of population structure are more accurate at very large sample sizes, even with extremely low sequencing depth. This all points to the conclusion that under various experimental scenarios, in cost-limited population genetics studies, large sample sizes at low sequencing depth are desirable to achieve high accuracy. These findings will help researchers design their experimental set-ups and guide further investigation on the effect of protocol design for genetic research.
Monoclonal antibodies identifying subsets of ectodermal, mesodermal, and endodermal cells in gastrulating and neurulating avian embryos

The goal of our laboratory research is to elucidate the mechanisms underlying gastrulation and neurulation, using the avian embryo as a model system. In previous studies, we used two approaches to map the morphogenetic movements involved in these processes: (1) we constructed quail/chick transplantation chimeras in which grafted quail cells could be identified within chick host embryos by the presence of nucleolarassociated heterochromatin, and (2) we microinjected exogenous cell markers. However, it would be advantageous to be able to detect endogenous markers to demarcate various subsets of cells within the unmanipulated embryo. To elucidate such a series of natural markers, we have used monoclonal antibodies to identify epitopes found on subsets of ectodermal, mesodermal, and endodermal cells. Antibodies were made by immunizing mice against either homogenized ectoderm (i. e., Prospective neural plate and surface ectoderm) or primitive streak, which had been microdissected from stage 3 chick embryos. Additionally, we screened a panel of antibodies made against soluble protein obtained from isolates of cell nuclei from late embryonic chick brain. Here, we describe the labeling patterns of three monoclonal antibodies, called MAb-GL1, GL2, and GL3 (GL, germ layer), during avian gastrulation and neurulation. Our results show that labeling early avian embryos with monoclonal antibodies can reveal previously undetected distributions of cells bearing shared epitopes, providing new labels for subsets of cells in each of the three primary germ layers. © 1993 Wiley-Liss, Inc.
The Selectivity of Vibrio cholerae H-NOX for Gaseous Ligands Follows the “Sliding Scale Rule” Hypothesis. Ligand Interactions with both Ferrous and Ferric Vc H-NOX

Vc H-NOX (or VCA0720) is an H-NOX (heme-nitric oxide and oxygen binding) protein from facultative aerobic bacterium Vibrio cholerae. It shares significant sequence homology with soluble guanylyl cyclase (sGC), a NO sensor protein commonly found in animals. Similar to sGC, Vc H-NOX binds strongly to NO and CO with affinities of 0.27 nM and 0.77 μM, respectively, but weakly to O2. When positioned on a “sliding scale” plot [Tsai, A.-l., et al. (2012) Biochemistry 51, 172–186], the line connecting log KD(NO) and log KD(CO) of Vc H-NOX can almost be superimposed with that of Ns H-NOX. Therefore, the measured affinities and kinetic parameters of gaseous ligands to Vc H-NOX provide more evidence to validate the “sliding scale rule” hypothesis. Like sGC, Vc H-NOX binds NO in multiple steps, forming first a six-coordinate heme–NO complex at a rate of 1.1 × 109 M–1 s–1, and then converts to a five-coordinate heme–NO complex at a rate that is also dependent on NO concentration. Although the formation of oxyferrous V...
Simple Model for Characterizing the Electrical Resistivity in A − 15 Superconductors

A discussion of some of the difficulties with previous analyses of the resistivity of $A\ensuremath{-}15$ compounds is given. Precise high-temperature data on $\ensuremath{\alpha}$-particle- and electron-damaged ${\mathrm{Nb}}_{3}$Ge and ${\mathrm{Nb}}_{3}$Sn samples with different defect concentrations are presented here and analyzed in a simple way with use of a phenomenological model based on the idea that the ideal resistivity must approach some limiting value in the regime where the mean free path becomes comparable to the interatomic spacing.
Wide-baseline optical interferometry with laser guide stars

Laser guide stars have been used successfully as a reference source for adaptive optics systems. We present a possible method for utilizing laser beacons as sources for interferometric phasing. The technique would extend the sky coverage for wide baseline interferometers and allow interferometric measurement and imaging of dim objects.
Biochemical analysis of toxic effects of 5-hydroxymethyl-2′-deoxyuridine in mammalian cells

Cellular and biochemical analyses of the toxic effects of the thymidine analog, 5-hydroxymethyl-2′-deoxyuridine (hmdUrd), were carried out using V79.5 Chinese hamster cells. It was found that the toxic effects of hmdUrd could be totally suppressed by the addition of thymidine at 1/10th the concentration of hmdUrd. When other pyrimidines were tested, deoxyuridine was found to also suppress toxicity, although not as well as thymidine, while orotate, uridine, cytidine, and deoxycytidine did not have significant effect. Biochemical analyses of the metabolic fate of hmdUrd demonstrated low but significant levels of hmdUrd triphosphate and the incorporation of 5-hydroxymethyluracil (hmUra) residues into DNA. Surprisingly, in addition to these metabolites, relatively high levels of free hmUra were also detected in the acid-soluble cell extracts. Further analysis demonstrated that when V79.5 cells were exposed to hmdUrd significant amounts of hmUra were released into the culture medium. In vitro assays provided evidence that hmdUrd was first phosphorylated to its monophosphate and then degraded to hmUra, possibly via the action of a new enzyme, hydroxymethyldeoxyuridylate phosphorylase. Exposure of cells to hmUra alone, at concentrations as high as 3 mM, had no effect on viability. However, when V79.5 cells were simultaneously exposed to low, nontoxic concentrations of hmdUrd and high, nontoxic concentrations of hmUra, a synergistic reduction in viability was observed. This synergistic effect was found to correlate with increased incorporation of hmUra into DNA, possibly via end-product inhibition of an hmUra-DNA glycosylase.
The historikerstreit and the critique of nationalism

In the recent debate among German historians and social scientists known as the Historikerstreit, Jurgen Habermas raised several philosophical questions concerning the concept of nationalism and its relation to historical self-consciousness. The terms of the debate between Habermas and several known, neo-conservative German historians (Sturmer, Hillgruber and Nolte) revolve around the issue of Germany's historical understanding of the Nazi period
Cultural Differences: A Cross-cultural Study of Urban Planners from Japan, Mexico, the U.S., Serbia-Montenegro, Russia, and South Korea

This study evaluates the efficacy of Hofstede’s indexes of national culture in the context of public planning agencies across six countries—US, Mexico, Serbia-Montenegro, Russia, Japan, and South Korea. We surveyed 343 planning employees and computed separate one-way, between groups analyses of variance to test for overall differences in Hofstede’s indexes. We found that public planning officials across countries are significantly different on all five dimensions of culture. We comment on how cultural differences might factor into urban planners’ attitudes toward advocacy and social equity planning, market-based planning, citizen participation, rational planning, and other issues relevant to planners’ roles.
Changes in cerebral perfusion during third-generation implantable cardioverter defibrillator testing.

Abstract Third-generation implantable cardioverter defibrillators (ICDs) are designed to provide tiered therapy for ventricular tachycardia and ventricular fibrillation. At present, however, therapy prescription does not take into account the hemodynamic consequences of ventricular dysrhythmias. Design of “intelligent” devices depends on their ability to assess hemodynamic consequences of tachyarrhythmias and end-organ perfusion. Quantitative electroencephalography (QEEG) and transcranial Doppler flow provide sensitive and specific measures of cerebral perfusion during ICD testing and programming. In response to prolonged hypotension (> 15 seconds), transient loss of α power (i.e., increase in δ power) in the EEG spectrum, accompanied by impaired cerebrovasomotor reactivity (CVR), was observed in 25 of 91 hypotensive episodes in 15 patients, ages 36 to 72 years, predicting intolerance to the programmed ICD therapy. Conversely, intact CVR prevented ischemia, slowing in the EEG, and predicted tolerance to the therapy prescription. These changes were exaggerated in the erect posture during tilt-table ICD testing. During ventricular tachycardia, signs of cerebral hypoxia detected by QEEG and Doppler techniques were accompanied by a fall in transcranial oxyhemoglobin saturation measured by near-infrared spectroscopy. We conclude that transcranial Doppler and QEEG are sensitive indicators of cerebral perfusion. These techniques could be used as indexes of perfusion against which hemodynamic sensors for future ICDs could be evaluated.
Photopolymerization of hydroxypropyl acrylate and tetraethylene glycol dimethacrylate initiated by uranyl ion

Uranyl nitrate, acetate, sulfate, and dibutyl phosphate were used in solution for the photoinitiation of homopolymerization and copolymerization of hydroxypropyl acrylate and tetraethylene glycol dimethacrylate. Solvents used included water, water-ethylene glycol mixtures, and dimethylformamide. Polymer yields in excess of 90% can readily be obtained by exposing solutions containing 0.014M UO22+ to light from a tungsten bulb for 1 hr. The rigidity of the polymers varied directly, the affinity for water in-versely, with the concentration of tetraethylene glycol dimethacrylate in the monomer mixture. Poly(hydroxypropy1 acrylate) contained 52% water and poly(tetraethy1ene glycol dimethacrylate) 34% water, a t equilibrium.
Occupation and COPD.

Time for action Chronic obstructive pulmonary disease (COPD) is now the fourth leading cause of death worldwide and, by all reasonable projections, its incidence will increase. The worldwide burden of COPD morbidity and mortality is already large, and will become staggering in this century. In this issue of the journal, Meldrum et al describe the impact of COPD on the UK.1 In their poignant review, they point out that while the main cause of COPD in the UK remains cigarette smoking, there is a substantial body of epidemiological evidence linking occupational exposures to dusts, gases/vapours, and …
Relationship of Rate of Thyroxine Secretion to Rate of Egg Production in the Domestic Fowl

Abstract IT has long been recognized that the activity of the thyroid gland is concerned in egg production, but the extent to which its activity affected production has not been reported. A number of earlier workers attempted to alter egg production by changing thyroid activity. Some of these investigators used desiccated thyroid; later workers have used iodinated casein. Most of the workers were unable to increase egg production with desiccated thyroid. Turner and his associates (1945a) and (1946) found that the feeding of 10 grams of iodinated casein per 100 pounds of feed to hens 2 to 5 years of age increased egg production. This increase in production was primarily in the late spring and summer months when production normally declines. Turner suggests that the normal decline in egg production in late spring and summer and with age is due to a drop in thyroxine secretion. Turner et al. (1945b) also . . .
Isolation of Inositol 1,3,4-Trisphosphate 5/6-Kinase, cDNA Cloning, and Expression of the Recombinant Enzyme

Inositol 1,3,4-trisphosphate 5/6-kinase was purified 12,900-fold from calf brain using chromatography on heparin-agarose and affinity elution with inositol hexakisphosphate. The final preparation contained proteins of 48 and 36-38 kDa. All of these proteins had the same amino-terminal sequence and were enzymatically active. The smaller species represent proteolysis products with carboxyl-terminal truncation. The Km of the enzyme for inositol 1,3,4-trisphosphate was 80 nM with a Vmax of 60 nmol of product/min/mg of protein. The amino acid sequence of the tryptic peptide HSKLLARPAGGLVGERTCNAXP matched the protein sequence encoded by a human expressed sequence tag clone (GB T09063) at 16 of 22 residues. The expressed sequence tag clone was used to screen a human fetal brain cDNA library to obtain a cDNA clone of 1991 base pairs (bp) that predicts a protein of 46 kDa. The clone encodes the amino-terminal amino acid sequence obtained from the purified calf brain preparation, suggesting that it represents its human homologue. The cDNA was expressed as a fusion protein in Escherichia coli and was found to have inositol 1,3,4-trisphosphate 5/6-kinase activity. Remarkably, both the purified calf brain and recombinant proteins produced both inositol 1,3,4,6-tetrakisphosphate and inositol 1,3,4,5-tetrakisphosphate as products in a ratio of 2.3-5:1. This finding proves that a single kinase phosphorylates inositol in both the D5 and D6 positions. Northern blot analysis identified a transcript of 3.6 kilobases in all tissues with the highest levels in brain. The composite cDNA isolated contains 3054 bp with a poly(A) tail, suggesting that 500-600 bp of 5′ sequence remains to be identified.
Neoliberalism and Social Security

The stagnant wages, worsening distribution of income, and slower economic growth that have resulted from neoliberalism have weakened Social Security’s future viability. Moreover, the prediction of ...
Stabilization of deoxyadenosine/polynucleotide complexes by 3',5'-di-O-benzoyl substituents.

Abstract 3′,5′-Di-O-benzoyldeoxyadenosine forms stable dT:dA:dT type complexes with poly(dT) and an oligo(dT)-cholesteryl conjugate in dilute aqueous solution. The benzoyl groups play an essential role in stabilizing these “triple stranded” complexes. This paper is dedicated in memory of Professor Tsujiaki Hata - a premier scientist, a creative leader in the field of nucleic acid chemistry, and a warm friend.
New antennas for the 1.5GHz band

Crowded radio communication bands have necessitated the opening up of new bands. A major expansion of the use of the 1.5 GHz band is now under way. New antennas have been designed to optimise the potential capacity of this band for the future
LIGHTCONE 2011 Summary: applications of Light-Cone Coordinates to Highly Relativistic Systems

The 2011 workshop of the International Light Cone Advisory Committee (ILCAC), Inc., took place at Southern Methodist University (SMU) in Dallas, Texas, 23–27 May. These workshops have been held at least annually since 1990, focusing on the formal and phenomenological application of light-cone coordinates to nuclear, particle, and string physics, especially via light-front quantization of field theory. In short, the field studies physics from the viewpoint of an observer travelling at the speed of light, a frame of reference that has some unique kinematical and dynamical advantages. LIGHTCONE 2011 had about 50 physicists, featuring a total of 45 presentations (invited talks and posters). The workshop was purposely limited in size to avoid parallel sessions and to allow all participants to present if they wished. Each day began with a 1-h thematic keynote talk, followed by 1/2 h talks; a relatively large and well-attended poster session generated a lot of discussion. About half the working time of the conference was given to informal discussion. The daily themes of this workshop reflected the current interests of the field: AdS/CFT/QCD, Partons, Ab Initio Calculations, Nuclear and Many-Body, with the final morning covering a variety of topics. Presentations have therefore been divided into those themes in this volume. Many phenomenological applications to hadrons were discussed using holographic QCD, covariant constituent models, and chiral perturbation theory. Light-front holography, which maps AdS/QCD directly to LF QCD in physical space–time, was treated in talks by Brodsky and de Teramond. Discussions on the kinematic issues in extracting GPDs (B. Bakker and C. Ji) were highly relevant to the analysis of DVCS experiments at JLab and DESY. A number of new directions were presented at this workshop, including the phenomenology of multi-parton distributions (M. Diehl) and new computational methods, such as Light-cone Coupled-cluster (J. Hiller and S. Chabysheva) and Singular Value Decomposition (M. Weinstein). The most lively discussion centered on ‘in-hadron’ condensates, which eliminate the 45 orders of magnitude conflict between the cosmological constant and QCD (talks by Roberts, Brodsky, Tandy, Glazek) and reminiscent of the trivial vacuum of regulated light-front quantization. The in-hadron condensate idea, which seems at odds with the traditional idea of Lorentz invariant vacuumexpectation values associated to spontaneous symmetry breaking, was supported by some but vigorously opposed by other participants. Many other interesting presentations can be found in this volume—they are only half the story however, as discussions outside of the lecture room were as important.
The machine in Utopia: Shaker women and technology

Synopsis Commonly believed devoted to handcrafts and opposed to technology, the nineteenth-century American Shakers were enthusiastic about the machine, viewing it as a means to a more humane life. Shaker women used, maintained, and even invented labor-saving devices, both in their domestic work and their commercial enterprises. The Shaker view toward women and technology emerged from their egalitarian religious principles that placed an equal value upon the lives of women and men. Shaker women invented the buzz saw, cut nails, and a successful revolving oven, and they were knowledgeable about the operation of machinery. Although they worked long hours at their machines, Shaker women emphasized that their lot was far better than that of unfortunate factory women, because they worked for themselves in pleasant surroundings and rotated work assignments frequently. Hard-working, they decried drudgery, and though they opposed capitalism and the factory system, they maintained a Utopian vision of technology as a source of a better American life.
Optimal transition from entry to cruising flight

Optimal angle of attack transition trajectories for space shuttle from atmospheric entry to cruising flight for conventional airport landing