cssi/SciSciGPT-SciSciNet huggingface dataset:
Design, synthesis, and in vitro evaluation of an activity-based protein profiling (ABPP) probe targeting agmatine deiminases

Agmatine deiminases (AgDs) belong to a family of enzymes known as guanidinium group modifying enzymes (GMEs). Many pathogenic bacteria encode an AgD that participates in the catabolism of agmatine (decarboxylated arginine). This catabolism may confer a competitive survival advantage, by virtue of energy production and increased acid tolerance, making this sub-family of enzymes a potential therapeutic target that warrants further study. Herein we report the development of an activity-based protein profiling (ABPP) probe that selectively targets the AgD from Streptococcus mutans. Due to the selectivity and covalent nature of the modification, this probe could prove to be a valuable tool for the study of other AgD family members.
Reaction of Benzo[a]pyrene-7,8-diol-9,10-epoxide with Human Hemoglobin and the Chromatographic Resolution of the Covalent Adducts

Abstract The formation of hemoglobin - carcinogen adducts has been detected in carcinogen treated animals and in human populations. Although polycyclic aromatic hydrocarbons are ubiquitous in the human environment and DNA - aromatic hydrocarbon adducts have been detected in human tissue, the occurrence of hemoglobin - polycyclic aromatic hydrocarbon adducts in humans has not been thoroughly described. In this study we examined the effects of reaction condition on the extent of in vitro reaction of human hemoglobin and (+) [3H]benzo[a]pyrene-7,8-diol-9,10-epoxide (anti)(BPDE), a metabolite thought to be largely responsible for the carcinogenic effect of benzo[a]pyrene. The chromatographic properties of the resulting hemoglobin - BPDE adducts were examined by conventional DEAE-cellulose ion exchange liquid chromatography and by reversed phase high performance liquid chromatography. Several adducts were formed which were chromatographically resolved from hemoglobin and from the individual globins. Some adduc...
Functionalization of carbon nanofibers with diamine and polyimide oligmer

Abstract This paper discusses the functionalization of oxidized carbon nanofibers (OCNF) with monomer and oligmer that mimic the structure of repeat unit of a polyimide (2,2-bis(3,4-dicarboxyphenyl) hexafluoropropane dianhydride-phenylene diamine). The goal was to covalently bind groups to the surface of OCNF that would both improve compatibility with the polyimide and potentially in case of the oligmer allow for chain entanglement in composite format. The reactions were carried out with or without initial activation by thionyl chloride (SOCl2). Functionalization following each reaction step was characterized using thermal gravimetric analysis (TGA), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). While quantitative analyzes indicated that the concentration of surface reactive oxygen groups was fairly low, the OCNFs were successfully functionalized with the aromatic diamine, dianhydride and the polyimide oligmer.
Fck1, a C-type cyclin-dependent kinase, interacts with Fcc1 to regulate development and secondary metabolism in Fusarium verticillioides.

Abstract In Fusarium verticillioides , the C-type cyclin Fcc1 is a global regulator of gene expression. In Saccharomyces cerevisiae and other organisms, C-type cyclins regulate the activity of specific cyclin-dependent kinases through physical association. We identified FCK1 , a gene encoding a cyclin-dependent kinase in F. verticillioides . The Fck1 protein is predicted to contain a cyclin-binding motif and a serine-threonine protein kinase domain homologous to previously described cyclin-dependent kinases. Disruption of FCK1 resulted in pleiotropic morphological defects including reduced growth, conidiation, fumonisin B 1 (FB 1 ) production, and enhanced pigmentation. Two-hybrid analysis indicated a strong physical interaction between Fcc1 and Fck1. This study presents the first description of the interaction between a C-type cyclin and a cyclin-dependent kinase in a filamentous fungus and provides new insight regarding a molecular mechanism that regulates aspects of maize kernel colonization by F. verticillioides .
Establishing Relationships Between the Geometric Structure and Chemical Reactivity of Alloy Catalysts Based on Their Measured Electronic Structure

While it is fairly straightforward to predict the relative chemical reactivity of pure metals, obtaining similar structure-performance relationships for alloys is more challenging. In this contribution we present experimental analysis supported with quantum chemical DFT calculations which allowed us to propose a simple, physically transparent model to predict the impact of alloying on the local electronic structure of different sites in alloys and on the local chemical reactivity. The model was developed through studies of a number of Pt alloys. The central feature of the model is that hybridization of d-orbitals in alloys does not lead to significant charge transfer between the constituent elements in the alloy, and therefore the width of the local density of d-states projected on a site, which is easily calculated from tabulated parameters, is an excellent descriptor of the chemical reactivity of the site.
Aminonucleoside Nephrosis in PRO/Re Mice

SummaryAdministration of aminonu-cleoside of puromycin to PRO/Re strain mice resulted in biochemical and renal glomerular alterations. The biochemical changes included hypoalbuminemia, hyper-alphaglobulinemia, hypercholesterolemia, and azotemia. Morphologically, there was approximation of visceral epithelial foot processes, intracytoplasmic vacuolization or percellular channel formation, and immense deposition of moderately electron-dense material in the subendothelial regions and lumens of glomerular capillaries. Attempts to induce similar changes in either of the parental and in other nonparental strains of mice of diverse genetic origins were unsuccessful.
Microorganisms in the gut of beetles: evidence from molecular cloning

We have regularly cultured yeasts from the gut of certain beetles in our ongoing research. In this study cloned PCR products amplified from the gut contents of certain mushroom-feeding and wood-ingesting beetles in four families (Erotylidae, Tenebrionidae, Ciidae, and Passalidae) were sequenced and compared with culture results. Cultural techniques detected some yeasts present in the gut of the beetles, including a Pichia stipitis-like yeast associated with wood-ingesting passalid beetles. Clone sequences similar to several ascomycete yeasts and Malassezia restricta, a fastidious basidiomycetous yeast requiring special growth media, however, were not detected by culturing. Unexpectedly, phylogenetic analysis of additional clone sequences discovered from passalid beetles showed similarity to members of the Parabasalia, protists known from other wood-ingesting insects, termites, and wood roaches. Examination of all gut regions of living passalids, however, failed to reveal parabasalids, and it is possible that they were parasites in the gut tissue present in low numbers.
Impurity effects on the adhesion of aluminum films on sapphire substrates

The adhesion of aluminum (Al) films onto sapphire substrates in the presence of controlled contaminants is being investigated. In this study, adhesion strength is evaluated by continuous scratch and nanoindentation tests to induce delamination of the Al film from the sapphire substrate. If delamination blisters or spallations can be induced, then fracture mechanics based models can be used to calculate the fracture energy or work of adhesion based on the radius of the blister. Initial specimens of 178 nm thick Al films were vapor deposited onto (0001) oriented sapphire substrates with a 5--19 nm layer of carbon sputter deposited onto the sapphire surface of selected samples. Continuous scratch tests promoted blistering of the film in specimens with carbon on the sapphire surface. Delamination blisters could not be induced by continuous indentation testing in samples with or without carbon at the interface. An overlayer of sputtered tantalum (Ta) was then used on a second set of 500 nm thick Al films with and without 10--20 nm of sputtered carbon on the sapphire surface to promote delaminations. With Ta overlayers, continuous nanoindentation techniques induced larger diameter delamination blisters in the specimens with carbon, than in the specimens without carbon. Resistance to blistering, or smaller induced blisters, indicates a higher interfacial strength.
Unusual Abnormalities in Adolescent Siblings with α1-Antitrypsin Deficiency

We studied, over a four-year period, two adolescents with a 1 -antitrypsin (AAT) deficiency who subsequently died from complications of hepatic cirrhosis. Serial pulmonary function studies indicated mild obstructive lung disease involving peripheral airways in both patients. Postmortem histologic and pulmonary morphometric studies indicated mild diffuse airspace and bronchial gland enlargement, and slight dilation of small airways. This airspace enlargement may represent the early stage of lung disease in AAT-deficient subjects and suggests that pulmonary anatomic changes may occur long before the onset of clinically and pathologically significant emphysema.
A NOTE ON FOREIGN EXCHANGE INTERVENTIONS AT ZERO INTEREST RATES

This note uses a nonlinear structural vector autoregression model to empirically investigate the effectiveness of official foreign exchange (FX) interventions in an economy when interest rates are constrained to the zero level, based on Japanese data in the 1990s. The model allows us to estimate the effects of FX interventions operating through different channels. We find that FX interventions are still capable of influencing the foreign exchange rate in a zero-interest-rate environment, even though their effects are greatly reduced by the zero lower bound on interest rates. Our results suggest that although it might be feasible to use the exchange rate as an alternative monetary policy instrument at zero interest rates as proposed by McCallum (Inflation Targeting and the Liquidity Trap, NBER working paper 8225, 2000), the exchange rate–based Taylor rule may not be very effective in achieving the ultimate policy goals.
An Analysis of Errors and Strategies in the Expository Writing of Learning Disabled Students

This study examined the expository writing errors of learning disabled students and two groups of regular class students. The results suggested that learning disabled students did exhibit quantitatively and qualitatively different writing performances than normally achieving students, and to a lesser extent, than regular class students who were matched to learning disabled writers on IQ and reading achievement. Learning disabled writers had significant difficulty sustaining their expository writing efforts, and their errors suggested a reliance on the knowledge-telling strategy as a basis for expository discourse production.
Diet, Genes, and Microbes: Complexities of Colon Cancer Prevention

Colorectal cancer is one of the leading causes of cancer-related deaths in the United States, and generally, as countries climb the economic ladder, their rates of colon cancer increase. Colon cancer was an early disease where key genetic mutations were identified as important in disease progression, and there is considerable interest in determining whether specific mutations sensitize the colon to cancer prevention strategies. Epidemiological studies have revealed that fiber- and vegetable-rich diets and physical activity are associated with reduced rates of colon cancer, while consumption of red and processed meat, or alcoholic beverages, and overconsumption as reflected in obesity are associated with increased rates. Animal studies have probed these effects and suggested directions for further refinement of diet in colon cancer prevention. Recently a central role for the microorganisms in the gastrointestinal tract in colon cancer development is being probed, and it is hypothesized that the microbes may integrate diet and host genetics in the etiology of the disease. This review provides background on dietary, genetic, and microbial impacts on colon cancer and describes an ongoing project using rodent models to assess the ability of digestion-resistant starch in the integration of these factors with the goal of furthering colon cancer prevention.
An experimental technique for measuring the unloaded Q of resonant antenna structures

The measurement technique places a resonant antenna structure; such as a patch or dielectric resonator antenna on a large reflecting plane. Two auxiliary antennas are employed in the measurement process. Antenna number 1 acts as a transmitting antenna and is oriented at an angle of approximately 45 degrees with respect to the x-y plane. Antenna number 2 acts as a receiving antenna and is oriented along the z-direction normal to the ground plane and is placed directly above the patch antenna. This orientation places it in a near minimum of the specular beam. Both antennas are properly polarized with respect to the desired radiation field of the patch antenna.
Layered video transmission over wireless multirate DS-CDMA links

In this paper, we consider the transmission of video over wireless direct-sequence code-division multiple access (DS-CDMA) channels. A layered (scalable) video source codec is used. The layers may be time-multiplexed and transmitted over a single CDMA channel or each layer can be transmitted over a different CDMA channel. For the latter case, spreading codes of different lengths are allowed for each CDMA channel (multirate CDMA). Thus, a different number of chips per bit can be used for the transmission of each scalable layer. For a given fixed energy value per chip and chip rate, the selection of a spreading code length affects the transmitted energy per bit and bit rate for each scalable layer. An MPEG-4 source encoder is used to provide a two-layer signal-to-noise-ratio scalable bit stream. Each of the two layers is channel-coded using rate-compatible punctured convolutional codes. Then, the data are interleaved, spread, carrier-modulated, and transmitted over the wireless channel. A multipath Rayleigh fading channel model is assumed. At the other end, the signal is collected by an antenna array front. After carrier demodulation, multiple-access-interference suppressing despreading is performed using adaptive space-time auxiliary-vector (AV) filters. The choice of the AV space-time receiver is dictated by realistic channel fading rates that limit the data record available for receiver adaptation and redesign. Our experimental results demonstrate the effectiveness of such a multirate DS-CDMA system for wireless video transmission.
Atmospheric transmittance measurements near 54 and 118 GHz

A zenith-scanning airborne imaging spectrometer, the Millimeter-wave Temperature Sounder (MTS), incorporating eight double-sideband channels centered around the 118.75-GHz oxygen resonance, was employed to measure atmospheric transmittances to space. Simultaneously, a zenith-viewing computer-controlled frequency-stepping spectrometer scanned roughly 3 GHz centered near 53.5 GHz. The observations were obtained continuously as a NASA ER-2 aircraft ascended to -20 km altitude and descended on multiple flights. Nearby radiosondes and air temperature and navigational data from the aircraft flight computer permit comparison of the radiometric data with theoretical transmittance expressions. Sensitivity of the measurements to aircraft altitude and attitude and to temperature and humidity profiles necessitates careful scrutiny of these data. The views of atmospheric radiance against the cosmic background provide sensitivity to conditions in the vicinity of the tropopause. Accurate calibration of the measurements through ascent and descent provides considerable challenges. >
The Rbf1, Hfl1 and Dbp4 of Candida albicans regulate common as well as transcription factor-specific mitochondrial and other cell activities

Our interest in Candida albicans mitochondria began with the identification of GOA1. We demonstrated its role in cell energy production, cross-talk among mitochondria and peroxisomes, non-glucose energy metabolism, maintenance of stationary phase growth, and prevention of premature apoptosis. Its absence results in avirulence. However, what regulated transcription of GOA1 was unknown. To identify transcriptional regulators (TRs) of GOA1, we screened a C. albicans TF knockout library (TRKO) and identified Rbf1p, Hfl1p, and Dpb4p as positive TRs of GOA1. The phenotypes of each mutant (reduced respiration, inability to grow on glycerol, reduced ETC CI and CIV activities) are reasonable evidence for their required roles especially in mitochondrial functions. While the integration of mitochondria with cell metabolic activities is presumed to occur, there is minimal information on this subject at the genome level. Therefore, microarray analysis was used to provide this information for each TR mutant. Transcriptional profiles of Rbf1p and Hfl1p are more similar than that of Dpn4p. Our data demonstrate common and also gene-specific regulatory functions for each TR. We establish their roles in carbon metabolism, stress adaptation, cell wall synthesis, transporter efflux, peroxisomal metabolism, phospholipid synthesis, rRNA processing, and nuclear/mtDNA replication. The TRs regulate a number of common genes but each also regulates specific gene transcription. These data for the first time create a genome roadmap that can be used to integrate mitochondria with other cell processes. Of interest, the TRs are fungal-specific, warranting consideration as antifungal drug targets.
Helium Atom Scattering from Graphene Grown on Rh(111)

Graphene growth on transition-metal surfaces leads to an ordered superlattice that appears as a series of hills and valleys in scanning tunneling microscopy. On Rh(111), the graphene forms an incommensurate epitaxial overlayer; the crystallographic axes of the graphene are closely aligned with the Rh(111) surface lattice vectors, but the Rh and graphene lattice constants are significantly different. Thus, the C atoms sit over different positions of the Rh(111) lattice and their height above the Rh(111) surface varies, but the different binding sites also affect the local electronic structure. Scanning tunneling microscopy is affected by both of these factors. He scattering is more a measure of the geometrical corrugation, the variation of the height of the graphene sheet relative to the Rh(111) surface. We compare the results of He diffraction measurements with those of previous scanning tunneling microscopy measurements to assess the relative geometric and electronic corrugations.
Crimean-Congo Hemorrhagic Fever Virus Glycoprotein Precursor Is Cleaved by Furin-Like and SKI-1 Proteases To Generate a Novel 38-Kilodalton Glycoprotein

Crimean-Congo hemorrhagic fever virus (genus Nairovirus, family Bunyaviridae) genome M segment encodes an unusually large (in comparison to members of other genera) polyprotein (1,684 amino acids in length) containing the two major structural glycoproteins, Gn and Gc, that are posttranslationally processed from precursors PreGn and PreGc by SKI-1 and SKI-1-like proteases, respectively. The characteristics of the N-terminal 519 amino acids located upstream of the mature Gn are unknown. A highly conserved furin/proprotein convertase (PC) cleavage site motif (RSKR247) is located between the variable N-terminal region that is predicted to have mucin-like properties and the rest of PreGn. Mutational analysis of the RSKR247 motif and use of a specific furin/PC inhibitor and brefeldin A demonstrate that furin/PC cleavage occurs at the RSKR247 motif of PreGn as the protein transits the trans Golgi network and generates a novel glycoprotein designated GP38. Immunoprecipitation analysis identified two additional proteins, GP85 and GP160, which contain both mucin and GP38 domain regions, and whose generation does not involve furin/PC cleavage. Consistent with glycosylation predictions, heavy O-linked glycosylation and moderate levels of N-glycans were detected in the GP85 and GP160 proteins, both of which contain the mucin domain. GP38, GP85, and GP160 are likely soluble proteins based on the lack of predicted transmembrane domains, their detection in virus-infected cell supernatants, and the apparent absence from virions. Analogy with soluble glycoproteins and mucin-like proteins encoded by other hemorrhagic fever-associated RNA viruses suggests these proteins could play an important role in viral pathogenesis.
Cohort Analysis of Patients With Localized, High-Risk, Extremity Soft Tissue Sarcoma Treated at Two Cancer Centers: Chemotherapy-Associated Outcomes

Purpose Patients with American Joint Committee on Cancer stage III soft tissue sarcoma (STS) have high risks of distant recurrence and death. The role of chemotherapy for these patients remains controversial despite several randomized trials and a meta-analysis. Methods We reviewed the treatments and outcomes of 674 consecutive adult patients presenting with primary stage III extremity STS between 1984 and 1999. Pre- or postoperative doxorubicin-based chemotherapy was used in a nonrandomized fashion in approximately half of this high-risk population. The objective of this review was to evaluate the impact of chemotherapy while accounting for known prognostic variables. Results Among 674 patients, 338 (50%) were treated with local therapy only, and 336 (50%) were treated with local therapy plus chemotherapy. The median follow-up for survivors was 6.1 years. Five-year local and distant recurrence-free interval probabilities were 83% and 56%, respectively, for the two groups combined. The 5-year disease-spec...
Metabolism of renal microvessels.

Abstract Metabolic profiles of renal arteriolar smooth muscle cells were constructed from semiquantitative histochemical analysis of biopsies from 20 mongrel dogs. Vessels ranging in outer wall diameter from 20 to 80 μm were analyzed for the presence and relative intensity of 14 enzymes and 3 substrates with attention being directed in particular to arteriolar smooth muscle cells. Enzymes representing glycolysis, the Krebs cycle, the hexose monophosphate shunt, lipid metabolism, the respiratory chain, and ATP hydrolysis were chosen. Glycogen, hydrophobic lipid, and free fatty acids were also studied. Renal arteriolar cells appear to be chiefly oxidative in their metabolism with a possible preference for free fatty acids as substrate. Anaerobic metabolism seems rather limited in these cells. Finally, arteriolar smooth muscle was found to be quite rich in myosin ATPase.
Guiding principles for collaborative research with 2-1-1.

ollaborations between 2-1-1 systems and aca- demic researchers should be based on a mutual dedication to helping populations in need, and will be most successful when they provide needed help to 2-1-1 callers, improve the 2-1-1 system's service to callers, and generate useful knowledge that is beneficial to both partners. Can a single collaboration do all that? It can, especially if it is designed that way. The researchers and 2-1-1 leaders involved with the projects reported in the papers in this supplement to the American Journal of Preventive Medicine 1-17 and elsewhere have faced some of the common challenges of research collaboration and emerged with successful research-service partnerships. This paper draws on their experiences as well as lessons from team science and participatory research to propose a set of guiding principles for conducting collaborative research with 2-1-1 systems. For decades, researchers have strived to build mutually beneficial partnerships with community organizations. This work has generated valuable new knowledge as well as recommendations and best practices for establishing and sustaining such partnerships. 18 -20 Developing re- search partnerships that integrate multiple disciplines, such as 2-1-1 and academic collaborations, requires that several processes be followed in the development phase. Hall et al., 21 in a model of transdisciplinary team-based research, identify some of these crucial processes as gen- erating a shared mission and goals, developing a critical awareness of the strengths and limitations that each part- ner brings to the team, defining the problem and creating a concrete representation of where each team member can contribute to the solution, and creating a psycholog- ically safe environment where partners are comfortable to share ideas and opinions openly in a mutually respect- ful discussion. When this environment is established, issues and challenges that arise during a partnership can be addressed in a constructive and productive manner, contributing to the success of the collaboration. Among partnerships applying these recommenda- tions, perhaps the most similar and relevant to the 2-1-1- academic collaborations described in this supplement is the Cancer Information Service Research Consortium (CISRC). The CISRC partnership joined the National Cancer Institute's Cancer Information Service (CIS)— like 2-1-1, a telephone information and referral system— and scientific investigators dedicated to cancer control research. The CISRC produced a laboratory for research advancing the field of health communication, which re- sulted in improvement in the reach, quality, and effec- tiveness of CIS service to its clients, as well as the publi- cation of five monographs compiling CISRC-based
PEPPeR, a Platform for Experimental Proteomic Pattern Recognition

Quantitative proteomics holds considerable promise for elucidation of basic biology and for clinical biomarker discovery. However, it has been difficult to fulfill this promise due to over-reliance on identification-based quantitative methods and problems associated with chromatographic separation reproducibility. Here we describe new algorithms termed "Landmark Matching" and "Peak Matching" that greatly reduce these problems. Landmark Matching performs time base-independent propagation of peptide identities onto accurate mass LC-MS features in a way that leverages historical data derived from disparate data acquisition strategies. Peak Matching builds upon Landmark Matching by recognizing identical molecular species across multiple LC-MS experiments in an identity-independent fashion by clustering. We have bundled these algorithms together with other algorithms, data acquisition strategies, and experimental designs to create a Platform for Experimental Proteomic Pattern Recognition (PEPPeR). These developments enable use of established statistical tools previously limited to microarray analysis for treatment of proteomics data. We demonstrate that the proposed platform can be calibrated across 2.5 orders of magnitude and can perform robust quantification of ratios in both simple and complex mixtures with good precision and error characteristics across multiple sample preparations. We also demonstrate de novo marker discovery based on statistical significance of unidentified accurate mass components that changed between two mixtures. These markers were subsequently identified by accurate mass-driven MS/MS acquisition and demonstrated to be contaminant proteins associated with known proteins whose concentrations were designed to change between the two mixtures. These results have provided a real world validation of the platform for marker discovery.
The self-employment experience of immigrants: evidence from the US General Social Survey, 1977–2004

This paper uses biennial data from the General Social Survey (GSS) to reexamine the self-employment experience of immigrants over the 1977–2004, yielding a database of 25 individual years with over 36,000 observations. The regression results suggest that the conditional probability of self-employment is higher among immigrants, though there is evidence that it has fallen, and then rebounded, over time. Self-employment is also significantly related to age, educational attainment, race, marital status, occupation, industry of employment and family background. However, these are generally less important in explaining self-employment among immigrants. Some variables such as marital status or homeownership (a proxy for access to capital) are associated with native self-employment, but not migrant self-employment. We look at ‘latent entrepreneurship’ and find no evidence that preferences for self-employment vary by immigrant status. Taking everything together, we speculate that immigrants may be self-selected into self-employment, independent of their individual characteristics and stated preferences.
Symmetries of three harmonically trapped particles in one dimension

We present a method for solving few-body problems for trapped particles and apply it to three equal-mass particles in a one-dimensional harmonic trap, interacting via a contact potential. By expressing the relative Hamiltonian in Jacobi cylindrical coordinates, i.e., the two-dimensional version of three-body hyperspherical coordinates, we discover an underlying ${C}_{6v}$ symmetry. This symmetry simplifies the calculation of energy eigenstates of the full Hamiltonian in a truncated Hilbert space constructed from the trap Hamiltonian eigenstates. Particle superselection rules are implemented by choosing the relevant representations of ${C}_{6v}$. We find that the one-dimensional system shows nearly the full richness of the three-dimensional system, and can be used to understand separability and reducibility in this system and in standard few-body approximation techniques.
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.
Asymmetric Localization of CK2α During Xenopus Oogenesis.

The establishment of the dorso-ventral axis is a fundamental process that occurs after fertilization. Dorsal axis specification in frogs starts immediately after fertilization, and depends upon activation of Wnt/β-catenin signaling. The protein kinase CK2α can modulate Wnt/β-catenin signaling and is necessary for dorsal axis specification in Xenopus laevis. Our previous experiments show that CK2α transcripts and protein are animally localized in embryos, overlapping the region where Wnt/β-catenin signaling is activated. Here we determined whether the animal localization of CK2α in the embryo is preceded by its localization in the oocyte. We found that CK2α transcripts were detected from stage I, their levels increased during oogenesis, and were animally localized as early as stage III. CK2α transcripts were translated during oogenesis and CK2α protein was localized to the animal hemisphere of stage VI oocytes. We cloned the CK2α 3’UTR and showed that the 2.8 kb CK2α transcript containing the 3’UTR was enriched during oogenesis. By injecting ectopic mRNAs, we demonstrated that both the coding and 3’UTR regions were necessary for proper CK2α transcript localization. This is the first report showing the involvement of coding and 3’UTR regions in animal transcript localization. Our findings demonstrate the pre-localization of CK2α transcript and thus, CK2α protein, in the oocyte. This may help restrict CK2α expression in preparation for dorsal axis specification.
Using Efficiency Tests to Reduce Revisions in Panel Data: The Case of Wage and Salary Estimates for U.S. States

This paper studies the preliminary estimates of state wage and salary growth produced by the U.S. Bureau of Economic Analysis (BEA), investigating whether they may be improved using basic efficiency tests. State wage and salary growth can be thought of as the sum of two components, an aggregate component equal to the currently prevailing national growth rate, and a state specific component, which we call the idiosyncratic variation in the estimates. BEA currently uses extrapolation techniques to compute the idiosyncratic component of the preliminary estimates, and this paper demonstrates some limitations to this approach. While revisions to BEA’s preliminary numbers are currently predictable, some simple regression-based generalizations of the extrapolation approach can reduce this predictability, cutting down mean squared and mean absolute revisions. While these reductions in revisions are not large, we can reject at conventional significance levels the hypothesis that they are equal to zero. ∗Bureau of Economic Analysis, 1441 L Street NW, Washington, DC 20230 (e-mail: jeremy.nalewaik@bea.gov). Thanks to Matthew Von Kerczek and Rob Brown for providing access to data, and to Rob Brown, Dennis Fixler, Bruce Grimm, Dave Lenze, and John Ruser for comments. The views expressed in this paper are soley those of the author and are not necessarily those of the U.S. Bureau of Economic Analysis or the U.S. Department of Commerce.
Going by Boat

In 1990, Binford argued that logistical mobility strategies… are the consequence of two major evolutionary changes that occurred long ago: (1) the “aquatic resource revolution” with its early occurrence primarily in higher latitudes. and (2) the perfection of transpon technologies, particularly water transport vessels and the use of pack and draft animals. (Binford 1990: 138)
Interpretation bias for uncertain threat: A replication and extension.

Background Intolerance of uncertainty (IU) has been proposed as an important transdiagnostic variable within various anxiety-related disorders. Research has suggested that individuals high in IU may interpret ambiguous information in a more threatening manner, suggesting a negative interpretation bias for uncertain information. However, interpretation biases within IU have not been adequately tested in the literature. Methods The current study evaluated negative interpretation biases for uncertain information by directly measuring an individual's interpretations of ambiguous information across two samples. Participants consisted of 76 (Study 1; 72.4% female) and 31 (Study 2; 81% female) undergraduate students. Results Results indicated that individuals high in IU interpret ambiguous scenarios as more threatening compared to negative and/or positive scenarios (β = .45, p = .02). In addition, individuals high in IU showed a negative interpretation bias for ambiguous information, but not benign information (Study 1: β = −.40, p < .001; Study 2: β = −.57, p = .002). Limitations Future research should attempt to replicate these findings within clinical populations. In addition, future work would benefit from the inclusion of behavioral assessments of IU. Conclusions These findings are the first to detect the presence of a negative interpretation bias for uncertain information among individuals high in IU utilizing a task designed to directly measure an individual's interpretation of information. Given the efficacy and low economic burden associated with interpretation bias modification protocols, and the transdiagnostic nature of IU, targeting IU within these protocols could have a tremendous public health impact.
Toward personalized pan-omic association analysis under complex structures and big data

Dr. Eric Xing is a Professor of Machine Learning in the School of Computer Science at Carnegie Mellon University, and Director of the CMU/UPMC Center for Machine Learning and Health. His principal research interests lie in the development of machine learning and statistical methodology, and large-scale computational system and architecture; especially for solving problems involving automated learning, reasoning, and decision-making in high-dimensional, multimodal, and dynamic possible worlds in artificial, biological, and social systems. Professor Xing received a Ph.D. in Molecular Biology from Rutgers University, and another Ph.D. in Computer Science from UC Berkeley. He servers (or served) as an associate editor of the Annals of Applied Statistics (AOAS), the Journal of American Statistical Association (JASA), the IEEE Transaction of Pattern Analysis and Machine Intelligence (PAMI), the PLoS Journal of Computational Biology, and an Action Editor of the Machine Learning Journal (MLJ), the Journal of Machine Learning Research (JMLR). He was a member of the DARPA Information Science and Technology (ISAT) Advisory Group, a recipient of the NSF Career Award, the Sloan Fellowship, the United States Air Force Young Investigator Award, and the IBM Open Collaborative Research Award. He was the Program Chair of ICML 2014.
Inorganic photochromic and cathodochromic recording materials

Discussion of studies at RCA Laboratories of the properties of rare-earth-doped CaF2, transition-metal-doped SrTiO3 and iron- or sulfur-doped sodalite as photochromic materials which change color during light or electron beam exposures. Particular attention is given to their photochromic characteristics in single-crystal and powder forms and to their cathodochromic properties in powder form. Details are given on the photochromic mechanisms, spectra, optical density, thermal decay rates, and coloring and bleaching efficiency of their single crystals and on the diffuse reflectance spectra, saturated photochromic contrast ratio, switching and erase sensitivities, and cathodochromic excitation of their photochromic powders. The many attractive characteristics of these materials when used in display storage systems are indicated.
Cyber-Attack Methods, Why They Work On Us, and What To Do

Basic cyber-attack methods are well documented, and even automated with user-friendly GUIs (Graphical User Interfaces). Entire suites of attack tools are legal, conveniently packaged, and freely downloadable to anyone; more polished versions are sold with vendor support. Our team ran some of these against a selected set of projects within our organization to understand what the attacks do so that we can design and validate defenses against them. Some existing defenses were effective against the attacks, some less so. On average, every machine had twelve easily identifiable vulnerabilities, two of them "critical". Roughly 5% of passwords in use were easily crack-able. We identified a clear set of recommendations for each project, and some common patterns that emerged among them all. Nomenclature
When the decision is what to decide: using evidence inventory reports to focus health technology assessments.

Objectives: Health systems frequently make decisions regarding acquisition and use of new technologies. It is desirable to base these decisions on clinical evidence, but often these technologies are used for multiple indications and evidence of effectiveness for one indication does not prove effectiveness for all. Here, we describe two examples of evidence inventory reports that were performed for the purposes of identifying how much and what type of published clinical evidence was available for a given technology, and the contexts in which those technologies were studied.Methods: The evidence inventory reports included literature searches for systematic reviews and health technology assessment (HTA) reports, and systematic searches of the primary literature intended to count and categorize published clinical studies. The reports did not include analysis of the primary literature.Results: The inventory reports were completed in 3 to 4 days each and were approximately ten pages in length, including references. Reports included tables listing the number of reported studies by specific indication for use, and whether or not there were randomized trials. Reports also summarized findings of existing systematic reviews and HTA reports, when available. Committees used the inventory reports to decide for which indications they wanted a full HTA report.Conclusions: Evidence inventory reports are a form of rapid HTA that can give decision makers a timely understanding of the available evidence upon which they can base a decision. They can help HTA providers focus subsequent reports on topics that will have the most influence on healthcare decision making.
An Iminium Salt Organocatalyst for Selective Aliphatic C–H Hydroxylation

The first examples of catalysis of aliphatic C–H hydroxylation by an iminium salt are presented. The method allows the selective organocatalytic hydroxylation of unactivated 3° C–H bonds at room temperature using hydrogen peroxide as the terminal oxidant. Hydroxylation of an unactivated 2° C–H bond is also demonstrated. Furthermore, improved functional group compatibility over other catalytic methods is reported in the form of selectivity for aliphatic C–H hydroxylation over alcohol oxidation. On the basis of initial mechanistic studies, an oxaziridinium species is proposed as the active oxidant.
The Emergence of the Levellers, 1647

The Levellers did not emerge as a separate political faction until October 1647. The previous six months saw the beginnings of a great climacteric of unsettlement in which the New Model Army and its Independent and sectarian allies unseated the dominant Presbyterian parliamentary faction. Historians often attribute the election of agitators in many regiments and the creation of a representative army General Council to the radical influence of a fully formed Leveller movement. However, the increasing disappointment and agitation of civilian and army radicals about the settlement proposals of the Independent leaders were really parallel developments. The Agreement of the People, which was brought to the General Council from London in late October, marked the clear development of a separate Leveller following.
Fern spores: evolutionary levels and ecological differentiation

The development of exospore relative to the perispore and type of aperture are used to assess evolutionary levels of spores in the major families of ferns. Spores of primitive families usually have trilete aperture and walls of thick exospore overlaid by a thin, conforming perispore; spores of derived families are largely monolete with thin exospore below a complex perispore. Spores at a specialized level have elaborate strata of either primitive or derived type.
4-Aminopyridine Reversal of Morphine Analgesia

Publisher Summary 4AP reversal of morphine analgesia has been assessed because while morphine sulfate (MS) inhibits the release of neurotransmitters involved with pain transmission, 4AP enhances calcium-dependent neurotransmitter release. 4AP has been used clinically to reverse nondepolarizing muscle relaxants and ketaminedlazepam anesthesia. The usefulness of 4AP in these circumstances may be because of an ability to block potassium conductance, create regenerative calcium current, and, thus, enhance neurotransmitter release. These events may also diminish morphine-induced analgesia. This chapter analyzes 4-aminopyridine (4AP) reversal of morphine analgesia. Analgesia was measured by tail flick and hot plate tests. It was found that 4AP did reverse MS analgesia. Analgesia reversal was not demonstrated by the hot plate latency (HPL) because the end point of the hot plate test was indicated by the animal's ability to lick or tap its hind paw. This behavior would require multisynaptic supraspinal function that was affected by the central excitatory action of 4AP. A clinical implication of these results is that while attempting to antagonize muscle relaxant or anesthetic effects in postoperative patients with 4AP, an incidental reversal of much needed narcotic analgesia may occur.
Self-assessment of team performance using T-NOTECHS in simulated pediatric trauma resuscitation is not consistent with expert assessment

Abstract Background The Trauma NOn-TECHnical Skills (T-NOTECHS) tool has been used to assess teamwork in trauma resuscitation, but its reliability and validity for self-assessment is unknown. Our purpose was to determine the reliability and validity of self-administered T-NOTECHS in pediatric trauma resuscitation. Methods Simulated in situ resuscitations were evaluated using T-NOTECHS in real time by experts and immediately afterwards by team members. Reliability was analyzed with linear-weighted kappa and intra-class correlation. T-NOTECHS scores were compared between expert (gold-standard) and self-assessment. Results Fifteen simulations were examined. T-NOTECHS scores were similar between self- and expert assessment for leadership. Self-assessment scores were higher than expert for the other domains and total composite score. Inter-rater reliability for total score was similar between the two groups, but differences were observed in the domains. Conclusions Self-assessment is not interchangeable with expert rating when using T-NOTECHS. Future studies need to determine how self-assessment can be best utilized. Level of evidence Studies of diagnostic accuracy – Level 2.
The relationship between visual field size and electroretinogram amplitude in retinitis pigmentosa.

PURPOSE To determine to what degree visual field size is correlated with electroretinogram (ERG) amplitude among patients with the common forms of retinitis pigmentosa (RP). METHODS Visual field equivalent diameter to the V4e white test light of the Goldmann perimeter was correlated with log ERG amplitude elicited by 0.5 Hz or 30 Hz full-field flashes of white light. Primary analyses were conducted on data from 583 patients with the common forms of RP. Subset analyses were performed on data from patients with ERG responses with different ranges of amplitude to assess to what extent the correlation depends on ERG amplitude, as well as on data from patients of a given genetic type to determine whether the correlation depends on the mode of transmission. Data from patients with the rhodopsin, Pro23His mutation (n = 38) or with the rhodopsin, Pro347Leu mutation (n = 24) were analyzed to determine the correlation between visual field size and ERG amplitude for patients with the same mutation. RESULTS Visual field size was significantly correlated with ERG amplitude for every comparison (P < or = 0.0003). Correlations generally were higher for ERGs elicited by 30 Hz flashes (r = 0.62 for the entire sample) than they were for those elicited by 0.5 Hz flashes (r = 0.53 for the entire sample). They were lower for truncated ranges of ERG amplitude, higher for patients with dominant or recessive disease than for patients with x-linked disease or for patients of all genetic types combined, and strong for patients with the same rhodopsin mutation (reaching a value of 0.87). CONCLUSIONS Visual field size is significantly correlated with ERG amplitude for patients with RP. Correlation depends on the range of ERG amplitudes, the inheritance type, and, particularly, on whether the analysis is confined to a single gene mutation.