cssi/SciSciGPT-SciSciNet huggingface dataset:
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.

Background: The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs). It is becoming increasingly apparent that many of these repetitive DNA sequence elements encode gene regulatory functions. This fact has important evolutionary implications, since repetitive DNA is the most dynamic part of the genome. We set out to assess the evolutionary rate and pattern of experimentally characterized human transcription factor binding sites (TFBS) that are derived from repetitive versus non-repetitive DNA to test whether repeat-derived TFBS are in fact rapidly evolving. We also evaluated the position-specific patterns of variation among TFBS to look for signs of functional constraint on TFBS derived from repetitive and non-repetitive DNA. Results: We found numerous experimentally characterized TFBS in the human genome, 7–10% of all mapped sites, which are derived from repetitive DNA sequences including simple sequence repeats (SSRs) and TEs. TE-derived TFBS sequences are far less conserved between species than TFBS derived from SSRs and non-repetitive DNA. Despite their rapid evolution, several lines of evidence indicate that TE-derived TFBS are functionally constrained. First of all, ancient TE families, such as MIR and L2, are enriched for TFBS relative to younger families like Alu and L1. Secondly, functionally important positions in TE-derived TFBS, specifically those residues thought to physically interact with their cognate protein binding factors (TF), are more evolutionarily conserved than adjacent TFBS positions. Finally, TE-derived TFBS show position-specific patterns of sequence variation that are highly distinct from random patterns and similar to the variation seen for non-repeat derived sequences of the same TFBS. Conclusion: The abundance of experimentally characterized human TFBS that are derived from repetitive DNA speaks to the substantial regulatory effects that this class of sequence has on the human genome. The unique evolutionary properties of repeat-derived TFBS are perhaps even more intriguing. TE-derived TFBS in particular, while clearly functionally constrained, evolve extremely rapidly relative to non-repeat derived sites. Such rapidly evolving TFBS are likely to confer species-specific regulatory phenotypes, i.e. divergent expression patterns, on the human evolutionary lineage. This result has practical implications with respect to the widespread use of evolutionary conservation as a surrogate for functionally relevant non-coding DNA. Most TE-derived TFBS would be missed using the kinds of sequence conservation-based screens, such as phylogenetic footprinting, that are used to help characterize non-coding DNA. Thus, the very TFBS that are most likely to yield human-specific characteristics will be neglected by the comparative genomic techniques that are currently de rigeur for the identification of novel regulatory sites.
Fast Camera Imaging of Hall Thruster Ignition

Hall thrusters provide efficient space propulsion by electrostatic acceleration of ions. Rotating electron clouds in the thruster overcome the space charge limitations of other methods. Images of the thruster start-up, taken with a fast camera, reveal a bright ionization period which settles into steady-state operation over 50 μs. The cathode introduces azimuthal asymmetry, which persists for about 30 μs into the ignition.
c-Kit Expression and Mutations in Phyllodes Tumors of the Breast

Background: Phyllodes tumors (PTs) represent uncommon fibroepithelial lesions of the breast that express c-Kit and platelet-derived growth factor receptor-alpha, similar to gastrointestinal stromal tumors (GISTs). 'Activating' mutations in these genes underlie responsiveness of GISTs to imatinib. Standard treatment for breast PTs is wide local excision, with no role for targeted therapies. Patients and Methods: c-Kit (CD117) expression was investigated by immunohistochemistry in 17 cases of breast PTs. Fourteen of these cases were also subjected to KIT mutation analysis by dideoxynucleotide sequencing. Results: Five out of 17 (29%) tumors showed weak stromal staining for CD117. No previously described 'activating' mutations were found in exons 9, 11, 13, or 17 of the KIT gene. A silent germline point mutation was found in exon 17 of one case. Conclusion: These data do not suggest a pathogenetic role for KIT in breast PTs. Inhibition of c-Kit signaling is unlikely to be helpful in this condition. Phyllodes tumors of the breast are uncommon fibroepithelial neoplasms that account for 0.3 to 1.5% of primary breast tumors (1). The typical patient is a middle-aged woman, and the
A Friend virus mutant that overcomes Fv-2rr host resistance encodes a small glycoprotein that dimerizes, is processed to cell surfaces, and specifically activates erythropoietin receptors.

The env gene of Friend spleen focus-forming virus (SFFV) encodes a membrane glycoprotein (gp55) that is inefficiently (3 to 5%) processed from the rough endoplasmic reticulum to form a larger dimeric plasma membrane derivative (gp55p). Moreover, the SFFV env glycoprotein associates with erythropoietin receptors (EpoR) to cause proliferation of infected erythroblasts [J.-P. Li, A. D. D'Andrea, H. F. Lodish, and D. Baltimore, Nature (London) 343:762-764, 1990]. Interestingly, the mitogenic effect of SFFV is blocked in mice homozygous for the Fv-2r resistance gene, but mutant SFFVs can overcome this resistance. Recent evidence suggested that these mutants contain partial env deletions that truncate the membrane-proximal extracellular domain of the encoded glycoproteins (M. H. Majumdar, C.-L. Cho, M. T. Fox, K. L. Eckner, S. Kozak, D. Kabat, and R. W. Geib, J. Virol. 66:3652-3660, 1992). Mutant BB6, which encodes a gp42 glycoprotein that has a large deletion in this domain, causes erythroblastosis in DBA/2 (Fv-2s) as well as in congenic D2.R (Fv-2r) mice. Analogous to gp55, gp42 is processed inefficiently as a disulfide-bonded dimer to form cell surface gp42p. Retroviral vectors with SFFV and BB6 env genes have no effect on interleukin 3-dependent BaF3 hematopoietic cells, but they cause growth factor independency of BaF3/EpoR cells, a derivative that contains recombinant EpoR. After binding 125I-Epo to surface EpoR on these factor-independent cells and adding the covalent cross-linking reagent disuccinimidyl suberate, complexes that had immunological properties and sizes demonstrating that they consisted of 125I-Epo-gp55p and 125I-Epo-gp42p were isolated from cell lysates. Contrary to a previous report, SFFV or BB6 env glycoproteins did not promiscuously activate other members of the EpoR superfamily. Although the related env glycoproteins encoded by dualtropic murine leukemia viruses formed detectable complexes with EpoR, strong mitogenic signalling did not ensue. Our results indicate that the SFFV and BB6 env glycoproteins specifically activate EpoR; they help to define the glycoprotein properties important for its functions; and they strongly suggest that the Fv-2 leukemia control gene encodes an EpoR-associated regulatory factor.
Mercury Release from FGD

Abstract The release of mercury from flue gas desulfurization (FGD) gypsum in the manufacture of 100% FGD wallboard was studied. Calcination, with product temperatures ranging from 150 to 180 °C, appears to be the most likely process to release mercury from the FGD. Two samples evaluated in trials conducted to simulate the calcining of FGD in flash calcining and kettle processes showed that the potential of mercury release exists. The differing amounts of mercury released by the two processes could be separated by orders of magnitude. Measurements in real production facilities are essential to developing a valid answer to the question of mercury release during FGD gypsum wallboard production.
Prevention of cyclosporine-induced nephrotoxicity with pentoxifylline.

Although cyclosporine (CSA) is established in the prevention of allograft rejection, its use has been associated with dose-limiting toxicities, most notably to the kidney and liver. To date, the pathogenesis of the acute form of nephrotoxicity is unclear but may be related to inhibition of vasodilatory prostagiandins resulting in vasoconstriction and ischemia. The present study investigated the coadministration of CSA with a unique hemorheologic agent, pentoxifylline (PTX), in the marine model. A total of 48 rats were orally dosed with CSA 25 mg/kgfor 10 days with either PTX 45 mg/kg i.p. or saline every 12 hr. Posttreatment renal function, assessed by creatinine (CCR) and inulin (CIN) clearances and renal electrolyte handling, was compared with baseline data and between groups. In an attempt to assess prostaglandin-mediated changes in enteral absorption, oral CSA pharmacokinetics with and without PTX were compared to the pharmacokinetics of similar groups (N = 8) administered i. v. CSA. Mean CIN of rats ...
ROMAN MOSAIC GLASS : A STUDY OF PRODUCTION PROCESSES, USING PIXE SPECTROMETRY

The most attractive Roman glass produced during the early part of the 1st century A.D. was mosaic ware ‐ bowls and dishes molded from arrays of multi-colored canes that created abstract floral and geometric designs. Yet ancient literature tells us little about the organization of the glassworking industry in which such wares were produced. We have focused upon two kinds of mosaic decoration that include a component of white glass in their cane construction and have purple glass as their matrix. A consistent pattern in the minor levels of lead in each kind of glass suggests that they were the products of two separate workshops, each with separate sources of supply for their glass stock. ” 1999 Elsevier Science B.V. All rights reserved.
View-Dependent Streamlines for 3D Vector Fields

This paper introduces a new streamline placement and selection algorithm for 3D vector fields. Instead of considering the problem as a simple feature search in data space, we base our work on the observation that most streamline fields generate a lot of self-occlusion which prevents proper visualization. In order to avoid this issue, we approach the problem in a view-dependent fashion and dynamically determine a set of streamlines which contributes to data understanding without cluttering the view. Since our technique couples flow characteristic criteria and view-dependent streamline selection we are able achieve the best of both worlds: relevant flow description and intelligible, uncluttered pictures. We detail an efficient GPU implementation of our algorithm, show comprehensive visual results on multiple datasets and compare our method with existing flow depiction techniques. Our results show that our technique greatly improves the readability of streamline visualizations on different datasets without requiring user intervention.
Spatial clustering of non-transported cardiac decedents: the results of a point pattern analysis and an inquiry into social environmental correlates.

Background People who die from heart disease at home before any attempt at transport has been made may represent missed opportunities for life-saving medical intervention. In this study, we undertook a point-pattern spatial analysis of heart disease deaths occurring before transport in a large metropolitan area to determine whether there was spatial clustering of non-transported decedents and whether there were significant differences between the clusters of non-transported cardiac decedents and the clusters of transported cardiac decedents in terms of average travel distances to nearest hospital and area socioeconomic characteristics. These analyses were adjusted for individual predictors of transport status.
Proton bremsstrahlung and its radiation effects in fusion reactors

Abstract Protons and neutrons are emitted in many fusion processes of light nuclei. In a fusion reactor, a proton and a neutron thus generated may again fuse with each other. Or they can in turn fuse with or be captured by an un-reacted nuclear fuel, for example deuterium. The average center-of-mass energy for such reaction is around 10 keV in a typical fusion reactor. At this low energy, the reacting nucleons are in an s-wave state in terms of their relative angular momentum. The single-gamma radiation process is thus strongly suppressed due to conservation laws. Instead the gamma ray released is likely to be accompanied by soft X-ray photons from a nuclear bremsstrahlung process. The generated soft X-ray has a continuous spectrum and peaks around a few hundred eV to a few keV. The average photon energy and spectrum properties of such a process are calculated with a semi-classical approach, with the explicit example of proton–neutron capture. This phenomenon may have been observed in some prior tokamak discharge experiments, and its interpretation is complicated by the presence of electron bremsstrahlung. However, it also opens up the possibility of new plasma diagnostics which are more sensitive to the ionic or nuclear degree of freedom.
The Saccharomyces cerevisiae Sgs1 helicase efficiently unwinds G-G paired DNAs

The Saccharomyces cerevisiae Sgs1p helicase localizes to the nucleolus and is required to maintain the integrity of the rDNA repeats. Sgs1p is a member of the RecQ DNA helicase family, which also includes Schizo-saccharomyces pombe Rqh1, and the human BLM and WRN genes. These genes encode proteins which are essential to maintenance of genomic integrity and which share a highly conserved helicase domain. Here we show that recombinant Sgs1p helicase efficiently unwinds guanine-guanine (G-G) paired DNA. Unwinding of G-G paired DNA is ATP- and Mg2+-dependent and requires a short 3' single-stranded tail. Strikingly, Sgs1p unwinds G-G paired substrates more efficiently than duplex DNAs, as measured either in direct assays or by competition experiments. Sgs1p efficiently unwinds G-G paired telomeric sequences, suggesting that one function of Sgs1p may be to prevent telomere-telomere interactions which can lead to chromosome non-disjunction. The rDNA is G-rich and has considerable potential for G-G pairing. Diminished ability to unwind G-G paired regions may also explain the deleterious effect of mutation of Sgs1 on rDNA stability, and the accelerated aging characteristic of yeast strains that lack Sgs1 as well as humans deficient in the related WRN helicase.
Microporous membranes of isotactic poly(4‐methyl‐1‐pentene) from a melt‐extrusion process. II. Effects of thermal annealing and stretching on porosity

A two-part study utilizing isotactic poly(4-methyl-1-pentene) (PMP) was undertaken to investigate a three-stage process (melt-extrusion/annealing/uniaxial stretching) (MEAUS) utilized to produce microporous films. In this report, the thermal-annealing (second stage) and subsequent uniaxial-stretching (third stage) results of selected PMP films from three resins, labeled A, B, and C, are discussed. From sequential analysis of the effect each stage had on the resulting microporosity, it was discovered that the melt-extruded precursor morphology and orientation, as a consequence of the first-stage extrusion parameters and resin characteristics, were crucial to controlling the membrane permeability. The annealing parameters were also critical, where a temperature of 205°C applied for 20 min under no tension was the optimum annealing condition for producing highly microporous PMP films upon stretching. For the conditions studied, the stretching parameters that were found to be the optimum for producing the desired characteristics in the final film were cold- and hot-stretch temperatures of 70 and 180°C, respectively. The cold- and hot-stretch extension levels concluded to be the best were a cold-stretch extension of 80%, followed by hot stretching to 90%, and, thus, a total overall extension level of 170% for the processing window studied. However, these results were only with respect to resin A films, while resin B and C samples could not be produced into microporous films via the MEAUS process. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 1076–1100, 2002; DOI 10.1002/app.10395
Human Robot Interaction using Face Pose Recognition

Face pose-based robot control plays an important role in natural human-robot interaction. In this paper, we propose a robust face pose estimation method based on manifold learning to control the wheeled robot. We represent each pose of a person's face as a connected low-dimensional appearance manifolds which are approximated by affine plane. Pose recognition task is to find sub-pose by computing the minimal distance from the given face image to sub-pose manifold. Based on the pose recognition result, the robot is controlled. Initial experiments are promising.
Polyribosome Profiles and Polyribosome-Associated RNA of Friend Leukaemia Cells Following DMSO-induced Differentiation

Differentiation along erythroid lines is greatly increased when Friend leukaemia cells (FLC) are grown in the presence of dimethylsulfoxide (DMSO). Maturation is accompanied by alterations in the polyribosome profiles of the DMSO-treated cells as compared to that of control cells grown for the same periods of time. The ribosomes of the differentiating cells are present primarily as trimers, tetramers and pentamers, with a low proportion of larger polysomes. Polyribosomes consisting of more than five ribosomes are much more common in the control untreated FLC. Agarose-acrylamide gel electrophoresis of radioactive uridine-labelled polysome-associated RNA from control and DMSO-treated cells demonstrates 4, 5, 5.5, 7, 9, 18 and 28S RNA species, as well as a series of RNAs which range from approximately 10S to 18S. The 5, 5.5, 18 and 28S RNAs have been tentatively identified as ribosomal RNAs, and the 4S and 7S RNAs may be transfer RNA and viral RNA respectively. The 9S RNA is probably the mRNA for histone, since its synthesis is inhibited in cells incubated with hydroxyurea. RNA which co-electrophoreses with the presumptive globin mRNA has been identified both in control, and in DMSO-treated cells. Although alterations in polyribosome patterns of DMSO-treated cells, as compared to control cells, have been readily demonstrable, no differences in the polyribosome-associated RNAs have been detected so far.
Sections of Toeplitz and Hilbert Forms

In this chapter we will discuss the spectral theory of Toeplitz integral operators and matrices, and applications of this theory to sections of the classical inequalities. We begin with integral equations of Toeplitz type, i.e., $$\lambda \phi (x) = \int\limits_{{ - A}}^{A} {\varrho (x - y)\phi (y)dy}$$ (2.1) .
Reexamining the Phosphorus–Protein Dilemma: Does Phosphorus Restriction Compromise Protein Status?

Dietary phosphorus restriction is recommended to help control hyperphosphatemia in hemodialysis patients, but many high-phosphorus foods are important sources of protein. In this review, we examine whether restricting dietary phosphorus compromises protein status in hemodialysis patients. Although dietary phosphorus and protein are highly correlated, phosphorus intakes can range up to 600 mg/day for a given energy and protein intake level. Furthermore, the collinearity of phosphorus and protein may be biased because the phosphorus burden of food depends on: (1) the presence of phosphate additives, (2) food preparation method, and (3) bioavailability of phosphorus, which are often unaccounted for in nutrition assessments. Ultimately, we argue that clinically relevant reductions in phosphorus intake can be made without limiting protein intake by avoiding phosphate additives in processed foods, using wet cooking methods such as boiling, and if needed, substituting high-phosphorus foods for nutritionally equivalent foods that are lower in bioavailable phosphorus.
Online Item Calibration for Q-Matrix in CD-CAT:

Item replenishment is important for maintaining a large-scale item bank. In this article, the authors consider calibrating new items based on pre-calibrated operational items under the deterministi...
Industry Evolution Revisited: The Role of Categories in Emerging Market Spaces

This panel symposium brings together a set of prominent scholars to discuss recent theoretical developments at the intersection of industry evolution and categorical dynamics. Technology scholars have long studied industry evolution and technological designs. More recently, organizational theorists have begun to explore the role of categories in industry dynamics. Yet, we do not fully understand how industry evolution and categorical dynamics are interrelated. Indeed, these literatures have evolved largely separate. This panel symposium tries to integrate these two theoretical streams by raising new theoretical questions such as: How and when does a “dominant category” emerge in an industry’s evolution? How does the relational structure of categories help shape industry evolution? What are the implications of defining the categories in an emerging market competitively as collections of organizations versus cognitively with an abstract language? How do categories interplay with functional attributes during...
Effect of testosterone on the involution of male rats' mammary glands.

SummaryAdult male rats were gonadec-tomized for 20 days. The mean DNA of their mammary glands was 3.59 ± 0.27 mg/100 g BW. Similar rats were injected for 20 days with 2 mg EB + 6 mg P/day. The mean...
Criegee intermediate reaction with CO: mechanism, barriers, conformer-dependence, and implications for ozonolysis chemistry.

Density functional theory and transition state theory rate constant calculations have been performed to gain insight into the bimolecular reaction of the Criegee intermediate (CI) with carbon monoxide (CO) that is proposed to be important in both atmospheric and industrial chemistry. A new mechanism is suggested in which the CI acts as an oxidant by transferring an oxygen atom to the CO, resulting in the formation of a carbonyl compound (aldehyde or ketone depending upon the CI) and carbon dioxide. Fourteen different CIs, including ones resulting from biogenic ozonolysis, are considered. Consistent with previous reports for other CI bimolecular reactions, the anti conformers are found to react faster than the syn conformers. However, this can be attributed to steric effects and not hyperconjugation as generally invoked. The oxidation reaction is slow, with barrier heights between 6.3 and 14.7 kcal/mol and estimated reaction rate constants 6–12 orders-of-magnitude smaller than previously reported literatur...
Reduced tonic inhibition in the dentate gyrus contributes to chronic stress‐induced impairments in learning and memory

It is well established that stress impacts the underlying processes of learning and memory. The effects of stress on memory are thought to involve, at least in part, effects on the hippocampus, which is particularly vulnerable to stress. Chronic stress induces hippocampal alterations, including but not limited to dendritic atrophy and decreased neurogenesis, which are thought to contribute to chronic stress-induced hippocampal dysfunction and deficits in learning and memory. Changes in synaptic transmission, including changes in GABAergic inhibition, have been documented following chronic stress. Recently, our laboratory demonstrated shifts in EGABA in CA1 pyramidal neurons following chronic stress, compromising GABAergic transmission and increasing excitability of these neurons. Interestingly, here we demonstrate that these alterations are unique to CA1 pyramidal neurons, since we do not observe shifts in EGABA following chronic stress in dentate gyrus granule cells. Following chronic stress, there is a decrease in the expression of the GABAA receptor (GABAA R) δ subunit and tonic GABAergic inhibition in dentate gyrus granule cells, whereas there is an increase in the phasic component of GABAergic inhibition, evident by an increase in the peak amplitude of spontaneous inhibitory postsynaptic currents (sIPSCs). Given the numerous changes observed in the hippocampus following stress, it is difficult to pinpoint the pertinent contributing pathophysiological factors. Here we directly assess the impact of a reduction in tonic GABAergic inhibition of dentate gyrus granule cells on learning and memory using a mouse model with a decrease in GABAA R δ subunit expression specifically in dentate gyrus granule cells (Gabrd/Pomc mice). Reduced GABAA R δ subunit expression and function in dentate gyrus granule cells is sufficient to induce deficits in learning and memory. Collectively, these findings suggest that the reduction in GABAA R δ subunit-mediated tonic inhibition in dentate gyrus granule cells contributes, at least in part, to deficits in learning and memory associated with chronic stress. These findings have significant implications regarding the pathophysiological mechanisms underlying impairments in learning and memory associated with stress and suggest a role for GABAA R δ subunit containing receptors in dentate gyrus granule cells. © 2016 Wiley Periodicals, Inc.
ORTHO: An APL Program for Measuring Predictor Variable Importance

This program is designed to compute and contrast four measures of predictor variable importance.
Whole Exome Sequencing, Familial Genomic Triangulation, and Systems Biology Converge to Identify a Novel Nonsense Mutation in TAB2‐encoded TGF‐beta Activated Kinase 1 in a Child with Polyvalvular Syndrome

Objective To use whole exome sequencing (WES) of a family trio to identify a genetic cause for polyvalvular syndrome. Methods and Results A male child was born with mild pulmonary valve stenosis and mild aortic root dilatation, and an atrial septal defect, ventricular septal defect, and patent ductus arteriosus that were closed surgically. Subsequently, the phenotype of polyvalvular syndrome with involvement of both semilunar and both atrioventricular valves emerged. His family history was negative for congenital heart disease. Because of hypotonia, myopia, soft pale skin, joint hypermobility, and mild facial dysmorphism, either Noonan syndrome- or William syndrome-spectrum disorders were suspected clinically. However, chromosomal analysis was normal and commercially available Noonan syndrome and William syndrome genetic tests were negative. Whole exome sequencing of the patient and both parents was performed. Variants were analyzed by sporadic and autosomal recessive inheritance models. A sporadic mutation, annotated as c.1491 T > A, in TAB2, resulting in a nonsense mutation, p.Y497X, in the TAB2-encoded TGF-beta activated kinase 1 (TAK1) was identified as the most likely disease-susceptibility gene. This mutation results in elimination of the terminal 197 amino acids, including the C-terminal binding motif critical for interactions with TRAF6 and TAK1. Conclusions The combination of WES, genomic triangulation, and systems biology has uncovered perturbations in TGF-beta activated kinase 1 signaling as a novel pathogenic substrate for polyvalvular syndrome.
High-speed GaAs PIN photodiodes grown on Si substrates by molecular beam epitaxy

The potential integration of the optoelectronic capabilities of GaAs with the highly developed integrated circuit technology of Si has motivated a great deal of effort toward fabricating GaAs devices—particularly lasers—in epitaxial layers grown on Si substrates. A GaAs-on-Si detector can take advantage of the high carrier mobilities and optical absorption coefficient of GaAs and serve as a high-speed receiver in a composite GaAs/Si optoelectronic circuit.
Learning an integrated hybrid image retrieval system

Current Web image search engines, such as Google or Bing Images, adopt a hybrid search approach in which a text-based query (e.g. “apple”) is used to retrieve a set of relevant images, which are then refined by the user (e.g. by re-ranking the retrieved images based on similarity to a selected example). This approach makes it possible to use both text information (e.g. the initial query) and image features (e.g. as part of the refinement stage) to identify images which are relevant to the user. One limitation of these current systems is that text and image features are treated as independent components and are often used in a decoupled manner. This work proposes to develop an integrated hybrid search method which leverages the synergies between text and image features. Recently, there has been tremendous progress in the computer vision community in learning models of visual concepts from collections of example images. While impressive performance has been achieved on standardized data sets, scaling these methods so that they are capable of working at web scale remains a significant challenge. This work will develop approaches to visual modelling that can be scaled to address the task of retrieving billions of images on the Web. Specifically, we propose to address two research issues related to integrated text- and image-based retrieval. First, we will explore whether models of visual concepts which are learned from collections of web images can be utilized to improve the image ranking associated with a text-based query. Second, we will investigate the hypothesis that the click-patterns associated with standard web image search engines can be utilized to learn query-specific image similarity measures that support improved query-refinement performance. We will evaluate our research by constructing a prototype integrated hybrid retrieval system based on the data from 300K real-world image queries. We will conduct user-studies to evaluate the effectiveness of our learned similarity measures and quantify the benefit of our method in real world search tasks such as target search.
Probability of emergence of novel temperature regimes at different levels of cumulative carbon emissions

The United Nations Paris Agreement creates new urgency and importance for understanding the emergence of climate impacts at different levels of cumulative carbon emissions. Using observations and climate models, we quantify the probability that different areas of the globe will experience permanent separation from the historical temperature regime, as a function of both time and cumulative emissions. We find that, in addition to a ~50% probability that global warming will exceed 2°C, cumulative emissions of 1000 gigatons of carbon (GtC) are likely to cause large areas of the tropics to transition to a new climate regime in which the annual temperature is never less than four standard deviations above the baseline mean. Although limiting cumulative emissions to 750 GtC substantially reduces these risks, the likelihood that some regions will still permanently experience extremely high annual temperatures suggests a critical role for adaptation, even if the Paris Agreement's mitigation targets are met.
Characterization of coherent receiver using polarization-multiplexed source generated from coherent transmitter

Intradyne coherent receiver (ICR) is an essential component for modern coherent systems. Critical parameters of ICR include frequency response, bandwidth, and gain imbalance. Conventionally one creates heterodyne beating between tunable laser source (TLS) and local oscillator, and sweeps frequency of TLS to measure those parameters. A complicated control loop aligns state of polarization (SoP) of TLS to 45/135 degree of principle axis of polarization beam splitter. Otherwise unequal amount of power will launch into two polarizations, leading to inaccurate result. To overcome this complexity, we present a novel scheme to characterize ICR using polarization-multiplexed laser source generated using internal components of coherent transmitter. The optical signals on two polarizations are modulated with sinusoidal signal at different frequencies. If frequency difference is larger than laser line width, the output at the coherent transmitter is a polarization-multiplexed laser source. This method allows on-board measurement of analog front-end of coherent receiver by connecting coherent transmitter with coherent receiver. Influence of automatic bias control and radio frequency amplifier is also discussed. Another method is to combine outputs of two separate TLSs with orthogonal polarization through a polarization beam combiner. Both methods lead to robust performance without active control of SoP. The measurement accuracy using polarization-multiplexed laser source is the same as that of the conventional method. The intrinsic resiliency to polarization change leads to simple setup and enables in-field characterization of ICR.
16 – DEMAND AND CONSUMER CHOICE

Publisher Summary This chapter presents fare rise in public buses in an attempt to describe demand and consumer choice. It reviews a case study that illustrates that public buses lost one eighth of their passengers—far more than the subways—during the first full month of the new 50-cent fare compared with the same period in 1974, the Metropolitan Transportation Authority disclosed. Bus ridership declined 12.7% to 46.2 million from 53 million, an average daily loss of 225,000 riders. There was no official explanation of the falloff in bus ridership. Unofficially, however, M.T.A. people noted that there is a greater element of discretion in whether to take the bus. The bus passenger usually takes a much shorter ride than the subway rider takes and may elect to walk in good weather. Another theory was that subway ridership, after a steady decline for years, had almost bottomed out and most riders were using it to go to work or because they had to. On the other hand, increase in the transit fare from 35 to 50 cents produced a 33.5% gain in subway revenue.
The Effect of High-Voltage Atmospheric Cold Plasma Treatment on the Shelf-Life of Distillers Wet Grains

There are currently limitations to storing and feeding distillers wet grains (DWG) due to their potential for spoilage and mycotoxin contamination in storage. In this study, in-package treatments of DWG using high-voltage atmospheric cold plasma (HVACP) treatment and storage in modified atmosphere with carbon dioxide were investigated with the primary purpose of increasing product shelf-life. The conditions investigated were (1) HVACP treatment and modified atmosphere packaging (MAP) storage, (2) carbon dioxide-modified atmosphere storage, and (3) HVACP treatment and carbon dioxide-modified atmosphere storage, compared with a control sample with no treatment under MAP storage. Treated samples and controls were stored for 0, 7, 14, 21, and 28 days at 10 and 25 °C, after which treated samples were evaluated for their efficacy to control mold growth indicated by pH, microbial count (CFU/g)/log reduction, and peroxide (H2O2) level. There was a significant difference among the treatments indicated by CFU/g (P 60% moisture), DWG for up to 28 days of storage at 10 and 25 °C. Both HVACP and the combination treatment showed high peroxide levels (100 mg/L) after treatment, which degraded in storage over time. It is thought that a better strategy for the combination treatment would be to treat substrate using HVACP with MAP having a high O2 concentration (65%) and store samples post-treatment in-package in a high CO2 environment.
Measurements of atmospheric ethene by solar absorption FTIR spectrometry

Abstract. Atmospheric ethene (C 2 H 4 ; ethylene) amounts have been retrieved from high-resolution solar absorption spectra measured by the Jet Propulsion Laboratory (JPL) MkIV interferometer. Data recorded from 1985 to 2016 from a dozen ground-based sites have been analyzed, mostly between 30 and 67 ∘ N. At clean-air sites such as Alaska, Sweden, New Mexico, or the mountains of California, the ethene columns were always less than 1 × 10 15 molec cm −2 and therefore undetectable. In urban sites such as JPL, California, ethene was measurable with column amounts of 20 × 10 15 molec cm −2 observed in the 1990s. Despite the increasing population and traffic in southern California, a factor 3 decrease in ethene column density is observed over JPL over the past 25 years, accompanied by a decrease in CO. This is likely due to southern California's increasingly stringent vehicle exhaust regulations and tighter enforcement over this period.
Rates and trends for inpatient surgeries in pediatric Crohn's disease in the United States from 2003 to 2012.

Abstract Background Pediatric Crohn's disease (CD) is increasing in incidence globally. Trends in specific types of inpatient pediatric CD-related surgical procedures have not been widely reported. Methods Patients ≤20 years of age with CD were identified in the Kids' Inpatient Database for 2003, 2006, 2009, and 2012. Bowel resection, stoma creation, and perianal or percutaneous drainage procedures were identified using ICD-9 procedure codes, and trends were identified. Logistic regression was used to identify factors associated with surgical intervention and trends. Results Rates of overall bowel resection (including ileocolic resection, other small bowel resection, or other colon resection) did not change significantly over time. However, the odds of having a laparoscopic colon resection increased by 41% annually (p Conclusions This study noted a stable rate of all types of bowel resections and increase in post resection ileostomy formation in US pediatric inpatients with CD from 2003–2012. Other rates of many CD-related procedures have remained stable. Further studies correlating the effects of biologic agents on surgical rates are warranted. Type of study Treatment Study Level of evidence Level III.
The Spanish ‘Shulamite Brides’: The Song of Songs in Teresa of Ávila, Mariana de San Joseph and María de Jesús de Ágreda

This essay examines the use and influence of the Song of Songs in the sixteenth- and seventeenth-century writings of three Castilian nuns. The biblical love poem provided a constitutive narrative that shaped the spiritual identity of the early modern religious who sought to become God's perfect spouse through imitation of the Song's protagonist, the Shulamite bride. Understanding the poem primarily as a portrayal of love between God and the soul, Hispanic nuns replicated the Shulamite bride's words, actions, and desires, which they refracted through their early modern spiritual concerns. In Meditaciones, Teresa of Avila viewed the Song as a script through which to guide her mystical ascent, thereby establishing an interpretive precedent for other nuns and religious to follow. Mariana de San Joseph's unique exegetical commentary, Sobre el libro de los cantares de Salomon, situated the meanings and messages of the Song within the context of daily convent life. In her Mistica ciudad de Dios, Maria de Jesus de Agreda promoted the Virgin Mary as the quintessential bride and role model. A fertile paradigm for spiritual advancement, the Song of Songs supplied significant elements that shaped and influenced early modern Hispanic spirituality.
Steady State Solutions to Circuit Problems

In this chapter we cover steady state methods which assume system has been running for a long time and all transient components have died out. The resulting solution is the steady state one. The applied stimulus is of the form e jωt and so will the resulting solution, which will be scaled based on the applied frequency ω. By either taking the real or imaginary part of the solution we can accommodate both sine and cosine inputs. By using superposition and using the Fourier series coefficients we can also accommodate other periodic stimuli such as the periodic pulse and periodic triangle and so forth. The method is applied on a range of circuits culminating in a 9-branch RLC network. We also touch on matrix solution of multi-branch circuits. Finally we compare to SPICE and observe excellent match, so far as the steady state part of the solution.
Increase in fertility following coal and oil power plant retirements in California

Few studies have explored the relationship between air pollution and fertility. We used a natural experiment in California when coal and oil power plants retired to estimate associations with nearby fertility rates. We used a difference-in-differences negative binomial model on the incident rate ratio scale to analyze the change in annual fertility rates among California mothers living within 0-5 km and 5-10 km of 8 retired power plants between 2001 and 2011. The difference-in-differences method isolates the portion of the pre- versus post-retirement contrast in the 0-5 km and 5-10 km bins, respectively, that is due to retirement rather than secular trends. We controlled for secular trends with mothers living 10-20 km away. Adjusted models included fixed effects for power plant, proportion Hispanic, Black, high school educated, and aged > 30 years mothers, and neighborhood poverty and educational attainment. Analyses included 58,909 live births. In adjusted models, we estimated that after power plant retirement annual fertility rates per 1000 women aged 15–44 years increased by 8 births within 5 km and 2 births within 5-10 km of power plants, corresponding to incident rate ratios of 1.2 (95% CI: 1.1–1.4) and 1.1 (95% CI: 1.0–1.2), respectively. We implemented a negative exposure control by randomly selecting power plants that did not retire and repeating our analysis with those locations using the retirement dates from original 8 power plants. There was no association, suggesting that statewide temporal trends may not account for results. Fertility rates among nearby populations appeared to increase after coal and oil power plant retirements. Our study design limited the possibility that our findings resulted from temporal trends or changes in population composition. These results require confirmation in other populations, given known methodological limitations of ecologic study designs.
Trapped in the Wrong Phraseology: O'Donnabhain v. Commissioner - Consequences for Federal Tax Policy and the Transgender Community

The U.S. Tax Court's 2010 decision in O'Donnabhain v. Commissioner reinterprets the scope of the medical expense deduction by authorizing the deduction of surgical treatment for Gender Identity Disorder (GID). After explaining the tax framework upon which the O'Donnabhain decision rests, this Recent Developments piece describes the decision and examines its consequences for the U.S. federal budget and the medicalization of the transgender community. The author concludes that O'Donnabhain will not significantly widen the pool of deductible medical care outside of sexual reassignment surgery and hormone therapy. The author applauds O'Donnabhain as a victory for those seeking to deduct expenses incurred in the treatment of GID but cautions that the decision may enforce a homogenous, medicalized model of the "ideal" transgender body. INTRODUCTION ...... 357 I. BACKGROUND OF THE CASE AND THE U.S. TAx FRAMEWORK 358 A. Rhiannon O'Donnabhain 358 B. The Itemized Deduction ...... 359 C. The Medical Expense Deduction ..... 361 D. The Appeals Process. 362 II. O'DONNABHAIN V. COMMISSIONER 363 A. Background of the Case 363 B. The Lead Opinion 365 t J.D. Candidate, University of California, Berkeley, School of Law (Boalt Hall). I would like to thank Professor Alan Auerbach for his guidance; Professor Anne Tamar-Mattis for her inspiration; Vikram Swaruup for his encouragement; and Alison Mollman and Ana Enriquez for their editorial assistance. All mistakes are my own. Finally, I dedicate this to Margaret Byer and to all gender-variant individuals everywhere. BERKELEY JOURNAL OF GENDER, LAW & JUSTICE 356 TRAPPED IN THE WRONG PHRASEOLOGY 1. Findings of Fact .. ....... 366 2. Opinion Section . 367 C. Judge Halpern's Concurrence 370 D. Judge Holmes's Concurrence. ...... 370 E. Judge Goeke's Opinion ..... 371 F. Judge Foley's Opinion ...... 372 G. Judge Gustafson's Opinion 373 III. O'DONNABHAIN'S CONSEQUENCES ........ 374 A. Implications for Tax Policy.... 374 1. Does O'Donnabhain Expand the Medical Deduction, and If So, How Much? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376 B. Implications for Transgender Individuals ..... 379 1. Recognition in the Law, But at a Cost ..... 379 2. Economic Realities: The Medical Model of Transition is Prohibitively Expensive 381 CONCLUSION 383
Experiential Roots of Intention, Initiative, and Trust

Intention, initiative, and trust have been considered to be developmental products of the first two years of living in human infants by widely disparate schools of thought. Since evidences of plasticity have weakened the traditional belief that early development is essentially predetermined in course and rate by heredity, an influential role in it may properly be attributed to experience, and especially early experience (Hunt, 1979a). It is common to call this influence “environmental.” Yet it is the functioning of the infant organism rather than the environment per se which modifies the course and rate of its development. Environmental circumstances are only indirectly of influence as they serve in the control of an infant’s functioning. Recent evidence has turned up hitherto unsuspected evidences of specificity between kinds of experience and the kinds of developmental achievements affected (see Hunt, 1977). These evidences of such specificity make it important for both the science of developmental psychology and the technology of early education to know as definitely and accurately as possible what kinds of experience are important for the various developmental achievements. The substance of this paper has been suggested by an unexpected consequence of an intervention in the infant rearing at an orphanage in Tehran (Hunt, Mohandessi, Ghodssi, & Akiyama, 1976). This intervention was planned to foster vocal imitation and, through it, language achievement (Hunt, 1979a). When the intervention turned out to produce also radical improvements in initiative, mood, and trust, it, combined with other new findings in the literature, suggested a need to revise my formulation of the role of intrinsic motivation in early psychological development.
Assessing the impact of antiretroviral therapy on tuberculosis notification rates among people with HIV: a descriptive analysis of 23 countries in sub-Saharan Africa, 2010–2015

HIV is a major driver of the tuberculosis epidemic in sub-Saharan Africa. The population-level impact of antiretroviral therapy (ART) scale-up on tuberculosis rates in this region has not been well studied. We conducted a descriptive analysis to examine evidence of population-level effect of ART on tuberculosis by comparing trends in estimated tuberculosis notification rates, by HIV status, for countries in sub-Saharan Africa. We estimated annual tuberculosis notification rates, stratified by HIV status during 2010–2015 using data from WHO, the Joint United Nations Programme on HIV/AIDS, and the United Nations Population Division. Countries were included in this analysis if they had ≥4 years of HIV prevalence estimates and ≥ 75% of tuberculosis patients with known HIV status. We compared tuberculosis notification rates among people living with HIV (PLHIV) and people without HIV via Wilcoxon rank sum test. Among 23 included countries, the median annual average change in tuberculosis notification rates among PLHIV during 2010–2015 was -5.7% (IQR -6.9 to -1.7%), compared to a median change of -2.3% (IQR -4.2 to -0.1%) among people without HIV (p-value = 0.0099). Among 11 countries with higher ART coverage, the median annual average change in TB notification rates among PLHIV was -6.8% (IQR -7.6 to -5.7%) compared to a median change of -2.1% (IQR -6.0 to 0.7%) for PLHIV in 12 countries with lower ART coverage (p = 0.0106). Tuberculosis notification rates declined more among PLHIV than people without HIV, and have declined more in countries with higher ART coverage. These results are consistent with a population-level effect of ART on decreasing TB incidence among PLHIV. To further reduce TB incidence among PLHIV, additional scale-up of ART as well as greater use of isoniazid preventive therapy and active case-finding will be necessary.