cssi/SciSciGPT-SciSciNet huggingface dataset:
The Electrogenic Reaction and Proton Release During Quinol Oxidation by the Cytochrome b/F Complex

The central element in electron transport between photosystem II and photosystem I is the cytochrome b/f complex that oxidizes plastoquinol and reduces plastocyanin. The complex includes four redox components, the Rieske-FeS center, cytochrome f, and two b-cytochromes (1–4). The mechanism of quinol oxidation and the role of the b-cytochromes is unresolved. in recent studies we have investigated the pathway of electrons in the cytochrome b/f complex and the release of protons during quinol oxidation (5–9). This work has led us to propose a model of quinol oxidation that is a modification of Mitchell’s Q-cycle (10). Here we examine two elements of this model. One is the origin of the slow electrogenic reaction associated with quinol oxidation by the cytochrome b/f complex. in an earlier study we proposed that the slow electrogenic reaction is due to two sequential reactions - (1) electron transfer from the b-cytochrome located near the inner surface of the thylakoid membrane to the b-cytochrome located near the outer surface, and (2) oxidation of the b-cytochrome located near the outer membrane surface (7,9). The other element is the amount of proton release into the inner aqueous space of the thylakoid vesicle associated with electron transfer from quinol to P700 (11). We found that for each electron transferred from quinol to photosystem I 1.7 to 2.0 protons are released into the thylakoid inner aqueous space.
Diagnosis of an unsuspected large left atrial tumor with intraoperative transesophageal echocardiography in a patient scheduled for coronary artery surgery

T RANSESOPHAGEAL echocardiography (TEE) is being used more frequently perioperatively. The primary indications include monitoring of ventricular function, assessment of valvular function after repair or replacement, and detection of intracardiac shunts, air, thrombi, and tumors. A case of an unsuspected left atria1 tumor diagnosed with intraoperative TEE in a patient scheduled for coronary artery bypass grafting (CABG) that helped avoid potentially disastrous complications is presented.
InP/In/sub 0.53/Ga/sub 0.47/As heterojunction bipolar transistors with a carbon-doped base grown by MOCVD

InP/In/sub 0.53/Ga/sub 0.47/As heterojunction bipolar transistors (HBTs) utilizing a carbon-doped base have been demonstrated. The devices were grown by low-pressure metalorganic chemical vapor deposition (LP-MOCVD) using carbon tetrachloride (CCl/sub 4/) as the p-type dopant source. These devices exhibit a DC common-emitter current gain of 50 and an emitter-base junction ideality factor of 1.29 in a structure for which no undoped spacer layer was employed at the emitter-base junction. These preliminary results suggest that C-doping of In/sub 0.53/Ga/sub 0.47/As may be a suitable alternative to Zn in MOCVD-grown InP/In/sub 0.53/Ga/sub 0.47/As HBTs. >
HEAR-SN: A New Hierarchical Energy-Aware Routing Protocol for Sensor Networks

Wireless sensor networks are becoming an integral part of numerous applications very quickly. Here, we present a new approach for sensor applications that requires coverage for a large area, stationary environment, and simplicity in the sensor nodes. Our protocol combines features such as data aggregation, energy aware routing, clustering and hierarchical routing into a single protocol. All these features combined allow for increased energy efficiency as well as extended network lifetime. Dynamic clustering is utilized to allow the sensors to change their cluster association dynamically. Data aggregation is incorporated to allow different data packets to be combined together in order to conserve energy and finally hierarchical routing is used to bridge large distances. We provide all the protocol specifications and our simulation results obtained with NS-2. Our simulations show that we could extend the network lifetime by a factor of two by using the proposed protocol HEAR-SN.
A novel non-migration nano-Ag conductive adhesive with enhanced electrical and thermal properties via self-assembled monolayers modification

Silver migration has long been one of the most critical issues in semiconductor electronic industry, while no effective approaches have been developed to control silver migration and maintain its excellent electrical and thermal properties. In this paper, we report a novel approach of using molecular self-assembled monolayers (SAMs) to dramatically reduce silver migration in the nano-Ag conductive adhesives. The protection of silver nano particles with molecular monolayers reduced the silver migration dramatically and no migration was observed upon application of high voltages (up to 500 V) due to the formation of surface chelating compounds between the SAM and nano silver fillers. The migration behavior of SAM passivated nano-Ag conductive adhesives was investigated by analyzing the results with DiGiacomo's model. In addition to a controlled migration, the SAM passivated nano Ag fillers also enhanced the electrical conductivity and current carrying capability of ACA joints significantly due to the improved interfacial properties and high current density of those molecular monolayers. Unlike typical anisotropic conductive adhesive (ACA) joints which showed high joint resistance and limited current carrying capability, the joint resistance of the SAM incorporated nano-Ag conductive adhesive could be achieved as low as 10/sup -5/ Ohm (the contact area is 100 /spl times/ 100 /spl mu/m ) and the maximum allowable current was higher than 3500 mA. Furthermore, the improved electrical performance of SAM treated nano Ag ACAs was also achieved with the increased thermal conductivity. As such, a fine pitch, high performance, non-migration and high reliability adhesives are developed for potential solder replacement in high voltage, high power device applications. The novel approach for silver migration control and electrical properties enhancement can also be applied in next generation high performance semiconductor devices to replace aluminum and copper metallization with the better performance silver.
Age and gender differences in children's and adolescents' adaptation to sexual abuse.

Abstract Objective: How children manifest psychological distress following the discovery of sexual abuse requires a better understanding of individual differences in developmental capacities and vulnerabilities. This study examined how age at the time of the abuse discovery and gender of victim are related to psychological distress. Method: One hundred and sixty-nine participants (96 children, 73 adolescents) were interviewed within 8 weeks of discovery of the abuse. Multivariate analyses were used to examine how age at discovery, and gender, with abuse characteristics as covariates, were related to shame, attribution style, depression, self-esteem, and traumatic events sequelae. Results: Adolescents compared to children report a higher level of depressive symptoms, negative reactions by others, and lower levels of self-esteem, social support, and sexual anxiety. Girls compared to boys report higher levels of intrusive thoughts, hyperarousal, sexual anxiety, personal vulnerability, and perceiving the world as a dangerous place and lower levels of eroticism. Conclusions: These findings suggest the importance of considering individual differences in age and gender for understanding patterns of symptom expression. Treatment strategies need to reflect these individual differences in adjustment, such as targeting issues of sexual anxiety for girls and self-esteem for adolescents.
A space–time discontinuous Galerkin method for the solution of the wave equation in the time domain

In recent years, the focus of research in the field of computational acoustics has shifted to the medium frequency regime and multiscale wave propagation. This has led to the development of new concepts including the discontinuous enrichment method. Its basic principle is the incorporation of features of the governing partial differential equation in the approximation. In this contribution, this concept is adapted for the simulation of transient problems governed by the wave equation. We present a space–time discontinuous Galerkin method with Lagrange multipliers, where the shape approximation in space and time is based on solutions of the homogeneous wave equation. The use of hierarchical wave-like basis functions is enabled by means of a variational formulation that allows for discontinuities in both the spatial and the temporal discretizations. Numerical examples in one space dimension demonstrate the outstanding performance of the proposed method compared with conventional space–time finite element methods. Copyright © 2008 John Wiley & Sons, Ltd.
Divergence between Archival and Perceptual Measures of the Environment: Causes and Consequences

Based on a review of previous theoretical and empirical research on environmental measurement, we develop a framework to explain both causes and consequences of divergence between archival and perceptual measures of the environment. Through this framework, we identity two central factors that account for this divergence: level of analysis and mediating filters. Research implications of this divergence between archival and perceptual characterizations are presented. Theoretical and methodological suggestions are advanced to improve the use of environmental measures.
Approximate shape fitting via linearization

Shape fitting is a fundamental optimization problem in computer science. The authors present a general and unified technique for solving a certain family of such problems. Given a point set P in R/sup d/, this technique can be used to /spl epsi/-approximate: (i) the min-width annulus and shell that contains P, (ii) minimum width cylindrical shell containing P, (iii) diameter, width, minimum volume bounding box of P, and (iv) all the previous measures for the case the points are moving. The running time of the resulting algorithms is O(n + 1//spl epsi//sup c/), where c is a constant that depends on the problem at hand. Our new general technique enables us to solve those problems without resorting to a careful and painful case by case analysis, as was previously done for those problems. Furthermore, for several of those problems our results are considerably simpler and faster than what was previously known. In particular, for the minimum width cylindrical shell problem, our solution is the first algorithm whose running time is subquadratic in n. (In fact we get running time linear in n.).
Static deformations from point forces and force couples located in welded elastic Poissonian half-spaces: Implications for seismic moment tensors

We present analytic expressions for the static deformations produced by point forces and point force couples embedded in two elastic Poissonian half-spaces that are welded on a horizontal interface. We show that the deformations from point forces and from vertically dipping strike-slip point double couples vary continuously (except at the strike-slip source) as the source is moved across the welded interface. We show that the pattern of deformations from vertically dipping (or horizontally dipping) dip-slip point double couples also vary continuously as the source is moved across the welded interface, but the amplitude of the deformations jumps by the ratio of the rigidities. Finally, we show that the pattern of deformation from a point explosion source or from a point double-couple source dipping at angles other than 0° or 90° jumps as the source is moved across the boundary. We demonstrate that integration of point double-couple sources on a plane of finite extent mimics the deformation of slip on a fault plane where the total moment of the double-couples is μAD. We also demonstrate that deformations from a distribution of double couples on a horizontally dipping finite plane just above the interface are indistinguishable from the deformations produced by a similar distribution of double couples located just below the interface but with a total moment that is different by the ratio of the rigidities. This demonstrates that the moment of a dislocation that occurs between two materials is ambiguously defined. We discuss reasons why seismic moment is not a very satisfying way to parameterize the size of an earthquake. We show that potency, defined to be the integral of the slip over the rupture surface, is a more natural size scaling parameter than seismic moment.
Intraoperative hyperthermia associated with intraventricular hemorrhage.

Abstract A case is presented of a 34-month-old child who developed hyperthermia with a temperature of 40°C while undergoing a suboccipital craniotomy for resection of a medulloblastoma. The presentation is followed by a discussion of the differential diagnosis of hyperthermia during anesthesia. Malignant hyperthermia, septicemia, thyroid storm, neuroleptic malignant syndrome, transfusion reaction, and exogenous causes of fever are discussed. The case serves as an illustration of the association between neurosurgical manipulation, intraventricular hemorrhage, and fever that may result from hypo-thalamic irritation.
Particulate flow simulations using lubrication theory solution enrichment

A technique for the numerical simulation of suspensions of particles in fluid based on the extended finite element method (X-FEM) is developed. In this method, the particle surfaces need not conform to the finite element boundaries, so that moving particles can be simulated without remeshing. The finite element basis is enriched with the Stokes flow solution for flow past a single particle and the lubrication theory solution for flow between particles. The latter enrichment allows the simulation of particles that come arbitrarily close together without refining the mesh in the gap between them. Example problems illustrating both types of enrichment are shown, along with a study of a 50% solution in channel flow. Copyright © 2003 John Wiley & Sons, Ltd.
COPYRIGHT, TRESPASS, AND THE FIRST AMENDMENT: AN INSTITUTIONAL PERSPECTIVE

In this paper I discuss one facet of the multifaceted question of whether strong protection for intellectual property rights—in particular, rights in expressive works and in information in digital form—is, in principle, at odds with the First Amendment guarantee of freedom of speech. The question has assumed particular urgency in recent years because the Internet and digital technology seem to have rendered formerly serviceable legal boundaries obsolete, and doctrines that sufficed in a print-on-paper world no longer seem adequate. Vigorous debate rages about what has come to be referred to as ‘propertization’. Commentators ask whether, and how, and based upon what empirical assumptions, old boundaries ought to be redrawn and doctrines modified. The academic literature tilts heavily away from endorsing strong property rights in digitized content, and toward expanded user rights and intensified First Amendment review in copyright cases. This paper tilts in a different direction. It swims against the academic tide not only in the direction of its analysis but, more importantly, in the kinds of questions it considers relevant and in its analytical focus. Readers should understand that the analysis is deliberately provisional and suggestive rather than completely developed, and the conclusions are tentative. The paper does not purport to be a definitive study that draws confident conclusions. It is offered as speculation and in the hope that readers will approach it in that spirit.
Reading the wind: how middle managers assess the context for selling issues to top managers

Issue selling is an important mechanism for creating change initiatives in organizations. This paper presents two studies that examine what middle managers think about as they decide whether or not to sell strategic issues to top management. In Study 1 middle managers identify themes that indicate a favorable or unfavorable context for issue selling. Top management’s willingness to listen and a supportive culture were the most often named contributors to context favorability, while fear of negative consequences, downsizing conditions and uncertainty were thought to signal that a context was unfavorable for issue selling. Study 2 identifies factors that middle managers associate with image risk in the context of issue selling. Violating norms for issue selling, selling in a politically vulnerable way and having a distant relationship with top management were regarded as major contributors to a middle manager’s level of image risk. Both studies enrich our understanding of the social psychological mechanisms that undergird the strategic change process.© 1997 by John Wiley & Sons, Ltd.
A dual role for Bub1 in the spindle checkpoint and chromosome congression.

The spindle checkpoint ensures faithful chromosome segregation by linking the onset of anaphase to the establishment of bipolar kinetochore–microtubule attachment. The checkpoint is mediated by a signal transduction system comprised of conserved Mad, Bub and other proteins. In this study, we use live-cell imaging coupled with RNA interference to investigate the functions of human Bub1. We find that Bub1 is essential for checkpoint control and for correct chromosome congression. Bub1 depletion leads to the accumulation of misaligned chromatids in which both sister kinetochores are linked to microtubules in an abnormal fashion, a phenotype that is unique among Mad and Bub depletions. Bub1 is similar to the Aurora B/Ipl1p kinase in having roles in both the checkpoint and microtubule binding. However, human Bub1 and Aurora B are recruited to kinetochores independently of each other and have an additive effect when depleted simultaneously. Thus, Bub1 and Aurora B appear to function in parallel pathways that promote formation of stable bipolar kinetochore–microtubule attachments.
General Hamiltonian form of Noether's theorem with applications to time-dependent nonlinear oscillators

We present a generalization of Noether's theorem to Hamiltonian mechanics and show that it can be used to obtain exact, explicit invariants. This generalizes earlier treatments using Noether's theorem in configuration space. As one of the examples, we treat a Hamiltonian which has recently been used to derive invariants using the method of dynamical algebras.
Stochastic Dominance and Security Design

Familiar results from expected utility theory are reapplied in a risk neutral setting of security issuance under asymmetric information. The main result is that if 1) issuer qualities are ranked by first-order stochastic dominance and 2) securities and the implied residual claims are both nondecreasing, then the severity of adverse selection problems is increasing in the value of investment opportunities. With second-order stochastic dominance and concave claims (convex residuals) the opposite is true. Finally, the ordering of issuer entry/exit is precisely reversed in these two scenarios. The model is used to explain why certain mathematical assumptions are useful in the equity literature but not the debt literature, and vice versa.
Information About Public Goods: Effects of Third-Party Ratings on Charitable Contributions

Private provision of public goods relies heavily on contributions to a wide variety of charities. But the quality of goods and services produced by charities is heterogeneous and essentially unknown to donors. To diminish the asymmetry, third-parties provide standardized information in the form of ratings. This paper bridges two relevant research areas, information disclosure and public goods, and isolates the effects on donations of one ratings group, using signals of 0-stars to 4-stars. One effect captures the change in a charity's contributions after ratings become available compared to before. The other effect characterizes the relationship between ratings levels and a charity's annual contributions. Using panel data for 5,400 rated charities, I estimate a higher star-rating significantly increases contributions. However, charities receive fewer contributions after being rated than before, from a negligible amount for 4-star charities to a 25% cut for 0-star charities. The results strongly demonstrate that voluntary giving responds to ratings.
Fed.R.Evid. 606(B): Actual Bias or Extraneous Information as Affecting Validity of Jury Verdict; Debunking 'Presumption of Prejudice'

The “presumption of prejudice” approach of Remmer was introduced 37 years prior to the United States Supreme Court in Fulminante recognizing the concept of structural/fundamental error. The “presumption of prejudice” test, in fact overruled by Smith and Fulminante, was based upon poor reasoning that somehow the government should have to establish that the alleged event asserted to give rise to the “actual bias” was somehow “harmless” to the defendant. Since the alleged event had no probative value as to an element of the charge or defense, theoretically it would have been extremely difficult if not impossible to establish either that a substantial right was affected, Fed.R.Evid.103(a), or conversely that the alleged contact was harmless. With the recognition of the concept of structural/fundamental error, “actual bias” of a juror now should occupy its rightful place in the short list of matters so construed by the United States Supreme Court along with “actual bias” of a judge, with which it is truly equivalent. Extraneous prejudicial information, on the other hand, should be addressed applying traditional reversible error harmless error constitutional right doctrine. It follows that the “presumption of prejudice” test as applied to attacking the validity of a jury verdict should be relegated to the trash heap where it has for so long belonged.
EFFECTS OF INDOLE DERIVATIVES ON MONOOXYGENASE ACTIVITY IN RABBIT LIVER MICROSOMES

Various physiological and pathological conditions may alter the levels of circulating indoles. We examined the interaction of various compounds containing the indole group with liver microsomes from phenobarbital treated rabbits, and studied the effects of these compounds on mono-oxygenase activity. Indoles that contain a 3 position free amine group, such as tryptamine and serotonin, were the most potent in inhibiting mixed-function oxidase activity. These compounds bound to oxidized microsomes to produce typical type II binding spectra with Ks values of 10–20 µM. Other indoles produced different binding spectra and bound less tightly to oxidized microsomes, with Ks values between 50 and 200 µM.
Quantitative Model and Metrics of Electrical Grids’ Resilience Evaluated at a Power Distribution Level

This paper presents a framework to systematically measure and assess power grids’ resilience with a focus on performance as perceived by customers at the power distribution level. The proposed framework considers an analogous measure of availability as a basic metric for resilience and defines other key resilience-related concepts and metrics, such as resistance and brittleness. This framework also provides a measurement for the degree of functional dependency of loads on power grids and demonstrates how the concepts of resilience and dependency are inherently related. It also discusses the implications of considering human-centered processes as fundamental constituting components of infrastructure systems. Thanks to its quantitative nature, the proposed resilience framework enables the creation of tools to evaluate power grids’ performance as a lifeline and to assess the effects of plans for optimal electrical power infrastructure deployment and operation. The discussion is supported by practical examples and empirical records from field damage assessments conducted after recent notable natural disasters.
Some Scattering Results on Organic-Inorganic Composites

A number of investigations are described to illustrate the use of small-angle x-ray and neutron scattering to characterize the structures of organic-inorganic composites. The organic phase in these materials is typically a polymer such as poly (dimethylsiloxane), and the inorganic phase a ceramic such as silica or titania (obtained by in-situ hydrolysis and condensation of an organosilane or organotitanate in the usual sol-gel approach). Other inorganic phases of interest include porous materials such as zeolites or Vycor glass. A major goal in such investigations is to correlate the structures of the composites with the synthetic techniques used to prepare them, and with the mechanical properties they exhibit. Carrying out scattering measurements as a function of time can also be used to obtain kinetic results on the sol-gel reactions used to generate the dispersed phase.
Why Do Firms Issue Equity? Right Issues in the Closed-End Funds Industry

We study 67 rights offerings by closed-end funds over 1988-1994 and gauge their impact on the fund's shareholders and managers. We find that funds conduct rights offerings while they are trading at a premium, reverts to a discount after the offering. Theories of asymmetric information about assets-in-place, growth and investment opportunities as well as downward sloping demand curves have little explanatory power in explaining the premium decline. Our proxies for managerial opportunism suggest that premium declines are related to agency problems between investment advisors and shareholders. Indeed, rights offerings result in a substantial increase in investment advisory fees.
Room-temperature optical inspection reliably indicates

A recently discovered phenomenon can be used to easily evaluate whether a cuprate contains superconducting grains. Quite simply, the room-temperature color of the microstructure, when viewed through crossed polarizers, indicates the presence or absence of superconducting phases. Regardless of the composition or desired product of processing, optical examination indicates the grains that are superconducting. Because the technique depends on reflectivity, automated detection of superconductivity is possible. The optical technique described also sheds light on the commonality and origin of superconductivity in the hisjh-temperature superconductors.
Lepidopteran Pests of Soybeans: Consumption of Soybean Foliage and Pods and Development Time

The foliage consumption potential by 6 lepidopteran larvae and the pod consumption potential by larvae of Heliothis zea (Boddie) were determined in laboratory feeding tests to be: Trichoplusia ni (Hubner)—119 cm2 of leaf/larva, Pseudoplusia includens (Walker)—114 cm2 Spodoptera exigua (Hubner)—52 cm, H. virescens (F.)—155 cm2 H. zea —336 cm2, and Anticarsia gemmatalis Hubner—84 cm2. For each species, ca. 90% of the feeding occurred during the final 2 larval stages. Larvae of T. ni held at 25°C consumed 23% more leaf area than those held at 20°C and 32% more area than those held at 30°C. Development of H. zea from the 4th through the 6th instar inclusive resulted in damage amounting to 8.2 pods and 7.1 seeds/larva.
Sexually transmitted diseases.

As sexual have become more liberal, so has the incidence of sexually transmitted diseases in this country’s children and adolescents.
UV Regulatory Strategies

Ultraviolet Radiation (UVR) is hazardous to human health. These hazards were recently detailed at a symposium held in Amsterdam entitled, “Human Exposure to Ultraviolet Radiation: Risks and Regulations” (Passchier and Bosnjakovic, 1987). This symposium brought together international experts on UVR risk and protection and was the first of its kind to focus specifically on health risks from UVR and outline current methods for risk reduction. The purpose of the present symposium, “UV Risks and Regulations”, has been to outline for a broader audience the results of the Amsterdam symposium along with new data and perspectives that have emerged in the last 20 months.
Chapter 30 – Radical Retropubic Prostatectomy

Radical prostatectomy for the treatment of prostate cancer has evolved over the last 60 years with surgical removal of the entire prostate becoming a standard treatment for localized prostate cancer. Of the two standard open radical prostatectomy techniques, the perineal and retropubic, radical retropubic prostatectomy has become the most common approach. The retropubic procedure is often considered technically demanding primarily due to the location of the prostate deep within the male pelvis; it also can be considered the most anatomic approach. In addition to ensuring the removal of the cancer, the surgeon must negotiate the risk of blood loss, and avoid damage to surrounding structures while performing reconstruction to preserve continence and maintain potency if present. Although robotically assisted laparoscopic radical prostatectomy has become the most common surgical procedure for radical prostatectomy in the United States, the open radical prostatectomy remains an important procedure. There are patients who are not suitable candidates for a robotically assisted radical prostatectomy or for whom the more costly robotic technology may not be readily available. This chapter reviews the current application of open retropubic radical prostatectomy.
Economic, Statistical, and Economic-Statistical X̄ Chart Designs

A FORTRAN program that enables users to determine economic, statistical, or economic-statistical X chart designs is presented. Economic designs are designs that minimize cost as measured by the Lo...
Water Quality Changes Shortly After Low-Head Dam Removal Examined With Cultural and Microbial Source Tracking Methods

Short-term effects of low head dam removal on water quality of urbanized stream were evaluated, focusing on fecal pollution indicators. Composite river samples were analyzed for Escherichia coli concentrations, nitrates, phosphates, turbidity and human-specific marker (HF183) and antibiotic resistance marker (tetQ) before and after dam removal during dry weather conditions. The sampled Olentangy River water in summer before the dam removal showed poor water quality with mean E. coli concentration of 439 colony forming unit (CFU)/100 mL, mean turbidity of 10 NTU and mean nutrient concentrations of 0.61 and 0.41 mg/L for nitrate and phosphate, respectively. Surprisingly, even one month after the dam removal, E. coli numbers doubled and nitrate concentration tripled compared to pre-removal concentrations. Although the detected HF183 concentrations were below the quantifiable levels, they did not correlate with E. coli concentrations, suggesting E. coli from other than human fecal origin. The correlation between turbidity and E. coli during dry weather further suggests E. coli accumulation in impoundment sediments and release once dam was removed. These short-term effects of dam removal on water quality should be further evaluated, especially if recreation and other beneficial uses of water in the area are expected. Copyright © 2016 John Wiley & Sons, Ltd.
Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa

Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Chimeric and hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify and classify AGPs, EXTs, PRPs, chimeric HRGPs, and hybrid HRGPs from the proteins predicted by the completed genome sequence of poplar (Populus trichocarpa). This bioinformatics approach is based on searching for biased amino acid compositions and for particular protein motifs associated with known HRGPs with a newly revised and improved BIO OHIO 2.0 program. Proteins detected by the program are subsequently analyzed to identify the following: 1) repeating amino acid sequences, 2) signal peptide sequences, 3) glycosylphosphatidylinositol lipid anchor addition sequences, and 4) similar HRGPs using the Basic Local Alignment Search Tool (BLAST). The program was used to identify and classify 271 HRGPs from poplar including 162 AGPs, 60 EXTs, and 49 PRPs, which are each divided into various classes. This is in contrast to a previous analysis of the Arabidopsis proteome which identified 162 HRGPs consisting of 85 AGPs, 59 EXTs, and 18 PRPs. Poplar was observed to have fewer classical EXTs, to have more fasciclin-like AGPs, plastocyanin AGPs and AG peptides, and to contain a novel class of PRPs referred to as the proline-rich peptides. The newly revised and improved BIO OHIO 2.0 bioinformatics program was used to identify and classify the inventory of HRGPs in poplar in order to facilitate and guide basic and applied research on plant cell walls. The newly identified poplar HRGPs can now be examined to determine their respective structural and functional roles, including their possible applications in the areas plant biofuel and natural products for medicinal or industrial uses. Additionally, other plants whose genomes are sequenced can now be examined in a similar way using this bioinformatics program which will provide insight to the evolution of the HRGP family in the plant kingdom.
PET image reconstruction with anatomical prior using multiphase level set method

Acquiring both anatomical and functional images during one scan, PET/CT systems improve the ability to distinguish pathology from normal uptake and to precisely localize abnormal loci. Researchers have investigated using anatomical boundary information in CT to regularize PET images. Here we propose a novel approach to maximum a posteriori (MAP) reconstruction of PET images with CT-based prior information. The image prior models both the smoothness of PET images and the similarity between functional boundaries in PET and anatomical boundaries in CT. Minimal smoothing is applied across functional boundaries to preserve shape edges. Level set functions are use to describe the anatomical boundaries from CT and to track the evolution of the functional boundaries in PET. The proposed method does not assume an exact match between PET and CT boundaries, but rather maximizes the similarity between the two boundaries, while allowing different region definition in the PET image. This is an important feature as mismatches between anatomical and functional boundaries have been observed in clinical images that could be caused either by inherent difference in the contrast mechanisms and/or subject motion. We conducted computer simulations to evaluate the performance of the proposed method. A digital phantom was built based on a PET/CT scan of a mouse. Two anatomical priors are obtained by modifying the segmented CT boundaries. The proposed method is compared with other methods including ML-EM, MAP with spatial-invariant and spatial-variant smoothing. The reconstructed images of the proposed method are locally smooth with sharp functional boundaries, while blurred boundaries appears in the results of other methods. The region of interest quantification study shows that the proposed method achieves less bias at the same noise level compared to the existing methods.
Reviews and Resources:Microbe, 2nd Edition: BOOKS

Twenty years ago, I took the transformative “Microbial Diversity” course at the Marine Biological Laboratories in Woods Hole, Mass., taught by the late Edward Leadbetter and the late Abigail Salyers. Awed by the depth and breadth of what I soon called “matters microbial,” and perplexed by textbook options for use in the classroom, Ed laughed and told me I needed three texts: one for the students, and two for me. Microbiology is changing constantly, and expanding its scope to so many other disciplines as it changes. There was simply, as he put it, not enough paper for the subject matter in one book.
New Directions for Special Collections: An Anthology of Practice . Eds. Lynne M. Thomas and Beth M. Whittaker. Santa Barbara, Calif.: Libraries Unlimited, 2017. 249p. $85.00 (ISBN 978-1-4408-4290-0).

In their introduction to New Directions for Special Collections: An Anthology of Practice , Lynne M. Thomas and Beth M. Whittaker outline their approach: rather than create a current guide or textbook for a field where best practices, technology, and expectations are changing rapidly, they endeavor to provide a “snapshot” of where the field is now. An open call for submissions, along with a few solicited contributions, has resulted in twenty-one chapters from a diverse group of special collections, metadata, and preservation librarians, as well as conservators, directors, and archivists, speaking to various components of their work as it stands today, and as they see it evolving in the future (descriptions of the individual authors’ background are included). Each chapter can stand alone, and there are no groupings according to subject (the index is perfectly adequate for searching within the chapters).
Neutrophil Extracellular Traps and Fibrin in Otitis Media: Analysis of Human and Chinchilla Temporal Bones

Background Bacterial resistance in acute otitis can result in bacterial persistence and biofilm formation, triggering chronic and recurrent infections. Objective To investigate the middle ear inflammatory response to bacterial infection in human and chinchilla temporal bones. Design, Setting, and Participants Six chinchillas underwent intrabullar inoculations with 0.5 mL of 10 6 colony-forming units (CFUs) of Streptococcus pneumoniae , serotype 2. Two days later, we counted bacteria in middle ear effusions postmortem. One ear from each chinchilla was processed in paraffin and sectioned at 5 µm. The opposite ear was embedded in epoxy resin, sectioned at a thickness of 1 µm, and stained with toluidine blue. In addition, we examined human temporal bones from 2 deceased donors with clinical histories of otitis media (1 with acute onset otitis media, 1 with recurrent infection). Temporal bones had been previously removed at autopsy, processed, embedded in celloidin, and cut at a thickness of 20 µm. Sections of temporal bones from both chinchillas and humans were stained with hematoxylin-eosin and immunolabeled with antifibrin and antihistone H4 antibodies. Main Outcome Measures Histopatological and imminohistochemical changes owing to otitis media. Results Bacterial counts in chinchilla middle ear effusions 2 days after inoculation were approximately 2 logs above initial inoculum counts. Both human and chinchilla middle ear effusions contained bacteria embedded in a fibrous matrix. Some fibers in the matrix showed positive staining with antifibrin antibody, others with antihistone H4 antibody. Conclusions and Relevance In acute and recurrent otitis media, fibrin and neutrophil extracellular traps (NETs) are part of the host inflammatory response to bacterial infection. In the early stages of otitis media the host defense system uses fibrin to entrap bacteria, and NETs function to eliminate bacteria. In chronic otitis media, fibrin and NETs appear to persist.
Launch of ‘Atlas Journal of Medical and Biological Sciences’

Why another biomedical journal? With the thousands of new journals launched each year, what new does “Atlas Journal of Medical and Biological Sciences” bring to scientific discourse? This is the same opening that meets every journal before it builds its own identity. Ours will, as other journals we edit, be characterized by openness for new ideas that have solid supporting documentation. Scientific advance requires dissemination of ideas that will advance scholarly inquiry and contrast with the many journals that focus on incremental advance of accepted dogma. This is an incredibly exciting period in biology-medicine, post genomic and soon to be post proteomic. After over half a century of dominance, reductionism is failing to assist in our understanding of disease. This is a period when by returning to basics of biology we have a chance to make major advances. Through your support, AJMBS will play a role in that transformation.
JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.
Can Understanding Spatial Equilibria Enhance Benefit Transfers for Environmental Policy Evaluation

A conceptual model of consumer sorting in markets for housing, labor and health care is outlined and used to make three points about how benefit transfers are used for environmental policy evaluation. First, the standard approach to assessing benefits of air quality improvements by transferring the value of a statistical life from labor market studies embeds several untested (but testable) assumptions. Second, if the cost of an environmental policy exceeds its capitalized effect on housing prices, then the capitalization effect is an insufficient statistic for determining whether benefits exceed costs. Third, there are several ways in which equilibrium sorting models may be usefully extended to assess distributional welfare effects of environmental policies.
Failures of Sacral Neuromodulation for Incontinence.

This study examines the reintervention rate associated with treatment failures and device malfunctions at 1, 3, and 5 years after sacral neuromodulation surgery.
HYVISUAL: A HYBRID SYSTEM MODELING FRAMEWORK BASED ON PTOLEMY II

Extended Abstract HyVisual is a hybrid systems modeling framework providing a block diagram visual syntax for specifying continuous dynamics and a bubble-and-arc syntax for specifying modal behavior. It is based on Ptolemy II, is written in Java, and is distributed open-source at http://ptolemy.eecs.berkeley.edu/hyvisual/. HyVisual has a rigorous operational semantics described in Lee and Zheng (2005). A key property is that it internally uses superdense time , where signals are modeled as partial functions of the form f : ℝ + Xℕ → V , where ℝ + is the non-negative real numbers and represents time, V is the value set (a data type, such as ℝ n ), and ℕ is the set of natural numbers. Continuous-time functions are total, whereas discrete-event functions are defined only on a discrete subset of ℝ + . The ℕ in the domain permits signals to have multiple values in a well-defined order at a particular time. Using this framework, HyVisual gives a rigorous semantics to discontinuous signals (which have multiple values at the point of discontinuity), to discrete-event signals with multiple events at the same time, and to transient states, where the time spent in the state is zero. An example of a HyVisual model that leverages this is shown in fig. 1, which shows many features of HyVisual. This models Newton's cradle, an apparatus with three (or more) balls hanging from strings (inspired by a one dimensional version in Mosterman (1999)). If the model is initialized with one of the balls displaced as shown in the HyVisual graphical animation at the lower left, then when the ball collides with the middle ball, a transient state results. At that time, the right ball transfers its momentum to the middle ball, and then, without any time elapsing, the middle ball transfers its momentum to the left ball. The two events (state transitions in the state machine at the middle left) are simultaneous but ordered. Other initial conditions can be chosen where two simultaneous events are unordered (e.g., starting with two balls appropriately displaced). HyVisual allows a model to permit nondeterministic choice of enabled transitions.
Inhomogeneities in La 1−x Sr x MnO 3 and Pr 1−x Ca x MnO 3

We start the analysis of inhomogeneities in LSMO by describing experimental results obtained using the pair-density-functional (PDF) technique. To understand this method, consider the density correlation function p(r) that describes the probability of finding an atom at a distance r from another atom, in the material under study. This function contains information about the atomic structure of the material expressed in real space. For a perfectly periodic crystal, p(r) peaks sharply at a, 2a, . . . where a is the lattice spacing. However, many real materials present substantial deviations from periodicity, and this occurs in manganites as well. In these materials, p(r) is a richer function, with peaks of finite width at several locations. This correlation function is important since it reveals features of the local structure, such as small deviations from average crystallographic positions due to tendencies to order at short distances that are not reflected in the dominant long-range order of atoms. In other words, not only are Bragg peaks revealed in this type of studies, but also those arising from diffuse scattering. The function p(r) can be obtained from X-ray or neutron diffraction techniques without assumptions about the periodicity of the lattice. The data is usually gathered in terms of momentum-space variables, and the results must be Fourier transformed to real space for their analysis. Details about this procedure and a more detailed introduction to PDF can be found in [14.1], and references therein.
Social subjective value in the primate midbrain.

How we value our own rewards depends on what others have. A new study shows that neurons in the medial prefrontal cortex selectively monitor the value of rewards received by oneself or by another individual, whereas midbrain dopaminergic neurons integrate these values to generate social subjective reward values.
Consortiums of ISP-Content Providers Formed by Nash Bargaining for Internet Content Delivery

The formation of consortiums of a broadband access Internet Service Provider (ISP) and multiple Content Providers (CP) is considered for large-scale content caching. The consortium members share costs from operations and investments in the supporting infrastructure. Correspondingly, the model’s cost function includes marginal and fixed costs; the latter has been important in determining industry structure. Also, if Net Neutrality regulations permit, additional network capacity on the ISP’s last mile may be contracted by the CPs. The number of subscribers is determined by a combination of users’ price elasticity of demand and Quality of Experience. The profit generated by a coalition after pricing and design optimization determines the game’s characteristic function. Coalition formation is by a bargaining procedure due to Okada (1996) based on random proposers in a non-cooperative, multi-player game-theoretic framework. A necessary and sufficient condition is obtained for the Grand Coalition to form, which bounds subsidies from large to small contributors. Hence, for the Grand Coalition to form it is necessary to administer Coalition Admission Control. Caching is generally supported even under Net Neutrality regulations. The Grand Coalition’s profit matches upper bounds. Numerical results illustrate the analytic results.