cssi/SciSciGPT-SciSciNet huggingface dataset:
Automatic non-rigid mismatch correction algorithm for CT-CT longitudinal oncology studies

Significant coverage mismatches, non-rigid motion, structural variability of anatomy, and intensity variations in contrast studies make automatic correction for multi-time point CT oncology studies a difficult problem. Also, since multiple volumes have to be non-rigidly co-aligned, it is important and challenging to maintain consistency of maps during non-rigid registration [NRR]. We present a fully automatic algorithm to handle above challenges using, 1) A novel graph-matching approach to initialize rigid registration under large coverage mismatches 2) An approximate, 1D diffeomorphic framework using patch based normalized image gradients to handle NRR. The above combination makes our method robust, fast (≈ 6 s for matching a pair of volumes on standard CPUs for high res. CT cases) and can be used to handle multiple volumes seamlessly. Validation of the proposed algorithm is shown on 17 pairwise NRR experiments on challenging multi-time point oncology studies.
Estimating demographic characteristics using the ratio-correlation method

Studies of the relative accuracy of methods of estimating the population at the substate level have generally found that the greatest degree of accuracy is provided by the ratio-correlation, or regression, method. This paper reports on research aimed at evaluating the effectiveness of this method in estimating the age and race composition of populations at the substate level. In addition to the basic multiple regression equation, variants such as stratification and the averaging of estimates from simple regression equations are also tested. Surprisingly, for Virginia localities the most satisfactory results are generated by the nonstratified multiple regression equation.
The Institutional Foundations of Democratic Cooperation in Costa Rica

Costa Rica's long-term standing as one of the few countries in Latin America with a stable democracy has prompted many to view its polity as an inevitable outcome of a racially homogeneous and relatively egalitarian society. Without ignoring the importance of sociological factors, this article contends that institutional arrangements played an equally important — if not more central — role in the development of a stable democratic regime in this country. The structure of Costa Rican presidentialism encouraged incumbents to maintain control of the state while it, as a consequence, incited the opposition to rebel against central state authorities. Political competition became more peaceful as parties that failed to hold or to capture the presidency were nevertheless compensated by being allowed to occupy legislative seats.
Neighborhood Characteristics and Outcomes After Traumatic Brain Injury

Abstract Corrigan JD, Bogner JA. Neighborhood characteristics and outcomes after traumatic brain injury. Objective To determine the extent to which characteristics of a person's neighborhood contribute to outcomes after traumatic brain injury (TBI). Design Prospective cohort. Setting A specialized brain injury unit providing acute rehabilitation care. Participants A consecutive sample of participants (N=200) in the Traumatic Brain Injury Model Systems (TBIMS) longitudinal study: 100 participants were 2 years postinjury, and 100 participants were 5 years postinjury. Interventions Not applicable. Main Outcome Measures U.S. Census Bureau block group descriptors of economic and social characteristics and initial and follow-up data from the TBIMS national dataset including the Glasgow Outcome Scale–Extended (GOS-E) and Satisfaction With Life Scale (SWLS). Results Economic and social characteristics of a person's neighborhood accounted for additional variance in outcomes beyond what could be accounted for by individual characteristics, including demographic, premorbid, and injury-related measures; concurrent measures of functioning; and the persons's perception of environmental influences. Individual characteristics predicted a substantial proportion of the variance in the GOS-E (69%); neighborhood characteristics contributed an additional 1.5%. Individual characteristics predicted 33.3% of the variance in SWLS, with neighborhood characteristics accounting for an additional 6.9%. Conclusions For both outcomes, a small but important proportion of the variance accounted for by neighborhood indices was unique to these environmental influences and was not accounted for by individual indices, including concurrent measures of functioning and the individual's perception of environmental influences. Further investigations of how neighborhood factors affect outcomes after TBI are warranted.
On securing networked real-time embedded systems

There has been an exponential growth of applications that rely on diverse types of embedded real-time end systems and devices, such as smart phones, play stations, home appliances, consumer and industrial electronics, smart sensors and actuators. These applications require diverse types of Quality-of-Service (QoS) including timeliness, dependability, security and privacy, from the end systems/devices which are usually networked together via heterogeneous networking technologies and procotols We now know how to guarantee timeliness and, to a lesser extent, how to provide fault-tolerance, on both end systems and their interconnection networks. However, how to secure them is far less known, despite the growing importance of protecting information stored in the end systems/devices and exchanged over their interconnection networks. Morever, timeliness, fault-tolerance, security and privacy—which I will call simply QoS—must be supported simultaneously, often with a tight resource budget such as memory, computation and communication bandwidth, and battery power. Also, different applications require different combinations of QoS components, and hence, one-fits-all solutions are not acceptable This talk will start with generic aspects of QoS and then detail how to secure a sensor network for surveillance applications. Sensor networks, usually built with a large number of small, low-cost sensor devices, are characterized by their large-scale and unattended deployment that invites many critical attacks, thereby necessitating high-level security support for their intended applications and services. However, making sensor networks secure is challenging due mainly to the fact that sensors are battery-powered and it is often very difficult to change or recharge their batteries. To meet this challenge, we have been developing Lightweight Security Protocols (LiSP) that cooperatively build a unified, energy-efficient security framework for sensor networks
Spanish Missions, Cultural Conflict and the Pueblo Revolt of 1680

Historians who try to understand encounters between red men and white men in the seventeenth century are immediately confronted with a problem: Indians were not literate, and they left no records of the sort we are accustomed to studying. For centuries the only information about aboriginal populations in the Americas was derived from European narratives, conditioned by viewpoints that harbored an outsider's values. Archaeology added some indigenous references, but the evidence has usually been too meager for adequate generalization. Historians have pursued the goal of avoiding white men's biases and viewing Indian cultures as having an integrity all their own, but that goal has remained an ideal, causing more despair than hope of eventual success. As far as the history of early New Mexico is concerned, the situation is worsened by the fact that most church and government archives were burned during the fighting of 1680–1696.
Improved anodic stripping voltammetric measurements of silver by codeposition with mercury

Significant improvements in the stripping voltammetric response of silver are observed in the presence of low levels (20 μg/L) of mercury. The formation of amalgam results in a higher sensitivity, sharper peak, improved reproducibility, and extended linear range when compared to analogous measurements in the absence of mercury. Even though mercury has a slightly more negative stripping potential than silver, no interference is observed because of its low level. The silver response is evaluated with respect to mercury and silver concentrations, deposition time and potential, coexisting metals, organic surfactants, and other variables. The detection limit is 1.4 × 10−10 M (16-min deposition), and the relative standard deviation (at 5 × 10−8 M) is 1.3%. Applicability to speciation work and river water samples is demonstrated. Additional work in this laboratory should lead to further improvements.
The egg, repagulum, and larva of Byas albistigma (Neuroptera: Ascalaphidae): morphology, behaviour and phylogenetic significance

The external morphology and habits of the larval instars of the Central American ascalaphid Byas albistigma (Walker) are described for the first time, and its eggs and repagula (abortive eggs) are compared to those of a Brazilian Byas sp. described by New (1971). In most respects, all immature stages of Byas are shown to be much like those of another neuroptyngine (entire-eyed) owlfly, Ascaloptynx furciger (McLachlan). However, larvae of Byas are arboreal rather than terrestrial and possess a number of important morphological characters that are more primitive than those seen in Ascaloptynx Shared features of the two genera that may constitute the ground plan of the Neuroptynginae are discussed in some detail and are weighted according to their primitive or derived status.
Maternal Receipt of Magnesium Sulfate Does Not Seem to Reduce the Risk of Neonatal White Matter Damage

Objective. To investigate whether in utero exposure to magnesium sulfate is associated with a lower incidence of cranial ultrasonographic abnormalities that predict cerebral palsy in infants who weigh less than 1501 g at birth. Design. For a prospective study of the antecedents of cranial ultrasonographic abnormalities, we enrolled infants who weighed 500 to 1500 g when born at five institutions. Data were collected by interview of the mothers and review of medical records. Protocol cranial ultrasonograms were obtained as close as possible to postnatal days 1, 7, and 21. Abnormality on cranial ultrasound scans was determined by a consensus committee of three sonologists. Results. Of the 1518 infants for whom we knew whether the mothers received magnesium sulfate, the first protocol cranial ultrasound scan was available for 1409 infants, the second for 1274 infants, and the third for 1050 infants. Forty-five percent of infants were exposed to magnesium sulfate before delivery. The major correlates of magnesium sulfate exposure were receipt of antenatal corticosteriods and a diagnosis of preeclampsia and/or pregnancy-induced hypertension. Maternal magnesium receipt was not associated with a reduced incidence of hypoechoic or hyperechoic images of white matter parenchyma, intraventricular hemorrhage, or ventriculomegaly, even when the sample was stratified by each of six potential confounders. When adjustment was made for gestational age, a measure of birth weight for gestational age, antenatal corticosteroid exposure, preeclampsia and pregnancy-induced hypertension, route of delivery, and the occurrence of any labor, the risk ratios for each cranial ultrasonographic abnormality associated with magnesium sulfate exposure hovered close to 1. Conclusion. Maternal receipt of magnesium sulfate does not seem to be associated with an appreciably reduced risk of cranial ultrasonographically defined neonatal white matter damage, intraventricular hemorrhage, or ventriculomegaly. low birth weight, magnesium sulfate, periventricular leukomalacia, antenatal corticosteriods, intraventricular hemorrhage, pregnancy-induced hypertension.
The Harmonic Mode of Oscillation in Barkhausen-Kurz Tubes

The phenomenon of harmonic operation of Barkhausen-Kurz tubes employing a resonating helical grid is investigated by the use of tubes with the plate cut transversely into three sections. It is shown that the fundamental or Barkhausen frequency may be elicited by exciting the grid at its central portion, but that if the grid is excited at its ends either symmetrically or unsymmetrically the oscillations occur at double the Barkhausen frequency. This doubled frequency is that usually generated by tubes of this type. It is also shown that it is essential to tune the filament circuit of the oscillator if maximum power output is desired.
Seasonality of rotavirus disease in the tropics: a systematic review and meta-analysis

Background To date little conclusive evidence exists on the seasonality of rotavirus incidence in the tropics. We present a systematic review and meta-analysis on the seasonal epidemiology of rotavirus in the tropics, including 26 studies reporting continuous monthly rotavirus incidence for which corresponding climatological data was available. Methods Using linear regression models that account for serial correlation between months, monthly rotavirus incidence was significantly negatively correlated with temperature, rainfall and relative humidity in 65%, 55% and 60% of studies, respectively. We carried out pooled analyses using a generalized estimating equation (GEE) that accounts for correlation from between-study variation and serial correlation between months within a given study. Results For every 1°C (1.8°F) increase in mean temperature, 1 cm (0.39 in.) increase in mean monthly rainfall, and 1% increase in relative humidity (22%) this analysis showed reductions in rotavirus incidence of 10% (95% CI: 6–13%), 1% (95% CI: 0–1%), and 3% (95% CI:0–5%), respectively. Conclusions On the basis of the evidence, we conclude that rotavirus responds to changes in climate in the tropics, with the highest number of infections found at the colder and drier times of the year.
Determination of all NOes in 1H–13C–Me-ILV-U−2H–15N Proteins with Two Time-Shared Experiments

We present two time-shared experiments that enable the characterization of all nOes in 1 H– 13 C-ILV methyl-labelled proteins that are otherwise uniformly deuterated and 15 N enriched and possibly selectively protonated for distinct residue types. A 3D experiment simultaneously provides the spectra of a 3D NOESY-HN-TROSY and of a 3D NOESY-HC-PEP-HSQC. Thus, nOes from any protons to methyl or amide protons are dispersed with respect to 15 N and 13 C chemical shifts, respectively. The single 4D experiment presented here yields simultaneously the four 4D experiments HC-HSQC-NOESYHC-PEP-HSQC, HC-HSQC-NOESY-HN-TROSY, HN-HSQC-NOESY-HN-TROSY and HN-HSQCNOESY-HC-PEP-HSQC. This allows for the unambiguous determination of all nOes involving amide and methyl protons. The method was applied to a ( 1 H, 13 C)-ILV)( 1 H)-FY-(U) 2 H, 15 N) sample of a 37 kDa di-domain of the E. coli enterobactin synthetase module EntF.
What covariance mechanisms underlie green:red equiluminance, luminance contrast sensitivity and chromatic (green:red) contrast sensitivity?

Abstract In order to investigate the mechanisms underlying green/red equiluminance matches in human observers and their relationship to mechanisms subserving luminance and/or chromatic (green/red) contrast sensitivity, we tested 21 human subjects along these dimensions at 16 different spatial and temporal frequencies (spatial frequency, 0.25–2 c/deg; temporal frequency, 2–16 Hz) and applied factor analysis to extract mechanisms underlying the data set. The results from our factor analysis revealed separate sources of variability for green/red equiluminance, luminance sensitivity and chromatic sensitivity, thus suggesting separate mechanisms underlying each of the three main conditions. When factor analysis was applied separately to green/red equiluminance data, two temporally-tuned factors were revealed (factor 1, 2–4 Hz; factor 2, 8–16 Hz), suggesting the existence of separate mechanisms underlying equiluminance settings at low versus high temporal frequencies. In addition, although the three main conditions remained separate in our factor analysis of the entire data set, our correlation matrix nonetheless revealed systematic correlations between equiluminance settings and luminance sensitivity at high temporal frequencies, and between equiluminance settings and chromatic sensitivity at low temporal frequencies. Taken together, these data suggest that the high temporal frequency factor underlying green/red equiluminance is governed predominantly by luminance mechanisms, while the low temporal frequency factor receives contribution from chromatic mechanisms.
Slotting Allowances and Optimal Product Variety

Some commentators believe that slotting allowances enhance social welfare by providing retailers with an efficient way to allocate scarce retail shelf space. The claim is that, by offering their shelf space to the highest bidders, retailers act as agents for consumers and ensure that only the most socially desirable products obtain distribution. I show that this claim does not hold in a model in which a dominant firm and competitive fringe compete for retailer patronage. By using slotting allowances to bid up the price of shelf space, the dominant firm can sometimes exclude the competitive fringe even when welfare would be higher if the fringe obtained distribution. Copyright Â© 1999-2005 Internet-Journals, Inc. All rights reserved.
NLTK: The Natural Language Toolkit

The Natural Language Toolkit is a suite of program modules, data sets and tutorials supporting research and teaching in computational linguistics and natural language processing. NLTK is written in Python and distributed under the GPL open source license. Over the past year the toolkit has been rewritten, simplifying many linguistic data structures and taking advantage of recent enhancements in the Python language. This paper reports on the simplified toolkit and explains how it is used in teaching NLP.
Identifying the sources of tuberculosis in young children: a multistate investigation.

To better understand the molecular epidemiology of tuberculosis (TB) transmission for culture-confirmed patients <5 years of age, data were analyzed from a population-based study conducted in seven U.S. sites from 1996 to 2000. Mycobacterium tuberculosis isolates were genotyped with IS6110-based restriction fragment length polymorphism analysis and spoligotyping. Case-patient data were obtained from the Centers for Disease Control and Prevention’s national tuberculosis registry and health department records. Routine public health investigations conducted by local health departments identified suspected source patients for 57 (51%) of 111 culture-confirmed patients <5 years of age. For 8 (15%) of 52 culture-confirmed patients <5 years of age and their suspected source patients with complete genotyping results, genotypes suggested infection with different TB strains. Potential differences between sources for patients <5 years of age and source patients that transmitted TB to adolescent and adult patients were identified. he occurrence of tuberculosis (TB) in children is an indicator of ongoing Mycobacterium tuberculosis transmis
Resolution of patch-type granuloma annulare lesions after biopsy

Abstract We describe a patient with patch-type granuloma annulare whose lesions resolved after biopsy on 2 occasions. The lesions not subjected to biopsy persisted. There is a paucity of literature on the relation between biopsy and resolution of granuloma annulare, with one frequently cited article implying that biopsy is not related to resolution. We briefly consider possible mechanisms through which involution of lesions of granuloma annulare could result after biopsy or other form of trauma. (J Am Acad Dermatol 2002;46:426-9.)
A Simple Unsupervised Learner for POS Disambiguation Rules Given Only a Minimal Lexicon

We propose a new model for unsupervised POS tagging based on linguistic distinctions between open and closed-class items. Exploiting notions from current linguistic theory, the system uses far less information than previous systems, far simpler computational methods, and far sparser descriptions in learning contexts. By applying simple language acquisition techniques based on counting, the system is given the closed-class lexicon, acquires a large open-class lexicon and then acquires disambiguation rules for both. This system achieves a 20% error reduction for POS tagging over state-of-the-art unsupervised systems tested under the same conditions, and achieves comparable accuracy when trained with much less prior information.
Work in progress - on introducing experiments in a Numerical Methods course

Several experiments have been developed and implemented in an undergraduate course in Numerical Methods. Most mathematical procedures that are taught in the course are covered in the analysis and interpretation of the data collected in these experiments. This paper describes the implementation of these experiments and how they are used in the course. Assessment data from two semesters for this WIP will be available at the time of the presentation.
Genoese Renaissance Villas: a Typological Introduction

This essay presents a typological introduction to Genoese Renaissance villas as an alternative building form to the urban palace and residential patterns of family life in the city. My survey focuses on Genoese villa architecture from the mid 15th through the late 16th century, following three historical phases of development: a late Lombard Gothic, an early Renaissance and a High Renaissance period. The close interrelationship of Genoese urban and suburban residences during this period of change is emphasized, as well as the underlying functions of the villa as a pleasure retreat from the city and a ceremonial (or formal entertainment) centre in nature. Finally, those stylistic influences from Northern and Central Italy are outlined that were so important for the development of a Genoese Renaissance villa style.
Mechanism for Improved Insulin Sensitivity after Gastric Bypass Surgery

Context: Surgical treatments of obesity have been shown to induce rapid and prolonged improvements in insulin sensitivity. Objective: The aim of the study was to investigate the effects of gastric bypass surgery and the mechanisms that explain the improvement in insulin sensitivity. Design: We performed a cross-sectional, nonrandomized, controlled study. Setting: This study was conducted jointly between the Departments of Exercise Science and Physiology at East Carolina University in Greenville, North Carolina. Subjects: Subjects were recruited into four groups: 1) lean [body mass index (BMI) 35 kg/m2; n = 43); and 4) postsurgery patients (BMI ≈ 30 kg/m2; n = 40). Postsurgery patients were weight stable 1 yr after surgery. Main Outcome Measures: Whole-body insulin sensitivity, muscle glucose transport, and muscle insulin signaling were assessed. Results: Postsurgery subjects had insulin sensitivity index value...
Design of Feedforward Input for Output-Settling Control With Dual-Stage Actuators

The settling problem is an output transition problem, i.e., given an initial state x(0), the goal is to bring the output to a desired value y(tf) = y macr and hold it constant after the end of settling, t > tf. This article develops the direct solution to the optimal-output-transition (OOT) problem for settling, and develops a method to use postactuation inputs to optimize the settling cost. The approach is illustrated with simulations on an example dual-stage system model. Simulations are also used to illustrate the reduction in the computational burden for online implementation by using linear combinations of precomputed inputs.
Bioactivation of halogenated hydrocarbons by cytochrome P4502E1.

Numerous halogenated hydrocarbons of the alkane, alkene, and alkyne classes are metabolized by P450 enzymes to products that elicit cytotoxic and/or carcinogenic effects. Such halogenated hydrocarbons include anesthetics (e.g., halothane and enflurane) and industrial solvents (e.g., carbon tetrachloride, chloroform, and vinylidine chloride). Formation of reaction intermediates from these compounds occurs via P450-promoted dehalogenation, reduction, or reductive oxygenation, with certain hydrocarbons undergoing all three reaction types. Of the multiple forms of P450 present in liver microsomes, P4502E1 has been identified as the primary catalyst of hydrocarbon bioactivation in animals and, most likely, in humans as well. As hepatic concentrations of this P450 enzyme are highly inducible by ethanol and similar agents, prior exposure to 2E1-inducing compounds can play a pivotal role in halogenated hydrocarbon toxicity. Considering that metabolism governs the cytotoxicity and carcinogenicity of halogenated hydrocarbons, an understanding of the mechanism(s) underlying 2E1 induction in man becomes all the more important.
Coalition Stability and Belief Change: Advocacy Coalitions in U.S. Foreign Policy and the Creation of Israel, 1922–44

This study examines whether advocacy coalitions are stable over time by examining legislative hearings data concerning U.S. foreign policy and the creation of Israel. It uses content analysis of 19 different policy core and deep core belief components applied to testimonies given in 1922 and in 1944. These belief components are used to identify members of advocacy coalitions and to test the coalitions' relative stability of membership over time. In addition, this research examines the stability of the belief systems of these advocacy coalitions. It finds that the structures of the advocacy coalitions remained relatively stable, yet new components of policy core beliefs emerged among all three advocacy coalitions, and such components are converging toward the belief system of the coalition advocating for the creation of Israel.
REDUCTIONISM AND PRACTICALITY

Like most domains of science, the study of the mind has been tackled at many scales of analysis, from the behavior of large groups of people (economics and ecology), to the diffusion of ions across cellular membranes (molecular biology and biophysics). At each of these scales, researchers often believe that the critical phenomena of interest, and the most powerful explanatory constructs and mechanisms, reside at their scale of analysis, with finer scales argued to be incapable of predicting the interesting phenomena, while coarser scales are purported to miss critical mechanistic subtleties. Here we argue by analogy that, for better or worse, researchers at all scales are correct: phenomena at each scale of analysis are intractable from other scales; thus, while reductionism is a useful scientific goal, it will not obviate the need for macroscopic research, constructs, and formalisms. At what scale should we study human behavior and the brain processes responsible? Fields at adjacent scales of analysis find themselves in similar disagreements, with every field condemning more abstract scales of analysis for failing to describe "how" various processes work, and more minute scales for missing the forest for the trees. Conveniently, the purportedly appropriate scale of analysis for studying "mechanisms" of mind and behavior usually coincides with that of the speakers' own research program. Computational cognitive scientists argue that understanding the brain requires a more abstract description of the organisms goals and available information, and claim cognitive psychologists face an insurmountably under constrained task in trying to describe the function of the whole organism by cobbling together isolated algorithms. Cognitive psychologists in turn condemn computational cognitive scientists for working with idealized learning models and glossing over specific errors and deviations from these idealizations found while studying particular psychological mechanisms.
Axial diffusion and Michaelis-Menten kinetics in oxygen delivery in rat peripheral nerve

Our simulation of the release, diffusion, and consumption of oxygen in the capillaries and surrounding tissue of peripheral nerve now includes axial diffusion in blood and in surrounding tissue, in addition to bulk flow of blood and radial diffusion of oxygen out of the capillary. Our simulation assumes that the oxygen consumption of nerve tissue obeys Michaelis-Menten kinetics rather than zero-order kinetics as had been assumed in the Krogh model. We can calculate the oxygen tension at all points in the capillary and surrounding tissue as a function of distance from the center of the nearest capillary and distance along the capillary from the arterial to the venous end. Using average measured values for microcirculatory parameters in rat nerve, we calculated a distribution of oxygen tension values that agrees with experimentally measured distributions. The effects of axial diffusion and of Michaelis-Menten kinetics on the oxygen distributions were noticeable under normal conditions, but these effects were much more important in situations in which oxygen delivery was adversely affected.
Evolution and Coevolution in Communities

Communities, broadly defined, are evident virtually from the beginning of the fossil record; the most general features of their structure may be said to arise automatically, but this cannot be said for more detailed aspects of structure, such as resource partitioning, even for contemporary communities. Diversity, although interrupted by major extinction events, tends to increase globally and probably locally. Although some guilds may approach the limits of species packing, new resources (species) emerge during evolution: these species and those that evolve to use them contribute to long-term increases in diversity. Trends toward greater ecological specialization may exist but are uncertain. Analogies between these trends and those that characterize ecological succession are probably just that. The taxonomic composition of a community is determined largely by ecological processes of invasion and extinction of species that owe their attributes more to phylogenetic history, to a long, extremely diffuse history of spatially, temporally, and phylogenetically discontinuous ecological interactions, than to immediate coevolutionary responses in situ or to coevolutionary adjustment of particular lineages over extended periods of ecological time.
Reevaluation of the Pyrazinamide Suppression Test

In 1961 Gutman and Yu proposed a three component system for the regulation of the renal excretion of uric acid in man. The first component of this system is filtration of plasma urate at the glomerulus. While this process is certain to be operative in the human kidney, its quantitative role in the renal excretion of uric acid in man depends upon the extent of urate binding to plasma proteins in vivo. This is a subject that is being discussed in another section of this symposium and will not be considered further in this paper. The second and third component of this system relate to uric acid reabsorption and secretion by the human nephron. Ample data is available to document that both of these processes are operable in the human kidney (Gutman and Yu, 1957; Gutman, et al., 1959), but the relative contribution of each to the final excretion of uric acid has been difficult to determine with conventional clearance techniques. However, a potential solution to this problem of bidirectional uric acid transport appeared in 1967 when Steele and Rieselbach introduced the “pyrazinamide suppression test”.
Structural Remodeling of Bacteriophage Φ29 during Infection of Gram-Positive Bacterium

Recent advances in cryo-electron tomography (cryo-ET) and the ability to isolate bacterial minicells have allowed direct visualization of the initial interactions between bacteriophages and their host bacteria. Thus far, studies have been limited to Gram-negative bacteria but the mechanism of infection of Gram-positive bacteria is unknown. Of particular interest is how phages penetrate the thick and highly cross-linked peptidoglycan layer of the Gram-positive cell wall. Here we detail the structural intermediates of phage Φ29 during infection of the Gram-positive Bacillus subtilis. As a member of the Podoviridae, Φ29 has an icosohedral head that contains the ∼20 kb genome with a short non-contractile tail. Minicells were generated from B. subtilis, infected with Φ29, and cryo-ET was then employed to study adsorption and the initial stages of infection. Many phages were observed adsorbed to the cell wall, in both pre- and post-DNA ejection states. Analysis of the structural intermediates suggests that phages first stably contact the cell wall at an angle using their appendages. In mature virions, appendages existed either in an extended or a downward conformation parallel to the tail. The phage then reorients to become perpendicular to the cell wall, a process that must involve conformational changes in at least some appendages. A peptidoglycan-degrading enzyme that is known to be present in the distal tail knob likely digests the cell wall, clearing a path towards the cytoplasmic membrane. Phage tail tubes were evident in direct contact with the outer face of the cytoplasmic membrane, suggesting contact likely triggers DNA ejection. Whether the phage tail directly penetrates the membrane into the cytoplasm is currently being addressed by subtomogram averaging of phages in contact with the membrane. This work was supported by grants from the NIGMS (GM110243) and the Welch Foundation (AU-1714).
In vitro granulocytic colony-forming potential of bone marrow from patients with granulocytopenia and aplastic anemia.

SummaryThe colony-forming potential in agar-gel of bone marrows from patients with aplastic anemia and granulocytopenia has been studied. It has been shown that bone marrow cells from these patients retain the ability to produce colonies in vitro, but that the number of colonies formed is reduced compared to normal human bone marrow. No inhibitory effect of serum or plasma from patients with aplastic or granulocytopenic states was found upon the colony growth of normal human bone marrow.
The discovery and early structural studies of arachidonic acid

Arachidonic acid and esterified arachidonate are ubiquitous components of every mammalian cell. This polyunsaturated fatty acid serves very important biochemical roles, including being the direct precursor of bioactive lipid mediators such as prostaglandin and leukotrienes. This 20 carbon fatty acid with four double bonds was first isolated and identified from mammalian tissues in 1909 by Percival Hartley. This was accomplished prior to the advent of chromatography or any spectroscopic methodology (MS, infrared, UV, or NMR). The name, arachidonic, was suggested in 1913 based on its relationship to the well-known arachidic acid (C20:0). It took until 1940 before the positions of the four double bonds were defined at 5,8,11,14 of the 20-carbon chain. Total synthesis was reported in 1961 and, finally, the configuration of the double bonds was confirmed as all-cis-5,8,11,14. By the 1930s, the relationship of arachidonic acid within the family of essential fatty acids helped cue an understanding of its structure and the biosynthetic pathway. Herein, we review the findings leading up to the discovery of arachidonic acid and the progress toward its complete structural elucidation.
Design and Realization of National Critical Infrastructure Model

More and more countries pay great attention to the modeling and simulation of their national critical infrastructure.In order to meet the requirement of simulating national critical infrastructure under crisis and search modeling and simulation methods of complex system,the basic concept and components of national critical infrastructure were clarified,and the necessity of using modeling and simulation as the only method to research the problem was analyzed.Then based on the design thought of X On Demand,a main structure of national critical infrastructure model was designed.The realization and integration method of each sub-model were also deeply studied.This model and its design method can offer a good reference for modeling complex social systems.In the end,the main problems to be resolved later were pointed out.
40 INVESTIGATING THE EXPRESSION PATTERNS OF TRANSCRIPTION FACTORS IMPORTANT DURING T-CELL DEVELOPMENT

During T-cell development, common lymphoid progenitors, undergo a stepwise loss of potential to become various lymphocytic cells and commit themselves to the T-cell lineage. T-cell development is characterized by several important and interesting events including TCR gene rearrangement, and transition from a double negative (DN) stage in which neither CD4 or CD8 receptors are expressed to a double positive (DP) stage where both are expressed, prior to final differentiation where only one is expressed and T-helper (CD4) cells can be distinguished from cytotoxic (CD8) T-cells. In order to understand the mechanisms of T-cell development, it is important to know which transcription factors are present at each of the developmental stages. Previous studies have shown unique patterns of expression for mRNA9s of 9 members of the ETS family of transcription factors, and an alternative and canonical form of a class A bHLH factor known as HEB. Here we investigated the patterns of expression of protein products of these mRNA9s and demonstrated that the protein products are expressed in similar patterns as the mRNA9s for three of these transcription factors, Erg, Fli-1, and PU.1 While Fli-1 seems to be expressed equally at all stages of development, Erg and PU.1 are present at higher levels in DN thymocytes. Results with HEB demonstrate higher expression levels of the protein in DN thymocytes than in DP thymocytes as seen with the alternative form of the mRNA. Comparison of western blots on mouse thymocytes and jurkat cells suggests that the HEB in mouse thymocytes is different in size than that of the jurkat cells, suggesting that the protein may be the alternative form.
Depression: Natural Responses

Many psychiatrists and psychologists view depression as frozen anger. In this theory when the depressed person cannot release his or her anger, it turns inward and the person becomes depressed. Sigmund Freud discussed the basic psychoanalysis of depression in his book, Mourning and Melancholia [1].
An Informatics Research Roadmap to Facilitate Precision Medicine

There is increasing recognition by practitioners, researchers, patients and policymakers of the promise of precision medicine for improving health. The intent of precision medicine is to integrate individual genetic data with existing health information to predict disease risk, develop prevention strategies, accurately establish disease course and tailor management plans. President Obama launched the National Institutes of Health Precision Medicine Initiative (PMI)2 in January 2015. The PMI consists of a near-term study focused on oncology and a longer-term goal to increase broad understanding of health and disease. A key component of the longer-term goal is the PMI-Cohort Program, which will assemble health data for 1 million volunteers that includes environmental exposures, lifestyle habits, longitudinal medical history and genetic information. The Food and …
Time-resolved Analysis of Proteome Dynamics by Tandem Mass Tags and Stable Isotope Labeling in Cell Culture (TMT-SILAC) Hyperplexing

Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples. The fractional labeling of multiple time-points can be measured in a single mass spectrometry run, providing temporally resolved measurements of protein turnover kinetics. To demonstrate the feasibility of the approach, we simultaneously measured the kinetics of protein clearance and accumulation for more than 3000 proteins in dividing and quiescent human fibroblasts and verified the accuracy of the measurements by comparison to established non-multiplexed approaches. The results indicate that upon reaching quiescence, fibroblasts compensate for lack of cellular growth by globally downregulating protein synthesis and upregulating protein degradation. The described methodology significantly reduces the cost and complexity of temporally-resolved dynamic proteomic experiments and improves the precision of proteome-wide turnover data.
Substructure of the Nucleon in the Chiral Quark Model

The spin and orbital angular momentum carried by different quark flavors in the nucleon are calculated in the SU(3) chiral quark model with symmetry-breaking. The similar calculation is also performed for other octet and decuplet baryons. Furthermore, the flavor and spin contents for charm and anti-charm quarks are predicted in the SU(4) symmetry breaking chiral quark model.
Multistage Stochastic Investment Planning With Multiscale Representation of Uncertainties and Decisions

We propose a multistage multiscale linear stochastic model to optimize electricity generation, storage, and transmission investments over a long planning horizon. The multiscale structure captures “large-scale” uncertainties, such as investment and fuel-cost changes and long-run demand-growth rates, and “small-scale” uncertainties, such as hour-to-hour demand and renewable-availability uncertainty. The model also includes a detailed treatment of operating periods so that the effect of dispatch decisions on long-term investments are captured. The proposed model can be large in size. The progressive hedging algorithm is applied to decompose the model by scenario, greatly reducing computation times. We also derive bounds on the optimal objective-function value, to assess solution quality. We use a case study based on the state of Texas to demonstrate the model and show the benefits of its detailed representation of the operating periods in making investment decisions.
Enhanced heterogeneous ice nucleation by special surface geometry

The freezing of water typically proceeds through impurity-mediated heterogeneous nucleation. Although non-planar geometry generically exists on the surfaces of ice nucleation centres, its role in nucleation remains poorly understood. Here we show that an atomically sharp, concave wedge can further promote ice nucleation with special wedge geometries. Our molecular analysis shows that significant enhancements of ice nucleation can emerge both when the geometry of a wedge matches the ice lattice and when such lattice match does not exist. In particular, a 45° wedge is found to greatly enhance ice nucleation by facilitating the formation of special topological defects that consequently catalyse the growth of regular ice. Our study not only highlights the active role of defects in nucleation but also suggests that the traditional concept of lattice match between a nucleation centre and crystalline lattice should be extended to include a broader match with metastable, non-crystalline structural motifs.
You Can Have It All – Fast Algorithms for Blind Deconvolution, Self-Calibration, and Demixing

We present new fast algorithms for solving the important problems of blind deconvolution, selfcalibration, and demixing. We disucss the performance of these algorithms, their theoretical foundations, and applications for image processing and for the Internet-of-Things.
Microbial community composition along the digestive tract in forage- and grain-fed bison.

Diversity and composition of microbial communities was compared across the 13 major sections of the digestive tract (esophagus, reticulum, rumen, omasum, abomasum, duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, and rectum) in two captive populations of American bison (Bison bison), one of which was finished on forage, the other on grain. Microbial diversity fell to its lowest levels in the small intestine, with Bacteroidetes reaching their lowest relative abundance in that region, while Firmicutes and Euryarchaeota attained their highest relative abundances there. Gammaproteobacteria were most abundant in the esophagus, small intestine, and colon. The forage-finished bison population exhibited higher overall levels of diversity, as well as a higher relative abundance of Bacteroidetes in most gut sections. The grain-finished bison population exhibited elevated levels of Firmicutes and Gammaproteobacteria. Within each population, different sections of the digestive tract exhibited divergent microbial community composition, although it was essentially the same among sections within a given region of the digestive tract. Shannon diversity was lowest in the midgut. For each section of the digestive tract, the two bison populations differed significantly in microbial community composition. Similarities among sections indicate that the esophagus, reticulum, rumen, omasum, and abomasum may all be considered to house the foregut microbiota; the duodenum, jejunum, and ileum may all be considered to house the small intestine or midgut microbiota; and the cecum, ascending colon, transverse colon, descending colon, and rectum may all be considered to house the hindgut microbiota. Acid from the stomach, bile from the gall bladder, digestive enzymes from the pancreas, and the relatively low retention time of the small intestine may have caused the midgut’s low microbial diversity. Differences in microbial community composition between populations may have been most strongly influenced by differences in diet (forage or grain). The clinical condition of the animals used in the present study was not evaluated, so further research is needed to establish whether the microbial profiles of some bison in this study are indeed indicative of dysbiosis, a predisposing factor to ruminal acidosis and its sequelae.
Reality, Process, and the Dialetical Relation between Man and Environment

An increasing desire for more complete levels of understanding of the relationship between man and environment led, in the later nineteen-sixties and early seventies, to a variety of research efforts focussing on the difference between form and process oriented approaches in human geography (e.g., Olsson (1969); Olsson and Gale (1968); King (1969); Golledge (1970); Olsson (1971) and Eichenbaum and Gale (1971)). Most of these papers discussed in some way the relative contribution of spatial form and spatial processes to our understanding of human behavior, and some specifically argued that more attention should be paid to human behavioral processes such as learning, perception, and attitude formation as part of the geographer’s explanatory schema. Concurrently there existed a growing concern for discovering what man knew of the various environments in which he existed (Lynch, 1960; Gould, 1965; Golledge, Briggs, and Demko, 1969; Appleyard, 1970; Downs, 1970). This latter research began uncovering various properties of ‘known’ environments that appeared to be somewhat different from the world of substance and fact which is experienced by our senses and which is usually described in terms of atomistic facts and mechanistic forces (Russell, 1918; Whitehead, 1933).
Recorded Maternal Voice, Recorded Music, or Live Intervention: A Bioecological Perspective

Introduction: The human infant develops in his or her expected bioecological niche based on experience-dependent regulation of physiology, motor control, and arousal, typically provided by close contact with the mother. Synchrony, intensity, tempo, and rhythm of a mother’s physical and vocal communication are embedded in what the infant experiences and lay the foundation for attachment relationships and optimal development. Infants who have significant medical issues or are early born experience a different developmental niche than would a typically developing infant. This chapter addresses the complexities of exposure of the newborn in intensive care to different models of intimate caregiving, including the mother’s recorded or live voice and recorded or live music, in the context of current knowledge of necessary species-specific, co-regulatory synchronous interactions. Additionally, the chapter explores opportunities and barriers to the provision of optimal mother-infant communication in intensive care.