cssi/SciSciGPT-SciSciNet huggingface dataset:
Scale formation in selected fundulid and cyprinodontid fishes

Patterns of scale formation (onset, points of origin, completion, and spatial pattern) were examined for six species of killifishes in two families (Cyprinodontidae: Cyprinodon variegatus, and Fundulidae: Fundulus confluentus, F. heteroclitus, F. luciae, F. majalis, and Lucania parva) to determine if the patterns are another useful indicator for the transition from the larval to juvenile periods. In some species, the patterns were very similar, with scale formation originating on/near the caudal peduncle, then the dorsal surface of the head (in fundulids only), and later on the lateral surfaces of the head, and on the ventral surface of the trunk at the level of the pectoral fin. The timing of scale formation, relative to fish size, was later than or overlapped with other morphological characters (e.g., fin ray formation, juvenile/adult body shape) often used to mark the larval/juvenile transition. The onset of scale formation, across all species, occurred between 8 and 13 mm TL. Completion of scale formation occurred between 18 and 23 mm TL. At completion, scales covered 86–99% of the trunk and head. Completion of scale formation in these fishes is one of the last external morphological changes to occur during the larval to juvenile transition. For these species, and other flatfishes we have examined in detail, it appears that scale formation may be useful in helping to define the end of the larval period and the beginning of the juvenile period. Further studies, of divergent groups of teleosts, are necessary to determine if this length-based approach has broad validity.
A TECHNIQUE FOR THE COMBINATION OF CLEARING, STAINING, AND INJECTING SMALL MAMMALS

A combined method for clearing soft tissues, staining cartilage and bone, and injecting the vascular system of small mammals was developed using Mus musculus (house mouse). Mammalian muscle tissue ...
Buffer-layer-assisted nanostructure growth via two-dimensional cluster-cluster aggregation

Physical vapor deposition of Au onto Xe multilayers on amorphous carbon at 20 K produces three-dimensional nanoclusters. Warming to room temperature desorbs the Xe and imparts limited mobility to the clusters. Coalescence occurs when two clusters come in contact, and the extent of coalescence depends on the buffer layer thickness. Using transmission electron microscopy images, we determined the spatial distribution of clusters as a function of Xe thickness and applied the scaling concepts of cluster–cluster aggregation to better understand processes associated with growth. Analysis shows a coverage dependent fractal dimension that extends from D � 1:42 to 1.72 for initial fractional surface coverages of q0 � 0:04–0.21, consistent with Monte Carlo simulations of two-dimensional diffusion-limited cluster aggregation (DLCA). Both the total number of clusters per unit area and the weighted average cluster size show a power law dependence on the Xe layer thickness, where the buffer layer thickness plays the role of time in DLCA modeling. These relationships will facilitate the design of nanostructure arrays generated by desorption-assisted coalescence. 2002 Elsevier Science B.V. All rights reserved.
Baiting the cross-face nerve graft with temporary hypoglossal hookup.

BackgroundCross-face nerve grafting yields inconsistent neural regeneration, and methods that promote more robust axonal traversing of the graft would expand the indications for this procedure. Obj...
A PHY-MAC Cross-Layer Protocol for Ad Hoc Networks with Multiple-Antenna Nodes

In this paper, we propose a physical (PHY) - medium access control (MAC) cross-layer protocol for ad hoc networks with antenna-array-equipped nodes that employ single-antenna transmission and multiple-antenna reception. Our protocol extends the progressive back-off algorithm (PBOA), proposed by Toumpis and Goldsmith, by integrating medium access and power control with optimum receive beamforming (ORB); hence it is named PBOA-ORB. The protocol performance is evaluated via simulations over a single-hop ad hoc network that is subject to a uniform traffic load. It is shown that PBOA-ORB significantly enhances both the aggregate throughput and the energy efficiency of PBOA by harnessing the interference suppression and array gains of receive beamforming. Specifically, for a small number of antennas compared to the number of nodes, the aggregate throughput increases linearly with the number of antennas while the average energy consumption per data packet decreases.
Data-Driven Professional Development: The Professional Development Plan for a Reading Excellence Act School.

Abstract The purpose of this article is to describe the professional development plan for an elementary school receiving federal funding through the Reading Excellence Act (REA). The Reading Excellence Act provided the school with a two‐year plan for literacy improvement. During the first year of the grant, assessment‐driven instruction and flexible grouping for instruction were the focus of professional development. This article focuses on the professional development of the second year of the grant during which school‐based data provided the REA grant coordinator with instructional needs of the staff, and disaggregated data provided specific needs for each grade level. Based upon the analysis of student achievement data, professional development for kindergarten and first grade teachers focused on training in word study to improve phonics and spelling achievement. Professional development for second through fourth grade teachers focused on fluency instruction and comprehension instruction, including nar...
Logarithmic Mori Program

The purpose of this chapter is twofold. The first is to review what we have learned so far by going over the main ingredients of the Mori program in the framework of the logarithmic category. The reader who feels confident of and comfortable with the material so far should have no trouble understanding this part and should even skip this review chapter. Mastery and understanding of the log minimal model program will be rewarded when we utilize it as an essential part of the Sarkisov program in Chapter 13. The second is to present some of the subtleties that inevitably arise as we go from the usual category to the logarithmic category. There are some open conjectures even in dimension 3, though their statements are the natural generalizations in the logarithmic category, according to Iitaka’s philosophy, of the corresponding ones in the usual category.
A Study of Quality of Internal Control in the US Federal Financial Management Systems

The primary purpose of this study is three-fold: to identify regulations designed to improve the United States government’s financial management, to examine the current state of the agencies’ financial statements’ audit and internal control and to investigate the changes, if any, in internal control over the past few years.The results demonstrate that while the US Congress has been vigilant in emphasising the importance of improving internal control over the federal financial statements, most agencies’ financial management systems are still marred with significant internal control weaknesses. More work is needed to strengthen the control systems in federal government and to develop a financial management system that is capable of producing reliable financial statements, and designed to generate financial statements that are comparable across the agencies and consistent from year to year.
Quantitative performance of internal standard platforms for absolute protein quantification using multiple reaction monitoring-mass spectrometry.

Stable-isotope-labeling mass spectrometry involves the addition of known quantities of stable-isotope labeled standards, which mimic native molecules, to biological samples. We evaluated three conventional internal standard platforms (synthetic peptides, QconCAT constructs, and recombinant proteins) for quantitative accuracy, precision, and inherent advantages and limitations. Internal standards for the absolute quantification of three human cytokine proteins (interferon gamma, interleukin-1 beta, and tumor necrosis factor alpha) were designed and verified. Multiple reaction monitoring assays, calibration curve construction, and regression analysis were used to assess quantitative performance of the internal standard platforms. We also investigated a strategy for methodological improvement to current platforms using natural flanking sequences. Data analysis revealed that full length protein standards have the broadest quantitative reliability with accuracy being peptide-dependent for QconCATs and syntheti...
Community Gardens for Refugee and Immigrant Communities as a Means of Health Promotion.

Refugees and new immigrants arriving in the United States (U.S.) often encounter a multitude of stressors adjusting to a new country and potentially coping with past traumas. Community gardens have been celebrated for their role in improving physical and emotional health, and in the Twin Cities of Minnesota, have been offered as a resource to immigrants and refugees. The purpose of this study is to present a mixed method evaluation of a refugee gardening project hosted by area churches serving primarily Karen and Bhutanese populations. Quantitative data were obtained from early and late season surveys (44 and 45 % response rates, respectively), and seven focus groups conducted at the end of the season provided qualitative data. Although few gardeners (4 %) identified food insecurity as a problem, 86 % indicated that they received some food subsidy, and 78 % reported vegetable intake increased between the early and late season surveys. Twelve percent of gardeners indicated possible depression using the PHQ-2 scale; in focus groups numerous respondents identified the gardens as a healing space for their depression or anxiety. Refugee gardeners expressed receiving physical and emotional benefits from gardening, including a sense of identity with their former selves. Gardens may serve as a meaningful health promotion intervention for refugees and immigrants adjusting to the complexity of their new lives in the U.S. and coping with past traumas.
Abstract IA20: Hypoxia, metabolism, and tumor progression

Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney malignancy. It is both chemotherapy and radiation resistant and current treatment options for this disease are limited, particularly because 1 out of 4 patients are diagnosed at a disseminated, metastatic disease state. Underlying these clinical characteristics are a number of changes at the molecular level, the most pronounced of which are metabolic alterations that promote malignancy. One of these modifications is to the urea cycle, which is the second most underexpressed metabolic pathway in ccRCC. The urea cycle occurs in the kidney and is involved in detoxification of free ammonia species. Two key enzymes in this cycle are arginase II (ARG2) and argininosuccinate synthase 1 (ASS1); ARG2 is included on chromosome 14q and loss of this region correlates with high malignancy grade and a poorer prognosis in ccRCC. Data from nearly 500 primary ccRCC tumors in The Cancer Genome Atlas (TCGA) dataset demonstrates that ARG2 exhibits copy number loss in 40% of ccRCC and is underexpressed at the mRNA level, whereas ASS1 is significantly underexpressed, but not deleted, in ccRCC compared to normal kidney tissue. In preliminary experiments, we have demonstrated that re-expressing these enzymes in ccRCC cell lines suppresses proliferation in vitro and in vivo during xenograft tumor growth. Furthermore, re-expression of ARG2 and ASS1 reduces glycolytic flux and decreases mTOR activity. The central hypothesis of our work is that ARG2 and ASS1 act as tumor suppressors by modulating urea cycle and glycolytic metabolism and by repressing mTORC1 dependent growth pathways. The objective is to define the molecular mechanisms by which ARG2 and ASS1 loss alters cellular metabolism to promote ccRCC tumor growth. Delineating these mechanisms will provide new therapeutic avenues to target in this disease. Citation Format: Marie Celeste Simon. Hypoxia, metabolism, and tumor progression. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr IA20.
Language and cultural contacts among Yukatekan Mayans.

The Yukatekan branch of the Maya language family, spread across the Yucatan Peninsula of Mexico, northern Guatemala, and Belize, began to diversify approximately 1, 000 years ago. Today it has four branches: Mopan Maya,Itzaj Maya, Lakantun Maya and Yukatek Maya proper, which have widely varying language statuses. Lakantun and Itzaj Maya are seriously threatened, while Mopan appears to have a stable or growing population of approximately 10,000 speakers and Yukatek has a very large number of speakers, perhaps 750,000. However, even many Yukateks believe that their language is threatened and that shift to Spanish is underway. During the past millennia there has been a series of contacts involving migration, trade, warfare, and flight among the different branches, as well as with other Mayan languages and with the Spanish. This paper examines a variety of different kinds of contact, and how the different language varieties were involved and affected. One goal of the paper is to better understand how the dynamics of inter-cultural contacts affects language practices resulting in very different language statuses and ideologies.
Later adults' cultural life scripts of middle and later adulthood.

ABSTRACTThe cultural life script (CLS) refers to expected prototypical life events, often including life transitions overwhelmingly occurring at ages 11-30. This study outlined CLS events at ages after the majority of these events typically occur. Participants, age 38-76, nominated events they expected a person of their age to experience in the future. Participants rated each event’s valence, importance, prevalence, and expected age of occurrence. Events were coded into three categories: the normative CLS for events listed by previous CLS studies, offspring’s CLS for experiencing CLS events of offspring, and later adulthood CLS for other events nominated by at least 4% of participants. Results suggest scripted events highlighting positivity and change. Offspring’s CLS was more positive and occurred earlier than others. Correlations emerged between event characteristics and well-being. Results affirm the prominence of transitions in memory, and suggest ways that older adults maintain well-being despite a c...
Simulation of GaN-based Light-Emitting Devices

Comprehensive physics-based simulations of GaN-based light-emitting diodes and laser diodes are presented. The talk discusses unique material properties of nitride compounds as well as performance-limiting physical mechanisms like self-heating, current crowding, and carrier leakage. Measurements are used to validate the models and to extract critical device parameters.
Becoming-academic in the neoliberal academy: A collective biography

ABSTRACTAs evidenced by the collection of articles in Gender and Education’s July 2015 issue and various articles that have circulated recently on social media [American Council on Education. 2016. “New report looks at the status of women in higher education.” January 15. http://www.acenet.edu/news-room/Pages/New-Report-Looks-at-the-Status-of-Women-in-Higher-Education.aspx; Donald, A. 2016. “Women are too often actively sidelined against their will.” Times Higher Education. https://www.timeshighereducation.com/blog/women-are-too-often-actively-sidelined-against-their-will; Higher Education Network. 2016. “How should we cope with sexism? That’s the wrong question.” The Guardian. April 15. https://www.theguardian.com/higher-education-network/2016/apr/15/how-should-we-cope-with-sexism-thats-the-wrong-question], the topic of gender in higher education is of concern to many in both academic and non-academic thought-spaces. In this collective biography, we explore entrance into the fraught and contested space o...
Quantifying flow interval–pollutant loading relationships in a rapidly urbanizing mixed-land-use watershed of the Central USA

Rapid urbanization and agricultural development have altered flow and pollutant loading regimes resulting in poorly understood pollutant transport regimes and inadequately conceived management practices. Four years of hydrologic and water quality data (i.e., stream flow, suspended sediment, nitrate, nitrite, total ammonium, total inorganic nitrogen, and total phosphorus) were collected using a five-site nested-scale study design in a representative mixed-land-use watershed. Cumulative nested sub-basin drainage areas ranged from 79 to 208 km2. Daily flow and load duration analyses were used to quantify land use impacts to flow-mediated pollutant loading at multiple flow intervals including high flows (0–10%), moist conditions (10–40%), mid-range flows (40–60%), dry conditions (60–90%), and low flows (90–100%). Pollutant loads ranged across four orders of magnitude for suspended sediments, and three orders of magnitude for nutrient loads during the high flow interval when nearly all of the total pollutant loads were transported (e.g., 99% of suspended sediments, 92% of total inorganic nitrogen, and 95% of total phosphorus loads). Results from stepwise multiple linear regression analyses showed significant relationships between land use, flow, and pollutant load at high flows, moist conditions, and mid-range flow intervals (R 2 > 75.7; p < 0.035). No significant relationships (p < 0.05) were detected during dry conditions, or low flow intervals. Results highlight the need for consideration of combined flow and pollutant loading targets appropriate for watersheds modified by current and ongoing land use and point to a need for long-term and broad-scale efforts to develop achievable hydrologic and water quality recommendations especially in rapidly urbanizing mixed-land-use watersheds.
Single Incision Laparoscopic Resection of a Giant Ovarian Mature Cystic Teratoma

Abstract Introduction: Ovarian tumors in the pediatric population are a rare occurrence, with an incidence of 2.6 cases per 100,000 girls per year.1 Ovarian teratomas are germ cell tumors further c...
Skinner’s Elementary Verbal Relations: Some New Categories

In Verbal Behavior (1957) B. F. Skinner identified and named five elementary verbal relations: mand, tact, intraverbal, textual and echoic. Because of their etymological commitment to visual and auditory stimuli respectively, the last two categories do not function well as general categories. Adding two more general categories, codic and duplic, to the first three results in a set of five mutually exclusive and collectively exhaustive groupings. Textual behavior and other relations involving point-to-point correspondence but no formal similarity fall into the codic category. Echoic behavior and other relations with formal similarity fall into the duplic category. This arrangement results in useful category names for all elementary forms and prevents potentially confusing extensions, such as referring to Braille reading as textual behavior, or sign imitation as echoic behavior.
Subglottic Tracheal Stenosis

The resection and reconstruction of benign laryngotracheal strictures demands from the surgeon a critical selection of patients and careful preoperative judgment. The technical execution of the operation depends on mucosal resurfacing of cartilaginous planes within a small subglottic lumen. Postoperative edema or mucosal compromise potentially threatens the airway and clinical outcome; this circumstance explains the somewhat higher early complication rate and the slightly inferior long-term results compared with simple tracheal end-to-end anastomosis. When carefully performed, however, laryngotracheal reconstruction offers effective treatment with excellent long-term results for both idiopathic and intubation stenosis.
Adiabatic Fock State Generation Scheme Using Kerr Nonlinearity

We introduce a theoretical scheme for generating Fock states using a Kerr cavity by adiabatic variation of the detuning and driving field amplitude. We perform numerical calculations to determine requirements for experimental feasibility.
Global and Local Sources of Mercury Deposition in Coastal New England Reconstructed from a Multiproxy, High-Resolution, Estuarine Sediment Record.

Historical reconstruction of mercury (Hg) accumulation in natural archives, especially lake sediments, has been essential to understanding human perturbation of the global Hg cycle. Here we present a high-resolution chronology of Hg accumulation between 1727 and 1996 in a varved sediment core from the Pettaquamscutt River Estuary (PRE), Rhode Island. Mercury accumulation is examined relative to (1) historic deposition of polycyclic aromatic hydrocarbons (PAHs) and lead (Pb) and its isotopes (206Pb/207Pb) in the same core, and (2) other reconstructions of Hg deposition in urban and remote settings. Mercury deposition in PRE parallels the temporal patterns of PAHs, and both track industrialization and regional coal use between 1850 and 1950 as well as rising petroleum use after 1950. There is little indication of increased Hg deposition from late 19th-century silver and gold mining in the western U.S. A broad maximum of Hg deposition during 1930–1980, and not found in remote sites, is consistent with the pr...
Gross Morphometry, Histomorphometry, and Immunohistochemistry Confirm Early and Persistent Jejunal Crypt Hyperplasia in Poults with Enteritis and Depressed Growth.

SUMMARY Phosphorylated histone 3 (PH3) and cleaved caspase 3 (CCASP3) were used to detect proliferating and apoptotic cells, respectively, in the jejunums of female sibling poults, with and without enteritis and depressed growth, from hatch to day 35. Poults that developed enteritis and depressed growth (SIB flock) were raised on a commercial farm in eastern North Carolina, whereas poults with normal growth and no enteritis (TAU flock) were raised in the Teaching Animal Unit at North Carolina State University College of Veterinary Medicine. Beginning on day 5 through day 35 and at processing, TAU poults were significantly heavier than SIB poults. Jejunal weights, relative jejunal weights, and jejunal densities were greater in SIB poults from day 10 through 35. Jejunal efficiency (body weight /jejunal length) was higher in TAU poults at day 5 and days 10 through 35. Mucosal thickness was greater in SIB poults between days 7 and 21 but greater in TAU poults at days 28 and 35. From day 7 to 35, villus-to-cry...
Time-averaged three-dimensional flow topology in the wake of a simplified car model using volumetric PIV

Fuel shortages and air pollution are two major incentives for improving the aerodynamics of vehicles. Reducing wake-induced aerodynamic drag, which is strongly dependent on flow topology, is important for improving fuel consumption rates which directly affect the environment. Therefore, a comprehensive understanding of the baseline flow topology is required to develop targeted drag reduction strategies. In this research, the near wake of a generic ground vehicle, a $$25^{\circ }$$ slant Ahmed model at a flow Reynolds number of $$Re =1.1\times 10^{6}$$ , is investigated and its flow topology elucidated. The flow field of this canonical bluff body is extremely rich, with complex flow features such as spanwise trailing wake and streamwise C-pillar vortices. The flow is characterized through stereoscopic and tomographic velocity field measurements. The large-scale, horseshoe vortex structures in the trailing wake, conventionally denoted as A- and B-vortices, are found to vary in size and shape along the spanwise direction, which in turn influence the pressure distribution on the rear vertical surface. The longitudinal C-pillar vortices are found to extend far downstream and also influence the trailing wake structures through a complex, three-dimensional interaction. The accuracy and cost of obtaining volumetric information in this complex flow field, by means of volume reconstruction, through Stacked Stereoscopic-Particle Image Velocimetry (PIV) and Tomographic PIV are also investigated.
Comment on "Accurate experimental values for the free energies of hydration of H+, OH-, and H3O+".

In the subject paper, Plascak and Shields claim to have derived accurate experimental values for the hydration free energies of H+, OH?, and H3O+. The purpose of this comment is to alert the community that, in fact, their values are less accurate than the values they are meant to replace. In what follows we show the errors PS made and, by example, give practical advice on how to ensure correct assignment of standard states for reactions with water as a reactant or product in gas and solution phases.
Radiation imaging: an interesting utilization of nuclear engineering methodology

Using well-established nuclear engineering methods, an interesting new radiation imaging technique has been developed. Scattered neutrons and photons have been found to carry detailed information a...
Head and Neck Cancer Surgery II: Reconstruction

Patients presenting for head and neck cancer resections may eventually require surgical reconstruction to fix anatomic defects and maintain aerodigestive and masseter function. Complex head and neck reconstructive surgery represents a unique interaction between the reconstructive surgeon and the anesthesiologist. The management of head and neck pathology including trauma, congenital deformities, as well as benign and malignant tumors requires a substantial array of reconstructive techniques. Over the last several decades the most significant reconstructive advancement from the surgical standpoint is the technique of free tissue transfer, the so-called “free flap.” This procedure involves harvesting distant tissues and transferring reconstructive elements such as bone, soft tissue, and muscle to ablative defects of the head and neck (see Fig. 16.1).
Serum osmolality in acute intoxication: a prospective clinical study.

The authors prospectively performed simultaneous determinations of serum delta osmolality (∆-Osm), enzymic (alcohol dehydrogenase [ADH]) quantitation of serum ethanol (EtOH), and urine drug screens on 339 acutely intoxicated patients. In addition, the authors established reference ranges for measured and calculated serum osmolalities in a group of 55 healthy volunteers. The authors determined the clinical utility of the combined ∆-Osm/ADH procedure for detecting the presence of EtOH or other low molecular weight (Mr) volatiles. In the reference population, the measured osmolality (M-Osm) and calculated osmolality (C-Osm) was 285.1 ± 4.3 (SD) mOsm/kg and 287.4 ± 5.1 (SD) mOsm/kg, respectively. The correlation between ∆-Osm and serum EtOH was 0.968 in 151 patients in whom EtOH was detected. The presence of drugs in 67 (44%) patients or absence of drugs in 84 (55.6%) patients was shown to have no significant effect on the ∆-Osm. The ∆-Osm/ADH method failed to detect a volatile other than EtOH in only two cases (0.6%) or in addition to EtOH in three cases (0.9%). The concentrations of these volatiles were not clinically significant. The sensitivity for detecting EtOH by means of the ∆-Osm calculation was 98.1% with a specificity of 98.2%. A disparity (∆-Osm > 10 mOsm/kg) between ∆-Osm and the EtOH determination suggested a volatile other than EtOH in five cases (1.5%), which was confirmed by headspace gas chromatographic (GC-HS) analysis. A volatile in addition to EtOH in seven cases (2.1%) was suggested but not confirmed by GC-HS analysis. The ∆-Osm/ADH procedure provides an efficient, rapid, and readily available method to evaluate the acutely intoxicated patient for the presence of EtOH and/or other low Mr volatiles.
Seasonal changes in morphology govern wettability of Katsura leaves.

Deciduous broad-leaf trees survive and prepare for winter by shedding their leaves in fall. During the fall season, a change in a leaf’s wettability and its impact on the leaf-fall are not well understood. In this study, we measure the surface morphology and wettability of Katsura leaves from the summer to winter, and reveal how leaf structural changes lead to wettability changes. The averaged contact angle of leaves decreases from 147° to 124° while the contact-angle hysteresis significantly increases by about 35°, which are attributed to dehydration and erosion of nano-wax. Due to such wettability changes, fall brown leaves support approximately 17 times greater water volume than summer leaves.
Genome-wide association analyses of invasive pneumococcal isolates identify a missense bacterial mutation associated with meningitis.

Bacterial mutations predisposing pneumococcus to causing meningitis, a more severe form of invasive pneumococcal disease (IPD), are largely unknown. Knowledge of such mutations may improve our understanding of pathogenesis and inform preventive strategies. Here we report a pneumococcal pbp1b gene mutation (pbp1bA641C causing N214T change in PBP1b transglycosylase domain) that is associated with meningitis in an exploratory cohort of IPD patients (n = 2054, p = 6.8 × 10−6), in an independent confirmatory cohort (n = 2518, p = 2.3 × 10−6), and in a combined analysis (n = 4572, p = 3.0 × 10−10). Patients infected by the pbp1b641C genotype pneumococci show 2.8-fold odds (95% CI 1.7 to 4.8) of meningitis compared to those infected by non-pbp1b641C pneumococci, after controlling for pneumococcal serotype, antibiotic resistance, and patient age. The pbp1bA641C change results in longer time needed for bacterial killing by antibiotic treatment and shows evidence of being under positive selection. Thus, a pneumococcal mutation conferring increased antibiotic tolerance is associated with meningitis among IPD patients. Meningitis is a severe form of invasive pneumococcal disease (IPD). To study the contribution of bacterial genomic variation, here Li et al. perform whole genome sequencing of pneumococcal isolates from IPD patients and identify an association for higher risk of meningitis with a pbp1bA641C variant
Beyond Cumulative Sum Charting in Non-Stationarity Detection and Estimation

In computer science, stochastic processes, and industrial engineering, stationarity is often taken to imply a stable, predictable flow of events and non-stationarity, consequently, a departure from such a flow. Efficient detection and accurate estimation of non-stationarity are crucial in understanding the evolution of the governing dynamics. Pragmatic considerations include protecting human lives and property in the context of devastating processes such as earthquakes or hurricanes. Cumulative Sum (CUSUM) charting, the prevalent technique to weed out such non-stationarities, suffers from assumptions on a priori knowledge of the pre and post-change process parameters and constructs such as time discretization. In this paper, we have proposed two new ways in which non-stationarity may enter an evolving system - an easily detectable way, which we term strong corruption, where the post-change probability distribution is deterministically governed, and an imperceptible way which we term hard detection, where the post-change distribution is a probabilistic mixture of several densities. In addition, by combining the ordinary and switched trend of incoming observations, we develop a new trend ratio statistic in order to detect whether a stationary environment has changed. Surveying a variety of distance metrics, we examine several parametric and non-parametric options in addition to the established CUSUM and find that the trend ratio statistic performs better under the especially difficult scenarios of hard detection. Simulations (both from deterministic and mixed inter-event time densities), sensitivity-specificity type analyses, and estimated time of change distributions enable us to track the ideal detection candidate under various non-stationarities. Applications on two real data sets sampled from volcanology and weather science demonstrate how the estimated change points are in agreement with those obtained in some of our previous works, using different methods. Incidentally, this study sheds light on the inverse nature of dependence between the Hawaiian volcanoes Kilauea and Mauna Loa and demonstrates how inhabitants of the now-restless Kilauea may be relocated to Mauna Loa to minimize the loss of lives and moving costs.
Endocarditis in Adults with Congenital Heart Disease

Endocarditis in adults with congenital heart disease can be traced to intermittent bacteremia owing to dental caries, drug addiction, and chronic infection. Turbulent flow associated with residual congenital lesions such as small ventricular septal defects (VSDs), patent arterial ducts (PAD), and coarctation of the aorta (CoA) cause endovascular damage that can attract and harbor cilia-forming bacteria. In addition, implanted devices such as valve prostheses, vascular grafts, and transcatheter devices can form niduses for bacterial growth and proliferation.
Material Transport in the Ocean Mixed Layer: Recent Developments Enabled by Large Eddy Simulations

Author(s): Chamecki, M; Chor, T; Yang, D; Meneveau, C | Abstract: Material transport in the ocean mixed layer (OML) is an important component of natural processes such as gas and nutrient exchanges. It is also important in the context of pollution (oil droplets, microplastics, etc.). Observational studies of small-scale three-dimensional turbulence in the OML are difficult, especially if one aims at a systematic coverage of relevant parameters and their effects, under controlled conditions. Numerical studies are also challenging due to the large-scale separation between the physical processes dominating transport in the horizontal and vertical directions. Despite this difficulty, the application of large eddy simulation (LES) to study OML turbulence and, more specifically, its effects on material transport has resulted in major advances in the field in recent years. In this paper we review the use of LES to study material transport within the OML and then summarize and synthesize the advances it has enabled in the past decade or so. In the first part we describe the LES technique and the most common approaches when applying it in OML material transport investigations. In the second part we review recent results on material transport obtained using LES and comment on implications.
Into and out of exile: an integrative phenomenological understanding of Attenuated Psychosis Syndrome

Understanding the experience of Attenuated Psychosis Syndrome (APS), apart from its risk for developing into psychosis, is important to evaluating and improving professional care for this populatio...
Crowdsourcing traffic simulation to improve signal timing

Inefficiency in automobile traffic light timing contributes to wasted time of travelers and wasted energy, but improving the timing of traffic lights is a difficult problem due to the inherent complexity of the problem. In this work, we present our crowdsourcing tool that allows Android mobile phone users to play a game challenging them to find optimal light timing for a simulated traffic intersection. To succeed at this game, players must configure the traffic light signals to optimize the throughput of vehicles. Scores and configurations of players are stored in a remote database, which is used to populate a high score list. The game uses crowdsourcing by allowing players to load configurations from the high score list to try to optimize them. We also present a case study of volunteers who tested our prototype.
Evaluating the Effectiveness of a Mindfulness App Among Academic Advisors

This yearlong study examined the impact of the 10% Happier phone app on levels of mindfulness and perceived stress among academic advisors. In addition, the study explored whether attending a one-time training session would influence app usage. To date, there is limited research regarding the effectiveness of mindfulness apps on the levels of mindfulness and perceived stress and the impact an in-person mindfulness training has on app usage. In this study, participants were given the choice to attend a one-time training session that included gaining access to the app or receive access to the app without attending training. A quantitative design was used to sample academic advisors (n = 33) at a large, state university in the Midwest. The results showed that in-person training appeared to increase app usage, and paired sample t-tests indicated increased levels of mindfulness on the Mindfulness Attention and Awareness Scale (MAAS) and decreased levels of perceived stress on the Perceived Stress Scale (PSS) among app users. There was no significant difference in changes in levels of mindfulness and perceived stress among those who did not use the app. A final result indicated 85% of participants agreed that practicing mindfulness was beneficial to their self-care and well-being.
Short communication: Detecting possibly frequent change-points: wild binary segmentation 2 and steepest-drop model selection

This article comments on the new version of wild binary segmentation in Fryzlewicz (Ann Stat 42(6):2243–2281, 2014).
Functional dissection of the Pol V large subunit CTD in RNA-directed DNA methylation

Plant multisubunit RNA Polymerase V transcription recruits Argonaute siRNA complexes that specify sites of RNA-directed DNA methylation (RdDM) for gene silencing. Pol V9s largest subunit, NRPE1, evolved from the largest subunit of Pol II but has a distinctive carboxyl-terminal domain (CTD). We show that the Pol V CTD is dispensable for catalytic activity in vitro, yet essential in vivo. One CTD subdomain (DeCL) is required for Pol V function at virtually all loci. Other CTD subdomains have locus-specific effects. In a yeast two-hybrid screen, the 3-prime to 5-prime exoribonuclease, RRP6L1 was identified as an interactor with the DeCL and glutamine-serine-rich (QS) subdomains, located downstream from an Argonaute-binding repeat subdomain. Experimental evidence indicates that RRP6L1 trims the 3-prime ends of Pol V transcripts sliced by ARGONAUTE 4 (AGO4), suggesting a model whereby the CTD enables the spatial and temporal coordination of AGO4 and RRP6L1 RNA processing activities.
Phase I study of a DNA-based vaccine targeting prostatic acid phosphatase (PAP) in patients with clinical stage D0 prostate cancer

1858 Background: Prostatic acid phosphatase (PAP) is a tumor antigen in prostate cancer. Clinical trials conducted in patients with metastatic prostate cancer targeting PAP by means of antigen presenting-cell vaccines have suggested clinical benefit in terms of disease progression and overall survival. Ultimately, however, tumor vaccines may be most effective in the setting of minimal residual disease. We have investigated plasmid DNA vaccines encoding PAP in rodent models. We found these to be safe and effective in eliciting PAP-specific CD8+ T cells and observed evidence of anti-tumor efficacy. We report here the initial clinical and immunological results from a dose-escalation phase I trial evaluating a DNA vaccine encoding PAP in patients with minimal residual prostate cancer, clinical stage D0. Methods: Patients with clinical stage D0 prostate cancer with rising serum PSA were vaccinated over a 12-week period, six times at 14-day intervals, with a plasmid DNA vaccine encoding PAP (pTVG-HP) in a dose-escalation trial. Vaccinations were administered intradermally with 100 mcg, 500 mcg, or 1500 mcg doses, and with 200 mcg of GM-CSF co-administered as a vaccine adjuvant. The primary endpoints of the trial were safety and immunological response, antigen-specific IFNγ-secreting CD8+ T cells as measured by ELISPOT. Other immunological responses were evaluated by antigen-specific T cell proliferation and IFNγ secretion and by ELISA for PAP-specific IgG. Results: Nine patients were enrolled and all completed the immunization series. No serious adverse events were observed, and no events greater than grade 2 were identified. Antibody responses to PAP were not observed, however 4/9 developed PAP-specific CD4+ or CD8+ proliferative T cell responses. 2/9 patients developed PAP-specific IFNγ-secreting CD8+ T cells, detectable without in vitro stimulation, as measured by ELISPOT, the primary immunological endpoint of the trial. 2/9 patients also demonstrated a marked increase in PSA doubling time, one of whom was found to have an ELISPOT response. Conclusions: Intradermal immunization of patients with stage D0 prostate cancer with pTVG-HP resulted in no significant adverse events in doses up to 1500 mcg. CD4+ and CD8+ T cell responses were elicited, consistent with a predominantly cellular immune response, at even the lowest dose of vaccine. The development of an antigen-specific CD8+ T cell response in conjunction with an increase in PSA doubling time in some patients suggests that further clinical evaluation is warranted.
Management of headaches in children and adolescents.

Pediatric headache impacts up to 80% of children, many recurrently, by the time they are 15 years old. Preventing the progression of episodic to chronic headache results in less truancy, staying current with schoolwork and improves children's quality of life. Lifestyle choices can play an important role in headache treatment. Early effective treatment of episodic headache can prevent transformation into a chronic form. While details of a child's headache are critical for making a proper diagnosis; patient education is critical and effective rescue and preventive treatment strategies enable patients to focus on enjoying activities of daily living. Recognizing “red flags” that may suggest a serious underlying etiology is critical in the early stages of diagnosing and preparing to treat children with headaches. Finally directing patients to manage their headaches at home and when to proceed to an emergency department, urgent care or infusion unit can lower the economic burden of acute headache management.
AI-driven high-throughput automation of behavioral analysis and dual-channel wireless optogenetics for multiplexing brain dynamics

Abstract Advances in behavioral optogenetics are limited by the absence of high-throughput pipelines for the automated analysis of behavior in freely behaving animals. Although a variety of AI algorithms has been proposed that enable automation of behavioral analysis, existing methods are generally low-throughput. In addition, optogenetic manipulation of neural circuits typically requires physical tethers to light sources, which limits the number of brain areas that can be targeted and thus constrains behavioral testing. Here, we develop a new wireless platform that combines a battery-free dual-channel optogenetic implant with an AI algorithm for high-throughput behavioral analysis. In our platform, a customized AI algorithm detected and quantified freezing behavior of rats that had undergone fear conditioning. Notably, our platform allows up to four enclosures to be monitored simultaneously. Wireless dual-channel optogenetic devices were implanted in the basolateral amygdala (BLA) to permit independent modulation of BLA principal neurons (red light, AAV-CaMKII-JAWS) or BLA interneurons (blue light, AAV-mDlx-ChR2) in freely behaving animals. In vivo validation with behaving rats demonstrates the utility of the telemetry system for large-scale optogenetic studies. Significance AI algorithms can enable automation of behavioral analysis and thereby facilitate the progress on behavioral optogenetics. Successful integration of advanced wireless dual-channel optoelectronic devices with biological systems can also yield new tools and techniques for neuroscience research, particularly in the context of techniques for optogenetics. Here, we propose a new approach that combines an advanced AI algorithm with a low power wireless telemetry system, yielding powerful capabilities in the understanding of brain functions and the evaluation of the behavioral consequences of neural circuit manipulations. In vivo studies using optimized systems demonstrate high-throughput automation of behavioral manipulation and analysis via AI-powered wireless telemetry.
Towards a Task-Level Programming Environment

To this point, we have discussed a mathematical framework for task-directed information gathering, described both the mean-square family of estimators and the grid-based method, and discussed their properties. The implementation of mean-square estimation methods is relatively simple and well-known, and a discussion thereof can be found in many of the cited references. The purpose of this chapter is to describe a concrete implementation of the grid-based techniques and to illustrate its application. We feel it is important to discuss this topic as it provides another means of gaining intuition about the flexibility, generality, and practicality of a method.
Either B7 Costimulation or IL-2 Can Elicit Generation of Primary Alloreactive CTL

B7-1 and B7-2 are important costimulatory molecules in the activation of T cell immunity. We have used mice made genetically deficient in either or both B7 molecules to determine the role of B7 molecules in activation of primary alloreactive CTL. The absence of either B7-1 or B7-2 did not alter generation of CTL from unfractionated lymphocytes, but the absence of B7-2 greatly decreased CTL generation from purified CD8+ responder cells. However, if B7-1 was induced on the stimulating cells then CTL generation was restored to wild-type levels. Absence of both B7-1 and B7-2 from MLR using whole splenocytes resulted in a profound reduction in generation of CTL. This could completely be reversed by the addition of IL-2. B7 molecules could directly costimulate CD8+ cells, as purified CD8+ cells developed into mature CTL when stimulated with wild-type APC, but not with B7-deficient APC. Again, IL-2 could drive CTL generation from purified CD8+ cells, even in the absence of B7 molecules. Taken together, these results demonstrate an important role for B7 costimulation in CTL generation.
Peering through the shroud: the effect of edge opacity on ip-based client identification

Online services often use IP addresses as client identifiers when enforcing access-control decisions. The academic community has typically eschewed this approach, however, due to the effect that NATs, proxies, and dynamic addressing have on a server's ability to identify individual clients. Yet, it is unclear to what extent these edge technologies actually impact the utility of using IP addresses as client identifiers. This paper provides some insights into this phenomenon. We do so by mapping out the size and extent of NATs and proxies, as well as characterizing the behavior of dynamic addressing. Using novel measurement techniques based on active web content, we present results gathered from 7 million clients over seven months. We find that most NATs are small, consisting of only a few hosts, while proxies are much more likely to serve many geographically-distributed clients. Further, we find that a server can generally detect if a client is connecting through a NAT or proxy, or from a prefix using rapid DHCP reallocation. From our measurement experiences, we have developed and implemented a methodology by which a server can make a more informed decision on whether to rely on IP addresses for client identification or to use more heavyweight forms of client authentication.
Energy, Economics and the Environment: Cases and Materials

This casebook integrates a legal assessment of energy resources with economic and environmental issues, thereby encouraging thoughtful analysis of energy policy issues confronting the U.S. and the world. Historical and contemporary legal issues confronting a range of energy resources are surveyed, including water power, coal, oil and gas, electricity, and nuclear power. Particular attention is paid to the need to reduce consumption of imported oil by motor vehicles. The third edition of the book contains considerable material on problems presented by climate change, including legal issues confronting renewable power projects and various conservation measures. We believe that the material can be taught in many different variations, and we continue to teach it in a somewhat different order every time it is offered.