cssi/SciSciGPT-SciSciNet huggingface dataset:
Impact of an antimicrobial stewardship program on healthcare-associated Clostridium difficile rates at a community-based teaching hospital:

We conducted a pre-intervention/post-intervention study to assess the rate of healthcare-associated Clostridium difficile infections (HA-CDI) before and after the implementation of an antimicrobial stewardship program (ASP). Upon implementation of our ASP, the usage of targeted antimicrobials, including ceftriaxone, clindamycin, fluoroquinolones and carbapenem antibiotics, were significantly reduced. There was also a significant reduction in HA-CDI/1000 patient-days following ASP implementation (0.84 vs. 0.28; P = 0.035).
An Interview with Van Jensen, author of Casino Royale (2018)

In March 2018, Dynamite Entertainment published a graphic novel adaptation of Ian Fleming's first James Bond novel, Casino Royale. In the following interview, author Van Jensen speaks to Ellen J. Stockstill about the process of adapting Fleming's novel, some of the challenges of working with an iconic character like James Bond, Fleming's writing style, Bond's cultural relevance, and the ways in which Fleming's legacy lives on in different media.
The fast flush test--is the clinical comparison equivalent to its in vitro simulation?

Objective. An in vitro simulation of the fast flush (FL) test has previously been used to prove that the FL test measures the dynamic response of entire the blood pressure monitoring system. This simulation has also been used to confirm that the FL test is equivalent to the “gold standard” test for determining dynamic response, namely the square wave (SW) test. The conditions of the in vitro simulation can be reproduced in vivo during cardiopulmonary bypass (CPB) and circulatory arrest. Therefore the present objective was to verify that the previous conclusions about the validity of the FL test, obtained from an in vitro model, are equally valid when applied to in vivoclinical conditions. A secondary objective was to determine whether the patient's arterial tree has any affect on the dynamic characteristics of fluid-filled manometers. Methods. Fourteen patients were studied during surgery that required CPB. We measured the dynamic response of the fluid filled arterial manometer during pulsatile conditions prior to the initiation of CPB, and then repeated the measurements during non-pulsatile CPB. In four of the fourteen patients we measured the dynamic response during circulatory arrest. A manometer, consisting of a fluid-filled tubing component, measured the patient's arterial blood pressure as well as the damped sinusoidal wave form created by the fast flush tests. The fluid-filled tubing was connected to a transducer (Utah Medical Products, Inc., Midvale, UT). The arterial pressures and the results of flush testing were recorded and displayed by a monitor (Marquette 7010, Marquette Electronics Inc., Milwaukee, WI). In an additional three patients we measured the dynamic response of the manometer in vitro and then in vivo. Results. The dynamic response of the arterial pressure measuring system was the same during normal pulsatile flow, CPB and circulatory arrest. In addition, the dynamic response of the fluid-filled manometer was the same in vivo as in vitro. Conclusions. The clinical conditions during CPB and particularly during circulatory arrest duplicate the in vitro FL test simulation model. These results confirm the validity of the FL test in vivo as well as proving that the dynamic characteristics of a fluid-filled manometer are independent of the patient's vasculature.
High-Resolution Numerical Models for Smoke Transport in Plumes from Wildland Fires

A high-resolution large-eddy simulation (LES) model is employed to examine the fundamental structure and dynamics of buoyant plumes arising from heat sources representative of wildland fires. Herein we describe several aspects of the mean properties of the simulated plumes. Mean plume trajectories are apparently well described by the traditional two-thirds law for plume rise; however, the spatial structure of the mean plume is significantly different from the Gaussian distributions typically assumed in simple plume models. This discrepancy arises from the fact that entrainment properties of a buoyant plume in a cross wind are significantly different from those of a buoyant plume in the absence of a cross wind, a result of the interaction of the buoyancy-generated vorticity in the plume with the vorticity in the ambient wind. The depth of the crosswind shear layer at the surface also appears to play a role in both the horizontal and vertical spread of the plume boundaries downwind, and in particular the increase in horizontal spread acts to increase the departure from a Gaussian distribution seen in the plume cross sections.
Nutrients with Special Functions: Essential Fatty Acids

The answer to the question in the title of this section goes beyond a simple listing of those acids with essential fatty acid (EFA) activity. Burr and Burr (1930), in their original account of the discovery of these substances, defined them as those fatty acids that could prevent or cure the deficiency symptoms seen in young rats fed a fat-free diet, and they considered three fatty acids to be essential:linoleic, linolenic, and arachidonic. We now know that almost all animals, including humans, can be made to show EFA deficiency symptoms and that a great many polyunsaturated fatty acids (PUFAs) have some EFA activity. Even if we extend the definition to encompass this information, it may still not be adequate. In their review of the subject, Le Breton and Ferret (1960) pointed out that such a definition has two requirements: first, that the substances fulfill some vital function and, second, that they cannot be synthesized from simple precursors. They preferred the term “acides gras indispensables” for these substances. It is now too late to change the terminology, but it may be profitable to consider the meaning of their definition as it applies to our present knowledge of the EFAs.
A SHARP UPPER BOUND FOR THE ENERGY OF A CONNECTED GRAPH

The energy of a graph is defined as the sum of the absolute values of the eigenvalues of the graph. A new upper bound for the energy of a connected graph is presented in this note. The upper bound involves the chromatic number and the rank of the graph.
Humoral Effects of the Pancreas Upon the Gastrointestinal Tract

Pancreatic hormones have been found to have a variety of actions upon the motor and secretory functions of the gut. Insulin directly depresses both gastric secretion and motility while both glucagon and gastrin play an important role in the normal control of gastric secretion. It is postulated that the diarrhea hormone is a humoral product or products produced by certain islet-cell tumor causing diarrhea in the absence of gastric hypersecretion. It has also been suggested that the mechanism of action of the diarrhea hormone is an inhibition of transfer of fluid and electrolyte by the small intestine. A probable cause of diarrhea is prostaglandins the fatty acid derivatives which have the property of readily contracting smooth muscle. Prostaglandins have been found in the human stomach and have been shown to stimulate contractions by strips of human gastric muscle. In the dog they inhibit gastric secretion stimulated by either food or histamine. Further studies are needed to determine whether prostaglandins cause diarrhea and whether the diarrhea hormone may have an effect on intestinal transport of water and electrolyte.
Total RNA Isolation from Separately Established Monolayer and Hydrogel Cultures of Human Glioblastoma Cell Line

Astrocytoma is an invasive carcinoma occurring in the nervous system and currently lacks effective treatment options. A deeper understanding of the mechanisms of tumorigenesis and tumor progression is needed in order to develop novel therapeutic strategies. Recent advances in in vitro culture systems have demonstrated that the use of three-dimensional (3D) culture models could be more relevant for this purpose as compared to monolayer or two-dimensional (2D) models due to their resemblance to in vivo cancer pathology. High-throughput techniques such as RNA sequencing, microarray analyses and cloning could provide useful insights into the relevance of these systems to the native tissue. Previous studies have reported RNA extraction protocols needed for such applications. We have modified these protocols to suit the isolation of total RNA from monolayer and hydrogel cultures of astrocytoma established using basement membrane matrix, Geltrex™. We have used this method to demonstrate the differences in the expression of genes involved in autophagy, a process deregulated in many cancer types, in monolayer and hydrogel cultures using quantitative polymerase chain reaction (qPCR). This protocol can be adopted by the researchers who wish to understand the molecular basis of gene expression in hydrogel cultures of normal as well as cancer cell lines.
Experimental investigation of sand particle erosion in a 90° elbow in annular two-phase flows

Abstract Upward gas-liquid-solid flows are often observed in oil and gas transmission pipelines. The presence of solids in such flows is a concern, as it can cause serious damage to pipe fittings, which are prone to erosion. These are normally components such as elbows and tees that can change the flow direction. The current work presents the results of an experimental erosion campaign including 56 tests in a 101.6-mm standard elbow (radius of curvature of 1.5) under gas-sand and gas-liquid-sand flow conditions. The latter included 38 tests (30 distinct conditions) mostly in the range of annular and unstable annular flows. Thickness loss measurements were made using a non-invasive ultrasonic technology instrument at 8 different points along the outer bend of the elbow to investigate effects of various factors on erosion. Additionally, flow visualization and paint erosion studies were performed to examine liquid distribution as well as the particulate phase behavior. Generally, when superficial liquid velocity increased, erosion ratio decreased for low liquid rate conditions. This trend, however, reversed for higher liquid rates. Also, the paint erosion experiments revealed that the location of the maximum erosion was around 40°–50° on the middle outer bend, for all cases examined.
Accuracy of virtual interocclusal records for partially edentulous patients.

Abstract Statement of problem Intraoral scans and virtual interocclusal records (VIRs) are widely used for contemporary prosthodontic treatment of patients with partial edentulism. The accuracy of VIRs in various clinical conditions is unclear. Purpose The purpose of this in vitro study was to investigate whether the span and location of edentulous areas affect the accuracy of VIRs. Material and methods Five sets of master stone casts were duplicated from a typodont model (Prosthetic Restoration Jaw Model; Nissin Dental) and then assigned into 5 study groups. Six pairs of interarch markers were placed on the master stone casts as reference points for measurements. The 5 study groups were group 1-Post: 1 posterior tooth missing; group 3-Post: 3 posterior teeth missing; group 6-Ant: 6 anterior teeth missing; group Bil-Post: bilateral posterior teeth missing; and group Dent: completely dentate arch. Master stone casts along with VIRs were scanned 10 times in each group by using an intraoral scanner (IOS) (Dental Wings Intraoral Scanner; Dental Wings Inc). Digital measurement of distances between the interarch markers was obtained on all digitally articulated casts and compared with the manual measurements (with electronic calipers with an accuracy of 0.02 mm). In addition, the differences (absolute values) between the digital and manual measurements were calculated at the edentulous locations for the groups 1-Post, 3-Post, 6-Ant, and Bil-Post and were compared with the corresponding interarch marker positions in the group Dent. Two-sample t tests were used for the statistical analysis (α=.05). Results The overall differences (mean ±standard deviation) between digital and manual measurements were group 1-Post: 0.10 ±0.19 mm, group 3-Post: 0.28 ±0.63 mm; group 6-Ant: 0.19 ±0.20 mm; group Bil-Post: 0.28 ±0.25 mm; and group Dent: 0.05 ±0.18 mm. Group Dent was the only group with no significant differences between digital and manual measurements at all 6 interarch marker positions and was used as the reference to analyze the measurements in the edentulous areas. No statistical difference was found (P=.237) at the group 1-Post's edentulous area when compared with the group Dent. In the group 3-Post, the edentulous areas showed statistically significant difference when compared with those of the group Dent (P=.002 and P=.003). In the group 6-Ant, the edentulous areas showed statistical differences when compared with those of the group Dent (P=.019 and P=.008). In the group Bil-Post, only 1 side of the edentulous areas showed statistical differences when compared with group Dent (P=.006 and P=.034). Conclusions The span and location of edentulous areas impact the accuracy of VIRs. For a single missing posterior tooth, VIRs could achieve a high level of accuracy comparable with that of the dentate condition. Unilateral and bilateral extended edentulous spans with 3 or more missing posterior teeth and the extended edentulous span in the anterior region all affected the accuracy of VIRs.
The AKP, party system change, and political representation by women in Turkey

In Turkey, the number of women in the Grand National Assembly has drastically increased from 24 in 2002 to 104 as of the June election of 2018. To date, the explanations for this rise and women’s e...
Hydrogen Peroxide Disproportionation with Manganese Macrocyclic Complexes of Cyclen and Pyclen

The catalase family of enzymes, which include a variety with a binuclear manganese active site, mitigate the risk from reactive oxygen species by facilitating the disproportionation of hydrogen peroxide into molecular oxygen and water. In this work, hydrogen peroxide disproportionation using complexes formed between manganese and cyclen or pyclen were investigated due to the spectroscopic similarities with the native MnCAT enzyme. Potentiometric titrations were used to construct speciation diagrams that identify the manganese complex compositions at different pH values. Each complex behaves as a functional mimic of catalase enzymes. UV-visible spectroscopic investigations of the H2O2 decomposition reaction yielded information about the structure of the initial catalyst and intermediates that include monomeric and dimeric species. The results indicate that rigidity imparted by the pyridine ring of pyclen is a key factor in increased TON and TOF values measured compared to cyclen.
Fulcrum: A Simplified Control and Access Mechanism Toward Flexible and Practical In-Situ Accelerators

In-situ approaches process data very close to the memory cells, in the row buffer of each subarray. This minimizes data movement costs and affords parallelism across subarrays. However, current in-situ approaches are limited to only row-wide bitwise (or few-bit) operations applied uniformly across the row buffer. They impose a significant overhead of multiple row activations for emulating 32-bit addition and multiplications using bitwise operations and cannot support operations with data dependencies or based on predicates. Moreover, with current peripheral logic, communication among subarrays is inefficient, and with typical data layouts, bits in a word are not physically adjacent. The key insight of this work is that in-situ, single-word ALUs outperform in-situ, parallel, row-wide, bitwise ALUs by reducing the number of row activations and enabling new operations and optimizations. Our proposed lightweight access and control mechanism, Fulcrum, sequentially feeds data into the single-word ALU and enables operations with data dependencies and operations based on a predicate. For algorithms that require communication among subarrays, we augment the peripheral logic with broadcasting capabilities and a previously-proposed method for low-cost inter-subarray data movement. The sequential processor also enables overlapping of broadcasting and computation, and reuniting bits that are physically adjacent. In order to realize true subarray-level parallelism, we introduce a lightweight column-selection mechanism through shifting one-hot encoded values. This technique enables independent column selection in each subarray. We integrate Fulcrum with Compress Express Link (CXL), a new interconnect standard. Fulcrum with one memory stack delivers on average (up to) 23.4 (76) speedup over a server-class GPU, NVIDIA P100, with three stacks of HBM2 memory, (ii) 70 (228) times speedup per memory stack over the GPU, and (iii) 19 (178.9) times speedup per memory stack over an ideal model of the GPU, which only accounts for the overhead of data movement.
Splenic artery angioembolization for high-grade splenic injury: Are we wasting money?

Abstract Background Non-operative management (NOM) is accepted treatment of splenic injury, but this may fail leading to splenectomy. Splenic artery embolization (SAE) may improve rate of salvage. The purpose is to determine the cost-utility of the addition of SAE for high-grade splenic injuries. Methods A cost-utility analysis was developed to compared NOM to SAE in patients with blunt splenic injury. Sensitivity analysis was completed to account for uncertainty. Utility outcome was quality-adjusted life years (QALY). Results For patients with grade III, IV and V injury NOM is the dominant strategy. The probability of NOM being the more cost-effective strategy is 87.5% in patients with grade V splenic injury. SAE is not the favored strategy unless the probability of failure of NOM is greater than 70.0%. Conclusion For grade III–V injuries, NOM without SAE yields more quality-adjusted life years. NOM without SAE is the most cost-effective strategy for high-grade splenic injuries.
Indocyanine green‐enhanced multimodal photoacoustic microscopy and optical coherence tomography molecular imaging of choroidal neovascularization

Photoacoustic microscopy (PAM) has great potential for visualization of the microvasculature with high spatial resolution and contrast. Early detection and differentiation of newly developed blood vessels named choroidal neovascularization (CNV) from normal vasculature remains a challenge in ophthalmology. Exogenous contrast agents can assist with improving PAM sensitivity, leading to differentiation of CNV. Here, an FDA-approved indocyanine green (ICG) was utilized as a PAM contrast agent. ICG was conjugated with RGD peptides, allowing the ICG to bind to the integrin expressed in CNV. Molecular PAM imaging showed that ICG-RGD can target CNV for up to 5 days post intravenous administration in living rabbits with a model of CNV. The PAM image sensitivity and image contrast were significantly enhanced by 15-fold at 24 h post-injection. Overall, the presented approach demonstrates the possibility of targeted ICG to be employed in PAM molecular imaging, allowing more precise evaluation of neovascularization. This article is protected by copyright. All rights reserved.
Identity as a Variable

As scholarly interest in the concept of identity continues to grow, social identities are proving to be crucially important for understanding contemporary life. Despite—or perhaps because of—the sprawl of different treatments of identity in the social sciences, the concept has remained too analytically loose to be as useful a tool as the literature’s early promise had suggested. We propose to solve this longstanding problem by developing the analytical rigor and methodological imagination that will make identity a more useful variable for the social sciences. This article offers more precision by defining collective identity as a social category that varies along two dimensions—content and contestation. Content describes the meaning of a collective identity. The content of social identities may take the form of four non-mutually-exclusive types: constitutive norms; social purposes; relational comparisons with other social categories; and cognitive models. Contestation refers to the degree of agreement within a group over the content of the shared category. Our conceptualization thus enables collective identities to be compared according to the agreement and disagreement about their meanings by the members of the group. The final section of the article looks at the methodology of identity scholarship. Addressing the wide array of methodological options on identity—including discourse analysis, surveys, and content analysis, as well as promising newer methods like experiments, agent-based modeling, and cognitive mapping—we hope to provide the kind of brush clearing that will enable the field to move forward methodologically as well.
The 2014 New York State Medicaid Expansion and Severe Maternal Morbidity During Delivery Hospitalizations.

Background Medicaid expansions under the Affordable Care Act have increased insurance coverage and prenatal care utilization in low-income women. However, it is not clear whether they are associated with any measurable improvement in maternal health outcomes. In this study, we compared the changes in the incidence of severe maternal morbidity (SMM) during delivery hospitalizations between low- and high-income women associated with the 2014 Medicaid expansion in New York State. Methods Data for this retrospective cohort study came from the 2006-2016 New York State Inpatient Database, a census of discharge records from community hospitals. The outcome was SMM during delivery hospitalizations, as defined by the Centers for Disease Control and Prevention. We used regression coefficients (β) from multivariable logistic models: (1) to compare independently in low-income women and in high-income women the changes in slopes in the incidence of SMM before (2006-2013) and after (2014-2016) the expansion, and (2) to compare low- and high-income women for the changes in slopes in the incidence of SMM before and after the expansion. Results A total of 2,286,975 delivery hospitalizations were analyzed. The proportion of Medicaid beneficiaries in parturients increased a relative 12.1% (95% confidence interval [CI], 11.8-12.4), from 42.9% in the preexpansion period to 48.1% in the postexpansion period, whereas the proportion of the uninsured decreased a relative 4.8% (95% CI, 2.8-6.8). Multivariable logistic modeling revealed that implementation of the 2014 Medicaid expansion was associated with a decreased slope during the postexpansion period both in low-income women (β = -0.0161 or 1.6% decrease; 95% CI, -0.0190 to -0.0132) and in high-income women (β = -0.0111 or 1.1% decrease; 95% CI, -0.0130 to -0.0091). The decrease in slope during the postexpansion period was greater in low- than in high-income women (β = -0.0042 or 0.42% difference; 95% CI, -0.0076 to -0.0007). Conclusions Implementation of the Medicaid expansion in 2014 in New York State is associated with a small but statistically significant reduction in the incidence of SMM in low-income women compared with high-income women.
Early Survivorship After Liver Transplantation: A Qualitative Study Identifying Challenges in Recovery From the Patient and Caregiver Perspective

Background Survivorship after liver transplantation (LT) is a novel concept providing a holistic view of the arduous recovery experienced after transplantation. We explored components of early survivorship including physical, emotional, and psychocological challenges to identify intervention targets for improving the recovery process of LT recipients and caregivers. Methods Twenty in-person interviews were conducted among adults 3-6 months post-LT. Trained qualitative research experts conducted interviews, coded, and analyzed transcripts to identify relevant themes and representative quotes. Results Early survivorship comprises overcoming: 1) physical challenges-the most-challenging experiences involving mobility, driving, dietary modifications, and medication adherence and 2) emotional and psychological challenges-including new health concerns, financial worries, body image/identity struggles, social isolation, dependency issues, and concerns about never returning to normal. Etiology of liver disease informed survivorship experiences including some patients with hepatocellular carcinoma expressing decisional regret or uncertainty in light of their post-LT experiences. Important topics were identified that framed LT recovery including setting expectations about waitlist experiences, hospital recovery, and ongoing medication requirements. Conclusion Early survivorship after LT within the first six months involves a wide array of physical, emotional and psychological challenges. Patients and caregivers identified what they wish they had known prior to transplant and strategies for recovery, which can inform targeted LT survivorship interventions.
EFFECTS OF HAZARDOUS ALCOHOL AND DRUG USE ON ANTIRETROVIRAL ADHERENCE AND HIV VIRAL SUPPRESSION: A MEDIATION ANALYSIS

Abstract Background: Little is known regarding the degree to which substance and alcohol use effects on HIV viral suppression are mediated through medication adherence. We hypothesized that the total effects of such use are mediated through adherence. Methods: We included patients with HIV (PWH) receiving care at an urban academic HIV clinic between 2014 and 2018. Eligible patients were those prescribed antiretroviral therapy who completed both patient reported outcome (PRO) questionnaires, and had subsequent plasma viral load (pVL) measurements. Measures included assessments of alcohol use (AUDIT-C), drug use (ASSIST), and self-reported adherence. Substances found in bivariate analysis to predict detectable pVL were modeled separately for mediation effects through adherence. We report natural direct (NDE) and indirect effect (NIE), marginal total effect (MTE) and percentage mediated. Results: Among 3125 Patients who met eligibility criteria, percentages of current use by category were: hazardous alcohol 25.8%, cannabis 27.1%, amphetamines 13.1%, inhalants 11.9%, cocaine 5.3%, sedative-hypnotics 4.5%, opioids 2.9%, and hallucinogens 2.3%. Excellent adherence was reported in 58% and 10% had detectable pVL. Except for sedatives use of other ascertained substances was significantly associated with worse adherence. Bivariate predictors of detectable pVL were [OR(95% CI)]: amphetamine use 2.4 (1.8 -3.2 ) and opioid use 2.3 (1.3 - 4.0) . The percentage mediated by adherence was 36% for amphetamine use, 26.5% for opioid use, and 39% for multiple substance use. Conclusion: Use of amphetamines, opioids, and multiple substances predicted detectable pVL. However, less than 40% of effects were mediated by self-reported adherence.
Exacerbation of human astrocyte inflammatory responses to bacterial pathogens by the neuropeptide substance P (MPF2P.742)

The neuropeptide substance P (SP) has increasingly been recognized to augment inflammatory immune responses. We have recently demonstrated that SP can significantly exacerbate the inflammatory responses of isolated murine glial cells to clinically relevant bacterial pathogens. Furthermore, we have shown that SP interactions with its receptor are an essential component in the initiation and/or progression of central nervous system (CNS) inflammation in in vivo mouse models of meningitis. In the present study, we demonstrate that SP similarly alters the inflammatory responses of human astrocytes to clinically relevant bacterial pathogens and their components. Specifically, we show that SP augments the production of inflammatory cytokines and the generation of nitric oxide by human astrocytes in response to Neisseria meningitidis . In addition, we showed that this effect is seen in astrocyte responses to the TLR4 ligand, LPS. However, such SP-mediated increases in inflammatory mediator production are not limited to TLR4 stimuli as human astrocyte responses to the disparate Gram-negative bacterial pathogen Borrelia burgdorferi , that does not express LPS, are also modulated in a dose and time dependent manner. Together, these results suggest that SP could play a significant role in the initiation and/or progression of bacterially induced CNS inflammation in humans in a similar manner to that previously seen in rodent models following infection.
Research on rational Capacity-Load Ratio of urban electric network

The index Capacity-Load Ratio (CLR) is a macro-technical indicator that is always used in urban electric network planning to reflect power supply capability. The value of CLR has significantly influenced the investment of construction and reformation about urban electric network. In today's competitive electricity market environment, the determination of a rational CLR is one of the major issues of power utilities. Rational CLR means that utilities have reasonable investment to ensure power supply with adequate quality and reliability.
Genome Sequence Databases: Sequencing and Assembly

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three-dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger) and 10 000 bp (PacBio)), great interest in analysis of microbial communities (metagenomes) of different complexities inhabiting seas, marshes and even the human gut raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 99.5% of the genome, very often, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/10 000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality (∼ 1 error/100 000 bp or better), validated through a number of computer and laboratory experiments.
Eya protein phosphatase activity regulates Six1–Dach–Eya transcriptional effects in mammalian organogenesis

The precise mechanistic relationship between gene activation and repression events is a central question in mammalian organogenesis, as exemplified by the evolutionarily conserved sine oculis (Six), eyes absent (Eya) and dachshund (Dach) network of genetically interacting proteins. Here, we report that Six1 is required for the development of murine kidney, muscle and inner ear, and that it exhibits synergistic genetic interactions with Eya factors. We demonstrate that the Eya family has a protein phosphatase function, and that its enzymatic activity is required for regulating genes encoding growth control and signalling molecules, modulating precursor cell proliferation. The phosphatase function of Eya switches the function of Six1-Dach from repression to activation, causing transcriptional activation through recruitment of co-activators. The gene-specific recruitment of a co-activator with intrinsic phosphatase activity provides a molecular mechanism for activation of specific gene targets, including those regulating precursor cell proliferation and survival in mammalian organogenesis.
Feeding dysfunction in single ventricle patients with feeding disorder.

Purpose To determine whether caregivers of children with single ventricle heart defects identified as having feeding disorder will report more frequent feeding dysfunction, or maladaptive mealtime behavior and/or interactions, when compared with reference populations. Methods As part of routine evaluation, parents of children evaluated at the Feeding, Swallowing, and Nutrition Center at the Children's Hospital of Wisconsin completed previously validated questionnaires to assess feeding dysfunction and parental stress. Parental responses for single ventricle patients were compared with all other children evaluated with a feeding disorder. Results Questionnaires were completed in eight patients with single ventricle heart defects. The mean age was 36 ± 23 months, with five females (63%). Mean weight-for-age z-score was −1.4 ± 0.9. Compared with noncardiac feeding clinic children, there was more reported child resistance to eating (83 ± 15% vs. 44 ± 2%; P = .05). Single ventricle parents were more likely to report distress (50 ± 18% vs. 21 ± 2%; P = .04) and a difficult child (63 ± 17% vs. 31 ± 2%; P = .05). There was also more defensive responding among parents of single ventricle children (63 ± 17% vs. 29 ± 2%; P = .04). Conclusion Single ventricle patients evaluated for disordered feeding more frequently showed resistance to eating and parental distress than noncardiac feeding clinic patients. Parents of these children underestimated the degree of feeding difficulty by defensive responding and had more parental distress. These findings suggest that feeding dysfunction can contribute to longer-term feeding and growth problems in single ventricle patients with feeding disorder.
The Intersection of Immigration and Housing Policies: Implications for the U.S. Housing Market and Economy

At no other time in the history of the United States have immigrants represented such a large share of the population. In 2012, 40.8 million or 13% of the U.S. population was foreign born (Migratio...
Just-so Stories: Vaccines, Autism, and the Single-bullet Disorder

When should we believe in science, especially in scientific explanations of the causes of health, ill or otherwise? One line of argumentation is that scientific evidence based in robust ecological data, supported by previously tested animal or biological models or double-blinded randomized control trials trumps intuition or just plain “common sense.” Another line of argumentation suggests that common sense is a powerful heuristic. For example, we pretty much know that parachutes work to cushion jumps from highflying planes even though there has not yet been a randomized control (RC) double blind study to support this intuition (however, see Smith and Pell [2003] for a counter opinion). Likewise, thousands of people think that Kipling’s (1912) explanation of why camels have humps makes a lot of sense. Recall that Kipling argues that the camel’s summary refusal to be a beast of burden—his “hmmphh”—led God to give him (and all other camels) a hump. Yet the weight of scientific opinion suggests otherwise perhaps because the “hmmphh” hypothesis lacks a plausible animal model or biological mechanism (not to mention support from a RC double-blind study). Who needs such models when the phenomenological reality of camels is precisely centered on their orneriness? How far should we trust just-so, common sense accounts of complex phenomena? Why are scientists and ordinary people so driven to embrace single-bullet explanations? What does all this say about trust in science? These are the questions considered in this essay, focusing on the purported relationship between autism and vaccines.
Fish Assemblage Structure and Habitat Associations in a Large Western River System

Longitudinal gradients of fish assemblage and habitat structure were investigated in the Kootenai River of northern Idaho. A total of 43 500-m river reaches was sampled repeatedly with several techniques (boat-mounted electrofishing, hoop nets and benthic trawls) in the summers of 2012 and 2013. Differences in habitat and fish assemblage structure were apparent along the longitudinal gradient of the Kootenai River. Habitat characteristics (e.g. depth, substrate composition and water velocity) were related to fish assemblage structure in three different geomorphic river sections. Upper river sections were characterized by native salmonids (e.g. mountain whitefish Prosopium williamsoni), whereas native cyprinids (peamouth Mylocheilus caurinus, northern pikeminnow Ptychocheilus oregonensis) and non-native fishes (pumpkinseed Lepomis gibbosus, yellow perch Perca flavescens) were common in the downstream section. Overall, a general pattern of species addition from upstream to downstream sections was discovered and is likely related to increased habitat complexity and additions of non-native species in downstream sections. Assemblage structure of the upper sections were similar, but were both dissimilar to the lower section of the Kootenai River. Species-specific hurdle regressions indicated the relationships among habitat characteristics and the predicted probability of occurrence and relative abundance varied by species. Understanding fish assemblage structure in relation to habitat could improve conservation efforts of rare fishes and improve management of coldwater river systems. Copyright © 2015 John Wiley & Sons, Ltd.
Syk: a new player in the field of breast cancer.

Breast tumor development and progression are thought to occur through a complex, multistep process, including oncogene activation (eg HER2/neu) and mutation or loss of tumor suppressor genes (eg p53). Determining the function of genetic alterations in breast carcinoma tumorigenesis and metastasis has been the focus of intensive research efforts for several decades. One group of proteins that play a critical role in breast cancer cell signaling pathways are tyrosine kinases. Overexpression of the tyrosine kinase HER2/neu is observed in many human breast cancers and is positively correlated with enhanced tumorigenesis [1]. Recently, another tyrosine kinase, Syk, has been implicated as an important inhibitor of breast cancer cell growth and metastasis [2]. This recent finding was unexpected, since Syk function has been predominantly linked to hematopoietic cell signaling, and is discussed further in this commentary.
An Extended Solid from the Solvothermal Decomposition of Co(Acac)3: Structure and Characterization of Co5(OH)2(O2CCH3)8·2H2O

The title compound can be isolated as well-formed single crystals from the partial solvothermal decomposition of Co(acac)3 in THF/H2O (25:1) at 255 °C. The acetate ligands are presumably derived fr...
Environment, Physical Activity, and Neurogenesis: Implications for Prevention and Treatment of Alzhemiers Disease

Age is the biggest risk factor for the development of neurodegenerative diseases. Consequently, as the population ages it becomes more critical to find ways to avoid the debilitating cost of neurodegenerative diseases such as Alzheimer's. Some of the non-invasive strategies that can potentially slow down the mental decline associated with aging are exercise and use of multi-sensory environmental stimulation. The beneficial effects of both exercise and multi-sensory environmental stimulation have been well-documented, thus it is possible that these strategies can either provide neuroprotection or increase resistance to the development of age-related cognitive problems.
Variation in Teacher Preparation: How Well Do Different Pathways Prepare Teachers to Teach?

Does teacher education influence what teachers feel prepared to do when they enter the classroom? Are there differences in teachers’experiences of classroom teaching when they enter through differe...
Speech-graphics dialogue systems

The central mechanism of a dialogue system must be a planner (Allen et al., 1994; Smith et al., 1995; Young et al., 1989) that seeks the dialogue goal and organizes all behaviors for that purpose. Our project uses a hybrid Prolog-like planner (Smith and Hipp, 1994) which first attempts to prove the top-most goal and then initiates interactions with the user when the proof cannot easily be achieved. Specifically, it attempts to discover key missing axioms in the proof that prevent its completion and that may be attainable with the help of the user. The purposes of the interaction are to gather the missing information and to eventually achieve the top-most goal.
In Search of Common Threads: Linking Multicultural, Feminist, and Social Justice Counseling Paradigms.

Multicultural, feminist, and social justice counseling theories are often viewed as disparate helping models. This article examines the complementary nature of these models and discusses the need to promote a clearer understanding of the ways in which these common threads can be used in counseling practice.
FDG Uptake on Positron Emission Tomography Correlates with Survival and Time to Recurrence in Patients with Stage I Non–Small-Cell Lung Cancer

Introduction Patients with stage I non–small-cell lung cancer (NSCLC) have a wide variation in outcomes, most likely because there are undetected metastases at presentation. We retrospectively reviewed patients with early stage lung cancer to determine if FDG uptake of the primary tumor as measured on positron emission tomography (PET) at the time of diagnosis was associated with overall survival (OS) or time to recurrence (TTR). Methods We reviewed the Tumor Registry at our institution and identified 336 consecutive patients diagnosed with stage I NSCLC over a 5-year period who underwent an FDG-PET/computed tomography within 90 days before surgery. Kaplan–Meier curves were used to describe the survival and TTR experience within subgroups defined by PET maximum standardized uptake value (SUVmax). Cox proportional hazards model was used to assess the impact of PET SUVmax as a continuous variable on OS and TTR. Logistic regression was used to analyze the effect of SUVmax on dichotomized outcomes. Results Three hundred thirty-six consecutive patients (176 women and 160 men) with stage I NSCLC were retrospectively reviewed. Mean SUVmax was 9.2 ± 6.9 (range 0.6–30.3). The hazard or risk of dying and recurrence increased significantly as SUVmax increased ( p = 0.0008 and 0.024, respectively). Conclusions Preoperative FDG uptake in the primary tumor in patients with stage I disease is associated with OS and TTR. This may be useful in identifying early stage patients who may benefit from more aggressive therapy after surgical resection.
Dynamic modeling of yeast meiotic initiation

Meiosis is the sexual reproduction process common to eukaryotes. The diploid yeast Saccharomyces cerevisiae undergoes meiosis in sporulation medium to form four haploid spores. Initiation of the process is tightly controlled by intricate networks of positive and negative feedback loops. Intriguingly, expression of early meiotic proteins occurs within a narrow time window. Further, sporulation efficiency is strikingly different for yeast strains with distinct mutations or genetic backgrounds. To investigate signal transduction pathways that regulate transient protein expression and sporulation efficiency, we develop a mathematical model using ordinary differential equations. The model describes early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signaling molecules for regulating protein activities. The mathematical model is capable of simulating the orderly and transient dynamics of meiotic proteins including Ime1, the master regulator of meiotic initiation, and Ime2, a kinase encoded by an early gene. The model is validated by quantitative sporulation phenotypes of single-gene knockouts. Thus, we can use the model to make novel predictions on the cooperation between proteins in the signaling pathway. Virtual perturbations on feedback loops suggest that both positive and negative feedback loops are required to terminate expression of early meiotic proteins. Bifurcation analyses on feedback loops indicate that multiple feedback loops are coordinated to modulate sporulation efficiency. In particular, positive auto-regulation of Ime2 produces a bistable system with a normal meiotic state and a more efficient meiotic state. By systematically scanning through feedback loops in the mathematical model, we demonstrate that, in yeast, the decisions to terminate protein expression and to sporulate at different efficiencies stem from feedback signals toward the master regulator Ime1 and the early meiotic protein Ime2. We argue that the architecture of meiotic initiation pathway generates a robust mechanism that assures a rapid and complete transition into meiosis. This type of systems-level regulation is a commonly used mechanism controlling developmental programs in yeast and other organisms. Our mathematical model uncovers key regulations that can be manipulated to enhance sporulation efficiency, an important first step in the development of new strategies for producing gametes with high quality and quantity.
Live Load Deflection Performance of Glued Laminated Timber Girder Bridges

To demonstrate and possibly to promote the increased use of timber bridges in U.S. transportation systems, various agencies, including the United States Department of Agriculture Forest Products Laboratory and FHWA, have supported research to develop improved glued laminated timber bridges. This project is part of this research and identifies acceptable live load deflection characteristics of timber bridges. The relationship between live load deflection and the condition of the asphalt wearing surface is of particular interest. To accomplish this, eight glued laminated timber girder bridges were selected for testing. The performance of the bridges was investigated under live load tests and through bridge inspections. The structures were load tested with fully loaded tandem-axle dump trucks, and global and differential deflection data were collected. Field tests revealed that a significant amount of the asphalt wearing-surface deterioration is the result of differential deck panel deflection.
WebEyeMapper and WebLogger: tools for analyzing eye tracking data collected in web-use studies

Eye trackers output a stream of points at which the eye was looking. To give these points meaning, researchers analyzing eye tracking data need to map the points onto the meaningful objects at which the eye was looking. Performing this mapping has proven to be a tedious, time-consuming task. We present a software system that automates this task for Web usabilty studies that incorporate eye tracking.
Normalized and Equilibrium Spectra of Wind Waves in Lake Michigan

Abstract An empirical spectral equation for fetch-limited deep-water wind waveswas derived by applying similarity analysis to wind and wave data recorded at the Lake Michigan Research Tower near Muskegon, Mich., during the autumn of 1967. The field data indicates that both the equilibrium range coefficient, β in S(ω) = βg2ω−5 and the dimensionless peak-frequency parameter, ωmU*/g, vary with Fo, where Fo = gF/U*2 is the dimensionless fetch parameter with respect to fetch F and friction velocity U*. The equation produces reasonably good results in estimating actual wave spectra, provided sufficient duration is achieved in the wind field. The equation also indicates that a fully-developed state will not be reached at a steady wind speed as the very low-frequency waves grow continuously with increasing fetch.