cssi/SciSciGPT-SciSciNet huggingface dataset:
Comparative ecology of bryozoan radiations; origin of novelties in cyclostomes and cheilostomes

Cyclostome and cheilostome bryozoans diversified at different times and consequently in different ecological contexts. Cyclostomes began their rebound from a Perm-Triassic bottleneck in the early Jurassic, prior to increases in bioturbation, durophagous predation, and other ecological changes of the Mesozoic Marine Revolution. Cheilostomes did not appear until the latest Jurassic and rapid diversification began only in the mid-Cretaceous, when the Mesozoic Revolution was well under way. We compare the radiations of these two groups to test for similarities in the within-group patterns of origin of biologically significant novelties, and for between-group differences that might be due to ecological context or group attributes. As seen for other invertebrate t a u , within-group novelties were not concentrated in onshore settings, in contrast to origination patterns at the ordinal level. Differences in environment of first occurrence and rapidity of novelty acquisition were not obviously related to the Mesozoic Revolution, or to the distinction between zooidand colony-level characters. The contrast in novelty acquisition rates may partly reflect group-specific constraints. In cyclostomes, novelties appeared rather evenly over 100 Ma, whereas in cheilostomes many of the novelties appeared in the Late Albian-Early Cenomanian during a period of rapid diversification. Despite a slow start (Late Jurassic-mid Cretaceous), the cheilostome radiation entered an explosive phase that may characterize successful establishment of groups founded late in the Phanerozoic.
Sexual Abuse of Young Children

For an 18-month period, all sexual abuse cases were referred to a project social worker. From her initial interview and the medical records, data were analyzed for 113 children who were 12 years of age or younger. It was found that half were five years or younger and three-fourths of the cases were female children. Reasons were discussed as to why females are more likely to be identified as sexually abused cases. A higher than average rate of gonorrhea was found among the pediatric group studied. While only 44 per cent of abusers were relatives of the abused, almost all (93%) were known to the family. If a relative were the alleged abuser, there was a high probability that it was a father, stepfather, or uncle.
Career Ladders: Messages Gleaned from Experience

The educational reform movement will begin to retreat from its goals if lessons from previous attempts at reforming the educational system are ignored. Career ladder and other incentive programs ar...
Detection of liposome membrane viscosity perturbations with ratiometric molecular rotors.

Molecular rotors are a form of fluorescent intramolecular charge-transfer complexes that can undergo intramolecular twisting motion upon photoexcitation. Twisted-state formation leads to non-radiative relaxation that competes with fluorescence emission. In bulk solutions, these molecules exhibit a viscosity-dependent quantum yield. On the molecular scale, the fluorescence emission is a function of the local free volume, which in turn is related to the local micro-viscosity. Membrane viscosity, and the inverse; fluidity, are characteristic terms used to describe the ease of movement withing the membrane. Often, changes in membrane viscosity govern intracellular processes and are indicative of a disease state. Molecular rotors have been used to investigate viscosity changes in liposomes and cells, but accuracy is affected by local concentration gradients and sample optical properties. We have developed self-calibrating ratiometric molecular rotors to overcome this challenge and integrated the new molecules into a DLPC liposome model exposed to the membrane-fluidizing agent propanol. We show that the ratiometric emission intensity linearly decreases with the propanol exposure and that the ratiometric intensity is widely independent of the total liposome concentration. Conversely, dye concentration inside liposomes influences the sensitivity of the system. We suggest that the new self-calibrating dyes can be used for real-time viscosity sensing in liposome systems with the advantages of lifetime measurements, but with low-cost steady-state instrumentation.
Delamination Growth Using Cohesive Zone Model for Adhesive Bonding Under Compression

Adhesive bonding of aircraft primary structures has been in use for many years. For example, joining the stringers to skins of fuselage and wing structures, metallic honeycomb to the skins of elevators, ailerons, tabs, and spoilers constitute the main uses of adhesives in aircraft structures. Due to this increasing use of bonded structures in recent years, for weight saving, considerable work has been done in the fracture testing of different types of adhesive joints. However, most previous work on adhesive bonded joints deals mostly with Mode I fracture, and very little work appears to have been done on compressive delamination of adhesive joints. The Chow and Ngan test, consisting of two slender beams with a blister at the centre of each, which were bonded together and loaded in compression, is an exception. In the present work, a cohesive finite element model was developed for this blister test-piece, and the geometric non-linearity was incorporated in the strain/displacement relations. The crack propagation in the adhesive joint under compression for the proposed test-piece was found to agree with the available experimental observation. Most importantly, the delamination in adhesive joint under compression for different constrained cases was studied by cohesive finite element with different interface mesh densities. Stronger adhesive joint was achieved for less constrained Double Cantilever Beam (DCB) specimen.
Are tropical forests near a high temperature threshold

We used leaf gas exchange, sap flow, and eddy covariance measurements to investigate whether high temperature substantially limits CO2 uptake at the LBA-ECO (Large-scale Biosphere-Atmosphere) km-83 tropical forest site in Brazil. Leaf-level temperature-photosynthesis curves, and comparisons of whole-canopy net ecosystem CO2 exchange (NEE) with air temperature, showed that CO2 uptake declined sharply during warm periods. Observations of ambient leaf microclimate showed that leaves oscillate between two states: a cool, dimly lit stage and a hot, brightly illuminated stage where leaf temperatures are often greater than 35°C. The leaf-level rates of photosynthesis decreased when shaded leaves (∼ambient air temperature and < 500 μmol m−2 s−1) were transferred into a prewarmed, brightly illuminated chamber (35° to 38°C and 1000 μmol m−2 s−1), coincident with increased leaf temperature, increased evaporative demand, and stomatal closure. The rates of whole-canopy CO2 uptake calculated at 5-min intervals increased initially at the onset of sunny periods that followed extended cloudy periods, but then decreased as the sunlight continued, leaf temperature and evaporative demand increased, and canopy conductance decreased. The forest at km-83 appears to be close to a high temperature threshold, above which CO2 uptake drops sharply. This sensitivity results in part from the covariance between leaf temperature and leaf illumination; the brightly illuminated leaves that contribute disproportionately to canopy photosynthesis are warmed to the point that leaf gas exchange is curtailed.
Probability hypothesis density filtering with multipath-to-measurement association for urban tracking

We consider the particle probability hypothesis density filter (PPHDF) for tracking multiple targets in urban terrain. This is a filtering technique based on random finite sets, implemented using the particle filter. Unlike data association methods, the PPHDF can be modified to estimate both the number of targets and their corresponding tracking parameters. We propose a modified PPHDF algorithm that employs multipath-to-measurement association (PPHDF-MMA) to automatically and adaptively estimate the available types of measurements. By using the best matched measurement at each time step, the new algorithm results in improved radar coverage and scene visibility. Numerical simulations demonstrate the effectiveness of the PPHDF-MMA in improving the tracking performance of multiple targets and targets in clutter.
Phase fluctuations and spectral properties of underdoped cuprates

We consider the effect of classical phase fluctuations on the quasiparticle spectra of underdoped high-${T}_{c}$ cuprate superconductors in the pseudogap regime above ${T}_{c}.$ We show that photoemission and tunneling spectroscopy data are well accounted for by a simple model in which mean-field $d$-wave quasiparticles are semiclassically coupled to supercurrents induced by fluctuating unbound vortex-antivortex pairs. We argue that the data imply that transverse phase fluctuations are important at temperatures above ${T}_{c},$ while longitudinal fluctuations are unimportant at all temperatures.
Handwritten character recognition using fuzzy logic

The present paper discusses an application of fuzzy set theory to handwritten character recognition. A nonmathematical, heuristic approach to structural pattern recognition is used. Entities are given in the form of fuzzy matrix and are processed by fuzzy logic according to the membership values in different categories of features stored. A computer simulation for English alphabets, and some results are presented.
Variation among Primary Care Physicians in the Use of Imaging for Older Patients with Acute Low Back Pain

BACKGROUND Diagnostic imaging is not recommended in the evaluation and management of non-specific acute low back pain.
Monoamniotic monochorionic twins discordant for noncompaction cardiomyopathy

Occasionally "identical twins" are phenotypically different, raising the question of zygosity and the issue of genetic versus environmental influences during development. We recently noted monochorionic-monoamniotic twins, one of which had an isolated cardiac abnormality, noncompaction cardiomyopathy, a condition characterized by cardiac ventricular hypertrabeculation. We examined the prenatal course and subsequent pathologic correlation since ventricular morphogenesis may depend on early muscular contraction and blood flow. The monochorionic-monoamniotic female twin pair was initially identified since one fetus presented with increased nuchal translucency. Complete heart block was later identified in the fetus with nuchal translucency who did not survive after delivery. In contrast, the unaffected twin had normal cardiac studies both prenatally and postnatally. Pathologic analysis of the affected twin demonstrated noncompaction of the left ventricle with dysplasia of the aortic and pulmonary valves. Dissection of the cardiac conduction system disclosed atrioventricular bundle fibrosis. Maternal lupus studies, amniocentesis with karyotype, and studies for 22q11.2 were normal. To test for zygosity, we performed multiple STR marker analysis and found that all markers were shared even using nonblood tissues from the affected twin. These studies demonstrate that monozygotic twins that are monochorionic monoamniotic can be discordant for cardiac noncompaction. The results suggest further investigation into the potential roles of pathologic fibrosis, contractility, and blood flow in cardiac ventricle development.
Do Higher Levels of Resilience Buffer the Deleterious Impact of Chronic Illness on Disability in Later Life

levels of resilience will have lower levels of disability and (b) resilience will moderate the association between the onset of a new chronic condition and subsequent disability. Design and Methods: This study used a sample of 1 0,753 Americans between the ages of 51 and 98, derived from 3 waves of the Health and Retirement Study (2006–2010). Ordinary least squares regression was used to estimate the impact of resilience on changes in disability (measured as difficulty with activities of daily living [ADLs] and instrumental activities of daily living [IADLs]) over a 2-year period using a simplified resilience score. Results: R esilience protects against increases in ADL and IADL limitations that are often associated with aging. Resilience mitigates a considerable amount of the deleterious consequences related to the onset of chronic illness and subsequent disability. Implications: Our results support our hypotheses and are consistent with claims that high levels of resilience can protect against the negative impact of disability in later life.
A Consideration of the Devolution of U.S. Agricultural Policy

Diverse needs and preferences across the United States provide justification for the devolution, or decentralization, of many Federal Government programs to the State or local level. The move toward devolution, however, has not been evidenced in U.S. agricultural policy, despite significant differences across States in such areas as commodity production, production costs, income distribution, and opportunities for off-farm work. The existing structure of USDA funding and program delivery already reflects an appreciation of the gains from devolution, with some programs accommodating differences in State and regional preferences. This report considers the implications of devolving $22 billion in 2003 budget outlays, mostly for domestic commodity and natural resource programs and rural development and housing programs. The local knowledge of needs and preferences is valuable and can provide the basis for increased program efficiency.
Perceived role of motivation and self-efficacy in smoking cessation: A secondary data analysis.

Abstract Background This secondary analysis tested whether smokers' perceived importance of willpower, ability to quit (i.e., self-efficacy), and use of treatment would prospectively predict occurrence of a quit attempt, duration of abstinence, or use of cessation aids. Methods Smokers (n = 143) who planned to quit sometime in the next 3 months were asked whether, for most smokers, a) willpower is necessary for quitting, b) willpower is sufficient for quitting, c) they could quit anytime, d) they were too addicted to quit, and e) they thought use of aids indicated weakness of character. Smokers then reported quit attempts and abstinence daily for 3 months. No treatment was provided. Results The two willpower beliefs were often endorsed (78% and 60% each); the can quit any time and being too addicted beliefs were endorsed less consistently (12% and 35% each); and the belief that use of aids indicates a weakness was rarely endorsed (8%). The beliefs were only modestly correlated. Those who more strongly endorsed the two willpower beliefs or use of aids as a weakness were less likely to make a quit attempt. None of the constructs predicted duration of quit attempt. Seeing treatment as a weakness predicted less use of treatment. Conclusions The large majority of smokers believe willpower is necessary and sufficient for quitting and this belief appears to impede quit attempts. Given this is a post-hoc finding, replication tests are needed. If replicated, clinical and media interventions to combat willpower beliefs may increase quit attempts.
Using chrome azurol S spectrophotometry to measure aluminium in extruded food

Objective:To establish a simple determination method for aluminum in extruded food.Methods:To determine the content of aluminum in extruded food with improved methods of chrome azurol S spectrophotometry.Results:Increased the linear range of the national standard method from 0~6 μg to 0~10 μg with the improved method.There was a linear relationship.The curve regression equation was Y=0.1174X-0.0236,the correlation coefficient was 0.9997,the recovery rate was between 93.0%~106.2%,the detection limit was 0.37 mg/kg.Conclusion:The improved aluminum determination method is simple,easy to control and can obtain accurate results.
Jump number of two-directional orthogonal ray graphs

We model maximum cross-free matchings and minimum biclique covers of two-directional orthogonal ray graphs (2-dorgs) as maximum independent sets and minimum hitting sets of an associated family of rectangles in the plane, respectively. We then compute the corresponding maximum independent set using linear programming and uncrossing techniques. This procedure motivates an efficient combinatorial algorithm to find a cross-free matching and a biclique cover of the same cardinality, proving the corresponding min-max relation. We connect this min-max relation with the work of Gyori [19], Lubiw[23], and Frank and Jordan [16] on seemingly unrelated problems. Our result can be seen as a non-trivial application of Frank and Jordan's Theorem. As a direct consequence, we obtain the first polynomial algorithm for the jump number problem on 2-dorgs. For the subclass of convex graphs, our approach is a vast improvement over previous algorithms. Additionally, we prove that the weighted maximum cross-free matching problem is NP-complete for 2-dorgs and give polynomial algorithms for some subclasses.
S15-3 Use of metabolomics in characterising occupational exposures to manganese in metalworkers

Metabolomics is an analysis technique used to characterise the set of small-molecule metabolites found in a biofluid, and has commonly been used to investigate biochemical differences between diseased and non-diseased groups. Limited research has looked at how metabolomics profiles differ in occupationally exposed and unexposed groups, and what the challenges and opportunities of using metabolomics in occupational exposure sciences are. Metabolomics has been proposed as a valuable tool in helping to characterise the exposome—though further study of its utility as an exposure assessment tool, particularly in occupational settings, is warranted. We explored metabolomics profiles related to manganese (Mn) exposure in urine, plasma, and whole blood in two geographically diverse metalworking cohorts. In the first cohort, a full-shift personal inhalable air sample was taken on all participants, and a spot urine sample was collected at the end of the day. In the second cohort, cumulative and recent exposures were modelled from an exposure questionnaire, and a whole blood sample, plasma sample, and spot urine sample were collected. All biofluids underwent global metabolomics analyses on a QTOF-LC/MS, and both exposed and unexposed individuals in each cohort were divided into a training set and demographically-matched internal validation set. For each biofluid, ions found to be significantly associated with exposure (adjusted p-value Results from this work could lead not only to a greater understanding of the biochemical pathways Mn perturbs after inhalation and risk interpretation for Mn exposure, but also inform future studies looking to use metabolomics to characterise exposure in occupational cohorts.
Reproducing a laser pointer dot on a secondary projected screen

Large lecture rooms typically contain more than one projector/screen pair, but the presenter can point a hand-held laser pointer at only one screen at a time. If the audience at the other side of the room has difficulty seeing the laser pointer dot, the presentation performance may be compromised. This paper introduces a robotic laser pointer system to solve such a problem. After calibration, a camera monitoring the primary screen continuously feeds images to a computer that detects and localizes the laser dot by comparing successive frames. The computer uses inverse kinematics to calculate the joint angles needed for a pan/tilt base holding another laser pointer to reproduce the laser position on the other screen. Quantitative evaluation verifies the system's capabilities and reveals potential improvements and further experiments needed to deploy the system in real lecture settings.
Recommendations about Pregnancy from Women with Mobility Disability to Their Peers.

Abstract Background Although growing numbers of women with mobility disability are becoming pregnant and desiring motherhood, relatively little is known about their pregnancy experiences or what they might recommend to other women with mobility disability contemplating pregnancy. Methods Using a semistructured, open-ended interview protocol, we conducted 2-hour telephone interviews with 22 women who had a significant mobility disability before becoming pregnant and had delivered babies within the prior 10 years. We recruited most interviewees through online social networks. We used NVivo software to sort interview transcript texts and performed conventional content analyses to identify major themes. Results Participants’ mean ± standard deviation age was 34.8 ± 5.3 years; most were White, well-educated, and middle income and 18 used wheeled mobility aids. Recommendations for other women with mobility disability coalesced around five themes: recognizing the possibility of giving birth, advocacy and support, being informed, approaches toward obstetrical practitioners, and managing fears about losing custody of their child. Lacking information about what to expect during their pregnancy was a significant problem. Women got information about pregnancy from diverse sources, but questions arose about accuracy and relevance of this information to individual circumstances. Women urged their peers to advocate for their preferences and needs with obstetrical practitioners. Conclusions Women with mobility disability who had delivered babies offered constructive advice for their peers who desire pregnancy. Increasing availability of accurate and relevant information about pregnancy among women with mobility disability is critically important, as is training obstetrical practitioners to provide patient-centered care to these women during pregnancy.
Debt, refugees and the failure of the European project in 2015

In December 2015, as French newspapers and magazines prepared their annual ‘closing of the year’ issues, the expression annus horribilis came up more than once. The year 2015 had opened with the ho...
Wideband air-coupled PZT piezoelectric micromachined ultrasonic transducer through DC bias tuning

Wide bandwidth for an air-coupled piezoelectric micromachined transducer (PMUT) is important to achieve short pulse transmission and reception in pulse-echo imaging with high axial resolution. Here, we report experimental results on an air-coupled PMUT with high displacement sensitivity up to 5500 nm/V, high 3 dB bandwidth of 20.3 kHz, and correspondingly short transmission time of 0.05 ms, achieved through dc bias tuning. The dc bias controls the polarization and intrinsic stress of the piezoelectric layer, tuning frequencies of two closely spaced resonance modes of the ribbon-shaped PMUT. The modes nearly overlapped when applying small dc bias around ±5 V, enabling wideband and short pulse transmission.
Effect of vinblastine on the brush border of proximal tubule cells of rat kidney

A vinblastine-induced lesion of the brush border of proximal tubule cells of rat kidney was studied by scanning and transmission electron microscopy. Adult rats were given two tail-vein injections of vinblastine sulfate and then sacrificed either three or sixteen hours after administration of the first injection. The proximal tubules of animals treated with the drug for three hours differed from those of saline-treated controls in possessing (1) well defined areas of apical cell surface devoid of microvilli and (2) fewer microcraters in the brush border. In tubules of animals treated with vinblastine for sixteen hours, the areas devoid of microvilli were much more extensive, and microcraters were less frequently seen. Cilia did not appear to be affected by exposure to the drug and were observed both in regions devoid of microvilli and in areas with a well developed brush border. The mechanism of action of vinblastine in eliciting focal loss of microvilli of proximal tubule cells is not known. Several hypotheses to account for this lesion of the brush border are discussed.
College Binge Drinking: A Problem of Perception - Letter Chicago Tribune

Parents can help clarifying college bound children's inaccurate perceptions of alcohol consumption on college campuses. Students believe that their peers drink more than the do consume. This may lead them to drink more to fit in. They do fit in, but do not know it. Parental involvement can help clarify their children's misperceptions before they leave for college..
Depressive Disorders and ADHD

Major and minor depressive disorders occur 5.5 times more often in people with attention-deficit/hyperactivity disorder (ADHD) than without it. Patients with depressive disorders and ADHD (Dep/ADHD) have significant long-term impairment and suicide risk. Dep/ADHD typically begins several years after the onset of the ADHD, offering the opportunity to prevent it in this predisposed group with ADHD. Impairment related to the ADHD and to other comorbid disorders, environmental adversities, and familial factors all may contribute to the increased risk of depressive disorders and suicide in patients with ADHD. Early identification could lead to earlier treatment, which could reduce the morbidity and mortality of Dep/ADHD, but is complicated by the overlap of depression symptoms with ADHD’s and other common comorbidities’ symptoms, and with the side effects of ADHD medications. Growing evidence suggests the benefit of treating Dep/ADHD with selective serotonergic reuptake inhibitor antidepressants, stimulants, and even atomoxetine or bupropion. Other evidence suggests the benefit of psychosocial treatments, alone or with pharmacotherapy, to target the depressive symptoms, psychosocial impairment, and contributing environmental factors. This chapter reviews the morbidity, etiological factors, and strategies for assessing and treating Dep/ADHD.
Detecting Visual Field Progression.

Timely detection of glaucomatous progression is crucial in the delivery of glaucoma care. Clinical judgment may be used to make this assessment, but relatively modest agreement among practitioners supports the use of complementary methods. Event-based analyses take into account expected localized test–retest variabilities in sensitivity, and trend-based analyses are helpful for determining and predicting overall visual function. Landmark clinical trials have used various visual field progression criteria as end points with variable performances. Short- and long-term fluctuations as well as inadequate testing frequency are limitations in visual field analysis for glaucomatous progression. Ongoing improvements in statistical techniques as well as incorporation of functional and structural measures into a single model likely will lead to an enhanced ability to detect glaucomatous progression and will allow for more timely and appropriate therapy.
Dabrafenib and Trametinib Treatment for Erdheim-Chester Disease With Brain Stem Involvement

Erdheim-Chester disease (ECD) is a rare form of non-Langerhans cell histiocytosis characterized by infiltration of organs by CD68+ and CD1a- lipid-laden histiocytes, including the central nervous system in more than a third of patients. Molecular analysis of ECD samples has demonstrated the prevalence of BRAF V600E mutations as high as 54%. Recently, vemurafenib became the only Food and Drug Administration-approved treatment for patients with ECD who carry the BRAF V600E mutation. However, dabrafenib has been suggested to have greater brain distribution. We describe a 44-year-old female patient treated from August of 2015 through November 2017. She presented with a 2-year history of light-headedness, fatigue, and vertigo. She was moderately dysmetric, diffusely hyperreflexic, and dysarthric in the bilateral upper and lower extremities. Her gait was wide-based. She had dysarthria and nystagmus on horizontal gaze bilaterally. Magnetic resonance imaging showed an extensive area of increased T2/fluid-attenuated inversion recovery signal in the brain stem, enhancement in the pons and midbrain, and thickening of the pituitary stalk. Positron emission tomography/computed tomography (PET/CT) and whole-body technetium Tc99m bone scintigraphy showed intense symmetrical radiotracer uptake in the distal femur and tibia bilaterally, which was biopsied. Immunohistochemistry was negative for BRAF V600E, but genomic sequencing revealed the mutation. The patient received combination therapy with dabrafenib and trametinib. Her nystagmus, dysarthria, dysmetria, and gait improved remarkably. Subsequent PET/CT and magnetic resonance imaging showed complete resolution of all radiographic evidence of disease. In this case report, we demonstrate the success of a combination therapy with dabrafenib and trametinib.
States and their genetic consequences in central Africa.

Archaeogenetic analyses are usually aimed at elucidating the demographic history of small-scale societies, although frequently over large geographic and temporal scales. There has been significantly less attention paid to the analysis of state-level societies, except sometimes as a political framework within which smaller-scale interactions took place. This is curious, because it is widely recognized that state policies can have important demographic consequences (1⇓–3). This relative lack of interest in the genetic impact of states may be associated with an assumption that historical sources provide sufficient information on such processes. In PNAS, the paper by van Dorp et al. (4) on the genetic effects of state formation in central Africa provides an example of such an analysis, indicating some of the likely consequences of state formation and functioning in the Kuba polity. Over the past 20 y, the archaeogenetic studies that have concerned themselves with state-level societies have done so through a variety of approaches, ranging from straightforward claims of correspondences between haplogroups and state ethnicities (5), to analysis of the demographic consequences of state collapse and regeneration (6), to analysis of different forms of sociopolitical hierarchy often associated with complex societies (7). The relatively small size and recent historical trajectory of the Kuba state allow van Dorp et al. (4) to take a more global approach, comparing variability in autosomal, Y-chromosomal, and mtDNA genetic features for a sample in individuals identifying as Kuba or non-Kuba, the latter from a variety of stateless societies historically situated beyond the boundaries of the Kuba state. These samples were not gathered within the historical territory of the Kuba state, but rather in Kananga, the modern capital of Kasai … [↵][1]1Email: scott.maceachern{at}dukekunshan.edu.cn. [1]: #xref-corresp-1-1
SeqOthello: Query over RNA-seq experiments at scale

We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. SeqOthello requires only five minutes to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets on a standard computer with 19.1 GB memory space. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and further reveals 270 novel fusion occurrences, all of which present as tumor-specific. The entire index is only 76 GB, achieving a 700:1 compression ratio relative to the original sequencing data and making it extremely portable. This is the first sequence search index constructed on the scale of TCGA data. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs. SeqOthello is currently available at https://github.com/LiuBioinfo/SeqOthello.
Restricting data’s use: A spectrum of concerns in need of flexible approaches

As researchers consider making their data available to others, they are concerned with the responsible use of data. As a result, they often seek to place restrictions on secondary use. The Research Connections archive at ICPSR makes available the datasets of dozens of studies related to childcare and early education. Of the 103 studies archived to date, 20 have some restrictions on access. While ICPSR’s data access systems were designed primarily to accommodate public use data (i.e. data without disclosure concerns) and potentially disclosive data, our interactions with depositors reveal a more nuanced notion range of needs for restricting use. Some data present a relatively low risk of threatening participants’ confidentiality, yet the data producers still want to monitor who is accessing the data and how they plan to use them. Other studies contain data with such a high risk of disclosure that their use must be restricted to a virtual data enclave. Still other studies rest on agreements with participants that require continuing oversight of secondary use by data producers, funders, and participants. This paper describes data producers’ range of needs to restrict data access and discusses how systems can better accommodate these needs.
Graph Convolutional Networks for Predicting Drug-Protein Interactions

In this paper, a heterogeneous graph of drug-target entities are constructed to predict drug-protein interactions. We use a deep learning approach and apply an encoder-decoder technique in an end-to-end manner directly on a full-scale heterogeneous graph. The proposed method not only achieves performance improvement over previous state-of-the-art techniques, but also integrates additional information into the model for a more comprehensive analysis.
1351. Pediatric Antibioitic Use in the North Carolina Medicaid Population

Background Antimicrobial resistance is increasing in the United States, with antibiotic use as the main driver. The majority of antibiotic use occurs in the outpatient setting. 6 of the 7 highest prescribing states are located in the Appalachian region of the country. Overall, the state of North Carolina (NC) has prescribing rates that are at the national average, but the geographic, patient and provider-level characteristics associated with antibiotic prescribing within the state are unknown.
Trustworthy scientific computing

Author(s): Peisert, S | Abstract: Addressing the trust issues underlying the current limits on data sharing.
Intramuscular hyaluronic acid expression following repetitive power training induced nonfunctional overreaching

Hyaluronic acid (HA) contributes to extracellular matrix viscosity and fiber regeneration. HA role in resistance training (RT) performance adaptations is unclear. RT men performed power training (n...
Quantum circuits for $${\mathbb {F}}_{2^{n}}$$F2n-multiplication with subquadratic gate count

One of the most cost-critical operations when applying Shor's algorithm to binary elliptic curves is the underlying field arithmetic. Here, we consider binary fields $${\mathbb {F}}_{2^n}$$F2n in polynomial basis representation, targeting especially field sizes as used in elliptic curve cryptography. Building on Karatsuba's algorithm, our software implementation automatically synthesizes a multiplication circuit with the number of $$T$$T-gates being bounded by $$7\cdot n^{\log _2(3)}$$7·nlog2(3) for any given reduction polynomial of degree $$n=2^N$$n=2N. If an irreducible trinomial of degree $$n$$n exists, then a multiplication circuit with a total gate count of $${\mathcal {O}}(n^{\log _2(3)})$$O(nlog2(3)) is available.
Irrepressible: An Interview with Mark Ptashne.

While winter storms crippled almost every state from Wisconsin to Florida, our own force of nature blew into California in January in the compact human form of Mark Ptashne (Fig 1). Mark, who holds the Ludwig Chair of Molecular Biology at Sloan-Kettering in New York, had arrived to give a series of seminars on the West Coast. And if that weren’t enough, he also came prepared for a soiree, with his violin in tow.
A multimethod analysis of shared decision-making in hospice interdisciplinary team meetings including family caregivers:

Background:Much of the existing research on shared decision-making in hospice and palliative care focuses on the provider–patient dyad; little is known about shared decision-making that is inclusive of family members of patients with advanced disease.Aim:We sought to describe shared decision-making as it occurred in hospice interdisciplinary team meetings that included family caregivers as participants using video-conferencing technology.Design:We conducted a multimethod study in which we used content and thematic analysis techniques to analyze video-recordings of hospice interdisciplinary team meetings (n = 100), individual interviews of family caregivers (n = 73) and hospice staff members (n = 78), and research field notes.Setting/participants:Participants in the original studies from which data for this analysis were drawn were hospice family caregivers and staff members employed by one of five different community-based hospice agencies located in the Midwestern United States.Results:Shared decision-ma...
Detection of SPO11-Oligonucleotide Complexes from Mouse Testes

The SPO11 protein generates programmed DNA double-strand breaks (DSBs) that initiate meiotic recombination. Endonucleolytic cleavage 3' to the DSB sites releases SPO11 from DNA, leaving SPO11 covalently associated with an oligonucleotide. This chapter describes detection of the release product, SPO11-oligonucleotide complexes, from mouse testis lysates. The method for determining the size of SPO11-associated oligonucleotides is also provided.
0 × 50—Preparing Seattle's Building Stock for a Carbon-neutral 2050

ABSTRACTSeattle's elected officials have set a target for transforming the city's “core energy”—including all of the energy serving its buildings and transportation, to be carbon-neutral by the year 2050. What does the city need to do with its building stock beginning today to ensure that it can hit that target in a single generation? The question was studied in part in the 2010 Stockholm Environment Institute (SEI) study Getting to Zero—A Pathway to a Carbon-Neutral Seattle (SEI 2010), as well as the 2013 Seattle Climate Action Plan (CAP 2013), both of which set targets and made general recommendations but necessarily stopped short of pinning down a detailed step-by-step solution. This paper proposes a set of potential strategies, centered on the concept of “zero-carbon-ready” communities. This set of strategies forms one of several possible pathways to carbon-neutrality that will be debated over the months and years to come. While a number of the components of this strategy are already incorporated into...
Cytochrome c interactions with membranes. A photoaffinity-labeled cytochrome c.

Abstract The aryl azide, 2,4-dinitro-5-fluorophenylazide, was reacted with horse heart cytochrome c to give a photoaffinity-labeled derivative of this heme protein. The modified cytochrome c, with one to two dinitroazidophenyl groups per mole of the enzyme, has a half-reduction potential the same (± 10 mV) as native cytochrome c. The dissociation constant for the modified cytochrome c from cytochrome c-depleted mitochondrial membranes and the apparent Km for the reaction with cytochrome c oxidase were each five to six times greater than the values for native cytochrome c. Irradiation of cytochrome c-depleted mitochondrial membranes supplemented with an excess of photoaffinity-labeled cytochrome c resulted in covalent binding of the derivative to the mitochondrial membranes. Fractionation of the irradiated mitochondria in the presence of detergents and salts followed by chromatography on agarose, Bio-Gel A, showed that labeled cytochrome c was bound covalently to cytochrome c oxidase in a 1:1 molar complex. The covalently linked cytochrome c-cytochrome c oxidase complex was active in mediating the electron transfer between N,N,N′,N′-tetramethyl-p-phenylenediamine/ascorbate and the oxidase.
Management of agitation in nursing home patients.

Agitation in demented nursing home residents is a major clinical problem with which patients, families and staff are required to cope. Agitation may be secondary to a variety of psychiatric, environmental and medical problems, and thus attempts must be made be clarify aetiological issues before initiating a treatment plan. Treatments for agitation are imperfect, and clinicians should be prepared to work through several to find the best for a given patient and clinical situation.
Mammalian Na+/H+ exchanger gene family: structure and function studies

Na+/H+ exchangers are integral plasma membrane proteins that exchange extracellular Na+ for intracellular H+ with a stoichiometry of one for one. They are inhibitable by the diuretic amiloride and have multiple cellular functions, including intracellular pH homeostasis, cell volume control, and electroneutral NaCl absorption in epithelia. The presence of multiple forms of the exchangers was demonstrated by the recent cloning of four mammalian Na+/H+ exchangers, NHE1, NHE2, NHE3, and NHE4. All of these cloned Na+/H+ exchangers have 10-12 putative transmembrane helixes and a long cytoplasmic carboxyl domain. Despite the structural similarity, these Na+/H+ exchanger isoforms differ in their tissue distribution, kinetic characteristics, and response to external stimuli. The present review deals with the recent developments in the molecular identification of the Na+/H+ exchanger gene family, the functional characteristics, and the short-term regulation of Na+/H+ exchange at molecular and cellular levels.
Validity of Hybrid Models for the Bidirectional Reflectance of Coated Rough Surfaces

Modeling of the bidirectional reflectance of thin-film coatings on rough surfaces has been an important and challenging problem. In the past, there have been studies that use thin-film optics to take account of the coating-induced interference effects and the geometric optics approximation to model the surface roughness. In an effort to delineate the validity regime of the hybrid method, the predicted bidirectional reflectance is compared with that obtained from the rigorous electromagnetic-wave solution for one-dimensional rough surfaces, considering the effect of coating thickness and roughness parameters. Two hybrid models are implemented using the Monte Carlo ray-tracing algorithm: the surface generation method and microfacet slope method. The former relies on statistically generated surfaces according to the root-mean-square roughness and the autocorrelation length, whereas the latter uses the microfacet whose orientation is stochastically determined, when a ray hits the surface, according to the slope distribution without creating deterministic rough surfaces a priori. The validity regimes of the hybrid models are established for silicon dioxide films on silicon substrates. The advantages and disadvantages of each hybrid model are discussed. Some useful guidelines are provided for the simulation of optical scattering from coated rough surfaces.
Diffusion and reaction in cellular media

Abstract This paper presents a general theoretical analysis of the problem of diffusion and chemical reaction in heterogeneous two-phase media in which membrane or interfacial resistances can be important. Volume-averaged transport equations are derived for both phases with a first-order, irreversible reaction occurring in the dispersed phase. From these equations, a one-equation model is derived and the constraints that the one-equation model must satisfy are identified. A method of closure is developed in order to determine effective diffusivities, and the influence of the membrane permeability on the effective diffusivity is illustrated for a wide range of the parameters that describe the system. Experimental data for the effective diffusivity in a cellular system are used in conjunction with our theoretical results to determine the membrane permeability of a biological system.
Heat transfer to a horizontal cylinder in a shallow bubble column

Abstract Heat transfer coefficient correlations for tall bubble columns are unable to predict heat transfer in shallow bubble columns, which have unique geometry and fluid dynamics. In this work, the heat transfer coefficient is measured on the surface of a horizontal cylinder immersed in a shallow air–water bubble column. Superficial velocity, liquid depth, and cylinder height and horizontal position with respect to the sparger orifices are varied. The heat transfer coefficient is found to increase with height until reaching a critical height, and a dimensionless, semi-theoretical correlation is developed that incorporates superficial velocity, liquid properties, and height. Additionally, the more minor effects of flow regime, column region, and bubble impact are discussed. Notably, the heat transfer coefficient can be as high in the region of bubble coalescence as in the bulk of the column, but only if bubbles impact the cylinder. The correlation and discussion provide a framework for modeling and designing shallow, coil-cooled bubble columns.
Auscultation cannot distinguish esophageal from tracheal passage of tube

We quantitatively compared the acoustic characteristics of passage of an endotracheal tube into the trachea with those of passage into the esophagus by analyzing the loudness and frequency (90% spectral edge frequency) of the sounds when auscultated at the suprasternal notch. We found that there was a significant difference (P<0.01) in maximum loudness between esophageal and tracheal intubations (0.15±0.05 and 0.25±0.06 V, respectively). However, there were no significant differences between the 90% spectral edge frequencies. We conclude that, without directly comparing the maximal acoustic amplitude of tracheal intubation with that of esophageal in each patient, one cannot distinguish between the two types of intubation by means of auscultation.
Trends in Health Care Coverage and Financing and Their Implications for Policy

The nation's preoccupation with the transformation of the health care delivery system to managed care has tended to obscure the importance of a number of other, simultaneous trends. These include t...
Influence of bathymetric fluctuations on coastal storm surge

Abstract Natural events constantly alter nearshore bathymetric properties. Hurricanes particularly affect bathymetry as they pass over a body of water. To compute an accurate forecast or recreate a hurricane's effects through hindcasting techniques, an operational bathymetry data set must be known in advance. However, obtaining and maintaining current and accurate bathymetric data can be costly and difficult to manage. In this paper we examine the extent to which variations in nearshore bathymetry affect the storm surge at the coast. A common question for wave and surge modeling is, “how good is the bathymetric data?” If we can allow for a range of fluctuations in the bathymetry without significantly adjusting the results of the surge predictions, we can potentially save months of field work and millions of dollars. A one-dimensional (1D) analytical solution for waves and water level is developed for initial testing. In the 1D case we find that as long as the amplitudes of the bathymetric fluctuations are less than 60% of the original depth, the surge at the coast is within ± 10% of the surge generated on the initial bottom slope. If the fluctuation produces a hole, a deepening of the local bathymetry, within 80% of the local water depth, the coastal storm surge calculated is still within 10% of the unperturbed value computed for bottom slopes shallower than 1:20. In addition, we find there is an optimum distance offshore for each sloped profile that corresponds to a depth between 25 and 40 m, beyond which the effects of bathymetric fluctuations begin to decrease. A coupled 2D modeling system is implemented to test our hypothesis along a realistic coastline. After selecting three study sites, we vary the bathymetry at the selected locations by ± 20%. Consistent with the 1D tests, the storm surge at the shoreline varies by less than 5%.
Pareto optimality and competitive equilibrium in infinite horizon economies

Abstract The paper presents a general model of a decentralized economy evolving over an infinite time horizon. Alternative notions of price systems, competitive equilibria, efficiency and optimality are introduced. The main results characterize conditions under which the two fundamental theorems of welfare economics are valid in such a general framework.