cssi/SciSciGPT-SciSciNet huggingface dataset:
On the detection and refinement of transcription factor binding sites using ChIP-Seq data

Coupling chromatin immunoprecipitation (ChIP) with recently developed massively parallel sequencing technologies has enabled genome-wide detection of protein–DNA interactions with unprecedented sensitivity and specificity. This new technology, ChIP-Seq, presents opportunities for in-depth analysis of transcription regulation. In this study, we explore the value of using ChIP-Seq data to better detect and refine transcription factor binding sites (TFBS). We introduce a novel computational algorithm named Hybrid Motif Sampler (HMS), specifically designed for TFBS motif discovery in ChIP-Seq data. We propose a Bayesian model that incorporates sequencing depth information to aid motif identification. Our model also allows intra-motif dependency to describe more accurately the underlying motif pattern. Our algorithm combines stochastic sampling and deterministic ‘greedy’ search steps into a novel hybrid iterative scheme. This combination accelerates the computation process. Simulation studies demonstrate favorable performance of HMS compared to other existing methods. When applying HMS to real ChIP-Seq datasets, we find that (i) the accuracy of existing TFBS motif patterns can be significantly improved; and (ii) there is significant intra-motif dependency inside all the TFBS motifs we tested; modeling these dependencies further improves the accuracy of these TFBS motif patterns. These findings may offer new biological insights into the mechanisms of transcription factor regulation.
Beyond Hysteria: Constructing New Narratives of Teachers and Teaching in the United States

This essay considers the influence of standardized testing in the construction of teachers in the United States. It calls on teacher educators to organize against neoliberal influences and create new narratives of what it means to be a teacher.
Learning Collaborative Behavior by Observation

This paper presents a multi-agent framework capable of learning teamwork by observation. The system combines proven single entity learning by observation techniques with a multi-agent system shown to exhibit effective teamwork. An effective simulated production team is observed. An off-line training algorithm uses the observed data to develop behavior maps for a Collaborative Context-based Reasoning framework. The Collaborative Context-based Reasoning framework provides generic base classes capable of recreating the behavior of the original agents using the behavior maps developed by the training algorithm. The resulting prototype effectively replaces the original team of agents and is capable of reproducing its behavior and generalizing the behavior to encompass similar situations.
Atomic Resolution Imaging of Au Nanocluster Dispersed in TiO2, SrTiO3, and MgO

Gold nanoclusters dispersed in single crystal TiO{sub 2}, MgO, and SrTiO{sub 3} have been prepared by ion implantation at 300-975 K and subsequent annealing at 1275 K for 10 h. High-resolution transmission electron microscopy and high-angle annular dark field (HAADF) imaging in aberration corrected scanning transmission electron microscope (STEM) have been used to characterize the microstructure of the gold nanoclusters dispersed materials. STEM-HAADF imaging with atomic resolution has directly revealed for all three materials that Au atoms partially occupy cation lattice positions. Cavities up to several tens of nanometers were observed in MgO and SrTiO{sub 3}. The cavities and gold clusters are spatially associated in MgO and SrTiO{sub 3}, indicating a strong interaction between the Au cluster and cavities. For MgO and SrTiO{sub 3}, the faceting planes appear to be the same for both nanometer-sized cavity and the Au cluster, demonstrating that both the surface energy and the interfacial energy between Au cluster and the matrix are lowest on these planes.
Misconduct Among Chinese American Adolescents The Role of Acculturation, Family Obligation, and Autonomy Expectations

This study examined the relation between acculturation and misconduct among Chinese American adolescents. The sample included 309 adolescents (mean age = 14.7 years, SD = 0.71; 54% female), recruited from two high schools in an ethnically diverse, urban city on the West Coast. Findings showed that acculturation (i.e., generational status and U.S. and Chinese cultural involvements) did not predict misconduct. But specific cultural values (i.e., family obligation and autonomy expectations) did. Specifically, youth with stronger family obligation and later autonomy expectations engaged in less misconduct. Such findings suggest that examining specific and developmentally-salient cultural values may be especially helpful in explaining why some Chinese Americans engage in misconduct.
Fast and Robust Part-of-Speech Tagging Using Dynamic Model Selection

This paper presents a novel way of improving POS tagging on heterogeneous data. First, two separate models are trained (generalized and domain-specific) from the same data set by controlling lexical items with different document frequencies. During decoding, one of the models is selected dynamically given the cosine similarity between each sentence and the training data. This dynamic model selection approach, coupled with a one-pass, left-to-right POS tagging algorithm, is evaluated on corpora from seven different genres. Even with this simple tagging algorithm, our system shows comparable results against other state-of-the-art systems, and gives higher accuracies when evaluated on a mixture of the data. Furthermore, our system is able to tag about 32K tokens per second. We believe that this model selection approach can be applied to more sophisticated tagging algorithms and improve their robustness even further.
Kay Wilson and the NIH Genetics Study Section

THE end of World War II brought massive changes to research in the United States. For science, it was a heady time. Vannevar Bush had written a book entitled “Science, the Endless Frontier” ([Bush 1945][1]). For the first time, the Federal Government assumed a major responsibility for research
Anyone for Tennis? The Monument to Captain Gervase Scrope in St Michael's, Coventry

The monument to Captain Gervase Scrope was destroyed in 1940, but a rubbing survives in the Society's collections. It alludes to Real Tennis, and in doing so takes part in a debate extending from Plautus to Stephen Hawking about the attitude of the Creator to the universe, although the side it takes is, in an ecclesiastical context, unexpected.
Auto-Calibrated Parallel Imaging Reconstruction for Arbitrary Trajectories Using ${\bf k}$ -Space Sparse Matrices (kSPA)

Image acquisition of magnetic resonance imaging (MRI) can be accelerated by using multiple receiving coils simultaneously. The problem of reconstructing an unaliased image from partially sampled k-space data can be formulated as a large system of sparse linear equations. The k-space sparse matrix (kSPA) algorithm proposes to solve the system of equations by finding a sparse approximate inverse. This algorithm has been shown to accelerate the image reconstruction for a large number of coils. The original kSPA algorithm requires knowledge of coil sensitivities. Here, we propose and demonstrate an auto-calibrated kSPA algorithm that does not require the explicit computation of the coil sensitivity maps. We have also shown that calibration data, in principle, can be acquired at any region of k-space. This property applies to arbitrary sampling trajectories and all reconstruction algorithms based on k-space. In practice, because of its higher SNR, calibration data acquired at the center of k-space performed more favorably. Such auto-calibration can be advantageous in cases where an accurate sensitivity map is difficult to obtain.
Instance Sense Induction from Attribute Sets

This paper investigates the new problem of automatic sense induction for instance names using automatically extracted attribute sets. Several clustering strategies and data sources are described and evaluated. We also discuss the drawbacks of the evaluation metrics commonly used in similar clustering tasks. The results show improvements in most metrics with respect to the baselines, especially for polysemous instances.
Chemical composition of HAL, an isotopically-unusual Allende inclusion

Thirty-seven major, minor and trace elements were determined by INAA and RNAA in samples of hibonite, black rim and portions of friable rim from an unusual Allende inclusion, HAL. The peculiar isotopic, mineralogical and textural properties of HAL are accompanied by very unusual trace element abundances. The most striking feature of the chemistry is the virtual absence of Ce from an inclusion otherwise highly enriched in REE compared to Cl chondrites. HAL is also depleted in Sr, Ba, U, V, Ru, Os and Ir, relative to other refractory elements. Of the lithophile elements determined which are normally considered to be refractory in a gas of solar composition, Sr, Ba, Ce, U and V are the most volatile in oxidizing gases. The distribution of REE between hibonite and rims seems to have been established when hibonite and other refractory minerals were removed at slightly different temperatures from a hot, oxidizing gas in which they previously coexisted as separate grains. On the basis of HAL's chemical and isotopic composition, possible locations for the chemical and mass dependent isotopic fractionation are in ejecta from the low temperature helium-burning zone of a supernova and in the locally oxidizing environment generated by evaporation of interstellar grains of near-chondritic chemical composition.
SALINITY OF INTERSTITIAL WATER IN A SANDY BEACH

The salinity in the upper 20 cm of intertidal sands was observed at two stations in Tomales Bay, California. In summer, there were no striking variations associated with elevation, except for the effect of evaporation. In winter, the influx of freshwater provides sufficient contrast between interstitial and open water to reveal features of circulation. High on the beach, the interstitial salinity at the lo- and 20-cm depth remains low through the tidal cycle. The salinity at 10 cm remains higher than at 20 cm. At an elevation of 1.0 m, the salinities at 10 and 20 cm converge. Below this elevation, interstitial salinity varies less than in the adjacent open waters of the bay. The environment of the infauna of the low intertidal zone is more stable than that of epifaunal or pelagic organisms in shallow water. The variations high in the intertidal zone must constitute a major obstacle to the spread of marine organisms into this area.
DISTRIBUTION AND RECRUITMENT OF SUBTIDAL GENICULATE CORALLINE ALAGE1

Geniculate coralline algae are common members of kelp forest communities. The structure provided by their stiff branches greatly influences the abundance and species composition of benthic animals and can affect associated algae by inhibiting recruitment, but the branches are themselves substrate for a large number of other taxa. However, other than qualitative observations, little is known about the within-site distribution, recruitment, and growth of these algae. We examined the distribution of the dominant corallines at a subtidal site in central California. Abundances of Calliarthron tuberculosum (Post. & Rupr.) Dawson, Bossiella californica ssp. schmittii (Manza) Johans., Calliarthron cheilosporioides Manza, Corallina vancouveriensis Yendo, and unidentifiable juveniles were determined at depths of 10, 15, and 20 m and on horizontal rock, vertical rock, and cobble. Calliarthron tuberculosum was most abundant (≤39% cover) at all depths, growing primarily on horizontal surfaces. Vertical surfaces and cobbles were dominated by B. californica ssp. schmittii (40 and 15% cover, respectively). These two most abundant species had the highest cover at 15 m. Calliarthron cheilosporioides and C. vancouveriensis were relatively rare (<1% cover) and generally grew on horizontal rocks and at shallower depths. Unidentified juveniles were also rare and occurred mainly on horizontal rocks and cobbles at 20 m. The settlement and growth rates of coralline crusts and the initiation and growth rates of young erect fronds from these crusts were determined in clearings made in the spring and fall at the three depths. Crust densities and diameters were highest at 10 m and in spring clearings. Settlement and growth tended to decrease with increasing depth. Trends were similar in fall clearings, but initial settlement was lower. Initiation and growth of fronds decreased with depth and were also higher in fall clearings. These variations in depth and substrata distribution, as well as settlement and growth, suggest there is considerable variation in the population biology between species in this group of subtidal plants.
Design of the Cryopumping Vacuum System for ESCAR

ESCAR is an experimental superconducting accelerating and storage ring for protons. Scattering collisions with residual gas degrades the quality of proton beams that are stored for long time periods. The loss of quality will be small if the average gas density in the path of the beam is kept less than about 106 molecules per cm3, depending upon the gas species. This density corresponds to a room temperature pressure for nitrogen-like gases of 3×10-ll Torr. We plan to achieve this vacuum goal in the ESCAR ring by distributed cryopumping at 4.5°K, the operating temperature of the superconducting magnets. In the magnet sections the cold bore of the magnet will provide the condensing surface. In the straight sections, 4.5°K beam tube or distributed cryopumps will be provided consistent with the function of the particular section. The large cryosurface area provides effective pumping capacity for H2 by utilizing sub-monolayer adsorption. The surfaces can be degassed of H2 by a temperature rise to 15°K. The cycle can be accomplished during routine maintenance periods. We expect the interval between the degassing of the magnet quadrants to be of the order of months. Because of the experimental nature of ESCAR, sector valves will be provided to permit the isolation of each straight section from the ring to allow ready accessibility for equipment testing and modification. Each section will have a roughing and conditioning pumping station.
Risk factors for coronary heart disease. Selected recent epidemiological advances.

Several recent advances in our understanding of the epidemiology and prevention of coronary artery disease are presented, highlighting the current status of the 3 major risk factors: blood cholesterol, blood pressure and cigarette smoking. There is a striking analogy between serum cholesterol and diastolic blood pressure in the pattern of the association with coronary heart disease (CHD). Mortality follow-up of the 361,662 middle-aged men screened for the Multiple Risk Factor Intervention Trial (MRFIT) shows that each of these risk factors identifies a large group of patients (the top 15% of the population distribution) who have a 4-fold higher risk of CHD death than those in the bottom 15%, and that each has a continuously rising gradient of risk for people with intermediary levels. The implication from these findings, and from the clinical trial data, is that public health and clinical policies directed at blood cholesterol should be made similar to those that have become widespread for blood pressure in the past 2 decades; i.e. measuring the level periodically in all adults and intervening to prevent CHD in those at highest risk. The public health campaign to reduce cigarette smoking has been bolstered by new evidence on the hazards of ambient smoke. One example comes from the clinical trial cohort of the MRFIT, in which non-smoking men who were married to smoking wives had nearly twice the all-cause mortality rate of non-smoking men who were married to non-smoking wives.(ABSTRACT TRUNCATED AT 250 WORDS)
Hypersexuality and couple relationships in bipolar disorder: A review

Abstract Background Although change in sexual behavior is recognized as an integral part of bipolar disorder, most of the relevant literature on sexual issues in patients with this illness concerns medication side effects and does not differentiate bipolar disorder from other serious mental disorders. Surprisingly, little has been published on mania-induced hypersexuality and the effects of mood cycling on couple relationships. In this review, we examine the extant literature on both of these subjects and propose a framework for future research. Methods A search of PsycINFO and PubMed was conducted using keywords pertaining to bipolar disorder, hypersexuality and couple relationships. A total of 27 articles were selected for review. Results Despite lack of uniformity in diagnosis of bipolar disorder and no formal definition of hypersexuality, the literature points to an increased incidence of risky sexual behaviors in bipolar patients during manic episodes compared to patients with other psychiatric diagnoses. Further, it appears that bipolar patients are more similar to healthy controls than to other psychiatric patients when it comes to establishing and maintaining couple relationships. Nonetheless, the studies that examined sexuality in couples with one bipolar partner found decreased levels of sexual satisfaction associated with the diagnosis, varying levels of sexual interest across polarities, increased incidence of sexual dysfunction during depressive episodes, and disparate levels of satisfaction in general between patients and their partners. Limitations Due to changes in diagnostic criteria over time, there is a lack of uniformity in the definition of bipolar disorder across studies. Hypersexuality is not systematically defined and therefore the construct was not consistent across studies. Some of the older articles date back more than 30 years, making them subject to the biases of sexual and gender norms that have since become outdated. Finally, the heterogeneity of the samples, which include patients with comorbid substance use as well as inpatient, outpatient, symptomatic and euthymic patients, may limit the generalizability of results. Conclusions Although bipolar patients experience disease-specific sexual problems of mania-induced hypersexuality and specific effects of mood cycling on couple relationships, the existing literature is mostly outdated and lacks a consistent definition of hypersexuality. Novel research is needed to address sexual symptomatology in bipolar disorder within the context of current sexual, cultural and gender norms.
The Role of Cloud Contamination, Aerosol Layer Height and Aerosol Model in the Assessment of the OMI Near-UV Retrievals Over the Ocean

Abstract. Retrievals of aerosol optical depth (AOD) at 388 nm over the ocean from the Ozone Monitoring Instrument (OMI) two-channel near-UV algorithm (OMAERUV) have been compared with independent AOD measurements. The analysis was carried out over the open ocean (OMI and MODerate-resolution Imaging Spectrometer (MODIS) AOD comparisons) and over coastal and island sites (OMI and AERONET, the AErosol RObotic NETwork). Additionally, a research version of the retrieval algorithm (using MODIS and CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) information as constraints) was utilized to evaluate the sensitivity of the retrieval to different assumed aerosol properties. Overall, the comparison resulted in differences (OMI minus independent measurements) within the expected levels of uncertainty for the OMI AOD retrievals (0.1 for AOD 0.3). Using examples from case studies with outliers, the reasons that led to the observed differences were examined with specific purpose to determine whether they are related to instrument limitations (i.e., pixel size, calibration) or algorithm assumptions (such as aerosol shape, aerosol height). The analysis confirms that OMAERUV does an adequate job at rejecting cloudy scenes within the instrument's capabilities. There is a residual cloud contamination in OMI pixels with quality flag 0 (the best conditions for aerosol retrieval according to the algorithm), resulting in a bias towards high AODs in OMAERUV. This bias is more pronounced at low concentrations of absorbing aerosols (AOD 388 nm ∼ In pixels where OMAERUV assigned a dust aerosol model, a fraction of them (
Freezing of gait is associated with increased saccade latency and variability in Parkinson’s disease

Abstract Objective Freezing of gait (FOG) is a locomotor disturbance in Parkinson disease (PD) related to impaired motor automaticity. In this study, we investigated the impact of freezing on automaticity in the oculomotor system using an anti-saccade paradigm. Methods Subjects with PD with (PD–FOG, n =13) and without (PD–NON, n =13) FOG, and healthy age-matched controls (CTRL, n =12) completed automatic pro-saccades and non-automatic anti-saccades. Primary outcomes were saccade latency, velocity, and gain. Results PD–FOG (pro-saccade latency=271ms, anti-saccade latency=412ms) were slower to execute both types of saccades compared to PD–NON (253ms, 330ms) and CTRL (246ms, 327ms). Saccade velocity and gain variability was also increased in PD–FOG. Conclusions Saccade performance was affected in PD–FOG for both types of saccades, indicating differences in automaticity and control in the oculomotor system related to freezing. Significance These results and others show that FOG impacts non-gait motor functions, suggesting global motor impairment in PD–FOG.
Properties of Alkylimidazoles as Solvents for CO2 Capture and Comparisons to Imidazolium-Based Ionic Liquids

Density, viscosity, and CO2 solubility of a series of 10 1-n-alkylimidazoles with chain lengths ranging from methyl (C1) to tetradecyl (C14) were characterized. Density and viscosity values were comparable to many common organic solvents over a temperature range of 20–80 °C. The measured data were utilized to develop empirical models for these physical properties with respect to temperature and the contribution of the n-alkyl chain. Solubility of CO2 in 1-n-alkylimidazoles at ambient temperature (25 °C) and low pressures (3–7 atm) was found to be less than most common organic solvents, even though the 1-n-alkylimidazole motif offers opportunities to tune the molecule’s solubility parameter. This effect was attributed to lower fractional free volume (FFV) that is available in molecules with systematically variable side chains. 1-n-Alkylimidazoles were less dense than most 1-n-alkyl-3-methylimidazolium-based ionic liquids (ILs), with differences ranging from 10 to 50%, based on contributions to increased de...
Some Thoughts on the Relation of Political Theory to Anthropology

The study of developing areas has, in recent years, caused political science and theory to be increasingly aware of realities of non-Western government and politics. Comparative politics and its theory no longer, therefore, can avoid utilizing the results of the research of anthropologists and ethnologists in a way comparable to the use of historical data if they wish to be comprehensively empirical. Since the political theorist will not, as a rule, be able to become a practising anthropologist, the basic problem of such cooperation turns upon whether the investigating anthropologist asks the crucial, the basic questions in the first place. A broad survey of their reports and writings, such as the Human Relations Area Files afford, shows that this is by no means generally the case. Nor is this easy to achieve, for political scientists and anthropologists differ in their objectives. It has been suggested that the anthropologist is primarily interested in diversity, in how many ways something could be done, whereas for the political scientist and theorist such divergencies are important mainly as they lead to political insight and verifiable generalization. The utility of the writings of anthropologists for the political scientist is seriously impeded by the over-simplified and misleading understanding of the nature of power and authority held by many of them.
NORMAL REFERENCE VALUES FOR TRANSCATHETER AORTIC VALVE REPLACEMENT WITH THE BALLOON-EXPANDABLE VALVE

There is a lack of data showing the expected mean gradients and calculated effective valve areas (EOA) by valve type and size for the transcatheter aortic valves (TAV). We sought therefore to describe the acceptable mean gradients and EOA for each iteration of SAPIEN valve. Mean gradients and EOA
Cerebral Resuscitation 2000 A.D.

As the brain is the most vulnerable vital organ, the clinical and socioeconomic importance of cerebral resuscitation is obvious. After the global brain ischaemia (GBI) of cardiac arrest (CA), the focal brain ischaemia (FBI) of stroke, or traumatic brain injury (TBI), we must aim for “good outcome” in terms of CPC 1 (cerebral performance category 1) (normal) or CPC 2 (moderate disability). In addition, we must learn to prevent long-term survival with “poor” outcome, i.e., CPC 3 (severe disability but conscious), CPC 4 (coma, persistent vegetative state), or CPC 5 (brain death or death). Thus, we must differentiate between overall and cerebral performance categories (OPC 1–5 vs CPC 1–5) [1].
Decreases in Suicide Deaths and Attempts Linked to the White Mountain Apache Suicide Surveillance and Prevention System, 2001-2012

Objectives. We evaluated the impact of a comprehensive, multitiered youth suicide prevention program among the White Mountain Apache of Arizona since its implementation in 2006.Methods. Using data from the tribally mandated Celebrating Life surveillance system, we compared the rates, numbers, and characteristics of suicide deaths and attempts from 2007 to 2012 with those from 2001 to 2006.Results. The overall Apache suicide death rates dropped from 40.0 to 24.7 per 100 000 (38.3% decrease), and the rate among those aged 15 to 24 years dropped from 128.5 to 99.0 per 100 000 (23.0% decrease). The annual number of attempts also dropped from 75 (in 2007) to 35 individuals (in 2012). National rates remained relatively stable during this time, at 10 to 13 per 100 000.Conclusions. Although national rates remained stable or increased slightly, the overall Apache suicide death rates dropped following the suicide prevention program. The community surveillance system served a critical role in providing a foundation ...
Architectural characterization of TCP/IP packet processing on the Pentium/spl reg/ M microprocessor

A majority of the current and next generation server applications (Web services, e-commerce, storage, etc.) employ TCP/IP as the communication protocol of choice. As a result, the performance of these applications is heavily dependent on the efficient TCP/IP packet processing within the termination nodes. This dependency becomes even greater as the bandwidth needs of these applications grow from 100 Mbps to 1 Gbps to 10 Gbps in the near future. Motivated by this, we focus on the following: (a) to understand the performance behavior of the various modes of TCP/IP processing, (b) to analyze the underlying architectural characteristics of TCP/IP packet processing and (c) to quantify the computational requirements of the TCP/IP packet processing component within realistic workloads. We achieve these goals by performing an in-depth analysis of packet processing performance on Intel's state-of-the-art low power Pentium/spl reg/ M microprocessor running the Microsoft Windows* Server 2003 operating system. Some of our key observations are - (i) that the mode of TCP/IP operation can significantly affect the performance requirements, (ii) that transmit-side processing is largely compute-intensive as compared to receive-side processing which is more memory-bound and (iii) that the computational requirements for sending/receiving packets can form a substantial component (28% to 40%) of commercial server workloads. From our analysis, we also discuss architectural as well as stack-related improvements that can help achieve higher server network throughput and result in improved application performance.
Examining the literature to reveal the nature of community EE/ESD programs and research

AbstractInterest in community environmental education (EE) and community education for sustainable development (ESD) is increasing, as evidenced by the increase in studies examining community EE/ESD approaches and NAAEE’s current development of the Community EE Guidelines for Excellence. Thus, the purpose of this paper is to: (1) provide a review of research which identifies as examining community EE/ESD issues from 1994 to 2013, (2) examine themes specific to community-oriented program implementation and outcomes, and (3) examine theoretical trends within this work. While no single framework emerged from the diverse studies on community EE/ESD, themes suggested greater success for programs that were rooted in community issues, involved multiple community partners, were oriented towards collaborative and civic action, and incorporated reflection on social institutions and power dynamics. These characteristics reflect an emancipatory approach to education which seeks to enhance human development through pu...
MPD: multiplex primer design for next-generation targeted sequencing.

Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches to targeted resequencing, including microfluidic PCR amplification, which may be enhanced by multiplex PCR. Currently, there is no open-source software that can design next-generation multiplex PCR experiments that ensures primers are unique at a genome-level and efficiently pools compatible primers. We present MPD, a software package that automates the design of multiplex PCR primers for next-generation sequencing. The core of MPD is implemented in C for speed and uses a hashed genome to ensure primer uniqueness, avoids placing primers over sites of known variation, and efficiently pools compatible primers. A JavaScript web application ( http://multiplexprimer.io ) utilizing the MPD Perl package provides a convenient platform for users to make designs. Using a realistic set of genes identified by genome-wide association studies (GWAS), we achieve 90% coverage of all exonic regions using stringent design criteria. Using the first 47 primer pools for wet-lab validation, we sequenced ~25Kb at 99.7% completeness with a mean coverage of 300X among 313 samples simultaneously and identified 224 variants. The number and nature of variants we observe are consistent with high quality sequencing. MPD can successfully design multiplex PCR experiments suitable for next-generation sequencing, and simplifies retooling targeted resequencing pipelines to focus on new targets as new genetic evidence emerges.
Pigmented purpuric lichenoid dermatitis of Gougerot-Blum mimicking Kaposi's sarcoma

A case of pigmented purpuric lichenoid dermatitis of Gougerot-Blum is presented and the pertinent literature is reviewed. This case is unusual in that the lesions were unilateral and very limited in extent. The patient presented with a localized pigmented purpuric eruption of plaques on the dorsum of one foot which mimicked Kaposi's sarcoma. However, a biopsy confirmed the diagnosis of pigmented purpuric lichenoid dermatitis of Gougerot-Blum.
Policy-driven process mapping (PDPM): Toward process design automation

Recently, many organizations are investing a great amount to revamp their business policies in order to comply with the new regulations related to Sarbanes-Oxley. For organizations with large-scale business processes, maintaining those processes to meet the changing policies is a non-trivial problem. In this paper, we present an innovative process mapping methodology named Policy-Driven Process Mapping (PDPM) that takes advantage of detailed organizational policies. In particular, we show how narrative process-related policies can be formalized and how process maps can be systematically created via a set of rules and algorithms. Our research contributes to business process management by providing a theoretical foundation for the development of advanced process mapping tools, thereby taking the first step toward automatable process design procedures.
Extraction of scattering centers for target recognition using ESPRIT

A target recognition system based on scattering centers extracted using ESPIRIT is investigated in this study. The scattering extraction approach is first tested on a synthetic target then applied to real radar targets with real radar data. The performance of the recognition system is evaluated under various adverse conditions.
Psychiatry residents' confidence in integrated care skills on a collaborative care rotation at a safety net health care system.

Abstract Objective This letter to the editor describes how psychiatry residents' confidence in delivering population based care improved after working within a collaborative care system. Methods An anonymous online survey was delivered to 24 psychiatry residents who matriculated through Cambridge Health Alliance residency from 2012 to 2014 and participated in the collaborative care rotation. During the rotation, residents provided direct and indirect consultations, used measurement-based care (MBC) and took a population approach to patient management. Items were asked about residents' level of confidence. Results Twenty of 24 residents responded to the survey (83% response rate) with no questions skipped. Among respondents, 80% were confident in the stepped care model, 65% were confident using MBC, 95% were confident communicating and coordinating with primary care teams, 65% felt they were likely to initiate lab checks (such as metabolic monitoring), and 95% had confidence the rotation helped clarify their role as a consultant to primary care teams. Only 30% were confident in providing indirect consultations to primary care teams. Conclusion After a 6 month rotation in a collaborative care model, psychiatry residents have gained confidence in multiple domains of integrated care. However, additional curriculum development and training is required to help residents improve confidence in indirect consultations.
On Analyzing Hegemony

Raymond Williams’s discussion of hegemony, a concept most fully developed in the work of Antonio Gramsci, provides an excellent summary of these points. It is Gramsci’s great contribution to have emphasized hegemony, and also to have understood it at a depth which is rare. The most helpful way of thinking through the complex characteristics, the scope and varied functions, of ideology is found in the concept of hegemony. Legitimation—Sociologists seem to agree that ideology is concerned with legitimation—the justification of group action and its social acceptance. Power Conflict—All of the sociological literature links ideology to conflicts between people seeking or holding power. Functionally, ideology has been evaluated historically as a form of false consciousness which distorts one’s picture of social reality and serves the interests of the dominant classes in a society. The chapter also presents an overview of the key concepts discussed in this book.
Prognostic Models for Patients with Myelodysplastic Syndromes

The myelodysplastic syndromes (MDS) are characterized by significant heterogeneity, both at the clinical and molecular levels. This translates in significant differences in terms of survival and response to therapy. A subgroup of patients may never require any intervention for MDS, whereas other patients will succumb to the disease shortly after diagnosis. To overcome this problem and to develop tools to predict survival and response to therapy, a number of groups over the last two decades have worked on the development of prognostic tools for patients with MDS. Since 1997, the standard prognostic tool has been the IPSS. This model has been fundamental for the most recent progress in MDS, including drug development and understanding of the impact of molecular alterations in this group of disorders. But with this progress has come the realization of the limitations of IPSS. This has resulted in the development of several new prognostic systems for patients with MDS, such as the WPSS, the Global MD Anderson model, and the models specific for patients with the so-called lower-risk disease or that incorporate comorbidities. These efforts have recently culminated in the development of the new revised IPSS. This prognostic system is the result of a large effort by multiple investigators in every continent and represents now the accepted standard prognostic system for MDS. In parallel with this effort, we have also witnessed significant advances in our understanding of the molecular basis and, in particular, mutational events in MDS. It is likely that this new molecular data will be rapidly incorporated into these classic clinical models, such as IPSS-R. Finally, we need better models to predict response to specific forms of therapy and outcomes once therapy is instituted.
Natural Languages and Formal Languages: A Tenable Dualism

Grammar intrigues philosophers. In ways only dimly understood, it binds together meaning-bearing elements and thus makes the articulation of thoughts, messages, and information possible. Some parts of language represent some parts of reality. Why are these parts of language combined the way they are? What does syntax contribute to understanding? Logicians and philosophers think that they have the answers to these questions in the case of artificially contructed formal languages. For the semantic complexes of these languages have a molecular structure. Syntax allows one to build up the semantic complexes from the semantic simples. In this way, in a formal language syntax mirrors semantic chemistry. Alternatively, it is the plaster that builds semantic bricks into a wall.
Coating Flows and Contact Line Models

A lubrication-type model is developed for gravity-driven coating flow down an inclined plane. The shear-stress singularity at the contact line and different approaches to removing it are discussed. Other topics include the classical Landau–Levich problem and capillary spreading of liquid droplets on flat solid surfaces. Stability of the two-dimensional gravity-driven coating flow and growth of fingering pattern in the strongly nonlinear regime are investigated.
THE INFINITE TIME QUADRATIC COST PROBLEM FOR CERTAIN CLASSES OF INFINITE DIMENSIONAL CONTROL SYSTEMS

Publisher Summary This chapter reviews the infinite time quadratic cost problem for certain classes of infinite dimensional control system. In understanding the problem, the author insists on an approach which clarifies the relationship between the system-theoretic issues of controllability (reachability), stabilizability, L2-stability and the existence of a positive solution to an operator equation of quadratic type. A system is said to be controllable if any initial state can be brought to the origin in a finite time interval [;O, T] using a control u ∈ L2 (0, T; U). The control system in state-equation form is said to be stabilizable if there exists a such that A + G defines an L2-stable system. Using the spectral properties of A, necessary and sufficient conditions for stabilizability can be given.
Quantification of Swell Energy and Its Impact on Wetlands in a Deltaic Estuary

The extensive coastal wetlands in Mississippi River Delta represent the seventh largest deltaic floodplain in the world, contributing to many services that sustain the economies of the region. Subsidence, sea level rise, saltwater intrusion, wave action from storms, and sediment depletion have contributed to chronic wetland losses, converting vegetated lands into open waters and increasing wind fetch. Among these factors listed, wave energy plays the largest role in marsh edge erosion in an open bay environment. Degrading barrier islands along the shoreline of this delta allow swell energy to enter protected bay areas, contributing to marsh edge erosion. Locally generated wind waves within enlarged bays also contribute to wetland loss. Quantifying the roles of swell and wind waves in marsh edge erosion is essential to any ecosystem restoration design. In this study, a numerical model is implemented to describe the wave climate of combined swell and wind waves in a deltaic estuary. Terrebonne Bay was chosen as the study area because it has experienced one of the largest reductions in barrier islands and wetland loss rates among Louisiana estuaries. A continuous wave measurement in upper Terrebonne Bay was obtained over the course of a year. A spectral wave model is used to hindcast the wave climate in the estuary. The model results are compared against the in situ wave measurement. The wave power is partitioned into swell and wind sea at different locations in Terrebonne Bay using the model results. An extensive analysis on a valid effective wave power range that directly impacts the marsh edge is performed and presented. Insight into the temporal and spatial variability of wave power is gained. Through differentiating swell and wind sea energies around the bay, improvements of long-term wave power computation for shoreline retreat prediction are made. It is found that the swell energy becomes the primary driver of marsh edge retreat in the southwest part of Terrebonne Bay as the barrier islands are degrading.
Parity-Time Symmetric Plasmonics

Plasmons are hybrid photon-electron waves bound between conducting and dielectric materials. They have enabled strongly enhanced light-matter interactions for light emission and sensing, sub-wavelength structuring of photonic devices, and exotic optical phenomena such as optical-frequency magnetism. To date, most control over plasmon dispersion has been achieved through structuring of the real part of the refractive index, while losses have been viewed as detrimental. Photonic Parity-Time (PT) symmetry takes advantage of these inherent losses, utilizing them in conjunction with balanced gain media to control eigenmode evolution. In this chapter, we review progress in PT-symmetric plasmonics, focusing on planar and coaxial geometries. We show how inclusion of balanced loss and gain gives rise to exceptional points, enabling a multitude of phenomena including: (1) subwavelength mode multiplexing; (2) chiral molecule sensing and discrimination; (3) subwavelength polarization conversion; and (4) nonreciprocal, nonlinear optical metamaterials. We also show a route towards thresholdless symmetry breaking. These results provide a foundation for ultra-compact optical components with almost complete control over scattering, reflection, and transmission by tuning the PT potential.
Perioperative Psychological Interventions

Surgery can be an emotionally stressful and potentially traumatic event. Physical complications from surgery, when they occur, are a significant predictor of long-term psychosocial adjustment. Other postoperative complications such as depression, post-traumatic stress disorder, pain, and delirium can also impact long-term outcome. This chapter presents the rationale for providing psychological intervention for these conditions within the perisurgical setting. Although few psychological interventions have been designed specifically for the postsurgical setting, numerous evidence-based psychotherapies can be successfully adapted to address symptoms of physical and emotional distress to aid perisurgical psychological adjustment.
‘Damned if you do, damned if you don’t:’ Black parents’ racial realist school engagement

Conventional scholarship frames parent involvement in schools as crucial for student success, often depicts Black and Brown parents as under-engaged, and implies their increased engagement would le...
Association between medical student debt and choice of specialty: a 6-year retrospective study.

The effect of rapidly increasing student debt on medical students’ ultimate career plans is of particular interest to residency programs desiring to enhance recruitment, including primary care specialties. Previous survey studies of medical students indicate that amount of student debt influences choice of medical specialty. Research on this topic to date remains unclear, and few studies have included the average income of different specialties in analyses. The purpose of this study is to observe whether empirical data demonstrates an association between debt of graduating medical students and specialties into which students match. This was a retrospective cross-sectional study of a public institution including data from graduation years 2010–2015. For each included student, total educational debt at graduation and matched specialty were obtained. Average income of each specialty was also obtained. Statistical hypothesis testing was performed to analyze any differences in average debt among specialties; subanalysis was performed assessing debt for primary care (PC) versus non-primary care (NPC) specialties. Correlation between student debt and average specialty income was also evaluated. One thousand three hundred ten students met the inclusion criteria and 178 were excluded for a final study population of 1132 (86%). The average debt was $182,590. Average debt was not significantly different among the different specialties (P = 0.576). There was no significant difference in average debt between PC and NPC specialties (PC $182,345 ± $64,457, NPC $182,868 ± $70,420, P = 0.342). There was no correlation between average specialty income and graduation debt (Spearman’s rho = 0.021, P = 0.482). At our institution, student indebtedness did not appear to affect matched medical specialty, and no correlation between debt and average specialty income was observed. Different subspecialties and residency programs interested in recruiting more students or increasing diversity may consider addressing alternative factors which may have a stronger influence on student choices.
Novel aqueous amine looping approach for the direct capture, conversion and storage of CO2 to produce magnesium carbonate

Designing novel integrated chemical pathways for the capture, conversion, and storage of CO2 is a crucial need for advancing sustainable energy conversion. The accelerated conversion of CO2 to water-insoluble and stable magnesium carbonate is a thermodynamically downhill route for permanently storing CO2. However, a practical constraint of carbon mineralization is the slow kinetics at low CO2 concentrations. In this study, we investigate a direct integrated mineralization approach, whereby CO2, amine solvents (such as monoethanolamine, MEA), water and alkaline Mg-bearing solids are reacted in a slurry reaction environment. About 70% conversion of magnesium oxide to magnesium carbonate was achieved at 50 °C after 3 hours. The looping of amine-bearing solvents between the CO2 loaded and release states, facilitates the accelerated conversion of magnesium-bearing oxides to magnesium carbonate. Hydrated magnesium carbonate and magnesium hydroxide phases were noted when less than complete conversion of magnesium oxide was achieved. The morphological features were determined using in operando ultra-small and small angle X-ray scattering (USAXS/SAXS) and grazing incidence-small angle X-ray scattering (GI-SAXS) measurements. The proposed pathway is an adaptive, low temperature, single-step approach for the direct capture, conversion and storage of CO2. By demonstrating the effectiveness of aqueous alkaline amine looping approach for the accelerated carbon mineralization of MgO, we aim to expand this approach to include heterogeneous alkaline industrial residues such as coal fly ash and steel slag and naturally occurring minerals such as magnesium silicate and calcium silicate.