cssi/SciSciGPT-SciSciNet huggingface dataset:
Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays.

Microbial forensics is important in tracking the source of a pathogen, whether the disease is a naturally occurring outbreak or part of a criminal investigation. A method and SPR Opt (S NP and P CR-R FLP Opt imization) software to perform a comprehensive, whole-genome analysis to forensically discriminate multiple sequences is presented. Tools for the optimization of forensic typing using Single Nucleotide Polymorphism (SNP) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) analyses across multiple isolate sequences of a species are described. The PCR-RFLP analysis includes prediction and selection of optimal primers and restriction enzymes to enable maximum isolate discrimination based on sequence information. SPR Opt calculates all SNP or PCR-RFLP variations present in the sequences, groups them into haplotypes according to their co-segregation across those sequences, and performs combinatoric analyses to determine which sets of haplotypes provide maximal discrimination among all the input sequences. Those set combinations requiring that membership in the fewest haplotypes be queried (i.e. the fewest assays be performed) are found. These analyses highlight variable regions based on existing sequence data. These markers may be heterogeneous among unsequenced isolates as well, and thus may be useful for characterizing the relationships among unsequenced as well as sequenced isolates. The predictions are multi-locus. Analyses of mumps and SARS viruses are summarized. Phylogenetic trees created based on SNPs, PCR-RFLPs, and full genomes are compared for SARS virus, illustrating that purported phylogenies based only on SNP or PCR-RFLP variations do not match those based on multiple sequence alignment of the full genomes. This is the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. As more sequence data becomes available for multiple strains and isolates of a species, automated, computational approaches such as those described here will be essential to make sense of large amounts of information, and to guide and optimize efforts in the laboratory. The software and source code for SPR Opt is publicly available and free for non-profit use at http://www.llnl.gov/IPandC/technology/software/softwaretitles/spropt.php .
Gerontology: Adding an Empowerment Paradigm

With gerontology boomers beginning to collect their social security checks, this article challenges gerontology professionals to transform the jobs, services, programs, and institutions that will a...
Scaling up production systems: Issues, approaches and targets

Production systems have successfully made the transition from a trendy research idea to a routinely used programming paradigm. An important cause of this transition has been the several orders of magnitude speedup in program execution achieved in the past few years by the combination of better match algorithms, efficient compilation techniques and faster hardware platforms.
Cell cycle, proteolysis and cancer

Research in the past 15 years has shown that the mammalian cell cycle is controlled by the action of cyclin-dependent kinases (CDKs). A crucial substrate of the CDKs in G1-phase is the retinoblastoma tumor suppressor (pRB), which restrains proliferation largely by repressing the activity of the E2F transcription factors. More recent work has shown that the cell cycle is also a tale of two classes of ubiquitin ligases, referred to as SCF and APC/C ligases. CDKs, E2F and ubiquitin ligases reciprocally regulate each other, resulting in complex feedback loops. Perturbation of this network of molecular machines is associated with proliferative diseases, including cancer.
Neuronal avalanches, epileptic quakes and other transient forms of neurodynamics.

Power-law behaviors in brain activity in healthy animals, in the form of neuronal avalanches, potentially benefit the computational activities of the brain, including information storage, transmission and processing. In contrast, power-law behaviors associated with seizures, in the form of epileptic quakes, potentially interfere with the brain’s computational activities. This review draws attention to the potential roles played by homeostatic mechanisms and multistable time-delayed recurrent inhibitory loops in the generation of power-law phenomena. Moreover, it is suggested that distinctions between health and disease are scale-dependent. In other words, what is abnormal and defines disease it is not the propagation of neural activity but the propagation of activity in a neural population that is large enough to interfere with the normal activities of the brain. From this point of view, epilepsy is a disease that results from a failure of mechanisms, possibly located in part in the cortex itself or in the deep brain nuclei and brainstem, which truncate or otherwise confine the spatiotemporal scales of these power-law phenomena.
637: Clinical estimated fetal weight at the end of labor compared to the beginning of labor

BEGINNING OF LABOR NATHAN FOX, STEPHEN T. CHASEN, Weill Cornell Medical College, Obstetrics and Gynecology, New York, New York OBJECTIVE: To determine if a clinical EFW performed at the end of labor is more or less accurate than one performed at the beginning of labor. STUDY DESIGN: Obstetricians were asked to obtain a clinical EFW at the beginning of labor and to repeat the EFW when the patient was fully dilated. Patients with singleton pregnancies at or beyond 37 0/7 weeks were included. RESULTS: 138 patients were included. Approximately 2/3 of providers changed their EFW over the course of labor. The repeat EFW was significantly more accurate than the original EFW. This was more pronounced in patients whose EFW was changed by more than 300g. Length and speed of labor and change in fetal station did not correlate with a smaller or larger repeat EFW or with repeat EFW accuracy. CONCLUSION: A clinical EFW performed at the end of labor is more accurate than one performed at the beginning of labor. A repeat EFW at the end of labor may be warranted when a clinical decision depends in part on the EFW, such as with operative vaginal delivery.
Salicylic Acid- And Nitric Oxide-Mediated Signal Transduction In Disease Resistance

Salicylic acid (SA) has been shown to play a critical role in signaling the activation of plant defense responses following pathogen infection. These responses include the induction of cell death and disease resistance in the infected leaf, as well as the activation of systemic disease resistance in the uninfected portions of the plant. SA has been shown to induce these phenomena through a variety of mechanisms that may include altering the activity or synthesis of certain enzymes, increasing the expression of various defense genes and/or potentiating the activation of certain defense responses.
In-Patient Trends and Complications After Total Ankle Arthroplasty in the United States

Introduction: Due to improvement in overall prosthesis designs and surgical methods, there have been increasing numbers of total ankle arthroplasty performed with encouraging intermediate results. While European registries have been able to perform long term follow-ups and analysis on total ankle arthroplasty patients, majority of the US studies have been based on experiences at a single institution. There is currently limited data on the recent trends of total ankle arthroplasty. The purpose of our study is to evaluate the in-patient demographics, complications and readmission rate in patients after total ankle arthroplasty at academic medical centers in United States. Patients & Methods: We queried the University Healthsystems Consortium (UHC) administrative database from 2007 to 2011 for patients who underwent total ankle arthrolasty by ICD-9 procedure code 81.56. A descriptive analysis of demographics was performed, followed by a similar analysis of patient clinical benchmarks, including hospital length of stay, hospital direct cost, in-hospital mortality, and 30-day readmission rates. Results: Our cohort consisted of 2,361 adult patients who underwent a total ankle arthroplasty at 95 different academic medical centers across the country during the specified time period. The annual surgical volume for individual surgeons who performed this procedure was 5 cases +/− 3. The cohort was comprised of 47% male and 53% female patients. The majority of the cohort 2,091 (88.5%) was white, 85 (3.6%) were black, 23 (1%) were Hispanic, and 162 (6.8%) other. The mean age of the cohort was 62 years old +/− 11. At least 70% of the cohort had one or more chronic medical conditions. The mean LOS for the cohort was 2.2 days +/− 1.26. The mean total direct cost for the hospital was $16,000 +/− 7,000 per case. 83% of the cohort had private insurance, 15% had Medicare, and 2% had Medicaid. In hospital mortality was less than 1% for the cohort during their index hospitalization. Inpatient complication rate include: DVT 2.3%, re-operation 0.7%, and infection 3.2%. There was a readmission rate of 2.6% within the first 30 days from the time of discharge. Discussion/Conclusion: Total ankle arthroplasty in the United States is a relatively safe procedure with low overall complication rates including infection (3.2%), DVT (2.3%), and re-operation (0.7%). Length of stay after the procedure is around 2 days with a total direct hospital cost of $16,000 +/− $7,000 and 2.6% readmission rate (30 days). Majority of the patients were Caucasian and had private insurance.
The Nature of Social Institutions

THE term "institution" has commonly been used in sociology and social psychology to refer to certain aggregations of people. Thus, a state or a social club or a church is described as an institution. It is the thesis of this paper that the people who are connected with an institution are, for purposes of scientific analysis, of minor importance. Complete analysis of any group of people shows the existence of certain fundamental psychological entities, such as language, public opinion, and fashion, which hold the group together. It is these basal psychological entities which are the true social institutions. They are as real as any objects in the physical world. They have natures which can be studied and can be described in terms of the laws of their own unique beings. The position taken in this paper can be expressed more concretely by saying that it is of no scientific importance whatsoever that John Smith is a member of a certain social group or of a certain church. The essential fact about the social group or the church is a body of beliefs and a body of established modes of behavior. The beliefs and established modes of behavior can be thought of as a psychological pattern quite independent of any individual. This psychological pattern must have a certain internal consistency or the institution cannot survive. Thus, an ecclesiastical organization which prescribes that its members submit themselves to certain ritualistic ceremonies must provide the ceremonies. Furthermore, its exercises over its members an influence which produces sectarian exclusiveness and repels all who do not submit to the prescribed ritualistic ceremonies. The coming or going of one or more members is an incidental occurrence. The institution can survive as a historical entity even if its whole membership disappears. To speak of the group of people as constituting the institution is to confuse a secondary, resultant fact with the institution's essential reality. The people who accept the beliefs and modes of behavior which constitute the essentials of an institution are not the only objective realities which exhibit the vitality of the institution. Asocial group has a constitution; a church has a creed. Both the social group and the church have fixed times and places for the assembling of their members and for the performance of other characteristic functions. It would be quite as proper to say that the reality of a church consists in the edifice in which its members meet or in the book in which its creed is printed as to say that its reality consists in its members. The fact is that
Room Temperature Growth of Silicon Dioxide Using a Low Energy Ion Beam

Ultra-thin films of silicon dioxide are formed on silicon surfaces at room temperature by direct bombardment with an oxygen-containing ion beam at energies of 150 eV or less. The process of film growth is studied through ellipsometric measurements of their properties as a function of ion energy and dose, oxygen partial pressure and substrate temperature. Typical oxide thicknesses of the order of 50 A are obtained by three minute or longer exposures to beams of current density 135 µA/cm2. Ion-beam grown oxides are compared to conventional thin oxide films grown at elevated temperatures and show the same stoichiometry. The growth rate decreases rapidly after a continuous oxide film has been formed. Performing the ion bombardment at elevated substrate temperatures leads to only small enhancement of the oxide growth indicating non-thermally driven reaction kinetics.
Protective Action of Desoxycorticosterone Acetate and Progesterone in Adrenalectomized Mice Exposed to Low Temperatures

SummaryBy the use of a precold treatment injection schedule it has been demonstrated that desoxycorticosterone acetate at dose levels of 250 γ and 500 γ and progesterone at 500 γ prolongs the life of adrenalectomized mice subjected to low temperatures. Peanut oil at the dose level of 0.2 cc has been shown to possess a significant toxic action.
Early commitment to neoplasia in murine B- and T-cell lymphomas arising late in life

Lymphomas arise spontaneously in C57BL/10.H-2aH-4b (2a4b) mice greater than 1 year old. The purpose of this study was to determine when cells become committed to neoplasia and whether genes linked to H-2a or H-4b are a factor in predisposition to genesis of lymphoma. Following transplantation of a pool of spleen cells in large groups of mice, lymphoma incidence increased 1.8- to 2.1-fold and mean latent periods decreased, compared with those in controls. Lymphomas arising in mice that received the same pool of spleen cells often displayed identical rearrangements of genes for immunoglobulin and T-cell receptor. This finding indicates that the lymphomas were derived from expanding clones of cells present in the donor mice prior to transfer. The age of the donor mice determined the latency of lymphomas arising after spleen cell transfer. When donors were 3-4 months old at the time of spleen cell transfer, lymphomas were detected in the recipients 1 year later. When mice 1.5-2 years old were used as donors, tumors were observed 3 months after transfer. Almost all of these tumors were clonally related B-cell lymphomas. We conclude that the lymphomas seen late in life arise from premalignant clones of cells that have become committed to neoplasia in relatively young animals. These clones normally follow an indolent course and are manifested clinically only in old age. Neither H-2a nor H-4b alone appeared to alter susceptibility to the genesis of lymphoma in similar experiments with H-2a and H-4b congenic mice.
Anterior Dentition of the Eocene Condylarth Thryptacodon: Convergence with the Tooth Comb of Lemurs

A new specimen of arctocyonid condylarth from the early Eocene (Clarkforkian) of Wyoming is represented by the anterior part of the snout and lower jaws. Molar teeth are lacking, but the size and spacing of the premolars most closely resemble those in the early Eocene arctocyonid Thryptacodon antiquus ; hence, the specimen is best referred to that species. The new specimen is most remarkable in preserving a well-developed tooth comb that closely resembles the tooth comb of Madagascan lemurs. Dental homologies of the teeth in the comb are different in cf. Thryptacodon and lemurs, and the tooth comb in the two is clearly a result of evolutionary convergence. Considering the whole dentition, a close modern analogue for Thryptacodon is the procyonid Nasua , which also has an incipient tooth comb. Nasua , like lemurs, uses its tooth comb for both food gathering and grooming.
Simplified procedure for reliability-based robust geotechnical design of drilled shafts in clay using spreadsheet

ABSTRACTThis paper provides a simplified procedure for reliability-based robust geotechnical design (RGD) using spreadsheet. In the RGD methodology, design robustness is achieved by adjusting “design parameters” without reducing the uncertainties in noise factors. This design approach generally involves a multi-objective optimisation, which is computationally challenging. To improve the efficiency of the RGD methodology, the design robustness is evaluated in terms of sensitivity index and the safety requirement is evaluated using mean value first order second moment (MFOSM). To ease the concern that the reliability index obtained with MFOSM may not be sufficiently accurate, a mapping function that relates MFOSM to a more accurate method such as first order reliability method is introduced. To further improve the efficiency of the proposed simplified RGD method, a new simplified procedure along with a more accurate robustness measure is developed that eliminates the need for multi-objective optimisation. W...
Cycle covers (II) - Circuit chain, Petersen chain and Hamilton weights

The Circuit Double Cover Conjecture is one of the most challenging open problems in graph theory. The main result of the paper is related to the characterization of circuit chain structure, which has been one of the most popular approaches to the conjecture. Let G be a bridgeless cubic graph associated with an eulerian weight w : E ( G ) ź { 1 , 2 } such that ( G , w ) does not have a faithful circuit cover. If, for every weight 2 edge e 0 of ( G , w ) , the eulerian weighted graph ( G - e 0 , w ) has a faithful circuit cover and ( G , w ) has no removable circuit avoiding e 0 , then it was proved (Alspach et al., 1993 1 or 1994 2) that G contains a Petersen minor. It was further conjectured by Fleischner and Jackson (1988) that this graph G must be the Petersen graph. This conjecture was verified (JCTB 2010) recently under the assumption of the Hamilton weight conjecture. These two earlier results are further strengthened in this paper as follows. If, for a given weight 2 edge e 0 , the eulerian weighted graph ( G - e 0 , w ) has a faithful circuit cover and ( G , w ) has no removable circuit avoiding e 0 , then, under the assumption of the Hamilton weight conjecture, G must be a Petersen chain. With a much weaker requirement "for a given e 0 " instead of "for every e 0 ", this strengthened result (structure of circuit chain joining a missing edge) is expected to be much more useful in future studies about circuit covering problems.
Epidemiological analysis of hand foot and mouth disease in Tianmen City from 2008-2011

[Objective]To analyze the epidemiological characteristics of hand foot and mouth disease(HFMD) in Tianmen City,explore the epidemic law,provide the basis for HFMD prevention and control.[Methods]By using the descriptive epidemiological method,the data of HFMD cases from the Information Network Direct Report System of Infectious Disease in Tianmen City during 2008-2011 were statistically analyzed with 2003 Excel software.[Results]A total of 1 770 HFMD cases were reported in Tianmen City from 2008-2011,and the average annual incidence rate was 27.10/lakh.The distribution of HFMD cases had obvious characteristics in season,age and sex,while the peak season was April to July.The key population was children aged 0-3 years old,which accounted for 89.72% of total cases.The peak occurred in 1-2 year-old age group,and cases of children over 10 years old were rare.There were 1208 male cases and 562 female cases with the male-to-female ratio of 2.15∶1,and the male cases were significantly more than female cases.The pathogen detection showed that 30(34.09%) cases were positive for EV71,19(21.59%) cases were positive for CoxA16,and 39(44.32%) cases were positive for other intestinal virus.20(22.73%) patients were infected with the above two viruses.[Conclusion]The epidemic situation of HFMD in Tianmen City is serious.It is necessary to pay attention to peak season(April to July) and high-risk population(children aged 0-3 years old),and strengthen the monitoring and control of HFMD.
Design and Establishment of Experimental Simulation System Concerning SF_6 Thermal Decomposition

In order to study the thermal decomposition characteristic and mechanism of SF6 systematically, so as to solidify the method by using SF6 decomposition theory to diagnose thermal fault of SF6 insulated equipment, we established an experimental simulation system of SF6 thermal decomposition. Focusing on the design parameters of system structure, function, main components and testing method, we conducted software simulation and experimental verification to prove the system's reliability. Results indicate that the experimental system can effectively control the temperature of simulated over-thermal fault, while the proposed testing method can availably produce local high temperature effect to cause SF6 decomposition and generate the main by-products of CO2, SOF2, SO2F2, H2 S, SO2, etc, so that the formation rules of main components under four different fault temperatures can be obtained initially. The results can provide solid experimental basis for final establishment of thermal fault diagnosis theory and method of gas-insulated devices.
The Application and Research of on-line Cleaning Pre-membrane Technology for Blast Furnace Closed Soft Water System

The on-line processing of blast furnace closed soft water system cleaning and pre-membrane technology were adopted in the paper.The technology is used to slove the problems of long shutdown time,internal circulation system equipment and pipeline scaling and internal corrosion.The solution of implementing cleaning pre-membrane technology is determined.It is proved that the effect of the blast furnace closed soft water system on line cleaning and prefilming is good.The corrosion rate of carbon steel hanging piece is 0.777 6 g/m2·h and the passivation film is 18.72 s,which achieve the desired requirements.
Radiographic Assessment of Peri-Implant Vertical Bone Loss: DICRG Interim Report No. 9

Vertical bone loss is being assessed radiographically as part of the Dental Implant Clinical Research Group studies through direct measurements on study radiographs taken longitudinally at surgery and recall appointments. Preliminary results and trends for the period between implant placement and 6 months after implant uncovering show more bone loss in implants that are 1) not coated with hydroxyapatite; 2) placed in the maxilla; 3) placed in anterior regions of the jaws; 4) in completely edentulous cases; and 5) placed in bone scored as having lower quality. Confounding relationships between predictor variables will require controlled statistical analyses when data collection is completed.
The search for standards.

The International Organization for Standardization (ISO) assigned the responsibility for developing valve standards to its technical committee on surgical implants. A sub-committee on cardiovascular implants and the working group for heart valves were formed more than 20 years ago. The working group has learned a great deal, not only from its experience with ISO, but most of all from the collaboration of its international experts representing science, engineering and manufacturing. The first valve standard was published in 1984, revised in 1989, and the next revision will probably be published in 1995. After the formation of this ISO working group in 1972, the U.S. Food and Drug Administration (FDA) developed regulations for the premarket approval of heart valves in the United States. The European Committee for Standardization (CEN) was subsequently formed and appointed a working group to develop heart valve standards for Europe. It rapidly became apparent that the lack of co-ordination and communication of three separate organizations writing documents with different requirements and tests would lead to inconsistent and conflicting requirements. The ultimate outcome could have been a threat to public welfare by limiting the availability of medical devices. The commitment to the harmonization of standards by CEN and ISO, and the recent FDA policy to participate actively in standards development, have greatly improved this situation. Past errors, omissions and inappropriate attitudes have often slowed the standards process or have resulted in incomplete standards. This learning experience, while painful, should point the way to more timely and complete standards development in the future.
Absence of the inferior vena cava associated with an atrophic right kidney and hypertension.

AbstractA 6-year-old girl presented with acute hypertension and urinary tract infection. Evaluation revealed congenital absence of the inferior vena cava associated with an atrophic right kidney. A possible embryologic mechanism is proposed in an effort to relate the renal findings and vascular anomaly. In addition, any possible relationships among the urinary tract infection, the hypertension and the renal abnormality are discussed.
Constructionist Social Problems Theory

Social constructionist approaches have transformed the sociology of social problems by shifting the analytic focus from social conditions to the processes by which issues come to public attention. ...
Medical Therapy of Gastroesophageal Reflux Disease Assessed by Twenty-Four-Hour Esophageal pH Monitoring

Depending on how one defines gastroesophageal reflux disease, there are three approaches that can be used in evaluating therapy. The symptomatic approach defines the disease as the experience of heartburn and regurgitation by the patient. With this definition, therapy is directed toward alleviating these two symptoms. The problem with this approach is that symptoms are not a reliable guide to the presence of reflux [1]. It is possible for a patient to have minimal complaints of heartburn or regurgitation and still have a chronic nocturnal cough, wheezing, or choking as a consequence of laryngotracheal aspiration secondary to gastroesophageal reflux. Consequently, the end point of alleviating heartburn and regurgitation is not reliable in indicating that the disease has abated. Furthermore, there can be associated conditions with gastroesophageal reflux such as duodenogastric reflux and/or a delayed gastric emptying [2], causing symptoms of epigastric pain, nausea, vomiting, and loss of appetite. These symptoms can be predominant and confused with those of heartburn and regurgitation. Often, when heartburn and regurgitation are alleviated by medical therapy, the symptoms of duodenogastric reflux increase and become more prominent. In this situation, even though the therapy has been judged to be effective in alleviating the primary symptoms of heartburn and regurgitation, it has not abated the disease as manifested by the other complaints that emerge in the treated patient.
Rubric Development and Inter-Rater Reliability Issues in Assessing Learning Outcomes

This paper describes the development of rubrics that help evaluate student performance and relate that performance directly to the educational objectives of the program. Issues in accounting for different constituencies, selecting items for evaluation, and minimizing time required for data analysis are discussed. Aspects of testing the rubrics for consistency between different faculty raters are presented, as well as a specific example of how inconsistencies were addressed. Finally, a considerat ion of the difference between course and programmatic assessment and the applicability of rubric development to each type is discussed.
Use of Veterans Affairs and Medicaid Services for Dually Enrolled Veterans.

Objectives To examine how dual coverage for nonelderly, low-income veterans by Veterans Affairs (VA) and Medicaid affects their demand for care. Data Sources Veterans Affairs utilization data and Medicaid Analytic Extract Files. Study Design A retrospective, longitudinal study of VA users prior to and following enrollment in Medicaid 2006–2010. Data Collection/Extraction Methods Veterans Affairs reliance, or proportion of care provided by VA, was estimated with beta-binomial models, adjusting for patient and state Medicaid program factors. Principal Findings In a cohort of 19,890 nonelderly veterans, VA utilization levels were similar before and after enrolling in Medicaid. VA outpatient reliance was 0.65, and VA inpatient reliance was 0.53 after Medicaid enrollment. Factors significantly associated with greater VA reliance included sociodemographic factors, having a service-connected disability, comorbidity, and higher state Medicaid reimbursement. Factors significantly associated with less VA reliance included months enrolled in Medicaid, managed care enrollment, Medicaid eligibility type, longer drive time to VA care, greater Medicaid eligibility generosity, and better Medicaid quality. Conclusion Veterans Affairs utilization following new Medicaid enrollment remained relatively unchanged, and the VA continued to provide the large majority of care for dually enrolled veterans. There was variation among patients as Medicaid eligibility and other program factors influenced their use of Medicaid services.
Making Queer and Trans of Color Counterpublics: Disability, Accessibility, and the Politics of Inclusion

Drawing on 2 years of ethnographic fieldwork, this article examines the accessibility organizing efforts of queer and transgender of color community initiatives in Toronto, Canada. I argue that the...
Generalization of Skills Acquired in Language for Learning by Young Children with Autism Spectrum Disorder

Language deficits are a characteristic of individuals with autism spectrum disorder (ASD). Language for Learning is a promising curriculum for this population; it directly addresses language skills and contains several effective instructional strategies for learners with ASD. However, research on this curriculum for learners with ASD is limited, and to date research has not examined whether skills acquired in Language for Learning generalize to novel stimuli. The purpose of this study was to evaluate the effects of Language for Learning for producing generalization of expressive labeling skills to untrained visual stimuli by two children with ASD using a multiple probe across behaviors design. Results indicate that Language for Learning was effective in producing generalization to untrained stimuli and to a novel person. Further, gains maintained 6–8 weeks after the intervention was terminated. The implications of these results for future research on Language for Learning are discussed.
ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models

Drawing integrated conclusions from diverse source data requires synthesis across multiple types of information. The ToxPi (Toxicological Prioritization Index) is an analytical framework that was developed to enable integration of multiple sources of evidence by transforming data into integrated, visual profiles. Methodological improvements have advanced ToxPi and expanded its applicability, necessitating a new, consolidated software platform to provide functionality, while preserving flexibility for future updates. We detail the implementation of a new graphical user interface for ToxPi (Toxicological Prioritization Index) that provides interactive visualization, analysis, reporting, and portability. The interface is deployed as a stand-alone, platform-independent Java application, with a modular design to accommodate inclusion of future analytics. The new ToxPi interface introduces several features, from flexible data import formats (including legacy formats that permit backward compatibility) to similarity-based clustering to options for high-resolution graphical output. We present the new ToxPi interface for dynamic exploration, visualization, and sharing of integrated data models. The ToxPi interface is freely-available as a single compressed download that includes the main Java executable, all libraries, example data files, and a complete user manual from http://toxpi.org .
Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces.

ABSTRACT The draft genome sequence of an isolate identified as Bifidobacterium longum is communicated herein. This strain was isolated from the feces of a 1-week-old Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is 2.39 Mb in length, with a G+C content of 60.1%.
Structure of Archaeological Explanation

This chapter presents several examples of archaeological explanation, varied in their completeness, and form and subject matter, against the background of various philosophical accounts of standards for scientific explanation. With respect to explanation of particular events, it has been argued that, statements to the contrary notwithstanding, such explanations are scientifically important. The chapter presents the Statistical–Relevance model, supplemented by causal features, that has been demonstrated to capture more fully than other available models the beneficiating aspects of such explanations in archaeology. Furthermore, this model, in addition to its ability to fit explanations implicity recognized as correct by archaeologists avoids certain problems that cannot be excised from the Inductive–Statistical model. The chapter presents a sound archaeological example that fits the Deductive–Statistical model. However, it has been noted that the fact that a good explanation fits a particular model does not guarantee correctness of that model as the explanation might fit other models as well. Models should be tested also by seeing whether or not any obviously bad explanations fit them.
URACIL-DNA GLYCOSYLASE MUTANTS ARE MUTATORS

ABSTRACT Spontaneous mutation to nalidixic acid or to rifampicin resistance is increased 5-fold in uracil-DNA glycosylase ( ung ) mutants of E. coli. By trpA reversion analysis we observed a 15-fold increase in the frequency of spontaneous G:C→A:T transition mutations while other transition and transversion frequencies were not affected. Duncan and Warner (Nature, 1978) have previously found that uracil-containing phage (30% uracil) are viable in ung − bacteria; the uracil is not removed from the DNA. Thus, uracil-DNA glycosylase appears to have evolved not to prevent uracil misincorporation into DNA (as A:U), but rather to edit (mutagenic) deaminated cytosine residues. This mechanism precludes the use of uracil as a “normal” DNA constituent.
Dynamics of water evaporation and flammability from the common “dogwood” (Cornus kousa) leaf

The leaves of Cornus kousa Dogwood were specifically analyzed for their ability to resist burning in three different conditions fresh oven dried and naturally fallen leaves Analyzing the different surface properties of each of the leaves was of particular importance and the special attributes of the epidermis layer were determined using Optical Water Contact Angle Microscopy Optical Microscopy and Confocal Microscopy Water droplets were displaced onto the surface of the leaves measuring each of the contact angles over a period of time until evaporation occurred which aided the understanding of the hydrophobic and hydrophilic properties of the leaves in different settings Optical and Confocal Microscopy were utilized to examine the topology of the leaf epidermis not only through a micro ndash analysis of the epidermal layer structures but also through a D model of the different course and smooth surfaces respectively Flame tests were conducted to contrast the pyrolyzing rates of the leaves under the three conditions Understanding properties specific to the Cornus kousa and more specifically the dynamics in water evaporation and flammability which is helpful for numerous applications ranging from wildfire prevention to horticulture
What's ours is yours: recall of history for lesser-known countries is guided by one's own national history.

The present studies examine how people recall history. Sometimes, certain national histories are well known and sometimes they are not. We propose that, under certain circumstances, culturally dist...
Failure of the Merger of the Mount Sinai and New York University Hospitals and Medical Schools: Part 2

This is the second of two articles in this issue of Academic Medicine that, together, report the author's findings from his study of the attempt by the leaders of Mount Sinai and New York University (NYU) medical centers in New York City to merge their medical schools and hospitals, and the failure of those attempts. After the unsuccessful effort of the trustees to merge the medical schools and hospitals--see the first article--the two institutions successfully created Mount Sinai NYU Health, a new company of the Mount Sinai and NYU hospitals in New York City. Members of the NYU faculty, worried that the new attempt would also include the medical schools, sued their university to prevent the merger. Although they lost the suit, the NYU medical school remained within the university as they had wanted. The hospital merger, like the more comprehensive hospital/medical school merger that failed, was favored by most of the trustees and executives at Mount Sinai. Although supported by many of the NYU trustees, both mergers were strongly opposed by some of the leadership and many of the faculty at the NYU medical center.The hospital merger came into effect in July 1998, but three years later, administration of the hospitals had returned to the separate campuses. In 2008, the merger was officially terminated. Although several of the back-office functions combined, no clinical programs did, as was also the case in other mergers of teaching hospitals. The author concludes with an analysis of why this merger failed while a few others succeeded.
Building Virtual Power Meters for Online Load Tracking

Many energy optimizations require fine-grained, load-level energy data collected in real time, most typically by a plug-level energy meter. Online load tracking is the problem of monitoring an individual electrical load’s energy usage in software by analyzing the building’s aggregate smart meter data. Load tracking differs from the well-studied problem of load disaggregation in that it emphasizes per-load accuracy and efficient, online operation rather than accurate disaggregation of every building load via offline analysis. In essence, tracking a particular load creates a virtual power meter for it, which mimics having a networked-connected power meter attached to the load, but notably does not require tracking every other load as well. We propose PowerPlay, a model-driven system for performing accurate, high-performance online load tracking. Our results from applying the system to real-world energy data demonstrate that PowerPlay (i) enables efficient online tracking on low-power embedded platforms, (ii) scales to thousands of loads (across many buildings) on server platforms, and (iii) improves per-load accuracy by more than a factor of two compared to a state-of-the-art load disaggregation algorithm. Our results point to the potential of replacing physical energy meters by “virtual” power meters using a system like PowerPlay.
Nucleotide Metabolism in Cardiac Activity II. Reactions in Systole

Relaxed mammalian hearts contain ATP as the predominant nucleotide, sometimes accompanied by smaller amounts of ADP, presumably formed during manipulation. In systole, one-tenth of the nucleotide is changed into a new compound, nucleotide H.
An Online System to Help With Mock Oral Examination Administration

Objective Describe an online system used to collect data, compute statistics, and provide reports for mock oral examinations. Design Forty general surgery residents, program directors, and faculty serving as examiners completed a survey regarding their experiences with the online mock oral examination system. Setting General surgery residency programs and national surgical conferences. Participants General surgery residents, program directors, and faculty. Results System users had very positive attitudes toward the online system in terms of usability and reporting functions. Conclusions The mock oral exam management online system is a useful tool that eases the burden of managing a mock oral exam session.
Creep behavior in Cu and Ag particle-reinforced composite and eutectic Sn-3.5Ag and Sn-4.0Ag-0.5Cu non-composite solder joints

Creep properties were determined for small, geometrically realistic Pb-free solder joints. Solder joints were prepared with eutectic Sn-3.5Ag and Sn-4.0Ag-0.5Cu solder alloys. Composite solder joints were made using the eutectic Sn-3.5Ag alloy as the matrix with 15 vol % of mechanically added ∼6 μm size Cu and ∼4 μm size Ag reinforcing particles. Creep tests were conducted on these joints at 25 °C, 65 °C and 105 °C representing homologous temperatures ranging from 0.61 to 0.78. Qualitative and quantitative evaluations of creep behavior were obtained from the distortion of excimer laser-induced surface ablation markings on the solder joint. Various creep parameters, such as global and localized creep strain, variation of creep strain and strain-rate, activation energy for creep, and the onset of tertiary creep were determined. General findings in this study revealed that the creep resistance in composite solder joints is significantly improved with Cu particle reinforcements. In contrast, the improvement in the creep properties of Ag particle-reinforced composite solder joints was far less even though highly uniform deformation in the joint was observed. The strain noted at the onset of tertiary creep for Cu and Ag reinforced composite solder joints was typically lower compared to non-composite solder joints. The activation energies for creep were similar for all the solder materials investigated in this study. © 2001 Kluwer Academic Publishers
Intermediate extensions of perverse constructible Fp-sheaves commute with smooth pullbacks

Abstract We prove that intermediate extensions of perverse constructible F p -sheaves commute with smooth pullbacks for embeddable schemes over a field of characteristic p. Along the way we also prove that the equivalence of categories of Cartier crystals with unit R [ F ] -modules commutes with f ! for a smooth morphism f : X → Y of embeddable schemes.
Examining the Immediate Effects of Recent Tax Law Changes on the Structure of Executive Compensation

As part of the “Tax Cuts and Jobs Act” (TCJA), Congress repealed a long-standing exception that allowed companies to deduct executives’ qualified performance-based compensation in excess of $1 million. The reason for the change was to reverse a shift in executive compensation away from cash compensation and towards performance pay, which Congress believed led executives to focus on short-term results rather than the long-term success of the company. The purpose of this study is to test the efficacy of this provision as part of the TCJA. Across a battery of tests, including a difference-in-differences design that exploits the staggered time-series implementation of the deduction limit, we find little evidence that the average firm changed the level or structure of CEO compensation after the TCJA as Congress intended. Overall, our findings suggest this change was ineffectual as enacted. Our results have implications for future policymakers who endeavor to adjust pay inequality or managerial myopia through tax laws targeted at executive compensation.
An Introduction to Space Anthropology

This chapter introduces two central concepts: first, human space settlement as adaptive evolution, and second, how evolutionary and anthropological sciences can aid in making the project of human space colonization more likely to succeed. I then continue by defining some basic concepts and terms, and the essential time- and space-thoughtscapes addressed in this book.
Confined Interlayer Water Promotes Structural Stability for High-Rate Electrochemical Proton Intercalation in Tungsten Oxide Hydrates

There is widespread interest in determining the structural features of redox-active electrochemical energy storage materials that enable simultaneous high power and high energy density. Here, we pr...
Updating urban design floods for changes in central tendency and variability using regression

Abstract Ordinary least squares (OLS) regression offers a decision-oriented approach for modeling trends in annual peak flows. We introduce a two-stage OLS approach for nonstationary flood frequency analysis that (i) models changes in their central tendency (median) in response to environmental perturbations with one regression and then (ii) examines changes in the coefficient of variation (Cv) by running a second regression on Anscombe-transformed residuals from the first regression. Monte Carlo simulations show that this approach yields 100-year flood estimates with mean squared errors comparable to estimates made with an advanced generalized linear model-based method. Also, this second-stage regression often produces approximately normal residuals, which permits statistical inferences on Cv trends. Case studies illustrate the dramatic impact that decreasing and increasing Cv trends can have on 100-year floods. Findings motivate the incorporation of trends in variability in infrastructure design along with further research examining asymmetric changes in urban flood variability.
Scanning offset-emission hyperspectral microscopy (SOHM) of waveguiding in single ZnO nanorod

We examine multiphoton-produced optical signals waveguided through single ZnO nanorod (NR) using a newly developed, scanning offset-emission hyperspectral microscopy (SOHM) technique. SOHM acquires spectrally indexed and spatially resolved intensity maps/spectra of waveguided light intensity, while excitation/emission collection positions and light polarization are scanned. Hence, the powerful measurement capabilities of SOHM enable quantitative analyses of the different ZnO NR waveguiding behaviors specific to the multiphoton-generated emissions as a function of measurement position, and the optical origin of the guided signal. We subsequently reveal the distinct waveguiding behaviors of single ZnO NRs pertaining to the variously originated signals and discuss particularly attractive ZnO NR properties in CARS waveguiding. In this talk, I will present the distinctive CARS waveguiding nature through single ZnO NR, exhibiting high position and polarization-dependence.
A Leading Log Approximation for Inflationary Quantum Field Theory

During inflation explicit perturbative computations of quantum field theories which contain massless, non-conformal fields exhibit secular effects that grow as powers of the logarithm of the inflationary scale factor. Starobinskii's technique of stochastic inflation not only reproduces the leading infrared logarithms at each order in perturbation theory, it can sometimes be summed to reveal what happens when inflation has proceeded so long that the large logarithms overwhelm even very small coupling constants. It is thus a cosmological analogue of what the renormalization group does for the ultraviolet logarithms of quantum field theory, and generalizing this technique to quantum gravity is a problem of great importance. There are two significant differences between gravity and the scalar models for which stochastic formulations have so far been given: derivative interactions and the presence of constrained fields. We use explicit perturbative computations in two simple scalar models to infer a set of rules for stochastically formulating theories with these features.