cssi/SciSciGPT-SciSciNet huggingface dataset:
Three-dimensional electron crystallography of protein microcrystals

X-ray crystallography has been used to work out the atomic structure of a large number of proteins. In a typical X-ray crystallography experiment, a beam of X-rays is directed at a protein crystal, which scatters some of the X-ray photons to produce a diffraction pattern. The crystal is then rotated through a small angle and another diffraction pattern is recorded. Finally, after this process has been repeated enough times, it is possible to work backwards from the diffraction patterns to figure out the structure of the protein. The crystals used for X-ray crystallography must be large to withstand the damage caused by repeated exposure to the X-ray beam. However, some proteins do not form crystals at all, and others only form small crystals. It is possible to overcome this problem by using extremely short pulses of X-rays, but this requires a very large number of small crystals and ultrashort X-ray pulses are only available at a handful of research centers around the world. There is, therefore, a need for other approaches that can determine the structure of proteins that only form small crystals. Electron crystallography is similar to X-ray crystallography in that a protein crystal scatters a beam to produce a diffraction pattern. However, the interactions between the electrons in the beam and the crystal are much stronger than those between the X-ray photons and the crystal. This means that meaningful amounts of data can be collected from much smaller crystals. However, it is normally only possible to collect one diffraction pattern from each crystal because of beam induced damage. Researchers have developed methods to merge the diffraction patterns produced by hundreds of small crystals, but to date these techniques have only worked with very thin two-dimensional crystals that contain only one layer of the protein of interest. Now Shi et al. report a new approach to electron crystallography that works with very small three-dimensional crystals. Called MicroED, this technique involves placing the crystal in a transmission electron cryo-microscope, which is a fairly standard piece of equipment in many laboratories. The normal ‘low-dose’ electron beam in one of these microscopes would normally damage the crystal after a single diffraction pattern had been collected. However, Shi et al. realized that it was possible to obtain diffraction patterns without severely damaging the crystal if they dramatically reduced the normal low-dose electron beam. By reducing the electron dose by a factor of 200, it was possible to collect up to 90 diffraction patterns from the same, very small, three-dimensional crystal, and then—similar to what happens in X-ray crystallography—work backwards to figure out the structure of the protein. Shi et al. demonstrated the feasibility of the MicroED approach by using it to determine the structure of lysozyme, which is widely used as a test protein in crystallography, with a resolution of 2.9 A. This proof-of principle study paves the way for crystallographers to study protein that cannot be studied with existing techniques.
Confessions of a Non-Designer Designer

The creation of a product design almost always involves competing visions within the team. Business, engineering, and design all have views on what makes for a successful product. News flash: The user should be the winner in that battle. If you are a consumer, you want this human factors engineer to be on the design team.
Secure detection in wireless sensor networks using a simple encryption method

The problem of binary hypothesis testing in a wireless sensor network is considered where observation of the sensors are quantized using identical binary quantizers and encrypted before transmission using a simple probabilistic cipher. The authorized or ally fusion center (AFC) is aware of the encryption process and the encryption parameters, whereas the unauthorized or third party fusion centers (TPFC) are unaware of the encryption parameters. The optimal threshold is evaluated for fixed values of the encryption parameters and numerical results are presented on the error probabilities of the two fusion centers. It is shown that by appropriate selection of the encryption parameters it is possible to degrade the performance of the TPFC significantly compared to that of AFC.
On the hydrodynamic lubrication of roller-bearings

Abstract An analysis is made of the lubrication of cylindrical roller-bearings in the hydrodynamic regime. Expressions are derived for the maximum film pressure, load capacity of the bearing, frictional moment on the shaft, and coefficient of friction. A numerical example is worked out and the limits of the theory investigated.
Just Say No to the Charges Against You: Alcohol Intoxication, Mental Capacity, and Criminal Responsibility

There have been many studies showing a high correlation between crime and alcohol use. Even the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders (DSM-111-R) cites that one significant complication of "alcohol intoxication" is its "frequent association with the commission of criminal acts."' Specifically, the DSM-111-R points out that "more than one-half of all murderers are believed to have been intoxicated at the time of the act."2 Yet because of the multiplicity of factors involved in analyzing alcohol's relation to crime, no study has conclusively proven any direct causal link.3 From the high correlation alone, many people may simply assume and expect that violence results from alcohol use. Some studies suggest that the lowering of inhibitions caused by alcohol may encourage the commission of violent
Gross nitrous oxide production drives net nitrous oxide fluxes across a salt marsh landscape

Sea level rise will change inundation regimes in salt marshes, altering redox dynamics that control nitrification - a potential source of the potent greenhouse gas, nitrous oxide (N2 O) - and denitrification, a major nitrogen (N) loss pathway in coastal ecosystems and both a source and sink of N2 O. Measurements of net N2 O fluxes alone yield little insight into the different effects of redox conditions on N2 O production and consumption. We used in situ measurements of gross N2 O fluxes across a salt marsh elevation gradient to determine how soil N2 O emissions in coastal ecosystems may respond to future sea level rise. Soil redox declined as marsh elevation decreased, with lower soil nitrate and higher ferrous iron in the low marsh compared to the mid and high marshes (P < 0.001 for both). In addition, soil oxygen concentrations were lower in the low and mid-marshes relative to the high marsh (P < 0.001). Net N2 O fluxes differed significantly among marsh zones (P = 0.009), averaging 9.8 ± 5.4 μg N m(-2) h(-1) , -2.2 ± 0.9 μg N m(-2) h(-1) , and 0.67 ± 0.57 μg N m(-2) h(-1) in the low, mid, and high marshes, respectively. Both net N2 O release and uptake were observed in the low and high marshes, but the mid-marsh was consistently a net N2 O sink. Gross N2 O production was highest in the low marsh and lowest in the mid-marsh (P = 0.02), whereas gross N2 O consumption did not differ among marsh zones. Thus, variability in gross N2 O production rates drove the differences in net N2 O flux among marsh zones. Our results suggest that future studies should focus on elucidating controls on the processes producing, rather than consuming, N2 O in salt marshes to improve our predictions of changes in net N2 O fluxes caused by future sea level rise.
Anasbaco janelas da alma: olhar o amado e o olhar do amado em baco e as Anas brasileiras de Yeda Schmaltz

Resumo O presente ensaio examina a autobiografia poetica generacional das Anas, alicercada na metafora alimento=amor. Ludicos, realistas e ironicos, os poemas mostram Baco (o homem brasileiro) a se pavonear ante as varias Anas. O amado se conhecera do exterior para o interior. E os oculos ora iluminam seu coracao, ora se tornam barreira a seu conhecimento. Abstract In Bacos e as Anas Brasileiras Yeda Schmaltz constructs masculinity through knowledge of the beloved. This poetical autobiography of a generation of women is based on the metaphor love=food. Ludic, realistic, and ironic, the poems show Bacchus (the Brazilian male) preening in front of the Anns who attempts to know the beloved from the outside to the inside. And his eyeglasses can either illuminate his soul or become a barrier.
Porous Silicon's Photoactivity in Water: Insights into Environmental Fate.

Interest in porous silicon (pSi) (and, more broadly, silicon nanoparticles (NPs)) has increased along with their concomitant use in various commercial and consumer products, yet little is known about their behavior in the natural environment. In this study, we have investigated the photosensitization, optical, and surface properties of pSi as a function of time in aqueous systems. Samples were prepared via an anodic electrochemical etching procedure, resulting in pSi particles with diameters of ca. 500 nm, composed of a porous network of Si nanocrystallites of 2–4 nm. Initially, pSi particles generated significant amounts of 1O2, yet they rapidly lost much of this ability due to the formation of an oxide layer on the surface, as determined by X-ray photoelectron spectroscopy, which likely prevented further photosensitization events. Addition of natural organic matter (NOM) did not significantly impact pSi’s photosensitization abilities. The pSi lacked any intrinsic bactericidal properties on Escherichia c...
GROWTH FIELDS IN THE DENTITION OF PEROMYSCUS

The sample of Peromyscus leucopus noveboracensis used and the measurements taken have been described elsewhere (Vanr Valen, 1962). There are three cheek teeth on each side of each jaw, and measurements of length and width were taken on each tooth. Correlations were computed for each measurement for each of the three possible pairs of teeth on each jaw, separately for each sex. The mean of the measurements on the two sides was used in each case. Fisher's normalizing corrected z transformation is used throughout. The correlation patterns are presented in table 1. Their most striking feature is the independence of the lengths of M3 and M3 from those of the other teeth. This is apparently not due to these teeth being vestigial in all respects, although they are somewhat the smallest of the three in each jaw, because the widths of M3 and of M3 show a strong correlation with those of the other teeth. Control of tooth width seems to be more important than control of tooth length. The correlation between each pair of teeth is greater for width, and the coefficients of variation (table 2) are less for all but one tooth. INTERPRETATION
Proportionally Reducing Sample-Size Requirements by Increasing Dependent-Variable Reliability:

Increasing dependent-variable reliability ρ(y,y) proportionally reduces both sample-size requirements and costs of independent-groups studies. This result is analytically considered in terms of the classical Z-test comparison of two means representing independent samples of size (N). Analysis reveals that the dependent-variable reliability directly trades-off with sample-size in its impacts on sensitivity, so that constant statistical-power is maintained by reducing sample-size with a proportionally increased ρ(y,y). Two illustrations (reflecting sample-size and associated cost reductions of up to 50% or more) are presented of the value of systematic efforts to enhance reliability: (a) Integrating performance measures in evaluation of worker exposure-effects, and (b) Quality and preferences in new-product development. Test-Retest Reliability analyses are recommended as means to evaluate (1) Potential for enhancing statistical-power via increases in ρ(y,y) and (2) Impacts of attempts to increase statistica...
HIV community viral load trends in South Carolina

Community viral load is an aggregate measure of HIV viral load in a particular geographic location, community, or subgroup. Community viral load provides a measure of disease burden in a community and community transmission risk. This study aims to examine community viral load trend in South Carolina and identify differences in community viral load trends between selected population subgroups using a state-wide surveillance dataset that maintains electronic records of all HIV viral load measurements reported to the state health department. Community viral load trends were examined using random mixed effects models, adjusting for age, race, gender, residence, CD4 counts, HIV risk group, and initial antiretroviral regimen during the study period, and time. The community viral load gradually decreased from 2004 to 2013 ( p < 0.0001). The number of new infections also decreased ( p = 0.0001) over time. A faster rate of decrease was seen among men compared to women ( p < 0.0001), men who have sex with men ( p = 0.0001) compared to heterosexuals, patients diagnosed in urban areas compared to that in rural areas ( p = 0.0004), and patients prescribed single-tablet regimen compared to multiple-tablet regimen ( p < 0.0001). While the state-wide community viral load decreased over time, the decline was not uniform among residence at diagnosis, HIV risk group, and single-tablet regimen versus multiple-tablet regimen subgroups. Slower declines in community viral load among females, those in rural areas, and heterosexuals suggest possible disparities in care that require further exploration. The association between using single-tablet regimen and faster community viral load decline is noteworthy.
Thermally activated features in 1 f noise in silicon on sapphire

Reproducible spectral features were found in the low-frequency noise in silicon-on-sapphire (SOS) wafers. These features moved in frequency as a function of temperature, with a range of activation energies from \ensuremath{\sim}0.4 to \ensuremath{\sim}0.7 eV. The relation between the log slope of the frequency spectrum and its temperature derivative was qualitatively similar to that predicted by a formula derived by Dutta et al. for noise with a range of activation energies. However, systematic quantitative deviations were found which demonstrate the existence of a wide range of temperatureindependent prefactors in the rate expressions.
Structural Integration Solution for the Texas A&M 2007 Solar Decathlon "GroHome"

The entry by the College of Architecture at Texas AM including manufacturing, welding, re-design, construction, and the extent of engineering supervision.
Cytological studies of the nematocysts of Hydra. I. Desmonemes, isorhizas, cnidocils, and supporting structures.

Entire hydras or tentacles were fixed in OsO4 or in KMnO4 and thereafter washed, dehydrated, and embedded in a methacrylate mixture. Ultrathin sections were cut on an experimental model, thermal expansion type ultramicrotome or on a Porter-Blume microtome. The sections were examined in an RCA electron microscope. Type EMU-2 D. "Squash preparations" for light microscopy, were made from the hydra mouth region and the attached tentacles. These were observed with an AO Baker interference microscope. In the mature organism, three of the four types of nematocysts normally found in hydra could be positively identified with the electron microscope. The desmonemes, the smallest type, have a dense matrix and a thin capsule. The two different types of mature isorhizas could not be distinguished with certainty. They are intermediate in size between the desmonemes and stenoteles and have a capsule with a dense matrix. The cnidocil, or triggering hair, which is composed of a dense core and a fibrillar sheath has nine supporting elements arranged in a semi-circle near its base. Twenty "supporting structures" are arranged around the nematocyst capsule and interconnections between the supporting elements and these latter structures have been observed. Development of the nematocysts involves an increase in density of the matrix. Spines can be seen in the interior of tubular structures within the capsules of the holotrichous isorhizas.
UV-vis spectroscopic properties of nC60 produced via extended mixing.

Colloidally stable C60 suspensions produced via extended mixing in water (aq/nC60) are highly heterogeneous with respect to particle size and morphology. Ultraviolet–visible (UV–vis) absorption spe...
A non von neumann continuum computer architecture for scalability beyond Moore's law

A strategic challenge confronting the continued advance of high performance computing (HPC) to extreme scale is the approaching near-nanoscale semiconductor technology and the end of Moore's Law. This paper introduces the foundations of an innovative class of parallel architecture reversing many of the conventional architecture directions, but benefiting from substantial prior art of previous decades. The Continuum Computer Architecture, or CCA, eschews traditional von Neumann-derived processing logic, instead employing structures composed of fine-grain cells (fontons) that combine functional units, memory, and network. The paper describes how CCA systems of various scales may be organized and implemented using currently available technology. As programming of such systems substantially differs from established practices, a still experimental ParalleX execution model is introduced to be used as a guide for the implementation of related software stack layers, ranging from the operating system to application level constructs. Finally, the HPX-5 runtime system, an advanced implementation of ParalleX core components, is presented as an intermediate software methodology for CCA system computation resource management.
Non-conduit repair of truncus arteriosus

Abstract Background Primary complete repair of truncus arteriosus (TA) is the goal in the current era of cardiac surgery. In the absence of valved conduits, non-conduit repair remains possible in spite of less optimal hemodynamics and could be a solution for this category of patients in the developing countries. Patients and methods This is a review of eight patients operated upon in the national heart institute from January 2013 to November 2015. They underwent non-conduit repair of truncus arteriosus by the modifications of the Barbero-Marcial technique through window like separation of the common trunk, approximating the pulmonary artery to right ventricular outflow tract and completed by autologous pericardial patch. Results The mean age was 43.75 days with range 20–80 days. The mean body weight was 3.5 kg with range 2.8–4.5 kg. There were two early mortality cases in the intensive care unit (ICU). The mean ventilation time was 38.6 h with range 18–66 h. The mean ICU stay was 6.3 days with range 3–11 days. Pre-discharge echocardiography revealed mean gradient across the right ventricular outflow tract (RVOT) 24 mmHg with range 14–34 mmHg and mean grade of pulmonary incompetence (PI) was 2.3 with range of 1–3. Conclusion The non-conduit repair is a good alternative for type I TA, especially when it is the only available solution.
The de Casteljau Algorithm

The algorithm described in this chapter is probably the most fundamental one in the field of curve and surface design, yet it is surprisingly simple. Its main attraction is the beautiful interplay between geometry and algebra: a very intuitive geometric construction leads to a powerful theory. Historically, it is with this algorithm that the work of de Casteljau started in 1959. The only written evidence is in [121] and [122], both of which are technical reports that are not easily accessible. De Casteljau's work went unnoticed until W. Boehm obtained copies of the reports in 1975. Prom then on, de Casteljau's name gained more popularity.
La política de la transgenericidad: Pierre du Ryer y su adaptación dramática de «Argenis» de John Barclay

John Barclay’s Argenis (1621) was an immediate smash hit in France, not least because the hero Poliarchus is a Frenchman. Indeed, it is rumored that Argenis was Cardinal Richelieu’s favorite novel, particularly because of the political dimension of this alleged roman a cle . Numerous French translations appeared between 1622 and 1630, and Nicolas Coeffeteau’s abridged version (1624) made the novel even more accessible to French readers. Taking advantage of the novel’s success, Pierre Du Ryer (1606-1658), one of the most popular playwrights of his generation, wrote two adaptations of Barclay’s novel: Argenis et Poliarque, ou Theocrine, tragicomedie (1630), focusses on the first encounter between Argenis and Poliarchus, whilst L’Argenis du sieur Du Ryer, tragi-comedie, derniere journee (1631) attempts to recount the entire plot. This article explores, through the prism of Du Ryer’s two plays, the poetics of adaptation of the neo-Latin novel to French tragicomedy. It approaches this question from narratological and performance viewpoints, and reflects on the politics of transgenericity, defined broadly as both the inscription of a genre in another and the passage from one mode of representation to another. This dual operation is political, in the sense that such a generic transformation is never insignificant, objective, or unmotivated. In fact, Du Ryer’s choice to adapt Argenis complicates the politics of spectacle at this time, especially since the dramatist’s patrons were not allies of Cardinal Richelieu, who was implementing reason of state policies and building an absolutist state.
Toll-like receptor signaling and stages of addiction

Athina Markou and her colleagues discovered persistent changes in adult behavior following adolescent exposure to ethanol or nicotine consistent with increased risk for developing addiction. Building on Dr. Markou’s important work and that of others in the field, researchers at the Bowles Center for Alcohol Studies have found that persistent changes in behavior following adolescent stress or alcohol exposure may be linked to induction of immune signaling in brain. This study aims to illuminate the critical interrelationship of the innate immune system (e.g., toll-like receptors [TLRs], high-mobility group box 1 [HMGB1]) in the neurobiology of addiction. This study reviews the relevant research regarding the relationship between the innate immune system and addiction. Emerging evidence indicates that TLRs in brain, particularly those on microglia, respond to endogenous innate immune agonists such as HMGB1 and microRNAs (miRNAs). Multiple TLRs, HMGB1, and miRNAs are induced in the brain by stress, alcohol, and other drugs of abuse and are increased in the postmortem human alcoholic brain. Enhanced TLR-innate immune signaling in brain leads to epigenetic modifications, alterations in synaptic plasticity, and loss of neuronal cell populations, which contribute to cognitive and emotive dysfunctions. Addiction involves progressive stages of drug binges and intoxication, withdrawal-negative affect, and ultimately compulsive drug use and abuse. Toll-like receptor signaling within cortical-limbic circuits is modified by alcohol and stress in a manner consistent with promoting progression through the stages of addiction.
Regression Discontinuity Designs With Sample Selection

This article extends the standard regression discontinuity (RD) design to allow for sample selection or missing outcomes. We deal with both treatment endogeneity and sample selection. Identificatio...
Teaching teachers about retirement and investments: A comparison of three interventions:

The authors describe a project that compared the effects of three interventions on the retirement investment knowledge of public school teachers in the Midwest. They interpret outcomes from three d...
Relative susceptibility of airway organisms to antimicrobial effects of nitric oxide

Background Nitric oxide (NO) is released in the airway as a critical component of innate immune defense against invading pathogenic organisms. It is well documented that bacteriostatic and bactericidal effects of NO are concentration-dependent. However, few data exist comparing relative susceptibility of common pathogens to NO at physiologic concentrations. In this study we evaluated the effects of NO on 4 common airway bacteria and 1 fungus, and examined the potential implications of discrepancies in sensitivity. Methods Staphylococcus epidermis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans cultures were adjusted to a uniform optical density (OD) and grown in log phase at 37°C with varying concentrations of NO formed by DETA NONOate. Both OD readings and colony forming units (CFUs) were measured at varying time-points to evaluate for inhibitory effects of NO. Results P aeruginosa and C albicans were significantly more sensitive to NO at physiologic concentrations typical of the human airway. S aureus was attenuated by NO to a lesser degree, and K pneumoniae and S epidermis were more resistant to NO at all concentrations tested. Air surface liquid from cultured human sinonasal epithelial cells had an additive effect in bacterial killing of P aeruginosa, but not in S aureus. Conclusion Common airway pathogens have varying levels of susceptibility to NO at physiologic concentrations of innate immune defense. Relative sensitivity of P aeruginosa and relative resistance of S epidermis may help explain the composition of the healthy microbiome, as well as opportunistic infection in the absence of induced NO release.
Pediatric Spondylolysis and Spondylolisthesis

Spondylolisthesis is the slipping of one vertebra on another. Spondylolysis is a disruption of the pars interarticularis. These two conditions can exist concomitantly or separately and are often seen in asymptomatic patients. However, these diagnoses are usually made because of complaints of back pain and/or deformity. Spondylolysis is associated with activities that involve repeated hyperextension of the spine. Spondylolisthesis can be of the developmental or acquired type. Severe slips are seen with the developmental type, and high-grade slips cause significant back deformity, loss of normal spinal alignment, and gait abnormalities. Diagnosis is made with plain radiographs with additional advanced imaging as indicated. The natural history is somewhat nebulous as many patients with even high-grade slips remain asymptomatic. Yet patients who only have spondylolysis may have severe low-back pain. The mainstay of treatment is periodic rest, physical therapy, and nonsteroidals. Persistent symptoms may require surgical treatment to either repair the pars in spondylolysis or to stabilize the spondylolisthesis with a fusion.
The Bayesian Bandwagon

We ended our discussion of Laplace’s principles of probability without exploring the tenth principle, which Laplace termed moral hope. We know this concept as utility.
Cognitive Effects of Cancer and Cancer Treatments

As the population of cancer survivors has grown into the millions, there has been increasing emphasis on understanding how the late effects of treatment affect survivors’ ability to return to work/school, their capacity to function and live independently, and their overall quality of life. This review focuses on cognitive change associated with cancer and cancer treatments. Research in this area has progressed from a pharmacotoxicology perspective to a view of the cognitive change as a complex interaction of aspects of the treatment, vulnerability factors that increase risk for posttreatment cognitive decline, cancer biology, and the biology of aging. Methodological advances include the development of (a) measurement approaches that assess more fine-grained subcomponents of cognition based on cognitive neuroscience and (b) advanced statistical approaches. Conceptual issues that arise from this multidimensional perspective are described in relation to future directions, understanding of mechanisms, and dev...
Reduction of Health Care Costs and Improved Appropriateness of Incoming Test Orders: the Impact of Genetic Counselor Review in an Academic Genetic Testing Laboratory

The goal of this study was to evaluate the impact of genetic counselor (GC) review of incoming test orders received in an academic diagnostic molecular genetics laboratory. The GC team measured the proportion of orders that could be modified to improve efficiency or sensitivity, tracked provider uptake of GC proposed testing changes, and calculated the health care dollar savings resulting from GC intervention. During this 6-month study, the GC team reviewed 2367 incoming test orders. Of these, 109 orders (4.6%) were flagged for review for potentially inefficient or inappropriate test ordering. These flagged orders corresponded to a total of 51 cases (1-5 orders for each patient), representing 54 individuals and including 3 sibling pairs. The GC team proposed a modification for each flagged case and the ordering providers approved the proposed change for 49 of 51 cases (96.08%). For the 49 modifications, the cost savings totaled $98,750.64, for an average of $2015.32 saved per modification. This study provides evidence of the significant contribution of genetic counselors in a laboratory setting and demonstrates the benefit of laboratories working with ordering providers to identify the best test for their patients. The review of test orders by a genetic counselor both improves genetic test ordering strategies and decreases the amount of health care dollars spent on genetic testing.
Development of Vignettes to Explore Workplace Bullying.

Incivility and bullying in healthcare can impact care delivery and quality. There are challenges in research to making a direct link between the behaviors and patient outcomes. One way to address t...
How Collaborative Learning Enhances Students’ Openness to Diversity

ABSTRACTWe investigated the influence of collaborative learning on students’ openness to diversity in the 1st year of college. Even in the presence of a host of potential confounders, we found that...
Exploring flexible communications for streamlining DNN ensemble training pipelines

Parallel training of a Deep Neural Network (DNN) ensemble on a cluster of nodes is a common practice to train multiple models in order to construct a model with a higher prediction accuracy, or to quickly tune the parameters of a training model. Existing ensemble training pipelines perform a great deal of redundant operations, resulting in unnecessary CPU usage, or even poor pipeline performance. In order to remove these redundancies, we need pipelines with more communication flexibility than existing DNN frameworks can provide. This project investigates a series of designs to improve pipeline flexibility and adaptivity, while also increasing performance. We implement our designs using Tensorflow with Horovod, and test it using several large DNNs in a large scale GPU cluster, the Titan supercomputer at Oak Ridge National Lab. Our results show that with the new flexible communication schemes, the CPU time spent during training is reduced by 2-11X. Furthermore, our implementation can achieve up to 10X speedups when CPU core limits are imposed. Our best pipeline also reduces the average power draw of the ensemble training process by 5--16% when compared to the baseline.
Automatically eliminating errors induced by suboptimal parameter choices in transcript assembly

The computational tools used for genomic analyses are becoming increasingly sophisticated and complex. While these applications provide more accurate results, a new problem is emerging in that these pieces of software have a large number of tunable parameters. The default parameter choices are designed to work well on average across all inputs, but the most interesting experiments are often not "average". Choosing the wrong parameter values for an application can lead to significant results being overlooked, or false results being reported. This problem is exacerbated when these applications are chained together in analysis pipelines where each step introduces errors due to parameter choices. We take some first steps towards generating a truly automated genomic analysis pipeline by developing a method for automatically choosing input-specific parameter values for reference-based transcript assembly. We apply the parameter advising framework, first developed for multiple sequence alignment, to optimize parameter choices for the Scallop transcript assembler. In doing so, we provide the first method for finding advisor sets for applications with large numbers of tunable parameters. This procedure can be parallelized, meaning it does not add any additional wall time. By choosing parameter values for each input, the area under the curve is increased by 28.9% over using only the default parameter choices on 1595 RNA-seq samples in the Sequence Read Archive. This approach is general, and when applied to StringTie it increases AUC by 13.1% on a set of 65 RNA-seq experiments from ENCODE.
PULS: Processor-Supported Ultra-Low Latency Scheduling

An increasing number of applications that will be supported by next generation wireless networks require packets to arrive before a certain deadline for the system to have the desired performance. While many time-sensitive scheduling protocols have been proposed, few have been experimentally evaluated to establish realistic performance. Furthermore, some of these protocols involve high complexity algorithms that need to be performed on a per-packet basis. Experimental evaluation of these protocols requires a flexible platform that is readily capable of implementing and experimenting with these protocols. We present PULS, a processor-supported ultra low latency scheduling implementation for testing of downlink scheduling protocols with ultra-low latency requirements. Based on our decoupling architecture, programmability of delay sensitive scheduling protocols is done on a host machine, with low latency mechanisms being deployed on hardware. This enables flexible scheduling policies on software and high hardware function re-usability, while meeting the timing requirements of a MAC. We performed extensive tests on the platform to verify the latencies experienced for per packet scheduling, and present results that show packets can be scheduled and transmitted under 1 ms in PULS. Using PULS, we implemented four different scheduling policies and provide detailed performance comparisons under various traffic loads and real-time requirements. We show that in certain scenarios, the optimal policy can maintain a loss ratio of less than 1% for packets with deadlines, while other protocols experience loss ratios of up to 65%.
Sediment Storage Partitioning in Alluvial Stratigraphy: The Influence of Discharge Variability

Abstract Numerical models of formation of alluvial stratigraphy often specify, either explicitly or implicitly, the proportion of channel and overbank sediments that are deposited during a given interval of time. However, little is known about the factors that affect the partitioning of sediment between channels and the overbank environment over long time intervals, and the fidelity with which that partition is preserved in the stratigraphic record. Here we use physical experiments to investigate the role that discharge variability plays in this partitioning in fluvial stratigraphy. We find that channels formed under constant flow conditions have low lateral mobility and act mostly as conduits for sediments to reach the shoreline. The bulk of the aggradation in this case is derived from sediment-laden flow that escapes the main channels. By contrast, including floods increases channel lateral mobility, and this change is recorded in stratigraphy as an increased proportion of channel deposits relative to overbank deposits. When variable flow is included as an input condition a large volume of in-channel deposition occurs, rendering the channels substantial contributors to stratigraphic volume on their own. The increase in channel deposit volume is driven mainly by a threefold increase in the average time that a location is subject to in-channel aggradation. Other factors include a slight increase of in-channel aggradation rates, and an increase in erosion of the overbank environment that results from energetic overbank flows. Our study shows that the character of a river's hydrograph exerts a significant influence on the proportion of channel to overbank sediment bodies in alluvial successions, which is an unexamined source of uncertainty in common stratigraphic models.
Nonlinear Oscillations of a Buckled Mechanism used as a Vibration Isolator

Various devices have been used to reduce the dynamic response of mechanical and structural systems connected to moving sources. A vibration isolator can be inserted between a system and source to absorb energy and reduce the system’s motion. The application of a buckled mechanism as a vibration isolator is investigated here. Harmonic motion is applied to the base, and the response of the supported weight is examined. Both parametric and external (forcing) excitations are present. Small applied motions and responses are considered first, and the steady-state harmonic motion of the weight is plotted as a function of the applied frequency. Then large responses are investigated. The buckled mechanism may snap from one side to the other. After some initial transient response, period-one, period-two, period-four, and chaotic responses are observed for various applied frequencies and given values of the applied amplitude, supported weight, damping coefficient, and stiffness parameter.
From Filters to Forests: Water Treatment and Supply

Physical, chemical and biological processes in the atmospheric, terrestrial, and aquatic environments establish the major characteristics of water supplies and affect the concentrations of pollutants in these supplies. The design and operation of water treatment facilities should reflect characteristics of the water source. Important natural processes and water quality characteristics are identified and their effects on water treatment systems are indicated. Forests affect filters.
Perioperative Management of Anticoagulation in the Patient with the Antiphospholipid Syndrome in Cardiac Surgery and Cardiac Interventions

The antiphospholipid syndrome (APS) is considered the most common acquired hypercoagulable disorder associated with thrombosis. It is an antibody-mediated prothrombotic state characterized by venous and/or arterial thrombosis or obstetrical morbidity in conjunction with laboratory identification of antiphospholipid antibodies (aPL). These antibodies, recently referred to as the “antiphospholipid triangle,” include anticardiolipin antibodies (aCL), anti-β2-glycoprotein I antibodies (aβ2GPI), and the lupus anticoagulant (LA) [1]. Antiphospholipid antibodies identified in otherwise healthy individuals after a venous or arterial thrombotic or obstetrical event is referred to as primary APS. Secondary APS is the term used when APS coexists with an underlying systemic autoimmune disease such as systemic lupus erythematosus (SLE). Antibodies also occur in asymptomatic individuals with no history of thrombosis. They can also be detected in persons on medications particularly important to the cardiac patient including procainamide, hydralazine, quinidine, and the angiotensin-converting enzyme (ACE) inhibitors [2].
Thresholds for shock formation in traffic flow models with nonlocal-concave-convex flux

Abstract We identify sub-thresholds for finite time shock formation in a class of non-local conservation law with concavity changing flux. From a class of non-local conservation laws, the Riccati-type ODE system that governs a solution's gradient is obtained. The changes in concavity of the flux function correspond to the sign changes in the leading coefficient functions of the ODE system. We identify the blow up condition of this structurally generalized Riccati-type ODE. The method is illustrated via the traffic flow models with nonlocal-concave-convex flux. The techniques and ideas developed in this paper is applicable to a large class of non-local conservation laws.
Soy protein supplementation is not androgenic or estrogenic in college-aged men when combined with resistance exercise training

It is currently unclear as to whether sex hormones are significantly affected by soy or whey protein consumption. Additionally, estrogenic signaling may be potentiated via soy protein supplementation due to the presence of phytoestrogenic isoflavones. Limited evidence suggests that whey protein supplementation may increase androgenic signalling. Therefore, the purpose of this study was to examine the effects of soy protein concentrate (SPC), whey protein concentrate (WPC), or placebo (PLA) supplementation on serum sex hormones, androgen signaling markers in muscle tissue, and estrogen signaling markers in subcutaneous (SQ) adipose tissue of previously untrained, college-aged men (n = 47, 20 ± 1 yrs) that resistance trained for 12 weeks. Fasting serum total testosterone increased pre- to post-training, but more so in subjects consuming WPC (p < 0.05), whereas serum 17β-estradiol remained unaltered. SQ estrogen receptor alpha (ERα) protein expression and hormone-sensitive lipase mRNA increased with training regardless of supplementation. Muscle androgen receptor (AR) mRNA increased while ornithine decarboxylase mRNA (a gene target indicative of androgen signaling) decreased with training regardless of supplementation (p < 0.05). No significant interactions of supplement and time were observed for adipose tissue ERα/β protein levels, muscle tissue AR protein levels, or mRNAs in either tissue indicative of altered estrogenic or androgenic activity. Interestingly, WPC had the largest effect on increasing type II muscle fiber cross sectional area values (Cohen’s d = 1.30), whereas SPC had the largest effect on increasing this metric in type I fibers (Cohen’s d = 0.84). These data suggest that, while isoflavones were detected in SPC, chronic WPC or SPC supplementation did not appreciably affect biomarkers related to muscle androgenic signaling or SQ estrogenic signaling. The noted fiber type-specific responses to WPC and SPC supplementation warrant future research.
Quality Assurance in Telehealth: Adherence to Evidence-Based Indicators

Abstract Background: Value enhancing telehealth (TH) lacks a robust body of formal clinically focused quality assessment studies. Innovations such as telehealth must always demonstrate that it pres...
Developing inclusive leaders with religious literacy in the workplace

There have been several incidents in the United States that point to significant problems with religious intolerance. Public debates and confrontations can have rippling effects beyond the politica...
Grown woman: Understanding what influences health behaviors in black female students at a HBCU

Objective: The purpose of this study was to understand what influences health behaviors in Black female students at a Historically Black College and University (HBCU).Participants and Methods: Twen...
Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO2 Capture by a Surface-Exposed [Fe4S4] Cluster.

Nitrogenase iron (Fe) proteins reduce CO2 to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-A crystal structure of the Fe protein from Methanosarcina acetivorans (MaNifH), which is generated in the presence of a reductant, dithionite, and an alternative CO2 source, bicarbonate. Structural analysis of this methanogen Fe protein species suggests that CO2 is possibly captured in an unactivated, linear conformation near the [Fe4S4] cluster of MaNifH by a conserved arginine (Arg) pair in a concerted and, possibly, asymmetric manner. Density functional theory calculations and mutational analyses provide further support for the capture of CO2 on MaNifH while suggesting a possible role of Arg in the initial coordination of CO2 via hydrogen bonding and electrostatic interactions. These results provide a useful framework for further mechanistic investigations of CO2 activation by a surface-exposed [Fe4S4] cluster, which may facilitate future development of FeS catalysts for ambient conversion of CO2 into valuable chemical commodities.IMPORTANCE This work reports the crystal structure of a previously uncharacterized Fe protein from a methanogenic organism, which provides important insights into the structural properties of the less-characterized, yet highly interesting archaeal nitrogenase enzymes. Moreover, the structure-derived implications for CO2 capture by a surface-exposed [Fe4S4] cluster point to the possibility of developing novel strategies for CO2 sequestration while providing the initial insights into the unique mechanism of FeS-based CO2 activation.
Adverse Metabolic Outcomes in Soil Pseudomonas Species Exposed to Polyethoxylated Tallow Amine and Glyphosate

Polyethoxylated tallow amine (POEA) is a common surfactant used in glyphosate-based herbicide formulations to enhance the bioavailability of the active herbicide ingredient. Toxic effects of POEA e...
Application of genetically modified animals in bone research

Abstract Genetically modified mice have had an enormous impact on our understanding of skeletal development, maintenance, and disease. Publicly supported efforts to generate and phenotype genes in the mouse have greatly expanded the ease of identifying and characterizing genes that play a role in skeletal tissues. CRISPR/Cas9 technology has led to rapid and cost-effective generation of mice carrying specific mutations. Conditional approaches, which enable cell-specific or temporal control over gene ablation, are the most powerful and precise means of genetic analysis. However, these approaches rely on the use of tissue-selective promoters. Understanding the temporal and spatial dynamics of these extensively used promoters is therefore vital to interpreting phenotypes or lineage studies in mice. We discuss some general features of transgenic overexpression and loss-of-function approaches, large-scale mutagenesis efforts and resources, and some of the most commonly used tissue-selective promoters and transgenic strains for tissue-specific gene analysis in skeletal cells.
Robotic assisted transaxillary thymectomy: Novel approach to thymic surgery.

BACKGROUND We present a video case with a novel, minimally invasive approach to the thymus, which does not require a sternotomy, thoracic incision, or entry into the pleural space. METHODS A 14-year-old girl was referred to our clinic with dysphagia and left sided thymic mass. A detailed video shows the operative techniques used to perform a thymectomy with robotic assistance via a transaxillary approach. RESULTS The procedure was tolerated well and without complication. The patient was discharged the day after surgery and was symptom free at her 2-week follow-up appointment. CONCLUSION We present a novel approach to thymic surgery that does not require a neck incision, sternotomy, or entry into the pleural space. There could be several benefits from this minimally invasive approach; however, concerns related to exposure and adequacy of resection need further research prior to recommending this technique for myasthenia or malignancy.
Morals from rationality alone? Some doubts:

Contractarians aim to derive moral principles from the dictates of instrumental rationality alone. It is well-known that contractarian moral theories struggle to identify normative principles that ...
Neutronic impact of Autonomous Reactivity Control system inclusion in a breed-and-burn core

Abstract This study examines the impacts induced in a large breed-and-burn core through the inclusion of Autonomous Reactivity Control (ARC) systems from the neutronics perspective. A combination of numerical and analytical techniques are used to conservatively quantify the reactivity penalty, amount of additional tritium production, and depletion of the system absorber fluid. The reactivity penalty is found to be negligibly small, with the largest impact resulting from the removal of fuel material to make room for the ARC system tubes. Similarly, the depletion of the absorber fluid is found to be negligible compared to the amount of fluid present. It is found that the production of tritium within the active core is also small in comparison to that which is nominally produced, while tritium production within the lower ARC system reservoir may be of concern if not adequately considered during the assembly design phase. This issue is explored and a mitigation technique is proposed. Ultimately this study concludes that there are no issues from the steady-state neutronics perspective preventing incorporation of ARC systems into typical breed-and-burn cores.