cssi/SciSciGPT-SciSciNet huggingface dataset:
A comparison of student performance on discipline-specific versus integrated exams in a medical school course

Curricular reform is a widespread trend among medical schools. Assessing the impact that pedagogical changes have on students is a vital step in review process. This study examined how a shift from discipline-focused instruction and assessment to integrated instruction and assessment affected student performance in a second-year medical school pathology course. We investigated this by comparing pathology exam scores between students exposed to traditional discipline-specific instruction and exams (DSE) versus integrated instruction and exams (IE). Exam content was controlled, and individual questions were evaluated using a modified version of Bloom's taxonomy. Additionally, we compared United States Medical Licensing Examination (USMLE) step 1 scores between DSE and IE groups. Our findings indicate that DSE students performed better than IE students on complete pathology exams. However, when exam content was controlled, exam scores were equivalent between groups. We also discovered that the integrated exams were composed of a significantly greater proportion of questions classified on the higher levels of Bloom's taxonomy and that IE students performed better on these questions overall. USMLE step 1 exam scores were similar between groups. The finding of a significant difference in content complexity between discipline-specific and integrated exams adds to recent literature indicating that there are a number of potential biases related to curricular comparison studies that must be considered. Future investigation involving larger sample sizes and multiple disciplines should be performed to explore this matter further.
The diagnosis of UTI: liquid gold and the problem of gold standards.

Why is urine yellow? Because it is liquid gold! Pediatric nephrologist William Primack* For >50 years, the gold standard for the diagnosis of urinary tract infections (UTIs) has been a positive culture result without regard for urinalysis findings. Both the definition of “positive” and the role of urinalysis stem from a publication in 1956.1 Edward Kass applied quantitative culture methods to urine specimens obtained from adults by catheterization to determine a dividing line between contamination and infection. The urine of most, but not all, patients with symptoms of acute pyelonephritis (chills, fever, flank pain, and dysuria) contained >100 000 CFU/mL. Urine specimens from some asymptomatic women also had such high colony counts but most were much lower. Kass concluded: “For survey purposes, a count of 105 bacteria or more per mL of urine has been designated arbitrarily as the dividing line between true bacilluria and contamination.” He acknowledged that for “individual clinical purposes,” lower colony counts needed to be considered and noted that pyuria did not reliably accompany bacteriuria in the asymptomatic women. During the subsequent decade, screening programs were widely conducted, applying ≥10 … Address correspondence to Kenneth B. Roberts, MD, 3005 Bramblewood Dr, Mebane, NC 27302. E-mail: kenrobertsmd{at}gmail.com
Selected papers from the 7th International Conference on Microtechnologies in Medicine and Biology (MMB 2013)

In this special section of Journal of Micromechanics and Microengineering are a collection of the best microengineering papers presented at the 7th International Conference on Microtechnologies in Medicine and Biology (MMB 2013) which took place in the seaside town of Marina del Rey, California, USA on 10?12 April, 2013. During the 3-day conference, participants enjoyed talks from 6 invited keynote speakers and 125 flash oral/poster presentations. The MMB conference is a biennial meeting with the primary purpose of fostering interactions between biologists and medical researchers, clinicians, chemists, physicists and engineers to enhance and strengthen the potential microtechnologies that will revolutionize the fields of medicine and biological sciences. The conference possesses a unique format where all poster presenters provide a brief 60?s oral presentation highlighting their research. This format was devised to provide training and exposure for young researchers, especially PhD students and postdocs, in the field and stimulate interdisciplinary exchanges. Therefore, MMB provides an intimate intellectual venue the facilitate discussions and collaborations to advance new research tools and technologies for medicine and biological sciences. The MMB conference series was co-founded by Professor David Beebe (University of Wisconsin?Madison) and Professor Andr? Dittmar (University of Lyon) and was the first international meeting to provide a forum focusing on emerging applications of microtechnologies to unmet needs in medicine and biology. The series was held for the first time in 2000, in Lyon, France and followed by Madison, USA (2002), Oahu Island in Hawaii, USA (2005), Okinawa, Japan (2006), Qu?bec City, Canada (2009), Lucerne, Switzerland (2011), and Marina del Rey, USA (2013). The next conference will be held in Seoul, Korea in 2015. This collection of articles highlights recent progress in microtechnologies with medical and biological applications. We are grateful to the many authors who contributed their research achievements to this exciting issue and to the anonymous reviewers for their invaluable insights and suggestions. We would also like to express our thanks to our colleagues on the international steering committee for their dedicated review of the selected presentations that appears at the conference. Finally, we appreciate the support of the editorial staff of Journal of Micromechanics and Microengineering for this inaugural MMB special issue. We look forward to continued collaboration in future MMB conferences.
A filtering approach to the two-dimensional volume conductor forward and inverse problems

Summary form only given. The volume conductor inverse problem is the problem of reconstructing a two-dimensional distributed voltage source from measurements of the electric field it produces at the surface of an intervening medium. The intervening medium may be homogeneous or horizontally layered, with differing conductivities in each layer. The problem is assumed to be quasistatic (a 'snapshot' in time); this is reasonable for the impedances encountered in biological tissues. The distributed source potential and the surface data are regarded as two-dimensional signals, and they are shown to be related by a linear two-dimensional filter. Implementation of the medium filter requires signal processing filtering techniques. This inverse problem is ill-conditioned for high-frequency signals and for large distances between source and measurements. The use of data-conditioning filters regularizes the inverse problem, with only minor effect on the reconstructed potential distribution. For typical signals under realistic signal-to-noise ratios, excellent numerical results have been obtained. In particular, a numerically stable recursive algorithm for computing the coefficients of the two-dimensional medium filter has been developed. >
Macrodynamics of Black Political Participation in the Post-Civil Rights Era

Research on black political life has demonstrated both the positive effects of black political empowerment and the negative effects of economic and social distress on black political participation. Using black respondents from the Roper Social and Political Trends data set, we estimate the effects of political, social, and economic factors on aggregate-levels of black civic activity in the time period from 1973 to 1994. We hypothesize that black political activity is stimulated by factors that enhance the political empowerment of black communities and is depressed by downward turns in the social and economic fortunes of black communities. We find that the positive influence of black political empowerment on macrolevels of black civic activity is countered by economic and social factors that swamp the benefits gained from black political success.
Climate and Culture: Anthropology in the Era of Contemporary Climate Change

This review provides an overview of foundational climate and culture studies in anthropology; it then tracks developments in this area to date to include anthropological engagements with contemporary global climate change. Although early climate and culture studies were mainly founded in archaeology and environmental anthropology, with the advent of climate change, anthropology's roles have expanded to engage local to global contexts. Considering both the unprecedented urgency and the new level of reflexivity that climate change ushers in, anthropologists need to adopt cross-scale, multistakeholder, and interdisciplinary approaches in research and practice. I argue for one mode that anthropologists should pursue—the development of critical collaborative, multisited ethnography, which I term “climate ethnography.”
Improving Crossover of Neural Networks in Evolution Through Speciation

Crossover is an important genetic operator that re-combines beneficial genes together and rapidly traverses the fitness landscape. Unfortunately, neuro-evolution (NE) has not experienced the benefits of crossover. Indeed, observations have shown that crossover has been detrimental to NE approaches. Tangentially, speciation has become an important feature in NE for diversity maintenance; however, such speciation research has focused on what measure is driving speciation versus how the measure determines species. This research posits that appropriate speciation implementations enable effective crossover by determining an individual’s potential mating partners. Prior speciation research demonstrated the impact of restricting the mating pools of genomes on search performance. This paper investigates these concepts in the context of NE and results demonstrate; (1) the impact of speciation implementation in NE, (2) crossover’s negative effect on search in NE, and (3) a novel speciation approach that enables effective crossover in NE.
Arthur Smith Woodward's fossil fish type specimens

Four years after joining the NaturalHistory Department of the British Museumin 1882, Arthur Smith Woodward published his first taxonomic paper erecting three new species based on sharks' teeth. He retired from the Natural History Museum in 1924 but continued to publish until his death in 1944 at the age of 80. In total he named 321 new fossil fishes, a remarkable achieve- ment, marking him out as the most influential palaeoichthyologist of his time. For the first time brief details of all his type specimens are brought together, accompanied in many cases by high- quality photographic images, in an online format readily available to anyone with access to the Internet. Supplementary material: Details of all the Smith Woodward type specimens, including images, are available at http://www.geolsoc.org.uk/SUP18874
Monitoring Genetic and Metabolic Potential for in situ Bioremediation: Mass Spectrometry

A number of DOE sites are contaminated with dense non-aqueous phase liquids (DNAPLs) such as carbon tetrachloride and trichloroethylene. At many of these sites, microbial bioremediation is an attractive strategy for cleanup, since it has the potential to degrade DNAPLs in situ. A rapid screening method to determine the broad range potential of a site's microbial population for contaminant degradation would greatly facilitate assessment for in situ bioremediation, as well as for monitoring ongoing bioremediation treatment. Current laboratory-based treatability methods are cumbersome and expensive. In this project, we are developing methods based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for rapid and accurate detection of polymerase chain reaction (PCR) products from microbial genes involved in biodegradation of pollutants. PCR primers are being developed to amplify DNA sequences that are amenable to MALDI-MS detection. This work will lay the foundation for development of a field-portable MS-based technique for rapid on site assessment and monitoring of bioremediation processes.
Spoken Language Recognition Based on Senone Posteriors

This paper explores in depth a recently proposed approach to spoken language recognition based on the estimated posteriors for a set of senones representing the phonetic space of one or more languages. A neural network (NN) is trained to estimate the posterior probabilities for the senones at a frame level. A feature vector is then derived for every sample using these posteriors. The effect of the language used in training the NN and the number of senones are studied. Speech-activity detection (SAD) and dimensionality reduction approaches are also explored and Gaussian and NN backends are compared. Results are presented on heavily degraded speech data. The proposed system is shown to give over 40% relative gain compared to a state-of-the-art language recognition system at sample durations from 3 to 120 seconds.
Scalable parallelization of the hybridized discontinuous Galerkin method for compressible flow

A distributed and parallel implementation of a hybridized discontinuous Galerkin (HDG) solver for the compressible Navier-Stokes equations is presented. This implementation exploits the characteristics of the HDG method. First, the global degrees of freedom are reduced to the numerical trace of the solution on the element boundaries. Second, the conserved quantities and their gradients on each element are obtained in terms of the numerical trace on the element boundary. For meshes composed by a large numer of elements, the cost of the solver is dominated by the first stage, since the second stage scales linearly with the number of elements and it can be parallelized. To accelerate the first stage, we use a distributed GMRES solver with restart pre-conditioned with an algebraic additive Schwarz domain decomposition with l-levels of overlap (ASDD(l)). Each sub-domain problem is approximated by an incomplete LU factorization with k-levels of fill-in (ILU(k)). From the considered tests cases, we conclude that ASDD(1)/ILU(0) presents good weak scaling characteristics for studying the periodic vortex shedding around an airfoil at low Reynolds and low Mach number.
Effects of a direct-fed microbial on digestive-tract morphology of Holstein bull calves and performance and carcass characteristics of Holstein steers1

Two experiments were conducted to evaluate the effects of live cultures of Lactobacillus acidophilus and Propionibacterium freudenreichii on digestivetract morphology of neonatal–transition Holstein bull calves and performance and carcass characteristics of calf-fed Holstein steers. In Exp. 1, forty-three 1-d-old Holstein bull calves (42 kg of BW) were supplemented with a direct-fed microbial (DFM) consisting of L. acidophilus and P. freudenreichii. Treatments consisted of a control (n = 21) and a treatment (n = 22) of direct-fed microbial (5 × 108 cfu) supplemented daily in a commercial milk replacer. At the conclusion of the milk-feeding stage (weaning), 11 calves from each treatment group were slaughtered at the University of Arizona Meats Laboratory for gastrointestinal-tract collection. The remaining calves were abruptly weaned and moved to concrete-floor pens for 14 d before slaughter (DFM treatments were mixed in the diet). Samples of the rumen and ileum were collected at the time of slaughter and examined for gastrointestinal-tract morphology. Before weaning, average ileal height, crypt depth, and total height (villus + crypt) were greater in DFM treatment (P 0.10) were noted in daily intake or G:F between treatments during the finishing period. Overall, steers fed 1 × 105 L. acidophilus had no difference in final BW and ADG versus steers fed the control diet.
Basal forebrain cholinergic modulation of sleep transitions.

Objectives The basal forebrain cholinergic system is involved in cognitive processes that require an attentive state, an increased level of arousal, and/ or cortical activation associated with low amplitude fast EEG activity. The activity of most neurons in the basal forebrain cholinergic space is tightly correlated with the cortical EEG and the activity state. While most cholinergic neurons fire maximally during waking and REM sleep, the activity of other types of basal forebrain neurons vastly differs across different arousal and sleep states. Numerous studies have suggested a role for the basal forebrain cholinergic neurons in eliciting cortical activation and arousal. However, the intricate local connectivity within the region requires the use of cell-specific manipulation methods to demonstrate such a causal relationship. Design and measurements Here we have combined optogenetics with surface EEG recordings in freely moving mice in order to investigate the effects of acute cholinergic activation on the dynamics of sleep-to-wake transitions. We recorded from naturally sleeping animals and analyzed transitions from NREM sleep to REM sleep and/ or wakefulness in response to photo-stimulation of cholinergic neurons in substantia innominata. Results and conclusions Our results show that optogenetic activation of BF cholinergic neurons during NREM sleep is sufficient to elicit cortical activation and facilitate state transitions, particularly transitions to wakefulness and arousal, at a time scale similar to the activation induced by other subcortical systems. Our results provide in vivo cell-specific demonstration for the role of basal forebrain cholinergic system in induction of wakefulness and arousal.
Drinking Your Own Kool-Aid: Self-Deception, Deception Cues, and Persuasion in Meetings

Two experiments show that face-to-face meetings help users discern reporters' true beliefs better than those who receive only a written report. Both experiments are based on a 'cheap talk' setting, modified to include two features common to accounting settings: reporters base reports on rich information, and (in a meeting condition) have rich channels of communication to users. Experiment 1 shows that meetings improve users' ability to discern the beliefs reporters held before they had an incentive to deceive the user. Once reporters learned of their incentive to deceive users, they revised their beliefs toward what they wanted users to believe (they self-deceived); those who revised more were more successful in their deception. Experiment 2 shows that users discerned reporters' beliefs through linguistic tone: reporters who believed their reports used more positive words. The results highlight the importance of face-to-face meetings and provide experimental support for Trivers' self-deception theory.
Mindfulness Practice and Its Relationship to the Five-Facet Mindfulness Questionnaire

Central to Mindfulness-Based Intervention (MBI) protocols are formal and informal mindfulness practice, both within and between weekly sessions. It is presumed that mindfulness practices foster increases in mindfulness, which in turn affect treatment outcomes. The current study assessed whether frequency and duration of between-session mindfulness practice predicted mindfulness as measured by the Five Facet Mindfulness Questionnaire (FFMQ) in a clinical sample of adults following Mindfulness-Based Relapse Prevention (N = 103). In the original trial, significantly greater changes in primary substance abuse outcomes were observed in the MBRP group. In the current study, it was hypothesized that type (formal versus informal), frequency (days/week), and duration (minutes) of practice would predict post-course FFMQ scores. However, no significant relationships were found between practice and either the total or subscale FFMQ scores. Results from the current study suggest that either mindfulness is not affected by mindfulness practices or that the FFMQ may need adaptation for specific clinical samples. Results suggest more objective indices of meditation practice, such as frequency and duration of practice, may be indicated in assessing how mindfulness practice relates to changes in mindfulness and to clinical outcomes, particularly in samples in which mindfulness measures have not been validated. Further investigation is needed to determine best methods of assessment to identify mechanisms of MBIs in different clinical populations.
Changing Patterns of Reye’s Syndrome

Trends in the clinical pattern of Reye’s syndrome in the British Isles between 1982 and 1990, and their relation to the June 1986 warnings against the use of aspirin in children, were analysed at the PHLS Communicable Disease Surveillance Centre, London, and other Centres in the UK.
Strong-coupling Bose polarons in a Bose-Einstein condensate

We use a nonperturbative renormalization group approach to develop a unified picture of the Bose polaron problem, where a mobile impurity is strongly interacting with a surrounding Bose-Einstein condensate (BEC). A detailed theoretical analysis of the phase diagram is presented and the polaron-to-molecule transition is discussed. For attractive polarons we argue that a description in terms of an effective Fr\"ohlich Hamiltonian with renormalized parameters is possible. Its strong-coupling regime is realized close to a Feshbach resonance, where we predict a sharp increase of the effective mass. Already for weaker interactions, before the polaron mass diverges, we predict a transition to a regime where states exist below the polaron energy and the attractive polaron is no longer the ground state. On the repulsive side of the Feshbach resonance we recover the repulsive polaron, which has a finite lifetime because it can decay into low-lying molecular states. We show for the entire range of couplings that the polaron energy has logarithmic corrections in comparison with predictions by the mean-field approach. We demonstrate that they are a consequence of the polaronic mass renormalization which is due to quantum fluctuations of correlated phonons in the polaron cloud.
Electrowetting-based microfluidic operations on rapid-manufactured devices for heat pipe applications

The heat transport capacity of traditional heat pipes is limited by the capillary pressure generated in the internal wick that pumps condensate to the evaporator. Recently, the authors conceptualized a novel heat pipe architecture, wherein wick-based pumping is replaced by electrowetting (EW)-based pumping of microliter droplets in the adiabatic section. An electrowetting heat pipe (EHP) can overcome the capillary limit to heat transport capacity and enable compact, planar, gravity-insensitive, and ultralow power consumption heat pipes that transport kiloWatt heat loads over extended distances. This work develops a novel technique for rapid, scalable fabrication of EW-based devices and studies critical microfluidic operations underlying the EHP, with the objective of predicting the key performance parameters of the EHP. Devices are fabricated on a printed circuit board (PCB) substrate with mechanically-milled electrodes, and a removable polyimide dielectric film. The first set of experiments uncovers the maximum channel gap (1 mm) for reliable EW-based pumping; this parameter determines the heat transport capacity of the EHP, which scales linearly with the channel gap. The second set of experiments uncovers the maximum channel gap (375 microns) at which EW voltages can successfully split droplets. This is an important consideration which ensures EHP operability in the event of unintentional droplet merging. The third set of experiments demonstrate and study EW-induced droplet generation from an open-to-air reservoir, which mimics the interface between the condenser and adiabatic sections of the EHP. The experimental findings predict that planar, water-based EHPs with a (10 cm by 4 mm) cross section can transport 1.6 kW over extended distances (>1 m), with a thermal resistance of 0.01 K W−1.
Comparing Diagnostic Performance of Digital Breast Tomosynthesis and Full-Field Digital Mammography in a Hybrid Screening Environment

OBJECTIVE. The purpose of this study is to compare the diagnostic performance of screening digital breast tomosynthesis (DBT) to that of full-field digital mammography (FFDM) in a mixed DBT and FFDM imaging environment. MATERIALS AND METHODS. This retrospective observational study consisted of all female patients undergoing screening DBT or FFDM at an academic medical center and outpatient imaging facility between October 2012 and May 2015. Patient demographics and personal history of breast cancer were collected from the electronic medical record. A natural language processing algorithm extracted patients' breast density, current or prior imaging findings, and BI-RADS category from their most recent prior imaging examinations. To control for differential selection of FFDM versus DBT, we applied propensity score matching based on patient age, imaging site, and prior imaging findings. An institutional breast cancer registry identified cancer diagnoses. Primary outcomes of recall rate, cancer detection rate...
Reactive sputter deposition and annealing of nanometer scale NiO thin films for metal-insulator-metal tunnel junction diodes

Abstract The increased switching speed of metal-insulator-metal (MIM) tunnel diodes over existing diodes has the potential to open new applications including infrared energy harvesting and high frequency detectors. The work here analyzes the effect of the insulator layer (NiOx) properties on performance of such Ni-NiOx-Cr based junctions. This work focuses on these films because they are critical for device performance. Thickness must be measured and controlled in the nanometer range for the requisite junction tunneling to take place. At the same time the other fabrication challenges, while significant, have practically been met. The films were deposited by reactive magnetron sputtering of a Ni target in an atmosphere containing oxygen. Test films ranged from 10 to 30 nm in thicknesses and were smooth as determined by atomic force microscopy. Initial ellipsometry examination showed that the as-deposited films were inhomogeneous in the growth direction and exhibited high optical absorption across the visible wavelength range (midrange k = 0.8 and up). While this is not unexpected considering what is known about nucleation and initial growth, it is undesirable for the intended use. Consequently treatment of the films was carried out by annealing in an oxygen atmosphere at 400 °C for 3, 6, and 12 min. This resulted in both a significant decrease in the optical absorption and a dramatic improvement in film homogeneity. Examination using Secondary Ion Mass Spectroscopy did not show significant increases in film oxygen suggesting that atomic rearrangement rather than oxidation occurred during annealing. To confirm test structure fabrication, performance of MIM junctions with the annealed films was investigated using current-voltage measurements. The results were correlated with capacitance-voltage measurements.
RESOLVING THE EUROGANG PARADOX

The goal of this volume is to share knowledge and ideas about street gangs, a matter that has long been an American staple and is now beginning to take on a European flavor. We are facing what I have come to call The Eurogang Paradox. The paradox has to do with denials that there are street gangs in Europe, because the gangs patterns don’t fit the American pattern of highly structured, cohesive, violent gangs. But then neither do most American gangs fit the pattern.
Franklian Existential Epistemology

Frankl’s existential psychology (logotherapy) generates a defensible epistemological framework for unusually personal research, including its most progressive manifestation, autoethnography. Major themes in this chapter include: each scholar’s uniqueness (based on disposition, situation, and position); valuing the particular and the general; validity; and perceptual metaphors for truth finding, including Frankl’s dimensional ontology. Border crossing, double consciousness, and intersectionality in inquiry practices are also explored from an existential framework. These concepts are explained and interpreted using examples from Frankl’s publications and the Part I Case Studies. The chapter concludes with a bulleted review and a list of existential questions for readers.
Prefigured Ordering and Protoselection in the Origin of Life

We are all indebted to Professor Oparin for reopening the origin of life problem in a scientific context (1,2). His writings were the original inspiration of what has become an impressive body of experimental research, especially in the last two decades. The immense value of Oparin’s general conceptions on biogenesis is that they provide the overall theoretical framework in which specific experiments are conducted and interpreted. In recent years the view that life is an inevitable outcome of the properties of matter and energy, a view long held by Professor Oparin, has gained increasing support. The alternative view that life was the result of a lucky random combination of chemical substances was popular when the experimental data on origins were still scanty. However, this erroneous view has persisted in uninformed discussion of the subject in many biology textbooks and in the recent criticism of the chemical theory of origins by the new creationists (3). The new data, taken in toto, indicate that the origin was in some sense, which must be carefully spelled out, foreordained from the beginning (4).
Response of Nine Herbaceous Flowering Perennials to Selected Herbicides

Abstract Nine herbicides registered for use on turf and ornamentals were applied semiannually for 2 years to 9 species of field grown herbaceous flowering perennials. The herbicides used were Balan (benefin), Betasan (bensulide), Dacthal (DCPA), Devrinol (napropamide), Fusilade (fluazifop), Ornamental Herbicide 2 (oxyfluorfen + pendimethalin), Pennant (metolachlor), Poast (sethoxydim), and Ronstar (oxadiazon). The perennials included fernleaf yarrow, shasta daisy, coreopsis, dianthus, daylily, candytuft, red hot poker, statice, and phlox. Betasan produced no visual phytotoxicity. All other treatments, excluding Ornamental Herbicide 2 (OH-2), caused less than 20% injury to all species tested. OH-2 caused 40%, 39%, and 30% injury to daylily, yarrow, and red hot poker, respectively. Economically tolerable (less than 25%) injury was exhibited by phlox and shasta daisy treated with OH-2, by daylily treated with Pennant, and by phlox treated with Ronstar. OH-2 increased flowering of coreopsis and statice by 97%...
Fully Automated Convolutional Neural Network Method for Quantification of Breast MRI Fibroglandular Tissue and Background Parenchymal Enhancement

The aim of this study is to develop a fully automated convolutional neural network (CNN) method for quantification of breast MRI fibroglandular tissue (FGT) and background parenchymal enhancement (BPE). An institutional review board-approved retrospective study evaluated 1114 breast volumes in 137 patients using T1 precontrast, T1 postcontrast, and T1 subtraction images. First, using our previously published method of quantification, we manually segmented and calculated the amount of FGT and BPE to establish ground truth parameters. Then, a novel 3D CNN modified from the standard 2D U-Net architecture was developed and implemented for voxel-wise prediction whole breast and FGT margins. In the collapsing arm of the network, a series of 3D convolutional filters of size 3 × 3 × 3 are applied for standard CNN hierarchical feature extraction. To reduce feature map dimensionality, a 3 × 3 × 3 convolutional filter with stride 2 in all directions is applied; a total of 4 such operations are used. In the expanding arm of the network, a series of convolutional transpose filters of size 3 × 3 × 3 are used to up-sample each intermediate layer. To synthesize features at multiple resolutions, connections are introduced between the collapsing and expanding arms of the network. L2 regularization was implemented to prevent over-fitting. Cases were separated into training (80%) and test sets (20%). Fivefold cross-validation was performed. Software code was written in Python using the TensorFlow module on a Linux workstation with NVIDIA GTX Titan X GPU. In the test set, the fully automated CNN method for quantifying the amount of FGT yielded accuracy of 0.813 (cross-validation Dice score coefficient) and Pearson correlation of 0.975. For quantifying the amount of BPE, the CNN method yielded accuracy of 0.829 and Pearson correlation of 0.955. Our CNN network was able to quantify FGT and BPE within an average of 0.42 s per MRI case. A fully automated CNN method can be utilized to quantify MRI FGT and BPE. Larger dataset will likely improve our model.
Abstract 4817: EP-100 sensitizes BRCA wild-type ovarian cancer cells to PARP inhibitor

EP-100 is a synthetic lytic peptide specific for targeting LHRH receptors on cancer cells that is being clinically tested for treatment of ovarian cancer. In this study, we aimed to identify combination approaches with EP-100 in ovarian cancer models. We carried out a series of in vitro (MTT assay, immunoblot analysis, Q-PCR, reverse phase protein array (RPPA), comet assay and immunofluorescence staining) and in vivo (orthotopic mouse model) experiments in ovarian cancer models to determine the biological effects of EP-100 alone and in combination with standard of care drugs. We first examined the cytotoxic effects of EP-100 alone on 8 ovarian cancer cell lines with variable expression level of LHRH receptors and the IC50 values ranged from 0.5 to 2.0 µM. We then tested the effect of combining EP-100 with standard drugs (e.g., cisplatin, paclitaxel, doxorubicin, topotecan, and olaparib) on ovarian cancer cells. Of those drugs, we found that combination of EP-100 and olaparib was highly synergistic in drug sensitive and multi-drug resistant ovarian cancer cell lines (HeyA8, HeyA8-MDR, A2780, and A2780CP20). The combination indices (CI) were Citation Format: Shaolin Ma, Sunila Pradeep, Sherry Wu, Mark Seungwook Kim, Wei Hu, Selanere Mangala, Robert L. Coleman, Anil K. Sood. EP-100 sensitizes BRCA wild-type ovarian cancer cells to PARP inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4817.
The Downside of High Status: Relating Status Level and Coworker Status to Stress in the Workplace

Informal status is an important aspect of organizational life. The many advantages of having higher status relative to one’s coworkers are well documented. This study extends research on status to hypothesize and show a downside of high status: stress. The study observed naturally occurring status hierarchies within a telecommunications organization in the Western U.S. and found that higher levels of status were positively related to higher levels of stress, after controlling for friendship levels, education, formal job level, tenure, job satisfaction, and perceptions of the organization’s culture. This effect was moderated by status distance, a dispersion measure drawn from the literature on relational demography, that shows how close in status a given individual is to the other individuals on his or her team. Specifically, high-status participants experienced more stress when on teams comprised of high-status others, as compared to low-status others. Implications for both practice and theory are discussed.
Bayesian-inferred Flexible Path Generation in Human-Robot Collaborative Networks

This paper presents a novel method for generating the trajectory of a robot assisting a human in servicing a set of tasks embedded in a convex 2-D domain. This method makes use of Bayesian inference to predict human intent in task selection. Rather than following optimal trajectory towards a single task, the robot computes a set of potentially optimal tasks each weighted by the human's posterior probability and superimposes them into a cost function that is designed to minimize the weighted Euclidean distance relative to set. The effect is a flexible path human-robot collaborative network that is shown in simulation to complete all tasks in a given domain in less time than existing methods for a certain class of highly impulsive humans, i.e., humans that tend to randomly switch tasks at times generated by a Poisson counting process. The algorithm is also illustrated through an experimental demonstration.
Temporal Thermal Covert Channels in Cloud FPGAs

With increasing interest in Cloud FPGAs, such as Amazon's EC2 F1 instances or Microsoft's Azure with Catapult servers, FPGAs in cloud computing infrastructures can become targets for information leakages via convert channel communication. Cloud FPGAs leverage temporal sharing of the FPGA resources between users. This paper shows that heat generated by one user can be observed by another user who later uses the same FPGA. The covert data transfer can be achieved through simple on-off keying (OOK) and use of multiple FPGA boards in parallel significantly improves data throughput. The new temporal thermal covert channel is demonstrated on Microsoft's Catapult servers with FPGAs running remotely in the Texas Advanced Computing Center (TACC). A number of defenses against the new temporal thermal covert channel are presented at the end of the paper.
Responding to God's Love

In lieu of an abstract, below is the essay's first paragraph. "In his complex, yet highly enlightening book Where the Hell is God? Richard Leonard writes: “We are invited to respond to God’s love, not forced or programmed by it” (25). Upon creating us, God gave each person the power of free will. However, because God granted us this ability, we sometimes give in to sin and temptation. My thesis is: With God’s gift of free will comes the biggest choice we as followers have, and that is to either love God or to turn away from him and sin." Cover Page Footnote Selected for the Essays on Religion prize. This essay on religion is available in Verbum: http://fisherpub.sjfc.edu/verbum/vol12/iss2/10
Robust online image processing for high-throughput super-resolution localization microscopy

Super-resolution localization microscopy is a powerful tool to visualize molecular structures at a nanoscale resolution. High-density emitter localization combined with a large field of view and fast imaging frame rate is an effective strategy to achieve a high throughput. But the complex algorithms used to precisely localize the overlapping molecules in dense emitter scenarios limits their usage to mostly small image size. Here we present a computationally simple non-iterative method for high-density emitter localization to enable online image processing that remains robust even for low signals and heterogeneous background. Through numerical simulation and biological experiments, we demonstrate that our approach improves the computation speed by two orders of magnitude on CPU and three orders of magnitude upon GPU acceleration to realize online image processing, without compromising localization accuracy for various image characteristics.
Modeling and state estimation of a Micro Ball-balancing Robot using a high yaw-rate dynamic model and an Extended Kalman Filter

The state estimation and control of a ball-balancing robot under high yaw rate is a challenging problem due to its highly nonlinear 3D dynamic. The small size and low-cost components in our Micro Ball-Balancing Robot makes the system inherently very noisy which further increases the complexity of the problem. In order to drive the robot more aggressively such as translating and spinning at the same time, a good state estimator which works well under high yaw rates is required. This paper presents the derivation of a high yaw-rate Ball-Balancing Robot dynamic model and the implementation of said model in an Extended Kalman Filter (EKF) using raw on-board sensor measurements. The EKF using the new model is then compared to a Kalman Filter which uses a linearized dynamic model. The accuracy of the attitude estimates and the controller performance under high yaw rates were verified using a motion capture system.
Can War Foster Institutional Change

Exposure to violent conflict increases prosocial behavior, which is a form of social capital or informal institutions. This article studies whether these changes to informal institutions map into change to formal institutions, and if this mapping is characterized by substitutability or complementarity between institutions. To test this hypothesis, we use the synthetic control method to construct a counterfactual path of formal institutions in Sierra Leone and Burundi during and after violent conflict. Results indicate that violence and the corresponding change to informal institutions leads to a persistent decline in the quality of the formal legal system and protections of private property. We interpret this as evidence of substitutability between informal and formal institutions.
Abstract B125: Targeting translation for the treatment of pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is currently the third leading cause of cancer deaths in the United States and is projected to be in second place by 2030. A key cellular aberration is the activating KRAS mutation (>90%) which in turn leads to stabilizing the MYC oncoprotein and stimulating the growth of PDAC tumors. Dense stroma with elevated levels of hyaluronic acid is another characteristic of PDAC tumors contributing to poor therapeutic response. We describe a novel approach for the treatment of PDAC involving the targeting of thetranslation initiation factor 4A (eIF4A) with a new class of Pateamine A derivatives, DMDA PatA and MZ735.Our data show that nanomolar concentrations of these compounds inhibit cell proliferation and cause G0/G1 arrest in PDAC cell lines. We observed reduction of c-MYC, CyclinD1 and hyaluronic acid synthase HAS3 following treatment with eIF4A targeting compounds. RNA-seq analysis of Miapaca-2 cells treated with MZ735 using the Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER) algorithm revealed that loss of several MYC gene sets was among the most significantly altered compared to the control cells. We further performed proteomics to better define the consequences of MZ735-induced translation inhibition and observed that several key oncoproteins in PDAC were among the most depleted including MYC, CCND1, and EGFR. Finally, confocal imaging confirmed the reduction of hyaluronic acid in the eIF4A inhibitor-treated PDAC cells. We believe these small molecule compounds represent a new class of anticancer agents that have the potential to address both altered cellular and microenvironment components in PDAC. Citation Format: Maryam Safari, Yu Ri Kim, Prabhjot S. Mundi, Changchun Deng, Susan E. Bates. Targeting translation for the treatment of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B125. doi:10.1158/1535-7163.TARG-19-B125
Inhibition of 15-PGDH Protects Mice from Immune-mediated Bone Marrow Failure

Aplastic anemia (AA) is a human immune mediated bone-marrow failure syndrome that is treated by stem cell transplantation for patients who have a matched related donor or immunosuppressive therapy (IST) for those who do not. Responses to IST are variable, with patients still at risk for prolonged neutropenia, transfusion-dependence, immune suppression, and severe opportunistic infections. Therefore, additional therapies to accelerate hematologic recovery in patients receiving front line IST are needed. We have shown that inhibiting 15-hydroxyprostaglandin dehydrogenase (15-PGDH) with the small molecule SW033291 (PGDHi) increases bone marrow (BM) prostaglandin E2 levels, expands hematopoietic stem cell (HSC) numbers, and accelerates hematologic reconstitution following murine BM transplantation. We now report that in a murine model of immune-mediated BM failure, PGDHi therapy mitigated cytopenias, increased BM HSC and progenitor cells, and significantly extended survival compared to vehicle-treated mice. PGDHi protection was not immune-mediated, as serum IFNγ levels and BM CD8+ T lymphocyte frequencies were not impacted. Moreover, dual administration of PGDHi plus low dose IST enhanced total white blood cell, neutrophil and platelet recovery, achieving responses similar to maximal dose IST at lesser toxicity. Together these data demonstrate that PGDHi can complement IST to accelerate hematologic recovery and reduce morbidity in severe AA.
Chapter 18 – Picoscopic Modeling

Traffic flow modeling evolves over time from simple to complex. At one end, there are macroscopic models which represent traffic flow as a compressible fluid and the emphasis is to study its dynamic states such as flow, speed, and density. Mesoscopic models offer more modeling details by looking more closely at the traffic. At present, the finest modeling details are achieved by microscopic models, which treat driver-vehicle units as particles and keep track of their motion and interaction. The next logical step is picoscopic modeling, which incorporates models for the driver, vehicle, and driving environment. The driver model collects information from the environment as well as the feedback from the vehicle and makes control decisions; the vehicle model executes the control decisions and dynamically responds to the environment; the motion and interaction of all driver-vehicle units constitute the changing environment, which is the basis of driver control in the next step. Thus, the mechanism described above can be modeled as a driver-vehicle-environment closed-loop control system, which is the basic building block of picoscopic modeling.
Detection and analysis of MP-DNA in BALF of mycoplasma pneumoniae pneumonia in children

Objective To study the value of MP-DNA in the early diagnosis of pneumonia by analyzing the result of MP-DNA in bronchoalveolar lavage fluid(BALF) and MP-IgM antibodies in serum.Methods 103 hospitalized children were detected for MP-DNA in BALF(positive:DNA copies ＞ 102/ml) and MP-IgM antibodies in serum.Results The MP-DNA positive in BALF and the MP-IgM positive in serum in children with pneumoina were significantly higher than those in children with foreign body in bronchus (x2 =13.00,4.11,all P ＜ 0.05).33.01％ of 103 children was MP-DNA positive,19.43％ of 103 children was MP-IgM positive.The MP-DNA positive in BALF was significantly higher than the MP-IgM positive in serum(x2 =4.92,P ＜0.05).Conclusion The samples of MP-DNA in BALF were collected more difficulty than the samples of MP-IgM in serum,but the detection of MP-DNA can avoid the false negative,which may be of value in the diagnosis and therapy of MPP. Key words: Mycoplasma pneumoniae pneumonia; Bronchoalveolar lavage fluid
The Betalain Secondary Metabolic Network

Betalains are a class of red and yellow pigments that replace the anthocyanins in most of the core families of the Caryophyllales order. No species is known that produces both pigments. The betalains color flowers, fruits, and epidermal tissues and respond to the same signals that anthocyanin pigments do. Many minor but important crops produce betalains including beets, quinoa, amaranth, spinach, and Opuntia. The evolutionary origin of this pathway is largely a mystery whose secrets are slowly being revealed. Betalains are based on tyrosine, as opposed to the phenylalanine-based anthocyanins. In this pathway, tyrosine is converted to l-3,4-dihydroxyphenylalanine (l-DOPA) via an unknown enzyme. l-DOPA is converted to the yellow compound, betalamic acid. Another molecule of l-DOPA is converted to colorless cyclo-DOPA. Betalamic acid and cyclo-DOPA condense to form the red betacyanins. If cyclo-DOPA is unavailable, betalamic acid will condense with other amine groups to form the yellow betaxanthins. Here, we discuss: the genetics of betalains; what is known about the discovery and function of biosynthetic genes encoding, an l-DOPA dioxygenase, a cytochrome P450, and several UDP glucosyltransferases; available resources for betalain research; and finally, the holes in our knowledge that need to be filled in through future research.