cssi/SciSciGPT-SciSciNet huggingface dataset:
Fast motif discovery in short sequences

Motif discovery in sequence data is fundamental to many biological problems such as antibody biomarker identification. Recent advances in instrumental techniques make it possible to generate thousands of protein sequences at once, which raises a big data issue for the existing motif finding algorithms: They either work only in a small scale of several hundred sequences or have to trade accuracy for efficiency. In this work, we demonstrate that by intelligently clustering sequences, it is possible to significantly improve the scalability of all the existing motif finding algorithms without losing accuracy at all. An anchor based sequence clustering algorithm (ASC) is thus proposed to divide a sequence dataset into multiple smaller clusters so that sequences sharing the same motif will be located into the same cluster. Then an existing motif finding algorithm can be applied to each individual cluster to generate motifs. In the end, the results from multiple clusters are merged together as final output. Experimental results show that our approach is generic and orders of magnitude faster than traditional motif finding algorithms. It can discover motifs from protein sequences in the scale that no existing algorithm can handle. In particular, ASC reduces the running time of a very popular motif finding algorithm, MEME, from weeks to a few minutes with even better accuracy.
Booms, Busts and Urban Variation Among ‘Resource-based Cities’ in China’s Northwest

China’s northwest is commonly portrayed in monolithic terms as poorer and less urbanised than the rest of the country. While this characterisation is partially true, it overlooks considerable variation at the local level and the dramatic socio-spatial changes in recent years that have transformed the region. Resource-based cities are under-examined, yet they constitute an important aspect of regional development. This article details recent dynamics of growth and decline in northwestern resource-based cities. It finds that booms and busts in extraction-oriented cities currently define urban growth in the region and urges greater attention be paid to these cities’ transformations.
Do Birds Alter Levels of Parental Investment Based on Nest‐Site Habitat Features?

Many habitats have undergone rapid changes over the past century as a result of anthropogenic activities. Organisms can respond to changes in their environment in many ways, including how much they invest in a given reproductive bout. Optimality theory and life history theory together have provided a framework for understanding how individuals make decisions about the risks and rewards of investing high levels of resources into their offspring within the context of current vs. future reproduction. Shrubland birds in the United States often breed in habitat that has been impacted by humans to varying degrees and provide an ideal system for examining whether organisms alter their levels of parental investment based on the habitat around the nest site. In this study, we assessed levels of nest-defense behavior during a simulated nest predation event in four shrubland birds: American robins (Turdus migratorius), gray catbirds (Dumetella carolinensis), brown thrashers (Toxostoma rufum), and northern cardinals (Cardinalis cardinalis). We found that thrashers and catbirds exhibited significantly higher levels of nest defense compared to robins and cardinals and that birds with larger broods acted more aggressively in defending them. We also found that thrashers acted less aggressively as the proportion of shrubland around the nest increased and as the proportion of developed land around the nest decreased and that cardinals acted less aggressively as the proportion of developed land around the nest increased. These patterns suggest that nest-defense behavior can covary with features of the landscape surrounding the nest, but that the factors shaping that behavior can differ by species.
Fluid landscapes, sovereign nature: Conservation and counterinsurgency in Indian-controlled Kashmir

This article analyzes how environmentalism reinscribed violent forms of state sovereignty in the disputed region of Kashmir in the aftermath of a decade-long uprising against Indian rule. After the return of an elected government, six years after its suspension in 1990, environmental restoration legitimized new forms of state and nature making in Kashmir. Nature rather than territory emerged as an arena of citizen activism, which further strengthened the state's ability to regulate the use and management of Kashmir's water resources. State and civic bodies deployed discourses of history and restoration to create new and imagined ecologies based on visions of nostalgia, commerce, and esthetics. By undermining place-based understandings of nature and ecology, discourses of environmental stewardship and conservation ended up fostering violent mechanisms of social and political control.
Optimism, Pessimism, and Pragmatism: Musings on the Cost of Medical Innovation.

The medical press and lay press are filled with commentary about the cost of U.S. health care and the marginal “value” it brings to our population. The foundation of this concern is variably blamed on physicians’ practice patterns, delivery of non–evidence-based care, the cost of durable
Assessment of Impact and Recovery Needs in Communities Affected by the Elk River Chemical Spill, West Virginia, April 2014.

Objectives:In January 2014, 4-methylcyclohexanemethanol spilled into the Elk River near Charleston, West Virginia, contaminating the water supply for about 120 000 households. The West Virginia Ame...
Understanding the Relationship of Cigarette Smoking Trajectories Through Adolescence and Weight Status in Young Adulthood in the United States.

Abstract Purpose Adolescent cigarette smoking has steadily declined since 1999, whereas adolescent obesity rates have quadrupled since the 1980s. Few studies address the longitudinal relationship of smoking and weight in youth and young adulthood. This study examines the relationship of smoking trajectories beginning in adolescence on weight status in young adulthood in a nationally representative longitudinal sample. Methods The study sample was drawn from the National Longitudinal Study of Adolescent to Adult Health Waves I–IV (N = 13,361). Four trajectories were generated through repeated-measures latent class analyses using current cigarette smoking status in Waves I–IV and age of initiation: nonsmokers (44%), early establishers (23%), late establishers (21%), and former smokers (12%). Wave IV weight status included self-reported body mass index (BMI) and measured waist circumference. Bivariate analyses addressed associations between smoking trajectory and BMI at each wave. Multivariate linear regression models tested the relationship of smoking trajectory and weight status at Wave IV. Results In bivariate analyses, early and late establishers had a significantly lower BMI at Wave III and all smoking trajectories had a significantly lower BMI at Wave IV versus nonsmokers. All smoking trajectories had a significantly lower BMI than nonsmokers (early establishers: β = −1.27, confidence interval [CI]: −1.56 to −.98]; late establishers: β = −.84, CI: −1.16 to −.52; and former smokers: β = −.63, CI: −.93 to −.34; p Conclusions This study reveals that weight status increased over time for all trajectories; thus smoking does not mitigate obesity risk. These results have implications for both research and interventions to help youth and young adults avoid both smoking and obesity.
Coculture of Two Developmental Stages of a Marine-Derived Aspergillus alliaceus Results in the Production of the Cytotoxic Bianthrone Allianthrone A

The genetically encoded, small-molecule chemical diversity of filamentous fungi is still largely unexplored and represents an attractive source for the discovery of new compounds. Here we report the production of new chlorinated bianthrones from coculture of two different developmental stages, or morphs, of a marine alga-derived Aspergillus alliaceus (teleomorph: Petromyces alliaceus) strain. The vegetative stage (asexual morph) can be separated from the morph that switched to sexual development (sclerotial morph); both produce distinct secondary metabolite patterns. Ochratoxin (1) was mainly found in the monoculture of the sclerotial morph, while the anthraquinone pigment nalgiovensin (2) was produced by the asexual morph. Surprisingly, combining cultures from both developmental stages in a coculture experiment changed the metabolite profile drastically. The chlorinated congener nalgiolaxin (3) was abundant, and newly produced bianthrones were found. Allianthrone A (4) and its two diastereomers [allianth...
Distribution of Mass and Charge in the Spontaneous Fission of 244 Cm

The distribution of mass and charge in the spontaneous fission of $^{244}\mathrm{Cm}$ has been investigated by radiochemical and mass spectrometric determination of the fission yields for 40 mass chains and 2 shielded nuclides (independent yields). The mass distribution is highly asymmetric with a relative probability of asymmetric-to-symmetric fission (peak-to-valley ratio) of greater than 5700. The average masses of the light and heavy groups are 103.1 and 138.7, respectively. The characteristics of the mass distribution, as well as the division of nuclear charge indicated by the independent yields of the two shielded nuclides, are consistent with the systematics established from other studies of low-energy fission.
Transcriptional repressor Kaiso promotes epithelial to mesenchymal transition and metastasis in prostate cancer through direct regulation of miR-200c.

Abstract The loss of miR-200 family, through DNA methylation, results in cancer cells undergoing an epithelial to mesenchymal transition (EMT), and metastasis. In this study, we established that the transcriptional repressor Kaiso directly binds methylated regions of the miR-200 family, and this is reversed with 5-aza treatment. sh-Kaiso PC-3 cells display increased miR-200-a/b/c, miR-141, and miR-429 expression, with miR-200c demonstrating the most significant increase. Interestingly, overexpression of EGFR or treatment with EGF decreases miR-200c expression and this is reversed after treatment with EGFR specific kinase inhibitor PD153035. However, EGF did not have a significant effect on miR-200c in sh-Kaiso DU-145 or PC-3 cell lines, suggesting Kaiso silences miR-200c through the activation of EGFR signaling. Overexpression of Kaiso in LNCaP cells results in decreased expression of miR-200-a/b/c, miR-141, and miR-429, along with increased expression of ZEB1, p-EGFR and total EGFR levels. Overexpression of miR200c in PC-3 cells results in decreased expression of EGFR, ZEB1, ERK1/2 and Kaiso. Additionally, sh-Kaiso PC-3 demonstrates reduced in vivo tumor formation and metastasis. Thus, our data suggests that EGFR signaling regulates the silencing of miR-200 family through Kaiso binding to methylated regions in the promoter.
Mass Mortality of Wood Frogs (Rana sylvatica) in the Ozark National Forest: Is it Acid Rain?

We describe observations of a continuing mass mortality event primarily involving wood frogs, but involving other amphibians to a lesser degree. The investigation took place from Spring 2000 through Spring 2004. No definitive correlations between environmental variables and mortality could be identified. Forensic analysis could not isolate causal pathogens. Although mortality fluctuated during the study, it may have spread to other species. Our report identifies population level problems in the eastern part of the Ozark National Forest but is unable to identify a cause. Future studies that more thoroughly address contaminants, pathogens/parasites, and other potential environmental problems in the Ozark National Forest are warranted.
Sex Differences in the Association between Heavy Drinking and Behavioral Distress Tolerance and Emotional Reactivity Among Non-Depressed College Students.

Background Heavy episodic drinking (HED) is a common behavior among college students that is associated with severe negative consequences. Negative reinforcement processes have been applied to elucidate mechanisms underlying relationships between consumption of alcohol and the desire to alleviate negative feelings. Distress tolerance (DT) and emotional reactivity are two mechanisms that are consistent with the self-medication model that may contribute to HED. The current study investigated relationships between DT, emotional reactivity, defined as frustration reactivity and irritability reactivity, and HED in a non-depressed college population. Given differential patterns of consumption and motivation for drinking between males and females, sex differences were also examined. Short summary The study examined two constructs consistent with negative reinforcement processes, behavioral distress tolerance (DT) and emotional reactivity (frustration reactivity and irritability reactivity), to explain heavy episodic drinking (HED) among non-depressed college students. Behavioral DT and frustration reactivity independently predicted HED. Higher HED was associated with higher frustration reactivity and lower behavioral DT in women, but nor in men. Methods One-hundred-ten college students without depressive symptoms completed alcohol use measures and the Paced Auditory Serial Attention Task (PASAT-C) to assess behavioral DT and emotional reactivity. Results DT and frustration reactivity independently predicted HED. The association between DT and HED was moderated by sex such that higher levels of DT predicted higher HED among females, but not among males. Higher frustration reactivity scores were associated with a greater number of HED. Conclusions Results provide supporting evidence that DT and emotional reactivity are distinct factors, and that they predict HED independently. Results underscore the importance of examining sex differences when evaluating the association between HED and negative reinforcement processes in this population.
Applications of Bayesian Neural Networks in Prostate Cancer Study

Abstract Prostate cancer is now the most common cancer in men in many western countries including USA. The causes are unknown but are probably related to lifestyle and dietary factors. Heredity and race play roles in causation as there are families with a high incidence of prostate cancer, and it is much more frequently found in African Americans than Caucasians. Prostate cancer can be locally confined or it can be spread outside the organ to the tissues outside of the prostate and to the lymph nodes or bone. Typically, cancers confined to organs of origin are potentially curable. Since surgery is the only option for most of the cases it is very much important to know, based on pre-surgery biopsy results how likely the cancer is organ confined or not. This article considers several hierarchical Bayesian neural network approaches for modeling posterior prediction probabilities of certain features indicative of non-organ confined prostate cancer like margin positivity (MP) and seminal vesicle positivity (SV). Two separate approaches are discussed one for predictions of MP and SV separately and another for MP and SV jointly. The effectiveness of the Bayesian neural network models for classification of non-organ confined prostate cancer with gene expression data is also established. In all the presented datasets Bayesian neural networks are shown to give superior result than most of the other common statistical approaches.
PROBABILITY AND RANDOM VARIABLES

Publisher Summary This chapter provides the foundation of the mathematical machinery necessary to come to grips with probabilistic phenomena, that is, to deal with random or nondeterministic variables. Most of the interesting variables in modern computer systems such as the response time of an on-line inquiry system or the retrieval time of a record from a direct access storage device are random variables. The chapter presents some formal definitions to explain the probability concept and examples to illustrate the definitions. It defines random variable and explains the way by which the probability distribution of a random variable is defined. It also provides some examples of random variables of the two main types, discrete and indiscrete, which are usually called continuous. The chapter presents the way by which some parameters of a random variable X such as expected value E[X] and variance Var[X] can be used to make interesting probability calculations and estimates and how transform methods such as the use of moment generating functions and the Laplace–Stieltjes transform simplify many probability calculations.
P.A. MacMahon: Ramanujan’s Distinguished Contemporary

P.A. MacMahon, a noted combinatorialist, wrote a famous treatise on Combinatory Analysis in which he included a discussion of the combinatorial significance of the Rogers–Ramanujan identities that neither Rogers nor Ramanujan emphasized. This article describes MacMahon’s life as a Major in the British Army stationed in India and later as an assistant to G.H. Hardy of Cambridge University. MacMahon’s mathematical connections with Ramanujan are not just due to the Rogers–Ramanujan identities, but also due the table of partitions he compiled in order to verify the famous Hardy–Ramanujan asymptotic formula for the partition function. The story of how Ramanujan discovered his famous partition congruences upon seeing this table is also described.
Drosha and DGCR8 in MicroRNA Biogenesis

Abstract Drosha and DGCR8 (also called Pasha), together known as the Microprocessor complex, are responsible for cleaving canonical microRNA primary transcripts (pri-miRNAs) to produce microRNA precursors (pre-miRNAs) in animals. This specific cleavage serves as the entrance to the microRNA (miRNA) maturation pathway. In this review, I summarize the current knowledge regarding how Drosha and DGCR8 recognize the pri-miRNA substrates, how pri-miRNA processing may be regulated through a variety of mechanisms, how a heme cofactor binds to DGCR8 and contributes to pri-miRNA processing, and how heterozygous deletion of DGCR8 causes abnormal miRNA expression and results in neurological defects observed in DiGeorge syndrome. Also discussed are potential functions of DGCR8 and Drosha in regulating the abundance of other RNAs, such as messenger RNAs and long noncoding RNAs.
Diamond-Blackfan Anemia

Diamond-Blackfan anemia (DBA) is a rare inherited bone marrow failure syndrome (IBMFS) that presents in early infancy and is characterized by severe anemia with mild macrocytosis, reticulocytopenia, and a normocellular bone marrow with a paucity of erythroid precursors. Clinically DBA is typified by failure of red cell terminal differentiation, an array of physical anomalies, and a predisposition to malignancy. Notably the study of DBA has defined a class of IBMFS referred to as “ribosomopathies” as the pathogenesis of DBA involves predominantly (in about 65–70% of patients) autosomal dominant mutations resulting in haploinsufficiency of ribosomal proteins (RP) encoded by 16 verified genes. X-linked mutations in two non-ribosomal genes, GATA1, encoding an erythroid transcription factor, and TSR2, encoding the putative RPS26 chaperone, are responsible for very rare instances of DBA. Tremendous progress using zebrafish and mouse models of DBA has advanced our understanding of the role of nucleolar stress (p53-dependent) and p53-independent mechanisms in the development of the DBA phenotype, providing strategies for therapeutic intervention. DBA is also confirmed to be a cancer predisposition syndrome. Our increasing understanding of the pathophysiology of DBA is leading to new therapeutic approaches such as ongoing open trials involving the modulation of mTOR and the TGFβ/activin pathways, with agents leucine and Sotatercept, respectively. In addition, trials with HDAC inhibitors, prolyl hydroxylase inhibitors, or PPAR-α agonists that are ongoing in other anemias may also provide useful insights for directing future therapies for patients with DBA.
Synchronous cerebral arteriovenous malformation and lung adenocarcinoma carcinoma brain metastases: A case study and literature review

Abstract Introduction While there are numerous published cases of arteriovenous malformations (AVMs) developing in the setting of malignancy, it is extremely rare to find them concurrently associated in the brain. Clinical case This is the case of a 55-year-old male who presented to the emergency department complaining of headaches, memory and visual changes. Neuro-imaging revealed a right temporal parietal AVM and an adjoining hyperenhancing occipitotemporal lobe lesion with concern for a possible evolving stroke. The patient was treated with radiosurgery for the AVM. His symptoms progressed one month later, and repeat imaging suggested interval enlargement of the previously presumed stroke that was intricately associated with the AVM, in addition to two new small enhancing lesions of the left temporal lobe. Microsurgical resection of the temporal lobe mass revealed adenocarcinoma of the lung. Conclusion This case represents a previously undocumented confluence of cranial AVM that initially masked a non-small cell lung cancer brain metastasis.
Fetal cardiac findings and hemodynamic changes associated with severe lower urinary tract obstruction in utero

OBJECTIVES To describe fetal echocardiographic findings associated with lower urinary tract obstruction (LUTO) and to compare anatomic and hemodynamic measurements between fetuses with LUTO and gestational age (GA)-matched controls, with an emphasis on quantitative indices of diastolic function and cardiac output. METHODS This was a retrospective cohort study of fetuses diagnosed with severe LUTO with giant bladder, which underwent at least one fetal echocardiogram at our center between January 2005 and June 2018. Fetuses with major congenital heart disease were excluded. Control fetuses did not have any structural or functional abnormalities and were GA-matched to the LUTO fetuses based on the time of the first fetal echocardiogram. Cardiac anatomy and hemodynamic measurements were compared between fetuses with LUTO and controls. In infants with LUTO, serial fetal and postnatal echocardiographic data were assessed, when available, and clinical outcomes were reviewed. RESULTS Twenty-six fetuses with LUTO and at least one fetal echocardiogram available were identified, one of which was excluded due to hypoplastic left heart syndrome, leaving 25 LUTO fetuses in the final cohort. The mean GA at the first fetal echocardiogram was 25.4 ± 5.1 weeks in the LUTO group and 25.3 ± 5.0 weeks in the control group. Common findings in fetuses with LUTO included cardiomegaly (40%), pericardial effusion (44%), right ventricular (RV) hypertrophy (64%) and left ventricular (LV) hypertrophy (48%). Compared with GA-matched controls, LUTO fetuses had lower ascending aorta Z-score (-0.10 ± 0.94 vs -0.93 ± 1.03; P = 0.02) and aortic isthmus Z-score (-0.14 ± 0.86 vs -1.62 ± 1.11; P < 0.001), shorter mitral valve inflow time indexed to cardiac cycle length (0.46 ± 0.04 vs 0.41 ± 0.06; P = 0.002), and worse (increased) LV myocardial performance index (0.39 ± 0.03 vs 0.44 ± 0.04; P < 0.001). In addition, the ratio of RV to LV cardiac index was higher in LUTO fetuses compared with controls (1.62 ± 0.13 vs 1.33 ± 0.11; P < 0.001). Of the 25 LUTO pregnancies, two were lost to follow-up, three underwent elective termination of pregnancy and three ended in intrauterine fetal demise. Four (16%) patients had mildly hypoplastic left-heart structures, comprising two with aortic arch hypoplasia and two with mitral and aortic stenosis. CONCLUSION In addition to presenting with cardiomegaly, pericardial effusion and ventricular hypertrophy, fetuses with LUTO demonstrate LV diastolic dysfunction and appear to redistribute cardiac output as compared to control fetuses, which may contribute to the development of left-heart hypoplasia. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
Recommendations for Thematic Issue on Kinesiology Doctoral Students' Perspectives.

ABSTRACTIn this thematic issue, we examined Doctoral Students’ (DS) perspectives on six topics: (a) dissertation, (b) teacher training, (c) research training, (d) advisors, (e) doctoral program and...
Copper Deficiency in Liver Diseases: A Case Series and Pathophysiological Considerations

Copper is an indispensable trace element. It serves as a cofactor for enzymes involved in cellular energy metabolism, antioxidant defense, iron transport, and fibrogenesis. Although these processes are central in the pathogenesis of liver disorders, few studies have attributed them to copper deficiency. We herein describe in detail a case series of liver disease patients (n = 12) who presented with signs of copper deficiency based on serum and liver copper measurements. Median age of the group at the time of presentation was 39 (range 18-64 years). Six patients were female. The median serum copper was 46 μg/dL (normal range: 80-155 μg/dL for women and 70-140 μg/dL for men). Seven of the 12 patients had hepatic copper concentration less than 10 μg/g dry weight (normal range: 10-35 μg/g). Most cases presented with acute-on-chronic liver failure (n = 4) and decompensated cirrhosis (n = 5). Only 3 patients had a condition known to be associated with copper deficiency (ileocolonic Crohn's disease following resection n = 1, Roux-en-Y gastric bypass n = 2) before presenting with hepatic dysfunction. Notable clinical features included steatohepatitis, iron overload, malnutrition, and recurrent infections. In 2 of the 3 patients who received copper supplementation, there was an improvement in serum copper, ceruloplasmin, and liver function parameters. Conclusion: Copper deficiency in the serum or liver occurs in a wide range of liver diseases. Given the biological essentiality of copper, the mechanism and clinical significance of this association require systematic study.
Design optimization for resilience for risk-averse firms

Abstract Designers should try to design systems that are resilient to adverse conditions during a system’s lifetime. The resilience of a system under time-dependent adverse conditions can be assessed by modeling the degradation and recovery of the system’s components. Decision makers in a firm should attempt to find the optimal design to make the system resilient to the various adverse conditions. A risk-neutral firm maximizes the expected profit gained from fielding the system, but a risk-averse firm may sacrifice some profit in order to avoid failure from these adverse conditions. The uniqueness of this paper lies in its model of a design firm’s risk aversion with a utility function or Value-at-Risk (VAR) and its use of that model to identify the optimal resilient design for the risk-averse firm. These risk-averse decision-making methods are applied to a design firm determining the resilience of a new engineered system. This paper significantly advances the engineering design discipline by modeling the firm’s appetite for risk within the context of designing a system that can fail due to degradation in the presence of adverse events and can respond to and recover from failure. Since the optimization model requires a complex Monte Carlo simulation to evaluate the objective function, we use a ranking and selection method and Bayesian optimization to find the optimal design. This paper incorporates the design of the wind turbine and the reliability and restoration of the turbine’s components for both risk-neutral and risk-averse decision makers. The results show that in order to make the system more resilient, risk-averse firms should pay a larger design cost to prevent catastrophic costs of failure. In this case, the system is less likely to fail due to the high resilience of its physical components.
Rigid-Rotor Vlasov Equilibrium for an Intense Charged-Particle Beam Propagating through a Periodic Solenoidal Magnetic Field

A new rigid-rotor Vlasov equilibrium is obtained for an intense, axisymmetric charged-particle beam with uniform density in the radial direction propagating through a periodic solenoidal focusing field. The beam envelope equation is derived, and examples of periodically focused rigid-rotor Vlasov equilibria are presented. Statistical properties and possible applications of the present beam equilibrium are also discussed. {copyright} {ital 1997} {ital The American Physical Society}
How Do Discrimination and Self-Esteem Control Beliefs Affect Prosociality? An Examination Among Black and Latinx Youth:

Black and Latinx youth are situated in a maladaptive discriminatory context in the United States; however, prosociality may be one way that youth can promote their own positive development in the f...
Safety and Monitoring During Pediatric ICU Sedation

Optimal sedation in the pediatric intensive care unit (ICU) is ideal but unfortunately far from the reality. Ensuring adequate sedation begins with appropriate assessment and treatment of pain, followed by assessment of sedation and agitation using developmentally appropriate and validated observational assessment tools. Safety during analgesia and sedation, whether for prolonged mechanical ventilation or a quick procedure, can further be achieved with standard use of cardiorespiratory monitoring and end-tidal capnography. Objective sedation monitoring through analysis of heart rate variability or processed electroencephalography (EEG) measures, such as the Bispectral Index score or amplitude-integrated EEG, has been investigated with varying levels of thoroughness. Current evidence does not support stand-alone use of objective monitoring devices; instead, analgesia and sedation management is dependent on integration of information from multiple sources, including observational assessment tools. In addition, current practice guidelines emphasize the importance of implementing standardized, goal-directed sedation protocols, which is currently lacking in many ICUs.
Societal Impacts of a Complete Street Project in a Mixed Urban Corridor: Case Study in Pittsburgh

AbstractComplete streets facilitate multimodal travel by improving both transportation access and safety by emphasizing the user, not the automobile. This case study evaluates the impacts of a comp...
Unassisted True Analog Neural Network Training Chip

Analog In-Memory Computing using Resistive Processing Unit (RPU) has been proposed for Neural Network (NN) training. However, hardware demonstration has been limited to using some digital emulation to assist the analog chip function. Using capacitor as analog weight, we report the first analog Neural Network training chip, where ALL Multiple and Accumulate (MAC) function are performed in analog cross-point arrays, and all weights are updated in parallel. The chip measure full MNIST training accuracy of 92.7% with run time faster than digital system in real time.
PrecisionProDB: improving the proteomics performance for precision medicine

Summary As the next-generation sequencing technology becomes broadly applied, genomics and transcriptomics are becoming more commonly used in both research and clinical settings. However, proteomics is still an obstacle to be conquered. For most peptide search programs in proteomics, a standard reference protein database is used. Because of the thousands of coding DNA variants in each individual, a standard reference database does not provide perfect match for many proteins/peptides of an individual. A personalized reference database can improve the detection power and accuracy for individual proteomics data. To connect genomics and proteomics, we designed a Python package PrecisionProDB that is specialized for generating a personized protein database for proteomics applications. PrecisionProDB supports multiple popular file formats and reference databases, and can generate a personized database in minutes. To demonstrate the application of PrecisionProDB, we generated human population-specific reference protein databases with PrecisionProDB, which improves the number of identified peptides by 0.34% on average. In addition, by incorporating cell line-specific variants into the protein database, we demonstrated a 0.71% improvement for peptide identification in the Jurkat cell line. With PrecisionProDB and these datasets, researchers and clinicians can improve their peptide search performance by adopting the more representative protein database or adding population and individual-specific proteins to the search database with minimum increase of efforts. Availability PrecisionProDB and pre-calculated protein databases are freely available at https://github.com/ATPs/PrecisionProDB and https://github.com/ATPs/PrecisionProDB_references. Supplementary information Supplementary data are available at Bioinformatics online.
Adjoint Sensitivity Analysis for Uncertain Material Parameters in Frequency-Domain 3-D FEM

We present an application of adjoint analysis for efficient sensitivity analysis and estimation of quantities of interest in the presence of uncertain model parameters in 3-D finite element method (FEM) scattering problems. We demonstrate that the adjoint solution may be leveraged to expedite quantification of uncertainty in the scattering model with extremely high accuracy and vast efficiency improvements in comparison to classic gradient approximation techniques and Monte Carlo (MC) methods. The proposed method is demonstrated for low- and high-dimensional parameter spaces for scattered electric field quantities of interest (QoIs). The results indicate strong agreement with equivalent Monte Carlo simulations for QoI responses and probability densities.
Trait irritability in adults is unrelated to face emotion identification

Abstract Irritability (i.e., a proneness to anger that is often accompanied by behavioral outbursts) is increasingly recognized as a clinically significant trait in adults, yet studies into its mechanisms and whether they differ from those observed in pediatric samples is largely unknown. Although face emotion identification deficits are associated with increased irritability in children, mixed findings exist in the two studies of trait irritability in adults. In an online sample of adults (N = 209, 18–62 years; M = 30.15), we sought to address some of the methodological limitations in prior studies to test whether irritability is associated with difficulties recognizing emotional expressions following frustration. Trait irritability was not associated with impaired face emotion identification, even after a frustration manipulation. This suggests that irritability-related mechanisms in adults may differ from those observed in pediatric samples or may be limited to adults with clinically significant irritability.
Atypical sonographic presentation of diabetic mastopathy: A case report and literature review

Diabetic fibrous mastopathy (DFM) is a relatively rare condition that most often occurs in insulin-dependent diabetics with a characteristic hypoechoic appearance on ultrasound (US). DFM frequently poses a diagnostic challenge in radiology due to malignant imaging similarities, and core needle biopsy is often required. If DFM is in the differential, fine-needle aspiration should not be considered as it will likely be non-diagnostic due to insufficient sampling and excisional biopsy should be avoided as it may worsen the disease process. Therefore, high clinical suspicion of DFM is important for diagnostic intervention consideration. We report the case of a 57-year-old who presented with a firm breast lump which on mammography was seen as a new 5.8 by 5.3 cm global asymmetry. US was performed and a diffuse area of increased echogenicity without posterior shadowing was identified. Given the appearance and patient history, DFM was considered unlikely. However, core needle biopsy revealed diabetic lymphocytic mastopathy consistent with DFM. Even though DFM is uncommon and has been reported to have a specific US appearance, it should be included in the differential for a palpable breast lump in any diabetic patient regardless of glucose control or atypical imaging findings.
A multi-agent approach for modeling oligarchs' campaign donations with simulated spatial elections.

We present the OLIGO model, a multi-agent simulation of oligarchy. We extend previous multi-agent-based, spatial models of democracy by adding a new class of agents, oligarchs, which represent leaders of firms in a common industry who lobby for beneficial subsidies through campaign donations. We test hypotheses from the literature in political economics on the behavior of oligarchs and political parties as they interact, under conditions of imperfect information and bounded rationality. By verifying that central hypotheses from the economics literature hold for the OLIGO model, we accomplish two goals: (1) We show that the simple rules agents follow in our model are sufficient to capture much of the complex dynamics of this politico-economic system; (2) we validate these results from prior studies that used analytic methods, using an alternative, agent-based modeling method; and (3) we derive support for the claim that the OLIGO model is a useful test environment for novel hypotheses about oligarchs’ campaign donation behavior.
Can erroneous examples help middle-school students learn decimals?

This paper reports on a study of learning with erroneous examples, mathematical problems presented to students in which one or more of the steps are incorrect. It is hypothesized that such examples can deepen student understanding of mathematics content, yet very few empirical studies have tested this in classrooms settings. In a classroom study, 255 6th, 7th, and 8th graders learned about decimals using a web-based system under one of three conditions - erroneous examples, worked examples, and partially-supported problem solving. Although students' performance improved significantly from pretest to posttest the learning effect for erroneous examples was not better than the other conditions, and unlike some earlier empirical work, the higher prior knowledge students did not benefit more from erroneous examples than from worked examples or problem solving. On the other hand, we were able to identify certain key decimal misconceptions that are held by a high percentage of students, confirming earlier mathematics education studies. Also, the incidence of misconceptions declined over the course of the lesson, especially for the worked example group. Overall, these results could indicate that erroneous examples are simply not as effective for learning as we (and other) researchers hypothesize. The results could also indicate that the manner in which erroneous examples were presented to the students in this study somehow missed the mark in promoting learning. It is also possible that erroneous examples, like some other e-learning techniques, do not work as well in classroom as they do in a laboratory setting. We discuss these possibilities and how we are redesigning the treatments to be more focused and appealing to learners for a subsequent study.
Ethical considerations in the selection of cells and the use of biologicals.

Dr. Bruce Dull has discussed in-depth the benefit risk assessment in the development of and usage of immunizing agents. It is my task to cover the wide range of other ethical considerations which face investigators and makers of public policy concerned with immunization. Many of the issues have been explored in-depth at a National Conference on Immunization sponsored by HEW in November 1976, and by a series of National Immunization Work Groups convened by the Assistant Secretary for Health of Health, Education and Welfare thereafter.
Temporal fluctuations in single molecule dipole orientation and single molecule energy transfer as a probe for protein conformational dynamics

Since the beginning of single molecule spectroscopy (SMS) at room temperature, it has often been suggested that it may be used for measuring the time trajectories of individidual biomolecule’s conformational dynamics. Such time trajectories can not be measured on ensembles because of the lack of synchronization.
Dietary Assimilation and its effect on health: A Study of International Students

This paper seeks to understand the effect of environment on obesity by studying the effect of acculturation on the health of a foreign population – who experience a relatively low prevalence of obesity – after they have been introduced to different environments, some are characterized by relatively low prevalence and others are characterized by relatively high rates of obesity. Acculturation for the purpose of this study is defined as a voluntary or involuntary adaptation of food habits and culture of the new country. The foreign population is defined to be the group of foreign students who come from various countries to the United States for short term or long-term habitation.
Spatiotemporal Analysis of Dairy Farm Productivity, Size, and Entry-Exit in the US

The US dairy industry has experienced significant structural changes in the last few decades. Dairy production has been consolidated into fewer but larger farms, and shifting toward Western and Southern states from traditional dairy regions including the Lake States and Corn Belt. The changes also involved significant entry and exit of small- and medium-sized farms. The paper attempts to characterize patterns of dynamic evolution of productivity, size, and entryexit of dairy farms over time and across major production regions in the US. The analysis sheds light on the contribution of farm and regional characteristics on farm-level productivity changes. Regional differences in climate and economic interconnection between farm productivity and entry-exit are also examined with a focus on the distinction among dairy farm sizes.
Stability Augmentation and Active Flutter Suppression of a Flexible Flying-Wing Drone

Integrated control laws are developed for stability augmentation and active flutter suppression of a flexible flying-wing research drone. The vehicle is a 12 lb unmanned flying-wing research aircraft with a 10 ft wingspan. Active flutter suppression is flight critical, since the subject vehicle is designed to flutter within its flight envelope. The critical flutter condition involves aeroelastic interactions between the rigid body and elastic degrees of freedom; hence, the control laws must simultaneously address both rigid-body stability augmentation and flutter suppression. The conventional control-synthesis approach is motivated by the concept of identically located force and acceleration, which was successfully applied on some previous operational aircraft. Based on the flutter characteristics and on conventional stability-augmentation concepts, two simple loop closures are suggested. It is shown that this control architecture robustly stabilizes the body-freedom-flutter condition, increases the dampi...
The economics of anti-corruption: Lessons from a widespread customs reform

Introduction Corruption is pervasive in developing countries, and is widely considered to be a major barrier to economic development. Yet systematic empirical evidence on the effectiveness of anti-corruption efforts is scarce. The seminal theoretical work of Gary Becker and George Stigler (1974) identified a pair of generic remedies for bureaucratic corruption in government: increased monitoring and higher wages. But for many reasons, anti-corruption reforms may fail in practice. For example, consider a reform that increases monitoring of potentially corrupt officials. Such a reform might fail if the monitors themselves were corrupt and so provide inaccurate information to higher authorities. In addition, higher-level officials may themselves be corrupt and not put the information gathered to good use. The monitoring program may simply be implemented to demonstrate the government's anti-corruption credentials. What is more, even if enforcers are honest, corrupt officials may be able to find alternative methods of continuing their corrupt dealings. Empirical work is therefore necessary to determine the effectiveness of any given anti-corruption effort. When there is a high probability that lower-level agents monitoring corrupt activity may themselves be corrupt, it may be reasonable for higher authorities to use monitors from outside the government—in particular, private firms. Hiring private firms to monitor potentially corrupt activity may make sense if competition among the private monitors generates incentives for integrity. A widely-recognized example of government-mandated monitoring by private firms is auditing by private accounting firms of the financial statements of publicly-traded companies, an essential foundation of securities regulation. Can "hiring integrity" from the private sector to collect information for government anti-corruption efforts be effective? This chapter analyzes a reform adopted by the customs services in many developing countries that does just that. Within a developing country government, the customs agency—the organization responsible for taxation of imported goods—is often singled out as having particularly severe problems with bureaucratic
A Characterization of Visibility Graphs for Pseudo-polygons

In this paper, we give a characterization of the visibility graphs of pseudo-polygons. We first identify some key combinatorial properties of pseudo-polygons, and we then give a set of five necessary conditions based off our identified properties. We then prove that these necessary conditions are also sufficient via a reduction to a characterization of vertex-edge visibility graphs given by O’Rourke and Streinu.
Computing minimum length representations of sets of words of uniform length

Motivated by text compression, the problem of representing sets of words of uniform length by partial words, i.e., sequences that may have some wildcard characters or holes, was recently considered and shown to be in P . Polynomial-time algorithms that construct representations were described using graph theoretical approaches. As more holes are allowed, representations shrink, and if representation is given, the set can be reconstructed. We further study this problem by determining, for a binary alphabet, the largest possible value of the size of a set of partial words that is important in deciding the representability of a given set S of words of uniform length. This largest value, surprisingly, is Σ i = 0 | S | - 1 2 ? ( i ) where ? ( i ) is the number of ones in the binary representation of i, a well-studied digital sum, and it is achieved when the cardinality of S is a power of two. We show that circular representability is in P and that unlike non-circular representability, it is easy to decide. We also consider the problem of computing minimum length representation (circular) total words, those without holes, and reduce it to a cost/flow network problem.