cssi/SciSciGPT-SciSciNet huggingface dataset:
Systems Biology through complex networks, signal processing, image analysis, and artificial intelligence

Comprehensive understanding of biology can only be achieved by integrating several type of data and models across wide time and space scales, ranging from molecules to ecology. While substantial advances have been obtained through the reductionist approach, where specific sybsystems are investigated separately, usually at microscopic scale, the integration of structural and dynamical concepts along several scales holds the key for major breakthroughs. Such endeavours are part of the so-called Systems Biology area. This article discusses and illustrates how complex networks, image analysis, signal processing and artificial intelligence can be integrated into systems biology research, providing an unprecedented opportunity for scientific and technologic advances. The generality of complex networks for system representation allows this type of structures to be effectively used to model both the architecture and function of virtually any biological entity. At the same time, image analysis paves the way not only for the characterization of phenotipic traits, but also for mapping several geometric biological structures (e.g. neuronal systems, bone canals, cell organelles, etc.) as complex networks. Several concepts and methods from signal processing can then be applied in order to characterize, classify and model the structure and dynamics in such network representations. Artificial intelligence approaches, especially pattern recognition, are also necessary in order to automate, integrate and interprete all such myriad of data and models. In addition to discussing, in a brief though accessible fashion, each of these areas as well as their integration into systems biology, the current work also illustrates the respective potential of this approach with respect to some of the author's recent works.
Observed Sacramento Basin streamflow response to precipitation and temperature changes and its relevance to climate impact studies

Abstract Observational studies of Sacramento Basin annual mean streamflow response to precipitation and temperature indicate that streamflow amounts in the basin are strongly sensitive to precipitation, but virtually insensitive to mean seasonal temperature. This result is in accord with studies of the climate mean sensitivity of streamflow amount to changes in climatological mean precipitation and temperature as simulated by conceptual hydrological models of the basin. Simpler regression models of the Sacramento Basin show a strong dependence of streamflow amount on temperature, which is not evident in the observation-based annual mean streamflow sensitivity. The interannual variability in Sacramento Basin streamflow response to precipitation exhibits substantial nonlinearity in that the partitioning of precipitation to runoff strongly depends on the precipitation volume. During very wet years in the basin, streamflow response to precipitation exhibits a proportionally greater change (increase) than during normal or dry years. For most dry years in the basin the streamflow response to precipitation is fairly linear. However, on the tails of droughts the streamflow response to precipitation is diminished relative to other dry years. This implies that a shift to a much drier or more drought-prone climate would result in a more substantial reduction in streamflow amounts than might at present be expected from observations of streamflow responses in isolated dry years. This conclusion assumes no changes in the features controlling water retention in the basin, which is an important issue to be addressed in basin climate change studies.
DENDRITIC CELLS ARE ABUNDANT IN NON-LESIONAL GRAY MATTER IN MULTIPLE SCLEROSIS

We have analyzed the localization of dendritic cells (DCs) in non-lesional gray matter (NLGM) in comparison to non-lesional white matter (NLWM) and acute or chronic active multiple sclerosis (MS) lesions. Immunohistochemistry was performed on cryostat sections for DCs markers (CD209, CD205, CD83) and other markers for inflammatory cells (CD68, CD8, CD4, CD3, CCR7, CCR5). We found cells expressing CD209 and containing myelin basic protein in both perivascular and parenchymal areas of NLGM. Our findings showing the expression of CD209+ cells in NLGM parenchymal areas are surprising relative to the previous literature which reported the presence of CD209+ DCs only in MS plaque perivascular areas. Although less numerous than CD209+ cells, NLGM cells expressing mature DCs marker CD205 were consistently detected in perivascular cuffs of most lesions. In double labeling experiments, some but not all of the CD209+ cells also expressed CD68 and CCR5. We also found CD209+ cells in close contact with CD3+ lymphocytes suggesting that DCs might contribute to the local activation of pathogenic T cells in the NLGM. Since injury to the NLGM is one of the key factors associated with disability accumulation, targeting DCs may represent a possible new therapeutic approach in MS to prevent disease progression.
Fabrication of self-apodized short-length fiber Bragg gratings

A new technique for writing extremely short-length Bragg gratings in optical fibers is demonstrated. A physical model describes the diffraction effects on the spatial and wavelength spectra of the Bragg gratings. Selection of appropriate diffraction patterns and related parameters permits self-apodized Bragg gratings with a typical spatial length of several hundred micrometers and a bandwidth of several nanometers to be obtained. These gratings with well-defined spectra are suitable for use as miniature distributed strain sensors and other applications requiring small physical dimensions and broadband spectra.
Generalized Linear Discriminant Analysis: A Unified Framework and Efficient Model Selection

High-dimensional data are common in many domains, and dimensionality reduction is the key to cope with the curse-of-dimensionality. Linear discriminant analysis (LDA) is a well-known method for supervised dimensionality reduction. When dealing with high-dimensional and low sample size data, classical LDA suffers from the singularity problem. Over the years, many algorithms have been developed to overcome this problem, and they have been applied successfully in various applications. However, there is a lack of a systematic study of the commonalities and differences of these algorithms, as well as their intrinsic relationships. In this paper, a unified framework for generalized LDA is proposed, which elucidates the properties of various algorithms and their relationships. Based on the proposed framework, we show that the matrix computations involved in LDA-based algorithms can be simplified so that the cross-validation procedure for model selection can be performed efficiently. We conduct extensive experiments using a collection of high-dimensional data sets, including text documents, face images, gene expression data, and gene expression pattern images, to evaluate the proposed theories and algorithms.
Code, Custom, and Contract: The Uniform Commercial Code as Law Merchant

Rooted in ancient and medieval mercantile experiences, the law of commercial transactions draws from private agreements, customs and usages, and legislation. In this century, three sources – contract, custom and code – have transcended national laws and legal institutions. Codification has occurred on an international scale. In particular, the United Nations Convention on Contracts for the International Sale of Goods (CISG) and Incoterms govern many international commercial transactions.
Percy Lavon JulianPioneer of Medicinal Chemistry Synthesis

Percy Lavon Julian (1899–1975) The contributions of Dr. Julian to the field of medicinal chemistry began humbly at the turn of the century in the segregated American South. Percy Lavon Julian was born on April 11, 1899, in Montgomery, AL. His formal public education was limited, while his secondary education ended at the eighth grade which was the norm for African Americans at that time. His father, who had been denied the opportunity to go to college, made it a priority to ensure that his children received this opportunity.14 Julian went on to complete two years of teacher training at the State Normal School for Negroes in Montgomery. In 1916, Julian became the first in his family to attend college when he was admitted to DePauw University in Green-castle, IN. During his first two years of college, Julian took remedial classes in addition to his college courses to make up for the academic deficiencies resulting from his limited primary education. Despite this, Julian was an excellent student in college and was elected as a member of both the Phi Beta Kappa and Sigma Xi honor societies. In 1920, Julian earned a bachelor’s degree in chemistry and was named valedictorian of his class. DePauw University circa 1916. A few African American students had been accepted to DePauw before Julian arrived; however, the culture was far from accepting. When he arrived, Julian was taken to off-campus housing because the dorms on campus were for “whites only.” Furthermore, it took a day and a half for Julian to find a diner that would serve him. This would be the beginning of many unwelcoming environments Julian would overcome and thrive in. Despite overcoming the barrier of obtaining a college education denied to his father, there were many more obstacles for Julian to overcome …
A Review of the Genus Eidmanniella (Mallophaga: Menoponidae) from the Pelecaniformes

Descriptions and a key are given for 6 recognized species, including a new species, Eidmanniella nancyae from Phalacrocorax nigrogularis . Neotypes are designated for E. pellucida (Rudow) and E. pustulosa (Nitzsch). There are 4 new synonymies: E. pellucida (= Menopon kuwani Kellogg & Chapman), E. subrotunda (= M. curum Piaget), and E. albescens (= M. singularis Kellogg & Kuwana and E. sula Tendeiro).
End-of-life care in a population-based cohort of cancer patients: clinical trial participation versus standard of care

Objectives To evaluate end-of-life care in a cohort of oncology patients in Olmsted County, Minnesota, USA, and compare differences between patients participating in clinical trials and those not in clinical trials. Methods A population-based cohort of subjects with active oncological disease who died between 2000 and 2002 was constructed retrospectively using institutional databases. Clinical trial participation and care during the last 2 months of life were analysed. Results A total of 395 eligible patients were identified. In the 2 months prior to death, 94 (24%) patients received chemotherapy, 232 (59%) were hospitalised, 249 (63%) were in hospice and 315 (80%) had a do not resuscitate (DNR) code status. Only 8 (2%) patients received cardiopulmonary resuscitation (CPR) and 26 (7%) patients participated in a clinical trial. Patients in clinical trials were more likely to receive chemotherapy (69.2% vs 20.6%; p Conclusions Although opportunities for improvement exist, high quality end-of-life care was found in this study of patients with active malignancy. A majority (over 60%) of patients enrolled in hospice prior to death, 80% had a DNR status and only 2% received CPR. Although clinical trial participants received more aggressive treatments during the last 2 months of life, they did not appear to have lower quality end-of-life care.
Sinkhole formation mechanisms and geostatistical-based prediction analysis in a mantled karst terrain.

Abstract Efforts to evaluate sinkhole formation and quantify the controlling factors are hindered by the lack of historical observations or coarse resolution datasets in many areas. We applied recent advances in GIS-based sinkhole mapping and spatial statistics to comprehensively investigate the factors controlling sinkhole formation in the mantled karst setting of Dougherty County, Georgia. Sinkholes form at varying spatial and temporal scales within the test site. A three-stage methodology was conducted. Firstly, 275 sinkholes that formed or were enlarged between 1999 and 2011 were detected by comparing the results of sinkhole inventories derived from two DEMs acquired in 1999 and 2011. Additionally, a LiDAR DEM (1 m resolution) was used to gather a spatially detailed sinkhole inventory of 3412 sinkholes. The sinkhole inventory data was converted into sinkhole density maps for subsequent analyses. Ordinary least squares (OLS) and geographically weighted regression (GWR) spatial statistical models were applied to quantify the impact of controlling factors on sinkhole density. Controlling factors included geologic, hydrologic, anthropogenic, hydrogeologic, and geomorphologic variables. For the two sinkhole inventory datasets analyzed, overburden thickness, aquifer fluctuations, and proximity to fractures, streams, and wetlands were the most influential controlling factors on sinkhole formation (GWR p-values
Der Blick auf eine bewegte Uhr

Wir wissen nun, dass jede Uhr, die sich mit der Geschwindigkeit v gegenuber einem Inertialsystem bewegt, in diesem System langsamer geht als eine dort ruhende Uhr. Der Verlangsamungsfaktor betragt $$s=\sqrt{1-v^{2}/c^{2}}.$$ (7.1) Man konnte dies leicht fur nicht mehr als einen kleinen Rechentrick halten – eine Schlussfolgerung, die nur auf ein paar intellektuellen Spielchen mit dem Begriff der Gleichzeitigkeit beruht. Wenn man tatsachlich auf eine bewegte Uhr schauen wurde, konnte man dann tatsachlich sehen, dass sie langsamer geht?
Research Progress on Bacterial Blight Resistance of New Rice Cultivars at Anren Experimental Station

Many years of research on rice bacteria blight by Rice Research Institute,Hunan Academy of Agricultural Science at Anren experimental station was conducted,and the occurrence regularity of rice bacterial blight was found,and the prevention measures were put forward,which included breeding multi-resistance varieties,medicament applied and cultivation management.In recent years,more then 50 000 materials were identified,and more the 500 resistance varieties and more than 100 high resistance varieties were screened.On this basis, a series of multi-resistance rice varieties were breeded,which produced very good economic,social and ecological benefits.The important targets of paddy rice breeding were screening of resistance resources and breeding of multi-resistance rice varieties to disease and pest.
An establishment of analysis of CYP2C9、UGT1A6 gene polymorphism on the metabolic enzyme of valproic acid

Objective:In order to study the effect of drug-metabolizing enzymes(DME) polymorphism on the metabolism of valproic acid(VPA),we set up a method to analyze the DME gene polymorphism.Methods:The GDNA were extracted from blood of human.The CYP2C9 and UGT1A6 gene were amplified with PCR.We used the restriction fragment length polymorphism(RFLP) to classify the CYP2C92,CYP2C93,CYP2C94,CYP2C95,UGT1A62 and UGT1A63 genotypes.Results:A successful design of the primers was used to contain expansion of CYP2C9 3,CYP2C9 4,CYP2C9 5 of the clips,and sequencing and verification were performed.Conclusions:We established a simple and reliable RFLP method to group the UGT1A6 and CYP2C9.
The Diagnosis And Treatment of Local Injection For Superficial Cavernous Hemangioma Among Children

Objective To study the role of B-ultrasonography and 3-dementional CT-angiography in the diagnosis and to compare the both therapeutic effects of the injection to tomor mass inside with dexamethasone and pingyangmycine(Bleomycin)for superficial cavernous hemangioma among suffered children.Methods Clinical records of the mentioned hemangioma underwent the two drugs injection to tumor mass inside treatment was retrospectively studied.80 of them was selected as group A;who received Dexamethasone,injections in the years of 1995 ～ 1999,another 80 was selected as group B who received Bleomycin in 2000 ～ 2005.Other conditions of both groups were comparable,including:age ranged from 2 mos to 10 yrs.,and sex ratio being one male to 3 females.Diagnosis of all cases were carried out by clinical signs and B-ultrasonography,but some by additional 3-dementional CT angiography for related detail structures.Drugs were given by intra-tumor injections,1 ～ 2 times weekly for 2 ～ 6 times until the regression remained stable.Results The cure rates were 75.0% in group A and 92.5% in group B;semi-cures in other 25.0% and 7.5% respectively.The total effectiveness rate was 100% in both groups.There was no remarkable scar formation or other complication.Evidently,Bleomycine group showed its superiority in cure rate.Conclusions For superficial cavernous hemangioma,with Bleomycin injection to tumor mass inside is preferred as the treatment of first choice.
Marxismo e Ecologia: fontes comuns de uma Grande Transição

Vincular o marxismo e a transicao ecologica pode parecer a primeira vista uma tentativade uniao de dois movimentos e discursos totalmente diferentes, cada qual com sua propriahistoria e logica: um que tem a ver principalmente com as relacoes de classe outro com arelacao entre os seres humanos e o meio ambiente. No entanto, historicamente o socialismoinfluenciou o desenvolvimento do pensamento e da pratica ecologicas, enquanto a ecologiainformou o pensamento e a pratica socialistas. Desde o seculo XIX, a relacao entre os doistem sido complexa, interdependente e dialetica.
The Impact of Behaviorism on Our Culture: Some Evidence and Conjectures

Current interest among behaviorists in public policy is contrasted with the minimal impact of behaviorism on contemporary American culture, in order to provide baseline information against which future developments might be compared.
Vector Space Models for Encoding and Retrieving Longitudinal Medical Record Data

Vector space models (VSMs) are widely used as information retrieval methods and have been adapted to many applications. In this paper, we propose a novel use of VSMs for classification and retrieval of longitudinal electronic medical record data. These data contain sequences of clinical events that are based on treatment decisions, but the treatment plan is not recorded with the events. The goals of our VSM methods are (1) to identify which plan a specific patient treatment sequence best matches and (2) to find patients whose treatment histories most closely follow a specific plan. We first build a traditional VSM that uses standard terms corresponding to the events found in clinical plans and treatment histories. We also consider temporal terms that represent binary relationships of precedence between or co-occurrence of these events. We create four alternative VSMs that use different combinations of standard and temporal terms as dimensions, and we evaluate their performance using manually annotated data on chemotherapy plans and treatment histories for breast cancer patients. In classifying treatment histories, the best approach used temporal terms, which had 87 % accuracy in identifying the correct clinical plan. For information retrieval, our results showed that the traditional VSM performed best. Our results indicate that VSMs have good performance for classification and retrieval of longitudinal electronic medical records, but the results depend on how the model is constructed.
Adaptive computation: the multidisciplinary legacy of John H. Holland

John H. Holland's general theories of adaptive processes apply across biological, cognitive, social, and computational systems.
Small Bowel Diameter in Short Bowel Syndrome as a Predictive Factor for Achieving Enteral Autonomy

Children with short bowel syndrome commonly have dilated small bowel. We found that the extent of dilation was associated with bowel length and that both were related to achieving enteral autonomy.
Back to School and Beyond Using Professional Resources to Overcome Everyday Challenges

As the excitement of the Back to School season begins to wane, connections with colleagues and professional development opportunities provide support in the face of everyday challenges.
PHEVs contribution to the self-healing process of distribution systems

Traditionally, distribution system takes a long time to recover after a major outage, due to its top-down operation strategy. As fast response energy resources, Plug-in Hybrid Electric Vehicles (PHEVs) can accelerate the load pickup process by compensating the imbalance between available generation and load in distribution system. In this paper, PHEVs are employed for reliable load pickup and faster self-healing process. The non-homogeneous Markov chain method has been employed for generation of synthetic driving behavior. The optimization problem of finding load pickup sequence to maximize restored energy is formulated as a Mixed Integer Linear Programming (MILP) problem. Simulation results on a 100-feeder test system demonstrate the benefit from PHEVs to restore more energy in a given recovery time. It also provides incentives to deploy a large amount of PHEVs to improve system resiliency.
Chapter 39 – Antipsychotic drugs

Neuroleptic medications, now referred to as antipsychotic drugs, were serendipitously discovered in the early 1950s when the phenothiazine chlorpromazine, which was used as an antihistaminic adjunct during surgery on mentally ill patients, was observed to ameliorate psychotic symptoms. Dozens of phenothiazine, and later many nonphenothiazine, antipsychotics were developed and all of them were noted to cause extrapyramidal movement disorders, which instigated the theory that schizophrenia is related to increased dopamine activity. The poor tolerability to, and nonadherence with, the first-generation antipsychotics due to akathisia, dystonia, dyskinesia, and parkinsonism led eventually to the development of the second-generation antipsychotics with more serotonin 5-HT2 than D2 receptor antagonism, resulting in far fewer acute and tardive movement disorders but more metabolic adverse effects, including obesity, hyperglycemia, and hyperlipidemia. Both generations have multiple effects on various organ systems, but the second-generation agents are now indicated or used not only in primary psychotic disorders and neurologically induced psychotic symptoms, but also in nonpsychotic conditions such as bipolar disorder and major depression. Future antipsychotic drugs may transcend the model of dopamine antagonism to one of glutamate modulation.
Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

Mycolactone is the exotoxin produced by Mycobacterium ulcerans and is the virulence factor behind the neglected tropical disease Buruli ulcer. The toxin has a broad spectrum of biological effects within the host organism, stemming from its interaction with at least two molecular targets and the inhibition of protein uptake into the endoplasmic reticulum. Although it has been shown that the toxin can passively permeate into host cells, it is clearly lipophilic. Association with lipid carriers would have substantial implications for the toxin's distribution within a host organism, delivery to cellular targets, diagnostic susceptibility, and mechanisms of pathogenicity. Yet the toxin's interactions with, and distribution in, lipids are unknown. Herein we have used coarse-grained molecular dynamics simulations, guided by all-atom simulations, to study the interaction of mycolactone with pure and mixed lipid membranes. Using established techniques, we calculated the toxin's preferential localization, membrane translocation, and impact on membrane physical and dynamical properties. The computed water-octanol partition coefficient indicates that mycolactone prefers to be in an organic phase rather than in an aqueous environment. Our results show that in a solvated membrane environment the exotoxin mainly localizes in the water-membrane interface, with a preference for the glycerol moiety of lipids, consistent with the reported studies that found it in lipid extracts of the cell. The calculated association constant to the model membrane is similar to the reported association constant for Wiskott-Aldrich syndrome protein. Mycolactone is shown to modify the physical properties of membranes, lowering the transition temperature, compressibility modulus, and critical line tension at which pores can be stabilized. It also shows a tendency to behave as a linactant, a molecule that localizes at the boundary between different fluid lipid domains in membranes and promotes inter-mixing of domains. This property has implications for the toxin's cellular access, T-cell immunosuppression, and therapeutic potential.
Outcome of facial palsy from Lyme disease in prospectively followed patients who had received corticosteroids.

Abstract Although a short course of corticosteroid therapy has been shown to improve the outcome of idiopathic facial nerve palsy (Bell's palsy), it is unclear whether corticosteroids, in addition to antibiotic therapy, are beneficial, are harmful, or have no impact on the outcome of facial palsy from Lyme disease (LDFP). From 2011 through 2016, 14 patients with LDFP were enrolled into a prospective study to determine the outcome of Lyme disease over the ensuing 12 months. Eleven (78.6%) had received corticosteroids in addition to oral antibiotics and entered the study within 24 days after onset of the LDFP (median 14 days, range 2–24 days). Overall, 6 of the corticosteroid-treated patients (54.5%, 95% C.I.: 28.0% to 78.7%) had evidence of residual dysfunction of the facial nerve at the last evaluation, which occurred at a mean of 13.1 months after the baseline visit (range 9.6–19.6 months). In conclusion, although corticosteroids are frequently prescribed for LDFP, the efficacy of this therapy has not been established. Like another recent report, our study raises concern about the safety of adjunctive corticosteroid treatment for LDFP. A well-designed, prospective clinical trial is needed to determine the risk-to-benefit ratio of corticosteroid therapy for LDFP.
Automated correlative segmentation of large Transmission X-ray Microscopy (TXM) tomograms using deep learning

Abstract A unique correlative approach for automated segmentation of large 3D nanotomography datasets obtained using Transmission X-ray Microscopy (TXM) in an Al-Cu alloy has been introduced. Automated segmentation using a Convolutional Neural Network (CNN) architecture based on a deep learning approach was employed. This extremely versatile technique is capable of emulating the manual segmentation process effectively. Coupling this technique with post-scanning SEM imaging ensured precise estimation of 3D morphological parameters from nanotomography. The segmentation process as well as subsequent analysis was expedited by several orders of magnitude. Quantitative comparison between segmentation performed manually and using the CNN architecture established the accuracy of this automated technique. Its ability to robustly process ultra-large volumes of data in relatively small time frames can exponentially accelerate tomographic data analysis, possibly opening up novel avenues for performing 4D characterization experiments with finer time steps.
Pharmacokinetic Aspects of Nonlinear Drug-Protein Binding

I have lived on the West Coast for about four years now and I have come to know what laid-back means. Although Sid Riegelman spent most of his professional career in the West, no one could ever accuse him of being laid-back. There are few if any among us who could match Sid in terms of unbounded energy, enthusiasm and intensity. Yet I know very well that occasionally Sid would stop to smell the flowers. From time to time, by note, or telephone or a tap on the shoulder Sid would tell me how much he enjoyed a particular paper or bit of work. The first time this occurred was many years ago. It concerned some studies on the role of bile salts in the dissolution of drugs in the gastrointestinal tract. The comment, the praise, were profoundly important; young assistant professors are not known for their high level of confidence. The last time this occurred was but a little while ago and it concerned some research we were doing in Buffalo on the consequences of nonlinear plasma protein binding. I have chosen to review this work, mostly because Sid thought it was very nice.
Toward an Understanding of Phonological Awareness

Numerous studies have documented a relationship between phonological awareness and reading achievement. Despite this work, phonological awareness and its development are not well understood. This chapter examines phonological awareness, first by considering how it has been measured, and then, by studying factors related to performance on a frequently used measure of phonological awareness. A review of the literature showed that numerous tasks have been used to measure children’s awareness of phonemes. These can be divided into phoneme segmentation, phoneme blending, and sound comparison tasks. It is proposed that performance on phoneme segmentation and phoneme blending tasks is heavily influenced by experience with an alphabetic writing system. An investigation of a commonly used sound comparison task, the oddity task, suggested that performance on this task was dependent in part on chidren’s perceptual and memory abilities.
Consumer Logistics: An Empirical Investigation

This paper reports the findings from an empirical investigation of consumer logistics. Cluster analysis grouped individuals according to their participation in consumer logistics activities and resulted in a four-group solution. Multiple discriminant analysis was then used to determine the relationship between the four group criterion variable and five sets of predictor variables. All analyses had at least one significant function at the .05 level of significance.
Listing Basic Combinatorial Objects

At a basic level, one would expect that constructive combinatorics would address the question of how one constructs the fundamental objects in combinatorics. In fact, “constructing” these objects could mean providing an algorithm for listing all of them, or it could mean generating one of them at random. While both questions are of interest, we shall concentrate on the first.
Cluster analysis of the origins of the new influenza A(H1N1) virus

In March and April 2009, a new strain of influenza A(H1N1) virus has been isolated in Mexico and the United States. Since the initial reports more than 10,000 cases have been reported to the World Health Organization, all around the world. Several hundred isolates have already been sequenced and deposited in public databases. We have studied the genetics of the new strain and identified its closest relatives through a cluster analysis approach. We show that the new virus combines genetic information related to different swine influenza viruses. Segments PB2, PB1, PA, HA, NP and NS are related to swine H1N2 and H3N2 influenza viruses isolated in North America. Segments NA and M are related to swine influenza viruses isolated in Eurasia.
Preparation of Three-dimensional (3-D) Human Liver (HepaRG) Cultures for Histochemical and Immunohistochemical Staining and Light Microscopic Evaluation:

The use of three-dimensional (3-D) in vitro culture systems (spheroids, organoids) in biomolecular and drug discovery research has become increasingly popular. The popularity is due, in part, to a diminished reliance on animal bioassays and a desire to develop physiologically relevant cell culture systems that simulate the in vivo tissue microenvironment. Most evaluations of 3-D cultures are by confocal microscopy and high-content imaging; however, these technologies do not allow for detailed cellular morphologic assessments or permit basic hematoxylin and eosin histologic evaluations. There are few studies that have reported detailed processes for preparing 3-D cultures for paraffin embedding and subsequent use for histochemical or immunohistochemical staining. In an attempt to do so, we have developed a protocol to paraffin-embed human liver spheroids that can be sectioned with a microtome and mounted onto glass slides for routine histochemical and immunohistochemical staining and light microscopic evaluations.
Impact of iron deficiency in patients with hepatocellular carcinoma: Data from the nationwide inpatient sample from 1999-2014.

e18751Background: Iron deficiency anemia (IDA) is a common condition in cancer patients (pts) and can have a deleterious effect on their outcomes. Pts with hepatocellular carcinoma (HCC) often have...
Sexual Inequality in the Cancer Cell.

Investigating sex differences in cancer will improve therapy for both sexes and discover sex-specific protective mechanisms. Two recent analyses by Lopes-Ramos and colleagues and Li and colleagues point to specific gene regulatory networks and genomic alterations associated with sex differences in tumor incidence and progression. Integrating this information with emerging concepts about sex biases in the genome may help focus attention on factors that shift the odds for tumor growth. Cancer Res; 78(19); 5504–5. ©2018 AACR . See related articles by Li et al., p. 5527, and Lopes-Ramos et al., p. 5538 .
Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models

Diverse signaling cues and attendant proteins work together during organogenesis, including craniofacial development. Lip and palate formation starts as early as the fourth week of gestation in humans or embryonic day 9.5 in mice. Disruptions in these early events may cause serious consequences, such as orofacial clefts, mainly cleft lip and/or cleft palate. Morphogenetic Wnt signaling, along with other signaling pathways and transcription regulation mechanisms, plays crucial roles during embryonic development, yet the signaling mechanisms and interactions in lip and palate formation and fusion remain poorly understood. Various Wnt signaling and related genes have been associated with orofacial clefts. This Review discusses the role of Wnt signaling and its crosstalk with cell adhesion molecules, transcription factors, epigenetic regulators and other morphogenetic signaling pathways, including the Bmp, Fgf, Tgfβ, Shh and retinoic acid pathways, in orofacial clefts in humans and animal models, which may provide a better understanding of these disorders and could be applied towards prevention and treatments.
The GTP-binding protein-dependent activation and deactivation of cyclic GMP phosphodiesterase in rod photoreceptors.

Cyclic GMP (cGMP) has a crucial role in visual transduction. Recent electrophysiological studies clearly indicate the existence of cGMP-activated conductance in photoreceptor plasma membranes. In darkness, Na{sup +}, Ca{sup ++}, and Mg{sup ++} enter rod outer segments (ROS) through cGMP-activated channels while light closes channels by lowering cGMP concentrations through activation of cGMP phosphodiesterase (PDE). Many excellent reviews reference the mechanism of PDE activation in photoreceptors. However, recent progress in understanding the mechanisms regulating cGMP hydrolysis has raised an important question in the PDE-regulation: how does the three-dimensional movement of a subunit of transducin (retinal G protein) relate to the PDE activation Associated with that question, the mechanism of PDE regulation appears to vary at different stages of evolution, for example, frog and bovine photoreceptors. This review examines recent progress of the cGMP hydrolysis mechanism by focusing on the subunit interactions between transducin and PDE. 36 refs., 2 figs.
Serum microRNAs in ASD: Association With Monocyte Cytokine Profiles and Mitochondrial Respiration

Our previous research has shown that purified peripheral blood monocytes (PRMo) from individuals who are diagnosed with autism spectrum disorders (ASDs) and have innate immune abnormalities reveal altered interleukin-1s (IL-1s)/IL-10 ratios. We also found, in separate studies, that microRNA (miRNA) expression in PBMo and mitochondrial respiration in peripheral blood mononuclear cells (PBMCs) differed in the IL-1s/IL-10-based ASD subgroups. This study explored whether serum miRNAs are associated with both altered innate immune responses and changes in mitochondrial respiration as a link of regulatory mechanisms for these two common abnormalities in ASD subjects. Serum miRNA levels were examined by high-throughput deep sequencing in ASD and non-ASD control sera with concurrent measurement of PBMo cytokine production and mitochondrial respiration by PBMCs. ASD samples were examined as a whole group and with respect to the previously defined IL-1s/IL-10-based ASD subgroups (high, normal, and low groups). Serum miRNA levels differed between the overall ASD sera (N = 116) and non-ASD control sera (N = 35) and also differed across the IL-1s/IL-10-based ASD subgroups. Specifically, miRNA levels were increased and decreased in eight and nine miRNAs, respectively, in the high-ratio ASD subgroup (N = 48). In contrast, the low- (N = 25) and normal- (N = 43) ratio ASD subgroups only showed decreased miRNAs levels (18 and 10 miRNAs, respectively). Gene targets of the altered miRNAs in the high and/or low IL-1β/IL-10 ratio ASD subgroups were enriched in pathways critical for monocyte functions and metabolic regulation. Gene targets of the altered miRNAs in all the ASD subgroups were enriched in pathways of neuronal development and synaptic plasticity, along with cell proliferation/differentiation. ASD subgroup-specific associations were observed between serum miRNA expression and IL-1s/IL-10 ratios, mitochondrial respiration, and monocyte cytokine profiles (IL-10, CCL2, and TNF-α). In summary, our results indicate that serum levels of select miRNAs may serve as promising biomarkers for screening and monitoring changes in innate immunity and mitochondrial respiration in ASD.
Real-time Model Predictive Control for Versatile Dynamic Motions in Quadrupedal Robots

This paper presents a new Model Predictive Control (MPC) framework for controlling various dynamic movements of a quadrupedal robot. System dynamics are represented by linearizing single rigid body dynamics in three-dimensional (3D) space. Our formulation linearizes rotation matrices without resorting to parameterizations like Euler angles and quaternions, avoiding issues of singularity and unwinding phenomenon, respectively. With a carefully chosen configuration error function, the MPC control law is transcribed into a Quadratic Program (QP) which can be solved efficiently in realtime. Our formulation can stabilize a wide range of periodic quadrupedal gaits and acrobatic maneuvers. We show various simulation as well as experimental results to validate our control strategy. Experiments prove the application of this framework with a custom QP solver could reach execution rates of 160 Hz on embedded platforms.
National Police Reform Commissions: Evidence-Based Practices or Unfulfilled Promises?:

The Kerner Commission devoted significant attention to the issue of policing and its impact on communities of color in particular. In light of the 50th anniversary of the Kerner Commission, the foc...
LinkShare: device-centric control for concurrent and continuous mobile-cloud interactions

Mobile applications have become increasingly sophisticated. Emerging cognitive assistance applications can involve multiple computationally intensive modules working continuously and concurrently, further straining the already limited resources on these mobile devices. While computation offloading to the edge or the cloud is still the de facto solution, existing approaches are limited by intra-application operations only or edge-/cloud-centric scheduling. Instead, we argue that operating system level coordination is needed on the mobile side to adequately support the prospects of multi-application offloading. Specifically, both the local mobile system resource and the network bandwidth to reach the cloud need to be allocated intelligently among concurrent offloading jobs. In this paper, we build a system-level scheduler service, LinkShare, that wraps over the operating system scheduler to coordinate among multiple offloading requests. We further study the scheduling requirements and suitable metrics, and find that the most intuitive approaches of minimizing the end-to-end processing time or earliest-deadline first scheduling do not work well. Instead, LinkShare adopts earliest-deadline first with limited sharing (EDF-LS), that balances real-time requirements and fairness. Extensive evaluation of an Android implementation of LinkShare shows that adding this additional scheduler is essential, and that EDF-LS reduces the deadline miss events by up to 30% compared to the baseline.
Regularity of solutions of quasi-linear elliptic equations with $L\log^m L$ coefficients

Let $D$ be an bounded region in ${\bf R}^n$. The regularity of solutions of a family of quasilinear elliptic partial differential equations is studied, one example being $\Delta_nu=Vu^{n-1}$. The coefficients are assumed to be in the space $L\log^{m}L(D)$ for $m>n-1$. Using a Moser iteration argument coupled with the Moser-Trudinger inequality, a local $L^{\infty}$ bound on the solution $u$ is proven. A Harnack-type inequality is then proven. These results are shown to be sharp with respect to $m$. Then essential continuity of $u$ is proven, and away from the boundary a bound on the modulus of continuity.
Gamma radiation shielding properties of poly (methyl methacrylate) / Bi2O3 composites

Abstract This work investigated the gamma-ray shielding performance, and the physical and mechanical properties of poly (methyl methacrylate) (PMMA) composites embedded with 0–44.0 wt% bismuth trioxide (Bi2O3) fabricated by the fast ultraviolet (UV) curing method. The results showed that the addition of Bi2O3 had significantly improved the gamma shielding ability of PMMA composites. Mass attenuation coefficient and half-value layer were examined using five gamma sources (Cs-137, Ba-133, Cd-109, Co-57, and Co-60). The high loading of Bi2O3 in the PMMA samples improved the micro-hardness to nearly seven times that of the pure PMMA. With these enhancements, it was demonstrated that PMMA/Bi2O3 composites are promising gamma shielding materials. Furthermore, the fast UV curing exerts its great potential in significantly shortening the production cycle of shielding material to enable rapid manufacturing.
N95 reprocessing by low temperature sterilization with 59% vaporized hydrogen peroxide during the 2020 COVID-19 pandemic.

Background Response to the COVID-19 pandemic by hospital systems has been strained by severe shortages in personal protective equipment (PPE), particularly N95 respirators. Recently, the Centers for Disease Control and Prevention endorsed decontamination strategies to prolong the lifespan of single use respirators. Battelle and Duke University have validated hospital protocols to decontaminate respirators using vaporized hydrogen peroxide (VHP) at 30%-35% concentrations. To prolong our supply of respirators, we evaluated and implemented VHP decontamination at 59% hydrogen peroxide concentration while detailing the effects of this process on the filtration efficiency and quantitative fit of single-use respirators. This study may help other health systems develop local solutions to their N95 mask shortage during this COVID-19 pandemic. Methods N95 respirators (3M 8211 FF and 9210 FF) that were treated with 5 and 10 cycles of VHP by the V-PRO maX Low Temperature Sterilization System were evaluated quantitatively for filtration efficiency as well as with quantitative fit testing per Occupational Safety and Health Administration standards. A decontamination protocol was concurrently implemented at our institution. This process involved depositing used masks, reprocessing, and re-distributing treated masks efficiently back to frontline providers. Furthermore, we implemented patient safety officers on COVID-19/person under investigation units to ensure optimized donning/doffing of respirators through frontline provider education. Results There were no statistically significant changes in mean filtration efficiency between the control and VHP-treated respirators. Furthermore, both treated and untreated respirators demonstrated fit factors above the minimum pass requirement. Conclusions We have successfully demonstrated that N95 respirator decontamination with VHP at 59% hydrogen peroxide can be safely utilized to decontaminate single-use N95 respirators without significant effects on filtration efficiency or quantitative fit testing. With the COVID-19 pandemic and N95 respirator shortage, health systems without access to commercial decontamination processes should investigate the viability of such a process in their facilities.
Identity as institution: power, agency, and the self

This paper addresses issues of agency and self-identity on the basis of a phenomenology of embodiment. It considers a tension in accounts of embodiment between, on the one hand, the body as the locus of subjectivity, lived experience, and agency, and, on the other hand, the body as constructed, as the site where discursive regimes of power are inscribed. In exploring this tension I consider Frantz Fanon’s and Sarah Ahmed’s phenomenological accounts of racism to illustrate the ways in which social power and violence come to be implicated in these conflicts within our embodied identities. I also consider Foucauldian “power” in relation to Merleau-Ponty’s concept of “institution.” I argue that only the phenomenological concept of institution, by drawing our attention to the ambiguities of lived embodiment, succeeds in offering us resources for thinking about the interplay between passivity and agency in the life of the subject, and, in particular, about a form of agency not wholly reducible to the effects of power.
Autonomous vs. Self-Driving Vehicles: The Power of Language to Shape Public Perceptions

Public perception of the next generation of vehicles will affect their design, deployment, and ultimately their use. As the engineering terms of self-driving, driverless, fully automated, and auton...
A spatiotemporal analysis of motorcyclist injury severity: Findings from 20 years of crash data from Pennsylvania.

Abstract Motorcyclists face higher risks of severe injuries in crashes compared to motor vehicle drivers who are often protected by seatbelts and airbags during collisions. A report by the National Highway Traffic Safety Administration reveals that motorcyclists have 27 times the risk of fatality in traffic crashes as much as motor vehicle drivers. Previous studies have identified a list of risk factors associated with motorcyclist injury severity and generated valuable insights for countermeasures to protect motorcyclists in crashes. These studies have shown that wearing helmets and/or motorcycle-specific reflective clothing and boots, driving alcohol/drug-free, and obeying traffic regulations are good practices for safe motorcycling. However, these practices and other risk factors are likely to interact with local geographic, socio-economic, and cultural contexts, leading to diversified correlations with motorcyclist injury severity, which remains under-explored. Such correlations may exhibit variations across space and time. The objective of this study is to revisit the correlates of motorcyclist injury severity with a focus on the spatial and temporal variations of correlations between risk factors and injury severity. This study employed an integrated spatiotemporal analytical approach to mine comprehensive statewide 20 years’ motorcycle-involved traffic crashes (N = 50,823) in Pennsylvania. Non-stationarity tests were performed to examine the significance of variations in spatially and temporally local correlations. The results show that most factors, such as helmet, engine size, vehicle age, pillion passenger, at-fault striking, and speeding, hold significant non-stationary relationships with motorcyclist injury severity. Furthermore, cluster analysis of estimations reveals the regional similarities of correlates, which may help practitioners develop regional motorcyclist safety countermeasures.