cssi/SciSciGPT-SciSciNet huggingface dataset:
Multiple Pathways for Repair of DNA Double-Strand Breaks in Mammalian Chromosomes

To study repair of DNA double-strand breaks (DSBs) in mammalian chromosomes, we designed DNA substrates containing a thymidine kinase (TK) gene disrupted by the 18-bp recognition site for yeast endonuclease I-SceI. Some substrates also contained a second defective TK gene sequence to serve as a genetic donor in recombinational repair. A genomic DSB was induced by introducing endonuclease I-SceI into cells containing a stably integrated DNA substrate. DSB repair was monitored by selection for TK-positive segregants. We observed that intrachromosomal DSB repair is accomplished with nearly equal efficiencies in either the presence or absence of a homologous donor sequence. DSB repair is achieved by nonhomologous end-joining or homologous recombination, but rarely by nonconservative single-strand annealing. Repair of a chromosomal DSB by homologous recombination occurs mainly by gene conversion and appears to require a donor sequence greater than a few hundred base pairs in length. Nonhomologous end-joining events typically involve loss of very few nucleotides, and some events are associated with gene amplification at the repaired locus. Additional studies revealed that precise religation of DNA ends with no other concomitant sequence alteration is a viable mode for repair of DSBs in a mammalian genome.
The effect of one positive reinforcement on helping with cost

Twenty male college student subjects were divided into two groups. One group received reinforcement when they helped a female confederate following a request for aid, the other group did not. The helping gesture involved the volunteering by the subject to take an electrical shock which he believed could go to the confederate. The reinforcement was a “Thank you” from the confederate. Subjects who received the reinforcement continued to volunteer for shock while those who did not disctontinued volunteering.
New Simple and Efficient Bounds on the Probability of Error in the Presence of Interference and Gaussian Noise

The problem of determining or of bounding the probability of error in the presence of intersymbol interference and Gaussian noise is an important one in data communications. In this concise paper we describe new upper and lower bounds for the probability of error when the peak distortion is finite (in practice, when the eye is open) and the data are independent. Over a range of S/N of interest in data communications; these bounds compare favorably with previously published bounds of similar complexity, especially when the eye opening is small. They can be applied to multilevel AM and CPSK transmission.
Gynecologic concerns in patients with cloacal anomaly

Children with anorectal malformations (ARM) constitute a significant group within a pediatric surgery practice. It is important with female cases of anorectal malformations to consider the association of gynecologic anomalies, especially at the time of the definitive repair. However, it is critical to consider the association of such gynecologic anomalies when caring for patients with a cloacal anomaly. If not recognized, an opportunity to diagnose and treat such anomalies may be missed with the possibility of negative implications for future reproductive capacity. With the knowledge of the associated anomalies and long-term sequelae, surgeons can provide better care for girls and important counseling for parents. Knowledge of reproductive related issues in females with cloaca allows the pediatric surgeon an opportunity both, to provide optimal surgical management in infancy, childhood, and into young adulthood and to collaborate medically and surgically with an experienced gynecologist in patients with more complex anatomic variations. Appropriate counseling for patients and families about potential reproductive concerns that may develop many years after the definitive surgical repair allows preparation and planning to preserve future fertility.
Airway pressure-release ventilation in pregnant patients with acute respiratory distress syndrome: a novel strategy

BACKGROUND: Airway pressure-release ventilation (APRV) is a novel mode of positive-pressure ventilation that has several advantages over low-tidal-volume, assist-control ventilation in patients with acute respiratory distress syndrome, specifically, lower airway pressures, lower minute ventilation, minimal effects on cardio-circulatory function, ability to spontaneously breathe throughout the entire ventilatory cycle, and decreased sedation requirements. APRV is consistent with lung-protective strategies that aim to limit lung injury associated with mechanical ventilation. APRV utilization in obstetrical patients has not previously been reported. CASES: We present 2 cases of pregnant women with severe life-threatening ARDS who were successfully managed with APRV. CONCLUSIONS: APRV may have particular utility in pregnant patients with ARDS. We believe APRV was life-saving in our cases. APRV ventilation should be considered in pregnant patients with ARDS.
Radiographic Diagnosis of Chronic Rhinosinusitis

With the concurrent evolution of endoscopic sinus surgery and the technological radiologic advances, radiographic imaging has become an important modality in the diagnosis and treatment of chronic rhinosinusitis (CRS). Computed tomography (CT) is considered the imaging modality of choice for evaluating CRS, primarily due to its ability to demonstrate bony anatomy in great detail. There are numerous anatomic variants within the sinonasal cavity that may contribute to the development of CRS, and prior knowledge of these structures is essential when performing endoscopic sinus surgery. MRI is used as an adjunctive and complimentary study due to its superior soft tissue characterization. There are several characteristic findings of CRS on CT and MRI which will aid in appropriate diagnosis and surgical planning.
Improving debugging education through applied learning

In this undergraduate research project, an extensive study on current software debugging methodologies and pedagogical approaches to debugging education in computer science curriculum is conducted. Based on the research findings, a web-based software tool is developed to assess the debugging skills for computer science students. Based on the outcome of the assessment, the tool can provide appropriate tutoring and practice exercises to target at the skill weakness of each individual. The benefits for this first-hand research and development experience in software debugging include the introduction of the debugging methodology research and education to freshmen and sophomores in computer science and the creation of a unique debugging skill assessment and tutoring software that can be adopted by undergraduate computer science education community.
Design of free-surface interfaces using RANS equations

In this paper, the continuous adjoint methodology to compute shape sensitivities in free-surface hydrodynamic design problems (RANS governing systems) has been developed. This technique will allow the specific design of the free-surface interface (typically air/water), which has a great potential in problems where the target is to reduce the wave energy, e.g. ship hull design. A detailed description of the methodology as well as numerical experiments to demonstrate the ability of this new technique to reduce the wave energy will be shown. I. Introduction In the past, lot of work has been done in shape optimization for ship hydrodynamics using Computational Fluid Dynamics. However, in most of the cases, the total resistance of the ship has been selected as the objective function to minimize (subject to geometrical constraints). In this particular paper, a new point of view is presented, and a di↵erent objective function has been defined to minimize the energy of the waves generated by an object submerged in the water. The complete adjoint methodology to evaluate the gradients will be presented in this article as well as some examples that demonstrate the ability of this technique to reduce the total resistance by minimizing the size of the waves. Hydrodynamic applications of optimal shape design in systems governed by partial di↵erential equations are formulated on a fluid domain ⌦ , delimited by disconnected boundaries divided into an inlet, outlet, and solid wall boundaries S. From now on we will restrict ourselves to the analysis of optimization problems involving a functional J defined on the solid wall S, and in the entire domain ⌦ , whose value depends on the flow variables U obtained from the solution of the fluid flow equations. In this context, the generic optimization problem can be succinctly stated as follows: find S min 2 Sad such that
A Pilot Study: The Effect of Bio-Energy on Stress for University Faculty, Staff, and Students During Finals Week

Aim: To examine the effectiveness of a bio-energy intervention on self-reported stress for a convenience sample of University students, faculty, and staff during finals week. We hypothesized that p...
Analysis on Surveillance Results of Death Causes Among Urban Residents in Changsha City from 2007 to 2010

Objective To investigate the death cause constitution among the urban residents in Changsha City during the period of 2007-2010,and to analyze the main diseases affecting the residents' health. Methods The data were classified according to ICD-10 and analyzed with DeathReg2005 and SPSS13.0 software. Results Totally 1,580,453 residents were monitored from 2007 to 2010.The total death cases of the residents were 8,555.The average mortality rate was 541.30/100,000.The average standardized mortality rate was 431.36/100,000.The male mortality rate was 622.70/100,000 and the female mortality rate was 458.08/100,000,the difference was statistically significant(χ2=196.73,P=0.000).Cardiovascular and cerebrovascular disease,cancer,respiratory disease,poisoning and injury,endocrine nutritional and metabolic diseases,infectious disease,and digestive disease were the top seven death causes that accounted for 94.47% of total mortality rate. Conclusions Cardiovascular and cerebrovascular disease,cancer and respiratory disease are the main death causes among the urban residents in Changsha City.It is necessary to adopt comprehensive countermeasures so as to reduce the death cases caused by noninfectious chronic diseases.
Massively Parallel Genetics

Human genetics has historically depended on the identification of individuals whose natural genetic variation underlies an observable trait or disease risk. Here we argue that new technologies now augment this historical approach by allowing the use of massively parallel assays in model systems to measure the functional effects of genetic variation in many human genes. These studies will help establish the disease risk of both observed and potential genetic variants and to overcome the problem of "variants of uncertain significance."
CD20-Specific Engineered Toxin Body Demonstrates Direct Cell Kill Of Multiple B-Cell Non-Hodgkin's Lymphoma Types

Abstract The B-cell membrane protein CD20 is expressed by both benign and neoplastic lymphocytes. It has been a superb target for immunotherapies targeting B-cell derived diseases. There are several anti-CD20 antibodies which have been developed for B-cell lymphoma therapy. The most successful example of this targeted approach is rituximab, which is approved for front and second line therapy of Non-Hodgkin lymphoma (NHL). However, rituximab has limited direct cell-kill effects, acting primarily through indirect immune responses induced by antibody-dependent cell-mediated cytotoxicity (ADCC) and/or complement dependent cytotoxicity (CDC). While CD20-targeted radiotherapeutics have shown promise, their administrative challenges have curtailed their clinical utility. Thus, a therapeutic approach with direct cell-kill activity against CD20-expressing cells would be clinically useful. We have developed an engineered toxin body (ETB) comprising a CD20 specific scFv and a modified Shiga-like Toxin A (3F7) capable of specifically recognizing and killing CD20 expressing cells. 3F7 is selectively cytotoxic against B-cell NHL cell lines and against NHL cells obtained from patients. It demonstrated potent cytotoxicity against Burkitt's lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma with IC (50) values ranging from 1.4 nM to 12 nM. Through immunofluorescent tracking, 3F7 internalizes within one hour after binding to CD20 (+) B cells. Consistent with the in vitro activity, 3F7 demonstrated anti-tumor efficacy in mice bearing Raji xenograft tumors. These results show that 3F7 is a promising targeted therapeutic agent against CD20 positive B-cell lymphomas and is currently under further development. Disclosures: Rajagopalan: Molecular Templates: Employment. Wirth: Molecular Templates: Employment. Erdman: Molecular Templates: Employment. Brieschke: Molecular Templates: Employment. Null: Molecular Templates: Employment. Liu: Molecular Templates: Employment. Willert: Molecular Templates: Employment. Higgins: Molecular Templates: Employment.
Hybridization as a facilitator of species range expansion.

Explaining the evolution of species geographical ranges is fundamental to understanding how biodiversity is distributed and maintained. The solution to this classic problem in ecology and evolution remains elusive: we still do not fully know how species geographical ranges evolve and what factors fuel range expansions. Resolving this problem is now more crucial than ever with increasing biodiversity loss, global change and movement of species by humans. Here, we describe and evaluate the hypothesis that hybridization between species can contribute to species range expansion. We discuss how such a process can occur and the empirical data that are needed to test this hypothesis. We also examine how species can expand into new environments via hybridization with a resident species, and yet remain distinct species. Generally, hybridization may play an underappreciated role in influencing the evolution of species ranges. Whether—and to what extent—hybridization has such an effect requires further study across more diverse taxa.
Using Radial Basis Function Networks for Watermark Determination in 3D Models

In this paper, we investigate the ability of a radial basis function network to determine the values of the watermark to be inserted in a 3D triangulated mesh model. The challenge in a watermarking algorithm is to achieve high watermark embedding capacity without causing perceptual distortion to the model. The proposed technique overcomes this challenge. The principal, mean and Gaussian curvature values computed at each vertex of the 3D model collectively represent the local geometry of the vertex and its neighborhood. These curvature values are used as input feature vectors to train the neural network. The amount of watermark to be inserted at a vertex is non-linearly proportional to these feature vectors. The neural network is trained with watermark values to learn this non-linear relationship. A wide range of 3D models are used to train the neural network such that the large variations in the geometry of the vertices is incorporated by the training phase. The algorithm adopts a non-blind extraction process to retrieve the watermark. Experimental results prove that the watermarking algorithm achieves imperceptibility, high capacity and robustness to noise and cropping attacks up to 20% level. I. INTRODUCTION
From Psychoanalysis to Group Analysis: The Pioneering Work of Trigant Burrow

(2015). From Psychoanalysis to Group Analysis: The Pioneering Work of Trigant Burrow. International Journal of Group Psychotherapy: Vol. 65, No. 3, pp. 459-477.
Perfect light absorption in ultrathin optical nanocavity and its application for color filters

We demonstrated perfect light absorption inultra-thin optical nanocavity made of a percolation aluminum film and a thin silicon film deposited on aluminum metal surface. Critical coupling to the optical nanocavity results in complete light absorption at specific wavelength, determined by the silicon film thickness. Due to light penetration into aluminum metal on top and bottom, the optical nanocavity silicon layer thickness can be one order of magnitude less than the perfect light absorption wavelength.
Toward integration of Big Data, technology and information systems competencies into the accounting curriculum

Abstract Recent initiatives of the American Accounting Association (AAA) and the Association to Advance Collegiate Schools of Business International (AACSB) have emphasized the importance of integrating Big Data and technology into the accounting curriculum. In response to these calls and to identify a common body of instructional resources toward this purpose, our paper uses the lens of the Competency Integration for Accounting Education framework to provide examples of Big Data and information systems integration into instructional resources. We loosely frame these instructional resources using accounting course subjects as the unit of analysis.
Investigation of simulated microgravity effects on Streptococcus mutans physiology and global gene expression.

Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight, host factors that could contribute to oral diseases such as caries and periodontitis. However, the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study, high aspect ratio vessel S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles, H2O2 resistance, and competence in sucrose-containing biofilm media. Stationary phase S. mutans simulated microgravity cultures displayed increased killing by H2O2 compared to normal gravity control cultures, but competence was not affected. RNA-seq analysis revealed that expression of 153 genes was up-regulated ≥2-fold and 94 genes down-regulated ≥2-fold during simulated microgravity high aspect ratio vessel growth. These included a number of genes located on extrachromosomal elements, as well as genes involved in carbohydrate metabolism, translation, and stress responses. Collectively, these results suggest that growth under microgravity analog conditions promotes changes in S. mutans gene expression and physiology that may translate to an altered cariogenic potential of this organism during space flight missions. The gene expression patterns, metabolism and physiology of tooth cavities-causing microbes change in a space-like gravity environment. These findings could help explain why astronauts are at a greater risk for dental diseases when in space. Kelly Rice and colleagues from the University of Florida, Gainesville, USA, cultured Streptococcus mutans bacteria under simulated microgravity and normal gravity conditions. The bacteria grown in microgravity were more susceptible to killing with hydrogen peroxide, tended to aggregate in more compact cellular structures, showed changes in their metabolite profile and expressed around 250 genes at levels that were either much higher or lower than normal gravity control cultures. These genes included many involved in carbohydrate metabolism, protein production and stress responses. The observed changes collectively suggest that space flight and microgravity could alter the cavities-causing potential of S. mutans.
Some Sort of Map or Chart of the Adventure of the Musgrave Ritual

When and where did the Musgrave Ritual germinate, when and where did Sherlock Holmes solve the mysteries of the Ritual and of the disappearance of Rachel Howells, and when and where did Holmes tell the whole story to John Watson? This map and its companion explain. Maybe.
Mothers of violent children with mental illness: how they perceive barriers to effective help

The goal of the present study was to understand how mothers perceive and experience barriers to effective help for their violent child with mental illness. Data from ethnographic interviews with 26 self-identified mothers of violent children with mental illness were analyzed using grounded theory and focused coding. Our study identified three themes that represent barriers to help: (1) denial of mental illness and severity of violence by treatment providers, extended family, and non-family members; (2) limited access to quality treatment and supports; and (3) a recurring cycle from optimism to hopelessness. To inform policy makers and practitioners on how best to remove these barriers, we draw comparisons between the current sample and survivors of intimate partner violence. Our paper concludes with recommendations for mental health practitioners and family intervention specialists.
The Silhouette: From the 18th Century to the Present Day

“The fact remains that the silhouette is governed by a norm, and that is inescapable.” (160)Georges Vigarello is a French sociologist and historian whose work has centered on the sociology of the b...
Exploring Trajectories of Pornography Use Through Adolescence and Emerging Adulthood

While the scholarly literature on pornography use is growing, much of this literature has examined pornography use as a static feature that does not change. Despite this trend, pornography use, like most sexual behaviors, is likely best viewed as a dynamic feature that may shift across the developmental life span. Using a sample of 908 adults from the United States, retrospective data on pornography use through adolescence and emerging adulthood were gathered to explore trajectories of pornography use across these developmental periods. Latent mixture models suggested the presence of common patterns of use across both developmental periods. Adolescence patterns appeared to largely be distinguished by those who either engaged or did not engage with pornography, while emerging adulthood data revealed the presence of a group of experimenters who engaged in pornography through adolescence but then decreased use through their 20s. Men were found to be more likely to have consistent profiles of pornography use,...
Time-Contrastive Networks: Self-Supervised Learning from Video

We propose a self-supervised approach for learning representations and robotic behaviors entirely from unlabeled videos recorded from multiple viewpoints, and study how this representation can be used in two robotic imitation settings: imitating object interactions from videos of humans, and imitating human poses. Imitation of human behavior requires a viewpoint-invariant representation that captures the relationships between end-effectors (hands or robot grippers) and the environment, object attributes, and body pose. We train our representations using a triplet loss, where multiple simultaneous viewpoints of the same observation are attracted in the embedding space, while being repelled from temporal neighbors which are often visually similar but functionally different. This signal causes our model to discover attributes that do not change across viewpoint, but do change across time, while ignoring nuisance variables such as occlusions, motion blur, lighting and background. We demonstrate that this representation can be used by a robot to directly mimic human poses without an explicit correspondence, and that it can be used as a reward function within a reinforcement learning algorithm. While representations are learned from an unlabeled collection of task-related videos, robot behaviors such as pouring are learned by watching a single 3rd-person demonstration by a human. Reward functions obtained by following the human demonstrations under the learned representation enable efficient reinforcement learning that is practical for real-world robotic systems. Video results, open-source code and dataset are available at sermanet.github.io/imitate
Putting the Radical Notion of Equality in the Service of Disrupting Inequality in Education: Research Findings and Conceptual Advances on the Infinity of Human Potential:

Research on disrupting inequality in education can benefit from situating it within the debates on varying and often conflicting meanings of equality and its perils and promises. Especially in the ...
Uncertain Futures: Essays about the Irish Past for Roy Foster: Pašeta, Senia, Ed. , Oxford: Oxford University Press 300 pp., $100.00, ISBN 9780198748274 Publication Date: August 2016

Uncertain Futures: Essays about the Irish Past for Roy Foster will be welcomed by anyone with an interest in modern Ireland, and especially by historians of the nineteenth and twentieth centuries. ...
Spatially Dispersive Shock Waves in Nonlinear Optics

We discuss recent experimental work demonstrating spatial dispersive shock waves (DSWs). These structures occur whenever nonlinearity enhances diffraction so that wave spreading becomes intensity-dependent. The mechanism of this spreading follows naturally from a hydrodynamic description of light flow, in which wave steepening from phase gradients allows faster parts of a beam to overtake slower parts. Scaling relationships are developed for this spreading and experimentally observed, in both local and nonlocal media.
Computer-aided diagnosis for the detection and classification of lung cancers on chest radiographs ROC analysis of radiologists' performance.

Rationale and Objectives The aim of the study is to investigate the effect of a computer-aided diagnostic (CAD) scheme on radiologist performance in the detection of lung cancers on chest radiographs. Materials and Methods We combined two independent CAD schemes for the detection and classification of lung nodules into one new CAD scheme by use of a database of 150 chest images, including 108 cases with solitary pulmonary nodules and 42 cases without nodules. For the observer study, we selected 48 chest images, including 24 lung cancers, 12 benign nodules, and 12 cases without nodules, from the database to investigate radiologist performance in the detection of lung cancers. Nine radiologists participated in a receiver operating characteristic (ROC) study in which cases were interpreted first without and then with computer output, which indicated locations of possible lung nodules, together with a five-color scale illustrating the computer-estimated likelihood of malignancy of the detected nodules. Results Performance of the CAD scheme indicated that sensitivity in detecting lung nodules was 80.6%, with 1.2 false-positive results per image, and sensitivity and specificity for classification of nodules by use of the same database for training and testing the CAD scheme were 87.7% and 66.7%, respectively. Average area under the ROC curve value for detection of lung cancers improved significantly ( P = .008) from without (0.724) to with CAD (0.778). Conclusion This type of CAD scheme, which includes two functions, namely detection and classification, can improve radiologist accuracy in the diagnosis of lung cancer.
121-P: PROSPECTIVE HEMATOPOIETIC STEM CELL RECIPIENT TYPING REVEALED AN INHERITED NOVEL DQB1 ALLELE – RAISING QUESTIONS FOR NMDP POTENTIAL DONOR SEARCHING

Aim Increased novel allele discovery has a huge contribution to HLA diversity, which could, however, complicate donor search. Currently, no clear guidelines of unrelated hematopoietic stem cell (HSC) donor search are available when novel alleles are involved. Novel alleles raise questions of the clinical significance of the substitution and its effect on unrelated donor search. In this study we present an approach to evaluate a novel allele for donor search. Methods HLA high resolution typing was performed by SBT. We examined the clinical significance of a novel DQB1 ∗ 06:XX allele for the difference between it and the common DQB1 ∗ 06:02, the nature of the changed amino acid, and the location of the changed amino acid on three dimensional structure (α helix or β sheet). Results DQB1 high resolution typing revealed a novel allele identical to DQB1 ∗ 06:02 with except for a mismatch at position 25 within exon 2. The Nucleotide changed from ‘G’ to ‘T’ which caused amino acid changing from Glycine to Valine at codon 13(β13) in the amino-terminal region. The mutation is located on the floor of groove accommodating anchor position pocket 4 (P4). The side group of Glycine in DQB1 ∗ 06:02 changed from –H to –C3H7 for Valine in novel DQB1 ∗ 06:XX. The replaced side group –C3H7 occupies more space and possesses more hydrogen bonds. Although the shape and affinity of the peptide binding pocket might be altered due to changing of the side chain, both Valine and Glycine still belong to hydrophobic amino acid group. High resolution HLA typing of his mother and three siblings were also performed. The novel allele was inherited from the mother. Conclusions Our findings suggest that the amino acid change of the novel allele DQB1 ∗ 06:XX might not be clinically significant based on its location and characteristics when compared to the common DQB1 ∗ 06:02. The method we used to evaluate a novel allele could be a practical approach for the unrelated donor search for a potential HSC recipient with a novel allele of any loci.
A Compressed Sensing Estimation Technique for Doubly Selective Channel in OFDM Systems

In this work, an estimation algorithm based on the compressive sensing (CS) technique is proposed for an orthogonal frequency division multiplexing (OFDM) system applied to multi-path time-varying channels. A fitting polynomial is used to approximate each channel path, and full-band training symbols are adopted. The variation of the channel response can then be evaluated according to the observation on the inter-carrier interference (ICI) from the determinate signals. The CS-based technique is introduced to explore the sparsity of the double-selective channel and the usage of high-order fitting polynomials is allowed. The orthogonal matching pursuit (OMP) algorithm is designed to cooperate with the fitting polynomial model, and more accurate channel estimation results can be provided compared to those provided by conventional least-square (LS) algorithms. When multiple transmission antennas are required, the advantage of the proposed polynomial-fitting OMP (PF-OMP) algorithm is more obvious as more transmission antennas are used.
Glass in Integrated Photonics

Integrated photonics, which generically refers to the technology of combining multiple optical components on a chip-scale platform to form a functional photonic circuit, is often hailed as the optical equivalent of electronic integrated circuits, which holds the potential to revolutionize communications, computing, sensing, and imaging. Similar to microelectronic integrated circuits, which assimilate more than half the Mendeleev periodic table into the manufacturing process, integrated photonics necessarily involves many classes of materials to enable different photonic functionalities essential to photonic circuit operation. Glassy materials, with their exceptional optical and structural properties, constitute critical building blocks in state-of-the-art integrated photonic systems. The progress in these materials will help diversify the choices of materials for novel devices and components and will, therefore, push forward the development of integrated photonics with advanced functionalities. This chapter addresses the key facets of glassy materials in the context of integrated photonics, including material characteristics and processing technologies with specific application examples based on different glass composition families.
Profiling of the reprogramome and quantification of fibroblast reprogramming to pluripotency

Pluripotent state can be established via reprogramming of somatic nuclei by factors within an oocyte or by ectopic expression of a few transgenes. Considered as being extensive and intensive, the full complement of genes to be reprogrammed, however, has never been defined, nor has the degree of reprogramming been determined quantitatively. Here, we propose a new concept of reprogramome, which is defined as the full complement of genes that need to be reprogrammed to the expression levels found in pluripotent stem cells (PSCs). This concept in combination with RNA-seq enables us to precisely profile reprogramome and sub-reprogramomes, and study the reprogramming process with the help of other available tools such as GO analyses. With reprogramming of human fibroblasts into PSCs as an example, we have defined the full complement of the human fibroblast-to-PSC reprogramome. Furthermore, our analyses of the reprogramome revealed that WNT pathways and genes with roles in cellular morphogenesis have to be extensively and intensely reprogrammed for the establishment of pluripotency. We further developed the first mathematical model to quantitate the overall reprogramming, as well as reprogramming in a specific cellular feature such as WNT signaling pathways and genes regulating cellular morphogenesis. We anticipate that our concept and mathematical model may be applied to study and quantitate other reprogramming (pluripotency reprogramming from other somatic cells, and lineage reprogramming), as well as transcriptional and epigenetic differences between any two types of cells including cancer cells and their normal counterparts.
Continuous growth phenomenon for direct synthesis of monodisperse water-soluble iron oxide nanoparticles with extraordinarily high relaxivity

The direct synthesis of highly water-soluble nanoparticles has attracted intensive interest, but systematic size control has not been reported. Here, we developed a general method for synthesizing monodisperse water-soluble iron oxide nanoparticles with nanometer-scale size increments from 4 nm to 13 nm in a single reaction. Precise size control was achieved by continuous growth in an amphiphilic solvent, diethylene glycol (DEG), where the growth step was separated from the nucleation step by sequential addition of a reactant. There was only one reactant in the synthesis and no need for additional capping agents and reducing agents. This study reveals the "living growth" character of iron oxide nanoparticles synthesised in an amphiphilic solvent. The synthetic method shows high reproducibility. The as-prepared iron oxide nanoparticles are extremely water soluble without any surface modification. Surprisingly, the synthesized 9 nm iron oxide nanoparticles exhibit extremely high transversal and longitudinal relaxivities of 425 mM-1 s-1 and 32 mM-1 s-1 respectively, which is among the highest transversal relaxivity in the literature for sub-10 nm spherical nanoparticles. This study will not only shed light on the continuous growth phenomenon of iron oxide nanoparticles in an amphiphilic solvent, but could also stimulate the synthesis and application of iron oxide nanoparticles. The continuous growth method could be further extended to other materials for the controlled synthesis of water-soluble nanoparticles.
A microfluidic computational fluid dynamics model for cellular interaction studies of sickle cell disease vaso-occlusions.

Abstract Individuals with sickle cell disease are plagued with vaso-occlusions, chronic blockages within the vasculature. Several factors including stiffer sickle red blood cells and increased cell aggregation contribute to vaso-occlusion formation; however much remains to be understood. We present a computational fluid dynamics blood flow simulation within a microfluidic platform using the Carreau model and Murray's law. Vaso-occlusions form preferentially near bifurcations within 60 s in the sickle cell disease simulation. Velocity profiles and shear rates align with clinical and experimental reports. We assert that results from this study can be utilized to inform experimental investigations and microfluidic system design decisions.
Evidence-Based Treatment for Victims of Child Sexual Abuse and Exploitation

This chapter is focused on evidence-based treatments (EBTs) for victims of child abuse and other exploitation. The introductory section addresses how the separate fields of child maltreatment and childhood trauma merged in the early 2000s. There is also a discussion of three major facets of EBTs for childhood trauma, including parental involvement, a phased-based approach, and trauma narration and processing. A brief review is provided of EBTs for childhood traumas that have some relevance for sexual abuse. The last part of the chapter is focused on trauma-focused cognitive behavioral therapy (TF-CBT) which is the EBT for the sequelae of childhood trauma that has the greatest amount of empirical support. There is an overview of the components of TF-CBT and the clinical implications of these interventions for children who have experienced sexual abuse or other sexual exploitation. Two major randomized clinical trials of TF-CBT for children who have been sexually victimized are described. Finally, the implications of this research for online sexual exploitation are discussed.
ATHLETE IDENTITY AND COMMON BENEFITS AND BARRIERS TO SPORT PARTICIPATION AMONGST ADOLESCENT SLED HOCKEY PLAYERS

Background:The physical, psychological, and social benefits of sports participation in adolescents have been well reported in the able-bodied population. However, those with physical disabilities e...
Clustering Analysis Methods for GNSS Observations: A Data-Driven Approach to Identifying California's Major Faults.

We present a data-driven approach to clustering or grouping Global Navigation Satellite System (GNSS) stations according to observed velocities, displacements or other selected characteristics. Clustering GNSS stations provides useful scientific information, and is a necessary initial step in other analysis, such as detecting aseismic transient signals (Granat et al., 2013, https://doi.org/10.1785/0220130039). Desired features of the data can be selected for clustering, including some subset of displacement or velocity components, uncertainty estimates, station location, and other relevant information. Based on those selections, the clustering procedure autonomously groups the GNSS stations according to a selected clustering method. We have implemented this approach as a Python application, allowing us to draw upon the full range of open source clustering methods available in Python's scikit-learn package (Pedregosa et al., 2011, https://doi.org/10.5555/1953048.2078195). The application returns the stations labeled by group as a table and color coded KML file and is designed to work with the GNSS information available from GeoGateway (Donnellan et al., 2021, https://doi.org/10.1007/s12145-020-00561-7; Heflin et al., 2020, https://doi.org/10.1029/2019ea000644) but is easily extensible. We demonstrate the methodology on California and western Nevada. The results show partitions that follow faults or geologic boundaries, including for recent large earthquakes and post-seismic motion. The San Andreas fault system is most prominent, reflecting Pacific-North American plate boundary motion. Deformation reflected as class boundaries is distributed north and south of the central California creeping section. For most models a cluster boundary connects the southernmost San Andreas fault with the Eastern California Shear Zone (ECSZ) rather than continuing through the San Gorgonio Pass.
Discrete-Time Survival Analysis in Prevention Science

Survival analysis refers to the general set of statistical methods developed specifically to model the timing of events. This chapter concerns a subset of those methods that deals with events measured or occurring in discrete-time or grouped-time intervals, sometimes referred to as event history analysis. The logistic hazard regression model linking the hazard odds of event occurrence in each time period to time-varying and time-invariant predictors is detailed. Survival models are illustrated with data on alcohol use onset in adolescence and early adulthood from the first seven waves of NLSY97. Advanced modeling extensions utilizing a structural equation modeling framework, similar to the latent class regression approach presented by Muthen and Masyn (Journal of Educational and Behavioral Statistics 30(1):27–58, 2005), are discussed.
Optical Properties of Simulated Astrophysical Grains and their Dynamics in the Near-Earth Environment LAUR 85-1978

Plans are underway to prepare simulated interplanetary grains and study their behavior when released into low-Earth orbit. The program is twofold: preparing and characterizing, in the laboratory, grains which simulate interstellar and interplanetary grains, and monitoring the optical properties of grains released into low-Earth orbit to study their dynamical behavior and interaction with the fields and plasma near the earth. Such phenomena as grain coagulation and alignment and also the effect of grains on the Earth’s plasma environment will be studied.
Causal Tendency, Necessitivity and Sufficientivity: An Updated Review

The tendency of one event F to cause a later event E was explicated by a simple formula in terms of probability by Good (1961/62), more specifically in terms of ‘weights of evidence’ (logarithms of Bayes factors). The argument was based on the concept of causal circuits. The same explication, and a generalization, are reached here without making use of that concept, and the mathematical level is elementary.
OLIGURIA AND ANURIA DUE TO INCREASED INTRARENAL PRESSURE

Excerpt The author's motive in publishing the results of this investigation was a desire to devise adequate treatment for the great number of victims of crush injury occurring in the war zones. Som...
Chapter 1 Molecular structure determination from spectroscopic data using scaled moments of inertia

Publisher Summary This chapter demonstrates the scaled moment of inertia (r ρ m ) structure method to yield an excellent approximation to the theoretically significant equilibrium (r e ) structure. A practical variant of Watson's r m procedure, the method requires only the spectroscopic data necessary to perform a complete ground state substitution (r s ) structure determination. The resulting r ρ m structure appears to be invariably a more reliable estimate of the true r e structure than is the r s structure. For polyatomic molecules, the heavy-atom distance parameters are expected to be within 0.001–0.002 A of the r e value in most cases. For hydrogen-containing molecules, a special empirical correction is needed to handle the data for the hydrogen isotopomers. This correction ensures that the quality of the heavy-atom parameters remains high, and leads to H-atom parameters of reduced, but useful, accuracy (0.002–0.004 A). The new procedure permits for the first time the practical estimation of reliable near-r e structures for polyatomic organic molecules from gas-phase spectroscopic ground state rotational constants. Along with gas electron diffraction and modem high-quality ab initio computations, the r ρ m methodology provides a reliable new tool for the high-precision structure determination of modest-sized polyatomic organic molecules.
Abstract P1-07-12: Defining the role of the kynurenine pathway in mediating anoikis resistance in triple negative breast cancer

Background: Anoikis resistance is thought to be a critical trait of metastatic cancer cells, enabling them to leave the primary tumor and travel through extracellular matrix, intravasate, and survive in the vasculature or lymphatics in transit to a metastatic site. This is particularly important for the triple-negative breast cancer (TNBC) subtype, which has a peak risk of recurrence within the first three years post-diagnosis and an increased mortality rate in the first five years as compared to other subtypes. We performed global profiling of TNBC cells in attached versus forced suspension culture conditions (using poly-HEMA coated plates) for 24 hours. These data revealed that TNBC cells surviving in suspension upregulate multiple genes involved in tryptophan catabolism, also known as the kynurenine pathway (KP), including the rate limiting enzyme tryptophan 2,3,-dioxygenase (TDO) and kynureninase (KYNU). A key metabolite of this pathway has been found to activate the aryl hydrocarbon receptor (AhR), which was also up-regulated in suspended cells. Hypothesis: We hypothesize that the ability to upregulate the kynurenine pathway (KP) facilitates TNBC cell survival in suspension and mediates the migratory/invasive potential of TNBC. Methods: We assessed mRNA and protein levels of TDO2, KYNU and AhR by RT-qPCR and western blot. AhR luciferase reporter activity, as well as known AhR regulated genes, were measured in suspension compared to adherent conditions. TNBC cells were treated with small molecule inhibitors of AhR and TDO2. Additionally, secretion of endogenous kynurenine was measured by high performance liquid chromatography (HPLC). Purified kynurenine was added to rescue AhR activity following TDO2 inhibition. Finally, anoikis sensitivity and migratory potential were measured following pharmacological inhibition of TDO2 and AhR. Results: Relative mRNA levels of TDO2, KYNU, and AhR increase 9, 7, and 2 fold respectively in suspended TNBC cells compared to adherent conditions (P Conclusions: Collectively, these results suggest that the kynurenine pathway may play a critical role in metastatic TNBC. Further mechanistic studies will focus on how the kynurenine pathway is mediating these tumorigenic properties either through the de novo synthesis of NAD+ and/or activation of AhR by kynurenine. Targeting the kynurenine pathway in the clinic may provide a therapeutic strategy to reduce TNBC mortality rates. Citation Format: Thomas Rogers, Nicholas D9Amato, Travis Nemkov, Michael Gordon, Kirk Hansen, Jennifer Richer. Defining the role of the kynurenine pathway in mediating anoikis resistance in triple negative breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P1-07-12.
Regulation of N-Nitrosodimethylamine Demethylase in Rat Liver and Kidney

Abstract In previous work, the low Km form of N-nitrosodimethylamine (NDMA) demethylase has been demonstrated to be due to a specific form of cytochrome P-450 (designated as P-450ac) and to be the enzyme required for the metabolic activation of NDMA. The present work deals with the regulation of P-450ac in rat liver during development as well as the mechanism of induction of P-450ac in rat liver and kidney by inducers. NDMA demethylase activity was almost undetectable in the liver of newborn rats, increased after day 4, and remained elevated throughout the first 17 days of the neonatal period. The enhancement of NDMA demethylase activity during development was accompanied by corresponding increases of P-450ac content and P-450ac mRNA levels as determined by Western and slot blot analyses, respectively. No sex differences with respect to this enzyme were observed in the developing rats. Acetone treatment on late-term pregnant rats for 2 days resulted in transplacental inductions of P-450ac and P-450ac mRNA in the newborn rats. Pretreatment of young male rats and adult female rats with acetone or isopropyl alcohol caused increases of NDMA demethylase activity and P-450ac content in the liver but no significant change in the P-450ac mRNA level. These facts suggest the possible existence of a posttranscription regulatory mechanism under these induction conditions. The presence of P-450ac in rat kidney was demonstrated by Western and Northern blot analyses. The renal form of P-450ac seemed to be regulated in a fashion similar to the hepatic P-450ac regarding its response to inducing factors such as fasting and acetone treatment.