cssi/SciSciGPT-SciSciNet huggingface dataset:
Modern NMR Spectroscopy and X-ray Crystallography : a Different Approach to Study the Structure and its Function of a Protein

The NMR spectroscopy has been utilized widely for a elucidation of the structural change of a protein caused by the change of pH, ionic strength, temperature, and ligand concentration in solution. The X-ray was less utilized for these study excutable easily in solution, but is utilized much for the structural determination of a protein. Such difference has ever lead to the situation that the NMR relied on the structure solved by X-ray and the X-ray argued its struture in reference to the conformational change elucidated by NMR. However, recent developments of NMR spectroscopy made it possible to determine the three-dimensional structure, and the X-ray techniques has also been developped to clarify the structural change of a protein. This review compares the recent development of these two techniques, and will discuss about the future collaborating interaction between NMR and X-ray.
Non-accidental Head Trauma

Non-accidental head trauma is the most common cause of death from inflicted injury in children. Discerning discrepancies between the history given by caretakers and the clinical presentation of the child is central to the evaluation of a child in whom intentional head trauma is suspected. Because signs and symptoms of abuse resulting in head injury may be similar to those seen in common childhood illnesses, serious injury often goes undetected or misdiagnosed. Non-accidental head trauma, which is commonly referred to as abusive head trauma, is a definable form of physical child abuse and should be considered in any case where there is a lack of history of trauma or insufficient history to explain a child’s injuries. There are specific signs that suggest abusive head trauma and the diagnosis should be considered when they are encountered. The medical work-up for abusive head trauma includes looking for intracranial injuries and skeletal trauma on radiographic studies, the assistance of ophthalmologic assessments to document possible associated intraocular injury, and laboratory tests, including hematologic and genetic work-ups to rule out any organic causes for intracranial bleeds. This medical work-up is always performed along with the evaluations and investigations of both Child Protective Services and law enforcement to obtain the most comprehensive assessment.
A game-theoretic approach for radar and LTE systems coexistence in the unlicensed band

Due to the tremendous growing demand for data traffic in cellular networks, and given how congested the RF environment has become, Long Term Evolution (LTE) has been proposed to be implemented in the unlicensed 5 GHz band. The 5 GHz band is occupied by several radar systems. So there is a definite need to develop a novel spectrum sharing techniques that takes into account maintaining the great performance of LTE technology without affecting the detection capability of the radar system. In this research, we plan to explore applying a game-theoretic approach to create a novel spectrum sharing algorithm between LTE and radar systems.
Source Control and Supporting Therapeutics: Integrating Bacterial Invasion, Host Defense, and Clinical Interventions with Source Control Procedures

While the concept of source control is not new and is in widespread practice, some of the underpinning that defines the practice has evolved. While source control is commonly interpreted as the drainage of purulent material, removal of infected medical devices, control of GI tract perforation, and debridement of devitalized tissue, all of those elements are reactionary in nature and are accompanied by adjunctive antibiotics for variable courses. Over the last decade, major advances have occurred in understanding the molecular basis of disease pathogenesis as well as the host response to injury, inflammation, and infection. These advances may enable proactive measures to be undertaken that target specific elements of host defense to optimize patient outcome in the emergency department (ED), operating room (OR), intensive care unit (ICU), or general ward. This chapter will address how one may integrate standard source control practices with recent data on potentially controllable elements that may enable host defense success.
Cooking up the nation: Spanish culinary texts and culinary nationalization in the late nineteenth and early twentieth century

Manuel Vazquez Montalban asked in 2001 if a Spanish cuisine exists (Contra los gourmets). He concluded that it is more appropriate to consider Spain’s multiple cuisines rather than a singular natio...
An Interval-based Algorithm for Adaptive IIR Filters

We present an algorithm for adaptive IIR filters that is designed to yield stable filters while guaranteeing convergence to the global minima of the mean square error (MSE) cost function. The algorithm is based on the global optimization technique of branch-and-bound along with interval arithmetic to compute bounds on the cost function. By so doing, we ensure that infinite precision results are not lost due to rounding errors that occur naturally in digital computations. The effectiveness of the algorithm is demonstrated through simulation results which show that it is capable of locating global minimum points in the presence of local minima.
Potential Inhibitory Influence of miRNA 210 on Regulatory T Cells during Epicutaneous Chemical Sensitization

Toluene diisocyanate (TDI) is a potent low molecular weight chemical sensitizer and a leading cause of chemical-induced occupational asthma. The regulatory potential of microRNAs (miRNAs) has been recognized in a variety of disease states, including allergic disease; however, the roles of miRNAs in chemical sensitization are largely unknown. In a previous work, increased expression of multiple miRNAs during TDI sensitization was observed and several putative mRNA targets identified for these miRNAs were directly related to regulatory T-cell (Treg) differentiation and function including Foxp3 and Runx3. In this work, we show that miR-210 expression is increased in the mouse draining lymph node (dLN) and Treg subsets following dermal TDI sensitization. Alterations in dLN mRNA and protein expression of Treg related genes/putative miR-210 targets (foxp3, runx3, ctla4, and cd25) were observed at multiple time points following TDI exposure and in ex vivo systems. A Treg suppression assay, including a miR-210 mimic, was utilized to investigate the suppressive ability of Tregs. Cells derived from TDI sensitized mice treated with miR-210 mimic had less expression of miR-210 compared to the acetone control suggesting other factors, such as additional miRNAs, might be involved in the regulation of the functional capabilities of these cells. These novel findings indicate that miR-210 may have an inhibitory role in Treg function during TDI sensitization. Because the functional roles of miRNAs have not been previously elucidated in a model of chemical sensitization, these data contribute to the understanding of the potential immunologic mechanisms of chemical induced allergic disease.
Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth–death (FBD) process provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, the FBD tree prior allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.
Meal pattern alterations associated with intermittent fasting for weight loss are normalized after high-fat diet re-feeding

Alternate day, intermittent fasting (IMF) can be an effective weight loss strategy. However, the effects of IMF on eating behaviors are not well characterized. We investigated the acute and residual effects of IMF for weight loss on meal patterns in adult obese male C57BL/6 mice. After 8weeks of ad libitum high-fat diet to induce diet-induced obesity (DIO), mice were either continued on ad libitum high-fat diet (HFD) or placed on one of 5 diet strategies for weight loss: IMF of high-fat diet (IMF-HFD), pair-fed to IMF-HFD group (PF-HFD), ad libitum low-fat diet (LFD), IMF of low-fat diet (IMF-LFD), or pair-fed to IMF-LFD group (PF-LFD). After the 4-week diet period, all groups were refed the high-fat diet for 6weeks. By the end of the diet period, all 5 groups had lost weight compared with HFD group, but after 6weeks of HFD re-feeding all groups had similar body weights. On (Day 2) of the diet period, IMF-HFD had greater first meal size and faster eating rate compared with HFD. Also, first meal duration was greater in LFD and IMF-LFD compared with HFD. At the end of the diet period (Day 28), the intermittent fasting groups (IMF-HFD and IMF-LFD) had greater first meal sizes and faster first meal eating rate compared with their respective ad libitum fed groups on similar diets (HFD and LFD). Also, average meal duration was longer on Day 28 in the low-fat diet groups (LFD and IMF-LFD) compared with high-fat diet groups (HFD and IMF-HFD). After 6weeks of HFD re-feeding (Day 70), there were no differences in meal patterns in groups that had previously experienced intermittent fasting compared with ad libitum fed groups. These findings suggest that meal patterns are only transiently altered during alternate day intermittent fasting for weight loss in obese male mice.
Next-generation sequencing of urine specimens: A novel platform for genomic analysis in patients with non-muscle-invasive urothelial carcinoma treated with bacille Calmette-Guérin.

BACKGROUND Biopsies from patients with high-risk (HR) non–muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guerin (BCG) treatment. METHODS Forty-one cytology slides from patients with HR NMIUC treated with intravesical BCG were selected for this study. Histological confirmation was available for all cases. The specimens were subjected to NGS analysis with a customized targeted exome capture assay composed of 341 genes. RESULTS In this cohort, genomic alterations were successfully identified in all cytology samples. Mutations were detected down to a 2% allele frequency and chromosomal rearrangements including copy number alterations and gene fusions were identified. The most frequently altered genes included telomerase reverse transcriptase (TERT), tumor protein 53 (TP53), Erb-B2 receptor tyrosine kinase 2 (ERBB2), and chromatin remodeling genes such as lysine demethylase 6A (KDM6A) and AT-rich interaction domain 1A (ARID1A). For patients with matched tumor tissue, cytology specimens revealed all mutations detected in tissue as well as additional mutations, and this suggested that urine might more effectively capture the full genetic heterogeneity of disease than an individual cystectomy. Alterations in multiple genes correlated with clinical and histopathological features, including responses to BCG treatment, flat architecture versus papillary architecture, and smoking history. CONCLUSIONS Urine specimens can replace tissue as a substrate for NGS analysis of HR NMIUC. Several genomic alterations identified in urine specimens might be associated with histological features and clinical characteristics. Cancer Cytopathol 2017;125:416–26. © 2017 American Cancer Society.
Internalized transphobia: Exploring perceptions of social messages in transgender and gender-nonconforming adults

ABSTRACTBackground: Transgender and gender nonconforming (TGNC) individuals encounter a variety of minority stressors that have yet to be fully articulated or explored within the research literature. The purpose of this study is to better understand internalized stigma—the experience of accepting and internalizing negative social messages and experiences about one's identity—an underexplored minority stressor for TGNC people.Method: We conducted in-depth interviews with 30 diverse TGNC participants using consensual qualitative research (CQR) methodology.Results: Following data saturation and analysis, six distinct themes emerged across participants: (1) TGNC identities are regarded negatively by society; (2) social messages are perceived as originating from the media and religious ideology; (3) TGNC individuals report emotional distress; (4) negative self-perceptions in response to social messages; (5) TGNC individuals report resilience processes in response to negative social messages; and (6) social mes...
CASAS: Cancer Survival Analysis Suite, a web based application

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis: quantile, landmark and competing risks, in addition to standard survival analysis. The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots. Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/ . The developmental repository is available at https://github.com/manalirupji/CASAS/ .
Effects of Free Energy and Solvent on Rates of Intramolecular Electron Transfer in Organic Radical Anions

Rates of intramolecular electron transfer from a 1,1 -biphenylyl radical anion to six different acceptors on an androstane scaffold are examined with the aid of a theory that was developed recently to include effects of vibrational relaxations and dephasing. The electronic- interaction matrix element and other parameters needed for the theory are obtained by quantum- mechanical/molecular-mechanical simulations of the reactions in five solvents ranging from iso-octane to methyltetrahydrofuran. Intramolecular vibrational modes that are coupled to electron transfer are resolved in simulations in iso-octane and cyclohexane. The energies and coupling factors for these modes allow the theory to be extended to incorporate transitions to and from excited vibrational levels. The calculated rates of electron transfer agree well with experimental measurements from the literature, except for reactions in which excited electronic states of the products become important.
Qualitative assessment of extractables from single-use components and the impact of reference standard selection

The advent of single-use bioprocess systems used for the delivery, storage or manufacture of biopharmaceuticals has introduced a new potential source for extractables and leachables (E&L) as these systems are comprised of polymeric materials. Several industry working groups, the FDA and USP have issued guidance and draft guidance on E&L analyses for a variety of applications. These documents typically indicate that mass spectrometry should be applied for discovery of E&L's but provide little guidance as to the exact analytical methodology which should be used. We investigated the extractable profiles of a model single-use bioprocessing system consisting of a single-use bioprocess bag, connector tubing, and a hydrophilic disk filter including filter housing. Extractions were performed in water, ethanol, ethanol/water (50:50) and saline solutions. Extracts were analyzed using a stepwise analytical methodology including a variety of screening and mass spectrometry methods We then used this model system to demonstrate the use of recursive feature finding to automatically detect unique extractables followed by statistical filtering to focus on differentially present extractables which were above the analytical evaluation threshold (AET). We further show the significant affects of standard selection on the number of compounds determined to be above AET when reducing liquid chromatography-mass spectrometry (LC/MS) data. A relative response factor database consisting of 14 structurally diverse commercially available polymer additives was used to arrive at an LC/MS identification threshold. The results of this study demonstrate that significant care should be taken when selecting standards for LC/MS analysis to avoid under reporting of extractables and leachables.
An iterative refinement approach to fitting clearing functions to data from simulation models of production systems

We examine the problem of fitting clearing functions that estimate the expected output of a production resource as a function of its expected workload from empirical data. Unlike most regression problems, the independent variables are not directly controllable due to the presence of a planning model that controls releases to the production system, and the release decisions made by the planning model are themselves dependent on the estimated clearing function. We propose an iterative refinement procedure that uses simulation experiments to resample data from the production system as the parameters of the clearing function are iteratively updated. We compare the iterative procedure to previously used approaches with promising results.
An Efficient Method for the Expression and Purification of Aβ(M1–42)

Advances in amyloid research rely on improved access to the β-amyloid peptide, Aβ. N-Terminal methionine-extended Aβ, Aβ(M1–42), is a readily expressed and widely used form of Aβ with properties comparable to those of the natural Aβ(1–42) peptide. Expression of Aβ(M1–42) is simple to execute and avoids an expensive and often difficult enzymatic cleavage step associated with expression and isolation of Aβ(1–42). This paper reports an efficient method for the expression and purification of Aβ(M1–42) and 15N-labeled Aβ(M1–42). This method affords the pure peptide at ∼19 mg/L of bacterial culture through simple and inexpensive steps in 3 days. This paper also reports a simple method for the construction of recombinant plasmids and the expression and purification of Aβ(M1–42) peptides containing familial mutations. We anticipate that these methods will enable experiments that would otherwise be hindered by insufficient access to Aβ.
Marine Metal Pollutants. A Small Set.

Abstract Three metal pollution episodes in the marine environment have certain commonalities: they involve elements associated with organic moieties: tributyltin, methyl mercury and organically chelated copper; two of the events were identified at maricultural activities; and catastrophes were necessary to bring the problems to the attention of the scientific community. Utilizing the lessons learned from these three events provides guidance to predicting potential problems in the future.
Grounding Zone and Associated Proglacial Seismic Facies from Bransfield Basin Antarctica

Bransfield Basin separates the South Shetland Islands and the western margin of the northern Antarctic Peninsula (Fig. 1). The basin is the youngest of several convergent margin basins formed on the Pacific margins of South America and Antarctica. The study area is characterized by elevated levels of precipitation and temperature relative to the rest of Antarctica [Reynolds, 1981].
Automatic Diacritization for Low-Resource Languages Using a Hybrid Word and Consonant CMM

We are interested in diacritizing Semitic languages, especially Syriac, using only dia-critized texts. Previous methods have required the use of tools such as part-of-speech taggers, segmenters, morphological analyzers, and linguistic rules to produce state-of-the-art results. We present a low-resource, data-driven, and language-independent approach that uses a hybrid word- and consonant-level conditional Markov model. Our approach rivals the best previously published results in Arabic (15% WER with case endings), without the use of a morphological analyzer. In Syriac, we reduce the WER over a strong baseline by 30% to achieve a WER of 10.5%. We also report results for Hebrew and English.
Regulation of B-cell differentiation by stromal cells

Publisher Summary Stromal cells are a cell type that supports the growth and differentiation of hematopoietic cells. The formation of a stromal cell matrix is necessary during development before other cell lineages, such as hematopoietic cells, can begin their developmental pathways. This chapter focuses on early stages of development in the B-lymphocyte pathway that require bone marrow stromal elements and are antigen independent. The B-cell development involves commitment of the pluripotent hematopoietic stem-cell to the B-cell pathway. The key issues of the B-cell differentiation pathway, to illuminate potential mechanisms by which B-cells develop, are also addressed. Moreover, the signals derived from stroma influencing B-cell growth and developments are studied. A positive or negative influence of cytokines on B-cell development is also discussed. Therefore, the natural and artificial mutations have given insight into the regulation of B cell development.
Huntington disease: A quarter century of progress since the gene discovery.

Abstract Huntington disease (HD) is an autosomal dominant neurodegenerative disorder characterized by motor, behavioral, and cognitive manifestations. It is caused by an expansion of a trinucleotide repeat in the huntingtin gene (HTT) on chromosome 4. Although disease onset is currently clinically defined by motor signs, the presence of non-motor symptoms prior to motor diagnosis is increasingly recognized. Complex multimodal symptoms adversely affect quality of life and longevity of patients. Thoughtful interdisciplinary symptomatic care can make a major positive impact for patients and families. A variety of symptomatic treatments are currently available, and new symptomatic and potentially disease modifying therapies are being actively developed. Functional and quality of life outcome measures can be used to assess efficacy of clinical interventions. These outcomes along with clinical data and novel longitudinal biomarkers are increasingly utilized in clinical trials, particularly those testing disease-modifying therapeutics. Recent advances in novel therapeutic strategies, including targeting mutant huntingtin (HTT) and the HTT gene, promise another wave of disease-modifying trials in the near future. Better appreciation of heterogeneous clinical phenomenology and immediate tractable treatment goals coupled with advances in new therapeutics heralds a golden age of HD treatment that will positively impact quality of life and longevity of HD patients and inform advances in other inherited and neurodegenerative neurological disorders.
Convection-Enhanced Delivery of Muscimol in Patients with Drug-Resistant Epilepsy.

Background Minimally invasive therapies for drug-resistant epilepsy (DRE) have been advocated. A study of convection-enhanced delivery (CED) of muscimol, a GABAA receptor agonist, was previously completed in non-human primates. Objective To investigate the safety and anti-epileptic effects of intracerebral muscimol infusion into the epileptic focus of patients with DRE. Methods In this phase 1 clinical trial, 3 adult patients with DRE underwent CED into the seizure focus of artificial CSF vehicle followed by muscimol for 12 to 24 h each using a crossover design. Basic pathophysiology of the epileptic focus was examined by assessing the infusions' effects on seizure frequency, electroencephalogram (EEG) spike-wave activity, and power-spectral EEG frequency. Results Inter-ictal neurological function remained normal in all patients. Pathological examination of resected specimens showed no infusion-related brain injuries. Seizure frequency decreased in 1 of 3 patients during muscimol infusion but was unchanged in all patients during vehicle infusion. Mean beta frequencies did not differ significantly before, during, or after infusion periods. Infused fluid provided insufficient MRI-signal to track infusate distribution. In the 2 yr after standard epilepsy surgery, 1 patient had temporary reduction in seizure frequency and 2 patients were seizure-free. Conclusion CED of muscimol into the epileptic focus of patients with DRE did not damage adjacent brain parenchyma or adversely affect seizure surgery outcome. This study did not confirm that intracerebral muscimol infusion effectively suppressed seizures. A surrogate tracer is recommended to track infusion distribution to the epileptic focus and surrounding structures in future studies using CED to suppress the seizure focus.
Interrelationships between Psychology and Medical Sciences

The area on psychological studies has extended in imitation of overpass the cutting-edge studies on Freudian, who has been especially worried including gangs, has flourished psychological diseases affect the organic side and organic diseases affect the psychological side. It is necessary because of professionals after drink outweighs over this twins aspects, focusing over the essential empirical development known namely the medical scanner, magnetic resonance imaging (MRI) imaging resonance the magnetic. A latter trend, referred to as the physical school, has been nee on the grounds that the sixties among France, who is concerned including both sides. The faculty emphasizes that the depressed or deteriorating psychological scenario is an essential factor among building the singular inclined in conformity with bodily illness, who is from time to time dangerous. It additionally holds so the sickness does now not usually have a bad cost as much that is, however, may carry a positive value, that is, the ailment affords the individual with entire the possibilities after reorganizing and resurface as postulate the ailment is a violation platform in imitation of restoring the individual after his equilibrium. Many clinicians have attached this theory, as has furnished them with useful field experiences, emphasizing the interplay about many psychological, bodily yet neighborly factors. The unaccompanied is a complicated embodied soul between who many elements overlap. With the creation then length about neurosciences about thirty years ago or its colorful results, a modern concept of bodily psychology referred to as neuropsychology, based totally over neuroscience between its research, has currently emerged, linking this principle in accordance with damage And adjustments in nerve centers, particularly the brain. In our intervention, we choice existing the almost vital field research including the findings, into kilter in accordance with hyperlink psychology, clinical sciences, and half other sciences.
Anesthesiologist Surgery Assignments using Policy Learning

Anesthesiologists are currently assigned to surgeries based primarily on anesthesiologist availability and specialty, but optimizing anesthesia time is not generally considered. If certain anesthesiologists perform faster on different patient or surgical cohorts, then incorporating patient-specific and surgery-specific features in scheduling decisions could reduce anesthesia time, and therefore improve operating room efficiency. We formulate the problem of assigning anesthesiologists to surgeries as a policy learning problem. We use random forests and generalized random forests to derive counterfactual estimates, and find the optimal decision tree based on these estimates. We formulate and solve the optimal decision tree problem as a mixed-integer program, and evaluate our decision tree policies using doubly robust estimation techniques. We also demonstrate how our methods can be used to solve a budget-constrained assignment problem by assigning individual costs to each anesthesiologist. The derived policies offer performance improvements over historical scheduling, but are unable to offer larger anesthesia time reductions due to anesthesiologist performance being primarily correlated with prior performance.
Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales

A novel picorna-like virus, provisionally named Aphis glycines virus 1 (ApGlV1) was discovered by high-throughput sequencing of soybean total RNAs and detected in suction trap-collected Aphis glycines. The ApGlV1 genome contains two large ORFs organized similar to those of dicipiviruses in the Picornaviridae where ORFs 1 and 2 encode structural and nonstructural proteins, respectively. Both ORFs are preceded by internal ribosome entry site (IRES) elements. The 5' IRES was more active in dual luciferase activity assays than the IRES in the intergenic region. The ApGlV1 genome was predicted to encode a serine protease instead of a cysteine protease and showed very low aa sequence identities to recognized members of the Picornavirales. In phylogenetic analyses based on capsid protein and RNA-dependent RNA polymerase sequences, ApGlV1 consistently clustered with a group of unclassified bicistronic picorna-like viruses discovered from arthropods and plants that may represent a novel family in the order Picornavirales.
Mitochondrial genetics cooperate with nuclear genetics to selectively alter immune cell development/trafficking

The nuclear genome drives differences in immune cell populations and differentiation potentials, in part regulated by changes in metabolism. Despite this connection, the role of mitochondrial DNA (mtDNA) polymorphisms (SNP) in this process has not been examined. Using mitochondrial nuclear exchange (MNX) mice, we and others have shown that mtDNA strongly influences varying aspects of cell biology and disease. Based upon an established connection between mitochondria and immune cell polarization, we hypothesized that mtDNA SNP alter immune cell development, trafficking, and/or differentiation. Innate and adaptive immune cell populations were isolated and characterizated from the peritoneum and spleen. While most differences between mouse strains are regulated by nuclear DNA (nDNA), there are selective changes that are mediated by mtDNA differences (e.g., macrophage (CD11c) differentiation), These findings highlight how nuclear-mitochondrial crosstalk may alter pathology and physiology via regulation of specific components of the immune system.
Characterization of intra-urban spatial variation in observed summer ambient temperature from the New York City Community Air Survey

Abstract Determining the relationship between within-city spatial variation of ambient temperatures and land-use characteristics would be useful for developing mitigation strategies for urban heat island effects in the warming climate, but relatively few published studies collected high-density ambient temperature data in large cities to date. We applied land-use regression (LUR) modeling to the ambient temperature data collected during 2009–2016 as part of the New York City Community Air Survey (NYCCAS), a high density air pollution monitoring network with up to 150 locations within New York City (NYC). The 3–5 AM average summer temperature, seasonally adjusted, was selected to avoid the influence of variation in shading across monitoring units. Environmental indicators, including normalized difference vegetation index (NDVI), high resolution land-cover, imperviousness and building density, were characterized at multiple buffer distances around each monitoring site, screened for explanatory value, and combined in a stepwise multivariable regression model using the first 7 years of data. We validated the model against 2016 data. Summer average temperature over the 8 years ranged from 17.1 to 25.8 °C and the spatial variation was well-explained by a nonlinear term of km2 tree, shrub, and grass cover at 200 m (negative association), a measure of live green vegetation (NDVI) within 1000 m (negative), interior built space within 600 m (positive), the summer average daily minimum temperature at the National Weather Service station at LaGuardia airport, and a nonlinear term based on the XY coordinates to model unexplained spatial autocorrelation (R2 = 0.82). This model predicted temperature very well at NYCCAS sites for summer 2016 (R2 = 0.87). We observed that there was a range of baseline vegetative cover where increasing cover was associated with the greatest decreases in temperature, suggesting specific urban micro-environments where increased tree canopy may be the most effective in reducing ambient temperature. Within-city variation of nighttime temperatures is well-explained by features of the built and natural environment. Interventions that target this combination of factors, such as converting paved vacant lots and derelict buildings into vegetated space or replacing city infrastructure that uses impermeable surfaces with vegetated ones wherever possible, may help to decrease ambient temperature in NYC. Our findings suggest that evaluations of neighborhood greening may not show temperature benefits until a certain level of live vegetative cover is established.
A clinical guideline for structured assessment of CT-imaging in congenital lung abnormalities.

Abstract Objectives To develop a clinical guideline for structured assessment and uniform reporting of congenital lung abnormalities (CLA) on Computed Tomography (CT)-scans. Materials and Methods A systematic literature search was conducted for articles describing CT-scan abnormalities of congenital pulmonary airway malformation (CPAM), bronchopulmonary sequestration (BPS), congenital lobar emphysema (CLE) and bronchogenic cyst (BC). A structured report using objective features of CLA was developed after consensus between a pediatric pulmonologist, radiologist and surgeon. Results Of 1581 articles identified, 158 remained after title-abstract screening by two independent reviewers. After assessing full-texts, we included 28 retrospective cohort-studies. Air-containing cysts and soft tissue masses are described in both CPAM and BPS while anomalous arterial blood supply is only found in BPS. Perilesional low-attenuation areas, atelectasis and mediastinal shift may be found in all aforementioned abnormalities and can also be seen in CLE as a cause of a hyperinflated lobe. We have developed a structured report, subdivided into five sections: Location & Extent, Airway, Lesion, Vascularization and Surrounding tissue. Conclusions CT-imaging findings in CLA are broad and nomenclature is variable. Overlap is seen between and within abnormalities, possibly due to definitions often being based on pathological findings, which is an unsuitable approach for CT imaging. We propose a structured assessment of CLA using objective radiological features and uniform nomenclature to improve reporting.
Wild type AAV, recombinant AAV, and Adenovirus super infection impact on AAV vector mobilization

Abstract Recombinant Adeno-associated viral vector (rAAV) mobilization is a largely theoretical process in which intact AAV vectors spread or “mobilize” from transduced cells and infect additional cells within, or external, of the initial host. This process can be replication independent (vector alone), or replication-dependent (de novo rAAV production facilitated by super-infection of both wild-type AAV (wtAAV) and Ad helper virus). Herein, rAAV production and mobilization with and without wtAAV were analyzed following plasmid transfection or viral transduction utilizing well established in vitro conditions and analytical measurements. During in vitro production, wtAAV produced the highest titer with rAAV-luc (4.1 Kb), rAAV-IDUA (3.7 Kb), and rAAV-NanoDysferlin (4.9 Kb) generating 2.5-, 5.9-, or 10.7-fold lower amounts, respectively. Surprisingly, cotransfection of a wtAAV and a rAAV plasmid resulted in a uniform decrease in production of wtAAV in all instances with a concomitant increase of rAAV such that wtAAV:rAAV titers were at a ratio of 1:1 for all constructs investigated. These results were shown to be independent of the rAAV transgenic sequence, size, transgene, or promoter choice and point to novel aspects of wtAAV complementation that enhance current vector production systems yet to be de fined. In a mobilization assay, a sizeable amount of rAAV recovered from infected 293 cell lysate remained intact and competent for a secondary round of infection (termed non-replicative mobilization). In rAAV infected cells co-infected with Ad5 and wtAAV, rAAV particle production was increased > 50-fold compared to non-replicative conditions. In addition, replicative dependent rAAV vectors mobilized and resulted in >1,000 -fold transduction upon a subsequent 2nd round infection, highlighting the reality of these theoretical safety concerns that can be manifested under various conditions. Overall, these studies document and signify the need for mobilization resistant vectors and the opportunity to derive better vector production systems.
CMU Array: A 3D Nano-Printed, Customizable Ultra-High-Density Microelectrode Array Platform

Abstract Microelectrode arrays (MEAs) provide the means to record electrophysiological activity fundamental to both basic and clinical neuroscience (e.g. brain-computer interfaces). Despite recent advances, current MEAs have significant limitations – including low recording density, fragility, expense, and the inability to optimize the probe to individualized study or patient needs. Here we address the technological limitations through the utilization of the newest developments in 3D nanoparticle printing.1 Our ‘CMU Arrays’ possess previously impossible electrode densities (> 6000 channels/cm2) with tip diameters as small as 10 μm. Most importantly, the probes are entirely customizable owing to the adaptive manufacturing process. Any combination of individual shank lengths, impedances, and layouts are possible. This is achieved in part via our new multi-layer, multi material, custom 3D-printed circuit boards, a fabrication advancement in itself. This device design enables new experimental avenues of targeted, large-scale recording of electrical signals from a variety of biological tissues.
A Point-Based Risk Calculator Predicting Mortality in Patients That Developed Postoperative Sepsis.

Background:Predicting the mortality from post-operative sepsis remains a continuing problem. We built a statistical model using national data to predict mortality in patients who developed post-ope...
Parametric study and optimization trends for the Von-Kármán-sodium dynamo experiment

We present magneto-hydrodynamic simulations of liquid sodium flow performed with the PLUTO compressible MHD code. We investigated the influence of the remanent magnetic field orientation and intensity, the impinging velocity field due to Ekman pumping as well as the impeller dimensions on the magnetic field collimation by helical flows in-between the impeller blades. For a simplified Cartesian geometry, we model the flow dynamics of a multi-blade impeller inspired by the Von-Karman-Sodium experiment. This study shows that a remanent magnetic field oriented in the toroidal direction is the less efficient configuration to collimate the magnetic field, although if the radial or vertical components are not negligible, the collimation is significantly improved. As the intensity of the remanent magnetic field increases, the system magnetic energy becomes larger, but the magnetic field collimation efficiency remains the same, so the gain of magnetic energy is smaller as the remanent magnetic field intensity incr...
Dynamics-based classification of semienclosed basins

Abstract This study is guided by other classifications of estuaries that are based on specified physical constraints. Previous classifications have been relevant and revealing of diagnostic functioning of estuaries in terms of their stratification and their baroclinically induced residual circulation. Those classifications, however, have disregarded residual circulations driven by tides, not only in estuaries, but in semienclosed basins in general. The classification proposed here uses tidally averaged, or residual, dynamics. Residual dynamics are explored via drivers, or forcing agents, of residual flow. Drivers are tides or density gradients and are counteracted by ‘modifiers,’ i.e., Earth’s rotation or friction. The relative influence between forcing agents is characterized by a scaled non-dimensional densimetric tidal Froude number, F r 0 2 , which hinges on tidal current amplitude, water depth and reduced gravity. The competition between modifiers is determined by a non-dimensional Ekman number, Ek, which depends on the kinematic eddy viscosity, the latitude and the depth of the basin. The classification suggested identifies all types of estuaries, whose dynamics is influenced by density gradients, but also recognizes frictionless tidal basins, tidal rivers, coastal lagoons, and basins that switch their dynamics from being baroclinically forced to being tidally forced. This classification can also be interpreted as an assessment of the strength of mixing (in Ek) versus the strength of baroclinicity (in F r 0 2 ), which determines the residual flows in semienclosed basins. Additionally, the classification incorporates basins forced by wind stress and/or baroclinicity, and basins forced by wind stress and/or tides.
Chapter 28 Automated Markets and Trading Agents

Abstract Computer automation has the potential, just starting to be realized, of transforming the design and operation of markets, and the behaviors of agents trading in them. We discuss the possibilities for automating markets, presenting a broad conceptual framework covering resource allocation as well as enabling marketplace services such as search and transaction execution. One of the most intriguing opportunities is provided by markets implementing computationally sophisticated negotiation mechanisms, for example combinatorial auctions. An important theme that emerges from the literature is the centrality of design decisions about matching the domain of goods over which a mechanism operates to the domain over which agents have preferences. When the match is imperfect (as is almost inevitable), the market game induced by the mechanism is analytically intractable, and the literature provides an incomplete characterization of rational bidding policies. A review of the literature suggests that much of our existing knowledge comes from computational simulations, including controlled studies of abstract market designs (e.g., simultaneous ascending auctions), and research tournaments comparing agent strategies in a variety of market scenarios. An empirical game-theoretic methodology combines the advantages of simulation, agent-based modeling, and statistical and game-theoretic analysis.
Landmark Direction and Distance Estimation in Large Scale Virtual Environments

The current paper describes our classification of errors participants made when estimating direction and distances in a large scale (2000 m × 2000 m) Virtual Environment (VE). Two VE configuration ...
Analysis of corneal development with monoclonal antibodies. I. Differentiation in isolated corneas.

Abstract Monoclonal antibodies highly selective for developmentally regulated antigens present in the cornea (Zak and Linsenmayer, Dev. Biol. 99, 373–381, 1983) have been used to immunohistochemically evaluate differentiation in intact chick corneas cultured on the chorioallantoic membrane (CAM) of host embryos. One antibody is directed against the epithelial cell layer and the other is against the corneal stromal matrix. It has been established that both antigens recognized by the antibodies are expressed de novo in young explanted corneas and that the stromal matrix antigen is a product of the corneal fibroblasts. Thus expression of the antigens can be used as criteria for overt differentiation of the respective cell types. The antibodies have been employed to assess when the corneal epithelial and stromal cells become capable of autonomous differentiation within isolated corneas. To accomplish this, corneas of various ages were explanted with and without adjacent pericorneal tissues. The results indicate that, under the culture conditions employed, corneal stromal differentiation is dependent on the presence of the lens until stage 28 ( 5 1 2 –6 days of development), which is the time when invasion of the stroma by pericorneal mesenchymal cells is initiated. After stage 28, the stromal matrix antigen was expressed by isolated corneas irrespective of the presence of the lens. Possibly the lens acts by maintaining the integrity of the corneal endothelial monolayer and thus promoting normal migration of pericorneal mesenchymal cells into the primary corneal stroma, where they undergo differentiation. Conversely, differentiation of the corneal epithelium was independent of any pericorneal structure from the earliest stage examined ( 4 1 2 –5 days of development). It was even independent of overt stromal differentiation, thus suggesting an early and strong determination for this tissue.