cssi/SciSciGPT-SciSciNet huggingface dataset:
Mechanisms of Mortality in Early and Late Sepsis

A recent hypothesis postulates that sepsis moves through different phases, with periods of enhanced inflammation alternating with periods of immune suppression. In this study we determined the levels of inflammation present during early and late septic deaths to examine whether death was due to hyperinflammation or immunosuppression. The murine model of sepsis induced by cecal ligation and puncture (CLP) was used. Complete blood counts, plasma interleukin-6 (IL-6) levels, and body weights were determined. Mice that died within the first 4 days had increased plasma levels of IL-6, indicating that there was activation of the immune system. Cecal resection on day 4 after CLP resulted in decreased abscess size, lower circulating neutrophil counts, decreased anemia, and improved survival compared to the results for mice that received only antibiotic and fluid therapy. All of the mice that died in the chronic phase of infection (after day 4) had positive peritoneal cultures containing significantly more bacteria than the cultures for surviving mice. After day 4, none of the surviving mice exhibited increases in the plasma levels of IL-6. Dying mice exhibited mixed IL-6 responses; for 41% of the mice there was never an increase in the IL-6 levels in the chronic phase, while for other mice the levels of IL-6 transiently increased prior to death. Peritoneal macrophages were obtained in the late phase of sepsis from moribund and healthy mice and were stimulated ex vivo. The cells from the moribund mice produced significantly less IL-6 than the cells obtained from healthy mice produced. These results indicate that in mice that die in the early phase there is uniformly increased inflammation. However, during the chronic phase of sepsis, some mice die with evidence of immunosuppression (increased bacterial growth and low IL-6 levels), while other mice die with immunostimulation (high IL-6 levels and bacterial growth). Determining the inflammatory status of individual patients may help guide appropriate, targeted therapy.
Combining multiple 2ν-SVM classifiers for tissue segmentation

In image classification problems, especially those involving tumor or precancerous lesion, we are usually faced with the situation in which the cost of mistakenly classifying samples in one class is much higher than that of the opposite mistake in the other class. Therefore it is essential to include cost information about classes in our classification methods. This paper applies a cost-sensitive 2v-SVM classification scheme to cervical cancer images to separate diseased regions from healthy tissue. Using this method, we are able to specify a higher weight to the class that is deemed more important. To the best of our knowledge, cost-sensitive SVM based medical image classification has not been done before. We specifically target segmenting disease regions in digitized uterine cervix images in a NCI/NLM archive of 60,000 images. Our second contribution is the introduction of a multiple classifier scheme instead of the traditional single classifier model. Using the multiple classifier scheme improves significantly classification accuracy as demonstrated by our experiments.
The rapid evolution of X-linked male-biased gene expression and the large-X effect in Drosophila yakuba, D. santomea and their hybrids

The X chromosome has a large effect on hybrid dysfunction, particularly on hybrid male sterility. Although the evidence for this so-called large-X effect is clear, its molecular causes are not yet fully understood. One possibility is that, under certain conditions, evolution proceeds faster in X-linked than in autosomal loci (i.e., faster-X effect) due to both natural selection and their hemizygosity in males, an effect that is expected to be greatest in genes with male-biased expression. Here, I study genome-wide variation in transcript abundance between Drosophila yakuba and D. santomea, within these species and in their hybrid males to evaluate both the faster-X and large-X effects at the level of expression. I find that in X-linked male-biased genes (MBGs) expression evolves faster than in their autosomal counterparts, an effect that is accompanied by a unique reduction in expression polymorphism. This suggests that Darwinian selection is driving expression differences between species, likely enhanced by the hemizygosity of the X chromosome in males. Despite the recent split of the two sister species under study, abundant changes in both cis- and trans-regulatory elements underlie expression divergence in the majority of the genes analyzed, with significant differences in allelic ratios of transcript abundance between the two reciprocal F(1) hybrid males. Cis-trans coevolution at molecular level, evolved shortly after populations become isolated, may therefore contribute to explain the breakdown of the regulation of gene expression in hybrid males. Additionally, the X chromosome plays a large role in this hybrid male misexpression, which affects not only MBG but also, to a lesser degree, nonsex-biased genes. Interestingly, hybrid male misexpression is concentrated mostly in autosomal genes, likely facilitated by the rapid evolution of sex-linked trans-acting factors. I suggest that the faster evolution of X-linked MBGs, at both protein and expression levels, contributes to explain the large effect of the X chromosome on hybrid male sterility, likely mediating widespread autosomal misexpression through the preferential recognition of cis-regulatory elements by conspecific trans-acting factors (i.e., cis-trans conspecific recognition).
Surgical management and associated complications of penetrating rectal injuries sustained in Iraq and Afghanistan.

ABSTRACTPurpose: The aim of this study was to analyze the surgical management and associated complications of penetrating rectal injuries sustained in Operation Iraqi Freedom and Operation Enduring Freedom. Methods: A retrospective review was performed using the Joint Theater Trauma Registry. U.S. military personnel injured in Iraq and Afghanistan from October 2003 to November 2008 were included. The surgical management of rectal injuries was evaluated, specifically looking at the utilization of diversion with ostomy, distal washout, and presacral drainage. Complications were compared between the treatment groups. Results: 57 patients who sustained a penetrating rectal injury were included in this study. Surgical management included diversion and ostomy alone in 34 patients (60%), diversion and distal washout in 11 patients (19%), diversion and drainage in 8 patients (14%), and diversion, distal washout, and drainage in 4 patients (7%). Complications were identified in 21% of patients. There were no death...
Can Single Protein and Protein Family Phylogenies be Resolved Better

Single gene or protein sequences have been used in protein biology and molecular biology studies to make inferences about the dynamics of evolution of their structure and function. In addition, single gene or protein phylogenies are required input in statistical tests for natural selection or in the determination of sites in proteins that are coevolving. Gene phylogenies using members of a multigene family (the globin genes are a classic example) are important too, because they can decipher the relationships of the members of the overall gene family and can address potential neofunctionalization phenomena [13]. While the issue of how single gene and single proteins contribute to the overall phylogeny of a group of organisms is an important and copiously addressed topic [4-7], the focus here is on the use of gene and protein sequences in single gene studies.
Ancestral Contributions to Roasted Peanut Attribute1

Abstract Estimates of broad-sense heritability for roasted flavor attribute of peanut (Arachis hypogaea L.) range from 9 to 24% on a single-plot basis. Response to selection is determined by the narrow-sense heritability, calculated from estimates of additive genetic variance which are not available for this trait. One way to assess the additive component of genetic variation is to determine how much of the total phenotypic variation can be predicted from genetic contributions of ancestors of the individuals measured. From 1986 to 1991, samples of 128 peanut cultivars and breeding lines were obtained from peanut research programs representing the three major production areas in the U.S. Samples were roasted to a nearly common color, ground into paste, and assessed for roasted flavor and fruity attribute by a trained sensory panel. CIELAB L* color was also measured for use as a covariate in statistical analysis to adjust for small differences in color. The sum of squares associated with the 128 genotypes a...
Improving Element-Boundary Alignment in All-Hex Meshes of Thin-Walled Solids by Side-Face Identification

This paper presents a new computational method for identifying side faces of thin-walled solids that can be excluded from the first step of conformal transformation from a tet mesh to an all-hex mesh. By excluding such side faces, all-hex meshes created by the conformal transformation method better align with the boundary of the side faces and tend to exhibit better scaled Jacobian quality. The proposed method first finds seeds of the candidate faces that may belong to the side faces. Then the candidate faces are grown across edges that have a low dihedral angle. Finally the candidate faces are retracted until no edge between a candidate face and non-candidate face has a low dihedral angle. Experimental results demonstrate clearly improvement of the element-boundary alignment and scaled Jacobian quality.
Learning representation and control in continuous Markov decision processes

This paper presents a novel framework for simultaneously learning representation and control in continuous Markov decision processes. Our approach builds on the framework of proto-value functions, in which the underlying representation or basis functions are automatically derived from a spectral analysis of the state space manifold. The proto-value functions correspond to the eigenfunctions of the graph Laplacian. We describe an approach to extend the eigenfunctions to novel states using the Nystrom extension. A least-squares policy iteration method is used to learn the control policy, where the underlying subspace for approximating the value function is spanned by the learned proto-value functions. A detailed set of experiments is presented using classic benchmark tasks, including the inverted pendulum and the mountain car, showing the sensitivity in performance to various parameters, and including comparisons with a parametric radial basis function method.
MicroRNAs regulating apolipoprotein B-containing lipoprotein production.

MicroRNAs (miRs) are small, non-coding RNAs that regulate gene expression and have been implicated in many pathological conditions. Significant progress has been made to unveil their role in lipid metabolism. This review aims at summarizing the role of different miRs that regulate hepatic assembly and secretion of apolipoprotein B (apoB)-containing lipoproteins. Overproduction and/or impaired clearance of these lipoproteins from circulation increase plasma concentrations of lipids enhancing risk for cardiovascular disease. So far, three miRs, miR-122, miR-34a, and miR-30c have been shown to modulate hepatic production of apoB-containing low density lipoproteins. In this review, we will first provide a brief overview of lipid metabolism and apoB-containing lipoprotein assembly to orient readers to different steps that have been shown to be regulated by miRs. Then, we will discuss the role of each miR on plasma lipids and atherosclerotic burden. Furthermore, we will summarize mechanistic studies explaining how these miRs regulate hepatic lipid synthesis, fatty acid oxidation, and lipoprotein secretion. Finally, we will briefly highlight the potential use of each miR as a therapeutic drug for treating cardiovascular diseases. This article is part of a Special Issue entitled: MicroRNAs and lipid/energy metabolism and related diseases edited by Carlos Fernandez-Hernando and Yajaira Suarez.
Sag during unfused tetanic contractions in rat triceps surae motor units.

Sag during unfused tetanic contractions in rat triceps surae motor units. Contractile properties and conduction velocity were studied in 202 single motor units of intact rat triceps surae muscles a...
Influence of Functional Groups on Organic Aerosol Cloud Condensation Nucleus Activity

Organic aerosols in the atmosphere are composed of a wide variety of species, reflecting the multitude of sources and growth processes of these particles. Especially challenging is predicting how these particles act as cloud condensation nuclei (CCN). Previous studies have characterized the CCN efficiency for organic compounds in terms of a hygroscopicity parameter, κ. Here we extend these studies by systematically testing the influence of the number and location of molecular functional groups on the hygroscopicity of organic aerosols. Organic compounds synthesized via gas-phase and liquid-phase reactions were characterized by high-performance liquid chromatography coupled with scanning flow CCN analysis and thermal desorption particle beam mass spectrometry. These experiments quantified changes in κ with the addition of one or more functional groups to otherwise similar molecules. The increase in κ per group decreased in the following order: hydroxyl ≫ carboxyl > hydroperoxide > nitrate ≫ methylene (where nitrate and methylene produced negative effects, and hydroperoxide and nitrate groups produced the smallest absolute effects). Our results contribute to a mechanistic understanding of chemical aging and will help guide input and parametrization choices in models relying on simplified treatments such as the atomic oxygen:carbon ratio to predict the evolution of organic aerosol hygroscopicity.
Measuring Human-Automation Function Allocation

Function allocation is the design decision in which work functions are assigned to all agents in a team, both human and automated. Building on the preceding companion papers’ review of the requirem...
Use of an optical clearing agent to enhance the visibility of subsurface structures and lesions from tooth occlusal surfaces

The purpose of this study is to show that optical clearing agents can be used to increase the visibility of deeply penetrating occlusal lesions that have reached the underlying dentin and spread laterally under the enamel. Previous studies have shown that high refractive index fluids can increase the contrast of caries lesions. Extracted teeth with natural occlusal lesions were imaged with optical coherence tomography (OCT) with and without the addition of a transparent vinyl polysiloxane impression material (VPS) currently used in vivo. The relative intensity of the reflectivity from the underlying lesion area for each sample was measured before and after application of the VPS. Lesion presence was confirmed with polarized light microscopy and microradiography. Application of VPS significantly increased (P<0.0001) the integrated reflectivity of subsurface dentinal lesions. This study shows that optical clearing agents can be used to increase the optical penetration and the visibility of subsurface lesions and the dentinal–enamel junction under sound and demineralized enamel in OCT images.
The Seed Program Case Studies

This chapter provides three case studies of what this book terms “Seed Programs.” These are the financial education programs of Grand Valley State University in Michigan, University of Texas at San Antonio and Purchase College in New York. The seed program or aspirational typology is used in this book to describe programs for which the “seed” of financial education has been planted, but there may be limited enthusiasm and/or resources to develop, sustain, or grow the program. Often managed by a program coordinator, the Seed Program Model is invariably not led by a program champion and is often little more than a symbol of need and aspiration, rather than an effective organization to address the financial education need. The seed programs may germinate from an administrator’s (or an influential person’s) belief that a financial education program is a good idea for the institution. That administrator may himself/herself have a passion for financial education but at the time is unable to devote the time or energy to the development of the program.
351 THE INTEGRA SPLIT-THICKNESS SKIN GRAFT “SINGLE-STAGE” APPLICATION: A NOVEL TECHNIQUE.

Background Many soft tissue defects are reconstructed using a two-stage procedure that requires placement of the Integra Bilayer Wound Dressing and separate split-thickness skin grafting 2 to 4 weeks later to allow dermal matrix incorporation. The need for two separate operations and the total time required for complete reconstruction at times makes this an inconvenient or nonfeasible process. We report a new method of soft tissue defect reconstruction using a single-stage placement of Integra Matrix Wound Dressing (IMWD) with concomitant skin grafting. Methods Five patients with soft tissue defects of the hand or head and neck after excision of nonmelanomatous skin cancers were reconstructed with “single-stage” Integra IMWD and split-thickness skin graft placement with a simple sterile sponge bolster dressing. Results All patients had excellent skin graft “take” after their bolsters were removed on average 8.5 days (range 7-9 days) postoperatively. Patients demonstrated excellent coloration, no evidence of hypertrophic scarring, and excellent tendon excursion when placed over extensor tendons of the hand. There were no skin graft losses, and all patients were spared a second step as part of a planned or “staged” reconstruction. Conclusion “Single-stage” reconstruction using IMWD and a split-thickness skin graft simultaneously is not only a successful and efficacious technique; it prevents the added morbidity of prolonged multistaged reconstructions and possible exposure to additional anesthetic agents. Additionally, many patients and surgeons who may not initially consider reconstruction with a skin substitute such as Integra because of the need for prolonged healing time and multiple procedures may reconsider as our technique produces excellent results in a single operation.
Physical and photoelectrochemical properties of Sb-doped SnO 2 thin films deposited by chemical vapor deposition: application to chromate reduction under solar light

Sb-doped SnO2 thin films (Sb-SnO2) are prepared by chemical vapor deposition. The X-ray diffraction indicates a rutile phase, and the SEM analysis shows pyramidal grains whose size extends up to 200 nm. The variation of the film thickness shows that the elaboration technique needs to be optimized to give reproducible layers. The films are transparent over the visible region. The dispersion of the optical indices is evaluated by fitting the diffuse reflectance data with the Drude–Lorentz model. The refractive index (n) and absorption coefficient (k) depend on both the conditions of preparation and of the doping concentration and vary between 1.4 and 2.0 and 0.2 and 0.01, respectively. Tin oxide is nominally non-stoichiometric, and the conduction is dominated by thermally electrons jump with an electron mobility of 12 cm2 V−1 s−1 for Sb-SnO2 (1 %). The (C2–V) characteristic in aqueous electrolyte exhibits a linear behavior from which an electrons density of 4.15 × 1018 cm−3 and a flat-band potential of −0.83 VSCE are determined. The electrochemical impedance spectroscopy shows a semicircle attributed to a capacitive behavior with a low density of surface states. The center lies below the real axis with a depletion angle (12°), due to a constant phase element, i.e., a deviation from a pure capacitive behavior, presumably attributed to the roughness and porosity of the film. The straight line at low frequencies is attributed to the Warburg diffusion. The energy diagram reveals the photocatalytic feasibility of Sb-SnO2. As application, 90 % of the chromate concentration (20 mg L−1, pH ~3) disappears after 6 h of exposure to solar light.
Nesselroade and Molenaar's Measurement Concerns and Proposals: An Introduction

ABSTRACTIn this special section Nesselroade and Molenaar (N & M) propose a provocative new approach to measurement invariance. When measures are collected repeatedly over time (e.g., daily diary studies), a potentially unique measurement model relating the items to the underlying construct can be created for each individual. If hypothesized causal paths specified between constructs (e.g., frustration → aggression) can be constrained to be equal across the individuals, a model with idiographic measurement of the constructs, but with nomothetic structural relationships can be specified. Three commentaries react to N & M's proposal. Revelle and Wilt challenge the priority given by N & M to unique individual measurement structures, arguing that between subjects differences in structural relationships are empirically important and meaningful. Markus's uses David Hume's framework to raise philosophy of science challenges for N & M's approach. Maydeu-Olivares challenges the incremental validity of N & M's approa...
Results of Epispadias Repair Using the Modified Cantwell-Ransley Technique

Objective To evaluate our results of epispadias repair with a modified Cantwell-Ransley (MCR) technique. Methods A retrospective Institutional Review Board-approved chart review of all patients who underwent an MCR epispadias repair was conducted between 1998 and 2015. Procedures were performed at birth or after the age of 8 months as part of the modern staged repair of exstrophy-epispadias complex (EEC) in patients with bladder exstrophy treated since birth, at presentation for older patients, and after the age of 6 months in isolated epispadias patients. Twenty-two children underwent MCR epispadias repair in our institute during the study period. Sixteen of them had EEC and 6 had isolated epispadias. Four patients underwent exstrophy and epispadias repair at the same session. Twelve children underwent epispadias repair as a second stage of modern staged repair at a mean age of 21 months (range 8-60). The procedures involved dissection of the corporeal bodies and urethral plate from the penile base to the tip of the penile glans. Results After a mean follow-up of 6.9 years (range 0.5-18), there were no complications in the isolated epispadias group and 4 complications in the bladder exstrophy group: urethrocutaneous fistula ( n = 1), residual dorsal curvature ( n = 1), and excess of penile skin ( n = 2). The meatal location was orthotopic in all cases. All of the complications were successfully addressed in a single subsequent surgical session. Conclusion MCR technique continues to be a reliable, reproducible option for epispadias repair in EEC patients and in cases of isolated epispadias.
Vaccination with Killed but Metabolically Active E. coli Over-expressing Hemagglutinin Elicits Neutralizing Antibodies to H1N1 Swine Origin Influenza A Virus.

There is a need for a fast and simple method for vaccine production to keep up with the pace of a rapidly spreading virus in the early phases of the influenza pandemic. The use of whole viruses produced in chicken eggs or recombinant antigens purified from various expression systems has presented considerable challenges, especially with lengthy processing times. Here, we use the killed but metabolically active (KBMA) Escherichia coli ( E. coli ) to harbor the hemagglutinin (HA) of swine origin influenza A (H1N1) virus (S-OIV) San Diego/01/09 (SD/H1N1-S-OIV). Intranasal vaccination of mice with KBMA E. coli SD/H1N1-S-OIV HA without adding exogenous adjuvants provoked detectable neutralizing antibodies against the virus-induced hemagglutination within three weeks. Boosting vaccination enhanced the titers of neutralizing antibodies, which can decrease viral infectivity in Madin-Darby canine kidney (MDCK) cells. The antibodies were found to specifically neutralize the SD/H1N1-S-OIV-, but not seasonal influenza viruses (H1N1 and H3N2), -induced hemagglutination. The use of KBMA E. coli as an egg-free system to produce anti-influenza vaccines makes unnecessary the rigorous purification of an antigen prior to immunization, providing an alternative modality to combat influenza virus in future outbreaks. Journal of Nature and Science (JNSCI), 3(2):e317, 2017
Nationwide review of hormonally active adrenal tumors highlights high morbidity in pheochromocytoma.

Abstract Background Adrenal adenomas are benign tumors often discovered incidentally, and >70% are hormonally inactive. The remaining subset may produce excess aldosterone, cortisol, or catecholamine. Perioperative outcomes after adrenalectomy for such “hormonally active” tumors remain unclear. This study examines in-hospital outcomes after unilateral adrenalectomy for hormonally active tumors. Methods A retrospective review was performed using the Nationwide Inpatient Sample (2006-2011) to identify patients undergoing unilateral adrenalectomy for hormonally active or inactive tumors. Malignant adrenal tumors were excluded. Demographics, comorbidities, and postoperative complications were evaluated by univariate analysis, using two-tailed Chi-square and t-tests and multivariate logistic regression. Results Of 27,312 patients who underwent adrenalectomy, 78% (n = 21,279) had hormonally inactive and 22% (n = 6033) had hormonally active adrenal tumors. Among the latter, 65% (n = 4000) had primary hyperaldosteronism (Conn's syndrome), 33% (n = 1996) had hypercortisolism (Cushing's syndrome), and 1.4% (n = 85) had pheochromocytoma. Patients with pheochromocytoma had higher rate of comorbidities including congestive heart failure, chronic lung disease, and malignant hypertension compared with remaining hormonally active tumors (12% versus 4%, 18% versus 11%, 6% versus 2%; P Conclusions Patients with pheochromocytoma have high rates of preoperative comorbidities, postoperative cardiopulmonary complications, and longer and more costly hospitalizations. Such high-risk patients should undergo appropriate preoperative medical optimization in preparation for adrenalectomy.
Critique of the Religion and Spirituality Discourse in Family Articles

The purpose of this article is to critically examine the emerging discourse of religion and spirituality in family research to clarify how each construct is defined and to make visible hidden ontological, epistemological, and culturally situated assumptions. The use of the term spirituality has increased dramatically in published articles and has undergone a distancing from religion. This separation creates a dichotomy that associates religion with conservative traditions and spirituality with liberalism and individualism, thus aligning the emergent spirituality discourse with dominant Western values.
Antioxidant supplementation and atrial arrhythmias in critically ill trauma patients.

Abstract Background The purpose of this study is to determine if antioxidant supplementation influences the incidence of atrial arrhythmias in trauma intensive care unit (ICU) patients. Materials and methods In this retrospective pre-post study, critically ill injured patients aged ≥18 years, admitted to a single-center trauma ICU for ≥48 hours were eligible for inclusion. The control group consists of patients admitted from January 2000 to September 2005, before routine antioxidant supplementation in our ICU. The antioxidant group consists of patients admitted from October 2005 to June 2011 who received an antioxidant protocol for ≥48 hours. The primary outcome is the incidence of atrial arrhythmias in the first 2 weeks of hospitalization or before discharge. Results Of the 4699 patients, 1622 patients were in the antioxidant group and 2414 patients were in the control group. Adjusted for age, sex, year, injury severity, past medical history, and medication administration, the unadjusted incidence of atrial arrhythmias was 3.02% in the antioxidant group versus 3.31% in the control group, with no adjusted difference in atrial arrhythmias among those exposed to antioxidants (odds ratio: 1.31 [95% confidence interval: 0.46, 3.75], P = 0.62). Although there was no change in overall mortality, the expected adjusted survival of patients in those without antioxidant therapy was lower (odds ratio: 0.65 [95% confidence interval: 0.43, 0.97], P = 0.04). Conclusions ICU antioxidant supplementation did not decrease the incidence of atrial arrhythmias, nor alter the time from admission to development of arrhythmia. A longer expected survival time was observed in the antioxidant group compared with the control group but without a change in overall mortality between groups.
Abstract 15020: Transcriptomic and Epigenomic Resemblance of Terminally Differentiated Cells Derived From Isogenic Human iPSCs and Nuclear Transfer Derived ESCs

Human pluripotent stem cells (PSCs) hold great promise for disease modeling, drug discovery, and regenerative medicine. Currently, patient-specific PSCs can be created via two approaches: somatic cell nuclear transfer (SCNT) by enucleated oocytes and iPSC reprogramming by ectopic expression of four transcription factors. Recent studies suggest that human SCNT-derived embryonic stem cells (nt-ESCs) are more similar to in vitro fertilized embryo derived ESCs (IVF-ESCs) than iPSCs at both transcriptomic and epigenomic levels. As terminally differentiated cells (i.e., cardiomyocytes, hepatocytes, neurons, and endothelial cells) are mostly desired for clinical application of human PSCs, here we assessed the molecular and functional similarity of terminally differentiated cells derived from human isogenic iPSCs and nt-ESCs. We differentiated three types of PSCs (iPSCs, nt-ESCs, and IVF-ESCs) into beating cardiomyocytes (PSC-CMs) and functional endothelial cells (PSC-ECs), respectively. During the process of induced differentiation, human nt-ESCs displayed closer dynamic marker gene expression profiles to IVF-ESCs than iPSCs. However, terminally differentiated cells (CMs and ECs) derived from iPSCs and nt-ESCs showed comparable differentiation efficiency, lineage marker gene expression, heterogeneity, nitric oxide release and tube formation capacity. Furthermore, iPSC-CMs were clustered more closely to nt-ESC-CMs than IVF-ESC-CMs at transcriptional level revealed by RNA-seq. DNA methylome analysis by RRBS-seq indicated that iPSC-CMs and iPSC-ECs were epigenetically similar to nt-ESC-CMs and nt-ESC-ECs, respectively, but were distinguishable from IVF-ESC derivatives. Thus, for generating terminally differentiated cells, human iPSCs are comparable to their isogenic nt-ESCs with respect to transcriptomic, epigenomic, and functional features.
Topical rifampin powder for orthopedic trauma part I: Rifampin powder reduces recalcitrant infection in a delayed treatment musculoskeletal trauma model

Open fractures become infected despite meticulous debridement and care. Locally applied antibiotics, commonly embedded in polymethylmethacrylate, deliver high doses of drug directly to the fracture site. Direct application of antibiotic powder, which is being applied prophylactically in spine surgery, is a recent interest in the trauma sector, where bacterial biofilms are more prevalent. Traditional antibiotics, such as vancomycin, are poor performers against bacterial biofilms thus are ineffective in delayed treatment. Rifampin is an effective eradicator of Staphylococcal biofilms. Here, a rat model of musculoskeletal trauma was used to evaluate the utility of locally applied rifampin powder for reducing established orthopedic Staphylococcal infections in a delayed treatment scenario that previously indicated the limited use of local vancomycin. By applying rifampin powder directly to the contaminated segmental defect, the number of bacteria, as well as clinical indications of infection, were significantly reduced compared to vancomycin and daptomycin. Considering the Infectious Disease Society of America's recommendation to use rifampin in combination with another antibiotic to reduce the onset of rifampin resistance, rifampin powder was also applied in combination with vancomycin or daptomycin with insignificant changes in eradication performance. No indications of rifampin resistance were identified. Clinical Significance: The use of locally applied rifampin is a promising therapy for mature and tolerant musculoskeletal infections. Published 2018. This article is a U.S. Government work and is in the public domain in the USA. J Orthop Res 36:3136-3141, 2018.
An Improved Recovery Algorithm for Decayed AES Key Schedule Images

A practical algorithm that recovers AES key schedules from decayed memory images is presented. Halderman et al. [1] established this recovery capability, dubbed the cold-boot attack, as a serious vulnerability for several widespread software-based encryption packages. Our algorithm recovers AES-128 key schedules tens of millions of times faster than the original proof-of-concept release. In practice, it enables reliable recovery of key schedules at 70% decay, well over twice the decay capacity of previous methods. The algorithm is generalized to AES-256 and is empirically shown to recover 256-bit key schedules that have suffered 65% decay. When solutions are unique, the algorithm efficiently validates this property and outputs the solution for memory images decayed up to 60%.
Concepts of Charge Density Analysis: The Experimental Approach

Though the potential for deriving electron distributions from elastic diffraction data was recognized in the decade following Von Laue’s discovery of X-ray diffraction, its practical application was delayed by many unrecognized problems of both experimental and theoretical nature. Only with the advent of four-circle diffractometers and high-speed computing could sufficiently accurate data be collected, corrected for physical effects like extinction, absorption and thermal diffuse scattering, and interpreted with a scattering factor formalism based on a more realistic description of bonded atoms.
On a Pedestal—Sport as an Arena for Admiration

ABSTRACTIn philosophical analyses of the value of sport, a relatively unheralded feature is the opportunity that sport offers for admiration. While we readily salute many of the things that people ...
Inside the prism of an invisible threat: Shining a light on the hidden work of contending with systemic stereotype threat in STEM fields

Abstract The purpose of the present research was to understand how individuals navigate careers in professional contexts that are infused with systemic stereotype threat. Systemic stereotype threat occurs when an individual is in a system that is characterized by gender or racial disparities and the implicit belief about the reason for these disparities is stereotypes about the deficits of women or people of color, rather than systemic inequalities. We conducted in-depth interviews with 26 women scientists in a top-tier academic research institution, a context that is steeped in negative stereotypes about women's ability and commitment as a reason for their underrepresentation. Stereotype threatening systems create the conditions for women scientists to experience heightened visibility due to their gender and heightened invisibility of the characteristics that make them successful scientists. We found that the strategies that women use to navigate in stereotype-threatening systems were patterned based on the goals that women had for managing their (in)visibility and that these goals were based on their understanding of the reasons for their underrepresentation in STEM fields. The three response patterns that emerged were: Fending Off the Threat; Confronting the Threat; and Sustaining Self in the Presence of the Threat. The importance of understanding the variety of strategies that individuals use to manage (in)visibility while working in stereotype-threatening systems is discussed.
Assessing CYP2C19 Ontogeny in Neonates and Infants Using Physiologically Based Pharmacokinetic Models: Impact of Enzyme Maturation Versus Inhibition.

The objective of this study was to develop pediatric physiologically based pharmacokinetic (PBPK) models for pantoprazole and esomeprazole. Pediatric PBPK models were developed by Simcyp version 15 by incorporating cytochrome P450 (CYP)2C19 maturation and auto-inhibition. The predicted-to-observed pantoprazole clearance (CL) ratio ranged from 0.96-1.35 in children 1-17 years of age and 0.43-0.70 in term infants. The predicted-to-observed esomeprazole CL ratio ranged from 1.08-1.50 for children 6-17 years of age, and 0.15-0.33 for infants. The prediction was markedly improved by assuming no auto-inhibition of esomeprazole in infants in the PBPK model. Our results suggested that the CYP2C19 auto-inhibition model was appropriate for esomeprazole in adults and older children but could not be directly extended to infants. A better understanding of the complex interplay of enzyme maturation, inhibition, and compensatory mechanisms for CYP2C19 is necessary for PBPK modeling in infants.
Abstract 5239: Cisplatin disrupts MDM2-DAXX-HAUSP complex, p53 accumulation, cell cycle regulation, and apoptosis in acute leukemia cells

Cisplatin (CDDP) is an antitumor drug successfully used in the treatment of various types of human malignancies. It enhances toxicity of arsenic trioxide (ATO) in head and neck squamous cell carcinoma cell, small cell lung cancer, ovarian cancer cells, and oral squamous cell carcinoma cells (, and chronic myelogenous leukemia cells. CDDP induces cytotoxicity, DNA damage, oxidative stress, and apoptosis in acute promyelocytes leukemia (APL) cells. However, the molecular mechanisms of CDDP-induced P53 activation, cell cycle arrest, and apoptosis in APL cells remain poorly understood. We hypothesized that CDDP inhibits proliferation of APL cells through MDM2-DAXX-HAUSP complex disruption, p53 activation leading to cell cycle arrest and apoptosis. To test hypothesis, we used three APL cell lines and mice model of APL and investigated CDDP effects on cells growth, complex disruption, cell cycle progression, and apoptosis by applying western blotting, IP, gene knockdown techniques, immune/histochemistry, and confocal imaging. We found that CDDP - induced stress signal transmitted by protein kinase (ATM, ATR) and its downstream targets (CHK1 & CHK2) phosphorylation leading to down-regulation of complex molecules expression and accumulation of p53. CDDP-induced p53 expression modulated cell cycle progression and apoptosis in APL cells, and stimulated the formation of more promyelocytes with dense granules through reduction of MDM2 expression in bone marrow cells. CDDP also activated p53 in APL mice liver tissues. This novel mechanism of action of CDDP in APL cells may help in the design of new anti-leukemic drugs for treatment of APL patients. Acknowledgements: This research was supported by National Institutes of Health NIMHD [grant # G12MD007581], through the RCMI-Center for Environmental Health at Jackson State University. Citation Format: Sanjay Kumar, Paul Tchounwou. Cisplatin disrupts MDM2-DAXX-HAUSP complex, p53 accumulation, cell cycle regulation, and apoptosis in acute leukemia cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5239.
The use of preoperative imaging in the treatment of sacral chordomas.

We greatly appreciate the thoughtful response by Munger and colleagues (1) to our original article on the predictive value of magnetic resonance imaging (MRI) findings on outcomes after en bloc resection of sacral chordomas (2). While we caution against over-interpretation given our sample size, we humbly believe that the preoperative imaging factors elucidated in our study may have prognostic implications that are important for both patients and surgeons.
Applied On-Chip Machine Learning for Dynamic Resource Control in Multithreaded Processors

In this paper, we propose a machine learning algorithm to control instruction fetch bandwidth in a simultaneous multithreaded CPU. In a simultaneous multithreaded CPU, multiple threads occupy pools...
Design and characterization of a porous pouch to prevent peritoneal adhesions during in vivo vascular graft maturation

Abstract Vein grafts for coronary artery bypass are not available in more than 30% of patients due to prior use or systemic vascular diseases. Tissue engineered vascular grafts (TEVGs) have shown promise, but intimal hyperplasia and graft thrombosis are still concerns when grafted in small-diameter arteries. In this study, we utilized the peritoneal cavity as an “in vivo” bioreactor to recruit autologous cells to electrospun conduits enclosed within porous pouches to improve the response after grafting. Specifically, we designed a new poly (ethylene glycol)-based pouch to avoid adhesion to the peritoneal wall and still allow the necessary peritoneal fluid to reach the enclosed conduit. The pouch mechanics in compression and bending were determined through experiments and finite element simulations to optimize the pouch design. This included poly (ethylene glycol) concentration, pore density, and pouch size. We demonstrated that the optimized pouch was able to withstand the estimated forces applied in the rat peritoneal cavity and it allowed maturation of the enclosed electrospun conduit. This pouch significantly reduced peritoneal adhesion formation compared to polytetrafluoroethylene pouches that have been used previously, which overcomes this potential limitation to clinical translation. After aortic grafting of pre-conditioned conduits, patent grafts with limited intimal hyperplasia were observed. Overall, this study demonstrated a new pouch design that allows the in vivo bioreactor strategy to be used for vascular tissue engineering without the potential side effect of peritoneal adhesion formation.
Content Analysis of ACGME Accredited Urology Residency Program Webpages

OBJECTIVE To provide an update on the web pages of academic Urology departments in the United States and to evaluate for consistency of information available to applicants. MATERIALS AND METHODS The American Urologic Association accredited listing of US urology residency programs was accessed in January 2018. One hundred and thirty-five urology residency program websites were then accessed and searched for the presence or absence of 44 criteria. Criteria were grouped into 7 categories: program overview and contact information, application information, program curriculum, current residents, alumni, faculty, and resident benefits. Programs were categorized based on US census bureau designated regions, program size, and by program ranking by the Doximity Urology Residency Program Navigator. RESULTS Out of 135, 134 (99%) of the AUA accredited listing of US urology residency programs had functional websites. The most commonly available information included clinical rotation sites (84%), resident curriculum (78%), number and names of current residents (76% and 77%, respectively), and faculty names and corresponding subspecialties (74% and 72%, respectively). These trends were similar across geographic regions. The top 20 residency programs on Doximity were more likely to list alumni names (70% vs 35%, P = .005), alumni fellowships (75% vs 30% P = .0003) and alumni jobs (75% vs 29%, P = .001) compared to all other residency programs. CONCLUSION There is high variability regarding comprehensiveness of urology residency websites. An informative and well-constructed website has the potential to improve optics and marketability of a residency program. Top notch residency programs are more likely to display fellowship and faculty information, both desirable prospects after residency.
Robustness of Sparse Bayesian Learning in Correlated Environments

In this paper we analyse the performance of Sparse Bayesian Learning (SBL) in an environment with correlated sources. We provide two new perspectives to understand SBL’s strategy for handling correlated sources. Using a Minimum Power Distortionless Response (MPDR) beamformer-based perspective of SBL, it is shown that the measured signal covariance strucure based on uncorrelated sources assumption used by SBL, infact provides immunity to source correlation. The MPDR based perspective is extended to formulate SBL’s misspecified model. This misspecified model is compared to the underlying true data distribution using Kullback-Leibler (KL) divergence metric and it is shown that SBL attempts to find an uncorrelated source covariance matrix that best fits the data. Theory on performance of misspecified models for the two source case is studied to gain further insights into the problem. Numerical results are provided to demonstrate SBL’s robustness as well as to quantify the model misfit when sources are correlated.
Hyperbaric oxygen therapy in malignant otitis externa: A systematic review of the literature.

Abstract Objective To review the role of adjuvant hyperbaric oxygen therapy (HBOT) in the treatment of malignant otitis externa (MOE). Data sources PubMed, Scopus, Web of Science, Science Direct, and Cochrane Library were searched for the following concepts: “hyperbaric oxygen” and “malignant or necrotizing otitis externa.” Methods Studies were included if they contained (1) patients with reported evidence of MOE, (2) employment of adjuvant HBOT, (3) details on patients’ medical condition, and (4) documented survival outcomes. Extracted information included patient demographics, underlying medical conditions, infectious etiology, signs and symptoms, medical and surgical treatments, duration of medical treatment, mean follow up time, HBOT setting, number of HBOT sessions, complications, survival rate, and all-cause mortality. Results A total of 16 studies comprising 58 patients (mean age 68.0 years) were included. Diabetes was present in 94.7% of cases and Pseudomonas spp (64.3%) was the most common infectious agent. Cranial nerve VII was involved in 55.2% of cases. Overall, the disease cure rate with adjuvant HBOT was 91.4% and all-cause mortality was 8.6%. Among those who had cranial nerve VII involvement, 72.0% had return of function and 93.8% of them survived. Conclusion HBOT may be an effective treatment option for refractory or advanced MOE but its efficacy remains unproven due to lack of strong scientific evidence. However, its therapeutic value should not be underestimated given good results and few adverse events reported in this study.
Analysis on site variation of amino acid of nucleoprotein of measles virus in Jilin province in 2013

Objective To study the site variation of amino acid of nucleoprotein (NP) of measles viruses in Jilin province in 2013.Methods All the throat swab specimen from measles cases in Jilin province in 2013 were detected the NP gene by the reverse transcription-polymerase chain reaction (RT-PCR) and then the RT-PCR positive products were sequenced.To analyze the variation of the deduced amino acid sequence.Results The measles virus genotype in Jilin province in 2013 were H1a genotype.There were 4 amino acids variations in NP in some of 50 specimen in 2013 compared with those of 2001.On the 3 amino acids variations on 422 site(G→S),457 site(S→G),497 site(R→K),there were only very few strains showed variation on these 3 sites in 2001-2008,and there were 100％,76.9％ and 32.0％-32.6％ of strains in 2009,2010 and 2013 respectively which showed variations on these 3 sites.There were 44.0％ of positive specimen of measles virus showed P→S variation only in 2013.Conclusions The measles virus showed diversified variations,remind us to pay close attention to the amino acids variations trend of the NP. Key words: Measles virus; Nucleoproteins; Amino acid sabstitution