cssi/SciSciGPT-SciSciNet huggingface dataset:
An approach to phylogenomic analysis of bacterial pathogens

From the beginning of the microbial genome sequencing era, researchers have shown a commendable commitment to phylogenetic diversity. The completion of one genome from each prokaryotic division or phylum is still a frequently articulated community goal. However, largely because of the interest in human pathogens and advances in sequencing technologies, there are also now a number of very closely related genomes whose organization and gene content can be directly compared. Studying genetic variability of pathogenic bacteria using whole-genome sequencing provides a way to understanding the mechanism of bacterial adaptation to rapid environmental changes and can be a source of useful information on virulence mechanisms. The bacterial genome datasets available in public archives represent a large collection of genome at different levels of sequence quality and assembly. A fast and reliable method of phylogenetic classification based on genome sequences provides a necessary foundation for a more detailed comparative analysis. NCBI has developed an approach of grouping bacterial organisms into phylogenetic clades using a genome dissimilarity measure based on the comparison of universally conserved markers. Special adjustments have been made to compensate for data inaccuracy and incompleteness. Tests performed on complete and draft genomes from phylum Proteobacteria demonstrated that the proposed robust genomic distance allows stable and reliable species-level clustering and can be used for forming phylogenetic clades. Since the tradeoff for the increased robustness of the method is its limited sensitivity at a very fine level, a phylogenomic refinement could be done within each constructed clade when file-level phylogenetic resolution of close genomes is necessary.
Computing the possible rest configurations of two interacting polygons

An algorithm that constructs the set of all possible equilibrium configurations for two interacting polygonal objects is described. Given two polygons, associated friction properties, and an applied force, the algorithm constructs the set of all configurations where the contact reaction force can balance the applied force, obeying friction constraints. The algorithm explicitly includes uncertainty in friction, applied force, and mass properties of the polygons. The algorithm has been implemented, and physical experiments have been performed to test the validity of the algorithm's predictions. The algorithm may be applied to a variety of physical systems to determine the possible rest states: examples include a part falling into a fixture and an object being pushed by a robot end-effector. >
The American Quarter Horse: Population Structure and Relationship to the Thoroughbred

A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred's influence on QH diversity. Results showed significant population structure among all QH performance groups excepting the comparison between the cutting and working cow horses; divergence was greatest between the cutting and racing QHs, the latter of which had a large contribution of Thoroughbred ancestry. Significant coancestry and the potential for inbreeding exist within performance groups, especially when considering the elite performers. Relatedness within performance groups is increasing with popular sires contributing disproportionate levels of variation to each discipline. Expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses suggest these QHs can be broadly classified into 3 categories: stock, racing, and pleasure/halter. Although the QH breed as a whole contains substantial genetic diversity, current breeding practices have resulted in this variation being sequestered into subpopulations.
WebMon: A performance profiler for web transactions

We describe WebMon, a tool for correlated, transaction-oriented performance monitoring of web services. Data collected with WebMon can be analyzed from a variety of perspectives: business, client, transaction, or systems. Maintainers of web services can use such analysis to better understand and manage the performance of their services. Moreover WebMon's data will enable the construction of more accurate performance prediction models for web services. Current web logging techniques create a log file per server making it difficult to correlate data from log files with respect to a given transaction. Additionally, data about the quality of service perceived by the client is missing entirely. WebMon overcomes these limitations by providing heterogenous instrumentation sensors and HTTP cookie-based correlators. In this paper, we present the design and implementation of of WebMon and our experience in applying WebMon to an HP Library web service.
CO 2 dissociation using the versatile atmospheric dielectric barrier discharge experiment (VADER)

To determine the viability of dielectric barrier discharges (DBDs) for CO 2 dissociation and other highly endothermic reactions, we developed a DBD-relevant chemical model for CO 2 dissociation and constructed a new DBD apparatus. The chemical model compares the chemical reaction rates during the different stages of a DBD discharge to determine which reactions control the chemical kinetics of a CO 2 plasma. The model showed that during the breakdown/cascade phase of the DBD electron impact dissociation, electron attachment and electron vibrational excitation are the dominant reactions within the plasma. However, relaxation of the dissociated components within the discharge afterglow determines the final chemical state of the system. The model also showed that the relaxation path taken is highly dependent on the gas temperature and the amount of product gas built up in the system. VADER is a planar DBD experiment used to determine the effects of different system parameters on the dissociation of CO 2 . These experiments showed that CO 2 dissociation efficiencies and rates are highly affected by multiple parameters including the power supply driving frequency (the most efficient dissociation occurs at a resonant frequency determined by the chemical kinetics), the gas composition (efficiency and rate improved with the addition of argon) and the addition of a photocatalyst into the reaction chamber (a photocatalyst improved CO 2 dissociation efficiencies and rates in a plasma operating at higher driving frequencies).
Modeling the effects of an H2 gas release on the equatorial ionosphere

Three simulated point releases of H2 gas are carried out at 1930 LT over the magnetic equator: 5 kg at 300 km, 10 kg at 350 km, and 20 kg at 300 km. The subsequent effects on the ionosphere in the vicinity of these releases are studied by calculating the densities of O(+), OH(+), H2O(+), and H3O(+) from coupled time-dependent ion continuity equations. It is found that the 5-kg release produces a depleted electron density region, while a 10-kg release produces an electron density hole. Increasing the release to 20 kg yields substantial amounts of the product ions OH(+), H2O(+), and H3O(+). The dominant ions at the times of 52, 276, and 1252 sec after release are 55% for H3O(+), 47.6% for OH(+), and 72.7% for O(+), respectively. Moreover, 276 sec after release, percent depletions in the integrated electron density and Pederson conductivity are 5.8% and 2.9%, respectively, for the 5-kg release; 7.4% and 5.2%, respectively, for the 10-kg release; and 11.8% and 4.3%, respectively, for the 20-kg release. Whether or not such initial depletions are sufficient remains to be seen.
Suicidality Among Battered Women in Tajikistan

This study examines the relationship between suicidality and women's experiences with marital violence in Tajikistan, including the type of abuser and help-seeking behaviors of battered women. This is a descriptive study that also includes comparisons based on women's demographics. Four hundred women in three districts of Khatlon Oblast, Tajikistan participated in this general population survey. Overall, women who experienced physical and/or sexual violence in their marriage and who told someone about the abuse were more likely to have suicidal thoughts and attempt suicide. The study's implications for future research on issues of marital violence against women and female suicide are discussed.
Absence of linkage between familial neural tube defects and PAX3 gene

Neural tube defects (NTD) are among the most common and disabling birth defects. The aetiology of NTD is unknown and their genetics are complex. The majority of NTD cases are sporadic, isolated, nonsyndromic, and generally considered to be multifactorial in origin. Recently, PAX3 (formerly HuP2, the human homologue of mouse Pax-3), on chromosome 2q35-37, was suggested as a candidate gene for NTD because mutations of Pax-3 cause the mouse mutant Splotch (Sp), an animal model for human NTD. Mutations in PAX3 were also identified in patients with Waardenburg syndrome type 1 (WS1). At least eight patients with both WS1 and NTD have been described suggesting pleiotropy or a contiguous gene syndrome. Seventeen US families and 14 Dutch families with more than one affected person with NTD were collected and 194 people (50 affected) from both data sets were genotyped using the PAX3 polymorphic marker. The data were analysed using affecteds only linkage analysis. The lod scores were -7.30 (US), -3.74 (Dutch), and -11.04 (combined) at theta = 0.0, under the assumption of the autosomal dominant model. For the recessive model, the lod scores were -3.30 (US), -1.46 (Dutch), and -4.76 (combined) at theta = 0.0. Linkage between PAX3 and familial NTD was excluded to 9.9 cM on either side of the gene for the dominant model and to 3.63 cM on either side of the gene for the recessive model in the families studied. No evidence of heterogeneity was detected using the HOMOG program. Our data indicate that PAX3 is not a major gene for NTD.
Osteoblasts Clock in for Their Day Job

The proteins encoded by clock genes regulate circadian variations of various cellular functions. In this issue of Cell, Fu, Karsenty, and colleagues (Fu et al., 2005) demonstrate that clock genes control the proliferation of osteoblasts, the cells that promote growth of bone. These findings indicate that the homeostatic regulation of bone mass is subject to circadian control.
Post-Traumatic Stress Disorder in Postpartum Patients: WHAT NURSES CAN DO

Women who have traumatic birth experiences, and even those who merely perceive their experiences as traumatic, may be at risk for PTSD. This article explains the condition and the role nurses can play in identifying patients at risk.
Newer teaching and learning techniques in the advancement of physiology education (531.15)

Instant access to content information is revolutionizing both the learning and teaching in higher education. The teacher-centered instruction is being replaced by active learning and other student-centered teaching methods. At St. Louis College of Pharmacy, a Flipped Classroom model is tested in the Advanced Physiology course where students are assigned homework in the form of lecture videos, PowerPoint presentations and reading assignments prior to their class meetings. The class time is dedicated to mini lectures, Team-Based Learning (TBL) activities and individual assessments. Clinical scenarios in the case discussion and the hands on lab activities are designed to provide ample opportunities to apply and review the lecture content. Additional support to help students’ cognitive skills is provided by weekly review sessions, walk-in tutoring opportunities and the availability of tutors for one-on-one instruction. The assessment includes a combination of factual details, problem solving, and comprehensio...
Boston Chicken Inc.: 4 1/2% Convertible Subordinated Debentures Due to 2004

Set in January 1994, this case concerns a discussion between a money manager and her assistant about approaches for analyzing an offering of convertible bonds by Boston Chicken. The analysis compares the insights available from standard descriptive ratios with those available from valuation analysis. The case is intended to be a student's first exercise in analyzing convertible bonds, and it assumes some familiarity with option-pricing theory and bond valuation. The format of the case (clear tasks and conversational style) is intended to disarm the novice. Nevertheless, the case raises many important and interesting points that will easily fill a class period.
Building Bridges for Refugee Empowerment

After the Syrian Humanitarian Crisis, the people of Turkey have long-established informal organizations to accommodate refugees. These local agencies often take responsibility as a cultural bridge between the refugee and the host community to establish peaceful relationships between two communities. In this paper, I examined the activities of one such local women’s organization in the Central Anatolia region. The organizational structure of this network of women was critically examined based on the principles of critical feminist theory. The findings showed that this organization challenged the dominant narratives of refugees as victims and helpers as liberators. In contrasts to much of the literature on refugee and migration studies, which avoided questioning the position of helpers, it unveiled some of the unacknowledged benefits accrued by the local women and presents an alternative humanitarian endeavor for improving refugees’ life standards.
A simple scaling normalization for comparing ChIP-Seq samples

In ChIP-Seq and DNase-Seq experiments, the density of background reads can vary from sample to sample. Differences in background read densities between samples do not necessarily correspond to proportional changes of read densities in true ChIP-Seq peaks. Therefore, scaling by total library size as a means for normalizing called ChIP-Seq peaks across samples may be ineffective. We suggest a simple easily implemented alternative to scaling by total library size that scales only by the total number of reads mapped to called peaks. We then demonstrate the effectiveness of the modified scaling in K4me3 and K27ac ChIP-Seq data from the BrainSpan project as well as DNase-Seq data from the ENCODE project.
A Review of A Color Atlas of Neuropathology

Neuropathology has long been an intimidating subdivision of anatomic pathology. Eponymous diseases (diagnosed by esoteric stains) seem to comprise an uncomfortable segment of the subspecialty, and yet a significant percentage of a forensic pathologist's cases involve neuropathologic conditions. C. S. Treip has added another volume to the Color Atlas series, and the result is a compact but surprisingly useful handbook. It makes a welcome complement to Fascicle 6 of the Tumor Pathology Series by covering, in addition to neoplasia, infectious and inflammatory disease, vascular disease, degenerative and demyelinating diseases, metabolic disorders, nutritional deficiencies, congenital malformations, and perinatal disorders. Also included is a section on traumatic lesions that is, unfortunately, very brief.
Hatching Egg Sanitization for Prevention or Reduction of Human Enteropathogens: A Review

Abstract Hatching egg sanitization has been a somewhat controversial issue for more than 50 yr. Many in the hatching egg industry oppose wetting of fertile eggs. Nevertheless, research has been published on the problem of lowering bacterial contamination of hatching eggs without adversely affecting hatchability. As on-farm and hatchery Hazard Analysis Critical Control Point programs become a reality, more and more companies will become interested in how to best prevent human enteropathogen colonization in chicks. It is possible to effectively lower bacterial contamination on the eggs and in the hatching cabinet and thus reduce the level of human enteropathogens being placed in grow houses with the chicks. Information gleaned from both early and recent egg-sanitizing efforts can be useful in designing the best overall egg and hatchery sanitization program.
Proof of Concept for Testing Acceleration Compensation Force Balance Techniques in Short Duration Flows with a CEV Capsule

is currently underway at CUBRC to design, build, calibrate and test a force/moment balance for use in short duration facilities. Due to the short test times it becomes paramount in the design of the force/moment balance to achieve the highest possible natural frequency for both the metric and non-metric components of the model to be tested. However, even with the most careful and well thought out design, there is still a strong possibility that the natural frequency of the model is to low to digitally filter without adversely aecting the true aerodynamic readings. It is therefore required to dynamically compensate the model to properly account for any low frequency response to accurately determine the true aerodynamics of the model being tested. The following paper briefly describes the design of such a model at CUBRC for an Apollo-like CEV re-entry vehicle.
Experimental Ablation of Posterior as Contrasted to Anterior Aortic Cusp on Cardiac Hypertrophy in the Rabbit.

During the progress of studies on the results of digitization on experimental aortic insufficiency hypertrophy it was observed that the gross configuration of the hypertrophied heart appeared to differ. Some were globular in form whereas others were elongated or boot shaped. The hearts were dissected by removal of the auricles and division of the ventricular mass by the midseptal method. It was found that the globular heart was associated with ablation of the posterior leaflet and the right ventricular wall appeared to be considerably thickened along with the increased mass of the left heart. The coeur en sabot type, on the other hand, was found occurring usually in those that had destruction of the left anterior cusp. In the latter group the thickness of the right ventricular wall did not appear to be conspicuously increased in thickness, while the left ventricular wall was strikingly so. In a few hearts with combined lesions the configuration depended upon which leaflet damage was the more extensive. Th...
Vasopressin and ACTH release.

SummaryA new method of testing for ACTH-releasing activity of neurohumoral substances has been described. The material to be tested is injected directly into the arterial blood supply of an ACTH-secreting pituitary tumor grafted in the hind leg of a hypophysectomized rat. The amount of ACTH released is measured by the difference in corti-costerone secretion rate before and after the injection. Amounts of vasopressin as minute as 1.0 μU to 10.0 μU release measurable quantities of ACTH. Doses of vasopressin 1,500 times this amount given intravenously have no effect on ACTH release. These findings suggest that vasopressin may be the ACTH-releasing neurohumor. It is suggested that the method may be used as an assay method for vasopressin.
Isolation and partial characterization of apiogalacturonans from the cell wall of Lemna minor

1. A mild, reproducible extraction procedure, using 0.5% ammonium oxalate, was developed for the isolation of polysaccharides containing d-apiose from the cell wall of Lemna minor. On a dry-weight basis the polysaccharide fractions extracted with ammonium oxalate made up 14% of the material designated cell walls and contained 20% of the d-apiose originally present in the cell walls. The cell walls, as isolated, contained 83% of the d-apiose present in L. minor. 2. After extraction with ammonium oxalate, purified polysaccharides were obtained by DEAE-Sephadex column chromatography and by fractional precipitation with sodium chloride. With these procedures the material extracted at 22°C could be separated into at least five polysaccharides. On a dry-weight basis two of these polysaccharides made up more than 50% of the material extracted at 22°C. There was a direct relationship between the d-apiose content of the polysaccharides and their solubility in sodium chloride solutions; those of highest d-apiose content were most soluble. 3. All the polysaccharides isolated appeared to be of one general type, namely galacturonans to which were attached side chains containing d-apiose. The d-apiose content of the apiogalacturonans varied from 7.9 to 38.1%. The content of esterified d-galacturonic acid residues in all apiogalacturonans was low, being in the range 1.0–3.5%. Hydrolysis of a representative apiogalacturonan with dilute acid resulted in the complete removal of the d-apiose with little or no degradation of the galacturonan portion. 4. Treatment of polysaccharide fractions with pectinase established that those of high d-apiose content and soluble in m-sodium chloride were not degraded, whereas those of low d-apiose content and insoluble in m-sodium chloride were extensively degraded. When the d-apiose was removed from a typical pectinase-resistant polysaccharide, the remainder of the polysaccharide was readily degraded by this enzyme. 5. Periodate oxidation of representative polysaccharide fractions and apiogalacturonans and determination of the formaldehyde released showed that about 50% of the d-apiose molecules were substituted at either the 3- or the 3′-position.
Inuit and non-Inuit alcohol consumption in the Baffin Region, NWT, Canada.

Stereotypes about Inuit drinking would have us believe they are much more likely to be users of alcohol compared to other segments of the population. As with many other stereotypes, however, this belief is primarily rooted in fiction and selective observation. As revealed in a number of self-report surveys regarding alcohol use, a smaller proportion of Inuit in the Northwest Territories (NWT) have reported drinking when compared to the non-aboriginal of the territory. The data presented here serve to further confirm the notion of comparatively less prevalent alcohol use among NWT Inuit. Rather than using survey data, however, this paper looks to alcohol use indicators derived from territorial liquor commission mail order invoices to show that the volume of alcohol consumed by Baffin Region Inuit is much less than that of non-Inuit in and outside the territory. Language: en
Abstract IA10: Regulating transcription elongation at stimulus responsive genes

The majority of mammalian protein-coding genes display transcription in both sense and anti-sense directions. At such bidirectional promoters, Pol II has been shown to initiate transcription and undergo promoter-proximal pausing near both the sense-strand mRNA transcription start site (TSS) and from within the upstream region in the anti-sense direction. This enigmatic, dual promoter structure raises fundamental questions about the specificity, purpose and regulation of upstream anti-sense transcription. Interestingly, transcription in the anti-sense direction is generally non-processive and creates short, unstable non-coding RNAs (ncRNAs). Intriguingly, many distal enhancer regions display bidirectional transcription and generate short unstable ncRNAs, raising parallels between enhancers and anti-sense promoters near protein-coding genes. Importantly, enhancers and upstream anti-sense promoters show exquisite cell type specificity in their location and activity, suggesting key roles in establishing cell state and behavior. Further, perturbation of either transcription or chromatin structure at such non-coding loci has been implicated in the development of cancer and disease, with a profound impact on maintenance of cell state and responsiveness to stimuli. These recent findings raise a number of intriguing questions about the communication between promoters and non-coding loci. Our work has recently defined a mechanism through which upstream anti-sense transcription impacts stimulus-responsive gene expression. Specifically, we found that the distance between sense and anti-sense TSSs at bidirectional promoters strongly influences activation of pro-inflammatory genes in macrophages. We discovered that anti-sense TSSs organize chromatin structure, creating a region of open chromatin between bidirectional TSSs that is optimal for recruitment of the transcription machinery and signal-dependent transcription factors like NF-kB. Further, we discovered that key inflammatory genes possess enhancer-like histone modifications around the anti-sense TSS, and that this characteristic selectively marks genes that are highly activated upon immune stimulation. Citation Format: Karen Adelman, Benjamin S. Scruggs, Telmo Henriques, Adam Burkholder, David C. Fargo. Regulating transcription elongation at stimulus responsive genes. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA10.
Postdivorce Parenting: A Study of Recently Divorced Mothers and Fathers

ABSTRACTDivorce is challenging for parents with children, commonly resulting in a series of individual and interpersonal adjustments. The time immediately following divorce can be particularly difficult. This study used a modified grounded theory approach to explore the experiences of 99 recently divorced mothers and fathers. Analysis of written narratives revealed 4 emergent groups of parents who described their postdivorce parenting experiences: good divorce, good enough, bad to better, and bad. Each group described their experiences across several areas including coparenting, father involvement, challenges of single parenting, personal turmoil, and their children’s adjustment. Implications for research and divorce education are discussed.
Recurrent SERPINB3 and SERPINB4 mutations in patients who respond to anti-CTLA4 immunotherapy

Immune checkpoint blockade has shown significant promise as an anticancer treatment, yet the determinants of response are not completely understood. Here we show that somatic mutations in SERPINB3 and SERPINB4 are associated with survival after anti-CTLA4 immunotherapy in two independent cohorts of patients with melanoma (n = 174). Interestingly, serpins are homologs of the well-known ovalbumin antigen and are associated with autoimmunity. Our findings have implications for the personalization of immunotherapy.
Abstract B66: Tumor-specific differences in virus-induced inflammation may determine therapeutic response to HSV virotherapy in sarcoma models

Ewing9s Sarcoma (EWS) is the second most common childhood bone cancer with high rate of metastasis (25%) and tumor recurrence (30~40%). Despite tremendous advances in the five-year survival rate of localized disease (70~80%), overall survival for patients with relapse or metastasis remains poor ( Citation Format: Chun-Yu Chen, Brian J. Hutzen, Pin-Yi Wang, Jennifer L. Leddon, Mark A. Currier, Nicholas Denton, Timothy Eubank, Timothy P. Cripe. Tumor-specific differences in virus-induced inflammation may determine therapeutic response to HSV virotherapy in sarcoma models. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr B66.
O-002 Presenting Diffusion-Restricted Core Volume, Not Time, Predicts Final Infarct Volume after Thrombectomy in Anterior Circulation Large Vessel Occlusion Stroke

Purpose With thrombectomy for anterior circulation large vessel occlusion (ACLVO) stroke, time to recanalization is considered important, but collateral status may be a more important driver of outcome than time. Here we used data from an institutional cohort to test the hypothesis that small DWI core volume on presenting MRI, a biomarker of robust collateral perfusion, is the dominant predictor of favorable outcome after thrombectomy. Methods A cohort of 56 ACLVO patients treated with thrombectomy at our institution between 11/1/2012 and 5/15/2015 was studied by logistic regression using final infarct volume ≤50 mL, a validated predictor of good clinical outcome, as the outcome variable. The following univariate predictor variables were assessed: age, NIHSS score, time to CTA, time to CTA ≤ 6 hours, presenting diffusion-restricting core volume, presenting core ≤ 50 mL, time to recanalization, time to recanalization ≤6 hours, time to recanalization ≤8 hours, and recanalization ≥ TICI2B. Finally, multiple logistic regression models were created comparing time and presenting core as predictors adjusting for age and TICI2B recanalization status. Results Of the univariate predictors studied, only presenting core volume, presenting core volume ≤50 mL, age, and post procedure TICI ≥ 2 B were significant predictors of the outcome variable at the α = 0.15 level (Table 1). Paradoxically, the administration of IV tPA was associated with larger core volumes in our dataset ( β = 1.53, p = 0.100). Of the time-based predictors, time to recanalization and time to recanalization ≤8 hours performed best, although none of them approached significance at the α = 0.15 level. The performances of time, core volume, age and TICI ≥ 2 B as predictors of small final infarct were then evaluated in a multiple logistic regression model. In that model, presenting core volume ≤50 mL, not time to recanalization, was the dominant predictor of small final infarct volume (OR 15.2 [95CI 1.3, 180] vs. 0.94 [95CI 0.78, 1.1]). Finally, a 3 variable logistic regression model incorporating presentation core volume, age, and TICI ≥ 2 B as covariates was constructed. The resulting model was statistically significant χ 2 (2) = 22.65, ( p Conclusion Presentation volume of diffusion-restricted core was a strong predictor of final infarct volume post-thrombectomy in this cohort of ACLVO patients, whereas time-based covariates showed little if any significant predictive value. For every 1 mL increase in presentation infarct volume, the odds of a small completed infarct were reduced by about 6%. A presentation core volume ≤50 mL improved the odds of a small final infarct by at least 26%, probably more. Disclosures B. Cristiano: None. M. Pond: None. S. Basu: None. U. Oyoyo: None. J. Jacobson: 4; C; GeneLux.
Allostatic breakdown of cascading homeostat systems: A computational approach.

Homeostasis posits that physiological systems compensate setpoint deviations in an attempt to maintain a state of internal constancy. Allostasis, on the other hand, suggests that physiological regulation is more appropriately described by predictive modulatory actions that, by adjusting setpoints, anticipate and react to changes in internal and external demand. In other words, “maintaining stability through change.” The allostatic perspective enabled the rationalization of predictive and reactive homeostasis. While the latter reflects external perturbations, the former refers to systemic adaptation in response to anticipated changes − not necessarily related to unexpected external disturbances. Therefore, the concept of allostasis accounts also for adaptation to circadian variations (seasonal, circannual or other predictive variability) and interprets the system’s adaptation of its setpoints not as reactive/subnormal adjustments, but rather as a proper response. Therefore, systemic entrainment to periodic demands is handled by predicting and implementing setpoint changes. Given the important role of circadian variability and regulation in maintaining health, and the loss of circadian entrainment as a predisposing factor and sequel of stress, we elaborate on an allostasis model which demonstrates the ability of the systems to adapt to circadian demands and quantifies the deteriorative natural wear and tear of a system constantly adapting, i.e. the irreversible damage and its consequences on system function and overall survival. While developing a system of cascaded nature, we demonstrate the importance of phase coordination and the implications of maintaining proper phase relations. The disruption of these relations is a hallmark of circadian disruption, a predisposing factor to increased vulnerability and/or a sequel to chronic stress.
How does regulation impact unregulated organizations? Evidence from the menu labeling regulation

Abundant organizational studies have examined the direct impact of regulations on its intended organizational targets. However, the existing literature has largely overlooked the spillover effects ...
Fetal and Placental Anatomy Visualized With Cinematic Rendering From Volumetric CT Data

Avoiding unnecessary radiation exposure in children, including fetuses or embryos, is of paramount importance. However, emergent clinical situations will arise that necessitate the use of ionizing radiation-based modalities, such as computed tomography (CT), in this patient population. In such circumstances, the use of advanced visualization methods may provide optimum diagnostic utility. We present the case of a pregnant patient with Loeys-Dietz syndrome who was evaluated with CT angiography to rule out an acute aortic syndrome. The CT data from the fetus and placenta were reconstructed using the new cinematic rendering technique that allows for photorealistic display. The potential advantages of cinematic rendering relative to traditional volume rendering are discussed.
The Obama Era: The View from Indonesia

US President Barack Obama’s election was watched particularly closely in Indonesia, where Obama had spent formative years of his childhood. For some scholars and policymakers, the election of the first US-Indonesian president in Washington, combined with a government in Jakarta interested in boosting Indonesia’s regional and global influence, offered a rare chance to transcend lingering and fundamentally transform the bilateral relationship.
Overcoming medication stigma in peer recovery: A new paradigm.

ABSTRACTBackground: Treatment for opioid use disorder involving opioid-based pharmacotherapies is considered most effective when accompanied by psychosocial interventions. Peer-led support groups are widely available and have been described by many as fundamental to the recovery process. However, some individuals using medications face stigma in these settings, which can be contradictory and counterproductive to their recovery. Methods: This paper describes the development of the “Ability, Inspiration and Motivation” or “AIM” group, an alternative peer support group that aims to remove medication stigma from peer recovery. Qualitative interviews with staff, peers, and clients of a community-based buprenorphine treatment program were used to establish the core components of the curriculum to support client needs. Results: Staff, peers, and clients of the buprenorphine program indicated a need and desire to establish a peer recovery group that recognizes persons on medication as being in recovery and destig...
Low Power Thermal Tuning in Resonant Vertical Junction Silicon Modulators Through Substrate Removal

We report on thermally tunable modulators, with efficiencies up to 2.16 nm/mW. Efficient performance was accomplished through integrated heater design and Si substrate removal, where the heavily N+ doped Si heater element is integrated into the body of the microdisk. For comparison, modulators with an external heater design were also tested with small diameter Si substrate removed. The external heavily doped N+Si heater bars were fabricated outside the diameter of the microdisk. Efficiency for external heater design was 0.68 nm/mW with substrate removed. Both types of thermal modulators were experimentally tested and simulated for a complete understanding of the Si substrate's influence on heat dissipation with both types benefiting significantly from substrate removal. Agreement between simulation and experimental results was greater than 80 $\%$ in all instances.
Dart-to-Heart Distance when Taser® Causes Ventricular Fibrillation in Pigs

Electromuscular incapacitating devices (EMDs), such as Tasers, deliver high current, short duration pulses that cause muscular contractions and temporarily incapacitate the human subject. Some reports suggest that EMDs can kill. To help answer the question, “Can the EMD directly cause ventricular fibrillation (VF)?,” ten tests were conducted to measure the dart-to-heart distance that causes VF in anesthetized pigs (mass = 64 kg ± 6.67 (SD)) for the most common X26 Taser. The dart-to-heart distance that caused VF was 17 mm ± 6.48 (SD) for the first VF event and 13.7 mm ± 6.79 (SD) for the average of the successive VF events. The result shows that when the stimulation dart is close enough to the heart, X26 Taser current will directly trigger VF in pigs. Echocardiography of erect humans shows skin-to-heart distances from 10 to 57 mm (dart-to-heart distances of 1 to 48 mm). These results suggest that the probability of a dart on the body landing in 1 cm2 over the ventricle and causing VF is 0.000172.
Photosystem-II repair and chloroplast recovery from irradiance stress: relationship between chronic photoinhibition, light-harvesting chlorophyll antenna size and photosynthetic productivity in Dunaliella salina (green algae)

High-light (HL) grown Dunaliella salina cells exhibit lower pigment content, a highly truncated chlorophyll (Chl) antenna size, and accumulation of photodamaged PS II centers in the chloroplast thylakoids (chronic photoinhibition). In HL-grown cells, the rate of photosynthesis saturated at higher irradiances and the quantum yield was lower compared to that of normally-pigmented low-light (LL) grown cells. In spite of these deficiencies, the light-saturated rate of photosynthesis for the HL-cells, when measured on a per chlorophyll basis, was ∼3 times greater than that of the LL-grown cells. To delineate the effect of photoinhibition from the Chl antenna size on quantum yield and rate of photosynthesis, HL-acclimated cells were switched to LL-conditions. Repair of photodamaged PS II, estimated from the recovery of functional PS II centers and from the increase in the quantum yield of photosynthesis, occurred with a half-time of ∼1 h. Chlorophyll accumulation in the cells occurred with a half-time of ∼4 h. The differential kinetics in repair versus Chl accumulation provided a ‘window of opportunity’, within about 2–3 h after the HL→LL shift, when cells exhibited a high quantum yield of photosynthesis, a small Chl antenna size and a light-saturated rate that was ∼6–9 times greater than that of the normally pigmented LL-grown cells. The work provides insight on the temporal sequence of events at the chloroplast and thylakoid membrane levels, leading from a chronic photoinhibition of PS II to repair and recovery. It is suggested that it is possible to maximize photosynthetic productivity and light utilization in mass microalgal cultures by minimizing the light-harvesting Chl antenna size of the photosystems.
Geometry of Planes over Nonassociative Algebras

In this paper the geometric interpretation of the exceptional Lie groups F4, E6, E7, and E8 is given. These groups are groups of motions of elliptic hyperbolic planes over nonassociative algebras of octaves and split octaves and their tensor products with algebras of usual and split complex numbers, quaternions and octaves. The explicit expressions of motions of these planes and their figures of symmetry are presented.
Overview of Non-Reactive Scattering

Non-reactive molecular scattering has been periodically reviewed from different points of view. Two volumes edited by Miller1 contain detailed chapters on theoretical approaches to the dynamics of molecular collisions. An encyclopedic theoretical guide to the experimentalist on atom-molecule collisions has recently been edited by Bernstein.2 Two reviews, by Dickinson3 and by DePriso and Rabitz,4 emphasize research areas developed by these authors. A monograph by Gianturco5 covers theoretical methods for both atomic and molecular collisions. Several contributions on inelastic collisions relating to chemical kinetics may be found in two issues of the Journal of Physical Chemistry,6,7 and also in the proceedings of a subsymposium on molecular collisions and electron scattering. Experimental work closely related to theoretical studies has been covered in reviews by Faubel and Toennies,9 by Bernstein,10 by Gentry,11 and most recently by Loesch.12
Recombination between mutants of Phycomyces with abnormal phototropism.

Sexual crosses were studied between mutants ofPhycomyces blakesleeanus with abnormal phototropism (phenotypemad). Recombination frequencies were determined among five genesmadA tomadE. No clear evidence was found for linkage between any of the genes. Inconsistent results in crosses involvingmadC are attributed to nonisogenicity between the particular strains used. Onemad strain was discovered to be a double mutant. A new gene, tentatively designatedmadG, was segregated from a cross involving that strain.
Evaluating the role of cough duration in the pertussis case definition among Michigan cases, 2000-2010.

Abstract Impressive reductions in pertussis have been achieved in the U.S. during the 20th century through childhood vaccination. Over the past two decades, increasing pertussis incidence has highlighted the need for accurate and timely reporting of cases to improve prevention and control efforts. We assessed components of the pertussis case definition, comparing use of clinical characteristics and laboratory results and their effects on internal validity, including an examination of the 2014 infant case definition. All reported pertussis cases in Michigan during 2000–2010 with data on cough length (N = 3310) were analyzed using multivariate statistics to internally validate reported cases, and calculate odds of meeting the clinical case definition, including a cough of at least 14 days. Cough duration of reported cases averaged 32 days and was longer with greater time interval between cough onset and initial presentation to a physician. Only about half of reported cases had positive laboratory results. Among cases seeking medical evaluation prior to meeting the cough duration required to fulfill the clinical case definition, the presence of positive lab results doubled the odds that the cough duration was not met compared to cases without a positive lab test. Clinical characteristics of pertussis are frequently ignored in applying the case classification. Relying solely on laboratory confirmation and disregarding clinical characteristics results in undiagnosed pertussis cases among those who are vaccinated, among adults, and among anyone who delays seeking care. This may prevent use of appropriate prevention and prophylaxis in contacts.
Relationship between uncertainty in illness and quality of life in patients with lung cancer

Objective To investigate uncertainty in illness and quality of life in patients with lung cancer and the relationship between them.Methods The scales of the Michel's Chinese version of uncertainty in illness and the scales of quality of life were tested in 280 hospitalized patients with lung cancer. Results ①The score of the uncertainty in illness was(105.15 ± 12.66).②The score of quality of life was(1.53 ± 0.58),each item followed by scoring high to low was cognitive function(1.78±0.92), emotional function(1.72±0.63), physical function(1.63±0.45), social function(1.56±0.68)and functional role(1.27±0.41).③There were positively correlations between the overall level of uncertainty in illness and the emotional function of the quality of life, uncertainty in information was positively correlated with the quality of life in the body function, emotional function, cognitive function, social function items;and the unpredictability of uncertainty in illness was negatively correlated with the cognitive function of the quality of life. Conclusion There is a high degree of uncertainty in illness in patients with lung cancer;and there are obvious correlations between the uncertainty in illness and the quality of life. Key words: Lung cancer; Uncertainly in illness; Quality of life
Interim results of prospective pilot phase II trial of concurrent anti-PD-1 and stereotactic radiosurgery (SRS) for melanoma and NSCLC patients with brain metastases (NCT02858869).

e22002Background: The safety and efficacy of concurrent radiotherapy (SRS) and single agent (anti-PD-1) checkpoint inhibitor have not been established. We report the first results of an interim ana...
Finding a state of sustainable wine: Implications for sustainable viticulture and oenology in New Jersey, USA

New Jersey is the most urbanised state in the USA, yet positioned as a sustainable wine region of the world. The methodology includes a thorough literature review of sustainable wine combined with a quantitative and qualitative survey of wineries in New Jersey. Data collected from 71% of wineries demonstrate sustainable opportunities for developing wine regions. A variety of conclusion is drawn from the research. First, farmers are generally sustainable at a small scale and employ a variety of sustainable best management practices. Second, support from the growers association and government would advance sustainability. Third, additional funding would expedite this move; many of New Jersey wines are already labelled or marketed as sustainable. By creating a certification, guidelines, or set of best management practices, New Jersey could differentiate and improve sales locally, nationally and even globally. These lessons can be applied to other developing wine regions of the world.
Loss of bound zinc facilitates amyloid fibril formation of leukocyte-cell-derived chemotaxin 2 (LECT2).

Aggregation of the circulating protein leukocyte-cell-derived chemotaxin 2 (LECT2) causes amyloidosis of LECT2 (ALECT2), one of the most prevalent forms of systemic amyloidosis affecting the kidney and liver. The I40V mutation is thought to be necessary but not sufficient for ALECT2, with a second, as-yet undetermined condition being required for the disease. EM, X-ray diffraction, NMR, and fluorescence experiments demonstrate that LECT2 forms amyloid fibrils in vitro in the absence of other proteins. Removal of LECT2’s single bound Zn2+ appears to be obligatory for fibril formation. Zinc-binding affinity is strongly dependent on pH: 9–13 % of LECT2 is calculated to exist in the zinc-free state over the normal pH range of blood, with this fraction rising to 80 % at pH 6.5. The I40V mutation does not alter zinc-binding affinity or kinetics but destabilizes the zinc-free conformation. These results suggest a mechanism in which loss of zinc together with the I40V mutation leads to ALECT2.
Mice Harboring a Non-Functional CILK1/ICK Allele Fail to Model the Epileptic Phenotype in Patients Carrying Variant CILK1/ICK

CILK1 (ciliogenesis associated kinase 1)/ICK (intestinal cell kinase) is a highly conserved protein kinase that regulates primary cilia structure and function. CILK1 mutations cause a wide spectrum of human diseases collectively called ciliopathies. While several CILK1 heterozygous variants have been recently linked to juvenile myoclonic epilepsy (JME), it remains unclear whether these mutations cause seizures. Herein, we investigated whether mice harboring either a heterozygous null Cilk1 (Cilk1+/−) mutation or a heterozygous loss-of-function Cilk1 mutation (Cilk1R272Q/+) have epilepsy. We first evaluated the spontaneous seizure phenotype of Cilk1+/− and Cilk1R272Q/+ mice relative to wildtype littermates. We observed no electrographic differences among the three mouse genotypes during prolonged recordings. We also evaluated electrographic and behavioral responses of mice recovering from isoflurane anesthesia, an approach recently used to measure seizure-like activity. Again, we observed no electrographic or behavioral differences in control versus Cilk1+/− and Cilk1R272Q/+ mice upon isoflurane recovery. These results indicate that mice bearing a non-functional copy of Cilk1 fail to produce electrographic patterns resembling those of JME patients with a variant CILK1 copy. Our findings argue against CILK1 haploinsufficiency being the mechanism that links CILK1 variants to JME.