cssi/SciSciGPT-SciSciNet huggingface dataset:
Genotyping Chlamydia trachomatis by PCR

Strain identification of Chlamydia trachomatis has historically been accomplished using serotyping as a phenotypic marker to differentiate chlamydial isolates (1). The target for serotyping is the major outer membrane protein (MOMP) which is the most antigenically diverse and abundant surface protein of the organism. Polyclonal antibodies (PAbs) were initially used for typing and were able to identify serovars D through K and LI, L2, and L3 as primarily genital pathogens, and serovars A, B, Ba, and C as trachoma pathogens. However, these groupings are somewhat imprecise. As immunotyping methods evolved, MOMP-specific monoclonal antibodies (MAbs) were produced that were able to detect additional serovars of the organism (2,3). These include Da, la, and L2a (2). MAbs recognize serovar-, subspecies-, and species-specific epitopes (4,5) that reflect many of the amino acid variations found among the 18 known serovars of C. trachomatis, and are located within three of the four variable sequence regions of MOMP, termed variable segments (VS) 1,2, 3, and 4. Sequence analysis of the MOMP gene (omp1) supports these findings in that VS 1,2, and 4, in contrast to VS 3, contain the greatest degree of nucleotide sequence variation (6,7).
The development and preliminary psychometric evaluation of an attachment Implicit Association Task.

The importance of measuring attachment insecurity is underscored by a vast literature tying attachment insecurity to numerous psychological disorders. Self-report measures assess explicit attachment beliefs and experiences, while interview measures, like the Adult Attachment Interview, assess implicit internal working models about the self as worthy of care and others as reliable sources of care. The present study is a preliminary psychometric evaluation of a potentially cost-effective method of assessing implicit internal working models of attachment through the development of an Implicit Association Test (IAT). A racially diverse sample of 104 college females was administered Internet-based versions of three IATs (assessing views of the self, mother, and father) as well as self-report measures of attachment and interpersonal problems. Analyses were conducted to evaluate the (a) internal consistency of each task, (b) correlations among the tasks, (c) concurrent validity, and (d) convergent validity. Adeq...
Clostridium difficile infection health disparities by race among hospitalized adults in the United States, 2001 to 2010

Recognition of health disparities in Clostridium difficile infection (CDI) is an initial step toward improved resource utilization and patient health. The purpose of this study was to identify health disparities by black vs. white race among hospitalized adults with CDI in the United States (U.S.) over 10 years. This was a retrospective analysis of the U.S. National Hospital Discharge Surveys from 2001 to 2010. Eligible cases included adults with an ICD-9-CM code for CDI (008.45). Patients with missing race or “other race” were excluded. The primary outcome, CDI incidence, was calculated as CDI discharges per 1,000 total discharges. Data weights were used to determine national estimates. Secondary outcomes included in-hospital mortality, hospital length of stay (LOS), and severe CDI. Comparisons were made using bivariable analyses. Race was assessed as an independent risk factor for CDI outcomes using logistic regression or proportional hazards models. These data represent 1.7 million CDI discharges, where 90 % of patients were identified as white and 10 % black. Blacks differed from whites with respect to all baseline characteristics (p 7 days (57 % vs. 52 %, p < 0.0001), and severe CDI (24 % vs. 19 %, p < 0.0001). In multivariable analyses, black race was a positive predictor of mortality (OR 1.12, 95 % CI 1.09–1.15) and severe CDI (OR 1.09, 95 % CI 1.07–1.11), and negative predictor for hospital LOS (OR 0.93, 95 % CI 0.93–0.94). CDI incidence was higher for white patients; however, black race was independently associated with mortality and severe CDI.
Redox Control of Aluminum Ring-Opening Polymerization: A Combined Experimental and DFT Investigation

The synthesis, characterization, and reactivity of an aluminum alkoxide complex supported by a ferrocene-based ligand, (thiolfan*)Al(OtBu) (1red, thiolfan* = 1,1′-di(2,4-di-tert-butyl-6-thiophenoxy)ferrocene), are reported. The homopolymers of l-lactide (LA), e-caprolactone (CL), δ-valerolactone (VL), cyclohexene oxide (CHO), trimethylene carbonate (TMC), and their copolymers were obtained in a controlled manner by using redox reagents. Detailed DFT calculations and experimental studies were performed to investigate the mechanism. Mechanistic studies show that, after the insertion of the first monomer, the coordination effect of the carbonyl group, which has usually been ignored in previous reports, can significantly change the energy barrier of the propagation steps, thus playing an important role in polymerization and copolymerization processes.
Rabies encephalitis presenting with new-onset refractory status epilepticus (NORSE)

A 15-year-old girl, previously healthy with normal developmental history, had an episode of unilateral arm jerking at school followed by transient loss of consciousness. Two weeks later, she presented to the emergency department with recurrent generalized convulsions despite treatment with lorazepam and fosphenytoin. In retrospect, her family reported a 1-month history of personality changes (i.e., listlessness) and decline in academic performance. There was no family history of epilepsy, metabolic disorders, or immunodeficiency. The patient resided in rural northeastern Kentucky. There was no recent travel history.
Determining total emissions and environmental drivers of methane flux in a Lake Erie estuarine marsh

Abstract Estuarine freshwater marshes can act as an important ecosystem for carbon storage and flux because of its strategic position in a watershed. We monitored CH4 and CO2 fluxes in Old Woman Creek, an estuarine wetland of Lake Erie, Ohio. The eddy covariance (EC) technique was used to measure fluxes of CH4 and CO2 continuously during the growing seasons of 2015 and 2016. Simultaneously, monthly sampling of gas exchange was conducted using non-steady state chambers in four distinct land-cover types in the wetland: open water, emergent vegetation (Typha spp.), floating vegetation (Nelumbo spp.) and mud flats. Chambers and EC measurements were combined to provide estimates of the continuous contributions of each land cover to the total methane emissions of the wetland. In addition, water and meteorological measurements were used to determine the most important environmental drivers of methane flux in the wetland. We found an average rate of emission from the Typha patch, the most abundant vegetated land cover, of 219.4 g CH4 C m−2 y−1, which was much higher than rates reported in similar emergent vegetation types in other wetlands. Mud flats had the highest rates of CH4 emission, followed by Nelumbo and Typha patches, and open water. Mud flats contributed 6.8% of the total CH4 emissions of the wetland despite occupying only 1.5% of the wetland area, whereas open water contributed 16.1% despite occupying 47% of the wetland area. Water temperature and wind speed were the strongest environmental drivers of CH4 flux to the atmosphere. Carbon fluxes were strongly correlated to methane fluxes. Fluctuating water levels above the wetland’s surface had a weak effect on overall CH4 emissions in the wetland, with stronger effects during the night than during the day. Providing an empirical model that predicts the influence of different environmental drivers CH4 emissions in the wetland can aid in the design of estuarine wetlands that retain nutrients and reduce coastal eutrophication while minimizing greenhouse gas emissions.
ADE: An ensemble approach for early Anomaly Detection

Proactive anomaly detection refers to anticipating anomalies or abnormal patterns within a dataset in a timely manner. Discovering anomalies such as failures or degradations before their occurrence can lead to great benefits such as the ability to avoid the anomaly happening by applying some corrective measures in advance (e.g., allocating more resources for a nearly saturated system in a data centre). In this paper we address the proactive anomaly detection problem through machine learning and in particular ensemble learning. We propose an early Anomaly Detection Ensemble approach, ADE, which combines results of state-of-the-art anomaly detection techniques in order to provide more accurate results than each single technique. Moreover, we utilise a a weighted anomaly window as ground truth for training the model, which prioritises early detection in order to discover anomalies in a timely manner. Various strategies are explored for generating ground truth windows. Results show that ADE shows improvements of at least 10% in earliest detection score compared to each individual technique across all datasets considered. The technique proposed detected anomalies in advance up to ∼16h before they actually occurred.
Off-Shell Higgs Probe of Naturalness

Examining the Higgs sector at high energy scales through off-shell Higgs production can potentially shed light on the naturalness problem of the Higgs boson mass. We propose such a study at the LHC by utilizing a representative model with a new scalar field (S) coupled to the standard model Higgs doublet (H) in a form |S|^{2}|H|^{2}. In the process pp→h^{*}→ZZ, the dominant momentum-dependent part of the one-loop scalar singlet corrections, especially above the new threshold at 2m_{S}, leads to a measurable deviation in the differential distribution of the Z-pair invariant mass, in accordance with the quadratic divergence cancellation to the Higgs mass. We find that it is conceivable to probe such new physics at the 5σ level at the high-luminosity LHC, improving further with the upgraded 27 TeV LHC, without requiring the precise measurement of the Higgs boson total width. The discovery of such a Higgs portal could also have important implications for thermal dark matter as well as for electroweak baryogenesis.
Using multirotor drones in engineering of systems curricula

This paper describes the usage of multirotor drones to support a sequence of systems engineering courses at the Naval Postgraduate School. These courses, Engineering Systems Conceptualization, Engineering Systems Design, and Engineering Systems Implementation & Operation, allow students to apply their knowledge and engineering skills to design future missions involving unmanned aerial systems, build and test a prototype drone to support these missions, and eventually demonstrate a mission execution in computer simulations and/or controlled environment indoors or outdoors. The paper provides some examples of following this process and designing the mission and unmanned system(s) to support it.
An Evaluation of Overcoming Barriers to Engage Consumers in the Use of Health Care Information Technology

ABSTRACTThe purpose of this review is to determine why consumers may not be adopting or engaging in the use of health information technology to successfully improve or maintain their health status. A literature search was completed to find articles related to consumer engagement in the use of health information technology. The literature found was then categorized based on a patient engagement framework defined by the National eHealth Collaborative. The barriers to engagement, issues with types of technology, and problems in study methodology were then synthesized for understanding consumer engagement. The results of the review showed the major barriers related to engaging consumers in the use of health information technology, including privacy, education, cost, literacy, accuracy of information, trust, meeting consumer needs, measures, integration, and policy. The most prevalent of these issues is that health information technology is often not designed with accurate and detailed user requirements in min...
Numerical investigation of two-phase flow encountered in electrically enhanced oil recovery

The study of two-phase immiscible flow in porous media using electrokinetics is important in different fields including the remediation of hydrocarbon contaminated soils and enhanced oil recovery. While electrokinetic technology has been traditionally used for treatment and decontamination of hydrocarbon polluted sites, electrically enhanced oil recovery (EEOR) is relatively new. Although a few laboratory and field experiments have investigated the potential promise of the EEOR method, further investigation is necessary to better understand the fundamentals and the importance of different parameters/processes that affect the oil production in this method. This study presents a numerical investigation of two-phase flow in EEOR method in an attempt to provide insight into the feasibility of, and the important parameters involved in this method. A sensitivity analysis is performed on important parameters involved in EEOR combined with water flooding. Most of the investigated reservoir and operational parameters were found to be significant and critical to the transport phenomena controlling the oil production. In addition, the results showed that the applied electrical gradient involved in EEOR combined with water flooding contributes to a small increase in oil production.
Review of "Exploratory Programming for the Arts and Humanities," by Montfort, N. (2016). Cambridge, MA: MIT Press.

Coding, like other forms of written communication, is both science and art. This is not a new or revolutionary idea. In 1974, Donald Knuth published "Computer Programming as an Art" and declared that "[a] programmer who subconsciously views himself as an artist will enjoy what he does and will do it better" (p. 673). In 1984, Steven Levy's Hackers: Heroes of the Computer Revolution introduced us to the Hacker Ethic, one tenet of which is that we can create art and beauty on the computer (p. 31). Many other authors and coders have argued similar cases about the socially situated nature of programming since.
Fiduciary Principles in Trust Law

This book chapter, prepared for the forthcoming Oxford Handbook of Fiduciary Law, canvasses the fiduciary principles applicable to a trustee of a donative, irrevocable private trust subject. The focus is on prevailing American law. The chapter examines (a) the trigger for finding a trust fiduciary relationship and the scope of that relationship; (b) the duty of loyalty; (c) the duty of prudence across the distribution, investment, custodial, and administrative functions of trusteeship; (d) other fiduciary duties in trust law, including the prominent duty of impartiality and the increasingly salient duty to give information to the beneficiaries; (e) the extent to which fiduciary principles in trust law are mandatory or may be waived by the settlor or by a beneficiary; and (f) the remedies available for a breach of duty by a trustee.
Modeling of structural failure of Zircaloy claddings induced by multiple hydride cracks

Zirconium alloys have been serving as primary structural materials for nuclear fuel claddings. Structural failure analysis under extreme conditions is critical to the assessment of the performance and safety of nuclear fuel claddings. This work focuses on simulating structural failure of Zircaloy tubes with multiple hydride defects through modeling explicit crack propagation in ductile media. First, we developed an integrated cladding failure model by taking into account both crack initiation induced by hydride/matrix interface separation and ligament tearing-off between activated hydride cracks. Second, to accommodate the initiation, propagation, and coalescence of multiple cracks in finite plastic media we incorporated this structural failure model into a coupled continuous/discontinuous Galerkin (DG) based finite element code, a traditionally preferred implicit numerical framework. Third, to improve the adaptive placement of DG interface elements for crack propagation and to identify potential coalescence of cracks due to the interaction between adjacent hydride cracks, we defined a special failure index for the assessment of potential failure zones using both true plastic strain developed and predicted failure strain based on the Johnson–Cook material failure criterion. Finally, by calibrating the proposed material failure model using a cluster of Zircaloy material experimental tests, we successfully simulated a complete failure process of a fuel cladding tube with multiple hydride cracks.
Deep convolutional networks do not classify based on global object shape.

Deep convolutional networks (DCNNs) are achieving previously unseen performance in object classification, raising questions about whether DCNNs operate similarly to human vision. In biological vision, shape is arguably the most important cue for recognition. We tested the role of shape information in DCNNs trained to recognize objects. In Experiment 1, we presented a trained DCNN with object silhouettes that preserved overall shape but were filled with surface texture taken from other objects. Shape cues appeared to play some role in the classification of artifacts, but little or none for animals. In Experiments 2–4, DCNNs showed no ability to classify glass figurines or outlines but correctly classified some silhouettes. Aspects of these results led us to hypothesize that DCNNs do not distinguish object’s bounding contours from other edges, and that DCNNs access some local shape features, but not global shape. In Experiment 5, we tested this hypothesis with displays that preserved local features but disrupted global shape, and vice versa. With disrupted global shape, which reduced human accuracy to 28%, DCNNs gave the same classification labels as with ordinary shapes. Conversely, local contour changes eliminated accurate DCNN classification but caused no difficulty for human observers. These results provide evidence that DCNNs have access to some local shape information in the form of local edge relations, but they have no access to global object shapes.
Differential oviposition and offspring success of gray treefrogs in the presence of an invasive fish

Females often decide where to place their eggs or offspring based on the relative risks and benefits of a location. One trade‐off may be between ovipositing with predators and ovipositing with competitors. Many amphibians show risk‐sensitive oviposition and select oviposition sites based on offspring performance. We examined differential oviposition and offspring success by gray treefrogs (Hyla versicolor) in response to the presence of caged or free‐ranging invasive western mosquitofish (Gambusia affinis) using cattletank mesocosms as experimental ponds. Our experiment sought to answer these questions by comparing the number of eggs laid and tadpoles produced among the experimental treatments: (1) Do gray treefrogs exhibit risk‐sensitive oviposition? and (2) What is the relative importance of pre‐colonization and post‐colonization consumptive and trait‐mediated effects of western mosquitofish? Gray treefrogs laid more eggs in control and caged predator mesocosms than in free‐ranging predator mesocosms. At the end of the experiment, there were more tadpoles in control and caged predator mesocosms than in free‐ranging predator mesocosms. Proportional yield was lower in free‐ranging predator mesocosms than control and caged predator mesocosms. Eggs were laid 7–8 d earlier in control mesocosms than caged and free‐ranging predator mesocosms. Western mosquitofish therefore had a negative effect on the successful colonization of experimental ponds by gray treefrogs, most likely through direct physical interactions. Our results also suggest gray treefrogs shift oviposition preferences as the number of conspecifics reaches a threshold where competition risk outweighs predation risk. Western mosquitofish therefore have great potential to affect the distribution of gray treefrogs through pre‐ and post‐colonization effects.
Characteristics of liposomal encapsulation of an archetypal multi-kinase inhibitor in terms of antitumor activity and avoidance of systemic toxicity.

e13589 Background: Staurosporine (STS) class drugs exhibit a unique and broad spectrum inhibition of intracellular signaling pathways, and even low doses potently overcome the chemotherapy resistan...
Early burn team consultation in the emergency department improves efficiency and patient throughput

Objective: The objective of the study is to assess the relationship between expedited burn surgery evaluation and total length of stay (LOS) in the emergency department (ED) in a high-volume tertiary burn care institution and extrapolate these results to the efficiency and cost-effectiveness of patient care. Methods: A retrospective review was performed of all patients evaluated by the burn surgery team and discharged from the University of Rochester Medical Center ED between November 2012 and June 2013. One hundred and three primary patients were identified and their time from arrival to discharge and the timing of burn surgery consultation were analyzed. Patients were stratified into two groups, early and late, based on how soon after arrival they were seen by the burn surgery service. Tests of statistical significance were performed, comparing total time in the ED, time to evaluation by ED provider, and time to evaluation by the burn surgery service. Results: Burn surgery was consulted and evaluated the early group significantly sooner than the late group (early mean: 63 min, late mean: 191 min; P Conclusions: Early burn surgery consultation is associated with a significantly reduced total ED LOS, arguing for immediate burn surgery consultation irrespective of ED provider contact so that patient throughput can be increased. Furthermore, the reduced LOS may translate into higher patient satisfaction, improved patient care, and lower opportunity cost of ED space.
Improving university students’ web savvy: An intervention study

Background Young people increasingly turn to the Internet for information about social and political issues. However, they struggle to evaluate the trustworthiness of the information they encounter online. Aims This pilot study investigated whether a focused curricular intervention could improve university students' ability to make sound judgements of credibility. Sample Participants (n = 67) were students in four sections of a 'critical thinking and writing' course at a university on the West Coast of the United States. Course sections were randomly assigned to treatment (n = 29) and control conditions (n = 38). Methods We conducted a pre-and-posttest, treatment/control experiment using a 2 × 2 × 2 design (treatment condition × order × time) with repeated measures on the last factor. Students in the treatment group received two 75-min lessons on evaluating the credibility of online content. An assessment of online reasoning was administered to students 6 weeks prior to the intervention and again 5 weeks after. Results Students in the treatment group were significantly more likely than students in the control group to have shown gains from pretest to posttest. Conclusions Results suggest that teaching students a small number of flexible heuristics that can be applied across digital contexts can improve their evaluation of online sources.
Interdisciplinary Training Program (ITP) in child abuse and neglect: Long term effects.

Abstract Background University of Oklahoma Health Sciences Center has offered Interdisciplinary Training Program (ITP) for Child Abuse and Neglect since 1987. However, there are limited evaluations on multidisciplinary/interprofessional training for early professionals in the field of child abuse and neglect. Objective This study aimed to examine the effects of the ITP on young professionals in developing their careers and taking leadership roles in the field of child abuse and neglect. Methods The anonymous online survey was conducted for students who completed in the ITP from 1989 to 2016 (n = 405, with contact information out of total 508 graduates). One hundred seventy nine alumni (44.2%) responded to the survey. Results Satisfaction for the ITP was high (m = 9.3, sd = 0.97 on a 10 point scale with higher numbers being positive). Their current contributions to the field of child abuse and neglect were widely seen in child advocacy (43.0%), clinical treatment (39.1%), primary prevention (29.6%), or research (27.9%). Graduates reported they made 133 presentations to civic or professional groups and published 69 articles since they finished the ITP. Conclusion The ITP trainees have made significant contributions to the field in clinical treatment, research, and child advocacy. Alumni were highly satisfied with their experience and continue to see the importance of the ITP to their jobs and career.
Sufficient Conditions for Zero Backscattering by a Uniaxial Dielectric-Magnetic Scatterer Endowed With Magnetoelectric Gyrotropy

As vector wavefunctions are available to represent incident and scattered fields in an isotropic dielectric-magnetic medium endowed with magnetoelectric gyrotropy, a transition matrix can be conceptualized to relate the scattered field coefficients to the incident field coefficients for scattering by an arbitrary scatterer composed of a linear medium. The elements of the transition matrix must satisfy certain conditions for zero backscattering. For a scatterer composed of a uniaxial dielectric-magnetic medium endowed with magnetoelectric gyrotropy, the extended boundary condition method (EBCM) can be formulated to determine the transition matrix. The numerical results obtained thereby lead to the formulation of a sufficient set of three zero-backscattering conditions: (i) the scatterer is a body of revolution with the incident plane wave propagating along the axis of revolution; (ii) the impedances of both mediums are identical; and (iii) the magnetoelectric-gyrotropy vectors of both mediums are aligned along the axis of revolution, whether or not both magnetoelectric-gyrotropy vectors are co-parallel.
Irradiation-Mediated Thymic Plasticity Is An Age-Related Phenomenon in Immunodeficient Mice.

Abstract 3677 Poster Board III-613 Successful T lymphopoiesis is essential for maintaining resistance to infection, mediating graft versus tumor activity, and as a platform for some immune based therapies. In mouse models of T cell immunodeficiency syndromes successful T cell reconstitution requires robust cellular reconstitution as well as remodeling of the thymic stroma. We have previously demonstrated that robust thymic lymphopoiesis in young IL-7 receptor deficient (IL7R−/−) mice can occur without prior irradiation and have linked this to the presence of intact stromal niches for DN3 precursors. In contrast to IL7R−/− mice, RAG−/− mice generate wild type T lymphocytes via thymic T lymphopoiesis after transfer of wild type precursors, but the thymus of transplanted RAG−/− mice remains hypocellular. As has been shown before, thymic cellularity of young RAG−/− mice can be rescued by irradiation followed by transfer of wild type precursors. We now demonstrate a profound difference between young and old RAG−/− mice in the thymic remodeling that occurs after irradiation and transfer of wild type hematopoietic stem cells. While the thymi of young RAG−/− mice undergo profound remodeling and develop normal cortico-medullary areas with segregation of single positive cells to the medulla, older RAG−/− mice do not undergo this remodeling and the cortical and medullary stroma remains less organized and more interdigitated. In addition, while the thymi of these older RAG−/− mice do develop small nests of medullary thymic epithelial cells (identified by flow cytometry and immunohistochemistry) not visualized in the untreated RAG−/− mice, these cells do not appropriately express MHC and these thymi do not appropriately segregate single positive developing T lymphocytes to these medullary areas. In vitro testing of sorted single positive thymocytes from these mice demonstrates failure of appropriate negative selection. Together these studies identify a specific defect in the thymic stroma of aging immunodeficient mice preventing appropriate de novo T lymphopoiesis. Disclosures: No relevant conflicts of interest to declare.
Outcomes of 210 Patients with Follicular and Marginal Zone Lymphomas Treated with 4 Gy of Radiation Therapy

Introduction Indolent lymphomas, such as follicular lymphoma (FL) and marginal zone lymphoma (MZL), are highly radiosensitive and often respond to very low dose radiation therapy (VLDRT). We investigated the outcomes of patients treated with 4 Gy from a large, contemporary, real world cohort, and a subset of potentially curable (PC) patients with early stage (Ann Arbor stage I-II) disease and no prior therapy to the targeted lesion(s) before VLDRT. Methods We analyzed 256 treated sites from 210 consecutive adult patients (Table 1) with FL or MZL who were treated with VLDRT of 2 Gy x 2 fractions between 2006 and 2019 at our comprehensive cancer center. Initial overall response rate (ORR) was defined as complete response (CR) or partial response (PR) using Lugano criteria at first follow-up post-RT (median: 2.1 months; Interquartile range: 1.6-2.5 months). Stable disease (SD) or progressive disease (PD) at 2 months post-RT were considered local failure (LF). Freedom from local failure (FFLF) was defined as time from VLDRT to LF. Patients were censored at the start of a subsequent line of therapy if the VLDRT-treated site had not progressed. Event-free survival (EFS) was calculated per patient from VLDRT to LF or distant PD. FFLF and EFS were estimated using Kaplan-Meier and compared using log-rank. Results Initial ORR for all sites was 88% (CR: 65%, PR: 23%); 12% (n=31) were initially nonresponding (SD: 7%, PD: 5%). Thirteen sites with initial PR/SD/PD received additional RT (median: 30 Gy) within 6 months of VLDRT and had subsequent CR (n=7), PR (n=5), and PD (n=1). With median follow-up of 21 months, 2-year FFLF was 70%. Initial response to VLDRT was prognostic with a significantly improved 2-year FFLF for sites with CR (n=166) compared to those with PR (n=58) (88% vs. 66%, p In the subset of PC patients (n=50), there were 52 lesions. The histology of these sites was split between FL (n=21, 41%), MZL (n=22, 42%) and indolent lymphoma not further classified (n=9, 17%). The majority of the lesions in the PC cohort were extranodal (n=42, 81%). Median follow-up was 1 year with a 1-year EFS of 82%. Of the 12 PC patients who progressed post VLDRT, two thirds developed a distant site of recurrence outside of the VLDRT field. In field recurrence alone was rare (n=4). Diffuse large B cell lymphoma transformation after VLDRT was rare in the PC (n=0) and overall (n=6, 3%) cohort; all cases of transformed DLBCL were diagnosed out of VLDRT field. Conclusions Overall, patients with FL and MZL treated with only 4 Gy have excellent initial ORR. Upfront CR is prognostic of improved disease control. Early evaluation following VLDRT identifies nonresponders who may benefit from additional RT and spares many patients from higher doses of RT with durable local control. Our analysis of PC patients suggests that VLDRT does not compromise the standard curative RT approach. Download : Download high-res image (247KB) Download : Download full-size image Disclosures No relevant conflicts of interest to declare.
Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".

Guidelines for variant interpretation incorporate variant hotspots in critical functional domains as evidence for pathogenicity (e.g., PM1 and PP2), but do not use “coldspots,” that is, regions without essential functions that tolerate variation, as evidence a variant is benign. To improve variant classification we evaluated BRCA1 and BRCA2 missense variants reported in ClinVar to identify regions where pathogenic missenses are extremely infrequent, defined as coldspots. We used Bayesian approaches to model variant classification in these regions. BRCA1 exon 11 (~60% of the coding sequence), and BRCA2 exons 10 and 11 (~65% of the coding sequence), are coldspots. Of 89 pathogenic (P) or likely pathogenic (LP) missense variants in BRCA1, none are in exon 11 (odds <0.01, 95% confidence interval [CI] 0.0–0.01). Of 34 P or LP missense variants in BRCA2, none are in exons 10–11 (odds <0.01, 95% CI 0.0–0.01). More than half of reported missense variants of uncertain significance (VUS) in BRCA1 and BRCA2 are in coldspots (3115/5301 = 58.8%). Reclassifying these 3115 VUS as likely benign would substantially improve variant classification. In BRCA1 and BRCA2 coldspots, missense variants are very unlikely to be pathogenic. Classification schemes that incorporate coldspots can reduce the number of VUS and mitigate risks from reporting benign variation as VUS.
Get-Rich-Quick and Ponzi Schemes

Many people have desired to become wealthy with a minimum of effort. Shrewd con artists exploited such desires. The get-rich schemes reveal dubious ethics on the part of both scammers and putative victims. Ponzi schemes not only provide insights into private scammers but also afford a comparison between business and government ethics. State governments displayed questionable ethics in running their lotteries; the federal government’s social security program also had its ethical blemishes. Businesspeople might insist that government ethics attain the level of business ethics.
Cell-free DNA Tissues-of-Origin Profiling to Predict Graft versus Host Disease and Detect Infection after Hematopoietic Cell Transplantation

ABSTRACT Allogeneic hematopoietic cell transplantation (HCT) provides effective treatment for hematologic malignancies and immune disorders. Monitoring for immune complications and infection is a critical component of post-HCT therapy, however, current diagnostic options are limited. Here, we propose a blood test that employs genome-wide profiling of methylation marks comprised within circulating cell-free DNA to trace the tissues-of-origin of cell-free DNA (cfDNA), to quantify tissue-specific injury, and to screen for microbial pathogens after allogeneic HCT. We applied this assay to 106 plasma samples collected from 18 HCT recipients at predetermined time points before and after allogeneic HCT. We observe marked dynamics in the composition and abundance of cfDNA from different tissues in response to conditioning chemotherapy and HCT. We find that the abundance of solid-organ derived cfDNA in the blood at one-month after HCT is an early predictor of acute graft-versus-host disease, a frequent immune-related complication of HCT that occurs when donor immune cells attack the patient’s own tissues (area under the curve, 0.9, p-value = 0.012). Metagenomic profiling of cfDNA was possible from the same assay and revealed the frequent occurrence of viral and bacterial infection in this patient population. This proof-of-principle study shows that cfDNA has the potential to improve the care of allogeneic HCT recipients by enabling earlier detection and better prediction of immune complications and infection after HCT.
Low-Rank Compression of Neural Nets: Learning the Rank of Each Layer

Neural net compression can be achieved by approximating each layer's weight matrix by a low-rank matrix. The real difficulty in doing this is not in training the resulting neural net (made up of one low-rank matrix per layer), but in determining what the optimal rank of each layer is—effectively, an architecture search problem with one hyperparameter per layer. We show that, with a suitable formulation, this problem is amenable to a mixed discrete-continuous optimization jointly over the ranks and over the matrix elements, and give a corresponding algorithm. We show that this indeed can select ranks much better than existing approaches, making low-rank compression much more attractive than previously thought. For example, we can make a VGG network faster than a ResNet and with nearly the same classification error.
Analysis of asynchronous multiprocessor algorithms with applications to sorting

Abstract : Efficient algorithms for asynchronous multiprocessor systems must achieve a balance between low process communication and high adaptability to variations in process speed. Algorithms which employ problem decomposition can be classified as static and dynamic. Static and dynamic algorithms are particularly suited for low process communication and high adaptability, respectively. In order to find the 'best' method, something about mean execution times must be known. Techniques for the analysis of the mean execution time are developed for each type of algorithm, including applications of order statistics and queueing theory. These techniques are applied in detail to (1) static generalizations of quicksort, (2) static generalizations of merge sort, and (3) a dynamic generalization of quicksort. (Author)
DBFOLD: An efficient algorithm for computing folding pathways of complex proteins

Abstract Atomistic simulations can provide valuable, experimentally-verifiable insights into protein folding mechanisms, but existing ab initio simulation methods are restricted to only the smallest proteins due to severe computational speed limits. The folding of larger proteins has been studied using native-centric potential functions, but such models omit the potentially crucial role of non-native interactions.Here, we present an algorithm, entitled DBFOLD, which can predict folding pathways for a wide range of proteins while accounting for the effects of non-native contacts. In addition, DBFOLD can predict the relative rates of different transitions within a protein’s folding pathway. To accomplish this, rather than directly simulating folding, our method combines equilibrium Monte-Carlo simulations, which deploy enhanced sampling, with unfolding simulations at high temperatures. We show that under certain conditions, trajectories from these two types of simulations can be jointly analyzed to compute unknown folding rates from detailed balance. This requires inferring free energies from the equilibrium simulations, and extrapolating transition rates from the unfolding simulations to lower, physiologically-reasonable temperatures at which the native state is marginally stable. As a proof of principle, we show that our method can accurately predict folding pathways and Monte-Carlo rates for the well-characterized Streptococcal protein G. We then show that our method significantly reduces the amount of computation time required to compute the folding pathways of large, misfolding-prone proteins that lie beyond the reach of existing direct simulation methods. Our algorithm, which is available online, can generate detailed atomistic models of protein folding mechanisms while shedding light on the role of non-native intermediates which may crucially affect organismal fitness and are frequently implicated in disease. Author summary Many proteins must adopt a specific structure in order to function. Computational simulations have been used to shed light on the mechanisms of protein folding, but unfortunately, realistic simulations can typically only be run for small proteins, due to severe limits in computational speed. Here, we present a method to solve this problem, whereby instead of directly simulating folding from an unfolded state, we run simulations that allow for computation of equilibrium folding free energies, alongside high temperature simulations to compute unfolding rates. From these quantities, folding rates can be computed using detailed balance. Importantly, our method can account for the effects of nonnative contacts which transiently form during folding and must be broken prior to adoption of the native state. Such contacts, which are often excluded from simple models of folding, may crucially affect real protein folding pathways and are often observed in folding intermediates implicated in disease.
Assessment of Arm Lean Mass, Fat Mass, and Bone Mineral Density in Breast Cancer Survivors Without Lymphedema.

Objectives To compare lean mass, fat mass, and bone mineral density (BMD) in the affected arm (the arm on the side where breast cancer was present) and unaffected arm of breast cancer survivors without lymphedema. Sample & setting 38 breast cancer survivors who had completed primary treatment were included in this analysis at a university in Florida. Methods & variables Arm lean mass, fat mass, and BMD were obtained using dual-energy x-ray absorptiometry. Paired t tests were used to compare tissue composition and BMD between the affected and unaffected arm. Independent t tests were used to compare interlimb differences between those participants whose affected arm was on the dominant and those whose affected arm was on the nondominant side. Significance was accepted at p Results The affected arm had lower fat mass and BMD as compared to the unaffected arm. Differences in lean mass were not statistically significant (p = 0.06). In breast cancer survivors whose nondominant arm was affected, lean mass, fat mass, and BMD were significantly lower in the affected arm. Implications for nursing The results show that the affected arm of breast cancer survivors is susceptible to negative tissue and BMD changes. This highlights the importance of educating individuals with breast cancer about these changes and supports the benefits of upper body resistance training.
Deep Learning-Enabled Resolution-Enhancement in Mini- and Regular Microscopy for Biomedical Imaging.

Abstract Artificial intelligence algorithms that aid mini-microscope imaging are attractive for numerous applications. In this paper, we optimize artificial intelligence techniques to provide clear, and natural biomedical imaging. We demonstrate that a deep learning-enabled super-resolution method can significantly enhance the spatial resolution of mini-microscopy and regular-microscopy. This data-driven approach trains a generative adversarial network to transform low-resolution images into super-resolved ones. Mini-microscopic images and regular-microscopic images acquired with different optical microscopes under various magnifications are collected as our experimental benchmark datasets. The only input to this generative-adversarial-network-based method are images from the datasets down-sampled by the Bicubic interpolation. We use independent test sets to evaluate this deep learning approach with other deep learning-based algorithms through qualitative and quantitative comparisons. To clearly present the improvements achieved by this generative-adversarial-network-based method, we zoom into the local features to explore and highlight the qualitative differences. We also employ the peak signal-to-noise ratio and the structural similarity, to quantitatively compare alternative super-resolution methods. The quantitative results illustrate that super-resolution images obtained from our approach with interpolation parameter α = 0.25 more closely match those of the original high-resolution images than to those obtained by any of the alternative state-of-the-art method. These results are significant for fields that use microscopy tools, such as biomedical imaging of engineered living systems. We also utilize this generative adversarial network-based algorithm to optimize the resolution of biomedical specimen images and then generate three-dimensional reconstruction, so as to enhance the ability of three-dimensional imaging throughout the entire volumes for spatial-temporal analyses of specimen structures.
Sodium Surface Lattice Plasmons

Metallic nanostructures can source, detect, and control light through surface plasmons with applications ranging from photocatalysis and biochemical sensors to light trapping in thin-film solar cel...
Minimizing Rate Variability with Effective Resource Utilization in 5G Networks

One of the main features of 5G networks is to provide high data rates with low variability to mobile users. However, this has been shown to be ineffective from the operator's perspective as it leads to abundantly unused network resources. Reallocating the unused resources to the same users increases back the data rate variability. A more efficient way is to provide different low-variability data rates to the users depending on their channel conditions, while not wasting network resources considerably. In this paper, the goal is to minimize the coefficient of variation across all users in the cell. To that end, we consider two approaches, one with reserved resources for every user and the other where the amount of allocated resources is decided on the fly. Then, for each of them, we look at different allocation policies and derive the maximum achievable constant rate for every user. We evaluate the performance on a real trace. Results show that utilizing policies with no-resource-reservation increases considerably the utilization of network resources and the achievable data rates at the expense of a slight increase in variability. Also, using our policies, the waste of resources drops to 15%, which is almost 4x lower than with other state-of-the-art techniques.
Ventrolateral hypothalamic lesions in obese-hyperglycemic mice (obob)

Bilateral electrolytic lesions were induced on the ventrolateral nucleus (VLN) of obese-hyperglycemic mice (obob) and lean littermates, with or without previous body weight reduction. All lean animals with VLN damage died within the first four post-operative days. In contrast, all obese mice (obob) with no prior body weight reduction recovered following an initial period of aphagia and rapid body weight loss. Three out of five reducedobob mice died following VLN lesions. - Two months after the operation the body weight of all lesionedobob mice stabilized at a level significantly lower than that of the “sham” operated obese; their serum immunoreactive insulin and blood glucose levels were also lower. - These data indicate thatobob mice respond normally to bilateral lesions of VLN and that their excess adiposity, by protecting them during the early post-operative period, facilitates their recovery. The final stabilization of the body weight of lesionedobob at a level lower than that of control mice is compatible with the view that the VLN acts as the low set point controller in the regulation of body weight.
Glucocorticosteroids increase beta 2-adrenergic receptor transcription in human lung

beta 2-Adrenergic receptors (beta 2R) are widely distributed and mediate a wide range of cellular responses in lung. Because glucocorticosteroids increase expression of beta 2R in cell lines, we have investigated the effects of glucocorticoids on the beta 2R mRNA level and the number of beta 2R in human peripheral lung in vitro. Incubation of lung tissues with dexamethasone (Dex) elevated both beta 2R mRNA level (as measured by Northern blot analysis) and beta 2R number (as measured by [125I]iodocyanopindolol binding). The increased accumulation of beta 2R mRNA could be detected at 15 min (1.27 +/- 0.1-fold) and the maximal accumulation occurred at 2 h (2.73 +/- 0.5-fold). The Dex-induced increase in beta 2R mRNA returned to the control level by 17 h. The increase in beta 2R number (1.58 +/- 0.2-fold) was slower, reaching a maximum between 17 and 24 h. Dex increased beta 2R mRNA in a time- and concentration-dependent manner that was abolished by the steroid receptor antagonist mifepristone (RU-38486 or RU-486). The stability of beta 2R mRNA was unchanged by Dex, and a nuclear run-on assay revealed that Dex approximately doubled the transcriptional rate of the beta 2R gene. These observations suggest that glucocorticoids act on steroid receptors to increase beta 2R expression by increasing the rate of beta 2R gene transcription.