cssi/SciSciGPT-SciSciNet huggingface dataset:
THU0417 Exposure, latent tuberculosis, or disseminated infection? The role of tst, quantiferon, and multisite cultures in high risk patients on TNF-inhibitors

Background Patients (pts) on tumor necrosis factor inhibitors (TNFi) are at risk for infections with Mycobacerium tuberculosis (MTB) and non-tuberculosis bacteria (NTM). Prior to TNFi therapy, pts are screened for latent TB infection (LTBI) with tuberculin skin test (TST) or Quantiferon (QFN) assay (Cellestis) and chest x-ray (CXR). High risk pts as defined by Centers for Disease Control, on long term TNFi are still at risk for exposure and development of new infections. 1 Guidelines on surveillance in pts on TNFi are currently lacking. Objectives To best identify mycobacterial infection in TNFi- naive and exposed pts using TST, QFN, or both. Additionally, to differentiate between latent or pre-symptomatic disseminated infection in new converters on TNFi using multi-site cultures (sputum, urine, and stool). Methods We evaluated 580 pts treated with TNFi between 11/1/2000 and 10/26/2011 at a single county institution. Screening TST and/or QFN, as well as CXR were obtained at baseline. Negative pts were serially re-tested while on TNFi. Those with new positive TST (>5mm induration) and/or QFN underwent multi-site cultures. Asymptomatic pts with negative cultures were treated as LTBI with Isoniazid for 9 months; those with positive cultures were referred for evaluation and treatment. Non-parametric and Fisher’s exact tests evaluated differences between groups. Results LTBI was prevalent at baseline; 169 of 580 (29%) pts were positive by either TST and/or QFN (figure 1). In TNFi-naive pts dual testing uncovered a higher LTBI rate (38.3%) compared to TST (24.5%) or QFN alone (32%, p-trend=0.04). New conversions while on TNFi remained high; 51 of 440 (11.6%) serial re-screens were positive by either test. Dual testing uncovered more new conversions (15.2%) compared to TST (8.8%) or QFN alone (8.8%, p-trend=0.1). Of 51 new asymptomatic converters on TNFi, 50 completed multisite cultures; 10 (20%) had positive cultures, 1 (2%) for MTB and 9 (18%) for NTM. Of 169 TNFi-naive pts with positivity for either test, 39 completed cultures; 4 (10%) were positive, 1 (2.6%) for MTB and 3 (7.4%) for NTM. Conclusions LTBI prevalence is significant at baseline and its incidence remains so in high-risk pts exposed to TNFi. Dual testing with TST and QFN captures a higher rate of mycobacterial infections especially in naive pts. A sizeable proportion of asymptomatic new converters on TNFi have positive cultures raising concern for dissemination. We therefore propose that both TNFi-naive and exposed, high-risk pts undergo dual baseline and serial testing. New converters by either TST or QFN should be further evaluated with multi-site cultures for possible dissemination. References CDC MMWR 2005; 54 (RR-17): 1-141 Disclosure of Interest None Declared
Pyrazine diazohydroxide (NSC-361456). Phase I clinical and pharmacokinetic studies.

Pyrazine diazohydroxide (NSC-361456) was identified as an active congener of pyridine 2-diazohydroxide with enhanced stability under physiologic conditions. In this phase I study, 35 patients with advanced cancer received 62 courses of PZDH administered intravenously every 3 weeks at doses ranging from 15–608 mg/m2. The dose-limiting toxicity was myelosuppression and the maximal tolerated dose was 487 mg/m2. Hematologie toxicity was delayed and prolonged with median time to recovery about 5 weeks. Mild gastrointestinal toxicity in the form of nausea and vomiting was fairly common. Ondansetron was effective in reducing nausea and vomiting at higher dose levels. Other less common reactions included stomatitis, diarrhea, fatigue, alopecia, and mild abnormalities of renal function and hepatic enzymes. PZDH pharmacokinetics were characterized in 16 patients who received doses of 100–608 mg/m2. Plasma elimination was fit to one (12/16) or two (4/16) compartment model with a mean k10 half-life of 11.5 min. Clearance was dose dependent. Hematologic toxicity was related to PZDH dose, AUC and peak plasma concentration. The sigmoidal relationships between hematologic toxicity and AUC or peak plasma concentration were well described by the Hill equation. There were no objective responses observed in this study. Based on this study, the recommended dose for phase II evaluation of PZDH using this schedule is 390 mg/m2.
Commentary on Steven H. Cooper’s Paper “Blurring Boundaries or Why Do We Refer to Sexual Misconduct With Patients as ‘Boundary Violation’”

In this commentary on Steven H. Cooper’s paper, the author acknowledges that the term boundary violation presents a vexing problem when we try to integrate it with the traditional use of the term boundary in psychoanalytic thought. He suggests that the two discourses represent two separate but somewhat related levels of discourse and that overlap occurs in some areas but not in others. While the use of “boundary violations” to describe ethical misconduct presents problems, the author suggests that it may be useful for some analysts who have experienced a collapse of analytic space and can no longer “play” in a symbolic realm. He also suggests that we may be stuck with the term because of the unconscious function it serves for the analytic community.
Hole Transport Dynamics in Mixed Sequence DNA Can Vary with Salt Concentration: An Experimental and Theoretical Analysis

Long-range hole transport (HT) through DNA is a well-established phenomenon with important applications in the fields of material science, biochemistry, and cell biology. However, the role that the surrounding environment plays in modulating DNA HT dynamics is not well understood and will impact the development of DNA HT theories. Here, we report that varying the bulk salt concentration can affect the dynamics of long-range HT in a mixed sequence DNA duplex. Using a previously described AQ-601 construct, we show that HT to distal guanines is maximal at physiological salt concentrations (100−200 mM), and declines as [NaCl] increases or decreases. Using circular dichroism, we observe that the 601 sequence has the unusual property of underwinding with increasing salt, but the connection of these changes in secondary structure to DNA HT dynamics is not clear. Using all-atom molecular dynamics simulations on decamer duplexes from AQ-601, we show that the changes in HT dynamics do not correlate with salt-depend...
Systematics and paleobiogeographic significance of the Upper Ordovician pterygometopine trilobite Achatella Delo, 1935

Abstract. Study of type and new material of the pterygometopine Achatella Delo, 1935 demonstrates the presence of four species in Upper Ordovician (Katian) strata of Laurentian North America, A. achates (Billings, 1860) from the northeastern United States and the St. Lawrence lowlands of Canada, A. carleyi (Meek, 1872) from the Cincinnati region, Ohio and Kentucky, A. katharina (Bradley, 1930), from Missouri and Oklahoma, and A. clivosa Lesperance and Weissenberger, 1998 from the Gaspe Peninsula, Quebec. Perhaps as many as five additional species are present in Sandbian—Katian strata of the Laurentian terranes of Scotland and Northern Ireland, although only three of these are known well enough to code for phylogenetic analysis. The oldest pterygometopines, including species of Achatella, are known from Middle Ordovician strata of Baltica. Phylogenetic analysis supports a single migration event from Baltica from Laurentia, followed by a modest diversification in the latter region.
Cyclooxygenase-2 targeted in vivo imaging of cancer

A59 Cyclooxygenase-2 (COX-2) enzyme is expressed in many malignant tumor types, even in very early stage pre-adenomas. Diagnostic imaging of cancer is still limited by the non-selective accumulation of imaging agents in normal tissues. In this regard, we have developed a novel COX-2-based imaging agent that is used as a tool for COX-2-targeted in vivo imaging of tumors with a >50:1 accumulation in the tumor over normal tissue. The fluorescent compound has adequate physicochemical properties to penetrate freely into living cells and allow direct imaging of COX-2 in four different mouse models: (a) liver metastasis model, (b) xenograft model, (c) C57BL/6 lung tumor model, and (d) min mouse intestinal polyp model. This imaging agent maintains adequate plasma concentration over a period of time sufficient for uptake into the target site for in vivo fluorescence imaging. Targeted COX-2 imaging and compound pharmacokinetics were assigned using bio-analytical methods that provided quantitative measurement of intact parent compound in the regions of interest. COX-2-targeted delivery was unambiguously confirmed by blocking the COX-2 active site with high affinity inhibitors in both in vitro and in vivo mouse models. It is noteworthy that in an in vivo mouse xenograft model, indomethacin blocked 92.6% (A‘Â±1.5%) of the COX-2 expressing tumor uptake of the lead compound. This novel strategy might be useful to develop tools to detect COX-2-expressing early stage human cancers using in vivo imaging techniques.
Resources Used to Detect Local Increases in Risk

This chapter focuses on the Los Angeles County Cancer Surveillance Program, which is the official registry for all cases of cancer occurring in residents of the United States. It was founded in 1971 as a resource designed to facilitate study of the causes of cancer, and is supported by the California State Department of Health Services, as part of the California Cancer Registry, and by the U.S. National Cancer Institute, as a component of its SEER (surveillance, epidemiology, and end results) system of nationally representative cancer registries. All California hospitals and pathologists are required by law to report every cancer diagnosis made in a person living in California. Completeness and accuracy of the case counts are routinely assessed by the California Department of Health Services, the National Institutes of Health, the Centers for Disease Control, and the World Health Organization. In addition to details about the malignancy itself, the registry gathers information about the affected person available in the hospital chart that might help to clarify the pattern of cancer occurrence. These items include age, sex, ethnicity, occupation, birthplace, and residential address as of the day of diagnosis. The address enables the registry, using census information, to roughly characterize the neighborhood level of social class, or socioeconomic status (SES). As no direct evidence about the income and education of each reported case is available, it must be presumed that the personal level of social class, that is, level of education and income, is similar to that of the typical person living in that neighborhood.
The End of the Nylon Era

The End of the Nylon Era (Konec nylonoveho věku, 1967) is the least well known of Skvorecký’s novels, one that was published in only a single edition and has never been translated into a foreign language. The timing of its origin was crucial for its fate. Written in 1950, two years after the Communist takeover, it was not harmful from the thematic viewpoint. But it was not written in the Socialist Realist mode and was therefore unpublishable until 1967, when the aesthetic dogmata of Socialist Realism were no longer enforced. This short novel (120 pages) reflects Skvorecký’s ambivalent attitude towards the life-style of the affluent, an attitude which is to a lesser degree present in The Cowards. Although the novel is to some extent a satire, it is also a psychological profile of the Czech bourgeoisie on the eve of its demise. The satirical scope is focused narrowly, showing the pro-Western, and especially pro-American, craze by which the affluent post-war Czech youth were obsessed. They all learned English, most of them mastering only the basics, idolised jazz, and dressed in a style copied from imported fashion magazines. Skvorecký himself actively participated in this life-style, and his negative portrayal of it might indicate the effect that the official anti-American propaganda had made on him, or it may simply result from self-doubt or an ability to see himself and his environment from a critical point of view. At the same time, the portrayal is not without touches of affection for the dying way of life.
The Non-Contractual Nature of the Student-University Contractual Relationship

A basic tenet of education law holds that the relationship between a student and a college or university is in large part contractual in nature. Many of the terms of that contract are found in the institution's various documents, its catalogues, bulletins, and circulars. Even the most superficial analysis of cases concerning student breach of contract actions against institutions of higher education reveals notions of contract law that are at great variance with accepted legal principles. Indeed, this discrepancy is so great, it will be argued, that the laws of contract are not in fact being applied in student-university cases. Nor should they be. Instead, theories of tort law should be applied more frequently to issues concerning the student-university relationship, as the basic conceptual premises of contract law are not truly reflective of that relationship and thus are not appropriate analytical tools in the education law area.
Juvenile Particulate Osteochondral Allograft for Treatment of Osteochondral Lesions of the Talus: Detection of Altered Repair Tissue Biochemical Composition Using 7 Tesla MRI and T2 Mapping

During the previous 2 decades, numerous surgical procedures have become available to treat osteochondral lesions of the talus. The objective of the present study was to use 7 Tesla (7T) magnetic resonance imaging (MRI) to quantify and compare T2 values (a marker of collagen architecture) of native tibiotalar cartilage and cartilage repair tissue in patients treated with a juvenile particulate allograft for osteochondral lesions of the talus. The institutional review board approved the present study, and all subjects provided written informed consent. We scanned the ankles of 7 cartilage repair patients using a 7T MRI scanner with a multi-echo spin-echo sequence to measure the cartilage T2 values. We assessed the cartilage T2 values in the talar repair tissue, adjacent native talar cartilage, and overlying tibial cartilage. We compared the differences between groups using the paired t test. The talar cartilage repair tissue demonstrated greater mean T2 relaxation times compared with the native adjacent talar cartilage (64.88 ± 12.23 ms versus 49.56 ± 7.82 ms; p = .043). The tibial cartilage regions overlying these talar cartilage regions demonstrated a trend toward greater T2 relaxation times (77.00 ± 31.29 ms versus 59.52 ± 7.89 ms; p = .067). 7T MRI can detect differences in T2 values in cartilage repair tissue compared with native cartilage and could be useful for monitoring the status of cartilage health after surgical intervention.
Impact of Malicious Node in MANETs

MANETs are known to possess unique and many vulnerable features. In such a case, security is again another crucial issue to be tackled. The attacks can affect the performance of the network critically. This paper therefore proposes a solution for maintain the optimum performance of the network even in presence of malicious nodes by modifying the existing DSR protocol. The simulation is performed in NS-2. The results of the scheme show that the network performance is not affected and proposed solution handles it well.
Abstract 509: Essential Role of Vascular Smooth Muscle Bmal1 in Diurnal Variations of Contraction and Blood Pressure

Bmal1 is an obligatory core clock gene that is ubiquitously expressed but has been demonstrated to have tissue specific functions. However, the vascular smooth muscle specific function of bmal1 is unknown. We generated a smooth muscle specific bmal1 knockout mouse model (SM-bmal1-ko) and investigated the role of bmal1 in vascular smooth muscle contraction and blood pressure regulation. Isometric contractions were measured in isolated right renal artery and 2 nd order branch of mesenteric artery helical strips. Blood pressure was monitored in conscious free-moving mice using radiotelemetry. We demonstrated that bmal1 was selectively deleted in smooth muscle enriched tissues like mesenteric arteries. Moreover, the diurnal variations of bmal1 target genes per1/2 were abolished in mesenteric arteries. The isometric contractions in response to alpha1 agonist phenylephrine and to 5-HT were significantly diminished in vascular helical strips isolated from SM-bmal1-ko mice compared to that from control flox mice. The contractile diurnal variations detected in the renal arteries isolated from control flox mice were significantly diminished in samples isolated from SM-bmal1-ko mice. Moreover, in vivo , the diurnal variations in the instantaneous pressor responses to intravenous phenylephrine injection were significantly diminished in SM-bmal1-ko mice compared to control flox mice. Twenty four hour mean arterial blood pressure was significantly decreased under 12:12 light:dark, constant light or constant dark conditions. Importantly, the amplitude of blood pressure diurnal variations was significantly diminished in SM-bmal1-ko mice. Importantly, neither the level nor the diurnal variations of locomotor activity was affected by bmal1 deletion. This indicates that the central SCN clock function is not affected in the SM-bmal1-ko mice and the blood pressure alterations in SM-bmal1-ko mice is not a consequence of changed locomotor activity. Taken together, our results demonstrate an essential role of bmal1 in the diurnal variations of vascular smooth muscle contraction and blood pressure.
Measurement of the 242mAm Neutron Fission Cross Section

The fission cross section of 241Am has been measured from 0.02 eV to 20 MeV using time-of-flight techniques at the Oak Ridge Electron Linear Accelerator. A “honeycomb” fission ionization chamber th...
Complete LabVIEW-Controlled HPLC Lab: An Advanced Undergraduate Experience

Virtually all modern chemical instrumentation is controlled by computers. While software packages are continually becoming easier to use, allowing for more researchers to utilize more complex instruments, conveying some level of understanding as to how computers and instruments communicate is still an important part of the undergraduate curriculum. Understanding how digital and analog signals are used to allow the smooth operation of an instrument allows the user to better understand the possible sources or problems when instruments stop working optimally. The experiment presented here allows students to investigate the communication between the computer and a high-performance liquid chromatography (HPLC) system by allowing them to construct a LabVIEW-based control program. Student understanding of instrument control is reinforced by having them control pump speed, detector zeroing, and a solvent recycling valve while also monitoring the injection port status and the detector output. Students gain an unde...
A Continuum of Severity of Sexual Intimate Partner Violence Among Black Women in the United States

Sexual intimate partner violence (IPV) continues to be a significant problem for women of all backgrounds. Sexual IPV occurs along a continuum of severity ranging from less severe forms (e.g., nonphysical controlling behaviors, verbal pressure, or manipulation) to more severe forms (e.g., physical force or threats thereof). In the United States, women of color experience higher lifetime and past year prevalence rates compared to non-Hispanic White women. Black women are more likely to suffer from social and structural barriers that further exacerbate the physical and mental health consequences of sexual IPV. This chapter aims to contextualize the experiences of sexual IPV along a continuum of severity among Black women. Through qualitative inquiry, a better understanding of the overlapping nature along the continuum, including disclosure experiences, women’s own perceptions of sexual violence, and the role of culture in the perceptions of the experiences, is achieved. Although most women struggle with the adverse effects of sexual IPV, some display high levels of resilience. Capitalizing on the cultural strengths of Black women, culturally tailored interventions are urgently needed at the individual, peer, community, and societal levels to maximize reductions in sexual IPV and improve health outcomes for those affected by sexual IPV.
NetAuth: supporting user-based network services

In User-Based Network Services (UBNS), the process servicing requests from user U runs under U's ID. This enables (operating system) access controls to tailor service authorization to U. Like privilege separation, UBNS partitions applications into processes in such a way that each process' permission is minimized. However, because UBNS fundamentally affects the structure of an application, it is best performed early in the design process. UBNS depends on other security mechanisms, most notably authentication and cryptographic protections. These seemingly straightforward needs add considerable complexity to application programming. To avoid this complexity, programmers regularly ignore security issues at the start of program construction. However, after the application is constructed, UBNS is difficult to apply since it would require significant structural changes to the application code. This paper describes easy-to-use security mechanisms supporting UBNS, and thus significantly reducing the complexity of building UBNS applications. This simplification enables much earlier (and hence more effective) use of UBNS. It focuses the application developer's attention on the key security task in application development, partitioning applications so that least privilege can be effectively applied. It removes vulnerabilities due to poor application implementation or selection of security mechanisms. Finally, it enables significant control to be externally exerted on the application, increasing the ability of system administrators to control, understand, and secure such services.
The relative persuasiveness of narrative versus non-narrative health messages in public health emergency communication: Evidence from a field experiment

Previous studies indicated that narrative health messages are more effective than non-narrative messages in influencing health outcomes. However, this body of evidence does not account for differences in health domain, and little is known about the effectiveness of this message execution strategy during public health emergencies. In this study, we examined the relative effectiveness of the two formats in influencing knowledge and perceived response efficacy related to prevention of pandemic influenza, and determined whether effects of message format vary across population sub-groups. Data for the study come from an experiment fielded in 2013 that involved a nationally representative sample of 627 American adults. Participants were randomly assigned to view either a narrative (n=322) or a non-narrative (n=305) video clip containing closely matched information about knowledge and preventive actions related to pandemic influenza, and completed pre- and post-viewing questions assessing knowledge and perceived response efficacy related to the prevention of pandemic influenza. Results indicated that participants in the non-narrative condition reported greater knowledge and rated pandemic influenza prevention measures as more effective compared with those in the narrative condition. Message format effects did not vary across population sub-groups; post-viewing scores of knowledge and perceptions related to pandemic influenza were consistently higher in the non-narrative condition compared with the narrative condition across five socio-demographic groups: age, gender, education, race/ethnicity and income. We concluded that didactic, non-narrative messages may be more effective than narrative messages to influence knowledge and perceptions during public health emergencies.
Low algebraic dimension matrix completion

Low rank matrix completion (LRMC) has received tremendous attention in recent years. The low rank assumption means that the columns (or rows) of the matrix to be completed are points on a low-dimensional linear variety. This paper extends this thinking to cases where the columns are points on low-dimensional nonlinear algebraic varieties. While others have recently studied matrix completion in such settings, existing results focus mainly on algorithms and experiments, without supporting theory. This paper proposes a new approach to what we call Low Algebraic-Dimension Matrix Completion (LADMC). We propose a new LADMC algorithm that leverages existing LRMC methods on a tensorized representation of the data. We also provide a formal mathematical justification for the success of our method. In particular, the new algorithm can succeed in many cases where traditional LRMC is guaranteed to fail. We also provide experimental results showing that the new approach significantly outperforms existing state-of-the-art methods for matrix completion in many situations.
Blooms of dinoflagellate mixotrophs in a lower Chesapeake Bay tributary: carbon and nitrogen uptake over diurnal, seasonal, and interannual timescales.

A multi-year study was conducted in the eutrophic Lafayette River, a sub-tributary of the lower Chesapeake Bay during which uptake of inorganic and organic nitrogen (N) and C compounds was measured during multiple seasons and years when different dinoflagellate species were dominant. Seasonal dinoflagellate blooms included a variety of mixotrophic dinoflagellates including Heterocapsa triquetra in the late winter, Prorocentrum minimum in the spring, Akashiwo sanguinea in the early summer, and Scrippsiella trochoidea and Cochlodinium polykrikoides in late summer and fall. Results showed that no single N source fueled algal growth, rather rates of N and C uptake varied on seasonal and diurnal timescales, and within blooms as they initiated and developed. Rates of photosynthetic C uptake were low yielding low assimilation numbers during much of the study period and the ability to assimilate dissolved organic carbon augmented photosynthetic C uptake during bloom and non-bloom periods. The ability to use dissolved organic C during the day and night may allow mixotrophic bloom organisms a competitive advantage over co-occurring phytoplankton that are restricted to photoautotrophic growth, obtaining N and C during the day and in well-lit surface waters.
Metabolic health and academic achievement in youth at risk for high school dropout in rural Mississippi: The role of classroom management.

Disparities in health and academic achievement affect large cross-sections of the same population subgroups. This study examined the relationship metabolic health and academic achievement in youth "at risk" for school dropout in rural Mississippi. Fifteen adolescents participated in a studio based learning educational summer camp and subsequent follow-up sessions during the regular school year that were aimed at developing knowledge of core curriculum subjects by developing design projects based on the camp STEM-related theme. These projects are characteristic of a pedagogical technique known as Studio Based Learning (SBL) and involve more movement than a traditional classroom setting. Participants' metabolic health was assessed via measurements of blood lipids and glucose, blood pressure, BMI and waist circumference, and examined individually and as a combined risk score. Academic achievement measurements were obtained from district standardized testing. Mean BMI for this sample was classified as overweight; however, other metabolic parameters (blood lipids and glucose, and resting blood pressure) were in normal ranges for this age group. Little association was found between metabolic health and academic achievement and in this sample for math of language (r = -0.56 and 0.20, respectively). Participants took part in notable amounts of moderate-to-vigorous physical activity during the SBL camp and very little in the traditional classroom setting (approximately 30 vs. 7 min/day, respectively). Actively engaging teaching strategies, such as SBL, may impart a meaningful impact on physical activity levels of school-aged children, which may have long term, positive health outcomes.
Transposition and Rearrangements in Plasmid Evolution

Transposable elements participate in two classes of replicative recombination events: (i) full transposition; and (ii) genome rearrangements. Transpositions mobilize DNA sequences internal to the transposable element, while rearrangements also mobilize sequences external to the transposable element. We will illustrate several ways in which rearrangements mediated by IS1 and mutant Tnl elements lead to the formation of new plasmid replicons. The effect of the Tnl/Tn3 tnpR + gene product leads to dissolution of new replicons formed by Tnl-mediated rearrangements. Replicons formed by IS1-mediated rearrangements are much more stable. This result indicates that IS1 employs a different pathway to full transposition. Thus, there are at least two classes of transposable elements in bacteria which play different roles in plasmid evolution.
Action and State Based Computation Tree Measurement Language and Algorithms

The computation tree measurement language (CTML) is a real-valued specification formalism, designed to express performance measures and dependability properties in a single framework. It is a further extension of probabilistic model checking logic in such a way that it expands the input and output value from the range of [0, 1] to the range of \([0, \infty )\). Unlike probabilistic computation tree logic (PCTL) or continuous stochastic logic (CSL), CTML can nest real values. As such, it turns out that CTML can express a nontrivial subset of probabilistic linear time logic (PLTL) formulas that cannot be expressed by PCTL while keeping the overall computational complexity being polynomial in the size of both an input formula and model. Moreover, it can express queries such as “when a message is sent, what is the expected time until it is received?” that cannot be expressed by an existing probabilistic logic, because they are“probabilistic” at most. While powerful, CTML is a state-based specification formalism. In this work, we introduce a stronger formal query language, called action and state based computation tree measurement language (asCTML). asCTML extends from CTML, for answering performance queries that operates over paths featured by a combination of states and actions. Inspired by the action and state based continuous stochastic logic (asCSL), asCTML supports multiple actions.
Evaluation of Dunphy et al.: Suggestions to Solidify, Clarify, and Focus without Substantial New Work

One snapshot of the peer review process for "Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa" (Dunphy et al., 2019).
Chemical and mechanical degradation and mitigation strategies for Si anodes

Abstract Atomistic and mesoscopic models are used to analyze cracking and stresses produced during charge of Si nanoparticles covered by a thin SEI film. Mechanical stresses coupled to chemical effects are investigated with classical molecular dynamics simulations and with a mesoscopic model. Rupture of the surface film is the main cause of capacity fade and damage evolution is strongly influenced by the structure of the solid film. For example, high currents can cause rapid amorphization and help preserving the bond integrity. But large damage occurs after the current is above a threshold. In agreement with the atomistic results, mesoscopic modeling reveals that rupture of the surface film is the primary cause of capacity fading for amorphous silicon exhibiting single phase diffusion. It also suggests that conjugated silicon-film fracture in crystalline silicon with two-phase diffusion further exacerbates this deterioration. Fracture damage is slightly diminished by decreasing the Young's modulus of the brittle coating for both amorphous and crystalline silicon; however, controlling the large volumetric expansion induced stress on surface film is crucial towards improving silicon anodes. Mitigation strategies examined by ab initio molecular dynamics and electronic density functional theory simulations show passivation effects of graphene and graphene oxide on lithiated Si surfaces.
Assessment of sampling adequacy using persistent homology for the evaluation of heterogeneity in 3D histology acquired through inverted selective plane illumination microscopy (iSPIM)

Diagnoses performed on the basis of histopathological evaluation depend on the premise that information derived from a small number of samples is valid for the entire tissue volume. By insufficiently sampling a biopsy volume the ability of pathologists to draw meaningful inferences from the sample is impeded. This work attempts to apply an information theoretic approach to biopsy sampling rates informed by variation in tissue morphology identified by persistent homology. By quantifying the diagnostic information present in a sample may be possible to prevent under sampling by the clinician by creating a “Nyquist limit" for histopathological sampling given the frequency of morphologically distinct regions in a single biopsy.
Comparing feature assistance between programming environments and their effect on novice programmers

Improving the novice's experience with learning to program has been an important research topic for some time. Appropriate programming environments for novices have been one research area. For example, many departments have adopted visual environments to teach programming as opposed to a command line environment at the beginning stages of a CS curriculum. Standard command line environments tend to possess less assistive features for programming than visual environments. In contrast, highly assistive visual environments could constrict a novice to learn a fixed set of foundational programming skills that exclude exposure to syntax checking, compilation and file systems. Therefore, novices may need to move to a less assistive environment to round out their skill set. A study was conducted in a CS1-laboratory class by examining three Python programming environments with varying levels of feature assistance (IDLE, PyScripter and Notepad). This study showed that students struggled with using a low assistive environment regardless of their prior experience and confidence with programming. Students were able to use moderately assistive environments more effectively.
Relative Average Look Duration and its Association with Neurophysiological Activity in Young Children with Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is characterized by early attentional differences that often precede the hallmark symptoms of social communication impairments. Development of novel measures of attentional behaviors may lead to earlier identification of children at risk for ASD. In this work, we first introduce a behavioral measure, Relative Average Look Duration (RALD), indicating attentional preference to different stimuli, such as social versus nonsocial stimuli; and then study its association with neurophysiological activity. We show that (1) ASD and typically developing (TD) children differ in both (absolute) Average Look Duration (ALD) and RALD to stimuli during an EEG experiment, with the most pronounced differences in looking at social stimuli; and (2) associations between looking behaviors and neurophysiological activity, as measured by EEG, are different for children with ASD versus TD. Even when ASD children show attentional engagement to social content, our results suggest that their underlying brain activity is different than TD children. This study therefore introduces a new measure of social/nonsocial attentional preference in ASD and demonstrates the value of incorporating attentional variables measured simultaneously with EEG into the analysis pipeline.
Unilateral Anterior Sacrospinous Ligament Hysteropexy: a Single-Center Experience

The objective was to present our experience with unilateral sacrospinous ligament hysteropexy performed through an anterior vaginal incision. This is a retrospective cohort study identifying women who underwent unilateral sacrospinous hysteropexy (CPT code 57282) performed through an anterior vaginal wall incision at the University of Rochester between January 2013 and October 2017. Exclusions included follow-up < 6 months, graft augmentation, bilateral sacrospinous ligament suspension, and a posterior approach. Data were compared using a t test, Wilcoxon rank sum test, Chi-square test, or Fisher’s exact test as appropriate; p < 0.05 was considered statistically significant. The cohort (n = 59) consists predominantly of Caucasian (93%), nonsmoking (54%), post-menopausal women (92%), and women with private insurance (59%). Median baseline values were age 63 years (range, 43–80 years), body mass index 26.8 kg/m2 (range, 18.9–43.1 kg/m2), and stage 3 prolapse (range, 2–3). The median operative time was 80 min (IQR 67, 94.5 min) and estimated blood loss 50 mL (IQR 25, 50 mL). Most women (81%) were discharged home on the day of surgery. Subjective recurrence, in any compartment, was 25.4% (n = 15). The recurrence rate was greatest at 44% during the first year (2013), reflecting a learning curve. In years after, recurrence rates averaged 17%. Recurrence was not associated with the surgeon, subject characteristics, obstetric history, or operative factors. Unilateral anterior sacrospinous hysteropexy is an efficient procedure with few complications. It provides a convenient approach for uterus-preservation pelvic organ prolapse repair with a recurrence comparable to anterior sacrospinous ligament vaginal vault suspension.
NDE OF MOISTURE ABSORPTION IN COMPOSITES USING NUCLEAR MAGNETIC RESONANCE

There are a number of NDE applications where nuclear magnetic resonance (NMR) can be useful for evaluating organic matrix composites and other polymer based materials. NMR is sensitive to molecular motions and structural changes and can be used to obtain both qualitative and quantitative information on the dynamic environment in which molecules are located. In particular, certain characteristics of NMR signals can provide information on 1) the presence of atoms in different physical states; 2) the type and strengths and interactions between atoms of both the same species and different species; 3) changes in molecular structure and intermolecular binding; and 4) transport (diffusion) phenomena. Although generally limited to detection of hydrogen in composites, NMR has been investigated for characterizing moisture, modulus variations, environmental degradation, aging, diffusion and degree of cure. Materials which have been examined include graphite, polyester and Kevlar composites in both cured and prepreg conditions, neat resins, and adhesives. In addition to laboratory studies, instrumentation approaches have been developed for practical application of NMR to nondestructive inspection problems involving composite or plastic components and structures. These approaches are based on the use of U-shaped magnets and flat detection coils to allow measurements to be made from a single surface. These one-sided NMR approaches also allow localized measurements to be made in order to map out spatially varying quantities such as moisture gradients and material inhomogeneities.
Conditional resampling improves calibration in single cell CRISPR screen analysis

Single cell CRISPR screens are an emerging biotechnology promising unprecedented insights into gene regulation. However, the analysis of these screens presents significant statistical challenges. For example, technical factors like sequencing depth impact not only expression measurement but also perturbation detection, creating a confounding effect. We demonstrate on a recent large-scale single cell CRISPR screen how these challenges cause calibration issues among existing analysis methods. To address these challenges, we propose SCEPTRE: analysis of single cell perturbation screens via conditional resampling. This methodology, designed to avoid calibration issues due to technical confounders and expression model misspecification, infers associations between perturbations and expression by resampling the former according to a working model for perturbation detection probability in each cell. Applying SCEPTRE to the CRISPR screen data yields excellent calibration on negative control perturbations and 217 regulatory relationships not found in the original study, many of which are supported by existing functional data.
Status Toward the Implementation of Precision Dosing in Children

Precision dosing is progressing beyond the conceptual and proof-of-concept stages toward implementation. As the availability of dosing algorithms, tools, and platforms increases, so do the investment in technology services and actual implementation of clinical services offering these solutions to patients. Nowhere is this needed more than in pediatric populations, which are still reliant on adult drug development and bridging strategies to support dosing, often in the absence of actual dose-finding studies in the target pediatric population. Still, there is more work to be done to ensure that proper governance of these services is maintained, and that sustainability of these early implementations is guided by new science as it evolves and meaningful outcome data to confirm that such services deliver on both clinical and economic return on investment. In addition, the field should ensure that all approaches beyond a therapeutic drug monitoring-driven, pharmacokinetic-centric approach should be considered as the tools and services evolve, especially when pediatric-specific pharmacokinetic/pharmacodyamic and pharmacogenetic data are available and shown to be useful to guide dosing. This review evaluates current pediatric precision dosing efforts, highlighting their utility, longevity, and sustainability and assesses the current process for implementing such approaches examining current barriers that stand in the way of broader implementation and the stakeholders that must engage to ensure its ultimate success.
Modeling a Grid-Forming Inverter Dynamics Under Ground Fault Scenarios Using Experimental Data From Commercially Available Equipment

In order to address the recent inclement weather-related energy events, electricity production is experiencing an important transition from conventional fossil fuel based resources to the use of Distributed Energy Resources (DER), providing clean and renewable energy. These DERs make use of power electronic based devices that perform the energy conversion process required to interface with the utility grids. For the particular cases where DC/AC conversion is required, grid-forming inverters (GFMI) are gaining popularity over their grid-following (GFLI) counterpart. This is due to the fact that GFMI do not require a dedicated Phase Locked Loop (PLL) to synchronize with the grid. The absence of a PLL allows GFMI to operate in stand-alone (off-grid) mode when needed. Nowadays, inverter manufacturers are already offering several products with grid-forming capabilities. However, modeling the dynamics of commercially available GFMI under heavy loads or faults scenarios has become a critical task not only for stability studies, but also for coordination and protection schemes in power grids (or microgrids) that are experiencing a steady growth in their levels of DERs. Based upon experimental low-impedance fault results performed on a commercially available GFMI, this paper presents a modeling effort to replicate the dynamics of such inverters under these abnormal scenarios. The proposed modeling approach relies on modifying previously developed GFMI models, by adding the proper dynamics, to match the current and voltage transient behavior under low-impedance fault scenarios. For the first inverter tested, a modified CERTS GFMI model provides matching transient dynamics under faults scenarios with respect to the experimental results from the commercially available inverter.
Towards Chloride-Free Organic Electrolytes for Rechargeable Aluminum Batteries

The corrosivity of chloride-based electrolytes is a major shortcoming in the practical realization of rechargeable aluminum batteries. Herein, the effect of Cl- on Al speciation and electrochemistry in tetrahydrofuran was measured by employing theoretical and experimental approaches for three systems: Al(OTF)3/THF, Al(OTF)3 plus LiCl in THF, and AlCl3/THF. The high consistency between measured and computed spectroscopic aspects associated with Al(OTF)3/THF electrolyte provided both a rationale for understanding Al complex-ion formation in a Cl- free environment and an approach for examining the effect of Cl- on Al speciation. Room-temperature Al plating was achieved from dilute solutions ([Al] = 0.1M) at potentials ≥ 0V (vs. Al⁄Al3+). Cl- is found to enable facile Al plating and SEM reveals that Al is electrochemically deposited as nanocrystalline grains.
Convolutive demixing with sparse discrete prior models for markov sources

In this paper we present a new source separation method based on dynamic sparse source signal models. Source signals are modeled in frequency domain as a product of a Bernoulli selection variable with a deterministic but unknown spectral amplitude. The Bernoulli variables are modeled in turn by first order Markov processes with transition probabilities learned from a training database. We consider a scenario where the mixing parameters are estimated by calibration. We obtain the MAP signal estimators and show they are implemented by a Viterbi decoding scheme. We validate this approach by simulations using TIMIT database, and compare the separation performance of this algorithm with our previous extended DUET method.
Loss of inorganic ions from host cells infected with Chlamydia psittaci.

Mouse fibroblasts (L cells) infected with the 6BC strain of Chlamydia psittaci released potassium ion (K + ) into the extracellular milieu in a way that depended on size of inoculum and time after infection. When the multiplicity of infection was 500 to 1,000 50% infectious units (ID 50 ) per L cell, loss of intracellular K + was first apparent 4 to 10 h after infection and was nearly complete at 6 to 20 h. Magnesium ion and inorganic phosphate (P i ) were also released. Similar multiplicities of ultraviolet-inactivated C. psittaci also caused release of K + . Leakage of inorganic ions probably resulted from immediate damage to the host-cell plasma membrane during ingestion of large numbers of chlamydiae. With multiplicities of 1 to 50 ID 50 per L cell, ingestion of C. psittaci was not by itself enough to cause release of K + and P i from infected L cells. There was a delay of 36 to 72 h between infection and massive leakage of intracellular ions during which time the chlamydiae multiplied extensively. Fifty ID 50 of ultraviolet-inactivated C. psittaci per L cell did not bring about significant leakage of K + , even after 72 h. The mechanism whereby these multiplicities of infection destroy the ability of host cells to retain intracellular molecules is not known. HeLa 229 cells also released K + and P i after infection, but these losses occurred more slowly than in comparably infected L cells, possibly because C. psittaci did not multiply as extensively in HeLa cells as it did in L cells. The significance of the inability of chlamydiae-infected cells to regulate the flow of molecules through their plasma membranes is discussed.
Construction of local fields in the bulk of AdS 5 and other spaces

In the Poincar\'e patch of Minkovski ${\mathrm{AdS}}_{5}$ we explicitly construct local bulk fields from the boundary operators, to leading order in $1/N,$ following the ideas of Banks et al. and Balasubramanian et al. We also construct the Green's function implicitly defined by this procedure. We generalize the construction of local fields for near horizon geometries of $\mathrm{D}p$-branes. We try to expand the procedure to the interacting case, with partial success.