cssi/SciSciGPT-SciSciNet huggingface dataset:
Gene Expression and Interferon

The regulation of gene expression in the interferon system falls into two distinct sub-topics. First is the induction of the interferon structural genes in cells infected with a virus or treated with some other inducer, such as double-stranded RNA or lectins. The second involves the mechanism of interferon action, in which several distinct genes are induced in interferon-treated cells to be transcribed and translated as the cells become virus resistant or cease their usual division cycle. In neither the induction of interferon nor its action is much known about specific effects on chromatin structure, but it is presumed that perturbations do occur as in other examples of regulated gene expression. Besides providing yet another “model” system, the interferons offer the following features: very rapid alterations in gene expression initiated at the cell surface by a relatively few inducing molecules (only one molecule in some cell types), leading to profound biological sequelae (refractility to viruses and blockade of cell cycle movements). The interferons are particularly interesting because cell division often stops in treated cells, in comparison to other hormonally-regulated systems where division rates are enhanced. The property of interferons to make cell cultures quiescent thus avoids the problem of studying cascades of gene expression which occur in growth-stimulated cells.
A Reconfigurable Architecture for the Detection of Strongly Connected Components

The Strongly Connected Components (SCCs) detection algorithm serves as a keystone for many graph analysis applications. The SCC execution time for large-scale graphs, as with many other graph algorithms, is dominated by memory latency. In this article, we investigate the design of a parallel hardware architecture for the detection of SCCs in directed graphs. We propose a design methodology that alleviates memory latency and problems with irregular memory access. The design is composed of 16 processing elements dedicated to parallel Breadth-First Search (BFS) and eight processing elements dedicated to finding intersection in parallel. Processing elements are organized to reuse resources and utilize memory bandwidth efficiently. We demonstrate a prototype of our design using the Convey HC-2 system, a commercial high-performance reconfigurable computing coprocessor. Our experimental results show a speedup of as much as 17× for detecting SCCs in large-scale graphs when compared to a conventional sequential software implementation.
Consumption Smoothing, Equivalence Scales, and Idiosyncratic Shocks: Evidence from a Quasi-Natural Experiment in Nicaragua

Rural households in developing countries are faced with a variety of risks to both income processes and consumption streams. Additionally, due to the lack of formal financial markets and credit institutions, and in general any formal insurance mechanisms, households are less equipped to respond to idiosyncratic income shocks. The empirical analysis presented here finds that under a systemic adverse shock, households are unable to fully insure themselves against idiosyncratic income shocks as the systemic shock reduces the effectiveness of informal consumption smoothing mechanisms. Additionally, I find that the ability of households to insure their consumption against fluctuations in income depends upon the equivalence scales used in the measurement of household consumption. Moreover, allowing for economies of scale in household consumption provides evidence that households are able to fully insure themselves within villages.
Solid-Phase-Epitaxial Growth of Ion Implanted Silicon Using CW Laser and Electron Beam Annealing

The nature of residual damage in As/sup +/, Sb/sup +/, and In/sup +/ implanted silicon after CW laser and e/sup -/ beam annealing has been studied using plan-view and cross-section electron microscopy. Lattice location of implanted atoms and their concentrations were determined by Rutherford backscattering and channeling techniques. Maximum substitutional concentrations achieved by furnace annealing in a temperature range of 500-600/sup 0/C have been previously reported and greatly exceeded the retrograde solubility limits for all dopants studied. Higher temperatures and SPE growth rates characteristic of electron or CW laser annealing did not lead to greater incorporation of dopant within the lattice and often resulted in dopant precipitation. Dopant segregation at the surface was sometimes observed at higher temperatures.
Orientational and motional narrowing of solid-state NMR lineshapes of uniaxially aligned membrane proteins.

A unified theory for the NMR line shapes of aligned membrane proteins arising from uniaxial disorder (mosaic spread) and global rotational diffusion about the director axis is presented. A superoperator formalism allows one to take into account the effects of continuous radiofrequency irradiation and frequency offsets in the presence of dynamics. A general method based on the Stochastic Liouville Equation makes it possible to bridge the static and dynamic limits in a single model. Simulations of solid-state NMR spectra are performed for a uniform α helix by considering orientational disorder and diffusion of the helix as a whole relative to the alignment axis. The motional narrowing of the resonance lines is highly inhomogeneous and can be used as an additional angular restraint in structure calculations. Experimental solid-state NMR spectra of Pf1 coat protein support the conclusions of the theory for two limiting cases. The static disorder dominates the 15N NMR spectra of Pf1 aligned on a phage, while f...
YY1 and NF-Y binding sites regulate the transcriptional activity of the dek and dek-can promoter

The mammalian protein DEK has been implicated in multiple cellular processes, including transcriptional regulation, mRNA processing, and chromatin remodeling, and is associated with a number of clinical autoimmune and neoplastic conditions. The connection between DEK and cancer exists at multiple levels: (a) the t(6;9) chromosomal translocation that characterizes a subtype of acute myelogenous leukemia cases results in the formation of a DEK-CAN fusion oncoprotein; (b) a fragment of dek cDNA is capable of partially reversing the radiation-sensitive phenotype of fibroblasts cultured from ataxia-telangiectasia patients; and (c) increased levels of dek mRNA have been found to be associated with hepatocellular carcinoma, glioblastoma, and melanoma. Despite the growing list of cancer subtypes with a connection to DEK, the factors that mediate its expression have yet to be characterized. Here we undertake the analysis of DEK regulation by mapping the discrete elements within the proximal promoter that are responsible for constitutive transcription of dek in transformed cells. We find that functional elements include an inverted CCAAT box and a YY1 consensus binding site, and the introduction of point mutations into these sites markedly diminishes transcriptional activity. In addition, we identify the transcriptional activator NF-Y as a member of the CCAAT-binding complex, and verify binding of the transcription factor YY1 at its consensus site in the dek promoter. The discovery of NF-Y and YY1 as regulatory determinants of DEK expression is consistent with the well-documented roles of these two factors in cellular proliferation and transformation.
Pulmonary artery pressure is associated with extracellular volume fraction in patients with normal left ventricular function

Background Elevated pulmonary artery pressures (PAP) from type II pulmonary hypertension (PH) is caused by a heterogeneous group of disorders. Myocardial fibrosis (MF) is a common pathological finding in many cardiovascular diseases; however its relationship with PAP is not well characterized. In particular, among patients with heart failure and preserved ejection fraction (HFpEF), MF may be a pathophysiologic mechanism contributing to disease severity and poor outcomes. This paradigm would be strengthened if MF were demonstrated to independently predict PAP in HFpEF. Cardiac MRI techniques quantifying extracellular volume matrix (ECV), are well validated markers of MF and may provide more comprehensive assessment over traditional late gadolinium enhancement (LGE) techniques. Thus, the goal of this study was to demonstrate that ECV is an independent predictor of PAP, particularly in patients with preserved left ventricular ejection fraction (EF).
On the significance of an anthropological approach to schizophrenia.

(1989). On the Significance of an Anthropological Approach to Schizophrenia. Psychiatry: Vol. 52, No. 1, pp. 45-65.
A Cross-sectional Study of KLKB1 and PRCP Polymorphisms in Patient Samples with Cardiovascular Disease.

Plasma kallikrein formed from prekallikrein (PK) produces bradykinin from kininogens and activates factor XII. Plasma PK is activated by factors XIIa, XIIa or prolylcarboxypeptidase (PRCP). A cross-sectional investigation determined if there is an association of PRCP and KLKB1 polymorphisms with cardiovascular disease. DNA was obtained from 2243 individuals from the PEACE trial. Two PRCP SNPs, rs7104980 and rs2298668 and 2 KLKB1 SNPs, rs3733402 and rs3087505, were genotyped. Logistic regression models were performed for history of diabetes, MI, stroke, angina, angiographic coronary disease, CABG, intermittent claudication, PTCA, and TIA. The PRCP SNP rs7104980 increased the odds of having a history of PTCA by 21% [OR = 1.211; 95% CI = (1.008, 1.454)]; P= 0.041, but was non significant after Bonferroni correction. Alternatively, having the G allele for rs3733402 (KLKB1 gene) decreased the odds of having a history of angiographic coronary disease by 24% [OR = 0.759; 95% CI = (0.622, 0.927)]; P = 0.007 that was statistically significant (p<0.01) after Bonferroni correction for multiple hypothesis testing. When the best-fit model based on the Akaike information criterion (AIC) controlled for age, weight, gender, hypertension, and history of angina. the G allele of KLKB1 rs3733402 that is associated with less plasma kallikrein activity correlated with reduced history of cardiovascular disease
Empirical Investigations of Development Status of Circular Agriculture in Shijiazhuang

The development status and problems of circular agriculture in Shijiazhuang were analyzed using the time sequence data from 1995 to 2006 and the random questionnaire.The main subject modes of improving the resource utilization and recycling of straw and feces were put forward,at the same time the increment potential of each mode was discussed.
Neutropenia-wise and pound-foolish: safe and effective chemotherapy in massively obese patients.

ABSTRACT:The massively obese patient has an increased risk of cancer and complications from therapy. Chemotherapy in massively obese patients may be complicated by difficulty in calculating body surface area. No guidelines exist for calculating doses by either actual or ideal weight, and the calcula
Dual Representation of the Semantic User Profile for Personalized Web Search in an Evolving Domain.

Several semantic based user profile approaches have been introduced in the literature to learn the users’ interests for personalized search. However, many of them are ill-suited to cope with a domain of information that evolves and user interests that may change over time. In this paper, we propose a novel dual representation of a user’s semantic profile to deal with this problem: (1) a lower-level semantic representation, consisting of an accumulated gathering of user activities over a long period of time, that uses a standard machine learning algorithm to detect user convergence, (2) a higher-level semantic representation that detects shifts in the user activitiesonce this shift is detected, the higher-level semantic representation automatically updates the user profiles and reinitialize the system. Our experimental results demonstrate the feasibility of this approach.
Structure-Based Search and In Vitro Analysis of Self-Cleaving Ribozymes

Detecting functional RNAs is increasingly accomplished through structure-based searches for patterns of conserved secondary structure. With large amounts of new sequencing data becoming available, there is a greater demand for efficient methods of identifying new RNAs. Here we present a method of identifying self-cleaving ribozymes and characterizing the in vitro activity.
Postoperative monitoring of free flap reconstruction: A comparison of external Doppler ultrasonography and the implantable Doppler probe.

Hypothesis The time to detection of vascular compromise and the postoperative time to re-exploration are shorter using the implantable Doppler (ID) probe, thereby resulting in earlier surgical re-exploration and a higher flap salvage rate. Methods A single-centre experience with 176 consecutive free flap reconstructions in 167 patients from 2000 to 2008 in a university-based teaching hospital by retrospective chart review is presented. Results There was a significant difference in overall flap survival (ID 98.0%, external Doppler [ED] 89.3%) and total flap loss (ID 2.0%, ED 10.7%) between the two groups (P=0.03). The difference in flap salvage rate was not significant (ID 90.9%, ED 63.6%; P=0.068). The false-positive (ID 0%, ED 3%; P=0.18) and false-negative rates (ID 0.0%, ED 4.5%; P=1.0) were not significantly different. There was also a lower median postoperative time to re-exploration for the ID group, from 48 h to one week after initial surgery (ID 74.5 h, ED 136.8 h; P=0.05). Conclusion The present analysis revealed a potential benefit for the ID probe in the postoperative monitoring of free tissue transfers.
Contradiction of space, centralization of capital, and the hybrid state oil company: the case of Russia

A new species of capital has emerged from the development of inter-capitalist competition in the oil industry. Oil-producing states have fused with financial and productive/extractive capital, fore...
Epilogue: The ‘Lessons’ of British Counterinsurgency

Although the Malayan emergency ended almost 30 years ago, it remains the principal example of counterinsurgency taught by the British army. While interpretations of the campaign vary from unqualified admiration to rank scepticism, no one has denied that the campaign represents the only clear-cut victory over a Communist revolution. Malaya can, however, only be understood against the background of internal security operations during the first half of the twentieth century. The British victory was not due entirely to chance or to fortuitous circumstances, although these played their part. Malaya could not have been won without the half century of experience that preceded it. No study of this experience would be quite complete without consideration of what part of it can be transferred to other times and places.
Dyspraxia in ASD: Impaired coordination of movement elements

Children with autism spectrum disorders (ASD) have long been known to have deficits in the performance of praxis gestures; these motor deficits also correlate with social and communicative deficits. To date, the precise nature of the errors involved in praxis has not been clearly mapped out. Based on observations of individuals with ASD performing gestures, we hypothesized that the simultaneous execution of multiple movement elements is especially impaired in affected children. We examined 25 school-aged participants with ASD and 25 age-matched controls performing seven simultaneous gestures that required the concurrent performance of movement elements and nine serial gestures, in which all elements were performed serially. There was indeed a group × gesture-type interaction (P < 0.001). Whereas both groups had greater difficulty performing simultaneous than serial gestures, children with ASD had a 2.6-times greater performance decrement with simultaneous (vs. serial) gestures than controls. These results point to a potential deficit in the simultaneous processing of multiple inputs and outputs in ASD. Such deficits could relate to models of social interaction that highlight the parallel-processing nature of social communication. Autism Res 2016,. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. Autism Res 2017, 10: 648-652. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.
Dynamic characteristics and applications of organic and polymer transistors

Summary form only given.Thin films of ordered organic semiconductors are being investigated as channel materials in field-effect transistors for a variety of applications. A detailed understanding of charge transport in such organic thin- film semiconductors used in field-effect transistors is of fundamental interest and is also essential to improve device performance. Our work examines the dynamic response of organic transistors in detail and extracts the drift velocity and mobility directly. The drift mobility and field-effect mobility are compared for pentacene and a liquid crystalline polymer with high mobility. The switching speed of FETs with channel length in the 2-8 micron range and scaling behavior of organic transistors (with channel lengths from 10 nm to 5 microns) are described. Frequency domain measurements have been made on diode connected transistors. Comparisons between frequency domain and time domain measurements will be presented. Finally, two important applications of organic transistors: RFID Tags and display drivers are discussed with regard to speed/mobility requirements and future trends.
The Holocaust: Telling and Retelling

Having spent part of the last twelve years studying 195 memoirs penned by 178 Holocaust survivors, interviewing scores of such men and women in many countries and studying related material in 48 Ho...
Trade and Democracy in Developing Countries: Granger Causality Tests

The relationship between trade and democracy according to the broad scholarship is controversial. The most significant advance in this field is empirical. However, the empirical tests that lack sound theoretical foundations imply correlation and not causation. This paper resolves the puzzle of democracy-trade literature, i.e. instability of democracy-trade relationship, by using a detailed analysis of the relationship stability and its direction across samples, datasets and different model specifications. The rolling regressions are used to identify the subsample instability of the relationship, whereas the Granger causality tests capture the asymmetries in the relationship between trade and democracy and allow testing for the direction of the causality. Among the results, first and foremost, the participation in international institutions in general mediates the relationship between trade and democracy. Second, the direction of causality depends on the number of the lags chosen. Thus, the tests signify the problems in lags selection and the importance to theoretically justify the number of lags that scholars use in the studies. Finally, I document the sample instability. Although the question, what “came first” democracy or trade, remained unanswered, this paper indicates avenues for future research and a call for solid theoretical grounds.
Time Pressure and Payoff Effects on Multidimensional Probabilistic Inference

Beginning with Miller (1960), numerous authors (e.g., Ben Zur & Breznitz, 1981; Maule & Mackie, 1990; Payne, Bettman, & Johnson, 1988; Svenson & Edland, 1987) have distinguished the possible effects of time pressure on decision processes on the assumption that a given decision requires a sequence of mental steps prior to its execution. Most authors have considered four possible time pressure effects. One, termed acceleration, is that processing does not fundamentally change, but rather, each step is simply accelerated under a deadline. A second, termed filtering, is that the processing sequence is altered so that only the most important subset of the information is attended to or handled prior to the decision. Third, the decision maker may select strategies that are appropriate for the available time. Although not generally pointed out, these latter two alternatives are not mutually exclusive. That is, strategies under time pressure may focus on only the most important facets of the information whereas those in the absence of time pressure may utilize the available information more completely. The fourth possibility is that time pressure has no effect on the strategic aspects of information processing. Rather, the person simply stops processing when the time is up and makes a decision.
Postquantum Opportunities: Lattices, Homomorphic Encryption, and Supersingular Isogeny Graphs

Supersingular isogeny graph–based cryptography has not yet been standardized, but the underlying hard problem has now been proposed as the basis for many cryptographic protocols. This motivates further investigation into the hardness of the underlying problem and the security of the proposed protocols.
Returning to the Past: The Use of History in Spanish Caribbean Theater

In this chapter uses each island’s history to examine how a theater of revisions aids the playwrights in shaping the present and the future. In this chapter, the three plays examined: La invasion (1970), Manuel Mendez Ballester from Puerto Rico, Cuban Gerardo Fulleda Leon’s Placido (1981), and Andromaca (1983) from Ivan Garcia Guerra from the Dominican Republic, use the events of the nineteenth century as the founding moments of the nation and therefore of the people. In this way, these events are re-examined or rescued in order to write a new future.
Intrapartum Fetal Heart Rate Monitoring: Nomenclature, Interpretation, and General Management Principles

Intrapartum monitoring is designed to detect fetal metabolic acidosis and to prevent hypoxia. Prior to its implementation, intrapartum fetal death rates were between 3 and 4 per 1000. A normal tracing reliably predicts a well-oxygenated fetus; however, an abnormal tracing is less predictive of fetal status. The three-tiered fetal heart rate interpretation system should be used to assist in determining fetal status [1].
Recurrent Xanthine Stone Formation in a Lesch-Nyhan Patient: A Case Report

Lesch-Nyhan disease is a rare genetic condition that presents as a deficiency in the hypoxanthine-guanine phosphoribosyltransferase (HGPRT) enzyme of the purine nucleotide recycling pathway. Patients with Lesch-Nyhan commonly present with uric acid urolithiasis, but rare cases of xanthine stone formation have been reported. Treatment for these recurrent xanthine stones has proven difficult and there remains no standard protocol for this presentation. Impaired renal function is of critical concern with current treatment practices and outcomes. We report a case of a 3-year-old boy with Lesch-Nyhan disease who presented with recurrent obstructing xanthine stones. World J Nephrol Urol. 2017;6(3-4):29-31 doi: https://doi.org/10.14740/wjnu311w
Simultaneous optimization of geometry and firing angles of in-wheel switched reluctance motor

Interests in using rare-earth free motors such as switched reluctance motors (SRMs) for electric and hybrid electric vehicles (EV/HEVs) continue to gain popularity, owing to their low cost and robustness. Optimal design of a SRM, to meet specific characteristics for an application, should involve simultaneous optimization of the motor geometry and control in order to achieve the highest performance with the lowest cost. This paper presents a constrained multi-objective optimization framework for design and control of a SRM based on a non-dominated sorting genetic algorithm II (NSGA-II). The proposed methodology optimizes SRM operation for high volume traction applications by considering multiple criteria including efficiency, average torque, and torque ripple. Several constraints are defined by the considered application, such as the motor stack length, outer diameter, minimum operating power, minimum desired efficiency, rated speed, rated current, and supply voltage. The outcome of this optimization includes an optimal geometry outlining variables such as air gap length, rotor inner diameter, stator pole arc angle, rotor pole arc angle, rotor back iron, stator pole height, and stator inner diameter as well as optimal turn-on and turn-off firing angles. Then the machine is manufactured according to the obtained optimal specifications. Comprehensive finite element analysis (FEA) and experimental results are provided to validate the theoretical findings.
Development of a miRNA surface-enhanced Raman scattering assay using benchtop and handheld Raman systems

DNA-functionalized nanoparticles, when paired with surface-enhanced Raman spectroscopy (SERS), can rapidly detect microRNA. However, widespread use of this approach is hindered by drawbacks associated with large and expensive benchtop Raman microscopes. MicroRNA-17 (miRNA-17) has emerged as a potential epigenetic indicator of preeclampsia, a condition that occurs during pregnancy. Biomarker detection using an SERS point-of-care device could enable prompt diagnosis and prevention as early as the first trimester. Recently, strides have been made in developing portable Raman systems for field applications. An SERS assay for miRNA-17 was assessed and translated from traditional benchtop Raman microscopes to a handheld system. Three different photoactive molecules were compared as potential Raman reporter molecules: a chromophore, malachite green isothiocyanate (MGITC), a fluorophore, tetramethylrhodamine isothiocyanate, and a polarizable small molecule 5,5-dithio-bis-(2-nitrobenzoic acid) (DTNB). For the benchtop Raman microscope, the DTNB-labeled assay yielded the greatest sensitivity under 532-nm laser excitation, but the MGITC-labeled assay prevailed at 785 nm. Conversely, DTNB was preferable for the miniaturized 785-nm Raman system. This comparison showed significant SERS enhancement variation in response to 1-nM miRNA-17, implying that the sensitivity of the assay may be more heavily dependent on the excitation wavelength, instrumentation, and Raman reporter chosen than on the plasmonic coupling from DNA/miRNA-mediated nanoparticle assemblies.
Reduction in Mortality Following Pediatric Rapid Response Team Implementation.

Objective To evaluate the effectiveness of a physician-led rapid response team program on morbidity and mortality following unplanned admission to the PICU. Design Before-after study. Setting Single-center quaternary-referral PICU. Patients All unplanned PICU admissions from the ward from 2005 to 2011. Interventions The dataset was divided into pre- and post-rapid response team groups for comparison. Measurements and main results A Cox proportional hazards model was used to identify the patient characteristics associated with mortality following unplanned PICU admission. Following rapid response team implementation, Pediatric Risk of Mortality, version 3, illness severity was reduced (28.7%), PICU length of stay was less (19.0%), and mortality declined (22%). Relative risk of death following unplanned admission to the PICU after rapid response team implementation was 0.685. Conclusions For children requiring unplanned admission to the PICU, rapid response team implementation is associated with reduced mortality, admission severity of illness, and length of stay. Rapid response team implementation led to more proximal capture and aggressive intervention in the trajectory of a decompensating pediatric ward patient.
Demystifying the Multiverse

In this section we discuss some misconceptions about the multiverse, often existing even in the scientific community.
CHI Doctoral Consortium: The Work of Cybersecurity Advocates

Cybersecurity advocates attempt to counter the tsunami of cyber attacks by promoting security best practices. However, little is known about the skills necessary for success and which advocacy techniques are the most effective. My research attempts to fill this gap by exploring the motivations, characteristics, and practices of cybersecurity advocates. The research informs educational recommendations to develop advocates and implications for how successful advocacy techniques can be incorporated into tools and interfaces that promote beneficial security behavior.
Remarks on properties of probability distributions determined by conditional moments

In this paper we consider some properties of rotation — invariant distributions onR n , which are determined by a form of conditional moment of order α>0. In particular we prove that the Gaussian distribution is determined uniquely by its conditional moments and we investigate the related question of finiteness of exponential moments. The case of general α>0 appears to be more difficult to analyze than the case α=2, studied previously by other authors.
Impact of Genomic Assay Testing and Clinical Factors on Chemotherapy Use After Implementation of Standardized Testing Criteria

Background For clinically appropriate early-stage breast cancer patients, reflex criteria for Oncotype DX ordering ("the intervention") were implemented at our comprehensive cancer center, which reduced time-to-adjuvant chemotherapy initiation. Our objective was to evaluate Oncotype DX ordering practices and chemotherapy use before and after implementation of the intervention. Materials and methods We examined medical records for 498 patients who had definitive breast cancer surgery at our center. The post-intervention cohort consisted of 232 consecutive patients who had Oncotype DX testing after reflex criteria implementation. This group was compared to a retrospective cohort of 266 patients who were diagnosed and treated prior to reflex criteria implementation, including patients who did and did not have Oncotype DX ordered. Factors associated with Oncotype DX ordering pre- and post-intervention were examined. We used multivariate logistic regression to evaluate factors associated with chemotherapy receipt among patients with Oncotype DX testing. Results The distribution of Oncotype DX scores, the proportion of those having Oncotype DX testing (28.9% vs. 34.1%) and those receiving chemotherapy (14.3% vs. 19.4%), did not significantly change between pre- and post-intervention groups. Age ≤65 years, stage II, grade 2, 1-3+ nodes, and tumor size >2 cm were associated with higher odds of Oncotype DX testing. Among patients having Oncotype DX testing, node status and Oncotype DX scores were significantly associated with chemotherapy receipt. Conclusion Our criteria for reflex Oncotype DX ordering appropriately targeted patients for whom Oncotype DX would typically be ordered by providers. No significant change in the rate of Oncotype DX ordering or chemotherapy use was observed after reflex testing implementation. Implications for practice This study demonstrates that implementing multidisciplinary consensus reflex criteria for Oncotype DX ordering maintains a stable Oncotype DX ordering rate and chemotherapy rate, mirroring what was observed in a specific clinical practice, while decreasing treatment delays due to additional testing. These reflex criteria appropriately capture patients who would likely have had Oncotype DX ordered by their providers and for whom the test results are predicted to influence management. This intervention serves as a potential model for other large integrated, multidisciplinary oncology centers to institute processes targeting patient populations most likely to benefit from genomic assay testing, while mitigating treatment delays.
Peculiar polygonal paths

Many microorganisms use light-sensitive receptors to migrate. A case in point is the microalga Euglena gracilis, which avoids light intensity increases by swimming in polygonal trajectories — providing an elegant solution to navigational challenges.
Improving the efficiency of the operating room environment with an optimization and machine learning model

The operating room is a major cost and revenue center for most hospitals. Thus, more effective operating room management and scheduling can provide significant benefits. In many hospitals, the post-anesthesia care unit (PACU), where patients recover after their surgical procedures, is a bottleneck. If the PACU reaches capacity, patients must wait in the operating room until the PACU has available space, leading to delays and possible cancellations for subsequent operating room procedures. We develop a generalizable optimization and machine learning approach to sequence operating room procedures to minimize delays caused by PACU unavailability. Specifically, we use machine learning to estimate the required PACU time for each type of surgical procedure, we develop and solve two integer programming models to schedule procedures in the operating rooms to minimize maximum PACU occupancy, and we use discrete event simulation to compare our optimized schedule to the existing schedule. Using data from Lucile Packard Children's Hospital Stanford, we show that the scheduling system can significantly reduce operating room delays caused by PACU congestion while still keeping operating room utilization high: simulation of the second half of 2016 shows that our model could have reduced total PACU holds by 76% without decreasing operating room utilization. We are currently working on implementing the scheduling system at the hospital.
Operational Calculus in One Variable

Let ℱ denote the algebra of all function f on –π≤θ≤π, with $$f(\theta ) = \sum\limits_{ - \infty }^\infty {{C_n}{e^{in\theta }}} ,\sum\limits_{ - \infty }^\infty {|{C_n}|}<\infty$$
Nuance in bilateral cleft lip repair

The management of patients with bilateral cleft lip and palate requires an understanding of anatomy and a focus on function. Comprehensive care in a collaborative multidisciplinary setting is crucial for the future development of these children. The operative technique begins with meticulous measurement and creation of symmetry to set the foundation for successful repair. In severely wide or asymmetric cases, preoperative orthopedics can be used to narrow the cleft prior to surgery. Consistency of design, anticipation of future growth and critical evaluation of results are essential for a cleft surgeon to obtain the best result.
Single-Molecule FRET of Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) are now widely recognized as playing critical roles in a broad range of cellular functions as well as being implicated in diverse diseases. Their lack of stable secondary structure and tertiary interactions, coupled with their sensitivity to measurement conditions, stymies many traditional structural biology approaches. Single-molecule Forster resonance energy transfer (smFRET) is now widely used to characterize the physicochemical properties of these proteins in isolation and is being increasingly applied to more complex assemblies and experimental environments. This review provides an overview of confocal diffusion-based smFRET as an experimental tool, including descriptions of instrumentation, data analysis, and protein labeling. Recent papers are discussed that illustrate the unique capability of smFRET to provide insight into aggregation-prone IDPs, protein-protein interactions involving IDPs, and IDPs in complex experimental milieus.
Anisotropic 2D excitons unveiled in organic–inorganic quantum wells

Two-dimensional (2D) excitons arise from electron–hole confinement along one spatial dimension. Such excitations are often described in terms of Frenkel or Wannier limits according to the degree of exciton spatial localization and the surrounding dielectric environment. In hybrid material systems, such as the 2D perovskites, the complex underlying interactions lead to excitons of an intermediate nature, whose description lies somewhere between the two limits, and a better physical description is needed. Here, we explore the photophysics of a tuneable materials platform where covalently bonded metal-chalcogenide layers are spaced by organic ligands that provide confinement barriers for charge carriers in the inorganic layer. We consider self-assembled, layered bulk silver benzeneselenolate, [AgSePh]∞, and use a combination of transient absorption spectroscopy and ab initio GW plus Bethe–Salpeter equation calculations. We demonstrate that in this non-polar dielectric environment, strongly anisotropic excitons dominate the optical transitions of [AgSePh]∞. We find that the transient absorption measurements at room temperature can be understood in terms of low-lying excitons confined to the AgSe planes with in-plane anisotropy, featuring anisotropic absorption and emission. Finally, we present a pathway to control the exciton behaviour by changing the chalcogen in the material lattice. Our studies unveil unexpected excitonic anisotropies in an unexplored class of tuneable, yet air-stable, hybrid quantum wells, offering design principles for the engineering of an ordered, yet complex dielectric environment and its effect on the excitonic phenomena in such emerging materials.
Computational Process Control Compatible Dimensional Metrology Tool: Through-focus Scanning Optical Microscopy

Using only two derived numbers based on a reference library, this paper shows how through-focus scanning optical microscopy (TSOM) is compatible with computational process control (CPC) for the complete 3Dshape process monitoring of nanoscale to microscale targets. This is demonstrated using three types of target switch widths (CDs) and depths ranging from 50 nm to1.0 μm, and 70 nm to 20 μm, respectively. TSOM is a high through put, low-cost and in-line capable optical dimensional metrology method ideally suited for high volume manufacturing (HVM), complementing other widely used metrology tools.
Photosynthetic and Respiratory Acclimation of Understory Shrubs in Response to in situ Experimental Warming of a Wet Tropical Forest

Despite the importance of tropical forests to global carbon balance, our understanding of how tropical plant physiology will respond to climate warming is limited. In addition, the contribution of tropical forest understories to global carbon cycling is predicted to increase with rising temperatures; however, in-situ warming studies of tropical forest plants to date focus only on upper canopies. We present results of an in-situ field-scale +4 C understory infrared warming experiment in Puerto Rico (Tropical Responses to Altered Climate Experiment; TRACE). We investigated gas exchange responses of two common understory shrubs, Psychotria brachiata and Piper glabrescens, after exposure to four and eight months warming. We assessed physiological acclimation in two ways: 1) by comparing plot-level physiological responses in heated versus control treatments before and after warming, and 2) by examining physiological responses of individual plants to variation in environmental drivers across all plots, seasons, and treatments. P. brachiata has the capacity to up-regulate (i.e., acclimate) photosynthesis through broadened thermal niche an up-regulation of photosynthetic temperature optimum (Topt) with warmer temperatures. P. glabrescens, however, did not upregulate any photosynthetic parameter, but rather experienced declines in the rate of photosynthesis at the optimum temperature (Aopt), corresponding with lower stomatal conductance under warmer daily temperatures. Contrary to expectation, neither species showed strong evidence for respiratory acclimation. P. brachiata down-regulated basal respiration with warmer daily temperatures during the wetter winter months only. P. glabrescens showed no evidence of respiratory acclimation. Unexpectedly, soil moisture, was the strongest environmental driver of daily physiological temperature responses, not vegetation temperature. Topt increased, while photosynthesis and basal respiration declined as soils dried, suggesting that drier conditions negatively affected carbon uptake for both species. Overall, P. brachiata, an early successional shrub, showed higher acclimation potential to daily temperature variations, potentially mitigating negative effects of chronic warming. The negative photosynthetic response to warming experienced by P. glabrescens, a mid-successional shrub, suggests that this species may not be able to as successfully tolerate future, warmer temperatures. These results highlight the importance of considering species when assessing climate change and relay the importance of soil moisture on plant function in large-scale warming experiments.
The simple past: by Driss Chraïbi, translated from the French by Hugh H. Harter, introduction by Adam Shatz, New York, New York Review Books, 2019, xiv + 226 pp., $15.95 (softcover), ISBN 978-1-68137-360-7

The new edition of Driss Chraibi’s The Simple Past, in the New York Review Books Classics series, is a testament to the enduring impact of this novel – first published in 1954 as Le passe simple, b...
Epitaxial growth of cubic WCy(001) on MgO(001)

Abstract Tungsten carbide films are sputter-deposited onto MgO(001) substrates at 400 °C in 5 mTorr Ar - CH4 gas mixtures with CH4 fractions fCH4 = 0.4–6%, yielding total C-to-W ratios x = 0.57–1.25 as determined by ion beam analyses and energy-dispersive X-ray spectroscopy. The C-to-W ratio y in the cubic WCy phase is smaller than x, ranging from y = 0.47–0.68, as determined from lattice constant ao measurements in combination with first-principle calculations that predict an increasing ao = (0.4053 + 0.0295 y) nm for y = 0.3–1.0. This suggests that the cubic phase is stabilized by carbon vacancies and that the layers contain amorphous C with a volume fraction increasing from 4% to 26% for fCH4 = 0.4–6%. X-ray diffraction (XRD) θ-2θ scans, ω-rocking curves, and reciprocal space maps in combination with high-resolution transmission electron microscopy (TEM) indicate the growth of epitaxial rock-salt structure WCy(001) layers with a cube-on-cube epitaxial relationship with the substrate: (001)WC || (001)MgO and [100]WC || [100]MgO. The measured XRD out-of-plane coherence length of 8 – 14 nm is nearly independent of the film thickness d = 10 or 600 nm, suggesting that growth beyond d = 10 nm leads to an epitaxial breakdown and the nucleation of misoriented hexagonal or orthorhombic W2C grains for fCH4 ≤ 1% and cubic nanocrystalline WCy grains for fCH4> 1%.
A qualitative study on Chinese visitors in Grand Teton National Park

Grand Teton (GRTE) and Yellowstone (YELL) National Parks are experiencing an increase in visitation of Chinese tourists over the last few years, but little is known about the expectations, behaviors, and actual experiences of these new visitors. Cultural differences and language barriers contribute to misunderstanding and confusion between park management and visitors, which may lead to regulation violations and conflicts. A better understanding of Chinese tourists’ expectations and experiences is essential for better communication strategies to facilitate preservation of natural resources. To address this, we interviewed Chinese tourists traveling individually or on tour buses, and tour guides for Chinese tourists in GRTE in summer 2018. Three major themes emerged from our interviews: 1) Factors that influence Chinese tourists’ decision-making process, among those the most significant ones are the reputation of YELL and different information sources in China; 2) Dominant expectations among Chinese tourists and the role these expectations are playing in tourists’ satisfaction; and, 3) Chinese tourists’ actual experience that may be different from those of domestic travelers. Recommendations for park management are provided based on the findings. Featured photo by Ken Lane on Flickr. https://flic.kr/p/VWD4Sm
Control of synthesis and wastage of ribosomal ribonucleic acid in lymphocytes. II. The role of protein synthesis.

Abstract Resting lymphocytes were found to accumulate rRNA in their cytoplasm at only half the rate at which the molecules were synthesized in the nucleus. This discrepancy was reversed by stimulating cell growth. This confirms, by independent means, conclusions reached previously on the basis of evidence showing rapid degradation of a large portion of newly synthesized 18 S rRNA in resting lymphocytes. By pulse chase studies with l-[methyl-3H]methionine it was shown that degradation of a fraction of newly synthesized 18 S rRNA molecules occurs shortly after cleavage of the 45 S pre-rRNA into 32 S and 18 S segments. Survival of new 18 S rRNA molecules was found to be dependent on continuous synthesis of a protein or proteins. Reduction of protein synthesis with cycloheximide caused exaggeration of 18 S RNA wastage normally occurring in resting cells. Increasing protein synthesis by temperature elevation reduced 18 S RNA wastage. Partial reduction of rRNA synthesis by low doses of actinomycin D caused an increased survival of those 18 S RNA molecules synthesized. This suggests that the protective protein acts on the new 18 S RNA molecule to prevent attack by ribonucleases, rather than acting on the degradative enzymes to alter their activity. The data support the conclusion that the survival of new 18 S rRNA molecules in resting lymphocytes is controlled by the rate of synthesis of a continuously produced protein. This control may act as a regulator of cell growth.
Model-Based Autonomous Systems for Robotic Space Exploration

A new generation of sensor rich, massively distributed systems is emerging that offers the potential for profound economic and environmental impact, including building energy systems, deep space probes and sensor webs that monitor the earth ecosystem. These robotic webs have the richness that comes from interacting with physical environments, together with the complexity of networked software systems. They must be efficient, capable and long lived, that is, able to survive decades of autonomous operation within unforgiving environments. Model-based autonomy meets this challenge through two ideas. First, we note that programmers generate the desired function based on their commonsense knowledge of how the software and hardware modules behave. The idea of model-based programming is to exploit this modularity by having engineers program reactive systems by simply articulating and plugging together these commonsense models. The second challenge is the infeasibility of synthesizing a set of codes at compile time that envision all likely failure situations and responses. Our solution is to develop real time systems, called model-based executives that respond to novel situations on the order of hundreds of milliseconds, while performing extensive deduction, diagnosis and planning within their reactive control loop.
Pharmacokinetics and pharmacodynamics of peginterferon beta-1a in patients with relapsing-remitting multiple sclerosis in the randomized ADVANCE study.

Aims To evaluate the pharmacokinetics (PK) and pharmacodynamics (PD) of subcutaneous peginterferon beta-1a in patients with relapsing-remitting multiple sclerosis (RRMS) in the phase 3 ADVANCE study (n = 1512). Methods During year 1, patients were randomized (1:1:1) to placebo or peginterferon beta-1a 125 μg every 2 or 4 weeks. After year 1, patients randomized to placebo were re-randomized to 125 μg peginterferon beta-1a administered every 2 weeks or every 4 weeks for year 2. Patients randomized to peginterferon beta-1a in year 1 remained on the same dosing regimen in year 2. Intensive blood samples for PK and PD (neopterin elevation; a biomarker of pharmacological activity induced by interferon beta-1a) measurements were collected from 44 patients pre-dosing and at intervals over 240 h post-dosing at weeks 4 and 24. Sparse samples were collected from all patients after each dosing at weeks 4, 12, 24, 56 and 84. Results The PK profile of peginterferon beta-1a did not change over time or between dosing regimens. No accumulation was observed. Peak serum concentrations were reached 1–1.5 days post-dosing, with a mono-phasic decline and a median half-life of approximately 2–3 days. Dosing every 2 weeks provided approximately two-fold greater monthly cumulative area under the curve than every 4 weeks. Neopterin elevation was sustained for 10−14 days following each dose, indicating doubled cumulative duration of pharmacological activity for dosing every 2 weeks vs. every 4 weeks. Conclusions These PK/PD profiles potentially explain the enhanced efficacy of dosing every 2 weeks in patients with RRMS.