cssi/SciSciGPT-SciSciNet huggingface dataset:
Cytological study of gibberellin regulated xylem development

We conducted the studies on xylem development of tobacco stem by over-expressed PtGA20ox and PtGA2ox1 genes,NtGA20ox RNAi transgenic lines and added extra different hormones with paraffin-cut section method and microscopic observation. The results showed that rapid elongation of internodes as well as xylem formation and development were stimulated by increasing endogenous gibberellins( GAs) levels or exogenous application of GA3,while xylem growth was delayed by decreasing endogenous GAs levels or exogenous application of PAC( GAs biosynthetic inhibitor). Thus our experiment proved that GAs played positive regulatory roles in the development process of xylem and this happened through a GAs concentration-dependent mechanism. Besides,we proved that the positive effects of IAA on xylem development were realized through increasing the level of GAs syntheses at least in some degree.
Reading Words and Images in the Description(s) of Sir John Soane’s Museum

In the 18th and early 19th centuries, London was a city filled with cabinets of curiosity, lusus naturae , and bourgeoning public museums. Most of these institutions publicized their holdings through newspaper advertisements, leaflets, and self-published, descriptive catalogs that were available for purchase on-site and through booksellers. Using Soane’s Museum as a case study, this paper will move beyond historiographical analysis of individual objects in collections catalogs to probe how the museum-produced guidebooks depicted spatial arrangements. Citing examples from the 19th to twenty-first centuries, this paper will examine how the curator-produced descriptions of Soane’s Museum manipulated text and graphics to guide visitors through a constructed narrative, recreated the ephemeral experiences of the museum, and advertise the site’s unparalleled union of painting, sculpture, and architecture to audiences abroad. Soane’s Description of the House and Museum, on the North Side of Lincoln‘s Inn-Fields, the Residence of Sir John Soane (privately printed 1830, 1832; revised 1835) paired spatial narratives with the architectural language of orthographic projection and perspective engravings. His Description set forth an agenda about the museum’s arrangement and established a compositional strategy for subsequent editions of the guidebook, renamed the General Description in the editions printed between 1840 and 1930 then rebranded as the New Description by Summerson in 1955. Through the study of the changing written and visual language published in the guides by the curators of Soane’s Museum, this article will examine the changing character of the visitor experience at the museum and question the form of future editions.
SU-F-T-134: Can We Use the Same Dose Constrains Learnt From Photon World to Plan Proton for Lung Cancer?

Purpose: To evaluate if the same DVH constrains used in photon plans can be safely used to plan proton therapy for lung cancer. Since protons and photons have different dose deposition patterns, the hypothesis is following DVH constrains derived from photon world is not safe for proton. Methods: We retrospectively evaluated plans for 11 lung cancer patients. Each patient was planned with photon and proton following the same dose constrains. Dose statistics on PTV, normal lung, heart and esophagus were extracted for comparison. gEUD for normal lung was calculated and compared between proton and photon plans. We calculated series of gEUDs for each plan by varying the parameter “a” in gEUD formula from 0.1 to 3, covering the whole confidence interval. Results: For all patients, proton plans yield similar PTV coverage and lower dose to heart and esophagus than photon plans. Normal lung V5 was 32.3 % on average in proton plans than 55.4 % in photon. Normal lung gEUD monotonically increased with increasing “a” for all proton and photon plans. For a given patient, the gEUD_proton(a) had a steeper slope than gEUD_photon(a). The two curves crossed for 8 out of 11 patients when “a” = [0.1, 3]. a_crossing ranged from 0.8 to 2.44 with an average of 1.15. For a<a_crossing, gEUD_proton was less than gEUD_photon and vice versa. Conclusion: The current clinical guideline is the lower normal lung V5 would associated with less complications. However, proton plans with a lower normal lung V5 could yield a higher gEUD than photon if the real “a” is larger than a_crossing. Since a_crossing was within the possible range of real “a”, simply following the normal lung V5 guideline for proton plan would not be a good practice. More comprehensive methods should be developed to evaluate the proton plan.
Cryo-quenched Fe-Ni-Cr alloy single crystals: A new decorative steel

Abstract A decorative steel is described that is formed by a process that is unlike that of the fabrication methods utilized in making the original Damascus steels over 2000 years ago. The decorative aspect of the steel arises from a three-dimensional surface pattern that results from cryogenically quenching polished austenitic alloy single crystals into the martensitic phase that is present below 190 K. No forging operations are involved – the mechanism is entirely based on the metallurgical phase properties of the ternary alloy. The symmetry of the decorative pattern is determined and controlled by the crystallographic orientation and symmetry of the 70%Fe,15%Ni,15%Cr alloy single crystals. In addition to using “cuts” made along principal crystallographic surface directions, an effectively infinite number of other random-orientation “cuts” can be utilized to produce decorative patterns where each pattern is unique after the austenitic-to-martensitic phase transformation.
Probabilistic insertion, deletion and substitution error correction using Markov inference in next generation sequencing reads

Error correction of noisy reads obtained from high-throughput DNA sequencers is an important problem since read quality significantly affects downstream analyses such as detection of genetic variation and the complexity and success of sequence assembly. Most of the current error correction algorithms are only capable of recovering substitution errors. In this work, Pindel, an algorithm that simultaneously corrects insertion, deletion and substitution errors in reads from next generation DNA sequencing platforms is presented. Pindel corrects insertion, deletion and substitution errors by modelling the sequencer output as emissions of an appropriately defined Hidden Markov Model (HMM). Reads are corrected to the corresponding maximum likelihood paths using an appropriately modified Viterbi algorithm. When compared with Karect and Fiona, the top two current algorithms capable of correcting insertion, deletion and substitution errors, Pindel exhibits superior accuracy across a range of datasets.
Simplifying network management using Software Defined Networking and OpenFlow

As the complexity of deployments increases, network managers face two problems that we address in this paper. First, the deployment of middleboxes in choke points (between two routers through which all traffic flows), raises concerns regarding robustness, correctness and efficiency. Second, dynamically managing traffic isolation in a network is a very tedious task. In this paper we propose using Software Defined Networks (SDN) and OpenFlow to simplify network management by addressing these two challenges. SDN consists of decoupling the control and data planes of a network. OpenFlow standardizes the way that the controller communicates with the network devices in an SDN architecture. To overcome the challenge faced by deploying middleboxes in choke points, we show how these appliances can be deployed at waypoints. In this architecture, a waypoint is only traversed by traffic that needs further processing. The remaining data flows through the network without being processed by the middlebox. We have developed an application that implements an encryption processing unit that works as a waypoint and we show how OpenFlow can be used to route through the encryption unit only the traffic that requires encryption. To overcome the challenge of dynamic traffic isolation, we show how a network manager can use an application to create, delete and modify virtual local area networks (VLANs) in a dynamic way to achieve traffic isolation. Our implementation provides a GUI to the user so that the administration of the VLANs is greatly simplified.
Incremental Value in Outcome Prediction with Molecular Signatures in Diffuse Large B-Cell Lymphoma,

Abstract 3687 INTRODUCTION: Multiple gene expression-based biomarkers have been identified in diffuse large B-cell lymphoma (DLBCL) that are predictive for survival outcomes. Most studies assess predictive significance based on p-value from multivariate Cox regression; few investigations have evaluated the incremental usefulness of these biomarkers in risk prediction. Using the recently developed concordance measures (e.g., C-statistics) on censored survival data, we assessed the usefulness of two published gene-based risk signatures and compared them to the known clinical prognostic factors; with an overall goal of investigating the added value. METHOD: The added value of biomarkers was assessed by C-statistic and the Integrated Discrimination Improvement (IDI). The overall C-statistic is an estimated concordance between prediction and observation (event vs. non-event) - the probability that predicted risk score is higher for subject with earlier time of event. The IDI measures overall improvement in sensitivity and specificity. The signatures we selected are a six-gene predictor by Lossos et al. (2004) and a three-component signature (∼400 genes) by Lenz et al. (2008). We used the Lenz dataset which include 233 patients with DLBCL who received R-CHOP therapy (median follow-up=2.81 yr), and focused on predicting 3-year survival outcome (42% censored). Clinical prognostic factors evaluated are the traditional IPI components (stage, performance status, age, LDH, and number of extra nodal sites). RESULTS: The C-statistic was 0.60 and 0.721 for six-gene predictor and three-component signature, suggesting good discrimination ability by molecular signature when used alone. However, the performance is inferior to IPI risk factors, with a C-statistic of 0.733. When integrating gene signatures with IPI risk factors, the C-statistic was increased to 0.744 and 0.762, an improvement of only 0.011 (95% CI, -0.049 to 0.071) and 0.029 (95% CI, -0.033 to 0.091) for six-gene predictor and three-component signature, respectively. Furthermore, assessment by IDI reveals an added value of only 0.011 (95% CI, -0.008 to 0.081) and 0.076 (95% CI, 0.013 to 0.16) for the two molecular signatures. Kaplan-Meier survival curves for the four quartile groups based on the predictor scores confirms the marginal benefit in risk prediction using molecular signatures. (Figure 1). CONCLUSIONS: These results indicate that molecular biomarkers are inferior to clinical factors for risk assessment in DLBCL and provide little added value in risk prediction. These calculations suggest we will need to consider more than gene expression to develop highly discriminatory risk prediction models. However, the study of gene expression and clinical outcomes retains considerable potential to enhance understanding of disease mechanisms and uncover new therapeutic targets. Disclosures: No relevant conflicts of interest to declare.
Turning Corners into Cameras: Principles and Methods

We show that walls, and other obstructions with edges, can be exploited as naturally-occurring “cameras” that reveal the hidden scenes beyond them. In particular, we demonstrate methods for using the subtle spatio-temporal radiance variations that arise on the ground at the base of a wall's edge to construct a one-dimensional video of the hidden scene behind the wall. The resulting technique can be used for a variety of applications in diverse physical settings. From standard RGB video recordings, we use edge cameras to recover 1-D videos that reveal the number and trajectories of people moving in an occluded scene. We further show that adjacent wall edges, such as those that arise in the case of an open doorway, yield a stereo camera from which the 2-D location of hidden, moving objects can be recovered. We demonstrate our technique in a number of indoor and outdoor environments involving varied floor surfaces and illumination conditions.
Does Sex Education Help Everyone?: Sex Education Exposure and Timing as Predictors of Sexual Health among Lesbian, Bisexual, and Heterosexual Young Women.

ABSTRACTUsing data from 2002 to 2013 collections of the National Survey of Family Growth, we explored how exposure and timing of sex education were associated with sexual health outcomes of 5,141 women between the ages of 15 and 20 years. Consistent with previous literature, sexual minority (e.g., lesbian and bisexual) women reported engaging in sexual intercourse with a male partner earlier than their heterosexual peers. Sexual minority women were also more likely to receive sex education after already engaging in sexual intercourse. Exposure to sex education was associated with poorer outcomes—such as an increased number of male sexual partners and higher reports of pregnancy—for sexual minority women but not for their heterosexual peers. Receiving sex education before engaging in intercourse was associated with an increase in birth control use among bisexual participants. Therefore, school psychologists and counselors should promote inclusive sex education programs that fully address the needs of sexua...
Cholesterol Trafficking and Esterification With Relation to Atherosclerosis and Neurodegenerative Diseases

Cholesterol is an important lipid molecule that is needed for the growth and viability of mammalian cells. The metabolites of cholesterol include bile acids, oxysterols, and steroid hormones; these substances also have important physiological functions. The sources of cholesterol are from the diet, and from endogenous biosynthesis. Genetically inherited and diet-induced hypercholesterolemia are major risk factors for causing atherosclerotic cardiovascular disease. This Chapter reviews our current knowledge on cellular cholesterol sources and trafficking routes in a mammalian cell. It also reviews the biochemical properties, and the cell biological and pathophysiological roles of the enzyme acyl coenzyme A:cholesterol acyltransferase (ACAT).
A logic programming and verification system for recursive quantificational logic

In this paper, we describe a logic programming and program verification system which is based on quantifier elimination techniques and axiomatization rather than on more common method of doing logic programming using the Herbrand-Prawitz-Robinson unification algorithm without occur-check. This system is shown to have interesting properties for logic programming and includes a number of advanced features. Among these features are user-defined data objects, user-defined recursive relations and functions, either of which may involve quantifiers in the body of their definitions, and automatic termination and consistency checking for recursively defined concept. In addition, it has a correct implementation of negation in contrast to PROLOG implementation of negation as failure, a smooth interaction between LISP-like functions and PROLOG-like relations, and a smooth interaction between specifications and programs. Finally, it provides a method of mathematical induction applicable to recursive definitions involving quantifiers.
Novel regeneration method for deactivated noble metal catalysts

The deactivation and regeneration of supported noble metal catalysts is a major problem encountered in a number of commercial processes. These types of catalyst systems are highly susceptible to loss of activity due to the accumulation of carbonaceous residues on the metal particle surfaces that necessitates the periodic utilization of a high temperature “de-coking” step that is generally performed in air. In the current investigation we have explored the potential of an alternative method to remove deposited carbonaceous species from a supported metal catalyst system that is based on a “surface cleaning” operation performed by adsorbed CO. The impetus for this study stems from the fact that there is a growing interest in the use of various forms of carbon as supporting media and the traditional methods of removing deposits from the catalyst would also result in the concomitant gasification of the support. As a consequence, we have been directed to search for regeneration methods that can be carried out at lower temperatures. The concept is predicated on the knowledge that the adsorption of CO on noble metals is relatively strong and such an action could possibly result in the preferential displacement of carbon species pre-adsorbed on the catalyst surface. The impact of this approach on the catalytic behavior of both carbon nanofiber and silica supported platinum, palladium and rhodium particles is discussed.
Complex Morpho-Hydrodynamic Response of Estuaries and Bays to Winter Storms: North-Central Gulf of Mexico, USA

Concepts pertaining to our understanding of estuarine dynamics have been heavily influenced by work carried out on the east and west coasts of the United States and western Europe (Pritchard, 1967). Antecedent geological controls have played an important role in predetermining the dominant type of estuaries along these coasts, namely drowned river valleys on coastal plains and fjord type systems tuned to moderate/high tidal regimes. Along the northern Gulf of Mexico (Fig. 1), however, estuaries are predominantly bar-built where the latest Holocene “stillstand” in sea level has permitted waves to build barrier islands/spits/beaches supplied by sediment from updrift and offshore sand sources (Stone et al., 1992; Stapor and Stone, 2004). Tides in the Gulf of Mexico are microtidal (0–0.3 m), predominantly diurnal and mixed (Marmer, 1954). Characteristically broad regions of low bathymetric relief result in minimal bathymetric steering of the otherwise low-frequency flow (Schroeder and Wiseman, 1999). Due to a high incidence of tropical cyclones in the northern Gulf (Stone et al., 1997; Muller and Stone, 2001), low profile barriers are susceptible to multiple breaches and inlet development. Such occurrences play an important role in estuarine circulation patterns due to phase lags in tidally driven waves. These interlinkages have, however, yet to be fully explored (Schroeder and Wiseman, 1999).
Neuroanatomy of the Kisspeptin Signaling System in Mammals: Comparative and Developmental Aspects

Our understanding of kisspeptin and its actions depends, in part, on a detailed knowledge of the neuroanatomy of the kisspeptin signaling system in the brain. In this chapter, we will review our current knowledge of the distribution of kisspeptin cells, fibers, and receptors in the mammalian brain, including the development, phenotype, and projections of different kisspeptin subpopulations. A fairly consistent picture emerges from this analysis. There are two major groups of kisspeptin cell bodies: a large number in the arcuate nucleus (ARC) and a smaller collection in the rostral periventricular area of the third ventricle (RP3V) of rodents and preoptic area (POA) of non-rodents. Both sets of neurons project to GnRH cell bodies, which contain Kiss1r, and the ARC kisspeptin population also projects to GnRH axons in the median eminence. ARC kisspeptin neurons contain neurokinin B and dynorphin, while a variable percentage of those cells in the RP3V of rodents contain galanin and/or dopamine. Neurokinin B and dynorphin have been postulated to contribute to the control of GnRH pulses and sex steroid negative feedback, while the role of galanin and dopamine in rostral kisspeptin neurons is not entirely clear. Kisspeptin neurons, fibers, and Kiss1r are found in other areas, including widespread areas outside the hypothalamus, but their physiological role(s) in these regions remains to be determined.
Pharmacogenetics: Single Gene Effects

Dr. Vesell and I have been asked to review some principles of pharmacogenetics that relate to the pharmacokinetic theme of this conference. We have divided the topic: Dr. Vesell will discuss multiple gene effects and their implications, and I will mention some single gene effects which can modify drug metabolism and drug response in man. We both are studying the way genetic factors account for rather remarkable person-to-person differences in drug responses and pharmacodynamics, and we hope that pharmacokinetic models will be designed that will take into account these genetically determined individual differences.
Reoperation for Bleeding in Patients Undergoing Coronary Artery Bypass Surgery Incidence, Risk Factors, Time Trends, and Outcomes

Background— Reoperation for bleeding represents an important complication in patients undergoing coronary artery bypass surgery (CABG). Yet, few studies have characterized risk factors and patient outcomes of this event. Methods and Results— We evaluated 528 686 CABG patients at >800 hospitals in the Society of Thoracic Surgeons National Cardiac Database (2004 to 2007). Clinical features and in-hospital outcomes were evaluated in patients with and without reoperation for bleeding after CABG. Logistic regression was used to identify predictors of risk of this event and to estimate weights for an additive risk score. A total of 12 652 CABG patients (2.4%) required reoperation for bleeding. These rates remained fairly stable over time (2.2%, 2.3%, 2.5%, and 2.4% from 2004 to 2007, respectively). Although overall operative mortality was 4.5-fold higher in patients requiring reoperation for bleeding versus those who did not (2.0% versus 9.1%), this mortality risk declined significantly over time (11.3%, 9.5%, ...
Fluid Chemistry of Mid-Ocean Ridge Hydrothermal Vents: A Comparison between Numerical Modeling and Vent Geochemical Data

Seawater-basalt interaction taking place at mid-ocean ridges was studied using numerical modeling to determine the compositional evolution of hydrothermal fluids and associated alteration mineralogy forming within newly emplaced crustal material. Geochemical modeling was carried out in a closed seawater-basalt system at discrete temperature intervals between 2 and 400°C at 500 bars, varying fluid/rock ratios, and secondary mineral assemblages representative of basalt alteration in natural systems. In addition to temperature, the fluid/rock ratio has a fundamental control on the resulting system chemistry. At rock-buffered conditions (low fluid/rock ratios), the mineral-solution equilibrium was characterized by high cation to proton activity ratios for aCa2+/(aH+)2 and aNa+/aH+ and very low dissolved Mg concentrations due to the precipitation of smectites and chlorite. A complex secondary mineral alteration assemblage dominated by Ca- and Na-bearing minerals including zeolites, calcite, epidote, prehnite, clinozoisite, and albite was predicted to form. The resulting fluid composition was alkaline and reduced relative to ambient seawater, with Eh values ranging between −0.2 and −0.6 V. In contrast, seawater-buffered conditions (high fluid/rock ratios) resulted in lower cation to proton activity ratios for aCa2+/(aH+)2 and aNa+/aH+ and higher dissolved Mg concentrations comparable to the value of this element in ambient seawater. A more simple mineral assemblage was predicted to form at these conditions with the predominance of Al-Si- and Mg-bearing minerals including kaolinite, quartz, and talc in addition to large amounts of anhydrite. The resulting fluid composition was mildly acidic and oxidized relative to seawater with Eh values ranging between −0.2 and 0 V. These modeling results were compared to a compilation of submarine hydrothermal vent fluid compositions from mid-ocean ridge settings and analogous basalt-dominated environments. The agreement obtained between the simulations and the compiled fluid data indicates that mid-ocean ridge hydrothermal processes can be closely reproduced by mineral-solution equilibria for a broad range of temperatures and fluid/rock ratios.
Passivation of Thin Channel Zinc Tin Oxide TFTs Using Al 2 O 3 Deposited by O 3 -Based Atomic Layer Deposition

Here, we fabricate solution processed zinc tin oxide bottom gate top contact thin film transistors (TFTs) with active layer thickness down to 6 nm by varying the solution molarity and number of layers. As-fabricated devices show hysteresis as large as 12.65 V. The hysteresis is then studied under vacuum to understand the important role of the back channel in electrical performance. After vacuum treatment, the hysteresis measured under vacuum was reduced to −0.05 V. Alumina deposited on the back channel using atomic layer deposition (ALD) is used for passivation. The TFTs passivated with an H2O-based ALD process show conductive behavior after passivation while an O3-based ALD process results in a negative threshold voltage shift dependent on the thickness of the active layer. O3-based passivated devices show good stability with a field effect mobility of 8.3 cm2V−1s−1, ${V}_{t}$ of 5.5 V, and hysteresis of 0.85 V.
A Buffer-Less Wideband Frequency Doubler in 45-nm CMOS-SOI With Transistor Multiport Waveform Shaping Achieving 25% Drain Efficiency and 46–89 GHz Instantaneous Bandwidth

A wideband high-efficiency frequency doubler leveraging transistor multiport waveform shaping is presented in this letter. Unlike the conventional push–push pair with grounded source terminals, both the gates and sources of the proposed doubler are simultaneously driven by 180° out-of-phase signals. As a result, the drain current bifurcation is greatly reduced, leading to suppression of the undesired 4th harmonic and significant enhancement of 2nd harmonic current. The EKV FET model is also adopted to mathematically analyze the current waveform shaping in both conventional and proposed topologies, which agrees well with the circuit simulations. Broadband fundamental matching and a dual-resonance 2nd harmonic trap filter together guarantee the wideband frequency doubling performance. Prototyped in 45-nm CMOS-silicon-on-insulator, the proposed doubler achieves 25% peak drain efficiency, instantaneously covering 46–89 GHz (64% fractional bandwidth).
Cultural Experiences, Patterns, and Practices of American Indian Women With Polycystic Ovary Syndrome: An Ethnonursing Study:

Introduction: Knowledge is needed about the cultural experiences, patterns, and practices of American Indian women with polycystic ovary syndrome (PCOS), so nurses can provide culturally congruent care. Method: A qualitative, ethnonursing study based on Leininger's theory of culture care diversity and universality. Data were collected from 13 key informants living on a reservation in the Western United States. Data were analyzed with Leininger's four phases of qualitative analysis. Results: Three universal themes were identified: (1) control of PCOS symptoms is important for the cultural well-being of tribal women, (2) culturally congruent PCOS education and health care are important with variations in approaches to treatment, and (3) tribal culture is important with variations in use of tribal practices. Discussion: Tribal culture affects the health care beliefs and practices of American Indian women with PCOS. The findings can be used to improve culturally congruent care for women with this chronic condition.
A “Visibilizing” Project: “Seeing” the Ontological Erasure of Disability in Teacher Education and Social Studies Curricula

In their consideration the quintessential questions of “What knowledge is of most worth? Who decides? Who benefits?” Nusbaum and Steinborn have arrived at a concept that they name ontological erasure. This concept goes beyond the absence of disability from curricular content, or silence around disability in educational justice frameworks—but rather is the active erasing of certain body-minds from “being” in the educational landscape. This paper traces their path in attempting to first understand what they both viewed as the absence or silence of disability from justice dialogues and curricular work that seeks to advance conceptions of diversity and underrepresented, marginalized groups. Then, they examine the genealogy of ableism in a brief survey of United States history and connected social studies curricula to demonstrate the necropolitical treatment and subsequent erasure of disability from academic spaces dedicated to social justice. Nusbaum and Steinborn hypothesize that pushing disability studies to the fore of those conversations requires interrogating whose histories are told, whose lives are given worth, and how the history taught in U.S. schools perpetuates a hierarchy of knowledge that is fundamentally ableist. This reconceptualization, thus, requires—demands—a “visibilizing” of disability within the educational landscapes from which it has been erased.
Two Conceptions of Embracing Ecological Change in Ecosystem Management and Species Conservation: Accommodation and Intervention

In this chapter I consider two different perspectives on what it means to acknowledge and embrace anthropogenic ecological change with respect to ecosystem management and species conservation. On one view, embracing anthropogenic change involves taking greater responsibility for and control of the ecological future. We ought to use our best science and technology to thoughtfully and intentionally manage, and where necessary design and modify, ecological systems and species. On another view, embracing ecological change involves reducing human influences and allowing systems and species space and opportunities to transition and reconfigure without intentionally designing them in accordance with how we think they need or ought to be. Anthropogenic change does not itself imply that there is a responsibility to take an interventionist and control-oriented approach to ecosystem management and species conservation. Whether and when people ought to do so will vary by case and context, not only in accordance with the relevant empirical information, but also in accordance with the operative values as stake.
Crosswalk Between Sullins’ 2016(1) and 2019(2) Add Health Longitudinal Analyses of Abortion and Mental Health

This brief paper explains the differences between the sample sizes and results reported in these two similar analyses using the same data.
Identification of the molecular components of a putative Jasus edwardsii (Crustacea; Decapoda; Achelata) circadian signaling system

Like all organisms, members of the crustacean order Decapoda must coordinate their physiology and behavior to accommodate recurring patterns of environmental change. Genetically encoded biological clocks are responsible, at least in part, for the proper timing of these organism-environment patternings. While biological clocks cycling on a wide range of timescales have been identified, the circadian signaling system, which serves to coordinate physiological/behavioral events to the solar day, is perhaps the best known and most thoroughly investigated. While many circadian patterns of physiology/behavior have been documented in decapods, few data exist concerning the identity of circadian genes/proteins in members of this taxon. In fact, large collections of circadian genes/proteins have been described from just a handful of decapod species. Here, a publicly accessible transcriptome, produced from tissues that included the nervous system (brain and eyestalk ganglia), was used to identify the molecular components of a circadian signaling system for rock lobster, Jasus edwardsii, a member of the decapod infraorder Achelata. Complete sets of core clock (those involved in the establishment of the molecular feedback loop that allows for ~ 24-h cyclical timing), clock-associated (those involved in modulation of core clock output), and clock input pathway (those that allow for synchronization of the core clock to the solar day) genes/proteins are reported. This is the first description of a putative circadian signaling system from any member of the infraorder Achelata, and as such, expands the decapod taxa for which complete complements of putative circadian genes/proteins have been identified.
Structure of Human ATG9A, the Only Transmembrane Protein of the Core Autophagy Machinery

Autophagy is a catabolic process involving capture of cytoplasmic materials into double-membraned autophagosomes that subsequently fuse with lysosomes for degradation of the materials by lysosomal hydrolases. One of the least understood components of the autophagy machinery is the transmembrane protein ATG9. Here, we report a cryoelectron microscopy structure of the human ATG9A isoform at 2.9-A resolution. The structure reveals a fold with a homotrimeric domain-swapped architecture, multiple membrane spans, and a network of branched cavities, consistent with ATG9A being a membrane transporter. Mutational analyses support a role for the cavities in the function of ATG9A. In addition, structure-guided molecular simulations predict that ATG9A causes membrane bending, explaining the localization of this protein to small vesicles and highly curved edges of growing autophagosomes.
Team Medical Coverage in College Basketball

Care of a college basketball team requires a broad set of skills by the team physician. The mix of intense aerobic exercise coupled with the explosive, multidirectional, contact-collision nature of the sport place basketball players at risk for a variety of sports-related conditions. Common injuries include lateral ankle sprains, anterior cruciate ligament (ACL) tears, finger injuries, facial trauma, and concussions. In addition, the cardiovascular demands of the sport may precipitate acute cardiac events in predisposed individuals, with greatest concern for hypertrophic cardiomyopathy as well as vascular complications of Marfan’s syndrome. College basketball players are subject to the usual illnesses of the general population but may have unique needs relating to their management as well as the rigors of travel, time zone change, and mental health concerns. Optimal care of the collegiate basketball team is by a sports medicine provider or group of providers who can meet each of these sport-related needs.
Bond strength of three chairside crown reline materials to milled polymethyl methacrylate resin

Abstract Statement of problem Information on the bond strength of milled polymethyl methacrylate interim restorations when relined with chairside reline materials is lacking. Purpose The purpose of this in vitro study was to measure the shear bond strength of various combinations of 3 different chairside reline materials bonded to milled polymethyl methacrylate blocks with 3 different types of surface treatments. Materials and methods Uniform blocks (10×10×22 mm) were milled from tooth-colored polymethyl methacrylate disks (Vivid PMMA; Pearson Dental Supply Co). The surface treatments tested were airborne-particle abrasion with 50-μm particle size aluminosilicate, application of acrylic resin monomer (Jet Liquid; Lang Dental Manufacturing Co) for 180 seconds, and airborne-particle abrasion with monomer application. The control groups were blocks with no surface treatment. The chairside reline materials tested were Jet acrylic resin (Jet Powder; Lang Dental Manufacturing Co), bis-acryl resin (Integrity; Dentsply Sirona), and flowable composite resin (Reveal; Bisco). All materials were applied through a O1.5×3-mm bonding ring. Ten specimens for each of the 12 groups were tested in a universal testing machine. Load was applied at a crosshead speed of 1 mm/min. Fracture surfaces were then analyzed for cohesive versus adhesive or mixed failure. Data were analyzed using 2-way ANOVA and Tukey-Kramer post hoc analysis (α=.05). Results The mean shear bond strength values ranged from 1.77 ±0.79 MPa to 28.49 ±5.75 MPa. ANOVA revealed that reline material (P Conclusions Of the materials tested, the most reliable material to bond to milled polymethyl methacrylate was Jet acrylic resin, and the bond strength values were increased substantially when the milled polymethyl methacrylate surface was airborne-particle abraded and monomer was applied.
Contribution of Free-Text Comments to the Burden of Documentation: Assessment and Analysis of Vital Sign Comments in Flowsheets.

Background: Documentation burden is a common problem with modern electronic health record (EHR) systems. To reduce this burden, various recording methods (eg, voice recorders or motion sensors) have been proposed. However, these solutions are in an early prototype phase and are unlikely to transition into practice in the near future. A more pragmatic alternative is to directly modify the implementation of the existing functionalities of an EHR system. Objective: This study aims to assess the nature of free-text comments entered into EHR flowsheets that supplement quantitative vital sign values and examine opportunities to simplify functionality and reduce documentation burden. Methods: We evaluated 209,055 vital sign comments in flowsheets that were generated in the Epic EHR system at the Vanderbilt University Medical Center in 2018. We applied topic modeling, as well as the natural language processing Clinical Language Annotation, Modeling, and Processing software system, to extract generally discussed topics and detailed medical terms (expressed as probability distribution) to investigate the stories communicated in these comments. Results: Our analysis showed that 63.33% (6053/9557) of the users who entered vital signs made at least one free-text comment in vital sign flowsheet entries. The user roles that were most likely to compose comments were registered nurse, technician, and licensed nurse. The most frequently identified topics were the notification of a result to health care providers (0.347), the context of a measurement (0.307), and an inability to obtain a vital sign (0.224). There were 4187 unique medical terms that were extracted from 46,029 (0.220) comments, including many symptom-related terms such as “pain,” “upset,” “dizziness,” “coughing,” “anxiety,” “distress,” and “fever” and drug-related terms such as “tylenol,” “anesthesia,” “cannula,” “oxygen,” “motrin,” “rituxan,” and “labetalol.” Conclusions: Considering that flowsheet comments are generally not displayed or automatically pulled into any clinical notes, our findings suggest that the flowsheet comment functionality can be simplified (eg, via structured response fields instead of a text input dialog) to reduce health care provider effort. Moreover, rich and clinically important medical terms such as medications and symptoms should be explicitly recorded in clinical notes for better visibility.
Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus .

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4 × after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.
Spectral dynamics of muscle fiber activation in response to exercise and acute fatigue

Skeletal muscles form an integrated multi-component system with complex dynamics of continuous myoelectrical activation of various muscle types with different functions and muscle fibers within muscles. To understand the multiscale dynamics of neuromuscular activity, we investigate spectral characteristics of different muscle types across timescales, and we track the evolution of the dynamics with progression of exercise and fatigue. We develop a protocol for young and elderly subjects of repeated squat exercise segments performed until exhaustion. We analyze differentiated spectral power responses over a range of frequency bands representing muscle fiber dynamics within leg and back muscle activation. We find that leg and back muscle are characterized by muscle-specific spectral profiles with differentiated frequency bands contribution and a muscle-specific evolution path in response to acute fatigue. Specifically, we observe that with increasing fatigue leg muscle spectral power increases for low, intermediate and high frequencies. In contrast, back muscle spectral power increases with fatigue only for low and intermediate frequencies below 50 Hz. Further, leg muscle shows higher spectral response to fatigue (35% and 40% for young and elderly subjects respectively; p < 0.05) compared to the back muscle (25% increase only for the young group; p = 0.03). The uncovered universality among subjects in the spectral profile, reveals a previously unrecognized multi-scale mechanism underlying differentiated response of distinct muscle types and muscle fibers to exercise-induced fatigue in young and elderly. Tracking changes in the spectral profiles could help quantify more precisely muscle adaptations after training interventions and may assist coaches with the selection of most appropriate and effective training programs.
Electron Paramagentic Resonance Investigation of Mechanism of Light- and Elevated-Temperature-Induced Degradation in Ga-doped Cz Si

We report on the electron paramagnetic resonance (EPR) spectra recorded at 6 K for Ga-doped Czochralski (Cz) Si in the initial stages of light- and elevated-temperature-induced degradation (LeTID). We show that the narrow-range EPR spectrum depends on the duration of simultaneous heat and light exposure. After prolonged LeTID, the EPR intensity increases at ~334 mT. The EPR signature at ~334 mT is characteristic of Si dangling bonds, and the increase in the dangling bond density can be attributed to the bulk and not the surface. Additionally, we show that the inverse of the minority carrier lifetime in Ga-doped Cz Si samples, measured by quasi-steady-state photoconductance (QSSPC) decay, correlates with the increase in the intensity of the Si dangling bond signal measured by EPR. Based on these observations, we put forth a hypothesis connecting H to LeTID and the corresponding defect structure.
The Mathematics Portfolio: An Alternative Tool to Evaluate Students’ Progress

This article describes the need for more thorough and varied forms of assessment to evaluate students’ level of understanding in mathematics. Portfolios are one type of assessment tool that, when added to a teacher’s repertoire can improve students’ comprehension and retention and enable students to monitor their own progress and to take more responsibility for their own learning. Portfolio assignments can also help students and teachers to detect and remedy weaknesses and misunderstandings and can increase students’ self-confidence in mathematics. This article discusses what a portfolio is, gives an example of a unit portfolio used in an undergraduate Finite Mathematics course to assess students understanding of Venn diagrams, describes the benefits and challenges of using unit portfolios, and discusses how teachers can evaluate portfolios with a rubric. By providing practical advice, this article can be used as a framework for teachers who have the desire to incorporate portfolio assignments, in addition to more traditional tools of assessment, at the undergraduate or K–12 grade levels.
Bigotry and Religious Belief

Attacks on religious doctrines are often characterized as a form of bigotry and traditional analyses of the concept support this view. I argue that regarding such attacks as bigotry is inconsistent with a variety of contemporary moral attitudes and social goals. I offer an improved account of when we should ascribe bigotry – one that is more coherent with views on tolerance and the importance of open debate. This account focuses upon the justification for hostile attitudes and also limits the target of bigoted thought to persons, not to doctrines, religious or otherwise. I argue that while it is indeed possible to adopt bigoted attitudes toward people classified on the basis of their religious beliefs, it is not possible to hold bigoted attitudes against the beliefs themselves.
Submicron CMOS MIL-STD-1750A based mission processor

The author describes the design of a MIL-STD-1750A mission processor (MP), which is generally based on the US Air Force Pave Pillar architecture. The MP is composed of a power conditioner unit, a chassis assembly, and a set of SEM-E (3/4 ATR)-size common modules. The common modules utilize a set of seven complex submicrometer CMOS integrated circuits as building blocks. The internal design architecture features a dual PI-Bus for intermodule communication and a dual TM-Bus for operational test and maintenance. The MP is capable of over 22-million-instruction/s performance on the Defense Avionics Instructions Set (DAIS) mix and contains up to 2.56 million words of random-access memory and 288 thousand words of read-only memory. The MP provides external interfaces to three dual redundant MIL-STD-1553B serial communication buses, two differential Small Computer System Interface (SCSI) buses, and IEEE-488 bus, and miscellaneous digital and analog discrete lines. >
Combined charged-particle and X-ray simulations using the Bmad open source software library

The open source Bmad software library, developed at Cornell University, has proved to be a useful tool for accelerator simulations owing to its modular, object-oriented design. Bmad has been used to simulate the storage ring CESR for many years, and to design and analyze the proposed Cornell Energy Recovery Linac. Work is ongoing to expand Bmad in a number of directions. In particular, the ability to be able to do a combined simulation of accelerated charged-particle beams and the x-ray beams they create is being developed. Ultimately a complete framework for simulations from the gun cathode (including space-charge) to x-ray generation, to x-ray tracking through to the experimental end-stations is envisioned. The flexibility of Bmad is such that multiple propagation algorithms can be accommodated with the user selecting the appropriate algorithm for each individual element. To this end, the integration of Bmad with the SHADOW tracking code is in development.