cssi/SciSciGPT-SciSciNet huggingface dataset:
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment

Motivation: It is well recognized that the effects of drugs are far beyond targeting individual proteins, but rather influencing the complex interactions among many relevant biological pathways. Genome-wide expression profiling before and after drug treatment has become a powerful approach for capturing a global snapshot of cellular response to drugs, as well as to understand drugs’ mechanism of action. Therefore, it is of great interest to analyze this type of transcriptomic profiling data for the identification of pathways responsive to different drugs. However, few computational tools exist for this task. Results: We have developed FacPad, a Bayesian sparse factor model, for the inference of pathways responsive to drug treatments. This model represents biological pathways as latent factors and aims to describe the variation among drug-induced gene expression alternations in terms of a much smaller number of latent factors. We applied this model to the Connectivity Map data set (build 02) and demonstrated that FacPad is able to identify many drug–pathway associations, some of which have been validated in the literature. Although this method was originally designed for the analysis of drug-induced transcriptional alternation data, it can be naturally applied to many other settings beyond polypharmacology. Availability and implementation: The R package ‘FacPad’ is publically available at: http://cran.open-source-solution.org/web/packages/FacPad/ Contact: hongyu.zhao/at/yale.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
OrganicPad: A Tablet PC Based Interactivity Tool for Organic Chemistry

This paper describes a software tool that utilizes the tablet PC's natural user interface to provide interactivity between an instructor and her students in an organic chemistry course. The instructor and the students are equipped with electronic tablets and wireless access to the Internet. The software tool, called OrganicPad, enables an instructor to engage her students in class by sending them problems to solve. The students develop answers to the problems guided by tips and hints provided by the software. All communication is through the web, using the HTTP communication protocol. At any time, the instructor can evaluate student submissions and can quickly understand where students are having difficulty. The instructor can hide students' identities and anonymously use the submissions pedagogically. Finally, the instructor can develop tutorial exercises that students can work on outside of class. We present how we have used OrganicPad and how we plan to extend its functionality in the future.
Distribution of particulate, colloidal, and dissolved mercury in San Francisco Bay estuary. 1. Total mercury

The phase speciation and estuarine behavior of monomethyl mercury (MeHg) were determined in surface waters of the San Francisco Bay estuary in September‐October 2000 (low flow) and March 2001 (high flow). Colloidally associated MeHg was isolated using a cross-flow ultrafiltration technique with a nominal molecular weight cutoff of 1 kDa. Filter-passing MeHg was 57 6 18% of the MeHg in unfiltered water in the fall and 39 6 12% in the spring. Colloidal MeHg averaged 34 6 11% of the filter-passing MeHg in the fall and 56 6 15% in the spring. Significantly higher particle‐water partition coefficients were observed between colloidal and dissolved MeHg (log KC 5 5.6 6 0.3, n 5 21) compared with those between particulate and dissolved MeHg (log KP 5 4.9 6 0.5, n 5 21), which suggests that MeHg is preferentially associated with colloidal material. Strong correlations of MeHg with organic carbon content in the filter-passing, colloidal, and dissolved fractions confirmed the importance of organic matter in the MeHg cycle. Both absolute and relative (as a percentage of Hg) MeHg concentrations were highest in the river water end-member under both flow regimes, which suggests that riverborne MeHg is the major source of MeHg introduced to the estuary. A nonconservative estuarine mixing model suggests that significant amounts of colloidal and dissolved MeHg are removed in the estuary under both flow regimes, standing in marked contrast to Hg, which had a source within the estuary under the low flow condition.
Delivery of Transforming Growth Factor-β2-Perturbing Antibody in a Collagen Vehicle Inhibits Cranial Suture Fusion in Calvarial Organ Culture

Abstract Objective: To determine whether antibody perturbation of Tgf-β, delivered in a collagen gel, could inhibit cranial suture fusion. Design: Attachment and proliferation of osteoblasts cultured on a collagen gel with or without anti-Tgf-β2 antibody were determined by AlamarBlue dye assay and cell morphology by toluidine-blue staining. In rat calvarial organ culture, collagen gel with and without anti-Tgf-β2 antibody was injected subperiosteally over the posterior frontal suture of postnatal day 15 rat calvariae. A quantitative analysis of suture fusion was used to measure suture bridging in histological serial sections at various time points. Results: Attachment and proliferation for cells cultured on collagen gel with anti-Tgf-β2 antibody were similar to collagen gel controls. Although proliferation was lower than on tissue culture plastic, cells treated with anti-Tgf-β2 antibody maintained an osteoblastic morphology. After 7, 10, and 15 days in organ culture, anti-Tgf-β2 antibody treatment caused ...
Feeding Deterrent Effects of Catnip Oil Components Compared with Two Synthetic Amides Against Aedes aegypti

Abstract Recently, catnip, Nepeta cataria L. (Lamiaceae), essential oil has been formulated and marketed as an alternative repellent for protection against biting arthropods by several vendors. We isolated the major active components of catnip oil, E,Z- and Z,E-nepetalactone, and quantitatively measured their antibiting efficacy compared with the repellents N,N-diethyl-3-methylbenzamide (deet) and chiral (1S,2′S)-2-methylpiperidinyl-3-cyclohexene-1-carboxamide (SS220) against the yellowfever mosquito, Aedes aegypti (L.), by using an in vitro assay and human volunteers at 24 nmol compound/cm2 (cloth or skin). Of all compounds tested in an in vitro assay, SS220 ranked as the most effective, whereas catnip oil and the nepetalactone compounds did not differ significantly from each other or from deet. However, in human volunteer bioassays, neither E,Z and Z,E-nepetalactone nor racemic nepetalactone deterred mosquito biting as effectively as SS220 or deet. All compounds differed significantly from the control. ...
Post-diagnosis social networks, and lifestyle and treatment factors in the After Breast Cancer Pooling Project.

Author(s): Kroenke, Candyce H; Michael, Yvonne L; Shu, Xiao-Ou; Poole, Elizabeth M; Kwan, Marilyn L; Nechuta, Sarah; Caan, Bette J; Pierce, John P; Chen, Wendy Y | Abstract: ObjectiveLarger social networks have been associated with better breast cancer survival. To investigate potential mediators, we evaluated associations of social network size and diversity with lifestyle and treatment factors associated with prognosis.MethodsWe included 9331 women from the After Breast Cancer Pooling Project who provided data on social networks within approximately two years following diagnosis. A social network index was derived from information about the presence of a spouse or intimate partner, religious ties, community participation, friendship ties, and numbers of living relatives. Diversity was assessed as variety of ties, independent of size. We used logistic regression to evaluate associations with outcomes and evaluated whether effect estimates differed using meta-analytic techniques.ResultsAssociations were similar across cohorts though analyses of smoking and alcohol included US cohorts only because of low prevalence of these behaviors in the Shanghai cohort. Socially isolated women were more likely to be obese (OR = 1.21, 95% CI:1.03-1.42), have low physical activity (l10 MET-hours/week, OR = 1.55, 95% CI:1.36-1.78), be current smokers (OR = 2.77, 95% CI:2.09-3.68), and have high alcohol intake (≥15 g/d, OR = 1.23, 95% CI:1.00-1.51), compared with socially integrated women. Among node positive cases from three cohorts, socially isolated women were more likely not to receive chemotherapy (OR = 2.10, 95% CI:1.30-3.39); associations differed in a fourth cohort. Other associations (nonsignificant) were consistent with less intensive treatment in socially isolated women. Low social network diversity was independently associated with more adverse lifestyle, but not clinical, factors.ConclusionsSmall, less diverse social networks measured post-diagnosis were associated with more adverse lifestyle factors and less intensive cancer treatment. Copyright © 2016 John Wiley a Sons, Ltd.
On the Distribution of Price Changes at a Bull Auction

T HE results presented here are a small step toward a more scientific th ory of exchange, which will distinguish between auctions, stores, etc., make predictions about actual trading outcomes, not about limits approached after innumerable replays, and recognize that actual outcomes are stochastic realizations. In practice, demand and supply are not known, and we can either generate them by simulation but suffer from artificiality, or study real markets but consider less important performance dimensions. Here we choose the latter alternative and focus on price changes, using data from 43 auctions of registered bulls at Red Bluff, California. Our conclusions can be summarized as follows: If the same person buys, the probability that price will rise more than two bidding increments, and the probability that price will fall more than two increments, both are about .2 if the later lot is equally desirable; the former increases and the latter decreases from .2 if the relative desirability of the later lot increases. If a different person buys, the probability that price will rise more than one increment is about .4 if the later lot is equally desirable and greater than .4 if its desirability is greater. Probabilities that apply given a change in buyers are almost equal to unconditional probabilities since the probability of repeating is small. The final price change has the same conditional distributions as an early price change but a different unconditional distribution, because the probability of repeating is greater. A theory of bidders' behavior consistent with these conclusions will be developed.
Neurobiology of Impulsive Aggression

Human aggression in various and extreme forms often results in injury to self, others, or objects. Aggressive behavior can be differentiated into different types, i.e., defensive versus offensive, adaptive versus maladaptive, and impulsive versus premeditated. Both impulsive and premeditated aggressive behaviors are commonly viewed as pathological. Using DSM-IV intermittent explosive disorder (IED) as a proxy for ‘‘recurrent, problematic aggression,’’ Coccaro et al. (1) reported that nearly 4% of a community sample met criteria for IED at any point in their lives. If so, asmany as 11million people in theUnited States alonemay have a lifetimehistory of recurrent, problematic, aggressive behavior. Since DSM-IV criteria discourage the diagnosis of IED in patients with borderline personality disorder (BPD), this ﬁgure underestimates the level of recurrent, problematic aggression since many, though certainly not all, patients with BPD have histories of problematic aggressive behavior.
Agency, Patiency, and The Good Life: the Passivities Objection to Eudaimonism

Many contemporary eudaimonists emphasize the role of agency in the good life. Mark LeBar, for example, characterizes his own eudaimonist view this way: “It is agentist, not patientist, because it emphasizes that our lives go well in virtue of what we do, rather than what happens, to us or otherwise”. Nicholas Wolterstorff, however, has argued that this prioritizing of agency over patiency is a fatal flaw in eudaimonist accounts of well-being. Eudaimonism must be rejected, Wolterstorff argues, because many life-goods are “passivities” that are out of a person’s hands, including how she is treated by others. In this paper, I defend eudaimonism against this passivities objection. I argue that eudaimonism can maintain its agentist character while also capturing the element of truth in the passivities objection—namely, that human well-being is vulnerable and social. I also argue that eudaimonists should avail themselves of the notion of receptivity to capture important aspects of the good life.
The Optimum Design of Stepped Shafts: A Study in Computational Optimization

Optimum stepped shaft designs are obtained through an application of Pontryagin’s Minimum Principle. Optimum designs are obtained for a given critical speed of specified order. Indexes of Performance to be minimized include mass and rotating inertia. A general problem formulation illustrates how constraints on stress, deflections, and geometric design are taken in account. Numerical solutions are obtained to nonlinear multi-point-boundary-value-problems. A Newton-Raphson algorithm was developed to determine step locations precisely in order to facilitate the convergence of the shooting method used to solve the boundary value problem. Numerical solutions are determined with an assumed critical speed; a Rayleigh quotient calculation is used to verify that the optimum design possesses the assumed value.Copyright © 1982 by ASME
Periprosthetic Infection: Management of Early Postoperative Infection

Deep periprosthetic joint infection (PJI) in the early postoperative period, defined as within the first 6 weeks postoperatively, is among the most dreaded complications following total knee arthroplasty. Diagnosis can be challenging as normal postoperative pain, swelling, and peri-incisional inflammation can cloud normal cues to diagnosis. Based on work from our center, we recommend the use of the serum C-reactive protein (CRP) as a screening test with an optimal threshold of approximately 100 mg/L (normal <10 mg/L); a value above or near this threshold should prompt an aspiration of the joint. Aspirated fluid should be sent for a synovial fluid white blood cell (WBC) count and differential, with optimal cutoff values during the first 6 weeks postoperatively of approximately 10,000 WBC/μ[mu]L and 90 %, respectively. In cases where the clinician is still unsure if a deep infection is present, synovial fluid cultures can be obtained and monitored, with the final decision on the treatment plan based on their results.
Performance Crime and Justice

Due to enhanced audience participation and involvement in content creation and distribution, crime and justice has changed. This change came about with the emergence of new digital social media and...
Surgical Anatomy of the Eyelids

The key to precision surgery of the eyelids and orbital area is a complete knowledge of surgical anatomy. The author reviews the form and function of individual anatomic constructs as they pertain to surgery.
Gamma-interferon modulates von Willebrand factor release by cultured human endothelial cells.

Endothelial cells (EC) synthesize and secrete von Willebrand factor (vWF), a multimeric glycoprotein required for normal hemostasis. Within human endothelial cells. vWF multimers of extremely high molecular weight are stored in rod-shaped organelles known as Weibel-Palade bodies. Inflammatory mediators, such as interleukin-1, induce in vitro a variety of procoagulant responses by EC, including the secretion of stored vWF. We postulated that other inflammatory mediators might act to balance this procoagulant reaction, thereby assisting in the maintainence of blood fluidity during immune activation. Both γ-interferon (γ-IFN) and tumor necrosis factor (TNF) were found to act independently and cooperatively to depress the stimulated release of vWF from EC. Analysis of stored vWF in either γ-IFN and/or TNF-treated EC demonstrated a loss of high molecular weight multimers while immunofluorescent studies documented a loss of visible Weibel-Palade bodies. This suggests that γ-IFN and TNF interfere with normal vWF storage. γ-IFN acted in a dose-, time-, and RNA-dependent fashion, and its inhibition of vWF release was reversible with time. No effect of γ-IFN on EC was noted when anti-serum to γ-IFN was added. Unlike γ-IFN, α-interferon did not effect EC vWF. Therefore, γ-IFN and TNF may be important in decreasing vWF release during inflammatory or immunologic episodes. This is a US government work. There are no restrictions on its use.
Picosecond Resonance Raman Spectroscopy: The Initial Photolytic Event in Rhodopsin and Isorhodopsin

We report here the first picosecond resonance Raman studies of visual pigments. Flowing samples of rhodopsin and isorhodopsin are photolysed and simultaneously probed by 30 psec pulses at 532 nm from a low-energy, high- repetition-rate doubled Nd:YAG laser. At intensities sufficient to cause moderate photoalteration during each pulse, both molecules exhibit Raman bands in the 850 to 940 cm−1 region that are distinctive to bathorhodopsin in a twisted all-trans configuration. The presence of these lines in our resonance Raman spectra indicates that the photoisomerization of retinal to its al1-trans form must be essentially complete within picoseconds after the absorption of a photon.
Sleep Duration and Neurocognitive Function in the Hispanic Community Health Study/Study of Latinos.

Study objectives To evaluate the association between sleep duration and neurocognitive function in a representative sample of middle-aged to older Hispanic/Latino adults in the US. We tested the hypothesis that sleep duration has a nonlinear, inverted U-shaped association with neurocognitive function. Methods We performed a cross-sectional analysis from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) participants ages 45-74 years (n = 8,676). HCHS/SOL is a community-based cohort from four US urban areas sampled using a probability design from 2008-2011. Self-reported sleep duration was calculated as a weighted average of the difference between habitual wake and bedtimes assessed by separate questions for weekdays and weekends. Neurocognitive function was measured with standardized scores for Word (Phonemic) Fluency (WF), Brief-Spanish English Verbal learning test (B-SEVLT), and Digit Symbol Substitution (DSS) tests. Results The mean age was 56.5 years; 55% were women; and 40.4% had less than high school education. Average sleep duration was 7.8 ± 1.7 hours. There was an inverted U-shaped association with sleep duration and WF, B-SEVLT sum, and the DSS, with no association with B-SEVLT delayed-recall. Participants with intermediate sleep duration had the best neurocognitive function, while long sleepers had worse neurocognitive function adjusting for demographic, behavioral, and medical factors, daytime sleepiness, and use of sleep medications. Conclusions Sleep duration had curvilinear inverted U-shaped associations with neurocognitive function, with worse scores among participants with longer sleep duration. These findings may provide a framework to further examine sleep duration in the prevention and treatment of neurocognitive disorders.
Microwave imaging of artificially induced magnetic anomalies: a feasibility study

The demand of effective, low cost and portable diagnostic tools for large scale preventive screening has addressed a huge interest in microwave imaging techniques. Moreover, the recently demonstrated capability of selectively targeting magnetic nanoparticles opens the way for new imaging strategies, that exploit nanoparticles as contrast agent. As a matter of fact, due to the nonmagnetic nature of human tissues, this artificially induced magnetic contrast can be exploited to enhance the response of small and hardly detectable anomalies. In this respect, two microwave imaging strategies, devoted to characterize magnetic targets embedded into an electric scenario, are proposed and a preliminary assessment of their reconstruction capabilities is given.
Case study: A tool centric approach for fault avoidance in microchip designs.

Achieving reliability in fault tolerant systems requires both avoidance and redundancy. This study focuses on avoidance as it pertains to the design of microchips. The lifecycle of a microchip is centered on the design of every block that makes up the hierarchy of the design. Early in the lifecycle the emphasis is on obtaining clean and fault free blocks for every CAD (Computer Aided Design) tool that the block is subjected to. A block is either a schematic or the artwork of a given functional circuit. As a block evolves, a regression of already released CAD tools is run to obtain predetermined levels of quality. Without running these regression suites, developers risk delaying the appearances of faults; which in the field of microchip development can prove extremely costly, especially when entering the manufacturing stages where the costs of making masks and test chips can be prohibitive. This study uses traditional data mining techniques to follow the evolution of a number of legacy blocks in a microchip and track the number of failures encountered per block and per tool over a period of time.
Recent trends in U.S. flood risk

Flooding is projected to become more frequent as warming temperatures amplify the atmosphere’s water holding capacity and increase the occurrence of extreme precipitation events. However, there is still little evidence of regional changes in flood risk across the USA. Here, we present a novel approach assessing the trends in inundation frequency above the National Weather Service’s four flood level categories in 2,042 catchments. Results reveal stark regional patterns of changing flood risk that are broadly consistent above the four flood categories. We show that these patterns are dependent on the overall wetness and potential water storage, with fundamental implications for water resources management, agriculture, insurance, navigation, ecology, and populations living in flood-affected areas. Our findings may assist in a better communication of changing flood patterns to a wider audience compared with the more traditional approach of stating trends in terms of discharge magnitudes and frequencies.
The jumping apparatus of flea beetles (Alticinae) — The metafemoral spring

Flea Beetles (Alticinae) is the largest subfamily of the Chrysomelidae with approximately 560 genera and 8000 species described. The scientific name of the type genus, Altica Fabricius 1775, is derived from the Greek ‘haltikos’ which means good at jumping. Although the Latinization of the original Greek name by Fabricius (1775) may not be entirely correct, following the rules of the International Code of Zoological Nomenclature the correct spelling for the type genus is Altica not Haltica (thus. Alticinae not Halticinae) (see detailed discussion in Furth 1981). The common name, Flea Beetle, is also basically derived (in several languages) from their ability to jump in an analagous fashion to the true fleas (Siphonaptera). Flea Beetles include, with the possible exception of some species of fleas (Rothschild et al 1975), the best jumpers among all insects and, indeed, among all living creatures. Most Alticinae use this jumping ability voluntarily in a very effective manner to avoid potential predators or entomologists. Lindroth (1971) observed that birds are not able to catch Flea Beetles that are on foliage because of the beetle’s effective escape by jumping. Jumping also serves as an efficient method of locomotion, especially for flightless populations. Flea Beetles can leap long distances relative to their body size (length). For example, a 7 mm long Blepharida sacra (Weise) has been measured to jump up to 70 cm or about 100 times its body length!
APT2 Inhibition Restores Scribble Localization and S-Palmitoylation in Snail-Transformed Cells.

The multidomain scaffolding protein Scribble (Scrib) organizes key signaling complexes to specify basolateral cell polarity and suppress aberrant growth. In many human cancers, genetically normal Scrib mislocalizes from cell-cell junctions to the cytosol, correlating with enhanced growth signaling and malignancy. Here we confirm that expression of the epithelial-to-mesenchymal transcription factor (EMT-TF) Snail in benign epithelial cells leads to Scrib displacement from the plasma membrane, mimicking the mislocalization observed in aggressive cancers. Upon further examination, Snail promotes a transcriptional program that targets genes in the palmitoylation cycle, repressing many protein acyl transferases and elevating expression and activity of protein acyl thioesterase 2 (APT2). APT2 isoform-selective inhibition or knockdown rescued Scrib membrane localization and palmitoylation while attenuating MEK activation. Overall, inhibiting APT2 restores balance to the Scrib palmitoylation cycle, promoting membrane re-localization and growth attenuation. These findings emphasize the importance of S-palmitoylation as a post-translational gatekeeper of cell polarity-mediated tumor suppression.
The MicroRNA-21 signaling pathway is involved in prorenin receptor (PRR) -induced VEGF expression in ARPE-19 cells under a hyperglycemic condition.

Purpose MicroRNAs (miRNAs/miRs) are involved in a large number of biological functions and diseases, such as cancer, cardiovascular diseases, and diabetes. MiR-21 has been reported to target Sprouty homolog 1 (SPRY1), SMAD7, and PTEN. In this study, we examined the underlying role of miR-21 in the regulation of prorenin receptor (PRR)-mediated induction of vascular endothelial growth factor (VEGF) expression via targeting SMAD7, SPRY1, and PTEN in a hyperglycemic condition. Methods PRR-mediated induction of VEGF under a hyperglycemic condition (high glucose, 33mM) was studied by treating ARPE-19 cells with perindopril (10 µmol/l), which inhibits angiotensin II-mediated signaling. ARPE-19 cells exposed to normal glucose (NG, 5.5 mM) were considered as the control. To examine the role of miR-21 in the regulation of SPRY1, SMAD7, PTEN, and VEGF, ARPE-19 cells cultured in NG or high glucose were transfected with scramble negative control (Scr), a miR-21 mimic, or a miR-21 antagomir. To investigate the role of PRR and the small GTP-binding protein RAC1 in the regulation of miR-21, the expression of PRR and RAC1 was silenced by transfecting ARPE-19 cells with their corresponding siRNAs. Results Compared with the NG control, high glucose significantly induced the expression of PRR, VEGF, VEGFR2, and miR-21 but significantly suppressed the expression of SPRY1, SMAD7, and PTEN at the transcript and protein levels. In contrast, silencing the expression of PRR significantly abolished the high glucose-induced expression of VEGF, VEGFR2, and miR-21. Knockdown of RAC1 significantly attenuated the high glucose-induced expression of LOX, CTGF, and miR-21, suggesting that PRR and RAC1 are involved in the CTGF/LOX-mediated regulation of miR-21. Furthermore, high glucose dramatically increased the levels of pERK (p44), hypoxia-inducible factor (HIF-1α), and VEGF. However, this effect was antagonized by the miR-21 antagomir, indicative of the involvement of high glucose-induced miR-21 in the regulation of VEGF through ERK signaling. Conclusions Our findings, for the first time, showed that the pleiotropic action of miR-21 induced the expression of pERK, HIF-1α, and VEGF in the high glucose condition by simultaneously targeting SPRY1, SMAD7, and PTEN in ARPE-19 cells. Therefore, miR-21 may serve as a potential therapeutic target for diabetes-induced retinal pathology.
Reliability and heat transfer performance of a miniature high-temperature thermosyphon-based thermal valve

Abstract Latent heat thermal energy storage systems have the advantages of near isothermal heat release and high energy density compared to sensible heat, generally resulting in higher power block efficiencies. Until now, there has been no highly effective and reliable method to passively extract that stored latent energy. Most modern attempts rely on external power supplied to a pump to move viscous heat transfer fluids from the phase change material (PCM) to the power block. In this work, the problem of latent heat dispatchability has been addressed with a redesigned thermosyphon geometry that can act as a “thermal valve” capable of passively and efficiently controlling the release of heat from a thermal reservoir. A bench-scale prototype with a stainless steel casing and sodium working fluid was designed and tested to be reliable for more than fifty “on/off” cycles at an operating temperature of 600 °C. The measured thermal resistances in the “on” and “off” states were 0.0395 K/W and 11.0 K/W respectively. This device demonstrated efficient, fast, reliable, and passive heat extraction from a PCM and may have application to other fields and industries using thermal processing.
Recovery of Aquaculture Treatment Constructed Wetlands Function After Prolonged Flood Inundation Events in South Texas

Constructed wetlands have been evaluated for many years as a means of low cost water treatment; however studies of performance evaluation and recovery after system upsets are not often reported. The Loma Alta Shrimp Aquaculture Facility (LASAF), located on the El Sauz Ranch in South Texas employs an innovative re-circulating aquaculture-wetland system where pond effluent is filtered through a constructed wetland and then re-circulated back into the shrimp production ponds. The goals of this study were to evaluate the relative water quality treatment ability for several wetland areas and evaluate the recovery of nutrient removal activity after major flooding damage and inundation in 2002. The practical implications of these results were incorporated into the design of a new constructed wetland that treats pond effluent in a sequential manner based on water depth. Despite variable loadings from aquaculture pond discharges, a steady state operation developed prior to harvest operations can be used to evaluate the nutrient removal performance of the wetlands, which can be determined through a change point statistical technique. The flooding events caused by storms and operator management requirements in 2002 resulted in diminished vegetation and wetland performance which was able to be restored in 2003, with the growth of primarily submerged vegetation. The smaller (8 ha) Phase III sequential basin design appeared to be able to effectively treat aquaculture effluent as well as the larger (19 ha) dual system Phase I and II wetlands. Close attention to water depth and recirculation rate management suggest a linkage to optimal performance for water treatment targets. It is suggested that techniques such as change-point analysis can help confirm as to when the retention time significantly changes in a dynamic wetland system as a result of changing water depth and provide insight as to the nature of its hydraulic efficiency.
Finitude as Clue to Embodiment

The reflections in the following paper are centered around what I take to be a central motivation in the work of Edmund Husserl, namely, the desire to uncover and clarify a transcendental basis for human communication. My thesis is that the study of the finite character of consciousness in the thought of Husserl can lead toward an understanding of both consciousness and of body which is helpful in creating the possibility for a genuine and grounded communication. In order to pursue this thesis I wish to consider three questions. The first question is whether and in what ways transcendental consciousness in Husserl can be properly thought of as finite consciousness? Second, how does the finitude of consciousness signal embodiment? Third, what is the meaning of body such that it can be the embodiment of transcendental consciousness? All three questions are posed in the framework of phenomenology understood as a practical task for transcendental consciousness rather than as a purely theoretical undertaking.
Prevalence and Clinical Correlations of MLL Gene Rearrangements in AML-M4/5

Rearrangements of the human trithorax gene (MLL, HRX, Htrx-1, All-1) were studied by Southern blotting in blast cells stored at presentation from 65 adults with de novo acute myelomonocytic (AML-M4) and acute monocytic leukemia (AML-M5). MLL rearrangements were demonstrated in 15 (23%) cases, including eight patients in whom karyotype analysis had failed to detect abnormalities of chromosome band 11q23. The patients with MLL rearrangements did not differ significantly from those with germline configurations in terms of the sex and age of the patients, the presence of lymphadenopathy, hepatosplenomegaly, or central nervous system involvement, and the absolute blast count at diagnosis. Kaplan-Meier analysis of the treated patients demonstrated no difference in survival for patients with MLL rearrangements compared with those without rearrangements. Therefore, in contrast to infantile acute leukemia, in adults with AML-M4 and AML-M5, MLL rearrangements do not identify a subgroup of patients with different clinical features or prognosis.
Computational Quantum Chemistry — Introductory Remarks

Methods currently used in quantitative molecular orbital computations are reviewed. Limitations of some of the simple, widely used techniques are pointed out.
Reconfigurable Anticounterfeiting Coatings Enabled by Macroporous Shape Memory Polymers

Here, we report a new type of reconfigurable anticounterfeiting coating enabled by integrating the scientific principles of photonic crystal and shape memory polymer (SMP). The autonomous infusion of uncured oligomers in a polydimethylsiloxane (PDMS) stamp into a templated macroporous SMP photonic crystal coating, which was confirmed by quantitative X-ray photoelectron spectroscopy analysis, can program an iridescent pattern on the transparent SMP membrane with deformed macropores. By manipulation of the unconventional all-room-temperature shape memory effects exhibited by the shape memory copolymer comprising polyethylene glycol diacrylate and ethoxylated trimethylolpropane triacrylate, the iridescent pattern can be easily and instantaneously concealed and revealed by immersing in common household liquids (e.g., ethanol and water). Systematic experiments and theoretical simulations using scanning electron microscopy, atomic force microscopy, optical spectroscopy, scalar wave approximation modeling, and c...
Is It Time for a Patient-Centered Quality Measure of Asthma Control?

Quality measures play a prominent role in the US health care system. They are used to monitor and report performance across health plans, providers, and health systems and are a foundational element of value-based payment. Measuring the quality of asthma care has been challenging because of a lack of reliable data to assess clinical processes and track patient-specific outcomes. Existing asthma Healthcare Effectiveness Data and Information Set measures rely on administrative claims–derived data on dispensed medications. These are proxy measures of appropriate prescribing but are not reflective of comprehensive asthma care. The increase in the volume and specificity of longitudinal clinical data in electronic health records, movement toward electronic quality measures, and advances in electronic clinical data systems enable the development of more meaningful measures. A patient-reported measure of asthma control would incorporate key clinical indicators such as a validated age- and culturally appropriate test, and would reflect the combined outcome of medical management, self-management education, reduction of environmental exposures, and appropriate support services. Although there is a current quality measure that includes a test of asthma control (the Optimal Asthma Control Measure), work is needed to address questions about usability, patient literacy, and the influence of setting on self-reported scores. Comprehensive reliability and validity testing of both clinical data and stratification across risk groups will be needed to determine whether a measure based on standardized assessments of asthma control indeed promote improved clinical outcomes.
Development of a Cross-Reactive Monoclonal Antibody for Detecting the Tumor Stroma

Here, we document the discovery of a monoclonal antibody that selectively binds to both human and murine fibroblast activation protein alpha (FAP), a serine protease that is overexpressed on cancer-associated fibroblasts (CAFs), making it an attractive therapeutic target for the aiding and abetting tumor microenvironment. The lead antibody, B12, was identified from a naive murine single-chain variable fragment antibody phage display library screened against recombinant human FAP on magnetic beads. The heavy and light chains of B12 were cloned into full-length human immunoglobulin 1 (IgG) vectors and expressed as a chimeric monoclonal antibody (B12 IgG). We engineered a drug-resistant prostate cancer cell line, CWR-R1-EnzR, to express human FAP for antibody characterization and validation (R1-EnzRFAP). B12 IgG selectively bound to the R1-EnzRFAP cells by flow cytometry and was internalized in vitro by confocal microscopy. B12 IgG was further evaluated as a near-infrared (NIR) optical imaging probe in R1-En...
Confidence interval, prediction interval and tolerance limits for a two-parameter Rayleigh distribution

ABSTRACTThe problems of interval estimating the parameters and the mean of a two-parameter Rayleigh distribution are considered. We propose pivotal-based methods for constructing confidence interva...
Listener impressions of foreigner-directed speech: A systematic review

Abstract Non-native speakers of a particular language face communicative challenges when interacting with native speakers in everyday life. A strategy frequently employed by native speakers to ensure smooth communication is speech accommodation in the form of foreigner-directed speech. Most of the research on foreigner-directed speech has focused on acoustic parameters, but few studies have examined non-native listener perceptions. This systematic review evaluates the published evidence for listener impressions of foreigner-directed speech. A systematic search of six databases and key journals identified 3,581 articles, eight of which met the inclusion criteria. Data were independently extracted and reviewed by two authors. The results show that by and large, native speakers perceived foreigner-directed speech negatively. Only two out of eight articles specifically asked foreigners about the listener impressions of foreigner-directed speech, and the results of these studies were not conclusive. Our findings demonstrate a need for research to further examine the nature of this phenomenon, particularly by focusing on non-native speaker's impressions of foreigner-directed speech.
Structure of the decorated ciliary doublet microtubule

The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility require a radially arranged set of doublet microtubules, each decorated in repeating patterns with non-tubulin components. We use single-particle cryo-electron microscopy to visualize and build an atomic model of the repeating structure of a native axonemal doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). The structure demonstrates how these proteins establish the unique architecture of doublet microtubules, maintain coherent periodicities along the axoneme, and stabilize the microtubules against the repeated mechanical stress induced by ciliary motility. Our work elucidates the architectural principles that underpin the assembly of this large, repetitive eukaryotic structure and provides a molecular basis for understanding the etiology of human ciliopathies.
Biallelic correction of sickle cell disease-derived induced pluripotent stem cells (iPSCs) confirmed at the protein level through serum-free iPS-sac/erythroid differentiation

New technologies of induced pluripotent stem cells (iPSCs) and genome editing have emerged, allowing for the development of autologous transfusion therapies. We previously demonstrated definitive β-globin production from human embryonic stem cell (hESC)-derived erythroid cell generation via hemangioblast-like ES-sacs. In this study, we demonstrated normal β-globin protein production from biallelic corrected sickle cell disease (SCD) iPSCs. We optimized our ES/iPS-sac method for feeder cell-free hESC maintenance followed by serum-free ES-sac generation, which is preferred for electroporation-based genome editing. Surprisingly, the optimized protocol improved yields of ES-sacs (25.9-fold), hematopoietic-like spherical cells (14.8-fold), and erythroid cells (5.8-fold), compared with our standard ES-sac generation. We performed viral vector-free gene correction in SCD iPSCs, resulting in one clone with monoallelic and one clone with biallelic correction, and using this serum-free iPS-sac culture, corrected iPSC-generated erythroid cells with normal β-globin, confirmed at DNA and protein levels. Our serum-free ES/iPS-sac protocol with gene correction will be useful to develop regenerative transfusion therapies for SCD.
Mycobacterium tuberculosis Sulfolipid-1 Activates Nociceptive Neurons and Induces Cough

Summary Pulmonary tuberculosis, a disease caused by Mycobacterium tuberculosis (Mtb), manifests with a persistent cough as both a primary symptom and mechanism of transmission. The cough reflex can be triggered by nociceptive neurons innervating the lungs, and some bacteria produce neuron-targeting molecules. However, how pulmonary Mtb infection causes cough remains undefined, and whether Mtb produces a neuron-activating, cough-inducing molecule is unknown. Here, we show that an Mtb organic extract activates nociceptive neurons in vitro and identify the Mtb glycolipid sulfolipid-1 (SL-1) as the nociceptive molecule. Mtb organic extracts from mutants lacking SL-1 synthesis cannot activate neurons in vitro or induce cough in a guinea pig model. Finally, Mtb-infected guinea pigs cough in a manner dependent on SL-1 synthesis. Thus, we demonstrate a heretofore unknown molecular mechanism for cough induction by a virulent human pathogen via its production of a complex lipid.
Exposure of Mycobacterium abscessus to Environmental Stress and Clinically Used Antibiotics Reveals Common Proteome Response among Pathogenic Mycobacteria

Mycobacterium abscessus subsp. abscessus (MAB) is a clinically important nontuberculous mycobacterium (NTM) causing pulmonary infection in patients such as cystic fibrosis and bronchiectasis. MAB is naturally resistant to the majority of available antibiotics. In attempts to identify the fundamental response of MAB to aerobic, anaerobic, and biofilm conditions (as it is encountered in patients) and during exposure to antibiotics, we studied bacterial proteome using tandem mass tag mass spectrometry sequencing. Numerous de novo synthesized proteins belonging to diverse metabolic pathways were found in anaerobic and biofilm conditions, including glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, oxidative phosphorylation, nitrogen metabolism, and glyoxylate and dicarboxylate metabolism. Upon exposure to amikacin and linezolid under stress environments, MAB displayed metabolic enrichment for glycerophospholipid metabolism and oxidative phosphorylation. By comparing proteomes of two significant NTMs, MAB and M. avium subsp. hominissuis, we found highly synthesized shared enzymes of oxidative phosphorylation, TCA cycle, glycolysis/gluconeogenesis, glyoxylate/dicarboxylate, nitrogen metabolism, peptidoglycan biosynthesis, and glycerophospholipid/glycerolipid metabolism. The activation of peptidoglycan and fatty acid biosynthesis pathways indicates the attempt of bacteria to modify the cell wall, influencing the susceptibility to antibiotics. This study establishes global changes in the synthesis of enzymes promoting the metabolic shift and enhancing the pathogen resistance to antibiotics within different environments.
Decreased BIM expression in BCL2-negative follicular lymphoma: a potential mechanism for resistance to apoptosis

Summary Follicular lymphoma (FL) is characterized by t(14; 18)(q32; q21), leading to overexpression of the antiapoptotic molecule BCL2; however, a subset of FLs lack BCL2 rearrangement and BCL2 expression as analyzed by immunohistochemistry (IHC). In this study, we evaluated expression of antiapoptotic (MCL1 and BCL-XL) and proapoptotic proteins (BIM) by IHC in both BCL2(−) and BCL2(+) FLs. FLs diagnosed between 2009 and 2019 were reviewed to identify BCL2(−) cases by IHC (assessed by clone 124). Immunohistochemical analyses for BCL2 (EP36), MCL1, BIM, BCL-XL, and Ki-67 were performed on tissue microarrays or whole slides. BCL2 (EP36) was interpreted as positive (≥10%) or negative (
Cataloging Children’s Materials: Issues and Solutions

Library catalogs remain challenging for children to use, especially because children have difficulty with multi-step processes, have less semantic and technical knowledge, and often search differen...
Learning by Playing Init2Winit: How Alignment Knowledge Increases Educational Aspirations and College Plans in High School

Init2Winit, a gamified mobile application designed to increase students’ alignment knowledge between college, career, and salary expectations has been beta-tested in midwestern urban and rural U.S....
Whiteness, Nationalism, and the U.S. Constitution: Constructing the White Nation through Legal Discourse

Overt expressions of White nationalism and White supremacy are once again mainstream in U.S. politics. Social movements advancing racist and nativist policies often do so through the language of co...
Printing Parameters of Fused Filament Fabrication Affect Key Properties of Four-Dimensional Printed Shape-Memory Polymers

Extrusion-based (fused filament fabrication) three-dimensional (3D) printing of shape-memory polymers (SMPs) has the potential to rapidly produce highly customized smart-material parts. Yet, the ef...
Validation of a lumped-mass mooring line model with DeepCwind semisubmersible model test data

Abstract This paper introduces a lumped-mass mooring line model and validates it against scale-model floating offshore wind turbine test data. The mooring model incorporates axial elasticity, hydrodynamic loading via Morison׳s equation, and bottom contact. It neglects bending and torsional stiffnesses for the sake of computation speed. A coupling with the floating wind turbine simulator FAST allows simulation of complete floating wind turbine systems including mooring dynamics. The DeepCwind semisubmersible floating wind turbine design was simulated and the results compared with data from previously-published 1:50-scale experiments. Uncoupled simulations in which the fairlead motions are prescribed according to the test data show very good agreement in fairlead tensions; predicted fatigue and extreme loads match the test data to within 10% and snap load conditions are predicted consistently. When the mooring model is coupled with FAST to simulate the entire floating wind turbine system, the fairlead tensions and the platform heave response are underpredicted relative to the test data, suggesting a limitation of the platform hydrodynamic model. In all cases, using a quasi-static mooring model significantly underpredicts the mooring loads, especially for fatigue. In general, the results suggest that the lumped-mass mooring model is suitable for predicting mooring line loads of the DeepCwind semisubmersible.