cssi/SciSciGPT-SciSciNet huggingface dataset:
Agonist-dependent phosphorylation of the formyl peptide receptor is regulated by the membrane proximal region of the cytoplasmic tail.

Formyl peptide receptor (FPR) is a chemoattractant G protein-coupled receptor (GPCR) involved in the innate immune response against bacteria. Receptor activation is terminated by receptor phosphorylation of two serine- and threonine-rich regions located in the distal half of the cytoplasmic tail. In this study we show that introduction of an amino acid with a bulky side chain (leucine or glutamine) adjacent to a single leucine, L320, in the membrane-proximal half of the cytoplasmic tail, significantly enhanced receptor phosphorylation, β-arrestin1/2 translocation, and receptor endocytosis, without affecting Gi-mediated ERK1/2 activation and release of intracellular calcium. In addition, the point mutations resulted in diminished susceptibility to trypsin, suggesting a conformation different from that of wild type FPR. Alignment of the FPR sequence with the rhodopsin sequence showed that L320 resides immediately C-terminal of an amphipathic region that in rhodopsin forms helix 8. Deletion of seven amino acids (Δ309–315) from the predicted helix 8 of FPR (G307–S319) caused reduced cell signaling as well as defects in receptor phosphorylation, β-arrestin1/2 translocation and endocytosis. Thus, the amino acid content in the N-terminal half of the cytoplasmic tail influences the structure and desensitization of FPR.
Bounds for truncation error in sampling expansions of finite energy band-limited signals (Corresp.)

An upper bound is established for the magnitude of the truncation error incurred when a real-valued finite energy signal that is bandlimited to -\pi r \leq \omega \leq \pi r, 0 , is approximated by 2N + 1 terms from its Shannon sampling series expansion with the samples taken at the integer points. The derived bound is an improvement on known results.
Design and fabrication of self-assembled thin films

Students experience the entire process of designing, fabricating and testing thin films during their capstone course. The films are fabricated by the ionic-self assembled monolayer (ISAM) technique, which is suited to a short class and is relatively rapid, inexpensive and environmentally friendly. The materials used are polymers, nanoparticles, and small organic molecules that, in various combinations, can create films with nanometer thickness and with specific properties. These films have various potential applications such as pH optical sensors or antibacterial coatings. This type of project offers students an opportunity to go beyond the standard lecture and labs and to experience firsthand the design and fabrication processes. They learn new techniques and procedures, as well as familiarize themselves with new instruments and optical equipment. For example, students learn how to characterize the films by using UV-Vis-NIR spectrophotometry and in the process learn how the instruments operate. This work compliments a previous exercise that we introduced where students use MATHCAD to numerically model the transmission and reflection of light from thin films.
Pseudo Self‐Consistent Estimation of a Copula Model with Informative Censoring

. We consider the case where a terminal event censors a non-terminal event, but not vice versa. When the events are dependent, estimation of the distribution of the non-terminal event is a competing risks problem, while estimation of the distribution of the terminal event is not. The dependence structure of the event times is formulated with the gamma frailty copula on the upper wedge, with the marginal distributions unspecified. With a consistent estimator of the association parameter, pseudo self-consistency equations are derived and adapted to the semiparametric model. Existence, uniform consistency and weak convergence of the new estimator for the marginal distribution of the non-terminal event is established using theories of empirical processes, U-statistics and Z-estimation. The potential practical utility of the methodology is illustrated with simulated and real data sets.
Development, Anatomy, and Physiology of the Larynx

The human larynx, located at the crossroads of the upper digestive tract and tracheobronchial tree, has evolved structural and functional components to safely facilitate respiration, swallowing, airway protection, and vocalization. The larynx, trachea, and lungs begin formation at 28 days of life. Development continues into the neonatal period and through puberty, with cartilage maturation and larynx and hyoid decent. Detailed knowledge of the laryngeal cartilage skeleton and neurovascular structures is vital for both the head and neck surgeon and speech pathologist. A complex set of afferent and efferent pathways govern neuromuscular physiology, which dictate basic laryngeal functions through a delicate coordination of precisely organized brainstem reflexes. Significant work has been invested into understanding the unique and phylogenetically advanced protective, respiratory, and phonatory reflexes of the human larynx.
DATED ROCK PAINTINGS AT RED CLIFFS, ARIZONA

ABSTRACTThis article presents radiocarbon dates for painted motifs at Red Cliffs, west of Sedona in the northeastern corner of Yavapai County, Arizona. All rock painting shields at the Red Cliffs sites have usually been attributed to the Sinagua. Black pigment from one shield motif and an overlying white dot on another motif yielded uncalibrated radiocarbon dates of 1080 and 550 years B.P., respectively. The black pigment sample dates to a time when the region was extensively used. Assuming that the two shields were painted contemporaneously, the age of the white dot sample suggests that a later cultural group altered Sinagua paintings at Red Cliffs after the Sinagua abandoned the region.
Human Red Cell Acid Phosphatase (ACP1): Genetic Typing at the DNA Level

Human red cell acid phosphatase (ACP1) is one of the best known of the forensically useful genetic polymorphisms. Two common alleles — ACP1*A and ACP1*B — are found in all major population groups. A third allele — ACP1*C — is common in Caucasians and a fourth — ACP1*R — is common in Blacks of African origin. A number of rare alleles have also been noted.
Long-Term Bone Marrow Suppression During Postoperative Chemotherapy in Rectal Cancer Patients After Preoperative Chemoradiation Therapy

Purpose/Objective(s) To quantify ensuing bone marrow (BM) suppression during postoperative chemotherapy resulting from preoperative chemoradiation (CRT) therapy for rectal cancer. Methods and Materials We retrospectively evaluated 35 patients treated with preoperative CRT followed by postoperative 5-Fluorouracil and oxaliplatin (OxF) chemotherapy for locally advanced rectal cancer. The pelvic bone marrow (PBM) was divided into ilium (IBM), lower pelvis (LPBM), and lumbosacrum (LSBM). Dose volume histograms (DVH) measured the mean doses and percentage of BM volume receiving between 5-40 Gy (i.e.: PBM-V5, LPBM-V5). The Wilcoxon signed rank tests evaluated the differences in absolute hematologic nadirs during neoadjuvant vs. adjuvant treatment. Logistic regressions evaluated the association between dosimetric parameters and ≥ grade 3 hematologic toxicity (HT3) and hematologic event (HE) defined as ≥ grade 2 HT and a dose reduction in OxF. Receiver Operator Characteristic (ROC) curves were constructed to determine optimal threshold values leading to HT3. Results During OxF chemotherapy, 40.0% (n=14) and 48% (n=17) of rectal cancer patients experienced HT3 and HE, respectively. On multivariable logistic regression, increasing pelvic mean dose (PMD) and lower pelvis mean dose (LPMD) along with increasing PBM-V (25-40), LPBM-V25, and LPBM-V40 were significantly associated with HT3 and/or HE during postoperative chemotherapy. Exceeding ≥36.6 Gy to the PMD and ≥32.6 Gy to the LPMD strongly correlated with causing HT3 during postoperative chemotherapy. Conclusions Neoadjuvant RT for rectal cancer has lasting effects on the pelvic BM, which are demonstrable during adjuvant OxF. Sparing of the BM during preoperative CRT can aid in reducing significant hematologic adverse events and aid in tolerance of postoperative chemotherapy.
Thermal effects of underground nuclear explosions.

Most of the energy of an underground nuclear explosion is deposited near the site of the explosion as heat. The heat remains localized for a long time because of the low thermal conductivity of rock. This heat plays a role in Plowshare applications by generating steam and, in the case of carbonate-bearing rocks, CO2. Applications to stimulate natural-gas production are complicated by the production of tritiated steam and CO2. The temperature of the rubble in the chimney fixes the steam partial pressure in the produced gas. Increasing chimney temperature, and thus steam pressure, is expected with increasing depth of explosion and also with decreasing spacing between detonations, in the case of multiple explosions. Laboratory experiments on shales that are mostly fine grain mixtures of quartz and carbonate show that CO2 is released at temperatures as low as 500°C, even under a CO2 pressure of 50 atm.In the future, the release of large amounts of CO2 may be used to advantage in secondary oil recovery and in ...
Leuconectria clusiae gen. nov. and its anamorph Gliocephalotrichium bulbilium with notes on Pseudonectria.

A new genus in the Hypocreales, Leuconectria, is described for Pseudonectria clusiae based on its unique perithecial wall anatomy and the anamorph Gliocephalotrichum bulbilium produced from single ...
Parental Marital Status and Self-Esteem of Boys and Girls

The purpose was to investigate the effects of parental marital status and sex on the self-esteem of children by assessing differences on mean self-esteem between boys and girls of divorced families as compared to boys and girls of intact families. The mean score on self-esteem of 54 children (27 boys, 27 girls) from divorced families was compared to that for 54 children (27 boys, 27 girls) from intact families using the Culture-free Self-esteem Inventory. Using factorial analysis, a statistically significant difference was found for sex but not for type of family or its interaction with sex.
Structural and Perceptual Influences on Intraindustry Stratification

This paper argues (1) that intraindustry stratification is a function of both structural parameters and top managers' responses to perceptions of their environments, and (2) that the notion of strategic groups can meaningfully extend to corporate and collective levels of strategy. We explored relevant research questions using survey data from 114 of the largest firms in the financial services industry. The results suggest that variables measuring managerial perceptions are useful predictors of intraindustry stratification and that the strength of the predictor variables differs across levels of strategies. Supragroupings of firms with similar configurations of strategies across levels also emerged.
EFFECTIVE DIFFERENCE IN INFLUENCE OF RELATIVE SIZE ON PERCEIVED RELATIVE DISTANCE.

Variations in relative perceived distance as a function of relative visual angle were studied. Variations in angular ratios which left the absolute size difference constant produced variations in relative distance. Variations in absolute difference without accompanying variations of angular ratios were ineffective.
Extensive subdural spinal enhancement mimicking leptomeningeal disease in a young child with posterior fossa tumour following lumbar puncture and surgery.

A 4-year-old girl presented to the emergency room with a 2-month history of progressive vomiting and ataxia. Initial workup included a lumbar puncture (LP) that led to rapid neurological decline. Emergent CT of the head revealed a large fourth ventricular tumour and hydrocephalus. Following emergent suboccipital craniotomy and resection, pathology confirmed the diagnosis of atypical teratoid rhabdoid tumour. MRI of the spine obtained on postoperative day 1 was concerning for widespread leptomeningeal disease (figure 1). However, …
Detection of Measles Virus-Specific Interferon-γ-Secreting T-Cells by ELISPOT

The enzyme-linked immunospot (ELISPOT) assay is a highly sensitive tool used to measure the frequency of antigen-specific T-cells in vitro. Among its many applications, this assay is useful for the characterization of cellular immune responses after immunization against measles and other viral pathogens. A description of the measles virus-specific interferon (IFN)-gamma ELISPOT assay optimized in our laboratory is described in detail in this chapter. Procedures for the preparation of measles virus, infection of peripheral blood mononuclear cells with measles virus, and the IFN-gamma ELISPOT assay are also outlined. These methods can also be broadly adapted to measure activated T-cells to other viral pathogens and/or pathogen-derived peptides. Therefore, the ELISPOT assay can be used for the design, development, and evaluation of new vaccines.
A molecular imaging biosensor detects in vivo protein folding and misfolding

Aberrant protein folding represents the molecular basis of many important human diseases. Although the discovery of new anti-misfolding drugs is a major priority in molecular therapeutics, there is currently no generalizable protein folding assay for use in cell-based high throughput screening (HTS) of chemical libraries, or for in vivo imaging. We molecularly engineered a bioluminescence-based biosensor composed of rationally split Firefly luciferase reporter fragments flanking a test protein, and used this in a protein-fragment complementation assay to quantitatively measure folding of the test protein. We comprehensively validated this biosensor in vitro, in cells, and by optically imaging protein folding and misfolding in living mice using several test proteins including enhanced green fluorescent protein, Renilla luciferase, Gaussia luciferase, and SIRT1. Applications of this novel biosensor are potentially far-reaching in both cell-based HTS approaches to discover new anti-misfolding drugs, and when using the same biosensor in validation studies of drug candidates in small animal models.
A hierarchical multiscale cohesive zone model and simulation of dynamic fracture in metals

Abstract In this work, a hierarchical higher order multi-scale cohesive zone model (MCZM) is developed to simulate the fracture and crack propagation in crystalline solids. The main novelties of the present work are: (1) the hierarchical cohesive zone model is developed, and higher order Cauchy–Born rules (up to the third order) are employed to model different orders of the process zones; (2) the finite element bubble mode is added into the lower order element to capture high-order strain gradient effects in the conventional bilinear quadrilateral element; (3) Barycentric finite element method is used to construct shape functions for hexagonal shaped cohesive zones, and (4) realistic EAM potential is implemented to simulate fracture in metals. Numerical simulations of fracture and crack propagation in both monocrystalline solids and polycrystalline solids are performed. Results show that the crack propagation velocity is in general agreement with that of a corresponding molecular dynamics simulation. Moreover, the transition from intergranular fracture to transgranular fracture in polycrystalline solids is found to be sensitive to both the grain size and the relative grain strength. Finally, it is revealed that the proposed multiscale model can capture the spall fracture in a copper plate under high-speed impact.
Operative Management of Crossover Femoral-femoral Graft Erosion into Bladder: A Case Report

Erosion of vascular grafts is not uncommon as seen in the recent literature. There have been many case reports documenting the work up and management of erosion of these grafts into bowel. We report a case of a crossover femoral-femoral graft that eroded into the anterior bladder wall and was incidentally found as an adherent bladder stone during cystoscopy. We demonstrate the importance of having a high level of clinical suspicion for eroding vascular grafts when preoperative imaging shows close proximity of graft to bladder.
Angle Scan and Frequency-Swept Ultrasonic Scattering Characterization of Tissue

Ultrasonic wave interference has been applied to characterize tissue by measuring scattered wave intensity as a function of frequency and angle. The measurements were made using a computer-based system for collection, processing, and display of data. Model studies consisted of data collection from deterministic targets of regular arrays of nylon filaments and random targets made from small spherical particles of cross-linked dextran in suspension. Angle and frequency scans have been made on post mortem human liver specimens. The model studies demonstrate that regular scatterer spacing can be inferred from measured diffraction data by Fourier inversion, and that scattering differences can be observed from particles of different sizes. Scattering from liver indicates the importance of off-axis scattering which may be related to scatterer size.
The “Glass Ceiling” and Hiring, Training, and Promotion

This chapter underscores issues of gender in hiring, training, promotion, and the proverbial glass ceiling in the workplace. Mayock explores here the language of job advertisements and of job interviewers, non-verbal signs communicated to potential employees, and the availability of and access to training. In addition, the concept of the “good fit” in hiring and promoting and the glass ceiling are analyzed through the lens of gender and other intersectional categories (perceived race, national origin, etc.).
CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort.

Motivation High throughput screening by fluorescence activated cell sorting (FACS) is a common task in protein engineering and directed evolution. It can also be a rate-limiting step if high false positive or negative rates necessitate multiple rounds of enrichment. Current FACS software requires the user to define sorting gates by intuition and is practically limited to two dimensions. In cases when multiple rounds of enrichment are required, the software cannot forecast the enrichment effort required. Results We have developed CellSort, a support vector machine (SVM) algorithm that identifies optimal sorting gates based on machine learning using positive and negative control populations. CellSort can take advantage of more than two dimensions to enhance the ability to distinguish between populations. We also present a Bayesian approach to predict the number of sorting rounds required to enrich a population from a given library size. This Bayesian approach allowed us to determine strategies for biasing the sorting gates in order to reduce the required number of enrichment rounds. This algorithm should be generally useful for improve sorting outcomes and reducing effort when using FACS. Availability and implementation Source code available at http://tyolab.northwestern.edu/tools/ . k-tyo@northwestern.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Path Integrals and The Relation Between Classical and Quantum Mechanics

Our perception of the world outside ourselves can best be described in the terms of classical physics. The phenomena on the atomic scale require the ideas of quantum mechanics for their understanding which remain rather formal and abstract in our mind. Hence the need to tie the two realms together. Many problems can be treated successfully, although only approximately, with the help of classical mechanics, e.g. transition rates in chemistry and self-bound states in quantum field theory (solitons and instantons).
Charges for Water and Access: What Explains the Differences Among West Virginian Municipalities?

Examining both spatial and non-spatial econometric analyses with a dataset of 125 municipal water utilities, we investigate utility cost and community factors that explain variation in residential ...
“Rich as a Jew”? Wealth and Lending among Anglo-Jews

Nowhere in medieval Europe are Jews thought to have been more wholly sunk in moneylending than in Anglo-Norman England.2 Rapid growth of royal administration in England generated copious records of Jewish loans and Jewish litigation over loans, Jewish tallages, and fines. An entire department of the Royal Exchequer was devoted to Jewish matters.3 These records seem to confirm the assumptions that Jews were rich, that their riches were gained from illicit usury, and that medieval kings used them as a sponge to sop up the surplus wealth of the country and squeeze it into the royal coffers. This is the interpretive framework used to make sense of the difficult and fragmentary medieval sources. But the legitimacy of this interpretive frame can be questioned from the English sources, as it can for the less-well-documented communities of Capetian France and central Europe.
Transesophageal Echocardiography Use in Diagnosis and Management of Embolized Intravascular Foreign Bodies.

The increasing use of endovascular interventions coupled with the large number of published case series detailing complications attest to the likelihood that anesthesiologists will encounter a case...
Role of afferent and efferent renal nerves in the development of AngII-salt hypertension in rats.

Abstract Hypertension is the leading modifiable risk factor for death worldwide, yet the causes remain unclear and treatment remains suboptimal. Catheter‐based renal denervation (RDNX) is a promising new treatment for resistant hypertension, but the mechanisms underlying its antihypertensive effect remain unclear. We recently found that RDNX attenuates deoxycorticosterone acetate‐salt hypertension and that this is dependent on ablation of afferent renal nerves and is associated with decreased renal inflammation. To determine if this is common to other models of salt‐sensitive hypertension, rats underwent complete RDNX ( n = 8), selective ablation of afferent renal nerves ( n = 8), or sham denervation ( n = 8). Mean arterial pressure (MAP) and heart rate were measure by telemetry and rats were housed in metabolic cages for measurement of sodium and water balance. Rats were then subjected to angiotensin II (AngII)‐salt hypertension (10 ng/kg/min, intravenous + 4% NaCl diet) for 2 weeks. At the end of the study, renal T‐cell infiltration was quantified by flow cytometry. AngII resulted in an increase in MAP of ~50 mmHg in all three groups with no between group differences, and a transient bradycardia that was blunted by selective ablation of afferent renal nerves. Sodium and water balance were unaffected by AngII‐salt treatment and similar between groups. Lastly, AngII infusion was not associated with T‐cell infiltration into the kidneys, and T‐cell counts were unaffected by the denervation procedures. These results suggest that AngII‐salt hypertension in the rat is not associated with renal inflammation and that neither afferent nor efferent renal nerves contribute to this model.
Crafting a Paper for Publication

The relationship between doing good research and getting the research published is not a causal one. At best, there is a correlation between the quality of a research paper and its being accepted for publication. A research paper’s becoming accepted for publication is ultimately a social process, which exists in addition to and is no less important than the content of the paper itself. In this article, I examine how the social process can influence the crafting of a paper for submission to a journal, and re-crafting it in the event that the journal’s editor asks for a revision.
Thermal Cyclobutane Ring Formation

This chapter reviews thermal [2 + 2] cycloadditions of alkenes to form cyclobutanes, extending the coverage provided by earlier summaries of the literature.1–8 It does not deal with [2 + 2] cycloadditions that are achieved photochemically, or that utilize allenes, arynes or ketenes, or that are deliberately catalyzed,9–14 or that result in heterocyclic four-membered rings, even though these other varieties of [2 + 2] cycloaddition reactions are important and of substantial interest.
Regulatory and electronic alphabet soup: Practice improvements and implications for providers

The growth of health information technology, the focus on patient safety and an increased degree of regulatory involvement in the practice of medicine have all transformed the way practitioners provide care. This paper reviews some of the recognized benefits of these advances, while outlining some of the challenges for providers at the bedside, utilizing a case study involving a hypothetical obstetric patient. The way external factors, such as information technology and regulatory requirements, influence the daily practice of medicine, should be carefully considered as the profession evolves.Integration and streamlining processes should remain a guiding principle to ensure patient safety and assist with workflow.
Mead, George Herbert (1863–1931)

American pragmatist philosopher George Herbert Mead (1863–1931) has had a major influence in the social sciences through his examinations of the processes of symbolic communication and the genesis of the social self. He developed his philosophy in dialogue with unique influences from empirical science, critical philosophy, and the progressive social reforms in which he was heavily involved during his eventful career. Although his ideas were known to colleagues and students at the University of Chicago in the early twentieth century, his subsequent influence has largely been through volumes compiled from disparate sources and published after his death.
FLOW SMOOTHING AND DENOISING: GRAPH SIGNAL PROCESSING IN THE EDGE-SPACE

This paper focuses on devising graph signal processing tools for the treatment of data defined on the edges of a graph. We first show that conventional tools from graph signal processing may not be suitable for the analysis of such signals. More specifically, we discuss how the underlying notion of a ‘smooth signal’ inherited from (the typically considered variants of) the graph Laplacian are not suitable when dealing with edge signals that encode a notion of flow. To overcome this limitation we introduce a class of filters based on the Edge-Laplacian, a special case of the Hodge-Laplacian for simplicial complexes of order one. We demonstrate how this Edge-Laplacian leads to low-pass filters that enforce (approximate) flow-conservation in the processed signals. Moreover, we show how these new filters can be combined with more classical Laplacian-based processing methods on the line-graph. Finally, we illustrate the developed tools by denoising synthetic traffic flows on the London street network.
The geology of earthquake swarms

Differences between earthquake sequences in the crust and adjacent uppermost mantle at oceanic transform faults are revealed by a seafloor seismic experiment at the Blanco Transform Fault.
Spectral Tuning by a Single Nucleotide Controls the Fluorescence Properties of a Fluorogenic Aptamer

Fluorogenic aptamers are genetically encoded RNA aptamers that bind and induce the fluorescence of otherwise nonfluorescent small molecule dyes. These RNA-fluorophore complexes can be highly fluorescent and useful for RNA visualization and genetically encoded biosensors. Notably, different RNA aptamers can bind the same fluorophore, resulting in complexes that exhibit spectrally distinct fluorescence properties. The basis for spectral tuning of small molecule fluorophores has not yet been studied. Here we explore the mechanism of spectral tuning in three highly related RNA aptamers, Broccoli, Orange Broccoli, and Red Broccoli, each of which binds the DFHO (3,5-difluoro-4-hydroxybenzylidene imidazolinone-2-oxime) fluorophore and generates distinct spectral emissions. We show that DFHO fluorescence spectral tuning is controlled by interaction of the oxime moiety of the fluorophore and one specific nucleotide that is different in each RNA aptamer. Our finding presents, for the first time, a mechanism by which RNA can control the properties of a bound small molecule fluorophore. More broadly, our finding can guide further development of fluorogenic aptamers with novel spectral properties.
Abstract 979: EGLN inhibition reduces gastrointestinal radiation toxicity and improves survival in a murine model of locally advanced pancreatic cancer

Rationale: Pancreatic cancer is almost always fatal since chemotherapy is only modestly effective and surgery is often not possible. Radiation therapy (RT) can be a definitive treatment in localized pancreatic cancer, but gastrointestinal toxicity to the nearby duodenum limits its efficacy. There are no known medications that can prevent or treat this gastrointestinal radiotoxicity, but we find that FG-4592, a small molecule inhibitor of EGLN proteins, reduces radiation damage to the intestines by selectively enhancing HIF expression within normal intestines but not within tumors. Methods: We developed a murine model of spontaneous pancreatic cancer (KrasLSL/+; Trp53FL/+; Ptf1aCre/+) that behaves similarly to locally advanced disease. KPC mice were screened for tumors by weekly ultrasounds and upon diagnosis were sequentially assigned to receive one of four possible treatments: Vehicle only (VEH), FG-4592 (FG), RT concurrent with vehicle (RT+VEH), or RT concurrent with FG-4592 (RT+FG). Mice were enrolled on a rolling basis and the total time from diagnosis to treatment end was approximately three weeks. Radiation treatments were planned to administer a total of 75Gy in 15 daily fractions. Results: A total of 70 KPC mice were evaluated. The administration of high-dose radiation therapy of >65Gy (high-dose) with or without radioprotection improved survival compared to all animals that received ≤65Gy (low-dose) of treatment or no RT (37 days [95% CI 33-41] vs. 15 days [10-21] vs. 15 days [10-20], respectively; p=0.005). KPC animals that received dose-escalated radiation lived significantly longer compared to unirradiated controls that received vehicle or FG-4592 alone. The median overall survival was compared amongst the treatment groups and was highest (p Citation Format: Cullen M. Taniguchi, Tara N. Fujimoto, Lauren E. Colbert, Jessica M. Moilkentine, Amit Deorukhkar, Laura J. Baseler, Ramesh Tailor, Gabriel O. Sawakuchi. EGLN inhibition reduces gastrointestinal radiation toxicity and improves survival in a murine model of locally advanced pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 979.
Improving plankton image classification using context metadata

Author(s): Ellen, JS; Graff, CA; Ohman, MD | Abstract: Advances in both hardware and software are enabling rapid proliferation of in situ plankton imaging methods, requiring more effective machine learning approaches to image classification. Deep Learning methods, such as convolutional neural networks (CNNs), show marked improvement over traditional feature-based supervised machine learning algorithms, but require careful optimization of hyperparameters and adequate training sets. Here, we document some best practices in applying CNNs to zooplankton and marine snow images and note where our results differ from contemporary Deep Learning findings in other domains. We boost the performance of CNN classifiers by incorporating metadata of different types and illustrate how to assimilate metadata beyond simple concatenation. We utilize both geotemporal (e.g., sample depth, location, time of day) and hydrographic (e.g., temperature, salinity, chlorophyll a) metadata and show that either type by itself, or both combined, can substantially reduce error rates. Incorporation of context metadata also boosts performance of the feature-based classifiers we evaluated: Random Forest, Extremely Randomized Trees, Gradient Boosted Classifier, Support Vector Machines, and Multilayer Perceptron. For our assessments, we use an original data set of 350,000 in situ images (roughly 50% marine snow and 50% non-snow sorted into 26 categories) from a novel in situ Zooglider. We document asymptotically increasing performance with more computationally intensive techniques, such as substantially deeper networks and artificially augmented data sets. Our best model achieves 92.3% accuracy with our 27-class data set. We provide guidance for further refinements that are likely to provide additional gains in classifier accuracy.
How to Engage with Social Media

Social media platforms have changed the ways in which people communicate and connect in the twenty-first century. Both faculty members and trainees in academic medicine would benefit from understanding the potential benefits and risks of engaging with social media. This chapter first describes different types of social media and the growth of these platforms in recent years. Next, this chapter explores how social media use can contribute to a productive and enjoyable career in academic medicine. Finally, this chapter reviews hazards of engaging with social media and provides suggestions for responsibly using such platforms.
Human Respiratory Viruses

Viruses are the leading causes of acute lower respiratory-tract infection in infancy. Respiratory syncytial virus (RSV) is the most common pathogen in severe disease, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory-tract disease.
Effects of positive college classroom motivational environments on procrastination and achievement

Understanding factors within college learning environments that can ameliorate maladaptive academic behaviours such as procrastination could contribute to enhancing college students’ success and persistence. Thus, the aims of the current study were to investigate: (a) the degree to which facets of the college classroom motivational environment predict college students’ academic procrastination after controlling for students’ level of conscientiousness (which is a strong predictor of procrastination); and (b) whether academic procrastination mediates the effect of classroom motivational environment facets on course grades. Participants were 223 students enrolled in two four-year institutions (one a Hispanic-serving institution) in southern US. Hierarchical regression analyses indicated that students who reported the presentation of course material in their classes as being more interesting (course situational interest) also tended to report procrastinating less. Furthermore, mediation analyses indicated that the positive effects on course grades of classroom motivational environments (in which instructors were perceived as providing academic and emotional support, promoting mutual respect and task-related interactions among students, and eliciting interest through the presentation of course material) were better explained as mediated by academic procrastination. These findings suggest that providing a supportive college classroom environment to engage students could cause them to procrastinate less and attain better academic outcomes.
The Establishment of Visual Equivalence Classes with a Go/No-Go Successive Matching-to-Sample Procedure

The current study evaluated the effectiveness of a successive matching-to-sample (S-MTS) procedure with a go/no-go preparation to establish three 3-member classes of visual stimuli with 24 undergraduate college students. At the start of each trial, participants touched a sample stimulus after which a comparison immediately appeared in the same location on the screen. Then, depending on the relation between sample and comparison, participants were required to either touch the comparison (i.e., go) or to refrain from touching it (i.e., no-go). The comparison remained on the screen for 8 s independent of participants’ responses. Following training of baseline relations (AB/BC), responses to untrained relations (i.e., BA/CB and AC/CA) were assessed. Overall, 22 out of 24 participants met emergence criterion on AC/CA tests, with reaction times to comparisons below 5 s indicating that S-MTS may be a viable alternative to traditional MTS to establish equivalence classes.
Lymphocyte soluble factors from pregnant cows modulate mRNA transcript abundances encoding for proteins associated with trophoblast growth and development

This study was conducted to determine whether T cell populations are responsible for modulating placental development during gestation in cattle. It was hypothesized that CD4+CD25+ and γ/δ+ T cells modulate gene expression, based on mRNA transcript abundances, and promote proliferation and survival of trophoblast cells. Peripheral blood was collected from cows at 160 to 180 days of gestation and non-pregnant cows, T cell populations CD8+, CD4+, CD4+CD25+, CD24+CD25-, and γ/δ+ T cells were isolated, cultured for 48 h, and supernatant was collected. Placental samples were digested, and trophoblast cells were cultured for 24 h. Trophoblast cells were cultured with 50 μL of T cell-conditioned media and 50 μL of fresh culture media for an additional 48 h. Samples in control wells were treated with unconditioned media. Trophoblast cell proliferation, apoptosis, and mRNA transcript assays were conducted. There was no effect of T cell population on trophoblast apoptosis rate, proliferation, and relative mRNA transcript abundances. The T cell supernatant from pregnant and non-pregnant cows induced greater apoptosis rates in trophoblast cells than unconditioned media. Trophoblast cells proliferated less when treated with T cell supernatant from pregnant compared to unconditioned medium and non-pregnant cows. Treatment with the T cell supernatant from pregnant cows resulted in larger abundances of BMP5, IGF1R, PAG10, FGF2, RSPO3 and TMED2 and also a lesser abundance of FGF2 mRNA transcript than non-pregnant group and unconditioned media treatments. Supernatant from T cell derived from pregnant cows modulates trophoblast mRNA transcript abundances differently from T cell supernatant of non-pregnant cows.
Are gun ownership rates and regulations associated with firearm incidents in American schools? A forty-year analysis (1980–2019)

Abstract Purpose This study examines the relationship between state gun ownership rates and school firearm incidents (n = 1275) and injured/killed victims (n = 2026) of these incidents over a forty-year period (1980–2019). It also investigates whether child access prevention, minimum age requirements for gun purchases, and mandatory gun safety training laws are associated with fewer school firearm incidents and injured/killed victims. Methods Data were linked together from the School Shootings Database, State Firearm Law Database, the National Center for Education Statistics, and the US Census Bureau. State fixed effects and interrupted time series analyses were performed. Results State gun ownership rates declined between 1980 and 2019 while school firearm incidents generally ranged between 20 and 40 incidents before skyrocketing to 102 incidents in 2018 and 110 incidents in 2019. Findings were mixed on the relationship between state gun ownership rates and school firearm incidents and injured/killed victims. Additionally, child access prevention, minimum age requirements for gun purchases, and mandatory gun safety training laws exhibited weak and inconsistent relationships with school firearm incidents. Discussion Although access to firearms plays an undeniable role in school shootings, it remains unclear what policies are needed to reduce these incidents. Future research may be needed to explore holistic approaches to addressing this problem.
Fast, Easy-to-use, Machine Learning-developed Models of Prediction of Flash Point, Heat of Combustion, and Lower and Upper Flammability Limits for Inherently Safer Design

Abstract This study proposes easy-to-apply machine learning-developed models, which predict four flammability properties of pure organic compounds: the flash point, heat of combustion, lower flammability limit (LFL), and upper flammability limit (UFL). These flammability properties pose a strong impact on the inherently safer design of industrial processes. Similar to quantitative structure-property relationship (QSPR) or group contribution models, machine learning algorithms are utilized in this study to establish predictive models. Compared to previous models, this study uses readily available variables (i.e., the numbers of atomic elements, molecular weights, and normal boiling points) as default variables without the analysis of detailed molecular structures or the in-depth knowledge of chemistry. This study consists of two steps: Step (1) building multiple linear regression (MLR) models by incorporating default input variables and Step (2) building MLR models by incorporating interaction and transformed variables to improve the predictions from the models in Step 1. In Step 1, an optimal subset of predictors is identified by constructing an MLR model via the sequential floating backward selection (SFBS) algorithm. As a result of Step 1, the two constructed models of the flash point and heat of combustion are found to be adequate, while the predictability of LFL and UFL are insufficient. In Step 2, MLR models incorporating nonlinearity and interaction terms are constructed via the sequential floating forward selection (SFFS) algorithm by selecting the optimal subset of default variables. The results show that all the constructed models in Step 2 are adequate as predictive models; the mean absolute errors (MAEs) of the flash point, heat of combustion, LFL, and UFL are 7.31 (5.67 via the SFBS) [K], 60.6 (61.87 via the SFBS) [kJ/mol], 0.21 (0.19 via the SFBS) [vol.%], and 2.44 (2.33 via the SFBS) [vol.%], respectively. Compared to previous models, the approved models in this study provide highly competitive performance with enhanced simplicity and interpretability.
Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders.

Abstract Understanding the exquisitely complex nature of the three-dimensional organization of the genome and how it affects gene regulation remains a central question in biology. Recent advances in sequencing- and imaging-based approaches in decoding the three-dimensional chromatin landscape have enabled a systematic characterization of gene regulatory architecture. In this review, we outline how chromatin architecture provides a reference atlas to predict the functional consequences of non-coding variants associated with human traits and disease. High-throughput perturbation assays such as massively parallel reporter assays (MPRA) and CRISPR-based genome engineering in combination with a reference atlas opened an avenue for going beyond observational studies to experimentally validating the regulatory principles of the genome. We conclude by providing a suggested path forward by calling attention to barriers that can be addressed for a more complete understanding of the regulatory landscape of the human brain.
Multiple Conformational Switches Control Co-translational Protein Targeting

The “GTPase switch” paradigm, in which a GTPase switches between an active, GTP-bound state and an inactive, GDP-bound state through the recruitment of nucleotide exchange factors (GEFs) or GTPase activating proteins (GAPs), has been used to interpret the regulatory mechanism of many GTPases. A notable exception to this paradigm is provided by two GTPases in the signal recognition particle (SRP) and the SRP receptor (SR) that control the co-translational targeting of proteins to cellular membranes. Instead of the classical “GTPase switch”, SRP and SR undergo a series of discrete conformational rearrangements during their interaction with one another, culminating in their reciprocal GTPase activation. Here, we show that this series of rearrangements during SRP–SR binding and activation provide important control points to drive and regulate protein targeting. Using real time fluorescence, we showed that the cargo for SRP—ribosomes translating nascent polypeptides with signal sequences—accelerates SRP–SR complex assembly over 100-fold, thereby driving rapid delivery of cargo to the membrane. A series of subsequent rearrangements in the SRP–SR GTPase complex provide important driving forces to unload the cargo during late stages of protein targeting. Further, the cargo delays GTPase activation in the SRP–SR complex by 8- to 12-fold, creating an important time window that could further improve the efficiency and fidelity of protein targeting. Thus the SRP and SR GTPases, without recruiting external regulatory factors, constitute a self-sufficient system that provides exquisite spatial and temporal control of a complex cellular process.
Generation of UV Radiation (250–260 nm) from Intracavity Doubling of a Single-Mode Ring Dye Laser

Molecules whose electronic transitions lie in the UV portion of the electromagnetic spectrum far outnumber those in the visible. Consequently, it is of considerable chemical interest to extend tunable coherent sources to shorter wavelengths. Potential applications are numerous, including photochemical, kinetic, analytical, and spectroscopic studies. We report here the construction of an intracavity-doubled cw ring dye laser producing single-mode UV output in the range 250–260 nm with a free-running jitter of about ±50 MHz over a time interval of a few seconds. High resolution spectra of the Hg 3P1 - 1S0 transition at 253.7 nm are presented. Fluorescence excitation of natural mercury in a bulb yields a spectrum in which the resolution of the hyperfine structure is Doppler limited, whereas excitation of an atomic beam allows subDoppler resolution of these features.
Learning to increase effective troubleshooting with an interactive expert system

A general overview is presented of an expert system design to replace advice from an instructor in digital logic circuit design at the level of small-scale-integrated components in a protoboard design. The expert system is available at all times to offer advice and answer students' questions on the topic. The interactive prototype system that has been implemented at the University of Connecticut is described. This system is intended to work at the troubleshooting stage to help a student identify the errors in the circuit and provide an environment in which the student can develop expertise in troubleshooting faulty circuits. >
Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem

We focus on the combinatorial analysis of physical mapping with repeated probes. We present computational complexity results, and we describe and analyze an algorithmic strategy. We are following the research avenue proposed by Karp [9] on modeling the problem as a combinatorial problem - the Hypergraph Superstring Problem - intimately related to the Lander-Waterman stochastic model [16]. We show that a sparse version of the problem is MAXSNP-complete, a result that carries over to the general case. We show that the minimum Sperner decomposition of a set collection, a problem that is related to the Hypergraph Superstring problem, is NP-complete. Finally we show that the Generalized Hypergraph Superstring Problem is also MAXSNP-hard.We present an efficient algorithm for retrieving the PQ-tree of optimal zero repetition solutions, that provides a constant approximation to the optimal solution on sparse data. We provide experimental results on simulated data.