cssi/SciSciGPT-SciSciNet huggingface dataset:
Detailing regulatory networks through large scale data integration

Motivation: Much of a cell's regulatory response to changing environments occurs at the transcriptional level. Particularly in higher organisms, transcription factors (TFs), microRNAs and epigenetic modifications can combine to form a complex regulatory network. Part of this system can be modeled as a collection of regulatory modules: co-regulated genes, the conditions under which they are co-regulated and sequence-level regulatory motifs. Results: We present the Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction (COALESCE) system for regulatory module prediction. The algorithm is efficient enough to discover expression biclusters and putative regulatory motifs in metazoan genomes (>20 000 genes) and very large microarray compendia (>10 000 conditions). Using Bayesian data integration, it can also include diverse supporting data types such as evolutionary conservation or nucleosome placement. We validate its performance using a functional evaluation of co-clustered genes, known yeast and Escherichea coli TF targets, synthetic data and various metazoan data compendia. In all cases, COALESCE performs as well or better than current biclustering and motif prediction tools, with high accuracy in functional and TF/target assignments and zero false positives on synthetic data. COALESCE provides an efficient and flexible platform within which large, diverse data collections can be integrated to predict metazoan regulatory networks. Availability: Source code (C++) is available at http://function.princeton.edu/sleipnir, and supporting data and a web interface are provided at http://function.princeton.edu/coalesce. Contact:ogt@cs.princeton.edu; hcoller@princeton.edu. Supplementary information:Supplementary data are available at Bioinformatics online.
Discrepancies in Reports of Support Exchanges Between Aging Parents and Their Middle-Aged Children

Methods. Participants included 337 dyads of parents (aged 59–96 years) and their children (aged 40–60 years). Multilevel models assessed the level of discrepancies between dyadic members and examined predictors accounting for the discrepancies. We considered downward (from parent to child) and upward (from child to parent) directions in support exchanges. Results. For upward support from adult children to their parents, children reported that they gave more than their aging parents reported receiving. For downward support from parents to children, the results differed depending on the type of support. Discrepancies between parents’ and children’s reports were associated with parents’ feelings of obligation toward children and children’s ratings of the importance of parent–child relationship. Discussion. These results suggest the importance of considering multiple perspectives and the direction of exchanges between generations. Discrepancies in reports of support reflect both self-enhancement and family context and may be an important source of misunderstanding and conflict between generations.
Grazer diversity effects on ecosystem functioning in seagrass beds

High plant species richness can enhance primary production, animal diversity, and invasion resistance. Yet theory predicts that plant and herbivore diversity, which often covary in nature, should have countervailing effects on ecosystem properties. Supporting this, we show in a seagrass system that increasing grazer diversity reduced both algal biomass and total community diversity, and facilitated dominance of a grazer-resistant invertebrate. In parallel with previous plant results, however, grazer diversity enhanced secondary production, a critical determinant of fish yield. Although sampling explained some diversity effects, only the most diverse grazer assemblage maximized multiple ecosystem properties simultaneously, producing a distinct ecosystem state. Importantly, ecosystem responses at high grazer diversity often differed in magnitude and sign from those predicted from summed impacts of individual species. Thus, complex interactions, often opposing plant diversity effects, arose as emergent consequences of changing consumer diversity, advising caution in extrapolating conclusions from plant diversity experiments to food webs.
Sleep deprivation and sustained attention performance: integrating mathematical and cognitive modeling.

A long history of research has revealed many neurophysiological changes and concomitant behavioral impacts of sleep deprivation, sleep restriction, and circadian rhythms. Little research, however, has been conducted in the area of computational cognitive modeling to understand the information processing mechanisms through which neurobehavioral factors operate to produce degradations in human performance. Our approach to understanding this relationship is to link predictions of overall cognitive functioning, or alertness, from existing biomathematical models to information processing parameters in a cognitive architecture, leveraging the strengths from each to develop a more comprehensive explanation. The integration of these methodologies is used to account for changes in human performance on a sustained attention task across 88 h of total sleep deprivation. The integrated model captures changes due to time awake and circadian rhythms, and it also provides an account for underlying changes in the cognitive processes that give rise to those effects. The results show the potential for developing mechanistic accounts of how fatigue impacts cognition, and they illustrate the increased explanatory power that is possible by combining theoretical insights from multiple methodologies.
Aggravated renal inflammatory responses in TRPV1 gene knockout mice subjected to DOCA-salt hypertension

To test the hypothesis that deletion of the transient receptor potential vanilloid type 1 (TRPV1) channel exaggerates hypertension-induced renal inflammatory response, wild-type (WT) or TRPV1-null mutant (TRPV1−/−) mice were subjected to uninephrectomy and deoxycorticosterone acetate (DOCA)-salt treatment for 4 wk. Mean arterial pressure (MAP) determined by radiotelemetry increased in DOCA-salt-treated WT or TRPV1−/− mice, whereas there was no difference in MAP between two strains at the baseline or after DOCA-salt treatment. DOCA-salt treatment increased urinary excretion of albumin and 8-isoprostane in both WT and TRPV1−/− mice, and the increases were greater in magnitude in the latter strain. Periodic acid-Schiff and Mason's trichrome staining showed that kidneys of DOCA-salt-treated TRPV1−/− mice exhibited more severe glomerulosclerosis and tubulointerstitial injury compared with DOCA-salt-treated WT mice. NF-κB assay showed that DOCA-salt treatment increased renal activated NF-κB concentrations in TRPV1−/− mice compared with WT mice. Immunostaining and ELISA assay revealed that DOCA-salt-treated TRPV1−/− mice had enhanced renal infiltration of monocyte/macrophage and lymphocyte, as well as increased renal levels of proinflammatory cytokine (TNF-α, IL-6) and chemokine (MCP-1) compared with DOCA-salt-treated WT mice. Renal ICAM-1 but not VCAM-1 expression was also greater in DOCA-salt-treated TRPV1−/− than WT mice. Dexamethasone (DEXA), an immunosuppressive drug, conveyed a renoprotective effect that was greater in DOCA-salt-treated TRPV1−/− compared with WT mice. These data show that renal inflammation is exacerbated in DOCA-salt hypertension when TRPV1 gene is deleted and that the deterioration is ameliorated by DEXA treatment, indicating that TRPV1 may act as a potential regulator of the inflammatory process to lessen renal injury in DOCA-salt hypertension.
Calnexin regulates mammalian Kv1 channel trafficking.

Abstract Voltage-gated Kv1 channels are key factors regulating excitability in the mammalian central nervous system. Diverse posttranslational regulatory mechanisms operate to determine the density, subunit composition, and localization of Kv1 channel complexes in the neuronal plasma membrane. In this study, we investigated the role of the endoplasmic reticulum chaperone calnexin in the intracellular trafficking of Kv1 channels. We found that coexpressing calnexin with the Kv1.2α subunit in transfected mammalian COS-1 cells produced a dramatic dose-dependent increase in cell surface Kv1.2 channel complexes. In calnexin-transfected COS-1 cells, the proportion of Kv1.2 channels with mature N-linked oligosaccharide chains was comparable to that observed in neurons. In contrast, calnexin coexpression exerted no effects on trafficking of the intracellularly retained Kv1.1 or Kv1.6α subunits. We also found that calnexin and auxiliary Kvβ2 subunit coexpression was epistatic, suggesting that they share a common pathway for promoting Kv1.2 channel surface expression. These results provide yet another component in the elaborate repertoire of determinants regulating the density of Kv1 channels in the plasma membrane.
Hardware based segmentation in iris recognition and authentication systems

Iris recognition algorithms depend on image processing techniques for proper segmentation of the iris. In the Ridge Energy Direction (RED) iris recognition algorithm, the initial step in the segmentation process searches for the pupil by thresholding and using binary morphology functions to rectify artifacts obfuscating the pupil. These functions take substantial processing time in software on the order of a few hundred million operations. Alternatively, a hardware version of the binary morphology functions is implemented to assist in the segmentation process. The hardware binary morphology functions have negligible hardware footprint and power consumption while achieving speed up of 200 times compared to the original software functions.
Analysis of floating point operations in microcontrollers

The purpose of this paper is to identify the advantages of including a floating point hardware / a mathematical co-processor in microcontrollers used for critical floating point operations. Three different microcontrollers are considered: Renesas M16C/62P (CISC without FPU), ATMEGA1280 (RISC without MCU) and Renesas RX62N (CISC with FPU). Gauss-Seidel and Jacobi iterations for a system of 2 and 3 variables using single precision and double precision floating point numbers are implemented. The time taken by each microcontroller is measured using the Timer in the microcontrollers. Based on the time taken, the advantages of the inclusion of the floating point unit are attributed against the cost incurred by the hardware.
Two Seventeenth-Century Conversion Narratives from Ipswich, Massachusetts Bay Colony

Two extraordinarily rare documents, the seventeenth-century spiritual autobiographies of William and Elisabeth Adams, residents of Ipswich, Massachusetts Bay Colony, are here introduced, transcribed, and annotated. So intense were the couple's spiritual struggles that, at one point, William fears that he might “cut the throat of my own soul.”
An Analytical Study of the Echelette Grating with Application to Open Resonators

Reflection coefficients of various order diffracted waves are calculated for an echelette grating which finds important use as a component of suboptical resonators. The classical optics approach has been found to be inadequate for deriving reliable results for this configuration. Accurate solution of the boundary value problem associated with the echelette grating is derived by a new method. The results are useful for the design of suboptical resonators which use the echelette grating as a coupling mirror to achieve a single wavelength operation.
Effects of radiodetoxified endotoxin on nitric oxide production in J774 macrophages and in endotoxin shock

Radiodetoxified lipopolysaccharide (RD-LPS) is a 60Co-gamma-irradiated LPS with a modified structure, which decreases its toxic effects. To obtain a better understanding of the mechanism of the reduced toxicity of RD-LPS, here we studied the effect of RD-LPS on the regulation of nitric oxide (NO) production in vitro and in vivo. In control cells, stimulation by native LPS (10 μg/ml) induced the expression of the inducible NO synthase (iNOS) and production of NO, as measured by increase in the concentration of nitrite, breakdown product of NO. Pre-exposure of the cells for 24 h to a subthreshold concentration of RD-LPS (10 ng/ml) induced a complete desensitization to the LPS-induced NO production in comparison to control cells (P < 0.01). On the contrary, pre-exposure of the cells with native LPS (10 ng/ml) did not reduce LPS-induced NO synthesis. RD-LPS induced a smaller production of tumor necrosis factor (TNF) than native LPS, but did not induce a desensitization against subsequent LPS-induced TNF synth...
Stability of planar stagnation flow of a highly viscoelastic fluid

Abstract Linear stability analysis is used to predict the onset of instabilities in inertialess viscoelastic planar stagnation flow. Beyond a critical value of the dimensionless flow rate, or Deborah number, the creeping base flow of similarity type, which is valid in the limit of vanishingly small Reynolds numbers, becomes unstable to localized three-dimensional disturbances. Stability calculations of the local similarity type viscoelastic flow in a small region near the stagnation plane are reported for the quasi-linear Oldroyd-B constitutive equation. The stability results for a range of Deborah numbers and viscosity ratio are presented to explore systematically the effects of elasticity and other rheological properties. The onset of instability and the temporal and spatial characteristics of the secondary flow predicted here resemble other purely elastic instabilities measured and predicted for viscoelastic flows in other simple and complex geometries with curved streamlines.
Internalized HIV Stigma and Mindfulness: Associations With PTSD Symptom Severity in Trauma-Exposed Adults With HIV/AIDS

Rates of both traumatic event exposure and posttraumatic stress disorder (PTSD; 22%-54%) are disproportionately elevated among people living with HIV/AIDS (PLHA). Trauma and related psychopathology significantly affect quality of life and disease management in this patient population. The current study examined associations between internalized HIV stigma, mindfulness skills, and the severity of PTSD symptoms in trauma-exposed PLHA. Participants included 137 PLHA (14.6% female; Mage = 48.94, SD = 8.89) who reported experiencing on average, five (SD = 2.67) traumatic events; 34% met diagnostic criteria for PTSD. Results indicate that after controlling for sex, age, education, and number of traumatic events, internalized HIV stigma was positively related to overall PTSD symptom severity (β = .16, p < .05) and severity of re-experiencing (β = .19, p < .05) and hyper-arousal (β = .16, p = .05), but not avoidance, PTSD symptom clusters. Among the mindfulness facets measured, acting with awareness was uniquely negatively related to the overall severity of PTSD symptoms (β = -.25, p < .01) and the severity of re-experiencing (β = -.25, p < .05), avoidance (β = -.25, p < .05), and hyper-arousal (β = -.29, p < .01) PTSD symptom clusters. These effects were observed after accounting for covariates and shared variance with other mindfulness facets. Theoretically, the present findings suggest that internalized HIV stigma may serve as a vulnerability factor for the severity of certain PTSD symptoms, whereas acting with awareness may function as a protective or resiliency factor for the severity of PTSD symptoms. Implications for the treatment of trauma-exposed PLHA are discussed.
The Infrastructure Of Critical Infrastructure: Vulnerability And Reliability Of Complex Networks

* Background & Objectives All critical infrastructure can be modeled as networks, or systems of nodes and connections, and many systems such as the electric grid, water supply, or telecommunications exist explicitly as networks. Infrastructures are interdependent, for instance, telecommunications depend on electric power, and control of the electric grid depends increasingly upon telecommunications, creating the possibility for a negative feedback loop following a disturbance. The performance of these systems under disturbance are related to their inherent network characteristics, and network architecture plays a fundamental role in reliability. What characteristics of networks affect their robustness? Could, for instance, the vulnerability of the electric grid to cascading failure be reduced? * Methods We create a failure model of the network where each node and connection is initially in the operative state. At the first discrete time step a network element is changed to the failed state. At subsequent ...
Prenatal Sonographic Diagnosis of a Buried Penis

Aburied or concealed penis is a relatively common diagnosis made in early infancy and childhood. It is characterized by a variable and at times short penile shaft length with an inadequately small amount of skin around it. 1 It is possible that the term penoscrotal transposition is also applied to the same congenital genital feature. Only 1 report about prenatal diagnosis of this condition was found in the literature, as reviewed by Pub Med. 2 .
Convective and Radiative Heat Transfer in Porous Media

Publisher Summary This chapter describes the convective and radiative heat transfer in porous media. Convective and radiative heat transfer and multiphase transport processes in porous media, both with or without phase change, have gained extensive attention. Several applications related to porous media require a detailed analysis of convective heat transfer in different geometrical shapes, orientations, and configurations. Based on the specific application, the flow in the porous medium may be internal or external. Forced convection over external boundaries in the presence of a porous medium constitutes a very important subject area. Analysis of convective heat transfer from this type of external boundary embedded in a porous medium has many important applications. It is shown that for the flow field the boundary effect is confined within a thin momentum boundary layer, which often plays an insignificant role in the overall flow consideration. The models developed for simultaneous heat and mass transfer processes in multiphase porous systems may have differences due to the various assumptions made in developing each model. The thermal radiation characteristics of porous beds are also elaborated.
Nitric oxide from perivascular nerves modulates cerebral arterial pH reactivity

In the isolated rat middle cerebral artery (MCA) we investigated the role of nitric oxide (NO)/cGMP in the vasodilatory response to extraluminal acidosis. Acidosis increased vessel diameter from 14...
A case of recurrent, self-inflicted handheld laser retinopathy

A 17-year-old young man presented with vision loss and discrete, bilateral foveal lesions. The patient returned 6 weeks later with worsening vision, prominent bilateral retinal lesions, and a full-thickness macular hole in the right eye consistent with recurrent self-inflicted handheld laser retinopathy. After instructing the family to remove the patient's access to laser pointers, follow-up examination revealed spontaneous closure of the macular hole but minimal vision improvement. Recurrent ocular exposure to handheld lasers can masquerade as an organic process in patients who withhold pertinent history. Clinicians should rely on the distinguishing features seen on examination and multimodal imaging to make the diagnosis of handheld laser retinopathy.
Partial Rotator Cuff Tears in Throwing Athletes

The throwing shoulder presents many challenges for the treating orthopeadic surgeon. High functional demands, season-specific schedules, and complex pathologies make proper evaluation and treatment difficult, and accurate diagnosis is especially important in decision-making in this difficult group of patients. Adaptive changes must be differentiated from pathologic injury, and a detailed and accurate history and physical examination is crucial. Often multiple abnormalities are seen on imaging. Advanced imaging must be paired with examination to determine the specific source of dysfunction. Rotator cuff injuries in overhead athletes have proven especially difficult despite extensive research spanning many decades. Surgery in a thrower's shoulder can be disabling, and surgery must be approached with caution. Nonoperative management serves a huge role and has high success rates, but when surgery is required, diagnosis must be accurate and surgery carefully planned and executed. Multiple surgical techniques have been described, and none of the techniques have clearly demonstrated the best results. The variability of presentation and severity makes every patient different, and treatment must be specifically tailored for each patient. This article provides a review of the history of management, theories of the mechanism of injury, our surgical technique, and current surgical results.
Interface stability during displacement reactions between Cu2O and Co1−XFeX alloys at 1223 K

The stability of the reactive interface during the solid-state displacement reaction, Cu2O+Co1−XFeX=2Cu+(Co1−XFeX)O, is studied as a function of Co-Fe alloy composition at 1223 K. For X≤0.03, the reaction zone has a layered structure, and the cation diffusion in (Co, Fe)O is the rate-limiting step. The interface is unstable in the early stages of the reaction; the instability decreases with time as the oxide thickness increases, and the interface becomes planar at long times. The time required for the attainment of interface planarity increases with the value of X. The reaction kinetics are consistent with the available cation-diffusion data in (Co, Fe)O. For X≥0.045, the product zone is a composite of Cu+(Co, Fe)O, and the rate is limited by the oxygen transport in copper. The transition to interface instability occurs when the oxide can support a cation flux that exceeds the maximum possible oxygen flux in copper. During the reaction, composition gradients develop in (Co, Fe)O because of higher diffusion rates for iron than for cobalt.
Research Progress on Mathematical Modeling of Blast Furnace Ironmaking Process

Blast furnace is one of the most complex metallurgical reactor. In order to achieve deep understanding, further optimization, and intelligent control of the blast furnace process, many mathematical models were developed. The paper firstly reviews the development course of reaction kinetics models of total blast furnace and focuses on introducing the typical research achievements on the creation and application of multi-fluid blast furnace model. Then, the development and application status of intelligent expert system at home and abroad are summarized. Some prospects of the development of blast furnace mathematical models in the future are put forward and pointed out that the future development on digital simulation and control for the blast furnace process is combining the CFD-DEM model, the whole comprehensive mathematical model of blast furnace with blast furnace expert system.
Should We Fear Folate

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA; Department of Urology, University of California at San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Mouse Mammary Tumor Virus

Mouse mammary tumor virus (MMTV) is a betaretrovirus that induces mammary carcinomas in mice. MMTV is transmitted through the germline (endogenous virus) as well as through maternal milk (milk-borne virus). Milk-borne MMTV exploits host immune responses and requires infection and amplification in lymphoid cells through the virally encoded superantigen (Sag). Infected B and T lymphocytes disseminate MMTV to epithelial cells in the mammary gland. MMTV replication is tightly controlled in these various cell types at the transcriptional level through both positive and negative elements in the viral long terminal repeats found at the ends of proviral DNA. Positive regulatory elements include the hormone response element, which binds several types of steroid receptors, as well as the mammary gland enhancer. The negative regulatory elements bind at least two homeodomain-containing proteins, SATB1 and CDP, which repress transcription in different cells and differentiation states to avoid insertional mutagenesis of host cells and the resulting tumors. Loss of repression and hormonal activation of milk-borne MMTV leads to efficient viral transcription in differentiated mammary cells to allow maximal transmission during lactation. Since a virally encoded RNA export protein, Rem, also controls post-transcriptional events, MMTV appears to be a complex retrovirus.
Unsteady Combustor Physics: Hydrodynamic Flow Stability I: Introduction

In Chapter 2, we showed that flow disturbances can be decomposed into fluctuations in vorticity, entropy, and volume. The next two chapters focus on the evolution of vorticity in flows, with particular emphasis on the development of coherent vortical structures. Such large-scale structures, embedded on a background of acoustic waves and broadband, smaller-scale turbulence, dominate the unsteady flow fields in combustors. These large-scale structures play important roles in processes such as combustion instabilities, mixing and entrainment, flashback, and blowoff. For example, we will discuss vortex–flame interactions repeatedly in discussions of combustion instabilities in later chapters. High Reynolds number flows are effectively inviscid outside the boundary layer. Vorticity in the flow largely originates, then, from boundary layers in approach flow passages or other walls. Free shear layers arise at points of boundary layer separation, initiating a sequence of large-scale flow instabilities as this vorticity is then stretched and amplified by the base flow. Coherent structures arise because the base flow configuration, u 0 ( y ) or ū ( y ), is unstable. Many of the same instabilities that are focused on in the next two chapters that play such important roles in unsteady combustor dynamics also manifest themselves in a variety of other instances, including in spectacular, large-scale fashion in nature. To illustrate, Figure 3–1(a) illustrates cloud patterns showing the Kelvin- Helmholtz instability, discussed in Sections 3.4 and 4.1. Figure 3–1(b) illustrates the Benard/von Karman instability over a Japanese island visualized from space, to be discussed in Section 4.2.
Deriving hierarchical complexity from simplistic colloidal templates

Establishing strategies for high-resolution micrometer to subnanometer structural control is an essential feature of any versatile materials design paradigm. Colloidal crystal (CC) templating not only establishes tunable replica pore topologies, but interfacial- and confinement-mediated phenomena extend its impact for tailoring properties such as pore hierarchy, topological diversity, and macroscopic morphology, as well as nucleation, growth, and crystallinity. Coupled with emerging strategies for “single-pot” template-replica co-assembly and efforts to expand the accessible materials palette, CC-templating offers promise for application-driven, rational materials design.
A 16 Gb/s 3.7 mW/Gb/s 8-Tap DFE Receiver and Baud-Rate CDR With 31 kppm Tracking Bandwidth

A 16 Gb/s I/O link receiver fabricated in 22 nm CMOS SOI technology is presented. Attenuation and ISI of transmitted NRZ data across PCB channels are equalized with a CTLE feeding an 8-tap DFE. The first tap uses digital speculation and the following seven taps are realized by means of the switched-capacitor technique. Timing recovery and control are performed with a Mueller-Muller type-A baud-rate CDR. The architecture is half-rate and requires one phase rotator. In total, each slice has six comparators to recover data and timing information. The secondorder digital CDR operates at quarter-rate and features a low-latency implementation of the proportional path. At 16 Gb/s, 1 Vppd PRBS31 data transmitted without FFE equalization is recovered across a PCB channel with 34 dB attenuation at 8 GHz. The measured tracking bandwidth is 31 kppm (16 GHz ± 496 MHz), and an amplitude of 3 UIPP is tolerated at 1 MHz sinusoidal jitter. The sinusoidal jitter amplitude tolerance measured at 10 Gb/s is 0.4 UIPP at 10 MHz and remains above 0.2 UIPP up to 1 GHz with PRBS31 data recovered (BER <; 10 -12 ) across a PCB channel with 27 dB attenuation at 5 GHz. The power efficiency is 3.7 mW/Gb/s, including the full-rate clock receiver.
Tunnelling for victory in particle physics

Adolf Hitler's promulgation of the "Civil Service Restitution Act" in April 1933 and Bill Clinton's signing of the bill that cancelled the Superconducting Supercollider (SSC) in October 1993 are set as the dramatic turning points in the ascendancy and decline of US particle physics in Gordon Fraser's The Quark Machines. If, indeed, the dominance in particle physics can be depicted as a pendulum swinging from Europe to the US and back again, it is an exceedingly erratic one. However; Fraser does not oversimplify things, but lays out in detail the bold steps, missed opportunities and occurrences of blind luck – in short, the jagged record of triumphs and failures on both sides of the Atlantic, from Rutherford's tabletop experiments to the current construction of the Large Hadron Collider (LHC) at CERN.
Continuous Glucose Monitoring with Multiple Daily Insulin Treatment: Outcome Studies

Continuous glucose monitoring (CGM) is developing into an increasingly useful tool for glucose monitoring and therapeutic guidance in the treatment of diabetes. Multiple daily doses of insulin (MDI) is the most common method for intensive insulin treatment of type 1 diabetes and is also becoming more common in the treatment of type 2 diabetes as an increasing population with type 2 diabetes experiences progressive beta cell loss. The clinical evidence demonstrating the benefit of CGM in the outcomes of patients treated with MDI is becoming clearer, particularly with the recent completion of several randomized clinical trials addressing both type 1 and 2 diabetes. This evidence is reviewed.
Experiment design for early molecular events in HIV infection

The recent introduction of integrase inhibitors to the HIV antiviral repertoire permits us to create in vitro experiments that reliably terminate HIV infection at the point of chromosomal integration. This allows us to isolate the dynamics of a single round of infection, without needing to account for the influence of multiple overlapping rounds of infection. By measuring the various nucleic acid concentrations in a population of infected target cells at multiple time points, we can infer the rates of these molecular events with great accuracy, which allows us to compare the rates between target cells with different functional phenotypes. This information will help in understanding the behavior of the various populations of reservoir cells such as active and quiescent T-cells which maintain HIV infection in treated patients. In this paper, we introduce a family of models of the early molecular events in HIV infection, with either linear dynamics or age-structured delays at each step. We introduce an experimental design metric based on the delta AIC (Akaike Information Criteria) between a model fit for simulated data from a matching model vs a mismatched model, which allows us to determine a candidate experiment design's ability to discriminate between models. Using parameters values drawn from experimentally-derived priors corrupted with appropriate measurement noise, we confirm that a proposed sampling schedule at different time points allows us to consistently discriminate between candidate models.
Ghetto: The invention of a place, the history of an idea, by Mitchell Duneier: New York, NY, Farrar, Straus and Giroux, 2016

In this new, very timely and well-written book, Mitchell Duneier takes on the complex challenge of documenting the history and ever-changing meaning of the now highly stigmatized word ghetto. The t...
Fluorescence ratio imaging microscopy.

Publisher Summary Rapid advancements in low-light-level imaging technology have made it possible to apply the fundamental principles of fluorescence spectroscopic analyses to living cells. The quantitation of an optical signal from living cells attached to a substrate is very difficult. Living cells move, change shape, and vary the local number density of membrane-bound organelles. Fluorescence ratio imaging provides a means of overcoming many of the problems associated with quantifying the complex temporal and spatial dynamics of molecules and organelles in living cells. This chapter describes the issues of fluorescence ratio imaging microscopy, including basic requirements of the instrumentation, validation of the basic tenets of ratioing as applied to microscopy, and some methods and issues in the application of ratio imaging. With continued development and improvement in fluorescent probes for ion measurements as well as the development of probes for other important molecules, the potential applicability of ratio imaging is enormous. Fluorescence ratio imaging is a spectroscopic technique and is usable for any technique that can be expressed by the relationship of signals at two or more wavelengths.
From Research Technique to Classroom Activity

Among the many techniques available for researchers in studying oral language production, elicited imitation (EI) stands out due to its ease of use, reliability, and versatility. The technique consists of a second language (L2) learner who simply listens to a sentence, typically 8–15 words in length, and then repeats verbatim what he or she has just heard.
Automatic relative RPC image model bias compensation through hierarchical image matching for improving DEM quality

Abstract The quality and efficiency of automated Digital Elevation Model (DEM) extraction from stereoscopic satellite imagery is critically dependent on the accuracy of the sensor model used for co-locating pixels between stereo-pair images. In the absence of ground control or manual tie point selection, errors in the sensor models must be compensated with increased matching search-spaces, increasing both the computation time and the likelihood of spurious matches. Here we present an algorithm for automatically determining and compensating the relative bias in Rational Polynomial Coefficients (RPCs) between stereo-pairs utilizing hierarchical, sub-pixel image matching in object space. We demonstrate the algorithm using a suite of image stereo-pairs from multiple satellites over a range stereo-photogrammetrically challenging polar terrains. Besides providing a validation of the effectiveness of the algorithm for improving DEM quality, experiments with prescribed sensor model errors yield insight into the dependence of DEM characteristics and quality on relative sensor model bias. This algorithm is included in the Surface Extraction through TIN-based Search-space Minimization (SETSM) DEM extraction software package, which is the primary software used for the U.S. National Science Foundation ArcticDEM and Reference Elevation Model of Antarctica (REMA) products.
Evolutionarily Conserved Coupling of Adaptive and Excitable Networks Mediates Eukaryotic Chemotaxis

Numerous models have been proposed to explain the remarkable ability of chemotactic cells to sense and migrate toward extremely shallow chemoattractant gradients independently of the ambient concentration. We carried out experiments to distinguish the various models of gradient sensing in migrating cells. First, signaling activity was strongly suppressed toward the low side of cells in a gradient or following sudden removal of uniform chemoattractant. Second, signaling activities displayed a rapid shut off and, with stimulation of increasing duration, a slower adaptation during which responsiveness to subsequent test stimuli declined. Simulations of existing classes of models indicated that these observations can only be explained by the coupling between an adaptive module and an excitable network. Moreover, stimulation of cells lacking G-protein function suppresses downstream activities, while constitutive G-protein activation induced persistent responses. This indicates that chemoattractant sensing is mediated by a G-protein-dependent excitor and a G-protein-independent inhibitor forming an incoherent feedforward loop. The salient features of the coupling between adaptive and excitable networks were observed for the chemoattractants cAMP and folic acid in Dictyostelium as well as fMLP in human neutrophils, suggesting an evolutionarily conserved mechanism for eukaryotic chemotaxis.
Finding Functionally Related Genes by Local and Global Analysis of MEDLINE Abstracts

Abstract : Discovery of biological relationships between genes is one of the keys to understanding the complex functional nature of the human genome. Currently, most of the knowledge about interrelating genes are found in immense amounts of various biomedical literature. Hence, extraction of biological contexts occurring in free text represents a valuable tool in gaining knowledge about gene interactions. We present a textual analysis of documents associated with pairs of genes, and describe how this approach can be used to discover and annotate functional relationships among genes. A study on a subset of human genes show that our analysis tool can act as a ranking mechanism for sets of genes based on their functional relatedness.
Diagnostic accuracy of intraoral film and direct digital images for detection of simulated recurrent decay.

UNLABELLED This study compared the diagnostic accuracy of bitewing images for detection of simulated recurrent caries using the following imaging modalities: Ektaspeed Plus film and different digital imaging system technologies comprised of a charge-coupled device (CCD) based digital imaging unit, a photo-stimulable phosphor (PSP) based unit and contrast- and brightness-enhanced PSP images. STUDY DESIGN Twenty-four extracted posterior teeth with MOD inlay preparations were secured in models simulating a natural arrangement of teeth. Lesions were created in proximal boxes using dental burs of varying sizes. Defects were filled with wax and plaster and preparations were restored with composite or amalgam. RESULTS Averages of receiver operating curve areas (Az) revealed diagnostic performances of Az = 0.74 for film, Az = 0.80 for CCD, Az = 0.73 for unenhanced PSP and Az = 0.64 for enhanced PSP. The differences between these means were significant (MANOVA p < 0.0001). Unenhanced PSP produced significantly poorer performance than other modalities. CCD performance was not significantly better than enhanced PSP. Lesions under radiopaque composite restorations were easier to detect, followed by those under amalgam and radiolucent composites across imaging modalities and lesion locations. Based on lesion location, those located at the buccal point angle were easiest to detect, followed by those at mid-gingival floor and lingual-point angle sites. CONCLUSIONS Contrast and brightness-enhanced digital images enabled better signal detection and a comparable performance with film for detection of artificially induced recurrent caries.
Spherical harmonic expansions of high-resolution directivity data

Quantifying the directivity patterns of sound sources provides not only deeper insights into understanding the source and its acoustical properties but also the potential to simulate the propagation of its sound in various settings. Being able to describe the detailed 3-dimensional directivity of highly complex and dynamic sound sources such as musical instruments and human speech in a simple way while at the same time preserving the fine details of the directivity patterns has broad applications. By using seventeenth-order spherical harmonic expansions of data collected on a 2,664-point spherical array, large amounts of the measured directivity of musical instruments and human speech was condensed in a simple, accurate, and powerful tool for understanding these complex systems.
NEON SIKE: Supersingular Isogeny Key Encapsulation on ARMv7

We present a highly-optimized implementation of Supersingular Isogeny Key Encapsulation (SIKE) mechanism on ARMv7 family of processors. We exploit the state-of-the-art implementation techniques and processor capabilities to efficiently develop post-quantum key encapsulation scheme on 32-bit ARMv7 Cortex-A processors. We benchmark our results on two popular ARMv7-powered cores. Our benchmark results show significant performance improvement of the key encapsulation mechanism in comparison with the portable implementation. In particular, we achieve almost 7.5 times performance improvement of the entire protocol over the SIKE 503-bit prime field on a Cortex-A8 core.
Cellular response to moderate chromatin architectural defects promotes longevity

Changes in chromatin organization occur during aging. Overexpression of histones partially alleviates these changes and promotes longevity. We report that deletion of the histone H3-H4 minor locus HHT1-HHF1 extended the replicative life span of Saccharomyces cerevisiae. This longevity effect was mediated through TOR signaling inhibition. We present evidence for evolutionarily conserved transcriptional and phenotypic responses to defects in chromatin structure, collectively termed the chromatin architectural defect (CAD) response. Promoters of the CAD response genes were sensitive to histone dosage, with HHT1-HHF1 deletion, nucleosome occupancy was reduced at these promoters allowing transcriptional activation induced by stress response transcription factors Msn2 and Gis1, both of which were required for the life-span extension of hht1-hhf1Δ. Therefore, we conclude that the CAD response induced by moderate chromatin defects promotes longevity.
Self-Triggered Interval Observers for Lipschitz Nonlinear Systems

This paper constructs observers for linear and Lipschitz nonlinear systems with self-triggered measurements by utilizing the interval observer framework, which guarantees that an upper bound on the error between the estimated state and the actual state are known. The self-triggered observers are designed based on periodically sampled interval observers which guarantees a positive uniform minimum inter-sampling time. Convex programs for constructing the observer gains and the triggering functions are proposed. Simulation results are given to show the effectiveness of the proposed algorithms.
The Radio Scream from black holes at Cosmic Dawn: a semi-analytic model for the impact of radio-loud black holes on the 21 cm global signal

We use a semi-analytic model to explore the potential impact of a brief and violent period of radio-loud accretion onto black-holes (The Radio Scream) during the Cosmic Dawn on the HI hyperfine 21 cm signal. We find that radio emission from super-massive black hole seeds can impact the global 21 cm signal at the level of tens to hundreds of percent provided that they were as radio loud as z ≈ 1 black holes and obscured by gas with column depths of N_H ≳ 10²³ cm⁻². We determine plausible sets of parameters that reproduce some of the striking features of the EDGES absorption feature including its depth, timing, and side steepness while producing radio/X-ray backgrounds and source counts that are consistent with published limits. Scenarios yielding a dramatic 21 cm signature also predict large populations of ∼μJy point sources that will be detectable in future deep surveys from the Square Kilometer Array (SKA). Thus, 21 cm measurements, complemented by deep point source surveys, have the potential to constrain optimistic scenarios where super-massive black-hole progenitors were radio-loud.
Is dyschloremia a marker of critical illness or euchloremia an interventional target to improve outcomes

Despite chloride being the most abundant extracellular anion, its significance in clinical practice was undervalued for years. In the past decade this has dramatically changed to the point of chloride receiving the distinction of “queen” of electrolytes (1); with several observational and interventional studies focused on the chloride content of crystalloid solutions used for fluid resuscitation.
Cross-Dataset Evaluation of Deep Learning Networks for Uterine Cervix Segmentation

Evidence from recent research shows that automatic visual evaluation (AVE) of photographic images of the uterine cervix using deep learning-based algorithms presents a viable solution for improving cervical cancer screening by visual inspection with acetic acid (VIA). However, a significant performance determinant in AVE is the photographic image quality. While this includes image sharpness and focus, an important criterion is the localization of the cervix region. Deep learning networks have been successfully applied for object localization and segmentation in images, providing impetus for studying their use for fine contour segmentation of the cervix. In this paper, we present an evaluation of two state-of-the-art deep learning-based object localization and segmentation methods, viz., Mask R-convolutional neural network (CNN) and MaskX R-CNN, for automatic cervix segmentation using three datasets. We carried out extensive experimental tests and algorithm comparisons on each individual dataset and across datasets, and achieved performance either notably higher than, or comparable to, that reported in the literature. The highest Dice and intersection-over-union (IoU) scores that we obtained using Mask R-CNN were 0.947 and 0.901, respectively.
The importance of words: revising the social insect lexicon

With the goal of creating a more open and inclusive scientific culture in the study of social insects, suggestions are made about word choice in publications on social insects. Scientists must acknowledge that the use of words with major human cultural associations can deter students and colleagues from engaging our field, and that students may feel emotionally harmed by the use of words like “slave” in scientific contexts. Specific reference in this commentary is made to the applications of slavery, caste, race, and social parasite, which have been used to describe aspects social insect biology. Cleptotecton, meaning stolen work, is suggested as a substitute term for slave, and cleptotectonic for slave-making. The use of geographic descriptors is also discussed. Better, and less culturally loaded, vocabulary is available for these concepts, and authors should reflect on the impacts of word choice on the community of social insect scientists.