cssi/SciSciGPT-SciSciNet huggingface dataset:
“Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated nucleases) is a powerful component of the prokaryotic immune system that has been adapted for targeted genetic engineering in higher organisms. A key element of CRISPR/Cas is the “guide” RNA (gRNA) that is ~20 nucleotides (nts) in length and designed to be complementary to the intended target site. An integral requirement of the CRISPR/Cas system is that the target site be followed by a protospacer adjacent motif (PAM). Care needs to be exercised during gRNA design to avoid unintended (“off-target”) interactions. We designed and implemented the Off-Spotter algorithm to assist with the design of optimal gRNAs. When presented with a candidate gRNA sequence and a PAM, Off-Spotter quickly and exhaustively identifies all genomic sites that satisfy the PAM constraint and are identical or nearly-identical to the provided gRNA. Off-Spotter achieves its extreme performance through purely algorithmic means and not through hardware accelerators such as graphical processing units (GPUs). Off-Spotter also allows the user to identify on-the-fly how many and which nucleotides of the gRNA comprise the “seed”. Off-Spotter’s output includes a histogram showing the number of potential off-targets as a function of the number of mismatches. The output also includes for each potential off-target the site’s genomic location, a human genome browser hyperlink to the corresponding location, genomic annotation in the vicinity of the off-target, GC content, etc. Off-Spotter is very fast and flexible and can help in the design of optimal gRNAs by providing several PAM choices, a run-time definition of the seed and of the allowed number of mismatches, and a flexible output interface that allows sorting of the results, optional viewing/hiding of columns, etc. A key element of Off-Spotter is that it does not have a rigid definition of the seed: instead, the user can declare both the seed’s location and extent on-the-fly. We expect that this flexibility in combination with Off-Spotter’s speed and richly annotated output will enable experimenters to interactively and quickly explore different scenarios and gRNA possibilities. This article was reviewed by Dr Eugene Koonin and Dr Frank Eisenhaber.
Infant-Feeding Beliefs and Experiences of Black Women Enrolled in WIC in the New York Metropolitan Area

In this ethnographic inquiry, the author explored infant-feeding beliefs and experiences of Black women enrolled in WIC (BWEW) in a New York metropolitan inner city. The study was conducted over an 18-month period and included 319 people (130 BWEW, 116 children, 20 grandmothers, 17 fathers, 11 friends, and 25 other relatives). From this group of BWEW, the author interviewed and observed 11 primiparous key informants during pregnancy and the first year postpartum to see how infant-feeding decisions fit into the context of their everyday lives. The major themes that emerged from analysis include (a) formula-feeding experiences were the norm for most BWEW, (b) life experiences of BWEW included a preponderance of loss and stress, and (c) infant-feeding beliefs of BWEW reflected responses to life experiences. These findings could be used to provide culturally sensitive care for BWEW.
Presumption of Incompetence: The Systematic Assignment of Guardianship Within the Transition Process

This article describes the potential impact that state guardianship laws may have on the transition planning process for students identified with intellectual and developmental disabilities under t...
Analysis of the Human Ferrochelatase Promoter in Transgenic Mice

Ferrochelatase catalyzes the chelation of ferrous iron and protoporphyrin to form heme. It is expressed as a housekeeping gene in all cells, but is upregulated during erythropoiesis. Ferrochelatase activity is deficient in the inherited disease protoporphyria as a result of heterogeneous mutations. Although human ferrochelatase is transcribed from a single promoter in both nonerythroid and erythroid cells, previous studies using transient transfection assays failed to demonstrate erythroid-specific increased expression from 4.0 kb of the human ferrochelatase promoter containing the erythroid cis-elements, GATA and NF-E2. The present study analyzes the in vivo regulation of the ferrochelatase gene to provide insights into the mechanism of its erythroid-specific enhancement. Transgenic (TG) mouse lines were generated in which the luciferase reporter gene was driven by either a 150-bp ferrochelatase minimal promoter (-0.15 TG) or by a 4.0 kb extended 5' upstream region (-4.0 TG). Expression of the -4.0 TG transgene was generally consistent with the endogenous gene during embryonic development and in nonerythroid and erythroid tissues as demonstrated by Northern blotting and mRNA in situ hybridization. The -4.0 TG was expressed at a higher level than the -0.15 TG in nonerythroid and erythroid tissues, including during extramedullary erythropoiesis induced by n-acetylphenylhydrazine injection. The enhanced erythroid expression of the -4.0 TG correlates with the appearance of a DNase I hypersensitive site in the 5' flanking region of the transgene. Therefore, in the context of chromosomal integration, the 5' flanking region of the ferrochelatase gene is necessary and sufficient to confer high levels of transgene expression in erythroid tissue.
DDT-Dehydrochlorinase Activity in House Fly Strains Resistant to Various Groups of Insecticides

DDT-ase activity of the soluble subcell fraction from strains of Musca domestica L. resistant to DDT, organophosphate, and carbamate insecticides by virtue of the second chromosomal resistance factors was approximately 10-fold that from the susceptible strains. A naphthalene-selected strain with unclassified resistance factors also exhibited high DDT-ase activity. The kdr-o strain with a third, and the Fc strain with both third (slower absorption) and fifth chromosomal factors for DDT resistance had DDT-ase activity approximately three-fold that of susceptible strains. The Fc strain showed high in vivo conversion of both DDT and DDE (2,2- bis -(p-chlorophenyl)-1, 1-dichloroethylene) to unknown metabolites, but no microsomal activity to oxidize these compounds. DDT-ase in a strain resistant to Isolan® (1-isopropyl-3-methyl-5-pyrozolyl dimethylcarbamate) was inherited through a dominant factor Deh on chromosome II.
Lymphomatoid granulomatosis of the lung, associated with a long history of benign lymphoepithelial lesions of the salivary glands and lymphoid interstitial pneumonitis. Report of a case.

A case of a man who had bilateral benign lymphoepithelial lesions of major salivary glands, subsequently had lymphoid interstitial pneumonitis at the age of 26 years, and progressed to lymphomatoid granulomatosis of the lung at the age of 42 years is reported, A labial gland biopsy was consistent with Sjogren's syndrome, which the patient was clinically suspected of having although his disease lacked many of the classic clinical features of that disorder. There was no evidence of malignant lymphoma of lymph nodes. Immunoglobulin distribances were minor, limited to slightly elevated IgG.
MP60-02 PRETREATMENT NEUTROPHIL-TO-LYMPHOCYTE RATIO IS AN INDEPENDENT PREDICTOR OF ADVANCED PATHOLOGIC STAGE AND CANCER-SPECIFIC SURVIVAL IN PATIENTS WITH UROTHELIAL CARCINOMA UNDERGOING RADICAL CYSTECTOMY

INTRODUCTION AND OBJECTIVES: The term acute kidney injury (AKI) has been proposed to encompass the spectrum of the syndrome from minor changes in renal function to the need for renal replacement therapy (RRT). AKI is seen after general surgery and is associated with morbidity and mortality. Although several studies have addressed the incidence and risk factors for AKI after cardiac and noncardiac surgery, little is known about AKI after urologic surgery. Radical cystectomy (RC) is one of the most invasive surgeries of the urogenital organs. The purpose of this study was to clarify the incidence and risk factors for AKI after RC based on the international Kidney Disease: Improving Global Outcomes (KDIGO) criteria. METHODS: A total of 210 patients underwent RC and urinary diversion (UD) in our institution from January 2006 through December 2012. Finally, evaluation of AKI associated with surgery was feasible for 145 patients, who were then enrolled in this study. Intraoperatively, a ureteral stent was inserted immediately after division of the ureter to avoid obstructive uropathy while minimizing the intraperitoneal urine exposure. The stent was removed 7 days after surgery. Postoperative AKI was assessed within 7 days after surgery according to the KDIGO definition. We evaluated their sex, age, body mass index, comorbidity, neoadjuvant chemotherapy (NAC), preoperative estimated glomerular filtration rate (eGFR), type of UD, operative time, amount of blood loss and postoperative NSAID use to determine the risk factors for postoperative AKI. The chi-square test and logistic regression analysis were used for univariate and multivariate analyses, respectively. RESULTS: Postoperative AKI was observed in 48 patients (33.1%), with stages 1, 2 and 3 in 33 (22.7%), 14 (9.6%) and 1 (0.7%), respectively. One patient (0.7%) required RRT. AKI had no influence on the postoperative course in any patient except the one who had stage 3 AKI and died of vascular complications. In univariate analysis, comorbid hypertension (P < 0.001) and preoperative eGFR < 60 ml/min/m2 (P 1⁄4 0.004) were significantly associated with postoperative AKI. Multivariate analysis revealed that hypertension (P < 0.001) and NAC (P 1⁄4 0.03) were independent risk factors for postoperative AKI. CONCLUSIONS: The incidence of AKI after RC is relatively high, althoughmost cases are low grade and can bemanaged conservatively. We should be aware of the risk for postoperative AKI, especially in patients who have comorbid hypertension and receive NAC.
The Causes of Progressive Stagnation

What accounts for the disconnect between the high end of elite progressive opinion and its other stratums? Why hasn’t there been a greater rejection of judicial review, or a more sustained and broad effort to discredit the courts? To be sure, there have been (and will continue to be) efforts to discredit particular opinions. For instance, many progressives denounced Citizens United v. FEC, with one doing so at the State of the Union. Yet there has been no persistent, general campaign to tear down the courts. Simple reasons account for the failure of the vanguard to convince the rearguard to humble the courts. Habit, identification, preference satisfaction, and the fact that courts remain the most meaningful constitutional game in town all contribute to the continued progressive preference for the courts as the locus of constitutional decision making.
Mechanism and Function of Angiogenin in Apoptosis Regulation

Angiogenin (ANG), a secreted ribonuclease, has been characterized recently as an anti-apoptosis factor involved in a variety of cellular anti-apoptosis process. ANG regulates intrinsic pathways-related major molecules such as anti-apoptotic protein Bcl-2, as well as extrinsic signaling pathways. Moreover, ANG regulates p53-regulated apoptosis, a process considered to be important in regulating both the extrinsic and the intrinsic pathways.
Determining the tensile response of materials at high temperature using DIC and the Virtual Fields Method

Abstract An experimental approach based on Digital Image Correlation (DIC) is successfully applied to predict the uniaxial stress-strain response of 304 stainless steel specimens subjected to nominally uniform temperatures ranging from room temperature to 900 °C. A portable induction heating device equipped with custom made water-cooled copper coils is used to heat the specimen. The induction heater is used in conjunction with a conventional tensile frame to enable high temperature tension experiments. A stereovision camera system equipped with appropriate band pass filters is employed to facilitate the study of full-field deformation response of the material at elevated temperatures. Using the temperature and load histories along with the full-field strain data, a Virtual Fields Method (VFM) based approach is implemented to identify constitutive parameters governing the plastic deformation of the material at high temperature conditions. Results from these experiments confirm that the proposed method can be used to measure the full field deformation of materials subjected to thermo-mechanical loading.
The Effects of Acidic Deposition and Ozone on Forest Tree Species in the Eastern United States: Results from the Forest Response Program

By the early 1980s in North America, several researchers reported problems in northeastern spruce-fir forests. Johnson and Siccama (1983) reported that since the early 1960s red spruce forests at high elevations in New York, Vermont, and New Hampshire have shown dieback and large reductions in basal area and density that are characteristic of a stress-related disease. Because of the locations of these forests, it was suggested that climatic stresses, such as drought, and pollutants in the form of acid deposition and airborne trace metals may contribute to the decline. Hornbeck and Smith (1985) used tree cores from a broad-scale survey of New England low-elevation, dominant, and codominant red spruce and found a large reduction in tree basal area increment occurring since the early 1960s. Reports of red spruce decline are not restricted to the northeast. Bruck (1984) and Adams et al. (1985) reported red spruce declines in the southern Appalachian Mountains.
The Origin of the State: Incentive Compatible Extraction under Environmental Circumscription

Theories of early state formation posit that the state enabled an emerging elite to extract resources in exchange for protection from outside groups. This paper formalizes and empirically evaluates these forces in a unified framework. The model shows that extraction is closely linked to the idea of environmental circumscription: only if outside options are sufficiently poor for potential extractees, (a) they are willing to accept extraction, and (b) extractors consider extraction capacity a worthwhile investment. In a global dataset of archaeological sites on a grid with 184,523 cells, we then show that circumscription is strongly associated with the location of early states, using the intersection of large rivers through arid regions as an instrument. Our estimates suggest that extraction was more important in the Old World civilizations of Egypt and China while other motives such as protection were more important in the New World.
Comparative approximations of criticality in a neural and quantum regime

Abstract Under a variety of conditions, stochastic and non-linear systems with many degrees of freedom tend to evolve towards complexity and criticality. Over the last decades, a steady proliferation of models re: far-from-equilibrium thermodynamics of metastable, many-valued systems arose, serving as attributes of a ‘critical’ attractor landscape. Building off recent data citing trademark aspects of criticality in the brain—including: power-laws, scale-free (1/f) behavior (scale invariance, or scale independence), critical slowing, and avalanches—it has been conjectured that operating at criticality entails functional advantages such as: optimized neural computation and information processing; boosted memory; large dynamical ranges; long-range communication; and an increased ability to react to highly diverse stimuli. In short, critical dynamics provide a necessary condition for neurobiologically significant elements of brain dynamics. Theoretical predictions have been verified in specific models such as Boolean networks, liquid state machines, and neural networks. These findings inspired the neural criticality hypothesis, proposing that the brain operates in a critical state because the associated optimal computational capabilities provide an evolutionarily advantage. This paper develops in three parts: after developing the critical landscape, we will then shift gears to rediscover another inroad to criticality via stochastic quantum field theory and dissipative dynamics. The existence of these two approaches deserves some consideration, given both neural and quantum criticality hypotheses propose specific mechanisms that leverage the same phenomena. This suggests that understanding the quantum approach could help to shed light on brain-based modeling. In the third part, we will turn to Whitehead's actual entities and modes of perception in order to demonstrate a concomitant logic underwriting both models. In the discussion, I briefly motivate a reading of criticality and its properties as responsive to the characterization of tenets from Eastern wisdom traditions.
Integrating Information Literacy and Evidence-Based Medicine Content within a New School of Medicine Curriculum: Process and Outcome

This column describes a process for integrating information literacy (IL) and evidence-based medicine (EBM) content within a new school of medicine curriculum. The project was a collaborative effort among health sciences librarians, curriculum deans, directors, and faculty. The health sciences librarians became members of the curriculum committees, developed a successful proposal for IL and EBM content within the curriculum, and were invited to become course instructors for Analytics in Medicine. As course instructors, the librarians worked with the other faculty instructors to design and deliver active learning class sessions based on a flipped classroom approach using a proprietary Information Mastery curriculum. Results of this collaboration may add to the knowledge base of attitudes and skills needed to practice as full faculty partners in curricular design and instruction.
Does matching for SNPs in the MHC gamma block in 10/10 HLA-matched unrelated donor-recipient pairs undergoing allogeneic stem cell transplant improve outcomes?

Abstract Background Matching at the HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 loci is important in donor selection for patients undergoing unrelated allogeneic hematopoietic stem cell transplantation (ASCT). Additional matching across the MHC gamma region may further improve outcomes. Methods The MHC gamma region was retrospectively genotyped in 66 adult recipients of ASCT and their 10/10 matched unrelated donors. A chart review was performed to determine whether MHC gamma matching impacted survival, relapse, or graft-versus-host disease. Results Of 66 donor-recipient pairs, 26(39.4%) were gamma-type matches, 34(51.5%) were mismatches, and 6(9.1%) were “indeterminate.” Matching status was not associated with overall survival (p = 0.43), relapse (p = 0.21), acute GVHD (p = 0.43), severe aGVHD (p = 0.31), or chronic GVHD (p = 0.23) in univariate analyses, nor in multivariate analyses (p = 0.28, 0.13, 0.29, 0.16, and 0.67, respectively), with or without adjusting for HLA-DPB1 matching status. Conclusions In our single institution study, gamma-type matching status was not associated with outcomes of adult ASCT recipients.
Evaluation of Compliance with a Weight-based Nurse-driven Heparin Nomogram in a Tertiary Academic Medical Center.

BACKGROUND Recently, our institution adopted a weight-based nurse-driven heparin titration protocol that relies on nurses ordering laboratories, adjusting doses, and initiating boluses. Numerous institutions have implemented similar protocols with reported success. METHODS A single-center retrospective analysis was conducted at the Brigham and Women's Hospital in Boston, Massachusetts that included all patients who were initiated on the weight-based nurse-driven heparin nomogram during a 30-day period. Nomogram compliance was defined as the rate of correct titrations per nomogram encounter and further separated into laboratory, titration, or dosing compliance. Spearman's coefficient was utilized to determine the correlation between noncompliance and percentage of activated partial thromboplastin time (aPTT) values in range. RESULTS Overall, 211 patients were evaluated for inclusion, of which 95 patients were determined to meet criteria for evaluation. The total nomogram compliance rate was 84.6% ± 10.5%. Laboratory, titration, and dosing compliances were 77.6% ± 19.2%, 87.2% ± 14.5%, and 91.8% ± 10.6%, respectively. The percent of aPTT values in therapeutic range was 39.6% ± 24.6%. A moderate negative correlation between the percentage of aPTT values in range and the nomogram error rate was observed (r = -0.452, P < 0.001). This relationship was found to be driven by the rate of dosing error, which showed the strongest correlation with percentage of aPTT values out of range (r = -0.465, P = 0.001). CONCLUSIONS Implementation of a nurse-driven heparin titration nomogram relies on compliance with the prescribed protocol. Dosing compliance had the lowest error rate, whereas dosing noncompliance had the strongest impact on percentage of aPTT values in range.
The virtual apprentice

Over the past couple of decades, virtual humans have been attracting more and more attention. Many applications including, video games, movies, and various training and tutoring systems have benefited from work in this area. While the visual quality of virtual agents has improved dramatically, their intelligence and socialization still needs improvement. In this paper, we present work towards endowing agents with social roles and exploiting Explanation-Based Learning (EBL) to enable them to acquire additional, contextual behaviors from other agents. These virtual humans are capable of learning and applying role related actions from multiple agents and only adopt behaviors that have been explained to them, meaning that their definition of a role may be a subset from one or more agents. This results in emergent behaviors in heterogeneous populations.
Agroforestry potential in the southeastern United States: perceptions of landowners and extension professionals

The first steps in developing an agroforestry extension and training program involve compilation, synthesis, and analysis of current knowledge on existing practices. Equally important is to understand the perceptions of landowners and professionals of agroforestry as a land use option. No systematic effort has been made to assess these critical issues in the southeastern United States. Therefore, needs assessment surveys were developed following an analysis of major demographic issues that frame land use in the region and synthesis of information obtained from informal site visits and interviews with people engaged in resource and land use in the Atlantic and Gulf Coastal Plain. Surveys of extension professionals and landowners were then undertaken in the states of Alabama, Florida, and Georgia to represent the southeastern region. In addition to getting insights into the perceived benefits and concerns about agroforestry practices, the surveys indicated that the extent of alley cropping, forest farming and silvopasture practiced by landowners was less than anticipated, and that the prominence of windbreaks was overlooked by professionals. Managed riparian forest buffers or streamside management zones and windbreak technologies were the most widely used forms of agroforestry in the study area, although landowners did not recognize influence of agroforestry practices on quality or quantity of water among benefits of highest importance to them. Multistrata patio- or home gardens were also a prominent landowner-practice and acknowledged by professionals. These survey results can be useful for developing a relevant agroforestry extension and training program in the subtropical Southeast and may be of interest to agroforestry efforts in other similar settings.
Glucocorticoid-Induced Death of Immune Cells: Mechanisms of Action

Cell death occurs in many physiological situations, including embryogenesis, differentiation, and metamorphosis. It is an important mechanism in maintaining homeostasis by providing a counterbalance to mitosis. There are at least two types of cell death that are now recognized: necrosis and apoptosis. In necrosis, the cell undergoes irreversible swelling and lysis in response to a variety of signals which are primarily nonphysiological; the plasma membrane disrupts and then spills the intracellular contents into the environment, resulting in activation of the immune response. Apoptosis, by contrast, is inherently “programmed” as part of the cellular processes, allowing the cell to die in response to a variety of signals without a deleterious effect on surrounding cells, i.e., it does not elicit an immune response. Details of the morphology of apoptosis have been extensively reported (Kerr et al. 1972; Arends and Wyllie 1991; Schwartzman and Cidlowski 1993a; Compton and Cidlowski 1992), but briefly, apoptosis involves separation of the cell from its neighbors, condensing of the cytoplasm, condensing of the chromatin, which moves to the margins of the nuclear envelope, convolution of the plasma membrane, and, finally, blebbing off of apoptotic bodies, which contain various organelles and chromatin fragments.
Multiexciton Lifetimes Reveal Triexciton Emission Pathway in CdSe Nanocrystals

Multiexcitons in emerging semiconducting nanomaterials play a critical role in potential optoelectronic and quantum computational devices. We describe photon resolved single molecule methods to directly probe the dynamics of biexcitons and triexcitons in colloidal CdSe quantum dots. We confirm that biexcitons emit from a spin-correlated state, consistent with statistical scaling. Contrary to current understanding, we find that triexciton emission is dominated by band-edge 1Se1S3/2 recombination rather than the higher energy 1Pe1P3/2 recombination.
Luther’s Biblical Hermeneutics as Ethics:

This article examines a thread that runs through Martin Luther’s biblical and catechetical writings: his appropriation of a Messianic logic in light of a creedal interpretation of the whole of Scripture. Situating my case in relation to recent philosophical scholarship on the apostle Paul, I contend that this biblical hermeneutic may well be Luther’s signal ethical contribution for our age. Drawing on the solae (sola gratia, sola fide, sola scriptura, and solus Christus) and relating them to three themes central to his biblical hermeneutics—the Word of God, Scripture, and the Creeds—I discuss how he develops (1) a Messianic ethics that intrinsically links faith and love in relation to (2) the biblical motifs of command and promise and (3) the Christological themes of cross and incarnation. I conclude by discussing the relevance of Luther’s biblical hermeneutics for a post-secular age.
Deploying Robust Security in Internet of Things

Popularization of the Internet-of-Things (IoT) has brought widespread concerns on IoT security, especially in face of several recent security incidents related to IoT devices. Due to the resource-constrained nature of many IoT devices, security offloading has been proposed to provide good-enough security for IoT with minimum overhead on the devices. In this paper, we investigate the inevitable risk associated with security offloading: the unprotected and unmonitored transmission from IoT devices to the offloaded security mechanisms. An important challenge in modeling the security risk is the dynamic nature of IoT due to demand fluctuations and infrastructure instability. We propose a stochastic model to capture both the expected and worst-case security risks of an IoT system. We then propose a framework to efficiently address the optimal robust deployment of security mechanisms in IoT. We use results from extensive simulations to demonstrate the superb performance and efficiency of our approach compared to several other algorithms.
Oxidation of Glucose Using Mono- and Bimetallic Catalysts under Base-Free Conditions

Oxidation of glucose to gluconic and glucaric acid using molecular O2 in aqueous solution is an environmentally friendlier alternative to the conventional method, which uses nitric acid as the oxidant. However, obtaining a satisfactory yield of the desirable product, glucaric acid, especially under base-free conditions, is still a challenge. In this paper, optimization of Pt-based mono- and bimetallic catalysts is reported by tuning four factors: support type, synthesis method, reductant used in the synthesis, and choice of the second metal. All four of these factors influence the glucaric acid selectivity. Among the tested combinations, the Pt–Cu/TiO2 bimetallic catalyst showed ∼60% glucaric acid selectivity in one-step glucose oxidation under base-free conditions at 90 °C and 15 bar O2. The catalyst consists of Pt metal particles (∼2.8 nm diameter on average) with a dominant presence of the alloyed Pt–Cu phase, as confirmed by X-ray diffraction and transmission electron microscopy analyses. These result...
Emphasizing Functional Relevance Over State Restoration in Post-Silicon Signal Tracing

The state restoration ratio (SRR) has been a de facto standard for evaluating the quality of signals selected for post-silicon tracing and debug. In this paper, we establish that SRR is intrinsically unsuitable as a metric for evaluating trace signal quality, as it captures neither the higher-level functionality of the design nor the constraints and requirements on trace signals. We present an algorithm, based on PageRank [PageRank on Netlist (PRoN)], for post-silicon trace signal selection. PageRank is not designed to maximize SRR and is applied to the circuit netlist. We demonstrate that optimizing for SRR typically generates signals that are functionally irrelevant to the design and unusable for debug, for a comprehensive set of SRR-based techniques. We assess the scalability of different signal selection algorithms by applying them to an industrial scale OpenSPARC T2 design. Our results show that our PRoN algorithm consistently outperformed other techniques with respect to scalability and functional relevance of signals selected. It also has higher restorability than the other algorithms, despite not being optimized for that metric.
Sensory neurons in the spinal cord of zebrafish and their local connectivity

Sensory neurons of the spinal cord provide critical information on the internal and external environment. We review recent work that has made significant strides in elucidating the structure and function of two such neurons, excitatory Rohon-Beard neurons and inhibitory cerebrospinal fluid contacting neurons. These studies provide newfound appreciation for the diversity within each of these cell types and for the high complexity of sensory inputs to motor circuits in the spinal cord. We highlight research that links sensory neurons and spinal circuits to behaviors, leveraging the zebrafish as a powerhouse system to interrogate whole, intact circuitry in a behaving animal.
Acute increases in O-GlcNAc indirectly impair mitochondrial bioenergetics through dysregulation of LonP1-mediated mitochondrial protein complex turnover

The attachment of O-linked β-N-acetylglucosamine (O-GlcNAc) to the serine and threonine residues of proteins in distinct cellular compartments is increasingly recognized as an important mechanism r...
Comprehensive Evaluation of Program Reliability with ComFIDet: An Integrated Fault Injection and Detection Framework for Embedded Systems

The study of program behavior in unreliable hardware infrastructure via fault injection is of great interest to researchers. By modeling the effect of faults on program behavior, programs can be tuned to be more fault resilient via fault-tolerant approaches, or to be tuned to saved energy via approximate computing techniques. Existing frameworks, however, do not adequately address the need of fault injection/detection simulation. To fill this gap, this paper proposes ComFIDet, a low-overhead and comprehensive instruction-level fault injection/detection framework. ComFIDet allows for the identification of both reliable and unreliable regions of a program via the simulation of a variety of hardware faults and can further be utilized in the tuning of a reliable design or an approximate computing technique through the implementation of run-time fault detection and effortless experiment replay. ComFIDet offers an easy to reconfigure process, iterative fault injection experiments, and requires zero modifications to the program under test. ComFIDet is evaluated through a comprehensive set of tests, exploring the effects of one possible configuration on program behavior.
Grafting metal complexes onto amorphous supports: From elementary steps to catalyst site populations: Via kernel regression

Ab initio computational studies have made tremendous progress in describing the behavior of molecular (homogeneous) catalysts and crystalline versions of heterogeneous catalysts, but not for amorphous heterogeneous catalysts. Even widely used industrial amorphous catalysts like atomically dispersed Cr on silica remain poorly understood and largely intractable to computational investigation. The central problems are that (i) the amorphous support presents an unknown quenched disordered structure, (ii) metal atoms attach to various surface grafting sites with different rates, and (iii) the resulting grafted sites have different activation and catalytic reaction kinetics. This study combines kernel regression and importance sampling techniques to efficiently model grafting of metal ions onto a non-uniform ensemble of support environments. Our analysis uses a simple model of the quenched disordered support environment, grafting chemistry, and catalytic activity of the resulting grafted sites.
Finite element analysis and simulation study on micromachining of hybrid composite stacks using Micro Ultrasonic Machining process

Abstract Hybrid composites stacks are multi-material laminates which find extensive applications in industries such as aerospace, automobile, and electronics and so on. Most hybrid composites consist of multiple layers of fiber composites and metal sheets stacked together. These composite stacks have excellent physical and mechanical properties including high strength, high hardness, high stiffness, excellent fatigue resistance and low thermal expansion. Micromachining of these materials require particular attention as conventional methods such as micro-drilling is extremely challenging considering the non-homogeneous structure and anisotropic nature of the material layers. Micro Ultrasonic Machining (μUSM) is a manufacturing process capable of machining such difficult-to-machine materials with ultraprecision. Experimental study showed that μUSM process could successfully machine hybrid composite stacks at micron scale with a relatively good surface finish. This research uses finite element simulation technique to investigate the material removal during the μUSM process for micromachining hybrid composite stacks. The effects of critical process parameters including the amplitude of vibration, feed rate and tool material on the cavity depth, cutting force and equivalent stress distribution are studied. The outcome of this research can be utilized to further our understanding of performing precision machining of hybrid composite stacks for use in several critical engineering applications.
A Surface Complexation Model of Alkaline-SmartWater Electrokinetic Interactions in Carbonates

Understanding the effect of injection water chemistry is becoming crucial, as it has been recently shown to have a major impact on oil recovery processes in carbonate formations. Various studies have concluded that surface charge alteration is the primary mechanism behind the observed change of wettability towards water-wet due to SmartWater injection in carbonates. Therefore, understanding the surface charges at brine/calcite and brine/crude oil interfaces becomes essential to optimize the injection water compositions for enhanced oil recovery (EOR) in carbonate formations. In this work, the physicochemical interactions of different brine recipes with and without alkali in carbonates are evaluated using Surface Complexation Model (SCM). First, the zeta-potential of brine/calcite and brine/crude oil interfaces are determined for Smart Water, NaCl, and Na2 SO4 brines at fixed salinity. The high salinity seawater is also included to provide the baseline for comparison. Then, two types of Alkali (NaOH and Na2 CO3 ) are added at 0.1 wt% concentration to the different brine recipes to verify their effects on the computed zeta-potential values in the SCM framework. The SCM results are compared with experimental data of zeta-potentials obtained with calcite in brine and crude oil in brine suspensions using the same brines and the two alkali concentrations. The SCM results follow the same trends observed in experimental data to reasonably match the zeta-potential values at the calcite/brine interface. Generally, the addition of alkaline drives the zeta-potentials towards more negative values. This trend towards negative zeta-potential is confirmed for the Smart Water recipe with the impact being more pronounced for Na2 CO3 due to the presence of divalent anion carbonate (CO3 )-2 . Some discrepancy in the zeta-potential magnitude between the SCM results and experiments is observed at the brine/crude oil interface with the addition of alkali. This discrepancy can be attributed to neglecting the reaction of carboxylic acid groups in the crude oil with strong alkali as NaOH and Na2 CO3 . The novelty of this work is that it clearly validates the SCM results with experimental zeta-potential data to determine the physicochemical interaction of alkaline chemicals with SmartWater in carbonates. These modeling results provide new insights on defining optimal SmartWater compositions to synergize with alkaline chemicals to further improve oil recovery in carbonate reservoirs.
Comment on "Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2)".

A very interesting report, for the first time, provided direct evidence that the ongoing pandemic etiological agent, SARS‐CoV‐2, may be able to directly infect central nervous system (CNS) through an endothelial route. If proven true, this may explain frequent neurological symptoms associated with severe COVID‐19 diseases. A corresponding therapeutic intervention will be urgently needed to prevent such dangerous infections of CNS and associated high mortality rate.This article is protected by copyright. All rights reserved.
Biomechanical Modeling of Aneurysms

Aneurysms are abnormal dilations in the arterial wall and predominantly occur in the aorta and in the cerebral vasculature. The aortic aneurysm is predominantly found in the infrarenal abdominal region and the cerebral aneurysms generally occur in or near the circle of Willis. There is considerable interest in understanding the mechanism underlying aneurysm growth, diagnosing their severity or propensity to rupture, and developing endovascular implants to treat the same. Biomechanical simulations are being employed to improve our understanding of factors that trigger aneurysms and mechanisms for growth/rupture of the lesions. In this chapter, studies on reconstruction of the three-dimensional geometry of the aneurysms, material modeling of the arterial wall and aneurysm components, and biomechanical analyses toward prediction of potential rupture are discussed.
Parent-child relationships in Latinx families: The role of immigrant concentration, residential stability, and generational status.

Prior research links neighborhood immigrant concentration and residential stability to individual health outcomes. It remains unclear how neighborhood social organization extend to family functioning among immigrant families. Expanding the scope of research on neighborhoods and family relationships, this study draws on data from 1417 Latinx families (Myouth age = 10.19 years, SDyouth age = 3.34) to: (1) examine associations between neighborhood immigrant concentration, residential stability, and parent-child warmth and conflict in Latinx families, and (2) test whether associations vary by family generational status. Multilevel mod3els revealed that associations between immigrant concentration and parent-child relationships were contingent on residential stability, and that the association differed according to generational status. In general, stable neighborhoods with larger immigrant populations were associated with more warmth and less conflict for first- and second-generation families relative to foreign-born families. Discussion centers on the conditional role of neighborhood structural characteristics for family relationships among Latinx families and advances directions for future research on neighborhoods and families.
Medicare Part D Plans Rarely Cover Brand-Name Drugs When Generics Are Available

Recent press reports and other evidence suggest that Medicare Part D plans may be encouraging the use of brand-name drugs instead of generics. However, the scope of such practices is unclear. We ex...
Variations in Perioperative Antibiotic Prescriptions Among Academic Urologists After Ambulatory Endoscopic Urologic Surgery: Impact on Infection Rates and Validation of 2019 Best Practice Statement

Abstract Objective To evaluate adherence to the American Urologic Association (AUA) best practice statement guidelines regarding antibiotic duration in the perioperative setting for endoscopic urologic surgery. We assessed concordance to these guidelines among adult urologists at a single academic institution and its correlation with postoperative positive urine cultures as it relates to the revised 2019 best practice statement. Methods We performed a retrospective review of all adult endoscopic ambulatory urologic surgeries performed over an 18-month period by urologists at our institution. Patient demographics, pre- and postoperative urine cultures, operative details, stent or foley use, and antibiotic prescriptions were reviewed. Chi-squared and linear regression analyses were done. Results Three hundred thirty patients were included for analysis. Sixty-two percent of patients were prescribed postoperative antibiotics, for an average of 4 days. Trimethoprim/Sulfamethoxazole and fluroquinolones were most often prescribed (43% and 38%, respectively). Intraoperative stent placement, positive urine culture within 30 days prior to surgery, and a positive urine culture within 1 year prior to surgery predicted antibiotic prescription. No significant differences were seen in rates of positive postoperative urine culture rates between cohorts that received antibiotics postoperatively vs those who did not. Conclusions At our academic institution, we observed poor concordance with the AUA best practice statement for perioperative antibiotic prescription after ambulatory endoscopic urologic surgery. Rates of positive postoperative cultures were low and not associated with receipt or duration of antibiotic prescription at the time of surgery, supporting minimal use of antibiotics for most endoscopic cases.
Mixture Solubility Parameters from Experimental Data and Perturbed-Chain Statistical Associating Fluid Theory

The solubility parameter is frequently used to screen potential solvents for a variety of applications. Solubility parameters for pure components are well documented; however, solvents used in indu...
Risk and Protective Factors for Preterm Birth Among Black Women in Oakland, California.

This project examines risk and protective factors for preterm birth (PTB) among Black women in Oakland, California. Women with singleton births in 2011–2017 (n = 6199) were included. Risk and protective factors for PTB and independent risk groups were identified using logistic regression and recursive partitioning. Having less than 3 prenatal care visits was associated with highest PTB risk. Hypertension (preexisting, gestational), previous PTB, and unknown Women, Infant, Children (WIC) program participation were associated with a two-fold increased risk for PTB. Maternal birth outside of the USA and participation in WIC were protective. Broad differences in rates, risks, and protective factors for PTB were observed.
Between the devil and the deep blue sea: Objectivity and political responsibility in the litigation of the Exxon Valdez oil spill:

Objectivity is widely recognized as a fundamental value in the sciences. Yet objectivity may be deployed as a filter or screen that discourages scientists from reflecting on the political consequen...
Privacy-Preserving Distributed Analytics in Fog-Enabled IoT Systems

The Internet of Things (IoT) has evolved significantly with advances in gathering data that can be extracted to provide knowledge and facilitate decision-making processes. Currently, IoT data analytics encountered challenges such as growing data volumes collected by IoT devices and fast response requirements for time-sensitive applications in which traditional Cloud-based solution is unable to meet due to bandwidth and high latency limitations. In this paper, we develop a distributed analytics framework for fog-enabled IoT systems aiming to avoid raw data movement and reduce latency. The distributed framework leverages the computational capacities of all the participants such as edge devices and fog nodes and allows them to obtain the global optimal solution locally. To further enhance the privacy of data holders in the system, a privacy-preserving protocol is proposed using cryptographic schemes. Security analysis was conducted and it verified that exact private information about any edge device’s raw data would not be inferred by an honest-but-curious neighbor in the proposed secure protocol. In addition, the accuracy of solution is unaffected in the secure protocol comparing to the proposed distributed algorithm without encryption. We further conducted experiments on three case studies: seismic imaging, diabetes progression prediction, and Enron email classification. On seismic imaging problem, the proposed algorithm can be up to one order of magnitude faster than the benchmarks in reaching the optimal solution. The evaluation results validate the effectiveness of the proposed methodology and demonstrate its potential to be a promising solution for data analytics in fog-enabled IoT systems.
Medication adherence to injectable glucagon-like peptide-1 (GLP-1) receptor agonists dosed once weekly vs once daily in patients with type 2 diabetes: A meta-analysis.

Background Suboptimal medication adherence has been associated with increased resource utilisation and mortality among patients with type 2 diabetes (T2D). Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are becoming increasingly important in the treatment of T2D. However, medications in this class differ considerably in their dosing frequency, which may impact adherence. We sought to perform a meta-analysis to compare adherence to injectable GLP-1RAs dosed once weekly vs once daily in patients with T2D. Methods Medline and Scopus were searched from 1/2005 to 7/2020 using keywords and MeSH terms pertaining to adherence and GLP-1RAs. Studies of adults with T2D were included if they compared adherence (as measured by proportion of days covered [PDC]) to injectable GLP-1RAs dosed once weekly vs once daily. A meta-analysis of non-overlapping studies was performed to evaluate the primary outcome of non-adherence, defined as the proportion of patients with a PDC Results A total of 7 studies evaluating 75 159 patients (range: 2886-30 097) with T2D were included. The follow-up periods of included studies ranged from 6 to 12 months. Injectable GLP-1RAs dosed once weekly were either dulaglutide, albiglutide or exenatide extended release; while liraglutide was the injectable once daily agent evaluated in all included studies. Upon meta-analysis, once weekly GLP-1RA dosing was associated with an 11% lower risk of non-adherence compared to once daily dosing (risk ratio = 0.89; 95% confidence interval = 0.83-0.95; I2 = 89%). Conclusion Once weekly dosing of injectable GLP-1RAs was associated with better adherence vs once daily dosing among patients with T2D. These findings coupled with the known detrimental consequences of non-adherence suggest that dosing frequency is an important factor to consider when selecting a GLP-1RA.