cssi/SciSciGPT-SciSciNet huggingface dataset:
FastSpot: Host-compiled thermal estimation for early design space exploration

Power and temperature of modern day systems have become important metrics in addition to performance. Static and dynamic power dissipation leads to an increase in temperature, which creates cooling and packaging issues. Furthermore, the transient thermal profile determines temperature gradients, hotspots and thermal cycles, which influence wear-out and reliability. Fast and accurate methodologies to facilitate estimation of temperature are needed during design space exploration. Traditional solutions rely on cycle-accurate simulations of detailed micro-architectural structures and are slow. We propose an approach that integrates accurate thermal estimation into existing host-compiled simulations. The developed methodology can incorporate different thermal models, such as HotSpot or discrete-time temperature evaluation models (DTTEMs). Using DTTEM as our thermal model, we show a 32000x increase in simulation throughput for temperature trace generation, incurring an average 0.06 K error in transient trace generation and 0.014 K error in steady state temperature measurements when compared to a cycle-accurate reference method. A comparative study between HotSpot and DTTEM based on speed/accuracy tradeoffs is reported for the thermal estimation process, showing that a 9x increase in simulation throughput can be achieved using DTTEM as the thermal model while incurring only marginal temperature measurement errors.
Heparan sulfate proteoglycans initiate dengue virus infection of hepatocytes

Dengue viruses (DEN) cause a broad spectrum of clinical manifestations including potentially life-threatening conditions such as hemorrhagic shock syndrome and less frequently acute hepatitis with liver failure and encephalopathy. In addition, dengue viruses provide a potential model to understand the initiation of hepatocyte infection by the structurally closely related hepatitis C virus (HCV), because this virus at present cannot be grown in cell culture. Although the initial steps of viral infection are a critical determinant of tissue tropism and therefore pathogenesis, little is known about the molecular basis of binding and endocytic trafficking of DEN or of any other flavivirus. Our studies revealed that binding of radiolabeled DEN to the human hepatoma cell line HuH-7 was strictly pH dependent and substantially inhibitable by the glycosaminoglycan heparin. Ligand-blot analysis, performed as a viral overlay assay, showed two heparan sulfate (HS) containing cell-surface binding proteins resolving at 33 and 37 kd. Based on the sensitivity of unprotected virus and the viral binding site on the cell surface to trypsin, viral internalization was quantified as an increase in trypsin protected virus over time. Virus trafficking to the site of degradation was inhibited by pH dissociation of the clathrin coat and dependent on IP(3)-mediated homotypic endosomal fusion. These findings confirm the hypothesis that binding and internalization of DEN by hepatocytes are mediated primarily by HS containing proteoglycans and suggest that flaviviruses traffic the major clathrin-dependent endocytic pathway during infection.
BeatTable: a tangible approach to rhythms and ratios

Frameworks that create synergies across disciplines provide a powerful means for learning by relating concepts from the different fields that are usually difficult to grasp individually. We discuss the design of the BeatTable, a microworld that uses the relation between mathematics and music to engage learners in using ratios and proportions to create rhythms and learn about musical composition. The BeatTable is a physical table with a digital environment that can be controlled by tangible instruments, and through immediate auditory and visual feedback makes salient the relationships between math and music. With a low-floor, high-ceiling design philosophy, BeatTable provides learners the opportunity to build on their conceptions about music and to practice and hone their use of ratios and proportions. We present what our design choices, the technology used, and a description of initial user feedback.
ICF-CY: A Universal Tool for Documentation of Disability

The International Classification of Functioning, Disability and Health—ICF (ICF-CY) conceptual framework offers a new paradigm and taxonomy of human functioning disability, which can be used to guide holistic and interdisciplinary approaches to assessment and intervention. In settings serving children, youth, or adults with disabilities, the ICF-CY can provide comprehensive documentation of its involvement in special education and rehabilitation. Implementation of the ICF-CY in early intervention, special education, and habilitation settings should build on the adoption of the dimensional framework for practice and correspond­ ing applications in assessment and intervention practices. An important priority in such applications is the identification and development of instruments and assessment tools that can provide evidence for assigning severity levels to ICF-CY codes.
Epigenetic regulation by Z-DNA silencer function controls cancer-associated ADAM-12 expression in breast cancer: cross-talk between MeCP2 and NF1 transcription factor family.

A disintegrin and metalloprotease domain-containing protein 12 (ADAM-12) is upregulated in many human cancers and promotes cancer metastasis. Increased urinary level of ADAM-12 in breast and bladder cancers correlates with disease progression. However, the mechanism of its induction in cancer remains less understood. Previously, we reported a Z-DNA–forming negative regulatory element (NRE) in ADAM-12 that functions as a transcriptional suppressor to maintain a low-level expression of ADAM-12 in most normal cells. We now report here that overexpression of ADAM-12 in triple-negative MDA-MB-231 breast cancer cells and breast cancer tumors is likely due to a marked loss of this Z-DNA–mediated transcriptional suppression function. We show that Z-DNA suppressor operates by interaction with methyl-CpG-binding protein, MeCP2, a prominent epigenetic regulator, and two members of the nuclear factor 1 family of transcription factors, NF1C and NF1X. While this tripartite interaction is highly prevalent in normal breast epithelial cells, both in vitro and in vivo, it is significantly lower in breast cancer cells. Western blot analysis has revealed significant differences in the levels of these 3 proteins between normal mammary epithelial and breast cancer cells. Furthermore, we show, by NRE mutation analysis, that interaction of these proteins with the NRE is necessary for effective suppressor function. Our findings unveil a new epigenetic regulatory process in which Z-DNA/MeCP2/NF1 interaction leads to transcriptional suppression, loss of which results in ADAM-12 overexpression in breast cancer cells. Cancer Res; 73(2); 736–44. ©2012 AACR.
A neurocontrol for automatic reconstruction of facial displays

Anthropomorphic representations of software agents (avatars) are being used as user interfaces in order to enhance communication bandwidth and interaction with human users. They have been traditionally programmed and controlled by ontologies designed according to intuitive and heuristic considerations. More recently, recurrent neural nets have been trained as neurocontrollers for emotional displays in avatars, on a continuous scale of negative, neutral, and positive feedback, that are meaningful to users in the context of tutoring sessions on a particular domain (computer literacy). We report on a new neurocontrol developed as a recurrent network to autonomously and dynamically generate and synchronize the movements of facial features such as lips, eyes, eyebrows, and gaze in order to produce facial displays that convey high information content on nonverbal behavior to untrained human users. The neurocontrol is modular and can be easily integrated with semantic processing modules of larger agents that operate in real-time, such as videoconference systems, tutoring systems, and more generally, user interfaces coupled with affective computing modules for naturalistic communication. A novel technique, cascade inversion, provides an alternative to backpropagation through time where the latter may fail to learn recurrent neural nets from previously learned modules playing a role in the final solution.
Magnetic Resonance Imaging Determination of Cardiac Prognosis

Background— Regional assessments of left ventricular (LV) wall motion obtained during MRI cardiac stress tests can be used to identify myocardial injury and ischemia, but the utility of MRI stress test results for the assessment of cardiac prognosis is not known. Methods and Results— Two hundred seventy-nine patients referred (because of poor LV endocardial visualization with echocardiography) for dobutamine/atropine MRI for the detection of inducible ischemia were followed for an average of 20 months. After MRI stress testing, the occurrence of myocardial infarction, cardiac death, death attributable to any cause, coronary arterial revascularization, and unstable angina or congestive heart failure requiring hospitalization was determined. In a multivariate analysis, the presence of inducible ischemia (hazard ratio 3.3, CI 1.1 to 9.7) or an LV ejection fraction <40% (hazard ratio 4.2, CI 1.3 to 13.9) was associated with future MI or cardiac death independent of the presence of risk factors for coronary arteriosclerosis. Conclusions— In patients with poor echocardiograms, the results of cardiac MRI stress tests can be used to forecast myocardial infarction or cardiac death. Received June 14, 2002; revision received August 14, 2002; accepted August 16, 2002.
Polytetrafluoroethylene Ingestion as a Way to Increase Food Volume and Hence Satiety Without Increasing Calorie Content

Since satiety is largely due to stretch of the stomach and people tend to eat a consistent weight of food, increasing food volume and mass increases satiety. This can be achieved without increasing the calories of food by mixing food with a material that cannot be metabolized. Such a material should be inert, safe, resistant to stomach acid, lack taste, available in powder form, smooth, resistant to heat, and cost effective. Polytetrafluoroethylene (PTFE) is an ideal substance for this purpose. It is a soft plastic that is widely considered to be the most inert material known and is extremely stable. Animal feeding trials showed that rats fed a diet of 25% PTFE for 90 days had no signs of toxicity and that the rats lost weight. This article publishes the data from these subchronic animal feeding trials, reviews the relevant available literature, and hypothesizes that increasing the volume of food by mixing the food with PTFE powder at a ratio of 3 parts food to 1 part PTFE by volume will substantially improve satiety and reduce caloric consumption in people.
Derivation of GMP-compliant integration-free hiPSCs using modified mRNAs

The clinical use of human induced pluripotent stem cells (hiPSCs) and the development of patients-specific gene and cell therapies rely on the development of fast, reliable, and integration-free methods of derivation of pluripotent stem cells from somatic tissues. Here we describe an integration-free protocol for the rapid derivation of hiPSCs from dermal fibroblasts using modified mRNAs. This method is inexpensive, highly efficient, and makes use of reagents that are xeno-free and chemically defined and can therefore be adopted by any Good Manufacturing Practice (GMP) facility.
GPU-Accelerated Computing with Gibbs Sampler for the 2PNO IRT Model

Item response theory (IRT) is a popular approach used for addressing large-scale statistical problems in psychometrics as well as in other fields. The fully Bayesian approach for estimating IRT models is usually memory and computational expensive due to the large number of iterations. This limits the use of the procedure in many applications. In an effort to overcome such restrictions, previous studies proposed to tackle the problem using massive core-based graphic processing units (GPU), and demonstrated the advantage of this approach over the message passing interface (MPI) by showing that a single GPU card could achieve a speedup of up to 50×. Given that GPU is practical, cost-effective, and convenient, this study aims to seek further improvements using a single GPU card.
A case study of right ventricular rupture in an elderly victim of motor vehicle crash: incorporating end-of-life care into trauma nursing.

Cardiac trauma fatalities occur in 22% of victims of motor vehicle crash. Blunt cardiac trauma may result in myocardial rupture. Mechanisms of injury include compression, deceleration, laceration, and "hydraulic ram" effect. Diagnosis is difficult because of coexisting injuries and the lack of evidence-based protocols. Physiological changes in the elderly and the presence of comorbid illness result in poor survival rates when myocardial rupture occurs. Trauma nurses must be prepared to provide end-of-life care related to the poor outcome associated with myocardial rupture. This case study reports a right ventricular rupture in an elderly patient involved in a frontal motor vehicle crash. Language: en
Intermittent hypoglycemia of childhood.

Seizures in an otherwise well child may be associated with intermittent hypoglycemia. Diagnostic laboratory tests are mandatory to exclude primary hormonal causes of hypoglycemia and certain rare inborn errors of metabolism. If the diagnosis of intermittent, or ketotic, hypoglycemia is established, simple therapeutic measures generally are effective.
Performance prediction of quantized SAR ATR algorithms

Automatic target recognition (ATR) of synthetic aperture radar (SAR) target chips is a difficult problem, complicated by the number of nuisance parameters typically present in SAR imagery. This also complicates performance analysis because fully sampling the space of nuisance parameters in an evaluation dataset is intractable. ATR algorithms that first quantize pixel intensity values have been shown to be effective for SAR ATR due to hypothetically reducing the sensitivity to these nuisance parameters. Here we study the performance of two such algorithms, multinomial pattern matching and quantized grayscale matching, and compare them with the traditional mean squared error (MSE) template matching based classification approach. Our approach is to approximate the decision statistic of each algorithm as a Gaussian random variable (RV) parameterized by the noise power, or alternatively signal-to-noise ratio (SNR). This allows the analytic prediction of algorithm performance when the noise process of test images differs from that of the dataset used to train each algorithm, without having to rely on costly empirical simulation. We verify our results in simulations utilizing the AFRL "Civilian Vehicle" dataset.
Continuum and molecular-dynamics simulation of nanodroplet collisions

The extent to which the continuum treatment holds in binary droplet collisions is examined in the present work by using a continuum-based implicit surface capturing strategy (volume-of-fluid coupled to Navier-Stokes) and a molecular dynamics methodology. The droplet pairs are arranged in a head-on-collision configuration with an initial separation distance of 5.3 nm and a velocity of 3 ms^{-1}. The size of droplets ranges from 10-50 nm. Inspecting the results, the collision process can be described as consisting of two periods: a preimpact phase that ends with the initial contact of both droplets, and a postimpact phase characterized by the merging, deformation, and coalescence of the droplets. The largest difference between the continuum and molecular dynamics (MD) predictions is observed in the preimpact period, where the continuum-based viscous and pressure drag forces significantly overestimate the MD predictions. Due to large value of Knudsen number in the gas (Kn_{gas}=1.972), this behavior is expected. Besides the differences between continuum and MD, it is also observed that the continuum simulations do not converge for the set of grid sizes considered. This is shown to be directly related to the initial velocity profile and the minute size of the nanodroplets. For instance, for micrometer-size droplets, this numerical sensitivity is not an issue. During the postimpact period, both MD and continuum-based simulations are strikingly similar, with only a moderate difference in the peak kinetic energy recorded during the collision process. With values for the Knudsen number in the liquid (Kn_{liquid}=0.01 for D=36nm) much closer to the continuum regime, this behavior is expected. The 50 nm droplet case is sufficiently large to be predicted reasonably well with the continuum treatment. However, for droplets smaller than approximately 36 nm, the departure from continuum behavior becomes noticeably pronounced, and becomes drastically different for the 10 nm droplets.
Structural regulation of state - owned economy and its institutional improvement

In view of the coming day when China becomes a member of WTO, the problem of structural regula- tion and institutional improvement for Chinese state - owned economy seems to be very pressing. The key move for the structural regulation of state - owned economy can be described as "governmental factors go marginally while non-governmental ones focussed on". Meanwhile, the private sector of economy should be developed in a great extent. In a word, it is critical to make all the workers become the subjects for the regulated institution of state - owned economy.
Comprehensive analysis of 3-D electromagnetic-fluid-thermal fields of oil-immersed transformer

A method based on the finite element method and the finite volume method is proposed to comprehensively analyze the 3-D electromagnetic-fluid-thermal fields of transformer. Based on the 3-D transformer model,the finite element method is applied to analyze the magnetic flux density distribution inside the transformer and obtain the core and winding losses,with which as the heat sources,the finite volume method is then applied to obtain the fluid-thermal field for analyzing the oil flow and temperature distributions inside the transformer. In order to improve the accuracy of solution,the transformer losses are revised according to the temperature distribution and the fluid-thermal field is iteratively solved to obtain the final temperature distribution inside the transformer. The 3-D electromagnetic-fluid-thermal fields are analyzed by the proposed method for a 35 k V oil-immersed transformer and the results are compared with the hot-spot temperatures calculated by the empirical formula,which verifies the correctness and effectiveness of the proposed method.
Evidence for uneven distribution of L-type calcium channels in rat pulmonary circulation

Experiments were performed on isolated, perfused rat lungs to determine the segmental sites of vasoconstriction in response to factors that open voltage-sensitive, L-type calcium channels on vascular smooth muscle cells. Lungs from male Sprague-Dawley rats were perfused at constant flow with a physiological saline solution (PSS) containing albumin. Measurements were made of pulmonary arterial and venous pressure, whereas capillary pressure was estimated by the double-occlusion technique. After equilibration, lungs were constricted with depolarizing PSS containing high K+ (35 or 45 mM). With both stimuli, approximately 80% of the observed increase in vascular resistance occurred on the arterial side of the circulation. Both nifedipine and verapamil reversed this response; however, reversal was more consistent in the arterial segment. In additional experiments, the L-type channel activator (-)BAY K 8644 caused increased resistance in the arterial but not the venous segment. Another group of lungs constricted with the thromboxane mimetic U-46619 demonstrated equal arterial and venous vasoconstriction. In U-46619-constricted lungs, nifedipine caused a 28% reversal of the agonist-induced increase in arterial resistance but was without effect on the venous circulation. These data suggest that a greater density of L-type calcium channels may exist within the arterial segment of the pulmonary circulation than in the veins.
Software for Analytics

Historically, data analysis and statistics were limited to individuals who could perform the computations, usually by hand with a slide rule. Modern computers have made the computation straightforward. However, knowing “what tests to use,” “how to use them,” and “how to interpret them” still requires an intensive understanding. This chapter addresses the tools available in modern software to accomplish visualization and computation, focusing primarily on advanced uses of Excel, Minitab, and “R.”
Reassessing the democratic advantage in interstate wars using k-adic datasets

Numerous studies have used monadic or dyadic data to show that democracies are more likely to win wars. Poast (2010; Political Analysis 18(4): 403–425) demonstrates that the use of dyadic data to model events that are really multilateral (or k-adic) can bias the statistical results. In this article, I discuss the potential consequences of that bias for previous studies on democracy and war outcomes. Then I replicate some of those studies using modified, k-adic versions of the original datasets. Finally, I conduct an original analysis using the updated dataset on wars by Reiter et al. (2014a; Journal of Conflict Resolution; doi: 10.1177/0022002714553107). Overall, I find several changes when using k-adic data. Most significantly, the relationship between democracy and war outcomes appears to be strongest for states that join the war effort after it has already started.
Detection of RSV Antibodies in Human Plasma by Enzyme Immunoassays

Enzyme immunoassays (EIAs) to detect and quantify antibodies against respiratory syncytial virus (RSV) and RSV proteins in human plasma or sera are described. The first EIA uses RSV lysate antigens produced in HEp-2 cell line. The second EIA uses RSV F or G gene-expressed antigen in HEp-2 cells. The third EIA uses 30-amino acid synthetic peptides from central conserved region of G protein of RSV A2 or RSV B1 virus and a peptide from the SARS CoV nucleoprotein as a negative control peptide. All three EIAs have been evaluated for detecting and quantifying the respective antibodies in human sera or plasma.
Left Ventricular Implantation of Biomaterials

In recent years, there has been a significant effort to restore heart function by the addition of stem cells directly into the myocardium. These cells are normally carried in a synthetic extracellular matrix and implanted into the injured heart. While there has been little demonstration of actual tissue regeneration using such methods, there has been long-term improvement from these techniques, and surprisingly, from the implantation of biomaterials alone, without any included cells. This has in fact led to therapies that directly add passive materials into the ventricle to help prevent heart failure. Therefore, theoretically evaluating the addition of passive material volumes into the myocardium is of clinical importance to understand the mechanisms for the improvement of ventricular mechanics and for optimizing such treatments. In this chapter we discuss the role of finite element studies in investigating the direct addition of non-contractile materials into the myocardium.
End user models for residential demand response

This paper presents a platform for Automated Demand Response (ADR) services in residential neighborhoods. While the platform is briefly introduced, main focus is on user behavior. A model of residential end user's behavior is defined. Next, a procedure to extract model parameters from available data is presented. Value of the behavior model is demonstrated on two use cases.
A dual substrate kinetic model for cytochrome P450BM3-F87G catalysis: simultaneous binding of long chain aldehydes and 4-fluorophenol

To develop a model for binding and catalysis associated with the stimulation of 4-fluorophenol (4-FP) oxidation in the presence of long chain aldehydes by the enzymatic catalyst, cytochrome P450BM3-F87G. A variation of the Michaeli–Menten kinetic model was employed to describe interactions at the active site of the enzyme, along with computer aided modeling approaches. In addition to the hydroquinone product arising from de-fluorination of 4-FP, a second product (p-fluorocatechol) was also observed and, like the hydroquinone, its rate of formation increased in the presence of the aldehyde. When only aldehyde was present with the enzyme, BM3-F87G catalyzed its oxidation to the corresponding carboxylic acid; however, this activity was inhibited when 4-FP was added to the reaction. A 3D computer model of the active site containing both aldehyde and 4-FP was generated, guided by these kinetic observations. Finally, partitioning between the two phenolic products was examined with an emphasis on the conditions directing the initial epoxidation at either the 2,3- or 3,4-positions on the substrate. Temperature, reaction time, substrate concentration, and the structure of the aldehyde had no substantial effect on the overall product ratios, however the NADPH coupling efficiency decreased when unsaturated aldehydes were included, or when the temperature of the reaction was reduced. The unsaturated aldehyde, trans-2-decenal, stimulates BM3-F87G catalyzed oxidation of 4-fluorophenol through a cooperative active site binding mode that doesn’t influence product distributions or coupling efficiencies, while 4-fluorophenol acts as a competitive inhibitor of aldehyde oxidation.
The Effect of ERP System Implementations on the Usefulness of Accounting Information

ERP systems have become the system of choice for the majority of publicly traded companies and have radically changed the way accounting information is processed, analyzed, audited, and disseminated. In this study, we examine whether ERP system implementations have impacted the decision usefulness of accounting information. We find that ERP adoptions lead to a trade-off between increased information relevancy and decreased information reliability for external users of financial statements. After implementing the system, firms concurrently experience both a decrease in reporting lag and an increase in the level of discretionary accruals. Contrary to expectations, adopting more ERP modules did not augment these effects. These results should be of interest to financial statement preparers initially adopting or implementing new versions of ERP applications, auditors serving clients with ERP systems, and regulators overseeing the financial markets and consolidation in the ERP industry.
On Distributed Observers for Linear Time-invariant Systems Under Intermittent Information Constraints

Abstract: We study the problem of estimating the state of a linear time-invariant plant in a distributed fashion over networks allowing only intermittent transmission of information. By attaching to each node an observer that employs information received from its neighbors in an intermittent fashion, we propose a distributed state observer that guarantees global asymptotic stability of the zero estimation error set. We also characterize the proposed observer’s robustness to measurement and communication noise in terms of ISS. The design of parameters is formulated as matrix inequalities. The properties of the proposed observer are shown analytically and validated numerically.
Obstacles Experienced by Care Managers in Managing Information for the Care of Chronically Ill Patients

ABSTRACTCare managers play a key role in coordinating care, especially for patients with chronic conditions. They use multiple health information technology (IT) applications in order to access, process, and communicate patient-related information. Using the work system model and its extension, the Systems Engineering Initiative for Patient Safety (SEIPS) model, we describe obstacles experienced by care managers in managing patient-related information. A web-based questionnaire was used to collect data from 80 care managers (61% response rate) located in clinics, hospitals, and a call center. Care managers were more likely to consider “inefficiencies in access to patient-related information” and “having to use multiple information systems” as major obstacles than “lack of computer training and support” and “inefficient use of case management software.” Care managers who reported “inefficient use of case management software” as an obstacle were more likely to report high workload. Future research should ex...
The effect of polarity on MOCVD growth of thick InGaN

The growth of thick III-polar and N-polar InGaN was investigated in order to understand the effect of polarity on the structural quality, surface morphology and optical properties of metalorganic chemical vapor deposition grown films. Our results demonstrate smooth (0.7 nm RMS) thick N-polar InGaN layers that are free of hexagonal hillocks and V-pits. An enhancement in the indium incorporation was observed in the N-polar InGaN (∼13.0%) when compared to III-polar films (∼7.5%) grown under identical conditions. These results provide an alternative route to the fabrication of thick InGaN for use in strain reducing schemes for deep-green and red emitters.
Deregulation of KSHV latency conformation by ER-stress and caspase-dependent RAD21-cleavage.

Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) is a human gammaherpesvirus recognized as the principal causative agent of KS and primary effusion lymphoma (PEL). KSHV establishes persistent latent infection in B lymphocytes where viral gene expression is restricted, in part, by a cohesin-dependent chromosome conformation. Here, we show that endoplasmic reticulum (ER) stress induces a rapid, caspase-dependent cleavage of cohesin subunit RAD21. ER stress-induced cleavage of RAD21 correlated with a rapid and strong viral lytic transcriptional activation. This effect was observed in several KSHV positive PEL cells, but not in other B-cells or non-B-cell models of KSHV latency. The cleaved-RAD21 does not dissociate from viral genomes, nor disassemble from other components of the cohesin complex. However, RAD21 cleavage correlated with the disruption of the latency genome conformation as revealed by chromosome conformation capture (3C). Ectopic expression of C-terminal RAD21 cleaved form could partially induce KSHV lytic genes transcription in BCBLI cells, suggesting that ER-stress induced RAD21 cleavage was sufficient to induce KSHV reactivation from latency in PEL cells. Taken together our results reveal a novel aspect for control and maintenance of KSHV genome latency conformation mediated by stress-induced RAD21 cleavage. Our studies also suggest that RAD21 cleavage may be a general regulatory mechanism for rapid alteration of cellular chromosome conformation and cohesin-dependent transcription regulation.
Live demonstration: Automated data acquisition and digital curation platform for enhancing research precision, productivity and reproducibility

A highly flexible software platform for automated data acquisition, production of research objects with data provenance and curation of experiment results throughout the life cycle of the data will be introduced and demonstrated along with a custom miniaturized electrochemical sensor system. The software platform, called eGor, allows users to define test procedures and components through a user friendly access point. Specific experiment definitions can be saved for later use or recalled as templates for modified tests. The user can then remotely execute the test on any connected physical experiment workbench in a real lab environment. Once the test is complete, eGor will capture an organized and metadata-rich research object that includes the raw test data, detailed definition of the test setup, and all procedural elements of the executed test such as the timings, test successions, device conditions, etc. The generated research object are stored for subsequent curating or data analysis, and any access or treatment of the results is automatically recorded to maintain data provenance. eGor also allows stored research objects to be shared with collaborators or provided to any institution that would be interested in reproducing the same results. The results may be inspected at various levels of detail, annotated and compared with other research objects. Thus, eGor would help researchers increase their confidence in their results and conclusions and promote improved research reproducibility. During this demonstrations the users will be allowed to interact with hardware blocks that mimic a simple lab setup, and the users may define, schedule and perform tests using these devices and save their test results as research objects.
Loss of inversin decreases transepithelial sodium transport in murine renal cells.

Type II nephronophthisis (NPHP2) is an autosomal recessive renal cystic disorder characterized by mutations in the inversin gene. Humans and mice with mutations in inversin have enlarged cystic kid...
Watershed export of fine sediment, organic carbon, and chlorophyll-a to Chesapeake Bay: Spatial and temporal patterns in 1984–2016

Chesapeake Bay has long experienced nutrient enrichment and water clarity deterioration. This study provides new quantification of loads and yields for sediment (fine and coarse grained), organic carbon (total, dissolved, and particulate), and chlorophyll-a from the monitored nontidal Chesapeake Bay watershed (MNTCBW), all of which are expected to drive estuarine water clarity. We conducted an integrated analysis of nine major tributaries to the Bay to understand spatial and temporal export patterns over the last thirty years (1984-2016). In terms of spatial pattern, export of these constituents from the MNTCBW was strongly dominated (~90%) by the three largest tributaries (i.e., Susquehanna, Potomac, and James). Among the nine tributaries, the ranking of constituent export generally follows the order of their watershed sizes, with other factors such as land use and reservoir playing important roles in some exceptions. In terms of partitioning, suspended sediment (SS) export was dominated by fine-grained sediment (SSfine) in all nine tributaries; overall, ~90% of the MNTCBW SS is SSfine. Total organic carbon (TOC) export was dominated by dissolved organic carbon (DOC) in all tributaries except Potomac River; overall, ~60% of the MNTCBW TOC is DOC. A comparison with literature shows that the MNTCBW SS and TOC yields were ~80% and ~60% of the respective medians of worldwide watersheds. In terms of temporal pattern, flow-normalized yields from the MNTCBW show overall increases in SS (both long-term [1984-2016] and short-term [2004-2016]), SSfine (long-term and short-term), TOC (long-term), and chlorophyll-a (short-term). The rises in SS, SSfine, and TOC were largely driven by Susquehanna River where Conowingo Reservoir's trapping efficiency has greatly diminished in the last twenty years. Overall, these new results on the status and trends of sediment, organic carbon, and chlorophyll-a provide the foundation for building potential linkages between riverine inputs and estuarine water clarity patterns.
Normalizing Extensions and the Second Layer Condition

We characterize the second layer condition for a link closed subset of Spec(S) where S is a Noetherian normalizing extension of a Noetherian ring R and R satisfies the second layer condition. The second layer condition is shown to depend on the R-module structure of tame injective S-modules that are naturally associated with prime ideals in the link closed set. This is used to demonstrate that certain twisted polynomial rings satisfy the second layer condition when R is the coefficient ring. In case S is a centralized extension, our characterization is applied to show that the strong second layer condition for S amounts to a diluted version of AR-separation for S whenever R is AR-separated.
EFFECT OF MORPHINE ON ATP-STIMULATED 45Ca++ UPTAKE IN SUBCELLULAR FRACTIONS OF RAT BRAIN

In the presence of ATP, significant uptake of 45Ca++ was observed in two subcellular components of rat brain (synaptic vesicles and synaptic plasma membranes). The addition of morphine in vitro to the incubation medium decreased 45Ca++ uptake. Chronic treatment with morphine markedly increased the uptake of 45Ca++ in synaptic vesicles and membranes as compared to those from naive animals, with the highest uptake occurring in the synaptic vesicles.
Sex- and Mode-specific Responses to Eccentric Muscle Fatigue.

The primary purpose of the present investigation was to examine sex-related differences as a result of fatiguing eccentric muscle actions on torque, muscle blood flow, electromyography, and mechanomyography. Eighteen men and 18 women performed peak torque trials prior to (pretest), immediately after (posttest), and 5-min after (recovery) completing 50 submaximal (60% of eccentric peak torque), eccentric, isokinetic (180°·s −1) muscle actions of the elbow flexors. Electromyographic and mechanomyographic responses were simultaneously recorded from the biceps brachii muscle, and muscle blood flow was measured at pretest, posttest and recovery. There were sex- and mode-specific responses for torque, but there were no sex-specific muscle blood flow or neuromuscular responses. From pretest to posttest, torque decreased (80.0–88.2% of pretest) for both the men and women. At recovery concentric peak torque recovered to a greater extent in women (95.0% of pretest) than men (88.0% of pretest), while eccentric peak torque recovered to a greater extent in men (88.9% of pretest) than women (86.9% of pretest). The sex-specific torque responses were not associated with different motor control strategies or differences in the occlusion of muscle blood flow between the men and women. For both men and women, eccentric fatiguing exercise is manifested similarly during isometric muscle actions, but not during eccentric and concentric muscle actions.
Inferring Insertion Times and Optimizing Error Penalties in Time-decaying Bloom Filters

Current Bloom Filters tend to ignore Bayesian priors as well as a great deal of useful information they hold, compromising the accuracy of their responses. Incorrect responses cause users to incur penalties that are both application- and item-specific, but current Bloom Filters are typically tuned only for static penalties. Such shortcomings are problematic for all Bloom Filter variants, but especially so for Time-decaying Bloom Filters, in which the memory of older items decays over time, causing both false positives and false negatives.We address these issues by introducing inferential filters, which integrate Bayesian priors and information latent in filters to make penalty-optimal, query-specific decisions. We also show how to properly infer insertion times in such filters. Our methods are general, but here we illustrate their application to inferential time-decaying filters to support novel query types and sliding window queries with dynamic error penalties.We present inferential versions of the Timing Bloom Filter and Generalized Bloom Filter. Our experiments on real and synthetic datasets show that our methods reduce penalties for incorrect responses to sliding-window queries in these filters by up to 70% when penalties are dynamic.
Analysis of the Length of Braille Texts in English Braille American Edition, the Nemeth Code, and Computer Braille Code versus the Unified English Braille Code.

This study compared the length of text in English Braille American Edition, the Nemeth code, and the computer braille code with the Unified English Braille Code (UEBC)—also known as Unified English...
Targeted quantitative proteomic analysis of drug metabolizing enzymes and transporters by nano LC-MS/MS in the sandwich cultured human hepatocyte model.

Abstract Introduction Sandwich-cultured human hepatocytes (SCHHs) are the most common in vitro hepatocyte model used for studying hepatic drug disposition and hepatotoxicity. Targeted quantification of key DME and transporter protein expression is useful for in vitro-in vivo extrapolation of drug and xenobiotic clearance and developing corresponding PBPK models. However, established methods for comprehensive quantification of drug metabolizing enzyme (DMEs) and transporter expression in SCHHs are lacking. In this study, a targeted quantitative proteomic isotope dilution nanoLC-MS/MS method developed in our laboratory was adapted to quantify a panel of phase I & II DMEs and transporter proteins in SCHHs under basal and induced conditions. Methods SCHHs were treated with known inducers of DMEs (Rifampin: PXR activator, CITCO: CAR activator) and transporters (CDCA: FXR activator) or with vehicle control (DMSO) for 72 h. Membrane protein was isolated from the SCHHs using a membrane extraction kit and 30 μg membrane protein was digested with trypsin. The resulting peptides were analyzed by isotope dilution nanoLC-MS/MS to quantify the DMEs and transporters. Results Using the method, we could quantify fourteen phase I and ten phase II DMEs, and twelve uptake/efflux transporters, under basal and induced conditions in the SCHHs. Analysis showed donor to donor variation in basal protein levels of CYP450s, UGTs and transporters, and that basal protein expression of CYP450s and UGTs was higher than that of transporters. In addition, induction of key proteins in response to rifampin, CITCO and CDCA was observed. Discussion We have successfully quantified protein abundance of multiple phase I and II DMEs and uptake and efflux transporters in SCHHs using a method previously developed in our laboratory. Our method is sufficiently sensitive to quantify inter-donor differences in protein concentrations at the basal level as well as changes in protein expression in response to endogenous and exogenous stimuli.
Postgrowth Imaginaries: New Ecologies and Counterhegemonic Culture in Post-2008 Spain - Prelims

This book brings together environmental cultural studies and postgrowth economics to examine counterhegemonic narratives and radical cultural shifts sparked by the global financial crisis of 2008. A number of critical voices worldwide have emphasized that in the context of a finite biosphere, constant economic growth is a biophysical impossibility. The problem is not a lack of growth but rather the globalization of an economic system addicted to constant growth, which destroys the ecological planetary systems that support life on Earth while failing to fulfil its social promises. Post-2008 Spain offers an optimal context to investigate these cultural processes, and this book demonstrates that a transition toward what Pradanos calls ‘postgrowth imaginaries’—the counterhegemonic cultural sensibilities that are challenging the growth paradigm in manifold ways—is well underway in the Iberian Peninsula today. Specifically, this book explores how emerging cultural sensibilities in Spain—reflected in fiction and nonfiction writing and film, television programs, photographs and graphic novels, op-eds, web pages, political manifestos, and socioecological movements—are actively detaching themselves from the dominant imaginary of economic growth. By approaching the counterhegemonic culture of the crisis though environmental criticism, this book uncovers a whole range of cultural nuances often ignored by Iberian cultural studies. The complex interrelations among cultural practices, economic paradigms, and ecological processes are vastly undertheorized. This book intends to fill this gap.
Age- and Race/Ethnicity-Specific Sex Partner Correlates of Condomless Sex in an Online Sample of Hispanic/Latino, Black/African-American, and White Men Who Have Sex with Men.

We sought to identify and compare correlates of condomless receptive anal intercourse with HIV-positive or unknown status partners (CRAI) for younger (< 25 years) and older (≥ 25 years) Hispanic/Latino, black/African-American, and white men who have sex with men (MSM). Baseline data from the Evaluation of Rapid HIV Self-Testing among MSM Project (eSTAMP), a randomized controlled trial with MSM (n = 2665, analytical sample size = 2421), were used. Potential correlates included participants’ sociodemographic characteristics and HIV status as well as the characteristics of participants’ partners. Younger Hispanic/Latino and black men were most likely to report having older sex partners (≥ 50% of partners being at least 5 years older), and having older partners was a significant correlate of CRAI among younger Hispanic/Latino and white men. Regardless of race/ethnicity, not knowing one’s HIV status was a significant correlate of CRAI among younger men, whereas having a black sex partner was a significant correlate among older men. HIV prevention initiatives could address these and other correlates specific to race/ethnicity groups to target their prevention resources and messaging.
Patient Surveillance in Total Joint Arthroplasty

Effective patient–provider communication is essential to the delivery of quality healthcare. Recent policy changes and technological advancements have catalyzed the implementation of various strategies to augment patient–provider communication, particularly in the field of total joint arthroplasty. Telemedical technologies, such as automated text messaging [short message service (SMS)], mobile applications, web-based platforms, structured telephone calls, videoconferencing, and wearable technologies, have been used as a means to provide patients with reminders, instructional content, and motivational messages, enhance data collection, and facilitate patient–provider communication. The incorporation of such forms of communication into healthcare not only has the potential to make providing and receiving healthcare more convenient, but also may increase the quality of care.
Smoother Judicial Reforms in Slovenia and Croatia: Does the Legacy of the Past Matter?

The feature shared by judicial reforms in Slovenia and Croatia is that in both countries, although they became EU member with very different timings, the EU-driven reforms in the judicial sector—especially the structural reforms—were adopted and implemented without particular conflict among political and judicial actors. The path of judicial reform in these two countries shows in particular that, in comparison with other countries such as Romania and Serbia, they were particularly rapid and efficient in solving problems to do with establishing an adequate institutional framework and guarantees of judicial independence.
Interactions between Litter Lignin and Soil Nitrogen Availability during Leaf Litter Decomposition in a Hawaiian Montane Forest

Previous work in a young Hawaiian forest has shown that nitrogen (N) limits aboveground net primary production (ANPP) more strongly than it does decomposition, despite low soil N availability. In this study, I determined whether (a) poor litter C quality (that is, high litter lignin) poses an overriding constraint on decomposition, preventing decomposers from responding to added N, or (b) high N levels inhibit lignin degradation, lessening the effects of added N on decomposition overall. I obtained leaf litter from one species, Metrosideros polymorpha, which dominates a range of sites in the Hawaiian Islands and whose litter lignin concentration declines with decreasing precipitation. Litter from three dry sites had lignin concentrations of 12% or less, whereas litter from two wet sites, including the study site, had lignin concentrations of more than 18%. This litter was deployed 2.5 years in a common site in control plots (receiving no added nutrients) and in N-fertilized plots. Nitrogen fertilization stimulated decomposition of the low-lignin litter types more than that of the high-lignin litter types. However, in contrast to results from temperate forests, N did not inhibit lignin decomposition. Rather, lignin decay increased with added N, suggesting that the small effect of N on decomposition at this site results from limitation of decomposition by poor C quality rather than from N inhibition of lignin decay. Even though ANPP is limited by N, decomposers are strongly limited by C quality. My results suggest that anthropogenic N deposition may increase leaf litter decomposition more in ecosystems characterized by low-lignin litter than in those characterized by high-lignin litter.