Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profile of Antithrombotic Protein C Defines New Mechanisms Modulating Inflammation and Apoptosis*

Human protein C is a natural anticoagulant factor, and a recombinant activated form of the molecule (rhAPC) is completing clinical evaluation for treatment of severe sepsis. Because of the pathophysiologic role of endothelial dysfunction in severe inflammatory disease and sepsis, we explored the possibility that rhAPC might directly modulate endothelial function, independent of its anticoagulant activity. Using broad transcriptional profiling, we show that rhAPC directly modulates patterns of endothelial cell gene expression clustering into anti-inflammatory and cell survival pathways. rhAPC directly suppressed expression of p50 and p52 NFκB subunits, resulting in a functional decrease in NFκB binding at target sites. Further, rhAPC blocked expression of downstream NFκB regulated genes following tumor necrosis factor α induction, including dose-dependent suppression of cell adhesion expression and functional binding of intracellular adhesion molecule 1, vascular cell adhesion molecule 1, and E-selectin. Further, rhAPC modulated several genes in the endothelial apoptosis pathway, including the Bcl-2 homologue protein and inhibitor of apoptosis protein. These pathway changes resulted in the ability of rhAPC to inhibit the induction of apoptosis by the potent inducer, staurosporine. This new mechanistic understanding of endothelial regulation and the modulation of tumor necrosis factor-induced endothelial dysfunction creates a novel link between coagulation, inflammation, and cell death and provides insight into the molecular basis for the efficacy of APC in systemic inflammation and sepsis.
From Findings to Theories: Institutionalizing Social Informatics

We focus here on the history, status, and future of social informatics. In doing this we build on the visionary work of the late Rob Kling. Social informatics research contributes insights and perspectives to the study of computing in our society that other approaches do not. We make the case that social informatics is on its way to becoming a scholarly institution: accepted as one of the several approaches to study computing, and in particular, the approach best suited to engage on computerization. In making this case, we highlight the value of social informatics, summarize its principles and common findings, point to current work and issues, illustrate the three perspectives through which to pursue this scholarship, and identify several current activities remaining for social informatics to institutionalize.
Two-Dimensional Voronoi-Based Model and Detection for Shingled Magnetic Recording

In this paper, we present a model of a shingled magnetic recording system, where Voronoi regions are used to model the grains of the magnetic medium. A probabilistic model is used to represent imperfections in the write process, i.e., the head failing to write some grains correctly. A two-dimensional model of the head response is used to calculate the signal read back by the head over any place on the medium, thereby including both intertrack and intersymbol interference effects in the model. We also present simulation results from tests of this model using a multitrack detector and an intertrack interference canceller and give performance results of the channel/detector combination for various track offsets.
USABILITY EVALUATION AND CORRESPONDENCE ANALYSIS OF SMARTPHONE OPERATING SYSTEMS

User-centered smartphone interface design is important so that consumers can easily learn about and begin to use newly purchased smartphones. This study first evaluates the effectiveness, efficiency, and user satisfaction of smartphone interfaces in Taiwan in terms of two representational operating systems: Android and iPhone OS. The usability evaluation includes observational experiments, user questionnaires, and the Wilcoxon sign-rank test. This study then conducts the correspondence analysis to summarize positive/ negative evaluations of usage and specification for smartphone OS. In observational experiments, a total of 48 participants with no previous smartphone experience on using smartphone with Android and iPhone OS are asked to perform five common phone tasks. All experiments are recorded and observed. Results and observations are discussed to attain a closer match between user needs and the performance of smartphone OS.
Prostaglandins: stimulation of bone resorption in tissue culture.

Prostaglandins (PG’s) stimulated resorption of fetal rat bone in 48–96 hr tissue culture. The effects of several PG’s were compared to the stimulation of bone resorption caused by parathyroid hormone (PTH). PGE1 and PGE2 caused increased release of previously incorporated radioactive calcium into the medium, losses of stable and labeled Ca from the bone and morphologic changes of osteoclastic resorption at 10−5-10−8M. The effects of PGE1 and PGE2 were similar to those of PTH (10−7- 10−8M) but in some experiments the effects of maximal doses of PTH were larger at 48 hr. Like PTH, the effects of PGE1 were inhibited by thyrocalcitonin and cortisol. PGA1 and PGFlα also stimulated bone resorption but only at higher doses (10−5M). In vivo studies demonstrated that injections of PGE1 in parathyroidectomized rats did not increase serum calcium concentration, while parathyroid extract (4–40 U/rat) was effective. (Endocrinology 86: 1436, 1970)
Under Consideration for Publication in Theory and Practice of Logic Programming Truth versus Information in Logic Programming

The semantics of logic programs was originally described in terms of two-valued logic. Soon, however, it was realised that three-valued logic had some natural advantages, as it provides distinct values not only for truth and falsehood, but also for " undefined ". The three-valued semantics proposed by Fitting and by Kunen are closely related to what is computed by a logic program, the third truth value being associated with non-termination. A different three-valued semantics, proposed by Naish, shared much with those of Fitting and Kunen but incorporated allowances for programmer intent, the third truth value being associated with underspecification. Naish used an (apparently) novel " arrow " operator to relate the intended meaning of left and right sides of predicate definitions. In this paper we suggest that the additional truth values of Fitting/Kunen and Naish are best viewed as duals. We use Belnap's four-valued logic, also used elsewhere by Fitting, to unify the two three-valued approaches. The truth values are arranged in a bilattice which supports the classical ordering on truth values as well as the " information ordering ". We note that the " arrow " operator of Naish (and our four-valued extension) is essentially the information ordering, whereas the classical arrow denotes the truth ordering. This allows us to shed new light on many aspects of logic programming, including program analysis, type and mode systems, declarative debugging and the relationships between specifications and programs, and successive executions states of a program. This paper is to appear in Theory and Practice of Logic Programming (TPLP).
Visualizing Relative Potential for Aquatic Ecosystem Toxicity Using the EPA Toxics Release Inventory and Life Cycle Assessment Methods

The U.S. EPA Toxic Release Inventory has been available since 1987 as a record of industrial releases of toxic chemicals following the 1986 Emergency Planning and Community Right-to-Know Act. Combining this release data with estimates of relative toxicity of these chemicals to aquatic systems increases the value of the database by providing a common basis for comparison. The Tool for Reduction and Assessment of Chemicals and Other Environmental Impacts is a database of characterization factors to assess environmental impacts. It was used to develop relative ecotoxicity impacts and interpreted using Life Cycle Assessment concepts. The visualization software Tableau was used to generate representations of the preliminary results in this communication. The major potential sources of aquatic toxicity have been identified for South Carolina by industry type and by year over the period 1987–2016. The possibility of toxicity from releases of zinc compounds from power generation and pulp and paper mills far exceeds all other sources. Zinc compounds dominated the potential ecotoxicity over the full time period 1987–2016.
Warming advances top-down control and reduces producer biomass in a freshwater plankton community

Global warming has been shown to affect ecosystems worldwide. Warming may, for instance, disrupt plant herbivore synchrony and bird phenology in terrestrial systems, reduce primary production in oceans, and promote toxic cyanobacterial blooms in freshwater lakes. Responses of communities will not only depend on direct species-specific temperature effects, but also on indirect effects related to bottom-up and top-down processes. Here, we investigated the impact of warming on freshwater phytoplankton community dynamics, and assessed the relative contribution of nutrient availability, fungal parasitism, and grazing therein. For this purpose, we performed an indoor mesocosm experiment following seasonal temperature dynamics of temperate lakes and a warmed (+4°C) scenario from early spring to late summer. We assessed phytoplankton biomass, C:N:P stoichiometry and community composition, dissolved nutrient availabilities, fungal parasite (i.e., chytrid) prevalence, and zooplankton abundance. Warming led to an overall reduction in phytoplankton biomass as well as lower C:P and N:P ratios, while phytoplankton community composition remained largely unaltered. Warming resulted in an earlier termination of the diatom spring bloom, and an epidemic of its fungal parasite ended earlier as well. Furthermore, warming advanced zooplankton phenology, leading to an earlier top-down control on phytoplankton in the period after the spring bloom. Linear model analysis showed that most of the observed variance in phytoplankton biomass was related to seasonal temperature dynamics in combination with zooplankton abundance. Our findings showed that warming advanced grazer phenology and reduced phytoplankton biomass, thereby demonstrating how bottom-up and top-down related processes may shape future phytoplankton dynamics.
Emergent management of pelvic ring injuries: an update.

Fractures of the pelvic ring comprise about 2% of all fractures, but the incidence is increasing due to increasing numbers of high-speed vehicular crashes and suicide attempts.1 Mortality associated with isolated pelvic injury, independent of severity, has been reported to be low: 1%–2%. 2 Among multiply injured victims of blunt trauma, however, almost 20% have injuries to the pelvic ring.3,4,5 In this group, when closed pelvic ring disruption is associated with multiple injuries, the mortality rate rises to 10%–15%. 6,7,8 Pelvic fractures associated with intra-cranial mass lesions or notable abdominal injuries have mortality rates as high as 50%. 3 The mortality associated with open pelvic fractures has been shown to be 30%–50%. 9,10 The parameters that predict mortality are age, injury severity score (ISS) and the existence of severe hemorrhage.11 Exsanguinating hemorrhage is the major cause of death in the first 24 hours after trauma.12,13,14,15,16 Immediate recognition of hemorrhagic shock and effective control of bleeding must be pivotal in every resuscitation effort. Appropriate recognition and management of serious pelvic fractures is also integral to resuscitative strategy. Management of these potentially lethal injuries requires expedited stabilization by a multidisciplinary team of trained personnel with a defined treatment protocol. Multidisciplinary clinical-pathway and coordinated joint decision-making improves patient survival.17 A post mortem study by Wright and colleagues18 has shown that the average ISS of patients dying from pelvic fractures was much higher in patients treated by a protocol of care than in those treated with a “non-system” approach on an ad-hoc basis. As the understanding of these potentially fatal injuries improves, priorities of early management of pelvic ring injuries are evolving. This review article summarizes the current trend in emergent management of pelvic fractures, based on available evidence. A protocol designed to facilitate organized and systematic care of the serious pelvic fracture in multi-system trauma is proposed.
Determination of Volatility Distributions of Primary Organic Aerosol Emissions from Internal Combustion Engines Using Thermal Desorption Gas Chromatography Mass Spectrometry

A new technique for measuring the primary organic aerosol (POA) emissions from internal combustion engines is presented. The method combines thermal-optical OC/EC analysis and thermal desorption gas chromatography mass spectrometry (TD-GC-MS) of quartz filter samples collected using a dilution sampler to quantify the total emissions of low-volatility organics and to distribute them across the volatility basis set. These data can be used in conjunction with partitioning theory to predict the gas-particle partitioning and thus the total amount of POA over the entire range of atmospheric conditions. The approach is evaluated using POA emissions data from two gas-turbine engines and one diesel generator. To evaluate the new method, we directly measured the effects of temperature and concentration on gas-particle partitioning of the emissions from each. Predictions based on the volatility distributions derived from the filter analyses are consistent with the direct partitioning measurements. The new approach represents a major improvement over the traditional assumption of nonvolatile POA emissions, which over predicts actual POA emissions from these sources by a factor of 2–4 at typical ambient concentration and temperature. By using quartz filter samples, this new technique is designed to be applied to routine source test data. Volatility distributions derived using this new approach can also be applied directly to the large catalog of quartz filter data used by existing emission inventories and models. The emissions data derived from this approach are designed for use in the next generation of chemical transport models and emissions inventories that employ the volatility basis set approach to explicitly track the gas-particle partitioning of POA emissions. Copyright 2012 American Association for Aerosol Research
A Lightweight Detection and Recovery Infrastructure of Kernel Objects for Embedded Systems

The kernel objects consist of critical kernel data structures and system call functions, which are the most important data for a system, should be protected as first-class candidates. In this paper, a lightweight system-level detection and recovery infrastructure is presented for embedded systems. Inside the infrastructure, specific runtime protections have been implemented for different kernel objects, kernel data structures are protected by the periodic detection and recovery, the interception of arguments is used to protect vulnerable system calls. At runtime once any system inconsistency has been detected, predefined recovery actions will be invoked. The consistency detection regulations and corresponding recovery actions can also be flexibly customized by system developers. The infrastructure requires few modifications to kernel source code, thus it is easy to integrate into existing embedded systems. The evaluation experiment results indicate our prototype system can correctly detect the inconsistent kernel data structures caused by security attacks and also prevent kernel from exploits due to vulnerable system calls with acceptable penalty to system performance. Moreover, it is fully software-based without introducing any specific hardware and requires no modifications to system call APIs, therefore legacy commercial-off-the-shelf (COTS) applications can be also easily reused.
A Study to Determine the Effects of Food and Multiple Dosing on the Pharmacokinetics of Vorinostat Given Orally to Patients with Advanced Cancer

Purpose: This phase I study, conducted in advanced-stage cancer patients, assessed the safety and tolerability of oral vorinostat (suberoylanilide hydroxamic acid), single-dose and multiple-dose pharmacokinetics of vorinostat, and the effect of a high-fat meal on vorinostat pharmacokinetics. Experimental Design: Patients (n = 23) received single doses of 400 mg vorinostat on day 1 (fasted) and day 5 (fed) with 48 hours of pharmacokinetic sampling on both days. Patients received 400 mg vorinostat once daily on days 7 to 28. On day 28, vorinostat was given (fed) with pharmacokinetic sampling for 24 hours after dose. Results: The apparent t1/2 of vorinostat was short (∼1.5 hours). A high-fat meal was associated with a small increase in the extent of absorption and a modest decrease in the rate of absorption. A short lag time was observed before detectable levels of vorinostat were observed in the fed state, and Tmax was delayed. Vorinostat concentrations were qualitatively similar following single-dose and multiple-dose administration; the accumulation ratio based on area under the curve was 1.21. The elimination of vorinostat occurred primarily through metabolism, with <1% of the given dose recovered intact in urine. The most common vorinostat-related adverse experiences were mild to moderate nausea, anorexia, fatigue, increased blood creatinine, and vomiting. Conclusions: Vorinostat concentrations were qualitatively similar after single and multiple doses. A high-fat meal increased the extent and modestly decreased the rate of absorption of vorinostat; this effect is not anticipated to be clinically meaningful. Continued investigation of 400 mg vorinostat given once daily in phase II and III efficacy studies is warranted.
Digital parenting: designing children's safety

In this paper, I describe an ethnographic study of children and parents looking at issues of domestic privacy and security. I will provide an overview of parental rules and strategies for keeping children safe and briefly discuss children's perspective on their online safety and how their parents shared the domestic work and responsibility for protecting them. As part of the discussion, I will present implications for design, and reflect on the problematic state of ethics, privacy, ethics review boards when working with children.
Changes in protein profiles of multiple myeloma cells in response to bortezomib

Abstract The objective of this study was to determine the changes in protein profiles of U-266 multiple myeloma cells in response to bortezomib. Bortezomib inhibited cell proliferation and increased the loss of mitochondrial membrane potential and caspase-3 activity in a dose-dependent manner. DECODON Delta2D Version 4.3 software demonstrated 37 differentially expressed protein spots: five proteins were newly formed, 10 proteins were lost, 12 proteins were up-regulated and 10 proteins were down-regulated in bortezomib-treated cells as compared to untreated cells. Some of the identified proteins after mass spectrometric analysis were as follows: apoptosis regulatory protein Siva (newly formed), caspase recruitment domain-containing protein 14 (lost), Ras-related protein Rab-25 (up-regulated), nuclear factor κB (NF-κB) p105 subunit (down-regulated). In summary, differentially expressed proteins of MM U-266 cells in response to bortezomib were analyzed and identified. The data obtained from this study may indicate the use of bortezomib for the treatment of various diseases.
An approach using Named Entities for Recognizing Textual Entailment

NESS, RALI’s summarization system for the TAC 2008’s update task, brings improvements and continuation to our last year’s “all-symbolic” approach. The most distinctive feature of our system is to rely on the syntactical parser FIPS to extract linguistic knowledge from source documents. NESS selects sentences based on linguistic metrics, especially tf · idf scores that measure the relevance of the newswire article sentences to the given topic. It also measures the similarity between candidate sentences and the previous articles already read by the user. NESS ranked well in the competition, obtaining excellent scores in linguistic quality and overall responsiveness.
Analysis of the coplanarity of functional pairs of semicircular canals using three-dimensional images reconstructed from temporal bone magnetic resonance imaging

Abstract Objectives: This study was conducted to investigate the angles and orientation of semicircular canals, and the coplanarity of functional canal pairs. Methods: Fluid signals in semicircular canals were reconstructed with three-dimensional reconstruction software using 20 temporal bone magnetic resonance images of normal subjects. The angles between each pair of semicircular canals were measured. Results: The mean angles between the anterior and horizontal semicircular canal plane, the horizontal and posterior semicircular canal plane, and the anterior and posterior semicircular canal plane were 83.7°, 82.5° and 88.4°, respectively. Pairs of contralateral synergistic canal planes were formed 15.1° between the right and left horizontal semicircular canal planes, 21.2° between the right anterior and left posterior semicircular canal, and 21.7° between the left anterior and right posterior semicircular canal. Conclusion: Each semicircular canal makes an almost right angle with other canals, but synergistically acting functional canal pairs of both ears do not lie in exactly the same plane.
Chapter 3 Zebrafish as a Model of Kidney Disease

The pronephros is the first kidney type to form in vertebrate embryos. The first step of pronephrogenesis in the zebrafish is the formation of the intermediate mesoderm during gastrulation, which occurs in response to secreted morphogens such as BMPs and Nodals. Patterning of the intermediate mesoderm into proximal and distal cell fates is induced by retinoic acid signaling with downstream transcription factors including wt1a, pax2a, pax8, hnf1b, sim1a, mecom, and irx3b. In the anterior intermediate mesoderm, progenitors of the glomerular blood filter migrate and fuse at the midline and recruit a blood supply. More posteriorly localized tubule progenitors undergo epithelialization and fuse with the cloaca. The Notch signaling pathway regulates the formation of multi-ciliated cells in the tubules and these cells help propel the filtrate to the cloaca. The lumenal sheer stress caused by flow down the tubule activates anterior collective migration of the proximal tubules and induces stretching and proliferation of the more distal segments. Ultimately these processes create a simple two-nephron kidney that is capable of reabsorbing and secreting solutes and expelling excess water—processes that are critical to the homeostasis of the body fluids. The zebrafish pronephric kidney provides a simple, yet powerful, model system to better understand the conserved molecular and cellular progresses that drive nephron formation, structure, and function.
On the performance of the Golden code in BICM-MIMO and in IEEE 802.11n cases

In 2times2 MIMO systems, the Golden code (GC) [1] was proposed when no binary outer code is applied at the transmitter. This code is optimal since it achieves full rate, full diversity and the Diversity Multiplexing Tradeoff [2], and it preserves the mutual information. We propose in this paper to study the performance of this code compared to Spatial Division Multiplexing (SDM) [3] in a BICM-MIMO system. We derive the Pairwise Error Probability (PER) in this context and we assess our results over a Rayleigh channel and in the 802.11n case. We show that the GC is also optimal for 2 times 2 BICM-MIMO systems. However, the impact of the additional gain provided by the Golden code is reduced when using binary outer code with high free distance case, as for instance in IEEE 802.11n standard.