Miracle-dz/UniFAR-FTUs huggingface dataset:
Parametric Timing Analysis

Embedded systems often have real-time constraints. Traditional timing analysis statically determines the maximum execution time of a task or a program in a real-time system. These systems typically depend on the worst-case execution time of tasks in order to make static scheduling decisions so that tasks can meet their deadlines. Static determination of worst-case execution times imposes numerous restrictions on real-time programs, which include that the maximum number of iterations of each loop must be known statically. These restrictions can significantly limit the class of programs that would be suitable for a real-time embedded system. This paper describes work-in-progress that uses static timing analysis to aid in making dynamic scheduling decisions. For instance, different algorithms with varying levels of accuracy may be selected based on the algorithm's predicted worst-case execution time and the time allotted for the task. We represent the worst-case execution time of a function or a loop as a formula, where the unknown values affecting the execution time are parameterized. This parametric timing analysis produces formulas that can then be quickly evaluated at run-time so dynamic scheduling decisions can be made with little overhead. Benefits of this work include expanding the class of applications that can be used in a real-time system, improving the accuracy of dynamic scheduling decisions, and more effective utilization of system resources.
Expression of Cancer Testis Antigens in Colorectal Cancer: New Prognostic and Therapeutic Implications

Background. While cancer/testis antigens (CTAs) are restricted in postnatal tissues to testes and germ line-derived cells, their role in cancer development and the clinical significance of their expression still remain to be better defined. Objective. The aim of this study was to investigate the level of CTA expression in colon samples from patients with colorectal cancer (CRC) in relation to patient clinical status. Methods. Forty-five patients with newly diagnosed colorectal cancer were included in the study. We selected a panel of 18 CTAs that were previously detected in CRC as well as some new gene candidates, and their expression was detected at the mRNA level by employing RQ-PCR. Additionally, we evaluated CTA expression in three colon cancer cell lines (CL-188, HTB-39, and HTB-37) after exposure to the DNA methylation-modifying drug 5-azacytidine. Results. We report that 6 out of 18 (33%) CTAs tested (MAGEA3, OIP5, TTK, PLU1, DKKL1, and FBXO39) were significantly (p < 0.05) overexpressed in tumor tissue compared with healthy colon samples isolated from the same patients. Conclusions. Moreover, we found that MAGEA3, PLU-1, and DKKL expression positively correlated with disease progression, evaluated according to the Dukes staging system. Finally, 5-azacytidine exposure significantly upregulated expression of CTAs on CRC cells, which indicates that this demethylation agent could be employed therapeutically to enhance the immune response against tumor cells.
A Denoising Method Based on Total Variation

Today large amounts of digital images are created by various modern devices such as digital cameras, X-Ray scanners, and so on. Noise reduces image quality and result of the processing. For example, biomedical images are a type of digital images. In these images, there is a combination of two types of noises: Gaussian noise and Poisson noise. In this paper, we propose a method to remove these noises. This method is based on the total variation of an image intensity (brightness) function. We combine two famous denoising models to remove this combination of noises.
Fabrication of microfluidic systems in poly(dimethylsiloxane)

Microfluidic devices are finding increasing application as analytical systems, biomedical devices, tools for chemistry and biochemistry, and systems for fundamental research. Conventional methods of fabricating microfluidic devices have centered on etching in glass and silicon. Fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS) by soft lithography provides faster, less expensive routes than these conventional methods to devices that handle aqueous solutions. These soft‐lithographic methods are based on rapid prototyping and replica molding and are more accessible to chemists and biologists working under benchtop conditions than are the microelectronics‐derived methods because, in soft lithography, devices do not need to be fabricated in a cleanroom. This paper describes devices fabricated in PDMS for separations, patterning of biological and nonbiological material, and components for integrated systems.
The star user interface: an overview

In April 1981 Xerox announced the 8010 Star Information System, a new personal computer designed for office professionals who create, analyze, and distribute information. The Star user interface differs from that of other office computer systems by its emphasis on graphics, its adherence to a metaphor of a physical office, and its rigorous application of a small set of design principles. The graphic imagery reduces the amount of typing and remembering required to operate the system. The office metaphor makes the system seem familiar and friendly; it reduces the alien feel that many computer systems have. The design principles unify the nearly two dozen functional areas of Star, increasing the coherence of the system and allowing user experience in one area to apply in others.
Two Human ARFGAPs Associated with COP-I-Coated Vesicles

ADP‐ribosylation factors (ARFs) are critical regulators of vesicular trafficking pathways and act at multiple intracellular sites. ADP‐ribosylation factor‐GTPase‐activating proteins (ARFGAPs) are proposed to contribute to site‐specific regulation. In yeast, two distinct proteins, Glo3p and Gcs1p, together provide overlapping, essential ARFGAP function required for coat protein (COP)‐I‐dependent trafficking. In mammalian cells, only the Gcs1p orthologue, named ARFGAP1, has been characterized in detail. However, Glo3p is known to make the stronger contribution to COP I traffic in yeast. Here, based on a conserved signature motif close to the carboxy terminus, we identify ARFGAP2 and ARFGAP3 as the human orthologues of yeast Glo3p. By immunofluorescence (IF), ARFGAP2 and ARFGAP3 are closely colocalized with coatomer subunits in NRK cells in the Golgi complex and peripheral punctate structures. In contrast to ARFGAP1, both ARFGAP2 and ARFGAP3 are associated with COP‐I‐coated vesicles generated from Golgi membranes in the presence of GTP‐γ‐S in vitro. ARFGAP2 lacking its zinc finger domain directly binds to coatomer. Expression of this truncated mutant (ΔN‐ARFGAP2) inhibits COP‐I‐dependent Golgi‐to‐endoplasmic reticulum transport of cholera toxin (CTX‐K63) in vivo. Silencing of ARFGAP1 or a combination of ARFGAP2 and ARFGAP3 in HeLa cells does not decrease cell viability. However, silencing all three ARFGAPs causes cell death. Our data provide strong evidence that ARFGAP2 and ARFGAP3 function in COP I traffic.
Local Common Property Exploitation with Rewards

This paper analyzes coalition formation in a livestock-pasture system where livestock are privately owned and the pasture is a common property. While standard models predict rather low prospects of cooperation, this paper introduces a cost advantage of cooperation based on Saami reindeer herding that may explain higher coalition participation. In contrast to the existing fishery literature on coalition formation, all players are assumed ex ante homogenous but may differ ex post due to the cost advantage. A stable equilibrium with cooperation can be reached and a moderate exploitation level can be sustained compared to the “tragedy of the commons” outcome. (JEL Q24)
STGC3 inhibits xenograft tumor growth of nasopharyngeal carcinoma cells by altering the expression of proteins associated with apoptosis

STGC3 is a potential tumor suppressor that inhibits the growth of the nasopharyngeal carcinoma cell line CNE2; the expression of this protein is reduced in nasopharyngeal carcinoma compared with normal nasopharyngeal tissue. In this study, we investigated the tumor-suppressing activity of STGC3 in nude mice injected subcutaneously with Tet/pTRE-STGC3/CNE2 cells. STGC3 expression was induced by the intraperitoneal injection of doxycycline (Dox). The volume mean of Tet/pTRE-STGC3/CNE2+Dox xenografts was smaller than that of Tet/pTRE/CNE2+Dox xenografts. In addition, Tet/pTRE-STGC3/CNE2+Dox xenografts showed an increase in the percentage of apoptotic cells, a decrease in Bcl-2 protein expression and an increase in Bax protein expression. A proteomic approach was used to assess the protein expression profile associated with STGC3-mediated apoptosis. Western blotting confirmed the differential up-regulation of prohibitin seen in proteomic analysis. These results indicate that overexpression of STGC3 inhibits xenograft growth in nude mice by enhancing apoptotic cell death through altered expression of apoptosis-related proteins such as Bcl-2, Bax and prohibitin. These data contribute to our understanding of the function of STGC3 in human nasopharyngeal carcinoma and provide new clues for investigating other STGC3-associated tumors.
Mating Intelligence : Sex, Relationships, and the Mind's Reproductive System

Contents: Part I: Introduction. D. Buss, Foreword. Preface. G. Geher, G. Miller, J. Murphy, Mating Intelligence: Towards an Evolutionarily Informed Construct. Part II: Mate Search and Mating Intelligence. L. Penke, P.M. Todd, A.P. Lenton, B. Fasolo, How Self-Assessments Can Guide Human Mating Decisions. C. De Backer, J. Braeckman, L. Farinpour, Mating Intelligence in Personal Ads. Part III: Strategic Flexibility in Mating Intelligence. N. Li, Intelligent Priorities: Adaptive Long- and Short-Term Mate Preferences. D. Nettle, H. Clegg, Personality, Mating Strategies, and Mating Intelligence. M. O'Sullivan, Deception and Self-Deception as Strategies in Short and Long-Term Mating. V.A. Weekes-Shackelford, J.A. Easton, E.A. Stone, How Having Children Affects Mating Psychology. Part IV: Mental Fitness Indicators and Mating Intelligence. M.C. Keller, The Role of Mutations in Human Mating. A. Shaner, G. Miller, J. Mintz, Mental Disorders as Catastrophic Failures of Mating Intelligence. Part V: Mating Intelligence and Other Individual Differences. S.B. Kaufman, A. Kozbelt, M.L. Bromley, G. Miller, The Role of Creativity and Humor in Mate Selection. J.J. Casey, J. Garrett, M.A. Brackett, S. Rivers, Emotional Intelligence, Relationship Quality, and Partner Selection. S. Kanazawa, Mating Intelligence and General Intelligence as Independent Constructs. Part VI: The Ecological Context of Mating Intelligence. J. Ash, G.G. Gallup, Jr., Brain Size, Intelligence, and Paleoclimatic Variation. A.J. Figueredo, B.H. Brumbach, D.N. Jones, J.A. Sefcek, G. Vasquez, W.J. Jacobs, Ecological Constraints on Mating Tactics. Part VII: Conclusions. G. Miller, Mating Intelligence: Frequently Asked Questions. G. Geher, M.A. Camargo, S. O'Rourke, Mating Intelligence: An Integrative Model and Future Research Directions.
Molecular Biology and DNA Microarray Technology for Microbial Quality Monitoring of Water

Public concern over polluted water is a major environmental issue worldwide. Microbial contamination of water arguably represents the most significant risk to human health on a global scale. An important challenge in modern water microbial quality monitoring is the rapid, specific, and sensitive detection of microbial indicators and waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. Rapid microbiological analyses and detection of rare events in water systems are important challenges in water safety assessment since culture methods present serious limitations from both quantitative and qualitative points of view. To circumvent lengthy culture methods, newer enzymatic, immunological, and genetic methods are being developed as an alternative. DNA microarray technology is a new and promising tool that allows the detection of several hundred or even thousands DNA sequences simultaneously. Recent advances in sample processing and DNA microarray technologies provide new perspectives to assess microbial water quality. The aims of this review are to (1) summarize what is currently known about microbial indicators, (2) describe the most important waterborne pathogens, (3) present molecular methods used to monitor the presence of pathogens in water, and (4) show the potential of DNA microarrays in water quality monitoring.
Acute Pathogenesis of Recombinant Vesicular Stomatitis Virus Vaccine Vectors is Linked to Interleukin-1

Acute Pathogenesis of Recombinant Vesicular Stomatitis Virus Vaccine Vectors is Linked to Interleukin-1 by Kathleen Constance Athearn Department of Pathology Duke University Date:_______________________ Approved: ___________________________ Elizabeth Ramsburg, Supervisor ___________________________ Herman Staats ___________________________ David Pickup An abstract of a thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the Department of Pathology in the Graduate School of Duke University 2011 Copyright by Kathleen Constance Athearn 2011
Measurement of Arterial and Venous Reactivity by an Advanced Strain Gauge Plethysmograph

The problems of applying mercury strain gauge venous occlusion plethys mography in quantitative measurements of high blood flow rates were studied in the extremities of humans and animals. The fast-acting ECG-controlled pneumatic Periflow system opens the possibility of measurements with reduced restriction of arterial inflow. In animal experiments the arterial inflow rate (about 0.25 vol%/min) during the arterial occlusion period was estimated by an indicator dilution technique. The accuracy of the perfusion rate estimation of a limb by plethysmography was tested in controlled perfused extremities of large dogs weighing about 60 kg. Strain gauges with different positions showed dif ferent—but for each filament quite proportional—relations to real values. The nonuniform venous capacities of the different segments of a limb, which have been shown by injections of a known volume and recording of pressure volume curves, may complicate blood flow measurements by volume displacements from low-compliance regions to high-compliance regions of the vein system. Estimations of the length resistance relation of mercury strain gauges agreed well with the theoretically expected function. If an inextensible part is inserted into the circumferential arrangement of the filament, a correcting calculation of volume changes is necessary.
Building Your Own Reading List Anytime via Embedding Relevance, Quality, Timeliness and Diversity

During every summer holidays, several editions of reading lists are recommended and emerged on mass media, e.g., New York Times, and BBC. However, these reading lists are built for whole people with general topics for some purposes. What if we expect the books of a specific topic at a specific moment? How to generate the requested reading list for our own automatically? In this paper, we propose a searching framework for building a topical reading list anytime, where the Relevance (between topics and books), Quality (of books), Timeliness (of popularities) and Diversity (of results) are embedded into vector representations respectively based on user-generated contents and statistics on social media. We collected 8,197 real-world topics from 198 diverse groups on Librarything.com. The proposed methods are evaluated on the topic collection and the public benchmarks Social Book Search 2012-2016 (SBS). Experimental results demonstrate the robustness and effectiveness of our framework.
Inducible expression of cre recombinase in the retinal pigmented epithelium.

PURPOSE The retinal pigmented epithelium (RPE) expresses many genes that play important roles in the support and maintenance of photoreceptors. The present study was conducted to develop a system amenable to the dissection of the temporal function of these genes, specifically within RPE cells. Transgenic mice were generated and characterized in which the expression of Cre recombinase could be specifically induced within the RPE. METHODS Transgenic mice carrying the human vitelliform macular dystrophy-2 (VMD2) promoter (P(VMD2))-directed reverse tetracycline-dependent transactivator (rtTA) and the tetracycline-responsive element (TRE)-directed cre were generated. Inducible Cre expression was achieved by feeding doxycycline to these mice and was characterized by using a Cre-activatable lacZ reporter mouse strain (R26R). RESULTS A beta-galactosidase assay of rtTA/Cre-R26R mice demonstrated that the basal level of Cre expression without doxycycline induction was negligible. Addition of doxycycline led to induction of RPE-specific Cre expression/function at least from embryonic day 9 to postnatal day 60. The highest induction occurred at approximately postnatal day 4. As measured by ERG and histology, retinal function and morphology were normal in 10-month-old rtTA/Cre mice that were treated with doxycycline at weaning age. CONCLUSIONS Transgenic mice were generated that express Cre recombinase in the RPE in an inducible fashion. These mice will be useful for studies of the RPE-specific role of genes that are expressed in the RPE as well as other cells, particularly for avoiding embryonic lethality and dissecting the function of genes that play dual roles in development and adulthood.
Withdrawal of Stimulation May Initiate the Transition of Effector to Memory CD4 Cells1

The initial steps that determine development of memory in CD4 cells are unknown. To distinguish an intrinsic capacity of effectors to become memory cells from contributions of as yet undefined survival factors, we analyzed the effects of withdrawal of signals via TCR, costimulation, and cytokines from Th1 or Th2 primary effectors induced in vitro from TCR-transgenic CD4 cells. Withdrawal of stimulation caused the transition of effectors to resting populations with a memory phenotype that did not undergo division following transfer to normal syngeneic recipients. The return of effectors to rest was accompanied by acquisition of the capacity to function as memory cells in vivo as defined by extended persistence and a more rapid response to Ag in vivo than naive cells in adoptive hosts. Upon challenge with Ag, these in vitro-rested Th1 and Th2 cells were similar to long-term in vivo-rested memory cells, but distinct from in vitro-generated primary effectors and in vivo-restimulated memory effectors by their ability to resist apoptosis. Cessation of stimulation may occur when activated CD4 cells exit lymphoid tissues after priming and transition to memory may be initiated if effectors either fail to gain access to Ag in peripheral tissues where restimulation can lead to activation-induced cell death or do not receive sufficient stimuli to continue a response. Our results suggest that the first stage leading to stable CD4 memory could occur stochastically and independently of instructional processes and as such, the development of memory may be a default pathway when signals that direct responses are not received.
Context Based Classification for Automatic Collaborative Learning Process Analysis

We present a publicly available tool called TagHelper that can be used to support the analysis of conversational data using automatic text classification technology. The contribution of this paper is to explore the limitations of the current simple approach to text processing employed by TagHelper tools with respect to identifying context-sensitive categories of conversational behavior. TagHelper can be downloaded from http://www.cs. cmu.edu/cprose/TagHelper.html.
The Influence of HLA Class I Alleles and Heterozygosity on the Outcome of Human T Cell Lymphotropic Virus Type I Infection1

The inflammatory disease human T cell lymphotropic virus type I (HTLV-I)-associated myelopathy (HAM/TSP) occurs in only 1–2% of HTLV-I-infected individuals and is associated with a high provirus load of HTLV-I. We hypothesize that a person’s risk of developing HAM/TSP depends upon the efficiency of their immune response to the virus, which differs between individuals because of polymorphism in genes that influence this response. Previously we showed that the possession of HLA-A*02 was associated with a lower risk of HAM/TSP, and with a lower provirus load in healthy carriers of HTLV-I. However, HLA-A*02 did not account for all the observed difference in the risk of HAM/TSP. Here we present evidence, in the same study population in Japan, that HLA-Cw*08 was also associated with disease protection (probability value, two-tailed test = 0.002) and with a lower proviral load in healthy carriers. Possession of the A*02 and/or Cw*08 genes prevented 36% of potential HAM/TSP cases. In contrast, HLA-B*5401 was associated with a higher susceptibility to HAM/TSP (probability value, two-tailed test = 0.0003) and with a higher provirus load in HAM/TSP patients. At a given provirus load, B*5401 appeared to increase the risk of disease. The fraction of HAM/TSP cases attributable to B*5401 was 17%. Furthermore, individuals who were heterozygous at all three HLA class I loci have a lower HTLV-I provirus load than those who were homozygous at one or more loci. These results are consistent with the proposal that a strong class I-restricted CTL response to HTLV-I reduces the proviral load and hence the risk of disease.
Squat exercise to estimate knee megaprosthesis rehabilitation: a pilot study

[Purpose] This study evaluated a specific rehabilitation protocol using a half squat after total knee reconstruction with distal femur megaprosthesis and tibial allograft-prosthesis composite. [Subject and Methods] Squat execution was recorded by a three-dimensional system before and after a specific rehabilitation program on a 28-year-old patient. Squat duration, body center of mass trajectory, and vertical range of motion were determined. Step width and joint angles and symmetry (hip flexion, extension, and rotation, knee flexion, and ankle dorsal and plantar flexion) were estimated. Knee and hip joint symmetry was computed using a bilateral cyclogram technique. [Results] After rehabilitation, the squat duration was longer (75%), step width was similar, and vertical displacement was higher. Hip flexion increased by over 20%, and ankle dorsiflexion diminished by 14%. The knee had the highest symmetry gain (4.1–3.4%). Angle-angle plot subtended areas decreased from 108° to 40°2 (hip) and from 204° to 85°2 (knee), showing improvement in movement symmetry. [Conclusion] We concluded that the squat is an effective multifactorial exercise to estimate rehabilitation outcomes after megaprosthesis, also considering that compressive and shear forces are minimal up to 60–70° of knee flexion.
PRELIMINARY AND INCOMPLETE DEVIATIONS BETWEEN STOCK PRICE AND FUNDAMENTAL VALUE FOR REAL ESTATE INVESTMENT TRUSTS

We document that real estate investment trust (REIT) stock prices deviate from net asset values (NAV), as measured by Green Street Advisors, a buy-side research firm. Using REIT data since 1990, we find large positive excess returns to a strategy of buying stocks that trade at a discount to NAV, and shorting stocks trading at a premium to NAV. Estimated alphas are between 1.2% and 1.8% per month, with little risk. Trading costs and short-sale constraints are not prohibitive. We find that some variation in P/NAV makes sense, as premiums are positively related to recent and future NAV growth. However, there appears to be too much variation in P/NAV, giving rise to potential profits from trading on mean reversion. These results are clearly related to similar findings in the closed-end fund literature. However, REITs have much higher institutional ownership. Thus, it is unlikely that these premiums and discounts reflect the investor sentiment hypothesis of Lee, Shleifer, and Thaler (1991).