Miracle-dz/UniFAR-FTUs huggingface dataset:
On the potential of transit surveys in star clusters: impact of correlated noise and radial velocity follow-up

We present an extension of the formalism recently proposed by Pepper and Gaudi to evaluate the yield of transit surveys in homogeneous stellar systems, incorporating the impact of correlated noise on transit time-scales on the detectability of transits, and simultaneously incorporating the magnitude limits imposed by the need for radial velocity (RV) follow-up of transit candidates. New expressions are derived for the different contributions to the noise budget on transit time-scales and the least-squares detection statistic for box-shaped transits, and their behaviour as a function of stellar mass is re-examined. Correlated noise that is constant with apparent stellar magnitude implies a steep decrease in detection probability at the high-mass end which, when considered jointly with the RV requirements, can severely limit the potential of otherwise promising surveys in star clusters. However, we find that small-aperture, wide-field surveys may detect hot Neptunes whose RV signal can be measured with present-day instrumentation in very nearby (<100 pc) clusters.
HIV-1 Envelope Subregion Length Variation during Disease Progression

The V3 loop of the HIV-1 Env protein is the primary determinant of viral coreceptor usage, whereas the V1V2 loop region is thought to influence coreceptor binding and participate in shielding of neutralization-sensitive regions of the Env glycoprotein gp120 from antibody responses. The functional properties and antigenicity of V1V2 are influenced by changes in amino acid sequence, sequence length and patterns of N-linked glycosylation. However, how these polymorphisms relate to HIV pathogenesis is not fully understood. We examined 5185 HIV-1 gp120 nucleotide sequence fragments and clinical data from 154 individuals (152 were infected with HIV-1 Subtype B). Sequences were aligned, translated, manually edited and separated into V1V2, C2, V3, C3, V4, C4 and V5 subregions. V1-V5 and subregion lengths were calculated, and potential N-linked glycosylation sites (PNLGS) counted. Loop lengths and PNLGS were examined as a function of time since infection, CD4 count, viral load, and calendar year in cross-sectional and longitudinal analyses. V1V2 length and PNLGS increased significantly through chronic infection before declining in late-stage infection. In cross-sectional analyses, V1V2 length also increased by calendar year between 1984 and 2004 in subjects with early and mid-stage illness. Our observations suggest that there is little selection for loop length at the time of transmission; following infection, HIV-1 adapts to host immune responses through increased V1V2 length and/or addition of carbohydrate moieties at N-linked glycosylation sites. V1V2 shortening during early and late-stage infection may reflect ineffective host immunity. Transmission from donors with chronic illness may have caused the modest increase in V1V2 length observed during the course of the pandemic.
On the degree of binder activity of reclaimed asphalt and degree of blending with recycling agents

It is common practice to assume full blending of the aged binder of reclaimed asphalt (RA) within the design of new asphalt mixtures. Although being practical, this assumption has often led designers to asphalt mixtures lacking binder. Hence, going towards recycled asphalt mixtures (RAM) there is a need to have a better understanding of the blending phenomena, to have a general agreement on terminology and finally adapting RA classification and mix design procedures accordingly. This manuscript aims at being both a reference and stimulus for the scientific community to work in this direction and on this basis provides a nomenclature and a theoretical framework of the blending phenomena. The study is built upon a literature review on definitions, methods and influencing factors related with the blending phenomena and as a result, an intrinsic property of RA, the Degree of binder Activity (DoA), is introduced for the sake of improving RA classification. Furthermore, the two well-known concepts of the Degree of Blending (DoB) and the Degree of binder Availability (DoAv) are redefined, within the proposed framework, together with practical suggestions to introduce them in mix design procedures.
Emerging types of Shiga toxin-producing E. coli (STEC) O178 present in cattle, deer, and humans from Argentina and Germany

More than 400 serotypes of Shiga toxin-producing Escherichia coli (STEC) have been implicated in outbreaks and sporadic human diseases. In recent years STEC strains belonging to serogroup O178 have been commonly isolated from cattle and food of bovine origin in South America and Europe. In order to explore the significance of these STEC strains as potential human pathogens, 74 German and Argentinean E. coli O178 strains from animals, food and humans were characterized phenotypically and investigated for their serotypes, stx-genotypes and 43 virulence-associated markers by a real-time PCR-microarray. The majority (n = 66) of the O178 strains belonged to serotype O178:H19. The remaining strains divided into O178:H7 (n = 6), O178:H10 (n = 1), and O178:H16 (n = 1). STEC O178:H19 strains were mainly isolated from cattle and food of bovine origin, but one strain was from a patient with hemolytic uremic syndrome (HUS). Genotyping of the STEC O178:H19 strains by pulsed-field gel electrophoresis revealed two major clusters of genetically highly related strains which differ in their stx-genotypes and non-Stx putative virulence traits, including adhesins, toxins, and serine-proteases. Cluster A-strains including the HUS-strain (n = 35) carried genes associated with severe disease in humans (stx2a, stx2d, ehxA, saa, subAB1, lpfAO113, terE combined with stx1a, espP, iha). Cluster B-strains (n = 26) showed a limited repertoire of virulence genes (stx2c, pagC, lpfAO113, espP, iha). Among O178:H7 strains isolated from deer meat and patients with uncomplicated disease a new STEC variant was detected that is associated with the genotype stx1c/stx2b/ehxA/subAB2/espI/[terE]/espP/iha. None of the STEC O178 strains was positive for locus of enterocyte effacement (LEE)- and nle-genes. Results indicate that STEC O178:H19 strains belong to the growing group of LEE-negative STEC that should be considered with respect to their potential to cause diseases in humans.
Modelling Advection and Diffusion in Microchannels

Mixing In Microchannels by Dan Beutel June 2003 This project will investigate mixing in microchannels. Specifically, the advection and diffusion of a passive scalar, using a split-step Monte Carlo method. Numerically the implementation of this method is well understood. The current experimental geometry is a rectangular pipe with grooves on one wall. Mixing results with straight walls agree closely with experiment. The velocity field over grooves is also studied.
Fast Java profiling with scheduling-aware stack fragment sampling and asynchronous analysis

Sampling is a popular approach to profiling because it typically has only a small impact on performance and does not modify the profiled application. Common sampling profilers collect data about an application by pausing the application threads, walking the stacks to create stack traces, and then adding the traces to their profile. Waiting threads are often sampled as well, even when they have not been active since their last sample. Sampling profilers for Java commonly rely on safepoints, which are locations in the Java code where a thread can pause to be sampled. However, restricting profiling to these locations affects the accuracy of the profile, and the safepoint mechanism itself imposes significant pause times on the application. We present stack fragment sampling, a new approach for Java applications that minimizes pause times and eliminates redundant samples altogether. It interrupts an application thread only to copy a fragment of its stack to a buffer and then immediately resumes its execution. Retrieving and decoding the stack fragments happens asynchronously and can run on a separate core or on another processor. Our approach integrates with the operating system to only take samples of threads while they are running in order to avoid redundant samples. We demonstrate that our approach has a very small impact on performance even at high sampling rates. Furthermore, we validate our approach by comparing our profiles to those from a profiler using safepoints as well as to a VM-internal profiler that does not use safepoints. The results show that the profiles agree.
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This Ph.D. progress report documents a combination of parti al evaluation and compilation that enables “just-in-time program specialization”. To th is end, we have composed a type-directed partial evaluator for OCaml programs with a r un-time code generator for the OCaml virtual machine. The composition is deforested, i . e. residual programs are directly expressed as byte code, which is then dynamically l oaded. The implementation seamlessly extends OCaml with two new keywords for generati ng code dynamically. The system has been applied to traditional examples of parti al evaluation and run-time code generation, such as the first Futamura projection for Ac tion Semantics and the BSD Packet Filter.
First steps towards probabilistic process mining

This paper presents some initial ideas on a probabilistic ve rsion of the process mining problem. We propose that a process model sele ction criteria to choose the “correct” model mined from a log should balance co mplexity (of the model) and fitness (how well the model predicts the frequenci es of the traces in the log). We propose the known statistical measure of χ to measure the fitness, and we point out some directions in this research line.
On non-abelian low energy effective action for D-branes

The connection between the partition function for the 2D sigma model with boundary pertubations and the low energy effective action for massless fields in the open string theory is discussed. In the non-abelian case with a stack of N D-branes, the terms up to the order of α'3 are found.
A Laboratory Test Expert System for Clinical Diagnosis Support in Primary Health Care

Clinical Decision Support Systems have the potential to reduce lack of communication and errors in diagnostic steps in primary health care. Literature reports have showed great advances in clinical decision support systems in the recent years, which have proven its usefulness in improving the quality of care. However, most of these systems are focused on specific areas of diseases. In this way, we propose a rule-based expert system, which supports clinicians in primary health care, providing a list of possible diseases regarding patient’s laboratory tests results in order to assist previous diagnosis. Our system also allows storing and retrieving patient’s data and the history of patient’s analyses, establishing a basis for coordination between the various health care levels. A validation step and speed performance tests were made to check the quality of the system. We conclude that our system could improve clinician accuracy and speed, resulting in more efficiency and better quality of service. Finally, we propose some recommendations for further research.
Limits of ultra-high-precision optical astrometry - Stellar surface structures

Aims. To investigate the astrometric effects of stellar surface structures as a practical limitation to ultra-high-precision astrometry (e.g. in the context of exoplanet searches) and to quantify the expected effects in different regions of the HR-diagram. Methods. Stellar surface structures (spots, plages, granulation, non-radial oscillations) are likely to produce fluctuations in the integrated flux and radial velocity of the star, as well as a variation of the observed photocentre, i.e. astrometric jitter. We use theoretical considerations supported by Monte Carlo simulations (using a starspot model) to derive statistical relations between the corresponding astrometric, photometric, and radial velocity effects. Based on these relations, the more easily observed photometric and radial velocity variations can be used to predict the expected size of the astrometric jitter. Also the third moment of the brightness distribution, interferometrically observable as closure phase, contains information about the astrometric jitter. Results.For most stellar types the astrometric jitter due to stellar surface structures is expected to be of the order of 10 micro-AU or greater. This is more than the astrometric displacement typically caused by an Earth-size exoplanet in the habitable zone, which is about 1-4 micro-AU for long-lived main-sequence stars. Only for stars with extremely low photometric variability (<0.5 mmag) and low magnetic activity, comparable to that of the Sun, will the astrometric jitter be of the order of 1 micro-AU, sufficient to allow the astrometric detection of an Earth-sized planet in the habitable zone. While stellar surface structure may thus seriously impair the astrometric detection of small exoplanets, it has in general a negligible impact on the detection of large (Jupiter-size) planets and on the determination of stellar parallax and proper motion. From the starspot model we also conclude that the commonly used spot filling factor is not the most relevant parameter for quantifying the spottiness in terms of the resulting astrometric, photometric and radial velocity variations. (Less)
Considerations on In-Band and Out-of-Band Signalling Constraints in OBS Networks

Most of previous works on optical burst switching (OBS) assume in their analysis that signalling does not affect network performance. In this paper we analyze under which conditions the effect of signalling is actually negligible, taking into account the effect of signalling in the evaluation of burst discard probability. We use two analytical models for two different signalling techniques in an OBS network: out-of-band and in-band technique. We evaluate the impact of these two signalling strategies in term of the probability of burst discard. We also discuss a new method to assign the correct amount of resources to the control plane. To verify the accuracy of the proposed models, analytical results are compared with results based on discrete-event simulations and are found to be in very satisfactory agreement.
Editorial - Augmenting Epithelial Barrier Function

The simplest multicellular animal organisms, coelenterates, are essentially floating intestines in the sea. More fundamentally, they are ‘barrier tubes’ that attempt to compartmentalize the environment they exist in. It is said that ontogeny recapitulates phylogeny. It is thus interesting that the blastocyst, among the earliest multicellular embryonic structures, is essentially a sac comprised of polarizing cells. Like the coelenterate, it is also compartmentalizing the environment that it exists in, creating an internal fluid compartment distinct from an external one. So on both an evolutionary basis and a developmental basis, the singular importance of fluid compartmentation and barrier cell linings was a concept that nature apparently grabbed hold of with both hands and never let go, as it kept ramifying the theme. The human body is in a sense a manifold of many different sacs and tubes: a respiratory tract, a GI tract, a urinary tract, the skin, a reproductive tract, a vasculature, a central nervous system encased in a medium (cerebrospinal fluid) quite distinct from blood. We are intimately and fundamentally divided into luminal and abluminal compartments.
Forces Shaping the Fastest Evolving Regions in the Human Genome

Comparative genomics allow us to search the human genome for segments that were extensively changed in the last ~5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202 genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements are dramatically changed in human but not in other primates, with seven times more substitutions in human than in chimp. The accelerated elements, and in particular the top five, show a strong bias for adenine and thymine to guanine and cytosine nucleotide changes and are disproportionately located in high recombination and high guanine and cytosine content environments near telomeres, suggesting either biased gene conversion or isochore selection. In addition, there is some evidence of directional selection in the regions containing the two most accelerated regions. A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome.
Novel Insight Into Intellectual Disability; A Review Article

: Intellectual disability or cognitive disturbance is a prevalent neurological problem determined by the low-level intelligence quotient (< 70). Intellectual disability affects approximately 1% to 3% of the general population. The collaboration of environmental factors and heterogeneous genetic agents can be a cause of intellectual disability in X-linked, autosomal dominant, recessive, and inheritance of mitochondria patterns. Spontaneous mutations in germ line may have vital phenotypic outcomes when involved in bases of the whole genome. Discovering the etiology of intellectual disability plays a role in precise diagnosis and can help the couple plan in the near future. Development of genome sequencing can improve mutation detection in a single experiment. These tools have been shown as a new way for the conception of the molecular pathway in a genetic disorder. This finding can have a profound implication for early diagnosis and treatment development. This study reviewed recent reports of de novo mutations detection of intellectual disability in the Iranian population by whole exome sequencing approaches.
Proof That Every Typed Formula Has a Normal Form Universal Turing Machine

16 bit architectures and simulated annealing, while appropriate in theory, have not until recently been considered natural. after years of unproven research into lambda calculus, we dis-confirm the analysis of spreadsheets, which embodies the unproven principles of theory. Our focus in this paper is not on whether DHTs can be made scalable, metamorphic, and interactive , but rather on presenting an application for event-driven configurations (Wae).
Source Retrieval Based on Learning to Rank and Text Alignment Based on Plagiarism Type Recognition for Plagiarism Detection

1Heilongjiang Institute of Technology, China 2Harbin Engineering University, China 3Harbin Institute of Technology, China kongleilei1979@gmail.com Abstract. For the task of source retrieval, the target is to retrieve all plagiarized sources while minimizing retrieval costs. It has become standard for plagiarism detection to retrieve plagiarism sources with query keywords selected from suspicious document. This paper regards the keywords selection problem as learning a ranking model to choose the method of keywords extraction over suspicious document segments. There are four basic methods which are used in our ranking function, which are BM25, TFIDF, TF and EW. Then, a ranking model based on Ranking SVM is proposed to rank the query keywords group which is contributed to get the higher evaluation measure F. In our ranking model, achieving the best performance measure F of source retrieval is used as the target of learning to rank and all kinds of statistic features are fused for searching the better query keywords groups.
UQ-DKE's Participation at MediaEval 2014 Placing Task

In this paper, we describe our approach as part of the MediaEval 2014 Placing Task evaluation. We first identify tags that are most indicative of geographic location by calculating the spatial-aware weighting for all tags in the training set. These weighting are applied to a language model-based retrieval framework. To address the geo-tagging problem, we find the most similar training item and propagate its location to the test item. Base on last year’s experience, we further improve the accuracy by utilizing the geo-location correlation of images/videos uploaded by the same user.
A fully GIS-integrated simulation approach for analyzing the spread of epidemics in urban areas

Human-to-human communicable diseases can be devastating in urban areas where large heterogeneous population groups are living in restricted spaces, causing serious concerns for public health, especially during epidemic outbreaks. Even though Geographic Information Systems (GIS) have been used to study a variety of public health issues in the last decade, their use to study human communicable diseases has been limited to the development of disease clustering, mapping and surveillance systems. These systems don't provide ways to understand and predict the dynamics of diseases spread across an urban region, taking into account the dynamics of human contacts and mobility, which are the main widely recognized mechanisms responsible for diseases' spread. In this paper we address such limits by presenting a GIS-based spatial-temporal simulation approach and software to support public health decision making in the context of communicable diseases in urban areas. The approach fully integrates epidemiological, mobility and GIS-data models at an aggregate population level in order to support spatialized interventions.
Anti-inflammatory effects of Rubus coreanus Miquel through inhibition of NF-κB and MAP Kinase

BACKGROUND/OBJECTIVES Rubus Coreanus Miquel (RCM), used as a traditional Korean medicine, reduces chronic inflammatory diseases such as cancer and rheumatoid arthritis. However, its mechanism has not been elucidated. In this study, we examine the anti-inflammatory effects of RCM and their possible mechanisms using RAW 264.7 cells. MATERIALS/METHODS Unripe RCM ethanol extract (UE), unripe RCM water extract (UH), ripe RCM ethanol extract (RE), and ripe RCM water extract (RH) were prepared. Inflammatory response was induced with LPS treatment, and expression of pro-inflammatory mediators (iNOS, COX-2, TNF-α, IL-1β, and IL-6) and NO and PGE2 productions were assessed. To determine the anti-inflammatory mechanism of RCM, we measured NF-κB and MAPK activities. RESULTS UE and UH treatment significantly reduced NF-κB activation and JNK and p38 phosphorylation and reduced transcriptional activities decreased iNOS, COX-2, and pro-inflammatory cytokines expressions, and NO and PGE2 productions. RE and RH treatments reduced IL-1β and IL-6 expressions through suppressions of JNK and p38 phosphorylation. CONCLUSIONS In this study, we showed that RCM had anti-inflammatory effects by suppression of pro-inflammatory mediator expressions. Especially, unripe RCM showed strong anti-inflammatory effects through suppression of NF-κB and MAPK activation. These findings suggest that unripe RCM might be used as a potential functional material to reduce chronic inflammatory responses.
A survey on design space exploration for heterogeneous multi-core

Design Space Exploration (DSE) plays an important role during the process of Hardware/Software co-design for heterogeneous multi-core architecture. DSE is the process of discovering and evaluating design alternatives, prior to implementation. The various designs can be compared with each other on the basis of required metrics and the optimized design can then be chosen to develop the system. The main goal of DSE is rapid prototyping and it is also used to find configurations and legal assemblies to satisfy a particular set of overall design constraints. This paper surveys the various DSE approaches used for heterogeneous multi-cores and compares them.