Miracle-dz/UniFAR-FTUs huggingface dataset:
The infectivity, growth, and virulence of the cestode Schistocephalus solidus in its first intermediate host, the copepod Macrocyclops albidus

In an experiment to study the infectivity, growth and virulence of Schistocephalus solidus in their first intermediate host, copepods of the species Macrocyclops albidus were kept singly and exposed to up to 9 coracidia. Eleven or 14 days post-infection (p.i.) the presence and growth of the cestode larvae relative to survival, growth and reproduction of their host was determined. As expected, the probability of a copepod becoming infected increased with increasing numbers of parasites administered. However, the chances of a single coracidium establishing in a copepod also increased with increasing numbers of coracidia administered, which indicates that the parasites profit from a dilution effect of the host's defence. Copepod size or developmental stage had no significant effect on the infection, but 14 days p.i. , constraining effects of copepod size on the growth of the parasites were apparent. Moreover, procercoids in multiple infections grew smaller and developed their cercomer at a smaller size than those in single infections. No significant effect of the parasite on host mortality was found within the observation period. However, growth between the 5th copepodid stage and adult stage was negatively affected by infection. An infection with S. solidus was also strongly linked with host reproduction: infected females were more likely to bear an egg sac at the end of the experiment than non-infected ones. These egg sacs, however, contained fewer eggs.
e-QRAQ: A Multi-turn Reasoning Dataset and Simulator with Explanations

In this paper we present a new dataset and user simulator e-QRAQ (explainable Query, Reason, and Answer Question) which tests an Agent's ability to read an ambiguous text; ask questions until it can answer a challenge question; and explain the reasoning behind its questions and answer. The User simulator provides the Agent with a short, ambiguous story and a challenge question about the story. The story is ambiguous because some of the entities have been replaced by variables. At each turn the Agent may ask for the value of a variable or try to answer the challenge question. In response the User simulator provides a natural language explanation of why the Agent's query or answer was useful in narrowing down the set of possible answers, or not. To demonstrate one potential application of the e-QRAQ dataset, we train a new neural architecture based on End-to-End Memory Networks to successfully generate both predictions and partial explanations of its current understanding of the problem. We observe a strong correlation between the quality of the prediction and explanation.
Exceptional situations and program reliability

It is difficult to write programs that behave correctly in the presence of run-time errors. Proper behavior in the face of exceptional situations is important to the reliability of long-running programs. Existing programming language features often provide poor support for executing clean-up code and for restoring invariants. We present a data-flow analysis for finding a certain class of exception-handling defects: those related to a failure to release resources or to clean up properly along all paths. Many real-world programs violate such resource usage rules because of incorrect exception handling. Our flow-sensitive analysis keeps track of outstanding obligations along program paths and does a precise modeling of control flow in the presence of exceptions. Using it, we have found over 1,300 exception handling defects in over 5 million lines of Java code. Based on those defects we propose a programming language feature, the compensation stack, that keeps track of obligations at run time and ensures that they are discharged. We present a type system for compensation stacks that tracks collections of obligations. Finally, we present case studies to demonstrate that this feature is natural, efficient, and can improve reliability.
Estimating Dynamic Traffic Matrices by Using Viable Routing Changes

In this paper we propose a new approach for dealing with the ill-posed nature of traffic matrix estimation. We present three solution enhancers: an algorithm for deliberately changing link weights to obtain additional information that can make the underlying linear system full rank; a cyclo-stationary model to capture both long-term and short-term traffic variability, and a method for estimating the variance of origin-destination (OD) flows. We show how these three elements can be combined into a comprehensive traffic matrix estimation procedure that dramatically reduces the errors compared to existing methods. We demonstrate that our variance estimates can be used to identify the elephant OD flows, and we thus propose a variant of our algorithm that addresses the problem of estimating only the heavy flows in a traffic matrix. One of our key findings is that by focusing only on heavy flows, we can simplify the measurement and estimation procedure so as to render it more practical. Although there is a tradeoff between practicality and accuracy, we find that increasing the rank is so helpful that we can nevertheless keep the average errors consistently below the 10% carrier target error rate. We validate the effectiveness of our methodology and the intuition behind it using commercial traffic matrix data from Sprint's Tier-1 backbone.
An Adaptive Multiresolution Method for Progressive Model Transmission

Although there are many adaptive (or view-dependent) multiresolution methods, support for progressive transmission and reconstruction has not been addressed. A major reason for this is that most of these methods require a large portion of the hierarchical data structure to be available at the client before rendering starts. This is due to the dependency constraints among neighboring vertices. In this paper, we present an efficient, adaptive, multiresolution method that allows progressive and selective model transmission. It is achieved by reducing the neighboring dependency to a minimum. The new method allows visually important parts of an object to be transmitted to the client at higher priority than the less important parts, and progressively reconstructed there for display. It is even possible to transmit only the visible parts of a model and reconstruct these visible parts at the client. The ability to selectively transmit allows the visualization of very large models across the network with minimal delay. We will present how our method works in a client-server environment. We will also show the data structure of the transmission record and some performance results of the method.
Grand Rounds: An Update on Convulsive Status Epilepticus

Status epilepticus (SE) is the term used to describe an abnormally prolonged state of self-perpetuating and evolving seizure activity, specifically defined by time, as a 5 minute seizure or an episode of briefer seizures with reduced recovery of awareness in between seizures1. SE can be convulsive or non-convulsive in type. Non-convulsive seizures represent states of various levels of altered awareness, associated with electroencephalographic (EEG) seizure activity, but without outwardly observable convulsive activity2. An important feature of convulsive seizures is their potential for evolution into non-convulsive seizures, where the patient can appear “post ictal” but is having electrical seizures, without obvious convulsive activity3. Other types of status epilepticus include simple partial status (with preserved awareness), complex partial status (with impaired consciousness) and myoclonic status (often associated with coma)4. Records from antiquity describe SE, but it has only been in the last century that there have been major advances in its understanding and treatment5. Many significant questions remain about the pathophysiology and management of this medical emergency which carries a substantial morbidity and mortality. This paper will present the current understanding of SE, identifying gaps in our knowledge. The evidence base for the pharmacological management of SE will be reviewed.
The Parallel Intensionally Fully Abstract Games Model of PCF

We describe a framework for truly concurrent game semantics of programming languages, based on Rideau and Winskel's concurrent games on event structures. The model supports a notion of innocent strategy that permits concurrent and non-deterministic behaviour, but which coincides with traditional Hyland-Ong innocent strategies if one restricts to the deterministic sequential case. In this framework we give an alternative interpretation of Plot kin's PCF, that takes advantage of the concurrent nature of strategies and formalizes the idea that although PCF is a sequential language, certain sub-computations are independent and can be computed in a parallel fashion. We show that just as Hyland and Ong's sequential interpretation of PCF, our parallel interpretation yields a model that is intensionally fully abstract for PCF.
Intravitreal Aflibercept in Recalcitrant Radiation Maculopathy due to External Beam Radiotherapy for Nasopharyngeal Cancer: A First Case Report

Purpose: To present the safety and efficacy of intravitreal aflibercept (Eylea) in a patient with radiation maculopathy secondary to external beam radiotherapy for nasopharyngeal cancer unresponsive to other therapeutic options. Methods: A 73-year-old female presented with decreased visual acuity in both eyes 18 months after completing 47 external beam cycles of radiation for nasopharyngeal cancer. On presentation, her best corrected visual acuity was 6/60 in the right eye and counting fingers from 1 meter in the left eye. She received 5 bevacizumab injections in the right eye and 7 bevacizumab injections in the left eye over the last year without any improvement. A treatment with intravitreal injections of aflibercept was recommended in both eyes. Results: The patient received 3 intravitreal aflibercept injections (2 mg/0.05 mL) in each eye every 4 weeks. The visual acuity improved from 6/60 to 6/12 in the right eye and from counting fingers to 6/36 in the left eye. Biomicroscopy showed less exudates, hemorrhages, and microaneurysms. Optical coherence tomography revealed reduced central retinal thickness in both eyes after 1–3 intravitreal aflibercept injections. Conclusion: Intravitreal aflibercept should be regarded a safe and effective treatment in patients with recalcitrant macular edema due to radiation maculopathy.
Core pathways controlling shoot meristem maintenance

Essential to the function of shoot meristems in plants to act as sites of continuous organ and tissue formation is the ability of cells within the meristem to remain undifferentiated and proliferate indefinitely. These are characteristics of the stem cells within meristems that are critical for their growth properties. Stem cells are found in tight association with the stem cell niche—those cells that signal to maintain stem cells. Shoot meristems are unique among stem cell systems in that the stem cell niche is a constantly changing population of recent daughter stem cells. Recent progress from Arabidopsis and other systems have uncovered a large number of genes with defined roles in meristem structure and maintenance. This review will focus on well‐studied pathways that represent signaling between the stem cells and the niche, that prevent ectopic differentiation of stem cells, that regulate the chromatin status of stem cell factors, and that reveal intersection of hormone signaling and meristem maintenance. WIREs Dev Biol 2013, 2:671–684. doi: 10.1002/wdev.110
Mitochondrial genome of the black flying fox, Pteropus alecto (Chiroptera: Megachiroptera: Pteropodidae)

Abstract In this article we report the complete mitochondrial genome of black flying fox, Pteropus alecto, with the sequence length of 16,739 bp for the first time. The mitogenome contained a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The base composition was A (33.1%), G (14.5%), C (27.2%) and T (25.2%), indicating that the percentage of A and T (58.3%) was higher than that of G and C. Most of these genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes. The mitochondrial genome analyzed here will provide new genetic information to study the evolution of bats.
Discovery of Rare Mutations in Populations: TILLING by Sequencing1[C][W][OA]

Discovery of rare mutations in populations requires methods, such as TILLING (for Targeting Induced Local Lesions in Genomes), for processing and analyzing many individuals in parallel. Previous TILLING protocols employed enzymatic or physical discrimination of heteroduplexed from homoduplexed target DNA. Using mutant populations of rice (Oryza sativa) and wheat (Triticum durum), we developed a method based on Illumina sequencing of target genes amplified from multidimensionally pooled templates representing 768 individuals per experiment. Parallel processing of sequencing libraries was aided by unique tracer sequences and barcodes allowing flexibility in the number and pooling arrangement of targeted genes, species, and pooling scheme. Sequencing reads were processed and aligned to the reference to identify possible single-nucleotide changes, which were then evaluated for frequency, sequencing quality, intersection pattern in pools, and statistical relevance to produce a Bayesian score with an associated confidence threshold. Discovery was robust both in rice and wheat using either bidimensional or tridimensional pooling schemes. The method compared favorably with other molecular and computational approaches, providing high sensitivity and specificity.
Effect of notch and crack initiating from notch on the behavior of adhesively bonded composite laminated plate

Reinforcing structures using bonded composites is an effective and economic method to increase the service life of damaged structures. In this study, we use the finite element method to analyze the behavior of a laminated structure by computing the stress concentration factor and the stress intensity factor at the crack tip in mode I. The effects of the mechanical properties of the laminate layers and the adhesive layer on the behavior of the assembly are highlighted. The results show that the factors of concentration and stress intensity are affected by the orientation of fibers and the presence of geometrical defects. The magnitude of the latter affects and amplifies the stress concentrations at the crack tip.
Adenovirus 2 peptide IX gene is expressed only on replicated DNA molecules

Transcription of the adenovirus type 2 peptide IX (pIX) gene was examined in transient expression assays. When a nonreplicating plasmid DNA containing the pIX gene was introduced into HeLa cells by the DEAE-dextran method, no pIX gene transcript was detected. In contrast, efficient transcription was observed in the cells transfected with a replicating plasmid containing the pIX gene. Adenovirus early genes did not affect the level of transcription of the pIX gene on either a nonreplicating or a replicating plasmid. Inhibition of plasmid replication with cytosine arabinoside prevented transcription of the pIX gene. By quantitative analysis of the amount of the pIX gene and its transcript in transfected cells, it was concluded that active transcription of the pIX gene occurred only on DNA molecules replicated in the cell.
Body-Based Perceptual Rescaling Revealed through the Size — Weight Illusion

An embodied approach to the perception of spatial layout contends that the body is used as a ‘perceptual ruler’ with which individuals scale the perceived environmental layout. In support of this notion, previous research has shown that the perceived size of objects can be influenced by changes in the apparent size of hand. The size – weight illusion is a well known phenomenon, which occurs when people lift two objects of equal weight but differing sizes and perceive that the larger object feels lighter. Therefore, if apparent hand size influences perceived object size, it should also influence the object's perceived weight. In this study, we investigated this possibility by using perceived weight as a measure and found that changes in the apparent size of the hand influence objects' perceived weight.
Convex hull covering of polygonal scenes for accurate collision detection in games

Decomposing a complex object into simpler pieces, e.g., convex patches or convex polyhedra, is a well-studied geometry problem. A well constructed decomposition can greatly accelerate collision detection since intersections with and between convex objects are fast to compute. In this paper, we look at a particular instance of the convex decomposition problem which arises from real-world game development. Given a collection of polyhedral surfaces (possibly with boundaries, holes, and complex interior structures) that model the scene geometry in a game environment, we wish to find a small set of convex hulls such that colliding objects in the scene against such a set of convex hulls produces the same game behavior as colliding against the original surfaces. The vague formulation of the problem is due to the difficulty of defining the space accessible by the objects involved in the game play. Under reasonable assumptions, we arrive at a set of conditions for valid convex decomposition and develop a construction algorithm via greedy merging driven by patch compactness. We show that our validity conditions ensure valid collision-related game behavior. The effectiveness of our decomposition algorithm is demonstrated through real examples from game development. To the best of our knowledge, no previous convex hull decomposition or surface decomposition algorithms were designed to handle the type of models we consider or be able to compute a set of convex hulls that ensure accurate collision detection results.
Three Facts About Marijuana Prices

Australians are among the largest consumers of marijuana in the world, and estimates show that their expenditure on marijuana is approximately twice that on wine. In the present paper, the evolution of Australian marijuana prices over the last decade is analysed, and a decline in real terms by almost 40 per cent is shown. This decline is far above that experienced by most agricultural products. Why has this occurred and what are the implications? One possible reason is the adoption of hydroponic growing techniques that have enhanced productivity and lowered costs and prices. Another reason is that laws have become softer and penalties reduced. Patterns in prices are found that divide the country into three broad regions: (i) Sydney, where prices are highest; (ii) Melbourne and Canberra, which have somewhat lower prices; and (iii) everywhere else, where marijuana is cheapest. An exploratory analysis indicates the extent to which the price declines have stimulated marijuana consumption and inhibited the consumption of a substitute product, alcohol.
Performance analysis of polymer based antenna-coils for RFID

Transponder-labels, -tags or -modules of inductively coupled RFID (Radio Frequency Identification)-systems commonly consist of a substrate with an appropriate transponder-chip or transponder-module mounted on top. The antenna coil is structured on this substrate, usually made of PET, PVC or polyimide and usually consists of a wound wire or etched copper or aluminium structures. As a low cost alternative, conductive polymeric thick film pastes can be used for the production of antenna coils for inductively coupled transponders. These pastes are applied by screen printing or dispensing. In mass production the consequence is a reduction of material costs and processing time. Most popular fillers of the conductive polymer pastes are silver flakes which get connected during the curing process. The conductivities of these compounds are lower in comparison with copper or aluminium. Therefore, the transponder coils made of conductive polymer pastes have substantially higher ohmic losses which influence the functionality of RFID transponders. In this paper, the minimum operating magnetic field strength and powering range of the transponder is considered in detail. A selected reference design with the size of a smart card inlay (47 /spl times/ 74 mm/sup 2/) is used.
Light transmission and haze of polyethylene blown thin films

The surface and bulk morphologies of polyethylene blown films are obtained using non-contact Atomic Force Microscopy (AFM). Based on these experimental observations, a model using the Mie Scattering theory is proposed to describe the forward transmission and scattering of a plane wave through the film. The light transmission properties are computed from the proposed model and the results are validated by experimental measurements.
Brane dimers and quiver gauge theories

We describe a technique which enables one to quickly compute an infinite number of toric geometries and their dual quiver gauge theories. The central object in this construction is a ``brane tiling,'' which is a collection of D5-branes ending on an NS5-brane wrapping a holomorphic curve that can be represented as a periodic tiling of the plane. This construction solves the longstanding problem of computing superpotentials for D-branes probing a singular non-compact toric Calabi-Yau manifold, and overcomes many difficulties which were encountered in previous work. The brane tilings give the largest class of = 1 quiver gauge theories yet studied. A central feature of this work is the relation of these tilings to dimer constructions previously studied in a variety of contexts. We do many examples of computations with dimers, which give new results as well as confirm previous computations. Using our methods we explicitly derive the moduli space of the entire Yp,q family of quiver theories, verifying that they correspond to the appropriate geometries. Our results may be interpreted as a generalization of the McKay correspondence to non-compact 3-dimensional toric Calabi-Yau manifolds.
Mycoplasma hyorhinis: a potential risk factor in gastric cancer progression

Persistent infection of Mycoplasma hyorhinis (M. hyorhinis) is associated with various types of cancer. However, to date, there is few study identifying host factors mediating its infection and its effect on cancer patients’ prognosis also remains unknown. Recently, we reported for the first time that M. hyorhinis infects mammalian cells and promotes gastric cancer cell invasiveness via its membrane protein p37, and host Annexin A2 (ANXA2) is the cell receptor mediating M. hyorhinis infection. Downstream of ANXA2, NF-kB pathway is activated and mediates M. hyorhinis -driven cell migration. Furthermore, we demonstrated that M. hyorhinis p37 protein expression in gastric cancer tissues positively correlates with tumor metastasis and predicts poor survival. In conclusion, our study uncovers the mechanism by which M. hyorhinis infects mammalian cells and promotes cancer cell migration and unveils the effect of M. hyorhinis infection on gastric cancer survival.