Miracle-dz/UniFAR-FTUs huggingface dataset:
Inbreeding depression and outbreeding depression in Digitalis purpurea: optimal outcrossing distance in a tetraploid

An optimal crossing distance exists within plant populations if inbreeding and outbreeding depression operate simultaneously. In a population of tetraploid Digitalis purpurea, maternal plants were pollinated with donors at four distances: 0 (self‐pollination), 1, 6 and 30 m. Lifetime fitness of F1 progeny was investigated in greenhouse experiments, and significant inbreeding and outbreeding depression were detected at five vs. three life history traits. Inbreeding depression increased at later life stages, whereas outbreeding depression was relatively constant. The existence of within‐population outbreeding depression suggests substantial genetic structuring at moderate distances in D. purpurea, and corroborates recent findings of significant outbreeding depression in F1 progeny in polyploids. The moderate inbreeding depression found in this predominately outcrossing population supports the notion that effects of inbreeding are less severe in polyploids than in diploids.
TRANSIT: specifying protocols with concolic snippets

With the maturing of technology for model checking and constraint solving, there is an emerging opportunity to develop programming tools that can transform the way systems are specified. In this paper, we propose a new way to program distributed protocols using concolic snippets. Concolic snippets are sample execution fragments that contain both concrete and symbolic values. The proposed approach allows the programmer to describe the desired system partially using the traditional model of communicating extended finite-state-machines (EFSM), along with high-level invariants and concrete execution fragments. Our synthesis engine completes an EFSM skeleton by inferring guards and updates from the given fragments which is then automatically analyzed using a model checker with respect to the desired invariants. The counterexamples produced by the model checker can then be used by the programmer to add new concrete execution fragments that describe the correct behavior in the specific scenario corresponding to the counterexample. We describe TRANSIT, a language and prototype implementation of the proposed specification methodology for distributed protocols. Experimental evaluations of TRANSIT to specify cache coherence protocols show that (1) the algorithm for expression inference from concolic snippets can synthesize expressions of size 15 involving typical operators over commonly occurring types, (2) for a classical directory-based protocol, TRANSIT automatically generates, in a few seconds, a complete implementation from a specification consisting of the EFSM structure and a few concrete examples for every transition, and (3) a published partial description of the SGI Origin cache coherence protocol maps directly to symbolic examples and leads to a complete implementation in a few iterations, with the programmer correcting counterexamples resulting from underspecified transitions by adding concrete examples in each iteration.
University of Groningen Interactions between Blood-Borne Streptococcus pneumoniae and the Blood-Brain Barrier Preceding Meningitis

Streptococcus pneumoniae (the pneumococcus) is a Gram-positive bacterium and the predominant cause of bacterial meningitis. Meningitis is thought to occur as the result of pneumococci crossing the blood-brain barrier to invade the Central Nervous System (CNS); yet little is known about the steps preceding immediate disease development. To study the interactions between pneumococci and the vascular endothelium of the blood-brain barrier prior to meningitis we used an established bacteremia-derived meningitis model in combination with immunofluorescent imaging. Brain tissue of mice infected with S. pneumoniae strain TIGR4, a clinical meningitis isolate, was investigated for the location of the bacteria in relation to the brain vasculature in various compartments. We observed that S. pneumoniae adhered preferentially to the subarachnoid vessels, and subsequently, over time, reached the more internal cerebral areas including the cerebral cortex, septum, and choroid plexus. Interestingly, pneumococci were not detected in the choroid plexus till 8 hours-post infection. In contrast to the lungs, little to no leukocyte recruitment to the brain was observed over time, though Iba-1 and GFAP staining showed that microglia and astrocytes were activated as soon as 1 hour post-infection. Our results imply that i) the local immune system of the brain is activated immediately upon entry of bacteria into the bloodstream and that ii) adhesion to the blood brain barrier is spatiotemporally controlled at different sites throughout the brain. These results provide new information on these two important steps towards the development of pneumococcal meningitis. Citation: Iovino F, Orihuela CJ, Moorlag HE, Molema G, Bijlsma JJE (2013) Interactions between Blood-Borne Streptococcus pneumoniae and the Blood-Brain Barrier Preceding Meningitis. PLoS ONE 8(7): e68408. doi:10.1371/journal.pone. 0068408 Editor: Riccardo Manganelli, University of Padova, Medical School, Italy Received March 7, 2013; Accepted May 29, 2013; Published July 16, 2013 Copyright: 2013 Iovino et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Parts of this work were funded by the National Institutes of Health (NIH) AI078972 (CJO). Part of the imaging analysis has been performed at the UMCG Microscopy and Imaging center (UMIC), which is sponsored by grants 40-00506-98-9021, and 175-010-2009-023 of the Netherlands Organisation for Scientific Research (NWO). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: j.j.e.bijlsma@umcg.nl
Group algebras whose units satisfy a group identity. II

Let K [ G ] be the group algebra of a torsion group G over an in-(cid:12)nite (cid:12)eld K , and let U = U ( G ) denote its group of units. A recent paper of A. Giambruno, S. K. Sehgal, and A. Valenti proved that if U satis(cid:12)es a group identity, then K [ G ] satis(cid:12)es a polynomial identity, thereby con(cid:12)rming a conjecture of Brian Hartley. Here we add a footnote to their result by showing that the commutator subgroup G 0 of G must have bounded period. Indeed, this additional fact enables us to obtain necessary and su(cid:14)cient conditions for U ( G ) to satisfy an identity.
Open Problem: Learning Dynamic Network Models from a Static Snapshot

In this paper we consider the problem of learning a graph generating process given the evolving graph at a single point in time. Given a graph of sufficient size, can we learn the (repeatable) process that generated it? We formalize the generic problem and then consider two simple instances which are variations on the well-know graph generation models by Erd˝ )
Development of an Immunocapture-Based Polymeric Optical Fiber Sensor for Bacterial Detection in Water

Conventional methods for pathogen detection in water rely on time-consuming enrichment steps followed by biochemical identification strategies, which require assay times ranging from 24 hours to a week. However, in recent years, significant efforts have been made to develop biosensing technologies enabling rapid and close-to-real-time detection of waterborne pathogens. In previous studies, we developed a plastic optical fiber (POF) immunosensor using an optoelectronic configuration consisting of a U-Shape probe connected to an LED and a photodetector. Bacterial detection was evaluated with the immunosensor immersed in a bacterial suspension in water with a known concentration. Here, we report on the sensitivity of a new optoelectronic configuration consisting of two POF U-shaped probes, one as the reference and the other as the immunosensor, for the detection of Escherichia coli. In addition, another methos of detection was tested where the sensors were calibrated in the air, before being immersed in a bacterial suspension and then read in the air. This modification improved sensor sensitivity and resulted in a faster detection time. After the immunocapture, the sensors were DAPI-stained and submitted to confocal microscopy. The histograms obtained confirmed that the responses of the immunosensors were due to the bacteria. This new sensor detected the presence of E. coli at 104 CFU/mL in less than 20 min. Currently, sub-20 min is faster than previous studies using fiber-optic based biosensors. We report on an inexpensive and faster detection technology when compared with conventional methods.
Interprocedural Type Specialization of JavaScript Programs Without Type Analysis

Dynamically typed programming languages such as Python and JavaScript defer type checking to run time. VM implementations can improve performance by eliminating redundant dynamic type checks. However, type inference analyses are often costly and involve tradeoffs between compilation time and resulting precision. This has lead to the creation of increasingly complex multi-tiered VM architectures. Lazy basic block versioning is a simple JIT compilation technique which effectively removes redundant type checks from critical code paths. This novel approach lazily generates type-specialized versions of basic blocks on-the-fly while propagating context-dependent type information. This approach does not require the use of costly program analyses, is not restricted by the precision limitations of traditional type analyses. This paper extends lazy basic block versioning to propagate type information interprocedurally, across function call boundaries. Our implementation in a JavaScript JIT compiler shows that across 26 benchmarks, interprocedural basic block versioning eliminates more type tag tests on average than what is achievable with static type analysis without resorting to code transformations. On average, 94.3% of type tag tests are eliminated, yielding speedups of up to 56%. We also show that our implementation is able to outperform Truffle/JS on several benchmarks, both in terms of execution time and compilation time.
Biopsy diagnosis of surgical infections.

A favorable outcome of necrotizing subcutaneous infections and other invasive soft-tissue infections that spread rapidly is dependent on early diagnosis followed by prompt surgical intervention to debride necrotic and infected tissue and prevent further extension and systemic spread of the septic process. In the early stages of many invasive infections originating in surface wounds, local signs are initially minimal and become more prominent as the disease progresses. Deep tissue pain with focal surface hypoesthesia and ecchymotic changes of intact skin overlying the infected tissue (considered to be characteristic of necrotizing fasciitis) indicate neural and vascular involvement, respectively, and signify the .
Effects of Viable and Heat-Inactivated Bifidobacterium longum D42 on Proliferation and Apoptosis of HT-29 Human Colon Cancer Cells

Bifidobacterium longum is a common probiotic; both viable and heat-inactivated Bifidobacterium longum have many probiotic effects, such as anticancer effects. But some mechanisms of anticancer effects are still unclear, especially for heat-inactivated probiotics. In this study, we analyzed the effects of viable and heat-inactivated Bifidobacterium longum D42 on human colon cancer cells (HT-29). Cell proliferation, membrane permeability and apoptosis were detected by using the CCK-8 method, LDH method and Annexin V-FITC/PI kits. The ROS level and mitochondrial membrane potential were examined using the fluorescent probes DCFH-DA and JC-1. Real-time fluorescence quantitative PCR (RT-qPCR) and Western blot were used to detect the expression of mitochondrial apoptosis pathway genes and proteins. The results showed that viable and heat-inactivated Bifidobacterium longum D42 at concentrations of 1 × 106 CFU/mL significantly inhibited the proliferation of and increased the level of LDH release of HT-29 colon cancer cells. We found that they could increase the apoptosis rate of HT-29 cells. Moreover, they could also induce apoptosis by inducing cells to produce ROS and destroying the mitochondrial membrane potential of cells. Further studies found that they could increase the mRNA transcription and protein expression levels of the Caspase-3, Caspase-9 and Bax genes in cells, and reduce the mRNA transcription and protein expression levels of the Bcl-2 gene. In summary, our findings revealed that viable and heat-inactivated Bifidobacterium longum D42 have inhibitory effects on proliferation and promote the apoptosis of human colon cancer cells, and also have certain adjuvant drug therapeutic effects and have potential application value in the adjuvant treatment of colon cancer.
Optical Character Recognition Technique using Intro Sort

In this study, we propose an optical character recognition technique using Intro Sort. Main feature of this proposed technique is that we segment images using intro sort. It reduces the comparison time for matching the pixels of an image. It reflects reduction in OCR time. Intro sort algorithm begins with quick sort and when recursion depth exceeds a level it switches to heap sort, based on the number of pixels being sorted. This approach also has advantage of recognizing number plates and text documents in very nominal time. Our approach is able to extract characters of different font sizes. Our technique is performed well in noisy images too. General Terms Optical character recognition
Individual wearable air purifier protects against pollen, house dust mite, and cat allergens: Report from an allergen exposure chamber

Purpose: Evaluation of a new individual wearable air purifier (Respiray Wear A+) for birch pollen, house dust mite (HDM), and cat-allergic rhinoconjunctivitis (ARC) patients in a standardized allergen exposure chamber (AEC). Materials and methods: Eligible allergic patients were exposed to birch pollen, HDM raw material, and cat allergen in an AEC for 60 minutes without (V1) and with (V3) the use of the Respiray device. Nasal, ocular, bronchial, and other symptoms were rated by the patients every 10 minutes, and their wellbeing, peak nasal inspiratory flow (PNIF), and lung function parameters were assessed every 30 minutes. The primary endpoint was the change in the median of the total symptom score (TSS) at V3 compared to V1 at 60 minutes of exposure. The secondary endpoints consisted of the total nasal symptom score (TNSS) and total eye symptom score (TESS). Results: 23 patients with birch pollen allergy, 37 patients with HDM allergy, and 41 patients with cat allergy were included in the analysis. Significant reduced symptom scores of ~ 49% were observed when using Respiray Wea A+ under birch pollen exposure (p < 0.05) in the primary endpoint TSS (V3 2.43 compared to V1 4.78). An 48% reduction of symptoms was seen in TSS in case of HDM exposure (V3 3.59; V1 6.92, (t-test: p < 0.01)) and the highest reduction of TSS (60%) under Respiray A+ using cat allergens (V3 2.95, V1 7.44, (t-test p < 0.01) after 60 minutes of exposure. The personal wellbeing revealed clinically meaningful improvements over time in all three studies which manifested in a lower symptom increase during the final allergen exposures. Conclusion: The individual wearable air purifier Respiray Wear A+ protects significantly against airborne pollen, HDM, and cat allergens and may be a very useful device for avoiding indoor allergens in a new way.
Context-coherent scenes of objects for camera pose estimation

We propose an approach to vision-based pose estimation using object recognition and identity. Whereas feature based scene recognition and pose estimation methods are well established as effective means for estimating motion and recognizing locations, feature-based methods depend critically on the detection of common local features from one view of a scene to another. We focus on place recognition and pose change estimation in the context of large changes in viewing position, even to the extent that no common surfaces are seen between the two views. Our approach is based on using object identities and their inter-relationship to compute pose change. An important secondary outcome of our method is that it simultaneously infers the 3D poses of objects in the scene that are used as features. Such an object-based approach is inspired by a vast literature on human perception and has the potential for great robustness, albeit at the expense of accuracy. We propose a formulation of the problem using pairwise contextual constraints and develop an efficient algorithmic solution. We validate the approach and quantify its performance using the publicly available TUM SLAM dataset [1].
Tag Suggestion Method Based on Association Pattern and Bigram Approach

Recently, the number of articles, blog posts, photos and videos on the web is dramatically increasing because of the increase of internet usage. In this situation, the web search is the most important thing in the web. When we search, we can use text information from articles or blog posts. In the case of photos and videos, we can only use a title. If there are tags − significant keywords of that multimedia, we can use tag information to search. Tag is a keyword of text, blog post, or multimedia. Users have already recognized about the value and importance of tags but only a few users are using tags. They might be annoying to add tags or they don't know what to add for good search result. This is why tag suggestion system is needed. Our method analyzes crawled tag data and suggests appropriate tags to user using association pattern and bigram approach. By experi-ments, we conclude that our tag suggestion method suggests appropriate tags.
Acquired and congenital ocular toxoplasmosis experimentally induced in Calomys callosus (Rodentia, Cricetidae).

An experimental model for acquired and congenital ocular toxoplasmosis as well as a model to induce experimental autoimmune uveitis (EAU) was investigated in Calomys callosus. Toxoplasma gondii, ME-49 strain, was used to infect males and pregnant- and not pregnant-females while S-antigen, a major glycoprotein of the retinal photoreceptor cell, was used to induce EAU. The ocular lesions elicited by T. gondii were characterized by the presence of cysts, free tachyzoites and inflammatory cells in the retina or related tissues. In the congenital form, 40% of the fetus presented ocular lesions, i.e., presence of cysts in the retina, vitreous, and extra-retinal tissues. In the acquired form, 75% of the females and 50% of the males presented unilateral ocular cysts both at 21 and 47 days post-infection. It was also demonstrated that S-antigen was not uveitogenic in the C. callosus model. No lesion was observed in the animals exclusively immunized with this retinal component, even when jacalin was used as additional adjuvant for polyclonal response to the retinal antigen. It can be concluded that C. callosus may constitute in a promising model for study both acquired and congenital ocular toxoplasmosis, particularly when it is important to make sure that a non autoimmune process is involved in the genesis of the ocular infection.
Does depression matter in neuropsychological performances in anorexia nervosa? A descriptive review.

OBJECTIVE This review aims to examine the impact of depressive symptoms on the assessment of cognitive flexibility, central coherence, and decision-making in individuals with anorexia nervosa (AN). METHOD An online search was carried out using PubMed and PsycInfo. Articles were selected for review if they were published in English between 1990 and 2014 and used the Wisconsin Card Sorting Test, the Trail Making Task parts A and B, the Brixton Test, the Rey-Osterrieth Complex Figure Test, and/or the Iowa Gambling Task. RESULTS Sixty-two studies were included. Thirty (48%) of the studies statistically assessed the association between depression and neurocognition in AN versus healthy controls. Where significant correlations were found, it became clear that the more serious the depression, the greater the neuropsychological impairment. Only six (10%) studies examined whether increased depressive symptoms were able to eliminate the differences between individuals with AN and healthy controls, and one study found that depressive symptoms did eliminate group differences in cognitive flexibility and decision-making. DISCUSSION Only a subgroup of articles on neuropsychology in AN adjusted for depression. However, given the role of depression that some articles suggest, future studies should pay closer attention to the evaluation of this potential confounder.
PEGASUS: 802.11 connectivity at high speed

Measurements and ongoing research have shown that WLAN connection for moving vehicles is feasible. However none of the previous works suggests a solution addressing a complete array of the challenges in vehicular WLAN communications. Our system, PEGASUS amends this by providing wireless connection roaming at high velocities. To the best of our knowledge, it is the first system that operates over "in situ" wifi networks, while at the same time offers transparency to user level applications by allowing a single IP address per user, and does not impose additional requirements to existing infrastructures. PEGASUS offers simple deployment, improved scalability, and is the first able to operate over secure "in situ" networks. It remains efficient under intermittent connectivity conditions and supports heterogeneous network mediums for increased robustness.
Directional cell movements downstream of Gbx2 and Otx2 control the assembly of sensory placodes

ABSTRACT Cranial placodes contribute to sensory structures including the inner ear, the lens and olfactory epithelium and the neurons of the cranial sensory ganglia. At neurula stages, placode precursors are interspersed in the ectoderm surrounding the anterior neural plate before segregating into distinct placodes by as yet unknown mechanisms. Here, we perform live imaging to follow placode progenitors as they aggregate to form the lens and otic placodes. We find that while placode progenitors move with the same speed as their non-placodal neighbours, they exhibit increased persistence and directionality and these properties are required to assemble morphological placodes. Furthermore, we demonstrate that these factors are components of the transcriptional networks that coordinate placode cell behaviour including their directional movements. Together with previous work, our results support a dual role for Otx and Gbx transcription factors in both the early patterning of the neural plate border and the later segregation of its derivatives into distinct placodes. Summary: Using spatial and temporally controlled perturbations followed by live cell tracking in vivo, this paper demonstrates that directional movements downstream of Gbx2 and Otx2 are important for otic and lens placode formation.
CSIM: a C-based process-oriented simulation language

CSIM is a process-oriented simulation language which is implemented as a superset of the C programming language. Using CSIM, a simulation programmer is able to quickly construct concise models of systems and then to execute these models in an efficient manner. In addition to supporting process-oriented simulation, CSIM as a number of additional features dealing with modeling system resources, message passing, data collection and debugging which ease the task of building simulation models.