Miracle-dz/UniFAR-FTUs huggingface dataset:
The demise of the marine cyanobacterium, Trichodesmium spp., via an autocatalyzed cell death pathway

We present experimental laboratory evidence and field observations of an autocatalyzed, programmed cell death (PCD) pathway in the nitrogen‐fixing cyanobacterium Trichodesmium spp. , which forms massive blooms in the subtropical and tropical oceans. The PCD pathway was induced in response to phosphorus and iron starvation as well as high irradiance and oxidative stress. Transmission electron microscopy revealed morphological degradation of internal components including thylakoids, carboxysomes, and gas vesicles, whereas the plasma membranes remained intact. Physiologically stressed cells displayed significantly elevated endonuclease activity and terminal d‐UTP nick‐end labeling. Nucleic acid degradation was concordant with increased immunoreactivity to human caspase‐3 polyclonal antisera and enhanced cleavage of a caspase‐specific substrate, DEVD. Caspase activity was positively correlated with mortality and was inhibited by the irreversible caspase inhibitor Z‐VAD‐FMK. A search of the Trichodesmium erythraeum genome identified several protein sequences containing a conserved caspase domain structure, including the histidine‐ and cysteine‐containing catalytic diad found in true caspases, paracaspases, and metacaspases. Induction of PCD by caspase‐like proteases in a bacterial photoautotroph with an ancient evolutionary history requires a reassessment about the origins and roles of cell death cascades. This process is a previously unappriciated mortality mechanism that can lead to the termination of natural Trichodesmium blooms and that can influence the fluxes of organic matter in the ocean.
Relationship between Antibody Susceptibility and Lipopolysaccharide O-Antigen Characteristics of Invasive and Gastrointestinal Nontyphoidal Salmonellae Isolates from Kenya

Background Nontyphoidal Salmonellae (NTS) cause a large burden of invasive and gastrointestinal disease among young children in sub-Saharan Africa. No vaccine is currently available. Previous reports indicate the importance of the O-antigen of Salmonella lipopolysaccharide for virulence and resistance to antibody-mediated killing. We hypothesised that isolates with more O-antigen have increased resistance to antibody-mediated killing and are more likely to be invasive than gastrointestinal. Methodology/Principal Findings We studied 192 NTS isolates (114 Typhimurium, 78 Enteritidis) from blood and stools, mostly from paediatric admissions in Kenya 2000–2011. Isolates were tested for susceptibility to antibody-mediated killing, using whole adult serum. O-antigen structural characteristics, including O-acetylation and glucosylation, were investigated. Overall, isolates were susceptible to antibody-mediated killing, but S. Enteritidis were less susceptible and expressed more O-antigen than Typhimurium (p<0.0001 for both comparisons). For S. Typhimurium, but not Enteritidis, O-antigen expression correlated with reduced sensitivity to killing (r = 0.29, 95% CI = 0.10-0.45, p = 0.002). Both serovars expressed O-antigen populations ranging 21–33 kDa average molecular weight. O-antigen from most Typhimurium were O-acetylated on rhamnose and abequose residues, while Enteritidis O-antigen had low or no O-acetylation. Both Typhimurium and Enteritidis O-antigen were approximately 20%–50% glucosylated. Amount of S. Typhimurium O-antigen and O-antigen glucosylation level were inversely related. There was no clear association between clinical presentation and antibody susceptibility, O-antigen level or other O-antigen features. Conclusion/Significance Kenyan S. Typhimurium and Enteritidis clinical isolates are susceptible to antibody-mediated killing, with degree of susceptibility varying with level of O-antigen for S. Typhimurium. This supports the development of an antibody-inducing vaccine against NTS for Africa. No clear differences were found in the phenotype of isolates from blood and stool, suggesting that the same isolates can cause invasive disease and gastroenteritis. Genome studies are required to understand whether invasive and gastrointestinal isolates differ at the genotypic level.
Three-limb Coupled Inductor Operation for Paralleled Multi-level Three-Phase Voltage Sourced Inverters

In high current applications, paralleling three-phase voltage sourced inverters represents a modular solution for improving the system power conversion quality. Single-phase output reactors are often inserted between the output terminals of the two inverters that supply the same phase output. One function of these inductors is to limit circulating currents between the two inverters. These currents are produced by common-mode voltage differences between the three-phase output terminals of the two inverters. Since standard interleaved pulse width modulation (PWM) techniques naturally produce high-frequency common-mode voltage differences between parallel connected inverters, this paper describes a modified discontinuous PWM scheme that eliminates these voltage differences. As a result, a three-phase parallel inverter system can be operated using a single three-limb coupled inductor, significantly improving the system power conversion density as a result. An experimental 3 kW prototype system is used to compare the operation of the resultant inverter against one using separate single-phase coupled inductors.
A Comparison of the Readability of Graphs Using Node-Link and Matrix-Based Representations

In this paper, we describe a taxonomy of generic graph related tasks and an evaluation aiming at assessing the readability of two representations of graphs: matrix-based representations and node-link diagrams. This evaluation bears on seven generic tasks and leads to important recommendations with regard to the representation of graphs according to their size and density. For instance, we show that when graphs are bigger than twenty vertices, the matrix-based visualization performs better than node-link diagrams on most tasks. Only path finding is consistently in favor of node-link diagrams throughout the evaluation
Your Morals Depend on Language

Should you sacrifice one man to save five? Whatever your answer, it should not depend on whether you were asked the question in your native language or a foreign tongue so long as you understood the problem. And yet here we report evidence that people using a foreign language make substantially more utilitarian decisions when faced with such moral dilemmas. We argue that this stems from the reduced emotional response elicited by the foreign language, consequently reducing the impact of intuitive emotional concerns. In general, we suggest that the increased psychological distance of using a foreign language induces utilitarianism. This shows that moral judgments can be heavily affected by an orthogonal property to moral principles, and importantly, one that is relevant to hundreds of millions of individuals on a daily basis.
Value conflicts in enterprise systems

Purpose – To identify, classify, and propose a preliminary theory of the value conflicts and social choices that arise in enterprise system use.Design/methodology/approach – Ethnographic case study of a medium‐sized manufacturing firm, using a participant‐observer approach.Findings – Three areas of value conflict are identified between functional areas: conflicts over work priorities, conflicts over dependency on the commitments of others, and conflicts over evaluation fairness. When participants perceived that the value conflicts were accommodated in a balanced and legitimate way, they chose to use information resources within the enterprise system. When the conflicts were perceived as too great, participants chose to ignore the enterprise system, or develop their own competing information resources.Research limitations/implications – This paper reports on theory building from one intensive case study. It implies, however, that previous attempts to account for the difficulty of enterprise resource planni.
Design and Analysis of Competition-Based Neural Networks

A simple and systematic approach to the design of neural networks for combinato rial op t imization is present ed in this paper. This approach is based on compe t it ion among the neurons of a network. Our approach relies on the use of simple heuristics in network design . The act ivat ion rul e govern ing neuron be havior is derived by breaking down the global constraints for a problem into local constraints for individual neurons. The local const rai nts can be expressed as simple heuristic rules for network design. Using this approach, high performance neural networks for optimiza t ion can be readil y designed and the global properties can be eas ily verified. Simulation results indicate that this approach can outpe rform some sequential heu ristic algorit hms and simulated annealing algorit hms.
Reasoning about human error by modeling cognition and interaction

In this paper we focus on system resilience from the perspective of understand- ing human error. In particular, we consider systematic cognitive slips, including post- completion errors, which are persistent, though infrequent. We outline the findings from empirical studies that have identified various factors that provoke or mitigate against such errors. We then describe approaches we are pursuing to encapsulate these insights in ways that can be re-used within system design. More broadly, we argue that an understanding of the factors that influence the likelihood of such errors can support organizations in design- ing systems and processes to minimize the likelihood of such errors.
Overexpression of the Prunus sogdiana NBS-LRR Subgroup Gene PsoRPM2 Promotes Resistance to the Root-Knot Nematode Meloidogyne incognita in Tobacco

Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are the most devastating soil-borne pathogens that significantly affect the production of Prunus spp. fruit. RKN infection is difficult to control and consequently causes massive yield losses each year. However, several germplasms of wild Prunus spp. have been shown to display resistance to M. incognita. Consequently, both the isolation of novel plant resistance (R) genes and the characterization of their resistance mechanisms are important strategies for future disease control. R proteins require the co-chaperone protein HSP90-SGT1-RAR1 to achieve correct folding, maturation, and stabilization. Here, we used homologous cloning to isolate the R gene PsoRPM2 from the RKN-resistant species Prunus sogdiana. PsoRPM2 was found to encode a TIR-NB-LRR-type protein and react with significantly elevated PsoRPM2 expression levels in response to RKN infection. Transient expression assays indicated PsoRPM2 to be located in both the cytoplasm and the nucleus. Four transgenic tobacco lines that heterologously expressed PsoRPM2 showed enhanced resistance to M. incognita. Yeast two-hybrid analysis and bimolecular fluorescence complementation analysis demonstrated that both PsoRAR1 and PsoRPM2 interacted with PsoHSP90-1 and PsoSGT1, but not with one another. These results indicate that the observed PsoRPM2-mediated RKN resistance requires both PsoHSP90-1 and PsoSGT1, further suggesting that PsoRAR1 plays a functionally redundant role in the HSP90-SGT1-RAR1 co-chaperone.
Influence of feed restriction during lactation on gonadotropic hormones and ovarian development in primiparous sows.

Effects of nutritional deficit during lactation on secretion of gonadotropic hormones and ovarian follicular populations around weaning were investigated in 24 primiparous crossbred sows. Sows were allocated to receive close to ad libitum intakes (H) or approximately 50% of this amount (L) during a 28-d lactation. Serial blood samples were collected 1 d before weaning (W-1), in the hours following weaning (W), and 1 d after (W+1). Their ovaries were removed on the day of weaning or 2 d later (W+2) and subjected to macroscopic and histological observations. Mean and basal LH concentrations were not influenced by the level of feeding. Frequency of LH pulses was reduced in L sows (.17, .5, and .5 vs 1.50, 1.17, and .83 pulses/6 h at d W-1, W, and W+1 respectively; P < .05). Mean and basal concentrations of LH were influenced by the day of sampling, being significantly increased within hours following weaning. Mean FSH concentrations were influenced neither by the level of feeding nor by the day of sampling. At weaning, the ovaries from L sows were lighter and had smaller follicles and fewer follicles > or = 4 mm (P < .05). Values of these macroscopic characteristics increased after weaning ( P < .05). At weaning, the percentage of healthy follicles was higher in the first class (< 1 mm) and lower in the second class (1 to 2.99 mm) in L compared to H sows (P < .05). Whatever the day of sampling, IGF-I concentrations in follicular fluid tended to be lower in L than in H sows. These results indicate that feed restriction during lactation inhibits LH pulsatility and ovarian activity.
Digraph visualization using a neural algorithm with a heuristic activation scheme

This paper presents an activation scheme for use with Hopfield neural network algorithms that guarantees a valid solution for a particular category of problems. The technique monitors the appropriate neurons and heuristically controls their activation function. As a result it has been possible to eliminate several constraint terms from the energy function that normally would have been required to drive the network toward a valid solution. This saves time and eliminates the need for empirically determining a larger number of constants. This technique has been applied to the combinatorial optimization problem called hierarchical digraph visualization that arises in many application areas where it is necessary to visually realize the relationship between entities in complex systems. Results are presented that compare this new approach with a more traditional neural network approach as well as heuristic approaches, performance improvement in terms of the solution quality as well as execution time relative to both alternative techniques was achieved.
The ATE Genes Are Responsible for Repression of Transdifferentiation into Xylem Cells in Arabidopsis1

We isolated three recessive mutants of Arabidopsis (Arabidopsis thaliana) showing ectopic expression of the xylem-specific marker, pAtxyn3::YFP. Genetic analysis indicated that the phenotypes were caused by mutations in three different genes, designated Abnormal Tracheary Element formation-related gene expression (ate1–3). The ate1 mutants showed a normal DR5::GUS gene expression pattern, and the ate1 mutation did not affect the abnormal vascular pattern formation in the van3 and pin1 mutants, indicating that the ate1 mutation does not affect the vascular pattern organization governed by auxin. The ate mutants showed ectopic lignin deposition, patterned secondary wall thickenings, and cell death, which are characteristic of mature tracheary elements (TEs) in cells ectopically expressing the pAtxyn3::YFP gene. Ectopic TE formation was rapidly induced in parenchymal tissue of the ate mutants in a TE-inducible system with excised hypocotyl. Furthermore, reverse transcription-polymerase chain reaction experiments showed that the expression of TE formation-related genes is up-regulated in the ate mutants. The ate1 mutation also caused ectopic expression of another xylem-specific marker gene, pAt3g62160::YFP. Overall, our results suggest that the ATE genes are responsible for the in situ repression of transdifferentiation into TEs in Arabidopsis and could be participants in the transdifferentiation-masking system.
A context-aware personalized travel recommendation system based on geotagged social media data mining

The proliferation of digital cameras and the growing practice of online photo sharing using social media sites such as Flickr have resulted in huge volumes of geotagged photos available on the Web. Based on users' traveling preferences elicited from their travel experiences exposed on social media sites by sharing geotagged photos, we propose a new method for recommending tourist locations that are relevant to users (i.e., personalization) in the given context (i.e., context awareness). We obtain user-specific travel preferences from his/her travel history in one city and use these to recommend tourist locations in another city. Our technique is illustrated on a sample of publicly available Flickr dataset containing photos taken in various cities of China. Results show that our context-aware personalized method is able to predict tourists' preferences in a new or unknown city more precisely and generate better recommendations compared to other state-of-the-art landmark recommendation methods.
Ants determine their next move at rest: motor planning and causality in complex systems

To find useful work to do for their colony, individual eusocial animals have to move, somehow staying attentive to relevant social information. Recent research on individual Temnothorax albipennis ants moving inside their colony’s nest found a power-law relationship between a movement’s duration and its average speed; and a universal speed profile for movements showing that they mostly fluctuate around a constant average speed. From this predictability it was inferred that movement durations are somehow determined before the movement itself. Here, we find similar results in lone T. albipennis ants exploring a large arena outside the nest, both when the arena is clean and when it contains chemical information left by previous nest-mates. This implies that these movement characteristics originate from the same individual neural and/or physiological mechanism(s), operating without immediate regard to social influences. However, the presence of pheromones and/or other cues was found to affect the inter-event speed correlations. Hence we suggest that ants’ motor planning results in intermittent response to the social environment: movement duration is adjusted in response to social information only between movements, not during them. This environmentally flexible, intermittently responsive movement behaviour points towards a spatially allocated division of labour in this species. It also prompts more general questions on collective animal movement and the role of intermittent causation from higher to lower organizational levels in the stability of complex systems.
Recent Advances in the Clinical Targeting of Hedgehog/GLI Signaling in Cancer

The Hedgehog/GLI signaling pathway plays an important role in normal embryonic tissue development and has been implicated in the pathogenesis of various human cancers. In this review article, we summarize pre-clinical evidence supporting the suitability of targeting this signaling pathway in cancers. We review agents blocking both the ligand-dependent and ligand-independent cascades, and discuss the clinical evidence, which has led to the FDA approval of Hedgehog receptor Smoothened inhibitors, vismodegib, and sonidegib, in different malignancies. Finally, we provide an overview of published and ongoing clinical trial data on single agent or combination therapeutic strategies, targeting Hedgehog/GLI signaling pathway, in both advanced solid tumors and hematologic malignancies.
A Simple-Transition Model for Relational Sequences

We use "nearly sound" logical constraints to infer hidden states of relational processes. We introduce a simple-transition cost model, which is parameterized by weighted constraints and a statetransition cost. Inference for this model, i.e. finding a minimum-cost state sequence, reduces to a single-state minimization (SSM) problem. For relational Horn constraints, we give a practical approach to SSM based on logical reasoning and bounded search. We present a learning method that discovers relational constraints using CLAUDIEN [De Raedt and Dehaspe, 1997] and then tunes their weights using perceptron updates. Experiments in relational video interpretation show that our learned models improve on a variety of competitors.
On the Recovery of Shape and Reflectance from a Single Multispectral Image

This paper presents a method for recovering the reflectance and shape of a surface from a single hyper spectral image. To do this, we depart from a reflectance model based on a physical interpretation of the reflection process where the geometry of the scene and the properties of the object surface describe the image formation process. With the model in hand, we propose a solution to the recovery of the reflection parameters via an optimisation approach that aims at recovering both the surface normals and the reflectance. This, in turn, allows for the application of the method by Frankot and Chellappa [8] so as to recover the surface depth at each pixel. We demonstrate the utility of our method for the recovery of both reflectance and surface depth on synthetic and real world images.
Pagetoid Squamous Cell Carcinoma In Situ (Pagetoid Bowen's Disease) of the External Genitalia

Approximately 5% of cutaneous squamous cell carcinomas in situ (SCCIS) have a nested pattern, referred to as pagetoid SCCIS, or pagetoid Bowen's disease. This growth pattern may simulate extramammary Paget's disease (EPD) when the external genitalia are involved. We report two cases of genital pagetoid SCCIS, including the first example affecting the vulva. Using several known cases each of classic (bowenoid) SCCIS of the vulva, primary cutaneous vulvar EPD, and cutaneous melanoma in situ as controls, we performed a battery of immunohistochemical and mucin stains to study the phenotype of pagetoid SCCIS. Both cases of pagetoid SCCIS were strongly positive for cytokeratin (CK) 7, a highly sensitive and popular marker for EPD. Stains with the high molecular weight cytokeratin marker Keratin-903 (34&bgr;E12) showed 4+ immunoreactivity, although not with the intensity seen in the juxtaposed normal keratinocytes or in the cells of classic SCCIS. Immunoreactivity scores were 2+ for CK5/6, 2+ for CK19, and 1+ to 3+ for CK 13. Unlike the Paget's cells of EPD, the nested cells of pagetoid SCCIS were devoid of mucin and were nonimmunoreactive with GCDFP-15, CEA, CAM5.2, and c-erbB2. Stains for CK20, S-100, and Melan A also were negative. Although CK7 is a sensitive marker for the Paget's cells of EPD, this study corroborates the unexpected CK7 positivity in pagetoid SCCIS, precluding its usefulness in distinguishing these two diseases. Combined with mucin stains, a limited immunohistochemical panel may be of diagnostic value in particularly difficult cases.
Alcohol Use and the Alcohol Use Disorders: A Developmental‐Biopsychosocial Systems Formulation Covering the Life Course

ALCOHOLISM AND THE ALCOHOL USE DISORDERS 620 HISTORICAL INTRODUCTION AND ISSUES FOR THE FIELD 621 EPIDEMIOLOGY 623 A MULTILEVEL NET FOR DEVELOPMENTAL VARIATION 625 VARIATIONS IN RISK AND COURSE OF THE DISORDER 628 Differences in Alcohol Nonspecific-Risk Structure for Later Disorder Are Present in Early Childhood 629 Heterogeneity in the Course of Risk and Heterogeneity of Nonspecific Risk 632 Heterogeneity of Alcohol-Specific Risk: Prolegomenon to Phenotypic Heterogeneity of Alcohol Use Disorder 635 Heterogeneity of Alcohol Use Disorder and Variations in Course of the DisorderlPhenotype 636 THE OTHER HALF OF THE STORY: ETIOLOGY FROM A NEUROBIOLOGICAL PERSPECTIVE 638 Alcoholism as a Genetic Disorder 638 Intermediate-Level Etiology in Brain 641 Developmental Significance of Neural Models in Late Adolescence 642 OTHER EPIGENETIC ISSUES 643 The Nestedness of Environmental, Behavioral, and Neurobiological Risk 643 Stability and Change in Alcohol Use Disorder Over Time: Factors Predicting Recovery, or Not 644 FUTURE WORK AND CONCLUDING SUMMARY 646 Redefining the Phenotype 646 Is the Child Father to the Man, or Mother to the Woman? Problems in Embracing a Developmental Psychopathology Paradigm 647 Articulating Specific Gene-Brain-BehaviorEnvironment Relationships 647 Summary and Concluding Remarks 648 REFERENCES 648