Miracle-dz/UniFAR-FTUs huggingface dataset:
A Vertex-Splitting Lemma, de Werra's Theorem, and Improper List Colourings

We prove a new vertex-splitting lemma which states that if a multigraphGhas maximum multiplicity of at mostp, then each vertex u can be split into ? (d(u)/p)? new vertices, ? (d(u)/p)? of degreep, with the multiple edges being shared out between the new vertices in such a way that each multiple edge remains intact at at least one of its two endpoints. We apply this lemma to deduce very simply the theorem of de Werra that each bipartite multigraph has a balancedk-edge-colouring for each positive integerk. We also apply the lemma to improve two earlier theorems of the first author which state that? s(G)=? (? (G)/s)? if either (1)Gis a bipartite multigraph, or (2)sis even andGis any multigraph; here? s(G) is thes-improper list chromatic index of G, i.e., the least possible value ofksuch that, if each edge ofGis provided with a list ? (e) of at leastkcolours, thenGhas ans-improper edge list colouring (so that at each vertex? not more than s edges incident with? receive the same colour), and, on each edge, the colour used lies in the list for that edge. The improvements that we obtain include that for each multiple edge of multiplicitym=mG(u, ? ), no colour is used on more than ? mG(u, ? )/? (? (G)/s)? +1 edges joininguand?
Whence the Expected Free Energy?

The expected free energy (EFE) is a central quantity in the theory of active inference. It is the quantity that all active inference agents are mandated to minimize through action, and its decomposition into extrinsic and intrinsic value terms is key to the balance of exploration and exploitation that active inference agents evince. Despite its importance, the mathematical origins of this quantity and its relation to the variational free energy (VFE) remain unclear. In this letter, we investigate the origins of the EFE in detail and show that it is not simply ”the free energy in the future. ” We present a functional that we argue is the natural extension of the VFE but actively discourages exploratory behavior, thus demonstrating that exploration does not directly follow from free energy minimization into the future. We then develop a novel objective, the free energy of the expected future (FEEF), which possesses both the epistemic component of the EFE and an intuitive mathematical grounding as the divergence between predicted and desired futures.
Generation and interpretation of morphogen gradients : a subject collection from Cold Spring Harbor perspectives in biology

Robust Generation and Decoding of Morphogen Gradients Naama Barkai and Ben-Zion Shilo Nodal Morphogens Alexander F. Schier Forming Patterns in Development Without Morphogen Gradients: Scattered Differentiation and Sorting Out Robert R. Kay and Christopher R.L. Thompson Graded Dorsal and Differential Gene Regulation in the Drosophila Embryo Gregory T. Reeves and Angelike Stathopoulos Establishing and Interpreting Graded Sonic Hedgehog Signaling during Vertebrate Neural Tube Patterning: The Role of Negative Feedback V. Ribes and J. Briscoe Signaling Gradients During Paraxial Mesoderm Development Alexander Aulehla and Olivier Pourqui e9 Gradients in the Brain: The Control of the Development of Form and Function in the Cerebral Cortex Stephen N. Sansom and Frederick J. Livesey Morphogen Gradient Formation Marcos Gonz e1 lez-Gait e1 n, Anna Kicheva, and Ortrud Wartlick Shaping Morphogen Gradients by Proteoglycans Dong Yan and Xinhua Lin Vertebrate Limb Development: Moving From Classical Morphogen Gradients to an Integrated 4D Patterning System Jean-Denis B e9 nazet and Rolf Zeller The Measure of Success: Constraints, Objectives, and Tradeoffs in Morphogen-Mediated Patterning Arthur D. Lander, Wing-Cheong Lo, Qing Nie and Frederic Y.M. Wan Regulation of Organ Growth by Morphogen Gradients Gerald Schwank and Konrad Basler Forming and Interpreting Gradients on the Early Xenopus Embryo J.C. Smith Gradients in Planarian Regeneration and Homeostasis T. Adell, F. Cebri e0 And E. Sal f3 Gradients and the Specification of Planar Polarity in the Insect Cuticle David Strutt Systems Biology of the Self-Regulating Morphogenetic Gradient of the Xenopus Gastrula Jean-Louis Plouhinec and E.M. De Robertis Axial Patterning in Hydra Hans R. Bode Chemical Gradients and Chemotropism in Yeast Robert A. Arkowitz Models for the Generation and Interpretation of Gradients Hans Meinhardt Index
PriVeil: Privacy-preserving threat information sharing

—Corporate cybersecurity is now more challenging than ever. Information infrastructures are susceptible attack targets, as their potential value gain is higher than that of domestic systems. Companies are unaware of all the security vulnerabilities present in their systems, because some of them are not known by anyone. Protection efforts can be leveraged by cooperating with other companies to identify and address security vulnerabilities together. However, trust cannot be fully placed on other parties by default, since their true intentions are not known. For this reason, existing solutions allow threat information to be shared yet using ﬁlters to prevent leakage of sensitive information. Nevertheless, relevant details can be lost during the anonymization process. All of these factors discourage companies to cooperate. This work proposes a threat information sharing system design that is able to match participants with identical security events, encouraging cooperation to identify the associated vulnerabilities while retaining full control over their private data. To this end, Privacy-preserving techniques like Homomorphic Encryption and Secure Multi-party Computation are used to assure that no sensitive information is unwillingly disclosed by the system. The system was evaluated qualitatively by fulﬁllment of a set of requirements and quantitatively through user and performance tests.
Doctoral research and scholarly communication : candidates, supervisors and information literacy

This thesis investigates scholarly communication within doctoral research. It focuses upon the notions of pedagogic continuity and information literacy, combined with the transition candidates make from a pedagogical orientation to that of an andragogical orientation and independence in research. The metaphor of a scholarly "Club" is used to articulate the findings.
Combined olanzapine plus fluoxetine modestly improves symptoms of acute bipolar I depression compared to lamotrigine

Brown EB, McElroy SL, Keck PE, et al. A 7-week, randomized, double-blind trial of olanzapine/fluoxetine combination versus lamotrigine in the treatment of bipolar I depression. J Clinical Psychiatry 2006;67:1025–33.
Pentoxifylline Ameliorates Renal Tumor Necrosis Factor Expression, Sodium Retention, and Renal Hypertrophy in Diabetic Rats

Background/Aim: Diabetic nephropathy contributes substantially to cardiovascular morbidity and mortality associated with diabetes. Urinary tumor necrosis factor (TNF) excretion is increased during diabetes and serves as an important mediator of pathological changes during the initial stages of diabetic nephropathy, including sodium retention and renal hypertrophy. We tested the hypothesis that pentoxifylline (PTF), an agent that inhibits TNF synthesis, could prevent sodium retention and renal hypertrophy during diabetes. Methods: Proximal and distal tubule TNF expression, urinary TNF excretion, sodium retention, and renal hypertrophy were examined in control, diabetic, and PTF-treated diabetic rats. Results: TNF mRNA and protein levels were increased in proximal tubule cells isolated from diabetic rats compared to control rats. In contrast, TNF expression in distal tubule cells was not increased during diabetes. PTF prevented the increase in TNF mRNA and protein in proximal tubule cells during diabetes and reduced urinary TNF excretion. PTF therapy decreased whole animal sodium retention by enhancing urinary sodium excretion in diabetic rats. In addition, PTF reduced renal hypertrophy in diabetic rats. Conclusions: The proximal tubule is an important site of TNF production during diabetes and PTF is an effective therapy for preventing the pathological changes accompanying early diabetic nephropathy.
Akkermansia muciniphila Adheres to Enterocytes and Strengthens the Integrity of the Epithelial Cell Layer

ABSTRACT Akkermansia muciniphila is a Gram-negative mucin-degrading bacterium that resides in the gastrointestinal tracts of humans and animals. A. muciniphila has been linked with intestinal health and improved metabolic status in obese and type 2 diabetic subjects. Specifically, A. muciniphila has been shown to reduce high-fat-diet-induced endotoxemia, which develops as a result of an impaired gut barrier. Despite the accumulating evidence of the health-promoting effects of A. muciniphila, the mechanisms of interaction of the bacterium with the host have received little attention. In this study, we used several in vitro models to investigate the adhesion of A. muciniphila to the intestinal epithelium and its interaction with the host mucosa. We found that A. muciniphila adheres strongly to the Caco-2 and HT-29 human colonic cell lines but not to human colonic mucus. In addition, A. muciniphila showed binding to the extracellular matrix protein laminin but not to collagen I or IV, fibronectin, or fetuin. Importantly, A. muciniphila improved enterocyte monolayer integrity, as shown by a significant increase in the transepithelial electrical resistance (TER) of cocultures of Caco-2 cells with the bacterium. Further, A. muciniphila induced interleukin 8 (IL-8) production by enterocytes at cell concentrations 100-fold higher than those for Escherichia coli, suggesting a very low level of proinflammatory activity in the epithelium. In conclusion, our results demonstrate that A. muciniphila adheres to the intestinal epithelium and strengthens enterocyte monolayer integrity in vitro, suggesting an ability to fortify an impaired gut barrier. These results support earlier associative in vivo studies and provide insights into the interaction of A. muciniphila with the host.
Isolation and functional analysis of fatty acid desaturase genes from peanut (Arachis hypogaea L.)

Background Fatty acid desaturases are enzymes that introduce double bonds into fatty acyl chains. Extensive studies of fatty acid desaturases have been done in many plants. However, less is known about the diversity of this gene family in peanut (Arachis hypogaea L.), an important oilseed crop that is cultivated worldwide. Results In this study, twelve novel AhFADs genes were identified and isolated from peanut. Quantitative real-time PCR analysis indicated that the transcript abundances of AhFAB2-2 and AhFAD3-1 were higher in seeds than in other tissues examined, whereas the AhADS and AhFAD7-1 transcripts were more abundant in leaves. AhFAB2-3, AhFAD3-2, AhFAD4, AhSLD-4, and AhDES genes were highly expressed in flowers, whereas AhFAD7-2, AhSLD-2, and AhSLD-3 were expressed most strongly in stems. During seed development, the expressions of AhFAB2-2, AhFAD3-1, AhFAD7-1, and AhSLD-3 gradually increased in abundance, reached a maximum expression level, and then decreased. The AhFAB2-3, AhFAD3-2, AhFAD4, AhADS, and AhDES transcript levels remained relatively high at the initial stage of seed development, but decreased thereafter. The AhSLD-4 transcript level remained relatively low at the initial stage of seed development, but showed a dramatic increase in abundance at the final stage. The AhFAD7-2 and AhSLD-2 transcript levels remained relatively high at the initial stage of seed development, but then decreased, and finally increased again. The AhFAD transcripts were differentially expressed following exposure to abiotic stresses or abscisic acid. Moreover, the functions of one AhFAD6 and four AhSLD genes were confirmed by heterologous expression in Synechococcus elongates or Saccharomyces cerevisiae. Conclusions The present study provides valuable information that improves understanding of the biological roles of FAD genes in fatty acid synthesis, and will help peanut breeders improve the quality of peanut oil via molecular design breeding.
Phosphorylation of Glutathione S-Transferase P1 (GSTP1) by Epidermal Growth Factor Receptor (EGFR) Promotes Formation of the GSTP1-c-Jun N-terminal kinase (JNK) Complex and Suppresses JNK Downstream Signaling and Apoptosis in Brain Tumor Cells*

Background: GSTP1 is a downstream EGFR phosphorylation target. Results: EGFR-dependent C-terminal Tyr-198 phosphorylation shifts GSTP1 to the monomeric state, facilitates JNK binding and inhibition, and suppresses apoptosis in brain tumor cells. Conclusion: Enhanced suppression of JNK signaling by EGFR-phosphorylated GSTP1 provides a survival advantage for tumors. Significance: The GSTP1-EGFR cross-talk is a mechanism of tumor cell survival and drug resistance. Under normal physiologic conditions, the glutathione S-transferase P1 (GSTP1) protein exists intracellularly as a dimer in reversible equilibrium with its monomeric subunits. In the latter form, GSTP1 binds to the mitogen-activated protein kinase, JNK, and inhibits JNK downstream signaling. In tumor cells, which frequently are characterized by constitutively high GSTP1 expression, GSTP1 undergoes phosphorylation by epidermal growth factor receptor (EGFR) at tyrosine residues 3, 7, and 198. Here we report on the effect of this EGFR-dependent GSTP1 tyrosine phosphorylation on the interaction of GSTP1 with JNK, on the regulation of JNK downstream signaling by GSTP1, and on tumor cell survival. Using in vitro and in vivo growing human brain tumors, we show that tyrosine phosphorylation shifts the GSTP1 dimer-monomer equilibrium to the monomeric state and facilitates the formation of the GSTP1-JNK complex, in which JNK is functionally inhibited. Targeted mutagenesis and functional analysis demonstrated that the increased GSTP1 binding to JNK results from phosphorylation of the GSTP1 C-terminal Tyr-198 by EGFR and is associated with a >2.5-fold decrease in JNK downstream signaling and a significant suppression of both spontaneous and drug-induced apoptosis in the tumor cells. The findings define a novel mechanism of regulatory control of JNK signaling that is mediated by the EGFR/GSTP1 cross-talk and provides a survival advantage for tumors with activated EGFR and high GSTP1 expression. The results lay the foundation for a novel strategy of dual EGFR/GSTP1 for treating EGFR+ve, GSTP1 expressing GBMs.
Processed and Unprocessed Red Meat Consumption and Risk of Heart Failure: Prospective Study of Men

Background—Epidemiological studies of red meat consumption in relation to risk of heart failure (HF) are scarce. We examined the associations of unprocessed and processed red meat consumption with HF incidence and mortality in men. Methods and Results—The population-based prospective Cohort of Swedish Men included 37 035 men, aged 45 to 79 years, with no history of HF, ischemic heart disease, or cancer at baseline. Meat consumption was assessed with a self-administered questionnaire in 1997. During a mean follow-up of 11.8 years, 2891 incidences and 266 deaths from HF were ascertained. Consumption of processed meat was statistically significant positively associated with risk of HF in both age- and multivariable-adjusted models. Men who consumed ≥75 g/d processed meat compared with those who consumed <25 g/d had a 1.28 (95% confidence interval, 1.10–1.48, P trend=0.01) higher risk of HF incidence and 2.43 (95% confidence interval, 1.52–3.88, P trend<0.001) higher risk of HF mortality. The consumption of unprocessed meat was not associated with increased risk of incidence of HF or mortality from HF. Conclusions—Findings from this prospective study of men with low to moderate red meat consumption indicate that processed red meat consumption, but not unprocessed red meat, is associated with an increased risk of HF.
Interpretation of Natural Language Rules in Conversational Machine Reading

Most work in machine reading focuses on question answering problems where the answer is directly expressed in the text to read. However, many real-world question answering problems require the reading of text not because it contains the literal answer, but because it contains a recipe to derive an answer together with the reader’s background knowledge. One example is the task of interpreting regulations to answer “Can I. ” or “Do I have to. ” questions such as “I am working in Canada. Do I have to carry on paying UK National Insurance? ” after reading a UK government website about this topic. This task requires both the interpretation of rules and the application of background knowledge. It is further complicated due to the fact that, in practice, most questions are underspecified, and a human assistant will regularly have to ask clarification questions such as “How long have you been working abroad? ” when the answer cannot be directly derived from the question and text. In this paper, we formalise this task and develop a crowd-sourcing strategy to collect 37k task instances based on real-world rules and crowd-generated questions and scenarios. We analyse the challenges of this task and assess its difficulty by evaluating the performance of rule-based and machine-learning baselines. We observe promising results when no background knowledge is necessary, and substantial room for improvement whenever background knowledge is needed.
Exploring Parallelism in Transactional Workloads

Multicores are now standard in most machines, which means that many programmers are faced with the challenge of how to take advantage of all the potential parallelism. Transactional Memory (TM) promises to simplify this task. Yet, at the same time, TM inhibits the programmer from fully exploring the latent parallelism in his application. In particular, it does not allow a transaction to contain parallel code. This fact limits the expressiveness of TM as a synchronization mechanism. Many applications contain large operations that must be performed atomically. These large sections may entail writing to shared data, which typically leads to many conflicts in optimistic concurrency control mechanisms such as those used by most TM systems. Yet, sometimes these operations could be executed faster if their latent parallelism was used efficiently, by allowing a transaction to be split in several parts that execute concurrently. In this paper we provide this increased flexibility by using parallel nesting. Moreover, we propose to overcome inherently sequential highly-conflicting workloads with the new expressiveness provided by TM. We additionally show that the use of conflict-aware scheduling provides an effective solution to maximize the benefits of parallel nesting. Finally, we show how the implementation of these ideas in a lock-free multi-version STM outperforms the original version on several known benchmarks by up to 2.8 times.
On Performance Optimization and System Design of Flash Memory based Solid State Drives in the Storage Hierarchy

As an emerging storage technology, Flash Memory based Solid tate Drive (SSD) has shown a high potential to fundamentally change the existing Hard Disk Drive (HDD) based storage systems. Unlike conventional magnetic disks, SSD i s built on semiconductor chips and has no mechanical components (e.g. rotating disk platte rs). This architectural difference brings many attractive technical features, such as hig h random data access performance and low power consumption. Most importantly, these un ique features could potentially address the long-existing technical limitations of c nventional magnetic disks. Due to this reason, SSD has been called a ‘pivotal technology’ that may completely revolutionize current computer storage systems. On the other hand, SSD also poses several critical challenge s to application and system designers. First, due to divergent internal structures, SS D is fundamentally different from rotating media, although they share the same logical and phy sical interfaces. To date we still lack an insightful understanding about the performan ce characteristics of SSDs, both the positive and negative sides, and their implications to a pplication and system designers. In this dissertation, we present a thorough experimental st udy on the unique features of SSDs. Second, although SSDs have shown a great performance p otential, especially for handling small and random data accesses, SSDs are much more e xpensive than conventional hard disks. Even considering the decreasing price tr end, the price gap between SSDs
Activation-induced Tumor Necrosis Factor Receptor-associated Factor 3 (Traf3) Alternative Splicing Controls the Noncanonical Nuclear Factor κB Pathway and Chemokine Expression in Human T Cells*

Background: Many pre-mRNAs are alternatively spliced upon T cell activation, but functional implications remain largely unexplored. Results: Alternative splicing of the signaling adaptor Traf3 controls expression of effector proteins in activated T cells. Conclusion: Cell type-specific and activation-dependent alternative splicing regulates signaling and gene expression in T cells. Significance: Alternative splicing plays a fundamental role in regulating functionality upon T cell activation. The noncanonical nuclear factor κB (ncNFκB) pathway regulates the expression of chemokines required for secondary lymphoid organ formation and thus plays a pivotal role in adaptive immunity. Whereas ncNFκB signaling has been well described in stromal cells and B cells, its role and regulation in T cells remain largely unexplored. ncNFκB activity critically depends on the upstream NFκB-inducing kinase (NIK). NIK expression is negatively regulated by the full-length isoform of TNF receptor-associated factor 3 (Traf3) as formation of a NIK-Traf3-Traf2 complex targets NIK for degradation. Here we show that T cell-specific and activation-dependent alternative splicing generates a Traf3 isoform lacking exon 8 (Traf3DE8) that, in contrast to the full-length protein, activates ncNFκB signaling. Traf3DE8 disrupts the NIK-Traf3-Traf2 complex and allows accumulation of NIK to initiate ncNFκB signaling in activated T cells. ncNFκB activity results in expression of several chemokines, among them B cell chemoattractant (CxCL13), both in a model T cell line and in primary human CD4+ T cells. Because CxCL13 plays an important role in B cell migration and activation, our data suggest an involvement and provide a mechanistic basis for Traf3 alternative splicing and ncNFκB activation in contributing to T cell-dependent adaptive immunity.