Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmid-Encoded RepA Proteins Specifically Autorepress Individual repABC Operons in the Multipartite Rhizobium leguminosarum bv. trifolii Genome

Rhizobia commonly have very complex genomes with a chromosome and several large plasmids that possess genes belonging to the repABC family. RepA and RepB are members of the ParA and ParB families of partitioning proteins, respectively, whereas RepC is crucial for plasmid replication. In the repABC replicons, partitioning and replication functions are transcriptionally linked resulting in complex regulation of rep gene expression. The genome of R. leguminosarum bv. trifolii TA1 (RtTA1) consists of a chromosome and four plasmids (pRleTA1a-d), equipped with functional repABC genes. In this work, the regulation of transcription of the individual repABC cassettes of the four RtTA1 plasmids was studied. The involvement of the RepA and RepB as well as parS-like centromere sites in this process was depicted, demonstrating some dissimilarity in expression of respective rep regions. RtTA1 repABC genes of individual plasmids formed operons, which were negatively regulated by RepA and RepB. Individual RepA were able to bind to DNA without added nucleotides, but in the presence of ADP, bound specifically to their own operator sequences containing imperfect palindromes, and caused operon autorepression, whereas the addition of ATP stimulated non-specific binding of RepA to DNA. The RepA proteins were able to dimerize/oligomerize: in general dimers formed independently of ATP or ADP, although ATP diminished the concentration of oligomers that were produced. By the comprehensive approach focusing on a set of plasmids instead of individual replicons, the work highlighted subtle differences between the organization and regulation of particular rep operons as well as the structures and specificity of RepA proteins, which contribute to the fine-tuned coexistence of several replicons with similar repABC cassettes in the complex bacterial genome.
Dietary wheat germ agglutinin modulates ovalbumin-induced immune responses in Brown Norway rats

The trend towards an increased consumption of minimally processed plant food results in a higher intake of non-nutritive compounds such as lectins. Lectins are typically globular proteins that are resistant to digestion in the gastrointestinal tract. They affect the integrity of the intestinal epithelium and the absorption of dietary antigens, and induce the release of allergic mediators from mast cells in vitro. Based on this information we have studied whether dietary wheat germ agglutinin (WGA) could be involved in triggering food allergies. Brown Norway rats were immunized intraperitoneally using ovalbumin (OVA; 10 μg/rat) and 10 d later treated for five consecutive days with WGA (10 mg/rat per d) administered intragastrically. Rats were then orally challenged with OVA (100 μg/rat) 1 h after the last WGA application, and blood was collected 4 h later. Immunological responses (anti-OVA immunoglobulins E and G, rat mast cell protease II, interferon-γ and lymphocyte proliferation) were measured and lymphocyte subpopulations were determined. In immunized rats WGA treatment resulted in increased serum rat mast cell protease II concentrations (pre-challenge 0.26 (SE 0.08) ΜG/ML, POST-CHALLENGE 0.49 (se 0.09) μg/ml; P<0.01) 4 h after the OVA challenge. After 5 d serum concentrations of anti-OVA immunoglobulin E were significantly increased only in the immunized controls (absorbance at 405 nm on days 14 and 19 was 0.09 (se 0.008) and 0.24 (se 0.046) respectively; P=0.02), while in WGA-treated rats no significant increase was seen (0.08 (se 0.004) and 0.15 (se 0.037 respectively; P=0.14). CD4+ : CD8+ T lymphocytes in the spleen was significantly increased at this time (OVA 1.1 (sd 0.2), OVA+WGA 1.4 (sd 0.1), P<0.05). The treatment did not impair the proliferation and interferon-γ production of mesenteric lymphocytes. In conclusion, these data suggest that high dietary intake of lectins such as WGA may affect the allergic response towards oral antigens in the gut-associated lymphoid tissue.
Identification of a Homophilic Binding Site in Immunoglobulin‐Like Domain 2 of the Cell Adhesion Molecule L1

Abstract: The cell adhesion molecule L1 plays an important role in neural development, and mutations in human L1 have been implicated in X‐linked hydrocephalus and related neurological diseases. We have previously demonstrated that recombinant proteins containing the second immunoglobulin‐like domain (Ig2) of L1 contain both homophilic binding and neuritogenic activities. In this report, the involvement of L1 Ig2 in cell‐cell adhesion and neuritogenesis was further evaluated in cell transfection studies. Transfectants expressing intact L1 were capable of undergoing L1‐dependent self‐aggregation and promoting neurite outgrowth from neural retinal cells. However, both activities were abolished in transfectants expressing L1Δ2, a mutant L1 with Ig2 deleted. In competition experiments, the wild‐type Ig2 fusion protein inhibited L1‐dependent cell aggregation, whereas an Ig2 fusion protein containing the hydrocephalus mutation R184Q did not. Oligopeptides flanking Arg184 were therefore synthesized and assayed for their effects on L1‐mediated cell‐cell binding and neuritogenesis. The peptide L1‐A, spanning the residues His178 and Gly191, inhibited both L1‐ and Ig2 fusion protein‐mediated homophilic binding. When neural retinal cells were cultured on substrate‐coated Ig2 fusion protein, peptide L1‐A also abolished L1‐dependent neurite outgrowth. Substitutions of several charged residues and hydrophobic residues with alanine in peptide analogues led to the loss of inhibitory effects, suggesting that multiple amino acids might be involved in L1‐L1 binding. Taken together, these results identify an L1 homophilic binding site within the sequence HIKQDERVTMGQNG of Ig2 and demonstrate the requirement of L1 homophilic binding in the promotion of neurite outgrowth.
Feed-Forward Rate Distortion Function and Markov Sources

The problem of channel coding with feedback has been extensively studied over the last 50 years. Using an ideal feedback link, the encoder knows all previously received channel outputs. Recently the duality between channel coding and rate distortion has been established in [15] and [3], leading to the problem of source coding with feed-forward. In this project we first study the general formula for the feed-forward rate distortion function given by Venkataramanan et al. [8]. They studied the source coding problem when a feed-forward link is available for general sources and general distortion measures. They derived the feed-forward rate distortion function for an arbitrary source in terms of the directed information which was originally introduced by Massey [5]. It is shown that the general formula given for source coding with feed-forward is closely related to the general formula for channel coding with feedback given by Tatikonda [4]. We then study another formula for the feed-forward rate distortion function recently proposed by Naiss et al. which is tractable and computable [17]. They also calculated the exact rate distortion function for first order asymmetric Markov sources. An original contribution of this project is an alternative achievability proof for the feed-forward rate distortion function of first order asymmetric Markov sources. I
Organizational Identity Formation and Change

Theory and research concerning organizational identity (“who we are as an organization”) is a burgeoning domain within organization study. A great deal of conceptual and empirical work has been accomplished within the last three decades—especially concerning the phenomenon of organizational identity change. More recently, work has been devoted to studying the processes and content associated with identity formation. Given the amount of scholarly work done to date, it is an appropriate time to reflect on the perspectives, controversies and outcomes of this body of work. Because organizational identity change has received the preponderance of attention, we first review that extensive literature. We consider the conceptual and empirical work concerning the three putative “pillars” of identity (i.e. that which is ostensibly central, enduring, and distinctive). We devote particular attention to the most controversial of these pillars—the debate pitting a view that sees identity as stable over time (a position .
Production , Manufacturing and Logistics The impacts of the full returns policy on a supply chain with information asymmetry

In contrast to the existing return policies literature assuming that information is symmetrical between the manufacturer and the retailer, we study the full returns policy’s impact on supply chains with information asymmetry. We first study the case that the base level of the demand follows a discrete distribution with two states. We find that the retailer benefits from the full returns policy in all circumstances, while the manufacturer and the supply chain are better off under some conditions. We then consider the situation in which the base level of the demand is a type of AR(1) process. 2006 Elsevier B.V. All rights reserved.
The role of practice in the development of performing musicians

A sample of 257 young people aged between eight and 18 who had undertaken individual instrumental tuition were interviewed in depth about their performing history from the start of playing. A subset of 94 of these individuals also kept a practice diary for a 42-week period. The data collected allowed estimates to be calculated of the amount of time devoted to various types of practice and other activities. The sample was selected in order to encompass a wide range of levels of musical achievement, from pupils at a highly selective specialist music school through to individuals who had abandoned instrumental study after less than a year of formal instruction. Data about formal examination successes confirmed the very wide range of achievement in the sample. It was discovered that there was a strong relationship between musical achievement and the amount of formal practice undertaken. Weaker relationships were discovered between achievement and amount of informal playing. There was no evidence that high achievers were able to gain a given level of examination success on less practice than low achievers. High achievers tended to be more consistent in their pattern of practice from week to week, and tended to concentrate technical practice in the mornings. These data lend strong support to the theory that formal effortful practice is a principal determinant of musical achievement.
Required for Thyroid Cell Transformation Induction of ETS-1 and ETS-2 Transcription Factors Is Updated

The proteins of the Ets family are transcription factors involved in signal transduction, cell cycle progression, and differentiation. In this study, we report that thyroid cell neoplastic transformation is associated with a dramatic increase in ETS transcriptional activity, which is dependent on the accumulation of Ets-1, Ets-2, and other Ets-related proteins. Inhibition of ETS transactivation activity by the Ets-dominant negative construct (Ets-Z) induced programmed cell death in human thyroid carcinoma cell lines but not in normal thyroid cells. Apoptotic cell death induced by Ets-Z was dependent on the reduction of c-MYC protein levels, because it was prevented by overexpression of c-myc. Taken together, these data indicate that the induction of Ets-1 and Ets-2 transcription factors plays a pivotal role in thyroid cell neoplastic transformation.
Towards a Conceptual Model and Reasoning Structure for Insider Threat Detection

The insider threat faced by corporations and governments today is a real and significant problem, and one that has become increasingly difficult to combat as the years have progressed. From a technology standpoint, traditional protective measures such as intrusion detection systems are largely inadequate given the nature of the ‘insider’ and their legitimate access to prized organisational data and assets. As a result, it is necessary to research and develop more sophisticated approaches for the accurate recognition, detection and response to insider threats. One way in which this may be achieved is by understanding the complete picture of why an insider may initiate an attack, and the indicative elements along the attack chain. This includes the use of behavioural and psychological observations about a potential malicious insider in addition to technological monitoring and profiling techniques. In this paper, we propose a framework for modelling the insider-threat problem that goes beyond traditional technological observations and incorporates a more complete view of insider threats, common precursors, and human actions and behaviours. We present a conceptual model for insider threat and a reasoning structure that allows an analyst to make or draw hypotheses regarding a potential insider threat based on measurable states from real-world observations.
Breaking the Split Incentive Hurdle via Time-Varying Monetary Rewards

Demand response is widely employed by today's data centers to response to the increasing of electricity cost. To incentivize users of data centers participate in the demand response programs, i.e., breaking the split incentive hurdle, some prior researches proposed market-based mechanisms such as dynamic pricing and static monetary rewards. However, these mechanisms are either intrusive or unfair. In this paper, we use time-varying rewards to incentivize users of data centers grant time-shifting of their requests. With a game-theoretic framework, we model/analyze the game between a single data center and its users. Further, we extend our design via integrating it with another emerging practical demand response strategies: server shutdown or local renewable energy generation. With real-world data traces, we show that a data center with our design can effectively shed its peak electricity load and overall electricity cost without reducing its profit, when compared with the current practice where no incentive mechanism is established.
The C.elegans ric‐3 gene is required for maturation of nicotinic acetylcholine receptors

Mutations in ric‐3 (resistant to inhibitors of cholinesterase) suppress the neuronal degenerations caused by a gain of function mutation in the Caenorhabditis elegans DEG‐3 acetylcholine receptor. RIC‐3 is a novel protein with two transmembrane domains and extensive coiled‐coil domains. It is expressed in both muscles and neurons, and the protein is concentrated within the cell bodies. We demonstrate that RIC‐3 is required for the function of at least four nicotinic acetylcholine receptors. However, GABA and glutamate receptors expressed in the same cells are unaffected. In ric‐3 mutants, the DEG‐3 receptor accumulates in the cell body instead of in the cell processes. Moreover, co‐expression of ric‐3 in Xenopus laevis oocytes enhances the activity of the C.elegans DEG‐3/DES‐2 and of the rat α‐7 acetylcholine receptors. Together, these data suggest that RIC‐3 is specifically required for the maturation of acetylcholine receptors.
Why European Integration Increases Leadership Autonomy within Political Parties

Party scholars have been arguing, at least since the 1960s, that party leaders are becoming more autonomous of their parties in respect of decision-making. This article analyses the impact of European integration on the balance of power in the national parties of EU member states. A theoretical model explaining why European integration increases the autonomy of party leadership is presented together with preliminary evidence. The main argument is that European integration consolidates centralization of decision-making through strengthening the agenda-setting powers of party leaders. Centralization and leadership autonomy should be greater in countries with weak parliamentary scrutiny over EU affairs. The level of control by national legislatures is in turn explained by party cohesion on integration. The concluding section presents questions for future research and discusses some of the main challenges national parties face in adapting to European integration.
The Endothelium in Sepsis

ABSTRACT Sepsis affects practically all aspects of endothelial cell (EC) function and is thought to be the key factor in the progression from sepsis to organ failure. Endothelial functions affected by sepsis include vasoregulation, barrier function, inflammation, and hemostasis. These are among other mechanisms often mediated by glycocalyx shedding, such as abnormal nitric oxide metabolism, up-regulation of reactive oxygen species generation due to down-regulation of endothelial-associated antioxidant defenses, transcellular communication, proteases, exposure of adhesion molecules, and activation of tissue factor. This review covers current insight in EC-associated hemostatic responses to sepsis and the EC response to inflammation. The endothelial cell lining is highly heterogeneous between different organ systems and consequently also in its response to sepsis. In this context, we discuss the response of the endothelial cell lining to sepsis in the kidney, liver, and lung. Finally, we discuss evidence as to whether the EC response to sepsis is adaptive or maladaptive. This study is a result of an Acute Dialysis Quality Initiative XIV Sepsis Workgroup meeting held in Bogota, Columbia, between October 12 and 15, 2014.
A Meta-Analysis of Culturally Sensitive Interventions Designed to Reduce High-Risk Behaviors Among African American Youth

ABSTRACT This study sought to determine the effectiveness of culturally sensitive interventions (CSIs) in reducing high risk behaviors with African American youth. A meta-analysis was conducted to assess the effectiveness of CSIs across seven studies. African American youth who participated in CSIs were less likely to engage in high risk behaviors compared to those who did not participate. The effect size was moderate (g = .35). Although the findings should be considered tentative, the results provide an initial quantitative assessment of CSI effectiveness that future evaluations and meta-analyses can build upon as CSI research expands.
Is current irrigation sustainable in the United States? An integrated assessment of climate change impact on water resources and irrigated crop yields

While climate change impacts on crop yields has been extensively studied, estimating the impact of water shortages on irrigated crop yields is challenging because the water resources management system is complex. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling framework, an integrated assessment model linking a global economic model to an Earth system model. We assess the effects of climate and socioeconomic changes on water availability for irrigation in the U.S. as well as subsequent impacts on crop yields by 2050, while accounting for climate change projection uncertainty. We find that climate and socioeconomic changes will increase water shortages and strongly reduce irrigated yields for specific crops (i.e., cotton and forage), or in specific regions (i.e., the Southwest) where irrigation is not sustainable. Crop modeling studies that do not represent changes in irrigation availability can thus be misleading. Yet, since the most water‐stressed basins represent a relatively small share of U.S. irrigated areas, the overall reduction in U.S. crop yields is small. The response of crop yields to climate change and water stress also suggests that some level of adaptation will be feasible, like relocating croplands to regions with sustainable irrigation or switching to less irrigation intensive crops. Finally, additional simulations show that greenhouse gas (GHG) mitigation can alleviate the effect of water stress on irrigated crop yields, enough to offset the reduced CO2 fertilization effect compared to an unconstrained GHG emission scenario.
Knowledge Graph and Corpus Driven Segmentation and Answer Inference for Telegraphic Entity-seeking Queries

Much recent work focuses on formal interpretation of natural question utterances, with the goal of executing the resulting structured queries on knowledge graphs (KGs) such as Freebase. Here we address two limitations of this approach when applied to open-domain, entity-oriented Web queries. First, Web queries are rarely wellformed questions. They are “telegraphic”, with missing verbs, prepositions, clauses, case and phrase clues. Second, the KG is always incomplete, unable to directly answer many queries. We propose a novel technique to segment a telegraphic query and assign a coarse-grained purpose to each segment: a base entity e1, a relation type r, a target entity type t2, and contextual words s. The query seeks entity e2 2 t2 where r(e1,e2) holds, further evidenced by schema-agnostic words s. Query segmentation is integrated with the KG and an unstructured corpus where mentions of entities have been linked to the KG. We do not trust the best or any specific query segmentation. Instead, evidence in favor of candidate e2s are aggregated across several segmentations. Extensive experiments on the ClueWeb corpus and parts of Freebase as our KG, using over a thousand telegraphic queries adapted from TREC, INEX, and WebQuestions, show the efficacy of our approach. For one benchmark, MAP improves from 0.2‐0.29 (competitive baselines) to 0.42 (our system). NDCG@10 improves from 0.29‐0.36 to 0.54.
Videoconference Capacity Leasing on Hybrid Clouds

This paper proposes a new methodology focused on implementing cost effective architectures on Cloud Computing systems. With this methodology the paper presents some disadvantages of systems that are based on single Cloud architectures and gives some advices for taking into account in the development of hybrid systems. The work also includes a validation of these ideas implemented in a complete videoconference service developed with our research group. This service allows a great number of users per conference, multiple simultaneous conferences, different client software (requiring transcodification of audio and video flows) and provides a service like automatic recording. Furthermore it offers different kinds of connectivity including SIP clients and a client based on Web 2.0. The ideas proposed in this article are intended to be a useful resource for any researcher or developer who wants to implement cost effective systems on several Clouds.
A Seed-specific Heat-shock Transcription Factor Involved in Developmental Regulation during Embryogenesis in Sunflower*

We report the cloning and functional characterization of the first heat-shock transcription factor that is specifically expressed during embryogenesis in the absence of environmental stress. In sunflower embryos this factor, HaHSFA9,trans-activated promoters with poor consensus heat-shockcis-elements, including that of the seed-specificHahsp17.6G1 gene. Mutations that improved the heat-shockcis-element consensus at the Hahsp17.7G4promoter impaired transient activation by HaHSFA9 in sunflower embryos. The same mutations did not affect heat-shock-induced gene expression of this promoter in transgenic tobacco plants but reduced the developmental activation by endogenous heat-shock transcription factors (HSFs) in seeds. Sunflower, and perhaps other plants such as tobacco, differs from the vertebrate animal systems in having at least one specialized HSF with expression and (or) activation patterns strictly restricted to embryos. Our results strongly indicate that HaHSFA9 is a transcription factor critically involved in the developmental activation of Hahsp17.6G1 and in that of similar target genes as Hahsp17.7G4.