julilili42/papers huggingface dataset:
Diversification of a Bacterial ADP‐Ribosyltransferase
2015-04-01

OBJECTIVE To accelerate the enzyme evolution, we diversified a bacterial ADP‐ribosyltransferase, cholix toxin catalytic fragment, to modify different substrates. METHODS Previously, we identified a diffusible intermediate that could modify target residues in a proximity dependent manner (submitted in the same meeting, Topic #2278‐ASBMB‐Enzyme Mechanism, Number 540). We utilized a phage display library screening strategy to select for variants to bind to different substrates of interests, followed by enzymatic screening for the selected variants retaining enzymatic activity. Site‐directed mutagenesis, enzymatic assays and 2‐D‐electrophoresis analysis were used to detect the in vitro modification of the substrates by the engineered enzymes. RESULTS We showed several examples of engineered cholix toxin catalytic fragment variants that can modify various substrates, including enhanced green fluorescent protein (EGFP) and mouse immunoglobulins. CONCLUSION We anticipate our findings to be a starting point for more sophisticated engineering. Such enzymes can be useful tools for basic research or therapeutic applications.
A Chemical Toolbox for Lysine Deacetylases
2015-04-01

Lysine acetylation is a well‐known post‐translation modification of proteins, which was discovered in the 1960s. Histone proteins and in particular their N‐terminal tail regions are among the most prominent targets of this modification. Histones package DNA into chromatin and lysine acetylation serves as an important regulator of chromatin condensation and accessibility and thereby gene expression. Recent proteome‐wide investigations have uncovered that lysine acetylation is not limited to histones but constitutes one of the most abundant protein modifications in nature with 3600 acetylation sites identified in the human proteome. Subsequent biochemical investigations have linked lysine acetylation to the regulatory networks of several cellular processes including signal transduction, apoptosis and metabolism. Lysine acetylation is catalyzed by lysine acetyltransferases and erased by lysine deacetylases. Especially the latter class of enzymes has gained considerable attention because lysine deacetylases have been identified as promising drug targets. However, biochemical research is hampered by the poor accessibility of these enzymes and as a result the overall knowledge about the substrate selectivity of lysine deacetylases is poor. In this talk recent developments and applications of chemical tools for probing the activity and specificity of lysine deacetylases will be presented.
Why and how does shared language affect subsidiary knowledge inflows? A social identity perspective
2015-04-02

We draw on social identity theory to conceptualize a moderated mediation model that examines the relationship between shared language among subsidiary and HQ managers, and subsidiaries’ knowledge inflows from HQ.&#13;\\n&#13;\\nSpecifically, we study (1) whether this relationship is mediated by the extent to which subsidiary managers share HQ goals and vision, and the extent to which HR decisions are centralized; and (2) whether subsidiary type moderates these mediated relationships. Building on a sample of 817 subsidiaries in nine countries/regions, we find support for our model. Implications for research on HQ-subsidiary knowledge flows, social identity theory and international HRM are discussed.
Keep Calm and Carry On: Improved Frustration Tolerance and Processing Speed by Transcranial Direct Current Stimulation (tDCS)
2015-04-02

Cognitive control (CC) of attention is a major prerequisite for effective information processing. Emotional distractors can bias and impair goal-directed deployment of attentional resources. Frustration-induced negative affect and cognition can act as internal distractors with negative impact on task performance. Consolidation of CC may thus support task-oriented behavior under challenging conditions. Recently, transcranial direct current stimulation (tDCS) has been put forward as an effective tool to modulate CC. Particularly, anodal, activity enhancing tDCS to the left dorsolateral prefrontal cortex (dlPFC) can increase insufficient CC in depression as indicated by a reduction of attentional biases induced by emotionally salient stimuli. With this study, we provide first evidence that, compared to sham stimulation, tDCS to the left dlPFC enhances processing speed measured by an adaptive version of the Paced Auditory Serial Addition Task (PASAT) that is typically thwarted by frustration. Notably, despite an even larger amount of error-related negative feedback, the task-induced upset was suppressed in the group receiving anodal tDCS. Moreover, inhibition of task-related negative affect was correlated with performance gains, suggesting a close link between enhanced processing speed and consolidation of CC by tDCS. Together, these data provide first evidence that activity enhancing anodal tDCS to the left dlPFC can support focused cognitive processing particularly when challenged by frustration-induced negative affect.
Opisthorchiasis: An Overlooked Danger
2015-04-02

BackgroundA group of helminth infections, caused by liver flukes of the trematode family Opisthorchiidae, were recently the focus of discussions at a meeting where scientists from Russia, Southeast Asia, Europe, and the United States came together in Tomsk city in Western Siberia (Russia) to form a Tomsk OPIsthorchiasis Consortium (TOPIC).This initiative starts a platform to raise awareness, to strengthen integrated control, and to conduct research on a neglected infectious disease that afflicts populations not only in the tropical regions of East Asia but also in temperate and semi-arctic areas of Europe and Asia [1].The Opisthorchiidae of importance to humans are Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis, each of which has a discrete, though occasionally overlapping, geographical distribution: O. felineus is endemic in Europe and Russia; C. sinensis in China, the Republic of Korea, and northern Vietnam; and O. viverrini in Southeast Asia.Together they affect more than 45 million people worldwide [2].Human infection with O. felineus results from eating raw or undercooked freshwater fish carrying the metacercariae of the parasite.The ingested larvae develop further and migrate to the bile ducts by chemotaxis, where adult worms feed on biliary epithelia and contents in the bile.Adult worms shed eggs that enter the gastrointestinal tract and are released with the faeces to the external environment.Freshwater snails of the family Bithyniidae ingest the eggs and, following the release of the miracidia from the eggs, several stages of development take place within the snail until cercariae have developed.Shed cercariae can penetrate freshwater fish, where they encyst in the skin or flesh [3].
Functional brain development in growth‐restricted and constitutionally small fetuses: a fetal magnetoencephalography case–control study
2015-04-02

Objective Fetal magnetoencephalography records fetal brain activity non‐invasively. Delayed brain responses were reported for fetuses weighing below the tenth percentile. To investigate whether this delay indicates delayed brain maturation resulting from placental insufficiency, this study distinguished two groups of fetuses below the tenth percentile: growth‐restricted fetuses with abnormal umbilical artery Doppler velocity ( IUGR ) and constitutionally small‐for‐gestational‐age fetuses with normal umbilical artery Doppler findings ( SGA ) were compared with fetuses of adequate weight for gestational age ( AGA ), matched for age and behavioural state. Design A case–control study of matched pairs. Setting Fetal magnetoencephalography‐Center at the University Hospital of Tuebingen. Population Fourteen IUGR fetuses and 23 SGA fetuses were matched for gestational age and fetal behavioural state with 37 healthy, normal‐sized fetuses. Methods A 156‐channel fetal magentoencephalography system was used to record fetal brain activity. Light flashes as visual stimulation were applied to the fetus. The Student's t ‐ test for paired groups was performed. Main outcome measure Latency of fetal visual evoked magnetic responses (VER). Results The IUGR fetuses showed delayed VER s compared with controls ( IUGR , 233.1 ms; controls, 184.6 ms; P = 0.032). SGA fetuses had similar evoked response latencies compared with controls ( SGA , 216.1 ms; controls, 219.9 ms; P = 0.828). Behavioural states were similarly distributed. Conclusion Visual evoked responses are delayed in IUGR fetuses, but not in SGA . Fetal behavioural state as an influencing factor of brain response latency was accounted for in the comparison. This reinforces that delayed brain maturation is the result of placental insufficiency.
Accounting for Linear Transformations of EEG and MEG Data in Source Analysis
2015-04-02

Analyses of electro- and magnetoencephalography (EEG, MEG) data often involve a linear modification of signals at the sensor level. Examples include re-referencing of the EEG, computation of synthetic gradiometer in MEG, or the removal of artifactual independent components to clean EEG and MEG data. A question of practical relevance is, if such modifications must be accounted for by adapting the physical forward model (leadfield) before subsequent source analysis. Here, we show that two scenarios need to be differentiated. In the first scenario, which corresponds to re-referencing the EEG and synthetic gradiometer computation in MEG, the leadfield must be adapted before source analysis. In the second scenario, which corresponds to removing artifactual components to 'clean' the data, the leadfield must not be changed. We demonstrate and discuss the consequences of wrongly modifying the leadfield in the latter case for an example. Future EEG and MEG studies employing source analyses should carefully consider whether and, if so, how the leadfield must be modified as explicated here.
Learning and Collective Knowledge Construction With Social Media: A Process-Oriented Perspective
2015-04-03

Social media are increasingly being used for educational purposes. The first part of this article briefly reviews literature that reports on educational applications of social media tools. The second part discusses theories that may provide a basis for analyzing the processes that are relevant for individual learning and collective knowledge construction. We argue that a systems-theoretical constructivist approach is appropriate to examine the processes of educational social media use, namely, self-organization, the internalization of information, the externalization of knowledge, and the interplay of externalization and internalization providing the basis of a co-evolution of cognitive and social systems. In the third part we present research findings that illustrate and support this systems-theoretical framework. Concluding, we discuss the implications for educational design and for future research on learning and collective knowledge construction with social media.
On the Link between Cognitive Diagnostic Models and Knowledge Space Theory
2015-04-03

The present work explores the connections between cognitive diagnostic models (CDM) and knowledge space theory (KST) and shows that these two quite distinct approaches overlap. It is proved that in fact the Multiple Strategy DINA (Deterministic Input Noisy AND-gate) model and the CBLIM, a competence-based extension of the basic local independence model (BLIM), are equivalent. To demonstrate the benefits that arise from integrating the two theoretical perspectives, it is shown that a fairly complete picture on the identifiability of these models emerges by combining results from both camps. The impact of the results is illustrated by an empirical example, and topics for further research are pointed out.
The Crucial Role of Confined Residual Additives on the Photostability of P3HT:PCBM Active Layers
2015-04-03

We have investigated the impact of\\nresidual additives such as diiodooctane\\n(DIO) and octanedithiol (ODT) on the photostability of state of the\\nart P3HT:PCBM active layers. A series of active layers prepared with\\nand without additives as well as neat additives were submitted to\\nlight irradiation in ambient air and analyzed by UV–vis and\\nIR spectroscopy. We show not only that residues are sensitive to the\\ncombined action of light and oxygen but also that their presence can\\ndramatically impact the polymer blend stability. DIO molecules are\\nhighly sensitive to light and can directly saturate the polymer conjugated\\nbackbone or be trapped by the fullerene moieties. ODT molecules can\\nbe photooxidized and may accelerate the intrinsic photooxidation of\\nthe active layer. Another important result is that the additives’\\nimpact is directly linked to the presence of a top layer above the\\nactive layer. The confinement makes that additives react within the\\nactive layer, and thus accelerate its photodegradation, rather than\\ndecomposing in the gas phase (irradiation without top layer). Thus,\\na light-soaking step before top layer deposition could allow a clean\\nremoving of additives without affecting the optimized morphology and\\npolymer blend stability. This process would be easily adaptable to\\nindustrial scale production.
Integrated whole‐genome screening for P seudomonas aeruginosa virulence genes using multiple disease models reveals that pathogenicity is host specific
2015-04-03

Summary P seudomonas aeruginosa is a multi‐host opportunistic pathogen causing a wide range of diseases because of the armoury of virulence factors it produces, and it is difficult to eradicate because of its intrinsic resistance to antibiotics. Using an integrated whole‐genome approach, we searched for P . aeruginosa virulence genes with multi‐host relevance. We constructed a random library of 57 360 Tn5 mutants in P . aeruginosa PAO1 ‐ L and screened it in vitro for those showing pleiotropic effects in virulence phenotypes (reduced swarming, exo‐protease and pyocyanin production). A set of these pleiotropic mutants were assayed for reduced toxicity in D rosophila melanogaster, C aenorhabditis elegans , human cell lines and mice. Surprisingly, the screening revealed that the virulence of the majority of P . aeruginosa mutants varied between disease models, suggesting that virulence is dependent on the disease model used and hence the host environment. Genomic analysis revealed that these virulence‐related genes encoded proteins from almost all functional classes, which were conserved among P . aeruginosa strains. Thus, we provide strong evidence that although P . aeruginosa is capable of infecting a wide range of hosts, many of its virulence determinants are host specific. These findings have important implication when searching for novel anti‐virulence targets to develop new treatments against P . aeruginosa .
Framing Protest and Insurgency: Boko Haram and MASSOB in Nigeria
2015-04-03

Why do some protest movements erupt into rebellion, whereas others protest peacefully under similar circumstances? Addressing this question, this paper investigates the cases of Boko Haram (rebellion) and MASSOB (non-violent protest) in contemporary Nigeria. Conventional explanations of rebellion focusing on opportunity, inequality, and repression cannot explain why these movements have pursued different protest strategies. This paper tries to explain this puzzle by investigating the signifying work and meaning construction of both movements drawing on the framing approach from social movement studies. The framing analysis shows that the different protest behavior largely results from the differing cultural context of both movements, from the agency of the framers, and from successful frame alignment, which results in frame resonance and, thereby, the successful mobilization for collective action.
rRNA regulation during growth and under stringent conditions in S taphylococcus aureus
2015-04-03

Summary The control of rRNA synthesis and, thereby, translation is vital for adapting to changing environmental conditions. The decrease of rRNA is a common feature of the stringent response, which is elicited by the rapid synthesis of (p)pp G pp. Here we analysed the properties and regulation of one representative rRNA operon of S taphylococcus aureus under stringent conditions and during growth. The promoters, P1 and P2, are severely downregulated at low intracellular guanosine triphosphate ( GTP ) concentrations either imposed by stringent conditions or in a guanine auxotroph guaBA mutant. In a (p)pp G pp 0 strain, the GTP level increased under stringent conditions, and rRNA transcription was upregulated. The correlation of the intracellular GTP levels and rRNA promoter activity could be linked to GTP nucleotides in the initiation region of both promoters at positions between +1 and +4. This indicates that not only transcriptional initiation, but also the first steps of elongation, requires high concentrations of free nucleotides. However, the severe downregulation of rRNA in post‐exponential growth phase is independent of (p)pp G pp, the composition of the initiation region and the intracellular nucleotide pool. In summary, rRNA transcription in S . aureus is only partially and presumably indirectly controlled by (p)pp G pp.
Violent vs. Non-Violent Struggle: Investigating the Impact of Frames on Movement Strategies in Yemen
2015-04-03

Why do some opposition movements escalate into armed conflict while others abide non-violently under very similar conditions? In order to account for this variance, the article proposes to transcend the limitations of existing structural theories within civil war studies by including a framing perspective. It accentuates and elucidates the agency component and the interactive dynamics of the construction and negotiation of meaning, which remain a 'black box' in current models. In a comparative study of two movements in Yemen, the article identifies and describes the respective collective action frames, establishes why and how strategic movement actors construct them in their specific particularity, and relates this to the question of why constituents take certain forms of action. The findings assert the theoretical contribution of an integrative approach.
Introduction: Framing Political Violence – A Micro-Approach to Civil War Studies
2015-04-03

The papers of the special issue analyse intra-state conflict escalation and armed rebellion from a framing perspective. Following Robert Benford and David Snow, framing is understood as strategic c...
Triggering verbal presuppositions
2015-04-03

This paper offers a predictive mechanism to derive the presuppositions of verbs. The starting point is the intuition, dating back at least to Stalnaker (1974), that the information conveyed by a sentence that is in some sense independent from its main point is presupposed. The contribution of this paper is to spell out a mechanism for deciding what will become the main point of the sentence and how to calculate independence. It is proposed that this can be calculated by making reference to event times. As a very rough approximation, the main point of an utterance is what (in a sense to be defined) has to be about the event time of the matrix predicate and the information that the sentence conveys but is not (or does not have to be) about the event time of the matrix predicate is presupposed. The notion of aboutness used to calculate independence is based on Demolombe and Farinas del Cerro (2000).
Data Freshness for Non-Trusted Environments Using Disposable Certificates
2015-04-03

Data stored in a non-trusted environment can be easily modified by attackers. In the context of a cloud, the attacker may be the cloud provider. Therefore, data should be protected against undetected modification. Conventional methods for protection of data integrity do not help if the data in the cloud is exchanged with a previous version of the data. That data is correct but not the latest version, it is not fresh.
Seuren/Rullmann ambiguities as plural comparisons
2015-04-03

This paper reexamines ambiguous comparatives of a kind made famous in Rullmann's (1995) dissertation, e.g. The helicopter was flying less high than a plane can fly. There is some disagreement in the semantic literature regarding whether the ambiguity is limited to less or also shows up in more-comparatives. Accordingly, the analyses suggested differ substantially, ranging from structural to pragmatic. My primary goal is to provide a more solid empirical basis for building semantic theories of the phenomenon. I report the results from a series of questionnaire studies that show (i) that the difference between more- and less-comparatives is not clear cut, and (ii) that we need to make more fine-grained distinctions among less-comparatives. I propose an analysis in terms of plural predication that captures the major effects found in the studies, and I begin to approach the more subtle data points.
Unrestrained beta reduction
2015-04-03

A major argument for syntactic reconstruction is based on the well-known fact that semantic reconstruction by beta-reduction is possible only if the term to be substituted for a variable does not contain any variable that would become bound as a result of substitution. This way, we derive a theoretical argument for syntactic reconstruction. However, syntactic reconstruction is not without its problems, simply because the surface form and the reconstructed form may still differ with respect to other syntactic, semantic, and information theoretic properties. This is particularly troublesome for minimalist theories which do not allow for multiple levels of representation. In this paper we propose a technique that might help to overcome these difficulties (ie. the limitation imposed by beta-reduction on semantic reconstruction) by defining a translation function T for expressions of a predicate logic L0 with lambda-abstraction into expressions of a higher-order language L1, with the desirable property that the translation of a formula in L0 is equivalent with the translation of its unrestricted reduction. In linguistic applications this will facilitate the binding of a pronoun without presupposing c-command. We will sketch a formal proof showing that unrestricted beta-reduction is a property of the target expressions in L1, the translations of L0 under T.
A Note on Phrasal Comparatives
2015-04-03

This paper investigates the various comparative operators that a language might employ and provides arguments for choosing a particular one. In particular, different phrasal comparatives are contrasted. We argue that Schoenfinkelization of the operator matters and reflects different crosslinguistic possibilities.
Sufficiency inference in anankastic conditionals
2015-04-03

The minimal sufficiency reading of anankastic conditionals, discussed in connection with Heim's (2001) ambiguities in comparative constructions and von Fintel &amp; Iatridou's (2007) 'Prejacent Problem' in the sufficiency modal construction, is argued to stem from the kind of ordering associated with anankastic modals.
A uniform analysis for concessive at least and optative at least
2015-04-03

This paper discusses a particular type of optative constructions (which are constructions that express a wish without containing an overt lexical item that means wish): If-clauses in which optativity is apparently licensed by 'at least'. I propose that the connection between 'at least' and optativity is indirect and can be explained as follows. On the one hand, if-clauses generally have an optative reading; on the other hand, optative 'at least' is an instance of concessive 'at least', which conveys desirability and thus supports ('cues') an optative reading. I propose that, as a consequence, the licensing of optativity by 'at least' is a semantic conspiracy: I argue that there is a pragmatic preference for using optativity cues, which blocks optative readings in cue-less utterances.