Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Regulation of xyn1, Encoding Xylanase I, in Hypocrea jecorina

ABSTRACT Two major xylanases (XYN I and XYN II) of the filamentous fungus Hypocrea jecorina (Trichoderma reesei) are simultaneously expressed during growth on xylan but respond differently to low-molecular-weight inducers. In vivo footprinting analysis of the xylanase1 (xyn1) promoter revealed three different nucleotide sequences (5′-GGCTAAATGCGACATCTTAGCC-3′ [an inverted repeat of GGCTAA spaced by 10 bp], 5′-CCAAT-3′, and 5′-GGGGTCTAGACCCC-3′ [equivalent to a double Cre1 site]) used to bind proteins. Binding to the Cre1 site is only observed under repressed conditions, whereas binding to the two other motifs is constitutive. Applying heterologously expressed components of the H. jecorina cellulase regulators Ace1 and Ace2 and the xylanase regulator Xyr1 suggests that Ace1 and Xyr1 but not Ace2 contact both GGCTAA motifs. H. jecorina transformants containing mutated versions of the xyn1 promoter, leading to elimination of protein binding to the left or the right GGCTAA box revealed either strongly reduced or completely eliminated induction of transcription. Elimination of Cre1 binding to its target released the basal transcriptional level from glucose repression but did not influence the inducibility of xyn1 expression. Mutation of the CCAAT box prevents binding of the Hap2/3/5 complex in vitro and is partially compensating for the loss of transcription caused by the mutation of the right GGCTAA box. Finally, evidence for a competition of Ace1 and Xyr1 for the right GGCTAA box is given. These data prompted us to hypothesize that xyn1 regulation is based on the interplay of Cre1 and Ace1 as a general and specific repressor with Xyr1 as transactivator.
Case–control genetic association study of fibulin‐6 (FBLN6 or HMCN1) variants in age‐related macular degeneration (AMD)

This article reports a well‐powered age‐related macular degeneration (AMD) case–control association study in the HMCN1 gene, showing that common variants do not account for a substantial proportion of AMD cases. Thus, the consistent linkage peak observed by several genome‐wide linkage scans within the 1q32 region is unlikely to be attributed to polymorphisms at the HMCN1 locus. In addition, the analysis provides comprehensive data suggesting that low‐frequency variants encoding possible functional amino acid polymorphisms in the HMCN1 gene may not contribute substantially to disease, although HMCN1 mutations may still confer disease susceptibility in a small subset of patients. Interestingly, the HMCN1 p.Gln5346Arg mutation, which is thought to be a causal mutation in a large AMD pedigree segregating the disease as a single‐gene trait, appears to occur in our control cohort as a low‐frequency polymorphism with an allele frequency of approximately 0.0026. Hum Mutat 28(4), 406–413, 2007. © 2007 Wiley‐Liss, Inc.
Prenatal mortality in the rabbit Oryctolagus cuniculus.

( ) The amount and distribution of prenatal mortality was estimated in three groups of does: Group i, a series of 126 first and second pregnancies in seventy-three control does; Group 2, fifteen superovulated and sixteen control does, and Group 3, sixteen does having five ova transferred to one uterine horn and either fifteen or twenty ova transferred to the other uterine horn. (2) Approximately 5 % of the untreated does suffered total loss of their ova before implanta¬ tion. In does in which implantation occurred, the loss amounted to 9-7% of the ova before implantation and 18% of the embryos after implantation. After implantation the loss was distributed as follows:
Speed, accuracy, and confidence in Google, Ovid, PubMed, and UpToDate: results of a randomised trial

Background The explosion of biomedical information has led to an ‘information paradox’—the volume of biomedical information available has made it increasingly difficult to find relevant information when needed. It is thus increasingly critical for physicians to acquire a working knowledge of biomedical informatics. Aim To evaluate four search tools commonly used to answer clinical questions, in terms of accuracy, speed, and user confidence. Methods From December 2008 to June 2009, medical students, resident physicians, and attending physicians at the authors' institution were asked to answer a set of four anaesthesia and/or critical care based clinical questions, within 5 min, using Google, Ovid, PubMed, or UpToDate (only one search tool per question). At the end of each search, participants rated their results on a four point confidence scale. One to 3 weeks after answering the initial four questions, users were randomised to one of the four search tools, and asked to answer eight questions, four of which were repeated. The primary outcome was defined as a correct answer with the highest level of confidence. Results Google was the most popular search tool. Users of Google and UpToDate were more likely than users of PubMed to answer questions correctly. Subjects had the most confidence in UpToDate. Searches with Google and UpToDate were faster than searches with PubMed or Ovid. Conclusion Non-Medline based search tools are not inferior to Medline based search tools for purposes of answering evidence based anaesthesia and critical care questions.
Back-Contacted Silicon Heterojunction Solar Cells: Optical-Loss Analysis and Mitigation

We analyze the optical losses that occur in interdigitated back-contacted amorphous/crystalline silicon heterojunction solar cells. We show that in our devices, the main loss mechanisms are similar to those of two-side contacted heterojunction solar cells. These include reflection and escape-light losses, as well as parasitic absorption in the front passivation layers and rear contact stacks. We then provide practical guidelines to mitigate such reflection and parasitic absorption losses at the front side of our solar cells, aiming at increasing the short-circuit current density in actual devices. Applying these rules, we processed a back-contacted silicon heterojunction solar cell featuring a short-circuit current density of 40.9 mA/cm2 and a conversion efficiency of 22.0%. Finally, we show that further progress will require addressing the optical losses occurring at the rear electrodes of the back-contacted devices.
Corporate Governance Theories: From Micro Theories to National Systems Theories

The objective of this article is to conduct a survey of the different corporate governance theories. In the first part, we present the micro theories by opposing the disciplinary view to the knowledge-based view. The second part deals with the macro or national systems theories. We separate the theories based on appropriation of the organizational rent from those attributing a dominant role to production. This survey highlights that the financial view of corporate governance is a very particular case and presents many limits.
Billiards and Brains: Cognitive Ability and Behavior in a p-Beauty Contest

"Beauty contests" are well-studied, dominance-solvable games that generate two interesting results. First, most behavior does not conform to the unique Nash equilibrium. Second, there is considerable unexplained heterogeneity in behavior. In this work, we evaluate the relationship between beauty contest behavior and cognitive ability. We find that subjects with high cognitive ability exhibit behavior that is closer to the Nash equlibrium. We examine this finding through the prism of economic and biological theory.
Operation and performance of the ATLAS semiconductor tracker

The semiconductor tracker is a silicon microstrip detector forming part of the inner tracking system of the ATLAS experiment at the LHC. The operation and performance of the semiconductor tracker during the first years of LHC running are described. More than 99% of the detector modules were operational during this period, with an average intrinsic hit efficiency of (99.74±0.04)%. The evolution of the noise occupancy is discussed, and measurements of the Lorentz angle, δ-ray production and energy loss presented. The alignment of the detector is found to be stable at the few-micron level over long periods of time. Radiation damage measurements, which include the evolution of detector leakage currents, are found to be consistent with predictions and are used in the verification of radiation background simulations.
The Effects of Extrinsic Motivations and Satisfaction in Open Source Software Development

As a new phenomenon in the software industry, Open Source Software (OSS) development has attracted a high level of research interest. Examining what motivates participants in OSS projects and how to enhance the effects of motivations has received increased attention in recent years. This study is prompted by the significant but detail-lacking examination of differential effects of various types of extrinsic motivations on participants’ task effort in OSS projects and their interaction effects with participants’ psychological states. Drawing upon self-determination theory, we establish four types of extrinsic motivations in OSS communities (i.e., external, introjected, identified, and integrated motivation) and investigate how these types affect task effort differently. Also, integrating self-determination theory with affective event theory, we study how satisfaction of needs for competence, autonomy, and relatedness moderates the relationships between extrinsic motivations and task effort. The research model is largely supported by data from 250 participants in various OSS projects. Theoretical contribution and practical implications are discussed.
Microcystins: measuring human exposure and the impact on human health

Abstract Context: Freshwater cyanobacterial toxins, microcystins, may be a contributing factor to the development of hepatocellular cancer and colorectal cancer. Objectives: This review summarizes the toxicity data, exposure routes and the methodologies available to determine exposure to elucidate the relationship to liver and colorectal cancer. Methods: Literature searches were conducted using Medline, PubMed and Web of Science. Results: There is evidence of human poisonings resulting from exposure to microcystins, however current methods rely on targeted approaches only suitable for acute exposure. No methods exist for the determination of chronic exposure to microcystins. Conclusions: With the growing evidence of exposure to microcystins and the possible links to cancer, methods to measure medium to long-term human exposure are needed. The identification and validation of candidate biomarkers are key to undertaking urgently required epidemiological studies.
If you're happy and you know it, clap your hands! Survey design and the analysis of satisfaction

Surveys differ in the way they measure satisfaction and happiness, so comparative research findings are vulnerable to distortion by survey design differences. We examine this using the British Household Panel Survey, exploiting its changes in question design and parallel use of different interview modes. We find significant biases in econometric results, particularly for gender differences in attitudes to the wage and hours of work. Results suggest that the common empirical finding that women care less than men about their wage and more about their hours may be an artifact of survey design rather than a real behavioural difference.
Programming of Mice Circadian Photic Responses by Postnatal Light Environment

Early life programming has important consequences for future health and wellbeing. A key new aspect is the impact of perinatal light on the circadian system. Postnatal light environment will program circadian behavior, together with cell morphology and clock gene function within the suprachiasmatic nucleus (SCN) of the hypothalamus, the principal circadian clock in mammals. Nevertheless, it is still not clear whether the observed changes reflect a processing of an altered photic input from the retina, rather than an imprinting of the intrinsic molecular clock mechanisms. Here, we addressed the issue by systematically probing the mouse circadian system at various levels. Firstly, we used electroretinography, pupillometry and histology protocols to show that gross retinal function and morphology in the adult are largely independent of postnatal light experiences that modulate circadian photosensitivity. Secondly, we used circadian activity protocols to show that only the animal's behavioral responses to chronic light exposure, but not to constant darkness or the acute responses to a light stimulus depend on postnatal light experience. Thirdly, we used real-time PER2::LUC rhythm recording to show long-term changes in clock gene expression in the SCN, but also heart, lung and spleen. The data showed that perinatal light mainly targets the long-term adaptive responses of the circadian clock to environmental light, rather than the retina or intrinsic clock mechanisms. Finally, we found long-term effects on circadian peripheral clocks, suggesting far-reaching consequences for the animal's overall physiology.
On Closedness and Test Complexity of Logic Circuits

The concept of closedness of a set of logic functions under stuck-type faults is introduced. All sets of logic functions closed under stuck-type faults are classified. For the sets of logic functions closed under stuck-type faults, the test complexity and the universal test sets are considered. It is shown that for each class of linear functions, OR functions, and AND functions, both the minimum numbers of multiple fault detection tests and multiple fault location tests are exactly n + 1, where n is the number of inputs of the circuits, and that there exists universal test sets with n + 1 tests to detect and locate all multiple faults in such circuits.
Recurrence of major depressive disorder: towards a model of risk

Objective: Knowledge of the risk of recurrence after recovery of a major depressive disorder (MDD) is of clinical and scientific importance. The purpose of this paper is to provide a systematic review of the prevalence and predictors of recurrence of MDD. Method: Studies were searched in Medline en PsychINFO using the search terms ‘recur*’, ‘relaps*’, ‘depress*’, ‘predict*’ and course. Results: Recurrence of major depressive disorder in specialised mental health care settings is high (60% after 5 years, 67% after 10 years and 85% after 15 years) and seems lower in the general population (35% after 15 years). Number of previous episodes and subclinical residual symptoms appear to be the most important predictors. Gender, civil status, and socioeconomic status seem not related to the recurrence of MDD. Conclusion: Clinical factors seem the most important predictors of recurrence. Data from studies performed in the general population and primary care on the recurrent course of major depressive disorder are scarce.
Flavin reduction activates Drosophila cryptochrome

Significance Cryptochromes (CRYs) are photosensors that play central roles in the circadian rhythms of plants and animals. CRYs are related to photolyase DNA-repair enzymes, but instead of binding DNA, insect CRYs bind a C-terminal tail (CTT) α-helix in the pocket that holds the light-sensing flavin molecule. There is no consensus on how light activates Drosophila CRY (dCRY). We show that reduction of the flavin to the anionic semiquinone by light or chemicals releases the CTT to activate dCRY. The target of dCRY, the protein Timeless, contains a sequence similar to the CTT, and dCRY recognizes this sequence selectively in the light. This study supports a model for CRY signaling in which flavin reduction is the critical step performed by light. Entrainment of circadian rhythms in higher organisms relies on light-sensing proteins that communicate to cellular oscillators composed of delayed transcriptional feedback loops. The principal photoreceptor of the fly circadian clock, Drosophila cryptochrome (dCRY), contains a C-terminal tail (CTT) helix that binds beside a FAD cofactor and is essential for light signaling. Light reduces the dCRY FAD to an anionic semiquinone (ASQ) radical and increases CTT proteolytic susceptibility but does not lead to CTT chemical modification. Additional changes in proteolytic sensitivity and small-angle X-ray scattering define a conformational response of the protein to light that centers at the CTT but also involves regions remote from the flavin center. Reduction of the flavin is kinetically coupled to CTT rearrangement. Chemical reduction to either the ASQ or the fully reduced hydroquinone state produces the same conformational response as does light. The oscillator protein Timeless (TIM) contains a sequence similar to the CTT; the corresponding peptide binds dCRY in light and protects the flavin from oxidation. However, TIM mutants therein still undergo dCRY-mediated degradation. Thus, photoreduction to the ASQ releases the dCRY CTT and promotes binding to at least one region of TIM. Flavin reduction by either light or cellular reductants may be a general mechanism of CRY activation.
Control of the endonuclease activity of type I restriction‐modification systems is required to maintain chromosome integrity following homologous recombination

A type I restriction‐modification enzyme will bind to an unmethylated target sequence in DNA and, while still bound to the target, translocate DNA through the protein complex in both directions. DNA breakage occurs when two translocating complexes collide. However, if type I restriction‐modification systems bind to unmodified target sequences within the resident bacterial chromosome, as opposed to incoming ‘foreign’ DNA, their activity is curtailed; a process known as restriction alleviation (RA). We have identified two genes in Escherichia coli, rnhA and recG, mutations in which lead to the alleviation of restriction. Induction of RA in response to these mutations is consistent with the production of unmodified target sequences following DNA synthesis associated with both homologous recombination and R‐loop formation. This implies that a normal function of RA is to protect the bacterial chromosome when recombination generates unmodified products. For EcoKI, our experiments demonstrate the contribution of two pathways that serve to protect unmodified DNA in the bacterial chromosome: the primary pathway in which ClpXP degrades the restriction endonucleas and a mechanism dependent on the lar gene within Rac, a resident, defective prophage of E. coli K‐12. Previously, the potential of the second pathway has only been demonstrated when expression of lar has been elevated. Our data identify the effect of lar from the repressed prophage.
Event related potential studies of recognition memory for faces

The retrieval processes supporting recognition memory for faces were investigated using event-related potentials (ERPs) and behavioural measures. The ERP old/new effects elicited by faces were investigated in five experiments in which participants were required to distinguish between old and new (studied and non-studied) faces. A direct comparison between the ERP old/new effects elicited by faces and words in an old/new recognition memory task in Experiment 1 provided evidence for at least one common old/new effect, as well as evidence for a material-specific retrieval effect that was only present for faces. The subsequent experiments employed 'recognition confidence judgments' (Experiments 2 and 3) and 'source memory' manipulations (Experiments 4 and 5) to separate neural activity that might be tied to the processes of recollection and familiarity. Across the two recognition confidence experiments, reliable old/new effects were evident mainly for responses that attracted high confidence judgments, and there was little evidence for modulations that were sensitive to the level of recognition confidence systematically. These data indicate that ERPs index memory processes supporting face judgments that are linked to recollection. The two source memory experiments also revealed superior old/new effects which covered both frontal and parietal scalps and which were larger for those correct old responses that attracted correct rather than incorrect source judgments. The ERP data thus provides strong evidence for neural indices of recollection across all experiments. It might be regarded as surprising that, given the findings in ERP studies with verbal materials, no strong evidence for an ERP correlate of familiarity was found in the ERP data. In Experiment 4, a mid-frontal old/new effect in the 300-500ms time window was present for all correct old responses, and was insensitive to the source judgments, suggesting that this modulation is a neural index of familiarity. This pattern of data, however, was not replicated in Experiment 5 when a more rigorous separation between familiarity- and recollection-based responding was employed. These ERP findings are considered in the context of dual-process theories of recognition memory and their broad application across markedly different kinds of studied materials.
Time Domain Signal Analysis Using Wavelet Packet Decomposition Approach

This paper explains a study conducted based on wavelet packet transform techniques. In this paper the key idea underlying the construction of wavelet packet analysis (WPA) with various wavelet basis sets is elaborated. Since wavelet packet decomposition can provide more precise frequency resolution than wavelet decomposition the implementation of one dimensional wavelet packet transform and their usefulness in time signal analysis and synthesis is illustrated. A mother or basis wavelet is first chosen for five wavelet filter families such as Haar, Daubechies (Db4), Coiflet, Symlet and dmey. The signal is then decomposed to a set of scaled and translated versions of the mother wavelet also known as time and frequency parameters. Analysis and synthesis of the time signal is performed around 8 seconds to 25 seconds. This was conducted to determine the effect of the choice of mother wavelet on the time signals. Results are also prepared for the comparison of the signal at each decomposition level. The physical changes that are occurred during each decomposition level can be observed from the results. The results show that wavelet filter with WPA are useful for analysis and synthesis purpose. In terms of signal quality and the time required for the analysis and synthesis, the Haar wavelet has been seen to be the best mother wavelet. This is taken from the analysis of the signal to noise ratio (SNR) value which is around 300 dB to 315 dB for the four decomposition levels.
Likelihood Estimation of Lévy�?Driven Stochastic Volatility Models Through Realized Variance Measures

This paper studies the impact of jumps and leverage‐type effects on return and realized variance calculations when the logarithmic asset price is given by a stochastically scaled Levy process. Realized variance is not a consistent estimator of the integrated squared volatility process in such a modelling framework, but it can nevertheless be used within a quasi‐maximum likelihood setup to draw inference on the model parameters. This paper introduces a new methodology for deriving all cumulants of the returns and of the realized variance in explicit form by solving a recursive system of inhomogeneous ordinary differential equations.