Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices

Recent technological developments in genetic screening approaches have offered the means to start exploring quantitative genotype-phenotype relationships on a large-scale. What remains unclear is the extent to which the quantitative genetic interaction datasets can distinguish the broad spectrum of interaction classes, as compared to existing information on mutation pairs associated with both positive and negative interactions, and whether the scoring of varying degrees of such epistatic effects could be improved by computational means. To address these questions, we introduce here a computational approach for improving the quantitative discrimination power encoded in the genetic interaction screening data. Our matrix approximation model decomposes the original double-mutant fitness matrix into separate components, representing variability across the array and query mutants, which can be utilized for estimating and correcting the single-mutant fitness effects, respectively. When applied to three large-scale quantitative interaction datasets in yeast, we could improve the accuracy of scoring various interaction classes beyond that obtained with the original fitness data, especially in synthetic genetic array (SGA) and in genetic interaction mapping (GIM) datasets. In addition to the known pairs of interactions used in the evaluation of the computational approach, a number of novel interaction pairs were also predicted, along with underlying biological mechanisms, which remained undetected by the original datasets. It was shown that the optimal choice of the scoring function depends heavily on the screening approach and on the interaction class under analysis. Moreover, a simple preprocessing of the fitness matrix could further enhance the discrimination power of the epistatic miniarray profiling (E-MAP) dataset. These systematic evaluation results provide in-depth information on the optimal analysis of the future, large-scale screening experiments. In general, the modeling framework, enabling accurate identification and classification of genetic interactions, provides a solid basis for completing and mining the genetic interaction networks in yeast and other organisms.
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

Transcription factor (TF) perturbation experiments give valuable insights into gene regulation. Genome-scale evidence from microarray measurements may be used to identify regulatory interactions between TFs and targets. Recently, Hu and colleagues published a comprehensive study covering 269 TF knockout mutants for the yeast Saccharomyces cerevisiae. However, the information that can be extracted from this valuable dataset is limited by the method employed to process the microarray data. Here, we present a reanalysis of the original data using improved statistical techniques freely available from the BioConductor project. We identify over 100 000 differentially expressed genes—nine times the total reported by Hu et al. We validate the biological significance of these genes by assessing their functions, the occurrence of upstream TF-binding sites, and the prevalence of protein–protein interactions. The reanalysed dataset outperforms the original across all measures, indicating that we have uncovered a vastly expanded list of relevant targets. In summary, this work presents a high-quality reanalysis that maximizes the information contained in the Hu et al. compendium. The dataset is available from ArrayExpress (accession: E-MTAB-109) and it will be invaluable to any scientist interested in the yeast transcriptional regulatory system.
Deformation Monitoring by Long Term D-InSAR Analysis in Three Gorges Area, China

After the Three Gorges Dam began to function in China in 2003, the water level of the Yangtze River in Three Gorges area rose more than 100 meters. The impact of the man-made reservoir caused by the dam on the surroundings is becoming the object of several studies. In this paper we make use of two long term D-InSAR techniques, the quasi-permanent scatterer technique (QPS) and the Stanford Method for Persistent Scatterer (StaMPS), to measure the deformation trends in Badong, Three Gorges area, China. The results obtained by the two processing tools with the same focused and co-registered data sets are analyzed and compared. Two subsidence areas are identified by both techniques. However, since the QPS analysis is able to process partially coherent targets, many more points are extracted than in StaMPS, and more information can be retrieved.
Determinants of Analyst Forecasting Accuracy

This paper examines recent trends in sell-side analyst forecast accuracy, with a particular focus on the industry of the firm being forecasted. Using median forecast data from 2000-2013 as provided by I/B/E/S, this study provides evidence indicating that forecast accuracy has been steadily decreasing over the sample period and that forecast dispersion has been steadily increasing. In addition, it finds that there are significant differences in forecast accuracy by industry. Finally, this study confirms the findings of prior research. Many of the factors found in prior studies as significant, remain significant even in the face of recent regulatory and economic changes. These factors include the size of the firm, the analyst coverage, the type of earnings and the change in earnings.
The Role of Spontaneous Retrieval, Monitoring and Sustained Attention in Prospective Memory

According to the Multiprocess Theory (Einstein and McDaniel, 1990), prospective memory is supported by two separate cognitive processes: monitoring and spontaneous retrieval. Successful monitoring during prospective memory tasks requires attention to be divided between separate stimuli and the attention needs to be sustained throughout the course of the task. However, this theoretical account also allows for prospective memory in the absence of monitoring, as in cases where memory is retrieved spontaneously in response to some cue. In the course of this study, support for the Multiprocess Theory has been found. Using a dual-task paradigm, prospective memory targets were displayed during a lexical decision task where participants were required to make a word/nonword decision to letter strings. Prospective memory targets were found using both monitoring and spontaneous retrieval, although displaying the target in the focus of attention or not did not differentially induce monitoring. A small increase from 2% target presentation rates (Experiments 1 through 3) to 3% target presentation rates (Experiment 4) did produce evidence of task interference that reflects monitoring; however, increasing target presentation rates to 5% did not increase reaction times above those found with 3% target presentation rates. Focal prospective memory targets (words) had higher accuracy rates than nonfocal prospective memory targets (words starting with letter "g"). Inhibiting responses to the lexical decision task to respond to prospective memory targets encouraged priorities to shift attention to the lexical decision task and increased the speed of lexical decision responding across the extended task. No evidence was found to support the hypothesis that sustained attention is identical to, or even a significant component of, monitoring. Sustained attention was not necessary to accomplish the prospective memory action, as variables affecting vigilance were not found to influence prospective-memory performance in the extended version of the dual-task paradigm used in this experiment. In Experiment 3, draining attention resources did negatively affect lexical decision reaction times and prospective memory performance with focal targets, but not with nonfocal targets. The strength of the lexical decision task routine was manipulated by varying the number of lexical decision practice trials given before the dual-task in Experiment 5. The strength of the routine did not affect task interference for focal or nonfocal targets. Overall, monitoring did not follow the sustainedattention pattern observed in vigilance. Prospective memory can be performed utilizing both cognitive mechanisms of monitoring and spontaneous retrieval. INDEX WORDS: Prospective memory, Attention, Vigilance, Sustained attention, Monitoring THE ROLE OF SPONTANEOUS RETRIEVAL, MONITORING AND SUSTAINED ATTENTION IN PROSPECTIVE
The hochschild cohomology ring of a class of special biserial algebras

We consider a class of self-injective special biserial algebras ΛN over a field K and show that the Hochschild cohomology ring of dΛN is a finitely generated K-algebra. Moreover, the Hochschild cohomology ring of ΛN modulo nilpotence is a finitely generated commutative K-algebra of Krull dimension two. As a consequence the conjecture of [N. Snashall and O. Solberg, Support varieties and Hochschild cohomology rings, Proc. London Math. Soc.88 (2004) 705–732], concerning the Hochschild cohomology ring modulo nilpotence, holds for this class of algebras.
Animal Diseases Caused by Orbiviruses, Algeria

Antibodies against bluetongue virus were detected in cattle, sheep, goats, and camels in Algeria in 2008. Antibodies against epizootic hemorrhagic disease virus were detected in cattle, but antibodies against African horse sickness virus were not detected in horses and mules. Epizootic hemorrhagic disease in northern Africa poses a major risk for the European Union.
Ocean Acoustic Waveguide Remote Sensing (OAWRS) of marine ecosystems

Abstract : Ocean Acoustic Waveguide Remote Sensing (OAWRS) has recently been shown to becapable of instantaneously imaging and continuously monitoring fish populations over continentalshelf-scale areas, covering thousands of km2. We show how OAWRS can be used in a variety ofoceanic ecosystems to remotely assess populations and study the behavior of fish and other marineorganisms, such as Antarctic krill, to help the study of marine ecology and the ecosystem-basedapproach to fisheries management.
Common Molecular Etiologies Are Rare in Nonsyndromic Tibetan Chinese Patients with Hearing Impairment

Background Thirty thousand infants are born every year with congenital hearing impairment in mainland China. Racial and regional factors are important in clinical diagnosis of genetic deafness. However, molecular etiology of hearing impairment in the Tibetan Chinese population living in the Tibetan Plateau has not been investigated. To provide appropriate genetic testing and counseling to Tibetan families, we investigated molecular etiology of nonsyndromic deafness in this population. Methods A total of 114 unrelated deaf Tibetan children from the Tibet Autonomous Region were enrolled. Five prominent deafness-related genes, GJB2, SLC26A4, GJB6, POU3F4, and mtDNA 12S rRNA, were analyzed. Inner ear development was evaluated by temporal CT. A total of 106 Tibetan hearing normal individuals were included as genetic controls. For radiological comparison, 120 patients, mainly of Han ethnicity, with sensorineural hearing loss were analyzed by temporal CT. Results None of the Tibetan patients carried diallelic GJB2 or SLC26A4 mutations. Two patients with a history of aminoglycoside usage carried homogeneous mtDNA 12S rRNA A1555G mutation. Two controls were homozygous for 12S rRNA A1555G. There were no mutations in GJB6 or POU3F4. A diagnosis of inner ear malformation was made in 20.18% of the Tibetan patients and 21.67% of the Han deaf group. Enlarged vestibular aqueduct, the most common inner ear deformity, was not found in theTibetan patients, but was seen in 18.33% of the Han patients. Common molecular etiologies, GJB2 and SLC26A4 mutations, were rare in the Tibetan Chinese deaf population. Conclusion The mutation spectrum of hearing loss differs significantly between Chinese Tibetan patients and Han patients. The incidence of inner ear malformation in Tibetans is almost as high as that in Han deaf patients, but the types of malformation vary greatly. Hypoxia and special environment in plateau may be one cause of developmental inner ear deformity in this population.
Contribution à une théorie explicative des systèmes de contrôle et d'incitation des responsables de divisions et de filiales

A travers cette recherche, nous tentons de construire une theorie explicative des systemes de controle et d'incitation des responsables de divisions et de filiales. Nous "rentrons" dans les grandes firmes industrielles pour analyser, a la lumiere des theories contractuelles des organisations et de la theorie de la contingence, les dimensions de ces systemes. Celles-ci consistent principalement en la repartition de l'autorite sur la prise de decision, l'evaluation et l'incitation. Au niveau des responsables d'unites, les mecanismes incitatifs qui jouent un grand role sont les promotions, les bonus et les plans d'options sur actions. Deux objectifs principaux sont poursuivis. Premierement, il s'agit d'etudier les relations entre, d'une part, les modalites de controle et d'incitation des responsables d'unites, et, d'autre part, les caracteristiques des firmes, des unites et des responsables eux-memes. Deuxiemement, il s'agit d'analyser les implications du choix du statut juridique de l'unite (division ou filiale a 100%) sur le controle de son responsable. Nous avons constitue un echantillon de 199 responsables d'unites qui appartiennent a 104 grandes firmes industrielles francaises et etrangeres. Nous avons obtenu de nombreux resultats concernant l'influence des caracteristiques des responsables et des entites auxquelles ils appartiennent sur les mecanismes de controle et d'incitation. Ensuite, un certain nombre d'interactions entre ces mecanismes ont ete mises en evidence. Enfin, nous avons eclaire les effets du choix du statut juridique de l'unite sur ces mecanismes.
An Exact Bayes Test of Asset Pricing Models with Application to International Markets

This paper develops and implements an exact finite-sample test of asset pricing models with time-varying risk premia using posterior probabilities. The strength of our approach is that it allows multiple conditional asset pricing specifications, both nested and nonnested, to be tested and compared simultaneously. We apply our procedure to international equity markets by testing and comparing the international Capital Asset Pricing Model (ICAPM) and conditional ICAPM versions of Fama and French (1998). The empirical evidence suggests that the best performing model is the ICAPM with the value premium constructed based on global earnings-to-price ratio.
Pushdown automata for user interface management

An interactive pushdown automaton is defined as a model for user interface management dialogue control. The relationships between dialogue control and device handling are defined in terms of acquiring, releasing, enabling, and disabling of devices. Input modes are defined by sets of acquired devices and input states are defined by sets of enabled devices. A specified automaton describes the dialogue. Semantic controls of parse transitions, as well as pervasive transitions for exceptional conditions, are supported in the automaton. Algorithms are given to convert a specified automaton into an executable automaton. For the executable automaton an interpretation algorithm, which incorporates the control of input modes and states, is given. Examples are given for how various features present in other user interface management systems are modeled using the IPDA.
Features of Gastric and Colonic Mucosa in Congenital Enteropathies: A Study in Histology and Immunohistochemistry

Congenital enteropathies comprise a constellation of rare clinicopathologic diagnoses characterized by intractable watery diarrhea and failure to thrive in infants. These diagnoses include, but are not limited to, tufting enteropathy (TE), microvillous inclusion disease (MID), and enteroendocrine cell dysgenesis (EED). Commonly, the diagnosis is based on identification of their characteristic histologic and/or ultrastructural features in small intestinal mucosa. In cases in which the changes in the small intestine are inconclusive or a small intestine biopsy is not performed, the diagnosis can be hampered or significantly delayed. We describe the histologic features and immunohistochemical staining patterns of gastric and colonic mucosa in patients with confirmed TE (3), MID (2), and EED (1). Specifically, focal epithelial tufts were found in the gastric mucosa of one TE patient and multifocally in the colonic mucosa of another. All TE patients showed complete loss of membranous epithelial EpCAM expression in gastric and colonic mucosa, characteristic of the diagnosis. Gastric biopsies were available in 1 patient with MID; this showed focal disruption of the gastric glandular architecture. Three colon biopsies and 1 resection from 2 patients with MID showed characteristic cytoplasmic vacuoles and periodic acid-Schiff/villin-positive cytoplasmic inclusions. Chromogranin stains showed complete absence of enteroendocrine cells within the colon and a normal distribution in the gastric mucosa of the EED patient. On the basis of our findings, we conclude that the characteristic histologic and immunohistochemical features associated with the small intestine can be confirmed within the gastric and/or colonic mucosa by careful histologic examination and immunohistochemistry.
Avoiding the Non-Detection Zone of Passive Loss-of-Mains (Islanding) Relays for Synchronous Generation by Using Low Bandwidth Control Loops and Controlled Reactive Power Mismatches

Generation connected to electrical distribution systems requires reliable and timely detection of loss-of-mains (islanding). Passive loss-of-mains detection relays typically use measurements of parameters such as frequency, phase, and the magnitudes of voltage and current. If a part of the power network becomes islanded and there is a very close match between generation and demand of both active and reactive power, there is a risk that the relay will not be able to detect the loss-of-mains (LOM) event quickly, or perhaps at all. This is the “non-detection zone” or NDZ. This paper proposes a combination of 2 generator control techniques which allow the NDZ to be avoided even when the generator has significant inertia. Firstly, the natural instability (when islanded) of a grid-connected control scheme consisting of integral and droop controls is recognized and exploited. Secondly, a simple strategy is added which makes occasional small, steady-state adjustments to the reactive power output of the generator. The scheme has been tested in the laboratory and shows that the 2 second detection time required by IEEE 1547 can be achieved, even when an exact match of active power generation and demand is initially configured, and the generator has a significant inertia.
African Women’s Theology, Gender Relations, and Family Systems Theory: Pastoral Theological Considerations and Guidelines for Care and Counseling

African women theologians have written extensively about problems in gender relations in African contexts, identifying oppressive elements and their effects on women's self-concept and status in the church, family, and society. This book provides much-needed pastoral theological attention and a response to the psychospiritual, relational, and sociocultural effects of gender injustice and marginalization of women. It critically examines concepts, methods, and principles of family systems theory, analyzes gender relations in African families and churches, and develops a theology of pastoral care (based on the Trinitarian concept of perichoresis) that offers pastoral guidelines for effective pastoral counseling with women and men, as well as recommendations for corrective and preventative care grounded in educational strategies. The paradigm of pastoral care that emerges attends both to women affected by gender injustice and to the sociocultural norms that cause distress and perpetuate gender oppression.
Graphical Representation of Climate-Based Daylight Performance to Support Architectural Design

Abstract Many conventional daylighting design tools are limited in that each simulation represents only one time of year and time of day (or a single, theoretical overcast sky condition). Since daylight is so variable – due to the movement of the sun, changing seasons, and diverse weather conditions – one moment is hardly representative of the overall quality of the daylighting design, which is why climate-based, dynamic performance metrics like Daylight Autonomy (DA) and Useful Daylight Illuminance (UDI) are so needed. Going one step further, the annual variation in performance (condensed to a percentage by DA and UDI) is also valuable information, as is the ability to link this data to spatial visualizations and renderings. Trying to realize this combination of analytical needs using existing tools would become an overly time-consuming and tedious process. The challenge is to provide all information necessary to early design stage decision-making in a manageable form, while retaining the continuity of annual data. This paper introduces a climate data simplification method based on a splitting of the year into 56 periods, over which weather conditions are “averaged” and simulated using Perez's ASRCCIE sky model, while information on sun penetration is provided at a greater resolution. The graphical output of the produced data in the form of “Temporal Maps” will be shown to be visually, and even numerically, comparable to reference case maps created using short time step calculations and based on illuminance data generated by Daysim.
Summary of "Growth and nutritional status in pediatric Crohn's disease" with a focus on sex differences in statural growth impairment.

Received March 20, 2011 From the UCSF Benioff C Francisco, California. Address correspondence 500 Parnassus Aven Hepatology, and Nutr Francisco, CA 94143 The author received supp Children’s Digestive Colitis Foundation of CCFA Career Develo PCRC Clinical Res UCSF-CTSI grant no The author reports no co Copyright # 2011 by E Hepatology, and Nut Gastroenterology, He DOI: 10.1097/MPG.0b01 Vasseur F, Gower-Rousseau C, Vernier-Massouille G, et al. Nutritional status and growth in pediatric Crohn’s disease: a population-based study. Am J Gastroenterol 2010;105:1893–90
Advantages and considerations in the confirmation of mitochondrial DNA mutations by denaturing HPLC and pyrosequencing

Human mitochondrial DNA (mtDNA) encodes 13 polypeptides essential for oxidative phosphorylation. Because of the unique features of “replicative segregation” and “threshold expression” of mtDNA genetics, identification of homoplasmy versus heteroplasmy status is critical. Results from various detection methods may lead to different interpretations on formation or outcome of mtDNA mutations, such as the conclusion of somatic mutation versus genetic drift in cancers. Denaturing high‐performance liquid chromatography (DHPLC) and pyrosequencing (PSQ) have recently been employed to confirm the presence of heteroplasmy of mtDNA because of their high sensitivity in detecting heteroplasmic mutations compared with direct sequencing. Moreover, PSQ has superior ability in quantifying percentage of heteroplasmy. However, there could be disagreement between these two techniques and several issues specific for mtDNA should be taken into consideration. Particularly, DHPLC analysis should be more prone to be interfered by nuclear mitochondrial sequences (Numts), if it is coamplified with mtDNA, than PSQ analysis.