Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitric Oxide Responsive Heavy Metal-Associated Gene AtHMAD1 Contributes to Development and Disease Resistance in Arabidopsis thaliana

Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.
On the distribution of the order and index of g(mod p) over residue classes

For a fixed rational number g 6∈ {−1, 0, 1} and integers a and d we consider the set Ng(a, d) of primes p for which the order of g(mod p) is congruent to a(mod d). For d = 4 and d = 3 we show that, under the Generalized Riemann Hypothesis (GRH), these sets have a natural density δg(a, d) and compute it. The results for d = 4 generalise earlier work by Chinen and Murata. The case d = 3 was apparently not considered before.
Data transfers in the grid: workload analysis of globus GridFTP

One of the basic services in grids is the transfer of data between remote machines. Files may be transferred at the explicit request of the user or as part of delegated resource management services, such as data replication or job scheduling. GridFTP is an important tool for such data transfers since it builds on the common FTP protocol, has a large user base with multiple implementations, and it uses the GSI security model that allows delegated operations. This paper presents a workload analysis of the implementation of the GridFTP protocol provided by the Globus Toolkit. We studied more than 1.5 years of traces reported from all over the world by Globus GridFTP installed components. Our study focuses on three dimensions: first, it quantifies the volume of data transferred and characterizes user behavior. Second, it attempts to show how tuning capabilities are used in practice. Finally, it quantifies the user base as recorded in the database and highlights the usage trends of this software component.
Complexity , Decision-Making and Cognitive Path Dependency : An Experimental Study

The development of path-dependent processes refers basically to positive feedback in terms of increasing returns as the main driving forces of such processes. It is assumed, however, that path dependency could also be affected by contextual factors such as different degrees of complexity. Up to now it is unclear whether and how complexity impacts path-dependent processes and the probability of lock-in. In this paper we investigate the relationship between complexity and path dependency by means of an experimental study. By focusing on the mode of information load and decision quality in chronological sequences, the study explores the impact of complexity on decision-making processes. The results are helpful for both the development of path-dependency theory and for a better understanding of decision-making behavior under conditions of positive feedback in different settings of complexity. As previous path research has applied qualitative case-study research and (to a minor part) simulations, this paper makes a further contribution by establishing experimental research for path-dependency issues.
Computing shortest paths with comparisons and additions

We present an undirected all-pairs shortest paths (APSP) algorithm which runs on a pointer machine in time <i>O</i>(<i>mn</i>α(<i>m,n</i>)) while making <i>O</i>(<i>mn</i>log α(<i>m, n</i>)) comparisons and additions, where <i>m</i> and <i>n</i> are the number of edges and vertices, respectively, and α(<i>m, n</i>) is Tarjan's inverse-Ackermann function. This improves upon all previous comparison & addition-based APSP algorithms when the graph is sparse, i.e., when <i>m</i> = <i>o</i>(<i>n</i> log <i>n</i>). At the heart of our APSP algorithm is a new single-source shortest paths algorithm which runs in time <i>O</i>(<i>m</i>α(<i>m, n</i>) + <i>n</i> log log <i>r</i>) on a pointer machine, where <i>r</i> is the ratio of the maximum-to-minimum edge length. So long as <i>r</i> < 2<sup><i>n</i><sup><i>o</i>(1)</sup></sup> this algorithm is faster than <i>any</i> implementation of Dijkstra's classical algorithm in the comparison-addition model.For <i>directed</i> graphs we give an <i>O</i>(<i>m + n</i> log <i>r</i>)-time comparison & addition-based SSSP algorithm on a pointer machine. Similar algorithms assuming integer weights or the RAM model were given earlier.
Send Orders of Reprints at Reprints@benthamscience.net a Comprehensive Study of Outcome after Lumber Discectomy for Lumbar Degenerative Spine Disease at 6 Months Post-operative Period

Study Design: A perspective case control study. Introduction and background data: The degenerative spine disease is a very common but complicated to treat and is prevalent in regions of Russia. The past decade has been witnessed with an increasing interest in evaluating the outcomes of medical care. Outcome research focuses on the meticulous measurement of symptoms, functional status, patient satisfaction with treatment, and health care costs associated with spinal treatment options. Whatsoever, no specific method exists that analyzes the effectiveness of the surgical procedures employed.
Entecavir plus tenofovir versus entecavir plus adefovir in chronic hepatitis B patients with a suboptimal response to lamivudine and adefovir combination therapy

Background/Aims We compared the efficacies of entecavir (ETV) plus tenofovir (TDF) and ETV plus adefovir (ADV) in chronic hepatitis B (CHB) patients with genotypic resistance to lamivudine (LAM) who showed a suboptimal response to LAM and ADV combination therapy. Methods We reviewed 63 CHB patients with genotypic resistance to LAM who showed a suboptimal response to LAM and ADV combination therapy. Among these patients, 30 were treated with ETV + ADV and 33 were treated with ETV + TDF for 12 months. Results The only baseline characteristic that differed significantly between the two groups was the ETV resistance profile. The rate of a virologic response [serum hepatitis B virus (HBV) DNA level of <20 IU/mL] was significant higher for ETV+TDF than for ETV+ADV over 12 months (57.6% vs. 23.3%, P=0.006, at 6 months; 84.8% vs. 26.7%, P<0.001, at 12 months). The probability of a virologic response was significantly increased in ETV+TDF (P<0.001, OR=54.78, 95% CI=7.15-419.54) and decreased in patients with higher baseline viral loads (P=0.001, OR=0.18, 95% CI=0.07-0.50) in multivariate analysis. No serious adverse event occurred during the study period. Conclusions In patients with CHB who showed a suboptimal response to LAM and ADV combination therapy, ETV+TDF was superior to ETV+ADV in achieving a virologic response regardless of the HBV resistance profile. Further large-scale and long-term follow-up prospective studies are needed to explain these results.
Perturbative and non-perturbative aspects of pure Script N = 1 super Yang-Mills theory from wrapped branes

The Maldacena-Nunez solution is generalized to include a number of integration constants, one of which controls the resolution of the singularity of the wrapped D5-brane background. Some features of the dual pure = 1 super Yang-Mills (SYM) theory are calculated, amongst which the gluino condensate, the beta function of the gauge coupling and a brane probe potential, which is related to the Veneziano-Yankielowicz effective potential. Each integration constant has a precise meaning in the dual SYM theory, e.g., the amount of non-perturbative SYM physics captured by the gravity configuration is described by the singularity resolution parameter.
Reduction in Noise-Induced Functional Loss of the Cochleae in Mice with Pre-Existing Cochlear Dysfunction Due to Genetic Interference of Prestin

Various cochlear pathologies, such as acoustic trauma, ototoxicity and age-related degeneration, cause hearing loss. These pre-existing hearing losses can alter cochlear responses to subsequent acoustic overstimulation. So far, the knowledge on the impacts of pre-existing hearing loss caused by genetic alteration of cochlear genes is limited. Prestin is the motor protein expressed exclusively in outer hair cells in the mammalian cochlea. This motor protein contributes to outer hair cell motility. At present, it is not clear how the interference of prestin function affects cochlear responses to acoustic overstimulation. To address this question, a genetic model of prestin dysfunction in mice was created by inserting an internal ribosome entry site (IRES)-CreERT2-FRT-Neo-FRT cassette into the prestin locus after the stop codon. Homozygous mice exhibit a threshold elevation of auditory brainstem responses with large individual variation. These mice also display a threshold elevation and a shift of the input/output function of the distortion product otoacoustic emission, suggesting a reduction in outer hair cell function. The disruption of prestin function reduces the threshold shifts caused by exposure to a loud noise at 120 dB (sound pressure level) for 1 h. This reduction is positively correlated with the level of pre-noise cochlear dysfunction and is accompanied by a reduced change in Cdh1 expression, suggesting a reduction in molecular responses to the acoustic overstimulation. Together, these results suggest that prestin interference reduces cochlear stress responses to acoustic overstimulation.
Sex Differences—A Silent Message? A Comparison Study of Parents’ Assessment and Junior High School Student's Self-Assessment of Learning Strengths and Interests

The relationship between the self-perceptions of twenty-three Junior High School gifted students from a middle- and upper-middle class socio-economic status community and their parents’ perceptions of learning strengths and interests on a forced-choice “Q-Sort” adapted by the author was examined to determine the effects of parents’ “self-fulfilling prophecies”. Special emphasis was given to correlations by sex of subjects and sex of parents, with particular focus on female subjects. Twenty-eight significant correlations (p = .05 or better) between mothers, fathers, and/or male/female subjects were determined. Results indicate that, despite efforts to avoid sexual stereotyping, parents generally favored “fundamentally male” characteristics for male subjects and “fundamentally female” characteristics for female subjects, while subjects themselves were less stereotypic than parents. A trend toward crossing traditional sex lines is indicated by subjects, leading to the conclusion that the way is open for gifted females to prophesy success for themselves and to reach self-fulfillment of these self-prophecies.
Mahalanobis-based one-class classification

Machine learning techniques have become very popular in the past decade for detecting nonlinear relations in large volumes of data. In particular, one-class classification algorithms have gained the interest of the researchers when the available samples in the training set refer to a unique/single class. In this paper, we propose a simple one-class classification approach based on the Mahalanobis distance. We make use of the advantages of kernel whitening and KPCA in order to compute the Mahalanobis distance in the feature space, by projecting the data into the subspace spanned by the most relevant eigenvectors of the covariance matrix. We also propose a sparse formulation of this approach. The tests are conducted on simulated data as well as on real data.
The Dynamics of Productivity in the Telecommunications Equipment Industry

Technological change and deregulation have caused a major restructuring of the telecommunications equipment industry over the last two decades. We estimate the parameters of a production function for the equipment industry and then use those estimates to analyze the evolution of plant level productivity over this period. The restructuring involved significant entry and exit and large changes in the sizes of incumbents. Since firms' choices on whether to liquidate and on the quantities of inputs demanded should they continue depend on their productivity, we use an equilibrium model to suggest an estimation algorithm that takes into account the relationship between productivity on the one hand. and both input demand and survival on the other. A fully parametric version of the estimation algorithm would be both computationally burdensome and require a host of auxiliary assumptions. So we develop a semi parametric technique which is both consistent with a quite general version of the theoretical framework and easy to use. The algorithm produces markedly different estimates of both production function parameters and of productivity movements than traditional estimation procedures. We find an increase in the rate of industry productivity growth after deregulation. This in spite of the fact there was no increase in the average of the plants' rates of productivity growth, and there was actually a fall in our index of the efficiency of the allocation of variable factors conditional on the existing distribution of fixed factors. Deregulation was, however, followed by a reallocation of capital towards more productive establishments (by a down sizing, often shutdown. of unproductive plants and by disproportionate growth of productive establishments) which more than offset the other factors' negative impacts on aggregate productivity.
Evaluation of Antioxidant and Antibacterial Potentials of Nigella sativa L. Suspension Cultures under Elicitation

Nigella sativa L. (family Ranunculaceae) is an annual herb of immense medicinal properties because of its major active components (i.e., thymoquinone (TQ), thymohydroquinone (THQ), and thymol (THY)). Plant tissue culture techniques like elicitation, Agrobacterium mediated transformation, hairy root culture, and so on, are applied for substantial metabolite production. This study enumerates the antibacterial and antioxidant potentials of N. sativa epicotyl suspension cultures under biotic and abiotic elicitation along with concentration optimization of the elicitors for enhanced TQ and THY production. Cultures under different concentrations of pectin and manganese chloride (MnCl2) elicitation (i.e., 5 mg/L, 10 mg/L, and 15 mg/L) showed that the control, MnCl2 10 mg/L, and pectin 15 mg/L suspension extracts greatly inhibited the growth of E. coli, S. typhimurium, and S. aureus (MIC against E. coli, i.e., 2.35 ± 0.8, 2.4 ± 0.2, and 2.46 ± 0.5, resp.). Elicitation decreased SOD enzyme activity whereas CAT enzyme activity increased remarkably under MnCl2 elicitation. MnCl2 10 mg/L and pectin 15 mg/L elicitation enhanced the DPPH radical inhibition ability, but ferric scavenging activity was comparable to the control. TQ and THY were quantified by LC-MS/MS in the cultures with high bioactive properties revealing maximum content under MnCl2 10 mg/L elicitation. Therefore, MnCl2 elicitation can be undertaken on large scale for sustainable metabolite production.
Fatty Acid Deposition on Broiler Meat in Chickens Supplemented with Tuna Oil

The aim of the present study was to evaluate the effect of feeding four levels of tuna oil on performance and fatty acid (FA) profiles of broiler chicken meat. 240 Ross broiler chickens were randomly assigned to 20 pens and divided into four treatments: 0%, 0.75%, 1%, and 1.25% of tuna oil. At 49 days, breast and legs-thighs muscles were processed for FA analysis. Concentrations of FA in legs and thighs meat were significantly higher when compared with breast meat. In both types of meats (breast and legs-thighs), the inclusion of 1.0% or 1.25% of tuna oil in the diet significantly increased (P < 0.05) the concentration of n-3 FA (especially docosahexaenoic and eicosapentaenoic acids). Fat in broiler breast contained a proportion of 29% saturated FA (SFA): 36% monosaturated FA (MFA): 35% polyunsaturated FA (PUFA); while legs and thighs meat had a proportion of 28% SFA: 38% MFA: 33% PUFA. The addition of tuna oil in the broiler diet significantly reduced the deposition of SFA, MFA, and PUFA in breast meat, while in legs and thighs these reductions were less noticeable. The significant reduction in the concentration of n-6 PUFA and the increment of n-3 PUFA were more evident in breast than in legs and thighs, and with the addition of 1% and 1.25% of tuna oil. The results of the present study suggest a difference in FA deposition attributable to supplementation with tuna oil. The addition of tuna oil could be recommendable to increase n-3 PUFA in both broiler chicken breast and legs-thighs meats, providing a healthier and functional chicken meat to consumer.
The expression pattern of Adam10 in the central nervous system of adult mice: Detection by in situ hybridization combined with immunohistochemistry staining

ADAM10 (a disintegrin and metalloprotease 10) is a member of the ADAMs family, which is key in the development of the nervous system, by regulating proliferation, migration, differentiation and survival of various cells, including axonal growth and myelination. Previous studies have investigated the embryonic or postnatal expression of ADAM10, however, detailed information regarding its cellular distribution in the adult stage, to the best of our knowledge, is not available. The present study investigated the expression pattern of the ADAM10 gene in the adult mouse central nervous system (CNS) using an ADAM10 complementary RNA probe for in situ hybridization (ISH). Immunohistochemical staining was used to identify the type of the ISH staining-positive cells with neuron- or astrocyte-specific antibodies. The results of the current study demonstrated that the ADAM10 gene was predominantly expressed in the neurons of the cerebral cortex, hippocampus, thalamus and cerebellar granular cells in adult mouse CNS.
Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons

Activating transcription factor 5 (ATF5) is a member of the ATF/cAMP response element-binding family of transcription factors, which compose a large group of basic region leucine zipper proteins whose members mediate diverse transcriptional regulatory functions. ATF5 has a well-established prosurvival activity and has been found to be overexpressed in several human cancers, in particular glioblastoma. However, the role(s) of ATF5 in development and normal physiology are unknown. Here we address this issue by deriving and characterizing homozygous Atf5 knockout mice. We find that Atf5−/− pups die neonatally, which, as explained below, is consistent with an olfactory defect resulting in a competitive suckling deficit. We show that Atf5 is highly expressed in olfactory sensory neurons (OSNs) in the main olfactory epithelium starting from embryonic stage 11.5 through adulthood. Immunostaining experiments with OSN-specific markers reveal that ATF5 is expressed in some immature OSNs and in all mature OSNs. Expression profiling and immunostaining experiments indicate that loss of Atf5 leads to a massive reduction in mature OSNs resulting from a differentiation defect and the induction of apoptosis. Ectopic expression of Atf5 in neural progenitor cells induces expression of multiple OSN-specific genes. Collectively, our results suggest a model in which Atf5 is first expressed in immature OSNs and the resultant ATF5 functions to promote differentiation into mature OSNs. Thus, ATF5 is required for terminal differentiation and survival of OSNs.
Author ' s personal copy Data-driven modeling of Alzheimer Disease pathogenesis

Alzheimer Disease (AD) is the most prevalent form of dementia and the sixth leading cause of death in developed world. A substantial amount of data concerning the pathogenesis of this neurological disorder is available, but the complexity of the interactions they reveal makes it difficult to reason about them. This paper describes a computational model that represents known facts concerning AD pathophysiology and demonstrates the implications of those facts in the aggregate. The computational model is written in a mathematical language known as Maude. Because a Maude specification is an executable mathematical theory, it can be used not only to simulate but also to logically analyze the system it models. This model is based on the amyloid hypothesis, which posits that AD results from the build-up of the peptide beta-amyloid. The AD model represents beta-amyloid regulation, and shows through model analysis how that regulation can be disrupted through the interaction of pathological processes such as cerebrovascular insufficiency, inflammation, and oxidative stress. The model demonstrates many other effects that depend in complex ways on interactions between elements. It also shows how treatments directed at multiple targets could be more effective at reducing betaamyloid than single-target therapies, and it makes several experimentally testable predictions. The work demonstrates that modeling AD as an executable mathematical theory using a specification language such as Maude is a viable adjunct to experiment, which allows insights and predictions to be derived that take more of the relevant biology into account than would be possible without the aid of the computational model. & 2011 Elsevier Ltd. All rights reserved.
Social Interaction History: A Framework for Supporting Exploration of Social Information Spaces

Social interaction history refers to traces of social interaction in information spaces. These traces have potential to help users explore and navigate through information spaces. In digital spaces, however, past records of social interaction are often hidden or underutilized. As a result, users cannot use social navigation to guide their movement while browsing information collections. We developed a conceptual framework for using social interaction history to improve information exploration. The basic hypothesis of our framework is that social interaction history can serve as a good indicator of the potential value of information items. We tested our hypothesis by performing statistical analysis of a data set from a social web application. The results supported our hypothesis: there were significant positive relationships between traces of social interaction and the degree of interestingness of web articles. We discuss the implications of these findings for the design of social applications and the potential applications of social interaction history in various domains.