Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth

Background The successful achievement of early ovarian folliculogenesis is important for fertility and reproductive life span. This complex biological process requires the appropriate expression of numerous genes at each developmental stage, in each follicular compartment. Relatively little is known at present about the molecular mechanisms that drive this process, and most gene expression studies have been performed in rodents and without considering the different follicular compartments. Results We used RNA-seq technology to explore the sheep transcriptome during early ovarian follicular development in the two main compartments: oocytes and granulosa cells. We documented the differential expression of 3,015 genes during this phase and described the gene expression dynamic specific to these compartments. We showed that important steps occurred during primary/secondary transition in sheep. We also described the in vivo molecular course of a number of pathways. In oocytes, these pathways documented the chronology of the acquisition of meiotic competence, migration and cellular organization, while in granulosa cells they concerned adhesion, the formation of cytoplasmic projections and steroid synthesis. This study proposes the involvement in this process of several members of the integrin and BMP families. The expression of genes such as Kruppel-like factor 9 (KLF9) and BMP binding endothelial regulator (BMPER) was highlighted for the first time during early follicular development, and their proteins were also predicted to be involved in gene regulation. Finally, we selected a data set of 24 biomarkers that enabled the discrimination of early follicular stages and thus offer a molecular signature of early follicular growth. This set of biomarkers includes known genes such as SPO11 meiotic protein covalently bound to DSB (SPO11), bone morphogenetic protein 15 (BMP15) and WEE1 homolog 2 (S. pombe)(WEE2) which play critical roles in follicular development but other biomarkers are also likely to play significant roles in this process. Conclusions To our knowledge, this is the first in vivo spatio-temporal exploration of transcriptomes derived from early follicles in sheep.
Agent based Protégé plugin for ontology alignment

Ontologies are extensively used to strcuture the domain knowledge. Nowadays, with the large amount of ontologies already available, there is a high demand for reusing the knowledge in existing ontologies. Since ontologies are complex structures, sharing of knowledge coming from various ontologies has become a tedious task. Ontology alignment is a popular knowledge sharing technique that is used to share information between heterogeneous information systems. There are numerous techniques for the alignment of ontologies, and the field still faces many challenges. Due to the inherent nature of multiple relationships among the ontologies, it postulates that the Multi-Agent System technology is a better technology to automate the ontology alignment with little human intervention. This paper presents multi-agent based approach for ontology alignment developed as a plug in for the popular ontological modelling environment known as Protégé. It simulates how different processes interactively operate inside the human mind to perform certain activities intelligently. Indeed, the proposed solution uses agent communication, negotiation, and coordination as the primary method of exploring the semantic relationships between the ontologies. The generated ontology could be used as a shared understanding between information systems that are running on input ontologies. The success of the proposed approach was evaluated by using two ontologies of agricultural domain. It was evident that the system could discover over 70% accurate semantic relationships, and thus, the authors claim that the proposed approach could resolve the complexity in ontology alignment for certain extend.
In vivo formation of 8-iso-prostaglandin f2alpha and platelet activation in diabetes mellitus: effects of improved metabolic control and vitamin E supplementation.

BACKGROUND Diabetes mellitus (DM) is associated with enhanced lipid peroxidation and persistent platelet activation. We tested the hypothesis that the in vivo formation of the F2-isoprostane 8-iso-prostaglandin (PG)F2alpha, a bioactive product of arachidonic acid peroxidation, is enhanced in DM and contributes to platelet activation. METHODS AND RESULTS Urine samples were obtained from 85 diabetic patients and 85 age- and sex-matched healthy subjects for measurement of immunoreactive 8-iso-PGF2alpha and 11-dehydro-thromboxane B2 (TXM), an in vivo index of platelet activation. Sixty-two had non-insulin-dependent (NID)DM, and 23 had insulin-dependent (ID) DM. Vitamin E supplementation, metabolic control, and cyclooxygenase inhibitors were used to investigate the mechanisms of formation of 8-iso-PGF2alpha in this setting. Urinary 8-iso-PGF2alpha excretion was significantly higher (P=0.0001) in NIDDM patients (419+/-208 pg/mg creatinine; range 160 to 1014) than in age-matched control subjects (208+/-92; 41 to 433). Urinary 8-iso-PGF2alpha was linearly correlated with blood glucose and urinary TXM. 8-iso-PGF2alpha excretion was also significantly (P=0. 0001) higher in IDDM patients (400+/-146; 183 to 702) than in control subjects (197+/-69; 95 to 353). Vitamin E supplementation (600 mg/d for 14 days) was associated with a statistically significant reduction in both urinary 8-iso-PGF2alpha (by 37%) and TXM (by 43%) in 10 NIDDM patients. Improved metabolic control was associated with a significant (P=0.0001) reduction in 8-iso-PGF2alpha and TXM excretion by 32% and 41%, respectively, in 21 NIDDM patients. 8-iso-PGF2alpha was unchanged after 2-week dosing with aspirin and indobufen despite profound suppression of TXM excretion. CONCLUSIONS We conclude that DM is associated with increased formation of F2-isoprostanes, as a correlate of impaired glycemic control and enhanced lipid peroxidation. This may provide an important biochemical link between impaired glycemic control and persistent platelet activation. These results provide a rationale for dose-finding studies of antioxidant treatment in diabetes.
A novel variable step size constant modulus algorithm based on autocorrelation of error signal for blind equalization

A novel variable step size constant modulus algorithm (VSS-CMA) based on autocorrelation of error signal has been proposed to improve the weakness of previous VSS-CMAs for application to blind equalization in this paper. Computer simulations have been performed to illustrate the performance of the proposed method in frequency selective Rayleigh fading channels. The obtained simulation results using WiMAX (IEEE 802.16–2004) radio standard have demonstrated that the proposed VSS-CMA algorithm has considerably better performance than conventional CMA, normalized CMA (N-CMA) and the other VSS-CMA algorithms.
Hierarchical VHDL libraries for DSP ASIC design

Methods are presented for the rapid design of DSP ASICs based on the use of hierarchical VHDL libraries. These are portable across many silicon foundries and allow complex DSP silicon systems to be developed in a fraction of the time normally required. Resulting designs are highly competitive with ones created using conventional methods. The approach is illustrated by its application to ADPCM codec and DCT cores.
The Impact of Impression Management on Purchase Intentions in Online Auctions: The Moderating Effects of Relationship Norms

The IT-mediated nature of e-commerce creates the uncertainty in online buyer-seller relationships where online buyers are difficult to personally scrutinize sellers, leading to many challenges for online sellers to win buyers’ trust. In order to overcome this problem, according to impression management theory and relationship theory, this research proposes a research framework for understanding how impression management tactics can be used by sellers to create a positive impression in the minds of buyers, affect buyers’ trust in the sellers, and subsequently purchase from them. This research further examines the moderating role of relationship norms on the relationship between impression management tactics and trust. A Web-based survey is then conducted in Yahoo! Taiwan auction to validate our proposed framework. Our research is expected to contribute to the theories by first examining the impression management theory and relationship theory in the context of online auctions. We also expect to contribute to the practice by illustrating that sellers should adjust their impression management tactics to suit buyers’ relationship norms. Specifically, self-focused tactics are more useful for buyers in an exchange relationship; other-focused tactics are more effective for buyers in a communal relationship.
Polycation gene delivery systems: escape from endosomes to cytosol

Clinical success of gene therapy based on oligonucleotides (ODNs), ribozymes, RNA and DNA will be greatly dependent on the availability of effective delivery systems. Polycations have gained increasing attention as a non‐viral gene delivery vector in the past decades. Significant progress has been made in understanding complex formation between polycations and nucleic acids, entry of the complex into the cells and subsequent entry into the nucleus. Sophisticated molecular architectures of cationic polymers have made the vectors more stable and less susceptible to binding by enzymes or proteins. Incorporation of specific ligands to polycations has resulted in more cell‐specific uptake by receptor‐mediated mechanisms. However, there are still other barriers limiting the transfection efficiency of polycation gene delivery systems. There is a consensus that polycation‐DNA complexes (polyplexes) enter cells via the endocytotic pathway. It is not clearly understood, however, how the polyplexes escape (if they do) from endosomes, how DNA is released from the polyplexes or how the released DNA is expressed. The primary focus of this article is to review various polycation gene delivery systems, which are designed to translocate DNA from endosomes into cytosol. Many polycation gene delivery systems have tried to mimic the mechanisms that viruses use for the endosomal escape. Polycation gene delivery systems are usually coupled with synthetic amphipathic peptides mimicking viral fusogenic peptides, histidine‐based gene delivery systems for pH‐responsive endosomal escape, polycations with intrinsic endosomolytic activity by the proton sponge mechanism and polyanions to mimic the anionic amphiphilic peptides.
Lithium ion batteries as key component for energy storage in automotive and stationary applications

The lithium ion technology was introduced to the market in 1990/1991 and series production has been established in the mid 1990ies. Within only a few years, the lithium ion system has become the market leader in the rechargeable small format battery market. Lithium ion batteries are used world-wide in practically all modern portable consumer electronics, such as notebooks, mobile phones, camcorders and cameras. Due to the local concentration of the consumer electronics production in the far east countries, the experience and know how with cell manufacturing is in a considerable part limited to these countries as well.
Brain MRI Measurements at a Term-Equivalent Age and Their Relationship to Neurodevelopmental Outcomes

BACKGROUND AND PURPOSE: An increased prevalence of disabilities is being observed as more preterm infants survive. This study was conducted to evaluate correlations between brain MR imaging measurements taken at a term-equivalent age and neurodevelopmental outcome at 2 years' corrected age among very low–birth-weight infants. MATERIALS AND METHODS: Of the various brain MR imaging measurements obtained at term-equivalent ages, reproducible measurements of the transcerebellar diameter and anteroposterior length of the corpus callosum on sagittal images were compared with neurodevelopmental outcomes evaluated by the Bayley Scales of Infant Development (II) at 2 years' corrected age (mean ± standard deviation, 16.1 ± 6.4 months of age). RESULTS: Ninety infants were enrolled. The mean gestational age at birth was 27 weeks and the mean birth weight was 805.5 g. A short corpus callosal length was associated with a Mental Developmental Index <70 (P = .047) and high-risk or diagnosed cerebral palsy (P = .049). A small transcerebellar diameter was associated with a Psychomotor Developmental Index <70 (P = .003), Mental Developmental Index <70 (P = .004), and major neurologic disability (P = .006). CONCLUSIONS: A small transcerebellar diameter and short corpus callosal length on brain MR imaging at a term-equivalent age are related to adverse neurodevelopmental outcomes at a corrected age of 2 years and could be a useful adjunctive tool for counseling parents about future developmental outcomes.
G-quadruplexes and their regulatory roles in biology

‘If G-quadruplexes form so readily in vitro, Nature will have found a way of using them in vivo’ (Statement by Aaron Klug over 30 years ago). During the last decade, four-stranded helical structures called G-quadruplex (or G4) have emerged from being a structural curiosity observed in vitro, to being recognized as a possible nucleic acid based mechanism for regulating multiple biological processes in vivo. The sequencing of many genomes has revealed that they are rich in sequence motifs that have the potential to form G-quadruplexes and that their location is non-random, correlating with functionally important genomic regions. In this short review, we summarize recent evidence for the in vivo presence and function of DNA and RNA G-quadruplexes in various cellular pathways including DNA replication, gene expression and telomere maintenance. We also highlight remaining open questions that will have to be addressed in the future.
Mechanized Network Origin and Path Authenticity Proofs

A secure routing infrastructure is vital for secure and reliable Internet services. Source authentication and path validation are two fundamental primitives for building a more secure and reliable Internet. Although several protocols have been proposed to implement these primitives, they have not been formally analyzed for their security guarantees. In this paper, we apply proof techniques for verifying cryptographic protocols (e.g., key exchange protocols) to analyzing network protocols. We encode LS2, a program logic for reasoning about programs that execute in an adversarial environment, in Coq. We also encode protocol-specific data structures, predicates, and axioms. To analyze a source-routing protocol that uses chained MACs to provide origin and path validation, we construct Coq proofs to show that the protocol satisfies its desired properties. To the best of our knowledge, we are the first to formalize origin and path authenticity properties, and mechanize proofs that chained MACs can provide the desired authenticity properties.
On the joint use of propensity and prognostic scores in estimation of the average treatment effect on the treated: a simulation study

Propensity and prognostic score methods seek to improve the quality of causal inference in non‐randomized or observational studies by replicating the conditions found in a controlled experiment, at least with respect to observed characteristics. Propensity scores model receipt of the treatment of interest; prognostic scores model the potential outcome under a single treatment condition. While the popularity of propensity score methods continues to grow, prognostic score methods and methods combining propensity and prognostic scores have thus far received little attention. To this end, we performed a simulation study that compared subclassification and full matching on a single estimated propensity or prognostic score with three approaches combining the estimated propensity and prognostic scores: full matching on a Mahalanobis distance combining the estimated propensity and prognostic scores (FULL–MAHAL); full matching on the estimated prognostic propensity score within propensity score calipers (FULL–PGPPTY); and subclassification on an estimated propensity and prognostic score grid with 5 × 5 subclasses (SUBCLASS(5*5)). We considered settings in which one, both, or neither score model was misspecified. The data generating mechanisms varied in the degree of linearity and additivity in the true treatment assignment and outcome models. FULL–MAHAL and FULL–PGPPTY exhibited strong to superior performance in root mean square error terms across all simulation settings and scenarios. Methods combining propensity and prognostic scores were no less robust to model misspecification than single‐score methods even when both score models were incorrectly specified. Our findings support the joint use of propensity and prognostic scores in estimation of the average treatment effect on the treated. Copyright © 2013 John Wiley & Sons, Ltd.
Poor sleep in middle-aged women is not associated with menopause per se

Whether sleep problems of menopausal women are associated with vasomotor symptoms and/or changes in estrogen levels associated with menopause or age-related changes in sleep architecture is unclear. This study aimed to determine if poor sleep in middle-aged women is correlated with menopause. This study recruited women seeking care for the first time at the menopause outpatient department of our hospital. Inclusion criteria were an age ≥40 years, not taking any medications for menopausal symptoms, and no sleeping problems or depression. Patients were assessed with the Pittsburgh Sleep Quality Index (PSQI), modified Kupperman Index (KI), and Menopause Rating Scale (MRS). A PSQI score of <7 indicated no sleep disorder and ≥7 indicated a sleep disorder. Blood specimens were analyzed for follicle-stimulating hormone and estradiol levels. A total of 244 women were included in the study; 103 (42.2%) were identified as having a sleep disorder and 141 as not having one. In addition, 156 (64%) women were postmenopausal and 88 (36%) were not menopausal. Follicle-stimulating hormone and estradiol levels were similar between the groups. Patients with a sleep disorder had a significantly higher total modified KI score and total MRS score (both, P<0.001) compared with those without a sleep disorder. Correlations of the PSQI total score with the KI and MRS were similar in menopausal and non-menopausal women. These results do not support that menopause per se specifically contributes to sleep problems.
Identifying Functional Groups by Finding Cliques and Near-Cliques in Protein Interaction Networks

Many cellular processes are performed by a group of proteins rather than by individual proteins. When visualized in a protein-protein interaction network, proteins in a same biological unit often form a highly connected subgraph but loosely connected to the rest of the network. Therefore, finding a highly connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a protein-protein interaction network. Analysis of the interaction network of yeast proteins demonstrates that 77% of the near-cliques identified by our algorithm have at least one function shared by all the proteins within a near- clique, and that 68% of the near-cliques show a good agreement with experimentally determined protein complexes catalogued in MIPS.
Measuring performance of continuous-time stochastic processes using timed automata

We propose deterministic timed automata (DTA) as a model-independent language for specifying performance and dependability measures over continuous-time stochastic processes. Technically, these measures are defined as limit frequencies of locations (control states) of a DTA that observes computations of a given stochastic process. Then, we study the properties of DTA measures over semi-Markov processes in greater detail. We show that DTA measures over semi-Markov processes are well-defined with probability one, and there are only finitely many values that can be assumed by these measures with positive probability. We also give an algorithm which approximates these values and the associated probabilities up to an arbitrarily small given precision. Thus, we obtain a general and effective framework for analysing DTA measures over semi-Markov processes.
On the non-phenomenological use of the word ‘ behaviour ’ in adaptive behaviour and robotics research

Since Simon[1] and Brooks[2], robotics researchers have understood that the behaviour of a robot system is a function of the structure and dynamics of its physical construction, the environment in which it finds itself, and its internal control system. Simultaneous with the growth in popularity of this view there has been an increasing use of the word ‘behaviour’ to refer to non-phenomenological objects. It is now common to refer to a subroutine in a robot controller as a ‘behaviour’, the word designating a set of instructions rather than the outcome of those instructions as they are executed. We believe that behaviour-as-subroutine is an unhelpful word, because it implies that the subroutine is the entire cause of the robot’s visible, external actions. It confuses the subroutine with the observable behaviour of the system. This is in conflict with the most important ideas behind adaptive systems, behaviour-based robotics and ethology, in which behaviour is considered the result of coupled interaction between active controller components, physical construction and environment. This paper presents some examples and a simple experiment to show that the two meanings of ‘behaviour’ are distinct and incompatible. We suggest that the non-phenomenological use of the word ‘behaviour’ is an unhelpful mistake and assert the usefulness of the classical meaning.
Experiences with performance tradeoffs in practical, continuous indoor localization

This paper describes our experiences and observations with a localization system that continuously tracks the indoor location of a large number of consumer mobile devices. Unlike past work that focuses principally on the accuracy of the location tracking algorithm, we study the performance of the localization system in terms of key additional metrics: scalability and energy-efficiency, which can sometimes conflict with the desire for high accuracy. To ensure that our solution can handle both Android and iOS-based mobile devices (& other closed mobile platforms), we adapt the conventional client-side fingerprinting-based localization approaches to develop a novel and practical infrastructure-based location tracking strategy. We study the relative accuracy to the two approaches in two different types of indoor buildings. Our studies establish how the building and its occupancy characteristics affect the accuracy achievable by different algorithms, and provide insights into why scalable, energy efficient and accurate indoor location tracking remains a challenge in practice.
ISERN 0005 1 Resource Estimation in Software Engineering

This paper presents a comprehensive overview of the state of the art in software resource estimation. We describe common estimation methods and also provide an evaluation framework to systematically compare and assess alternative estimation methods. Though we have tried to be as precise and objective as possible, it is inevitable that such a comparison exercise be somewhat subjective. We however, provide as much information as possible, so that the reader can form his or her own opinion on the methods to employ. We also discuss the applications of such estimation methods and provide practical guidelines.