Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Applications in Genetics and Molecular Biology

Peer ReviewedTitle:Validation in Genomics: CpG Island Methylation RevisitedAuthor:Segal, Mark R, University of California, San FranciscoPublication Date:12-01-2006Publication Info:Center for Bioinformatics and Molecular Biostatistics, UC San FranciscoPermalink:http://escholarship.org/uc/item/835236jgKeywords:multiple testing, cross-validation, local false discovery rate, classification, sequence featuresAbstract:In a recent article in PLoS Genetics, Bock et al., (2006) undertake an extensive computationalepigenetics analysis of the ability of DNA sequence-derived features, capturing attributes such astetramer frequencies, repeats and predicted structure, to predict the methylation status of CpGislands. Their suite of analyses appears highly rigorous with regard to accompanying validationprocedures, employing stringent Bonferroni corrections, stratified cross-validation, and follow-upexperimental verification. Here, however, we showcase concerns with the validation steps, in partascribable to the genome scale of the investigation, that serve as a cautionary note and indicatethe heightened need for careful selection of analytic and companion validation methods. A seriesof new analyses of the same CpG island methylation data helps illustrate these issues, not justfor this particular study, but also analogous investigations involving high-dimensional predictorswith complex between-feature dependencies.
A Qualitative Analysis of Edge Closure in Information Networks

Social Networks Analysis is one of the cutting edge research areas which finds applications in Information Retrieval and Data Mining and which deals with very large amounts of data. A considerable amount of research in this field has focused on mining useful information patterns in networks. Other applications have focused primarily on structure of networks. Several models have been proposed to address both issues. Existing models have been developed and replaced with better ones. One direction of this research has focused on how to implement one method of analysis on several data associations in order to understand how different data models behave. Responses to such questions account for the underlying differences in properties of the data considered. In its broadest sense, a community is a large set of nodes that have been collected over a period of time. In the present scenario efforts are being made to develop a complete model that can correctly explain and predict how links are formed in networks and how a network of nodes dynamically ”progresses” into a bigger and more diverse one. If an idea is implemented on networks derived from different domains the results can account for the underlying differences in the properties of the data. Such an approach is useful because it helps to find not only differences based on domain but also identify similarity and therefore to correlate one domain with another.
Diffuse porous melt flow and melt‐rock reaction in the mantle lithosphere at a slow‐spreading ridge: A structural petrology and LA‐ICP‐MS study of the Othris Peridotite Massif (Greece)

Harzburgites and plagioclase‐peridotites from the Othris Peridotite Massif in Central Greece preserve microstructural and petrological evidence for interaction with a melt which became saturated in orthopyroxene while migrating by km‐scale diffuse porous flow through the thermal boundary layer (TBL) and the base of the thermal lithosphere. The melt precipitated orthopyroxene, and eventually also plagioclase and clinopyroxene within the peridotites. Major and trace element geochemistry suggests that the melt was a depleted melt, i.e., a melt fraction from the melting column underneath a spreading centre produced by shallow melting of refractory peridotites. We see no evidence for the presence of boninitic melts. We argue that the melts in Othris migrated by diffuse porous flow as they crystallised orthopyroxenes and were therefore inherently unable to create their own high‐permeability melt channels. We propose that depleted melt fractions can remain isolated from deeper melt fractions, possibly already aggregated into a MORB‐like magma, because they migrate by different mechanisms through the TBL and the lithosphere.
Modeling parallel and reactive empathy in virtual agents: an inductive approach

Humans continuously assess one another's situational context, modify their own affective state, and then respond based on these outcomes through empathetic expression. Virtual agents should be capable of similarly empathizing with users in interactive environments. A key challenge posed by empathetic reasoning in virtual agents is determining whether to respond with parallel or reactive empathy. Parallel empathy refers to mere replication of another's affective state, whereas reactive empathy exhibits greater cognitive awareness and may lead to incongruent emotional responses (i.e., emotions different from the recipient's and perhaps intended to alter negative affect). Because empathy is not yet sufficiently well understood, it is unclear as to which type of empathy is most effective and under what circumstances they should be applied. Devising empirically informed models of empathy from observations of "empathy in action" may lead to virtual agents that can accurately respond in social situations. This paper proposes a unified inductive framework for modeling parallel and reactive empathy. First, in training sessions, a trainer guides a virtual agent through a series of problem-solving tasks in a learning environment and encounters empathetic characters. The proposed inductive architecture tracks situational data including actions, visited locations, intentions, and the trainer's physiological responses to generate models of empathy. Empathy models are used to drive runtime situation-appropriate empathetic behaviors by selecting suitable parallel or reactive empathetic expressions. An empirical evaluation of the approach in an interactive learning environment suggests that the induced empathy models can accurately assess social contexts and generate appropriate empathetic responses for virtual agent control.
The Efficacy and Safety of Imeglimin as Add-on Therapy in Patients With Type 2 Diabetes Inadequately Controlled With Metformin Monotherapy

OBJECTIVE A 12-week study assessed the efficacy and safety of a new oral antidiabetic agent, imeglimin, as add-on therapy in type 2 diabetes patients inadequately controlled with metformin alone. RESEARCH DESIGN AND METHODS A total of 156 patients were randomized 1:1 to receive imeglimin (1,500 mg twice a day) or placebo added to a stable dose of metformin (1,500–2,000 mg/day). Change in A1C from baseline was the primary efficacy outcome; secondary outcomes included fasting plasma glucose (FPG) and proinsulin/insulin ratio. RESULTS After 12 weeks, the placebo-subtracted decrease in A1C with metformin-imeglimin was −0.44% (P < 0.001). Metformin-imeglimin also significantly improved FPG and the proinsulin/insulin ratio from baseline (−0.91 mg/dL and −7.5, respectively) compared with metformin-placebo (0.36 mg/dL and 11.81). Metformin-imeglimin therapy was generally well-tolerated with a comparable safety profile to metformin-placebo. CONCLUSIONS Addition of imeglimin to metformin improved glycemic control and offers potential as a new treatment for type 2 diabetes.
Business analysis of web service repairability

In web-services compositions, in which a number of services is composed to create new value-added services, there can be failures of web services participating in the composition. In this work, two different repair actions on unsuccessful web services are considered, namely retry and substitution, and the impact of those repair actions has been analyzed from the business perspective. To analyze the impacts of these repair actions, we present a mathematical model for computing the economic value of the application. A tool based on this mathematical model has been implemented to give a comparative analysis of the repair actions.
Ambient wood: designing new forms of digital augmentation for learning outdoors

Ubiquitous and mobile technologies provide opportunities for designing novel learning experiences that move out of the classroom. Information can be presented and interacted with in a variety of ways while exploring a physical environment. A key issue this raises is when, where, what and how much? Our research is concerned with the design, delivery and interaction of digital information when learning about ecology outdoors. We present a framework of the different forms of digital augmentation and the different processes by which they can be accessed. Using the framework, we designed an outdoors learning experience, aimed at encouraging students to carry out contextualized scientific enquiry and to reflect on their interactions. Pairs of 11-12 year olds explored a woodland and were presented at certain times with different forms of digital augmentation. Our study showed that this kind of exploration promoted interpretation and reflection at a number of levels of abstraction.
Cellular Morphology and Physiology of the Perinatal Rat Cerebral Cortex

The cellular morphology and electrophysiology of the rat neocortex between embryonic day (E) 18 and postnatal day (P) 3 was studied in vitro by extracellular biocytin injections and whole-cell recordings, respectively. Most neurons were characterized by a small number of short-range dendrites and a main axon that was directed towards the white matter. Biocytin injections into the marginal zone and the cortical plate labeled far-reaching connections extending up to 2 mm in horizontal direction, indicating the existence of a dense network of long-range intrinsic projections in the neonatal cortex. Action potentials could be elicited as early as E18 and repetitive firing could first be observed at P0. Electrical stimulation of the immature cortex at various positions elicited polyphasic and long-lasting (up to 1 s) excitatory postsynaptic potentials and currents, which were significantly reduced in amplitude by a selective N-methyl-D-aspartate receptor antagonist. Our data indicate that the perinatal cortex manifests the structural and functional conditions for powerful excitatory interactions, which increase the likelihood for the generation of epileptiform activity during this developmental period.
Systems development methodologies: the problem of tenses

Presents two fundamental arguments. First, it is proposed that most of the currently available systems development methodologies are founded on concepts which emerged in the period from about 1967 to 1977. This argument is presented through the use of literature references. The second argument is that the profile of the development environment now faced in organizations is very different from that which prevailed in the period 1967 to 1977. This is illustrated through original empirical research which supports this argument, and by contrasting these findings with those of previous studies in the literature. It is therefore argued that there is a need to update “tenses” by deriving new methodological canons more appropriate to the needs of the current development environment. Some suggestions for new methodological canons appropriate to the current development environment are provided.
A robust framework for estimating linguistic alignment in social media conversations

When people talk, they tend to adopt the behaviors, gestures, and language of their conversational partners. This “accommodation” to one’s partners is largely automatic, but the degree to which it occurs is influenced by social factors, such as gender, relative power, and attraction. In settings where such social information is not known, this accommodation can be a useful cue for the missing information. This is especially important in web-based communication, where social dynamics are often fluid and rarely stated explicitly. But connecting accommodation and social dynamics on the web requires accurate quantification of the different amounts of accommodation being made. We focus specifically on accommodation in the form of “linguistic alignment”: the amount that one person’s word use is influenced by another’s. Previous studies have used many measures for linguistic alignment, with no clear standard. In this paper, we lay out a set of desiderata for a linguistic alignment measure, including robustness to sparse and short messages, explicit conditionality, and consistency across linguistic features with different baseline frequencies. We propose a straightforward and flexible model-based framework for calculating linguistic alignment, with a focus on the sparse data and limited social information observed in social media. We show that this alignment measure fulfills our desiderata on simulated data. We then analyze a large corpus of Twitter data, both replicating previous results and extending them: Our measure’s improved resolution reveals a previously undetectable effect of interpersonal power in social media interactions.
Evaluating the potential of IP-10 and MCP-2 as biomarkers for the diagnosis of tuberculosis

The aim of the present study was to evaluate the potential of diagnostic tests based on interferon-γ inducible protein (IP)-10 and monocyte chemotactic protein (MCP)-2, and compare the performance with the QuantiFERON TB® Gold In-Tube (QFT-IT; Cellestis, Carnagie, Australia) test. IP-10 and MCP-2 were determined in supernatants from whole blood stimulated with Mycobacterium tuberculosis-specific antigens. Samples were obtained from 80 patients with culture- and/or PCR-proven tuberculosis (TB), and 124 unexposed healthy controls: 86 high school students and 38 high school staff. IP-10 and MCP-2 test cut-offs were established based on receiver operating characteristic curve analysis. TB patients produced significantly higher levels (median) of IP-10 (2158 pg·mL−1) and MCP-2 (379 pg·mL−1) compared with interferon (IFN)-γ (215 pg·mL−1). The QFT-IT, IP-10 and MCP-2 tests detected 81, 83 and 71% of the TB patients; 0, 3 and 0% of the high school students and 0, 16 and 3% of the staff, respectively. Agreement between tests was high (>89%). By combining IP-10 and IFN-γ tests, the detection rate increased among TB patients to 90% without a significant increase in positive responders among the students. In conclusion, interferon-γ inducible protein-10 and monocyte chemotactic protein-2 responses to Mycobacterium tuberculosis-specific antigens could be used to diagnose infection. Combining interferon-γ inducible protein-10 and interferon-γ may be a simple approach to increase the detection rate of the Mycobacterium tuberculosis-specific in vitro tests.
Document Classification Using Expectation Maximization with Semi Supervised Learning

As the amount of online document increases, the demand for document classification to aid the analysis and management of document is increasing. Text is cheap, but information, in the form of knowing what classes a document belongs to, is expensive. The main purpose of this paper is to explain the expectation maximization technique of data mining to classify the document and to learn how to improve the accuracy while using semi-supervised approach. Expectation maximization algorithm is applied with both supervised and semi-supervised approach. It is found that semi-supervised approach is more accurate and effective. The main advantage of semi supervised approach is "Dynamically Generation of New Class". The algorithm first trains a classifier using the labeled document and probabilistically classifies the unlabeled documents. The car dataset for the evaluation purpose is collected from UCI repository dataset in which some changes have been done from our side.
Extending Web Application IDS Interface: Visualizing Intrusions in Geographic and Web Space

Web application intrusion detection systems (IDSs) are developed with the main objective is to detect web based intrusions as automatically as possible. As a result, these systems' user interfaces tend to be simple. This creates difficulties when further analyses based on these results are required. To make the outputs of web application IDSs more useful to security administrators, we propose an information visualization technique that displays intrusions as directed links starting in a geographic space and ending in a web space. The benefits in doing so are that it makes the display of intrusions clear, shows the overall results in a compact way, and supports user analysis in a natural manner. To evaluate the proposed technique, we implement a working prototype and use it to experiment with some test scenarios. The experiment results confirm the advantages of our approach compared to the traditional text based display.
Normal Molecular Repair Mechanisms in Regenerative Peripheral Nerve Interfaces Allow Recording of Early Spike Activity Despite Immature Myelination

Clinical use of neurally controlled prosthetics has advanced in recent years, but limitations still remain, including lacking fine motor control and sensory feedback. Indwelling multi-electrode arrays, cuff electrodes, and regenerative sieve electrodes have been reported to serve as peripheral neural interfaces, though long-term stability of the nerve-electrode interface has remained a formidable challenge. We recently developed a regenerative multi-electrode interface (REMI) that is able to record neural activity as early as seven days post-implantation. While this activity might represent normal neural depolarization during axonal regrowth, it can also be the result of altered nerve regeneration around the REMI. This study evaluated high-throughput expression levels of 84 genes involved in nerve injury and repair, and the histological changes that occur in parallel to this early neural activity. Animals exhibiting spike activity increased from 29% to 57% from 7 to 14 days following REMI implantation with a corresponding increase in firing rate of 113%. Two weeks after implantation, numbers of neurofilament-positive axons in the control and REMI implanted nerves were comparable, and in both cases the number of myelinated axons was low. During this time, expression levels of genes related to nerve injury and repair were similar in regenerated nerves, both in the presence or absence of the electrode array. Together, these results indicate that the early neural activity is intrinsic to the regenerating axons, and not induced by the REMI neurointerface.
Achieving computational and unconditional security in authentication watermarking: analysis, insights, and algorithms

This paper focuses on the analysis and enhancement of watermark-based security strategies for multimedia authentication. Based on an authentication game between a transmitter and its authorized receiver, and an opponent, security of authentication watermarking is measured by the opponent's inability to launch a successful attack. In this work, we consider two traditional classes of security for authentication: computational security and unconditional security. First we identify authentication watermarking as an error detection problem, which is different from error correction coding in robust watermarking. Then we analyze the computational and unconditional security requirements of an error detection code structure associated with quantization-based authentication watermarking schemes. We propose a novel security enhancement strategy that results in efficient and secure quantization-based embedding and verification algorithms. For computational security, cryptographic message authentication codes are incorporated while unconditional security is obtained by using unconditionally secure authentication codes. Both theoretical analysis and experimental results are presented. They show that using our approach, protection is achieved without significant increase in embedding distortion, and without sacrificing computational efficiency of the embedding and verification algorithms.
Antibody targeting of doxorubicin-loaded liposomes suppresses the growth and metastatic spread of established human lung tumor xenografts in severe combined immunodeficient mice.

Beta1 integrins, expressed on the cell surface of human non-small cell lung carcinomas, are used here as a target for the selective delivery of anti-cancer drug-loaded liposomes. Fab' fragments of a monoclonal antibody specific for human beta1 integrins were conjugated to sterically stabilized liposomes. Confocal microscopy of beta1 integrin-positive lung tumor cells incubated with fluorescently labeled anti-beta1 Fab immunoliposomes revealed a tumor-specific binding and efficient internalization of the liposomes into the tumor cells. The ability of these liposomes to deliver cytotoxic drugs to the tumor and kill these cells was demonstrated in vitro by incubating tumor cells with doxorubicin-loaded anti-beta1 Fab' immunoliposomes. The drug-loaded immunoliposomes were >30-fold more cytotoxic to the tumor cells than drug-loaded liposomes without antibody, nonspecific Fab' control immunoliposomes with drug or immunoliposomes without drug. The therapeutic efficacy of doxorubicin-loaded immunoliposomes was also evaluated in a metastatic human lung tumor xenograft/severe combined immunodeficient (SCID) mouse model. SCID mice that received i.v. injections of human lung tumor cells developed primary tumor nodules in the lung that subsequently metastasized to the liver and adrenal gland. Treatment of SCID mice bearing established lung tumor xenografts with doxorubicin-loaded anti-beta1 Fab immunoliposomes resulted in a significant suppression of tumor growth (monitored periodically by quantifying serum levels of a tumor marker), whereas tumors grew progressively in mice treated with control formulations. In addition to suppressing the growth of the primary lung tumor nodules, the immunoliposomes prevented the metastatic spread of the tumor to the liver and adrenal glands and increased the median survival time of the tumor-bearing mice. We conclude that Fab' immunoliposomes directed to tumor-associated integrins represent a potentially viable approach clinically for the selective delivery of drugs to solid tumors and may be useful in preventing the metastatic spread of lung cancer.
SocialStegDisc: Application of steganography in social networks to create a file system

In this paper, the concept named SocialStegDisc was introduced. This concept is as an application of the original idea of StegHash method which uses multimedia files as a carrier of hidden information and connects them logically with a mechanism of hashtags. SocialStegDisc is a new kind of mass-storage characterized by unlimited space and provides the set of operations on files: creation, reading, deletion and modification. Furthermore, the attempts to improve the operation of StegHash by trade-off between memory requirements and computation time are presented: a) an application of linked list structure; b) introduction of a dynamic verification of free addresses to the multimedia objects. The features, limitations and opportunities of the design were discussed.