Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression analysis of microRNA cluster based on isomiRs from high throughput DNA sequencing data

MicroRNAs (miRNAs) are single-stranded noncoding small RNAs, frequently expressed as clusters. The co-expressed miRNA clusters are pivotal in coordinately regulating multiple processes, including embryonic development, cell cycles and cell differentiation. In the study, relative expression analysis of miRNA cluster was performed based on isomiRs from high throughput DNA sequencing data using SOLiD2122; system. Similar expression pattern of miRNA cluster was detected by analyzing the most abundant isomiR and multiple isomiRs, respectively. According to all the multiple isomiRs, miRNA* species always had fewer sequence counts and indicated different expression patterns with their miRNAs. Although co-transcribed from a single promoter as a single polycistronic transcript, miRNAs in gene cluster showed distinct levels. Inconsistent expression levels also could be detected after normalization of sequence counts despite degree of divergence was largely reduced. The difference of expression pattern might result from miRNA half-life because of degradation degree and rate. Inconsistent expression levels of members in miRNA cluster maybe contribute to complex biological processes in particular developmental contexts at specific times. The expression patterns according to the most abundant isomiR and all the multiple isomiRs are consistent, and relative expression analysis based on sequence counts and isomiRs from high throughput sequencing data provides a feasible method to analyze different miRNAs.
Can Human Verb Associations Help Identify Salient Features for Semantic Verb Classification?

This paper investigates whether human associations to verbs as collected in a web experiment can help us to identify salient verb features for semantic verb classes. Assuming that the associations model aspects of verb meaning, we apply a clustering to the verbs, as based on the associations, and validate the resulting verb classes against standard approaches to semantic verb classes, i.e. GermaNet and FrameNet. Then, various clusterings of the same verbs are performed on the basis of standard corpus-based types, and evaluated against the association-based clustering as well as GermaNet and FrameNet classes. We hypothesise that the corpus-based clusterings are better if the instantiations of the feature types show more overlap with the verb associations, and that the associations therefore help to identify salient feature types.
Acquisition of Scientific Literatures based on Citation-reason Visualization

When carrying out scientific research, the first step is to acquire relevant papers. It is easy to grab vast numbers of papers by inputting a keyword into a digital library or an online search engine. However, reading all the retrieved papers to find the most relevant ones is agonizingly time-consuming. Previous works have tried to improve paper search by clustering papers with their mutual similarity based on reference relations, including limited use of the type of citation (e.g. providing background vs. using specific method or data). However, previously proposed methods only classify or organize the papers from one point of view, and hence not flexible enough for user or context-specific demands. Moreover, none of the previous works has built a practical system based on a paper database. In this paper, we first establish a paper database from an open-access paper source, then use machine learning to automatically predict the reason for each citation between papers, and finally visualize the resulting information in an application system to help users more efficiently find the papers relevant to their personal uses. User studies employing the system show the effectiveness of our approach.
Learning about Art History by Exploratory Search, Contextual View and Social Tags

In order to develop a learning environment for art history, we adopted concepts from art education and information technology. In contrast to other user-interfaces for art-databases, we created the explorARTorium1 to compare artworks along different dimensions without having to rely on textual information that excludes people without sophisticated knowledge of art history. Instead, artworks are presented in context among different categories like the oeuvre of the artist, the topic and theme of an artwork as well as the geographical region and time period the artwork was created in. Additional concepts of the explorARTorium are social tagging and tag- clouds. By evaluating the main concepts of the explorARTorium we provide proof that users follow and apply these concepts.
The Need for Trauma-Sensitive Language Use in Literacy and Health Literacy Screening Instruments

The authors recently began a research study, funded by the National Institute of Mental Health, aimed at increasing the understanding of the ways in which limited literacy affects the lives of people with serious mental illness. In preparing for the study, the authors reviewed many health literacy screens and assessments for their appropriateness in public urban mental health settings. The Rapid Estimate of Adult Literacy in Medicine and the Test of Functional Health Literacy in Adults, perhaps the most frequently used assessments of health literacy, involve assessments that include lists of words that the test-taker must choose from or read. Each of these instruments includes language that is potentially triggering for trauma survivors, particularly those with posttraumatic stress disorder (PTSD). The research participants for the current project are consumers of mental health services, and thus, the authors believe it is essential to remove the problematic language, given that the likelihood of a diagnosis of PTSD and/or a history of abuse is higher than average among this population. However, the authors argue that this issue applies to anyone who administers these instruments, because sexual assault and abuse, as well as PTSD diagnoses, are certainly not confined to those who seek mental health services. The authors' aim is not only to call attention to the use of triggering language in existing literacy and health-related assessments and research instruments, but also to advocate that others take similar steps toward embracing more sensitive language by removing or replacing words that may cause unnecessary stress, anxiety, or pain to those who are at increased risk of retraumatization.
An Intervention Based on Video Feedback and Questioning to Improve Tactical Knowledge in Expert Female Volleyball Players

This study applied an intervention program, based on video feedback and questioning, to expert female volleyball players to improve their tactical knowledge. The sample consisted of eight female attackers (26 ± 2.6 years old) from the Spanish National Volleyball Team, who were divided into an experimental group (n = 4) and a control group (n = 4). The video feedback and questioning program applied in the study was developed over eight reflective sessions and consisted of three phases: viewing of the selected actions, self-analysis and reflection by the attacker, and joint player–coach analysis. The attackers were videotaped in an actual game and four clips (situations) of each of the attackers were chosen for each reflective session. Two of the clips showed a correct action by the attacker, and two showed an incorrect decision. Tactical knowledge was measured by problem representation with a verbal protocol. The members of the experimental group showed adaptations in long-term memory, significantly improving their tactical knowledge. With respect to conceptual content, there was an increase in the total number of conditions verbalized by the players; with respect to conceptual sophistication, there was an increase in the indication of appropriate conditions with two or more details; and finally, with respect to conceptual structure, there was an increase in the use of double or triple conceptual structures. The intervention program, based on video feedback and questioning, in addition to on-court training sessions of expert volleyball players, appears to improve the athletes’ tactical knowledge.
Improving Electrical Safety in the Workplace: Applying Prevention Through Design to Voltage Testing

Fundamental to an electrical safety program is establishing electrically safe work conditions. De-energizing equipment, following adequate lockout/tagout procedures, and verifying the absence of voltage are key to accomplishing this. As industry strives to make the practice of de-energizing equipment before performing electrical work standard practice, verifying the absence of voltage has become one of the most frequent tasks performed by qualified electrical workers.
Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3

Integrins are heterodimeric cell surface adhesion and signaling receptors that are essential for metazoan existence. Some integrins contain an I-domain that is a major ligand binding site. The ligands preferentially engage the active forms of the integrins and trigger signaling cascades that alter numerous cell functions. Here we found that the adenylate cyclase toxin (CyaA), a key virulence factor of the whooping cough agent Bordetella pertussis, preferentially binds an inactive form of the integrin complement receptor 3 (CR3), using a site outside of its I-domain. CyaA binding did not trigger downstream signaling of CR3 in human monocytes and CyaA-catalyzed elevation of cAMP effectively blocked CR3 signaling initiated by a natural ligand. This unprecedented type of integrin-ligand interaction distinguishes CyaA from all other known ligands of the I-domain-containing integrins and provides a mechanistic insight into the previously observed central role of CyaA in the pathogenesis of B. pertussis. DOI: http://dx.doi. org/10.7554/eLife.10766. 001
Source transformation, analysis and generation in TXL

The TXL transformation framework has been widely used in practical source transformation tasks in industry and academia for many years. At the core of the framework is the TXL language, a functional programming language specifically designed for expressing source transformation tasks. TXL programs are self-contained, specifying and implementing all aspects of parsing, pattern matching, transformation rules, application strategies and unparsing in a single uniform notation with no dependence on other tools or technologies. Programs are directly interpreted by the TXL processor without any compile or build step, making it particularly well suited to rapid turnaround, test-driven development. In this paper we provide a practical introduction to using TXL in rapidly developing source transformations from concrete examples, and review experience in applying TXL to a number of practical large scale applications in source code analysis, renovation and migration.
On the security of HMM-based speaker verification systems against imposture using synthetic speech

For speaker verification systems, security against imposture is one of the most important problems, and many approaches to reducing false acceptance of impostors as well as false rejection of clients have been investigated. On the other hand, imposture using synthetic speech has not been considered. In this paper, we investigate imposture against speaker verification systems using synthetic speech. We use an HMM-based text-prompted speaker verification system with a false acceptance rate of 0% for human impostors as a reference system, and adopt a trainable HMM-based speech synthesis system for imposture. Experimental results show that false acceptance rates for synthetic speech reached over 70% by training the synthesis system using only 1 sentence from each customer, and current security of HMM-based speaker verification systems against synthetic speech is inadequate.
Histopathological changes in venous grafts and in varicose and non-varicose veins.

AIMS--To examine veins histologically from different sites in the body to study the effect of venous pressure; and to examine veins used as aortocoronary grafts. METHODS--The axillary vein, femoral vein at the inguinal ligament, the short saphenous vein at the knee and the long saphenous vein at the ankle were removed from 24 necropsy cases of patients aged 2 months to 80 years. Fifteen varicose saphenous veins and 12 aortocoronary grafts removed at surgery were obtained. All were examined histologically. RESULTS--Varying degrees of intimal thickening composed of collagen, elastin, and smooth muscle were found. These changes were most noticeable in the varicose veins. Intimal changes were also seen related to valves and to adjacent arteries. No clinically relevant lipid was seen in the native veins, though atheromatous changes were seen in the grafts. CONCLUSIONS--Venous changes are related to venous pressure, to local haemodynamic effects, and probably to hypoxia. The changes are often focal and seem to be sequential in their formation. True atheroma is seen in the aortocoronary grafts but is not seen in native veins and this may be the result of additional factors.
Approaching multi-lingual emotion recognition from speech - on language dependency of acoustic/prosodic features for anger recognition

In this paper, we describe experiments on automatic Emotion Recognition using comparable speech corpora collected from real-life American English and German Interactive Voice Response systems. We compute the optimal set of acoustic and prosodic features for mono-, crossand multi-lingual anger recognition, and analyze the differences. When an emotion recognition system is confronted with a language it has not been trained on we normally observe a severe system degradation. Analyzing this loss we report on strategies to combine the feature spaces with and without combining and retraining the mono-lingual systems. We report classification scores and feature sets for various cases, and estimate the relative importance of features on both databases. We compare the feature distribution and feature ranks by evaluating information gain ratio. After final system integration, we obtain a single bi-lingual anger recognition system which performs just as well as two separate mono-lingual systems on the test data.
Dynamic Database Integration in a JDBC Driver

Current integration techniques are unsuitable for large-scale integrations involving numerous heterogeneous data sources. Existing methods either require the user to know the semantics of all data sources or they impose a static global view that is not tolerant of schema evolution. These assumptions are not valid in many environments. We present a different approach to integration based on annotation. The contribution is the elimination of the bottleneck of global view construction by moving the complicated task of identifying semantics to local annotators instead of global integrators. This allows the integration to be more automated, scaleable, and rapidly deployable. The algorithms are packaged in an embedded database engine contained in a JDBC driver capable of dynamically integrating data sources. Experimental results demonstrate that the Unity JDBC driver efficiently integrates data located in separate data sources with minimal overhead.
Characterization of molecular and atomic species adsorbed on ferroelectric and semiconductor surfaces

BHARATH, SATYAVEDA CHAVI. Characterization of Molecular and Atomic Species Adsorbed on Ferroelectric and Semiconductor Surfaces. (Under the direction of Thomas P. Pearl and Gerd Duscher). In order to clarify the mechanisms behind the adsorption of atomic and molecular species adsorbed on ferroelectric surfaces, single crystalline lithium niobate (LiNbO3, LN), ‘Z-cut’ along the (0001) plane, has been prepared, characterized and subsequently exposed to molecular and atomic species. 4-n-octyl-4′-cyanobiphenyl (8CB) liquid crystal was chosen as a polar molecule for our model system for this study. Low-energy electron diffraction (LEED), atomic force microscopy (AFM), surface contact angles (CA), and X-ray photoelectron spectroscopy (XPS) were used to characterize the surface of LN as well as the nature of the liquid crystal films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. Also, for the purpose of gaining a fundamental understanding of low coverage interactions of metal atoms on ferroelectric surfaces, we choose to deposit gold onto the LN surface. These gold atomic layers were grown under UHV conditions and characterized. Understanding anchoring mechanisms and thin film organization for LC molecules and metal atoms on uniformly poled surfaces allows for a fuller appreciation of how molecular deposition of other polarizable molecules on patterned poled LN surfaces would occur as well as yielding greater insight on the atomic characteristics of metal on ferroelectric interfaces. Also, to reveal the mechanisms involved in the adsorption of organic aromatic molecules on high-index Si surfaces, thiophene (C4H4S) and pyrrole (C4H5N) molecules were dosed on prepared Si(5 5 12)-2x1 surfaces as our experimental system. The Si(5 5 12) surface was prepared to produce a 2x1 reconstruction after which molecules were dosed at low exposure to observe the preferred adsorption sites on the surface. All surface preparation and experiments were performed in UHV and measurements of the surface before and after deposition were performed using scanning tunneling microscopy (STM). Fundamental understanding of organic nanostructures on Si(5 5 12) surfaces will yield a broader appreciation of the mechanisms that drive the creation of these nanostructures for specific potential applications. Characterization of Molecular and Atomic Species Adsorbed on Ferroelectric and Semiconductor Surfaces by Satyaveda Chavi Bharath A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Materials Science and Engineering Raleigh, North Carolina 05/28/09
Rapidly Sequential and Fatal Hemorrhaging in a Case of Cerebral Amyloid Angiopathy

Patient: Female, 63 Final Diagnosis: Cerebral amyloid angiopathy Symptoms: Altered mental state • aphasia • hemiplegia Medication: — Clinical Procedure: — Specialty: Neurology Objective: Unusual clinical course Background: Cerebral amyloid angiopathy (CAA) is an increasingly recognized cause of lobar intracerebral hemorrhage (ICH) and cognitive impairment in the aging population. Magnetic resonance imaging (MRI) of cerebral microbleeds is the most reliable option for clinical diagnosis of suspected CAA. The pathophysiology of microbleeds and ICH in CAA is not well understood, but it is thought to be the result of vessel weakening and rupture secondary to amyloid deposition. Little evidence has been established pertaining to the time course of recurrent CAA-related microbleeds or larger hemorrhages. Although several risk factors have been associated with an increased risk of ICH in CAA, there are no current treatment guidelines for recurrent hemorrhaging in CAA. Case Report: We present a rare case of rapidly sequential and fatal lobar hemorrhaging in the setting of suspected CAA, diagnosed by numerous microbleeds on MRI, compounded by the use of subcutaneous heparin in a 63-year-old female patient. Conclusions: This case broadens our understanding of a rarely identified progression of CAA and illustrates the need for further investigation of the use of subcutaneous heparin in the setting of probable CAA.
Space-filling curve RFID tags

A completely passive radio frequency tag is proposed, utilizing the scattering from electrically small but resonant inclusions. When placing these space-filling curve inclusions in an array and scaling each element within the array such that each element has its own separate resonant frequency, a radio frequency barcode can be developed from the radar cross section of the array. The narrow bandwidth inherent to such inclusions can be helpful in packing the overall signature into a relatively small frequency spectrum. Such radio frequency tags may have potential use in some applications of radio frequency identification systems.
Effect of Curcumin Supplementation on Physiological Fatigue and Physical Performance in Mice

Curcumin (CCM) is a well-known phytocompound and food component found in the spice turmeric and has multifunctional bioactivities. However, few studies have examined its effects on exercise performance and physical fatigue. We aimed to evaluate the potential beneficial effects of CCM supplementation on fatigue and ergogenic function following physical challenge in mice. Male ICR mice were divided into four groups to receive vehicle or CCM (180 μg/mL) by oral gavage at 0, 12.3, 24.6, or 61.5 mL/kg/day for four weeks. Exercise performance and anti-fatigue function were evaluated after physical challenge by forelimb grip strength, exhaustive swimming time, and levels of physical fatigue-associated biomarkers serum lactate, ammonia, blood urea nitrogen (BUN), and glucose and tissue damage markers such as aspartate transaminase (AST), alanine transaminase (ALT), and creatine kinase (CK). CCM supplementation dose-dependently increased grip strength and endurance performance and significantly decreased lactate, ammonia, BUN, AST, ALT, and CK levels after physical challenge. Muscular glycogen content, an important energy source for exercise, was significantly increased. CCM supplementation had few subchronic toxic effects. CCM supplementation may have a wide spectrum of bioactivities for promoting health, improving exercise performance and preventing fatigue.
Relationships between Body Composition and Fundamental Movement Skills among Children and Adolescents

Abstract The purpose of this study was to examine associations of fundamental movement skills (FMS) with measures of body composition among children and adolescents. Secondary analyses of cross-sectional data collected from 4,363 children and adolescents in Grades 4, 6, 8, and 10 as part of the 1997 New South Wales Schools Fitness and Physical Activity Survey were conducted. Six FMS (run, vertical jump, throw, catch, kick, and strike) were assessed by observation. Height and weight (used to calculate body mass index; BMI) and waist circumference were directly measured. Results indicated that the children's and adolescents' ability to perform FMS was significantly related to BMI and waist circumference. Specifically, BMI and waist circumference were significant predictors for FMS in six of the eight demographic groups. Adjusted odds ratios revealed that overweight boys and girls in all grades were less likely to possess high levels of FMS and more likely to possess low levels of FMS than those who weren't overweight. When FMS were partitioned into locomotor and object-control skills, nonoverweight boys and girls in each grade were two to three times more likely to possess more advanced locomotor skills than overweight boys and girls. However, for object-control skills, the only demographic groups in which nonoverweight students possessed a greater number of advanced skills than overweight students were boys in Grades 6 and 10. There appear to be significant and important associations between performance of locomotor skills and weight status among children and adolescents. This would suggest that intervention strategies to prevent unhealthy weight gain among children and youth might usefully include increasing proficiency of locomotor skills as a key component.