Miracle-dz/UniFAR-FTUs huggingface dataset:
RIPGA: RNA-RNA interaction prediction using genetic algorithm

Non-coding RNAs are RNA molecules that do not translate into proteins. These RNAs are functional important in many biological processes. Their biological functions are highly related to their interaction partners. RNA-RNA interactions are one of the possibilities. It is desired to use computational methods to study and predict the interaction partners of non-coding RNAs. Most recent programs for RNA-RNA interaction prediction programs are based on Turner Energy Model. Some papers show that the free energy of RNA-structures is lower than random sequences but it is not statistically significant. It shows that we may need to modify the energy model for different RNA structures applications. In this paper, we first study the RNA-RNA interaction pattern using experimental validated RNA-RNA interaction data, which are extracted from sRNATarBase. We study the sRNA-mRNA interaction data and extract some features of the RNA-RNA interaction patterns. Then we combine these features about interaction sites into the Turner Energy Model. We develop a genetic algorithm based program RIPGA to solve the RNA-RNA interaction prediction problem. We use genetic algorithm because the RNA-RNA interaction prediction is NP-hard and we are interested to find out good suboptimal solutions. We use an sRNA-mRNA interaction dataset to evaluate the performance of the modified energy model and compare the results with two state-of-the-art programs. The comparison of the original model and the modified model shows that the modified energy model has better performance in both sensitivity and positive predictive value (PPV). Comparing RIPGA with state-of-the-art programs, RIPGA have better sensitivity and comparable positive predictive value.
Feasibility and Initial Efficacy of a Comprehensive School-Based Intervention for High-Functioning Autism Spectrum Disorders.

This study examined the feasibility and initial efficacy of a comprehensive school-based intervention (CSBI) for 12 children with high-functioning autism spectrum disorders, aged 6 to 9 years. Treatment included a 3-week summer preparation program followed by a 10-month CSBI, comprising social skills groups, therapeutic activities, face and voice emotion recognition instruction, an individual daily note, and parent training. Feasibility was supported in high levels of treatment fidelity and teacher- and parent-reported acceptability and satisfaction. Pre–post comparisons suggested that children significantly improved their knowledge of target social skills, ability to identify emotions in facial and vocal expressions taught in the program, and broader emotion recognition skills in child faces. According to parent and teacher ratings, children displayed gains in their use of target social skills and broader social performance. Parents also reported a significant reduction in autism spectrum disorder-related features.
Phosphoglycerate dehydrogenase is dispensable for breast tumor maintenance and growth

Cancer cells rely on aerobic glycolysis to maintain cell growth and proliferation via the Warburg effect. Phosphoglycerate dehydrogenase (PHDGH) catalyzes the first step of the serine biosynthetic pathway downstream of glycolysis, which is a metabolic gatekeeper both for macromolecular biosynthesis and serine-dependent DNA synthesis. Here, we report that PHDGH is overexpressed in many ER-negative human breast cancer cell lines. PHGDH knockdown in these cells leads to a reduction of serine synthesis and impairment of cancer cell proliferation. However, PHGDH knockdown does not affect tumor maintenance and growth in established breast cancer xenograft models, suggesting that PHGDH-dependent cancer cell growth may be context-dependent. Our findings suggest that other mechanisms or pathways may bypass exclusive dependence on PHGDH in established human breast cancer xenografts, indicating that PHGDH is dispensable for the growth and maintenance of tumors in vivo.
Beyond reducing ﬁre hazard: fuel treatment impacts on overstory tree survival.

Fuel treatment implementation in dry forest types throughout the western United States is likely to increase in pace and scale in response to increasing incidence of large wildﬁres. While it is clear that properly implemented fuel treatments are effective at reducing hazardous ﬁre potential, there are ancillary ecological effects that can impact forest resilience either positively or negatively depending on the speciﬁc elements examined, as well as treatment type, timing, and intensity. In this study, we use overstory tree growth responses, measured seven years after the most common fuel treatments, to estimate forest health. Across the ﬁve species analyzed, observed mortality and future vulnerability were consistently low in the mechanical- only treatment. Fire-only was similar to the control for all species except Douglas-ﬁr, while mechanical-plus-ﬁre had high observed mortality and future vulnerability for white ﬁr and sugar pine. Given that overstory trees largely dictate the function of forests and services they provide (e.g., wildlife habitat, carbon sequestration, soil stability) these results have implications for understanding longer-term impacts of common fuel treatments on forest resilience.
An energy-aware algorithm for TDMA MAC protocols in real-time wireless networks

In distributed embedded systems operated by battery, energy management is a critical issue that has to be addressed at different architecture levels. For systems that tightly interact with the environment, an additional goal is to enforce a set of real-time constraints to guarantee a desired performance. A lot of research has focused on power management at the communication level, especially for MAC protocols. However, not many authors considered both real-time and energy requirements in wireless communication systems. In this paper we present El-MAC, an elastic energy-aware algorithm at the MAC level for wireless distributed systems with real-time constraints. Under this framework, each node can adapt its bandwidth requirements to balance performance versus energy consumption, taking both lifetime and message deadlines into account. We describe the algorithm for a generic TDMA MAC protocol.
An adaptive fitness function based on branch hardness for search based testing

Search based software testing has received great attention as a means of automating the test data generation, and the goal is to improve various criteria. There are different types of coverage criteria. In this paper, we deal with the path coverage. Concretely, we focus on the path that is the most difficult to cover. One major limitation of search based testing is the inefficient and insufficiently informed fitness function. To address this problem, we propose an adaptive fitness function based on branch hardness. The branch hardness is measured by the expected number of visits of each branch in the program, which is modeled by an absorbing discrete time Markov chain. By tuning the parameters of branch hardness heuristically, the search hardness, evaluated by the variation coefficient of the fitness function, of generating test data can be minimized. Therefore, this new fitness function is more flexible than the traditional counterparts. In addition, we point out that the present definition of branch distance and the use of normalizing functions are problematic, and propose some improvements. Finally, the empirical study reveals the promising result of our proposal in this paper.
Investigating the “Self” in Deliberate Self-Harm

In this study, the authors explored how a group of young people aged 16 to 26 years (who identified themselves as having engaged in deliberate self-harm) made sense of the self by conducting two online focus groups and four e-mail interviews. They analyzed data using interpretive phenomenological analysis. The concept of validation was the primary means of making sense of the self and concerned the desire to be considered legitimate and of worth. This desire was clearly evident across three realms of conflict: (a) the intrinsic or extrinsic self, which marked the distinction between objective fact and subjective opinion; (b) the accepted or denied self; and (c) the notion of normality. It is possible that having one’s denied self validated online might lead to an exacerbation of an individual’s self-harming behavior. Further work is needed to explore the effects of online discussion forums on such taboo forms of behavior.
A 3D grasping system based on multimodal visual and tactile processing

Purpose – The purpose of this paper is to present a novel multimodal approach to the problem of planning and performing a reliable grasping action on unmodeled objects.Design/methodology/approach – The robotic system is composed of three main components. The first is a conceptual manipulation framework based on grasping primitives. The second component is a visual processing module that uses stereo images and biologically inspired algorithms to accurately estimate pose, size, and shape of an unmodeled target object. A grasp action is planned and executed by the third component of the system, a reactive controller that uses tactile feedback to compensate possible inaccuracies and thus complete the grasp even in difficult or unexpected conditions.Findings – Theoretical analysis and experimental results have shown that the proposed approach to grasping based on the concurrent use of complementary sensory modalities, is very promising and suitable even for changing, dynamic environments.Research limitations/i.
Developing teacher candidate identity in the context of a rural internship

This qualitative study focused on the experiences and perceptions of 12 teacher candidates as they completed a six‐week rural internship experience. The main objectives of the study were to: (a) describe the learning experiences of teacher candidates as they live and teach in rural communities; (b) examine how teaching and living in rural communities influence teacher identity; and (c) ascertain if living and teaching in rural communities affect teacher candidates' willingness to accept future teaching assignments in rural communities. Several data collection procedures and sources were used, including open‐ended pre‐ and post‐questionnaires, pre‐ and post‐internship interviews (40–60 minutes each), university‐based classroom observations, and online reflections. During the rural internship, teacher candidates engaged in a variety of professional activities that were classroom‐, school‐, and/or community‐based; examined the nature of teaching in rural schools and communities in relation to their own beliefs, values, and aspirations; and reflected on the opportunities and challenges associated with living and teaching in a rural community.
Growing a Syntax

In this paper we present a macro system for the Fortress programming language. Fortress is a new programming language designed for scientific and high-performance computing. Features include: implicit parallelism, transactions, and concrete syntax that emulates mathematical notation. Fortress is intended to grow over time to accommodate the changing needs of its users. Our goal is to design and implement a macro system that allows for such growth. The main challenges are (1) to support extensions to a core syntax rich enough to emulate mathematical notation, (2) to support combinations of extensions from separately compiled macros, and (3) to allow new syntax that is indistinguishable from core language constructs. To emulate mathematical notation, Fortress syntax is specified as a parsing expression grammar (PEG), supporting unlimited lookahead. Macro definitions must be checked for well-formedness before they are expanded and macro uses must be well encapsulated (hygienic, composable, respecting referential transparency). Use sites must be parsed along with the rest of the program and expanded directly into abstract syntax trees. Syntax errors at use sites of a macro must refer to the unexpanded program at use sites, never to definition sites. Moreover, to allow for many common and important uses of macros, mutually recursive definitions should be supported. Our design meets these challenges. The result is a flexible system that allows us not only to support new language extensions, but also to move many constructs of the core language into libraries. New grammar productions are tightly integrated with the Fortress parser, and use sites expand into core abstract syntax trees. Our implementation is integrated into the open-source Fortress reference interpreter.To our knowledge, ours is the first implementation of a modular hygienic macro system based on parsing expression grammars. ∗ Work partially done while visiting Sun Microsystems Laboratories. † Supported by the SIMAP Project under the Danish Strategic Research Council NABIIT-program. Copyright is held by Sun Microsystems, Inc. FOOL ’09 24 January, 2009, Savannah, Georgia, USA. ACM .
Integrated cervical smear screening using liquid based cytology and bioimpedance analysis

Objective: To minimize the false negativity in cervical cancer screening with Papanicolaou (Pap) test, there is a need to explore novel cytological technique and identification of unique and important cellular features from the perspectives of morphological as well as biophysical properties. Materials and Methods: The present study explores the feasibility of low-cost cervical monolayer techniques in extracting cyto-pathological features to classify normal and abnormal conditions. The cervical cells were also analyzed in respect to their electrical bioimpedance. Result: The results show that newly developed monolayer technique for cervical smears is cost effective, capable of cyto-pathological evaluation. Electrical bioimpedance study evidenced distinction between abnormal and normal cell population at more than two order of magnitude difference. Conclusion: The integration of bioimpedance observation along with the proposed low-cost monolayer technology could increase the efficiency of the cervical screening to a greater extent thereby reducing the rates of faulty diagnosis.
Molecular Identification and Characterization of an Essential Pyruvate Transporter from Trypanosoma brucei*

Background: Pyruvate transport is vital for growth and survival of T. brucei bloodstream form. Results: TbPT0 is a unique monocarboxylate transporter with preference for pyruvate and essential for bloodstream form viability. Conclusion: TbPT0 represents the first molecular identification of essential pyruvate transporters in T. brucei. Significance: Unique T. brucei pyruvate transporters provide a potential drug target against the bloodstream form parasites. Pyruvate export is an essential physiological process for the bloodstream form of Trypanosoma brucei as the parasite would otherwise accumulate this end product of glucose metabolism to toxic levels. In the studies reported here, genetic complementation in Saccharomyces cerevisiae has been employed to identify a gene (TbPT0) that encodes this vital pyruvate transporter from T. brucei. Expression of TbPT0 in S. cerevisiae reveals that TbPT0 is a high affinity pyruvate transporter. TbPT0 belongs to a clustered multigene family consisting of five members, whose expression is up-regulated in the bloodstream form. Interestingly, TbPT family permeases are related to polytopic proteins from plants but not to characterized monocarboxylate transporters from mammals. Remarkably, inhibition of the TbPT gene family expression in bloodstream parasites by RNAi is lethal, confirming the physiological relevance of these transporters. The discovery of TbPT0 reveals for the first time the identity of the essential pyruvate transporter and provides a potential drug target against the mammalian life cycle stage of T. brucei.
The impact of incorrectly speculated memory operations in a multithreaded architecture

The speculated execution of threads in a multithreaded architecture, plus the branch prediction used in each thread execution unit, allows many instructions to be executed speculatively, that is, before it is known whether they actually needed by the program. In this study, we examine how the load instructions executed on what turn out to be incorrectly executed program paths impact the memory system performance. We find that incorrect speculation (wrong execution) on the instruction and thread-level provides an indirect prefetching effect for the later correct execution paths and threads. By continuing to execute the mispredicted load instructions even after the instruction or thread-level control speculation is known to be incorrect, the cache misses observed on the correctly executed paths can be reduced by 16 to 73 percent, with an average reduction of 45 percent. However, we also find that these extra loads can increase the amount of memory traffic and can pollute the cache. We introduce the small, fully associative wrong execution cache (WEC) to eliminate the potential pollution that can be caused by the execution of the mispredicted load instructions. Our simulation results show that the WEC can improve the performance of a concurrent multithreaded architecture up to 18.5 percent on the benchmark programs tested, with an average improvement of 9.7 percent, due to the reductions in the number of cache misses.
Surfactant Secretion in LRRK2 Knock-Out Rats: Changes in Lamellar Body Morphology and Rate of Exocytosis

Leucine-rich repeat kinase 2 (LRRK2) is known to play a role in the pathogenesis of various diseases including Parkinson disease, morbus Crohn, leprosy and cancer. LRRK2 is suggested to be involved in a number of cell biological processes such as vesicular trafficking, transcription, autophagy and lysosomal pathways. Recent histological studies of lungs of LRRK2 knock-out (LRRK2 -/-) mice revealed significantly enlarged lamellar bodies (LBs) in alveolar type II (ATII) epithelial cells. LBs are large, lysosome-related storage organelles for pulmonary surfactant, which is released into the alveolar lumen upon LB exocytosis. In this study we used high-resolution, subcellular live-cell imaging assays to investigate whether similar morphological changes can be observed in primary ATII cells from LRRK2 -/- rats and whether such changes result in altered LB exocytosis. Similarly to the report in mice, ATII cells from LRRK2 -/- rats contained significantly enlarged LBs resulting in a >50% increase in LB volume. Stimulation of ATII cells with ATP elicited LB exocytosis in a significantly increased proportion of cells from LRRK2 -/- animals. LRRK2 -/- cells also displayed increased intracellular Ca2+ release upon ATP treatment and significant triggering of LB exocytosis. These findings are in line with the strong Ca2+-dependence of LB fusion activity and suggest that LRRK2 -/- affects exocytic response in ATII cells via modulating intracellular Ca2+ signaling. Post-fusion regulation of surfactant secretion was unaltered. Actin coating of fused vesicles and subsequent vesicle compression to promote surfactant expulsion were comparable in cells from LRRK2 -/- and wt animals. Surprisingly, surfactant (phospholipid) release from LRRK2 -/- cells was reduced following stimulation of LB exocytosis possibly due to impaired LB maturation and surfactant loading of LBs. In summary our results suggest that LRRK2 -/- affects LB size, modulates intracellular Ca2+ signaling and promotes LB exocytosis upon stimulation of ATII cells with ATP.
Synthetic Speech Discrimination using Pitch Pattern Statistics Derived from Image Analysis

In this paper, we extend the work by Ogihara, et al. to discriminate between human and synthetic speech using features based on pitch patterns. As previously demonstrated, significant differences in pitch patterns between human and synthetic speech can be leveraged to classify speech as being human or synthetic in origin. We propose using mean pitch stability, mean pitch stability range, and jitter as features extracted after image analysis of pitch patterns. We have observed that for synthetic speech, these features lie in a small and distinct space as compared to human speech and have modeled them with a multivariate Gaussian distribution. Our classifier is trained using synthetic speech collected from the 2008 and 2011 Blizzard Challenge along with Festival pre-built voices and human speech from the NIST2002 corpus. We evaluate the classifier on a much larger corpus than previously studied using human speech from the Switchboard corpus, synthetic speech from the Resource Management corpus, and synthetic speech generated from Festival trained on the Wall Street Journal corpus. Results show 98% accuracy in correctly classifying human speech and 96% accuracy in correctly classifying synthetic speech. Index Terms: Speaker recognition, Speech synthesis, Security
Hepatic response after high-dose melphalan and stem cell transplantation in patients with AL amyloidosis associated liver disease

In patients with AL amyloidosis and liver involvement, treatment with high-dose melphalan chemotherapy and autologous peripheral blood stem cell transplantation resulted in 61% overall survival at 5 years. Moreover, the transplant-related mortality (13%) was similar to that of patients with AL amyloidosis without associated liver disease. High-dose melphalan chemotherapy and autologous peripheral blood stem cell transplantation has been shown to result in durable hematologic response and prolonged overall survival in systemic AL amyloidosis. In this retrospective study, we evaluated clinical and hematologic responses in 69 patients with predominant liver involvement who were treated with high-dose intravenous melphalan and autologous stem cell transplantation from 1998 to 2006. Nine patients (13%) died from treatment-related mortality, similar to patients without hepatic involvement. The overall survival was 81% at one year and 61% at five years, by Kaplan-Meier estimates. A hematologic complete response was achieved by 53% (31/58) of patients at one year. A hepatic response occurred in 57% (33/58) at one year after high-dose intravenous melphalan and autologous stem cell transplantation and 63% (19/30) at two years after high-dose intravenous melphalan and autologous stem cell transplantation. In conclusion, hepatic disease improves in almost 2/3 patients treated with high-dose intravenous melphalan and autologous stem cell transplantation who have a complete or partial hematologic response to treatment.
Impact of depression on health utility value in cancer patients

The quality‐adjusted life year, which is usually calculated from the health utility value, is now a standard measurement used in political decision‐making in health. Although depression is the leading cause of decrement in health utility in general population, impact of comorbid depression among cancer patients has not been studied sufficiently. Therefore, this study aimed to measure the impact of depression on cancer patients' health utility score, according to the severity of depression.