Miracle-dz/UniFAR-FTUs huggingface dataset:
Upstream ORFs are prevalent translational repressors in vertebrates

Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post‐transcriptional regulation. Previous studies have predicted thousands of ORFs in 5′ UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high‐resolution ribosome footprinting, we find that (i) uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii) uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Reporter experiments reveal clear repression of downstream translation by uORFs/oORFs. uORF number, intercistronic distance, overlap with the CDS, and initiation context most strongly influence translation. Evolution has targeted these features to favor uORFs amenable to regulation over constitutively repressive uORFs/oORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.
A Methodology to Evaluate Agent Oriented Software Engineering Techniques

Systems using software agents (or multi-agent systems, MAS) are becoming more popular within the development mainstream because, as the name suggests, an agent aims to handle tasks autonomously with intelligence. To benefit from autonomous control and reduced running costs, system functions are performed automatically. Agent-oriented considerations are being steadily accepted into the various software design paradigms. Agents may work alone, but most commonly, they cooperate toward achieving some application goal(s). MAS's are components in systems that are viewed as many individuals living in a society working together. From a SE perspective, solving a problem should encompass problem realization, requirements analysis, architecture design and implementation. These steps should be implemented within a life-cycle process including testing, verification, and reengineering to proving the built system is sound. In this paper, we explore the various applications of agent-based systems categorized into different application domains. A baseline is developed herein to help us focus on the core of agent concepts throughout the comparative study and to investigate both the object-oriented and agent-oriented techniques that are available for constructing agent-based systems. In each respect, we address the conceptual background associated with these methodologies and how available tools can be applied within specific domains
A mobile agent infrastructure for the mobility support

The mobility of terminals and users is a crucial issue in the open global system represented by the Internet. Supporting terminal and user mobility requires a middleware infrastructure capable of efficiently answering the needs of scalable resource discovery, of security and interoperability, of Quality of Service (QoS) monitoring and adaptation. Some proposals address mobility at the network level and some others focus on application-level solutions. By following the latter approach, the paper proposes the adoption of the mobile agent technology to model and implement mobility. In particular, the paper concentrates on the components and modules implemented in the SOMA mobile agent programming framework to specifically support terminal and user mobility. The SOMA tracing and discovery system extends the SOMA basic naming service to identify and keep track of all mobile entities in the environment. The SOMA QoS adaptation support exploits the functionality of the SOMA monitoring tools and permits to dynamically adjust service provision in response to the changing network and nodes conditions. These features are integrated in a mobility add-on module that pursues also the goals of security and interoperability when moving users and roaming terminals.
The Stability of Moving Average Technical Trading Rules on the Dow Jones Index

This paper reafirms previous results that show a distinct change in performance of moving average trading rules on the Dow Jones Index over the past 10 years relative to the previous 90 years. The performance in forecasting conditional means has changed significantly. In contrast to this is the fact that technical rules continue to forecast conditional variances in a similar fashion to the previous 90 years. Several tests are performed to demonstrate the robustness of these results over alternative trading mechnasims. Finally, the results are discussed in the context of datasnooping versus structural changes in the Dow.
Campus greenhouse monitoring with a simple ZigBee-based sensor network

The concept of greenhouse is to create a controllable environment suitable for vegetation growth. By stabilizing environmental parameters including lighting, temperature, humidity, and soil moisture, the yield of vegetable and fruit can be effectively increased. Commonly, greenhouse is a non-open space and lighted with solar-like sources. The light source will emit infrared ray that can heat the room and cause loss water in soil. Automatically monitoring the parameters can not only save man power but also facilitate growing environment control. ZigBee with low cost, low power and long communication distance is an efficient wireless communication device widely used in home-network. In this paper, a simple ZigBee-based sensor network is proposed for the campus greenhouse monitoring with mobile device. The system consists of three modules, a mesh structure network, data processing center, and mobile application program (APP). The network involves three functional nodes and is responsible for sensed data delivering. These nodes are modularly designed. Considering self-healing, a simple network operation system that applies ‘token’, data flow, and, hand shaking techniques.is also built. There are three functions for the data processing center. The first is filtering received data and saving correct data in a database, the second is data analysis and control action, and the third serves the requests of mobile device. APP installed in mobile device is a simple function that enables remote monitoring for sensor status and environment parameters. The framework has been implemented for performance evaluation. The experimental results validate the feasibility of the new ZigBee-based transducer structure.
Gate delay modeling for static timing analysis of body-biased circuits

Body biasing is a well-known circuit technique to compensate for increasing process variations. A static body biasing, in which fixed amount of bias voltage is applied after chips are sorted out according to process corners, is a convenient and viable approach in ASIC designs. The key question in this approach is how we generate new gate delays without re-characterizing all the gates, which is expensive. We notice, for the first time, that the ratio of delay (of original gate and the gate after body biasing) from the time input starts to change to the time output crosses Vdd=2 can be regarded invariant, i.e. it is a function of input transition time and load capacitance, but not a function of gate type. Therefore, once the ratio is characterized using a sample gate such as an inverter, it can be used to derive delay of all the other gates. We also propose some refinement techniques to improve accuracy. Experiments with industrial 32-nm library indicate that the average error over re-characterization is about 4% with maximum error being 11%, when maximum body bias voltage is assumed. The errors decrease as smaller bias voltage is applied.
Human Cortical during Free Exploration Encodes Space and Predicts Subsequent Memory

Joseph Snider,1 Markus Plank,1 Gary Lynch,2 Eric Halgren,3,4 and Howard Poizner1,4 1Institute for Neural Computation, University of California, San Diego, La Jolla, California 92093, 2Departments of Psychiatry and Human Behavior and Anatomy and Neurobiology, University of California, Irvine, Irvine, California 92697, 3Departments of Radiology, Neuroscience, and Psychiatry, University of California, San Diego, La Jolla, California 92093, and 4Program in Neurosciences, University of California, San Diego, La Jolla, California, 92093
A New Performance Enhancement Technique of the Current Feedback Amplifier

An improved performance current feedback amplifier circuit referred to as CFA feedback current feedback amplifier (CCFA) is described in this paper. This circuit is developed as an augmentation to the operational current feedback amplifier which employs a technique involving the incorporation of the input circuit of the current feedback amplifier in the feedback loop of an operational amplifier to reduce the input impedance at the inverting terminal of the current feedback amplifier. The proposed circuit replaces the operational amplifier with AD8004 CFA and the circuit possesses the gain accuracy and bandwidth of the current feedback amplifier. The new realization significantly enhanced the bandwidth accuracy and bandwidth gain-independence. The simulation of the proposed circuit has been performed using PSPICE. Various configurations using AD8004 CFA and LT1364 OPA have been simulated and the satisfactory results were obtained.
Cathepsin B is a New Drug Target for Traumatic Brain Injury Therapeutics: Evidence for E64d as a Promising Lead Drug Candidate

There is currently no therapeutic drug treatment for traumatic brain injury (TBI) despite decades of experimental clinical trials. This may be because the mechanistic pathways for improving TBI outcomes have yet to be identified and exploited. As such, there remains a need to seek out new molecular targets and their drug candidates to find new treatments for TBI. This review presents supporting evidence for cathepsin B, a cysteine protease, as a potentially important drug target for TBI. Cathepsin B expression is greatly up-regulated in TBI animal models, as well as in trauma patients. Importantly, knockout of the cathepsin B gene in TBI mice results in substantial improvements of TBI-caused deficits in behavior, pathology, and biomarkers, as well as improvements in related injury models. During the process of TBI-induced injury, cathepsin B likely escapes the lysosome, its normal subcellular location, into the cytoplasm or extracellular matrix (ECM) where the unleashed proteolytic power causes destruction via necrotic, apoptotic, autophagic, and activated glia-induced cell death, together with ECM breakdown and inflammation. Significantly, chemical inhibitors of cathepsin B are effective for improving deficits in TBI and related injuries including ischemia, cerebral bleeding, cerebral aneurysm, edema, pain, infection, rheumatoid arthritis, epilepsy, Huntington’s disease, multiple sclerosis, and Alzheimer’s disease. The inhibitor E64d is unique among cathepsin B inhibitors in being the only compound to have demonstrated oral efficacy in a TBI model and prior safe use in man and as such it is an excellent tool compound for preclinical testing and clinical compound development. These data support the conclusion that drug development of cathepsin B inhibitors for TBI treatment should be accelerated.
Cancer Prediction using Mining Gene Expression Data

Cancer is a major cause of all natural mortalities and morbidities throughout the world.Pointed out the exact tumour types provides an optimized solution for the better treatment and toxicity minimization due to medicines on the patients. To get a clear picture on the insight of a problem, a clear cancer classification analysis system needs to be pictured followed by a systematic approach to analyse global gene expression which provides an optimized solution for the identified problem area. Molecular diagnostics provides a promising option of systematic human cancer classification, but these tests are not widely applied because characteristic molecular markers for most solid tumor save yet to be identified. Recently, DNA microarray-based tumor gene expression profiles have been used for cancer diagnosis. Existing system focussed in ranging from old nearest neighbour analysis to support vector machine manipulation for the learning portion of the classification model. We don’t have a clear picture of supervised classifier (Supervised Multi Attribute Clustering Algorithm) which can manage knowledge attributes coming two different knowledge streams. Our proposed system takes the input from multiple source, create an ontological store, cluster the data with attribute match association rule and followed by classification with the knowledge acquired
Neonatal Co‐Infection with Helicobacter Species Markedly Accelerates the Development of Inflammation‐Associated Colonic Neoplasia in IL‐10−/–Mice

Background: Inflammatory bowel disease (IBD) is hypothesized to represent an aberrant immune response against enteric bacteria that occurs in a genetically susceptible host. Humans and mice with IBD are at markedly increased risk for colonic neoplasia. However, the long lead time required before development of inflammation‐associated colon neoplasia in commonly used murine models of IBD slows the development of effective chemopreventative therapies.
Rubber Concentrations on Rheology of Aged Asphalt Binders

Three different concentrations of crumb rubber were mixed with two different asphalts by means of a wet process to investigate the effect of rubber particles on the fundamental internal structure of asphalt binders with respect to their long-term aging performance. The rheological properties of unaged and aged unmodified and rubber-modified asphalt binders were studied as a function of long-term oxidative aging. Master curves were constructed by shifting the aging time-frequency data to assist in the interpretation. A generalized power-law model used in neat asphalt based on the time–temperature superposition principle was applied to construct the master curves of the rheological parameters. Based on a limited study, the results indicate that the amount of rubber particles added into the asphalt binder is asphalt dependent. The results also show that the stiffness effect of crumb rubber to one less-compatible asphalt is higher than the other highly compatible asphalt. Addition of crumb rubber to both asph.
Quantifying the role of steric constraints in nucleosome positioning

Statistical positioning, the localization of nucleosomes packed against a fixed barrier, is conjectured to explain the array of well-positioned nucleosomes at the 5′ end of genes, but the extent and precise implications of statistical positioning in vivo are unclear. We examine this hypothesis quantitatively and generalize the idea to include moving barriers as well as nucleosomes actively packed against a barrier. Early experiments noted a similarity between the nucleosome profile aligned and averaged across genes and that predicted by statistical positioning; however, we demonstrate that aligning random nucleosomes also generates the same profile, calling the previous interpretation into question. New rigorous results reformulate statistical positioning as predictions on the variance structure of nucleosome locations in individual genes. In particular, a quantity termed the variance gradient, describing the change in variance between adjacent nucleosomes, is tested against recent high-throughput nucleosome sequencing data. Constant variance gradients provide support for generalized statistical positioning in ∼50% of long genes. Genes that deviate from predictions have high nucleosome turnover and cell-to-cell gene expression variability. The observed variance gradient suggests an effective nucleosome size of 158 bp, instead of the commonly perceived 147 bp. Our analyses thus clarify the role of statistical positioning in vivo.
Folate Metabolism Polymorphisms Influence Risk of Colorectal Adenoma Recurrence

Folate intake is inversely related to risk of developing colorectal neoplasia. Associations between risk of colorectal neoplasia and polymorphisms in genes coding for enzymes involved in folate metabolism have also been reported, suggesting a relationship between genotype and development of colorectal neoplasia. To further investigate the effects of folate metabolism genotypes on colorectal neoplasia, we genotyped 546 patients participating in a randomized controlled trial of folate supplementation for the prevention of colorectal adenoma recurrence. A significantly reduced risk of recurrence was observed in patients heterozygous for the MTRR A66G polymorphism [relative risk (RR), 0.64; 95% confidence interval (95% CI), 0.46-0.90] or heterozygous for the MTHFR A1298C polymorphism (RR, 0.71; 95% CI, 0.52-0.97). Furthermore, a significant reduction in recurrence risk was seen in MTRR A66G heterozygotes who received folate supplements but not in those who did not receive folate. Patients heterozygous for the MTHFR C677T polymorphism had a nonsignificant risk reduction (RR, 0.92; 95% CI, 0.69-1.23), as did patients with one or two variant alleles for the MTR A2756G polymorphism (RR, 0.82; 95% CI, 0.60-1.12). No influence on recurrence risk was observed for the TSER, TSER 3R G>C, and TS 1494del6 variants. These findings provide additional support for the hypothesis that germ line variants in folate metabolism genes influence the development of colorectal adenomas. (Cancer Epidemiol Biomarkers Prev 2006;15(9):1607–13)
Effects of ELL-associated factor 2 on ultraviolet radiation-induced cataract formation in mice

ELL-associated factor 2 (Eaf2) has an important role in crystalline lens development and maturation; however, its role in ultraviolet radiation (UV)-induced cataract formation has remained elusive. The present study compared UV-induced cell apoptosis, activation of caspase-3 and caspase-9 and changes in protein expression levels of B-cell lymphoma 2 (bcl-2), bcl-2-associated X protein (bax) and phosphorylated extracellular signal-regulated kinase in wild-type and Eaf2-knockout mice. The results showed that Eaf2 knockout can reduce UV-induced apoptosis in crystalline lenses and mitigate the formation of cataracts. Further functional studies indicated that Eaf2 can induce the activation of caspase-3 and caspase-9, increase the protein expression of the pro-apoptotic protein bax and inhibit the expression of the anti-apoptotic protein bcl-2; thereby, Eaf2 promotes cell apoptosis and is implicated in the formation and development of cataracts. The present study laid a theoretical foundation for the development of drugs for cataract treatment.
The Use of Thin Silicon Films in Flat Panel Displays

We review some recent developments in the industry of flat panel displays, based on the use of thin films of amorphous silicon or polycrystalline silicon. In particular, we show that the field of application of active matrix liquid crystal displays (AMLCDs) is continuously expanding. In the Far East, AMLCD manufacturers are now competing for the TV-on-the-wall market, with displays measuring 40 in diagonal and over. AMLCDs are in the process of becoming the universal technology for displaying multimedia images (computer or video) on a flat panel. Low temperature polysilicon (LTPS) technology is also actively developed, for application to AMLCDs and also for the addressing of organic light emitting materials.
A de novo nonsense mutation in ZBTB18 plus a de novo 15q13.3 microdeletion in a 6‐year‐old female

ZBTB18 has been proposed as candidate gene for microcephaly and abnormalities of the corpus callosum based on overlapping microdeletions of 1q43q44. More recently, de novo mutations of ZBTB18 have been identified in patients with syndromic and non‐syndromic intellectual disability. Heterozygous microdeletions of 15q13.3 encompassing the candidate gene CHRNA7 are associated with developmental delay or intellectual disability with speech problems, hypotonia, and seizures. They are characterized by significant variability and reduced penetrance. We report on a patient with a de novo ZBTB18 nonsense mutation and a de novo 15q13.3 microdeletion, both in a heterozygous state, identified by next generation sequencing and array‐CGH. The 6‐year‐old girl showed global developmental delay, absent speech, therapy‐refractory seizures, ataxia, muscular hypotonia, and discrete facial dysmorphisms. Almost all of these features have been reported for both genetic aberrations, but the severity could hardly been explained by the microdeletion 15q13.3 alone. We assume an additive effect of haploinsufficiency of ZBTB18 and CHRNA7 in our patient. Assembling the features of our patient and the published patients, we noted that only one of them showed mild anomalies of the corpus callosum. Moreover, we hypothesize that nonsense mutations of ZBTB18 are associated with a more severe phenotype than missense mutations. This report indicates that haploinsufficiency of additional genes beside ZBTB18 causes the high frequency of corpus callosum anomalies in patients with microdeletions of 1q43q44 and underlines the importance of an NGS‐based molecular diagnostic in complex phenotypes.
Comparison of Electrochemical Behaviors of Chalcopyrite, Bornite, Chalcocite and Covellite in 9K Medium

Electrochemical behaviors of chalcopyrite, covellite, chalcocite and bornite in 9K medium at 65 °C were compared in this paper to verify they whether or not the intermediate products of chalcopyrite. The results confirmed that bornite, chalcocite and covellite are the intermediate products of chalcopyrite. Chalcocite and bornite can both oxidize to covellite.
Flip-Mirror-Rotate: An Architecture for Bit-write Reduction and Wear Leveling in Non-volatile Memories

This paper proposes Flip-Mirror-Rotate (FMR), an architecture for bit-write reduction and endurance enhancement in emerging non-volatile memories (NVMs). FMR comprises three components: adaptive Flip-N-Write (aFNW), Mirror-N-Write (MNW), and Rotate-N-Write (RNW). aFNW and MNW focus on word-level bit-write reduction, which reduces NVM dynamic energy while also improving endurance. RNW is an intra-word wear leveling scheme that operates at cache line granularity. The proposed FMR architecture is integrated with frequent pattern compression (FPC) to simultaneously reduce bit-writes and wear in NVMs. Trace-based simulations of the SPEC CPU2006 benchmarks show that for the same memory overhead and < 1% loss in memory bandwidth, FMR reduces bit-writes (dynamic energy) by 48% (29%) in comparison to classical read-modify-write (DCW), 39% (13%) in comparison to Flip-N-Write (FNW), and 21% (14%) in comparison to FPC. Simultaneously, FMR also reduces the peak bit-writes per cell by 47% in comparison to DCW, 34% in comparison to FNW, and 47% in comparison to FPC, improving NVM endurance.