Miracle-dz/UniFAR-FTUs huggingface dataset:
Generating Super Stimulated-Echoes in MRI and Their Application to Hyperpolarized C-13 Diffusion Metabolic Imaging

Stimulated-echoes in MR can be used to provide high sensitivity to motion and flow, creating diffusion and perfusion weighting as well as T1 contrast, but conventional approaches inherently suffer from a 50% signal loss. The super stimulated-echo, which uses a specialized radio-frequency (RF) pulse train, has been proposed in order to improve the signal while preserving motion and T1 sensitivity. This paper presents a novel and straightforward method for designing the super stimulated-echo pulse train using inversion pulse design techniques. This method can also create adiabatic designs with an improved response to RF transmit field variations. The scheme was validated in phantom experiments and shown in vivo to improve signal-to-noise ratio (SNR). We have applied a super stimulated-echo to metabolic MRI with hyperpolarized 13C-labeled molecules. For spectroscopic imaging of hyperpolarized agents, several repetition times are required but only a single stimulated-echo encoding is feasible, which can lead to unwanted motion blurring. To address this, a super stimulated-echo preparation scheme was used in which the diffusion weighting is terminated prior to the acquisition, and we observed a SNR increases of 60% in phantoms and 49% in vivo over a conventional stimulated-echo. Experiments following injection of hyperpolarized [1-13C] -pyruvate in murine transgenic cancer models have shown improved delineation for tumors since signals from metabolites within tumor tissues are retained while those from the vasculature are suppressed by the diffusion preparation scheme.
Predicting program behavior using real or estimated profiles

There is a growing interest in optimizations that depend on or benefit from an execution profile that tells where time is spent. How well does a profile from one run describe the behavior of a different run, and how does this compare with the behavior predicted by static analysis of the program? This paper defines two abstract measures of how well a profile predicts actual behavior. According to these measures, real profiles indeed do better than estimated profiles, usually. A perfect profile from an earlier run with the same data set, however, does better still, sometimes by a factor of two. Unfortunately, using such a profile is unrealistic, and can lead to inflated expectations of a profile-driven optimization.
Generif Quality Assurance as Summary Revision

Like the primary scientific literature, GeneRIFs exhibit both growth and obsolescence. NLM's control over the contents of the Entrez Gene database provides a mechanism for dealing with obsolete data: GeneRIFs are removed from the database when they are found to be of low quality. However, the rapid and extensive growth of Entrez Gene makes manual location of low-quality GeneRIFs problematic. This paper presents a system that takes advantage of the summary-like quality of GeneRIFs to detect low-quality GeneRIFs via a summary revision approach, achieving precision of 89% and recall of 77%. Aspects of the system have been adopted by NLM as a quality assurance mechanism.
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/.
Comparison of Uniaxial Wafer Bending and Contact-Etch-Stop-Liner Stress Induced Performance Enhancement on Double-Gate FinFETs

Longitudinal piezoresistance (pi) coefficients for n- and p-type double-gate (DG) FinFETs with sidewall channels along (110) surface and (110) channel direction are measured via wafer-bending experiments (51.4 and -37 X 10 -11 Pa-1 for n- and p-FinFETs, respectively) and are found to differ from bulk Si (110) (31.2 and -71.8 X 10 -11 Pa-1 for n- and p-Si, respectively). Compressive and tensile contact-etch-stop liners (CESLs) are fabricated on DG FinFETs and are found to induce higher channel stress than in planar MOSFETs, with 30% enhancement in the saturation current for the shortest channel-length devices in both n- and p-MOSFETs, whereas the long devices show little or no enhancement. The channel-length dependence of the enhancement suggests that stress coupling into the FinFET channels from the CESL occurs via the fin extensions and not through the gate.
Efficient parameter estimation for RNA secondary structure prediction

MOTIVATION Accurate prediction of RNA secondary structure from the base sequence is an unsolved computational challenge. The accuracy of predictions made by free energy minimization is limited by the quality of the energy parameters in the underlying free energy model. The most widely used model, the Turner99 model, has hundreds of parameters, and so a robust parameter estimation scheme should efficiently handle large data sets with thousands of structures. Moreover, the estimation scheme should also be trained using available experimental free energy data in addition to structural data. RESULTS In this work, we present constraint generation (CG), the first computational approach to RNA free energy parameter estimation that can be efficiently trained on large sets of structural as well as thermodynamic data. Our CG approach employs a novel iterative scheme, whereby the energy values are first computed as the solution to a constrained optimization problem. Then the newly computed energy parameters are used to update the constraints on the optimization function, so as to better optimize the energy parameters in the next iteration. Using our method on biologically sound data, we obtain revised parameters for the Turner99 energy model. We show that by using our new parameters, we obtain significant improvements in prediction accuracy over current state of-the-art methods. AVAILABILITY Our CG implementation is available at http://www.rnasoft. ca/CG/.
Prevention of the Disrupted Enamel Phenotype in Slc4a4-Null Mice Using Explant Organ Culture Maintained in a Living Host Kidney Capsule

Slc4a4-null mice are a model of proximal renal tubular acidosis (pRTA). Slc4a4 encodes the electrogenic sodium base transporter NBCe1 that is involved in transcellular base transport and pH regulation during amelogenesis. Patients with mutations in the SLC4A4 gene and Slc4a4-null mice present with dysplastic enamel, amongst other pathologies. Loss of NBCe1 function leads to local abnormalities in enamel matrix pH regulation. Loss of NBCe1 function also results in systemic acidemic blood pH. Whether local changes in enamel pH and/or a decrease in systemic pH are the cause of the abnormal enamel phenotype is currently unknown. In the present study we addressed this question by explanting fetal wild-type and Slc4a4-null mandibles into healthy host kidney capsules to study enamel formation in the absence of systemic acidemia. Mandibular E11.5 explants from NBCe1−/− mice, maintained in host kidney capsules for 70 days, resulted in teeth with enamel and dentin with morphological and mineralization properties similar to cultured NBCe1+/+ mandibles grown under identical conditions. Ameloblasts express a number of proteins involved in dynamic changes in H+/base transport during amelogenesis. Despite the capacity of ameloblasts to dynamically modulate the local pH of the enamel matrix, at least in the NBCe1−/− mice, the systemic pH also appears to contribute to the enamel phenotype. Extrapolating these data to humans, our findings suggest that in patients with NBCe1 mutations, correction of the systemic metabolic acidosis at a sufficiently early time point may lead to amelioration of enamel abnormalities.
Zebrafish acvr2a and acvr2b exhibit distinct roles in craniofacial development

To examine the roles of activin type II receptor signaling in craniofacial development, full‐length zebrafish acvr2a and acvr2b clones were isolated. Although ubiquitously expressed as maternal mRNAs and in early embryogenesis, by 24 hr postfertilization (hpf), acvr2a and acvr2b exhibit restricted expression in neural, hindbrain, and neural crest cells (NCCs). A morpholino‐based targeted protein depletion approach was used to reveal discrete functions for each acvr2 gene product. The acvr2a morphants exhibited defects in the development of most cranial NCC‐derived cartilage, bone, and pharyngeal tooth structures, whereas acvr2b morphant defects were largely restricted to posterior arch structures and included the absence and/or aberrant migration of posterior NCC streams, defects in NCC‐derived posterior arch cartilages, and dysmorphic pharyngeal tooth development. These studies revealed previously uncharacterized roles for acvr2a and acvr2b in hindbrain and NCC patterning, in NCC derived pharyngeal arch cartilage and joint formation, and in tooth development. Developmental Dynamics 233:1405–1418, 2005. © 2005 Wiley‐Liss, Inc.
Association Rule Mining and Classifier Approach for 48-Hour Rainfall Prediction Over Cuddalore Station of East Coast of India

The methodology of data mining techniques has been presented for the rain forecasting models for the Cuddalore (11°43' N/79°49' E) station of Tamilnadu in East Coast of India. Data mining approaches like classification and association mining was applied to generate results for rain prediction before 48 hour of the actual occurrence of the rain. The objective of this study is to demonstrate what relationship models are there between various atmospheric variables and to interconnect these variables according to the pattern obtained out of data mining technique. Using this approach rainfall estimates can be obtained to support the decisions to launch cloud- seeding operations. There are 3 main parts in this study. First, the obtained raw data was filtered using discretization approach based on the best fit ranges. Then, association mining has been performed on it using Predictive Apriori algorithm. Thirdly, the data has been validated using K * classifier approach. Results show that the overall
Simultaneous Learning of Several Bayesian Discriminant Functions by a Neural Network with Additional Nodes

We construct a one-hidden-layer neural network which can simultaneously learn several Bayesian discriminant functions. The method can be applied if there exists a common transformation which transforms them to sums of a common main function and simple additional functions respectively. In this paper, we treat concretely the case where the state-conditional probability distributions are normal and the additional simple functions are supposed to be linear. Corresponding to this decomposition, the neural network has a main structure and additional linear nodes.
Differential Modulation of TREM2 Protein during Postnatal Brain Development in Mice

During postnatal development, microglia, the resident innate immune cells of the central nervous system are constantly monitoring the brain parenchyma, cleaning the cell debris, the synaptic contacts overproduced and also maintaining the brain homeostasis. In this context, the postnatal microglia need some control over the innate immune response. One such molecule recently described to be involved in modulation of immune response is TREM2 (triggering receptor expressed on myeloid cells 2). Although some studies have observed TREM2 mRNA in postnatal brain, the regional pattern of the TREM2 protein has not been described. We therefore characterized the distribution of TREM2 protein in mice brain from Postnatal day (P) 1 to 14 by immunostaining. In our study, TREM2 protein was expressed only in microglia/macrophages and is developmentally downregulated in a region-dependent manner. Its expression persisted in white matter, mainly in caudal corpus callosum, and the neurogenic subventricular zone for a longer time than in grey matter. Additionally, the phenotypes of the TREM2+ microglia also differ; expressing CD16/32, MHCII and CD86 (antigen presentation markers) and CD68 (phagocytic marker) in different regions as well as with different intensity till P7. The mannose receptor (CD206) colocalized with TREM2 only at P1–P3 in the subventricular zone and cingulum, while others persisted at low intensities till P7. Furthermore, the spatiotemporal expression pattern and characterization of TREM2 indicate towards its other plausible roles in phagocytosis, progenitor’s fate determination or microglia phenotype modulation during postnatal development. Hence, the increase of TREM2 observed in pathologies may recapitulate their function during postnatal development, as a better understanding of this period may open new pathway for future therapies.
Climatic Correlates of Tree Mortality in Water- and Energy-Limited Forests

Recent increases in tree mortality rates across the western USA are correlated with increasing temperatures, but mechanisms remain unresolved. Specifically, increasing mortality could predominantly be a consequence of temperature-induced increases in either (1) drought stress, or (2) the effectiveness of tree-killing insects and pathogens. Using long-term data from California’s Sierra Nevada mountain range, we found that in water-limited (low-elevation) forests mortality was unambiguously best modeled by climatic water deficit, consistent with the first mechanism. In energy-limited (high-elevation) forests deficit models were only equivocally better than temperature models, suggesting that the second mechanism is increasingly important in these forests. We could not distinguish between models predicting mortality using absolute versus relative changes in water deficit, and these two model types led to different forecasts of mortality vulnerability under future climate scenarios. Our results provide evidence for differing climatic controls of tree mortality in water- and energy-limited forests, while highlighting the need for an improved understanding of tree mortality processes.
Apolipoprotein E isoforms and lipoprotein metabolism

Apolipoprotein (apo) E is a 299‐residue protein which functions as a key regulator of plasma lipid levels. Human apoE exists as three common isoforms and the parent form, apoE3, operates optimally in promoting clearance of triglyceride (TG)‐rich lipoproteins and is associated with normal plasma lipid levels. This result occurs because apoE3 possesses both the requisite lipid‐binding ability and affinity for the low density lipoprotein receptor (LDLR) to mediate appropriate lipolytic processing and endocytosis of TG‐rich lipoprotein remnant particles. ApoE2 which differs from apoE3 by the single amino acid substitution Arg158Cys located near the LDLR recognition site exhibits impaired binding to the receptor and an inability to promote clearance of TG‐rich lipoprotein remnant particles; this isoform is associated with Type‐III hyperlipoproteinemia. ApoE4 which differs from apoE3 by the single amino acid substitution Cys112Arg is also associated with dyslipidemia although binding of this isoform to the LDLR is unaffected. The amino acid substitution affects the organization and stability of both the N‐terminal helix bundle domain and separately folded C‐terminal domain so that apoE4 has enhanced lipid binding ability. As a consequence, apoE4 binds better than apoE3 to the surface of very low density lipoprotein (VLDL) particles and impairs their lipolytic processing in the circulation so that apoE4 is associated with a more pro‐atherogenic lipoprotein‐cholesterol distribution (higher VLDL‐cholesterol/high density lipoprotein‐cholesterol ratio). This review summarizes current understanding of the structural differences between apoE2, apoE3, and apoE4, and the molecular mechanisms responsible for the alterations in lipoprotein metabolism resulting from this polymorphism of apoE. Detailed knowledge of how expression of structurally distinct apoE variants modifies lipoprotein metabolism provides a basis for developing ways to manipulate the functionality of apoE in vivo. © 2014 IUBMB Life, 66(9):616–623, 2014
Functional Assessment of Cardiac Responses of Adult Zebrafish (Danio rerio) to Acute and Chronic Temperature Change Using High-Resolution Echocardiography

The zebrafish (Danio rerio) is an important organism as a model for understanding vertebrate cardiovascular development. However, little is known about adult ZF cardiac function and how contractile function changes to cope with fluctuations in ambient temperature. The goals of this study were to: 1) determine if high resolution echocardiography (HRE) in the presence of reduced cardiodepressant anesthetics could be used to accurately investigate the structural and functional properties of the ZF heart and 2) if the effect of ambient temperature changes both acutely and chronically could be determined non-invasively using HRE in vivo. Heart rate (HR) appears to be the critical factor in modifying cardiac output (CO) with ambient temperature fluctuation as it increases from 78 ± 5.9 bpm at 18°C to 162 ± 9.7 bpm at 28°C regardless of acclimation state (cold acclimated CA– 18°C; warm acclimated WA– 28°C). Stroke volume (SV) is highest when the ambient temperature matches the acclimation temperature, though this difference did not constitute a significant effect (CA 1.17 ± 0.15 μL at 18°C vs 1.06 ± 0.14 μl at 28°C; WA 1.10 ± 0.13 μL at 18°C vs 1.12 ± 0.12 μl at 28°C). The isovolumetric contraction time (IVCT) was significantly shorter in CA fish at 18°C. The CA group showed improved systolic function at 18°C in comparison to the WA group with significant increases in both ejection fraction and fractional shortening and decreases in IVCT. The decreased early peak (E) velocity and early peak velocity / atrial peak velocity (E/A) ratio in the CA group are likely associated with increased reliance on atrial contraction for ventricular filling.
Positron Emission Tomography Reporter Genes and Reporter Probes: Gene and Cell Therapy Applications

Positron emission tomography (PET) imaging reporter genes (IRGs) and PET reporter probes (PRPs) are amongst the most valuable tools for gene and cell therapy. PET IRGs/PRPs can be used to non-invasively monitor all aspects of the kinetics of therapeutic transgenes and cells in all types of living mammals. This technology is generalizable and can allow long-term kinetics monitoring. In gene therapy, PET IRGs/PRPs can be used for whole-body imaging of therapeutic transgene expression, monitoring variations in the magnitude of transgene expression over time. In cell or cellular gene therapy, PET IRGs/PRPs can be used for whole-body monitoring of therapeutic cell locations, quantity at all locations, survival and proliferation over time and also possibly changes in characteristics or function over time. In this review, we have classified PET IRGs/PRPs into two groups based on the source from which they were derived: human or non-human. This classification addresses the important concern of potential immunogenicity in humans, which is important for expansion of PET IRG imaging in clinical trials. We have then discussed the application of this technology in gene/cell therapy and described its use in these fields, including a summary of using PET IRGs/PRPs in gene and cell therapy clinical trials. This review concludes with a discussion of the future direction of PET IRGs/PRPs and recommends cell and gene therapists collaborate with molecular imaging experts early in their investigations to choose a PET IRG/PRP system suitable for progression into clinical trials.
Pla2g2a Attenuates Colon Tumorigenesis in Azoxymethane-Treated C57BL/6 Mice; Expression Studies Reveal Pla2g2a Target Genes and Pathways

Background: The group IIA secretory phospholipase A2 gene, Pla2g2a, confers resistance to intestinal tumorigenesis in the ApcMin/+ mouse model. However, it is unclear how Pla2g2a exerts its tumor-suppressive effects and whether its mode of action depends on Apc-germline mutations. Methods: We tested whether expression of a Pla2g2a transgene provides protection against carcinogen-induced colon tumors, and examined whether the normal colon microenvironment is modulated by Pla2g2a expression. Results: Pla2g2a strongly inhibited colon tumorigenesis in mice following treatment with the DNA alkylating agent azoxymethane (AOM). Moreover, AOM-induced duodenal tumors were also attenuated by Pla2g2a expression. These tumors demonstrated upregulation of β-catenin, indicative of involvement of the Wnt signaling pathway. Comparison of genome-wide microarray expression profiles of healthy (non-pathologic) colon tissues from Pla2g2a-transgenic to non-transgenic mice revealed 382 genes that were differentially expressed, comprising clusters of genes involved in inflammation and microbial defense, cell signaling and cell cycle, transactivation, apoptosis and mitochondrial function, DNA repair, and lipid and energy metabolism. Pathway analysis using Gene Set Enrichment Analysis (GSEA) indicated that Pla2g2a suppresses the expression of interferon-induced genes. Conclusion: Our results demonstrate that Pla2g2a attenuates colon tumorigenesis independent of Apc-germline mutations, and reveal Pla2g2a target genes and pathways in non-pathologic colon microenvironment that influence conditions for colorectal cancer development.
Clinical efficacy and safety of statins in managing cardiovascular risk

Since their introduction in the 1980s, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors (statins) have emerged as the one of the best-selling medication classes to date, with numerous trials demonstrating powerful efficacy in preventing cardiovascular outcomes. As our understanding of low-density lipoprotein cholesterol (LDL-C) and atherosclerosis continues to grow, the concept of ‘lower is better’ has corresponded with a ‘more is better’ approach to statin-based therapy. This review provides a detailed understanding of the clinical efficacy and safety of statins with a particular emphasis on the third generation drug, rosuvastatin.
Wireless power transmission technologies for solar power satellite

Solar Power Satellite (SPS) is an energy system which collects solar energy in space and transmits it to the ground. It has been believed as a promising infrastructure to resolve global environmental and energy problems for human beings. One of the most important technologies for the SPS is the wireless power transmission from the geostationary orbit to the ground. Microwave power transmission has been investigated and demonstrated for more than 40 years, but still requires further research regarding high-efficiency power conversion and high-accuracy beam control for SPS application. This paper introduces the concept of SPS, and presents microwave power transmission technologies necessary for SPS, their demonstration experiments both on the ground and in space in the near future, and future prospects towards commercial SPS.