Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorodopa is a Promising Fluorine‐19 MRI Probe for Evaluating Striatal Dopaminergic Function in a Rat Model of Parkinson's Disease

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra projecting to the striatum. It has been estimated that approximately 80% of the striatal dopamine and 50% of nigral dopaminergic neurons are lost before the onset of typical motor symptoms, indicating that early diagnosis of PD using noninvasive imaging is feasible. Fluorine‐19 (19F) magnetic resonance imaging (MRI) represents a highly sensitive, easily available, low‐background, and cost‐effective approach to evaluate dopaminergic function using non‐radioactive fluorine‐containing dopaminergic agents. The aim of this study was to find a potent 19F MRI probe to evaluate dopaminergic presynaptic function in the striatum. To select candidates for 19F MRI probes, we investigated the following eight non‐radioactive fluorine‐containing dopaminergic agents: fluorodopa (F‐DOPA), F‐tyrosine, haloperidol, GBR13069 duhydrochloride, GBR12909 duhydrochloride, 3‐bis‐(4‐fluorophenyl) methoxytropane hydrochloride, flupenthixol, and fenfluramine. In 19F nuclear magnetic resonance measurements, F‐tyrosine and F‐DOPA displayed a relatively higher signal‐to‐noise ratio value in brain homogenates than in others. F‐DOPA, but not F‐tyrosine, induced the rotational behavior in a 6‐hydroxydopamine (6‐OHDA)‐induced hemiparkinsonian rat model. In addition, a significantly high amount of F‐DOPA accumulated in the ipsilateral striatum of hemiparkinsonian rats after the injection. We performed 19F MRI in PC12 cells and isolated rat brain using a 7T MR scanner. Our findings suggest that F‐DOPA is a promising 19F MRI probe for evaluating dopaminergic presynaptic function in the striatum of hemiparkinsonian rats. © 2016 Wiley Periodicals, Inc.
Informed Single Channel Speech Separation with time-frequency exemplar GMM-HMM model

In recent studies, the problem of Single Channel Speech Separation (SCSS) have been efficiently tackled by introducing additional cues from the original target source in the form of Informed Source Separation (ISS). In this paper, a more realistic situation is considered where an additional user/listener generated Exemplar source is introduced to aid the separation process instead of using the original target source. The Exemplar source consists of patterns that need to be transformed, extracted, regulated and calibrated to generate an utterance dependent (UD) model that could statistically represent the target source. The proposed method uses general speaker independent (SI) features along with the generated UD features are modelled and combined in a joint probability model to achieve reliable separation. Unlike most model-based approaches, the proposed method does not require Speaker Dependent training on individual sources of the mixture, and is therefore much more efficient and less restrictive.
Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

Abstract Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site‐associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285–621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R 2 adj = .66–.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random‐forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.
RI-COTS: Trading performance for reliability improvements in commercial of the shelf systems

The flexibility of software-based fault tolerant approaches in providing the required level of reliability Commer-cial-Off-The Shelf (COTS) devices made them the first choice in designing safety-critical systems. In this paper, we propose a reliability improvement method for COTS-based systems, so-called, RI-COTS. The main idea behind RI-COTS is to establish a tradeoff between reliability and performance of COTS system through controlling redundant execution at instruction level. RI-COTS is implemented on LEON2 processor VHDL model. Our simulation results show that comparing with the most related studies, RI-COTS can improve the fault detection capability by 20% with only 4% performance overhead.
Gaussian pulse approximation using standard CMOS and its application for sub‐GHz UWB impulse radio

Gaussian pulse is widely used in communication systems. The true Gaussian function is not physically realizable, but it can be approximated through linear functions. This paper presents a Gaussian pulse approximation approach to generate a quasi‐Gaussian pulse by using the transient response of a CMOS inverter. The basic structure of the proposed design includes a digital variable square pulse generator, a Gaussian pulse generator and a small antenna model. The digital variable square pulse generator makes the amplitude and width of the generated quasi‐Gaussian pulse tunable. The proposed pulse generator works well for three different electrical small antenna models. The simulation results show that the generated pulse approximates the Gaussian shape very well and the radiated signal at the antennas is compliant with the Federal Communication Commission's spectral mask for the 0–960 MHz band. The simple structure of this Gaussian pulse generator lends itself to a low‐power, single‐chip UWB transceiver solution. Copyright © 2008 John Wiley & Sons, Ltd.
Influence of Processing Temperature on Microcellular Injection-Moulded Wood–Polypropylene Composites

Microcellular wood fibre reinforced polymer materials are significant because of their possibility to reduce the density of automotive components through microcellular structure, process and product part advantages, and as a new development with bio-fibre strengthened plastics. Soft wood fibre reinforced PP composites in box part and panel shape were prepared by an injection moulding process. Polymeric microspheres as a chemical foaming agent (endothermic) were used to produce the microcellular composites. The influence of injection moulding processing temperature on the microcellular structure and properties (tensile and flexural properties, notched charpy impact strength) was investigated by varying the temperature over the 150-170°C, 160-180 °C and 170-190 °C. A comparative study of cell morphology, weight reduction and mechanical properties was conducted between box part and panel. Microcell morphology, cell size, shape and distribution were investigated using scanning electron micrographs. The results indicated that the lower processing temperature should be below the range of 170-190 °C and processing temperature at 160-180 °C, where the composites showed finer cellular structure compared to other processing temperatures. The mechanical properties did not differ with the variation of processing temperature regardless of composite types (box part or panel). Cellular structure changes in the box part were found considering near or far from injecting point.
Age and cellular composition influence overall survival in a collective of non-immunocompromised patients with EBV-positive diffuse large B-cell lymphoma from a German lymphoma center

Abstract We investigated 41 diffuse large B-cell lymphomas (DLBCL) diagnosed at one center harboring ≥50% of latently Epstein–Barr virus (EBV)-infected neoplastic cells occurring in 34 patients aged ≥50 years and in 7 patients younger than 50 years in the absence of any known immunodeficiency for the expression patterns of EBV latent and immediate-early proteins, for the differentiation stage of the neoplastic cells, the presence of cytogenetic alterations and a possible co-infection with the human herpes virus (HHV)-8. Here, we show that EBV-positive DLBCLs rarely arise from naïve and more frequently from post-germinal center B-cells that often contain crippling immunoglobulin gene mutations. Most of the lymphomas did not exhibit breaks in the BCL2, BCL6, and MYC genes and none of the cases investigated contained HHV-8 sequences. Patients aged <50 years performed better than older ones while in patients aged ≥50 years only the cellular composition had an impact on overall survival.
Conserved S-Layer-Associated Proteins Revealed by Exoproteomic Survey of S-Layer-Forming Lactobacilli

ABSTRACT The Lactobacillus acidophilus homology group comprises Gram-positive species that include L. acidophilus, L. helveticus, L. crispatus, L. amylovorus, L. gallinarum, L. delbrueckii subsp. bulgaricus, L. gasseri, and L. johnsonii. While these bacteria are closely related, they have varied ecological lifestyles as dairy and food fermenters, allochthonous probiotics, or autochthonous commensals of the host gastrointestinal tract. Bacterial cell surface components play a critical role in the molecular dialogue between bacteria and interaction signaling with the intestinal mucosa. Notably, the L. acidophilus complex is distinguished in two clades by the presence or absence of S-layers, which are semiporous crystalline arrays of self-assembling proteinaceous subunits found as the outermost layer of the bacterial cell wall. In this study, S-layer-associated proteins (SLAPs) in the exoproteomes of various S-layer-forming Lactobacillus species were proteomically identified, genomically compared, and transcriptionally analyzed. Four gene regions encoding six putative SLAPs were conserved in the S-layer-forming Lactobacillus species but not identified in the extracts of the closely related progenitor, L. delbrueckii subsp. bulgaricus, which does not produce an S-layer. Therefore, the presence or absence of an S-layer has a clear impact on the exoproteomic composition of Lactobacillus species. This proteomic complexity and differences in the cell surface properties between S-layer- and non-S-layer-forming lactobacilli reveal the potential for SLAPs to mediate intimate probiotic interactions and signaling with the host intestinal mucosa.
Absolute quantification of BCR-ABL1 fusion transcripts in pediatric chronic myeloid leukemia

Yanjing Tang*, Xiaoyuan Wei*, Jing Chen*, Yunzhi Du, Huiling Chu, Louise Mao, Jun Chen, Qing Xu, Jingyan Tang, Shuhong Shen and Mao Mao Department of Hematology and Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Translational Bioscience and Diagnostics, WuXi AppTec Co., Ltd., Waigaoqiao Free Trade Zone, Shanghai, China; Department of Cognitive Science, University of California Berkeley, Berkeley, CA, USA
A platform for functional assessment of large variant libraries in mammalian cells

Abstract Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created. Second, a single variant from a library of transfected, promoter-less plasmids is recombined into the landing pad in each cell. Thus, every cell in the recombined pool expresses a single variant, allowing for parallel, sequencing-based assessment of variant effect. We describe a method for incorporating a single landing pad into a defined site of a cell line of interest, and show that our approach can be used generate more than 20 000 recombinant cells in a single experiment. Finally, we use our platform in combination with a sequencing-based assay to explore the N-end rule by simultaneously measuring the effects of all possible N-terminal amino acids on protein expression.
Natural Variation in Decision-Making Behavior in Drosophila melanogaster

There has been considerable recent interest in using Drosophila melanogaster to investigate the molecular basis of decision-making behavior. Deciding where to place eggs is likely one of the most important decisions for a female fly, as eggs are vulnerable and larvae have limited motility. Here, we show that many natural genotypes of D. melanogaster prefer to lay eggs near nutritious substrate, rather than in nutritious substrate. These preferences are highly polymorphic in both degree and direction, with considerable heritability (0.488) and evolvability. Relative preferences are modulated by the distance between options and the overall concentration of ethanol, suggesting Drosophila integrate many environmental factors when making oviposition decisions. As oviposition-related decisions can be efficiently assessed by simply counting eggs, oviposition behavior is an excellent model for understanding information processing in insects. Associating natural genetic polymorphisms with decision-making variation will shed light on the molecular basis of host choice behavior, the evolutionary maintenance of genetic variation, and the mechanistic nature of preference variation in general.
A Rough Set Approach to Data Imputation and Its Application to a Dissolved Gas Analysis Dataset

Missing values are a common occurrence in a number of real world databases, and various statistical methods have been developed to address this problem, which is referred to as missing data imputation. In the detection and prediction of incipient faults in power transformers using Dissolved Gas Analysis (DGA), the problem of missing values is influential and has resulted in inconclusive decision-making. Previous methods used for handling missing data (e.g., Deleting cases with incomplete information or substituting the missing values with estimated mean scores), although simple to implement, are problematic because those methods may result in biased data models. Fortunately, recent advances in theoretical and computational statistics have led to more feasible techniques to address the missing data problem.
An improved template-matching method for real-time detection of abnormal heartbeats

This study proposes an improved template-matching method which can automatically update the normal template heartbeats with the change in heart rate, and compare the input heartbeats with the template to detect abnormal heartbeats in real time. If an input heartbeat has a cross-correlation coefficient of less than 0.6 or a mean-square difference larger than 1.0 in comparison with the template, it is identified as abnormal. The study results show that if the normal template is not updated with the heart rate, normal heartbeats may be misjudged as abnormal when exercise changes the heart rate and heartbeat waveforms. The results also demonstrate that the proposed method can accurately identify abnormal heartbeats of ventricular fibrillation (VF) and ventricular tachycardia (VT) using ECG records 426 and 607 from the Malignant Ventricular Arrhythmia Database.
Acupuncture for peripheral joint osteoarthritis: a systematic review and meta-analysis.

OBJECTIVE To evaluate the evidence for the effectiveness of acupuncture in peripheral joint osteoarthritis (OA). METHODS Systematic searches were conducted on Medline, Embase, AMED, Cochrane Library, CINAHL, British Nursing Index, PsychINFO and CAMPAIN until July 2005. Hand-searches included conference proceedings and our own files. There were no restrictions regarding the language of publication. All randomized controlled trials (RCTs) of acupuncture for patients with peripheral joint OA were considered for inclusion. Trials assessing needle acupuncture with or without electrical stimulation were considered if sham- or placebo-controlled or controlled against a comparator intervention. Trials testing other forms of acupuncture were excluded. Methodological quality was assessed and, where possible, meta-analyses were performed. RESULTS Thirty-one possibly relevant studies were identified and 18 RCTs were included. Ten trials tested manual acupuncture and eight trials tested electro-acupuncture. Overall, ten studies demonstrated greater pain reduction in acupuncture groups compared with controls. The meta-analysis of homogeneous data showed a significant effect of manual acupuncture compared with sham acupuncture (standardized mean difference 0.24, 95% confidence interval 0.01-0.47, P = 0.04, n = 329), which is supported by data for knee OA. The extent of heterogeneity in trials of electro-acupuncture prevented a meaningful meta-analysis. CONCLUSIONS Sham-controlled RCTs suggest specific effects of acupuncture for pain control in patients with peripheral joint OA. Considering its favourable safety profile acupuncture seems an option worthy of consideration particularly for knee OA. Further studies are required particularly for manual or electro-acupuncture in hip OA.
Updated regulation curation model at the Saccharomyces Genome Database

Abstract The Saccharomyces Genome Database (SGD) provides comprehensive, integrated biological information for the budding yeast Saccharomyces cerevisiae, along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms. We have recently expanded our data model for regulation curation to address regulation at the protein level in addition to transcription, and are presenting the expanded data on the ‘Regulation’ pages at SGD. These pages include a summary describing the context under which the regulator acts, manually curated and high-throughput annotations showing the regulatory relationships for that gene and a graphical visualization of its regulatory network and connected networks. For genes whose products regulate other genes or proteins, the Regulation page includes Gene Ontology enrichment analysis of the biological processes in which those targets participate. For DNA-binding transcription factors, we also provide other information relevant to their regulatory function, such as DNA binding site motifs and protein domains. As with other data types at SGD, all regulatory relationships and accompanying data are available through YeastMine, SGD’s data warehouse based on InterMine. Database URL: http://www.yeastgenome. org
Placenta and Placental Derivatives in Regenerative Therapies: Experimental Studies, History, and Prospects

Placental structures, capable to persist in a genetically foreign organism, are a natural model of allogeneic engraftment carrying a number of distinctive properties. In this review, the main features of the placenta and its derivatives such as structure, cellular composition, immunological and endocrine aspects, and the ability to invasion and deportation are discussed. These features are considered from a perspective that determines the placental material as a unique source for regenerative cell therapies and a lesson for immunological tolerance. A historical overview of clinical applications of placental extracts, cells, and tissue components is described. Empirically accumulated data are summarized and compared with modern research. Furthermore, we define scopes and outlooks of application of placental cells and tissues in the rapidly progressing field of regenerative medicine.
Randomized controlled trial of mindfulness-based therapy for dyspnea in chronic obstructive lung disease.

OBJECTIVES Patients with chronic obstructive lung disease (COPD) suffer from significant dyspnea and may benefit from complementary and alternative medicine (CAM) therapies aimed at mitigating symptoms. The objective of this study was to test the efficacy of a mindfulness-based breathing therapy (MBBT) on improving symptoms and health-related quality of life in those with COPD. DESIGN We conducted a randomized controlled trial of 8-week mindfulness-based breathing therapy (MBBT) compared to support groups to test efficacy on improving symptoms and health-related quality of life in those with COPD. SETTING The setting for this study was an academic-affiliated veterans healthcare system. SUBJECTS The subjects consisted of 86 patients with COPD. INTERVENTIONS MBBT included weekly meetings practicing mindfulness mediation and relaxation response. OUTCOME MEASURES The main outcome measure was a post 6-minute-walk test (6MWT) Borg dyspnea assessment. Other outcome measures included health-related quality of life measures, 6MWT distance, symptom scores, exacerbation rates, and measures of stress and mindfulness. Analysis of covariance compared differences in outcomes between groups; paired t test evaluated changes within groups. RESULTS Participants were predominantly elderly men with moderate to severe COPD. We found no improvements in dyspnea (post 6MWT Borg difference between the MBBT and support group was 0.3 (95% confidence interval [CI]: -1.1, 1.7). We found no differences between groups in almost all other outcome measures by either intention-to-treat analysis or within the subset that completed assigned group sessions. For the physical summary scale of the generic Short Form-36 for Veterans, the difference between outcomes favored the support group (4.3, 95% CI: 0.4, 8.1). Participant retention was low compared to mind-body trials that randomize from CAM wait lists. CONCLUSIONS This trial found no measurable improvements in patients with COPD receiving a mindfulness-based breathing CAM therapy compared to a support group, suggesting that this intervention is unlikely to be an important therapeutic option for those with moderate-to-severe COPD.
Sequential Hypothesis Testing based Polling Interval Adaptation in Wireless Sensor Networks for IoT Applications

It is well known that duty-cycling control by dynamically adjusting the polling interval according to the traffic loads can effectively achieve power saving in wireless sensor networks. Thus, there has been a significant research effort in developing polling interval adaptation schemes. Especially, Dynamic Low Power Listening (DLPL) scheme is one of the most widely adopted open-looping polling interval adaptation techniques in wireless sensor networks. In DLPL scheme, if consecutive idle (busy) samplings reach a given fixed threshold, the polling interval is increased (decreased). However, due to the trial-and-error based approach, it may significantly deteriorate the system performance depending on given threshold parameters. In this paper, we propose a novel DLPL scheme, called SDL (Sequential hypothesis testing based Dynamic LPL), which employs sequential hypothesis testing to decide whether to change the polling interval conforming to various traffic conditions. Simulation results show that SDL achieves substantial power saving over state-of-the-art DLPL schemes.