Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Value of microRNA for Alzheimer’s Disease: A Systematic Review and Meta-Analysis

Sound evidence indicates that microRNAs (miRNAs) are aberrantly expressed in Alzheimer’s disease (AD) patients. We performed a systematic review and meta-analysis to investigate the role of miRNA in AD pathogenesis and their clinical diagnostic value; a systematic review of literature and meta-analysis of clinical trials were performed. In the systematic review, 236 papers were included, and we reviewed the dysregulated miRNA expression in different parts of AD patients in order to identify the relationship between aberrantly expressed miRNAs and AD pathology. In the subsequent meta-analysis, seven studies were statistically analyzed with the following results: pooled sensitivity 0.86 (95%CI 0.79–0.90), pooled specificity 0.87 (95%CI 0.72–0.95), diagnostic odds ratio (28.29), and the area under the curve (0.87). In conclusion, our review indicated that aberrant expression of various miRNAs plays an important role in the pathological process of AD, and statistical analysis of quantitative studies reveal the potential value of specific miRNAs in the diagnosis of AD.
Relationships between social norms, social network characteristics, and HIV risk behaviors in Thailand and the United States.

OBJECTIVE Social norms have been associated with a wide range of health behaviors. In this study, the authors examined whether the social norms of HIV risk behaviors are clustered within social networks and whether the norms of network members are linked to the risk behaviors of their social network members. DESIGN Data were collected from the baseline assessment of 354 networks with 933 participants in a network-oriented HIV prevention intervention targeting injection drug users in Philadelphia, United States, and Chiang Mai, Thailand. MAIN OUTCOME MEASURES Four descriptive HIV risk norms of sharing needles, cookers, and cotton and front- or back-loading among friends who inject were assessed. RESULTS Three of 4 injection risk norms (sharing needle, cookers, and cotton) were found to be significantly clustered. In Philadelphia, 1 network member's (the index participant) norms of sharing needles and front- or back-loading were found to be significantly associated with the network members' risk behaviors, and the norm of sharing cotton was marginally associated. CONCLUSION The results of this study suggest that among injection drug users, social norms are clustered within networks; social networks are a meaningful level of analyses for understanding how social norms lead to risk behaviors, providing important data for intervening to reduce injection-related HIV risks.
TiProD: the Tissue-specific Promoter Database

TiProD is a database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures of individual tissues, and to retrieve sets of promoters according to their tissue-specific activity or according to individual Gene Ontology terms the corresponding genes are assigned to. We have defined a measure for tissue-specificity that allows the user to discriminate between ubiquitously and specifically expressed genes. The database is accessible at .
Resistive Associative Processor

Associative Processor (AP) combines data storage and data processing, and functions simultaneously as a massively parallel array SIMD processor and memory. Traditionally, AP is based on CMOS technology, similar to other classes of massively parallel SIMD processors. The main component of AP is a Content Addressable Memory (CAM) array. As CMOS feature scaling slows down, CAM experiences scalability problems. In this work, we propose and investigate an AP based on resistive CAM-the Resistive AP (ReAP). We show that resistive memory technology potentially allows scaling the AP from a few millions to a few hundred millions of processing units on a single silicon die. We compare the performance and power consumption of a ReAP to a CMOS AP and a conventional SIMD accelerator (GPU) and show that ReAP, although exhibiting higher power density, allows better scalability and higher performance.
Asymptotically Optimal Scalar Quantizers for QIM Watermark Detection

This paper investigates asymptotically optimal scalar quantizers to address QIM watermark detection with i.i. d. host data and additive noise. False-alarm probability of detection is chosen as the cost to be minimized, keeping the embedding distortion and the miss probability upper-bounded. To avoid the intractability of false-alarm probability, Kullback distance between watermarked and non-watermarked data is adopted instead. The problem is then to seek the quantizer which maximizes the false-alarm error exponent under distortion constraint. Using Lagrange multiplier minimization, a quantizer updating Lloyd-Max-like procedure is used to solve the optimization. For experimental aspects, host data and noise have been set Gaussian. In comparison with uniform or Lloyd-Max quantizers, it turns out that detection performances can be notably enhanced by using proposed application-optimized quantizers. The gain is effective even for small number TV of sample at the detector input. However, this gain becomes more substantial as TV grows. This also emphasises that good quantizers in terms of distortion are not suitable for detection task
SPECIAL T OPIC: S CALING-UP I N E COLOGY

How to scale up from local-scale interactions to regional-scale dynamics is a critical issue in field ecology. We show how to implement a systematic approach to the problem of scaling up, using scale transition theory. Scale transition theory shows that dynamics on larger spatial scales differ from predictions based on the local dynamics alone because of an interaction between local- scale nonlinear dynamics and spatial variation in density or the environment. Based on this theory, a systematic approach to scaling up has four steps: (1) derive a model to translate the effects of local dynamics to the regional scale, and to identify key interactions between nonlin- earity and spatial variation, (2) measure local-scale model parameters to determine nonlinearities at local scales, (3) measure spatial variation, and (4) combine nonlinearity and variation measures to obtain the scale transition. We illustrate the approach, with an example from benthic stream ecology of caddisflies living in rif- fles. By sampling from a simulated system, we show how collecting the appropriate data at local (riffle) scales to measure nonlinearities, combined with measures of spatial variation, leads to the correct inference for dynamics at the larger scale of the stream. The approach provides a way to investigate the mechanisms and con- sequences of changes in population dynamics with spa- tial scale using a relatively small amount of field data.
Connexin‐specific cell‐to‐cell transfer of short interfering RNA by gap junctions

The purpose of this study was to determine whether oligonucleotides the size of siRNA are permeable to gap junctions and whether a specific siRNA for DNA polymerase β (pol β) can move from one cell to another via gap junctions, thus allowing one cell to inhibit gene expression in another cell directly. To test this hypothesis, fluorescently labelled oligonucleotides (morpholinos) 12, 16 and 24 nucleotides in length were synthesized and introduced into one cell of a pair using a patch pipette. These probes moved from cell to cell through gap junctions composed of connexin 43 (Cx43). Moreover, the rate of transfer declined with increasing length of the oligonucleotide. To test whether siRNA for pol β was permeable to gap junctions we used three cell lines: (1) NRK cells that endogenously express Cx43; (2) Mβ16tsA cells, which express Cx32 and Cx26 but not Cx43; and (3) connexin‐deficient N2A cells. NRK and Mβ16tsA cells were each divided into two groups, one of which was stably transfected to express a small hairpin RNA (shRNA), which gives rise to siRNA that targets pol β. These two pol β knockdown cell lines (NRK‐kcdc and Mβ16tsA‐kcdc) were co‐cultured with labelled wild type, NRK‐wt or Mβ16tsA‐wt cells or N2A cells. The levels of pol β mRNA and protein were determined by semiquantitative RT‐PCR and immunoblotting. Co‐culture of Mβ16tsA‐kcdc cells with Mβ16tsA‐wt, N2A or NRK‐wt cells had no effect on pol β levels in these cells. Similarly, co‐culture of NRK‐kcdc with N2A cells had no effect on pol β levels in the N2A cells. In contrast, co‐culture of NRK‐kcdc with NRK‐wt cells resulted in a significant reduction in pol β in the wt cells. The inability of Mβ16tsA‐kcdc cells to transfer siRNA is consistent with the fact that oligonucleotides of the 12 nucleotide length were not permeable to Cx32/Cx26 channels. This suggested that Cx43 but not Cx32/Cx26 channels allowed the cell‐to‐cell movement of the siRNA. These results support the novel hypothesis that non‐hybridized and possible hybridized forms of siRNA can move between mammalian cells through connexin‐specific gap junctions.
The SPOROCYTELESS/NOZZLE Gene Is Involved in Controlling Stamen Identity in Arabidopsis1[W][OA]

The stamen, which consists of an anther and a filament, is the male reproductive organ in a flower. The specification of stamen identity in Arabidopsis (Arabidopsis thaliana) is controlled by a combination of the B genes APETALA3 (AP3) and PISTILLATA, the C gene AGAMOUS (AG), and the E genes SEPALLATA1 (SEP1) to SEP4. The “floral organ-building” gene SPOROCYTELESS/NOZZLE (SPL/NZZ) plays a central role in regulating anther cell differentiation. However, much less is known about how “floral organ identity” and floral organ-building genes interact to control floral organ development. In this study, we report that ectopic expression of SPL/NZZ not only affects flower development in the wild-type background but also leads to the transformation of petal-like organs into stamen-like organs in flowers of ap2-1, a weak ap2 mutant allele. Moreover, our loss-of-function analysis indicates that the spl/nzz mutant enhances the phenotype of the ag weak allele ag-4. Furthermore, ectopic expression and overexpression of SPL/NZZ altered expression of AG, SEP3, and AP2 in rosette leaves and flowers, while ectopic expression of SPL/NZZ resulted in ectopic expression of AG and SEP3 in the outer whorls of flowers. Our results indicate that the SPL/NZZ gene is engaged in controlling stamen identity via interacting with genes required for stamen identity in Arabidopsis.
Applying Model Learning and Domain Specific Languages to Refactor Legacy Software

Many organizations have serious challenges in maintaining complex legacy software systems to continue being competitive in today’s fast-changing business. The challenges include a lack of documentation, absence of original developers, and embedded business knowledge in the source code. The challenges to maintain legacy industrial software and the benefits of developing new software implementation are investigated. In addition, a combination of model learning, model transformations, and equivalence checking is applied to refactor complex legacy software and to improve future maintainability. This combination of approaches can produce a new software implementation that has the same behavior as its legacy version and reduces its complexity.
The Amsterdam Resting-State Questionnaire reveals multiple phenotypes of resting-state cognition

Resting-state neuroimaging is a dominant paradigm for studying brain function in health and disease. It is attractive for clinical research because of its simplicity for patients, straightforward standardization, and sensitivity to brain disorders. Importantly, non-sensory experiences like mind wandering may arise from ongoing brain activity. However, little is known about the link between ongoing brain activity and cognition, as phenotypes of resting-state cognition—and tools to quantify them—have been lacking. To facilitate rapid and structured measurements of resting-state cognition we developed a 50-item self-report survey, the Amsterdam Resting-State Questionnaire (ARSQ). Based on ARSQ data from 813 participants assessed after 5 min eyes-closed rest in their home, we identified seven dimensions of resting-state cognition using factor analysis: Discontinuity of Mind, Theory of Mind, Self, Planning, Sleepiness, Comfort, and Somatic Awareness. Further, we showed that the structure of cognition was similar during resting-state fMRI and EEG, and that the test-retest correlations were remarkably high for all dimensions. To explore whether inter-individual variation of resting-state cognition is related to health status, we correlated ARSQ-derived factor scores with psychometric scales measuring depression, anxiety, and sleep quality. Mental health correlated positively with Comfort and negatively with Discontinuity of Mind. Finally, we show that sleepiness may partially explain a resting-state EEG profile previously associated with Alzheimer's disease. These findings indicate that the ARSQ readily provides information about cognitive phenotypes and that it is a promising tool for research on the neural correlates of resting-state cognition in health and disease.
Template Switches during Plus-Strand DNA Synthesis of Duck Hepatitis B Virus Are Influenced by the Base Composition of the Minus-Strand Terminal Redundancy

ABSTRACT Two template switches are necessary during plus-strand DNA synthesis of the relaxed circular (RC) form of the hepadnavirus genome. The 3′ end of the minus-strand DNA makes important contributions to both of these template switches. It acts as the donor site for the first template switch, called primer translocation, and subsequently acts as the acceptor site for the second template switch, termed circularization. Circularization involves transfer of the nascent 3′ end of the plus strand from the 5′ end of the minus-strand DNA to the 3′ end, where further elongation can lead to production of RC DNA. In duck hepatitis B virus (DHBV), a small terminal redundancy (5′r and 3′r) on the ends of the minus-strand DNA has been shown to be important, but not sufficient, for circularization. We investigated what contribution, if any, the base composition of the terminal redundancy made to the circularization process. Using a genetic approach, we found a strong positive correlation between the fraction of A and T residues within the terminal redundancy and the efficiency of the circularization process in those variants. Additionally, we found that the level of in situ priming increases, at the expense of primer translocation, as the fraction of A and T residues in the 3′r decreases. Thus, a terminal redundancy rich in A and T residues is important for both plus-strand template switches in DHBV.
The Role of Serum Adiponectin for Outcome Prediction in Patients with Dilated Cardiomyopathy and Advanced Heart Failure

Clinical interpretation of patients' plasma adiponectin (APN) remains challenging; its value as biomarker in dilated cardiomyopathy (DCM) is equivocal. We evaluated whether circulating APN level is an independent predictor of composite outcome: death, left ventricle assist device (LVAD) implantation, and heart transplantation (HT) in patients with nonischemic DCM. 57 patients with nonischemic DCM (average LV diastolic diameter 6.85 cm, LV ejection fraction 26.63%, and pulmonary capillary wedge pressure 22.06 mmHg) were enrolled. Patients underwent echocardiography, right heart catheterization, and endomyocardial biopsy. During a mean follow-up of 33.42 months, 15 (26%) patients died, 12 (21%) patients underwent HT, and 8 (14%) patients were implanted with LVAD. APN level was significantly higher in patients who experienced study endpoints (23.4 versus 10.9 ug/ml, p = 0.01). APN was associated with worse outcome in univariate Cox proportional hazards model (HR 1.04, CI 1.02–1.07, p = 0.001) but lost significance adjusting for other covariates. Average global strain (AGS) is an independent outcome predictor (HR 1.42, CI 1.081–1.866, p = 0.012). Increased circulating APN level was associated with higher mortality and may be an additive prognostic marker in DCM with advanced HF. Combination of serum (APN, BNP, TNF-α) and echocardiographic (AGS) markers may increase the HF predicting power for the nonischemic DCM patients.
IEEE 1451 Standard in 6LoWPAN Sensor Networks Using a Compact Physical-Layer Transducer Electronic Datasheet

The adoption of the Internet Protocol version 6 (IPv6) networking in IEEE 802.15. 4 sensor networks, using IEEE 1451 standardization, increases the interoperability of low-power smart-sensor devices over IP networks. This paper explains the design and implementation of the IPv6 sensor network over low-power wireless personal-area networks (6LoWPANs), and it uses the IEEE 1451 standard in IEEE 802.15. 4 sensor networks. We propose the design of the 6LoWPAN physical-layer transducer electronic datasheet (PHY-TEDS) using data-type redefinition with the header compression. Each TEDS was analyzed in terms of memory size, obtaining a reduction of 48% in the PHY-TEDS and 25% in the meta-TEDS with respect to the standard definition. Finally, the IEEE 1451 commands are encapsulated in User Datagram Protocol datagrams to establish communication from the network capable application processor to the wireless transducer interface module in an environmental monitoring application.
Carbon stock in aboveground biomass of vegetation at the High Tatra Mts. twelve years after disturbance

Abstract The paper focused on the estimation of aboveground biomass and its carbon stock in the vegetation cover on the territory of the High Tatras twelve years after a large-scale wind disturbance. Besides biomass quantification of main plant groups (i.e. trees and ground vegetation) we considered plant components with special regard to carbon rotation rate. The measurements were performed on two transects each containing 25 plots sized 4 × 4 m. Height and stem diameter of all trees on the plots were measured and used for biomass estimation. To quantify the biomass of ground vegetation, six subplots sized 20 × 20 cm were systematically placed on each plot and the aboveground biomass was harvested. The plant material was subjected to chemical analyses to quantify its carbon concentration. The study showed that while the wind disturbance caused dramatic decrease of carbon stock, young post-disturbance stands with abundant ground vegetation, represented large carbon flux via litter fall. Twelve years after the wind disturbance, the trees contributed to carbon stock more than the ground vegetation. However, the opposite situation was recorded for the carbon flux to litter that was related to the dominance of annual plants in the above-ground biomass of ground vegetation. The carbon stock in the biomass of young trees and ground vegetation represented about 8,000 kg per ha. The young stands manifested a dynamic growth, specifically the aboveground biomass increased annually by one third. The results confirmed different carbon regimes in the former old (pre-disturbance) and sparse young (post-disturbance) stands.
Directional Total Variation

This paper introduces a “directional total variation” (TV) where the gradients are weighted depending on their direction. The introduced directional TV has increased (and tunable) sensitivity to variations at a selected direction. In order to demonstrate the utility of the directional TV, we consider an image denoising formulation. This formulation requires the realization of the “proximal map” of the directional TV. Therefore, it is relevant for more general inverse problem settings as well. We derive an algorithm that solves the problem and use the algorithm to study the effects of the parameters of the directional TV.
REE partition among zircon, orthopyroxene, amphibole and garnet in a high-grade metabasic system

Abstract A mafic amphibole-bearing granulite with porphyroblastic garnet was investigated to evaluate: (1) the rare earth element (REE) partition among garnet, zircon, orthopyroxene and amphibole during the metamorphic evolution; (2) the significance of the REE distribution along lobes and bights of reabsorbed garnet rim; and (3) REE distribution coefficient values (DREE) suggestive of chemical equilibrium, assuming garnet as a reference. The results have been compared with those deriving from an intermediate granulite containing porphyroblastic garnet, without amphibole. Porphyroblastic garnet from both samples is rimmed by a continuous corona formed during post-peak decompression characterized by REE-enriched lobes and REE-poor bights. The amphiboles from corona have various REE abundances, reflecting a different dissolution rate of original garnet rim. The initial slow rate of garnet dissolution caused high REE concentration in the new garnet rim due to intra-crystalline diffusion, leading to the formation of REE-poorer amphiboles in corona. Subsequently, under an increasing geothermal gradient and fluid-present conditions, the faster dissolution of garnet determined the formation of bights and the transfer of REEs towards the corona. The timing of garnet growth and its dissolution were checked by U–Pb zircon ages. The zircons dated from 339 Ma to 303 Ma in two rock types combined with the garnet domains (core, outer core, rim) show similar distribution of patterns relative to heavy rare earth elements for zircon and garnet (DHREEzrn/grt), suggesting chemical equilibrium. Zircons dated at c. 300 Ma do not appear in equilibrium with REE-rich garnet lobes, and younger zircons (278 Ma) show a new equilibrium with REE-poor garnet bights. On this basis, the DHREEamph/grt values obtained in specific textural sites might be interpreted as suggestive of equilibrium under granulite conditions.
The Kinesin Walk: A Dynamic Model with Elastically Coupled Heads

Recently individual two-headed kinesin molecules have been studied in in vitro motility assays revealing a number of their peculiar transport properties. In this paper we propose a simple and robust model for the kinesin stepping process with elastically coupled Brownian heads that show all of these properties. The analytic and numerical treatment of our model results in a very good fit to the experimental data and practically has no free parameters. Changing the values of the parameters in the restricted range allowed by the related experimental estimates has almost no effect on the shape of the curves and results mainly in a variation of the zero load velocity that can be directly fitted to the measured data. In addition, the model is consistent with the measured pathway of the kinesin ATPase.
Reading Performance in Older Adults with Good Acuity

Purpose. This study evaluated factors affecting reading performance in a sample (N = 544) of older adults (mean age 72.8 years, range 58 to 102) with good high-contrast acuity (≥20/32). Methods. Using the Pepper Reading Test, the relationship between reading rate and several vision measures was assessed. Results. Mean corrected reading rate fell substantially over the age range tested despite the fact that these individuals all had good acuity. However, multiple regression analysis indicated that when other measures were taken into account (most notably, low-contrast vision, motor ability, and attentional field integrity), age was not a significant independent predictor of corrected reading rate. Conclusion. Reading is an important skill, and ways of enhancing reading performance should be explored. Good high-contrast acuity does not assure that older individuals can read satisfactorily.