Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliability of White Matter Microstructural Changes in HIV Infection: Meta-Analysis and Confirmation

BACKGROUND: Diffusion tensor imaging has been widely used to measure HIV effects on white matter microarchitecture. While many authors have reported reduced fractional anisotropy and increased mean diffusivity in HIV, quantitative inconsistencies across studies are numerous. PURPOSE: Our aim was to evaluate the consistency across studies of HIV effects on DTI measures and then examine the DTI reliability in a longitudinal seropositive cohort. DATA SOURCES: Published studies and investigators. STUDY SELECTION: The meta-analysis included 16 cross-sectional studies reporting fractional anisotropy and 12 studies reporting mean diffusivity in the corpus callosum. DATA ANALYSIS: Random-effects meta-analysis was used to estimate study standardized mean differences and heterogeneity. DTI longitudinal reliability was estimated in seropositive participants studied before and 3 and 6 months after beginning treatment. DATA SYNTHESIS: Meta-analysis revealed lower fractional anisotropy (standardized mean difference, −0.43; P < .001) and higher mean diffusivity (standardized mean difference, 0.44; P < .003) in seropositive participants. Nevertheless, between-study heterogeneity accounted for 58% and 66% of the observed variance (P < .01). In contrast, the longitudinal cohort fractional anisotropy was higher and mean diffusivity was lower in seropositive participants (both, P < .001), and fractional anisotropy and mean diffusivity measures were very stable during 6 months, with intraclass correlation coefficients all >0.96. LIMITATIONS: Many studies pooled participants with varying treatments, ages, and disease durations. CONCLUSIONS: HIV effects on WM microstructure had substantial variations that could result from acquisition, processing, or cohort-selection differences. When acquisition parameters and processing were carefully controlled, the resulting DTI measures did not show high temporal variation. HIV effects on WM microstructure may be age-dependent. The high longitudinal reliability of DTI WM microstructure measures makes them promising disease-activity markers.
Station Location - Complexity and Approximation

We consider a geometric set covering problem. In its original form it consists of adding stations to an existing geometric transportation network so that each of a given set of settlements is not too far from a station. The problem is known to be NP-hard in general. However, special cases with certain properties have been shown to be efficiently solvable in theory and in practice, especially if the covering matrix has (almost) consecutive ones property. In this paper we are narrowing the gap between intractable and efficiently solvable cases of the problem. We also present an approximation algorithm for cases with almost consecutive ones property.
Can cognitive exercise prevent the onset of dementia? Systematic review of randomized clinical trials with longitudinal follow-up.

OBJECTIVES Epidemiological and preclinical studies suggest that mental activity levels may alter dementia risk. Clinical trials are now beginning to address the key issues of persistence of effect over extended follow-up and transfer of effect to nontrained domains. The aim of this report was to therefore systematically review results from clinical trials, which have examined the effect of cognitive exercise on longitudinal cognitive performance in healthy elderly individuals. METHODS MEDLINE, PubMed, and key references were used to generate an initial list of relevant studies (N = 54). These were reviewed to identify randomized controlled trials, which tested the effect of a discrete cognitive exercise training regime on longitudinal (>3 months) posttraining neuropsychological performance in healthy older adults. Seven RCTs met entry criteria. Prechange and postchange scores were integrated using a random effects weighted mean difference (WMD) meta-analytic approach (Review Manager Version 4.2). RESULTS A strong effect size was observed for cognitive exercise interventions compared with wait-and-see control conditions (WMD = 1.07, CI: 0.32-1.83, z = 2.78, N = 7, p = 0.006, N = 3,194). RCTs with follow-up greater than 2 years did not appear to produce lower effect size estimates than those with less extended follow-up. Quality of reporting of trials was in general low. CONCLUSION Cognitive exercise training in healthy older individuals produces strong and persistent protective effects on longitudinal neuropsychological performance. Transfer of these effects to dementia-relevant domains such as general cognition and daily functioning has also been reported in some studies. Importantly, cognitive exercise has yet to be shown to prevent incident dementia in an appropriately designed trial and this is now an international priority.
Extended Coreferential Relations and Bridging Anaphora in the Prague Dependency Treebank

The present paper outlines the coding scheme for annotating extended nominal coreference and bridging relations in the Prague Dependency Treebank. We compare our annotation scheme to the existing ones with respect to the language to which the scheme is applied. We identify the annotation principles and demonstrate their application to the large­scale annotation of Czech texts. We further present our classification of coreferential relations and bridging relations types and discuss some problematic aspects in this area. An automatic pre­annotation and some helpful features of the annotation tool, such as maintaining coreferential chain, underlining candidates for antecedents, etc. are presented and discussed. Statistical evaluation is performed on the already annotated part of the Prague Dependency Treebank. We also present the first results of the inter­annotator agreement measurement and explain the most frequent cases of disagreement. 1 Introduction The Prague Dependency Treebank (henceforth PDT) is a large collection of linguistically annotated data and documentation [2]. In PDT 2.0, Czech newspaper texts are annotated using a three layer annotation scenario. The most abstract (tectogrammatical) layer includes among other mark­ups the annotation of coreferential links. The whole corpus PDT 2.0 contains almost 50 thousand sentences. In PDT 2.0, two types of coreference are (mainly manually) annotated: grammatical and textual coreference. The grammatical coreference typically occurs within a single sentence, the antecedent being able to be derived on the basis of grammatical rules of the given language. It includes coreference of relative pronouns, arguments of verbs of control, reflexive pronouns, reciprocity and verbal complements. As for textual coreference (which is not realized by grammatical means alone, but also on the basis of the context), it has been restricted up to now to cases, in which a demonstrative this or an anaphoric pronoun of the 3 rd person, also in its zero form, are used [8].
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity. DOI: http://dx.doi. org/10.7554/eLife.00731. 001
Molecular Analysis of Thymoma

Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patients with thymomas and followup data was available. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed with Partek Genomics Suite®, and Ingenuity Pathways Analysis (IPA). Unsupervised clustering of gene expression data, representing one of the largest series in literature, resulted in identification of four molecular clusters of tumors (C1–C4), which correlated with histology (P = 0.002). However, neither histology nor clusters correlated with clinical outcomes. Correlation of gene expression data with clinical data showed that a number of genes were associated with either advanced stage at diagnosis or development of recurrence or metastases. The top pathways associated with metastases were amino acid metabolisms, biosynthesis of steroids and glycosphingolipids, cell cycle checkpoint proteins and Notch signaling. The differential expression of some of the top genes related to both metastases and stage was confirmed by RT-PCR in all cases of metastases and matched nonmetastatic cases. A number of potential candidates for therapeutics were also identified.
Characterization and Ectopic Expression of CoWRI1, an AP2/EREBP Domain-Containing Transcription Factor from Coconut (Cocos nucifera L.) Endosperm, Changes the Seeds Oil Content in Transgenic Arabidopsis thaliana and Rice (Oryza sativa L.)

Coconut (Cocos nucifera L.) is a key tropical crop and a member of the monocotyledonous family Arecaceae (Palmaceae). Few genes and related metabolic processes involved in coconut endosperm development have been investigated. In this study, a new member of the WRI1 gene family was isolated from coconut endosperm and was named CoWRI1. Its transcriptional activities and interactions with the acetyl-CoA carboxylase (BCCP2) promoter of CoWRI1 were confirmed by the yeast two-hybrid and yeast one-hybrid approaches, respectively. Functional characterization was carried out through seed-specific expression in Arabidopsis and endosperm-specific expression in rice. In transgenic Arabidopsis, high over-expressions of CoWRI1 in seven independent T2 lines were detected by quantitative real-time PCR. The relative mRNA accumulation of genes encoding enzymes involved in either fatty acid biosynthesis or triacylglycerols assembly (BCCP2, KASI, MAT, ENR, FATA, and GPDH) were also assayed in mature seeds. Furthermore, lipid and fatty acids C16:0 and C18:0 significantly increased. In two homozygous T2 transgenic rice lines (G5 and G2), different CoWRI1 expression levels were detected, but no CoWRI1 transcripts were detected in the wild type. Analyses of the seed oil content, starch content, and total protein content indicated that the two T2 transgenic lines showed a significant increase (P < 0.05) in seed oil content. The transgenic lines also showed a significant increase in starch content, whereas total protein content decreased significantly. Further analysis of the fatty acid composition revealed that palmitic acid (C16:0) and linolenic acid (C18:3) increased significantly in the seeds of the transgenic rice lines, but oleic acid (C18:1) levels significantly declined.
Densities of Agrilus auroguttatus and Other Borers in California and Arizona Oaks

We investigated within-tree population density of a new invasive species in southern California, the goldspotted oak borer, Agrilus auroguttatus Schaeffer (Coleoptera: Buprestidae), with respect to host species and the community of other borers present. We measured emergence hole densities of A. auroguttatus and other borers on the lower stem (bole) of naïve oaks at 18 sites in southern California and on co-evolved oaks at seven sites in southeastern Arizona. We sampled recently dead oaks in an effort to quantify the community of primary and secondary borers associated with mortality—species that were likely to interact with A. auroguttatus. Red oaks (Section Lobatae) produced greater densities of A. auroguttatus than white oaks (Section Quercus). On red oaks, A. auroguttatus significantly outnumbered native borers in California (mean ± SE of 9.6 ± 0.7 versus 4.5 ± 0.6 emergence holes per 0.09 m2 of bark surface), yet this was not the case in Arizona (0.9 ± 0.2 versus 1.1 ± 0.2 emergence holes per 0.09 m2). In California, a species that is taxonomically intermediate between red and white oaks, Quercus chrysolepis (Section Protobalanus), exhibited similar A. auroguttatus emergence densities compared with a co-occurring red oak, Q. kelloggii. As an invasive species in California, A. auroguttatus may affect the community of native borers (mainly Buprestidae and Cerambycidae) that feed on the lower boles of oaks, although it remains unclear whether its impact will be positive or negative.
Quantifying the damage susceptibility to extreme events of mountain stream check dams using Rough Set Analysis

In this work, a Rough Set Analysis‐based approach is proposed to quantify the damage susceptibility of check dams through specific indexes, which all require expert judgment to be quantified. The indexes are the Post‐Event Damage Condition (DamPost), the induced Condition Change (DamCh), the Residual Condition (RC), and the Post‐Event Functionality (FPost). Preliminarily, an existing data set, containing a quantification of the damage indexes, the associated characterisation of the flow process type of three torrential hazard events occurred in South Tyrol (Italy), the identification of construction material and the determination of age of the structure, was statistically analysed. To predict the damage indexes based on Rough Set Analysis, a general model, which considered all check dams regardless of their construction material, two specific models, for concrete and for masonry structures respectively, and a simplified version of the general model were set up. The derived rule bases exhibited satisfactory prediction accuracies only when the post‐event functionality, FPost, was chosen. Prediction accuracies were 68% for the general model, 79% for the material category concrete, 60% for the material category masonry, and 86% could be obtained by simplifying the decision attribute to a binary form (functionality given or not).
An optimal MIMO mode selection method for D2D transmission in cellular networks

Device-to-Device (D2D) communication is one of the new features introduced for Long Term Evolution-Advanced (LTE-A) and beyond networks. In this paper we address the problem of communication mode selection for a pair of User Equipments (UEs). In particular we assume that the paired UEs can choose from the reuse, dedicated, and cellular modes. While this problem was treated in the literature for Single-Input-Single-Output (SISO) case, we derive models for networks where UEs and evolved-Node-Bs (eNBs) exploit Multiple-Input-Multiple-Output (MIMO) techniques with four antennas at each side. This approach requires design of the pre-coding matrices at each node which poses a challenge in the reuse mode due to the non-convexity problem. To solve this issue we propose a distributed iterative algorithm. The numerical study compares the performance of the MIMO based approach with that of the SISO case, and the results show that the presented MIMO based mode selection method provides significantly higher network throughput than that of the SISO based mode selection method for the same D2D transmission range.
Patterns of stress response and tolerance based on transcriptome profiling of rice crown tissue under zinc deficiency

Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Several studies have investigated how rice plants respond to Zn deficiency and examined the differences between Zn-efficient (ZE) and Zn-inefficient (ZI) genotypes. ZE genotypes reallocate more Zn to roots and are better at maintaining crown root development than ZI genotypes in response to Zn deficiency. However, little is known about the molecular mechanisms controlling these differences. Moreover, the role of the crown, the part of the stem from which crown roots emerge, has yet to be examined. In this study we highlight the molecular mechanisms triggered by early Zn deficiency in crown tissue through RNA sequencing of two contrasting groups of several ZE and ZI genotypes. This method allowed us to (i) identify several novel and well-known Zn transporters involved in Zn retranslocation from the crown to the shoot and roots in response to Zn deficiency; (ii) determine that Zn deficiency triggers the conversion of soluble sugars into starch; and (iii) detect several candidate genes possibly conferring Zn efficiency, including a monosaccharide transporter, a Zn finger domain-containing protein, a gibberellin-stimulated family protein and a plasma membrane polypeptide family protein.
Joint Bandwidth Optimization and Media Access Control for Multihop Underwater Acoustic Sensor Networks

Multihop underwater acoustic sensor networks (UASNs) suffer from low throughput caused by low channel utilization and unreasonable bandwidth allocation. The existing media access control (MAC) protocols for UASNs mainly aim to improve channel utilization but neglect to optimize bandwidth, so that they cannot achieve high throughput in miltihop networks. We propose the idea of joint bandwidth optimization and MAC in this paper. We first present a system model to optimize bandwidth for miltihop UASNs. Both the complicated interference relations between links and the different transmission demands of nodes are modeled. Thus, it can accurately reflect the characteristics of miltihop UASNs. By analyzing a 1-D linear miltihop network, we find and formulate a maximum hop number which is determined by nodes' traffic load and channel capacity. The other finding is that an optimal scheduling needs to allocate the bandwidth based on traffic load, and the nodes with more traffic load should be allocated more bandwidth. This finding inspire us to develop a distributed traffic-based scheduling MAC protocol. This protocol can optimize bandwidth allocation by letting the older packet to be transmitted preferentially. To improve channel utilization, multiple packets are allowed to be transmitted in each data transmission round. Simulation results have confirmed that our protocol can achieve excellent performance owing to its core idea of joint bandwidth optimization and MAC.
English-Spanish Large Statistical Dictionary of Inflectional Forms

The paper presents an approach for constructing a weighted bilingual dictionary of inflectional forms using as input data a traditional bilingual dictionary, and not parallel corpora. An algorithm is developed that generates all possible morphological (inflectional) forms and weights them using information on distribution of corresponding grammar sets (grammar information) in large corpora for each language. The algorithm also takes into account the compatibility of grammar sets in a language pair; for example, verb in past tense in language L normally is expected to be translated by verb in past tense in Language L'. We consider that the developed method is universal, i.e. can be applied to any pair of languages. The obtained dictionary is freely available. It can be used in several NLP tasks, for example, statistical machine translation.
Effects of Reclaimed Water Irrigation on Microbial Diversity and Composition of Soil with Reducing Nitrogen Fertilization

Reclaimed water (RW) is an alternative water resource that has been utilized all over the world, but its environmental effects are not fully understood. Soil biodiversity is an important indicator of soil tolerance and resilience. In the present study, the impact of RW irrigation on the microbial community diversity and chemical properties of topsoil was investigated by monitoring nitrogen (N) rates. Tomato plants were grown on plots which had been irrigated with reclaimed water for 5 years with varying levels of N fertilization (N270, 270 kg ha−1; N216, 216 kg ha−1; N189, 189 kg ha−1; and N135, 135 kg ha−1). Soil bacterial community composition was analyzed by PCR amplification of the 16S rDNA gene and Illumina MiSeq high-throughput sequencing technology of a total of 770,066 quality sequences. The results showed that long-term RW irrigation altered the bacterial composition of soil in an N-dependent manner. RW irrigation increased the abundances of Gemmatimonadetes, Actinobacteria, Firmicutes, and Nitrospirae in soils. The Chao, ACE, and H indices revealed no significant difference under RW irrigation with varying levels of N fertilization. The tomato yield and partial factor productivity from applied N for RN216 increased significantly under RW irrigation with reducing N fertilization. RW irrigation increased the yield of tomato and the abundance of functional microorganisms, which eventually improved the practice of irrigating with reclaimed municipal wastewater. Meanwhile, the potential environmental and health risks of long-term RW irrigation warrant further investigation.
Learning to Search More Efficiently from Experience: A Multi-Heuristic Approach

Learning from experience can significantly improve the performance of search based planners, especially for challenging problems like high-dimensional planning. Experience Graph (E-Graph) is a recently developed framework that encodes experiences, obtained from solving instances in the past, into a single bounded-admissible heuristic, and uses it to guide the search. While the E-Graph approach was shown to be very useful for repetitive problems, it suffers from two issues. First, computing the E-Graph heuristic is time consuming as it maintains the bounded admissibility constraints. Second, a single heuristic can get stuck in a local minimum, and thereby, degrade the performance. In this work, we present an alternative approach to improving the runtime of search from experience, based on a recently developed search algorithm Multi-heuristic A* (MHA*). This framework provides an improvement over the E-Graph planner for two reasons: a) MHA* uses multiple heuristics simultaneously to explore the search space, which reduces the probability of getting stuck in a local minimum, and b) the heuristics in MHA* can be arbitrarily inadmissible, which makes it very easy to compute them. The paper describes the framework, explains how to compute these (inadmissible) heuristics through offline and online processing and presents experimental analysis on two domains, motion planning for a 6D planar arm and large sliding tile puzzles.