Miracle-dz/UniFAR-FTUs huggingface dataset:
Radial Growth and Wood Density Reflect the Impacts and Susceptibility to Defoliation by Gypsy Moth and Climate in Radiata Pine

Drought stress causes a reduction in tree growth and forest productivity, which could be aggravated by climate warming and defoliation due to moth outbreaks. We investigate how European gypsy moth (Lymantria dispar dispar L., Lepidoptera: Erebidae) outbreak and related climate conditions affected growth and wood features in host and non-host tree species in north-western Spain. There, radiata pine (Pinus radiata D. Don) plantations and chestnut (Castanea sativa Mill.) stands were defoliated by the moth larvae, whereas Maritime pine (Pinus pinaster Ait.) was not defoliated. The gypsy moth outbreak peaked in 2012 and 2013, and it was preceded by very warm spring conditions in 2011 and a dry-warm 2011–2012 winter. Using dendrochronology we compared growth responses to climate and defoliation of host species (radiata pine, chestnut) with the non-host species (Maritime pine). We also analyzed wood density derived from X-ray densitometry in defoliated and non-defoliated trees of radiata pine. We aimed to: (i) disentangle the relative effects of defoliation and climate stress on radial growth, and (ii) characterize defoliated trees of radiata pine according to their wood features (ring-width, maximum and minimum density). Radial growth during the outbreak (2012–2013) decreased on average 74% in defoliated (>50% of leaf area removed) trees of radiata pine, 43% in defoliated trees of chestnut, and 4% in non-defoliated trees of Maritime pine. After applying a BACI (Before-After-Control-Impact) type analysis, we concluded that the difference in the pattern of radial growth before and during the defoliation event was more likely due to the differences in climate between these two periods. Radiata pines produced abundant latewood intra-annual density fluctuations in 2006 and 2009 in response to wet summer conditions, suggesting a high climatic responsiveness. Minimum wood density was lower in defoliated than in non-defoliated trees of radiata pine prior to the outbreak, but increased during the outbreak. The pre-outbreak difference in minimum wood density suggests that the trees most affected by the outbreak produced tracheids with wider lumen and were more susceptible to drought stress. Results of this study illustrate (i) that the pattern of radial growth alone may be not a good indicator for reconstructing past defoliation events and (ii) that wood variables are reliable indicators for assessing the susceptibility of radiata pine to defoliation by the gypsy moth.
Regulatory discrimination of mRNAs by FMRP controls mouse adult neural stem cell differentiation

Significance Fragile X syndrome (FXS) is the most common form of inherited intellectual disability and autism. FXS results from the loss of functional fragile X mental retardation protein (FMRP), an RNA binding protein involved in translational regulation. However, the impact of FMRP on gene expression has not been evaluated comprehensively. Here, we present simultaneous high-resolution ribosome profiling and RNA-sequencing data from the same wild-type and FMRP-deficient adult neural stem cells. We find remarkable and heretofore unknown forms of regulation by FMRP critical for neural differentiation. Importantly, our data also show that FMRP controls RNA expression in six distinct ways. Thus, we have uncovered a molecular foundation for pathophysiologies associated with FXS. Fragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), an RNA binding protein whose deficiency impacts many brain functions, including differentiation of adult neural stem cells (aNSCs). However, the mechanism by which FMRP influences these processes remains unclear. Here, we performed ribosome profiling and transcriptomic analysis of aNSCs in parallel from wild-type and Fmr1 knockout mice. Our data revealed diverse gene expression changes at both mRNA and translation levels. Many mitosis and neurogenesis genes were dysregulated primarily at the mRNA level, while numerous synaptic genes were mostly dysregulated at the translation level. Translational “buffering”, whereby changes in ribosome association with mRNA are compensated by alterations in RNA abundance, was also evident. Knockdown of NECDIN, an FMRP-repressed transcriptional factor, rescued neuronal differentiation. In addition, we discovered that FMRP regulates mitochondrial mRNA expression and energy homeostasis. Thus, FMRP controls diverse transcriptional and posttranscriptional gene expression programs critical for neural differentiation.
A notification-oriented solution for data-intensive enterprise information systems – A cloud manufacturing case

ABSTRACT The application of Industrial Internet of Things (IIoT) has brought a series of new challenges to the traditional Enterprise Information Systems (EIS). More and more networked manufacturing entities are combined with data sensing, collection, transmission, and actuation capabilities. EIS are now facing large amounts of heterogeneous data. To address this issue, this paper proposes a notification-oriented solution for the data-intensive EIS within a distributed, collaborative, and heterogeneous environment. The solution is then applied in terms of model to a cloud-based smart factory prototype. This work indicates the suitability of the proposition and discusses the existing drawbacks and perspectives that include the manual modelling process and the application on a prototype.
Phonemic and Semantic Verbal Fluency in Sex Chromosome Aneuploidy: Contrasting the Effects of Supernumerary X versus Y Chromosomes on Performance

Abstract Objectives: Past research suggests that youth with sex chromosome aneuploidies (SCAs) present with verbal fluency deficits. However, most studies have focused on sex chromosome trisomies. Far less is known about sex chromosome tetrasomies and pentasomies. Thus, the current research sought to characterize verbal fluency performance among youth with sex chromosome trisomies, tetrasomies, and pentasomies by contrasting how performance varies as a function of extra X number and X versus Y status. Methods: Participants included 79 youth with SCAs and 42 typically developing controls matched on age, maternal education, and racial/ethnic background. Participants completed the phonemic and semantic conditions of a verbal fluency task and an abbreviated intelligence test. Results: Both supernumerary X and Y chromosomes were associated with verbal fluency deficits relative to controls. These impairments increased as a function of the number of extra X chromosomes, and the pattern of impairments on phonemic and semantic fluency differed for those with a supernumerary X versus Y chromosome. Whereas one supernumerary Y chromosome was associated with similar performance across fluency conditions, one supernumerary X chromosome was associated with relatively stronger semantic than phonemic fluency skills. Conclusions: Verbal fluency skills in youth with supernumerary X and Y chromosomes are impaired relative to controls. However, the degree of impairment varies across groups and task condition. Further research into the cognitive underpinnings of verbal fluency in youth with SCAs may provide insights into their verbal fluency deficits and help guide future treatments. (JINS, 2018, 24, 917–927)
Outcome of Juvenile Idiopathic Arthritis Associated Uveitis in Two Disease Subtypes.

Objectives This study aims to evaluate the efficacy of adalimumab as a first line biologic agent in specific subtypes of juvenile idiopathic arthritis (JIA) patients with associated uveitis. Patients and methods We retrospectively analyzed the data of 11 JIA patients (8 males, 3 females; mean age 14.5 years; range 9 to 18 years) with associated uveitis treated with biologic therapy. All patients were diagnosed as oligoarticular/extended oligoarticular or enthesitis-related JIA subtypes, treated with methotrexate, and had active or previous history of uveitis for which adalimumab was prescribed. We tested all patients for anti-nuclear antibody presence and human leukocyte antigen genotype. We assessed disease activity and therapy efficacy by American College of Rheumatology 50%, 70%, and 100% improvement criteria. We evaluated uveitis activity by slit-lamp biomicroscopy and recorded adverse events. Results Of the JIA patients, three (27.27%) had oligoarticular/extended oligoarticular JIA and eight (72.73%) had enthesitis-related arthritis. Anti-nuclear antibody positivity was present in 27.27% (all females) while human leukocyte antigen-B51 was determined in 62.5% and human leukocyte antigen-B27 in 12.5% of patients. Mean uveitis duration before adalimumab introduction was 12.3 months. After two years of follow-up, there were no relapses of uveitis and visual acuity was stable while on adalimumab and methotrexate treatment. All patient were gradually tapered and discontinued treatment with topical steroids. Disease activity improved and seven patients (63.64%) achieved American College of Rheumatology 100% response rate (attained remission), while four patients (36.36%) achieved American College of Rheumatology 70% response rate. Conclusion Anti-nuclear antibody positivity with oligoarticular/extended oligoarticular and enthesitis-related arthritis JIA subtypes, which are known for their high risk to develop uveitis, may benefit from adalimumab as a first line anti-tumor necrosis factor agent.
Copy Number Variants Account for a Tiny Fraction of Undiagnosed Myopathic Patients

Next-generation sequencing (NGS) technologies have led to an increase in the diagnosis of heterogeneous genetic conditions. However, over 50% of patients with a genetically inherited disease are still without a diagnosis. In these cases, different hypotheses are usually postulated, including variants in novel genes or elusive mutations. Although the impact of copy number variants (CNVs) in neuromuscular disorders has been largely ignored to date, missed CNVs are predicted to have a major role in disease causation as some very large genes, such as the dystrophin gene, have prone-to-deletion regions. Since muscle tissues express several large disease genes, the presence of elusive CNVs needs to be comprehensively assessed following an accurate and systematic approach. In this multicenter cohort study, we analyzed 234 undiagnosed myopathy patients using a custom array comparative genomic hybridization (CGH) that covers all muscle disease genes at high resolution. Twenty-two patients (9.4%) showed non-polymorphic CNVs. In 12 patients (5.1%), the identified CNVs were considered responsible for the observed phenotype. An additional ten patients (4.3%) presented candidate CNVs not yet proven to be causative. Our study indicates that deletions and duplications may account for 5–9% of genetically unsolved patients. This strongly suggests that other mechanisms of disease are yet to be discovered.
Adaptation of a Fungal Pathogen to Host Quantitative Resistance

Impact of host quantitative resistance on pathogen evolution is still poorly documented. In our study, we characterized the adaptation of the pathogenic fungus Colletotrichum gloeosporioides, to the quantitative resistance of its host, the water yam (Dioscorea alata). Genetic and pathogenic diversities of C. gloeosporioides populations were specified at the field scale. We used nuclear markers to describe fungal population structuring within and between six fields of three cultivars differently susceptible to the fungus. Strain aggressiveness was then quantified in the laboratory through cross-inoculation tests. The high level of genetic diversity and significant linkage disequilibrium revealed a significant influence of clonal reproduction in the C. gloeosporioides evolution. The recorded fungal migration between fields was weak (evidence for a dispersion mode via tubers rather than splashing dispersal), which provides the first molecular evidence for limited C. gloeosporioides migration via yam tuber exchanges. C. gloeosporioides’s populations are adapted to their host resistance. The aggressiveness of the fungal clones seems to have evolved toward an accumulation of components specific to each host cultivar. Despite the remaining marks of adaptation to the former widely cultivated host, adaptation to current cultivars was clearly depicted.
Plasma levels of IL‐1Ra are associated with schizophrenia

Although peripheral low‐grade inflammation and brain‐derived neurotrophic factor (BDNF) levels have been implicated in schizophrenia (SCZ), the interactions between them remain to be fully revealed. We aimed to compare BDNF and cytokines in patients with SCZ and healthy controls (HC). Additionally, we aimed to investigate the association between peripheral levels of cytokines and BDNF in patients with SCZ.
Learning and Inference in Hilbert Space with Quantum Graphical Models

Quantum Graphical Models (QGMs) generalize classical graphical models by adopting the formalism for reasoning about uncertainty from quantum mechanics. Unlike classical graphical models, QGMs represent uncertainty with density matrices in complex Hilbert spaces. Hilbert space embeddings (HSEs) also generalize Bayesian inference in Hilbert spaces. We investigate the link between QGMs and HSEs and show that the sum rule and Bayes rule for QGMs are equivalent to the kernel sum rule in HSEs and a special case of Nadaraya-Watson kernel regression, respectively. We show that these operations can be kernelized, and use these insights to propose a Hilbert Space Embedding of Hidden Quantum Markov Models (HSE-HQMM) to model dynamics. We present experimental results showing that HSE-HQMMs are competitive with state-of-the-art models like LSTMs and PSRNNs on several datasets, while also providing a nonparametric method for maintaining a probability distribution over continuous-valued features.
Subword Encoding in Lattice LSTM for Chinese Word Segmentation

We investigate subword information for Chinese word segmentation, by integrating sub word embeddings trained using byte-pair encoding into a Lattice LSTM (LaLSTM) network over a character sequence. Experiments on standard benchmark show that subword information brings significant gains over strong character-based segmentation models. To our knowledge, this is the first research on the effectiveness of subwords on neural word segmentation.
Efficacy of Azithromycin and Miltefosine in Experimental Systemic Pythiosis in Immunosuppressed Mice

We evaluated the efficacy of azithromycin (50 mg/kg, every 12 h [q12h] orally) and miltefosine (25 mg/kg, q24h orally) treatments in an experimental model of vascular/disseminated pythiosis in immunosuppressed mice. Azithromycin was the only treatment able to reduce mortality. ABSTRACT We evaluated the efficacy of azithromycin (50 mg/kg, every 12 h [q12h] orally) and miltefosine (25 mg/kg, q24h orally) treatments in an experimental model of vascular/disseminated pythiosis in immunosuppressed mice. Azithromycin was the only treatment able to reduce mortality. The histopathological findings showed acute vascular inflammation, pathogen dissemination, necrotizing myositis, neuritis, and arteritis. The results suggest that azithromycin, but not miltefosine, may have clinical relevance in the treatment of vascular/disseminated pythiosis.
Posterior Reversible Encephalopathy Syndrome in a Patient With Multiple System Atrophy

Posterior Reversible Encephalopathy Syndrome (PRES) is a clinicoradiological syndrome of reversible subcortical vasogenic brain oedema that can arise in the setting of renal failure, cytotoxic drugs, autoimmune disorders, (pre)eclampsia or blood pressure fluctuations. An insufficient cerebral blood pressure autoregulatory response with disruption of the blood-brain barrier is a leading theory of the pathophysiological changes underlying PRES1. Multiple System Atrophy (MSA) is a neurodegenerative disorder characterized by a combination of parkinsonism, cerebellar, pyramidal and autonomic signs. The consequence of the latter is often blood pressure variations with clinically invalidating orthostatic hypotension. This article is protected by copyright. All rights reserved.
A novel role for acid‐sensing ion channels in Pavlovian reward conditioning

Pavlovian fear conditioning has been shown to depend on acid‐sensing ion channel‐1A (ASIC1A); however, it is unknown whether conditioning to rewarding stimuli also depends on ASIC1A. Here, we tested the hypothesis that ASIC1A contributes to Pavlovian conditioning to a non‐drug reward. We found effects of ASIC1A disruption depended on the relationship between the conditional stimulus (CS) and the unconditional stimulus (US), which was varied between five experiments. In experiment 1, when the CS preceded the US signaling an upcoming reward, Asic1a−/− mice exhibited a deficit in conditioning compared to Asic1a+/+ mice. Alternatively, in experiment 2, when the CS coinitiated with the US and signaled immediate reward availability, the Asic1a−/− mice exhibited an increase in conditioned responses compared to Asic1a+/+ mice, which contrasted with the deficits in the first experiment. Furthermore, in experiments 3 and 4, when the CS partially overlapped in time with the US, or the CS was shortened and coinitiated with the US, the Asic1a−/− mice did not differ from control mice. The contrasting outcomes were likely because of differences in conditioning because in experiment 5 neither the Asic1a−/− nor Asic1a+/+ mice acquired conditioned responses when the CS and US were explicitly unpaired. Taken together, these results suggest that the effects of ASIC1A disruption on reward conditioning depend on the temporal relationship between the CS and US. Furthermore, these results suggest that ASIC1A plays a critical, yet nuanced role in Pavlovian conditioning. More research will be needed to deconstruct the roles of ASIC1A in these fundamental forms of learning and memory.
To Clean or Not to Clean

Web document collections such as WT10G, GOV2, and ClueWeb are widely used for text retrieval experiments. Documents in these collections contain a fair amount of non-content-related markup in the form of tags, hyperlinks, and so on. Published articles that use these corpora generally do not provide specific details about how this markup information is handled during indexing. However, this question turns out to be important: Through experiments, we find that including or excluding metadata in the index can produce significantly different results with standard IR models. More importantly, the effect varies across models and collections. For example, metadata filtering is found to be generally beneficial when using BM25, or language modeling with Dirichlet smoothing, but can significantly reduce retrieval effectiveness if language modeling is used with Jelinek-Mercer smoothing. We also observe that, in general, the performance differences become more noticeable as the amount of metadata in the test collections increase. Given this variability, we believe that the details of document preprocessing are significant from the point of view of reproducibility. In a second set of experiments, we also study the effect of preprocessing on query expansion using RM3. In this case, once again, we find that it is generally better to remove markup before using documents for query expansion.
A Randomized Controlled Trial: Regenerative Effects, Efficacy and Safety of Erythropoietin in Burn and Scalding Injuries

In adult’s burn injuries belong to the top 15 causes of injury. Annually more than a million patients receive specialized treatment. Improving burned patients’ outcomes is still a challenge. Effects of erythropoietin (EPO) are reported to be pro-angiogenic, pro-regenerative, anti-inflammatory, immunomodulatory and hypoxia/ischemia protective. Study objectives were to demonstrate cytoprotective and regenerative effects of EPO in burned patients in terms of improved wound healing, reduced morbidity and mortality. This was a prospective, placebo-controlled, randomized, double-blind trial. The trial was conducted in 13 specialized burn care centers in Germany. Adult Patients with 2b° or 3° burn injuries were included. Patients received state of the art burn care including obligatory split skin graft transplantation. Study medication was EPO or placebo every other day for 21 days. Between 12/08 and 06/14, 116 patients were randomized, 84 received study medication (EPO 45, Placebo 39). Primary endpoint analysis revealed inconclusive results, as only a minority of patients reached the primary endpoint [100% re-epithelialization: EPO: 23% (9/40); Placebo 30% (11/37)]. Several secondary endpoints such as SOFA score (morbidity), EPO level in blood and wound healing onset revealed clinical, and statistically significant results in favor of the EPO group. Adverse Events (AEs) and Severe Adverse Events (SAEs) were in expected ranges; AEs EPO: 80%, (36/45), Placebo: 77%, (30/39); SAEs EPO: 24%, (11/45), Placebo: 24%, (8/39). Out of 84 patients two died, one per group, thus mortality was lower than expected. Results (SOFA score) indicate a lower morbidity of the EPO group, suggesting pro-regenerative effects of EPO in burned patients. Higher EPO levels might influence the faster onset of re-epithelialization in the first 10 days of the treatment. Both effects could reveal new therapeutic options. Clinical Trial Registration: ISRCT Number: ISRCTN95777824 and EudraCT Number: 2006-002886-38, Protocol Number: 0506.
A Randomized Clinical Trial of Atomoxetine for Mild Cognitive Impairment in Parkinson's Disease

Mild cognitive impairment in Parkinson's disease (PD‐MCI) is associated with diminished norepinephrine from the locus coeruleus to the prefrontal cortex. Atomoxetine is a specific norepinephrine reuptake inhibitor that has been approved by the US Food and Drug Administration to treat attention deficit hyperactivity disorder in adults. The authors hypothesized that atomoxetine would improve attention and executive functioning in patients with PD‐MCI.
Genetic abnormalities seen on CVS in early pregnancy failure

Abstract Objective: To determine the frequency and distribution of chromosome abnormalities in women with early pregnancy failure (EPF) detected by cytogenetic testing on chorionic villus sampling. Method: Retrospective observational cohort study of chromosomal analysis from transvaginal chorionic villus sampling (CVS) or reflex products of conception (POC) karyotype. CVS was offered as a training tool for Maternal Fetal Medicine fellows prior to manual vacuum aspiration for EPF 9-week gestation. POC were analyzed for cytogenetics if no results were obtained on CVS. Results: One hundred thirty samples were collected from December 2011 to April 2015. 33 (27.3%) cases had a normal karyotype and 88 (73.0%) cases had an abnormal karyotype. The most common group of abnormalities were trisomy, (n = 50, 41.3%), triploidy/tetraploidy, (n = 17, 14.0%), monosomy (n = 15, 12.4%), and structural rearrangements (n = 6, 5.0%). Nine (6.9%) samples were maternal decidua only. Abnormal karyotype in EPF was significantly increased in women by age group (p < .01) but not in women with a history of prior miscarriage (p = .5). Conclusion: Our cohort had a high detection rate of aneuploidy. The most common chromosomal abnormalities in EPF were: trisomy, followed by triploidy/tetraploidy, monosomy, and structural rearrangements. Maternal age had the strongest correlation with EPF associated with aneuploidy.