Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality of nonstructured and structured abstracts of original research articles in the British Medical Journal, the Canadian Medical Association Journal and the Journal of the American Medical Association.

OBJECTIVE To assess and compare the quality of nonstructured and structured abstracts of original research articles in three medical journals. DESIGN Blind, criterion-based observational study. SAMPLE Random sample of 300 abstracts (25 abstracts per journal each year) of articles published in the British Medical Journal (BMJ), the Canadian Medical Association Journal and the Journal of the American Medical Association (JAMA) in 1988 and 1989 (nonstructured abstracts) and in 1991 and 1992 (structured abstracts). MAIN OUTCOME MEASURES The quality of abstracts was measured against 33 objective criteria, which were divided into eight categories (purpose, research design, setting, subjects, intervention, measurement of variables, results and conclusions). The quality score was determined by dividing the number of criteria present by the number applicable; the score varied from 0 to 1. RESULTS The overall mean quality scores for nonstructured and structured abstracts were 0.57 and 0.74 respectively (p < 0.001). The frequency in meeting the specific criteria was generally higher for the structured abstracts than for the nonstructured ones. The mean quality score was higher for nonstructured abstracts in JAMA than for those in BMJ (0.60 v. 0.54, p < 0.05). The scores for structured abstracts did not differ significantly between the three journals. CONCLUSIONS The findings support recommendations that promote the use of structured abstracts. Further studies should be performed to assess the effect of time on the quality of abstracts and the extent to which abstracts reflect the content of the articles.
Seasonal, interannual and decadal drivers of tree and grass productivity in an Australian tropical savanna

Tree–grass savannas are a widespread biome and are highly valued for their ecosystem services. There is a need to understand the long‐term dynamics and meteorological drivers of both tree and grass productivity separately in order to successfully manage savannas in the future. This study investigated the interannual variability (IAV) of tree and grass gross primary productivity (GPP) by combining a long‐term (15 year) eddy covariance flux record and model estimates of tree and grass GPP inferred from satellite remote sensing. On a seasonal basis, the primary drivers of tree and grass GPP were solar radiation in the wet season and soil moisture in the dry season. On an interannual basis, soil water availability had a positive effect on tree GPP and a negative effect on grass GPP. No linear trend in the tree–grass GPP ratio was observed over the 15‐year study period. However, the tree–grass GPP ratio was correlated with the modes of climate variability, namely the Southern Oscillation Index. This study has provided insight into the long‐term contributions of trees and grasses to savanna productivity, along with their respective meteorological determinants of IAV.
Bid Regulates the Pathogenesis of Neurotropic Reovirus

Reovirus infection leads to apoptosis in both cultured cells and the murine central nervous system (CNS). NF-κB-driven transcription of proapoptotic cellular genes is required for the effector phase of the apoptotic response. Although both extrinsic death-receptor signaling pathways and intrinsic pathways involving mitochondrial injury are implicated in reovirus-induced apoptosis, mechanisms by which either of these pathways are activated and their relationship to NF-κB signaling following reovirus infection are unknown. The proapoptotic Bcl-2 family member, Bid, is activated by proteolytic cleavage following reovirus infection. To understand how reovirus integrates host signaling circuits to induce apoptosis, we examined proapoptotic signaling following infection of Bid-deficient cells. Although reovirus growth was not affected by the absence of Bid, cells lacking Bid failed to undergo apoptosis. Furthermore, we found that NF-κB activation is required for Bid cleavage and subsequent proapoptotic signaling. To examine the functional significance of Bid-dependent apoptosis in reovirus disease, we monitored fatal encephalitis caused by reovirus in the presence and absence of Bid. Survival of Bid-deficient mice was significantly enhanced in comparison to wild-type mice following either peroral or intracranial inoculation of reovirus. Decreased reovirus virulence in Bid-null mice was accompanied by a reduction in viral yield. These findings define a role for NF-κB-dependent cleavage of Bid in the cell death program initiated by viral infection and link Bid to viral virulence.
High prevalence of S. Stercoralis infection among patients with Chagas disease: A retrospective case-control study

Background We evaluate the association between Trypanosoma cruzi infection and strongyloidiasis in a cohort of Latin American (LA) migrants screened for both infections in a non-endemic setting. Methodology Case-control study including LA individuals who were systematically screened for T. cruzi infection and strongyloidiasis between January 2013 and April 2015. Individuals were included as cases if they had a positive serological result for Strongyloides stercoralis. Controls were randomly selected from the cohort of individuals screened for T. cruzi infection that tested negative for S. stercoralis serology. The association between T. cruzi infection and strongyloidiasis was evaluated by logistic regression models. Principal findings During the study period, 361 individuals were screened for both infections. 52 (14.4%) individuals had a positive serological result for strongyloidiasis (cases) and 104 participants with negative results were randomly selected as controls. 76 (48.7%) indiviuals had a positive serological result for T. cruzi. Factors associated with a positive T. cruzi serology were Bolivian origin (94.7% vs 78.7%; p = 0.003), coming from a rural area (90.8% vs 68.7%; p = 0.001), having lived in an adobe house (88.2% vs 70%; p = 0.006) and a referred contact with triatomine bugs (86.7% vs 63.3%; p = 0.001). There were more patients with a positive S. stercoralis serology among those who were infected with T. cruzi (42.1% vs 25%; p = 0.023). Epidemiological variables were not associated with a positive strongyloidiasis serology. T. cruzi infection was more frequent among those with strongyloidiasis (61.5% vs 42.3%; p = 0.023). In multivariate analysis, T. cruzi infection was associated with a two-fold increase in the odds of strongyloidiasis (OR 2.23; 95% CI 1.07–4.64; p = 0.030). Conclusions T. cruzi infection was associated with strongyloidiasis in LA migrants attending a tropical diseases unit even after adjusting for epidemiological variables. These findings should encourage physicians in non-endemic settings to implement a systematic screening for both infections in LA individuals.
Prediction of acute coronary syndromes by urinary proteome analysis

Identification of individuals who are at risk of suffering from acute coronary syndromes (ACS) may allow to introduce preventative measures. We aimed to identify ACS-related urinary peptides, that combined as a pattern can be used as prognostic biomarker. Proteomic data of 252 individuals enrolled in four prospective studies from Australia, Europe and North America were analyzed. 126 of these had suffered from ACS within a period of up to 5 years post urine sampling (cases). Proteomic analysis of 84 cases and 84 matched controls resulted in the discovery of 75 ACS-related urinary peptides. Combining these to a peptide pattern, we established a prognostic biomarker named Acute Coronary Syndrome Predictor 75 (ACSP75). ACSP75 demonstrated reasonable prognostic discrimination (c-statistic = 0.664), which was similar to Framingham risk scoring (c-statistics = 0.644) in a validation cohort of 42 cases and 42 controls. However, generating by a composite algorithm named Acute Coronary Syndrome Composite Predictor (ACSCP), combining the biomarker pattern ACSP75 with the previously established urinary proteomic biomarker CAD238 characterizing coronary artery disease as the underlying aetiology, and age as a risk factor, further improved discrimination (c-statistic = 0.751) resulting in an added prognostic value over Framingham risk scoring expressed by an integrated discrimination improvement of 0.273 ± 0.048 (P < 0.0001) and net reclassification improvement of 0.405 ± 0.113 (P = 0.0007). In conclusion, we demonstrate that urinary peptide biomarkers have the potential to predict future ACS events in asymptomatic patients. Further large scale studies are warranted to determine the role of urinary biomarkers in clinical practice.
Antithrombotic Therapy for Venous Thromboembolism and Prevention of Thrombosis in Otolaryngology–Head and Neck Surgery: State of the Art Review

Objective The aim of this report is to present a cohesive evidence-based approach to reducing venous thromboembolism (VTE) in otolaryngology–head and neck surgery. VTE prevention includes deep venous thrombosis and pulmonary embolism. Despite national efforts in VTE prevention, guidelines do not exist for otolaryngology–head and neck surgery in the United States. Data Sources PubMed/MEDLINE. Review Methods A comprehensive review of literature pertaining to VTE in otolaryngology–head and neck surgery was performed, identifying data on incidence of thrombotic complications and the outcomes of regimens for thromboprophylaxis. Data were then synthesized and compared with other surgical specialties. Conclusions We identified 29 articles: 1 prospective cohort study and 28 retrospective studies. The overall prevalence of VTE in otolaryngology appears lower than that of most other surgical specialties. The Caprini system allows effective individualized risk stratification for VTE prevention in otolaryngology. Mechanical and chemoprophylaxis (“dual thromboprophylaxis”) is recommended for patients with a Caprini score ≥7 or patients with a Caprini score of 5 or 6 who undergo major head and neck surgery, when prolonged hospital stay is anticipated or mobility is limited. For patients with a Caprini score of 5 or 6, we recommend dual thromboprophylaxis or mechanical prophylaxis alone. Patients with a Caprini score ≤4 should receive mechanical prophylaxis alone. Implications for Practice Otolaryngologists should consider an individualized and risk-stratified plan for perioperative thromboprophylaxis in every patient. The risk of bleeding must be weighed against the risk of VTE when deciding on chemoprophylaxis.
Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions

The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.
Quantitative modeling of category learning deficits in various patient populations.

OBJECTIVE To provide a select review of our applications of quantitative modeling to highlight the utility of such approaches to better understand the neuropsychological deficits associated with various neurologic and psychiatric diseases. METHOD We review our work examining category learning in various patient populations, including individuals with basal ganglia disorders (Huntington's Disease and Parkinson's disease), amnesia and Eating Disorders. RESULTS Our review suggests that the use of quantitative models has enabled a better understanding of the learning deficits often observed in these conditions and has allowed us to form novel hypotheses about the neurobiological bases of their deficits. CONCLUSIONS We feel that the use of neurobiologically inspired quantitative modeling holds great promise in neuropsychological assessment and that future clinical measures should incorporate the use of such models as part of their standard scoring. Appropriate studies need to be completed, however, to determine whether such modeling techniques adhere to the rigorous psychometric properties necessary for a valid and reliable application in a clinical setting. (PsycINFO Database Record
Dimerization of sortilin regulates its trafficking to extracellular vesicles

Extracellular vesicles (EVs) play a critical role in intercellular communication by transferring microRNAs, lipids, and proteins to neighboring cells. Sortilin, a sorting receptor that directs target proteins to the secretory or endocytic compartments of cells, is found in both EVs and cells. In many human diseases, including cancer and cardiovascular disorders, sortilin expression levels are atypically high. To elucidate the relationship between cardiovascular disease, particularly vascular calcification, and sortilin expression levels, we explored the trafficking of sortilin in both the intracellular and extracellular milieu. We previously demonstrated that sortilin promotes vascular calcification via its trafficking of tissue-nonspecific alkaline phosphatase to EVs. Although recent reports have noted that sortilin is regulated by multiple post-translational modifications, the precise mechanisms of sortilin trafficking still need to be determined. Here, we show that sortilin forms homodimers with an intermolecular disulfide bond at the cysteine 783 (Cys783) residue, and because Cys783 can be palmitoylated, it could be shared via palmitoylation and an intermolecular disulfide bond. Formation of this intermolecular disulfide bond leads to trafficking of sortilin to EVs by preventing palmitoylation, which further promotes sortilin trafficking to the Golgi apparatus. Moreover, we found that sortilin-derived propeptide decreased sortilin homodimers within EVs. In conclusion, sortilin is transported to EVs via the formation of homodimers with an intermolecular disulfide bond, which is endogenously regulated by its own propeptide. Therefore, we propose that inhibiting dimerization of sortilin acts as a new therapeutic strategy for the treatment of EV-associated diseases, including vascular calcification and cancer.
Low-Frequency rTMS Ameliorates Autistic-Like Behaviors in Rats Induced by Neonatal Isolation Through Regulating the Synaptic GABA Transmission

Patients with autism spectrum disorder (ASD) display abnormalities in neuronal development, synaptic function and neural circuits. The imbalance of excitatory and inhibitory (E/I) synaptic transmission has been proposed to cause the main behavioral characteristics of ASD. Repetitive transcranial magnetic stimulation (rTMS) can directly or indirectly induce excitability and synaptic plasticity changes in the brain noninvasively. However, whether rTMS can ameliorate autistic-like behaviors in animal model via regulating the balance of E/I synaptic transmission is unknown. By using our recent reported animal model with autistic-like behaviors induced by neonatal isolation (postnatal days 1–9), we found that low-frequency rTMS (LF-rTMS, 1 Hz) treatment for 2 weeks effectively alleviated the acquired autistic-like symptoms, as reflected by an increase in social interaction and decrease in self-grooming, anxiety- and depressive-like behaviors in young adult rats compared to those in untreated animals. Furthermore, the amelioration in autistic-like behavior was accompanied by a restoration of the balance between E/I activity, especially at the level of synaptic transmission and receptors in synaptosomes. These findings indicated that LF-rTMS may alleviate the symptoms of ASD-like behaviors caused by neonatal isolation through regulating the synaptic GABA transmission, suggesting that LF-rTMS may be a potential therapeutic technique to treat ASD.
A versatile plasmid system for reconstitution and analysis of mammalian ubiquitination cascades in yeast

Ubiquitination is a posttranslational protein modification that regulates most aspects of cellular life. The sheer number of ubiquitination enzymes that are present in a mammalian cell, over 700 in total, has thus far hampered the analysis of distinct protein ubiquitination cascades in a cellular context. To overcome this complexity we have developed a versatile vector system that allows the reconstitution of specific ubiquitination cascades in the model eukaryote Saccharomyces cerevisae (baker’s yeast). The vector system consists of 32 modular yeast shuttle plasmids allowing inducible or constitutive expression of up to four proteins of interest in a single cell. To demonstrate the validity of the system, we show that co-expression in yeast of the mammalian HECT type E3 ubiquitin ligase E6AP (E6-Associated Protein) and a model substrate faithfully recapitulates E6AP-dependent substrate ubiquitination and degradation. In addition, we show that the endogenous sumoylation pathway of S. cerevisiae can specifically sumoylate mouse PML (Promyelocytic leukemia protein). In conclusion, the yeast vector system described in this paper provides a versatile tool to study complex post-translational modifications in a cellular setting.
of Geophysical Research : Solid Earth Seismic Amplitude Ratio Analysis of the 2014 – 2015 Bár ð arbunga-Holuhraun Dike Propagation and Eruption

Magma is transported in brittle rock through dikes and sills. This movement may be accompanied by the release of seismic energy that can be tracked from the Earth’s surface. Locating dikes and deciphering their dynamics is therefore of prime importance in understanding and potentially forecasting volcanic eruptions. The Seismic Amplitude Ratio Analysis (SARA) method aims to track melt propagation using the amplitudes recorded across a seismic network without picking the arrival times of individual earthquake phases. This study validates this methodology by comparing SARA locations (filtered between 2 and 16 Hz) with the earthquake locations (same frequency band) recorded during the 2014–2015 Bárðarbunga-Holuhraun dike intrusion and eruption in Iceland. Integrating both approaches also provides the opportunity to investigate the spatiotemporal characteristics of magma migration during the dike intrusion and ensuing eruption. During the intrusion SARA locations correspond remarkably well to the locations of earthquakes. Several exceptions are, however, observed. (1) A low-frequency signal was possibly associated with a subglacial eruption on 23 August. (2) A systematic retreat of the seismicity was also observed to the back of each active segment during stalled phases and was associated with a larger spatial extent of the seismic energy source. This behavior may be controlled by the dike’s shape and/or by dike inflation. (3) During the eruption SARA locations consistently focused at the eruptive site. (4) Tremor-rich signal close to ice cauldrons occurred on 3 September. This study demonstrates the power of the SARA methodology, provided robust site amplification; Quality Factors and seismic velocities are available. Plain Language Summary Locating earthquakes usually implies picking phase arrivals (P and S waves). Another technique called Seismic Amplitude Ratio Analysis (SARA) was recently introduced to locate them only by using the amplitude recorded at different pairs of seismic stations. However, this technique was never proven to be true. This study shows that the earthquake locations derived by SARA compares remarkably well with the locations of 30,000 seismic events triggered when magma migrated in the Icelandic crust prior to the 2014–2015 Holuhraun eruption. But the results also provide new insight into the magma dynamics that led to the largest eruption of the last two centuries in Europe. We show that ground vibration was continuously triggered during the 2 week period preceding the eruption when magma forced its way toward the eruption site but also during the eruption itself. Several intriguing features were observed including low-frequency vibrations possibly associated with eruption below the ice, or large patches of seismic activity when the magma stopped propagating toward the eruption site. This methodology performs very well, provided some parameters are available, and allows to gain insights into the complex dynamics associated with magma movements.
Data-based fuzzy rules extraction method for classification

In this study, a two-stage method which extracts fuzzy rules directly from samples is proposed for classification. First, we introduce a neighborhood based attribute significance algorithm to select r of the most important attributes from the original attribute set. Second, the proposed algorithm generates fuzzy rule from each sample described by the selected attribute subset and finally simplifies the returned fuzzy rule-base. A confidence degree is assigned for each of the extracted fuzzy rules by counting the number of training samples covered by the rule to solve the conflicts among the rules and then the rule-base is pruned. The performance of the proposed classification method have been compared with other five classification approaches including C4.5, DTable, OneR, NNge, and PART on seven UCI data sets. The experimental results show that the proposed method is better than other methods in two aspects: the higher classification accuracy and the smaller rule-base.