Miracle-dz/UniFAR-FTUs huggingface dataset:
Is suicidal behaviour a stronger predictor of later suicide than suicidal ideation? A systematic review and meta-analysis

Objective: Suicidal ideation and suicidal behaviour are both regarded as important risk factors for suicide, but it is usually believed that suicidal ideation is less strongly linked to suicide than suicidal behaviours. In this study, we assessed and compared the strengths of the associations that suicidal ideation and suicidal behaviour have with later suicide using meta-analysis of primary studies reporting both these independent variables and the dependent variable of suicide. Methods: A total of 51 English language publications describing cohort or controlled studies that reported on both the association between suicidal ideation and suicide and the association between suicidal behaviours and suicide were located using searches for titles in PubMed containing variants of the word suicide (suicid*). Suicides were considered to include reported suicides and open verdicts from mortality registers. The strengths of the two associations were examined in separate random effects meta-analyses and were then compared using mixed effects meta-regression. Subgroups were examined according to study characteristics including the definitions of suicidal ideation or behaviour used, setting (psychiatric or non-psychiatric), diagnostic mix of the study population, study design (cohort or control) and study quality. Results: Suicidal ideation (odds ratio = 3.11, 95% confidence interval = 2.51, 3.86) and suicidal behaviours (odds ratio = 4.09, 95% confidence interval = 3.05, 5.49) were both significantly associated with suicide but there was no significant difference in the strengths of association (p = 0.14). Nor were there significant differences in the strengths of the two associations in multiple subgroup analyses. Conclusion: Suicidal ideation and suicidal behaviour are both moderately associated with suicide. Existing data cannot conclusively demonstrate that suicidal behaviours are more strongly associated with suicide than suicidal ideation. Clinicians should not strongly prioritise suicidal behaviour over suicidal ideation when considering suicide risk.
Pilot Multi-Omic Analysis of Human Bile from Benign and Malignant Biliary Strictures: A Machine-Learning Approach

Cholangiocarcinoma (CCA) and pancreatic adenocarcinoma (PDAC) may lead to the development of extrahepatic obstructive cholestasis. However, biliary stenoses can also be caused by benign conditions, and the identification of their etiology still remains a clinical challenge. We performed metabolomic and proteomic analyses of bile from patients with benign (n = 36) and malignant conditions, CCA (n = 36) or PDAC (n = 57), undergoing endoscopic retrograde cholangiopancreatography with the aim of characterizing bile composition in biliopancreatic disease and identifying biomarkers for the differential diagnosis of biliary strictures. Comprehensive analyses of lipids, bile acids and small molecules were carried out using mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (1H-NMR) in all patients. MS analysis of bile proteome was performed in five patients per group. We implemented artificial intelligence tools for the selection of biomarkers and algorithms with predictive capacity. Our machine-learning pipeline included the generation of synthetic data with properties of real data, the selection of potential biomarkers (metabolites or proteins) and their analysis with neural networks (NN). Selected biomarkers were then validated with real data. We identified panels of lipids (n = 10) and proteins (n = 5) that when analyzed with NN algorithms discriminated between patients with and without cancer with an unprecedented accuracy.
Detection of piscine nodaviruses from apparently healthy wild marine fish in Korea

Piscine nodaviruses are the causative agent of viral encephalopathy and retinopathy in cultured and wild marine fish. A total of 663 apparently healthy wild marine fish (70 species) were collected near aquaculture facilities in three different coastal areas (Donghae, Hwanghae and Namhae) of Korea. The brains of fish were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR to detect the coat protein gene of nodavirus. Fourteen samples collected in Donghae and 80 from Hwanghae were negative for nodavirus in both RT-PCR and nested PCR tests. Two and 48 of 569 samples collected in Namhae were positive for nodavirus in RTPCR and nested PCR, respectively. Samples from 21 species have been definitively found positive: Indian perch, white croakers, spearnose grenadier, moon dragonet, blue fin sea robin, robust tonguefish, black throat sea perch, moontail puffer, silver ponyfish, yellow goosefish, daggertooth pike conger, skate ray fish, red sea bream, marbled sole, five spots flounder, chub mackerel, silver whiting, grass puffer, Japanese jack mackerel, John dory and blotched eel pout. These results indicate that nodavirus occurs at a considerably level in populations of wild marine fish in the Southern part of Korea, suggesting an importance of these fish as carriers of virus.
A Joint Neural Model for Information Extraction with Global Features

Most existing joint neural models for Information Extraction (IE) use local task-specific classifiers to predict labels for individual instances (e.g., trigger, relation) regardless of their interactions. For example, a victim of a die event is likely to be a victim of an attack event in the same sentence. In order to capture such cross-subtask and cross-instance inter-dependencies, we propose a joint neural framework, OneIE, that aims to extract the globally optimal IE result as a graph from an input sentence. OneIE performs end-to-end IE in four stages: (1) Encoding a given sentence as contextualized word representations; (2) Identifying entity mentions and event triggers as nodes; (3) Computing label scores for all nodes and their pairwise links using local classifiers; (4) Searching for the globally optimal graph with a beam decoder. At the decoding stage, we incorporate global features to capture the cross-subtask and cross-instance interactions. Experiments show that adding global features improves the performance of our model and achieves new state of-the-art on all subtasks. In addition, as OneIE does not use any language-specific feature, we prove it can be easily applied to new languages or trained in a multilingual manner.
Effect of Nutritional Restriction on the Hair Follicles Development and Skin Transcriptome of Chinese Merino Sheep

Simple Summary The morphogenesis hair follicles begins in the embryonic stage. The first follicles formed are the primary wool follicles (PF), followed by secondary wool follicles (SF), and then secondary-derived follicles that branch from the SF in Merino sheep. The morphogenesis and development of SF in sheep determine wool yield and quality. At present, the mechanism of SF development and branching is still unclear. In this study, hair follicle morphogenesis and development were inhibited through nutritional restrictions during pregnancy, and transcriptome sequencing was performed to screen for differentially expressed genes related to the SF development in the fetus. Our findings are helpful to understand the mechanisms of SF development and branching of Merino sheep. Abstract The high concentration of secondary branched wool follicles is a distinctive feature of the Merino sheep. At present, the molecular control of the development and branching of secondary wool follicles (SF) remains elusive. To reveal the potential genes associated with the development of hair follicles, we investigated the characteristics of prenatal and postnatal development of wool follicles, and the transcriptional expression profile in fetuses/lambs from dams under either maternal maintenance or sub-maintenance (75% maintenance) nutrition. The density of SF and the ratio of SF to primary wool follicles (PF) were reduced (p < 0.05) in fetuses from day 105 to 135 of gestation under sub-maintenance nutrition. Differentially expressed genes were enriched in the binding, single-organism process, cellular process, cell and cell part Gene Ontology (GO) functional categories and metabolism, apoptosis, and ribosome pathways. Four candidate genes, SFRP4, PITX1, BAMBI, and KRT16, which were involved in secondary wool follicles branching and development, were identified. Our results indicate that nutritional intervention imposed on pregnant ewes by short-term sub-maintenance nutrition could provide a strategy for the study of wool follicle development. Overall insight into the global gene expression associated with SF development can be used to investigate the underlying mechanisms of SF branching in Merino sheep.
Genetic variability of Potato virus Y (PVY) and Tobacco etch virus (TEV) from naturally infected pepper fields in the Hatay region of Turkey

The genetic structure of Potato virus Y (PVY) and Tobacco etch virus (TEV) (Potyvirus) populations was investigated in pepper fields in two regions in Turkey. The diversity of PVY and TEV populations according to coat protein (CP) and VPg coding regions showed some similarity. All the isolates built a monophyletic group due to a single introduction event or multiple introductions of genetically similar isolates. All the isolates of both viruses showed evidence to the diversification for a long time. Based on VPg and CP sequences, all PVY isolates corresponded to clade C1. Turkish potyvirus isolates were only able to break the pvr21 resistance allele and therefore belonged to pathotype (0, 1). The Pvr4 dominant gene was found to be efficient and durable against PVY but not at all efficient against TEV. Consequently, the pvr22 resistance allele, efficient resistance against PVY and TEV pathotype (0, 1) isolates, would be the most suitable strategy to control potyviruses.
Simultaneous Detection of NF1, SPRED1, LZTR1, and NF2 Gene Mutations by Targeted NGS in an Italian Cohort of Suspected NF1 Patients

Neurofibromatosis type 1 (NF1) displays overlapping phenotypes with other neurocutaneous diseases such as Legius Syndrome. Here, we present results obtained using a next generation sequencing (NGS) panel including NF1, NF2, SPRED1, SMARCB1, and LZTR1 genes on Ion Torrent. Together with NGS, the Multiplex Ligation-Dependent Probe Amplification Analysis (MLPA) method was performed to rule out large deletions/duplications in NF1 gene; we validated the MLPA/NGS approach using Sanger sequencing on DNA or RNA of both positive and negative samples. In our cohort, a pathogenic variant was found in 175 patients; the pathogenic variant was observed in NF1 gene in 168 cases. A SPRED1 pathogenic variant was also found in one child and in a one year old boy, both NF2 and LZTR1 pathogenic variants were observed; in addition, we identified five LZTR1 pathogenic variants in three children and two adults. Six NF1 pathogenic variants, that the NGS analysis failed to identify, were detected on RNA by Sanger. NGS allows the identification of novel mutations in five genes in the same sequencing run, permitting unambiguous recognition of disorders with overlapping phenotypes with NF1 and facilitating genetic counseling and a personalized follow-up.
Glyph2Vec: Learning Chinese Out-of-Vocabulary Word Embedding from Glyphs

Chinese NLP applications that rely on large text often contain huge amounts of vocabulary which are sparse in corpus. We show that characters’ written form, Glyphs, in ideographic languages could carry rich semantics. We present a multi-modal model, Glyph2Vec, to tackle Chinese out-of-vocabulary word embedding problem. Glyph2Vec extracts visual features from word glyphs to expand current word embedding space for out-of-vocabulary word embedding, without the need of accessing any corpus, which is useful for improving Chinese NLP systems, especially for low-resource scenarios. Experiments across different applications show the significant effectiveness of our model.
Vegetation Landscape Analysis Due to Land Use Changes on Arid Lands

ABSTRACT Fast land use changes have strongly affected arid and semi-arid regions at a global scale, affecting food security of the inhabitants of these regions. This study evaluated the fragmentation degree in the Chihuahua´s desert region of Mexico by using data from the Landsat TM sensor. Nine scenes, taken with Landsat TM5 sensor from the years 1990, 2000, and 2012, were used for the analysis. The coverage of seven land uses (grasslands, shrubland, croplands, sandy desert vegetation, forest, water bodies, and urban areas) was obtained under supervised classification techniques and the accuracy level was evaluated through the Kappa multi-varied discrete index. The classification showed a good reliance level having global accuracies of 93, 93.2 and 90.3% for the years 1990, 2000 and 2012, respectively. The fragmentation analysis showed an increase in the number of patches, an indicator of the ecosystem degradation process. The patches number increased from 8,354.23 in 1990 to 9,658.36 in 2000 and to 11,469 in 2012. Simpson and Shannon diversity indexes proved a clear fragmentation process. During the period of 1990−2012, grasslands were the most affected vegetation type with a reduction of 30.7% in its area. Such reduction was mainly attributed to invasions of shrubland communities and to an increase in cropland areas.
On the use of osteoderm features in a phylogenetic approach on the internal relationships of the Chroniosuchia (Tetrapoda: Reptiliomorpha)

Abstract: Chroniosuchians are an enigmatic Permian to Triassic group of crocodile‐like basal tetrapods. Their conspicuous dorsal osteoderm systems include most of the group’s yet documented postcranial morphological variability but have hardly been considered in cladistic approaches. Aiming at the clarification of the internal relationships of the Chroniosuchia, we have carried out a parsimony analysis including, among others, 23 morphological and osteohistological osteoderm characters and 12 chroniosuchian taxa. According to the most parsimonious trees, taxa usually referred to Chroniosuchidae form a paraphyletic succession with Madygenerpeton pustulatus and Chroniosaurus dongusensis as the basalmost chroniosuchians and Uralerpeton tverdochlebovae as the sister group of Bystrowianidae (hypothesis A). However, the concurrent hypothesis of a basal split into monophyletic subtaxa Chroniosuchidae and Bystrowianidae (hypothesis B) is only slightly less parsimonious and supported by an alternative analysis which includes embolomeres as the only reptiliomorph outgroup. Searching for the better hypothesis, we compare the respective order of branching to the order of first occurrences in the fossil record, demonstrating that hypothesis A provides a better stratigraphic fit than hypothesis B. Accordingly, the last common ancestor of the yet known chroniosuchians had a series of broad complexly interlocking ‘chroniosuchid’ osteoderms that served as a protection carapace apart from supporting the trunk during terrestrial locomotion. The later evolution of chroniosuchian carapaces was marked by a stepwise increase in flexibility and size reduction, which resulted in a loss of protective function and in a reduction in trunk support function. The flexibility increase is paralleled by the evolution of the Crocodylomorpha whose extant members do not possess as extensively interlocking osteoderm systems as some of their Mesozoic relatives.
Identification of a Blood-Based Protein Biomarker Panel for Lung Cancer Detection

Lung cancer is the deadliest cancer worldwide, mainly due to its advanced stage at the time of diagnosis. A non-invasive method for its early detection remains mandatory to improve patients’ survival. Plasma levels of 351 proteins were quantified by Liquid Chromatography-Parallel Reaction Monitoring (LC-PRM)-based mass spectrometry in 128 lung cancer patients and 93 healthy donors. Bootstrap sampling and least absolute shrinkage and selection operator (LASSO) penalization were used to find the best protein combination for outcome prediction. The PanelomiX platform was used to select the optimal biomarker thresholds. The panel was validated in 48 patients and 49 healthy volunteers. A 6-protein panel clearly distinguished lung cancer from healthy individuals. The panel displayed excellent performance: area under the receiver operating characteristic curve (AUC) = 0.999, positive predictive value (PPV) = 0.992, negative predictive value (NPV) = 0.989, specificity = 0.989 and sensitivity = 0.992. The panel detected lung cancer independently of the disease stage. The 6-protein panel and other sub-combinations displayed excellent results in the validation dataset. In conclusion, we identified a blood-based 6-protein panel as a diagnostic tool in lung cancer. Used as a routine test for high- and average-risk individuals, it may complement currently adopted techniques in lung cancer screening.
Environmental Drivers for Persistence of Escherichia coli and Salmonella in Manure-Amended Soils: A Meta-Analysis.

ABSTRACT Application of organic amendments to agricultural land improves soil quality and provides nutrients essential for plant growth; however, they are also a reservoir for zoonotic pathogens whose presence poses a significant risk to public health. The persistence of bacteria in manure-amended soil, and differences in manure handling practices, are important issues from a food safety perspective. The primary objective of this study was to quantitatively summarize the variations in the rate of decline of Escherichia coli and Salmonella spp. in manure-amended soil under laboratory and field conditions, and to assess the impact of environmental factors. Available literature data on persistence of E. coli and Salmonella spp. in manure-amended soil from 42 primary research studies were extracted and statistically analyzed using a mixed-effect regression model. The results indicated that temperature (soil and air combined) was the most prominent factor affecting persistence of both E. coli and Salmonella spp. under laboratory conditions (P < 0.001), and of E. coli under field conditions (P < 0.05). The time required for a log reduction of E. coli under field conditions was significantly higher at low temperature (0 to 10°C) than at high temperature (greater than 20°C) (P < 0.05). In addition, application method was identified as a significant factor, with manure incorporation to soil inducing longer survival compared with surface application by approximately 1.2 times. The significant variation observed among primary research studies of bacterial persistence has highlighted that mitigation strategies associated with the use of manures in fresh produce production need to be improved by addressing factors such as climate, soil management, application method, and initial microbial levels. These findings may be used to support guidelines establishing exclusion periods between manure fertilization and the grazing or harvesting of crops, and may be useful for the generation of quantitative microbial risk models for fresh produce. HIGHLIGHTS
AMR Parsing with Latent Structural Information

Abstract Meaning Representations (AMRs) capture sentence-level semantics structural representations to broad-coverage natural sentences. We investigate parsing AMR with explicit dependency structures and interpretable latent structures. We generate the latent soft structure without additional annotations, and fuse both dependency and latent structure via an extended graph neural networks. The fused structural information helps our experiments results to achieve the best reported results on both AMR 2.0 (77.5% Smatch F1 on LDC2017T10) and AMR 1.0 ((71.8% Smatch F1 on LDC2014T12).
The Key Psychological Beliefs Underlying Student Participation in Recreational Sport

The first year of university study provides an ideal opportunity to target student participation in many health behaviors such as recreational sport. The study used the theory of planned behavior to identify the key behavioral, normative, and control beliefs underlying student participation in recreational sport. A cross-sectional design was used with a 4-week follow-up. A purposive sample of 206 participants responded to a theoretically informed questionnaire measuring baseline cognitions. Follow-up behavior was measured using self-report questionnaires. All beliefs correlated with intention, and seven beliefs correlated with behavior. Four key beliefs predicted intention (“enjoyable,” “time consuming,” “friends,” and “family members”) and two key beliefs predicted behavior (“enjoyable” and “time consuming”). Interventions successfully targeting these specific beliefs may lead to a greater number of students participating in recreational sport.
Constitutive NF-κB/Rel Activation in Philadelphia Chromosome Positive (Ph+) Acute Lymphoblastic Leukemia (ALL)

The Bcr-Abl translocation t(9;22)(q34;q11) defines a subgroup of ALL patients with a dismal prognosis despite the introduction of intensified induction and consolidation regimen. Although BcrAbl induced NF-kB/Rel activation has previously been shown, the role of NF-kB/Rel in Ph+ leukemia is unclear. Using DNA binding assays, we demonstrate constitutive NF-kB/Rel activity in nuclear extracts from Ph+ ALL blasts, whereas Ph7 primary blast cells and B-precursor cell lines lack NF-kB/Rel activity. NF-kB/Rel activity was shown in the e1a2 and the b2a2 subtypes. Constitutive NF-kB/Rel activity in Ph+ blasts is not due to elevated endogenous IkB kinase (IKK) activity as shown by immune complex kinase assays. Since NF-kB/Rel is a transcriptional regulator of inhibitors of apoptosis we examined the expression of anti-apoptotic genes known to be induced by NF-kB/Rel by real time PCR analysis. We found no induction of TRAF1, TRAF2, cIAP1, cIAP2, XIAP, A20 or Bfl/A1 in Ph+ ALL samples as compared to Ph7negative ALL controls. In summary, constitutive NF-kB/Rel activation independent of endogenous IKK activation may be a common finding in Ph+ ALL. However, targets of NF-kB/Rel mediated transcriptional regulation in this disease remain to be identified.
Genetic control of mineral concentration and yield in perennial ryegrass (Lolium perenne L.), with special emphasis on minerals related to grass tetany

Grass tetany is a common metabolic disorder of ruminants in southern Australia. To investigate the genetic control of mineral concentrations leading to this disorder, replicate populations of perennial ryegrass half-sib families were grown at Hamilton and Timboon in southern Australia. Variation in herbage yield, and Mg, P, K, Ca, Na, Cl, S, Mn, Fe, Cu, Zn, and K/(Mg+Ca) (tetany ratio) concentrations in the herbage of these families was measured in the early spring of 1994. Large environmental effects on herbage mineral concentration were detected, with location differences accounting for 60–80% of the total variance. Both the mean and range for mineral concentration were similar for each population. As expected, Mg, Ca, and K were significantly correlated with tetany ratio; however, the concentrations of other minerals were not consistently associated with tetany ratio. Tetany ratio and Mg showed a negative genetic correlation in both groups. The genetic correlation for tetany ratio with K or Ca was less repeatable across groups. Significant family variance components (σ2f) were detected for yield, Mg, Ca, K, and tetany ratio, and narrow-sense heritabilities for these traits were moderate to high (h2 = 0·46–0·81). However, family location interactions were also significant, with σ2fl often >σ2f. A large proportion of the family location interaction for K and Mg concentration was associated with non-rank family changes indicating that family selection for low K or high Mg concentration would be effective across environments. However, family × location effects for Ca and tetany ratio were associated with substantial rank changes across locations. Selection for increased Mg concentration would appear the most suitable strategy for reducing the tetany ratio of perennial ryegrass, with possibly different cultivars required for the environments represented by Hamilton and Timboon.