bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporally informed random forests for suicide risk prediction
Authors: Bayramli Ilkin , Castro Victor , Barak-Corren Yuval , Madsen Emily M , Nock Matthew K , Smoller Jordan W , Reis Ben Y 
Published: October 2021

Abstract

Objective
Suicide is one of the leading causes of death worldwide, yet clinicians find it difficult to reliably identify individuals at high risk for suicide. Algorithmic approaches for suicide risk detection have been developed in recent years, mostly based on data from electronic health records (EHRs). Significant room for improvement remains in the way these models take advantage of temporal information to improve predictions.

Materials and Methods
We propose a temporally enhanced variant of the random forest (RF) model—Omni-Temporal Balanced Random Forests (OT-BRFs)—that incorporates temporal information in every tree within the forest. We develop and validate this model using longitudinal EHRs and clinician notes from the Mass General Brigham Health System recorded between 1998 and 2018, and compare its performance to a baseline Naive Bayes Classifier and 2 standard versions of balanced RFs.

Results
Temporal variables were found to be associated with suicide risk: Elevated suicide risk was observed in individuals with a higher total number of visits as well as those with a low rate of visits over time, while lower suicide risk was observed in individuals with a longer period of EHR coverage. RF models were more accurate than Naive Bayesian classifiers at predicting suicide risk in advance (area under the receiver operating curve = 0.824 vs. 0.754, respectively). The proposed OT-BRF model performed best among all RF approaches, yielding a sensitivity of 0.339 at 95% specificity, compared to 0.290 and 0.286 for the other 2 RF models. Temporal variables were assigned high importance by the models that incorporated them.

Discussion
We demonstrate that temporal variables have an important role to play in suicide risk detection and that requiring their inclusion in all RF trees leads to increased predictive performance. Integrating temporal information into risk prediction models helps the models interpret patient data in temporal context, improving predictive performance.
Resistance of Soybean Genotypes toAnticarsia gemmatalis(Lepidoptera: Erebidae): Antixenosis and Antibiosis Characterization
Authors: Ongaratto S , Silveira C M , Santos M C , Gorri J E R , Sartori M M P , Hunt Thomas E , Lourenção A L , Baldin E L L 
Published: October 2021

AbstractInjury by herbivores is a major biotic stress that limits soybean [Glycine max (L.) Merrill] crop production. Among the main soybean insect pests, Anticarsia gemmatalis Hübner is responsible for causing significant economic damage in soybean. The primary management strategy for this insect is chemical control and use of Bt transgenic soybean. Alternative strategies, such as host plant resistance, are considered an efficient and less-aggressive method, especially in association with other strategies as part of an integrated pest management (IPM) approach. In this study, we evaluated 30 soybean genotypes to verify antixenosis expression through oviposition, attractiveness, and food consumption tests. From this, we selected 13 promising genotypes to verify the possible presence of antibiosis. Our results suggest that antixenosis was found in genotypes ‘TMG 133’ RR, ‘TMG 1179’ RR, ‘IAC 19’, ‘IAC 17’, ‘IAC 100’, D75-10169, and IAC 78-2318. By influence on behavior and negative impact on larval viability, antixenosis and antibiosis were indicated for the genotypes IAC 74-2832, ‘IAC 19’, ‘IAC 17’, ‘IAC 100’, and PI 274454. ‘TMG 7062’ IPRO was found to provide antibiosis resistance by negatively affecting larval development and viability. Because of reduced food consumption by larvae, antixenosis was indicated for ‘IAC 24’. These genotypes should be considered in soybean breeding programs focusing on soybean resistance to A. gemmatalis.
Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV
Authors: Clavel Marion , Lechner Esther , Incarbone Marco , Vincent Timothée , Cognat Valerie , Smirnova Ekaterina , Lecorbeiller Maxime , Brault Véronique , Ziegler-Graff Véronique , Genschik Pascal 
Published: October 2021

Abstract
In plants and some animal lineages, RNA silencing is an efficient and adaptable defense mechanism against viruses. To counter it, viruses encode suppressor proteins that interfere with RNA silencing. Phloem-restricted viruses are spreading at an alarming rate and cause substantial reduction of crop yield, but how they interact with their hosts at the molecular level is still insufficiently understood. Here, we investigate the antiviral response against phloem-restricted turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana. Using a combination of genetics, deep sequencing, and mechanical vasculature enrichment, we show that the main axis of silencing active against TuYV involves 22-nt vsiRNA production by DCL2, and their preferential loading into AGO1. Moreover, we identify vascular secondary siRNA produced from plant transcripts and initiated by DCL2-processed AGO1-loaded vsiRNA. Unexpectedly, and despite the viral encoded VSR P0 previously shown to mediate degradation of AGO proteins, vascular AGO1 undergoes specific post-translational stabilization during TuYV infection. Collectively, our work uncovers the complexity of antiviral RNA silencing against phloem-restricted TuYV and prompts a re-assessment of the role of its suppressor of silencing P0 during genuine infection.
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents
Authors: Zhou Ying , Zhang Yintao , Lian Xichen , Li Fengcheng , Wang Chaoxin , Zhu Feng , Qiu Yunqing , Chen Yuzong 
Published: October 2021

Abstract
Drug discovery relies on the knowledge of not only drugs and targets, but also the comparative agents and targets. These include poor binders and non-binders for developing discovery tools, prodrugs for improved therapeutics, co-targets of therapeutic targets for multi-target strategies and off-target investigations, and the collective structure-activity and drug-likeness landscapes of enhanced drug feature. However, such valuable data are inadequately covered by the available databases. In this study, a major update of the Therapeutic Target Database, previously featured in NAR, was therefore introduced. This update includes (a) 34 861 poor binders and 12 683 non-binders of 1308 targets; (b) 534 prodrug-drug pairs for 121 targets; (c) 1127 co-targets of 672 targets regulated by 642 approved and 624 clinical trial drugs; (d) the collective structure-activity landscapes of 427 262 active agents of 1565 targets; (e) the profiles of drug-like properties of 33 598 agents of 1102 targets. Moreover, a variety of additional data and function are provided, which include the cross-links to the target structure in PDB and AlphaFold, 159 and 1658 newly emerged targets and drugs, and the advanced search function for multi-entry target sequences or drug structures. The database is accessible without login requirement at: https://idrblab.org/ttd/.
Cat Scratch Disease as a Mimicker of Malignancy
Authors: Dhal Udit , Hicklen Rachel S , Tarrand Jeffrey , Kontoyiannis Dimitrios P 
Published: October 2021

Abstract
Cat scratch disease (CSD) infrequently mimics malignancy. We reviewed 11 such cases at MD Anderson Cancer Center and an additional 36 reported from the literature. Breast cancer, sarcoma, and lymphoma were the most commonly suspected malignancies. Most patients were young, female, had prior cat exposure, and had no systemic symptoms. Regional lymphadenopathy was the most common finding.
Capitalism’s future is Africa’s future
Authors: Songwe Vera 
Published: October 2021

AbstractThis article looks at the role of finance within a traditional form of capitalism. In essence, it was a component of a dynamic process which relied on classical production functions to create value. This contrasts with its more recent role in which financial value creation happens in isolation of production. It tries to tease out the implications for Africa as well as for the future of capitalism. The conclusion reached is that Africa is ripe for that traditional role of finance, but not for its modern variant. Policy choices will determine which options dominate investment decisions.
Politics of delegated governance: reforming vocational education and training
Authors: Özel Isik D 
Published: October 2021

AbstractFollowing decades-long inertia, many countries started reforming vocational education and training (VET). Yet, respective reform processes that entail certain traits of the German dual system face challenges linked to domestic constraints. Focusing on secondary education and drawing on the Turkish case, this article examines VET’s transformation from a centralized, school-based, state-dominated system to a system based on school–industry collaboration. It suggests that effective adoption of VET reforms may be facilitated by bipartite coordination between government and employers’ organizations representing small- and medium-sized enterprises (SMEs). It unveils how such coordination led an institutional transformation, fostered by a broad cross-class VET coalition formed in a polarized fashion. Highlighting the role of political ownership and organizational capacity in VET reforms, it traces how the Justice and Development Party (AKP) accommodated SMEs’ demands, while sidelining labor. The article undertakes a power-distributional analysis tackling political conflicts and coalitions as drivers of institutional change and continuity.
More than 100 years of neglect: a bibliometric analysis of global research on noma (cancrum oris)
Authors: Dominic Catherine , Farley Elise , Elkheir Natalie 
Published: October 2021

ABSTRACT

Background
Research plays a significant role in quantifying and addressing the burden of disease, improving healthcare delivery and developing evidence-based policy for neglected tropical diseases (NTDs). Since noma is not a recognised NTD by the World Health Organization (WHO), research activity is hypothesised to be low. This study aims to understand patterns and trends of research conducted on noma, to understand the patterns of citations, highlight networks of collaboration and analyse stakeholders in noma research.

Methods
The SCOPUS database was selected and searched. Data analysis was conducted using the bibliometrix package for R in RStudio. Areas of interest included the distribution of research output on noma by year and location, the academic impact of publication output, mapping the major academic community and conducting a thematic analysis of high-frequency keywords.

Results
A total of 208 documents were identified. The annual growth rate of publications is 4.3%. The average number of citations per publication was 11.0 (rounded from 10.98) and the average citations per year per publication was 0.57. The USA was the country with the highest percentage 10.6% (n=22) of corresponding authors, followed by Nigeria (6.7% [n=14]), the UK (6.3% [n=13]) and India (5.8% [n=12]). For those papers with multiple authors, there was an average of 3.22 co-authors per document. The collaboration index was 3.3. Upon plotting collaboration networks between authors, only 11 clusters were identified (frequency and intensity of collaboration). Mapping of trending topics showed a focus on skin grafting and transplantation within the literature.

Conclusions
In order to progress towards eventual elimination of noma it is key that more research should be undertaken and more interest and funding should be dedicated to work on noma. Recognition of noma as an NTD by the WHO would be a first step in moving towards increased awareness.
Mechanisms of damage prevention, signalling, and repair impact disease tolerance
Authors: Prakash Arun , Monteith Katy M. , Vale Pedro F. 
Published: October 2021

AbstractThe insect gut is frequently exposed to pathogenic threats and must not only clear these potential infections, but also tolerate relatively high microbe loads. In contrast to the mechanisms that eliminate pathogens, we currently know less about the mechanisms of disease tolerance. We investigated how well-described mechanisms that either prevent, signal, control, or repair damage during infection contribute to the phenotype of disease tolerance. We established enteric infections with the bacterial pathogen Pseudomonas entomophila in transgenic lines of Drosophila melanogaster fruit flies affecting dcy (a major component of the peritrophic matrix), upd3 (a cytokine-like molecule), irc (a negative regulator of reactive oxygen species) and egfr1 (epithelial growth factor receptor). Flies lacking dcy experienced the highest susceptibility, while loss of function of either irc or upd3 reduced tolerance in both sexes. The disruption of egfr1 resulted in a severe loss in tolerance in male flies but had no substantial effect on the ability of female flies to tolerate P. entomophila infection, despite carrying greater microbe loads than males. Together, our findings provide evidence for the role of damage limitation mechanisms in disease tolerance and highlight how sex differences in these mechanisms could generate sexual dimorphism in disease tolerance.
PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets
Authors: Zhang Susu , Wang Jing , Liu Qi , McDonald W. Hayes , Bomber Monica L. , Layden Hillary M. , Ellis Jacob , Borinstein Scott C. , Hiebert Scott W. , Stengel Kristy R. 
Published: October 2021

AbstractTranscriptional control is a highly dynamic process that changes rapidly in response to various cellular and extracellular cues1. Thus, it is difficult to achieve a mechanistic understanding of transcription factor function using traditional genetic deletion or RNAi methods, because these slow approaches make it challenging to distinguish direct from indirect transcriptional effects. Here, we used a chemical-genetic approach to rapidly degrade a canonical transcriptional activator, PAX3-FOXO12-6 to define how the t(2;13)(q35;q14) disrupts normal gene expression programs to trigger cancer. By coupling rapid protein degradation with the analysis of nascent transcription over short time courses, we identified a core transcriptional network that rapidly collapsed upon PAX3-FOXO1 degradation. Moreover, loss of PAX3-FOXO1 impaired RNA polymerase pause release and transcription elongation at regulated gene targets. The activity of PAX3-FOXO1 at enhancers controlling this core network was surprisingly selective and often only a single element within a complex super-enhancer was affected. In addition, fusion of the endogenous PAX3-FOXO1 with APEX2 identified proteins in close proximity with PAX3-FOXO1, including ARID1A and MYOD1. We found that continued expression of PAX3-FOXO1 was required to maintain chromatin accessibility and allow neighboring DNA binding proteins and chromatin remodeling complexes to associate with this small number of regulated enhancers. Overall, this work provides a detailed mechanism by which PAX3-FOXO1 maintains an oncogenic transcriptional regulatory network.
β-amyloid−driven synaptic depression requires PDZ protein interaction at AMPA-receptor subunit GluA3
Authors: Reinders Niels R. , van der Spek Sophie , Klaassen Remco V. , Koymans Karin J. , Li Ka Wan , Smit August B. , Kessels Helmut W. 
Published: October 2021

AbstractSoluble oligomeric amyloid-β (Aβ) is a prime suspect to cause cognitive deficits in Alzheimer’s disease and weakens synapses by removing AMPA-type glutamate receptors (AMPARs). We show that synapses of CA1 pyramidal neurons become vulnerable to Aβ when they express AMPAR subunit GluA3. We found that Aβ-oligomers reduce the levels of GluA3 immobilized at spines, indicating they deplete GluA3-containing AMPARs from synapses. These Aβ-driven effects critically depended on the PDZ-binding motif of GluA3. When GluA3 was expressed with a single amino acid mutation in its PDZ-binding motif that prevents GRIP binding, it did not end up at spines and Aβ failed to trigger synaptic depression. GluA3 with a different point mutation in the PDZ-motif that leaves GRIP-binding intact but prevents its endocytosis, was present at spines in normal amounts but was fully resistant to effects of Aβ. Our data indicate that Aβ-mediated synaptic depression requires the removal of GluA3 from synapses. We propose that GRIP-detachment from GluA3 is a critical early step in the cascade of events through which Aβ accumulation causes a loss of synapse.
Brain networks in human conscious visual perception
Authors: Kronemer Sharif I. , Aksen Mark , Ding Julia , Ryu Jun Hwan , Xin Qilong , Ding Zhaoxiong , Prince Jacob S. , Kwon Hunki , Khalaf Aya , Forman Sarit , Jin David , Wang Kevin , Chen Kaylie , Hu Claire , Agarwal Akshar , Saberski Erik , Wafa Syed Mohammad Adil , Morgan Owen P. , Wu Jia , Christison-Lagay Kate L. , Hasulak Nicholas , Morrell Martha , Urban Alexandra , Constable R. Todd , Pitts Michael , Richardson R. Mark , Crowley Michael J. , Blumenfeld Hal 
Published: October 2021

AbstractConsciousness is not explained by a single mechanism, rather it involves multiple specialized neural systems overlapping in space and time. We hypothesize that synergistic, large-scale subcortical and cortical attention and signal processing networks encode conscious experiences. To identify brain activity in conscious perception without overt report, we classified visual stimuli as perceived or not using eye measurements. Report-independent event-related potentials and functional magnetic resonance imaging (fMRI) signals both occurred at early times after stimuli. Direct recordings revealed a novel thalamic awareness potential linked to conscious visual perception based on report. fMRI showed thalamic and cortical detection, arousal, attentional salience, task-positive, and default mode networks were involved independent of overt report. These findings identify a specific sequence of neural mechanisms in human conscious visual perception.One-Sentence SummaryHuman conscious visual perception engages large-scale subcortical and cortical networks even without overt report.
Differential timing for glucose assimilation in Prochlorococcus and coexistent microbial populations at the North Pacific Subtropical Gyre
Authors: Muñoz-Marín María del Carmen , Duhamel Solange , Björkman Karin M. , Magasin Jonathan D. , Díez Jesús , Karl David M. , García-Fernández José M. 
Published: October 2021

AbstractThe marine cyanobacterium Prochlorococcus can utilize glucose as a source of carbon. However, the relative importance of inorganic and organic carbon assimilation and the timing of glucose assimilation are still poorly understood in these numerically dominant cyanobacteria. Here we investigated whole microbial community and group-specific primary production and glucose assimilation, using incubations with radioisotopes combined with flow cytometry cell sorting. We also studied changes in the microbial community structure in response to glucose enrichments and analyzed the transcription of Prochlorocccus genes involved in carbon metabolism and photosynthesis.Our results showed a circadian rhythm for glucose assimilation in Prochlorococcus, with maximum assimilation during the midday and minimum at midnight, which was different compared with that of the total microbial community. This suggests that rhythms in glucose assimilation have been adapted in Prochlorococcus to couple the active transport to photosynthetic light reactions producing energy, and possibly to avoid competition from the rest of the microbial community. High-light Prochlorococcus strains showed most transcriptional changes upon glucose enrichment. Pathways involved in glucose metabolism as the pentose phosphate, the Entner-Dudoroff, glycolysis, respiration and glucose transport showed an increase in the transcript level. A few genes of the low-light strains showed opposite changes, suggesting that glucose assimilation has been subjected to diversification along the Prochlorococcus evolution.
Robust T cell activation requires an eIF3-driven burst in T cell receptor translation
Authors: De Silva Dasmanthie , Ferguson Lucas , Chin Grant H. , Smith Benjamin E. , Apathy Ryan A. , Roth Theodore L. , Blaeschke Franziska , Kudla Marek , Marson Alexander , Ingolia Nicholas T. , Cate Jamie H. D. 
Published: October 2021

ABSTRACTActivation of T cells requires a rapid surge in cellular protein synthesis. However, the role of translation initiation in the early induction of specific genes remains unclear. Here we show human translation initiation factor eIF3 interacts with select immune system related mRNAs including those encoding the T cell receptor (TCR) subunits TCRA and TCRB. Binding of eIF3 to theTCRAandTCRBmRNA 3’-untranslated regions (3’-UTRs) depends on CD28 coreceptor signaling and regulates a burst in TCR translation required for robust T cell activation. Use of theTCRAorTCRB3’-UTRs to control expression of an anti-CD19 chimeric antigen receptor (CAR) improves the ability of CAR-T cells to kill tumor cellsin vitro. These results identify a new mechanism of eIF3-mediated translation control that can aid T cell engineering for immunotherapy applications.
Effect of cow’s milk with different PUFA n-6: n-3 ratios on performance, serum lipid profile, and blood parameters of grower gilts
Authors: Reis Leriana Garcia , da Silva Thiago Henrique , Salles Márcia Saladini Vieira , Andrade André Furugen Cesar , Martins Simone Maria Massami Kitamura , Takeuchi Paula Lumy , Vidal Ana Maria Centola , Netto Arlindo Saran 
Published: October 2021

ABSTRACTThe concern with human health has increased the interest in producing foods enriched with polyunsaturated fatty acids (PUFA), directly or naturally by inclusion in the animals’ diet. The positive effects such as antithrombotic, anti-inflammatory, and hypolipidemic have been observed in pigs and rats, used as human models for study. The present study evaluated the effect of cow’s milk with different lipid profiles on performance, serum fatty acid profile, biochemical analysis, and a complete blood count of gilts used as a human model. At 34 days, thirty gilts were equally distributed in three treatments. Experimental treatments were milk from cows without the oil supplementation (C), milk from cows fed an enriched diet with linseed oil (n-3), and milk from cows fed an enriched diet with soybean oil (n-6). Milk supplementation was performed until the age of 190 days, provided once in the morning. The n-3 and n-6 milk reduced the concentration of myristic acid in the blood and increased the leukocytes. Milk enriched with n-3 compared to n-6 reduced stearic acid. In conclusion, milk with a better PUFA profile can reduce saturated fatty acids in the blood and alter the concentration of cells in the defense system.