bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controllability of a class of swarm signalling networks
Authors: Sun Peng , Kooij Robert E , Bouffanais Roland 
Published: November 2022

Abstract
In this article, we propose closed-form analytical expressions to determine the minimum number of driver nodes that is needed to control a specific class of networks. We consider swarm signalling networks with regular out-degree distribution where a fraction $p$ of the links is unavailable. We further apply our method to networks with bi-modal out-degree distributions. Our approximations are validated through intensive simulations. Results show that our approximations have high accuracy when compared with simulation results for both types of out-degree distribution.
Impact of a national screening programme on obesity and cardiovascular risk factors
Authors: Nakao Yoko M , Gale Chris P , Miyazaki Kei , Kobayashi Hajime , Matsuda Ayako , Nadarajah Ramesh , Motonishi Taizo 
Published: November 2022

Abstract

Aims
The benefits of nationwide screening and tailored health guidance on improving obesity and cardiovascular risk factors is uncertain. The aim of the present study was to investigate the association of the national health screening and tailored health guidance with population health outcomes.

Methods and results
A fuzzy regression discontinuity design analysed data of men and women aged 40–74 years who participated in a nationwide health screening programme in Japan from 1 April 2008 to 31 March 2019 and were recorded in the Japanese National Database. Exposure was assignment to the national health guidance of counselling on healthy lifestyle and clinical follow-up for individuals found to have waist circumference ≥85 cm for men ≥90 cm for women with one or more cardiovascular risk factors during annual national health screening. The primary outcomes were changes in obesity status and cardiovascular risk factors 1 year after screening. Of 3 490 112 men and 2 328 929 women, the assignment to the health guidance resulted in small reductions in obesity parameters: waist circumference; men, −0.27 cm [95% confidence interval (CI) −0.29 to −0.26]; women −0.34 (−0.41 to −0.27); body mass index, −0.07 kg/m2 (−0.075 to −0.066); −0.11 kg/m2 (−0.13 to −0.10); weight, −0.21 kg (−0.22 to −0.19); −0.28 kg (−0.32 to −0.24) that attenuated over time. Short-term improvements were also observed in blood pressure, haemoglobin A1c, fasting glucose and triglycerides across both sexes.

Conclusion
A nationwide health screening programme was associated with only small, and transient improvements in obesity and cardiovascular risk factors.
Artificial intelligence in gastric cancer: applications and challenges
Authors: Cao Runnan , Tang Lei , Fang Mengjie , Zhong Lianzhen , Wang Siwen , Gong Lixin , Li Jiazheng , Dong Di , Tian Jie 
Published: November 2022

Abstract
Gastric cancer (GC) is one of the most common malignant tumors with high mortality. Accurate diagnosis and treatment decisions for GC rely heavily on human experts' careful judgments on medical images. However, the improvement of the accuracy is hindered by imaging conditions, limited experience, objective criteria, and inter-observer discrepancies. Recently, the developments of machine learning, especially deep-learning algorithms, have been facilitating computers to extract more information from data automatically. Researchers are exploring the far-reaching applications of artificial intelligence (AI) in various clinical practices, including GC. Herein, we aim to provide a broad framework to summarize current research on AI in GC. In the screening of GC, AI can identify precancerous diseases and assist in early cancer detection with endoscopic examination and pathological confirmation. In the diagnosis of GC, AI can support tumor-node-metastasis (TNM) staging and subtype classification. For treatment decisions, AI can help with surgical margin determination and prognosis prediction. Meanwhile, current approaches are challenged by data scarcity and poor interpretability. To tackle these problems, more regulated data, unified processing procedures, and advanced algorithms are urgently needed to build more accurate and robust AI models for GC.
Evolutionary Conservation and Transcriptome Analyses Attribute Perenniality and Flowering to Day-Length Responsive Genes in Bulbous Barley (Hordeum bulbosum)
Authors: Fuerst Dana , Shermeister Bar , Mandel Tali , Hübner Sariel 
Published: November 2022

Abstract
Rapid population growth and dramatic climatic turnovers are challenging global crop production. These challenges are spurring plant breeders to enhance adaptation and sustainability of major crops. One intriguing approach is to turn annual systems into perennial ones, yet long-term classical breeding efforts to induce perenniality have achieved limited success. Here, we report the results of our investigation of the genetic basis of bulb formation in the nonmodel organism Hordeum bulbosum, a perennial species closely related to barley. To identify candidate genes that regulate bulb formation in H. bulbosum, we applied two complementary approaches. First, we explored the evolutionary conservation of expressed genes among annual Poaceae species. Next, we assembled a reference transcriptome for H. bulbosum and conducted a differential expression (DE) analysis before and after stimulating bulb initiation. Low conservation was identified in genes related to perenniality in H. bulbosum compared with other species, including bulb development and sugar accumulation genes. We also inspected these genes using a DE analysis, which enabled identification of additional genes responsible for bulb initiation and flowering regulation. We propose a molecular model for the regulation of bulb formation involving storage organ development and starch biosynthesis genes. The high conservation observed along a major part of the pathway between H. bulbosum and barley suggests a potential for the application of biotechnological techniques to accelerate breeding toward perenniality in barley.
Whole-exome sequencing study identifies four novel gene loci associated with diabetic kidney disease
Authors: Pan Yang , Sun Xiao , Mi Xuenan , Huang Zhijie , Hsu Yenchih , Hixson James E , Munzy Donna , Metcalf Ginger , Franceschini Nora , Tin Adrienne , Köttgen Anna , Francis Michael ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium TOPMed Kidney Function Working Group, Brody Jennifer A , Kestenbaum Bryan , Sitlani Colleen M , Mychaleckyj Josyf C , Kramer Holly , Lange Leslie A , Guo Xiuqing , Hwang Shih-Jen , Irvin Marguerite R , Smith Jennifer A , Yanek Lisa R , Vaidya Dhananjay , Chen Yii-Der Ida , Fornage Myriam , Lloyd-Jones Donald M , Hou Lifang , Mathias Rasika A , Mitchell Braxton D , Peyser Patricia A , Kardia Sharon L R , Arnett Donna K , Correa Adolfo , Raffield Laura M , Vasan Ramachandran S , Cupple L Adrienne , Levy Daniel , Kaplan Robert C , North Kari E , Rotter Jerome I , Kooperberg Charles , Reiner Alexander P , Psaty Bruce M , Tracy Russell P , Gibbs Richard A , Morrison Alanna C , Feldman Harold , Boerwinkle Eric , He Jiang , Kelly Tanika N ,   the CRIC Study Investigators
Published: November 2022

AbstractDiabetic kidney disease (DKD) is recognized as an important public health challenge. However, its genomic mechanisms are poorly understood. To identify rare variants for DKD, we conducted a whole-exome sequencing (WES) study leveraging large cohorts well-phenotyped for chronic kidney disease and diabetes. Our two-stage WES study included 4372 European and African ancestry participants from the Chronic Renal Insufficiency Cohort and Atherosclerosis Risk in Communities studies (stage 1) and 11 487 multi-ancestry Trans-Omics for Precision Medicine participants (stage 2). Generalized linear mixed models, which accounted for genetic relatedness and adjusted for age, sex and ancestry, were used to test associations between single variants and DKD. Gene-based aggregate rare variant analyses were conducted using an optimized sequence kernel association test implemented within our mixed model framework. We identified four novel exome-wide significant DKD-related loci through initiating diabetes. In single-variant analyses, participants carrying a rare, in-frame insertion in the DIS3L2 gene (rs141560952) exhibited a 193-fold increased odds [95% confidence interval (CI): 33.6, 1105] of DKD compared with noncarriers (P = 3.59 × 10−9). Likewise, each copy of a low-frequency KRT6B splice-site variant (rs425827) conferred a 5.31-fold higher odds (95% CI: 3.06, 9.21) of DKD (P = 2.72 × 10−9). Aggregate gene-based analyses further identified ERAP2 (P = 4.03 × 10−8) and NPEPPS (P = 1.51 × 10−7), which are both expressed in the kidney and implicated in renin–angiotensin–aldosterone system modulated immune response. In the largest WES study of DKD, we identified novel rare variant loci attaining exome-wide significance. These findings provide new insights into the molecular mechanisms underlying DKD.
In situ digestion of alcohol-fixed cells for quantitative proteomics
Authors: Hatano Atsushi , Takami Tomoyo , Matsumoto Masaki 
Published: November 2022

Abstract
Currently, the bottom-up approach, in which proteins are digested by enzymes such as trypsin prior to mass spectrometry, is the mainstream approach in mass spectrometer-based proteomics. In this approach, the enzymatic digestion process strongly affects the reproducibility of protein identification and quantification. Here, we quantitatively evaluated the enzymatic digestion of proteins under various conditions by quantitative proteomics using data-independent acquisition and found that proteins precipitated with acetone after solubilization with SDS were fully digestible without re-solubilization. This result implies that organic solvent treatment makes cells amenable to trypsin digestion. Direct trypsin digestion of methanol-fixed cells achieved the same digestion efficiency and quantitative reproducibility as the conventional method. Furthermore, this method was found to be equally applicable to mouse liver samples. The establishment of this method indicates that the sample preparation process in bottom-up proteomics can be simplified while maintaining high digestion efficiency and is expected to become a general method for sample preparation in bottom-up proteomics in the future.
Circ_0000253 promotes the progression of osteosarcoma via the miR-1236-3p/SP1 axis
Authors: Xu Lijun , Duan Jun , Li Mingwu , Zhou Cong , Wang Qinzhi 
Published: November 2022

Abstract

Objective
Circular RNAs (circRNAs) play important roles in modulating tumour progression. This study investigated the role of circ_0000253 in osteosarcoma (OS).

Methods
We downloaded the chip dataset GSE140256 from the Gene Expression Omnibus database and the circRNAs differentially expressed in OS tissue and normal tissue samples were analysed. Quantitative real-time PCR (qRT-PCR) was carried out to examine circ_0000253 expression in OS tissues and cells. Cell counting kit-8, BrdU and flow cytometry assays were performed to verify the effects of circ_0000253 on OS cell growth and apoptosis. Bioinformatics analysis was conducted to predict, and RNA immunoprecipitation assay and dual-luciferase reporter gene assay were performed to verify the targeted relationships of miR-1236-3p with circ_0000253 and Sp1 transcription factor (SP1) mRNA 3ʹUTR. The effects of miR-1236-3p and circ_0000253 on SP1 expression in OS cells were detected through Western blot.

Key findings
Circ_0000253 was upregulated in OS tissues and cell lines. Circ_0000253 overexpression facilitated OS cell growth and suppressed apoptosis, whereas knocking down circ_0000253 inhibited OS cell growth and facilitated apoptosis. Circ_0000253 targeted miR-1236-3p directly and negatively modulated its expression. SP1 was miR-1236-3p’s target gene and positively regulated by circ_0000253.

Conclusion
Circ_0000253 promotes OS cell proliferation and suppresses cell apoptosis via regulating the miR-1236-3p/SP1 molecular axis.
Pharos 2023: an integrated resource for the understudied human proteome
Authors: Kelleher Keith J , Sheils Timothy K , Mathias Stephen L , Yang Jeremy J , Metzger Vincent T , Siramshetty Vishal B , Nguyen Dac-Trung , Jensen Lars Juhl , Vidović Dušica , Schürer Stephan C , Holmes Jayme , Sharma Karlie R , Pillai Ajay , Bologa Cristian G , Edwards Jeremy S , Mathé Ewy A , Oprea Tudor I 
Published: November 2022

AbstractThe Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for users to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.
Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation
Authors: Ares-Arroyo Manuel , Coluzzi Charles , Rocha Eduardo P C 
Published: November 2022

Abstract
Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.
On a Turán Conjecture and random multiplicative functions
Authors: Angelo Rodrigo , Xu Max Wenqiang 
Published: November 2022

Abstract
We show that if f is the random completely multiplicative function, the probability that $\sum_{n\le x}\frac{f(n)}{n}$ is positive for every x is at least $1-10^{-45}$, while also strictly smaller than 1. For large x, we prove an asymptotic upper bound of $O(\exp(-\exp( \frac{\log x}{C\log \log x })))$ on the exceptional probability that a particular truncation is negative, where C is some positive constant.
Natural annual transcriptome dynamics ofEucalyptusreveal seasonal adaptation of tropical/sub-tropical trees
Authors: Dai Xiaokang , Lin Ying , Zhou Tingting , Li Yue , Liao Xiaoli , Cao Jianbo , Ding Jihua 
Published: November 2022

AbstractSeasonal environment cues are primary factors that influence a plant’s growth and adaptation. The molecular basis of seasonal phenology has been well studied in trees growing in boreal and temperate ecosystems. However, little is known about the molecular phenology of trees belonging to tropical/sub-tropical regions. Here, we characterize the annual transcriptome dynamics of Eucalyptus dunnii, one of the world’s most widely planted tropical/sub-tropical hardwoods, in natural environments. Our transcriptome analysis combined with the geographical distribution, environmental cues, microscopic observations and heterologous transformation analyses provides a molecular timetable of seasonal regulatory events of E. dunnii and its planting prospects in China. We further investigated the molecular mechanisms of the flowering phenology of E. dunnii. Our results suggest that low temperature is one of environment triggers for its seasonal flowering. In addition, a comparative transcriptome and cell ultrastructure analysis between Eucalyptus and Populus reveals the molecular bases of different shoot apex growth habits of trees originating from tropical/sub-tropical and boreal/temperate regions. Our study will provide cues for further investigating the molecular mechanisms underlying the seasonal phenology of trees from tropical/sub-tropical regions.
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales
Authors: Li Nien-Kung , Corander Jukka , Grad Yonatan H , Chang Hsiao-Han 
Published: November 2022

AbstractIncomplete selection makes it challenging to infer selection on genes at short time scales, especially for microorganisms, due to stronger linkage between loci. However, in many cases, the selective force changes with environment, time, or other factors, and it is of great interest to understand selective forces at this level to answer relevant biological questions. We developed a new method that uses the change in dN/dS, instead of the absolute value of dN/dS, to infer the dominating selective force based on sequence data across geographical scales. If a gene was under positive selection, dN/dS was expected to increase through time, whereas if a gene was under negative selection, dN/dS was expected to decrease through time. Assuming that the migration rate decreased and the divergence time between samples increased from between-continent, within-continent different-country, to within-country level, dN/dS of a gene dominated by positive selection was expected to increase with increasing geographical scales, and the opposite trend was expected in the case of negative selection. Motivated by the McDonald–Kreitman (MK) test, we developed a pairwise MK test to assess the statistical significance of detected trends in dN/dS. Application of the method to a global sample of dengue virus genomes identified multiple significant signatures of selection in both the structural and non-structural proteins. Because this method does not require allele frequency estimates and uses synonymous mutations for comparison, it is less prone to sampling error, providing a way to infer selection forces within species using publicly available genomic data from locations over broad geographical scales.
Treatment of adrenocortical carcinoma: oncological and endocrine outcomes
Authors: Brönimann Stephan , Garstka Nathalie , Remzi Mesut 
Published: November 2022

Purpose of review
Adrenocortical carcinoma (ACC) is a rare, aggressive disease with a paucity of data and great variability between published studies regarding its treatment. This review provides information on current clinical management and oncological and endocrine outcomes.

Recent findings
Complete surgical resection is the only potentially curative treatment for adrenocortical carcinoma (ACC). Adjuvant mitotane treatment is recommended in patients with favourable/intermediate prognosis. As part of the endocrine follow-up, steroid hormones and thyroid hormones may be decreased or increased and may need to be substituted or suppressed. Recurrences are common. If the disease-free interval is more than 12 months, surgery is a treatment if complete resection is feasible. In advanced/metastatic ACC patients, the prognosis is poor. Mitotane monotherapy is only appropriate for patients with low tumour burden and indolent disease. Patients with unfavourable prognosis should be treated with aggressive cytotoxic therapy. Patients requiring third-line treatment should be considered for clinical trials. Immunotherapy and targeted therapy are currently being investigated, but have so far yielded only unsatisfactory results.

Summary
There is scarce evidence for the treatment of ACC, which often complicates clinical decision-making. Patients who progress on EDP-M should be treated in clinical trials.
Rhinoplasty in the COVID-19 Era: Practice and Safety Considerations
Authors: Rohrich Rod J. , Abraham Jasson T. , Alleyne Brendan , Bellamy Justin 
Published: November 2022

Summary:
The COVID-19 pandemic has required changes in health care practices to decrease the risk of disease transmission during the provision of medical care. The risk of transmission is high in procedures involving the nasopharyngeal and oropharyngeal tissues. This article describes simple preventative strategies at a single institution to minimize the risk of disease transmission during rhinoplasty procedures. In particular, the utility of povidone-iodine in prophylaxis during the perioperative period is discussed.
The Associations Between Intracranial Stenosis, Brain Amyloid-beta, and Cognition in a Memory Clinic Sample
Authors: Lim Mervyn J.R. , Tan Jaclyn , Gyanwali Bibek , Tanaka Tomotaka , Reilhac Anthonin , Vrooman Henri A. , Chen Christopher , Hilal Saima 
Published: November 2022

Background:
Intracranial stenosis (ICS) and brain amyloid-beta (Aβ) have been associated with cognition and dementia. We aimed to investigate the association between ICS and brain Aβ and their independent and joint associations with cognition.

Methods:
We conducted a cross-sectional study of 185 patients recruited from a memory clinic. ICS was measured on 3-dimensional time-of-flight magnetic resonance angiography and defined as stenosis ≥50%. Brain Aβ was measured with [11C] Pittsburgh compound B–positron emission tomography imaging. Cognition was assessed with a locally validated neuropsychological battery.

Results:
A total of 17 (9.2%) patients had ICS, and the mean standardized uptake value ratio was 1.4 (±0.4 SD). ICS was not significantly associated with brain Aβ deposition. ICS was significantly associated with worse global cognition (β: −1.26, 95% CI: −2.25; −0.28, P=0.013), executive function (β: −1.04, 95% CI: −1.86; −0.22, P=0.015) and visuospatial function (β: −1.29, 95% CI: −2.30; −0.27, P=0.015). Moreover, in ICS patients without dementia (n=8), the presence of Aβ was associated with worse performance on visuomotor speed.

Conclusions:
ICS was significantly associated with worse cognition and showed interaction with brain Aβ such that patients with both pathologies performed worse on visuomotor speed specifically in those without dementia. Further studies may clarify if ICS and brain Aβ deposition indeed have a synergistic association with cognition.