bluuebunny/crossref_metadata_2025_split huggingface dataset:
Keeping score: an empirical analysis of the interventions in Ukraine v Russia
Authors: Wigard Kyra , Pomson Ori , McIntyre Juliette 
Published: June 2023

Abstract
The Allegations of Genocide under the Convention on the Prevention and Punishment of the Crime of Genocide (Ukraine v Russia) case involves an unprecedented number of Article 63 declarations of intervention. We consider the specific arguments made in individual declarations, but also the mass nature of the declarations. In order to do this in a systematic manner, we employ empirical methods to identify those declarations and arguments that are more central and those that are more unique. Using citation network analysis, we identify the main and central arguments presented by states in their declarations. Moreover, we find evidence that states have co-operated in the preparation of their intervention declarations, using Article 63 as an opportunity to collectively condemn Russia as well as offer their joint interpretation of the Genocide Convention. But while all states come to support Ukraine, the interventions are not necessarily helpful to Ukraine’s case.
Resolving intergenotypic Striga resistance in sorghum
Authors: Mutinda Sylvia , Mobegi Fredrick M , Hale Brett , Dayou Olivier , Ateka Elijah , Wijeratne Asela , Wicke Susann , Bellis Emily S , Runo Steven 
Published: June 2023

Abstract
Genetic underpinnings of host–pathogen interactions in the parasitic plant Striga hermonthica, a root parasitic plant that ravages cereals in sub-Saharan Africa, are unclear. We performed a comparative transcriptome study on five genotypes of sorghum exhibiting diverse resistance responses to S. hermonthica using weighted gene co-expression network analysis (WGCNA). We found that S. hermonthica elicits both basal and effector-triggered immunity—like a bona fide pathogen. The resistance response was genotype specific. Some resistance responses followed the salicylic acid-dependent signaling pathway for systemic acquired resistance characterized by cell wall reinforcements, lignification, and callose deposition, while in others the WRKY-dependent signaling pathway was activated, leading to a hypersensitive response. In some genotypes, both modes of resistance were activated, while in others either mode dominated the resistance response. Cell wall-based resistance was common to all sorghum genotypes but strongest in IS2814, while a hypersensitive response was specific to N13, IS9830, and IS41724. WGCNA further allowed for pinpointing of S. hermonthica resistance causative genes in sorghum, including glucan synthase-like 10 gene, a pathogenesis-related thaumatin-like family gene, and a phosphoinositide phosphatase gene. Such candidate genes will form a good basis for subsequent functional validation and possibly future resistance breeding.
Rhetorical militarism, humanitarian law, and public space: a study on military interventions in Brazil
Authors: Nagamine Renata , Roriz João 
Published: June 2023

Abstract
In Rio de Janeiro, the laws of war have contributed to the transformation of symbolically and materially violent means and practices into an experience of everyday life. Political actors contribute to rationalizing violence in certain areas of Brazil, disregarding expectations related to citizenship and human rights.
Over-expression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo
Authors: Mendez Ruiz Shannon , Chalk Alistair M , Goradia Ankita , Heraud-Farlow Jacki , Walkley Carl R 
Published: June 2023

Abstract
Adenosine to inosine editing (A-to-I) in regions of double stranded RNA (dsRNA) is mediated by adenosine deaminase acting on RNA 1 (ADAR1) or ADAR2. ADAR1 and A-to-I editing levels are increased in many human cancers. Inhibition of ADAR1 has emerged as a high priority oncology target, however, whether ADAR1 overexpression enables cancer initiation or progression has not been directly tested. We established a series of in vivo models to allow overexpression of full-length ADAR1, or its individual isoforms, to test if increased ADAR1 expression was oncogenic. Widespread over-expression of ADAR1 or the p110 or p150 isoforms individually as sole lesions was well tolerated and did not result in cancer initiation. Therefore, ADAR1 overexpression alone is not sufficient to initiate cancer. We demonstrate that endogenous ADAR1 and A-to-I editing increased upon immortalization in murine cells, consistent with the observations from human cancers. We tested if ADAR1 over-expression could co-operate with cancer initiated by loss of tumour suppressors using a model of osteosarcoma. We did not see a disease potentiating or modifying effect of overexpressing ADAR1 or its isoforms in the models assessed. We conclude that increased ADAR1 expression and A-to-I editing in cancers is most likely a consequence of tumor formation.
CrypticProteinDB: an integrated database of proteome and immunopeptidome derived non-canonical cancer proteins
Authors: Othoum Ghofran , Maher Christopher A 
Published: June 2023

Abstract
Translated non-canonical proteins derived from noncoding regions or alternative open reading frames (ORFs) can contribute to critical and diverse cellular processes. In the context of cancer, they also represent an under-appreciated source of targets for cancer immunotherapy through their tumor-enriched expression or by harboring somatic mutations that produce neoantigens. Here, we introduce the largest integration and proteogenomic analysis of novel peptides to assess the prevalence of non-canonical ORFs (ncORFs) in more than 900 patient proteomes and 26 immunopeptidome datasets across 14 cancer types. The integrative proteogenomic analysis of whole-cell proteomes and immunopeptidomes revealed peptide support for a nonredundant set of 9760 upstream, downstream, and out-of-frame ncORFs in protein coding genes and 12811 in noncoding RNAs. Notably, 6486 ncORFs were derived from differentially expressed genes and 340 were ubiquitously translated across eight or more cancers. The analysis also led to the discovery of thirty-four epitopes and eight neoantigens from non-canonical proteins in two cohorts as novel cancer immunotargets. Collectively, our analysis integrated both bottom-up proteogenomic and targeted peptide validation to illustrate the prevalence of translated non-canonical proteins in cancer and to provide a resource for the prioritization of novel proteins supported by proteomic, immunopeptidomic, genomic and transcriptomic data, available at https://www.maherlab.com/crypticproteindb.
Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs
Authors: Arnesen Spencer , Polaski Jacob T , Blanchard Zannel , Osborne Kyle S , Welm Alana L , O’Connell Ryan M , Gertz Jason 
Published: June 2023

Abstract
Estrogen receptor α (ER) mutations occur in up to 30% of metastatic ER-positive breast cancers. Recent data has shown that ER mutations impact the expression of thousands of genes not typically regulated by wildtype ER. While the majority of these altered genes can be explained by constant activity of mutant ER or genomic changes such as altered ER binding and chromatin accessibility, as much as 33% remain unexplained, indicating the potential for post-transcriptional effects. Here, we explored the role of microRNAs in mutant ER-driven gene regulation and identified several microRNAs that are dysregulated in ER mutant cells. These differentially regulated microRNAs target a significant portion of mutant-specific genes involved in key cellular processes. When the activity of microRNAs is altered using mimics or inhibitors, significant changes are observed in gene expression and cellular proliferation related to mutant ER. An in-depth evaluation of miR-301b led us to discover an important role for PRKD3 in the proliferation of ER mutant cells. Our findings show that microRNAs contribute to mutant ER gene regulation and cellular effects in breast cancer cells.
From Leiden to Tel-Aviv University (TAU): exploring clustering solutions via a genetic algorithm
Authors: Gilad Gal , Sharan Roded 
Published: June 2023

Abstract
Graph clustering is a fundamental problem in machine learning with numerous applications in data science. State-of-the-art approaches to the problem, Louvain and Leiden, aim at optimizing the modularity function. However, their greedy nature leads to fast convergence to sub-optimal solutions. Here, we design a new approach to graph clustering, Tel-Aviv University (TAU), that efficiently explores the solution space using a genetic algorithm. We benchmark TAU on synthetic and real data sets and show its superiority over previous methods both in terms of the modularity of the computed solution and its similarity to a ground-truth partition when such exists. TAU is available at https://github.com/GalGilad/TAU.
Systematic study of the relationship between nuclear structure and reactions for the 10Be nucleus
Authors: Furumoto T , Suhara T , Itagaki N 
Published: June 2023

Abstract
We systematically investigate the relationship between the nuclear structure and reaction in the 10Be nucleus using a theoretical framework. The structure of the 10Be nucleus is constructed with a cluster model based on a microscopic viewpoint. In this paper, the 10Be nucleus is prepared with different structures by manipulating the parameters of an effective nucleon–nucleon interaction. The nuclear structure and expectation values of physical quantities are drastically changed by the modification. We summarize such changes and show the effects on the elastic and inelastic scatterings for proton and 12C targets in the microscopic coupled-channel calculation. Of especial interest, we recently reported the visualization of the dineutron correlation in 10Be on proton inelastic scattering in [Phys. Rev. C 104, 034613 (2021)]. In this preceding work, we found that changing the degree of dineutron correlation in 10Be leads to drastic changes of the inelastic cross section for the 2$_2^+$ state. The development (or breaking) of the dineutron correlation is governed by the strength of the spin–orbit interaction of the structure calculation. However, in the previous work, some of the realistic physical points were missing, for example, the binding energy (BE). Therefore, we reconstruct the 10Be nucleus by adjusting the effective nucleon–nucleon interaction to obtain a reasonable BE of the ground state. With this improvement, we again discuss the dineutron correlation in the 10Be nucleus. We reconfirm the way to measure the degree of development (or breaking) of the dineutron cluster structure: its sensitivity to the inelastic cross section of the 2$_2^+$ state of 10Be. Subject Index cluster model, folding model, dineutron correlation, effective nucleon-nucleon interaction.
Milton, Boccaccio, and Demogorgon
Authors: Pigman G W 
Published: June 2023

Abstract
For years scholars have realized that Demogorgon owes his existence to a misreading of demiurgus in a commentary on Statius’ Thebaid and that Boccaccio’s Genealogy of the Pagan Gods was the most important text for establishing Demogorgon as the ancestor of the gods for the Renaissance. But the extent of scepticism about Demogorgon in Milton’s day is not widely known. In an early example of the polemical imitation that characterizes much of his mature poetry, Milton indicates his own scepticism in Prolusion I by extensively correcting Boccaccio’s account of Demogorgon and his progeny. Unlike his frighteningly powerful namesake in Boiardo, Ariosto, and Spenser, the Demogorgon of Paradise Lost is simply one member of the court of Chaos. The multivalent periphrasis—‘the dreaded name $|$ Of Demogorgon’—suggests that Boccaccio’s ancestor of the gods is nothing more than a name.
Analysis of occupational radiation dose data and determination of suitable probability distribution
Authors: Patil Sandeep , Bakshi Ashok 
Published: June 2023

Abstract
The first study on fitting dose data for workers was performed by Gale( 1) in 1965 where log-normal and normal distributions were used. Since then, various models of dose distribution have been proposed. The log-normal distribution and its different forms have been widely used for fitting the dose data. Most of the studies included one or two distributions under consideration. In this study five distributions are considered for fitting and four distributions are selected based on observation of Cullen–Frey graph. The Akaike’s Information criteria (AIC) and Bayesian Information criteria (BIC) are applied to find the suitable distribution to fit the occupational dose data. The maximum likelihood method was used for calculation of AIC, BIC values and parameter estimation. A computer code is written in R-language and environment for statistical computing and graphics for analysis of occupational dose data of three institutions.
Analysis of distributions reveals real differences on dichotic listening scores between left- and right-handers
Authors: Karlsson Emma M , Hugdahl Kenneth , Hirnstein Marco , Carey David P 
Published: June 2023

Abstract
About 95% of right-handers and 70% of left-handers have a left-hemispheric specialization for language. Dichotic listening is often used as an indirect measure of this language asymmetry. However, while it reliably produces a right-ear advantage (REA), corresponding to the left-hemispheric specialization of language, it paradoxically often fails to obtain statistical evidence of mean differences between left- and right-handers. We hypothesized that non-normality of the underlying distributions might be in part responsible for the similarities in means. Here, we compare the mean ear advantage scores, and also contrast the distributions at multiple quantiles, in two large independent samples (Ns = 1,358 and 1,042) of right-handers and left-handers. Right-handers had an increased mean REA, and a larger proportion had an REA than in the left-handers. We also found that more left-handers are represented in the left-eared end of the distribution. These data suggest that subtle shifts in the distributions of DL scores for right- and left-handers may be at least partially responsible for the unreliability of significantly reduced mean REA in left-handers.
Dissecting the effects of paraquat-induced pulmonary injury in rats using UPLC-Q-TOF-MS/MS-based metabonomics
Authors: Liu Xiehong , Li Chi , Hou Changmiao , Jiang Yu , Chen Fang , Zhu Yimin , Zou Lianhong 
Published: June 2023

Abstract

Objective
Paraquat (PQ) is a toxic compound that selectively accumulates in the lungs, inducing severe pulmonary inflammation and fibrosis. However, data on the metabolomic changes induced by the PQ remain scant. This study aimed to determine the metabolic changes in Sprague–Dawley rats subjected to PQ using UPLC-Q-TOF-MS/MS.

Methods
We established groups of PQ-induced pulmonary injury rats for 14 or 28 days.

Results
Our data showed that PQ decreased the survival of the rats and induced pulmonary inflammation at day 14 or pulmonary fibrosis at day 28. There was upregulation of IL-1β expression in the inflammation group as well as upregulation of fibronectin, collagen and α-SMA in the pulmonary fibrosis group. OPLS-DA revealed differential expression of 26 metabotites between the normal and the inflammation groups; 31 plasma metabotites were also differently expressed between the normal and the fibrosis groups. There was high expression of lysoPc160-, hydroxybutyrylcarnitine, stearic acid, and imidazolelactic acid in the pulmonary injury group compared to the normal group.

Conclusion
Metabolomics analysis confirmed that the PQ-induced lung injury was not only related to the aggravation of inflammation and apoptosis but also to mediated histidine, serine, glycerophospholipid, and lipid metabolism. This study gives insights into the mechanisms of PQ-induced lung injury and highlights the potential therapeutic targets.

Nonstructured abstract
The effect of PQ on lung injury in rats was detected by metabonomics, and the possible metabolic mechanism was investigated by KEGG analysis. OPLS-DA revealed the differential expression of 26 metabotites and 31 plasma metabotites between the normal and the pulmonary injury groups. Metabolomics analysis confirmed that the PQ-induced lung injury was not only related to the aggravation of inflammation and apoptosis but also to mediated histidine, serine, glycerophospholipid, and lipid metabolism. Oleoylethanolamine, stearic acid, and imidazolelactic acid are potential molecular markers in PQ-induced pulmonary injury.
Machine learning noise exposure detection of rail transit drivers using heart rate variability
Authors: Sun Zhiqiang , Liu Haiyue , Jiao Yubo , Zhang Chenyang , Xu Fang , Jiang Chaozhe , Yu Xiaozhuo , Wu Gang 
Published: June 2023

Abstract
Previous studies have found that drivers’ physiological conditions can deteriorate under noise conditions, which poses a potential hazard when driving. As a result, it is crucial to identify the status of drivers when exposed to different noises. However, such explorations are rarely discussed with short-term physiological indicators, especially for rail transit drivers. In this study, an experiment involving 42 railway transit drivers was conducted with a driving simulator to assess the impact of noise on drivers’ physiological responses. Considering the individuals’ heterogeneity, this study introduced drivers’ noise annoyance to measure their self-noise-adaption. The variances of drivers’ heart rate variability (HRV) along with different noise adaptions are explored when exposed to different noise conditions. Several machine learning approaches (support vector machine, K-nearest neighbour and random forest) were then used to classify their physiological status under different noise conditions according to the HRV and drivers’ self-noise adaptions. Results indicate that the volume of traffic noise negatively affects drivers’ performance in their routines. Drivers with different noise adaptions but exposed to a fixed noise were found with discrepant HRV, demonstrating that noise adaption is highly associated with drivers’ physiological status under noises. It is also found that noise adaption inclusion could raise the accuracy of classifications. Overall, the random forests classifier performed the best in identifying the physiological status when exposed to noise conditions for drivers with different noise adaptions.
The Complete Genome Sequence of Pseudomonas syringae pv. actinidifoliorum ICMP 18803
Authors: Templeton Matthew D. , Arshed Saadiah , Andersen Mark T. , Jayaraman Jay 
Published: June 2023

The genome of Pseudomonas syringae pv. actinidifoliorum ICMP18803 (Pfm) was sequenced using the Oxford Nanopore MinION platform to an average read depth of 123-fold. The genome assembled into a single chromosome of 6,353,853 bp after error correction with Illumina short reads using Pilon. No plasmids were detected. Despite Pfm only being a relatively weak pathogen of kiwifruit, a set of 31 effectors, 26 of which were full length, was identified by mapping the comprehensive effector library generated by previous researchers to the assembled chromosome. A revised Pfm genome with the effector complement correctly named and annotated was resubmitted to GenBank (CP081457). [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Targeted metabolomics unravels altered phenylalanine levels in piglets receiving total parenteral nutrition
Authors: Jiang Lu , Liu Yang , Zhou Yongchang , Xu Qingyang , Cheng Siyang , Yan Junkai , Xiao Yongtao , Han Lianshu , Wang Ying , Cai Wei 
Published: June 2023

AbstractParenteral nutrition, received by many patients with intestinal failure, can induce hepatobiliary complications, which is termed as parenteral nutrition‐associated liver disease (PNALD). The spectrum of PNALD ranges from cholestasis and steatosis to fibrosis and cirrhosis. Although many factors contribute to the pathogenesis of PNALD, the underlying mechanisms remain unclear. In this study, we performed targeted metabolomics to characterize the metabolomic profile in neonatal piglets receiving total parenteral nutrition (TPN) or enteral nutrition (EN) for 1 or 2 weeks. Overall, the metabolomic signature of TPN groups differed from EN groups at both time points. Among the 20 acylcarnitines identified, a majority of them were significantly reduced in TPN groups. KEGG pathway analysis showed that phenylalanine metabolism‐associated pathways were dysregulated accompanied by more progressive liver steatosis associated with TPN. Next, we evaluated phenylalanine catabolism and its association with fatty acid oxidation in piglets and rats with PNALD. We showed that the hepatic expression of phenylalanine‐degrading enzyme phenylalanine hydroxylase (PAH) was reduced and systemic phenylalanine levels were increased in both animal models of PNALD. Moreover, carnitine palmitoyltransferase 1A, a central regulator of fatty acid oxidation, was downregulated and its expression was negatively correlated with phenylalanine levels in TPN‐fed animals. To explore the effects of phenylalanine accumulation on lipid metabolism, we treated HepG2 cells with phenylalanine co‐cultured with sodium palmitate or soybean oil emulsion to induce lipid accumulation. We found that phenylalanine treatment exacerbated lipid accumulation by inhibiting fatty acid oxidation without affecting fatty acid synthesis. In summary, our findings establish a pathogenic role of increased phenylalanine levels in driving liver steatosis, linking dysregulation of phenylalanine catabolism with lipid accumulation in the context of PNALD.
The surgical management of scheurmann’s kyphosis: Efficacy and safety of a low density posterior pedicle screw construct
Authors: Khattab Mohamed Fawzy , Saad Moustafa Mohamed , El Hawary Youssry 
Published: June 2023

Background:
To see if employing a low pedicle screw density in the posterior therapy of Scheuermann kyphosis is safe, radiologically effective, and clinically effective.

Methods:
Patients with Scheuermann kyphosis underwent posterior surgical correction between 2016 and 2019. Low Screw Density, peri apical Ponte osteotomies and cantilever correction maneuver were our surgical technique for deformity correction. Two observers performed a radiological evaluation of the before and postoperative Spinopelvic parameters. Validated Arabic version of Scoliosis Research Society 22 questionnaire were used to assess the preoperative and postoperative clinical results. Cost saving analysis was performed.

Results:
This study enlisted the participation of thirty patients. The patients mean age 21.8 ±3.4 years and mean follow up 34.8±7.9 months. The mean surgical time was 165.33 ±17.9 minutes , the mean number of osteotomies was 4.2± 0.8 , and the mean blood loss was 770± 139.3cc.The mean preoperative dorsal kyphosis 87.5°±4.6 °and the mean postoperative dorsal kyphosis 43.1°± 3.7° at final follow up (P<0.001).The mean preoperative scoliosis research society 22 questionnaire 2.8±0.4 and the mean postoperative scoliosis research society 22 questionnaire 4.3±0.8 at final follow up (P<0.001).

Conclusions:
Posterior Surgical Intervention with low Screw Density construct and periapical Ponte osteotomies is safe , radiologically , clinically and cost effective way in surgical management of Scheuermann kyphosis.

Study Design:
Prospective Cohort Study.

Level of Evidence:
Level IV.