bluuebunny/crossref_metadata_2025_split huggingface dataset:
The autotetraploid potato genome provides insights into highly heterozygous species
Authors: Wang Fang , Xia Zhiqiang , Zou Meiling , Zhao Long , Jiang Sirong , Zhou Yun , Zhang Chenji , Ma Yongzhen , Bao Yuting , Sun Haihong , Wang Wenquan , Wang Jian 
Published: June 2022

SummaryPotato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day‐dependent tuber development. Herein, we present a high‐quality, chromosome‐scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein‐coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome‐wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.
Pain avoidance and functional connectivity between insula and amygdala identifies suicidal attempters in patients with major depressive disorder using machine learning
Authors: Hao Ziyu , Li Huanhuan , Ouyang Lisheng , Sun Fang , Wen Xiaotong , Wang Xiang 
Published: June 2022

AbstractPain avoidance can effectively classify suicide attempters from non‐attempters among patients with major depressive disorder (MDD). However, the neural circuits underlying pain processing in suicide attempters have not been described comprehensively. In Study 1, we recruited MDD patients with a history of suicide attempts (MDD‐SA), and those without (MDD‐NSA) to examine the patterns of psychological pain using the latent profile analysis. Further, in Study 2, participants including the MDD‐SA, MDD‐NSA, and healthy controls underwent resting‐state functional magnetic resonance imaging. We used machine learning that included features of gray matter volume (GMV), the functional connectivity (FC) brain patterns of the region of interest, and behavioral data to identify suicide attempters. The results identified three latent classes of psychological pain in MDD patients: the low pain class (18.9%), the painful feeling class (37.2%), and the pain avoidance class (43.9%). Furthermore, the proportion of suicide attempters with high pain avoidance was the highest. The accuracy of multimodality classifiers (63%–92%) was significantly higher than that of brain‐only classifiers (56%–85%) and behavior‐only classifiers (64%–73%). Pain avoidance ranked first in the optimal feature set of the suicide attempt classification model. The crucial brain imaging features were FC between the left amygdala and right insula, right orbitofrontal and left thalamus, left anterior cingulate cortex and left insula, right orbitofrontal, amygdala, and the GMV of right thalamus. Additionally, the optimal feature set, including pain avoidance and crucial brain patterns of psychological pain neural circuits, was provided for the identification of suicide attempters.
The methyl‐CpG‐binding domain family member PEM1 is essential for Ubisch body formation and pollen exine development in rice
Authors: Song Yunyun , Tang Yongyan , Liu Lingtong , Xu Yunyuan , Wang Tai 
Published: June 2022

SUMMARYPollen exine is composed of finely‐organized nexine, bacula and tectum, and is crucial for pollen viability and function. Pollen exine development involves a complicated molecular network that coordinates the interaction between pollen and tapetal cells, as well as the biosynthesis, transport and assembly of sporopollenin precursors; however, our understanding of this network is very limited. Here, we report the roles of PEM1, a member of methyl‐CpG‐binding domain family, in rice pollen development. PEM1 expressed constitutively and, in anthers, its expression was detectable in tapetal cells and pollen. This predicted PEM1 protein of 240 kDa had multiple epigenetic‐related domains. pem1 mutants exhibited abnormal Ubisch bodies, delayed exine occurrence and, finally, defective exine, including invisible bacula, amorphous and thickened nexine and tectum layer structures, and also had the phenotype of increased anther cuticle. The mutation in PEM1 did not affect the timely degradation of tapetum. Lipidomics revealed much higher wax and cutin contents in mutant anthers than in wild‐type. Accordingly, this mutation up‐regulated the expression of a set of genes implicated in transcriptional repression, signaling and diverse metabolic pathways. These results indicate that PEM1 mediates Ubisch body formation and pollen exine development mainly by negatively modulating the expression of genes. Thus, the PEM1‐mediated molecular network represents a route for insights into mechanisms underlying pollen development. PEM1 may be a master regulator of pollen exine development.
Comparison of median sternotomy closure‐related complication rates using orthopedic wire or suture in dogs: A multi‐institutional observational treatment effect analysis
Authors: Pilot Mariette A. , Lutchman Aaron , Hennet Julie , Anderson Davina , Robinson William , Rossanese Matteo , Chrysopoulos Angelos , Demetriou Jackie , De la Puerta Benito , Mullins Ronan A. , Brissot Hervé , Jeffery Nicholas , Chanoit Guillaume 
Published: June 2022

AbstractObjectiveTo determine and compare median sternotomy (MS) closure‐related complication rates using orthopedic wire or suture in dogs.Study designMulti‐institutional, retrospective observational study with treatment effect analysis.Animals331 client‐owned dogs, of which 68 were excluded.MethodsMedical records of dogs with MS were examined across nine referral centers (2004–2020). Signalment, weight, clinical presentation, surgical details, complications, and outcomes were recorded. Follow‐up was performed using patient records and email/telephone contact. Descriptive statistics, treatment effect analysis and logistic regression were performed.ResultsMedian sternotomy closure was performed with wire in 115 dogs and suture in 148. Thirty‐seven dogs experienced closure‐related complications (14.1%), 20 in the wire group and 17 in the suture group. Twenty‐three were listed as mild, four as moderate and 10 as severe. Treatment effect analysis showed a mean of 2.3% reduction in closure‐related complications associated with using suture versus wire (95% CI: −9.1% to +4.5%). In multivariable logistic regression, the only factor associated with increased risk of closure‐related complications was dog size (p = .01). This effect was not modified by the type of closure used (interaction term: OR = 0.99 [95% CI: 0.96/1.01]).ConclusionThe incidence of closure‐related complication after MS was low compared to previous reports. The likelihood of developing a closure‐related complication was equivalent between sutures and wires, independent of dog size, despite a higher proportion of complications seen in larger dogs (≥20 kg).Clinical significanceUse of either orthopedic wire or suture appear to be an appropriate closure method for sternotomy in dogs of any size.
Neogastropod (Mollusca, Gastropoda) phylogeny: A step forward with mitogenomes
Authors: Lemarcis Thomas , Fedosov Alexander E. , Kantor Yuri I. , Abdelkrim Jawad , Zaharias Paul , Puillandre Nicolas 
Published: June 2022

AbstractThe Neogastropoda (Mollusca, Gastropoda) encompass more than 15,000 described species of marine predators, including several model organisms in toxinology, embryology and physiology. However, their phylogenetic relationships remain mostly unresolved and their classification unstable. We took advantage of the many mitogenomes published in GenBank to produce a new molecular phylogeny of the neogastropods. We completed the taxon sampling by using an in‐house bioinformatic pipeline to retrieve mitochondrial genes from 13 transcriptomes, corresponding to five families not represented in GenBank, for a final dataset of 113 taxa. Because mitogenomic data are prone to reconstruction artefacts, eight different evolutionary models were applied to reconstruct phylogenetic trees with IQTREE, RAxML and MrBayes. If the over‐parametrization of some models produced trees with aberrant internal long branches, the global topology of the trees remained stable over models and softwares, and several relationships were revealed or found supported here for the first time. However, even if our dataset encompasses 60% of the valid families of neogastropods, some key taxa are missing and should be added in the future before proposing a revision of the classification of the neogastropods. Our study also demonstrates that even complex models struggle to satisfactorily handle the evolutionary history of mitogenomes, still leading to long‐branch attractions in phylogenetic trees. Other approaches, such as reduced‐genome strategies, must be envisaged to fully resolve the neogastropod phylogeny.
Parametric Study and Correlation of Racetrack Shaped Jets for Leading Edge Impingement
Authors: Kulkarni Ritwik V. , Wright Lesley M. 
Published: June 2022

Abstract
This paper provides a detailed experimental investigation of heat transfer and pressure loss for leading edge jet impingement using square-edged, racetrack jets. Experiments were carried out over various parameters: jet-to-jet spacings (s/d) of 2, 4, 8; jet-to-target surface spacings (z/d) of 2 and 4; jet plate thicknesses (l/d) of 1.33, 2.6, and 4; and Reynolds numbers from 10,000 to 100,000. The results show that pressure loss and heat transfer decrease with increasing s/d and z/d. There is an interesting observation for jet plate thickness at l/d = 2.6—a local minima for both heat transfer and pressure loss is measured with the racetrack shaped jets. Using the exhaustive experimental data, design correlations are developed to estimate the surface Nusselt number and discharge coefficients within the domain of geometric and flow parameters. The novel correlations account for the parametric effects and can accurately predict the Nusselt number and discharge coefficient with deviations of 19.8% and 15.9%, respectively. These provide a capability for the engine designers to predict the heat transfer and pressure loss for leading edge jet impingement.
Halogen ratios in crustal fluids through time—Proxies for the emergence of aerobic life?
Authors: Fusswinkel Tobias , Niinikoski-Fusswinkel Paula , Wagner Thomas 
Published: June 2022

Abstract
Halogens (Cl, Br, I) are exceptional provenance tracers in crustal fluids because their ratios are not strongly altered during most fluid-rock interaction processes. The halogen systematics of metamorphic fluids are of particular interest because such fluids are key drivers of crustal-scale element fluxes and ore formation in orogenic belts, but they remain poorly studied due to analytical challenges. We present novel triple-halogen laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) fluid-inclusion data from metamorphic systems ranging in age from Archean to Phanerozoic. Our results show that the halogen signatures in Phanerozoic metamorphic fluids are controlled by variable degrees of organic-matter interaction in their source rocks, leading to increased I/Cl and decreased Br/I ratios relative to seawater. By contrast, Archean metamorphic fluids from organic matter–rich source rocks have low I/Cl and very high Br/I ratios, distinctly different from any known fluid source signature. We propose that these signatures nevertheless are consistent with organic-matter interaction because dominantly prokaryotic Archean lifeforms did not yet produce iodine-bearing metabolites. This prevented biosequestration and accumulation of iodine-rich organic matter in sediments and imposed halogen signatures onto Archean metamorphic fluids entirely unlike those in younger fluids.
Afghan Agenda in Current Canadian Politics
Authors: Issraelyan E. V. 
Published: June 2022

Abstract
Canada’s operation in Afghanistan has been unfolding during a critically important domestic political event, i.e., the federal elections of 2021. The election campaign had pooled the main attention and resources of the Canadian leadership, limiting its ability to act in Afghanistan. Despite the difficulties, the Liberal Government of Justin Trudeau has achieved a lot. Firstly, they have organized the evacuation of Canadians and of Afghans who worked with the Canadian Armed Forces during the US and NATO military mission. Secondly, Ottawa has defined its attitude towards the Taliban regime by refusing diplomatic recognition. Thirdly, the admission of Afghan refugees to Canada has begun. In each of these areas, the Liberal Government has successes and failures, which have caused acute controversy in the country.
Peasant Studies As a New Direction in Modern Studies of Russian Agrarian History
Authors: Babashkin V. 
Published: June 2022

Abstract
This article describes the circumstances under which a permanent interdisciplinary international seminar “Modern Concepts of Agrarian Development” arose in 1992. The roles of the Russian historian V.P. Danilov at the Institute of Russian History, Russian Academy of Sciences (IRH RAS) and the English historian-sociologist T. Shanin (Manchester University, Britain), as well as the role of the problems discussed at the meetings at the seminar and the publication of the seminar’s materials by the journal Otechestvennayaistoriya (Russian History) in the development of a new direction in Russian agrarian historical research, in the creation of this forum are shown. Suggestions are made about why the methodological approaches that gained popularity in the 1960s in Western Peasant Studies are difficult to apply to Russian-language historical publications on agrarian issues. An idea is given of some works of modern domestic historians that can rightfully be attributed to the direction of research called peasant studies.
Market Transformations in the 1990s in the Russian Village
Authors: Verbitskaya Olga 
Published: June 2022

Abstract
This article examines the agrarian reform of the 1990s in Russia. It is noted that its first version was developed by domestic agricultural scientists and was designed for the phased implementation of transformations for a period of at least 10 years. However, later, under pressure from Western experts, this project underwent significant adjustments, in accordance with which the market reform in the agrarian sector was carried out more radically and at a faster pace. It is shown that the main methods of market transformations in the countryside were price liberalization, denationalization and privatization of land, distribution of land shares to farmers, creation of a farmer’s way of life, disaggregation of former collective agricultural enterprises, their transfer to market forms of work, etc. The author believes that basically these transformations in the countryside were carried out formally and did not achieve their true goal. The reformers' hopes for the economic success of farms also turned out to be untenable, since their real number was extremely small, and their actual role in agricultural production was scanty. More than half of all products of the agricultural sector were produced by subsidiary farms, which were significantly replenished by the peasants who lost their jobs. At the end of the article, it was concluded that the agrarian reform, conceived with the aim of significantly increasing the efficiency of agriculture, did not justify the hopes: the tasks set were not fulfilled, and it only actually ruined agriculture. Over the 10 years of market transformations, the area under crops has significantly decreased, the number of livestock has decreased, production has fallen by more than 50%, and the level of labor mechanization has decreased by about 33%. As a result of the market transformations in the 1990s, the agricultural industry of Russia in terms of its main indicators was thrown back 30–40 years.
Participation of the Organs of the OGPU-NKVD of the Soviet Union in the Collectivization of Agriculture
Authors: Mozokhin O. B. 
Published: June 2022

Abstract
This article analyzes the role of the OGPU-NKVD in carrying out the policy of the All-Union Communist Party of Bolsheviks on the collectivization of agriculture, and it reports on the protest movements of the peasantry, on individual and collective protests against collectivization, and the suppression of these movements by punitive bodies. The measures of the authorities for the “liquidation of the kulaks as a class” and the organs of the OGPU-NKVD as a mechanism for carrying out repressions are specially studied.
Incidence and outcomes of pulmonary hypertension in the Ireland
Authors: Cullivan Sarah , Lennon Denise , Meghani Salima , Minnock Caitriona , McCullagh Brian , Gaine Sean 
Published: June 2022

IntroductionPulmonary hypertension (PH) is a progressive disease of the pulmonary vasculature, which is characterised by premature morbidity and mortality. The aim of this study is to define the characteristics of PH in the national PH unit (NPHU) in Ireland between 2010 and 2020.MethodsCases of PH which were referred to the NPHU between 2010 and 2020 were included. PH was defined as a mean pulmonary artery pressure ≥25 mm Hg at right heart catheterisation.ResultsFour hundred and fifteen cases of PH were identified during the study period. Group 1 pulmonary arterial hypertension (PAH) accounted for 39% (n=163) of cases, with a calculated annual incidence of 3.11 per million population (95% CI 1.53 to 4.70). The leading PAH subgroup was connective tissue disease-associated PAH (CTD-PAH), which was responsible for 49% of PAH referrals. This was followed by idiopathic PAH, with an estimated annual incidence of 0.63 cases per million population. The mean age at PAH diagnosis was 56±15 years and 86% (n=111) received double-combination or triple-combination therapy within the first 12 months of diagnosis. The 1-year, 3-year and 5-year transplant-free survival for PAH was 89%, 75% and 65%. This was significantly lower for individuals with CTD-PAH relative to other PAH subgroups (p<0.05).DiscussionThis study describes the incidence and outcomes of PH in Ireland. While the outcomes are comparable to other centres, the incidence of PAH and specific subgroups appears low, suggesting that improved disease awareness and case recognition are required. Furthermore, the survival of individuals with CTD-PAH is poor and requires additional exploration.
NY-ESO-1-specific redirected T cells with endogenous TCR knockdown mediate tumor response and cytokine release syndrome
Authors: Ishihara Mikiya , Kitano Shigehisa , Kageyama Shinichi , Miyahara Yoshihiro , Yamamoto Noboru , Kato Hidefumi , Mishima Hideyuki , Hattori Hiroyoshi , Funakoshi Takeru , Kojima Takashi , Sasada Tetsuro , Sato Eiichi , Okamoto Sachiko , Tomura Daisuke , Nukaya Ikuei , Chono Hideto , Mineno Junichi , Kairi Muhammad Faris , Diem Hoang Nguyen Phuong , Simoni Yannick , Nardin Alessandra , Newell Evan , Fehlings Michael , Ikeda Hiroaki , Watanabe Takashi , Shiku Hiroshi 
Published: June 2022

BackgroundBecause of the shortage of ideal cell surface antigens, the development of T-cell receptor (TCR)-engineered T cells (TCR-T) that target intracellular antigens such as NY-ESO-1 is a promising approach for treating patients with solid tumors. However, endogenous TCRs in vector-transduced T cells have been suggested to impair cell-surface expression of transduced TCR while generating mispaired TCRs that can become self-reactive.MethodsWe conducted a first-in-human phase I clinical trial with the TCR-transduced T-cell product (TBI-1301) in patients with NY-ESO-1-expressing solid tumors. In manufacturing TCR-T cells, we used a novel affinity-enhanced NY-ESO-1-specific TCR that was transduced by a retroviral vector that enables siRNA (small interfering RNA)-mediated silencing of endogenous TCR. The patients were divided into two cohorts. Cohort 1 was given a dose of 5×108cells (whole cells including TCR-T cells) preconditioned with 1500 mg/m2cyclophosphamide. Cohort 2 was given 5× 109cells preconditioned with 1500 mg/m2cyclophosphamide.ResultsIn vitro study showed that both the CD8+and CD4+T fractions of TCR-T cells exhibited cytotoxic effects against NY-ESO-1-expressing tumor cells. Three patients and six patients were allocated to cohort 1 and cohort 2, respectively. Three of the six patients who received 5×109cells showed tumor response, while three patients developed early-onset cytokine release syndrome (CRS). One of the patients developed a grade 3 lung injury associated with the infiltration of the TCR-T cells. No siRNA-related adverse events other than CRS were observed. Cytokines including interleukin 6 I and monocyte chemotactic protein-1/chemokine (C-C motif) ligand (CCL2)increased in the sera of patients with CRS. In vitro analysis showed these cytokines were not secreted from the T cells infused. A significant fraction of the manufactured T cells in patients with CRS was found to express either CD244, CD39, or both at high levels.ConclusionsThe trial showed that endogenous TCR-silenced and affinity-enhanced NY-ESO-1 TCR-T cells were safely administered except for grade 3 lung injury. The TCR-T cell infusion exhibited significant tumor response and early-onset CRS in patients with tumors that express NY-ESO-1 at high levels. The differentiation properties of the manufactured T cells may be prognostic for TCR-T-related CRS.Trial registration numberNCT02366546.