bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser
Authors: Fu Jine , Wan Lingyun , Song Lisha , He Lili , Jiang Ni , Long Hairong , Huo Juan , Ji Xiaowen , Hu Fengyun , Wei Shugen , Pan Limei 
Published: April 2022

Abstract
The hemiparasitic Taxillus chinensis (DC.) Danser is a root-parasitizing medicinal plant with photosynthetic ability, which is lost in other parasitic plants. However, the cultivation and medical application of the species are limited by the recalcitrant seeds of the species, and even though the molecular mechanisms underlying this recalcitrance have been investigated using transcriptomic and proteomic methods, genome resources for T. chinensis have yet to be reported. Accordingly, the aim of the present study was to use nanopore, short-read, and high-throughput chromosome conformation capture sequencing to construct a chromosome-level assembly of the T. chinensis genome. The final genome assembly was 521.90 Mb in length, and 496.43 Mb (95.12%) could be grouped into nine chromosomes with contig and scaffold N50 values of 3.80 and 56.90 Mb, respectively. In addition, a total of 33,894 protein-coding genes were predicted, and gene family clustering identified 11 photosystem-related gene families, thereby indicating photosynthetic ability, which is a characteristic of hemiparasitic plants. This chromosome-level genome assembly of T. chinensis provides a valuable genomic resource for elucidating the genetic basis underlying the recalcitrant characteristics of T. chinensis seeds and the evolution of photosynthesis loss in parasitic plants.
On Degenerations of Projective Varieties to Complexity-One T-Varieties
Authors: Kaveh Kiumars , Manon Christopher , Murata Takuya 
Published: April 2022

Abstract
Let $R$ be a positively graded finitely generated $\textbf {k}$-domain with Krull dimension $d+1$. We show that there is a homogeneous valuation ${\mathfrak {v}}: R \setminus \{0\} \to {\mathbb {Z}}^d$ of rank $d$ such that the associated graded $\operatorname {gr}_{\mathfrak {v}}(R)$ is finitely generated. This then implies that any polarized $d$-dimensional projective variety $X$ has a flat deformation over ${\mathbb {A}}^1$, with reduced and irreducible fibers, to a polarized projective complexity-one $T$-variety (i.e., a variety with a faithful action of a $(d-1)$-dimensional torus $T$). As an application we conclude that any $d$-dimensional complex smooth projective variety $X$ equipped with an integral Kähler form has a proper $(d-1)$-dimensional Hamiltonian torus action on an open dense subset that extends continuously to all of $X$.
Developing a novel DNA methylation risk score for survival and identification of prognostic gene mutations in endometrial cancer: a study based on TCGA data
Authors: Shen Po-Chien , Wang Ying-Fu , Chang Hao-Chih , Huang Wen-Yen , Lo Cheng-Hsiang , Su Yu-Fu , Yang Jen-Fu , Lin Chun-Shu , Dai Yang-Hong 
Published: April 2022

Abstract

Background
Few studies have focused on DNA methylation in endometrial cancer. The aim of our study is identify its role in endometrial cancer prognosis.

Methods
A publicly available dataset was retrieved from The Cancer Genome Atlas. For validation of expression alteration due to methylation, RNA sequencing data were obtained from other independent cohorts. MethSurv was used to search for candidate CpG probes, which were then filtered by least absolute shrinkage and selection operator Cox regression and multivariate Cox regression analyses to identify final set of CpG probes for overall survival. A methylation-based risk model was developed and receiver operating characteristic analysis with area under curve was used for evaluation. Patients were divided into high- and low-risk groups using an optimal cut-off point. Comprehensive bioinformatic analyses were conducted to identify hub genes, key transcription factors, and enriched cancer-related pathways. Kaplan–Meier curve was used for survival analysis.

Results
A 5-CpG signature score was established. Its predictive value for 5-year overall survival was high, with area under curve of 0.828, 0.835 and 0.816 for the training, testing and entire cohorts. cg27487839 and cg12885678 had strong correlation with their gene expression, XKR6 and PTPRN2, and lower PTPRN2 expression was associated with poorer survival in both The Cancer Genome Atlas and the validation datasets. Low-risk group was associated with significantly better survival. Low-risk group harboured more mutations in hub genes and key transcription factors, and mutations in SP1 and MECP2 represented favourable outcome.

Conclusion
We developed a methylation-based prognostic stratification system for endometrial cancer. Low-risk group was associated with better survival and harboured more mutations in the key regulatory genes.
Population Structure of German Cockroaches (Blattodea: Ectobiidae) in an Urban Environment Based on Single Nucleotide Polymorphisms
Authors: Fan X , Wang C , Bunker D E 
Published: April 2022

Abstract
German cockroaches (Blattella germanica L.) harbor and disperse medically important pathogens and are a source of allergens that impact human health and wellbeing. Management of this pest requires an understanding of their distribution and dispersal. In this study, we collected German cockroaches from three apartment buildings in New Jersey, USA. We identified single-nucleotide polymorphisms (SNPs) from DNA extractions using next generation sequencing. We analyzed the SNPs and characterized cockroach population genetic structure using Fst, principal component, phylogenetic, and STRUCTURE analyses. We found significant differences in German cockroach population structure among the buildings. Within buildings, we found variable population structure that may be evidence for multiple colonization events. This study shows that SNPs derived from next generation sequencing provide a powerful tool for analyzing the genetic population structure of these medically important pests.
Spontaneous splenic rupture from indeterminate dendritic cell proliferation: a case report
Authors: Iqbal Shaikh B , Chittal Abhinandan R , Rao Shiavax J , Lakra Pallavi , Bhansali Deepty , Pyrgos George 
Published: April 2022

Abstract
Spontaneous splenic rupture is a rare and life-threatening phenomenon, usually associated with an underlying infectious, inflammatory, hematological, neoplastic or rheumatologic condition. Indeterminate cell tumor is a rare neoplastic dendritic cell disorder that is poorly understood but shares immunophenotypic markers for Langerhans cells without Birbeck granules. A 73-year-old man presented with upper abdominal pain after an unwitnessed fall. Computed tomography angiography showed splenomegaly and a large ruptured splenic subcapsular hematoma. Intraoperative findings from an emergency laparotomy revealed a large hemoperitoneum and a ruptured spleen. Microscopic sections identified numerous, mostly poorly formed, small nodules classified as a proliferation of indeterminate dendritic cell tumors.
Putting the pea in photoPEAriod
Authors: Chapman Mark A 
Published: April 2022

This article comments on:
Williams O, Vander Schoor JK, Butler JB, Ridge S, Sussmilch FC, Hecht VFG, Weller JL. 2022. The genetic architecture of flowering time changes in pea from wild to crop. Journal of Experimental Botany 73,3978–3990.
3D mapping of the Wolf–Rayet nebula M 1-67: clues for post-common envelope evolution in massive stars
Authors: Zavala S , Toalá J A , Santamaría E , Ramos-Larios G , Sabin L , Quino-Mendoza J A , Rubio G , Guerrero M A 
Published: April 2022

ABSTRACT
We present a 3D mapping of the Wolf–Rayet (WR) nebula M 1-67 around WR 124. We obtained high-resolution San Pedro Mártir (SPM) Manchester Echelle Spectrograph (MES) observations along 17 long-slit positions covering all morphological features in M 1-67. We are able to unveil the true morphology of M 1-67 and its kinematics by interpreting the SPM MES observations by means of the 3D modelling tool for Astrophysics shape. Our shape model that best reproduces the SPM MES data includes three concentric bipolar structures composed by a hollow ellipsoidal structure and a torus. In addition, the model requires the presence of expanding jets and broken blisters in order to reproduce specific spectral features. Our results are consistent with the idea that M 1-67 and its progenitor star WR 124 have formed through a common envelope scenario that occurred 11.8$^{+4.6}_{-0.8}$ kyr ago. Our bipolar model strongly questions previous suggestions of the presence of a bow shock structure surrounding M 1-67. We interpret that the bright structures detected in the spectra extracted from the central regions are produced by wind compression at the receding region of the innermost structure in M 1-67. Furthermore, WR 124 is moving through a low-density region above the Galactic plane that has negligibly affected the formation history of M 1-67.
Host galaxies of ultrastrong Mg ii absorbers at z ∼ 0.5
Authors: Guha Labanya Kumar , Srianand Raghunathan , Dutta Rajeshwari , Joshi Ravi , Noterdaeme Pasquier , Petitjean Patrick 
Published: April 2022

ABSTRACT
From a sample of 109 candidate ultrastrong Mg ii (USMg ii; having rest equivalent width of Mg ii, W2796 &gt; 3.0 Å) systems at z = 0.4–0.6, we confirm 27 and identify host galaxies of 20 systems based on associated nebular line emission from our SALT observations or from Sloan Digital Sky Survey (SDSS) fiber spectra. The measured impact parameter, [O ii] luminosity, star formation rate, B-band luminosity, and stellar mass are in the ranges 7.3 ≤ D[kpc] ≤ 79, $0.2\le L_{[\mathrm{ O}\,~\small {\rm II}]}[ 10^{41}~\mathrm{ erg} \mathrm{ s}^{-1}]\le 4.5$, 2.59 ≤ SFR[M⊙yr−1] ≤ 33.51, $0.15L_B^{*}\le L_B\le 1.63L_B^{*}$, and 10.21 ≤ log[M*/ M ⊙] ≤ 11.62, respectively. The impact parameters found are larger than that predicted by the W2796 versus D relationship of the general population of Mg ii absorbers. At a given D, USMg ii host galaxies are more luminous and massive compared to typical Mg ii absorbers. However, the measured SFRs are slightly lower than that of main-sequence galaxies with same M⋆ at z ∼ 0.5. We report a correlation between $L_{[\mathrm{ O}\,\small {\rm II}]}$ and W2796 for the full population of Mg ii absorbers, driven mainly by the host galaxies of weak Mg ii absorbers that tend to have low $L_{[\mathrm{ O}\,\small {\rm II}]}$ and large impact parameters. We find at least ∼33 per cent of the USMg ii host galaxies (with a limiting magnitude of mr &lt; 23.6) are isolated and the large W2796 in these cases may originate from gas flows (infall/outflow) in single haloes of massive but not starburst galaxies. We also find galaxy interactions could be responsible for large velocity widths in at least ∼17 per cent cases.
Deep phenotyping: symptom annotation made simple with SAMS
Authors: Steinhaus Robin , Proft Sebastian , Seelow Evelyn , Schalau Tobias , Robinson Peter N , Seelow Dominik 
Published: April 2022

Abstract
Precision medicine needs precise phenotypes. The Human Phenotype Ontology (HPO) uses clinical signs instead of diagnoses and has become the standard annotation for patients’ phenotypes when describing single gene disorders. Use of the HPO beyond human genetics is however still limited. With SAMS (Symptom Annotation Made Simple), we want to bring sign-based phenotyping to routine clinical care, to hospital patients as well as to outpatients. Our web-based application provides access to three widely used annotation systems: HPO, OMIM, Orphanet. Whilst data can be stored in our database, phenotypes can also be imported and exported as Global Alliance for Genomics and Health (GA4GH) Phenopackets without using the database. The web interface can easily be integrated into local databases, e.g. clinical information systems. SAMS offers users to share their data with others, empowering patients to record their own signs and symptoms (or those of their children) and thus provide their doctors with additional information. We think that our approach will lead to better characterised patients which is not only helpful for finding disease mutations but also to better understand the pathophysiology of diseases and to recruit patients for studies and clinical trials. SAMS is freely available at https://www.genecascade.org/SAMS/.
Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain
Authors: Kojima Shin , Shiochi Naoya , Sato Kazuki , Yamaura Mamiko , Ito Toshiaki , Yamamura Nodoka , Goto Naoki , Odamoto Mika , Kobayashi Shin , Kimura Tohru , Sekita Yoichi 
Published: April 2022

Abstract
The Dlk1-Dio3 imprinted domain is controlled by an imprinting control region (ICR) called IG-DMR that is hypomethylated on the maternal allele and hypermethylated on the paternal allele. Although several genetic mutation experiments have shown that IG-DMR is essential for imprinting control of the domain, how DNA methylation itself functions has not been elucidated. Here, we performed both gain and loss of DNA methylation experiments targeting IG-DMR by transiently introducing CRISPR/Cas9 based-targeted DNA methylation editing tools along with one guide RNA into mouse ES cells. Altered DNA methylation, particularly at IG-DMR-Rep, which is a tandem repeat containing ZFP57 methylated DNA-binding protein binding motifs, affected the imprinting state of the whole domain, including DNA methylation, imprinted gene expression, and histone modifications. Moreover, the altered imprinting states were persistent through neuronal differentiation. Our results suggest that the DNA methylation state at IG-DMR-Rep, but not other sites in IG-DMR, is a master element to determine whether the allele behaves as the intrinsic maternal or paternal allele. Meanwhile, this study provides a robust strategy and methodology to study core DNA methylation in cis-regulatory elements, such as ICRs and enhancers.
A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA
Authors: Nir Ronit , Hoernes Thomas Philipp , Muramatsu Hiromi , Faserl Klaus , Karikó Katalin , Erlacher Matthias David , Sas-Chen Aldema , Schwartz Schraga 
Published: April 2022

AbstractRNA can be extensively modified post-transcriptionally with &gt;170 covalent modifications, expanding its functional and structural repertoire. Pseudouridine (Ψ), the most abundant modified nucleoside in rRNA and tRNA, has recently been found within mRNA molecules. It remains unclear whether pseudouridylation of mRNA can be snoRNA-guided, bearing important implications for understanding the physiological target spectrum of snoRNAs and for their potential therapeutic exploitation in genetic diseases. Here, using a massively parallel reporter based strategy we simultaneously interrogate Ψ levels across hundreds of synthetic constructs with predesigned complementarity against endogenous snoRNAs. Our results demonstrate that snoRNA-mediated pseudouridylation can occur on mRNA targets. However, this is typically achieved at relatively low efficiencies, and is constrained by mRNA localization, snoRNA expression levels and the length of the snoRNA:mRNA complementarity stretches. We exploited these insights for the design of snoRNAs targeting pseudouridylation at premature termination codons, which was previously shown to suppress translational termination. However, in this and follow-up experiments in human cells we observe no evidence for significant levels of readthrough of pseudouridylated stop codons. Our study enhances our understanding of the scope, ‘design rules’, constraints and consequences of snoRNA-mediated pseudouridylation.
MEOX2homeobox gene promotes growth of malignant gliomas
Authors: Schönrock Anna , Heinzelmann Elisa , Steffl Bianca , Demirdizen Engin , Narayanan Ashwin , Krunic Damir , Bähr Marion , Park Jong-Whi , Schmidt Claudia , Özduman Koray , Pamir M Necmettin , Wick Wolfgang , Bestvater Felix , Weichenhan Dieter , Plass Christoph , Taranda Julian , Mall Moritz , Turcan Şevin 
Published: April 2022

AbstractBackgroundGlioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10, and aberrantly activated receptor tyrosine kinase signaling pathways. Previously, we identified Mesenchyme Homeobox 2 (MEOX2), a gene located on chromosome 7, as an upregulated transcription factor in GBM. Overexpressed transcription factors can be involved in driving GBM. Here, we aimed to address the role of MEOX2 in GBM.MethodsPatient-derived GBM tumorspheres were used to constitutively knockdown or overexpress MEOX2 and subjected to in vitro assays including western blot to assess ERK phosphorylation. Cerebral organoid models were used to investigate the role of MEOX2 in growth initiation. Intracranial mouse implantation models were used to assess the tumorigenic potential of MEOX2. RNA-sequencing, ACT-seq, and CUT&Tag were used to identify MEOX2 target genes.ResultsMEOX2 enhanced ERK signaling through a feed-forward mechanism. We identified Ser155 as a putative ERK-dependent phosphorylation site upstream of the homeobox-domain of MEOX2. S155A substitution had a major effect on MEOX2 protein levels and altered its subnuclear localization. MEOX2 overexpression cooperated with p53 and PTEN loss in cerebral organoid models of human malignant gliomas to induce cell proliferation. Using high-throughput genomics, we identified putative transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor.ConclusionsWe identified MEOX2 as an oncogenic transcription regulator in GBM. MEOX2 increases proliferation in cerebral organoid models of GBM and feeds into ERK signaling that represents a core signaling pathway in GBM.
Human capital and welfare
Authors: Bosi Stefano , Camacho Carmen , Desmarchelier David 
Published: April 2022

AbstractWe introduce the Human Development Index (HDI) in a growth model to show that if households cared about human capital, even if infinitesimally, then human capital would increase forever protecting economies indirectly. Here, human capital will have an additional positive effect on social welfare through the quality of individual health and education. In a simple economy with a Cobb–Douglas technology and logarithmic preferences, we provide the explicit trajectories for human capital, consumption, and the HDI, which correspond to the balanced growth path (BGP). Using a two-step maximization strategy, we compute the optimal initial value of the control variable, in this case, the initial optimal labour supply. In other words, we prove the optimality of the BGP. We highlight a HDI crossing property: the propensity to consume has a positive effect on the HDI in the short run, but negative in the long run.
Clinical characteristics and risk factors associated with lymphoma in patients with systemic lupus erythematosus: a nationwide cohort study
Authors: Martín-López María , Galindo Maria , Pego-Reigosa José María , Jiménez Norman , Olivé Marqués Alejandro , Tomero Eva , Freire Mercedes , Martínez-Barrio Julia , Boteanu Alina , Salgado-Perez Eva , Fernández-Nebro Antonio , Calvo Jaime , Menor-Almagro Raul , Rúa-Figueroa Iñigo 
Published: April 2022

Abstract

Objectives
To assess the characteristics and risk of lymphoma in a large cohort of patients with SLE.

Methods
A case–cohort analysis was performed within a dynamic cohort of SLE patients from the Spanish Society of Rheumatology Lupus Registry (RELESSER). Clinical and analytical features were compared between the lymphoma SLE group and the control SLE group using an independent-sample Student’s t-test or Mann–Whitney test for continuous variables and the χ2 test for categorical variables with Fisher’s exact test if necessary. The multivariate analysis was based on a generalized linear model.

Results
Twenty-one patients with SLE and lymphoma and 3965 non-lymphoma controls with SLE were studied. Most lymphomas were of B cell origin (n = 15/21), with diffuse large B cell lymphoma being the most frequent histological type (8/21, 38.1%). As in the general population, the risk of lymphoma in SLE was higher in male than in female patients and increased with age. In the lymphoma SLE group, bivariate analysis showed a significantly higher percentage of pericarditis, organic brain syndrome, seizures, vasculitis, haemolytic anaemia, splenomegaly, venous thrombosis and mean modified (excluding lymphoma) SLICC/ACR damage index. In contrast, renal involvement, positive anti-dsDNA, and antimalarials ever were less frequent.

Conclusions
In this large multicentre Spanish cohort, we identified characteristics of SLE that are associated with a higher risk of lymphoma. Antimalarials were significantly negatively associated with risk of lymphoma in SLE patients. Nevertheless, further prospective studies are needed to clarify these findings.
PERFORMANCE OF BARC NEUTRON PERSONAL DOSEMETER IN EURADOS INTERCOMPARISON EXERCISE IC2017N – A LESSON LEARNT
Authors: Bakshi A K , Beck Mudit , Shah Pankaj 
Published: April 2022

Abstract
Bhabha Atomic Research Centre (BARC) conducts fast neutron personnel monitoring service to radiation workers involved in reactors, accelerators, spent fuel processing plants, oil-well industries, etc., using CR-39 detector based dosemeter. In this study, performance of the BARC fast neutron personnel dosemeter has been checked through EURADOS intercomparison exercise for simulated workplace neutron fields. The overall performance of the dosemeter in the lower dose equivalent (≤ 5 mSv) was found to be acceptable as per ISO-14146. The performance (ratio of estimated to reference dose equivalent) of the dosemeter in the higher dose equivalent (12 mSv) was found to be in the range of 0.48–0.44 and not satisfactory as per the ISO-14146 criteria for any dosimetry service. Based on this performance, a new imaging system was developed and performance of the dosemeters were improved and found to be acceptable (within ±20%) as per ISO.
In Vitro Pain Assay Using Human iPSC-Derived Sensory Neurons and Microelectrode Array
Authors: Odawara Aoi , Shibata Mikako , Ishibashi Yuto , Nagafuku Nami , Matsuda Naoki , Suzuki Ikuro 
Published: April 2022

Abstract
Drug-induced peripheral neuropathy occurs as an adverse reaction of chemotherapy. However, a highly accurate method for assessing peripheral neuropathy and pain caused by compounds has not been established. The use of human-induced pluripotent stem cell (hiPSC)-derived sensory neurons does not require animal experiments, and it is considered an effective method that can approach extrapolation to humans. In this study, we evaluated the response to pain-related compounds based on neural activities using in vitro microelectrode array (MEA) measurements in hiPSC-derived sensory neurons. Cultured sensory neurons exhibited gene expression of the Nav1.7, TRPV1, TRPA1, and TRPM8 channels, which are typical pain-related channels. Channel-dependent evoked responses were detected using the TRPV1 agonist capsaicin, a TRPA1 agonist, allyl isothiocyanate (AITC), and TRPM8 agonist menthol. In addition, the firing frequency increased with an increase in temperature from 37°C to 46°C, and temperature sensitivity was observed. In addition, the temperature of the peak firing rate differed among individual neurons. Next, we focused on the increase in cold sensitivity, which is a side effect of the anticancer drug oxaliplatin, and evaluated the response to AITC in the presence and absence of oxaliplatin. The response to AITC increased in the presence of oxaliplatin in a concentration-dependent manner, suggesting that the increased cold sensitivity in humans can be reproduced in cultured hiPSC-derived sensory neurons. The in vitro MEA system using hiPSC-derived sensory neurons is an alternative method to animal experiments, and it is anticipated as a method for evaluating peripheral neuropathy and pain induced by compounds.