bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient disruption of CmHk1 using CRISPR/Cas9 ribonucleoprotein delivery in Cordyceps militaris
Authors: Choi Hyeongju , Park Sung-Won , Oh Junsang , Kim Cheol Soo , Sung Gi-Ho , Sang Hyunkyu 
Published: July 2023

Abstract
Cordyceps militaris, an entomopathogenic ascomycete, produces edible medicinal mushrooms known to have medicinal and therapeutic functions. To develop the genetic transformation system in C. militaris, green fluorescent protein (GFP) mutants of C. militaris were generated by PEG-mediated protoplast transformation. The CRISPR/Cas9 ribonucleoprotein (RNP) targeting the class III histidine kinase of C. militaris (CmHk1) was then delivered into protoplasts of C. militaris through the transformation system. Mutations induced by the RNP in selected mutants were detected: 1 nt deletion (6 mutants), 3 nt deletion with substitution of 1 nt (1 mutant), insertion of 85 nts (1 mutant), 41 nts (2 mutants), and 35 nts (5 mutants). An in vitro sensitivity assay of the mutants indicated that knockout of CmHk1 reduced sensitivity to two fungicides, iprodione and fludioxonil, but increased sensitivity to osmotic stresses compared to the wild type. Summing up, the CRISPR/Cas9 RNP delivery system was successfully developed, and our results revealed that CmHk1 was involved in the fungicide resistance and osmotic stress in C. militaris.
Assessing Progression of Biologic Therapies Based on Smoking Status in Patients With Crohn’s Disease
Authors: Alizadeh Madeline , Ali Osman , Cross Raymond K 
Published: July 2023

Abstract

Background
Active smoking is a well-established risk factor for developing Crohn’s disease (CD) and negatively impacts overall disease progression. Patients who start or continue smoking after CD diagnosis are at risk for poor outcomes, higher therapeutic requirements, and have higher rates of relapse. However, it remains unclear if the exposure to smoking leads to increased sequencing through treatment therapies, especially biologics.

Methods
The Study of Prospective Adult Research Cohort with IBD (SPARC IBD) registry has been collecting patient-reported outcomes data in real-time, as well as laboratory, endoscopic, and pathologic samples from 17 tertiary referral centers since 2016. In this study, we conducted a retrospective review of the SPARC clinical registry collected between December 2016 and January 2021 from 1 participating site, the University of Maryland School of Medicine’s Inflammatory Bowel Disease Program. A total of 619 patients were enrolled in the SPARC IBD database. Four hundred twenty-five patients with CD were included for initial review of completeness of data; of these, 144 patients were excluded due to missing data on smoking status and/or biologic treatment, resulting in a final cohort of 281 patients. We collected and analyzed baseline demographic and clinical characteristics. The final cohort was categorized into 3 exposure groups: current, former, and never smokers. Our outcome of interest was number biologics used, categorized into 3 groups: 0, 1, or ≥2 biologics.

Results
One hundred seventy-two never smokers, 70 former smokers, and 39 current smokers were identified. Current, former, and never smokers had no statistically significant differences in number of biologics used (ie, biologic sequencing). However, statistically significant independent risk factors for increased sequencing of biologics were identified. These risk factors included female sex, ileocolonic disease location, younger age at diagnosis, and prolonged disease duration; none of these factors remained significant in adjusted analyses.

Conclusion
To date, this is the first study assessing the association of smoking and sequencing of biologics. Although current or former smokers were not found to sequence through more biologics when compared with never smokers, smoking is a well-established risk factor for poor health outcomes, and efforts should be made to counsel patients to quit. Further, additional research must be done to stratify risk to patients based on amount of tobacco exposure.
SARS-CoV-2 mRNA vaccine-induced immune responses in rheumatoid arthritis
Authors: Limoges Marc-André , Lortie Audrey , Demontier Élodie , Quenum Akouavi Julite Irmine , Lessard Félix , Drouin Zacharie , Carrier Nathalie , Nguimbus Leopold Mbous , Beaulieu Marie-Claude , Boire Gilles , Piché Alain , Allard-Chamard Hugues , Ramanathan Sheela , Roux Sophie 
Published: July 2023

Abstract
Our objective was to characterize T and B cell responses to vaccination with SARS-CoV-2 antigens in immunocompromised rheumatoid arthritis (RA) patients. In 22 RA patients, clinical and biological variables were analyzed before and 4 weeks after each of 3 messenger RNA (mRNA) vaccine doses and compared with unmatched healthy individuals. Sequentially sampled peripheral blood mononuclear cells and sera were collected to determine immune profiles and to analyze the T cell response to a spike peptide pool and B cell specificity to the receptor-binding domain (RBD). Anti-spike antibodies were detectable in 6 of 22 RA patients after 1 dose of vaccine with increasing titers after each booster dose, although the overall response was lower compared with that in healthy control individuals. Responding patients after the first dose were more likely to have RA antibodies and a higher baseline proportion of circulating follicular B cells. In RA patients, the mRNA vaccine elicited a robust CD4+ T response to a spike peptide pool following the first and second doses. Consistent with the serologies, RBD-specific B cells exhibited a modest increase after the first dose and the second dose resulted in marked increases only in a fraction of the RA patients to both ancestral and omicron RBD. Our results highlight the importance of multidose COVID-19 vaccination in RA patients to develop a protective humoral response. However, these patients rapidly develop specific T CD4+ responses, despite delayed B cell responses.
Caveolin-1 is essential for the increased release of glutamate in the anterior cingulate cortex in neuropathic pain mice
Authors: Yang Jun-Xia , Zhao Wei-Nan , Jiang Yan-Yu , Ma Yu , Chen Dan-Dan , Lin Zhi-Hua , Yin Meng-Bing , Ren Kun-Peng 
Published: July 2023

Abstract
Neuropathic pain has a complex pathogenesis. Here, we examined the role of caveolin-1 (Cav-1) in the anterior cingulate cortex (ACC) in a chronic constriction injury (CCI) mouse model for the enhancement of presynaptic glutamate release in chronic neuropathic pain. Cav-1 was localized in glutamatergic neurons and showed higher expression in the ACC of CCI versus sham mice. Moreover, the release of glutamate from the ACC of the CCI mice was greater than that of the sham mice. Inhibition of Cav-1 by siRNAs greatly reduced the release of glutamate of ACC, while its overexpression (induced by injecting Lenti-Cav-1) reversed this process. The chemogenetics method was then used to activate or inhibit glutamatergic neurons in the ACC area. After 21 days of injection of AAV-hM3Dq in the sham mice, the release of glutamate was increased, the paw withdrawal latency was shortened, and expression of Cav-1 in the ACC was upregulated after intraperitoneal injection of 2 mg/kg clozapine N-oxide. Injection of AAV-hM4Di in the ACC of CCI mice led to the opposite effects. Furthermore, decreasing Cav-1 in the ACC in sham mice injected with rAAV-hM3DGq did not increase glutamate release. These findings suggest that Cav-1 in the ACC is essential for enhancing glutamate release in neuropathic pain.
Low-ionization iron-rich broad absorption-line quasar SDSS J 1652+2650: physical conditions in the ejected gas from excited Fe ii and metastable He i
Authors: Balashev S A , Ledoux C , Noterdaeme P , Boissé P , Krogager J-K , López S , Telikova K N 
Published: July 2023

ABSTRACT
We present high-resolution VLT/UVES spectroscopy and a detailed analysis of the unique broad absorption-line system towards the quasar SDSS J 165252.67+265001.96. This system exhibits low-ionization metal absorption lines from the ground states and excited energy levels of Fe ii and Mn ii, and the meta-stable $2\, ^3S$ excited state of He i. The extended kinematics of the absorber encompasses three main clumps with velocity offsets of −5680, −4550, and −1770 km s−1 from the quasar emission redshift, z = 0.3509 ± 0.0003, derived from [O ii] emission. Each clump shows moderate partial covering of the background continuum source, Cf ≈ [0.53; 0.24; 0.81]. We discuss the excitation mechanisms at play in the gas, which we use to constrain the distance of the clouds from the active galactic nucleus (AGN) as well as the density, temperature, and typical sizes of the clouds. The number density is found to be nH ∼ 104 cm−3 and the temperature Te ∼ 104 K, with longitudinal cloudlet sizes of ≳0.01 pc. cloudy photoionization modelling of He i⋆, which is also produced at the interface between the neutral and ionized phases, assuming the number densities derived from Fe ii, constrains the ionization parameter to be log U ∼ −3. This corresponds to distances of a few 100 pc from the AGN. We discuss these results in the more general context of associated absorption-line systems and propose a connection between FeLoBALs and the recently identified molecular-rich intrinsic absorbers. Studies of significant samples of FeLoBALs, even though rare per se, will soon be possible due to large dedicated surveys paired with high-resolution spectroscopic follow-ups.
Towards ultra metal-poor DLAs: linking the chemistry of the most metal-poor DLA to the first stars
Authors: Welsh Louise , Cooke Ryan , Fumagalli Michele , Pettini Max 
Published: July 2023

ABSTRACT
We present new Keck/HIRES data of the most metal-poor damped Ly α (DLA) system currently known. By targeting the strongest accessible Fe ii features, we have improved the upper limit of the [Fe/H] abundance determination by ∼1 dex, finding [Fe/H] &lt; −3.66 (2σ). We also provide the first upper limit on the relative abundance of an odd-atomic number element for this system [Al/H] &lt; −3.82 (2σ). Our analysis thus confirms that this zabs ≃ 3.08 DLA is not only the most metal-poor DLA but also the most iron-poor DLA currently known. We use the chemistry of this DLA, combined with a stochastic chemical enrichment model, to probe its enrichment history. We find that this DLA is best modelled by the yields of an individual Population III progenitor rather than multiple Population III stars. We then draw comparisons with other relic environments and, particularly, the stars within nearby ultra-faint dwarf galaxies. We identify a star within Boötes I, with a similar chemistry to that of the DLA presented here, suggesting that it may have been born in a gas cloud that had similar properties. The extremely metal-poor DLA at redshift zabs ≃ 3.08 (i.e. ∼2 Gyr after the Big Bang) may reside in one of the least polluted environments in the early Universe.
EYA2 tyrosine phosphatase inhibition reduces MYC and prevents medulloblastoma progression
Authors: Wolin Arthur R , Vincent Melanie Y , Hotz Taylor , Purdy Stephen C , Rosenbaum Sheera R , Hughes Connor J , Hsu Jessica Y , Oliphant Michael U J , Armstrong Brock , Wessells Veronica , Varella-Garcia Marileila , Galbraith Matthew D , Pierce Angela , Wang Dong , Venkataraman Sujatha , Danis Etienne , Veo Bethany , Serkova Natalie , Espinosa Joaquin M , Gustafson Daniel L , Vibhakar Rajeev , Ford Heide L 
Published: July 2023

Abstract

Background
Medulloblastoma is the most common pediatric brain malignancy. Patients with the Group 3 subtype of medulloblastoma (MB) often exhibit MYC amplification and/or overexpression and have the poorest prognosis. While Group 3 MB is known to be highly dependent on MYC, direct targeting of MYC remains elusive.

Methods
Patient gene expression data were used to identify highly expressed EYA2 in Group 3 MB samples, assess the correlation between EYA2 and MYC, and examine patient survival. Genetic and pharmacological studies were performed on EYA2 in Group 3 derived MB cell models to assess MYC regulation and viability in vitro and in vivo.

Results
EYA2 is more highly expressed in Group 3 MB than other MB subgroups and is essential for Group 3 MB growth in vitro and in vivo. EYA2 regulates MYC expression and protein stability in Group 3 MB, resulting in global alterations of MYC transcription. Inhibition of EYA2 tyrosine phosphatase activity, using a novel small molecule inhibitor (NCGC00249987, or 9987), significantly decreases Group 3 MB MYC expression in both flank and intracranial growth in vivo. Human MB RNA-seq data show that EYA2 and MYC are significantly positively correlated, high EYA2 expression is significantly associated with a MYC transcriptional signature, and patients with high EYA2 and MYC expression have worse prognoses than those that do not express both genes at high levels.

Conclusions
Our data demonstrate that EYA2 is a critical regulator of MYC in Group 3 MB and suggest a novel therapeutic avenue to target this highly lethal disease.
An arginine-to-histidine mutation in flavanone-3-hydroxylase results in pink strawberry fruits
Authors: Xu Pengbo , Li Xinyu , Fan Junmiao , Tian Shuhua , Cao Minghao , Lin Anqi , Gao Qinhua , Xiao Kun , Wang Chong , Kuang Huiyun , Lian Hongli 
Published: July 2023

Abstract
Fruit color is a very important external commodity factor for consumers. Compared to the most typical red octoploid strawberry (Fragaria × ananassa), the pink strawberry often sells for a more expensive price and has a higher economic benefit due to its outstanding color. However, few studies have examined the molecular basis of pink-colored strawberry fruit. Through an EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified a mutant with pink fruits and green petioles. Bulked-segregant analysis sequencing analysis and gene function verification confirmed that the responsible mutation resides in a gene encoding flavanone-3-hydroxylase (F3H) in the anthocyanin synthesis pathway. This nonsynonymous mutation results in an arginine-to-histidine change at position 130 of F3H. Molecular docking experiments showed that the arginine-to-histidine mutation results in a reduction of intermolecular force-hydrogen bonding between the F3H protein and its substrates. Enzymatic experiments showed a greatly reduced ability of the mutated F3H protein to catalyze the conversion of the substrates and hence a blockage of the anthocyanin synthesis pathway. The discovery of a key residue in the F3H gene controlling anthocyanin synthesis provides a clear target of modification for the molecular breeding of strawberry varieties with pink-colored fruits, which may be of great commercial value.
An Anatomy Lesson for Democrats
Authors: Huq Aziz Z 
Published: July 2023

Abstract
The extensive political science, sociology, and legal literatures on democratic backsliding all tend to approach the issue in the same way: Start with a recent example of democratic decay. Then reason back from that example to generate a more extensive account of backsliding mechanisms or consequences. In contrast, Norwegian political scientist and sociologist Stein Ringen, in a book called How Democracies Live: Power, Statecraft, and Freedom in Modern Societies, offers a diagnosis of democratic backsliding that flips this standard sequence of analysis. Rather than beginning with case studies, Ringen offers an investigation of five “core” concepts of political theory. Those who seek to ameliorate democracy's current woes, he contends, should start with this sort of very general anatomy lesson. Only with the resulting conceptual map of political theory can they develop specific lessons for the task of managing democratic revival today. By negative implication, Ringen suggests, reformers will be led astray by starting with a specific case. The latter approach, he implies, causes them to overlook or misconstrue basic elements of the political order that must be fixed before the democratic ship can be righted. This review considers whether Ringen's anatomy-inspired method yields insights and, further, whether, more generally, an anatomical approach to political concepts can deepen our understanding of democracy and its present travails. It offers reasons for skepticism on both counts. It may well be possible to construct a taxonomy of political concepts to clarify the terms of democratic survival. But the specific taxonomy of core concepts offered in How Democracies Live does not plainly succeed.
Whole exome sequencing of a German sarcoidosis family with four affected and one spontaneous remission case
Authors: Kvacskay Peter , El Jammal Thomas , Lorenz Hanns-Martin , Pacheco Yves , Calender Alain 
Published: July 2023

Abstract

Objectives
To analyse genetic mechanisms triggering familial sarcoidosis, whole exome screening of a family of six persons with four cases of sarcoidosis and two healthy controls was performed integrating progressive and spontaneous remission cases and evaluating involved genetic alterations that could potentially determine the individual course of the disease.

Methods
Clinical diagnostic criteria in patients of the selected sarcoidosis family were according to American Thoracic Society/European Respiratory Society/World Association of Sarcoidosis and other Granulomatous Disorders guidelines. Exome screening of four patients and the two intrafamilial healthy relatives was performed by paired-end (2 × 100 bp) sequencing. We then selected the gene variants considered pathogenic on the basis of a series of prediction software applications and presence only in members of the family affected by sarcoidosis, after subtracting the common variations observed in healthy subjects.

Results
Four persons out of six family members were affected by sarcoidosis. Fifty genes with uncommon in silico pathogenic variants could be identified that differentiated affected and healthy family members. One patient with sarcoidosis showed spontaneous remission whereas the remaining three patients required immunosuppressive treatment. Subtraction analysis revealed 18 genes that distinguished the three progressive cases from the patient with spontaneous remission.

Conclusion
The genetic analysis of these cases with familial sarcoidosis identified several involved genes and functional pathways that could help in understanding the basic mechanisms that determine the development of the disease and that discriminate spontaneously regressive and progressive forms.
Prognostic significance of pericardial effusion in systemic sclerosis-associated pulmonary hypertension: analysis from the PHAROS Registry
Authors: Luo Yiming , Gordon Jessica K , Xu Jiehui , Kolstad Kathleen D , Chung Lorinda , Steen Virginia D , Bernstein Elana J ,   PHAROS Investigators, Csuka Mary E , Derk Chris T , Domsic Robyn T , Fischer Aryeh , Frech Tracy , Goldberg Avram Z , Hant Faye , Hinchcliff Monique , Horn Evelyn , Hummers Laura , Hsu Vivien , Kafaja Susanna , Khanna Dinesh , Molitor Jerry , Saketkoo Lesley , Shapiro Lee , Silver Rick , Simms Robert 
Published: July 2023

Abstract

Objectives
Pulmonary hypertension (PH) is a leading cause of death in patients with SSc. The purpose of this study was to determine the prognostic significance of pericardial effusion in patients with SSc-PH.

Methods
Pulmonary Hypertension Assessment and Recognition of Outcomes in Scleroderma (PHAROS) is a prospective multicentre registry which enrolled patients with newly diagnosed SSc-PH from 2005 to 2016. The prognostic impact of pericardial effusion status, including those who ever or never had pericardial effusion, and those who had persistent or intermittent pericardial effusion, was analysed. Kaplan–Meier survival analyses, log-rank test, and multivariable Cox proportional hazards regression were performed.

Results
Of the 335 patients with SSc-PH diagnosed by right heart catheterization and documentation of pericardial effusion presence or absence on echocardiogram, 166 (50%) ever had pericardial effusion. Ever having pericardial effusion was not predictive of survival (log-rank test P = 0.49). Of the 245 SSc-PH patients who had at least two echocardiograms, 44% had a change in pericardial effusion status over an average of 4.3 years of follow up. Having a persistent pericardial effusion was an independent predictor of survival [adjusted hazard ratio (aHR)=2.34, 95% CI 1.20, 4.64, P = 0.002], while intermittent pericardial effusion was not a predictor of survival (aHR = 0.89, 95% CI 0.52, 1.56, P = 0.68), in a multivariable-adjusted analysis.

Conclusion
Persistent pericardial effusion, but not ever having had pericardial effusion or intermittent pericardial effusion, was independently associated with poorer survival. Incorporating information from serial echocardiograms may help clinicians better prognosticate survival in their SSc-PH patients.
Construct validity and reliability of the Assessment of Systemic Sclerosis-Associated Raynaud’s Phenomenon (ASRAP) questionnaire
Authors: Pauling John D , Yu Lan , Frech Tracy M , Herrick Ariane L , Hummers Laura K , Shah Ami A , Denton Christopher P , Saketkoo Lesley Ann , Withey Jane , Khanna Dinesh , Domsic Robyn T 
Published: July 2023

Abstract

Objectives
Assessment of construct validity and reliability of a novel patient-reported outcome (PRO) instrument for assessing the severity and impact of RP in SSc.

Methods
An international multicentre study validation study of the 27-item Assessment of Systemic Sclerosis-Associated Raynaud’s Phenomenon (ASRAP) and 10-item short-form (ASRAP-SF) questionnaires. The relationship between ASRAP questionnaires and demographics, clinical phenotype and legacy instruments for assessing SSc-RP severity, disability and pain was assessed. Repeatability was evaluated at 1 week. Anchor-based statements of health status facilitated assessment of ASRAP thresholds of meaning.

Results
A total of 420 SSc subjects were enrolled. There was good correlation between ASRAP (and ASRAP-SF) with RP visual analogue scale (VAS) and Scleroderma Health Assessment Questionnaire RP VAS (rho range 0.648–0.727, P &lt; 0.001). Correlation with diary-based assessment of SSc-RP attack frequency and duration was lower (rho range 0.258–0.504, P &lt; 0.001). ASRAP questionnaires had good correlation with instruments for assessing disability, hand function, pain and global health assessment (rho range 0.427–0.575, P &lt; 0.001). Significantly higher ASRAP scores were identified in smokers, patients with active digital ulceration (DU), previous history of DU and calcinosis (P &lt; 0.05 for all comparisons). There was excellent repeatability at 1 week among patients with stable SSc-RP symptoms (intra-class coefficients of 0.891 and 0.848, P &lt; 0.001). Patient-acceptable symptom state thresholds for ASRAP and ASRAP-SF were 45.34 and 45.77, respectively. A preliminary Minimally Important Clinical Difference threshold of 4.17 (95% CI 0.53, 7.81, P = 0.029) was estimated.

Conclusion
ASRAP and ASRAP-SF questionnaires are valid and reliable novel PRO instruments for assessing the severity and impact of SSc-RP.