bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana
Authors: Corona-Gomez Jose Antonio , Coss-Navarrete Evelia Lorena , Garcia-Lopez Irving Jair , Klapproth Christopher , Pérez-Patiño Jaime Alejandro , Fernandez-Valverde Selene L. 
Published: August 2022

AbstractLong non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.
Large-scale vivid metasurface color printing using advanced 12-in. immersion photolithography
Authors: Khaidarov Egor , Eschimese Damien , Lai Keng Heng , Huang Aihong , Fu Yuan Hsing , Lin Qunying , Paniagua-Dominguez Ramon , Kuznetsov Arseniy I. 
Published: August 2022

AbstractNanostructures exhibiting optical resonances (so-called nanoantennas) have strong potential for applications in color printing and filtering with sub-wavelength resolution. While small scale demonstrations of these systems are interesting as a proof-of-concept, their large scale and volume fabrication requires deeper analysis and further development for industrial adoption. Here, we evaluate the color quality produced by large size nanoantenna arrays fabricated on a 12-in. wafer using deep UV immersion photolithography and dry etching processes. The color reproduction and quality are analyzed in context of the CIE color diagram, showing that a vivid and vibrant color palette, almost fully covering the sRGB color space, can be obtained with this mass-manufacturing-ready fabrication process. The obtained results, thus, provide a solid foundation for the potential industrial adoption of this emerging technology and expose the limits and challenges of the process.
Rapid evolution of a novel protective symbiont into keystone taxon in Caenorhabditis elegans microbiota
Authors: Wu-Chuang Alejandra , Bates Kieran A. , Obregon Dasiel , Estrada-Peña Agustín , King Kayla C. , Cabezas-Cruz Alejandro 
Published: August 2022

AbstractProtective microbes have a major role in shaping host–pathogen interactions, but their relative importance in the structure of the host microbiota remains unclear. Here, we used a network approach to characterize the impact of a novel, experimentally evolved ‘protective microbial symbiont’ (Enterococcus faecalis) on the structure and predicted function of the natural microbiota of the model organism Caenorhabditis elegans. We used microbial network analysis to identify keystone taxa and describe the hierarchical placement of protective and non-protective symbionts in the microbiota. We found that early colonization with symbionts produce statistically significant changes in the structure of the community. Notably, only the protective E. faecalis became a keystone taxon in the nematode microbiota. Non-protective lineages of the same bacterial species remained comparatively unimportant to the community. Prediction of functional profiles in bacterial communities using PICRUSt2 showed that the presence of highly protective E. faecalis decreased the abundance of ergothioneine (EGT) biosynthesis pathway involved in the synthesis of the antioxidant molecule EGT, a potential public good. These data show that in addition to direct antagonism with virulent pathogens, keystone protective symbionts are linked to modified bacterial community structure and possible reductions in public goods, potentially driving decreased antioxidant defense. We suggest that this response could suppress infection via wholesale microbial community changes to further benefit the host. These findings extend the concept of protective symbionts beyond bodyguards to ecosystem engineers.
Effects of online parietal transcranial electric stimulation on associative memory: a direct comparison between tDCS, theta tACS, and theta-oscillatory tDCS
Authors: Živanović Marko , Bjekić Jovana , Konstantinović Uroš , Filipović Saša R. 
Published: August 2022

AbstractAssociative memory (AM) is the ability to remember and retrieve multiple items bound together. Previous studies aiming to modulate AM by various transcranial electric stimulation (tES) techniques were inconclusive, although overall suggestive that tES could be a tool for AM enhancement. However, evidence from a direct comparison between different tES techniques is lacking. Here, in a sham-controlled cross-over experiment, we comparatively assessed the effects of three types of tES—anodal tDCS, theta-band transcranial alternating current stimulation (tACS), and theta-oscillatory tDCS (otDCS), delivered over the left posterior parietal cortex, during a short-term digit-color AM task with cued-recall. The effects were tested in 40 healthy young participants while both oscillatory tES were delivered at a previously determined individual theta frequency (4–8 Hz). All three active stimulations facilitated the overall AM performance, and no differences could be detected between them on direct comparison. However, unlike tDCS, the effects of which appeared to stem mainly from the facilitation of low-memory demand trials, both theta-modulated tACS and otDCS primarily promoted AM in high memory demand trials. Comparable yet differential effects of tDCS, theta tACS, and otDCS could be attributed to differences in their presumed modes of action.
Occupations and their impact on the spreading of COVID-19 in urban communities
Authors: Hâncean Marian-Gabriel , Lerner Jürgen , Perc Matjaž , Oană Iulian , Bunaciu David-Andrei , Stoica Adelina Alexandra , Ghiţă Maria-Cristina 
Published: August 2022

AbstractThe current pandemic has disproportionally affected the workforce. To improve our understanding of the role that occupations play in the transmission of COVID-19, we analyse real-world network data that were collected in Bucharest between August 1st and October 31st 2020. The data record sex, age, and occupation of 6895 patients and the 13,272 people they have interacted with, thus providing a social network from an urban setting through which COVID-19 has spread. Quite remarkably, we find that medical occupations have no significant effect on the spread of the virus. Instead, we find common transmission chains to start with infected individuals who hold jobs in the private sector and are connected with non-active alters, such as spouses, siblings, or elderly relatives. We use relational hyperevent models to assess the most likely homophily and network effects in the community transmission. We detect homophily with respect to age and anti-homophily with respect to sex and employability. We note that, although additional data would be welcomed to perform more in-depth network analyses, our findings may help public authorities better target under-performing vaccination campaigns.
Study on the water-richness law and zoning assessment of mine water-bearing aquifers based on sedimentary characteristics
Authors: Wang Yang , Pu Zhiguo , Ge Qin , Liu Jinhui 
Published: August 2022

AbstractTo study and prevent the water hazards of deep coal mines roof in the Inner Mongolia–Shaanxi (IM–S) mining area, it is essential to correctly evaluate the water-richness distributions of water-bearing aquifers in roof. This paper puts forward a sediment control method for water-richness law and zoning in the roof aquifers of deep Jurassic coals. To determine the vertical distance of direct water-bearing aquifers, the height of fractured water-conducting zone was detected by an underground network parallel electrical method. The plane and lateral spatial distribution patterns of the water-bearing aquifers and the control of the water-richness distribution was analyzed with the sediment control method. An evaluation system that consisted of four indicators, i.e., sedimentary environmental impact index, interlayer ratio of sandstone and mudstone, sandstone thickness, geophysical water-richness anomaly index was constructed. Furthermore, an Analytic Hierarchy Process (AHP) was introduced to establish the comprehensive zoning map. Finally, through the example analysis of Muduchaideng coal mine, the zoning evaluation results of water-richness were verified by the mine inflow. The findings of this study provide scientific guidance for prevention and control of mine water hazards in the IM–S mining area.
STUB1 is an intracellular checkpoint for interferon gamma sensing
Authors: Ng Simon , Lim Shuhui , Sim Adrian Chong Nyi , Mangadu Ruban , Lau Ally , Zhang Chunsheng , Martinez Sarah Bollinger , Chandramohan Arun , Lim U-Ming , Ho Samantha Shu Wen , Chang Shih Chieh , Gopal Pooja , Hong Lewis Z. , Schwaid Adam , Fernandis Aaron Zefrin , Loboda Andrey , Li Cai , Phan Uyen , Henry Brian , Partridge Anthony W. 
Published: August 2022

AbstractImmune checkpoint blockade (ICB) leads to durable and complete tumour regression in some patients but in others gives temporary, partial or no response. Accordingly, significant efforts are underway to identify tumour-intrinsic mechanisms underlying ICB resistance. Results from a published CRISPR screen in a mouse model suggested that targeting STUB1, an E3 ligase involved in protein homeostasis, may overcome ICB resistance but the molecular basis of this effect remains unclear. Herein, we report an under-appreciated role of STUB1 to dampen the interferon gamma (IFNγ) response. Genetic deletion of STUB1 increased IFNGR1 abundance on the cell surface and thus enhanced the downstream IFNγ response as showed by multiple approaches including Western blotting, flow cytometry, qPCR, phospho-STAT1 assay, immunopeptidomics, proteomics, and gene expression profiling. Human prostate and breast cancer cells with STUB1 deletion were also susceptible to cytokine-induced growth inhibition. Furthermore, blockade of STUB1 protein function recapitulated the STUB1-null phenotypes. Despite these encouraging in vitro data and positive implications from clinical datasets, we did not observe in vivo benefits of inactivating Stub1 in mouse syngeneic tumour models—with or without combination with anti-PD-1 therapy. However, our findings elucidate STUB1 as a barrier to IFNγ sensing, prompting further investigations to assess if broader inactivation of human STUB1 in both tumors and immune cells could overcome ICB resistance.
Characteristics of major and macular branch retinal vein occlusion
Authors: Choi Yu-Jin , Jee Donghyun , Kwon Jin-woo 
Published: August 2022

AbstractWe compared the aqueous profiles, baseline characteristics, and clinical outcomes of 54 eyes with macular edema secondary to major branch retinal vein occlusion (BRVO) and macular BRVO. We also identified the characteristics of poor responders to anti-vascular endothelial growth factor (VEGF) injections. Aqueous inflammatory cytokine and VEGF concentrations were significantly higher in major BRVO. In optical coherence tomography, major BRVO had a higher proportion with subretinal fluid, disorganization of retinal inner layers, and ellipsoid zone disruption. Comparing the clinical outcomes, major BRVO required more intravitreal anti-VEGF injections and had a poorer visual prognosis in the first 12 months. A significantly higher proportion of patients with major BRVO required additional treatments after 6 months compared to macular BRVO. Patients who responded poorly to anti-VEGF had higher aqueous VEGF levels and central subfield thickness (CST) at baseline. In conclusion, major BRVO patients required more and longer treatments, and had worse visual prognoses. BRVO that responds poorly to anti-VEGF had greater CST and higher aqueous VEGF levels at baseline.
Effectiveness of ozone generated by a dielectric barrier discharge plasma reactor against multidrug-resistant pathogens and Clostridioides difficile spores
Authors: Bong Cheolwoo , Choi Ji Young , Bae Jinseung , Park Sungsu , Ko Kwan Soo , Bak Moon Soo , Cheong Hae Suk 
Published: August 2022

AbstractThe contaminated healthcare environment plays an important role in the spread of multidrug-resistant organisms (MDROs) and Clostridioides difficile. This study aimed to evaluate the antimicrobial effects of ozone generated by a dielectric barrier discharge (DBD) plasma reactor on various materials that were contaminated by vancomycin-resistant Enterococcus faecium (VRE), carbapenem-resistant Klebsiella pneumoniae (CRE), carbapenem-resistant Pseudomonas aeruginosa (CRPA), carbapenem-resistant Acinetobacter baumannii (CRAB) and C. difficile spores. Various materials contaminated by VRE, CRE, CRPA, CRAB and C. difficile spores were treated with different ozone concentrations and exposure times. Atomic force microscopy (AFM) demonstrated bacterial surface modifications following ozone treatment. When an ozone dosage of 500 ppm for 15 min was applied to VRE and CRAB, about 2 or more log10 reduction was observed in stainless steel, fabric and wood, and a 1–2 log10 reduction in glass and plastic. Spores of C. difficile were more resistant to ozone than were all other tested organisms. On AFM, the bacterial cells, following ozone treatment, were swollen and distorted. The ozone generated by the DBD plasma reactor provided a simple and valuable decontamination tool for the MDROs and C. difficile spores, which are known as common pathogens in healthcare-associated infections.
Design, synthesis, and in silico studies of quinoline-based-benzo[d]imidazole bearing different acetamide derivatives as potent α-glucosidase inhibitors
Authors: Noori Milad , Davoodi Ali , Iraji Aida , Dastyafteh Navid , Khalili Minoo , Asadi Mehdi , Mohammadi Khanaposhtani Maryam , Mojtabavi Somayeh , Dianatpour Mehdi , Faramarzi Mohammad Ali , Larijani Bagher , Amanlou Massoud , Mahdavi Mohammad 
Published: August 2022

AbstractIn this study, 18 novel quinoline-based-benzo[d]imidazole derivatives were synthesized and screened for their α-glucosidase inhibitory potential. All compounds in the series except 9q showed a significant α-glucosidase inhibition with IC50 values in the range of 3.2 ± 0.3–185.0 ± 0.3 µM, as compared to the standard drug acarbose (IC50 = 750.0 ± 5.0 µM). A kinetic study indicated that compound 9d as the most potent derivative against α-glucosidase was a competitive type inhibitor. Furthermore, the molecular docking study revealed the effective binding interactions of 9d with the active site of the α-glucosidase enzyme. The results indicate that the designed compounds have the potential to be further studied as new anti-diabetic agents.
High rates of COVID-19 vaccine refusal among Afghan pregnant women: a cross sectional study
Authors: Nemat Arash , Yaftali Sumaira , Danishmand Tamim Jan , Nemat Haroon , Raufi Nahid , Asady Abdullah 
Published: August 2022

AbstractSevere Acute Respiratory Syndrome Corona Virus Type-2 (SARS-COV-2) was first detected in China and created a global pandemic rapidly. Subsequently after serious efforts different types of vaccines produced against the virus and recommended for all people including pregnant women. The aim of this study was to realize the willingness of pregnant women to accept the COVID-19 vaccine in Kabul Afghanistan. For this purpose, a cross-sectional study was conducted in gynecology wards of several hospitals in Kabul, Afghanistan from 10th of July to 20th of August 2021 through direct interview with the pregnant women who had come for prenatal care to the healthcare centers. The collected data were analyzed through Statistical Package for Social Studies (SPSS) version 25. Simple descriptive analysis computed for demographic characteristics and bi-variable (Chi-square) analysis was carried out to find out the associations of taking vaccine with demographic variables. A p-value of < 0.05 was considered significant at 95% confidence interval. A total of 491 who were completed the inclusion criteria included in the analysis. A small portion of pregnant women (8.6%) illustrated the intent to get the COVID-19 vaccine if it is recommended by the health authorities in Afghanistan. Our study found a high rate of COVID-19 vaccine refusal among pregnant women in Kabul, Afghanistan. They showed the concern on adverse effects of the vaccine as the main reason for refusal, emphasizing the need to reduce the misconception on vaccine efficacy and campaigns to enhance awareness on the vaccine safety and benefits for mothers and babies.
Subtype and cell type specific expression of lncRNAs provide insight into breast cancer
Authors: Bjørklund Sunniva Stordal , Aure Miriam Ragle , Häkkinen Jari , Vallon-Christersson Johan , Kumar Surendra , Evensen Katrine Bull , Fleischer Thomas , Tost Jörg ,   OSBREAC, Bathen Tone F. , Borgen Elin , Børresen-Dale Anne-Lise , Engebråten Olav , Fritzman Britt , Hartmann-Johnsen Olaf Johan , Garred Øystein , Geisler Jürgen , Geitvik Gry Aarum , Hofvind Solveig , Kåresen Rolf , Langerød Anita , Lingjærde Ole Christian , Mælandsmo Gunhild Mari , Naume Bjørn , Russnes Hege G. , Sauer Torill , Skjerven Helle Kristine , Schlichting Ellen , Sørlie Therese , Sahlberg Kristine K. , Mathelier Anthony , Bhanot Gyan , Ganesan Shridar , Tekpli Xavier , Kristensen Vessela N. 
Published: August 2022

AbstractLong non-coding RNAs (lncRNAs) are involved in breast cancer pathogenesis through chromatin remodeling, transcriptional and post-transcriptional gene regulation. We report robust associations between lncRNA expression and breast cancer clinicopathological features in two population-based cohorts: SCAN-B and TCGA. Using co-expression analysis of lncRNAs with protein coding genes, we discovered three distinct clusters of lncRNAs. In silico cell type deconvolution coupled with single-cell RNA-seq analyses revealed that these three clusters were driven by cell type specific expression of lncRNAs. In one cluster lncRNAs were expressed by cancer cells and were mostly associated with the estrogen signaling pathways. In the two other clusters, lncRNAs were expressed either by immune cells or fibroblasts of the tumor microenvironment. To further investigate the cis-regulatory regions driving lncRNA expression in breast cancer, we identified subtype-specific transcription factor (TF) occupancy at lncRNA promoters. We also integrated lncRNA expression with DNA methylation data to identify long-range regulatory regions for lncRNA which were validated using ChiA-Pet-Pol2 loops. lncRNAs play an important role in shaping the gene regulatory landscape in breast cancer. We provide a detailed subtype and cell type-specific expression of lncRNA, which improves the understanding of underlying transcriptional regulation in breast cancer.
Maternal anxiety affects embryo implantation via impairing adrenergic receptor signaling in decidual cells
Authors: Wu Jinxiang , Lin Shu , Huang Pinxiu , Qiu Lingling , Jiang Yufei , Zhang Ying , Meng Nan , Meng Meiqing , Wang Lemeng , Deng Wenbo , Liu Zhao , Guo Chuanhui , Lu Jinhua , Wang Haibin , Kong Shuangbo 
Published: August 2022

AbstractRecurrent implantation failure (RIF) is defined as the failed pregnancy after good embryo transfer over 3 cycles during in vitro fertilization (IVF).The human endometrium plays a vital role in providing the site for embryo implantation, with several factors implicated in unsatisfactory endometrial receptivity in RIF. Our present results revealed that women with pregnancy loss or infertility have a higher serum epinephrine level, indicating a potential correlation between psychological stress and pregnancy failure. RNA-sequencing of the tissues collected at the endometrial receptive phase in normal and RIF women showed that stress hormones could affect the functional status of endometrial receptivity. Subsequent analysis revealed that the epinephrine signaling acts as an important regulator of endometrial receptivity through the PI3K-AKT and FOXO1 signaling pathways. We also found that patients with RIF show attenuated expression of the alpha-2C-adrenergic receptor (ADRA2C) and that its down regulation induced by high level epinephrine could inhibit the decidualization. Early pregnant mice treated with stress showed high serum epinephrine levels, defective uterine adrenergic receptor expression, and low pregnancy rates. Altogether, our findings indicate that mental stress during early pregnancy can alter the functional status of endometrial receptivity.
Reassigning the shapes of the 0+ states in the 186Pb nucleus
Authors: Ojala Joonas , Pakarinen Janne , Papadakis Philippos , Sorri Juha , Sandzelius Mikael , Cox Daniel M. , Auranen Kalle , Badran Hussam , Davies Paul J. , Grahn Tuomas , Greenlees Paul T. , Henderson Jack , Herzáň Andrej , Herzberg Rolf-Dietmar , Hilton Joshua , Jakobsson Ulrika , Jenkins David G. , Joss David T. , Julin Rauno , Juutinen Sakari , Kibédi Tibor , Konki Joonas , Lane Gregory J. , Leino Matti , Liimatainen Jarkko , McPeake Christopher G. , Neuvonen Olavi , Page Robert D. , Parr Edward , Partanen Jari , Peura Pauli , Rahkila Panu , Revill John , Ruotsalainen Panu , Sarén Jan , Scholey Catherine , Stolze Sanna , Uusitalo Juha , Ward Andrew , Wadsworth Robert 
Published: August 2022

AbstractAcross the physics disciplines, the 186Pb nucleus is the only known system, where the two first excited states, together with the ground state, form a triplet of zero-spin states assigned with prolate, oblate and spherical shapes. Here we report on a precision measurement where the properties of collective transitions in 186Pb were determined in a simultaneous in-beam γ-ray and electron spectroscopy experiment employing the recoil-decay tagging technique. The feeding of the $${0}_{2}^{+}$$

0

2

+

state and the interband $${2}_{2}^{+}\to {2}_{1}^{+}$$

2

2

+

→

2

1

+

transition have been observed. We also present direct measurement of the energies of the electric monopole transitions from the excited 0+ states to the 0+ ground state. In contrast to the earlier understanding, the obtained reduced transition probability $$B(E2;{2}_{1}^{+}\to {0}_{2}^{+})$$
B

(

E
2
;

2

1

+

→

0

2

+

)

value of 190(80) W.u., the transitional quadrupole moment $$| {Q}_{t}({2}_{1}^{+}\to {0}_{2}^{+})| =7.7$$
∣

Q

t

(

2

1

+

→

0

2

+

)

∣
=
7.7
(33) eb and intensity balance arguments provide evidence to reassign the $${0}_{2}^{+}$$

0

2

+

and $${0}_{3}^{+}$$

0

3

+

states with predominantly prolate and oblate shape, respectively. Our work demonstrates a step-up in experimental sensitivity and paves the way for systematic studies of electric monopole transitions in this region. These electric monopole transitions probe the nuclear volume in a unique manner and provide unexploited input for development of the next-generation energy density functional models.