bluuebunny/crossref_metadata_2025 huggingface dataset:
Robust single nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity
Authors: So Jisun , Strobel Olivia , Wann Jamie , Kim Kyungchan , Paul Avishek , Acri Dominic J. , Dabin Luke C. , Peng Gang , Kim Jungsu , Roh Hyun Cheol
Published: April 2024

Single nucleus RNA sequencing (snRNA-seq), an alternative to single cell RNA sequencing (scRNA-seq), encounters technical challenges in obtaining high-quality nuclei and RNA, persistently hindering its applications. Here, we present a robust technique for isolating nuclei across various tissue types, remarkably enhancing snRNA-seq data quality. Employing this approach, we comprehensively characterize the depot-dependent cellular dynamics of various cell types underlying adipose tissue remodeling during obesity. By integrating bulk nuclear RNA-seq from adipocyte nuclei of different sizes, we identify distinct adipocyte subpopulations categorized by size and functionality. These subpopulations follow two divergent trajectories, adaptive and pathological, with their prevalence varying by depot. Specifically, we identify a key molecular feature of dysfunctional hypertrophic adipocytes, a global shutdown in gene expression, along with elevated stress and inflammatory responses. Furthermore, our differential gene expression analysis reveals distinct contributions of adipocyte subpopulations to the overall pathophysiology of adipose tissue. Our study establishes a robust snRNA-seq method, providing novel insights into the biological processes involved in adipose tissue remodeling during obesity, with broader applicability across diverse biological systems.
DNA targeting by compact Cas9d and its resurrected ancestor
Authors: Ocampo Rodrigo Fregoso , Bravo Jack P. K. , Dangerfield Tyler , Nocedal Isabel , Jirde Samatar , Alexander Lisa M. , Das Anjali , Nielsen Sarah , Johnson Kenneth A. , Brown Christopher T. , Butterfield Cristina N. , Goltsman Daniela S. A. , Taylor David W.
Published: April 2024

The type II-A CRISPR effector SpCas9 has gained widespread popularity as an efficient and programmable genome editing tool. However, much remains to be known about novel compact variants that may overcome some limitations of current systems1,2. Recently, alternative CRISPR-Cas systems with highly compact nucleases capable of genome editing in mammalian cells have been discovered through metagenomic analysis of uncultivated microbes, including Cas9d (a type II-D CRISPR-Cas effector)3. Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains and facilitate DNA target recognition. We find that the sgRNA can be truncated by up to ∼25% yet still retain activityin vivo. We also show that despite preferentially targeting an NGG PAM, Cas9d exhibits a unique mechanism for PAM recognition. Finally, we identify the first Cas9d smaller than 800 amino acids exhibiting robust nuclease activity in mammalian cells. Using ancestral sequence reconstruction, we demonstrate that it is possible to generate compact nucleases capable of efficient genome editing by expanding the diversity of Cas9d families. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a molecular blueprint for future rational re-engineering of minimal RNA-guided DNA nucleases.
Use of steric blocking antisense oligonucleotides for the targeted inhibition of junction containing precursor microRNAs
Authors: Ma Sicong , Howden Samantha A. , Keane Sarah C.
Published: April 2024

Antisense oligonucleotides (ASOs) are widely used as therapeutics for neurodegenerative diseases, cancers, and virus infections. One class of ASOs functions to enhance protein expression by sequestering the mature microRNA (miRNA) in a double-stranded structure within the RNA-induced silencing complex (RISC). An alternative approach for the targeted control of gene expression is to use ASOs that bind to the pre-elements of miRNAs (pre-miRNAs) and modulate their enzymatic processing. Here, we demonstrate that ASOs can be used to disrupt a specific structural feature, “junction,” within pre-miR-31 that is important in directing efficient processing by the Dicer/TRBP complex. Furthermore, we extend and validate this strategy to pre-miR-144, which has a similar junction-dependent structure-function relationship. We found that a significant number of human pre-miRNAs are predicted to contain junctions, and validated our ASO approach on several members of this group. Importantly, we also verified the application of junction-targeting ASOs for the specific inhibition of pre-miRNA processingin cell. Our study reemphasizes the important roles of RNA structure in regulating Dicer/TRBP processing of pre-miRNAs and provides the framework to develop structure-informed ASOs that serve to inhibit miRNA production.
Identification and characterization of a synaptic active zone assembly protein
Authors: Lützkendorf J. , Matkovic-Rachid T. , Götz T. , Liu S. , Ghelani T. , Maglione M. , Grieger M. , Putignano S. , Gao L. , Gimber N. , Schmoranzer J. , Stawrakakis A. , Walter A.M. , Heine M. , Wahl M.C. , Mielke T. , Liu F. , Sigrist S.J.
Published: April 2024

At presynaptic active zones (AZs), scaffold proteins play a crucial role in coordinating synaptic vesicle (SV) release and forming intricate nanoarchitectures essential for synaptic function. Despite their suspected importance, factors governing the assembly of nanoscale AZ scaffolds have remained elusive. Here, we identify “Blobby” as a novel regulator of AZ nanopatterning, localized within the AZ scaffold. Genetic loss of the extended Blobby protein led to aberrant accumulation of AZ scaffold proteins (“blobs”) and disrupted the nanoscale architecture of the AZ scaffold, resulting in a significant reduction in the packing density of voltage-gated Ca2+channels at AZs, as observed through intravital single-molecule imaging. This disruption correlated with decreased evoked synaptic currents and SV release probability. Our findings suggest that Blobby plays a crucial role in switching the AZ scaffold into a state which allows to fine-tune the dynamic nanopatterning of Ca2+channels to maintain proper release.
A postnatal molecular switch drives the activity-dependent maturation of parvalbumin interneurons
Authors: Moissidis Monika , Abbasova Leyla , Alis Rafael , Bernard Clémence , Domínguez Yaiza , Qin Shenyue , Kelly Audrey , Oozeer Fazal , Mòdol Laura , Hamid Fursham , Lavender Paul , Flames Nuria , Marín Oscar
Published: April 2024

Cortical neurons are specified during embryonic development but often only acquire their mature properties at relatively late stages of postnatal development. This delay in terminal differentiation is particularly prominent for fast-spiking parvalbumin-expressing (PV+) interneurons, which play critical roles in regulating the function of the cerebral cortex. We found that the maturation of PV+ interneurons is triggered by neuronal activity and mediated by the transcriptional cofactor peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC-1α). Developmental loss of PGC-1α prevents PV+ interneurons from acquiring unique structural, electrophysiological, synaptic, and metabolic features and disrupts their diversification into distinct subtypes. PGC-1α exerts its function as a master regulator of the differentiation of PV+ interneurons by directly controlling gene expression through a transcriptional complex that includes ERRγ and Mef2c. Our results uncover a molecular switch that translates neural activity into a specific transcriptional program promoting the maturation of PV+ interneurons at the appropriate developmental stage.
A functional screen uncovers circular RNAs regulating excitatory synaptogenesis in hippocampal neurons
Authors: Kelly Darren , Bicker Silvia , Winterer Jochen , Nanda Prakruti , Germain Pierre-Luc , Dieterich Christoph , Schratt Gerhard
Published: April 2024

Circular RNAs (circRNAs) are an expanding class of largely unexplored RNAs which are prominently enriched in the mammalian brain. Here, we systematically interrogated their role in excitatory synaptogenesis of rat hippocampal neurons using RNA interference. Thereby, we identified seven circRNAs as negative regulators of excitatory synapse formation, many of which contain high-affinity microRNA binding sites. Knockdown of one of these candidates, circRERE, surprisingly promoted the formation of electrophysiologically silent synapses. Mechanistically, circRERE knockdown resulted in a preferential upregulation of synaptic mRNAs containing binding sites for miR-128-3p because of a reduced protective interaction between miR-128-3p and circRERE. Accordingly, overexpression of circRERE rescued exaggerated synapse formation upon circRERE knockdown in a miR-128-3p binding site-specific manner. Overall, our results uncover circRERE-mediated stabilization of miR-128-3p as a novel mechanism to restrict the formation of silent excitatory synaptic co-clusters and more generally implicate circRNA-dependent microRNA regulation in the control of synapse development and function.
Empirical evidence for the validity of the job crafting scale (JCS) in a Portuguese setting
Authors: Viseu João , Santos Joana , Semedo Carla Santarém , Bakker Arnold B. , Tims Maria , Agrela Sara , Lagareiro Beatriz
Published: April 2024

Purpose

This study aims to adapt and validate the Job Crafting Scale (JCS), a measure based on the conceptualization of job crafting of the job demands–resources theory, for a sample of Portuguese workers and to test its psychometric properties regarding validity (factor, convergent, discriminant, and criterion) and reliability.

Design/methodology/approach

Two subsamples (n1 = 315 and n2 = 329) of Portuguese workers aged 18 years old and over participated in this research. Exploratory factor analysis and confirmatory factor analysis were used to assess the factor structure.

Findings

The results indicated that the Portuguese version of the JCS, with 18 items, has a factor structure composed of four-correlated factors. Furthermore, the results demonstrated the existence of factor, discriminant, and criterion validity, as well as reliability.

Originality/value

This study provides a job crafting measure adapted to the Portuguese language that can serve as a diagnostic tool for workers and organizations.
Whole‐genome resequencing reveals novel sex‐related markers and candidate gene in the Chinese soft‐shelled turtle (Pelodiscus sinensis)
Authors: Zeng Dan , Chen Mengying , Zeng Jiawei , Tu Yangyang , Zhang Yucheng , Tan Meiling , Wang Xiaoqing
Published: April 2024

An apparent sexual dimorphism, such as growth rate and immunocompetence, is observed in the Chinese soft‐shelled turtle (Pelodiscus sinensis). The identification of sex‐related markers and candidate genes holds significance for the sex‐controlled breeding of P. sinensis. In this study, through an integration of whole‐genome resequencing and Sanger sequencing, 21 female‐specific single nucleotide polymorphisms (SNPs) were identified. Based on these SNPs, the rapid and cost‐effective molecular methodologies for genetic sex identification in P. sinensis were established. Of note, 19 validated SNPs are located within the zinc and ring finger 3 (ZNRF3) gene, which has been reported to be testis‐determining in mammals. Cloning of the ZNRF3 gene from P. sinensis (PsZNRF3) and analysis of its expression profile in tissues and in response to sex steroid hormone treatment demonstrated exhibiting a female‐biased expression pattern. These findings not only provide molecular markers for sex‐controlled breeding in P. sinensis but also open up a solid basis for revealing the sex‐determination mechanism of this species.
Breaking Borders, Bridging Fields: Unveiling the Transculturality of Anti‐Asian Racism in a Global Context
Authors: Luo Zhifan , Yang X. Alvin , Li Muyang
Published: April 2024

Despite the recent surge in scholarly attention to anti‐Asian racism, what is largely missing in this growing body of literature is a bridge connecting studies on this subject to the broader field of race and ethnicity studies. In this special issue, we propose to use the concept of transculturality, which is defined as the process of cultural interaction, interpenetration, and hybridization that transcends the traditional borders of individual cultures, to establish this connection. In this introductory article, we first critically review the concepts of culture, interculturality, and multiculturality in the studies of race and ethnicity. Upon this review, we explain how transculturality advances the knowledge of racial and ethnic identity, ideas, and practices. This introduction concludes with an overview of each contribution, setting the stage for a comprehensive exploration of this complex and multifaceted issue. Collectively, this special issue aims to not only provide theoretical and empirical insights into the transculturality of anti‐Asian racism but also build a bridge between the studies of the Asian diaspora and the general research on race and ethnicity.
Prevalence and clinical implications of heightened plastic chemical exposure in pediatric patients undergoing cardiopulmonary bypass
Authors: Guerrelli Devon , Desai Manan , Semaan Youssef , Essa Yasin , Zurakowski David , Cendali Francesca , Reisz Julie , D'Alessandro Angelo , Luban Naomi , Posnack Nikki Gillum
Published: April 2024

Background

Phthalate chemicals are used to manufacture plastic medical products, including many components of cardiopulmonary bypass (CPB) circuits. We aimed to quantify iatrogenic phthalate exposure in pediatric patients undergoing cardiac surgery and examine the link between phthalate exposure and postoperative outcomes.

Study Design and Methods

The study included pediatric patients undergoing (n=122) unique cardiac surgeries at Children's National Hospital. For each patient, a single plasma sample was collected preoperatively and two additional samples were collected postoperatively upon return from the operating room and the morning after surgery. Concentrations of di(2‐ethylhexyl) phthalate (DEHP) and its metabolites were quantified using ultra high‐pressure liquid chromatography coupled to mass spectrometry.

Results

Patients were subdivided into three groups, according to surgical procedure: (1) cardiac surgery not requiring CPB support, (2) cardiac surgery requiring CPB with a crystalloid prime, and (3) cardiac surgery requiring CPB with red blood cells (RBCs) to prime the circuit. Phthalate metabolites were detected in all patients, and postoperative phthalate levels were highest in patients undergoing CPB with an RBC‐based prime. Age‐matched (<1 year) CPB patients with elevated phthalate exposure were more likely to experience postoperative complications. RBC washing was an effective strategy to reduce phthalate levels in CPB prime.

Discussion

Pediatric cardiac surgery patients are exposed to phthalate chemicals from plastic medical products, and the degree of exposure increases in the context of CPB with an RBC‐based prime. Additional studies are warranted to measure the direct effect of phthalates on patient health outcomes and investigate mitigation strategies to reduce exposure.
Skeletal muscle mitochondrial correlates of critical power and W' in healthy active individuals
Authors: Peden Donald L. , Rogers Robert , Mitchell Emma A. , Taylor Suzanne M. , Bailey Stephen J. , Ferguson Richard A.
Published: April 2024

The asymptote (critical power; CP) and curvature constant (W') of the hyperbolic power–duration relationship can predict performance within the severe‐intensity exercise domain. However, the extent to which these parameters relate to skeletal muscle mitochondrial content and respiratory function is not known. Fifteen males (peak O2 uptake, 52.2 ± 8.7 mL kg−1 min−1; peak work rate, 366 ± 40 W; and gas exchange threshold, 162 ± 41 W) performed three to five constant‐load tests to task failure for the determination of CP (246 ± 44 W) and W' (18.6 ± 4.1 kJ). Skeletal muscle biopsies were obtained from the vastus lateralis to determine citrate synthase (CS) activity, as a marker of mitochondrial content, and the ADP‐stimulated respiration (P) and maximal electron transfer (E) through mitochondrial complexes (C) I–IV. The CP was positively correlated with CS activity (absolute CP, r = 0.881, P < 0.001; relative CP, r = 0.751, P = 0.001). The W' was not correlated with CS activity (P > 0.05). Relative CP was positively correlated with mass‐corrected CI + IIE (r = 0.659, P = 0.038), with absolute CP being inversely correlated with CS activity‐corrected CIVE (r = −0.701, P = 0.024). Relative W' was positively correlated with CS activity‐corrected CI + IIP (r = 0.713, P = 0.021) and the phosphorylation control ratio (r = 0.661, P = 0.038). There were no further correlations between CP or W' and mitochondrial respiratory variables. These findings support the assertion that skeletal muscle mitochondrial oxidative capacity is positively associated with CP and that this relationship is strongly determined by mitochondrial content.
Recombinant bivalent subunit vaccine combining truncated VP4 from P[7] and P[23] induces protective immunity against prevalent porcine rotaviruses
Authors: Tang Xuechao , Li Sufen , Zhou Jinzhu , Bian Xianyu , Wang Jianxin , Han Nan , Zhu Xuejiao , Tao Ran , Wang Wei , Sun Min , Li Peng , Zhang Xuehan , Li Bin
Published: April 2024

Porcine rotaviruses (PoRVs) cause severe economic losses in the swine industry. P[7] and P[23] are the predominant genotypes circulating on farms, but no vaccine is yet available. Here, we developed a bivalent subunit PoRV vaccine using truncated versions (VP4*) of the VP4 proteins from P[7] and P[23]. The vaccination of mice with the bivalent subunit vaccine elicited more robust neutralizing antibodies (NAbs) and cellular immune responses than its components, even at high doses. The bivalent subunit vaccine and inactivated bivalent vaccine prepared from strains PoRVs G9P[7] and G9P[23] were used to examine their protective efficacy in sows and suckling piglets after passive immunization. The immunized sows showed significantly elevated NAbs in the serum and colostrum, and the suckling piglets acquired high levels of sIgA antibodies from the colostrum. Challenging subunit-vaccinated or inactivated-vaccinated piglets with homologous virulent strains did not induce diarrhea, except in one or two piglets, which had mild diarrhea. Immunization with the bivalent subunit vaccine and inactivated vaccine also alleviated the microscopic lesions in the intestinal tissues caused by the challenge with the corresponding homologous virulent strain. However, all the piglets in the challenged group displayed mild to watery diarrhea and high levels of viral shedding, whereas the feces and intestines of the piglets in the bivalent subunit vaccine and inactivated vaccine groups had lower viral loads. In summary, our data show for the first time that a bivalent subunit vaccine combining VP4*P[7] and VP4*P[23] effectively protects piglets against the diarrhea caused by homologous virulent strains.

IMPORTANCE

PoRVs are the main causes of diarrhea in piglets worldwide. The multisegmented genome of PoRVs allows the reassortment of VP4 and VP7 genes from different RV species and strains. The P[7] and P[23] are the predominant genotypes circulating in pig farms, but no vaccine is available at present in China. Subunit vaccines, as nonreplicating vaccines, are an option to cope with variable genotypes. Here, we have developed a bivalent subunit candidate vaccine based on a truncated VP4 protein, which induced robust humoral and cellular immune responses and protected piglets against challenge with homologous PoRV. It also appears to be safe. These data show that the truncated VP4-protein-based subunit vaccine is a promising candidate for the prevention of PoRV diarrhea.
Supplemental Material: Paleomagnetic investigation of the basal Maieberg Formation (Namibia) cap carbonate sequence (635 Ma): Implications for Snowball Earth postglacial dynamics
Authors: Pescarini Thales , al. et
Published: April 2024

Complementary rock magnetism information and sample-level directional statistics. 
PECT Composite Defect Detection Algorithm Based on DualGAN
Authors: Gao Ming , Zhou Zhiyan , Huang Jinjie , Ding Kewei
Published: April 2024

To address the problems of insufficient accuracy and slow reconstruction speed of Planar Electrical Capacitance Tomography (PECT) detection of damaged specimens, a Dual Generative Adversarial Networks (DualGAN)-based PECT image defect detection method is proposed in this paper. The improved particle swarm algorithm with adaptive particle number and L2-norm is used to optimize the sensitivity field, combined with the parallel Landweber algorithm to solve the PECT inverse problem to obtain the dielectric constant distribution map. In the DualGAN network, the Unet generator utilizes an Adam-based local attention mechanism to adjust module weights, facilitating feature extraction and the generation of high-quality transformation images of the Landweber dielectric constant distribution. A PatchGAN discriminator is employed to distinguish between transformation images and real images, using the generated transformation images as target images. Experimental results demonstrate that the sensitivity field, enhanced by the improved particle swarm algorithm and L2-norm normalization, achieves better balance. Furthermore, the addition of a network transformation using the Adam-based local attention weight mechanism on the DualGAN network reduces artifacts in the reconstructed images, resulting in more accurate PECT reconstructions. The PECT image defect detection method, integrating DualGAN, an improved particle swarm optimization algorithm, and a local attention mechanism, has made significant strides in addressing challenges related to image reconstruction accuracy and speed. This technological advancement has enhanced the precision and efficiency of defect detection in carbon fiber composite materials, thereby fostering the broader utilization of planar capacitance tomography technology in industrial damage detection and material defect analysis.
Verifiable secret sharing with changeable access structure
Authors: Ghebleh Mohammad , Kanso Ali , Abuhasan Haya
Published: April 2024

We propose a verifiable [Formula: see text]-threshold secret sharing scheme using Lagrange interpolation and secure cryptographic hash functions. This scheme is an improvement of Shao’s scheme [Inform. Sci. 278 (2014) 104–109]. In our variant, verification of shares is achieved through computation of their multiplicative inverses in conjunction with a secure hash function such as SHA-3. This idea results in a significant size reduction, in comparison with Shao’s scheme, to the shares assigned to each participant. Applications of the proposed scheme include sharing of cryptographic keys, access codes, etc. Furthermore, we improve our construction to present a method for secret sharing with adjustable access structure. This can further be extended to a secret sharing scheme with essential participants, where any authorized set of participants must meet a threshold in the number of essential participants it contains. While our proposal has smaller share sizes compared to Shao’s scheme, it also adds the capabilities of changeable parameters and essential participants.
Perception of Healthcare Professionals towards Electronic-Prescribing at University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia: A Cross-Sectional Study
Authors: Sema Faisel Dula , Kebede Abel Getu , Soworsu Girum Zeleke , Mengistu Tigist Tsegaye , Assen Hussien Endris , Muche Esileman Abdela , Abebe Rahel Belete , Kemal Leila Kenzu , Jara Abdisa Gemedi , Seid Abdulwase Mohammed
Published: April 2024

Background. Electronic-prescribing (e-prescribing) is the most recent technological advancement in the medication use process. Its adoption and consequent realization of its potential benefits, however, mainly depend on the healthcare professionals’ perception, willingness to accept, and engagement with the technology. Objectives. This study is aimed at assessing the perception of healthcare professionals towards e-prescribing at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia, from June 1 to August 30, 2021. Method. A cross-sectional study was conducted using a simple random sampling technique. A self-administered questionnaire was used for data collection. Data were entered into and analyzed by using the Statistical Package for the Social Sciences (SPSS® (IBM Corporation)) version 24. Both descriptive and inferential statistics like the Kruskal-Wallis and Mann–Whitney tests were used for data analysis. A statistical significance was declared at a p value < 0.05. Result. From 401 participants, the majority of study participants had a neutral perception of e-prescribing. More than two-thirds (68.8%) of them had a neutral perception towards the perceived usefulness of e-prescribing with a median (interquartile range (IQR)) perceived usefulness of 43.0 (7.0) (maximum score=60). The perceived ease of use of e-prescribing was also neutral in the case of more than three-fourths (79.8%) of participants with a median (IQR) perceived ease of use of 49.0 (6) (maximum score=75). Similarly, more than half (56.6%) of the participants had a neutral perception towards the perceived fitness of e-prescribing with a median (IQR) perceived fitness of 15.0 (2.5) (maximum score=15). The perception of the participants showed a significant difference based on their qualifications and work and computer use experience. Participants who heard about e-prescribing and e-prescribing software had a significantly higher mean rank score of perceived usefulness, perceived ease of use, and perceived fitness of e-prescribing. Participants who previously used e-prescribing had also a significantly higher mean rank score of perceived usefulness. Conclusion and Recommendation. The majority of healthcare professionals had a neutral perception of e-prescribing. The perception of healthcare professionals differs based on their qualifications, work and computer use experience, and their exposure to e-prescribing. The hospital should take all expectations and concerns of all HCPs into consideration and provide experience-sharing opportunities for all healthcare professionals who may potentially be involved in e-prescribing.
Supplementary Table 3 from Inhibition of NEK2 Promotes Chemosensitivity and Reduces KSHV-positive Primary Effusion Lymphoma Burden
Authors: White Maria C. , Wong Jason P. , Damania Blossom
Published: April 2024

Table S3. T-1101 tosylate IC50 values in PEL cell lines
Table S1 from Overcoming Xenoantigen Immunity to Enable Cellular Tracking and Gene Regulation with Immune-competent “NoGlow” Mice
Authors: Trotter Timothy N. , Wilson Andrea , McBane Jason , Dagotto Carina E. , Yang Xiao-Yi , Wei Jun-Ping , Lei Gangjun , Thrash Hannah , Snyder Joshua C. , Lyerly Herbert Kim , Hartman Zachary C.
Published: April 2024

Description of animal models used in the study
Supplementary Table 1 from Inhibition of NEK2 Promotes Chemosensitivity and Reduces KSHV-positive Primary Effusion Lymphoma Burden
Authors: White Maria C. , Wong Jason P. , Damania Blossom
Published: April 2024

Table S1. JH295 IC50 values in PEL cell lines
Figure S4 from Overcoming Xenoantigen Immunity to Enable Cellular Tracking and Gene Regulation with Immune-competent “NoGlow” Mice
Authors: Trotter Timothy N. , Wilson Andrea , McBane Jason , Dagotto Carina E. , Yang Xiao-Yi , Wei Jun-Ping , Lei Gangjun , Thrash Hannah , Snyder Joshua C. , Lyerly Herbert Kim , Hartman Zachary C.
Published: April 2024

Confirming triple-transgenic GFP rtTA-Luc construct in E0771 cells
Supplementary Figure 4 from Inhibition of NEK2 Promotes Chemosensitivity and Reduces KSHV-positive Primary Effusion Lymphoma Burden
Authors: White Maria C. , Wong Jason P. , Damania Blossom
Published: April 2024

Figure S4. NEK2 inhibition in PEL results in decreased expression of the transcription factor, beta-catenin, and the pro-survival protein, Bcl-xL. (A) Western blot for total beta-catenin, phosphorylated beta-catenin (Ser33/Ser37/Thr41, ~92 kDa band), and Bcl-xL in PEL cells treated with or without JH295 for 48h. GAPDH was used as the loading control. Data are representative of three independent biological replicates. (B) Western blot for phosphorylated beta-catenin (Ser33/Ser37/Thr41) and Bcl-xL in PEL cells with intact NEK2 expression (NTC) or depleted NEK2 expression (shRNA). GAPDH was used as the loading control. Data are representative of two-three independent biological replicates. (C) Viability of PEL cells treated with vehicle control (DMSO) or the Bcl-xL inhibitor, A-1155463, for 48h. Data are plotted as individual values from three-four independent biological replicates and normalized to the DMSO control values for each treatment. Data represent mean ± SD and were analyzed using two-way ANOVA with Dunnett’s multiple comparisons. ****p < 0.0001.
Supplementary Figure 1 from Inhibition of NEK2 Promotes Chemosensitivity and Reduces KSHV-positive Primary Effusion Lymphoma Burden
Authors: White Maria C. , Wong Jason P. , Damania Blossom
Published: April 2024

Figure S1. Purity of primary B cells isolated from bulk PBMCs. (A) Flow cytometry analysis of primary B cell purity before (bulk PBMCs) and after (purified B cells) B cell purification from donor PBMCs using the STEMCELL EasySep system. Analyzed populations were gated on single cells and B cells were denoted as CD20-positive CD3-negative, while T cells were denoted as CD3-positive CD20-negative.
FIGURE 2 from Inhibition of NEK2 Promotes Chemosensitivity and Reduces KSHV-positive Primary Effusion Lymphoma Burden
Authors: White Maria C. , Wong Jason P. , Damania Blossom
Published: April 2024

JH295 treatment results in death of PEL cells but has no impact on normal B cells. A, IC50 curves of PEL cell lines treated with a range of JH295 concentrations and normalized to the DMSO control values. Curves were fitted using nonlinear regression and are connected by means. Data are four independent biological replicates, each performed in triplicate. See also Supplementary Table S1. B, Quantification of PEL cell death via Trypan blue staining following JH295 treatment. Individual data points from three independent biological replicates are plotted as mean ± SD and analyzed using one-way ANOVA with Dunnett multiple comparisons. ****, P < 0.0001; **, P = 0.0003; *, P = 0.04. C, PEL cell viability via Trypan blue count following mock or JH295 treatment. Individual data points from three independent biological replicates are plotted as mean ± SD and analyzed using one-way ANOVA with Dunnett multiple comparisons. ****, P < 0.0001; **, P < 0.007. D, IC50 curve of bulk PBMCs treated with JH295 and normalized to the DMSO control values, overlayed on the PEL data from A. Curves were fitted using nonlinear regression and are connected by means. Data are three individual biological replicates, each performed in triplicate, using two unique PBMC donors. E, Cell viability of PBMCs versus PEL cells treated with JH295, each normalized to the corresponding DMSO control values. Individual data points from two independent biological replicates using two unique PBMC donors and performed in triplicate are plotted as mean + SEM and analyzed using one-way ANOVA with Dunnett multiple comparisons. ****, P < 0.0001. F, Cell viability of purified primary B cells treated with either DMSO or JH295. Data representing fold change in luminescence relative to the DMSO control, are plotted as individual data points of three to six independent biological replicates using three to six unique cell donors, and analyzed using unpaired two-tailed t test. ns, not significant. See also Supplementary Fig. S1. G, Cell viability of purified primary B cells following mock or LPS stimulation. Data are fold change in luminescence relative to mock-stimulated cells, are plotted as individual data points of three to six independent biological replicates using three-six unique cell donors, and analyzed using unpaired two-tailed t test. **, P = 0.0031. H, Cell viability of stimulated purified primary B cells treated with and without JH295. Data are fold change in luminescence relative to the LPS control, are plotted as individual data points of three to six independent biological replicates using three to six unique cell donors, and analyzed using unpaired two-tailed t test. ns, not significant.
FIGURE 2 from Overcoming Xenoantigen Immunity to Enable Cellular Tracking and Gene Regulation with Immune-competent “NoGlow” Mice
Authors: Trotter Timothy N. , Wilson Andrea , McBane Jason , Dagotto Carina E. , Yang Xiao-Yi , Wei Jun-Ping , Lei Gangjun , Thrash Hannah , Snyder Joshua C. , Lyerly Herbert Kim , Hartman Zachary C.
Published: April 2024

Mutant GFP and luciferase induce immune responses comparable with wild-type (WT) proteins. A, WT male Balb/c mice were vaccinated with Ad encoding WT or mutant copies of GFP (ΔT64; n = 5/group) and serum antibody responses were measured after 3 weeks. Mice showed equivalent anti-GFP responses whether vaccinated with WT or mutant GFP. B, WT female C57Bl/6 mice were vaccinated with Ad-GFP-Luc WT or Ad-Luc mutant (G315A; n = 5/group) and serum antibody responses were measured after 3 weeks revealing similar levels of anti-Luc antibodies. P values for A, B are at 1:50 dilution by two-way ANOVA with Tukey multiple comparisons test. C, Male WT Balb/c mice were vaccinated with Ad encoding WT or mutant GFP (ΔT64) or Luc (H245R) and anti-GFP or -Luc T-cell responses in the spleens were detected after 3 weeks via ELISpot. Both WT and mutant forms of GFP and Luc were able to elicit robust T-cell responses compared with mice naïve for the respective antigen. P values were determined by two-way ANOVA with Tukey post hoc analysis. D, E0771 GFP-Luc cells were implanted in MFPs of female WT C57Bl/6 mice and were vaccinated with Ad encoding WT GFP, mutant GFP (ΔT64), WT Luc, mutant Luc (ΔH245), or LacZ control (n = 5 per group) after three days. Compared with LacZ control vaccination, GFP WT/mutant, or Luc WT/mutant vaccines resulted in a comparable reduction in tumor growth. P values are at time of euthanasia by two-way ANOVA with Tukey multiple comparisons test. All P values represent mean ± SEM.
TABLE 4 from Artificial Intelligence–Assisted Cancer Status Detection in Radiology Reports
Authors: Arya Ankur , Niederhausern Andrew , Bahadur Nadia , Shah Neil J. , Nichols Chelsea , Chatterjee Avijit , Philip John
Published: April 2024

Classification metric of the multiclass classifier model to predict cancer status using one versus rest approach on held out test data
La literatura peruana en proceso: ecos de Mariátegui en el “Primer Encuentro de Narradores Peruanos”
Authors: Cunha Roseli Barros
Published: April 2024

En el “Primer Encuentro de Narradores Peruanos” ocurrido en Arequipa, 1965, se reunieron autores y críticos literarios de por lo menos dos distintas generaciones. A lo largo de tres debates discutieron temas relacionados a la creación literaria canónica y a la producción de la época. El renombrado intelectual José Carlos Mariátegui, así como la corriente del indigenismo, fueron varias veces citados por los participantes. La propuesta en este artículo es, a partir de las actas de los debates (publicadas en 1969 y republicadas en 1986) y de las reflexiones posteriores de críticos como Chang-Rodríguez (1986), Sánchez (1976), Escajadillo ([1980] 2004) y Sobrevilla (2012), realizar un breve rastreo de la influencia del Amauta y del indigenismo en las declaraciones y polémicas suscitadas en el encuentro.
Mais que trezentos anos de beleza – uma entrevista com Angela-Lago
Authors: Araújo Hanna
Published: April 2024

Entrevista com Angela-Lago.
Livros, infâncias e materialidades: uma reflexão sobre mediação de leitura
Authors: Feltre Camila , Rogério Cristiane
Published: April 2024

O artigo busca discutir sobre a materialidade dos livros e suas possíveis relações com os leitores, aproximando-se de temas como acessibilidade, experiência de leitura, intimidade e formas de mediação. Os “livros ilustrados”, ou picture books em inglês, são livros que podem nos causar dúvidas sobre como manuseá-los e explorar seus limites devido a seus diferentes formatos, sendo eles sanfonados, inseridos em caixas, com conteúdo na frente e no verso, podendo também ter capa dura e ser muito grandes ou muito pequenos. Colocamos como parte deste grupo – e também do desafio na mediação – os livros em que é necessário apresentar o objeto “livro” para narrar uma história, porque o texto está sob uma perspectiva e a imagem sob outra, por exemplo. Porém, entendemos que estes livros, em que a intenção com a materialidade está mais clara, podem afetar as mediações possíveis com outros livros, pessoas, mundos. Afinal, dos bebês aos adultos, como podemos convidá-los à leitura com estes livros-objetos? Como notamos as sutilezas da materialidade como parte da narrativa? Como propor esta dança da leitura que estes livros permitem? Leituras que vêm e vão, abrem e fecham, mostram surpresas e instigam leituras sem fim. Sinta-se convidado à leitura deste artigo.
The struggle for industrial democracy in Sweden: A sociological macro-meso analysis 1960–2020
Authors: Tengblad Stefan , Andersson Thomas
Published: April 2024

Sweden has the reputation of being one of the most progressive countries in the world concerning work-life development and industrial democracy. In this article, an analytical overview of the development in these areas is provided, which includes the antecedents, major events, actor positioning and also the broad-term outcomes. Two major reform movements are described: one aiming to create a radically different work-life where workers control their own work with a power balance between labour and capital, and one a reformist movement aiming to create a degree of co-determination and a more engaging work-life without any major changes in power relations. The case shows that the radical movement was not able to generate radical change and that the reformistic movement achieved only partial success. The outcome over time has been a decreased interest in work-life development where co-determination practices are heavily institutionalized but perhaps do not provide better conditions for workers than in many other advanced industrial countries with a lesser degree of formal co-determination.
Renal calculus composition analysis using dual-energy CT: a prospective observational study
Authors: Johnson Jithin P. , Dhall Arushi , Chawla Arun , Prakashini K
Published: April 2024

Background

To analyze preoperatively the composition of renal calculi using dual-energy computed tomography (DECT) and compare it with reference standard biochemical stone analysis.

Methods

Eighty-one participants who were diagnosed with renal calculi underwent DECT at 80 kVp and 140 kVp. Spectral analysis was performed, and the energy map generated was used to classify the calculus based on available preset data. Average Hounsfield units (HU) were calculated for the two energy levels, and ratio of HU was derived (DE ratio) and calculus was categorized into different stone compositions. Hounsfield units of each calculus was measured at 120 kVp standard dose CT, and Hounsfield density (HU/largest transverse diameter) was derived. Comparison of results of spectral analysis and DE ratio was done and correlated with the biochemical laboratory analysis as reference standard wherever available.

Results

Spectral analysis and CT prediction of stone were performed for all 81 patients. CT prediction of stone based on DE ratio into “uric acid,” “struvite,” “calcium oxalate” and “calcium carbonate apatite” was performed. Assessment of stone composition by biochemical analysis was done for 65 patients who eventually underwent PCNL for stone extraction.

Both DE ratio and spectral analysis were able to differentiate calculus into various types based on composition with statistically significant p values. However, spectral analysis proved to be marginally better in renal stone characterization particularly for mixed stones. The DE ratio for uric acid stones was derived as 0.9–1.1, 0.9–2.3 for mixed stones and 1.0–2.4 for calcium stones.

Conclusions

Spectral analysis promises a practical approach to predicting calculus composition preoperatively, thereby avoiding unnecessary surgical intervention.
Genome-wide analysis and expression profiling of the HD-ZIP gene family in kiwifruit
Authors: Ye Kai-yu , Li Jie-wei , Wang Fa-ming , Gao Jian-you , Liu Cui-xia , Gong Hong-juan , Qi Bei-bei , Liu Ping-ping , Jiang Qiao-sheng , Tang Jian-min , Mo Quan-hui
Published: April 2024

The homeodomain-leucine zipper (HD-Zip) gene family plays a pivotal role in plant development and stress responses. Nevertheless, a comprehensive characterization of the HD-Zip gene family in kiwifruit has been lacking. In this study, we have systematically identified 70 HD-Zip genes in the Actinidia chinensis (Ac) genome and 55 in the Actinidia eriantha (Ae) genome. These genes have been categorized into four subfamilies (HD-Zip I, II, III, and IV) through rigorous phylogenetic analysis. Analysis of synteny patterns and selection pressures has provided insights into how whole-genome duplication (WGD) or segmental may have contributed to the divergence in gene numbers between these two kiwifruit species, with duplicated gene pairs undergoing purifying selection. Furthermore, our study has unveiled tissue-specific expression patterns among kiwifruit HD-Zip genes, with some genes identified as key regulators of kiwifruit responses to bacterial canker disease and postharvest processes. These findings not only offer valuable insights into the evolutionary and functional characteristics of kiwifruit HD-Zips but also shed light on their potential roles in plant growth and development.
Vineyard microclimate alterations induced by black inter-row mulch through transcriptome reshaped the flavoromics of cabernet sauvignon grapes
Authors: Tian Meng-Bo , Wang Yu , Gao Xiao-Tong , Lu Hao-Cheng , Zhang Qi , Han Xiao , Li Hui-Qing , Shi Ning , Duan Chang-Qing , Wang Jun
Published: April 2024

Background

Weed control is essential for agricultural floor management in vineyards and the inter-row mulching is an eco-friendly practice to inhibit weed growth via filtering out photosynthetically active radiation. Besides weed suppression, inter-row mulching can influence grapevine growth and the accumulation of metabolites in grape berries. However, the complex interaction of multiple factors in the field challenges the understanding of molecular mechanisms on the regulated metabolites. In the current study, black geotextile inter-row mulch (M) was applied for two vintages (2016–2017) from anthesis to harvest. Metabolomics and transcriptomics analysis were conducted in two vintages, aiming to provide insights into metabolic and molecular responses of Cabernet Sauvignon grapes to M in a semi-arid climate.

Results

Upregulation of genes related to photosynthesis and heat shock proteins confirmed that M weakened the total light exposure and grapes suffered heat stress, resulting in lower sugar-acid ratio at harvest. Key genes responsible for enhancements in phenylalanine, glutamine, ornithine, arginine, and C6 alcohol concentrations, and the downward trend in ε-viniferin, anthocyanins, flavonols, terpenes, and norisoprenoids in M grapes were identified. In addition, several modules significantly correlated with the metabolic biomarkers through weighted correlation network analysis, and the potential key transcription factors regulating the above metabolites including VviGATA11, VviHSFA6B, and VviWRKY03 were also identified.

Conclusion

This study provides a valuable overview of metabolic and transcriptomic responses of M grapes in semi-arid climates, which could facilitate understanding the complex regulatory network of metabolites in response to microclimate changes.
Focal ischemic myocardial fibrosis assessed by late gadolinium enhancement cardiovascular magnetic resonance in patients with hypertrophic cardiomyopathy
Authors: Zhi Yang , Gui Fu-dan , Xue Meng , Long Yi-tian , Miao Wen , Yi You , Gao Liang-chao , Bing Fu , Pan Shu-yue
Published: April 2024

Background

In patients with hypertrophic cardiomyopathy (HCM), ischemic myocardial fibrosis assessed by late gadolinium enhancement (I-LGE) using cardiovascular magnetic resonance (CMR) have been reported. However, the clinical significance of I-LGE has not been completely understood. We aim to evaluate the I-LGE differ phenotypically from HCM without LGE or nonischemic myocardial fibrosis assessed by late gadolinium enhancement (NI-LGE) in the left ventricle (LV).

Methods

The patients with HCM whom was underwent CMR were enrolled, using cine cardiac magnetic resonance to evaluate LV function and LGE to detect the myocardial fibrosis. Three groups were assorted: 1) HCM without LGE; 2) HCM with LGE involved the subendocardial layer was defined as I-LGE; 3) HCM with LGE not involved the subendocardial layer was defined as NI-LGE.

Results

We enrolled 122 patients with HCM in the present study. LGE was detected in 58 of 122 (48%) patients with HCM, and 22 (18%) of patients reported I-LGE. HCM with I-LGE had increased higher left ventricular mass index (LVMI) (P < 0.0001) than HCM with NI-LGE or without LGE. In addition, HCM with I-LGE had a larger LV end- systolic volume (P = 0.045), lower LV ejection fraction (LVEF) (P = 0.026), higher LV myocardial mass (P < 0.001) and thicker LV wall (P < 0.001) more than HCM without LGE alone. The I-LGE were significantly associated with LVEF (OR: 0.961; P = 0.016), LV mass (OR: 1.028; P < 0.001), and maximal end-diastolic LVWT (OR: 1.567; P < 0.001). On multivariate analysis, LVEF (OR: 0.948; P = 0.013) and maximal end-diastolic LVWT (OR: 1.548; P = 0.001) were associated with higher risk for I-LGE compared to HCM without LGE. Noticeably, the maximal end-diastolic LVWT (OR: 1.316; P = 0.011) was the only associated with NI-LGE compared to HCM without LGE.

Conclusions

I-LGE is not uncommon in patients with HCM. HCM with I-LGE was associated with significant LV hypertrophy, extensive LGE and poor LV ejection fraction. We should consider focal ischemic myocardial fibrosis when applying LGE to risk stratification for HCM.
Impact of the COVID-19 outbreak and interventions on hand, foot and mouth disease in Zhengzhou, China, 2014–2022: a retrospective study
Authors: Jia Wanyu , Zhang Xue , Sun Ruiyang , Li Peng , Song Chunlan
Published: April 2024

Background

Since December 2019, COVID-19 has spread rapidly around the world, and studies have shown that measures to prevent COVID-19 can largely reduce the spread of other infectious diseases. This study explored the impact of the COVID-19 outbreak and interventions on the incidence of HFMD.

Methods

We gathered data on the prevalence of HFMD from the Children’s Hospital Affiliated to Zhengzhou University. An autoregressive integrated moving average model was constructed using HFMD incidence data from 2014 to 2019, the number of cases predicted from 2020 to 2022 was predicted, and the predicted values were compared with the actual measurements.

Results

From January 2014 to October 2022, the Children’s Hospital of Zhengzhou University admitted 103,995 children with HFMD. The average number of cases of HFMD from 2020 to 2022 was 4,946, a significant decrease from 14,859 cases from 2014 to 2019. We confirmed the best ARIMA (2,0,0) (1,1,0)12 model. From 2020 to 2022, the yearly number of cases decreased by 46.58%, 75.54%, and 66.16%, respectively, compared with the forecasted incidence. Trends in incidence across sexes and ages displayed patterns similar to those overall.

Conclusions

The COVID-19 outbreak and interventions reduced the incidence of HFMD compared to that before the outbreak. Strengthening public health interventions remains a priority in the prevention of HFMD.