bluuebunny/crossref_metadata_2025 huggingface dataset:
What Did They Learn? Objective Assessment Tools Show Mixed Effects of Training on Science Communication Behaviors
Authors: Capers Robert S. , Oeldorf-Hirsch Anne , Wyss Robert , Burgio Kevin R. , Rubega Margaret A.
Published: February 2022

There is widespread agreement about the need to assess the success of programs training scientists to communicate more effectively with non-professional audiences. However, there is little agreement about how that should be done. What do we mean when we talk about “effective communication”? What should we measure? How should we measure it? Evaluation of communication training programs often incorporates the views of students or trainers themselves, although this is widely understood to bias the assessment. We recently completed a 3-year experiment to use audiences of non-scientists to evaluate the effect of training on STEM (Science, Technology, Engineering and Math) graduate students’ communication ability. Overall, audiences rated STEM grad students’ communication performance no better after training than before, as we reported in Rubega et al. 2018. However, audience ratings do not reveal whether training changed specific trainee communication behaviors (e.g., jargon use, narrative techniques) even if too little to affect trainees’ overall success. Here we measure trainee communication behavior directly, using multiple textual analysis tools and analysis of trainees’ body language during videotaped talks. We found that student use of jargon declined after training but that use of narrative techniques did not increase. Flesch Reading Ease and Flesch-Kincaid Grade Level scores, used as indicators of complexity of sentences and word choice, were no different after instruction. Trainees’ movement of hands and hesitancy during talks was correlated negatively with audience ratings of credibility and clarity; smiling, on the other hand, was correlated with improvement in credibility, clarity and engagement scores given by audience members. We show that objective tools can be used to measure the success of communication training programs, that non-verbal cues are associated with audience judgments, and that an intensive communication course does change some, if not all, communication behaviors.
Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes
Authors: Chen Si , Guo Xiaofei , He Xiaoyun , Di Ran , Zhang Xiaosheng , Zhang Jinlong , Wang Xiangyu , Chu Mingxing
Published: February 2022

The pituitary is a remarkably dynamic organ with roles in hormone (FSH and LH) synthesis and secretion. In animals with the FecB (fecundity Booroola) mutation, the pituitary experiences hormone fluctuations during the follicular–luteal transition, which is implicated in the expression and regulation of many genes and regulators. Long non-coding RNAs (lncRNAs) are a novel type of regulatory factors for the reproductive process. Nevertheless, the expression patterns of lncRNAs and their roles in FecB-mediated follicular development and ovulation remain obscure. Thus, we profiled the pituitary transcriptome during the follicular (F, 45 h after evacuation vaginal sponges) and luteal (L, 216 h after evacuation vaginal sponges) phases in FecB-mutant homozygous (BB) and wild-type (WW) Small Tail Han sheep. We identified 78 differentially expressed genes (DEGs) and 41 differentially expressed lncRNAs (DELs) between BB_F and BB_L, 32 DEGs and 26 DELs between BB_F and WW_F, 16 DEGs and 29 DELs between BB_L and WW_L, and 50 DEGs and 18 DELs between WW_F and WW_L. The results of real-time quantitative PCR (RT-qPCR) correlated well with the transcriptome data. In both the follicular and luteal phases, DEGs (GRID2, glutamate ionotropic receptor delta type subunit 2; ST14, ST14 transmembrane serine protease matriptase) were enriched in hormone synthesis, secretion, and action. MSTRG.47470 and MSTRG.101530 were the trans-regulated elements of ID1 (inhibitor of DNA binding 3, HLH protein) and the DEG ID3 (inhibitor of DNA binding 3, HLH protein), and EEF2 (eukaryotic translation elongation factor 2), respectively; these factors might be involved in melatonin and peptide hormone secretion. In the FecB-mediated follicular phase, MSTRG.125392 targeted seizure-related 6 homolog like (SEZ6L), and MSTRG.125394 and MSTRG.83276 targeted the DEG KCNQ3 (potassium voltage-gated channel subfamily Q member 3) in cis, while MSTRG.55861 targeted FKBP4 (FKBP prolyl isomerase 4) in trans. In the FecB-mediated luteal phase, LOC105613905, MSTRG.81536, and MSTRG.150434 modulated TGFB1, SMAD3, OXT, respectively, in trans. We postulated that the FecB mutation in pituitary tissue elevated the expression of certain genes associated with pituitary development and hormone secretion. Furthermore, this study provides new insights into how the pituitary regulates follicular development and ovulation, illustrated by the effect of the FecB mutation.
Roadmap for Long-Term Macroplastic Monitoring in Rivers
Authors: van Emmerik Tim , Vriend Paul , Copius Peereboom Eric
Published: February 2022

Macroplastic pollution in and around rivers negatively impacts human livelihood, and aquatic ecosystems. Monitoring data are crucial for better understanding and quantifying this problem, and for the design of effective intervention strategies. However, current monitoring efforts are often of short duration, or study single river compartments. We present a “Roadmap” to overcome the challenges related to the design and implementation of long-term riverine macroplastic monitoring strategies. This “Roadmap” can help accelerating the process of achieving structural monitoring through providing a stepwise approach, which links monitoring goals and research questions to the data and methods required to answer them. We identify four monitoring goals: 1) policy, 2) knowledge development, 3) operations, and 4) solutions. Linked to these, we provide a non-exhaustive list of 12 globally common research questions that are important to answer to reach these goals. The “Roadmap” takes these questions and links them to development levels of monitoring methods for each river compartment: 1) method development, 2) baseline assessment, and 3) long-term monitoring. At each level, specific questions can only be answered if the level is achieved for specific river compartments. For questions at higher levels, the previous levels need to be achieved first. This creates a clear stepwise approach to solve open challenges. With the “Roadmap”, we provide a new tool to support decision-making and planning of specific projects by policy makers. The “Roadmap” is a clear and stepwise, yet flexible framework that allows to add and remove elements based on new insights, available resources, and other relevant changes.
Dynamic Supervision and Control of VOCs Emission From China’s Furniture Manufacturing Based on Big Data and IoT
Authors: Chen Zi-Gui , Wu Wei-Ping , Li Jing , Zeng Yu-Heng
Published: February 2022

How to effectively monitor and prevent volatile organic compounds (VOCs) in furniture manufacturing has become the key to solving the dilemma between furniture industry development and public health. Based on the combination of VOCs emission standards and prevention policies of China’s furniture manufacturing, this article explores the path of dynamic monitoring, intelligent prevention, and control of VOCs embedded in furniture manufacturing with big data and IoT and puts forward feasible VOCs control technologies in the whole process of China’s furniture manufacturing, including source, process, and end. Herein, dynamic monitoring, intelligent prevention, and control of VOCs in furniture manufacturing have important reference significance for the prevention and control of VOCs in other industries, such as coal chemical industry, rubber products, engineering machinery, and coiled materials.
Seasonal Variation in Terrestrial Invertebrate Subsidies to Tropical Streams and Implications for the Feeding Ecology of Hart’s Rivulus (Anablepsoides hartii)
Authors: Owens David C. , Heatherly Thomas N. , Eskridge Kent M. , Baxter Colden V. , Thomas Steven A.
Published: February 2022

Terrestrial invertebrates are important subsidies to fish diets, though their seasonal dynamics and importance to tropical stream consumers are particularly understudied. In this year-round study of terrestrial invertebrate input to two Trinidadian headwater streams with different forest canopy densities, we sought to (a) measure the mass and composition of terrestrial inputs with fall-in traps to evaluate the influences of seasonality, canopy cover, and rainfall intensity, and; (b) compare terrestrial and benthic prey importance to Anablepsoides hartii (Hart’s Rivulus), the dominant invertivorous fish in these streams, by concurrently measuring benthic and drifting invertebrate standing stocks and the volume and composition of invertebrates in Rivulus guts throughout the year. The biomass of terrestrial invertebrate fall-in was 53% higher in the wet versus dry season; in particular, ant input was 320% higher. Ant biomass fall-in also increased with the density of canopy cover among sampling locations within both streams. Greater precipitation correlated with increased ant inputs to the more open-canopied stream and increased inputs of winged insects in the more closed canopy stream. Concurrently, the biomass of benthic invertebrates was reduced by more than half in the wet season in both streams. We detected no differences in the total volume of terrestrial prey in Rivulus diets between seasons, though ants were a greater proportion of their diet in the wet season. In contrast, benthic prey were nearly absent from Rivulus diets in the wet season in both streams. We conclude that terrestrial invertebrates are a substantial year-round prey subsidy for invertivores in tropical stream ecosystems like those we studied, which may contrast to most temperate streams where such terrestrial inputs are significantly reduced in the cold season. Interestingly, the strongest seasonal pattern in these tropical streams was observed in benthic invertebrate biomass which was greatly reduced and almost absent from Rivulus diets during the wet season. This pattern is essentially the inverse of the pattern observed in many temperate streams and highlights the need for additional studies in tropical ecosystems to better understand how spatial and temporal variation in terrestrial subsidies and benthic prey populations combine to influence consumer diets and the structure of tropical stream food webs.
Genome-Wide Identification and Characterization of GASA Gene Family in Nicotiana tabacum
Authors: Li Zhaowu , Gao Junping , Wang Genhong , Wang Shuaibin , Chen Kai , Pu Wenxuan , Wang Yaofu , Xia Qingyou , Fan Xiaorong
Published: February 2022

The gibberellic acid stimulated Arabidopsis (GASA) gene family is critical for plant growth, development, and stress response. GASA gene family has been studied in various plant species, however, the GASA gene family in tobacco (Nicotiana tabacum) have not been characterized in detail. In this study, we identified 18 GASA genes in the tobacco genome, which were distributed to 13 chromosomes. All the proteins contained a conserved GASA domain and highly specific 12-cysteine residues at the C-terminus. Phylogenetic analysis divided the NtGASA genes into three well-conserved subfamilies. Synteny analysis suggested that tandem and segmental duplications played an important role in the expansion of the NtGASA gene family. Cis-elements analysis showed that NtGASA genes might influence different phytohormone and stress responses. Tissue expression analysis revealed that NtGASA genes displayed unique or distinct expression patterns in different tissues, suggesting their potential roles in plant growth and development. We also found that the expression of NtGASA genes were mostly regulated by abscisic and gibberellic acid, signifying their roles in the two phytohormone signaling pathways. Overall, these findings improve our understanding of NtGASA genes and provided useful information for further studies on their molecular functions.
Development and Validation of a Three-Gene Prognostic Signature Based on Tumor Microenvironment for Gastric Cancer
Authors: Wang Qian , Li Xiangmei , Wang Yahui , Qiu Jiayue , Wu Jiashuo , He Yalan , Li Ji , Kong Qingfei , Han Junwei , Jiang Ying
Published: February 2022

Gastric cancer (GC), which has high morbidity and low survival rate, is one of the most common malignant tumors in the world. The increasing evidences show that the tumor microenvironment (TME) is related to the occurrence and progression of tumors and the prognosis of patients. In this study, we aimed to develop a TME-based prognostic signature for GC. We first identified the differentially expressed genes (DEGs) related to the TME using the Wilcoxon rank-sum test in a training set of GC. Univariate Cox regression analysis was used to identify prognostic-related DEGs. To decrease the overfitting, we performed the least absolute shrinkage and selection operator (LASSO) regression to reduce the number of signature genes and obtained three genes (LPPR4, ADAM12, NOX4). Next, the multivariate Cox regression was performed to construct the risk score model, and a three-gene prognostic signature was developed. According to the signature, patients were classified into high-risk and low-risk groups with significantly different survival. The signature was then applied to three independent validated sets and obtained the same results. We conducted the time-dependent Receiver Operating Characteristic (ROC) curve analysis to evaluate our signature. We further evaluated the differential immune characters between high-risk and low-risk patients to reveal the potential immune mechanism of the impact on the prognosis of the model. Overall, we identified a three-gene prognostic signature based on TME to predict the prognosis of patients with GC and facilitate the development of a precise treatment strategy.
Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome
Authors: Yao Yining , Sun Kuan , Yang Qinrui , Zhou Zhihan , Shao Chengchen , Qian Xiaoqin , Tang Qiqun , Xie Jianhui
Published: February 2022

Multiple mutational events of insertion/deletion occurring at or around InDel sites could form multi-allelic InDels and multi-InDels (abbreviated as MM-InDels), while InDels with random DNA sequences could imply a unique mutation event at these loci. In this study, preliminary investigation of MM-InDels with random sequences was conducted using high-throughput phased data from the 1000 Genomes Project. A total of 3,599 multi-allelic InDels and 6,375 multi-InDels were filtered with multiple alleles. A vast majority of the obtained MM-InDels (85.59%) presented 3 alleles, which implies that only one secondary insertion or deletion mutation event occurred at these loci. The more frequent presence of two adjacent InDel loci was observed within 20 bp. MM-InDels with random sequences presented an uneven distribution across the genome and showed a correlation with InDels, SNPs, recombination rate, and GC content. The average allelic frequencies and prevalence of multi-allelic InDels and multi-InDels presented similar distribution patterns in different populations. Altogether, MM-InDels with random sequences can provide useful information for population resolution.
CCR6 and CXCR6 Identify the Th17 Cells With Cytotoxicity in Experimental Autoimmune Encephalomyelitis
Authors: Hou Lifei , Yuki Koichi
Published: February 2022

Due to the plasticity of IL-17-producing CD4 T cells (Th17 cells), a long-standing challenge in studying Th17-driven autoimmune is the lack of specific surface marker to identify the pathogenic Th17 cells in vivo. Recently, we discovered that pathogenic CD4 T cells were CXCR6 positive in experimental autoimmune encephalomyelitis (EAE), a commonly used Th17-driven autoimmune model. Herein, we further revealed that peripheral CXCR6+CD4 T cells contain a functionally distinct subpopulation, which is CCR6 positive and enriched for conventional Th17 molecules (IL-23R and RORγt) and cytotoxic signatures. Additionally, spinal cord-infiltrating CD4 T cells were highly cytotoxic by expressing Granzyme(s) along with IFNγ and GM-CSF. Collectively, this study suggested that peripheral CCR6+CXCR6+CD4 T cells were Th17 cells with cytotoxic property in EAE model, and highlighted the cytotoxic granzymes for EAE pathology.
An Immunoproteomic Survey of the Antibody Landscape: Insights and Opportunities Revealed by Serological Repertoire Profiling
Authors: Ionov Steven , Lee Jiwon
Published: February 2022

Immunoproteomics has emerged as a versatile tool for analyzing the antibody repertoire in various disease contexts. Until recently, characterization of antibody molecules in biological fluids was limited to bulk serology, which identifies clinically relevant features of polyclonal antibody responses. The past decade, however, has seen the rise of mass-spectrometry-enabled proteomics methods that have allowed profiling of the antibody response at the molecular level, with the disease-specific serological repertoire elucidated in unprecedented detail. In this review, we present an up-to-date survey of insights into the disease-specific immunological repertoire by examining how quantitative proteomics-based approaches have shed light on the humoral immune response to infection and vaccination in pathogenic illnesses, the molecular basis of autoimmune disease, and the tumor-specific repertoire in cancer. We address limitations of this technology with a focus on emerging potential solutions and discuss the promise of high-resolution immunoproteomics in therapeutic discovery and novel vaccine design.
Topographical Relationship Between Acute Macular Neuroretinopathy and Choroidal Watershed Zone or Patchy Choroidal Filling
Authors: Duan Jialiang , An Jianbin , Li Minhao , Zhang Zhengwei , Zhou Liang , Yin Pengfei , Ma Jingxue , Shang Qingli
Published: February 2022

Purpose

To study the topographical relationship between acute macular neuroretinopathy (AMN) lesions and the choroidal watershed zone (CWZ) or patchy choroidal filling (PCF) using multimodal imaging.

Methods

Lesions in patients diagnosed with AMN were clinically examined using multimodal imaging, including fundus photography, near-infrared reflectance imaging, spectral-domain optical coherence tomography (OCT), fluorescein angiography, indocyanine green angiography, OCT angiography, and microperimetry. The topographical relationship between AMN and the CWZ or PCF was evaluated.

Results

Seven eyes of six patients were included in the study. The mean age of the patients was 35.8 ± 11.7 years. The AMN lesions were collocated with the CWZ in five eyes and the PCF in one eye. Among these eyes, three had complete patterns, and three had partial patterns. Only one eye showed no topographical relationship between AMN and the CWZ or PCF.

Conclusion

The colocation of AMN and CWZ/PCF suggests that the AMN lesions were within an area with a dual-watershed zone: the watershed zone between the retinal deep capillary plexus and choriocapillaris, and the choroidal watershed zone or patchy choroidal filling. This retinal area was highly vulnerable to hypoperfusion. Our results suggest a novel pathophysiological mechanism for AMN.
Association Between Frailty and Inpatient Services Utilization Among Older Adults in Rural China: The Mediating Role of Multimorbidity
Authors: Yuan Yemin , Li Jie , Fu Peipei , Zhou Chengchao , Li Shixue
Published: February 2022

Introduction

Developed and developing countries have different health systems and disease patterns. There is little evidence that frailty is related to inpatient services utilization in developing countries. In addition, the underlying mechanism of this relationship also remains unclear. This study aimed to examine the association between frailty and inpatient services utilization, and further explore whether multimorbidity play a mediating role in this association.

Methods

A total of 3,242 rural older adults aged 60 and older were included in the analysis. Frailty was measured by the physical frailty phenotype (PFP). Multimorbidity and inpatient services utilization was measured based on participants' self-report and validated by village doctors. Ordered logistic regression analyses were performed to examine the association between frailty, multimorbidity and inpatient services utilization. Bootstrap analysis was further to explore the mediation effect of multimorbidity on frailty and inpatient services utilization.

Results

The utilization of inpatient services was 20.1% (one: 15.8%, two or more: 4.3%). The prevalence of prefrailty and frailty was 64.7 and 18.1%, respectively. Frail older adults experienced a higher risk of multimorbidity and inpatient services utilization. Multimorbidity partially mediated the association between frailty and inpatient services utilization [95% confidence interval (CI): 0.005-0.016, p < 0.001]. The mediating effect of multimorbidity accounted for 19.0% of the total effect.

Conclusions

Among Chinese rural older adults, frailty is associated with higher inpatient services utilization, and multimorbidity mediates this association. Recommendations are to increase frailty risk screening, chronic disease monitoring, and to do timely interventions.
Immigrant IBD Patients in Spain Are Younger, Have More Extraintestinal Manifestations and Use More Biologics Than Native Patients
Authors: Gutiérrez Ana , Zapater Pedro , Ricart Elena , González-Vivó María , Gordillo Jordi , Olivares David , Vera Isabel , Mañosa Míriam , Gisbert Javier P. , Aguas Mariam , Sánchez-Rodríguez Eugenia , Bosca-Watts Maia , Laredo Viviana , Camps Blau , Marín-Jiménez Ignacio , Zabana Yamile , Martín-Arranz María Dolores , Muñoz Roser , Navarro Mercè , Sierra Eva , Madero Lucía , Vela Milagros , Pérez-Calle José Lázaro , Sainz Empar , Calvet Xavier , Arias Lara , Morales Victor , Bermejo Fernando , Fernández-Salazar Luis , Van Domselaar Manuel , De Castro Luisa , Rodríguez Cristina , Muñoz-Villafranca Carmen , Lorente Rufo , Rivero Montserrat , Iglesias Eva , Herreros Belén , Busquets David , Riera Joan , Martínez-Montiel María Pilar , Roldón Marta , Roncero Oscar , Hinojosa Esther , Sierra Mónica , Barrio Jesús , De Francisco Ruth , Huguet José , Merino Olga , Carpio Daniel , Ginard Daniel , Muñoz Fernando , Piqueras Marta , Almela Pedro , Argüelles-Arias Federico , Alcaín Guillermo , Bujanda Luis , Manceñido Noemí , Lucendo Alfredo J. , Varela Pilar , Rodríguez-Lago Iago , Ramos Laura , Sempere Laura , Sesé Eva , Barreiro-de Acosta Manuel , Domènech Eugeni , Francés Rubén
Published: February 2022

Background

Previous studies comparing immigrant ethnic groups and native patients with IBD have yielded clinical and phenotypic differences. To date, no study has focused on the immigrant IBD population in Spain.

Methods

Prospective, observational, multicenter study comparing cohorts of IBD patients from ENEIDA-registry who were born outside Spain with a cohort of native patients.

Results

We included 13,524 patients (1,864 immigrant and 11,660 native). The immigrants were younger (45 ± 12 vs. 54 ± 16 years, p < 0.001), had been diagnosed younger (31 ± 12 vs. 36 ± 15 years, p < 0.001), and had a shorter disease duration (14 ± 7 vs. 18 ± 8 years, p < 0.001) than native patients. Family history of IBD (9 vs. 14%, p < 0.001) and smoking (30 vs. 40%, p < 0.001) were more frequent among native patients. The most prevalent ethnic groups among immigrants were Caucasian (41.5%), followed by Latin American (30.8%), Arab (18.3%), and Asian (6.7%). Extraintestinal manifestations, mainly musculoskeletal affections, were more frequent in immigrants (19 vs. 11%, p < 0.001). Use of biologics, mainly anti-TNF, was greater in immigrants (36 vs. 29%, p < 0.001). The risk of having extraintestinal manifestations [OR: 2.23 (1.92–2.58, p < 0.001)] and using biologics [OR: 1.13 (1.0–1.26, p = 0.042)] was independently associated with immigrant status in the multivariate analyses.

Conclusions

Compared with native-born patients, first-generation-immigrant IBD patients in Spain were younger at disease onset and showed an increased risk of having extraintestinal manifestations and using biologics. Our study suggests a featured phenotype of immigrant IBD patients in Spain, and constitutes a new landmark in the epidemiological characterization of immigrant IBD populations in Southern Europe.
Multi-Gene Phylogeny of the Ciliate Genus Trachelostyla (Ciliophora, Hypotrichia), With Integrative Description of Two Species, Trachelostyla multinucleata Spec. nov. and T. pediculiformis (Cohn, 1866)
Authors: Zhang Tengyue , Shao Chen , Zhang Tengteng , Song Weibo , Vd’ačný Peter , Al-Farraj Saleh A. , Wang Yurui
Published: February 2022

Many hypotrich genera, including Trachelostyla, are taxonomically challenging and in a need of integrative revision. Using morphological data, molecular phylogenetic analyses, and internal transcribed spacer 2 (ITS2) secondary structures, we attempt to cast more light on species relationships within the genus Trachelostyla. The present multifaceted approach reveals that (1) a large-sized species with numerous macronuclear nodules, isolated from sandy littoral sediments in southern China, is new to science and is endowed here with a name, T. multinucleata spec. nov.; (2) two other Chinese populations previously identified as T. pediculiformis represent undescribed species; and (3) multigene phylogeny is more robust than single-gene trees, recovering the monophyly of the genus Trachelostyla with high bootstrap frequency. Additionally, ITS2 secondary structures and the presence of compensatory base changes in helices A and B indicate the presence of four distinct taxa within the molecularly studied members of the genus Trachelostyla. Molecular data are more suitable for delimitation of Trachelostyla species than morphological characters as interspecific pairwise genetic distances of small subunit (18S) rDNA, ITS1-5.8S-ITS2, and large subunit (28S) rDNA sequences do not overlap, whereas ranges of multiple morphometric features might transcend species boundaries.
Engineering Infrequent DNA Nicking Endonuclease by Fusion of a BamHI Cleavage-Deficient Mutant and a DNA Nicking Domain
Authors: Xu Shuang-yong
Published: February 2022

Strand-specific DNA nicking endonucleases (NEases) typically nick 3–7 bp sites. Our goal is to engineer infrequent NEase with a >8 bp recognition sequence. A BamHI catalytic-deficient mutant D94N/E113K was constructed, purified, and shown to bind and protect the GGATCC site from BamHI restriction. The mutant was fused to a 76-amino acid (aa) DNA nicking domain of phage Gamma HNH (gHNH) NEase. The chimeric enzyme was purified, and it was shown to nick downstream of a composite site 5′ GGATCC-N(4-6)-AC↑CGR 3′ (R, A, or G) or to nick both sides of BamHI site at the composite site 5′ CCG↓GT-N5-GGATCC-N5-AC↑CGG 3′ (the down arrow ↓ indicates the strand shown is nicked; the up arrow↑indicates the bottom strand is nicked). Due to the attenuated activity of the small nicking domain, the fusion nickase is active in the presence of Mn2+ or Ni2+, and it has low activity in Mg2+ buffer. This work provided a proof-of-concept experiment in which a chimeric NEase could be engineered utilizing the binding specificity of a Type II restriction endonucleases (REases) in fusion with a nicking domain to generate infrequent nickase, which bridges the gap between natural REases and homing endonucleases. The engineered chimeric NEase provided a framework for further optimization in molecular diagnostic applications.
Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333T Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species
Authors: Oh Eom-Ji , Hwang In Sun , Park In Woong , Oh Chang-Sik
Published: February 2022

Clavibacter michiganensis, a Gram-positive, plant-pathogenic bacterium belonging to Actinobacteria, is a causal agent of bacterial canker in tomatoes. Although LMG7333T is the type strain of C. michiganensis, it has not been used in many studies, probably because of a lack of the complete genome sequence being available. Therefore, in this study, the complete genome sequence of this type strain was obtained, and comparative genome analysis was conducted with the genome sequences of two other C. michiganensis strains and type strains of Clavibacter species, of which their complete genome sequences are available. C. michiganensis LMG7333T carries one chromosome and two plasmids, pCM1 and pCM2, like two other C. michiganensis strains. All three chromosomal DNA sequences were almost identical. However, the DNA sequences of two plasmids of LMG7333T are similar to those of UF1, but different from those of NCPPB382, indicating that both plasmids carry distinct gene content among C. michiganensis strains. Moreover, 216 protein-coding sequences (CDSs) were only present in the LMG7333T genome compared with type strains of other Clavibacter species. Among these 216 CDSs, approximately 83% were in the chromosome, whereas others were in both plasmids (more than 6% in pCM1 and 11% in pCM2). However, the ratio of unique CDSs of the total CDSs in both plasmids were approximately 38% in pCM1 and 30% in pCM2, indicating that the high gene content percentage in both plasmids of C. michiganensis are different from those of other Clavibacter species, and plasmid DNAs might be derived from different origins. A virulence assay with C. michiganensis LMG7333T using three different inoculation methods, root-dipping, leaf-clipping, and stem injection, resulted in typical disease symptoms, including wilting and canker in tomato. Altogether, our results indicate that two plasmids of C. michiganensis carry distinct gene content, and the genome information of the type strain LMG7333T will help to understand the genetic diversity of the two plasmids of Clavibacter species, including C. michiganensis.
Update on the Pathogenesis, Clinical Diagnosis, and Treatment of Hirayama Disease
Authors: Wang Hongwei , Tian Ye , Wu Jianwei , Luo Sushan , Zheng Chaojun , Sun Chi , Nie Cong , Xia Xinlei , Ma Xiaosheng , Lyu Feizhou , Jiang Jianyuan , Wang Hongli
Published: February 2022

Hirayama disease (HD) is characterized by the juvenile onset of unilateral or asymmetric weakness and amyotrophy of the hand and ulnar forearm and is most common in males in Asia. A perception of compliance with previous standards of diagnosis and treatment appears to be challenged, so the review is to update on HD. First, based on existing theory, the factors related to HD includes, (1) cervical cord compression during cervical flexion, (2) immunological factors, and (3) other musculoskeletal dynamic factors. Then, we review the clinical manifestations: typically, (1) distal weakness and wasting in one or both upper extremities, (2) insidious onset and initial progression for 3–5 years, (3) coarse tremors in the fingers, (4) cold paralysis, and (5) absence of objective sensory loss; and atypically, (1) positive pyramidal signs, (2) atrophy of the muscles of the proximal upper extremity, (3) long progression, and (4) sensory deficits. Next, updated manifestations of imaging are reviewed, (1) asymmetric spinal cord flattening, and localized lower cervical spinal cord atrophy, (2) loss of attachment between the posterior dural sac and the subjacent lamina, (3) forward displacement of the posterior wall of the cervical dural sac, (4) intramedullary high signal intensity in the anterior horn cells on T2-weighted imaging, and (5) straight alignment or kyphosis of cervical spine. Thus, the main manifestations of eletrophysiological examinations in HD include segmental neurogenic damages of anterior horn cells or anterior roots of the spinal nerve located in the lower cervical spinal cord, without disorder of the sensory nerves. In addition, definite HD needs three-dimensional diagnostic framework above, while probable HD needs to exclude other diseases via “clinical manifestations” and “electrophysiological examinations”. Finally, the main purpose of treatment is to avoid neck flexion. Cervical collar is the first-line treatment for HD, while several surgical methods are available and have achieved satisfactory results. This review aimed to improve the awareness of HD in clinicians to enable early diagnosis and treatment, which will enable patients to achieve a better prognosis.
Contextual Modulation of Feedforward Inputs to Primary Visual Cortex
Authors: Lankow Benjamin S. , Usrey W. Martin
Published: February 2022

Throughout the brain, parallel processing streams compose the building blocks of complex neural functions. One of the most salient models for studying the functional specialization of parallel visual streams in the primate brain is the lateral geniculate nucleus (LGN) of the dorsal thalamus, through which the parvocellular and magnocellular channels, On-center and Off-center channels, and ipsilateral and contralateral eye channels are maintained and provide the foundation for cortical processing. We examined three aspects of neural processing in these streams: (1) the relationship between extraclassical surround suppression, a widespread visual computation thought to represent a canonical neural computation, and the parallel channels of the LGN; (2) the magnitude of binocular interaction in the parallel streams; and (3) the magnitude of suppression elicited by perceptual competition (binocular rivalry) in each stream. Our results show that surround suppression is almost exclusive to Off channel cells; further, we found evidence for two different components of monocular surround suppression—an early-stage suppression exhibited by all magnocellular cells, and a late-stage suppression exhibited only by Off cells in both the parvocellular and magnocellular pathways. This finding indicates that stream-specific circuits contribute to surround suppression in the primate LGN and suggests a distinct role for suppression in the Off channel to the cortex. We also examined the responses of LGN neurons in alert macaque monkeys to determine whether neurons that supply the cortex with visual information are influenced by stimulation of both eyes. Our results demonstrate that LGN neurons are not influenced by stimulation of the non-dominant eye. This was the case when dichoptic stimuli were presented to classical receptive fields of neurons, extraclassical receptive fields of neurons, and when stimuli were appropriate to produce the perception of binocular rivalry.
Associations of the Dietary Iron, Copper, and Selenium Level With Metabolic Syndrome: A Meta-Analysis of Observational Studies
Authors: Ding Jun , Liu Qi , Liu Ze , Guo Hongbin , Liang Jieyu , Zhang Yi
Published: February 2022

Background

Epidemiological studies have investigated the associations of dietary iron, copper, and selenium level with metabolic syndrome (MetS). However, their results are conflicting. This meta-analysis of observational study was, therefore, employed to investigate the associations above.

Methods

A comprehensive literature search was employed using PubMed, Web of Science, Embase, and Scopus database up to October 2021 (no restriction was set for the initiate time). The pooled relative risk (RR) of MetS for the highest vs. lowest dietary iron, copper, and selenium level was estimated, respectively.

Results

A total of 14 observational studies (55,131 participants) were identified as meeting the inclusion criteria. Specifically, 7 studies were related to the dietary iron level. The overall multivariable adjusted RR demonstrated that the dietary iron level was positively associated with MetS (RR = 1.27, 95% CI: 1.12–1.44; p < 0.001). With regard to the dietary copper level, 7 studies were included for meta-analysis. The overall multivariable adjusted RR showed that the dietary copper level was inversely associated with MetS (RR = 0.85, 95% CI: 0.78–0.93; p < 0.001). In addition, 4 studies were specified for the dietary selenium level. The overall multivariable adjusted RR indicated that the dietary selenium level was inversely associated with MetS (RR = 0.77, 95% CI: 0.63–0.95; p = 0.01) as well.

Conclusion

Our results suggest that the dietary iron level is positively associated with MetS, whereas a negative association between the dietary copper and selenium level and MetS is obtained. Further large well-designed prospective cohort studies are warranted to elaborate on the issues examined in this study.
Acute Myeloid Leukemia With CEBPA Mutations: Current Progress and Future Directions
Authors: Su Long , Shi Yuan-Yuan , Liu Zeng-Yan , Gao Su-Jun
Published: February 2022

Mutations in CCAAT enhancer binding protein A gene (CEBPA) are one of the common genetic alterations in acute myeloid leukemia (AML). Recently, the emergence of new evidence makes it necessary to reconsider the subsets and treatment of AML patients with CEBPA mutations. This review will summarize the history of research progress of CEBPA mutations in AML, the heterogeneities of AML with CEBPA double mutations (CEBPAdm), and two special subtypes of CEBPA mutated AML. We will discuss the treatment of AML with CEBPA mutations as well, and finally propose a new algorithm for the treatment of these patients, including both familial and sporadic CEBPA mutated AML patients. This review may be beneficial for further investigation and optimizing clinical management of AML patients with CEBPA mutations.
Levels and Health Risk of Pesticide Residues in Chinese Herbal Medicines
Authors: Wang Ying , Gou Yan , Zhang Lei , Li Chun , Wang Zhao , Liu Yuanxi , Geng Zhao , Shen Mingrui , Sun Lei , Wei Feng , Zhou Juan , Gu Lihong , Jin Hongyu , Ma Shuangcheng
Published: February 2022

In the present study, 168 pesticides in 1,017 samples of 10 Chinese herbal medicines (CHMs) were simultaneously determined by high-performance liquid (HPLC-MS/MS) and gas (GC-MS/MS) chromatography–tandem mass spectrometry. A total of 89.2% of the samples encompassed one or multiple pesticide residues, and the residue concentrations in 60.5% of samples were less than 0.02 mg kg−1, revealing the relatively low residue levels. The hazard quotient and hazard index methods were used to estimate the health risk for consumers. For a more accurate risk assessment, the exposure frequency and exposure duration of CHMs were involved into the exposure assessment, which was obtained from a questionnaire data of 20,917 volunteers. The results of chronic, acute, and cumulative risk assessment indicated that consumption of CHMs is unlikely to pose a health risk to consumers. Ranking the risk of detected pesticides revealed that phorate, BHC, triazophos, methidathion, terbufos, and omethoate posed the highest risk. Our results also showed that pollution of the aboveground medicinal part was more serious. Although exposure to pesticides in tested CHMs was below dangerous levels, more strict controlled management should be carried out for banned pesticides due to the high detection rate and illegal use in the actual planting practice.
α-Conotoxin TxIB Improved Behavioral Abnormality and Changed Gene Expression in Zebrafish (Danio rerio) Induced by Alcohol Withdrawal
Authors: Mao Kailin , Li Xiaodan , Chen Zongde , Dong Xiaoqian , Zhangsun Dongting , Zhu Xiaopeng , Luo Sulan
Published: February 2022

Background and Purpose: Alcohol use disorder (AUD) is a serious public health issue and affects the lives of numerous people. Previous studies have shown a link between nicotinic acetylcholine receptors (nAChR) and alcohol addiction. However, the role of α6β2* nAChR in alcohol addiction remains obscure, and whether α6β2* nAChR can be used as a potential drug target for alcohol withdrawal need to be studied.

Methods: Zebrafish (Danio rerio) were exposed to 0.2% alcohol for 14 days followed by 7 days of repeated withdrawal and then retro-orbitally injected with α-conotoxin TxIB (a selective α6β2* nAChR antagonist). Open Field Test was applied to characterize zebrafish behavior parameters. The monoamine neurotransmitter amounts and their mRNA expression in the zebrafish brain were identified using ELISA and quantitative real-time PCR (RT-PCR). RNA-sequencing (RNA-seq) and subsequent bioinformatics analysis were employed to explore the potential network regulation of TxIB after alcohol withdrawal.

Results: The max speed in the center area of the Open Field Test was significantly higher in the withdrawal group whereas TxIB injection corrected this abnormality. The amount and mRNA expression of monoamine neurotransmitters did not change significantly after alcohol withdrawal and TxIB administration. RNA sequencing of zebrafish brain indicated a total of 657 genes showed aberrant expression and among which 225 were reversed after TxIB injection. These reversed genes were significantly enriched in the calcium ion binding pathway and the gene expression profile was further validated by RT-PCR.

Conclusion: Our finding suggests α-conotoxin TxIB improved behavioral abnormality induced by alcohol-withdrawal, and changed gene expression mainly in the calcium signaling pathway. Therefore, α-conotoxin TxIB is expected to become a potential therapeutic agent for alcohol withdrawal.
Circulating Collagen Metabolites and the Enhanced Liver Fibrosis (ELF) Score as Fibrosis Markers in Systemic Sclerosis
Authors: Chen Chen , Wang Lingbiao , Wu Jinfeng , Lu Meijuan , Yang Sen , Ye Wenjing , Guan Ming , Liang Minrui , Zou Hejian
Published: February 2022

Background: Serum fibrosis markers for systemic sclerosis (SSc) remain limited. The Enhanced Liver Fibrosis (ELF) score is a collagen marker set consisting of procollagen type III amino terminal propeptide (PIIINP), tissue inhibitor of metalloproteinases 1 (TIMP-1), and hyaluronic acid (HA). This longitudinal study aimed to examine the performance of the ELF score and its single analytes as surrogate outcome measures of fibrosis in SSc.

Methods: Eighty-five SSc patients fulfilling the 2013 ACR/EULAR criteria with the absence of chronic liver diseases were enrolled. Serum PIIINP, TIMP-1, HA, and the ELF score were measured and correlated with clinical variables including the modified Rodnan skin score (mRSS) and interstitial lung disease (ILD). Twenty SSc patients underwent a follow-up serological testing and mRSS evaluation during treatment with immunosuppressants and/or anti-fibrotic drugs.

Results: Serum PIIINP, TIMP-1, and ELF score were significantly higher in patients with SSc than in healthy controls [PIIINP: 10.31 (7.83–14.10) vs. 5.61 (4.69–6.30), p < .001; TIMP-1: 110.73 (66.21–192.45) vs. 61.81 (48.86–85.24), p < .001; ELF: 10.34 (9.91–10.86) vs. 9.68 (9.38–9.99), p < .001]. Even higher levels of PIIINP, TIMP-1, and ELF score were found in patients with diffuse cutaneous SSc than those with limited cutaneous SSc. At baseline, both PIIINP and ELF score showed good correlation with mRSS (PIIINP: r = .586, p < .001; ELF: r = .482, p < .001). Longitudinal analysis showed that change in PIIINP positively correlated with change in mRSS (r = 0.701, p = .001), while change in ELF score were not related, in a statistical context, to the change in mRSS (ELF: r = .140, p = .555). Serum TIMP-1 was significantly higher in SSc patients with ILD, compared to the matched group of patients without ILD [109.45 (93.05–200.09) vs. 65.50 (40.57–110.73), p = 0.007].

Conclusion: In patients with SSc, the ELF score well correlates with the extent of skin fibrosis, while serum PIIINP is a sensitive marker for longitudinal changes of skin fibrosis. In the future, circulating collagen metabolites may potentially be used to evaluate therapeutic effects of anti-fibrotic treatments in the disease.
Review of Incoherent Digital Holography: Applications to Multidimensional Incoherent Digital Holographic Microscopy and Palm-Sized Digital Holographic Recorder—Holosensor
Authors: Tahara Tatsuki
Published: February 2022

We review advancements in incoherent digital holography (IDH) with an image sensor and its applications to multidimensional microscopy and a palm-sized hologram recorder termed “holosensor”. There are two types of representative IDH technique: IDH with a structured illumination and a single photodetector termed optical scanning holography and self-interference IDH. The latter IDH is a technique to obtain an incoherent digital hologram by modulating an incoherent light wave between an object and an image sensor. Multidimensional information such as three-dimensional space and wavelengths is simultaneously recorded without changing optical filters by introducing interferometric techniques invented in laser holography. Applications to high-speed color-multiplexed holographic fluorescence microscopy, single-shot incoherent full-color holographic microscopy with white light, and a palm-sized multidimensional incoherent hologram recorder have been developed using multidimensional IDH systems. Schematics and experimental results obtained using IDH techniques, incoherent holographic microscopy systems, and compact IDH systems are introduced.
Engineering Macromolecular Trafficking Into the Citrus Vasculature
Authors: Calderón-Pérez Berenice , Ramírez-Pool José Abrahán , Núñez-Muñoz Leandro Alberto , Vargas-Hernández Brenda Yazmín , Camacho-Romero Abel , Lara-Villamar Mariana , Jiménez-López Domingo , Xoconostle-Cázares Beatriz , Ruiz-Medrano Roberto
Published: February 2022

The plant vasculature is a central organ for long-distance transport of nutrients and signaling molecules that coordinate vegetative and reproductive processes, and adaptation response mechanisms to biotic and abiotic stress. In angiosperms, the sieve elements are devoid of nuclei, thus depending on the companion cells for the synthesis of RNA and proteins, which constitute some of the systemic signals that coordinate these processes. Massive analysis approaches have identified proteins and RNAs that could function as long-range signals in the phloem translocation stream. The selective translocation of such molecules could occur as ribonucleoprotein complexes. A key molecule facilitating this movement in Cucurbitaceae is the phloem protein CmPP16, which can facilitate the movement of RNA and other proteins into the sieve tube. The CmPP16 ortholog in Citrus CsPP16 was characterized in silico to determine its potential capacity to associate with other mobile proteins and its enrichment in the vascular tissue. The systemic nature of CsPP16 was approached by evaluating its capacity to provide phloem-mobile properties to antimicrobial peptides (AMPs), important in the innate immune defense. The engineering of macromolecular trafficking in the vasculature demonstrated the capacity to mobilize translationally fused peptides into the phloem stream for long-distance transport. The translocation into the phloem of AMPs could mitigate the growth of Candidatus Liberibacter asiaticus, with important implications for crop defense; this system also opens the possibility of translocating other molecules to modulate traits, such as plant growth, defense, and plant productivity.