bluuebunny/crossref_metadata_2025 huggingface dataset:
Physiological Characteristics and Comparative Secretome Analysis of Morchella importuna Grown on Glucose, Rice Straw, Sawdust, Wheat Grain, and MIX Substrates
Authors: Cai YingLi , Ma XiaoLong , Zhang QianQian , Yu FuQiang , Zhao Qi , Huang Wei , Song JiaXin , Liu Wei
Published: May 2021

Morels (Morchella sp.) are economically important edible macro-fungi, which can grow on various synthetic or semi-synthetic media. However, the complex nutritional metabolism and requirements of these fungi remain ill-defined. This study, based on the plant biomass commonly used in the artificial cultivation of morels, assessed and compared the growth characteristics and extracellular enzymes of Morchella importuna cultivated on glucose, rice straw, sawdust, wheat grain, and a mixture of equal proportions of the three latter plant substrates (MIX). M. importuna could grow on all five tested media but displayed significant variations in mycelial growth rate, biomass, and sclerotium yield on the different media. The most suitable medium for M. importuna was wheat and wheat-containing medium, followed by glucose, while rice straw and sawdust were the least suitable. A total of 268 secretory proteins were identified by liquid chromatography coupled with tandem mass spectrometry detection. Functional classification and label-free comparative analysis of these proteins revealed that carbohydrate-active enzyme (CAZYme) proteins were the predominant component of the secretome of M. importuna, followed by protease, peptidase, and other proteins. The abundances of CAZYme proteins differed among the tested media, ranging from 64% on glucose to 88% on rice straw. The CAZYme classes of glycoside hydrolases and carbohydrate-binding module were enriched in the five secretomes. Furthermore, the enzyme activities of CMCase, lignase, amylase, xylase, pNPCase, and pNPGase were detected during the continuous culture of M. importuna in MIX medium, and the relative expression of the corresponding genes were detected by quantitative real-time PCR. The combined data of growth potential, secretome, extracellular enzyme activity, and gene expression on different substrates inferred that M. importuna was weak in lignocellulose degradation but a good starch decomposer. Specifically, in terms of the degradation of cellulose, the ability to degrade cellulose into oligosaccharides was weaker compared with further degradation into monosaccharides, and this might be the speed-limiting step of cellulose utilization in M. importuna. In addition, M. importuna had a strong ability to decompose various hemicellulose glycosidic bonds, especially α- and β-galactosidase. Only a very few lignin-degradation-related proteins were detected, and these were in low abundance, consistent with the presence of weak lignin degradation ability. Furthermore, the presence of lipase and chitinase implied that M. importuna was capable of decomposition of its own mycelia in vitro. The study provides key data that facilitates a further understanding of the complex nutritional metabolism of M. importuna.
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities
Authors: Iablokov Stanislav N. , Novichkov Pavel S. , Osterman Andrei L. , Rodionov Dmitry A.
Published: May 2021

The profiling of 16S rRNA revolutionized the exploration of microbiomes, allowing to describe community composition by enumerating relevant taxa and their abundances. However, taxonomic profiles alone lack interpretability in terms of bacterial metabolism, and their translation into functional characteristics of microbiomes is a challenging task. This bottom-up approach minimally requires a reference collection of major metabolic traits deduced from the complete genomes of individual organisms, an accurate method of projecting these traits from a reference collection to the analyzed amplicon sequence variants (ASVs), and, ultimately, an approach to a microbiome-wide aggregation of predicted individual traits into physiologically relevant cumulative metrics to characterize and compare multiple microbiome samples. In this study, we extended a previously introduced computational approach for the functional profiling of complex microbial communities, which is based on the concept of binary metabolic phenotypes encoding the presence (“1”) or absence (“0”) of various measurable physiological properties in individual organisms that are termed phenotype carriers or non-carriers, respectively. Derived from complete genomes via metabolic reconstruction, binary phenotypes provide a foundation for the prediction of functional traits for each ASV identified in a microbiome sample. Here, we introduced three distinct mapping schemes for a microbiome-wide phenotype prediction and assessed their accuracy on the 16S datasets of mock bacterial communities representing human gut microbiome (HGM) as well as on two large HGM datasets, the American Gut Project and the UK twins study. The 16S sequence-based scheme yielded a more accurate phenotype predictions, while the taxonomy-based schemes demonstrated a reasonable performance to warrant their application for other types of input data (e.g., from shotgun metagenomics or qPCR). In addition to the abundance-weighted Community Phenotype Indices (CPIs) reflecting the fractional representation of various phenotype carriers in microbiome samples, we employ metrics capturing the diversity of phenotype carriers, Phenotype Alpha Diversity (PAD) and Phenotype Beta Diversity (PBD). In combination with CPI, PAD allows to classify the robustness of metabolic phenotypes by their anticipated stability in the face of potential environmental perturbations. PBD provides a promising approach for detecting the metabolic features potentially contributing to disease-associated metabolic traits as illustrated by a comparative analysis of HGM samples from healthy and Crohn’s disease cohorts.
Infection of Two Heterologous Mycoviruses Reduces the Virulence of Valsa mali, a Fungal Agent of Apple Valsa Canker Disease
Authors: Yang Shian , Dai Ruoyin , Salaipeth Lakha , Huang Lili , Liu Jie , Andika Ida Bagus , Sun Liying
Published: May 2021

Mycovirus infection has been widely shown to attenuate the virulence of phytopathogenic fungi. Valsa mali is an agriculturally important fungus that causes Valsa canker disease in apple trees. In this study, two unrelated mycoviruses [Cryphonectria hypovirus 1 (CHV1, genus Hypovirus, and single-stranded RNA) and Mycoreovirus 1 (MyRV1, genus Mycoreovirus, double-stranded RNA)] that originated from Cryphonectria parasitica (chestnut blight fungus) were singly or doubly introduced into V. mali via protoplast fusion. CHV1 and MyRV1 stably infected V. mali and caused a reduction in fungal vegetative growth and virulence. Co-infection of both viruses further reduced the virulence of V. mali but compromised the stability of CHV1 infection and horizontal transmission through hyphal anastomosis. Infections of MyRV1 and, to a lesser extent, CHV1 up-regulated the transcript expression of RNA silencing-related genes in V. mali. The accumulation of CHV1 (but not MyRV1) was elevated by the knockdown of dcl2, a key gene of the RNA silencing pathway. Similarly, the accumulation of CHV1 and the efficiency of the horizontal transmission of CHV1 during co-infection was restored by the knockdown of dcl2. Thus, CHV1 and MyRV1 are potential biological control agents for apple Valsa canker disease, but co-infection of both viruses has a negative effect on CHV1 infection in V. mali due to the activation of antiviral RNA silencing by MyRV1 infection.
An Inventory of CiaR-Dependent Small Regulatory RNAs in Streptococci
Authors: Jabbour Nancy , Lartigue Marie-Frédérique
Published: May 2021

Bacteria adapt to the different environments encountered by rapid and tightly controlled regulations involving complex networks. A first line of control is transcriptional with regulators such as two-component systems (TCSs) that respond to physical and chemical perturbations. It is followed by posttranscriptional regulations in which small regulatory RNAs (sRNAs) may affect RNA translation. Streptococci are opportunistic pathogens for humans and farm animals. The TCS CiaRH is highly conserved among this genus and crucial in bacterial survival under stressful conditions. In several streptococcal species, some sRNAs belong to the CiaRH regulon and are called csRNAs for cia-dependent sRNAs. In this review, we start by focusing on the Streptococcus species harboring a CiaRH TCS. Then the role of CiaRH in streptococcal pathogenesis is discussed in the context of recent studies. Finally, we give an overview of csRNAs and their functions in Streptococci with a focus on their importance in bacterial adaptation and virulence.
A Turntable Setup for Testing Visual and Tactile Grasping Movements in Non-human Primates
Authors: Buchwald Daniela , Schaffelhofer Stefan , Dörge Matthias , Dann Benjamin , Scherberger Hansjörg
Published: May 2021

Grasping movements are some of the most common movements primates do every day. They are important for social interactions as well as picking up objects or food. Usually, these grasping movements are guided by vision but proprioceptive and haptic inputs contribute greatly. Since grasping behaviors are common and easy to motivate, they represent an ideal task for understanding the role of different brain areas during planning and execution of complex voluntary movements in primates. For experimental purposes, a stable and repeatable presentation of the same object as well as the variation of objects is important in order to understand the neural control of movement generation. This is even more the case when investigating the role of different senses for movement planning, where objects need to be presented in specific sensory modalities. We developed a turntable setup for non-human primates (macaque monkeys) to investigate visually and tactually guided grasping movements with an option to easily exchange objects. The setup consists of a turntable that can fit six different objects and can be exchanged easily during the experiment to increase the number of presented objects. The object turntable is connected to a stepper motor through a belt system to automate rotation and hence object presentation. By increasing the distance between the turntable and the stepper motor, metallic components of the stepper motor are kept at a distance to the actual recording setup, which allows using a magnetic-based data glove to track hand kinematics. During task execution, the animal sits in the dark and is instructed to grasp the object in front of it. Options to turn on a light above the object allow for visual presentation of the objects, while the object can also remain in the dark for exclusive tactile exploration. A red LED is projected onto the object by a one-way mirror that serves as a grasp cue instruction for the animal to start grasping the object. By comparing kinematic data from the magnetic-based data glove with simultaneously recorded neural signals, this setup enables the systematic investigation of neural population activity involved in the neural control of hand grasping movements.
MBOAT7-TMC4 rs641738 Is Not Associated With the Risk of Hepatocellular Carcinoma or Persistent Hepatitis B Infection
Authors: Wang Peng , Li Ying , Li Lu , Zhong Rong , Shen Na
Published: May 2021

Objective

A hot genetic variant, rs641738 within the membrane-bound O-acyltransferase domain containing 7(MBOAT7) and transmembrane channel-like 4 (TMC4), was recently reported to be associated with several liver diseases. However, the results remain controversial. Therefore, this study aimed to explore the role of MBOAT7-TMC4 rs641738 in the risk of hepatocellular carcinoma (HCC) and persistent hepatitis B virus (HBV) infection.

Methods

We first conducted a case-control study that included 779 HCC cases and 1412 cancer-free controls. Controls consisted of 678 persistent HBV carriers and 734 spontaneously recovered subjects. The gene variant rs641738 was genotyped using the MassARRAY platform. The results were analyzed in five genetic models using multivariate logistic regression analyses. Next, we performed a systematic review and meta-analysis to further explore the role of this variant in HCC risk.

Results

The results suggested no association between MBOAT7-TMC4 rs641738 and HCC risk in most genetic models (all P > 0.05). Although a marginally significant association was observed in TT vs. CC (P = 0.037) and the recessive models (P = 0.044). The meta-analysis of 2135 HCC cases and 4388 controls supported that this variant was not related to HCC risk, even in the TT vs. CC and recessive models. We also determined that this variant did not influence persistent HBV infection.

Conclusion

Our work highlights that MBOAT7-TMC4 rs641738 is not associated with the risk of HCC or persistent HBV infection. This study provides some clues to identify the “truth” of potential disease-related genetic factors in the post-genome era.
A Prospective Investigation of Bispecific CD19/22 CAR T Cell Therapy in Patients With Relapsed or Refractory B Cell Non-Hodgkin Lymphoma
Authors: Zhang Ying , Li Jiaqi , Lou Xiaoyan , Chen Xiaochen , Yu Zhou , Kang Liqing , Chen Jia , Zhou Jin , Zong Xiangping , Yang Zhen , Li Minghao , Xu Nan , Jia Sixun , Geng Hongzhi , Chen Guanghua , Dai Haiping , Tang Xiaowen , Yu Lei , Wu Depei , Li Caixia
Published: May 2021

Background

The use of T cells expressing chimeric antigen receptor (CAR T) engineered to target CD19 constitutes breakthrough treatment for relapsed or refractory B cell non-Hodgkin lymphoma (R/R B-NHL). Despite improved outcomes, high relapse rate remains a challenge to overcome. Here, we report the clinical results and the pharmacokinetics of bispecific CD19/22 CAR T in patients with R/R B-NHL.

Methods

We performed a prospective, single-arm study of bispecific CD19/22 CAR T cells in R/R B-NHL. We analyzed the safety and efficacy and investigated the kinetic profiles of the CAR T cells. CAR transgene levels were measured using quantitative polymerase chain reaction, and correlation analyses of pharmacodynamic markers and product characteristics, disease conditions, clinical efficacy and adverse events were performed.

Results

From August 2017 to September 2020, a total of 32 patients with CD19/22 CAR T administration were analyzed. The overall response rate was 79.3%, and the complete response rate was 34.5%. The progression-free survival (PFS) and overall survival (OS) rates at 12 months were 40.0% and 63.3%, respectively. Among patients who had a CR at 3 months, the PFS and OS rates at 12 months were 66.7% and 100%, respectively. Severe cytokine release syndrome (sCRS) (grade 3 and higher) occurred in nine patients (28.1%). Grade 3 or higher neurologic events occurred in four patients (12.5%). One patient died from irreversible severe CRS-associated acute kidney injury. Long-term CAR T cells persistence correlated with clinical efficacy (133 days vs 22 days, P = 0.004). Patients treated with more than three prior therapies and presenting extranodal organ involvement had lower maximal concentration (Cmax) values than other patients. Responders had higher Cmax and area under the curve values than non-responders. Tumour burden and Cmax were potentially associated with the severity of CRS.

Conclusions

This study demonstrates the safety and potential clinical efficacy of bispecific CD19/22 CAR T cells in patients with R/R B-NHL and highlights the importance of measuring kinetic parameters in PB to predict efficacy and safety in clinical applications of CAR T cell therapy.

Clinical Trial Registration

https://www.clinicaltrials.gov/ct2/show/NCT03196830, identifier NCT03196830.
Case Report: A Novel Compound Heterozygous Mutation in IL-10RA in a Chinese Child With Very Early-Onset Inflammatory Bowel Disease
Authors: Dong Fang , Xiao Fangfei , Ge Ting , Li Xiaolu , Xu Wuhen , Wu Shengnan , Zhang Ting , Wang Yizhong
Published: May 2021

Very early-onset inflammatory bowel disease (VEO-IBD) is defined as IBD diagnosed in children younger than 6 years of age. VEO-IBD is often associated with a monogenic etiology or primary immune deficiency. Here, we report the case of a 7-month-old Chinese girl diagnosed with VEO-IBD who had a variant in the interleukin-10 receptor A (IL-10-RA) gene. The patient presented with recurrent fevers, abdominal pain, diarrhea, perianal abscesses, and oral ulcers. Whole-exome sequencing (WES) identified a novel compound heterozygote mutation, c.395T>G (p.Leu132Arg)/ex.1del (p.?), in the IL-10RA gene of the patient. The missense mutation c.395T>G (p.Leu132Arg) was inherited from her mother, and ex.1del (p.?) was inherited from her father. Neither mutation has been reported previously. The IL-10RA function of the patient was defective, as demonstrated by a failure of signal transducer and activator of transcription 3 (STAT3) activation in peripheral blood mononuclear cells (PBMCs) stimulated with recombinant IL-10. The patient underwent matched unrelated peripheral blood hematopoietic stem cell transplantation (HSCT), and the clinical manifestations were dramatically improved. In summary, we identified a novel compound heterozygote mutation, c.395T>G (p.Leu132Arg)/ex.1del (p.?), in IL-10RA that caused VEO-IBD in a Chinese child, which further expands the mutational spectrum of IL-10RA.
Optogenetic Manipulations of Amygdala Neurons Modulate Spinal Nociceptive Processing and Behavior Under Normal Conditions and in an Arthritis Pain Model
Authors: Mazzitelli Mariacristina , Marshall Kendall , Pham Andrew , Ji Guangchen , Neugebauer Volker
Published: May 2021

The amygdala is an important neural substrate for the emotional–affective dimension of pain and modulation of pain. The central nucleus (CeA) serves major amygdala output functions and receives nociceptive and affected–related information from the spino-parabrachial and lateral–basolateral amygdala (LA–BLA) networks. The CeA is a major site of extra–hypothalamic expression of corticotropin releasing factor (CRF, also known as corticotropin releasing hormone, CRH), and amygdala CRF neurons form widespread projections to target regions involved in behavioral and descending pain modulation. Here we explored the effects of modulating amygdala neurons on nociceptive processing in the spinal cord and on pain-like behaviors, using optogenetic activation or silencing of BLA to CeA projections and CeA–CRF neurons under normal conditions and in an acute pain model. Extracellular single unit recordings were made from spinal dorsal horn wide dynamic range (WDR) neurons, which respond more strongly to noxious than innocuous mechanical stimuli, in normal and arthritic adult rats (5–6 h postinduction of a kaolin/carrageenan–monoarthritis in the left knee). For optogenetic activation or silencing of CRF neurons, a Cre–inducible viral vector (DIO–AAV) encoding channelrhodopsin 2 (ChR2) or enhanced Natronomonas pharaonis halorhodopsin (eNpHR3.0) was injected stereotaxically into the right CeA of transgenic Crh–Cre rats. For optogenetic activation or silencing of BLA axon terminals in the CeA, a viral vector (AAV) encoding ChR2 or eNpHR3.0 under the control of the CaMKII promoter was injected stereotaxically into the right BLA of Sprague–Dawley rats. For wireless optical stimulation of ChR2 or eNpHR3.0 expressing CeA–CRF neurons or BLA–CeA axon terminals, an LED optic fiber was stereotaxically implanted into the right CeA. Optical activation of CeA–CRF neurons or of BLA axon terminals in the CeA increased the evoked responses of spinal WDR neurons and induced pain-like behaviors (hypersensitivity and vocalizations) under normal condition. Conversely, optical silencing of CeA–CRF neurons or of BLA axon terminals in the CeA decreased the evoked responses of spinal WDR neurons and vocalizations, but not hypersensitivity, in the arthritis pain model. These findings suggest that the amygdala can drive the activity of spinal cord neurons and pain-like behaviors under normal conditions and in a pain model.
Identification of Resistance Sources and Genome-Wide Association Mapping of Septoria Tritici Blotch Resistance in Spring Bread Wheat Germplasm of ICARDA
Authors: Louriki Sara , Rehman Sajid , El Hanafi Samira , Bouhouch Yassine , Al-Jaboobi Muamar , Amri Ahmed , Douira Allal , Tadesse Wuletaw
Published: May 2021

Septoria tritici blotch (STB) of wheat, caused by the ascomycete Zymoseptoria tritici (formerly Mycosphaerella graminicola), is one of the most important foliar diseases of wheat. In Morocco, STB is a devastating disease in temperate wheat-growing regions, and the yield losses can exceed up to 50% under favorable conditions. The aims of this study were to identify sources of resistance to STB in Septoria Association Mapping Panel (SAMP), which is composed of 377 advanced breeding lines (ABLs) from spring bread wheat breeding program of ICARDA, and to identify loci associated with resistance to STB at seedling (SRT) as well as at the adult plant (APS) stages using genome-wide association mapping (GWAM). Seedling resistance was evaluated under controlled conditions with two virulent isolates of STB (SAT-2 and 71-R3) from Morocco, whereas adult plant resistance was assessed at two hot spot locations in Morocco (Sidi Allal Tazi, Marchouch) under artificial inoculation with a mixture of STB isolates. At seedling stage, 45 and 32 ABLs were found to be resistant to 71-R3 and SAT-2 isolates of STB, respectively. At adult plant stage, 50 ABLs were found to be resistant at hot spot locations in Morocco. Furthermore, 10 genotypes showed resistance in both locations during two cropping seasons. GWAM was conducted with 9,988 SNP markers using phenotypic data for seedling and the adult plant stage. MLM model was employed in TASSEL 5 (v 5.2.53) using principal component analysis and Kinship Matrix as covariates. The GWAM analysis indicated 14 quantitative trait loci (QTL) at the seedling stage (8 for isolate SAT-2 and 6 for isolate 71-R3), while 23 QTL were detected at the adult plant stage resistance (4 at MCH-17, 16 at SAT-17, and 3 at SAT-18). SRT QTL explained together 33.3% of the phenotypic variance for seedling resistance to STB isolate SAT-2 and 28.3% for 71-R3, respectively. QTL for adult plant stage resistance explained together 13.1, 68.6, and 11.9% of the phenotypic variance for MCH-17, SAT-17, and SAT-18, respectively. Identification of STB-resistant spring bread wheat germplasm in combination with QTL detected both at SRT and APS stage will serve as an important resource in STB resistance breeding efforts.
Transcriptome Profile Analysis of Arabidopsis Reveals the Drought Stress-Induced Long Non-coding RNAs Associated With Photosynthesis, Chlorophyll Synthesis, Fatty Acid Synthesis and Degradation
Authors: Chen Kang , Huang Yang , Liu Chunni , Liang Yu , Li Maoteng
Published: May 2021

Long non-coding RNAs (lncRNAs) play an important role in the response of plants to drought stress. The previous studies have reported that overexpression of LEA3 and VOC could enhance drought tolerance and improve the oil content in Brassica napus and Arabidopsis thaliana, and most of the efforts have been invested in the gene function analysis, there is little understanding of how genes that involved in these important pathways are regulated. In the present study, the transcriptomic results of LEA3 and VOC over-expressed (OE) lines were compared with the RNAi lines, mutant lines and control lines under long-term and short-term drought treatment, a series of differentially expressed lncRNAs were identified, and their regulation patterns in mRNA were also investigated in above mentioned materials. The regulation of the target genes of differentially expressed lncRNAs on plant biological functions was studied. It was revealed that the mutant lines had less drought-response related lncRNAs than that of the OE lines. Functional analysis demonstrated that multiple genes were involved in the carbon-fixing and chlorophyll metabolism, such as CDR1, CHLM, and CH1, were regulated by the upregulated lncRNA in OE lines. In LEA-OE, AT4G13180 that promotes the fatty acid synthesis was regulated by five lncRNAs that were upregulated under both long-term and short-term drought treatments. The key genes, including of SHM1, GOX2, and GS2, in the methylglyoxal synthesis pathway were all regulated by a number of down-regulated lncRNAs in OE lines, thereby reducing the content of such harmful compounds produced under stress in plants. This study identified a series of lncRNAs related to the pathways that affect photosynthesis, chlorophyll synthesis, fatty acid synthesis, degradation, and other important effects on drought resistance and oil content. The present study provided a series of lncRNAs for further improvement of crop varieties, especially drought resistant and oil content traits.
Genetic Analysis of a Horizontal Resistance Locus BLMR2 in Brassica napus
Authors: Zhang Qiang , Dandena Hanna , McCausland Madison , Liu Huizhi , Liu Zheng , Xu Wen , Li Genyi
Published: May 2021

Leptosphaeria maculans causes blackleg disease in Brassica napus. The blackleg disease is mainly controlled by resistance genes in B. napus. Previous studies have shown that the blackleg resistant BLMR2 locus that conferred horizontal resistance under field conditions, is located on chromosome A10 of B. napus. The purpose of this study is to fine map this locus and hence identify a candidate gene underlying horizontal resistance. The spectrum of resistance to L. maculans isolates of the resistance locus BLMR2 was analyzed using near isogenic lines, resistant, and susceptible cultivars. The results showed that this locus was horizontally resistant to all isolates tested. Sequence characterized amplified regions (SCAR), simple sequence repeats (SSR), and single nucleotide polymorphism (SNP) markers were developed in the chromosome region of BLMR2 and a fine genetic map was constructed. Two molecular markers narrowed BLMR2 in a 53.37 kb region where six genes were annotated. Among the six annotated genes, BnaA10g11280D/BnaA10g11290D encoding a cytochrome P450 protein were predicted as the candidate of BLMR2. Based on the profiling of pathogen induced transcriptome, three expressed genes in the six annotated genes were identified while only cytochrome P450 showed upregulation. The candidate corresponds to the gene involved in the indole glucosinolate biosynthesis pathway and plant basal defense in Arabidopsis thaliana. The molecular markers identified in this study will allow the quick incorporation of the BLMR2 allele in rapeseed cultivars to enhance blackleg resistance.
Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments
Authors: Sica Pietro , Scariolo Francesco , Galvao Aline , Battaggia Domiziana , Nicoletto Carlo , Maucieri Carmelo , Palumbo Fabio , Franklin Dorcas , Cabrera Miguel , Borin Maurizio , Sambo Paolo , Barcaccia Gianni
Published: May 2021

Common bean (Phaseolus vulgarisL.) is an essential source of food proteins and an important component of sustainable agriculture systems around the world. Thus, conserving and exploiting the genetic materials of this crop species play an important role in achieving global food safety and security through the preservation of functional and serependic opportunities afforded by plant species diversity. Our research aimed to collect and perform agronomic, morpho-phenological, molecular-genetic, and nutraceutical characterizations of common bean accessions, including lowland and mountain Venetian niche landraces (ancient farmer populations) and Italian elite lineages (old breeder selections). Molecular characterization with SSR and SNP markers grouped these accessions into two well-separated clusters that were linked to the original Andean and Mesoamerican gene pools, which was consistent with the outputs of ancestral analysis. Genetic diversity in the two main clusters was not distributed equally the Andean gene pool was found to be much more uniform than the Mesoamerican pool. Additional subdivision resulted in subclusters, supporting the existence of six varietal groups. Accessions were selected according to preliminary investigations and historical records and cultivated in two contrasting Venetian environments: sea-level and mountain territories. We found that the environment significantly affected some nutraceutical properties of the seeds, mainly protein and starch contents. The antioxidant capacity was found significantly greater at sea level for climbing accessions and in the mountains for dwarf accessions. The seed yield at sea level was halved than mountain due to a seeds reduction in weight, volume, size and density. At sea level, bean landraces tended to have extended flowering periods and shorter fresh pod periods. The seed yield was positively correlated with the length of the period during which plants had fresh pods and negatively correlated with the length of the flowering period. Thus, the agronomic performance of these genetic resources showed their strong connection and adaptation to mountainous environments. On the whole, the genetic-molecular information put together for these univocal bean entries was combined with overall results from plant and seed analyses to select and transform the best accessions into commercial varieties (i.e., pure lines) suitable for wider cultivation.
Enacting Media. An Embodied Account of Enculturation Between Neuromediality and New Cognitive Media Theory
Authors: Fingerhut Joerg
Published: May 2021

This paper argues that the still-emerging paradigm of situated cognition requires a more systematic perspective on media to capture the enculturation of the human mind. By virtue of being media, cultural artifacts present central experiential models of the world for our embodied minds to latch onto. The paper identifies references to external media within embodied, extended, enactive, and predictive approaches to cognition, which remain underdeveloped in terms of the profound impact that media have on our mind. To grasp this impact, I propose an enactive account of media that is based on expansive habits as media-structured, embodied ways of bringing forth meaning and new domains of values. We apply such habits, for instance, when seeing a picture or perceiving a movie. They become established through a process of reciprocal adaptation between media artifacts and organisms and define the range of viable actions within such a media ecology. Within an artifactual habit, we then become attuned to a specific media work (e.g., a TV series, a picture, a text, or even a city) that engages us. Both the plurality of habits and the dynamical adjustments within a habit require a more flexible neural architecture than is addressed by classical cognitive neuroscience. To detail how neural and media processes interlock, I will introduce the concept of neuromediality and discuss radical predictive processing accounts that could contribute to the externalization of the mind by treating media themselves as generative models of the world. After a short primer on general media theory, I discuss media examples in three domains: pictures and moving images; digital media; architecture and the built environment. This discussion demonstrates the need for a new cognitive media theory based on enactive artifactual habits—one that will help us gain perspective on the continuous re-mediation of our mind.
Factors Associated With Ruminative Thinking in Individuals With Gender Dysphoria
Authors: Silva Dhiordan Cardoso , Salati Leonardo Romeira , Villas-Bôas Anna Paula , Schwarz Karine , Fontanari Anna Martha , Soll Bianca , Costa Angelo Brandelli , Hirakata Vania , Schneider Maiko , Lobato Maria Inês Rodrigues
Published: May 2021

This study aimed to examine psychosocial factors and medical history as well as symptoms of depression, anxiety, and stress associated with ruminative thinking in transgender people with gender dysphoria (GD) before undergoing gender affirmation surgery (GAS). This study evaluated 189 participants with GD (111 trans women and 78 trans men) from a specialized service for GAS in southern Brazil. Semi-structured interviews were conducted, and participants were asked to complete self-report questionnaires. We recovered participants' sociodemographic and psychosocial data (e.g., history of sexual abuse, expulsion from home, and history of drug use) and data regarding their clinical history (e.g., medication, history of suicidal ideation and attempted suicide, and HIV status). Further, we implemented the Depression, Anxiety and Stress Scale (DASS-21) to examine participants' psychological state, as well as the Ruminative Response Scale (RRS) to assess ruminative thinking, which includes brooding and reflection. The predictor variables were those that exhibited a minimum level of significance of p ≤ 0.05 in multivariate linear regression. The ruminative thinking scores for trans women were higher than those of trans men (Brooding p = 0.014; Reflection p = 0.052).In the multivariate model, suicidal ideation, moderate depression, and severe/very severe anxiety were associated with both brooding and reflection. Feminine gender identity and stress symptoms moderated only brooding, while anxiety symptoms moderated only reflection. Our findings show that trans women had the highest ruminative thinking scores, and that depression, anxiety, stress, and suicidal ideation were associated with ruminative thinking in total sample. Psychological symptoms should be examined in the context of gender affirmation surgery to minimize the possibility of adverse mental health outcomes. Follow-up studies are required to measure ruminative thinking levels more accurately and to identify its predictors.
Carer's Attachment Anxiety, Stressful Life-Events and the Risk of Childhood-Onset Type 1 Diabetes
Authors: Turin Anja , Dovč Klemen , Klemenčič Simona , Bratina Nataša , Battelino Tadej , Lipovšek Jasna Klara , Uršič Katarina , Shmueli-Goetz Yael , Drobnič-Radobuljac Maja
Published: May 2021

Background/Objective: Type 1 diabetes (T1D) is among the most common chronic diseases in children/adolescents, and the incidence continues to rise worldwide. Different environmental factors have been evaluated in the etiology. In the present study, we investigated the role of attachment examining whether insecure attachment to carers or carers' own attachment insecurity was related to a higher risk of T1D in children.

Methods: We included 101 children with T1D (mean age 11.8 years), 106 healthy controls (11.6 years), and one of their carers. We assessed children's attachment using the Child Attachment Interview and carers' attachment using the Relationship Structures Questionnaire. We constructed binary multinomial logistic regression models using attachment to mothers, carers' attachment representations, and stressful life-events as T1D predictors.

Results: Higher carer attachment anxiety was associated with the child's T1D diagnosis (p < 0.05; R2 = 0.0613) while security of attachment to mothers showed no significant association. When mothers' education was included in the model, both attachment anxiety in higher educated mothers and stressful life events showed a significant association with the child's T1D (p < 0.001; R2 = 0.293).

Conclusions: Our findings suggest that higher attachment-related anxiety in carers with high education and stressful life events are associated with T1D in children.
Athletes' and Coaches' Attitudes Toward Protective Headgear as Concussion and Head Injury Prevention: A Scoping Review
Authors: Tjønndal Anne , Austmo Wågan Frida
Published: May 2021

The purpose of this article is to map existing research literature on athletes and coaches' attitudes toward protective headgear in sport in relation to concussion and head injury prevention, and to identify and analyse knowledge gaps in the field. A scoping review was conducted in three databases; PubMed, Scopus, SportDiscus, and reference lists were searched to identify relevant grey literature. This process lead to an in-depth analysis of 18 peer-reviewed journal articles. Of the 18 studies identified, the majority focused on athletes (n = 14), only two studies focused on coaches, and two studies included a sample of both athletes and coaches. The findings in this scoping review suggests that there is a discrepancy between attitudes and beliefs about the protective effects of headgear, athletes' behaviour as far as wearing protective headgear, and coaches' behaviour in terms of recommending use of protective headgear to their athletes. The majority of athletes in most of the reviewed literature believed that headgear had protective effects against concussion and other head injuries, however relatively few athletes report wearing this protective headgear unless it was mandatory by competition rules.
Biological Nitrogen Fixation and Denitrification in Rhizosphere of Potato Plants in Response to the Fertilization and Inoculation
Authors: Volkogon Vitaliy V. , Dimova Svitlana B. , Volkogon Kateryna I. , Sidorenko Vasyl P. , Volkogon Mykola V.
Published: May 2021

The study aim was to evaluate the potential nitrogen fixation and denitrification in the rhizosphere soil of potato plants, crop yield and output quality in response to the different fertilization systems and the inoculation with Azospirillum brasilense 410. Field stationary experiment was conducted between 2016 and 2019 with potato in a crop rotation system on leached chernozem soil. Farmyard manure, 40 t/ha, applied prior to potatoes planting promotes nitrogen fixation (0.8–2.0 times compared to control). However, it has also affected denitrification (in 1.4–2.2 times higher compared to control). The lowest rate of mineral fertilizers used in the experiment, N40P40K40, was shown as most environmentally feasible. Under its use the increase of soil nitrogenase activity and low denitrification levels were observed. Same trends were also noted for the medium fertilizer rate, N80P80K80. The highest doses of mineral fertilizers, N120P120K120, substantially affected the denitrification process and reduced the nitrogen fixation activity (in 1.9–2.2 times). The combination of manure with the medium fertilizers rate has also resulted in high denitrification levels, while the soil nitrogen fixation activity has restored only at flowering stage. Crop inoculation with A. brasilense combined with the manure application, has not affected studied processes. However, crop inoculation after the green manure intercropping has shown the growth of nitrogenase activity. Used on the mineral fertilizers background inoculation has activated nitrogen fixation and has ensured the decrease of denitrification levels, subject to the fertilization background. High fertilizer rates have hampered the inoculation efficiency. Inoculation has promoted crop yields on unfertilized and mineral backgrounds or following green manure. Crop inoculation following organic and the organo-mineral backgrounds had no significant effect, probably due to the competition for A. brasilense from microorganisms that have created a competitive environment for A. brasilense. Despite its environmental expediency, inoculation combined with the low fertilizer doses underperforms the action of inoculation combined with the medium fertilizer rates showing the latter as the compromise between the environmental requirements and crop productivity. The use of inoculation has promoted the accumulation of starch and ascorbic acid and has contributed to the reduction of nitrate contents in the tubers of inoculated plants.
Rumen Microbiota of Tibetan Sheep (Ovis aries) Adaptation to Extremely Cold Season on the Qinghai-Tibetan Plateau
Authors: Fan Qingshan , Cui Xiongxiong , Wang Zhaofeng , Chang Shenghua , Wanapat Metha , Yan Tianhai , Hou Fujiang
Published: May 2021

The Qinghai-Tibet Plateau is characterized by low temperatures and hypoxia, and this feature is more obvious in the winter. However, it is not clear how Tibetan sheep adapt to extreme cold climates. To address this, we used physiological methods combined with next-generation sequencing technology to explore the differences in growth performance, forage nutrient digestion, serum biochemical indexes, and rumen microbial communities of Tibetan sheep (Ovis aries) between the summer and winter. In the summer, owing to the high nutritional quality of the forage, the Tibetan sheep showed enhanced forage degradation and fermentation though increased counts of important bacteria in the rumen, such as Bacteroidetes, Prevotella_1, Prevotellaceae_UCG-003, Ruminococcus_1, Saccharofermentans, and Ruminococcaceae_UCG-014, to improve the growth performance and increase serum immunity and antioxidant status. In the winter, owing to the low nutritional quality of the forage, the Tibetan sheep presented low values of forage degradation and fermentation indicators. The relative abundance of Firmicutes, the Firmicutes/Bacteroidetes ratio, microbial diversity, interactive activity between microorganisms, and metabolism were significantly increased, implying that the rumen microbiota could promote the decomposition of forage biomass and the maintenance of energy when forage nutritional value was insufficient in the winter. Our study helps in elucidating the mechanism by which Tibetan sheep adapt to the high-altitude harsh environments, from the perspective of the rumen microbiota.
New Numerical and Measurements Flow Analyses Near Radars
Authors: Salinas Manuel Flores , Botez Ruxandra Mihaela , Gauthier Guy
Published: May 2021

An experimental and numerical investigation of the flow near a blunt body has been conducted in this study. Most experimental methods of flow studies use flow visualization and probes introduction into the flow field. The main goal of this research was the development of a new methodology to analyze flows, and to measure flow characteristics without taking into account the distorting effects of measuring probes. A series of experiments were performed on a ground surveillance radar in the Price-Païdoussis subsonic wind tunnel. Forces and moments were measured as functions of wind speeds and angular positions by the use of a six-component aerodynamic scale. A Computational Fluid Dynamics three-dimensional model was employed to analyze the wake region of the ground surveillance radar. A turbulence reduction system was proposed and analyzed in this research. The use of the proposed turbulence reduction system was found to be an effective way to reduce turbulent flow intensity by 50%, drag coefficients by 9.6%, and delay the flow transition point by 7.6 times.
Departure from Flux-Gradient Relation in the Planetary Boundary Layer
Authors: Santos Pedro , Peña Alfredo , Mann Jakob
Published: May 2021

It is well known that when eddies are small, the eddy fluxes can be directly related to the mean vertical gradients, the so-called flux-gradient relation, but such a relation becomes weaker the larger the coherent structures. Here, we show that this relation does not hold at heights relevant for wind energy applications. The flux–gradient relation assumes that the angle (β) between the vector of vertical flux of horizontal momentum and the vector of the mean vertical gradient of horizontal velocity is zero, i.e., these vectors are aligned. Our observations do not support this assumption, either onshore or offshore. Here, we present analyses of a misalignment between these vectors from a Doppler wind lidar observations and large-eddy simulations. We also use a real-time mesoscale model output for inter-comparison with the lidar-observed vertical profiles of wind speed, wind direction, momentum fluxes, and the angle between the horizontal velocity vector and the momentum flux vector up to 500 m, both offshore and onshore. The observations show this within the height range 100–500 m, β=−18∘ offshore and β=−12∘ onshore, on average. However, the large-eddy simulations show β≈0∘ both offshore and onshore. We show that observed and mesoscale-simulated vertical profiles of mean wind speed and momentum fluxes agree well; however, the mesoscale results significantly deviate from the wind-turning observations.
MiR-139 Modulates Cancer Stem Cell Function of Human Breast Cancer through Targeting CXCR4
Authors: Cheng Chun-Wen , Liao Wen-Ling , Chen Po-Ming , Yu Jyh-Cherng , Shiau Hui-Ping , Hsieh Yi-Hsien , Lee Huei-Jane , Cheng Yu-Chun , Wu Pei-Ei , Shen Chen-Yang
Published: May 2021

Elevated expression of C-X-C motif chemokine receptor 4 (CXCR4) correlates with chemotaxis, invasion, and cancer stem cell (CSC) properties within several solid-tumor malignancies. Recent studies reported that microRNA (miRNA) modulates the stemness of embryonic stem cells. We aimed to investigate the role of miRNA, via CXCR4-modulation, on CSC properties in breast cancer using cell lines and xenotransplantation mouse model and evaluated miR-193 levels in 191 patients with invasive ductal carcinoma. We validated miR-139 directly targets the 3′-untranslated region of CXCR4. Hoechst 33342 fluorescence-activated cell sorting (FACS) and sphere-forming assay were used to identify CSCs. MiR-139 suppressed breast CSCs with mesenchymal traits; led to decreased migration and invasion abilities through down-regulating CXCR4/p-Akt signaling. In lung cancer xenograft model of nude mice transplanted with human miR-139-carrying MDA-MB-231 cells, metastatic lung nodules were suppressed. Clinically, microdissected breast tumor tissues showed miR-139 reduction, compared to adjacent non-tumor tissues, that was significantly associated with worse clinicopathological features, including larger tumor size, advanced tumor stage and lymph node metastasis; moreover, reduced miR-139 level was predominately occurred in late-stage HER2-oreexpression tumors. Collectively, our findings highlight miR-139-mediated suppression of CXCR4/p-Akt signaling and thereby affected mesenchymal stem-cell genesis, indicating its potential as a therapeutic target for invasive breast cancer.
Identification of Candidate Protein Biomarkers for CIN2+ Lesions from Self-Sampled, Dried Cervico–Vaginal Fluid Using LC-MS/MS
Authors: Gutiérrez Ariadna Lara , Lindberg Julia Hedlund , Shevchenko Ganna , Gustavsson Inger , Bergquist Jonas , Gyllensten Ulf , Enroth Stefan
Published: May 2021

Molecular screening programs for cervical cancer detect the presence of human papilloma virus (HPV) in cell material or vaginal fluids. Persistent infection with high-risk HPV is a necessary pre-requisite, but the majority of infections do not lead to pathological states. Additional biomarkers are needed to increase the specificity of the molecular tests. Here, we have investigated the possibility of detecting protein biomarkers using mass spectrometry from dried self-sampled cervico–vaginal fluid deposited on FTA cards. We found significant intra-individual correlations (p < 2.2 × 10−16), although heterogenous protein profiles were obtained between individuals. Out of 3699 proteins found in total, 169 were detected in at least 95% of the samples. Using a discovery/replication design, 18 proteins were found to be significant in the discovery cohort, with higher values in those cases compared to controls. All of these were found to also have higher levels among the cases in the replication cohort, with one protein (DEAD-Box Helicase) remaining statistically significant. Finally, a predictive 7-protein multivariate model was developed with a sensitivity and specificity of 0.90 and 0.55, respectively. Our results demonstrate that robust measurements of protein biomarkers can be obtained from self-sampled dried CVF and that these could be used to predict cervical cancer pre-stages.