bluuebunny/crossref_metadata_2025 huggingface dataset:
Religion & Transitional Justice
Authors: Murphy Colleen
Published: June 2020

Transitional justice refers to the process of dealing with human rights abuses committed during the course of ongoing conflict or repression, where such processes are established as a society aims to move toward a better state, and where a constitutive element of that better state includes democracy. A philosophical theory of transitional justice articulates what the moral criteria or standards are that processes of transitional justice must satisfy to qualify as just responses to past wrongdoing. This essay focuses on the roles of religion in transitional justice. I first consider the multiple and conflicting roles of religion during periods of conflict and repression. I then argue against conceptualizing transitional justice in a theologically grounded manner that emphasizes the importance of forgiveness. Finally, I discuss the prominent role that religious actors often play in processes of transitional justice. I close with the theoretical questions about authority and standing in transitional contexts that warrant further examination, questions that the roles of religious actors highlight. Thinking through the relationship between religion and democracy from the perspective of transitional justice is theoretically fruitful because it sheds more light on additional dimensions to the issue of authority than those scholars of liberal democracy have traditionally taken up.
What Does Dorsal Cortex Contribute to Perception?
Authors: Freud Erez , Behrmann Marlene , Snow Jacqueline C.
Published: June 2020

According to the influential “Two Visual Pathways” hypothesis, the cortical visual system is segregated into two pathways, with the ventral, occipitotemporal pathway subserving object perception, and the dorsal, occipitoparietal pathway subserving the visuomotor control of action. However, growing evidence suggests that the dorsal pathway also plays a functional role in object perception. In the current article, we present evidence that the dorsal pathway contributes uniquely to the perception of a range of visuospatial attributes that are not redundant with representations in ventral cortex. We describe how dorsal cortex is recruited automatically during perception, even when no explicit visuomotor response is required. Importantly, we propose that dorsal cortex may selectively process visual attributes that can inform the perception of potential actions on objects and environments, and we consider plausible developmental and cognitive mechanisms that might give rise to these representations. As such, we consider whether naturalistic stimuli, such as real-world solid objects, might engage dorsal cortex more so than simplified or artificial stimuli such as images that do not afford action, and how the use of suboptimal stimuli might limit our understanding of the functional contribution of dorsal cortex to visual perception.
Beyond networks: Aligning qualitative and computational science studies
Authors: Cambrosio Alberto , Cointet Jean-Philippe , Abdo Alexandre Hannud
Published: June 2020

This article examines the thorny issue of the relationship (or lack thereof) between qualitative and quantitative approaches in Science and Technology Studies (STS). Although quantitative methods, broadly understood, played an important role in the beginnings of STS, these two approaches subsequently strongly diverged, leaving an increasing gap that only a few scholars have tried to bridge. After providing a short overview of the origins and development of quantitative analyses of textual corpora, we critically examine the state of the art in this domain. Focusing on the availability of advanced network structure analysis tools and Natural Language Processing workflows, we interrogate the fault lines between the increasing offer of computational tools in search of possible uses and the conceptual specifications of STS scholars wishing to explore the epistemic and ontological dimensions of techno-scientific activities. Finally, we point to possible ways to overcome the tension between ethnographic descriptions and quantitative methods while continuing to avoid the dichotomies (social/cognitive, organizing/experimenting) that STS has managed to discard.
The Development, Preservation and Loss of Differential Case Marking in Inner Asia Minor Greek
Authors: Karatsareas Petros
Published: June 2020

In Cappadocian and Pharasiot, the two main members of the inner Asia Minor Greek dialect group, the head nouns of NPs found in certain syntactic positions are marked with the accusative if the relevant NPs are definite and with the nominative if the NPs are indefinite. This differential case marking (dcm) pattern contrasts with all other Modern Greek dialects, in which the accusative is uniformly used in the relevant syntactic positions. After revisiting recent proposals regarding the synchronic status of dcm in Cappadocian and Pharasiot, I show how the two dialects developed this ‘un-Greek’ feature in the model of Turkish, which marks the head nouns of direct object NPs with an accusative suffix only if they take a specific reading leaving non-specific direct object NPs unmarked. I subsequently trace the diachronic trajectory of this contact-induced innovation within the two dialectal systems, seeking to explain why dcm was gradually lost in Cappadocian but preserved in Pharasiot.
Evaluation of the Overall 5-Year Survival of Breast Cancer at INO: Data from the 5-Year Prospective Database
Authors: Kaddi NA , Berrada NA , Errihani HA
Published: June 2020

Background:

Breast cancer is both the most common and deadliest cancer among women in the world. The objective of this study was to assess breast cancer survival rates.

Material and Methods:

Prospective study conducted at the National Institute of oncology (INO) Sidi Mohamed Ben Abdellah Rabat .diagnosed patients with cancer from 2013 to 2015. The date of inclusion in the study is the date of histological confirmation of cancer. The survival assessment performed by the Kaplan Meier method, and the comparison between the different classes of a variable was performed by the Log Rank test.

Results:

931 cases were collected during this study. According to molecular classification 59% of luminal patients, 25% positive human epidermal growth factor receptors (her2 positive) and 16% basal. The percentage of survival at 5 years, for luminal stage I 93%, stage II 92%, stage III 74% and stage IV 25% ;as well as for basal stage I 92%, stage II 80%, stage III 53% and stage IV 10% ; then the her2 positive stage I 100%, stage II 75% and stage III 70%.

Conclusion:

The discovery of metastatic cancer decreased breast cancer survival rate, hence the importance of Early Detection Awareness.
The Long-Term Effects of Bullying, Victimization, and Bystander Behavior on Emotion Regulation and Its Physiological Correlates
Authors: Camodeca Marina , Nava Elena
Published: June 2020

Bullying at school is a serious social problem that influences the wellbeing of everyone involved, that is, victims, perpetrators, and bystanders. Among the many health and psychological problems that these individuals may develop, emotion dysregulation appears to be a common marker. To date, however, it remains unclear whether bullying experienced during the school years is associated with emotion dysregulation also in adulthood. In this study, by adopting a retrospective approach, we investigated whether involvement in bullying at school—either as a bully, victim, or bystander—could put these individuals at risk of presenting deficits in emotion regulation in adulthood, as assessed with behavioral (explicit) and physiological (implicit) indexes (i.e., skin conductance), and whether the association between the involvement in bullying and emotion regulation was direct or mediated by other factors, such as somatic complaints and sensation seeking. A total of 58 young adults were asked to control their emotional reactions in front of images with strong emotional content, and to explicitly evaluate them with ratings, while their arousal was measured through skin conductance. They also responded to questionnaires about retrospective involvement in bullying, somatic complaints, and sensation seeking. Results revealed that victimization and bystander behavior were directly and negatively associated with emotion regulation as assessed with skin conductance, whereas bullying was positively associated with implicit emotion regulation through the mediation of sensation seeking. Interestingly, emotion regulation as assessed with explicit ratings was not associated with any of the characteristics of the participants. Our study suggests that being directly (as victim) but also indirectly (as bystander) involved in bullying at school time is associated with difficulties in emotional wellbeing in adulthood. Furthermore, it reveals that behavioral and physiological indexes associated with emotion regulation dissociate, suggesting that subtle physiological changes may remain hidden from explicit behavior.
Gender and education inequalities in parental employment and earnings when having a child with increased care needs: Belgium versus Norway
Authors: Vinck Julie , Brekke Idunn
Published: June 2020

Caring for children with increased care needs can be demanding and the time required to provide such care hampers parents’ employment participation. Especially, mothers and lower educated parents are affected by the increased care burden and reduce or stop their employment participation. So far, the literature lacks studies investigating the employment impact in a comparative perspective. We fill this gap by comparing Belgium and Norway. We use comparable administrative datasets, identifying children with increased care needs as those receiving a cash benefit designed to financially compensate for the extra private care. The results confirm that gender and education inequalities exist in both countries. Moreover, we find that the negative care burden gap in employment depends on the country of residence, with significantly larger inequalities in Belgium. Our analyses suggest that increased support on multiple fronts is needed for these families.
Evaluating telephone and online psychological support and referral
Authors: Hawkins Andrew , Odgers Jasper , Reeves Amanda , McCoy Alicia
Published: June 2020

Mental health counselling and support over the telephone or internet is increasingly common. Evaluating effectiveness requires outcome measures and understanding factors driving behaviour. This article describes a theory-driven evaluation of the one-month outcomes of a short-term solution-focused support session for anxiety or depression with a counsellor. The primary aim of the evaluation was to measure the outcomes of this session on service users’ help-seeking behaviour. It also sought to understand reasons for behaviour based on behaviour change theory. A secondary aim was to measure changes in feelings of stress and coping before and after the session, and collect evidence of the value of the service in terms of ‘consumer-defined recovery’. The evaluation found the service was effective, with the overwhelming majority taking some action, being more engaged with a health professional, having reduced feelings of distress, increased confidence to cope and less hopelessness. Improvements for service users included ‘reality testing’ the advice given and building commitment or intent to follow the advice, and ‘rehearsing’ so service users can demonstrate to themselves they have the skills required and can overcome any obstacles to following the advice.
A Retrospective Thematic Analysis of Patient, Family, and Staff Creative Art Tiles Developed on a Tertiary Palliative Care Unit
Authors: Collins Andrew , Ayre Sandy , Brulotte Tiffany , Crowe Kim , Nekolaichuk Cheryl
Published: June 2020

Objectives:

Clinical use of the creative arts in palliative care is well established, yet there are few evaluation studies of these programs.

Methods:

In this first phase of a 3-phase evaluation of a creative arts program entitled “Tile Tales,” we conducted a retrospective thematic analysis of 85 painted tiles and accompanying stories that were publically displayed on a tertiary palliative care unit. Each story was independently coded, using content analysis. Themes were derived through consensus, using the constant comparative method.

Results:

Tiles were created by staff (n = 36, 42%), family (n = 32, 38%), patients (n = 9, 11%), or patients and family (n = 8, 9%). Six major themes emerged from the artwork: “Spirituality,” “Relationships,” “Journey,” “Story,” “Symbolism,” and “Paradox.”

Significance of Results:

These results illustrate how the creative arts can support the expression of diverse palliative care experiences, for patients, their families and palliative care staff, when words alone may not suffice.
Is it possible to achieve gender equality in Kazakhstan: Focus on employment and social protection
Authors: Khamzina Zhanna , Buribayev Yermek , Yermukanov Yerkin , Alshurazova Aizhan
Published: June 2020

International ratings confirm that Kazakhstan is a leader in Central Asia in addressing the causes of gender inequality; however, there are still significant gender differences in key areas. In particular, gender discrimination in the labor market is complex: when hiring or dismissing, while restricting access to certain professions and positions, in matters of promotion and career growth, when remuneration is paid for performing the same work, not related to differences in labor efficiency. Discrimination is especially sensitive in relation to pregnant women and women with young children. Discrimination continues with access to social measures for avoiding poverty and in the pension system. Further progress requires more strategically significant and focused actions to identify and bridge the remaining factors of systemic discrimination and gender gaps. In the article, we show the insufficient attention of the legal science of Kazakhstan to the problems of regulation of equality. We present the author’s methodology for analyzing labor and social legislation from the perspective of regulating gender equality, consisting of several assessments: Kazakhstan’s fulfillment of international obligations; implementation of the principle of nondiscrimination in labor and social legislation; administrative and judicial mechanisms to protect against discrimination based on sex; and opportunities for implementing best foreign and international practices for the regulation of equality.
Maxillary sinus osteoma: A case report and literature review
Authors: Hania Mohamed , Sharif Mohammad Owaise
Published: June 2020

This case report describes a rare presentation of an osteoma in the maxillary sinus picked up from an incidental finding on an orthopantomogram that was obtained to inform orthodontic treatment. While orthodontists principally use this radiograph to assess the developing dentition, aid treatment planning and monitor treatment, several peripheral anatomical sites are evident on this radiograph. We review the literature in relation to osteomas presenting in the craniofacial area along with its management. We provide examples of common radiopaque lesions along with their radiographic features that dental healthcare clinicians may encounter.
Curcumin Nanoparticles Improved Diabetic Wounds Infected With Methicillin-Resistant Staphylococcus aureus Sensitized With HAMLET
Authors: Taghavifar Saeed , Afroughi Fatemeh , Saadati Keyvan Maryam
Published: June 2020

Accurately orchestrated course of events normally observed in healing are not followed in diabetic wounds, and bacterial colonization/infection further messes up the process. Novel therapeutic options for treatment of infections caused by multidrug-resistant Staphylococcus aureus are urgently needed. HAMLET (human α-lactalbumin made lethal to tumor cells) has been reported to be able to sensitize bacterial pathogens to traditional antimicrobial agents. The aim was to assess the wound healing activity of curcumin nanoparticles in diabetic wounds infected with methicillin-resistant Staphylococcus aureus (MRSA) sensitized with HAMLET. Fifty male rats were randomized into 5 groups of 10 animals each. In CONTROL group, 0.1-mL sterile saline 0.9% solution was added to the wounds with no infection. In MRSA group, the wounds were infected with MRSA and only treated with 0.1-mL sterile saline 0.9% solution. In MRSA/HAMLET group, infected wounds were treated with HAMLET (100 µg). In MRSA/CNP group, animals with infected wounds were treated with 0.1 mL topical application of 1 mg/mL curcumin nanoparticles. In MRSA/CNP/HAMLET group, animals with infected wounds were treated with topical application of 0.1 mL solution of curcumin nanoparticles (1 mg/mL) and HAMLET (100 µg). All test formulations were applied for 10 days, twice a day, starting from first treatment. Microbiological examination; planimetric, biochemical, histological, and quantitative morphometric studies; immunohistochemical staining for angiogenesis; determination of hydroxyproline levels; and reverse transcription polymerase chain reaction for caspase 3, Bcl-2, and p53 showed that there was significant difference between animals in MRSA/CNP/HAMLET group compared with other groups ( P < .05). Curcumin nanoparticles improved diabetic wounds infected with MRSA sensitized with HAMLET and had the potential to offer more attention to this safer agent for topical use in infected diabetic wounds.
Treatment Modality of Distal Ulnar Head and Neck Fractures Associated With Operatively Treated Distal Radius Fractures Does Not Affect Outcomes
Authors: Glogovac Georgina , Perry Allison K. , Wigton Michael D. , Stern Peter J.
Published: June 2020

Background: This study compares the functional outcomes and complications between operatively and nonoperatively treated distal ulnar head and neck fractures associated with internal fixation of concomitant distal radius fractures. Methods: A 7-year retrospective chart review was performed to identify patients with operatively treated distal radius fractures associated with distal ulnar head and neck fractures. Ulnar styloid fractures were excluded. Fifty-eight patients who had a minimum of 6 months of follow-up were identified. Patients were divided into 3 treatment groups: nonoperative, open reduction internal fixation (ORIF), and distal ulna resection. Reviewed data included demographics, injury and treatment details, complications, and patient-reported outcome measures. Outcomes measures included Patient-Reported Outcomes Measurement Information System (PROMIS) Upper Extremity and Patient-Rated Wrist Evaluation (PRWE) surveys. Due to inadequate power, 5 patients treated with distal ulna resection were excluded from statistical analysis. Results: The average patient age was 56 years, with an average follow-up of 27 months. All patients underwent ORIF of the distal radius fracture. Distal ulna fractures were treated nonoperatively in 25 patients, with ORIF in 28 patients, and with distal ulna resection in 5 patients. There were no statistically significant differences in wrist or forearm range of motion, complication rates, secondary procedure rates, PRWE scores, or PROMIS scores between ORIF and nonoperative treatment. Conclusion: No differences in wrist or forearm range of motion, complication rates, secondary procedure rates, PRWE scores, or PROMIS scores were observed between ORIF and nonoperative treatment of distal ulnar head and neck fractures associated with operatively treated distal radius fractures.
Recommendations for participation in leisure-time physical activity and competitive sports in patients with arrhythmias and potentially arrhythmogenic conditions: Part 1: Supraventricular arrhythmias. A position statement of the Section of Sports Cardiology and Exercise from the European Association of Preventive Cardiology (EAPC) and the European Heart Rhythm Association (EHRA), both associations of the European Society of Cardiology
Authors: Heidbuchel Hein , Adami Paolo E , Antz Matthias , Braunschweig Frieder , Delise Pietro , Scherr Daniel , Solberg Erik E , Wilhelm Matthias , Pelliccia Antonio ,   EHRA/EAPC Scientific Review Group, Heinzel Frank R , Veltmann Christian , Odening Katja E , Boldt Leif Hendrik , Anne Wim , Napolitano Carlo , Davos Constantinos , Piepoli Massimo , Biffi Alessandro , van Buuren Frank
Published: June 2020

Symptoms attributable to arrhythmias are frequently encountered in clinical practice. Cardiologists and sport physicians are required to identify high-risk individuals harbouring such conditions and provide appropriate advice regarding participation in regular exercise programmes and competitive sport. The three aspects that need to be considered are: (a) the risk of life-threatening arrhythmias by participating in sports; (b) control of symptoms due to arrhythmias that are not life-threatening but may hamper performance and/or reduce the quality of life; and (c) the impact of sports on the natural progression of the underlying arrhythmogenic condition. In many cases, there is no unequivocal answer to each aspect and therefore an open discussion with the athlete is necessary, in order to reach a balanced decision. In 2006 the Sports Cardiology and Exercise Section of the European Association of Preventive Cardiology published recommendations for participation in leisure-time physical activity and competitive sport in individuals with arrhythmias and potentially arrhythmogenic conditions. More than a decade on, these recommendations are partly obsolete given the evolving knowledge of the diagnosis, management and treatment of these conditions. The present document presents a combined effort by the Sports Cardiology and Exercise Section of the European Association of Preventive Cardiology and the European Heart Rhythm Association to offer a comprehensive overview of the most updated recommendations for practising cardiologists and sport physicians managing athletes with supraventricular arrhythmias, and provides pragmatic advice for safe participation in recreational physical activities, as well as competitive sport at amateur and professional level. A companion text on recommendations in athletes with ventricular arrhythmias, inherited arrhythmogenic conditions, pacemakers and implantable defibrillators is published as Part 2 in Europace.
The BET inhibitor CPI203 promotes ex vivo expansion of cord blood long-term repopulating HSCs and megakaryocytes
Authors: Hua Peng , Hester Joanna , Adigbli George , Li Rong , Psaila Bethan , Roy Anindita , Bataille Carole J. R. , Wynne Graham M. , Jackson Thomas , Milne Thomas A. , Russell Angela J. , Davies James , Roberts Irene , Issa Fadi , Watt Suzanne M.
Published: June 2020

Although cytokine-mediated expansion of human hematopoietic stem cells (HSCs) can result in high yields of hematopoietic progenitor cells, this generally occurs at the expense of reduced bone marrow HSC repopulating ability, thereby limiting potential therapeutic applications. Because bromodomain-containing proteins (BCPs) have been demonstrated to regulate mouse HSC self-renewal and stemness, we screened small molecules targeting various BCPs as potential agents for ex vivo expansion of human HSCs. Of 10 compounds tested, only the bromodomain and extra-terminal motif inhibitor CPI203 enhanced the expansion of human cord blood HSCs without losing cell viability in vitro. The expanded cells also demonstrated improved engraftment and repopulation in serial transplantation assays. Transcriptomic and functional studies showed that the expansion of long-term repopulating HSCs was accompanied by synchronized expansion and maturation of megakaryocytes consistent with CPI203-mediated reprogramming of cord blood hematopoietic stem and progenitor cells. This approach may therefore prove beneficial for ex vivo gene editing, for enhanced platelet production, and for the improved usage of cord blood for transplantation research and therapy.
Exosomal miR-200c-3p negatively regulates the migration and invasion of lipopolysaccharide (LPS)-stimulated colorectal cancer (CRC)
Authors: Jiang Yimei , Ji Xiaopin , Liu Kun , Shi Yiqing , Wang Changgang , Li You , Zhang Tao , He Yonggang , Xiang Ming , Zhao Ren
Published: June 2020

Background

Colorectal cancer (CRC) is a leading cancer and a major cause of death. Lipopolysaccharide (LPS), an abundant component in gut microbiome, is involved in CRC progression and metastasis, potentially through regulating the miRNA composition of CRC-derived exosomes. In this study, we aimed to identify miRNA species in exosome which regulates CRC progression after LPS stimulation.

Results

Firstly, we discovered a shift of miRNA profile in CRC exosome after LPS stimulation. Among the differentially expressed miRNAs, we identified miR-200c-3p as a potential key regulator of CRC progression and metastasis. Retrospective analysis revealed that miR-200c-3p was elevated in CRC tumor tissues, but decreased in the serum exosome in CRC patients. In vitro experiments demonstrated that exosomal miR-200c-3p expression did not influence CRC cell proliferation, but negatively regulated their capacity of migration and invasion in the presence of LPS. miR-200c-3p level in exosome influenced exosomal expression of Zinc finger E-box-binding homeobox-1 (ZEB-1) mRNA, one of the miR-200c targets which affects migration and invasion capacity, and further altered ZEB-1 protein expression in CRC cell. In addition, exosomal miR-200c-3p promotes apoptosis of HCT-116 cells.

Conclusions

Our findings indicate that exosomal miR-200c-3p inhibits CRC migration and invasion, and promotes their apoptosis after LPS stimulation. It is suggested as a potential diagnostic marker and therapeutic target of CRC.
Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis
Authors: Ma Xiao , Cen Shuangshuang , Wang Luming , Zhang Chao , Wu Limin , Tian Xue , Wu Qisheng , Li Xuejun , Wang Xiaoqing
Published: June 2020

Background

The gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction have been investigated in some species. However, the regulatory patterns of miRNA and lncRNA in the sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of Pelodiscus sinensis.

Results

We identified 10,446 mature miRNAs, 20,414 mRNAs and 28,500 lncRNAs in the ovaries and testes, and 633 miRNAs, 11,319 mRNAs, and 10,495 lncRNAs showed differential expression. A total of 2814 target genes were identified for miRNAs. The predicted target genes of these differentially expressed (DE) miRNAs and lncRNAs included abundant genes related to reproductive regulation. Furthermore, we found that 189 DEmiRNAs and 5408 DElncRNAs showed sex-specific expression. Of these, 3 DEmiRNAs and 917 DElncRNAs were testis-specific, and 186 DEmiRNAs and 4491 DElncRNAs were ovary-specific. We further constructed complete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 103 DEmiRNAs, 636 DEmRNAs, and 1622 DElncRNAs. The target genes for the differentially expressed miRNAs and lncRNAs included abundant genes involved in gonadal development, including Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1.

Conclusions

In animals, miRNA and lncRNA as master regulators regulate reproductive processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for studying the molecular processes involved in sexual reproduction and genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproductive traits for aquaculture.
mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
Authors: Kaspi Antony , Ziemann Mark
Published: June 2020

Background

Inference of biological pathway activity via gene set enrichment analysis is frequently used in the interpretation of clinical and other omics data. With the proliferation of new omics profiling approaches and ever-growing size of data sets generated, there is a lack of tools available to perform and visualise gene set enrichments in analyses involving multiple contrasts.

Results

To address this, we developed mitch, an R package for multi-contrast gene set enrichment analysis. It uses a rank-MANOVA statistical approach to identify sets of genes that exhibit joint enrichment across multiple contrasts. Its unique visualisation features enable the exploration of enrichments in up to 20 contrasts. We demonstrate the utility of mitch with case studies spanning multi-contrast RNA expression profiling, integrative multi-omics, tool benchmarking and single-cell RNA sequencing. Using simulated data we show that mitch has similar accuracy to state of the art tools for single-contrast enrichment analysis, and superior accuracy in identifying multi-contrast enrichments.

Conclusion

mitch is a versatile tool for rapidly and accurately identifying and visualising gene set enrichments in multi-contrast omics data. Mitch is available from Bioconductor (https://bioconductor.org/packages/mitch).
Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani
Authors: Motyka-Pomagruk Agata , Zoledowska Sabina , Misztak Agnieszka Emilia , Sledz Wojciech , Mengoni Alessio , Lojkowska Ewa
Published: June 2020

Background

Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.

Results

High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.

Conclusions

The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.
Health status and infections in patients with symptomatic primary and secondary immunoglobulin G (IgG) deficiencies receiving intravenous IgG replacement
Authors: Weide Rudolf , Schnell Roland , Schardt Christof , Koenigsmann Michael , Otremba Burkhard , Zahn Mark-Oliver , Wierecky Jan , Braun Ute , Hensel Manfred , Klausmann Martine , Fleckenstein Doris , Ehscheidt Peter , Feiten Stefan
Published: June 2020

Background

The effects of intravenous immunoglobulin G replacement on perceived health and infection susceptibility of patients suffering from immunoglobulin G (IgG) deficiencies should be evaluated in a prospective analysis.

Methods

Patients with symptomatic primary or secondary IgG deficiencies were interviewed prior to the first IgG infusion (t0) and over the course of their treatment (t1- t6). The respondents rated their current health using a 100 point scale (EQ-5D-5L), ranging from 0 (‘worst imaginable health’) to 100 (‘best imaginable health’). The patients also provided information on the frequency of infections and of infections requiring antibiotics in the past 8 weeks. A healthy control group (CG) without oncologic diseases answered the questions once.

Results

One hundred six patients with a median age of 65 years (21–85 years) were investigated. The median serum IgG concentration changed from 500 mg/dl (t0) to 772 mg/dl (t6). The mean number of infections and of infections requiring antibiotics decreased during IgG replacement significantly. Current health according to EQ-5D-5L improved from 57 (t0) to 68 (t6), compared to 73 in the CG.

Conclusion

During the course of IgG replacement patients reported fewer and less severe infections. Their health assessment improved but still was inferior to the healthy CG.
Integrated transcriptomics and metabolomics analysis of catechins, caffeine and theanine biosynthesis in tea plant (Camellia sinensis) over the course of seasons
Authors: Gong An-Dong , Lian Shuai-Bin , Wu Nan-Nan , Zhou Yong-Jie , Zhao Shi-Qi , Zhang Li-Min , Cheng Lin , Yuan Hong-Yu
Published: June 2020

Background

Catechins, caffeine, and theanine as three important metabolites in the tea leaves play essential roles in the formation of specific taste and shows potential health benefits to humans. However, the knowledge on the dynamic changes of these metabolites content over seasons, as well as the candidate regulatory factors, remains largely undetermined.

Results

An integrated transcriptomic and metabolomic approach was used to analyze the dynamic changes of three mainly metabolites including catechins, caffeine, and theanine, and to explore the potential influencing factors associated with these dynamic changes over the course of seasons. We found that the catechins abundance was higher in Summer than that in Spring and Autumn, and the theanine abundance was significantly higher in Spring than that in Summer and Autumn, whereas caffeine exhibited no significant changes over three seasons. Transcriptomics analysis suggested that genes in photosynthesis pathway were significantly down-regulated which might in linkage to the formation of different phenotypes and metabolites content in the tea leaves of varied seasons. Fifty-six copies of nine genes in catechins biosynthesis, 30 copies of 10 genes in caffeine biosynthesis, and 12 copies of six genes in theanine biosynthesis were detected. The correlative analysis further presented that eight genes can be regulated by transcription factors, and highly correlated with the changes of metabolites abundance in tea-leaves.

Conclusion

Sunshine intensity as a key factor can affect photosynthesis of tea plants, further affect the expression of major Transcription factors (TFs) and structural genes in, and finally resulted in the various amounts of catechins, caffeine and theaine in tea-leaves over three seasons. These findings provide new insights into abundance and influencing factors of metabolites of tea in different seasons, and further our understanding in the formation of flavor, nutrition and medicinal function.
Characterisation of early responses in lead accumulation and localization of Salix babylonica L. roots
Authors: Xue Wenxiu , Jiang Yi , Shang Xiaoshuo , Zou Jinhua
Published: June 2020

Background

Lead (Pb) is a harmful pollutant that disrupts normal functions from the cell to organ levels. Salix babylonica is characterized by high biomass productivity, high transpiration rates, and species specific Pb. Better understanding the accumulating and transporting Pb capability in shoots and roots of S. babylonica, the toxic effects of Pb and the subcellular distribution of Pb is very important.

Results

Pb exerted inhibitory effects on the roots and shoots growth at all Pb concentrations. According to the results utilizing inductively coupled plasma atomic emission spectrometry (ICP-AES), S. babylonica can be considered as a plant with great phytoextraction potentials as translocation factor (TF) value > 1 is observed in all treatment groups throughout the experiment. The Leadmium™ Green AM dye test results indicated that Pb ions initially entered elongation zone cells and accumulated in this area. Then, ions were gradually accumulated in the meristem zone. After 24 h of Pb exposure, Pb accumulated in the meristem zone. The scanning electron microscopy (SEM) and energy-dispersive X-ray analyses (EDXA) results confirmed the fluorescent probe observations and indicated that Pb was localized to the cell wall and cytoplasm. In transverse sections of the mature zone, Pb levels in the cell wall and cytoplasm of epidermal cells was the lowest compared to cortical and vessel cells, and an increasing trend in Pb content was detected in cortical cells from the epidermis to vascular cylinder. Similar results were shown in the Pb content in the cell wall and cytoplasm of the transverse sections of the meristem. Cell damage in the roots exposed to Pb was detected by propidium iodide (PI) staining, which was in agreement with the findings of Pb absorption in different zones of S. babylonica roots under Pb stress.

Conclusion

S. babylonica L. is observed as a plant with great potential of Pb-accumulation and Pb-tolerance. The information obtained here of Pb accumulation and localization in S. babylonica roots can furthers our understanding of Pb-induced toxicity and its tolerance mechanisms, which will provide valuable and scientific information to phytoremediation investigations of other woody plants under Pb stress.
Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods
Authors: Kippes Nestor , VanGessel Carl , Hamilton James , Akpinar Ani , Budak Hikmet , Dubcovsky Jorge , Pearce Stephen
Published: June 2020

Background

Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutations in eitherPHYBorPHYCresult in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod.

Results

We found that under non-inductive short-day (SD) photoperiods,phyB-null andphyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type (WT) plants. The delay in heading between WT andphymutants was greater in LD than in SD, confirming the importance ofPHYBandPHYCin accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods,PHYBregulated more genes thanPHYC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated byPHYBandPHYCin either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genesVRN-A1andPPD-B1inphyBandphyCmutants compared to the WT.

Conclusions

Our study confirms the major role of bothPHYBandPHYCin flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in thephyB-null andphyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.
Identification of small RNAs during cold acclimation in Arabidopsis thaliana
Authors: Tiwari Bhavika , Habermann Kristin , Arif M. Asif , Weil Heinrich Lukas , Garcia-Molina Antoni , Kleine Tatjana , Mühlhaus Timo , Frank Wolfgang
Published: June 2020

Background

Cold stress causes dynamic changes in gene expression that are partially caused by small non-coding RNAs since they regulate protein coding transcripts and act in epigenetic gene silencing pathways. Thus, a detailed analysis of transcriptional changes of small RNAs (sRNAs) belonging to all known sRNA classes such as microRNAs (miRNA) and small interfering RNA (siRNAs) in response to cold contributes to an understanding of cold-related transcriptome changes.

Result

We subjected A. thaliana plants to cold acclimation conditions (4 °C) and analyzed the sRNA transcriptomes after 3 h, 6 h and 2 d. We found 93 cold responsive differentially expressed miRNAs and only 14 of these were previously shown to be cold responsive. We performed miRNA target prediction for all differentially expressed miRNAs and a GO analysis revealed the overrepresentation of miRNA-targeted transcripts that code for proteins acting in transcriptional regulation. We also identified a large number of differentially expressed cis- and trans-nat-siRNAs, as well as sRNAs that are derived from long non-coding RNAs. By combining the results of sRNA and mRNA profiling with miRNA target predictions and publicly available information on transcription factors, we reconstructed a cold-specific, miRNA and transcription factor dependent gene regulatory network. We verified the validity of links in the network by testing its ability to predict target gene expression under cold acclimation.

Conclusion

In A. thaliana, miRNAs and sRNAs derived from cis- and trans-NAT gene pairs and sRNAs derived from lncRNAs play an important role in regulating gene expression in cold acclimation conditions. This study provides a fundamental database to deepen our knowledge and understanding of regulatory networks in cold acclimation.
Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam)
Authors: Qin Zhen , Hou Fuyun , Li Aixian , Dong Shuxu , Huang Chengxing , Wang Qingmei , Zhang Liming
Published: June 2020

Background

Sweet potato (Ipomoea batatas (L.) Lam.) is a highly heterozygous autohexaploid crop with high yield and high anthocyanin content. Purple sweet potato is the main source of anthocyanins, and the mechanism of anthocyanin biosynthesis in storage roots has not been fully revealed.

Results

In order to reveal the mechanism of anthocyanin biosynthesis and identify new homologous genes involved in anthocyanin biosynthesis in the storage roots of sweet potato, we used Ningzishu 1 and Jizishu 2 as parents to construct a F1 hybrid population. Seven anthocyanin-containing lines and three anthocyanin-free lines were selected for full-length and second-generation transcriptome analyses. A total of 598,375 circular consensus sequencing reads were identified from full-length transcriptome sequencing. After analysis and correction of second-generation transcriptome data, 41,356 transcripts and 18,176 unigenes were obtained. Through a comparative analysis between anthocyanin-containing and anthocyanin-free groups 2329 unigenes were found to be significantly differentially expressed, of which 1235 were significantly up-regulated and 1094 were significantly down-regulated. GO enrichment analysis showed that the differentially expressed unigenes were significantly enriched in molecular function and biological process. KEGG enrichment analysis showed that the up-regulated unigenes were significantly enriched in the flavonoid biosynthesis and phenylpropanoid biosynthesis pathways, and the down-regulated unigenes were significantly enriched in the plant hormone signal transduction pathway. Weighted gene co-expression network analysis of differentially expressed unigenes revealed that anthocyanin biosynthesis genes were co-expressed with transcription factors such as MYB, bHLH and WRKY at the transcription level.

Conclusions

Our study will shed light on the regulatory mechanism of anthocyanin biosynthesis in sweet potato storage roots at the transcriptome level.
Characterization of Brazilian hospital admissions due to cardiovascular diseases: a longitudinal study
Authors: de Araújo Fonseca Luiza Gabriela , Lima Illia Nadinne Dantas Florentino , Gualdi Lucien Peroni
Published: June 2020

Background

Cardiovascular diseases (CVD) are the main cause of death and comorbidities worldwide. It is estimated that three quarters of all deaths related to CVD occur in low and middle income countries such as Brazil. Furthermore, it is estimated that emerging countries will present the highest worldwide prevalence of such diseases by 2050. In view of the above, this study aims to characterize Brazilian hospital admission distribution classified by the ICD-10 in adults between 2008 and 2017 in Brazil.

Methods

This is a longitudinal descriptive study in which all data regarding hospital admissions registered in the Brazilian Hospital Information System of “Sistema Único de Saúde” (SIH/SUS) due to cardiovascular diseases (ICD-10) were included. All admissions from private or public services linked to the SUS from 2008 and 2017 were evaluated. The following variables were collected: number of hospital admissions, place of hospitalization classified by the ICD-10 and mortality rate at the federal level and according to regions. Absolute values and frequency of hospital admissions were grouped according to sex, age and living region as well as the number of deaths. The extracted data was stored in a Microsoft Excel 2013 program spreadsheet. Statistical analysis was performed by GraphPad Prism version 5.0 software.

Results

There was a total of 11,345,821 hospital admissions due to CVD registered between 2008 and 2017. Individuals from 50 to 79 years old were the most affected. Heart failure (21.3%), other ischemic heart diseases (13.3%) and stroke (11.4%) were responsible for almost half of the hospital admissions associated to CVD. The number of registered deaths caused by any CVD was 867,838 and the national mortality rate was 7.82.

Conclusion

CVD were responsible for around 10% of all hospital admissions in Brazil between 2008 and 2017. Moreover, it was possible to observe a decrease in hospital admissions as well as mortality rate over time after implementing governmental strategies to prevent cardiovascular diseases.