bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA let-7 and viral infections: focus on mechanisms of action
Authors: Letafati Arash , Najafi Sajad , Mottahedi Mehran , Karimzadeh Mohammad , Shahini Ali , Garousi Setareh , Abbasi-Kolli Mohammad , Sadri Nahand Javid , Tamehri Zadeh Seyed Saeed , Hamblin Michael R. , Rahimian Neda , Taghizadieh Mohammad , Mirzaei Hamed 
Published: February 2022

AbstractMicroRNAs (miRNAs) are fundamental post-transcriptional modulators of several critical cellular processes, a number of which are involved in host defense mechanisms. In particular, miRNA let-7 functions as an essential regulator of the function and differentiation of both innate and adaptive immune cells. Let-7 is involved in several human diseases, including cancer and viral infections. Several viral infections have found ways to dysregulate the expression of miRNAs. Extracellular vesicles (EV) are membrane-bound lipid structures released from many types of human cells that can transport proteins, lipids, mRNAs, and miRNAs, including let-7. After their release, EVs are taken up by the recipient cells and their contents released into the cytoplasm. Let-7-loaded EVs have been suggested to affect cellular pathways and biological targets in the recipient cells, and can modulate viral replication, the host antiviral response, and the action of cancer-related viruses. In the present review, we summarize the available knowledge concerning the expression of let-7 family members, functions, target genes, and mechanistic involvement in viral pathogenesis and host defense. This may provide insight into the development of new therapeutic strategies to manage viral infections.
Characteristic and affecting factors of wetland herbs’ distribution in the radiant belt toward land of lake–terrestrial ecotone in Tibet, China
Authors: Zheng Pei-Ru , Li Chun-Hua , Ye Chun , Wang Hao , Wei Wei-Wei , Zheng Ye , Zheng Xiang-yong 
Published: February 2022

Abstract
Background
Lake is a critical part of Tibet's hydrological cycle, the lake–terrestrial ecotone is the most sensitive area in the water and terrestrial ecosystem. For the ecological protection and maintenance of the lakeside zone, defining the upper boundary of the lake–terrestrial ecotone is a key issue that needs to be solved urgently. However, the ecological characteristics of lake–terrestrial ecotone made it difficult to delimit. Wetland herbs are characteristic plants of the lake–terrestrial ecotone, and their distribution width can be used to reflect the upper boundary of the lake–terrestrial ecotone. We took Baksum Lake, Yamdroktso, Namtso, Siling Co as examples, based on the spatial structure of the lake–terrestrial ecotone, used the moving split-window technology (MSWT) delimited the width of wetland herbs.

Results
The results of the MSWT showed the distribution width of wetland herbs in each lake–terrestrial ecotone with the natural-wetland type sampling line of Baksum Lake, Yamdroktso, Namtso, Siling Co was 51 m, 56 m, 33 ~ 53 m, 19 ~ 31 m. The detrended correspondence analysis (DCA) showed quantity of wetland herbs species, BK1 > YT1 = NT1 > NT2 > SC1 = SC2. The principal component analysis (PCA) and the (redundancy analysis) RDA showed soil moisture content (SMO), pH, soil moisture content (SSC), and soil nutrient content had obvious correlation with distribution width.

Conclusion
The MSWT was a feasible method to determine the width of lake–terrestrial ecotone. SMO, pH, SSC, and soil nutrient content were all important environmental factors affecting the wetland herbs distribution width of the four lakes; and the SMO was the most important factor. Besides, compared with the lakes in the Middle-Lower Yangtze Plain, the high-density population distribution, high-intensive human activity invaded the plants' growth area, resulting in a smaller distribution width. The distribution edge of wetland herbs is equivalent to the upper boundary of lake–terrestrial ecotone. It determines the management boundary of the lake–terrestrial ecotone, provides a theoretical basis for the construction of environmental protection projects, and is of great significance to the lake ecological restoration and management in watershed control planning.
gcaPDA: a haplotype-resolved diploid assembler
Authors: Xie Min , Yang Linfeng , Jiang Chenglin , Wu Shenshen , Luo Cheng , Yang Xin , He Lijuan , Chen Shixuan , Deng Tianquan , Ye Mingzhi , Yan Jianbing , Yang Ning 
Published: February 2022

Abstract
Background
Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity.

Results
Here, Using robust programs, we build a diploid genome assembly pipeline called gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We demonstrate the effectiveness of gcaPDA based on simulated HiFi reads of maize genome which is highly heterozygous and repetitive, and real data from rice.

Conclusions
With applicability of coping with complex genomes and fewer restrictions on application than most of diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes.
Degeneracy measures in biologically plausible random Boolean networks
Authors: Kocaoglu Basak , Alexander William H. 
Published: February 2022

Abstract
Background
Degeneracy—the ability of structurally different elements to perform similar functions—is a property of many biological systems. Highly degenerate systems show resilience to perturbations and damage because the system can compensate for compromised function due to reconfiguration of the underlying network dynamics. Degeneracy thus suggests how biological systems can thrive despite changes to internal and external demands. Although degeneracy is a feature of network topologies and seems to be implicated in a wide variety of biological processes, research on degeneracy in biological networks is mostly limited to weighted networks. In this study, we test an information theoretic definition of degeneracy on random Boolean networks, frequently used to model gene regulatory networks. Random Boolean networks are discrete dynamical systems with binary connectivity and thus, these networks are well-suited for tracing information flow and the causal effects. By generating networks with random binary wiring diagrams, we test the effects of systematic lesioning of connections and perturbations of the network nodes on the degeneracy measure.

Results
Our analysis shows that degeneracy, on average, is the highest in networks in which ~ 20% of the connections are lesioned while 50% of the nodes are perturbed. Moreover, our results for the networks with no lesions and the fully-lesioned networks are comparable to the degeneracy measures from weighted networks, thus we show that the degeneracy measure is applicable to different networks.

Conclusions
Such a generalized applicability implies that degeneracy measures may be a useful tool for investigating a wide range of biological networks and, therefore, can be used to make predictions about the variety of systems’ ability to recover function.
Genetic characterization and genome-wide association mapping for stem rust resistance in spring bread wheat
Authors: Shewabez Elias , Bekele Endashaw , Alemu Admas , Mugnai Laura , Tadesse Wuletaw 
Published: February 2022

Abstract
Background
Emerging wheat stem rust races have become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economic and environmentally sound strategy to combat this problem. Thus, this study was aimed at characterizing the genetic diversity and identifying the genetic loci conferring resistance to the stem rust of wheat. To accomplish this, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were evaluated under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The single nucleotide polymorphisms (SNP) marker data was retrieved from a 15 K SNP wheat array. A mixed linear model was used to investigate the association between SNP markers and the best linear unbiased prediction (BLUP) values of the stem rust coefficient of infection (CI).

Results
Phenotypic analysis revealed that 46% of the lines had a coefficient of infection (CI) in a range of 0 to 19. Genome-wide average values of 0.38, 0.20, and 0.71 were recorded for Nei’s gene diversity, polymorphism information content, and major allele frequency, respectively. A total of 46 marker-trait associations (MTAs) encompassed within eleven quantitative trait loci (QTL) were detected on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A for CI. Two major QTLs with –log10 (p) ≥ 4 (EWYP1B.1 and EWYP1B.2) were discovered on chromosome 1B.

Conclusions
This study identified several novel markers associated with stem rust resistance in wheat with the potential to facilitate durable rust resistance development through marker-assisted selection. It is recommended that the resistant wheat genotypes identified in this study be used in the national wheat breeding programs to improve stem rust resistance.
The interplay between infection risk factors of SARS-CoV-2 and mortality: a cross-sectional study from a cohort of long-term care nursing home residents
Authors: Soldevila Laura , Prat Núria , Mas Miquel À. , Massot Mireia , Miralles Ramón , Bonet-Simó Josep M. , Isnard Mar , Expósito-Izquierdo Marta , Garcia-Sanchez Irene , Rodoreda-Noguerola Sara , Moreno Nemesio , Badia Esther , López Genís , Sevilla Javier , Estrada Oriol , Vallès Xavier 
Published: February 2022

Abstract
Background
Covid-19 pandemic has particularly affected older people living in Long-term Care settings in terms of infection and mortality.

Methods
We carried out a cross-sectional analysis within a cohort of Long-term care nursing home residents between March first and June thirty, 2020, who were ≥ 65 years old and on whom at least one PCR test was performed. Socio-demographic, comorbidities, and clinical data were recorded. Facility size and community incidence of SARS-CoV-2 were also considered. The outcomes of interest were infection (PCR positive) and death.

Results
A total of 8021 residents were included from 168 facilities. Mean age was 86.4 years (SD = 7.4). Women represented 74.1%. SARS-CoV-2 infection was detected in 27.7% of participants, and the overall case fatality rate was 11.3% (24.9% among those with a positive PCR test). Epidemiological factors related to risk of infection were larger facility size (pooled aOR 1.73; P < .001), higher community incidence (pooled aOR 1.67, P = .04), leading to a higher risk than the clinical factor of low level of functional dependence (aOR 1.22, P = .03). Epidemiological risk factors associated with mortality were male gender (aOR 1.75; P < .001), age (pooled aOR 1.16; P < .001), and higher community incidence (pooled aOR 1.19, P = < 0.001) whereas clinical factors were low level of functional dependence (aOR 2.42, P < .001), Complex Chronic Condition (aOR 1.29, P < .001) and dementia (aOR 1.33, P <0.001). There was evidence of clustering for facility and health area when considering the risk of infection and mortality (P < .001).

Conclusions
Our results suggest a complex interplay between structural and individual factors regarding Covid-19 infection and its impact on mortality in nursing-home residents.
Analysing the protection from respiratory tract infections and allergic diseases early in life by human milk components: the PRIMA birth cohort
Authors: van Stigt Arthur H. , Oude Rengerink Katrien , Bloemenkamp Kitty W. M. , de Waal Wouter , Prevaes Sabine M. P. J. , Le Thuy-My , van Wijk Femke , Nederend Maaike , Hellinga Anneke H. , Lammers Christianne S. , den Hartog Gerco , van Herwijnen Martijn J. C. , Garssen Johan , Knippels Léon M. J. , Verhagen Lilly M. , de Theije Caroline G. M. , Lopez-Rincon Alejandro , Leusen Jeanette H. W. , van’t Land Belinda , Bont Louis ,   PRIMA Initiative Group, Knulst André C. , van der Ent C. Kors , van Baarle Debbie , Wauben Marca H. M. , Rots Nynke Y. , Sanders Elisabeth A. M. , Benders Manon J. N. L. , Meulenbroek Laura A. M. P. , Stahl Bernd , Kraneveld Aletta D. , Buiteman Brigitte J. M. , Voogt Tanja , van der Meij Barbara , Lerkvaleekul Butsabong , Voogd Eline , Lammers Christianne S. , Lalmahomed Tariq A. , Brus Iris M. , van Meerwijk Daphne M. M. , Jepma Sophie I. E. 
Published: February 2022

AbstractBackgroundMany studies support the protective effect of breastfeeding on respiratory tract infections. Although infant formulas have been developed to provide adequate nutritional solutions, many components in human milk contributing to the protection of newborns and aiding immune development still need to be identified. In this paper we present the methodology of the “Protecting against Respiratory tract lnfections through human Milk Analysis” (PRIMA) cohort, which is an observational, prospective and multi-centre birth cohort aiming to identify novel functions of components in human milk that are protective against respiratory tract infections and allergic diseases early in life.MethodsFor the PRIMA human milk cohort we aim to recruit 1000 mother–child pairs in the first month postpartum. At one week, one, three, and six months after birth, fresh human milk samples will be collected and processed. In order to identify protective components, the level of pathogen specific antibodies, T cell composition, Human milk oligosaccharides, as well as extracellular vesicles (EVs) will be analysed, in the milk samples in relation to clinical data which are collected using two-weekly parental questionnaires. The primary outcome of this study is the number of parent-reported medically attended respiratory infections. Secondary outcomes that will be measured are physician diagnosed (respiratory) infections and allergies during the first year of life.DiscussionThe PRIMA human milk cohort will be a large prospective healthy birth cohort in which we will use an integrated, multidisciplinary approach to identify the longitudinal effect human milk components that play a role in preventing (respiratory) infections and allergies during the first year of life. Ultimately, we believe that this study will provide novel insights into immunomodulatory components in human milk. This may allow for optimizing formula feeding for all non-breastfed infants.
COVID-19 vaccine hesitancy among different population groups in China: a national multicenter online survey
Authors: Huang Yiman , Su Xiaoyou , Xiao Weijun , Wang Hao , Si Mingyu , Wang Wenjun , Gu Xiaofen , Ma Li , Li Li , Zhang Shaokai , Yang Chunxia , Yu Yanqin , Qiao Youlin 
Published: February 2022

Abstract
Background
COVID-19 vaccine has been available in China since the beginning of the 2021, however, certain numbers of people are reluctant for some reasons to vaccinate. The high vaccine coverage is crucial for controlling disease transmission, however, the vaccine hesitancy might be a barrier to the establishment of sufficient herd immunization. This study aims to investigate the prevalence of the COVID-19 vaccine hesitancy among different population groups, and explore common barriers and facilitators to vaccination decisions.

Methods
The current survey was performed among Chinese students, public health professionals, medical workers and general population from January to March 2021 from seven cities in China. The questionnaire contained sociodemographic information, concerns about infection with COVID-19, general vaccination behaviors and attitudes, the General Vaccine Hesitancy Scale, the COVID-19 Vaccine Hesitancy Scale and other potential factors. Univariate analysis was conducted by chi-squared test, and variables significant at P < 0.10 were then included in a multivariable regression model.

Results
The prevalence of COVID-19 vaccine hesitancy was 15.6% in our study, and 23.9% of students, 21.2% of the general population, 13.1% of medical workers, and 10.4% of public health professionals had vaccine hesitancy. The results of multivariate analysis indicated that participants who had received negative information of COVID-19 vaccine (OR: 1.563, 95% CI: 1.229–1.986) and who had doubts about the information source (OR: 2.157, 95% CI: 1.697–2.742) were more likely to have vaccine hesitancy. While those who needed transparent information about COVID-19 vaccine (OR: 0.722, 95% CI: 0.535–0.973) and who would get COVID-19 vaccine if doctors recommended (OR: 0.176, 95% CI: 0.132–0.234) were less likely to have COVID-19 vaccine hesitancy.

Conclusions
Given recommendations from medical workers about vaccination can motivate people to accept COVID-19 vaccination, appropriate training in knowledge about vaccines and communication skills are necessary for them to increase public’s willingness of vaccination. Reducing the spread of misinformation and disseminating facts in a timely and accurate way will likely reduce vaccine hesitancy. Moreover, to establish suitable communication strategies and information exchange platforms between the government and the public and a warning system on infodemic would be helpful to improve public’s confidence in vaccination.
What are the strategies for implementing primary care models in maternity? A systematic review on midwifery units
Authors: Batinelli Laura , Thaels Ellen , Leister Nathalie , McCourt Christine , Bonciani Manila , Rocca-Ihenacho Lucia 
Published: February 2022

Abstract
Background
Midwifery Units (MUs) are associated with optimal perinatal outcomes, improved service users’ and professionals’ satisfaction as well as being the most cost-effective option. However, they still do not represent the mainstream option of maternity care in many countries. Understanding effective strategies to integrate this model of care into maternity services could support and inform the MU implementation process that many countries and regions still need to approach.

Methods
A systematic search and screening of qualitative and quantitative research about implementation of new MUs was conducted (Prospero protocol reference: CRD42019141443) using PRISMA guidelines. Included articles were appraised using the CASP checklist. A meta-synthesis approach to analysis was used. No exclusion criteria for time or context were applied to ensure inclusion of different implementation attempts even under different historical and social circumstances. A sensitivity analysis was conducted to reflect the major contribution of higher quality studies.

Results
From 1037 initial citations, twelve studies were identified for inclusion in this review after a screening process. The synthesis highlighted two broad categories: implementation readiness and strategies used. The first included aspects related to cultural, organisational and professional levels of the local context whilst the latter synthesised the main actions and key points identified in the included studies when implementing MUs. A logic model was created to synthesise and visually present the findings.

Conclusions
The studies selected were from a range of settings and time periods and used varying strategies. Nonetheless, consistencies were found across different implementation processes. These findings can be used in the systematic scaling up of MUs and can help in addressing barriers at system, service and individual levels. All three levels need to be addressed when implementing this model of care.
Randomised controlled trial of Interpersonal and Social Rhythm Therapy and group-based Cognitive Remediation versus Interpersonal and Social Rhythm Therapy alone for mood disorders: study protocol
Authors: Douglas Katie M. , Inder Maree L. , Crowe Marie T. , Jordan Jennifer , Carlye Dave , Lacey Cameron , Beaglehole Ben , Mulder Roger , Eggleston Kate , Donovan Katherine A. , Frampton Christopher M. A. , Bowie Christopher R. , Porter Richard J. 
Published: February 2022

Abstract
Background
Individuals with mood disorders frequently experience cognitive impairment, which impacts on the long-term trajectory of the disorders, including being associated with persisting difficulties in occupational and psychosocial functioning, residual mood symptoms, and relapse. Current first-line treatments for mood disorders do little to improve cognitive function. Targeting cognition in clinical research is thus considered a priority. This protocol outlines a prospectively-registered randomised controlled trial (RCT) which examines the impact of adding group-based Cognitive Remediation (CR) to Interpersonal and Social Rhythm Therapy (IPSRT-CR) for individuals with mood disorders.

Methods
This is a pragmatic, two-arm, single-blinded RCT comparing IPSRT-CR with IPSRT alone for adults (n = 100) with mood disorders (Major Depressive Disorder or Bipolar Disorder) with subjective cognitive difficulties, on discharge from Specialist Mental Health Services in Christchurch, New Zealand. Both treatment arms will receive a 12-month course of individual IPSRT (full dose = 24 sessions). At 6 months, randomisation to receive, or not, an 8-week group-based CR programme (Action-based Cognitive Remediation – New Zealand) will occur. The primary outcome will be change in Global Cognition between 6 and 12 months (treatment-end) in IPSRT-CR versus IPSRT alone. Secondary outcomes will be change in cognitive, functional, and mood outcomes at 6, 12, 18, and 24 months from baseline and exploratory outcomes include change in quality of life, medication adherence, rumination, and inflammatory markers between treatment arms. Outcome analyses will use an intention-to-treat approach. Sub-group analyses will assess the impact of baseline features on CR treatment response. Participants’ experiences of their mood disorder, including treatment, will be examined using qualitative analysis.

Discussion
This will be the first RCT to combine group-based CR with an evidence-based psychotherapy for adults with mood disorders. The trial may provide valuable information regarding how we can help promote long-term recovery from mood disorders. Many issues have been considered in developing this protocol, including: recruitment of the spectrum of mood disorders, screening for cognitive impairment, dose and timing of the CR intervention, choice of comparator treatment, and choice of outcome measures.

Trial registration
Australian and New Zealand Clinical Trials Registry, ACTRN12619001080112. Registered on 6 August 2019.