bluuebunny/crossref_metadata_2025 huggingface dataset:
How Mentors Contribute to Latinx Adolescents’ Social Capital in the Sciences
Authors: Sánchez Bernadette , Mroczkowski Alison L. , Flores Lisa Y. , de los Reyes Wendy , Ruiz Jesus , Rasgado-Flores Hector
Published: January 2021

The aim of this study was to examine how mentors provide social capital to Latinx adolescents in science education. Participants were drawn from a long-term, comprehensive science support program at a medical university in the Midwest. Using a case study approach, various stakeholders participated in one-on-one, in-depth qualitative interviews: 11 Latinx high school and college students, three staff members, 12 graduate student mentors, and 13 faculty mentors. Protocols were approved by an Institutional Review Board. The qualitative analysis was guided by a modified grounded theory approach, which involved three steps: initial coding, focused coding, and modified axial coding. Participants described how mentors promoted youth’s social capital through bridging and bonding behaviors, which were related to students’ (a) enhanced professional development, (b) broadened perspectives about science specifically and education broadly, (c) exploration opportunities, and (d) increased interest in science. This study fills gaps in the literature by showing how bridging and bonding social capital are provided in mentoring relationships and by examining STEM mentoring in a Latinx adolescent sample. Study findings have implications for increasing Latinx students in the science education pipeline. Future directions for research on STEM mentoring and social capital are discussed.
Ethnic Socialization in Current and Prospective Parents
Authors: Wojda Kayla , Tram Jane M. , Truong Arthur , Anderson Danielle M.
Published: January 2021

Few studies have examined whether the manner in which one has been parented impacts one’s subsequent parenting style regarding ethnic socialization. We examined this question in current and prospective parents. First, we found that receiving greater familial ethnic socialization is significantly correlated with stronger subsequent parental ethnic socialization (PES) for both current and prospective parents. Second, we found that PES did not significantly differ between current and prospective parents. Third, given the limited research examining the ethnic socialization experiences of those who are White, we examined these questions specifically for our White participants. Our findings persisted when we examined all ethnicities together and when we examined White participants alone.
When Journalists See Themselves as Villains: The Power of Negative Discourse
Authors: Moon Ruth
Published: January 2021

This article examines the way journalists talk about themselves and negotiate authority with sources, audiences, and media policy in a postconflict, developmental authoritarian state. Grounded in concepts of metajournalistic discourse and authority, the study shows how members of the journalism field in some contexts embrace a narrative that limits autonomy and situates them as untrustworthy social actors. Interviews collected over a 7-month period in Rwanda show that a shared sense of untrustworthiness defines the contemporary boundaries of the Rwandan journalism field. The findings also suggest that consensus-oriented or postconflict social contexts might encourage journalists to adopt less autonomous social roles.
Pathophysiology of the comorbidity of glaucoma with obstructive sleep apnea: A postulation
Authors: Goyal Manish , Tiwari Uma Sharan , Jaseja Harinder
Published: January 2021

Glaucoma is a serious and progressive optic neuropathy, the exact pathophysiology of which is still poorly understood. Furthermore, glaucoma exhibits significant comorbidity with obstructive sleep apnea (OSA) that warrants an in-depth study in view of highly probable beneficial and far-reaching clinical implications. In this brief paper, the authors have studied the existing theories in an attempt to explain the comorbidity and its underlying pathophysiology. From the ensuing evidence, the role of connective tissue strength has emerged as a major factor and which appears to play a pivotal role not only in the development of glaucoma but also in the underlying pathophysiology of its enigmatic comorbidity with OSA. Understanding the pathophysiology of the comorbidity can stimulate newer therapeutic strategies targeted toward strengthening of connective tissues that may at least retard if not arrest the progression of glaucomatous changes and their complications.
Using WhatsApp for focus group discussions: ecological validity, inclusion and deliberation
Authors: Colom Anna
Published: January 2021

WhatsApp’s ubiquity in many people’s everyday lives points at new possibilities for conducting online and mobile focus groups. Yet, research on the benefits and potential pitfalls of this is negligible. This paper offers new empirical insights from using the method as part of a digital ethnography with young activists in Western Kenya. The presence of WhatsApp in participants’ everyday lives offers a context with high ecological validity. The paper suggests that this opens up new options for designing online focus groups, transcending the traditional categorisation between synchronous and asynchronous interactions and some limitations of both approaches. WhatsApp also offers opportunities for creating more inclusive group discussions. Using discourse analysis of the WhatsApp focus group, the paper also finds that this familiarity and inclusivity affords the potential for group deliberation, which can be particularly valuable in participatory research.
Comparative higher education research in times of globalisation of higher education: Theoretical and methodological insights
Authors: Hauptman Komotar Maruša
Published: January 2021

In times of globalisation of higher education, alternative theoretical and methodological approaches were introduced in the field of comparative higher education research. To stimulate the debate on this issue, this paper firstly addresses them theoretically by combining the concept of institutional isomorphism and the ‘glonacal’ analytical heuristic. On this basis, it discusses arguments in favour of convergence and diversity from the perspective of the internationalisation of higher education and also points to the limits of institutional isomorphism resulting from ‘glonacal’ influences of agencies and agency on the development of (internationalisation of) higher education. Secondly, the paper also draws attention to the influence of globalisation on the selection of methodology in comparative higher education research by exposing the limits of methodological nationalism. Along these lines, it portrays the reversed pyramid model of different horizontal and vertical levels of comparisons with which it establishes the (missing) link between the selected theoretical and methodological framework of comparative (higher education) research. In conclusion, it acknowledges the need to integrate the contextual element into the comparative framework which allows thorough analysis of complex relationships between globalisation and higher education both theoretically and methodologically.
Primary Crime Prevention Apps: A Typology and Scoping Review
Authors: Wood Mark A. , Ross Stuart , Johns Diana
Published: January 2021

In the last decade, an array of smartphone apps have been designed to prevent crime, violence, and abuse. The evidence base of these apps has, however, yet to analyzed systematically. To rectify this, the aims of this review were (1) to establish the extent, range, and nature of research into smartphone apps with a primary crime prevention function; (2) to locate gaps in the primary crime prevention app literature; and (3) to develop a typology of primary crime prevention apps. Employing a scoping review methodology and following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, studies were identified via Web of Science, EBSCOhost, and Google Scholar. We included English-language research published between 2008 and 2020 that examined smartphone applications designed explicitly for primary crime prevention. Sixty-one publications met our criteria for review, out of an initial sample of 151 identified. Our review identified six types of crime prevention app examined in these publications: self-surveillance apps, decision aid apps, child-tracking apps, educational apps, crime-mapping/alert apps, and crime reporting apps. The findings of our review indicate that most of these forms of primary crime prevention apps have yet to be rigorously evaluated and many are not evidence-based in their design. Consequently, our review indicates that recent enthusiasm over primary crime prevention apps is not supported by an adequate evidence base.
Successful Aortic Valve Replacement With Perceval Bioprosthesis for Aortic Stenosis With Membranous Ventricular Septum Aneurysm
Authors: Nishijima Shuhei , Nakamura Yoshitsugu , Gersak Borut , Namiki Shigetaka , Kouzaki Tsunashi , Tsuchiya Yoshiki
Published: January 2021

Membranous ventricular septum aneurysm (MVSA) is extremely rare, especially when coexisting with aortic stenosis (AS), and reports regarding the available treatment for MVSA with AS are limited. Aortic valve replacement (AVR) can be challenging because of anatomical reasons. In this case report, a patient with MVSA and severe AS was treated with AVR with the sutureless Perceval bioprosthesis. After implantation, no paravalvular leakage was detected in echocardiography, and no other postoperative complications were observed. Postoperative electrocardiography-gated computed tomography revealed no contrast enhancement for MVSA. The MVSA was closed by the Perceval bioprosthetic valve. Thus, patients with simultaneous MVSA and AS may be effectively treated with AVR using a Perceval bioprosthesis.
A modular framework for early-phase seamless oncology trials
Authors: Boonstra Philip S , Braun Thomas M , Chase Elizabeth C
Published: January 2021

Background:

As our understanding of the etiology and mechanisms of cancer becomes more sophisticated and the number of therapeutic options increases, phase I oncology trials today have multiple primary objectives. Many such designs are now “seamless,” meaning that the trial estimates both the maximum tolerated dose and the efficacy at this dose level. Sponsors often proceed with further study only with this additional efficacy evidence. However, with this increasing complexity in trial design, it becomes challenging to articulate fundamental operating characteristics of these trials, such as (1) what is the probability that the design will identify an acceptable, that is., safe and efficacious, dose level? or (2) how many patients will be assigned to an acceptable dose level on average?

Methods:

In this manuscript, we propose a new modular framework for designing and evaluating seamless oncology trials. Each module is comprised of either a dose assignment step or a dose-response evaluation, and multiple such modules can be implemented sequentially. We develop modules from existing phase I/II designs as well as a novel module for evaluating dose-response using a Bayesian isotonic regression scheme.

Results:

We also demonstrate a freely available R package called seamlesssim to numerically estimate, by means of simulation, the operating characteristics of these modular trials.

Conclusions:

Together, this design framework and its accompanying simulator allow the clinical trialist to compare multiple different candidate designs, more rigorously assess performance, better justify sample sizes, and ultimately select a higher quality design.
Functional bias of morphine and oliceridine under conditions of minor injury
Authors: Nwaneshiudu Chinwe , Shi Xiao-Yu , Sahbaie Peyman , David Clark J
Published: January 2021

Recent reports suggest pain from surgical injury may influence the risks associated with exposure to opioids. In mice, hind-paw incision attenuates morphine-primed reinstatement due to kappa opioid receptor activation by dynorphin. In this focused group of studies, we examined the hypotheses that kappa-opioid receptor activation in the nucleus accumbens mediates attenuated drug- primed reinstatement after incisional surgery, and the G-protein biased mu-opioid agonist, oliceridine, leads to less priming of the dynorphin effect in comparison to morphine. To address these hypotheses, adult C57BL/6 male mice underwent intracranial cannulation for administration of the selective kappa-opioid antagonist norBNI directly into the nucleus accumbens. After recovery, they were conditioned with morphine or oliceridine after hind-paw incisional injury, then underwent extinction followed by opioid-primed reinstatement. Intra-accumbal administration of norBNI was carried out prior to testing. The nucleus accumbens and medial prefrontal cortex were extracted and analyzed for expression of prodynorphin. We observed that animals conditioned with morphine in the setting of incisional injury demonstrated blunted responses to opioid-primed reinstatement, and that the blunted responses were reversed with intra-accumbal norBNI administration. Persistently elevated levels of prodynorphin expression in the medial prefrontal cortex and nucleus accumbens were observed in the incised morphine-treated animals. However, both behavioral and molecular changes were absent in animals with incisional injury conditioned with oliceridine. These findings suggest a role for prodynorphin expression in the nucleus accumbens with exposure to morphine after surgery that may protect individuals from relapse not shared with biased mu- opioid receptor agonists.
A phase II study of cisplatin plus vinorelbine combined with atezolizumab as adjuvant therapy for completely resected non-small-cell lung cancer with EGFR mutation (West Japan Oncology Group 11719L/ADJUST study)
Authors: Shibaki Ryota , Akamatsu Hiroaki , Kato Terufumi , Nishino Kazumi , Okada Morihito , Mitsudomi Tetsuya , Wakuda Kazushige , Yoshimura Kenichi , Yamamoto Nobuyuki , Nakagawa Kazuhiko
Published: January 2021

Background:

Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) is a standard treatment in EGFR-mutated advanced non-small-cell lung cancer (NSCLC); however, previous data have suggested that EGFR-TKI has limited potential as adjuvant therapy. On the contrary, based on subset analysis with the immune checkpoint inhibitor (ICI) plus platinum-doublet chemotherapy in advanced NSCLC with EGFR mutation, we hypothesized that this combination was worth testing as adjuvant therapy in patients with EGFR-mutated NSCLC.

Methods:

Herein, we introduce our phase II study of cisplatin plus vinorelbine combined with atezolizumab as adjuvant therapy for completely resected NSCLC with EGFR mutation. Accrued patients will be pathological stage II–IIIA with completely resected NSCLC and whose tumors have EGFR mutation. Treatment comprises four cycles of cisplatin plus vinorelbine combined with atezolizumab followed by maintenance with atezolizumab. The primary endpoint is the disease-free survival (DFS) rate at 2 years. Secondary endpoints are DFS, overall survival, and safety. In total, 18 patients will be enrolled in this study.

Discussion:

Ongoing phase III trials of adjuvant ICI allow the inclusion of patients with EGFR mutation, but our current trial will provide the earliest clinical data on the efficacy of platinum-doublet chemotherapy with atezolizumab.
The Impact of Exogenous Insulin Input on Calculating Hepatic Clearance Parameters
Authors: McHugh Alexander D. , Chase J. Geoffrey , Knopp Jennifer L. , Ormsbee Jennifer J. , Kulawiec Diana G. , Merry Troy L. , Murphy Rinki , Shepherd Peter R. , Burden Hannah J. , Docherty Paul D.
Published: January 2021

Objective:

Model-based metabolic tests require accurate identification of subject-specific parameters from measured assays. Insulin assays are used to identify insulin kinetics parameters, such as general and first-pass hepatic clearances. This study assesses the impact of intravenous insulin boluses on parameter identification precision.

Method:

Insulin and C-peptide data from two intravenous glucose tolerance test (IVGTT) trials of healthy adults ( N = 10 × 2; denoted A and B), with (A) and without (B) insulin modification, were used to identify insulin kinetics parameters using a grid search. Monte Carlo analysis ( N = 1000) quantifies variation in simulation error for insulin assay errors of 5%. A region of parameter values around the optimum was identified whose errors are within variation due to assay error. A smaller optimal region indicates more precise practical identifiability. Trial results were compared to assess identifiability and precision.

Results:

Trial B, without insulin modification, has optimal parameter regions 4.7 times larger on average than Trial A, with 1-U insulin bolus modification. Ranges of optimal parameter values between trials A and B increase from 0.04 to 0.12 min-1 for hepatic clearance and from 0.07 to 0.14 for first-pass clearance on average. Trial B’s optimal values frequently lie outside physiological ranges, further indicating lack of distinct identifiability.

Conclusions:

A small 1-U insulin bolus improves identification of hepatic clearance parameters by providing a smaller region of optimal parameter values. Adding an insulin bolus in metabolic tests can significantly improve identifiability and outcome test precision. Assay errors necessitate insulin modification in clinical tests to ensure identifiability and precision.
Teacher Perceptions of Barriers to Providing Work-Based Learning Experiences
Authors: Rooney-Kron Magen , Dymond Stacy K.
Published: January 2021

This study investigated teachers’ perceptions of barriers to planning and organizing work-based learning experiences (WBLEs) for students with intellectual disability. Participants were high school special education teachers who had at least one student with an intellectual disability age 14 or older on their caseload ( N = 256). Teachers were asked to complete an online questionnaire about WBLEs. We used content analysis procedures to analyze teacher’s responses to two open-ended questions about barriers to WBLEs that occur in the school and community. Although teachers reported barriers to school and community settings separately, their responses were similar across settings and collapsed into one set of themes. Barriers to planning and organizing WBLEs included opportunities, resources, stakeholder support, time, and support for students. We discuss the need for additional research about contextual factors that may relate to barriers as well as practical implications for how schools and teachers can address barriers.
The Application of Neurodiagnostic Studies to Inform the Acute Management of a Newborn Presenting With Carbamoyl Phosphate Synthetase 1 Deficiency
Authors: McGowan Meaghan , Ferreira Carlos , Whitehead Matthew , Basu Sudeepta K. , Chang Taeun , Gropman Andrea
Published: January 2021

Neonatal-onset urea cycle disorders (UCDs) may result in hyperammonemic (HA) encephalopathy presenting with several neurologic sequelae including seizures, coma, and death. However, no recommendations are given in how and when neurodiagnostic studies should be used to screen or assess for these neurologic complications. We present a case of carbamoyl phosphate synthetase 1 (CPS1) deficiency in a newborn female in which electroencephalogram monitoring to assess encephalopathy and seizures, and magnetic resonance imaging measurements of brain metabolites were used to guide care during her hyperammonemic crisis. Her neurologic course and response to treatment characterizes the significant neurologic impact of HA encephalopathy. Our group herein proposes a clinical neurodiagnostic pathway for managing acute HA encephalopathy.
Epi-Bowman keratectomy versus alcohol-assisted photorefractive keratectomy: wound healing and complications
Authors: Taneri Suphi , Kießler Saskia , Rost Anika , Schultz Tim , Dick H. Burkhard
Published: January 2021

Purpose:

In Epi-Bowman Keratectomy™ (EBK), a new dynamic multi-blade single-use device (Epi-Clear™, Orca Surgical, Israel) is utilized to remove the epithelium by sweeping movements across the corneal surface. Epithelial cells are discarded. Alcohol or other chemical agents are not utilized. We wanted to compare clinical results of Epi-Clear photorefractive kertectomy (PRK) to alcohol-assisted PRK.

Study design:

Retrospective, comparative study.

Methods:

Consecutive case series: Adult patients seeking laser vision correction of myopia or myopic astigmatism without ocular diseases or prior surgery were included. The Epi-Clear PRK group comprised 50 consecutive eyes of 27 patients and the PRK group 50 eyes of 25 patients.

Results:

No intraoperative complications occurred. Epi-Clear PRK: At day 1, day 4, and 3 months, uncorrected distance visual acuity (UDVA) was 0.41/0.47/0.93 (decimal scale); epithelial defect diameter was 4.7/0.2/0 (mm); pain level was 3.8/0.3/0 (visual analogue scale, 0–10), respectively. At 3 months, efficacy index was 0.86 and spherical aberrations were unchanged. Three eyes (6%) showed (presumably sterile) infiltrates. PRK: At day 1, day 4, and 3 months, UDVA was 0.56/0.46/1.15; epithelial defect diameter was 6.3/0.2/0 (mm); pain level was 5.0/0.3/0, respectively. At 3 months, efficacy index was 1.1 and spherical aberrations were unchanged.

Conclusion:

The new method of epithelial debridement with Epi-Clear before laser ablation seems to offer fast epithelial removal without nicking Bowman’s layer (as observed with the laser microscope). However, we found significantly inferior results of Epi-Clear PRK compared to alcohol-assisted PRK. Furthermore, after Epi-Clear PRK corneal infiltrates as a new type of postoperative complication were observed.
E-Peer Coaching: A Model to Support Rural Special Education Field Placements
Authors: Gugino Jessica , Raimondi Sharon , Maheady Larry
Published: January 2021

Providing adequate supervision for pre-service teachers enrolled in special education field placements is a challenge. Rural placements often exacerbate this challenge due to the large geographical areas in which these placements are located. The purpose of this article is to describe one approach to early field supervision in rural settings that may provide solutions to this dilemma. E-peer coaching utilizes video-facilitated peer coaching to provide novice pre-service teachers (NPTs) with accurate feedback that is both frequent and timely. This study investigated the use of a Google App that allowed NPTs to record instructional sessions and provide feedback to one another under the supervision of a course instructor. Recommendations for implementation are discussed.
Unified Principal S–N Equation for Friction Stir Welding of 5083 and 6061 Aluminum Alloys
Authors: Li Xiangwei , Fang Ji , Guan Xiaoli
Published: January 2021

With the popularization of friction stir welding (FSW), 5083-H321 and 6061-T6 aluminum alloy materials are widely used during the FSW process. In this study, the fatigue life of friction stir welding with two materials, i.e., 5083-H321 and 6061-T6 aluminum alloy, are studied. Fatigue tests were carried out on the base metal of these two materials as well as on the butt joints and overlapping FSW samples. The principle of the equivalent structural stress method is used to analyze the FSW test data of these two materials. The fatigue resistances of these two materials were compared and a unified principal S–N curve equation was fitted. Two key parameters of the unified principal S–N curve obtained by fitting, Cd is 4222.5, and h is 0.2693. A new method for an FSW fatigue life assessment was developed in this study and can be used to calculate the fatigue life of different welding forms with a single S–N curve. Two main fatigue tests of bending and tension were used to verify the unified principal S–N curve equation. The results show that the fatigue life calculated by the unified mean 50% master S–N curve parameters are the closest to the fatigue test results. The reliability, practicability, and generality of the master S–N curve fitting parameters were verified using the test data. The unified principal S–N curve acquired in this study can not only be used in aluminum alloy materials but can also be applied to other materials.
Renocolic fistula following a partial nephrectomy: a case study
Authors: Dergamoun Hamza , Zaoui Youssef , Amielh David , Volpe Pascal , El Kharroubi Amine
Published: January 2021

Background

Uro-digestive fistulae are uncommon. They frequently manifest themselves with mild symptoms but can, in some cases, be life-threatening leading to septic shock and death. The diagnosis is facilitated by radiological explorations and their management remains mainly surgical.

Case presentation

We report the case of a diabetic 62-year-old patient who developed a renocolic fistula revealed by a digestive symptomatology, following a partial nephrectomy that was surgically treated with positive overall outcome.

Conclusion

The development of a fistula between the colon and the kidney is very rare. Although the outcome was positive at the price of total nephrectomy and partial colectomy, the diagnosis and management of the fistula were challenging. Urologists should keep in mind the possibility of a fistula developing in the aftermath of a partial nephrectomy.
An Anatolian study on the current knowledge and attitudes of urology operating room staff on ionizing radiation
Authors: Girgin Reha
Published: January 2021

Background

To evaluate current approaches to ionizing radiation by personnel working in urology operating room at all levels of health service in Anatolia, Turkey.

Methods

A questionnaire was e-mailed to urology operating room personnel including MDs at different academic levels, between August and September 2020 in Anatolia, Turkey. The questionnaire included demographic questions and questions about ionizing radiation, exposure and protection.

Results

Of the 173 (11.9%) respondents, 44.5% were doctors, 24.9% were nurses, 20.8% were radiology technicians, and 9.8% were other operating room personnel. While most participants (73.4%) had some knowledge of radiation, only 42.2% stated they had received radiation-specific training. The two most commonly used personal protective equipments (PPEs) among respondents (79.8%) were lead aprons and thyroid protectors. Interestingly, both types of PPE were preferred among those who had not received radiation safety training. Conversely, besides lead aprons and thyroid protectors; gonadal protection, goggles and gloves were the preferred PPEs among respondents who had received radiation training (p < 0.001). Radiology technicians exhibited the highest compliance rate for dosimeter usage (100%), followed by faculty members (37.5%), urology specialists (36.7%) nurses (27.9%), operating room staff (17.6%) and assistants (15%). While differences in compliance were statistically significant (p < 0.001), no significant relationship was found between radiation protection measures and years of experience, daily fluoroscopy exposure or education level.

Conclusions

Despite advances in medical science, our findings suggest that many hospital personnel are still insensitive to the dangers of fluoroscopy, which is of great importance in urology operating rooms.
Mining influential genes based on deep learning
Authors: Kong Lingpeng , Chen Yuanyuan , Xu Fengjiao , Xu Mingmin , Li Zutan , Fang Jingya , Zhang Liangyun , Pian Cong
Published: January 2021

Background

Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-expanding gene expression profile, a new, low-cost, high-throughput reduced representation expression profiling method called L1000 was proposed, with which one million profiles were produced. Although a set of ~ 1000 carefully chosen landmark genes that can capture ~ 80% of information from the whole genome has been identified for use in L1000, the robustness of using these landmark genes to infer target genes is not satisfactory. Therefore, more efficient computational methods are still needed to deep mine the influential genes in the genome.

Results

Here, we propose a computational framework based on deep learning to mine a subset of genes that can cover more genomic information. Specifically, an AutoEncoder framework is first constructed to learn the non-linear relationship between genes, and then DeepLIFT is applied to calculate gene importance scores. Using this data-driven approach, we have re-obtained a landmark gene set. The result shows that our landmark genes can predict target genes more accurately and robustly than that of L1000 based on two metrics [mean absolute error (MAE) and Pearson correlation coefficient (PCC)]. This reveals that the landmark genes detected by our method contain more genomic information.

Conclusions

We believe that our proposed framework is very suitable for the analysis of biological big data to reveal the mysteries of life. Furthermore, the landmark genes inferred from this study can be used for the explosive amplification of gene expression profiles to facilitate research into functional connections.
Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics
Authors: Shen Pan , Xu Aishi , Hou Yushan , Wang Huqiang , Gao Chao , He Fuchu , Yang Dong
Published: January 2021

Background

One striking feature of the large KRAB domain-containing zinc finger protein (KZFP) family is its rapid evolution, leading to hundreds of member genes with various origination time in a certain mammalian genome. However, a comprehensive genome-wide and across-taxa analysis of the structural and expressional features of KZFPs with different origination time is lacking. This type of analysis will provide valuable clues about the functional characteristics of this special family.

Results

In this study, we found several conserved paradoxical phenomena about this issue. 1) Ordinary young domains/proteins tend to be disordered, but most of KRAB domains are completely structured in 64 representative species across the superclass of Sarcopterygii and most of KZFPs are also highly structured, indicating their rigid and unique structural and functional characteristics; as exceptions, old-zinc-finger-containing KZFPs have relatively disordered KRAB domains and linker regions, contributing to diverse interacting partners and functions. 2) In general, young or highly structured proteins tend to be spatiotemporal specific and have low abundance. However, by integrated analysis of 29 RNA-seq datasets, including 725 samples across early embryonic development, embryonic stem cell differentiation, embryonic and adult organs, tissues in 7 mammals, we found that KZFPs tend to express ubiquitously with medium abundance regardless of evolutionary age and structural disorder degree, indicating the wide functional requirements of KZFPs in various states. 3) Clustering and correlation analysis reveal that there are differential expression patterns across different spatiotemporal states, suggesting the specific-high-expression KZFPs may play important roles in the corresponding states. In particular, part of young-zinc-finger-containing KZFPs are highly expressed in early embryonic development and ESCs differentiation into endoderm or mesoderm. Co-expression analysis revealed that young-zinc-finger-containing KZFPs are significantly enriched in five co-expression modules. Among them, one module, including 13 young-zinc-finger-containing KZFPs, showed an ‘early-high and late-low’ expression pattern. Further functional analysis revealed that they may function in early embryonic development and ESC differentiation via participating in cell cycle related processes.

Conclusions

This study shows the conserved and special structural, expressional features of KZFPs, providing new clues about their functional characteristics and potential causes of their rapid evolution.
Activation of metabolic and stress responses during subtoxic expression of the type I toxin hok in Erwinia amylovora
Authors: Peng Jingyu , Triplett Lindsay R. , Sundin George W.
Published: January 2021

Background

Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia amylovora, the causative agent of fire blight disease on pome fruit trees. A high-level induction of the hok gene was lethal to E. amylovora cells through unknown mechanisms. The molecular targets or regulatory roles of Hok were unknown.

Results

Here, we examined the physiological and transcriptomic changes of Erwinia amylovora cells expressing hok at subtoxic levels that were confirmed to confer no cell death, and at toxic levels that resulted in killing of cells. In both conditions, hok caused membrane rupture and collapse of the proton motive force in a subpopulation of E. amylovora cells. We demonstrated that induction of hok resulted in upregulation of ATP biosynthesis genes, and caused leakage of ATP from cells only at toxic levels. We showed that overexpression of the phage shock protein gene pspA largely reversed the cell death phenotype caused by high levels of hok induction. We also showed that induction of hok at a subtoxic level rendered a greater proportion of stationary phase E. amylovora cells tolerant to the antibiotic streptomycin.

Conclusions

We characterized the molecular mechanism of toxicity by high-level of hok induction and demonstrated that low-level expression of hok primes the stress responses of E. amylovora against further membrane and antibiotic stressors.
Association of mitochondrial DNA haplogroups J and K with low response in exercise training among Finnish military conscripts
Authors: Kiiskilä Jukka , Jokelainen Jari , Kytövuori Laura , Mikkola Ilona , Härkönen Pirjo , Keinänen-Kiukaanniemi Sirkka , Majamaa Kari
Published: January 2021

Background

We have previously suggested that some of the mutations defining mitochondrial DNA (mtDNA) haplogroups J and K produce an uncoupling effect on oxidative phosphorylation and thus are detrimental for elite endurance performance. Here, the association between haplogroups J and K and physical performance was determined in a population-based cohort of 1036 Finnish military conscripts.

Results

Following a standard-dose training period, excellence in endurance performance was less frequent among subjects with haplogroups J or K than among subjects with non-JK haplogroups (p = 0.041), and this finding was more apparent among the best-performing subjects (p < 0.001).

Conclusions

These results suggest that mtDNA haplogroups are one of the genetic determinants explaining individual variability in the adaptive response to endurance training, and mtDNA haplogroups J and K are markers of low-responders in exercise training.
A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
Authors: Li Douyue , Pan Saichao , Zhang Hongxi , Fu Yongzhuo , Peng Zhuli , Zhang Liang , Peng Shan , Xu Fei , Huang Hanrou , Shi Ruixue , Zheng Heping , Peng Yousong , Tan Zhongyang
Published: January 2021

Background

Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences.

Results

The maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA.

Conclusions

These 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA.
Correction to: Differential production and secretion of potentially toxigenic extracellular proteins from hypervirulent Aeromonas hydrophila under biofilm and planktonic culture
Authors: Barger Priscilla C. , Liles Mark R. , Beck Benjamin H. , Newton Joseph C.
Published: January 2021

An amendment to this paper has been published and can be accessed via the original article.
Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties
Authors: Zhang Yan , Wang Wei , Shen Zhangjun , Wang Jingjing , Chen Yajun , Wang Dong , Liu Gang , Han Maozhen
Published: January 2021

Background

Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health.

Results

In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective.

Conclusions

This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.
Off-pump coronary artery bypass concomitant with retrieval of broken guide wire stuck in the brachial artery: a case report
Authors: Xue Yuan , Dai Lu , Jiang Wenjian , Zhang Hongjia
Published: January 2021

Background

The broken guide wire could get stuck anywhere during coronary artery angiography, but the broken guide wire in the brachial artery is extremely rare.

Case presentation

In this report, we describe our experience with a case of off-pump coronary artery bypass (OPCABG) concomitant with the retrieval of a broken guide wire stuck in the brachial artery: a 56-year-old male patient was referred to our hospital because of tri-vessel disease and a broken guide wire stuck in the right brachial artery. He received OPCABG concomitant with the retrieval of the broken guide wire stuck in the brachial artery under general anesthesia. The patient was discharged uneventfully, and 12 months follow-up showed an excellent surgical outcome.

Conclusion

Open surgery is an effective means for treating patients with a guide wire stuck in the brachial artery during percutaneous coronary intervention.
Macrophage migration inhibitory factor is an early marker of severe acute pancreatitis based on the revised Atlanta classification
Authors: Shen Dingcheng , Tang Caixi , Zhu Shuai , Huang Gengwen
Published: January 2021

Background

Various serum markers for early identification of severe acute pancreatitis (SAP) have been studied. Serum macrophage migration inhibitory factor (MIF) was reported to be correlated with severity of acute pancreatitis (AP) based on the 1992 Atlanta classification. However, MIF has never been proven to be predictive of disease severity based on the revised Atlanta classification (RAC). The potential predictive value of MIF needs to be further validated.

Methods

Consecutive patients with AP within 48 h after symptom onset and 10 healthy control volunteers were enrolled prospectively. Serum MIF levels were measured by enzyme-linked immunosorbent assay (ELISA). The predictive value of MIF, clinical scores and other serum markers were determined.

Results

Among 143 patients with AP, there were 52 (36.4%), 65 (45.5%) and 26 (18.1%) with mild, moderate and severe disease based on the RAC respectively. Compared with healthy volunteers, serum levels of MIF were significantly higher in AP patients, especially those with SAP (P < 0.001). Multivariate regression analysis indicated that increased serum MIF (cut-off 2.30 ng/ml, OR = 3.16, P = 0.008), IL-6 (cut-off 46.8 pg/ml, OR = 1.21, P = 0.043), APACHE II score (cut-off 7.5, OR = 2.57, P = 0.011) and BISAP score (cut-off 1.5, OR = 1.01, P = 0.038) were independent risk factors for predicting SAP (P < 0.05). By using the area under the receiver operating characteristic (ROC) curve (AUC), MIF (AUC 0.950) demonstrated more excellent discriminative power for predicting SAP than APACHE II (AUC 0.899), BISAP (AUC 0.886), and IL-6 (AUC 0.826).

Conclusions

Serum MIF is a valuable early marker for predicting the severity of AP based on the RAC.
Effects of hearing impairment and hearing aid use on the incidence of cognitive impairment among community-dwelling older adults: evidence from the Taiwan Longitudinal Study on Aging (TLSA)
Authors: Tai Chi-Jung , Tseng Tzyy-Guey , Hsiao Yu-Han , Kuo Tsu-Ann , Huang Ching-Ya , Yang Yi-Hsin , Lee Meng-Chih
Published: January 2021

Background

Previous studies have reported associations between hearing impairment (HI) and cognitive impairment, but the evidence is not conclusive while considering concurrent geriatric syndromes. Especially, evidence from previous studies rarely came from Asian studies. This study aimed to evaluate the independent effects of HI and hearing aid use on the incidence of cognitive impairment while considering most geriatric confounders.

Methods

This population-based, propensity-score matched cohort study used cohort from Waves IV–VII (1999–2011) survey of the Taiwan Longitudinal Study on Aging (TLSA). Cognitive impairment was identified based on Short Portable Mental Status Questionnaire (SPMSQ) scores. The hazard ratio (HR) was calculated using the Cox proportional hazard regression adjusting for age, sex, comorbidities, socioeconomic status, Center for Epidemiologic Studies Depression (CES-D) scores, the instrumental activities of daily living scale, mobility condition and quality of life. In addition, social support and participation were also considered as confounders in the analysis. To assess the robustness of our findings, we conducted a sensitivity analysis designed to access unmeasured confounding factors by calculating E-values.

Results

After 1:1 propensity-score matching, we included 709 participants in both the HI and non-HI groups with a mean age of 73.4 years and 39.4% of participants were female. The mean follow-up was 8.9 ± 3.9 years. The HI group had a higher incidence of cognitive impairment than the non-HI group (74.5% vs. 69.1%, respectively), with an adjusted HR of 1.16 (95% confidence interval [CI], 1.03–1.32) based on a 12-year follow up. The E-value was 1.45 for the estimate, which provided evidence for this study’s robustness. Although, a subgroup analysis showed that hearing aid use was associated with lower incidences of cognitive impairment (66.3% vs. 75.6%) when compared to non-users in the HI group, the adjusted HR of 0.82 (95% CI, 0.61–1.09) revealed no significant differences.

Conclusions

HI was an independent risk factor of incident cognitive impairment on top of concurrent geriatric syndromes. Early HI detection may thus be effective for preventing cognitive decline. Further studies are needed to evaluate the effect of hearing aid use on the prevention of cognitive decline.
Association between renal function and platelet reactivity during aspirin therapy in elderly patients with atherosclerotic cardiovascular disease
Authors: Liang Wenyi , Zhang Peng , Liu Meilin
Published: January 2021

Background

Aspirin is the key treatment in the secondary prevention of atherosclerotic cardiovascular disease. High on-treatment platelet reactivity (HTPR) to aspirin has been reported to partially account for the enhanced risk of thrombotic events. In particular, HTPR has been described more frequently among elderly patients. The aim of this study was to identify the clinical and biological factors associated with HTPR in a real-life elderly population.

Methods

In this retrospective study, elderly patients with atherosclerotic cardiovascular disease on regular aspirin treatment were enrolled. Cardiovascular risk factors, routine biological parameters, comorbidities, and concomitant medications were recorded. The upper quartile of the platelet aggregation rate, determined by light transmission aggregometry with arachidonic acid, was defined as the HTPR group.

Results

A total of 304 patients were included (mean age 77 ± 8 years, 76% men). Patients in the HTPR group were older than the patients in the non-HTPR group (mean age: 79 ± 7 vs. 76 ± 8 years, p = 0.008). Patients with moderately decreased estimated glomerular filtration rate (eGFR) had a higher frequency of HTPR than patients with slightly decreased eGFR or normal eGFR (35.8, 22.5, 12.2%, respectively, p < 0.05). In multivariate analysis, an independent risk factor for HTPR was the eGFR (OR: 0.984, 95% CI: 0.980–0.988, p < 0.001).

Conclusions

Advanced age and decreased eGFR are correlated with poor pharmacodynamic response to aspirin.