bluuebunny/crossref_metadata_2025 huggingface dataset:
Schools, Justice, and Immigrant Students: Assimilation, Race, Ethnicity, Gender, and Perceptions of Fairness and Order
Authors: Peguero Anthony A. , Bondy Jennifer M.
Published: November 2021

Background/Context

Students’ perceptions of justice, fairness, and order within their schools are arguably key building blocks of socialization to participation within a democratic society. The ideals of justice, fairness, and order within their schools are particularly imperative because the educational system is founded on a belief of democracy and meritocracy. It is also known that students’ perceptions of school justice can vary by race, ethnicity, and gender. What remains uncertain is how the fastest growing segment of the United States, students in immigrant families, perceive the school justice, fairness, and order within their school.

Purpose

The aim of this study is to explore if straight-line assimilation, segmented assimilation, and immigrant optimism hypotheses explain the relationships between schools, justice, and immigration, as well as the potential role of gender, race, and ethnicity in immigrant youth perceptions of justice, fairness, and order.

Participants/Subjects

This study utilizes the Education Longitudinal Study of 2002 (ELS), a nationally representative sample of high school sophomores.

Research Design

This study's research design includes statistical analysis of secondary data.

Findings/Results

Findings do suggest that the students’ perceptions of justice, fairness, and order are indeed moderated by immigrant generation, race, ethnicity, and gender.

Conclusions/Recommendations

Educators and educational researchers who are seeking to better understand the schooling experiences of immigrant youth might benefit from questioning assimilation and Americanization as processes that inevitably promote educational progress. Given that immigrant youth are and have historically been marginalized within U.S. schools, it appears that socialization, Americanization, gender, and immigrant generational status are germane to creating democratic education for all students. Attentiveness to democratic school justice, order, and fairness is, therefore, imperative.
Virtual Coaching for Instructional Leaders: A Multi-Method Investigation of Technology-Enabled External Assistance
Authors: Ermeling Bradley A. , Tatsui Timothy T. , Young Kelly R.
Published: November 2021

Background

Education reforms over the last several decades have relied heavily on external assistance to help schools increase capacity for improving outcomes, but investing in sustained outside coaching and support is increasingly difficult with diminishing federal, state, and district resources. One under-investigated possibility for maintaining affordable external assistance is to leverage new virtual technologies.

Purpose

This proof-of-concept study explored the potential of virtual coaching as a means for providing a cost-effective, alternative model of ongoing external assistance to principals and leadership teams engaged in collaborative instructional improvement.

Intervention

Researchers adapted an existing assistance framework from an established instructional improvement model, with published studies of effectiveness in the traditional face-to-face context, and substituted virtual methods of coaching and support for ongoing monthly settings with school leaders.

Research Design

The study used a mixed-methods design, including video-recorded meetings, rubric-based coding and ratings, interviews, focus groups, and coaching logs to investigate implementation at three elementary and two middle schools during one full academic year.

Findings

Evidence suggests that the blended coaching model served as an adequate and cost-effective substitute for traditional face-to-face coaching at all five pilot schools. The virtual coaching format was particularly effective for conducting one-on-one planning meetings with principals and served as a catalyst to expand principals’ growth and ownership of the instructional improvement process. The authors also document several challenges that emerged related to limitations of human interaction in the virtual context.

Conclusions

Findings suggest that blended or virtual models are worth consideration as one potential solution for maintaining external support in the midst of diminishing fiscal resources. For schools with verified leadership and technology readiness, the availability of virtual models might translate to greater distribution of outside expertise across a wider number of schools, or enable some funds to be repurposed for other critical priorities. Findings also have implications for the design of external assistance programs and services. Evidence from the study highlights distinct benefits of the virtual format, which might enable more strategic distribution of monthly support, increase capacity building, and improve access to high-quality expertise. Lastly, findings provide guidance for research and policy around technology-supported professional learning, pointing to the importance of aligning solutions with contexts, attending to sound quality and room configuration, and addressing challenges with the naturalness of interaction.
African American Males Navigate Racial Microaggressions
Authors: Hotchkins Bryan K.
Published: November 2021

Background/Context

High school educational environments find Black males experience systemic racial microaggressions in the form of discipline policies, academic tracking and hegemonic curriculum. Black males in high school are more likely than their White male peers to have high school truancies and be viewed as intentionally sinister. African American males are labeled by White teachers and administrators as deviant for issues like talking in class, dress code violations and being tardy. Deficit perceptions about African American students as held by White teachers and administrators serve as racial microaggressions within K–12 context.

Purpose/Objective/Research Question/Focus of Study

Racial microaggressions based on prejudicial White beliefs of teachers impedes the learning process of participants. Racial microaggressive acts are problematic due to being a symptom of the overarching campus racial climate, which is often indicative of the negative historic treatment of Black males by Whites. The cumulative impact of racial microaggressions on Black males negatively impacts self-image, academic performance, and social navigation skills. Examining how Black males responded to racial microaggressions by White teachers and administrators at culturally diverse high school settings was the impetus for this study.

Research Design

To understand how African American male students responded to racial microaggressions qualitative research was used. Conducting a study that focuses on multiple individualistic lived experiences, I am mindful that “human actions cannot be understood unless the meaning that humans assign to them is understood.” This comparative case study allowed for narrative expression, which informed the experiential meanings participants assigned to enduring racial microaggressions by gathering in-depth information through multiple sources to understand participants’ real life meanings to situations.

Conclusions/Recommendations

Participants’ engaged in pro-active navigation strategies to minimize and counter racial microaggressions. Navigation strategies were influenced by in- and out-of-class interactions with White teachers and student peers. Analysis of the data gathered during interviews, focus groups, and observations confirmed the racial microaggressive lived experiences of participants. Three themes emerged: (1) monolithic targeting; (2) integrative fluidity; and (3) behavioral vacillation. Participants avoided monolithic targeted racial microaggression(s) by creating meaningful alliances within other racialized student populations by utilizing social and extracurricular relationships as protective barriers to lessen the adverse effects of racial microaggressive experiences.
Race, Test Scores, and Educational Outcomes
Authors: Yeh Stuart
Published: November 2021

Background

Policymakers wish to know what changes must be made to the primary and secondary education system so that when students apply to college they are highly prepared, ready to perform at high levels, and likely to be successful in college.

Purpose

The purpose of the current study was to investigate the significance of strong educational preparation for all students—and especially for minority students—as measured by standardized test scores. While the importance of educational preparation may already seem well established, previous studies have tended to minimize or obscure the significance of the type of preparation that is measured by test scores. Existing studies are not adequate for the purpose of estimating the total effect of a hypothetical intervention that raises student achievement by one standard deviation (SD).

Research Design

The current study employed logistic regression with a nationally-representative dataset, controlled for key covariates, and analyzed the hypothetical effect of raising student test scores by one SD.

Findings

Raising test scores by one SD would substantially reduce the probabilities that black, Hispanic, Asian, and white students would drop out of high school, and would greatly increase the probabilities that both minority and white students would compile a rigorous high school record, complete algebra 2 in high school, enroll at a 4-year institution, and attain a baccalaureate degree.

Recommendation

The results reported here underline the importance of swiftly adopting the most efficient approaches for raising student achievement. To the extent that existing approaches for raising student achievement are unproductive, inefficient, and disproportionately affect minority students, current policies may serve to depress baccalaureate attainment rates and to perpetuate the disadvantaged status of minorities.
The Discipline Gap: What's Trust Got to Do with It?
Authors: Romero Lisa S.
Published: November 2021

Background/Context

If we are serious about eliminating the racial achievement gap, we need to address the discipline gap as well. The scholarly literature generally paints a positive picture of the potential of trust to transform schools. Research on student trust has shown that students who trust their teachers and schools are suspended and expelled less frequently and have more positive academic outcomes. However, we know little about if or how the impact of trust may vary by race or gender.

Research Question

Do the benefits of trusting relationships accrue equally to all students? Do trusting student–teacher relationships pay off in less discipline and improved academic outcomes for all students, or do the benefits of trust depend on the race and gender of the student?

Research Design

Structural equation modeling was used to model the relationships between student trust, behavior, and high school outcomes, controlling for socioeconomic status, school size, and prior achievement. Data, drawn from the Educational Longitudinal Survey of 2002, includes responses from more than 6,000 public high school students (n = 6,352) who identify as African American or White. Comparisons are made between results for White, African American, and African American male students.

Findings/Results

Student trust is associated with fewer disciplinary incidents and better academic outcomes; however, the benefits of trust do not accrue equally to all students. Black students, particularly males, benefit less from trust. Controlling for trust, behavior, and standardized measures of math and reading ability, Black students are penalized multiple times for a single disciplinary incident: by the suspension (or other consequence), by missed instruction, and by the impact on their grades (and possibly their future course placement and postsecondary plans). In other words, there are unequal consequences of equal discipline.

Conclusions/Recommendations

This research found that Black and White students with roughly equivalent discipline records, scores on achievement tests, and levels of trust still have substantially different high school outcomes. Although efforts to implement restorative justice or positive behavior support programs are a step in the right direction, results suggest that they will not be enough. Schools must deal with implicit bias and the unequal consequences of equal discipline. To do this, we must scrutinize course placement practices, grading, and the messages that we send to students. Failure to do so will continue to leave us with a vast education debt and will continue to fuel the achievement gap.
How Did that Happen? Teachers’ Explanations for Low Test Scores
Authors: Evans Margaret , Teasdale Rebecca M. , Gannon-Slater Nora , Londe Priya G. La , Crenshaw Hope L. , Greene Jennifer C. , Schwandt Thomas A.
Published: November 2021

Context

Educators often engage with student performance data to make important instructional decisions, yet limited research has analyzed how educators make sense of student performance data. In addition, scholars suggest that teachers recognize a relationship between their instruction and student performance data, but this is a relatively untested assumption.

Focus of Study

We investigated if and how teachers referenced instruction as a contributing factor for why students performed in particular ways on assessments. We also studied other explanations that teachers offered for student performance data.

Research Design

Our research team conducted a qualitative case study of six grade-level teams of teachers who met biweekly to make meaning of student performance data. Using data collected from 44 hours of observation of teacher team meetings, 16 individual interviews, and six group interviews with participating teachers, we analyzed the ways in which and the extent to which teachers referenced instruction as a contributing factor to student performance data. Findings: Teachers connected student performance data to their instruction approximately 15% of the time. Teachers more frequently connected student performance data to student characteristics. Notably, student behavior accounted for 32% of all teacher explanations for student performance. We offer five distinct categories of teachers’ explanations of student performance and the extent to which teachers invoked each category.

Conclusions

The findings in this study build on research on teachers’ attributions for assessment data. In contrast to other studies, our findings suggest that teachers invoked student characteristics in distinct ways when explaining student performance. At times, teachers were knowledgeable about student characteristics, which offered verifiable insights into the “problem” of low achievement. At other times, teachers voiced negative viewpoints of students that served to blame students for their poor performance. We suggest that the practice of data-driven decision making offers an opportunity to bolster educators’ informed judgment and undermine negative, unverifiable claims about children.
Beyond Posters and Pennants: College-Going Messaging at Three Racially and Economically Diverse Public Schools
Authors: Martinez Melissa A. , Torres Isaac , Lewis Katherine
Published: November 2021

Context

It has been argued that high schools with a majority of students of color and from low-income backgrounds must be purposeful in fostering a college-going culture in order to address the challenges and inequities historically underserved students face in preparing for and accessing a higher education. However, what this looks and sounds like in practice is not always clear, leaving schools seeking common ground on how to create a college-going environment.

Purpose

Through a symbolic and ecological model of college readiness framework, the messaging associated with the college-going culture at three racially and economically diverse Texas high schools that had consistently high college ready graduate rates was examined. The research questions that guided the study included: What types of college-going culture messages are conveyed at the schools, and how? How might such messaging impact students, school staff and leaders?

Research Design

This study drew on data from a three-year, multi-site descriptive case study of three public high schools in different regions of Texas that all served approximately 50% or more of students with financial need and 72% to 97% students of color, specifically Latina/o and Black students.

Data Collection and Analysis

Data was collected during week-long, yearly visits to the three schools and included: school and district documents; individual and group semi-structured interviews with 194 individuals including administrators, teachers, support staff, students, parents, and community members; observations of common areas and classrooms; archival data; and researcher-derived documents including field notes, memos, and photographs of the school grounds and school activities. This paper primarily drew on the pictures taken of the schools (in hallways, classrooms, and shared spaces like cafeterias and libraries), field notes, memos, and interview data that specifically spoke to the visual and verbal messaging associated with the college-going culture. Analysis of data revealed six themes: college is a revered goal with many options; varying degrees of integration; support and resources are at your reach; think college and career; finding funding for college is vital; college is an individual and shared success.

Conclusions

This study's findings suggest the need to: reconsider what a strong college-going culture entails, re-envision college-going cultures as dynamic, multi-layered, and responsive, reframe postsecondary opportunities so they are more expansive and varied, and re-evaluate inequities in college-going messaging and academic rigor.
Then and Now: Depicting a Changing National Profle of STEM Career and Technical Education Course Takers
Authors: Plasman Jay Stratte , Gottfried Michael A. , Hutt Ethan L.
Published: November 2021

Background

After nearly a century of federal policies focusing on career-related high school coursework, a 2006 policy reauthorization especially called for increased rigor in STEM-themed career and technical education (CTE) courses and increased participation from all students, and particularly women and those with disabilities. We explore whether this reauthorization helped meet these calls for increased participation.

Research Questions

We asked the following research questions in exploring the implementation of the Perkins IV act: (1) How have the predictors of participation in AS-CTE coursework changed during the decade between 2004 and 2013? (2) Were students in the class of 2013 more likely to participate in AS-CTE than those in the class of 2004? (3) Is there a specific difference in AS-CTE participation for female students and students with disabilities in the class of 2013 as compared to the class of 2004?

Research Design

To respond to these questions, we merged two nationally representative datasets—the Education Longitudinal Study of 2002 (ELS:2002) and the High School Longitudinal Study of 2009 (HSLS:2009). We employed basic logistic regression to explore changes in participation and ordinary least squares regression to explore changes in credit accumulation. We also utilized double hurdle and state fixed-effects models to account for various potential biases.

Results

We found that there were slight changes in predictors of applied STEM CTE course-taking, though female students remained significantly less likely than male students to participate in each cohort. Exploring across cohorts, we found students in the later cohort (HSLS:2009) to be both more likely to participate in applied STEM CTE and more likely to complete more units. Finally, when exploring female students and students with IEPs, we found that these students were more likely to participate in applied STEM CTE, but were not more likely to complete more units.

Conclusions

A first implication from these findings is that it appears the national efforts and sentiments around increasing high schoolers’ participation in CTE course-taking have taken hold. Second, it appears there may be a specific role for states as they look to grow participation in applied STEM CTE—and CTE in general. Finally, additional focus needs to be placed on increasing CTE participation for underrepresented students.
Feasibility of percutaneous endoscopic gastrostomy insertion in children receiving peritoneal dialysis
Authors: Kempf Caroline , Holle Johannes , Berns Susanne , Henning Stephan , Bufler Philip , Müller Dominik
Published: November 2021

Background:

Peritoneal dialysis (PD) is the preferred dialysis modality for paediatric patients with end-stage kidney disease. Frequently, malnutrition is encountered. Percutaneous endoscopic gastrostomy (PEG) is the preferred mode of feeding because of its minimal invasive mode of placement and easy handling in daily life. However, reports of a high risk for early post-interventional peritonitis hampered this procedure during PD and controlled studies on the benefit of peri-interventional management to prevent peritonitis are lacking. Here, we report the safety profile of PEG insertion among a cohort of children on PD by using a prophylactic antibiotic and antifungal regimen as well as modification of the PD programme.

Methods:

We performed a single-centre analysis of paediatric PD patients receiving PEG placement between 2015 and 2020. Demographic data, peri-interventional prophylactic antibiotic and antifungal treatment as well as modification of the PD programme were gathered and the incidence of peritonitis within a period of 28 days after PEG was calculated.

Results:

Eight PD patients (median weight 6.7 kg) received PEG insertion. Antibiotic and antifungal prophylaxis were prescribed for median time of 4.0 and 5.0 days, respectively. After individual reduction of PD intensity, all patients continued their regular PD programme after a median of 6 days. One patient developed peritonitis within 24 h after PEG insertion and simultaneous surgery for hydrocele.

Conclusions:

Applying an antibiotic and antifungal prophylactic regime as well as an adapted PD programme may reduce the risk for peritonitis in paediatric PD patients who receive PEG procedure.
Anti-inflammatory secondary metabolites from Scrophularia kotschyana
Authors: Renda Gülin , Kadıoğlu Mine , Kılıç Merve , Korkmaz Büşra , Kırmızıbekmez Hasan
Published: November 2021

The species belonging to Scrophularia genus grow mainly in Irano-Turanian and Mediterranean regions and have been used as folk remedy for inflammatory-related diseases since ancient times. The present study was aimed to evaluate the anti-inflammatory activity of the extracts of Scrophularia kotschyana as well as the isolated compounds. The aerial parts and the roots of the plant were separately extracted with methanol. Anti-inflammatory activities of both extracts were evaluated with formalin test in mice. As the methanolic extract of the aerial parts significantly ( p < .05) inhibited inflammation, it was then submitted to successive solvent extractions with n-hexane, dichloromethane, ethyl acetate and n-butanol to yield subextracts. Anti-inflammatory activities of the subextracts were evaluated within the same test system. Among the subextracts tested, the n-butanol subextract produced a significant ( p < .05) anti-inflammatory activity at all doses (5, 10, and 30 mg/kg, ip.). Sequential chromatographic separation of the n-butanol subextract yielded 8-O-acetyl-4′- O-( E)- p-coumaroylharpagide, 8- O-acetyl-4′- O-( Z)- p-coumaroylharpagide, β-sitosterol 3- O-β-glucopyranoside, apigenin 7- O-β-glucopyranoside, apigenin 7- O-rutinoside, luteolin 7- O-β-glucopyranoside and luteolin 7- O-rutinoside. The anti-inflammatory activities of the isolates were evaluated at 5 mg/kg dose. Luteolin 7- O-β-glucopyranoside and apigenin 7- O-rutinoside caused a significant ( p < .05) inhibition of oedema formation.
Expressing MLH1 in HCT116 cells increases cellular resistance to radiation by activating the PRKAC
Authors: Huang Yuling , Feng Liu , Bao Yongqiang , Zhang Yun , Liang Jinghui , Mao Qingfeng , Li Jingao , Jiang Chunling
Published: November 2021

Mut L homolog-1 (MLH1) is a key DNA mismatch repair protein which participates in the sensitivity to DNA damaging agents. However, its role in the radiosensitivity of tumor cells is less well characterized. In this study, we investigated the role of MLH1 in cellular responses to ionizing radiation (IR) and explored the signaling molecules involved. The isogenic pair of MLH1 proficient (MLH1+) and deficient (MLH1–) human colorectal cancer HCT116 cells was exposed to IR for 24 h at the dose of 3 cGy. The clonogenic survival was examined by the colony formation assay. Cell cycle distribution was analyzed with flow cytometry. Changes in the protein level of MLH1, DNA damage marker γH2AX, and protein kinase A catalytic subunit (PRKAC), a common target for anti-tumor drugs, were examined with Western blotting. The results showed that the HCT116 (MLH1+) cells demonstrated increased radio-resistance with increased S population, decreased G2 population, a low level of γH2AX, a reduced ratio of phosphorylated PRKACαβ to total PRKAC, and an elevated level of total PRKAC and phosphorylated PRKACβII following IR compared with the HCT116 (MLH1–) cells. Importantly, silencing PRKAC in HCT116 (MLH1+) cells increased the cellular radiosensitivity. In conclusion, MLH1 may increase cellular resistance to IR by activating PRKAC. Our finding is the first to demonstrate the important role of PRKAC in MLH1-mediated radiosensitivity, suggesting that PRKAC has potential as a biomarker and a therapeutic target for increasing radio-sensitization.
Eco-Friendly and Community Sustainable Textile Fabric Dyeing Methods From Thai Buffalo Manure: From Pasture to Fashion Designer
Authors: Bureekhampun Suthasini , Maneepun Chanida
Published: November 2021

The research objective was to study local traditional wisdom of the art of producing fabric dye from fresh buffalo manure (FBM). Data were collected from rural weaving community cooperative (co-op) members and experts in Thailand’s northeastern Mekong River province of Nakhon Phanom. The study’s Method 1 added buffalo dung water, salt, and a mordant together, which was brought to a boil for 30 minutes. Method 2 added buffalo dung water and salt, which was brought to a boil for 10 minutes, after which a mordant agent was added, then boiled for an additional 30 minutes. There were five different formulas for each method using a different mordant. Results revealed that Method 1 had the best dyeing solution and produced a consistent, commercially usable, washable fabric with three-tone coloring and long-lasting yarn. Method 1 also used a hot dyeing technique in which cotton yarn and FBM were disinfected in a boiling vat while natural odor-reducing additives were added. Moreover, Method 1 consisted of either (1) FBM, salt, and lye, (2) FBM, salt, and muddy water, or (3) only salt added to FBM. These three solutions yielded a material in which testing by the Thailand Textile Institute (THTI) using ISO standards was determined to have a moderate degree of lightfastness, as well as an excellent resistance to color fading after washing. The study is important as it adds a wealth of knowledge to the literature concerning eco-friendly eco-fashion, sustainable products, and economically viable traditional handicraft textile production techniques.
The role of absolute humidity in respiratory mortality in Guangzhou, a hot and wet city of South China
Authors: Chen Shutian , Liu Chao , Lin Guozhen , Hänninen Otto , Dong Hang , Xiong Kairong
Published: November 2021

Background

For the reason that many studies have been inconclusive on the effect of humidity on respiratory disease, we examined the association between absolute humidity and respiratory disease mortality and quantified the mortality burden due to non-optimal absolute humidity in Guangzhou, China.

Methods

Daily respiratory disease mortality including total 42,440 deaths from 1 February 2013 to 31 December 2018 and meteorological data of the same period in Guangzhou City were collected. The distributed lag non-linear model was used to determine the optimal absolute humidity of death and discuss their non-linear lagged effects. Attributable fraction and population attributable mortality were calculated based on the optimal absolute humidity, defined as the minimum mortality absolute humidity.

Results

The association between absolute humidity and total respiratory disease mortality showed an M-shaped non-linear curve. In total, 21.57% (95% CI 14.20 ~ 27.75%) of respiratory disease mortality (9154 deaths) was attributable to non-optimum absolute humidity. The attributable fractions due to high absolute humidity were 13.49% (95% CI 9.56 ~ 16.98%), while mortality burden of low absolute humidity were 8.08% (95% CI 0.89 ~ 13.93%), respectively. Extreme dry and moist absolute humidity accounted for total respiratory disease mortality fraction of 0.87% (95% CI − 0.09 ~ 1.58%) and 0.91% (95% CI 0.25 ~ 1.39%), respectively. There was no significant gender and age difference in the burden of attributable risk due to absolute humidity.

Conclusions

Our study showed that both high and low absolute humidity are responsible for considerable respiratory disease mortality burden, the component attributed to the high absolute humidity effect is greater. Our results may have important implications for the development of public health measures to reduce respiratory disease mortality.
Effect of AMY1 copy number variation and various doses of starch intake on glucose homeostasis: data from a cross-sectional observational study and a crossover meal study
Authors: Farrell Mary , Ramne Stina , Gouinguenet Phébée , Brunkwall Louise , Ericson Ulrika , Raben Anne , Nilsson Peter M. , Orho-Melander Marju , Granfeldt Yvonne , Tovar Juscelino , Sonestedt Emily
Published: November 2021

Background

Copy number (CN) variation (CNV) of the salivary amylase gene (AMY1) influences the ability to digest starch and may influence glucose homeostasis, obesity and gut microbiota composition. Hence, the aim was to examine the association of AMY1 CNV with fasting glucose, BMI, and gut microbiota composition considering habitual starch intake and to investigate the effect of AMY1 CNV on the postprandial response after two different starch doses.

Methods

The Malmö Offspring Study (n = 1764, 18–71 years) was used to assess interaction effects between AMY1 CNV (genotyped by digital droplet polymerase chain reaction) and starch intake (assessed by 4-day food records) on fasting glucose, BMI, and 64 gut bacteria (16S rRNA sequencing). Participants with low (≤ 4 copies, n = 9) and high (≥ 10 copies, n = 10) AMY1 CN were recruited for a crossover meal study to compare postprandial glycemic and insulinemic responses to 40 g and 80 g starch from white wheat bread.

Results

In the observational study, no overall associations were found between AMY1 CNV and fasting glucose, BMI, or gut microbiota composition. However, interaction effects between AMY1 CNV and habitual starch intake on fasting glucose (P = 0.03) and BMI (P = 0.05) were observed, suggesting inverse associations between AMY1 CNV and fasting glucose and BMI at high starch intake levels and positive association at low starch intake levels. No associations with the gut microbiota were observed. In the meal study, increased postprandial glucose (P = 0.02) and insulin (P = 0.05) were observed in those with high AMY1 CN after consuming 40 g starch. This difference was smaller and nonsignificant after consuming 80 g starch.

Conclusions

Starch intake modified the observed association between AMY1 CNV and fasting glucose and BMI. Furthermore, depending on the starch dose, a higher postprandial glucose and insulin response was observed in individuals with high AMY1 CN than in those with low AMY1 CN.

Trial registration

ClinicalTrials.gov, NCT03974126. Registered 4 June 2019—retrospectively registered.
A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
Authors: Utro Filippo , Levovitz Chaya , Rhrissorrakrai Kahn , Parida Laxmi
Published: November 2021

Background

All diseases containing genetic material undergo genetic evolution and give rise to heterogeneity including cancer and infection. Although these illnesses are biologically very different, the ability for phylogenetic retrodiction based on the genomic reads is common between them and thus tree-based principles and assumptions are shared. Just as the different frequencies of tumor genomic variants presupposes the existence of multiple tumor clones and provides a handle to computationally infer them, we postulate that the different variant frequencies in viral reads offers the means to infer multiple co-infecting sublineages.

Results

We present a common methodological framework to infer the phylogenomics from genomic data, be it reads of SARS-CoV-2 of multiple COVID-19 patients or bulk DNAseq of the tumor of a cancer patient. We describe the Concerti computational framework for inferring phylogenies in each of the two scenarios.To demonstrate the accuracy of the method, we reproduce some known results in both scenarios. We also make some additional discoveries.

Conclusions

Concerti successfully extracts and integrates information from multi-point samples, enabling the discovery of clinically plausible phylogenetic trees that capture the heterogeneity known to exist both spatially and temporally. These models can have direct therapeutic implications by highlighting “birth” of clones that may harbor resistance mechanisms to treatment, “death” of subclones with drug targets, and acquisition of functionally pertinent mutations in clones that may have seemed clinically irrelevant. Specifically in this paper we uncover new potential parallel mutations in the evolution of the SARS-CoV-2 virus. In the context of cancer, we identify new clones harboring resistant mutations to therapy.
Evaluation validation of a qPCR curve analysis method and conventional approaches
Authors: Zhang Yashu , Li Hongping , Shang Shucheng , Meng Shuoyu , Lin Ting , Zhang Yanhui , Liu Haixing
Published: November 2021

Background

Reverse Transcription quantitative polymerase chain reaction (RT-qPCR) is a sensitive and reliable method for mRNA quantification and rapid analysis of gene expression from a large number of starting templates. It is based on the statistical significance of the beginning of exponential phase in real-time PCR kinetics, reflecting quantitative cycle of the initial target quantity and the efficiency of the PCR reaction (the fold increase of product per cycle).

Results

We used the large clinical biomarker dataset and 94-replicates-4-dilutions set which was published previously as research tools, then proposed a new qPCR curve analysis method——CqMAN, to determine the position of quantitative cycle as well as the efficiency of the PCR reaction and applied in the calculations. To verify algorithm performance, 20 genes from biomarker and partial data with concentration gradients from 94-replicates-4-dilutions set of MYCN gene were used to compare our method with various publicly available methods and established a suitable evaluation index system.

Conclusions

The results show that CqMAN method is comparable to other methods and can be a feasible method which applied to our self-developed qPCR data processing and analysis software, providing a simple tool for qPCR analysis.
Evaluation of microRNA expression in a sheep model for lung fibrosis
Authors: Perera Udari Eshani , Derseh Habtamu B. , Dewage Sasika N. V. , Stent Andrew , Wijayarathna Rukmali , Snibson Kenneth J.
Published: November 2021

Background

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibroproliferative disorder that has one of the poorest prognoses amongst interstitial lung diseases. Recently, the finding of aberrant expression levels of miRNAs in IPF patients has drawn significant attention to the involvement of these molecules in the pathogenesis of this disease. Clarification of the differential expression of miRNAs in health and disease may identify novel therapeutic strategies that can be employed in the future to combat IPF. This study evaluates the miRNA expression profiles in a sheep model for lung fibrosis and compares them to the miRNA profiles of both IPF patients and the mouse bleomycin model for pulmonary fibrosis. Pathway enrichment analyses were performed on differentially expressed miRNAs to illustrate which biological mechanisms were associated with lung fibrosis.

Results

We discovered 49 differentially expressed miRNAs in the sheep fibrosis model, in which 32 miRNAs were significantly down regulated, while 17 miRNAs were significantly upregulated due to bleomycin-induced lung injury. Moreover, the miRNA families miR-29, miR-26, miR-30, let-7, miR-21, miR-19, miR-17 and miR-199 were aberrantly expressed in both sheep and mouse models, with similar differential miRNAs expression observed in IPF cases. Importantly, 18 miRNAs were aberrantly expressed in both the sheep model and IPF patients, but not in mice.

Conclusion

Together with pathway enrichment analyses, these results show that the sheep model can potentially be used to characterize previously unrecognized biological pathways associated with lung fibrosis.
Human papillomavirus-associated anal squamous intraepithelial lesions in men who have sex with men and transgender women living with and without HIV in Karachi Pakistan: implications for screening and prevention
Authors: Ejaz Muslima , Mubarak Muhammad , Ali Tazeen Saeed , Andersson Sören , Ekström Anna Mia
Published: November 2021

Background

Anal squamous intraepithelial lesions (ASIL), strongly related to human papilloma virus (HPV) infection, is more prevalent among men who have sex with men (MSM). However, no such data are available for Pakistan yet, and neither HPV vaccination nor anal-cytology screening is implemented in Pakistan. The purpose of this first ever study was to assess the prevalence of HPV-related anal cytological abnormalities among MSM and transgender women living with and without HIV infection in Pakistan.

Methods

We conducted a cross-sectional study from March 2016 to November 2017 at sexual health centers run by the Perwaaz Trust and the National AIDS Control Program in Karachi. The study enrolled MSM and transgender women aged greater-than-and-equal-to-18-years who reported anal sex in the preceding 6 months. We collected two anal samples for liquid-based cytology and HPV type testing by PCR, and socio-demographic and behavioral data were collected through face-to face interviews. ASIL and its associations with biological and behavioral risk factors were analyzed through Cox regression for prevalence ratios (PR) and corresponding 95% confidence intervals (CIs).

Results

Out of 271 qualifying participants, 79% were MSM and 21% transgender women. The mean age was 28.8 (± 8) years. Almost 35% (93/271) of the study population had ASIL detected, ASIL was significantly more common among participants living with HIV than in HIV negative ((50/118) 42.4%; vs. (43/153) 28.1%) (p ≤ 0.001). Among ASIL, 66% (61/93) had low-grade squamous intraepithelial lesions (LSIL), and 3.6% (3/93) had high-grade squamous intraepithelial lesions (HSIL). The overall, HPV16 positivity was 35.5% (33/93) among all abnormal anal lesions and all 3 HSIL were HPV16 positive, however, HPV16 positivity could show its association with ASIL detection in univariate model only (PRcrude: 2.11(1.39–3.18)). Moreover, any HR-HPV type (PR 3.04; 95% CI 1.75–5.26), concurrent sexually transmitted infection (STI) (2.13; (1.28–3.55)) and HIV + /HPV + coinfection (1.75; (1.07–2.88)) remained independently associated with ASIL in the multivariate model.

Conclusions

Abnormal anal cytology among MSM and transgender is prevalent enough to consider optimal screening regimens. Further studies are required to see if periodic anal cytology can be made part of HIV care and treatment programs among MSM in Pakistan.
Clinical outcomes and temporal trends of immunological and non-immunological rare diseases in adult kidney transplant
Authors: Gallo Ester , Mingozzi Silvia , Mella Alberto , Fop Fabrizio , Presta Roberto , Burdese Manuel , Boaglio Elena , Torazza Maria Cristina , Giraudi Roberta , Leonardi Gianluca , Lavacca Antonio , Gontero Paolo , Sedigh Omidreza , Bosio Andrea , Verri Aldo , Dolla Caterina , Biancone Luigi
Published: November 2021

Background

Rare diseases (RDs) encompass many difficult-to-treat conditions with different characteristics often associated with end-stage renal disease (ESRD). However, data about transplant outcomes in adult patients are still lacking and limited to case reports/case series without differentiation between immunological/non-immunological RDs.

Methods

Retrospective analysis among all adult kidney transplanted patients (KTs) with RDs (RDsKT group) performed in our high-volume transplantation center between 2005 and 2016. RDs were classified according to the Orphanet code system differentiating between immunological and non-immunological diseases, also comparing clinical outcomes and temporal trends to a control population without RDs (nRDsKT).

Results

Among 1381 KTs, 350 patients (25.3%) were affected by RDs (RDsKTs). During a f/up > 5 years [median 7.9 years (4.8–11.1)], kidney function and graft/patient survival did not differ from nRDsKTs. Considering all post-transplant complications, RDsKTs (including, by definition, patients with primary glomerulopathy except on IgA nephropathy) have more recurrent and de-novo glomerulonephritis (14.6% vs. 9.6% in nRDsKTs; p = 0.05), similar rates of de-novo cancers, post-transplant diabetes, dysmetabolism, hematologic disorders, urologic/vascular problems, and lower infectious episodes than nRDsKTs (63.7% vs 72.7%; p = 0.013). Additional stratification for immunological and non-immunological RDsKTs or transplantation periods (before/after 2010) showed no differences or temporal trends between groups.

Conclusions

Kidney transplant centers are deeply involved in RDs management. Despite their high-complex profile, both immunological and non-immunological RDsKTs experienced favorable patients’ and graft survival.
Covid-19 transmission in fitness centers in Norway - a randomized trial
Authors: Helsingen Lise M. , Løberg Magnus , Refsum Erle , Gjøstein Dagrun Kyte , Wieszczy Paulina , Olsvik Ørjan , Juul Frederik E. , Barua Ishita , Jodal Henriette C. , Herfindal Magnhild , Mori Yuichi , Jore Solveig , Lund-Johansen Fridtjof , Fretheim Atle , Bretthauer Michael , Kalager Mette ,   for the TRAiN study group, Aalby Anita , Berli Madeleine , Furholm Siv , Horvli Anne-Lise , Norum Line , Lauvstad Halvor , Somogyi Judit , Myers Alexander , Poulsson Tonje , Evertsen Wenche , Sandvoll Hilde , Oppen Kjersti
Published: November 2021

Background

Closed fitness centers during the Covid-19 pandemic may negatively impact health and wellbeing. We assessed whether training at fitness centers increases the risk of SARS-CoV-2 virus infection.

Methods

In a two-group parallel randomized controlled trial, fitness center members aged 18 to 64 without Covid-19-relevant comorbidities, were randomized to access to training at a fitness center or no-access. Fitness centers applied physical distancing (1 m for floor exercise, 2 m for high-intensity classes) and enhanced hand and surface hygiene. Primary outcomes were SARS-CoV-2 RNA status by polymerase chain reaction (PCR) after 14 days, hospital admission after 21 days. The secondary endpoint was SARS-CoV-2 antibody status after 1 month.

Results

3764 individuals were randomized; 1896 to the training arm and 1868 to the no-training arm. In the training arm, 81.8% trained at least once, and 38.5% trained ≥six times. Of 3016 individuals who returned the SARS-CoV-2 RNA tests (80.5%), there was one positive test in the training arm, and none in the no-training arm (risk difference 0.053%; 95% CI − 0.050 to 0.156%; p = 0.32). Eleven individuals in the training arm (0.8% of tested) and 27 in the no-training arm (2.4% of tested) tested positive for SARS-CoV-2 antibodies (risk difference − 0.87%; 95%CI − 1.52% to − 0.23%; p = 0.001). No outpatient visits or hospital admissions due to Covid-19 occurred in either arm.

Conclusion

Provided good hygiene and physical distancing measures and low population prevalence of SARS-CoV-2 infection, there was no increased infection risk of SARS-CoV-2 in fitness centers in Oslo, Norway for individuals without Covid-19-relevant comorbidities.

Trial registration

The trial was prospectively registered in ClinicalTrials.gov on May 13, 2020. Due to administrative issues it was first posted on the register website on May 29, 2020: NCT04406909.
Students’ initial perspectives on online learning experience in China during the COVID-19 outbreak: expanding online education for future doctors on a national scale
Authors: Li Li , Wu Hongbin , Xie A’na , Ye Xiaoyang , Liu Cheng , Wang Weimin
Published: November 2021

Background

During the early stage of COVID-19 outbreak in China, most medical undergraduate programs have to eventually embrace the maneuver of transferring to nearly 100% online-learning as a new routine for different curricula. And there is a lack of empirical evidence of effective medical education curriculum that has been completely implemented in an online format. This study summarizes medical students’ perspectives regarding online-learning experience during the COVID-19 outbreak and presents reflection on medical education.

Methods

From February 21st to March 14th, 2020, the authors conducted survey of a nationally representative sample of undergraduate medical students from 90 medical schools in China. Participant demographics and responses were tabulated, and independent sample t-tests as well as multiple logistic regression models were used to assess the associations of demographic characteristics, prior online learning experience, and orientation with students’ perspectives on the online learning experience.

Results

Among 118,030 medical students participated in the survey (response rate 52.4%), 99,559 provided valid data for the analysis. The sample is fairly nationally representative. 65.7% (65,389/99,559) supported great orientation and 62.1% (61,818/99,559) reported that they were satisfied with the ongoing online-learning experience. The most common problem students would encounter was the network congestion (76,277/99,559; 76.6%). Demographics, learning phases, and academic performance were associated with online-learning engagement and perceptions. Formal orientation and prior PU (perceived usefulness of online learning) were significantly positively associated with the satisfaction and evaluation of the online learning experience (p <  0.001).

Conclusions

Data from this national survey indicates a relatively positive role of online learning as a formal teaching/learning approach in medical education. Considerations should be made regarding such application in aspects of students’ different learning phases. We suggest that further policy interventions should be taken from technological, organizational, environmental, as well as individual aspects, to help improve the outcome of online learning for future doctors.