bluuebunny/crossref_metadata_2025 huggingface dataset:
Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist
Authors: Mei Hong , Zha Zhao , Wang Wei , Xie Yusang , Huang Yuege , Li Wenping , Wei Dong , Zhang Xinxin , Qu Jieming , Liu Jia
Published: October 2021

Background

Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance.

Results

Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner.

Conclusion

Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors.
Differential regulation of transposable elements (TEs) during the murine submandibular gland development
Authors: Valdebenito-Maturana Braulio , Torres Francisca , Carrasco Mónica , Tapia Juan Carlos
Published: October 2021

The submandibular gland (SG) is a relatively simple organ formed by three cell types: acinar, myoepithelial, and an intricate network of duct-forming epithelial cells, that together fulfills several physiological functions from assisting food digestion to acting as an immune barrier against pathogens. Successful SG organogenesis is the product of highly controlled and orchestrated genetic and transcriptional programs. Mounting evidence links Transposable Elements (TEs), originally thought to be selfish genetic elements, to different aspects of gene regulation in mammalian development and disease. To our knowledge, the role of TEs during murine SG organogenesis has not been studied. Using novel bioinformatic tools and publicly available RNA-Seq datasets, our results indicate that a significant number of genic and intergenic TEs are differentially expressed during the SG development. Furthermore, changes in expression of specific TEs correlated with that of genes involved in cellular division and differentiation, critical aspects for SG maturation. Altogether, we propose that TEs modulate gene networks that operate during SG development.
Performance of the plasma Aβ42/Aβ40 ratio, measured with a novel HPLC-MS/MS method, as a biomarker of amyloid PET status in a DPUK-KOREAN cohort
Authors: Jang Hyemin , Kim Ji Sun , Lee Hye Joo , Kim Chi-Hun , Na Duk L. , Kim Hee Jin , Allué José Antonio , Sarasa Leticia , Castillo Sergio , Pesini Pedro , Gallacher John , Seo Sang Won ,   on behalf of DPUK
Published: October 2021

Background

We assessed the feasibility of plasma Aβ42/Aβ40 determined using a novel liquid chromatography-mass spectrometry method (LC-MS) as a useful biomarker of PET status in a Korean cohort from the DPUK Study.

Methods

A total of 580 participants belonging to six groups, Alzheimer’s disease dementia (ADD, n = 134), amnestic mild cognitive impairment (aMCI, n = 212), old controls (OC, n = 149), young controls (YC, n = 15), subcortical vascular cognitive impairment (SVCI, n = 58), and cerebral amyloid angiopathy (CAA, n = 12), were included in this study. Plasma Aβ40 and Aβ42 were quantitated using a new antibody-free, LC-MS, which drastically reduced the sample preparation time and cost. We performed receiver operating characteristic (ROC) analysis to develop the cutoff of Aβ42/Aβ40 and investigated its performance predicting centiloid-based PET positivity (PET+).

Results

Plasma Aβ42/Aβ40 were lower for PET+ individuals in ADD, aMCI, OC, and SVCI (p < 0.001), but not in CAA (p = 0.133). In the group of YC, OC, aMCI, and ADD groups, plasma Aβ42/Aβ40 predicted PET+ with an area under the ROC curve (AUC) of 0.814 at a cutoff of 0.2576. When adding age, APOE4, and diagnosis, the AUC significantly improved to 0.912.

Conclusion

Plasma Aβ42/Aβ40, as measured by this novel LC-MS method, showed good discriminating performance based on PET positivity.
Metastatic choriocarcinoma in a young woman presenting as thyroid storm: a case report
Authors: Saleem Muhammad , Sethi Sher M. , Ali Abrar , Kiran Zareen
Published: October 2021

Background

Thyroid storm is an endocrine emergency and life-threatening condition discovered in 1926. There is no specific laboratory parameter that can differentiate or distinguish between thyroid storm and primary hyperthyroidism. Diagnosis is made on a clinical scoring system, including the Burch–Wartofsky point scale and Japanese Thyroid Association scoring system. The management is early diagnosis, immediate initiation of anti-thyroid medications, intensive care monitoring, and prevention of multiorgan failure.

Case presentation

A 30-year-old Pakistani female presented with complaint of headache, vomiting, and generalized weakness for 3 weeks. She had an episode of seizure-like activity at home, and so was rushed to the emergency department. A detailed thyroid examination revealed a soft, nontender gland with no enlargement or bruit and no exophthalmos. Her thyroid-stimulating hormone was extremely low, with high free triiodothyronine and thyroxine. Thyroglobulin was 425 ng/ml (normal reference range ≤ 55 ng/ml), and thyroid-stimulating hormone receptor antibody was 0.87 IU/L (normal reference range 0–1.75 IU/L). She had high levels of beta-human chorionic gonadotropin hormone on initial presentation. Transvaginal ultrasound showed no intrauterine pregnancy, but an echogenic focus was found adherent to the right ovary with no vascularity. With the chief complaint of headache, she underwent magnetic resonance imaging of the brain that showed multiple scattered hemorrhagic lesions in supratentorial and infratentorial brain parenchyma that were highly suspicious for metastases. Computed tomography scan of the chest, abdomen, and pelvis revealed multiple neoplastic lesions in the lung, liver, spleen, and kidneys. A Tru-Cut liver biopsy showed linear cores of liver tissue with metastatic carcinoma with morphological features consistent with choriocarcinoma. Our patient scored 65 on the Burch–Wartofsky point scale. As per the Japanese Thyroid Association scoring system, our patient met the criteria for a “definite thyroid storm.” She had initiated propranolol to achieve adequate control of her heart rate and dexamethasone. Carbimazole was started to control her thyroid function. Her thyroid function after 2 weeks of treatment showed significant improvement. Methotrexate and etoposide were given for choriocarcinoma. She made a good recovery and was discharged home. She will undergo rehabilitation along with ongoing chemotherapy (methotrexate and etoposide weekly till beta-human chorionic gonadotropin levels normalize). Unless her source of beta-human chorionic gonadotropin is carefully under control, she will continue to take anti-thyroid medications.

Conclusion

Choriocarcinoma is not only associated with hyperthyroidism but can induce thyroid storm. Beta-human chorionic gonadotropin is directly associated with promoting thyroid dysfunction. Patients with gestational trophoblastic disease should be under close surveillance to prevent thyroid storms.
Use of heparinized saline flush during endovascular thrombectomy for acute ischemic stroke; a survey of clinical practice in the Netherlands
Authors: Benali Faysal , van der Leij Christiaan , Staals Julie , van Zwam Wim H.
Published: October 2021

Background and introduction

Information about optimal use of heparin in flush fluids during endovascular thrombectomy (EVT) for acute ischemic stroke (AIS) is lacking. Variables that determine total heparin dose entering the patient by flush fluids are mostly unknown. We aim to provide insight in these unknown but highly relevant variables.

Methods and results

We performed a survey including all Dutch interventionists performing EVT (n = 79) collecting data on used concentration of heparin in infusion bags, number of infusion bags connected, timing of connecting the flush line and the dripping rate (ml/sec). We calculated potential heparin dose entering the patient per hour through flush fluids (IU/h). Twenty-eight interventionists (35%) representing 17 Dutch stroke centers completed the survey. Eight interventionists responded not to add any heparin to flush fluids (18%). The highest amount of heparin entering the patients was 13,500 IU/h, reported by 2 interventionists from the same center (4%).

Conclusions

We provide insight in the use of heparinized flush during EVT in the Netherlands. Total amounts of heparin administered via flush fluids may go up to 13,500 IU/h. With this paper we intend to set a starting for future research and development of guidelines on the use of heparinized flush fluids during EVT for AIS.
Supporting Scientific Practice through Model-Based Inquiry: A Students’-Eye View of Grappling with Data, Uncertainty, and Community in a Laboratory Experience
Authors: Bolger Molly S. , Osness Jordan B. , Gouvea Julia S. , Cooper Alexandra C.
Published: October 2021

This article reports on students’ experiences with scientific modeling as they engaged in authentic inquiry within a laboratory course, Authentic Inquiry through Modeling in Biology (AIM-Bio). Case study analysis of student interviews revealed the importance of agency, uncertainty, collaboration, and model-based reasoning in students’ modeling practice.
Kiowa at the Battle of the Washita, 27 November 1868
Authors: Meadows William C.
Published: October 2021

While the Battle of the Washita of 27 November 1868 is a well-documented event in Native American and Southern Plains history, especially regarding the Cheyenne, Kiowa involvement is little known. This work sheds light on which Kiowa were at the battle and their participation, through an examination of US military records, Kiowa ledger art, oral histories, onomastics, photographs, and an unpublished account from Kein-taddle of her husband’s (Chiefs Call Him) participation and later naming of three family members from his personal war actions in the battle. The account suggests not only that Chiefs Call Him was involved in the action against Major Joel Elliott and his detachment, who were killed that day, but that he also witnessed Elliott’s death and counted coup on him.
Wyroki sądów specjalnych Polskiego Państwa Podziemnego na żołnierzach ZWZ-AK i kolaborantach z terenu Obszaru Lwowskiego w latach 1940-1943
Authors: Chudzicka Joanna
Published: October 2021

JUDGMENTS OF THE SPECIAL COURTS OF THE POLISH UNDERGROUND STATE REGARDING SOLDIERS OF THE UNION OF ARMED STRUGGLE – THE HOME ARMY (ZWZ-AK) AND COLLABORATIONISTS FROM THE LVIV AREA IN 1940-1943 The present article aims to analyse the functioning of the underground judiciary during World War II, primarily in relation to people associated with the Lviv area of the ZWZ-AK in 1940-1943. First, the article presents the development of Special Courts of the ZWZ, and then as Special Military Courts. In addition, legal regulations in the field of court proceedings and adjudication of criminal sanctions are discussed. The main part of the work, based on the Files of Military Special Courts from the collections of the Archives of Modern Records in Warsaw, describes exemplary court proceedings against members of the armed underground from Area No. 3 of the ZWZ-AK in Lviv, against whom the death penalty was imposed. Moreover, based on one of the underground publications, “Information Bulletin of the Czerwieński Region”, the decisions of the Judging Commissions for Civil Combat in the matter of minor offenses and crimes committed by civilians are discussed.
„Biuletyn Informacyjny” żołnierzy 27 Wołyńskiej Dywizji Piechoty Armii Krajowej jako świadectwo wspomnień walk i głos pamięci o losach ofiar ludobójstwa – analiza zawartości treści i struktury kwartalnika
Authors: Polaczek-Bigaj Marta
Published: October 2021

“INFORMATION BULLETIN” OF THE SOLDIERS OF THE 27TH VOLHYNIAN INFANTRY DIVISION OF THE HOME ARMY (WDPAK) AS A TESTIMONY TO THE MEMORIES OF STRUGGLES AND COMMEMORATION THE FATE OF GENOCIDE VICTIMS – ANALYSIS OF THE CONTENT AND STRUCTURE OF THE QUARTERLY The “Information Bulletin” of the 27th WDPAK, which had been published for 29 years, played a significant role for the milieu of former soldiers of the Volhynia Division and their families. The analysis of its content reveals a very interesting research material. The author of the study made a comparison of approx. 9,000 pages of source material, published in the years 1984-2012. The publication provides answers to the questions of what the “Bulletin” was, who created it, what its purpose was and what roles it played. The work discusses particular columns and changing structure of the quarterly. The author notices links between published articles and the political situation during the publication of subsequent issues of the magazine. Polish-Ukrainian relations, which changed over the years, were also of particular importance. The disagreements between these two nations, genocide and the difficult road to truth were among the main themes presented in the “Bulletin”. The author analyses and compares articles on particular topics that appeared in the quarterly over the years and discusses these issues in the literature on the subject.
JD.com Improves Delivery Networks by a Multiperiod Facility Location Model
Authors: Kang Ningxuan , Shen Hao , Xu Ye
Published: October 2021

Because delivery systems play an increasingly significant role in modern life, it is of strategical importance to design an efficient and adaptive delivery network. JD.com is the largest business-to-consumer e-commerce company by revenue in China and has built the largest amount of logistics infrastructure nationwide. In this study, we developed an optimization model to automatically make annual plans of the delivery stations that minimize operational costs. We built an optimization algorithm by adopting a multiperiod facility location model a using mixed-integer linear programming (MILP) method and proposing applicable techniques to solve the model. The results demonstrate that our model generates improved plans compared with manually planning in terms of both operational cost and delivery distance. The tool described in this paper helps JD.com save on delivery costs and gain operational benefits in designing delivery networks.
The killing and thereafter: intimate partner homicides in a process perspective, part II
Authors: Enander Viveka , Krantz Gunilla , Lövestad Solveig , Örmon Karin
Published: October 2021

This article puts intimate partner homicide (IPH) into a process perspective, and describes the latter two stages of the IPH process, that is, ‘changing the project’ and ‘the aftermath’. The focus of analysis is on the moment when the perpetrator chooses to kill the victim, and what s/he does and says in the wake of the killing. Fifty court files, from cases involving 40 male and 10 female perpetrators, underwent thematic analysis. Regarding the final trigger pertaining to changing the project, some situational factors that trigger male-perpetrated IPH seem to differ from the corresponding factors in female-perpetrated IPH. Feelings of rejection and jealousy seemed to be more common as triggers to kill for men than for women, while some cases of female-perpetrated IPH were linked to self-defence in response to IPV. Moreover, as noted previously, no female perpetrators displayed possessiveness.

Regarding the aftermath, after the homicide the perpetrators generally contacted someone and admitted to having killed their partners. Only a few perpetrators denied culpability and even fewer, mainly male, perpetrators concealed their crimes and denied knowledge of them. However, even in cases where the perpetrator admitted to having killed their victims, their courtroom narratives were apparently constructed to minimise resposibility.
PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes
Authors: Carpenter Charlie M. , Zhang Weiming , Gillenwater Lucas , Severn Cameron , Ghosh Tusharkanti , Bowler Russell , Kechris Katerina , Ghosh Debashis
Published: October 2021

High-throughput data such as metabolomics, genomics, transcriptomics, and proteomics have become familiar data types within the “-omics” family. For this work, we focus on subsets that interact with one another and represent these “pathways” as graphs. Observed pathways often have disjoint components, i.e., nodes or sets of nodes (metabolites, etc.) not connected to any other within the pathway, which notably lessens testing power. In this paper we propose the Pathway Integrated Regression-based Kernel Association Test (PaIRKAT), a new kernel machine regression method for incorporating known pathway information into the semi-parametric kernel regression framework. This work extends previous kernel machine approaches. This paper also contributes an application of a graph kernel regularization method for overcoming disconnected pathways. By incorporating a regularized or “smoothed” graph into a score test, PaIRKAT can provide more powerful tests for associations between biological pathways and phenotypes of interest and will be helpful in identifying novel pathways for targeted clinical research. We evaluate this method through several simulation studies and an application to real metabolomics data from the COPDGene study. Our simulation studies illustrate the robustness of this method to incorrect and incomplete pathway knowledge, and the real data analysis shows meaningful improvements of testing power in pathways. PaIRKAT was developed for application to metabolomic pathway data, but the techniques are easily generalizable to other data sources with a graph-like structure.
CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation
Authors: Daouda Tariq , Dumont-Lagacé Maude , Feghaly Albert , Benslimane Yahya , Panes Rébecca , Courcelles Mathieu , Benhammadi Mohamed , Harrington Lea , Thibault Pierre , Major François , Bengio Yoshua , Gagnon Étienne , Lemieux Sébastien , Perreault Claude
Published: October 2021

MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neoplastic cells by CD8 T cells. However, accurately predicting the MAP repertoire remains difficult, because only a fraction of the transcriptome generates MAPs. In this study, we investigated whether codon arrangement (usage and placement) regulates MAP biogenesis. We developed an artificial neural network called Codon Arrangement MAP Predictor (CAMAP), predicting MAP presentation solely from mRNA sequences flanking the MAP-coding codons (MCCs), while excluding the MCCper se. CAMAP predictions were significantly more accurate when using original codon sequences than shuffled codon sequences which reflect amino acid usage. Furthermore, predictions were independent of mRNA expression and MAP binding affinity to MHC-I molecules and applied to several cell types and species. Combining MAP ligand scores, transcript expression level and CAMAP scores was particularly useful to increase MAP prediction accuracy. Using anin vitroassay, we showed that varying the synonymous codons in the regions flanking the MCCs (without changing the amino acid sequence) resulted in significant modulation of MAP presentation at the cell surface. Taken together, our results demonstrate the role of codon arrangement in the regulation of MAP presentation and support integration of both translational and post-translational events in predictive algorithms to ameliorate modeling of the immunopeptidome.
Factors associated with diarrheal disease among children aged 1–5 years in a cholera epidemic in rural Haiti
Authors: Dolstad Hilary A. , Franke Molly F. , Vissieres Kenia , Jerome Jean-Gregory , Ternier Ralph , Ivers Louise C.
Published: October 2021

Diarrheal illness is a major cause of morbidity and mortality among children in Haiti, and the impact of diarrheal illness was compounded by a cholera outbreak between 2010 and 2019. Our understanding of risk factors for diarrhea among children during this outbreak is limited. We conducted a secondary analysis of data collected as part of a cholera vaccine effectiveness study to identify factors associated with medically attended diarrhea among children in central Haiti from October of 2012 through November of 2016. We identified 47 children aged one to five years old who presented to medical clinics with acute, watery diarrhea, and 166 matched controls who did not have diarrhea, and we performed conditional logistic regression to identify factors associated with diarrhea. Discontinuing exclusive breastfeeding within one month of birth was associated with increased risk of diarrhea (RR 6.9, 95% CI 1.46–32.64), and diarrhea was inversely associated with reported history of supplementation with vitamin A (RR 0.05, 95% CI 0.004–0.56) and zinc (reported among 0% of cases vs. 17% of controls). Because of the concordance in supplementation patterns, it was not possible to attribute the association to vitamin A or zinc independently. While having a respondent who correctly identified ≥3 means of avoiding cholera was associated with reduced risk of diarrhea (RR 0.43, 95% CI 0.19–1.01), reported household sanitation practices and knowledge of cholera were not consistently associated with risk of diarrhea. These findings support ongoing efforts to reduce barriers to breastfeeding and promote pediatric supplementation with vitamin A and zinc in Haiti. Given the reduced efficacy of current oral cholera vaccines (OCV) among children, the results reinforce the importance of breastfeeding and micronutrient supplementation in preventing all-cause pediatric diarrheal illness generally and during cholera outbreaks.
Analysis of an evolutionary game of pallet pooling with participation of third-party platform
Authors: Liu Cuiping , Li Xinchun , Liu Quanlong
Published: October 2021

Pallet pooling has been widely recognized as an important part of the green supply chain. The development of pallet pooling is an essential component for the transformation and upgrade of the logistics industry in China. Pallet pooling can, however, lead to a conflict over potential benefits among the players. One of the main problems of pallet pooling in China is the reasonable benefit allocation mechanism has not been formed. The pallet pooling system (PPS) with participation of the third-party platform (PPSWPTPP) is one of the pilot modes of pallet pooling in China. Based on evolutionary game theory and a penalty mechanism for breach of contract, this paper constructs a tripartite evolutionary game model of the PPSWPTPP. Eight propositions are set in two basic scenarios regarding whether pallet pooling is adapted to the logistics market to study the stability and dynamic evolution process of the players in the PPSWPTPP. Theoretical and numerical simulation results indicate that these will affect the smooth development of the PPS. The suitable setting of penalties and bonuses, the precise estimation of the pooling benefits, the intention intensity of the players to the pallet pooling, and whether to adapt to the logistics market demand are explored.
The effects of dietary saturated fat source on weight gain and adiposity are influenced by both sex and total dietary lipid intake in zebrafish
Authors: Fowler Lauren A. , Powers Audrey D. , Williams Michael B. , Davis James L. , Barry Robert J. , D’Abramo Louis R. , Watts Stephen A.
Published: October 2021

The effects of saturated fat intake on obesity and cardiovascular health remain inconclusive, likely due in part to their varied nature and interactions with other nutrients. Investigating the synergistic effects of different saturated fat sources with other dietary lipid components will help establish more accurate nutritional guidelines for dietary fat intake. Over the past two decades, zebrafish (Danio rerio) have been established as an attractive model system to address questions regarding contributions of dietary lipid intake to diet-induced obesity in humans. The goal of the present study was to assess interactions of three different saturated fat sources (milk fat, palm oil, and coconut oil) with sex and total dietary lipid intake on weight gain and body composition in adult zebrafish. Larvae were raised on live feeds until 28 days post fertilization, and then fed a formulated maintenance diet until three months of age. An eight-week feeding trial was then initiated, in which zebrafish were fed nine experimental low- and high-fat diets varying in saturated fatty acid and long-chain polyunsaturated fatty acid content, in addition to a low-fat and high-fat control diet. At termination of the feeding trial, each treatment was evaluated according to body mass, moisture content, and adiposity. Sex and diet significantly interacted in their effects on body mass (P = 0.026), moisture content (P = 0.044), and adiposity (P = 0.035). The influence of saturated fat source on body mass was observed to be dependent on intake of total dietary lipid. In females, all three saturated fat sources had similar effects on adiposity. From these observations, we hypothesize that impacts of saturated fat intake on energy allocation and obesity-related phenotypes are influenced by both sex and intake of other dietary lipid components. Our results suggest that current nutritional guidelines for saturated fat intake may need to be re-evaluated and take sex-specific recommendations into consideration.
Trade vulnerability assessment in the grain-importing countries: A case study of China
Authors: Duan Jian , X. U. Yong , Jiang Haining
Published: October 2021

Since the 2008 global food crisis, food security vulnerability has been a prominent topic in the food policy debate. However, vulnerability is inherently difficult to conceptualize and is more challenging to operationalize and measure. This study constructs a mathematical model and takes China as a case study to measure the vulnerability and sensitivity of China with its partners in the international grain trade. The results show that 1) the degree of interdependence between China and its grain trading partners is asymmetric, which generates trade vulnerability or economic power; 2) the vulnerability of China’s food trade shows a high spatiotemporal heterogeneity among countries: the higher vulnerability zones are concentrated in North America and Northeast Asia, and the scope of the higher vulnerability zones tends to expand; 3) Our results also reveal that China also has different sensitivities to fluctuations in grain markets from different countries, and the higher sensitive zones of the grain trade in China are mainly distributed in America, Europe, and Oceania. The main contribution of this paper is the development of a methodology for food trade vulnerability assessment and examines the influence of international food trade on food security in importing countries, measured using the vulnerability index and sensitivity index. Nevertheless, the conclusions of this study can be considered preliminary, and there remains great potential for future studies to deepen and broaden our analyses further.
Racial and ethnic differences in foveal avascular zone in diabetic and nondiabetic eyes revealed by optical coherence tomography angiography
Authors: Laotaweerungsawat Sawarin , Psaras Catherine , Haq Zeeshan , Liu Xiuyun , Stewart Jay M.
Published: October 2021

Purpose

The purpose of this study was to examine whether racial and ethnic differences in retinal microvasculature are detectable with quantitative measures derived from optical coherence tomography angiography (OCTA).

Methods

OCTA scans and fundus photography were obtained in 447 eyes from 271 patients with and without diabetes between April and October 2018. Fundus photos were graded by the hospital reading center for diabetic retinopathy (DR) severity. Eight OCTA parameters relating to the foveal avascular zone (FAZ), superficial vascular perfusion, and deep vascular perfusion were analyzed for significant differences between race and ethnicity groups, self-reported by patients and organized according to National Center for Health Statistics groupings. Multiple regression was then used to adjust estimates for possible confounding by age, gender, hypertension, and last hemoglobin A1c level.

Results

Significant differences in FAZ area were found between white and non-white patients. After adjustment, the differences between white and all non-white groups were statistically significant (p<0.05) among patients with mild to moderate DR. In those without diabetes, the Hispanic and Asian groups had significantly larger FAZ areas (p<0.005) than NH white patients. In those with mild to moderate non-proliferative diabetic retinopathy (NPDR), NH Black, Hispanic, and Asian patients also had significantly larger FAZ areas than NH white patients (p<0.005).

Conclusion

Significant differences in FAZ area exist among different racial and ethnic groups. These results highlight the importance of considering and further studying race and ethnicity in OCTA analyses of the retinal microvasculature.
Impaired semen quality, an increase of sperm morphological defects and DNA fragmentation associated with environmental pollution in urban population of young men from Western Siberia, Russia
Authors: Kleshchev Maxim , Osadchuk Alexander , Osadchuk Ludmila
Published: October 2021

Poor sperm morphology and an elevated DNA fragmentation level are considered to be related to spermiogenesis malfunctions as a result of genetic mutations and effects of environmental factors, including industrial pollution. Standardized cross-sectional population studies of sperm morphology defects and sperm DNA fragmentation, especially in regions with increased environmental pollution may be helpful to investigate an influence of industrial pollution and other population-related factors on spermiogenesis process. The aim of present study was to estimate an influence industrial pollution on sperm morphogenesis and sperm DNA fragmentation in men from the general population of the Western Siberia. The Novosibirsk and Kemerovo cities are located to same climatic conditions in Western Siberia but the Kemerovo city is characterized by increased environmental pollution especially by particulate matter (PM). The male volunteers living in Novosibirsk (n = 278) and Kemerovo (n = 258) were enrolled. Percentages of sperm morphological defects are counted after staining native ejaculate smears by Diff-Quick kits. DNA fragmentation was estimated by a SCSA technique. The residents of Kemerovo were characterized by lowered sperm count and sperm motility, elevated DNA fragmentation, poor sperm morphology and increased incidence of morphological effects of head (pyriform, elongated, round, abnormal acrosome and vacuolated chromatine), asymmetrical neck insertion and excess residual cytoplasm. Moreover, elevated DNA fragmentation was associated with lowered sperm count, sperm motility and increased percentages of several sperm morphology defects, with the place of residence affecting the relationships between conventional semen parameters, sperm morphology and DNA fragmentations. Our study suggests that excessive sperm head elongation and impaired acrosome formation can contribute to sperm morphology deterioration in men from polluted areas. Regional features in the relationships between sperm morphology, sperm count and DNA fragmentation were shown, suggesting an importance of studying sperm morphology pattern in men from different regions.
A flipped classroom, same-level peer-assisted learning approach to clinical skill teaching for medical students
Authors: Chan Enoch , Botelho Michael George , Wong Gordon Tin Chun
Published: October 2021

Background

Clinical procedural skills are vital components of medical education. Increased student intake and limited capacity of medical schools necessitate more efficient ways to deliver clinical skill teaching. This study employed a flipped classroom, peer-assisted learning approach to deliver clinical skill teaching. It aimed to determine the influence of pre-class demonstration video watching and in-class student-student interactions on clinical skill acquisition.

Methods

In 2017, a cohort of 205 medical students in their penultimate year of undergraduate medical study were recruited, and they learned bag mask ventilation and intravenous cannulation during this study. The participants watched a demonstration video before class, and then underwent self-directed practice as triads. Afterwards, each participant video-recorded their skill performance and completed post-class questionnaires. The videos were evaluated by two blinded assessors.

Results

A hundred and thirty-one participants (63.9%) completed the questionnaire. For bag mask ventilation, participants who claimed to have watched the corresponding demonstration video before class achieved higher performance scores (those who watched before class: 7.8 ± 1.0; those who did not: 6.3 ± 1.7; p < 0.01). For intravenous cannulation, while there is no significant difference in performance scores (those who watched before class: 14.3 ± 1.3; those who did not: 14.1 ± 1.4; p = 0.295), those who watched the video before class received less interventions from their peers during triad practice (those who watched before class: 2.9 ± 1.8; those who did not: 4.3 ± 2.9; p < 0.05). The questionnaire results showed that most participants preferred the new approach of clinical skill teaching and perceived it to be useful for skill acquisition.

Conclusion

The flipped classroom, same-level peer-assisted learning model is potentially an effective way to address the current challenges and improve the efficiency of clinical procedural skill teaching in medical schools.
Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach
Authors: Shafie Alaa , Khan Shama , Batra Sagar , Anjum Farah , Mohammad Taj , Alam Shoaib , Yadav Dharmendra Kumar , Islam Asimul , Hassan Md. Imtaiyaz
Published: October 2021

PIM1, is a serine/threonine proto-oncogene kinase, involved in many biological functions, including cell survival, proliferation, and differentiation, thus play a key role in oncogenesis. It plays a crucial role in the onset and progression of various hematopoietic and non-hematopoietic malignancies, including acute myeloid leukemia and prostate cancer. Mutations in PIM1, especially in its kinase domain, can induce abnormal structural changes and thus alter functionalities that can lead to disease progression and other complexities. Herein, we have performed an extensive analysis of the PIM1 mutations at sequence and structure level while utilizing state-of-the-art computational approaches. Based on the impact on PIM1, numerous pathogenic and destabilizing mutations were identified and subsequently analyzed in detail. Finally, two amino acid substitutions (W109C and F147C) in the kinase domain of PIM1 were selected to explore their impact on the PIM1 structure in a time evolution manner using all-atom molecular dynamics (MD) simulations for 200 ns. MD results indicate significant conformational altercations in the structure of PIM1, especially upon F147C mutation. This study provides a significant insight into the PIM1 dysfunction upon single amino acid substitutions, which can be utilized to get insights into the molecular basis of PIM1-associated disease progression.
Analysis of rDNA reveals a high genetic diversity of Halophila major in the Wallacea region
Authors: Nguyen Xuan-Vy , Nguyen-Nhat Nhu-Thuy , Nguyen Xuan-Thuy , Dao Viet-Ha , M. Liao Lawrence , Papenbrock Jutta
Published: October 2021

The genusHalophilashows the highest species diversity within the seagrass genera. Southeast Asian countries where several boundary lines exist were considered as the origin of seagrasses. We hypothesize that the boundary lines, such as Wallace’s and Lydekker’s Lines, may act as marine geographic barriers to the population structure ofHalophila major. Seagrass samples were collected at three islands in Vietnamese waters and analyzed by the molecular maker ITS. These sequences were compared with published ITS sequences from seagrasses collected in the whole region of interest. In this study, we reveal the haplotype and nucleotide diversity, linking population genetics, phylogeography, phylogenetics and estimation of relative divergence times ofH.majorand other members of theHalophilagenus. The morphological characters show variation. The results of the ITS marker analysis reveal smaller groups ofH.majorfrom Myanmar, Shoalwater Bay (Australia) and Okinawa (Japan) with high supporting values. The remaining groups including Sri Lanka, Viet Nam, the Philippines, Thailand, Malaysia, Indonesia, Two Peoples Bay (Australia) and Tokushima (Japan) showed low supporting values. The Wallacea region shows the highest haplotype and also nucleotide diversity. Non-significant differences were found among regions, but significant differences were presented among populations. The relative divergence times between some members of sectionHalophilawere estimated 2.15–6.64 Mya.
Quality Assessment of Heterogeneous Training Data Sets for Classification of Urban Area with Landsat Imagery
Authors: Lyimo Neema Nicodemus , Luo Fang , Cheng Qimin , Peng Hao
Published: October 2021

Quality assessment of training samples collected from heterogeneous sources has received little attention in the existing literature. Inspired by Euclidean spectral distance metrics, this article derives three quality measures for modeling uncertainty in spectral information of open-source
heterogeneous training samples for classification with Landsat imagery. We prepared eight test case data sets from volunteered geographic information and open government data sources to assess the proposed measures. The data sets have significant variations in quality, quantity, and data type.
A correlation analysis verifies that the proposed measures can successfully rank the quality of heterogeneous training data sets prior to the image classification task. In this era of big data, pre-classification quality assessment measures empower research scientists to select suitable data
sets for classification tasks from available open data sources. Research findings prove the versatility of the Euclidean spectral distance function to develop quality metrics for assessing open-source training data sets with varying characteristics for urban area classification.
O uso do seminário como facilitador no processo de ensino e aprendizagem de linguagens computacionais
Authors: Cunha Arielly Kizzy , Bozzo Anderson Valentino , Silva Alexander Vinicius Leite da
Published: October 2021

Neste trabalho, procura-se realizar uma abordagem em relação ao uso da prática pedagógica “Seminário em sala de aula”, como instrumento facilitador do processo ensino-aprendizagem na disciplina Lógica de Programação, do Curso Técnico em Informática da Escola Técnica de Praia Grande. O planejamento e a estruturação da aplicação desta prática pedagógica, nos moldes em que foi desenvolvida, basearam-se no Caderno de Orientações do Curso Formação Pedagógica para Educação Profissional e foi fomentado pela observância dos repetidos relatos advindos de alunos de turmas distintas sobre sua dificuldade de aprendizagem das atuais três disciplinas de programação aplicadas no segundo módulo do curso.
A pesquisa como princípio pedagógico no contexto do PROEJA
Authors: Castaman Ana Sara , De Bortoli Lis Ângela , Tommasini Angélica
Published: October 2021

Este estudo tem por objetivo conhecer os fundamentos que norteiam os Institutos Federais de Educação, Ciência e Tecnologia (IF), de modo a compreender as bases conceituais da pesquisa como princípio pedagógico no contexto do Programa de Integração da Educação Profissional ao Ensino Médio na Modalidade de Educação de Jovens e Adultos (PROEJA). Caracteriza-se como pesquisa exploratória e descritiva, pautando-se em uma perspectiva qualitativa e dialética e pela técnica bibliográfica. Está organizado em 02 (duas) seções: a) aborda as bases conceituais dos IF, enfatizando a pesquisa como um princípio pedagógico; b) apresenta a análise de um relato de experiência do ensino com pesquisa no contexto do PROEJA. Conclui-se que a pesquisa em sala de aula está indissociável do ensino. Assim, há que criar espaços efetivos no PROEJA para que os estudantes possam lidar com elementos inerentes à pesquisa como o questionamento, a construção de argumentos, a produção escrita e o diálogo.
Kinetic model of the dispersive interaction between a particle with an erythrocyte
Authors: Riaño-Rivera Ángela Johana , Rodríguez-Patarroyo Diego Julián , Pantoja-Benavides Jaime Francisco
Published: October 2021

A kinetic model of interaction between nanomicroparticle (NMP) and an erythrocyte (RC) was developed considering an elastic type collision, taking into account that the main dispersion center in the delivery of drugs through the bloodstream are the RC. For the analysis of the model, three cases were considered where the position and speed of the MPN were varied. In case 1, the initial position of the MPN was varied with respect to the x axis; In case 2, there was a variation of the position with respect to the y axis, and finally, the speed with respect to the x axis was varied. This study allowed calculating the angle of dispersion (α) based on the impact parameter (s) with respect to the axis of symmetry of the RC. It was verified that in frontal collisions with s values close to the center of the axis of symmetry, the NMP presents the same incident trajectory, with a null angle of dispersion. In an oblique collision, the dispersion is greater and dependent on the initial position and the speed in its Cartesian components, thus a dependency with respect to the initial position is identified, as well as the direction of movement given by the speed components, which it is reflected in the variation of the angle of dispersion.
SANI: Assistant for Information Security Auditing on ISO/IEC 27001
Authors: Franco-Mora Diana Cristina , Porras-Castro Hernán Oswaldo , Corredor-Chavarro Felipe Andrés , Calderón-Bogotá Cristian
Published: October 2021

Information security is a fundamental aspect to any organization, not something exclusive to large companies. Implementing good practices in security management is relevant to being competitive in the context, however, adopting a standard in this regard is a tedious and expensive process for small companies. Audits are part of the proper management of information security, as these help to prevent incidents and mitigate risks on information assets. Many auditing applications are developed and executed in private technological settings, are expensive and not available to the community, or focus on functionality, but have serious difficulties in guaranteeing or documenting confidentiality and anonymity services. With this problem in mind, SANI, an alternative tool that implements these capabilities, was designed, developed, and tested in a real operating scenario.
A Proposal for Improving the Essence Standard by Using Terminology Unification
Authors: Zapata Jaramillo Carlos Mario , Henao Roqueme Antony
Published: October 2021

Context: SEMAT (Software Engineering Method and Theory) is promoting a software engineering theory with adequate terminology to improve the transference of methods and practices between teams. Terminologies should be uniform in order to eliminate ambiguity, improve communication among teams, and support new concepts. Method: The process of reaching uniformity is called terminology unification. In this paper we propose a method for improving the Essence standard based on terminology unification. This method comprises four stages: selection of base models and definitions for structuring terms, identification of terminology problems by comparing the base models and definitions, unification of terms among the base models and definitions, and measurement of the gap between the current standard terms and the proposed changes. Results: We propose a set of modifications to the Essence standard in constructs like: alpha state cards, relationships among alphas, and names of activity spaces. Conclusions: By solving such conflicts, we can define a common, unambiguous terminology for software engineering teams.
Vision-based Software Tool System for Position Estimation Using a Smartphone
Authors: Urbano-López Julio , Bacca Cortes Eval Bladimir , Buitrago-Molina José
Published: October 2021

Context: Current smartphone models have a very interesting set of sensors such as cameras, IMUs, GPS, and environmental variables. This combination of sensors motivates the use of smartphones in scientific and service applications. One of these applications is precision agriculture, specifically drone position estimation using computer vision in GPS-denied environments for remote crop measurements.
Method: This work presents the development of EVP, a vision-based position estimation system using a modern smartphone and computer vision methods. EVP consists of two software applications: an Android app (mobile station) running on a smartphone capable of controlling the drone’s flight, acquiring images, and transmitting them through a wireless network; and another application (base station) running on a Linux-based computer capable of receiving the images, processing them and running the position estimation algorithms using the acquired images. In this work, the mobile station is placed in a quadcopter. Using EVP, users can configure the mobile and base station software, execute the vision-based position estimation method, observe position graph results on the base station, and store sensor data in a database.
Results: EVP was tested in three field tests: an indoor environment, an open field flight, and a field test over the Engineering Department’s square at Universidad del Valle. The root mean square errors obtained in XY were 0,166 m, 2,8 m, and 1,4 m, respectively, and they were compared against the GPS-RTK measurements.
Conclusions: As a result, a vision-based position estimation system called EVP was developed and tested in realworld experiments. This system can be used in GPS-denied environments to perform tasks such as 3D mapping, pick-up and delivery of goods, object tracking, among others.
CULTURAL JUSTICE, BASIC INCOME AND THE CAPABILITY APPROACH
Authors: YAMAMORI TORU
Published: October 2021

In this paper, we elaborate on a theory of an evolutionary political economy capable of accommodating the issue of cultural justice by taking seriously the redistribution–recognition dilemma, a normative analysis of which has been put forth by Nancy Fraser. While accepting Fraser’s articulation of the dilemma, we resist her concluding that Sen’s capability approach is insensitive to cultural justice or the recognition of difference. There is no automatic guarantee, yet an intermediate theory of recognition or cultural justice could in theory be brought to bear on what is, after all, ‘a framework’. We argue that Fraser’s analysis is well suited to be such an intermediate theory, and propose a theoretical device for an evolutional perspective on redistribution and recognition. We concentrate on identifying the stage of the market process at which policy intervenes to remedy redistribution, and the stage of the communication process at which policy intervenes to remedy recognition. Interventions at the entrance stages of both processes are relatively effective and one possibility for such an intervention is to propose Basic Income, which would make it not inconsistent with the capability approach, even though this approach neither directly suggests such a policy not excludes others.