bluuebunny/crossref_metadata_2025 huggingface dataset:
The old and the new about the contractile vacuole of Trypanosoma cruzi
Authors: Jimenez Veronica , Miranda Kildare , Augusto Ingrid
Published: August 2022

Osmoregulation is a conserved cellular process required for the survival of all organisms. In protists, the need for robust compensatory mechanisms that can maintain cell volume and tonicity within physiological range is even more relevant, as their life cycles are often completed in different environments. Trypanosoma cruzi, the protozoan pathogen responsible for Chagas disease, is transmitted by an insect vector to multiple types of mammalian hosts. The contractile vacuole complex (CVC) is an organelle that senses and compensates osmotic changes in the parasites, ensuring their survival upon ionic and osmotic challenges. Recent work shows that the contractile vacuole is also a key component of the secretory and endocytic pathways, regulating the selective targeting of surface proteins during differentiation. Here we summarize our current knowledge of the mechanisms involved in the osmoregulatory processes that take place in the vacuole, and we explore the new and exciting functions of this organelle in cell trafficking and signaling.
Toward an efficient recycling system: Evaluating recyclability of end‐of‐life stainless steels by considering elements distribution during a remelting process
Authors: Lu Xin , Ohno Hajime , Takeda Osamu , Miki Takahiro , Sasaki Yasushi , Zhu Hongmin , Nagasaka Tetsuya
Published: August 2022

Stainless steel is a special category of steel and contains high chromium and nickel. With particular attention to chromium and nickel, the solvent metal phase of recycling of end‐of‐life (EoL) ferritic and austenitic stainless steels by remelting is considered Fe–Cr alloy and Fe–Cr–Ni alloy instead of pure iron, respectively. Understanding the element elimination behavior from the solvent metal phase during the remelting process is important for the improvement of the resource efficiency of the stainless steel recycling. The elimination behavior of 23 alloying elements from Fe–Cr alloy and 22 alloying elements from Fe–Cr–Ni alloy were quantitatively evaluated by the thermodynamic method. The conventional metallurgical process, including slagging (oxidation) and evaporation, can efficiently eliminate lots of alloying elements but has its limitation for the elimination of some alloying elements such as copper, antimony, and tin. Moreover, improvement of the elimination is hard to expect with optimizing remelting conditions. Developing novel metallurgical refining processes, such as chlorination and sulfurization, is efficient for eliminating specific alloying elements. However, besides the effort from metallurgical technologies, developing advanced physical separation technologies of collected EoL products in the short term and optimizing the alloy/products design principle in the long term are much more important for improving the resource efficiency of recycling of EoL stainless steel products. Feedback of the alloying elements' elimination behavior during the remelting process to the upstream of the stainless steel cycle is critical.
Serum hepatic biomarkers in women with obstetric cholestasis and a concurrent SARS‐CoV‐2 infection
Authors: D'Ambrosi Francesco , Di Maso Matteo , Viscardi Anna , Ossola Manuela W. , Soldavini Chiara M. , Cetera Giulia E. , Erra Roberta , Ferrazzi Enrico
Published: August 2022

Aim

The aim of the study was to evaluate the association between SARS‐CoV‐2 infection and serum hepatic biomarker levels among women with obstetric cholestasis.

Methods

In this prospective study, we recruited all pregnant women admitted in our hospital with obstetric cholestasis. Among those with a concurrent SARS‐CoV‐2 infection, we evaluated the following serum hepatic biomarkers: aspartate aminotransferase (AST), alanine aminotransferase (ALT), and biliar acids (BA).

Results

Among the 88 women enrolled in the study, 20 presented with a SARS‐CoV‐2 infection while 68 were negative. SARS‐CoV‐2 infected women were younger (mean age 30.5 ± 5.7 vs. 34.3 ± 5.4; p < 0.01) and in a greater percentage of non‐Caucasian ethnicity when compared to noninfected women (60.0% vs. 17.6%; p < 0.01). Regarding levels of hepatic biomarkers, they showed higher levels of AST (111.5 ± 134.1 vs. 37.3 ± 43.4 UI/L; p = 0.02), ALT (132.2 ± 115.7 vs. 50.5 ± 73.173.1 UI/L; p < 0.01), and BA (41.4 ± 46.8 vs. 18.4 ± 13.4 μmol/L; p = 0.04) compared to noninfected patients. No significant differences in maternal or fetal outcomes were found between infected and noninfected women.

Conclusion

SARS‐CoV‐2 infection was associated with higher levels of liver enzymes in patients with obstetric cholestasis. This could be the result of a possible hepatic involvement in patients with SARS‐CoV‐2 infection.
Circulating trimethylamine N‐oxide levels do not predict 10‐year survival in patients with or without coronary heart disease
Authors: Bjørnestad Espen Ø. , Dhar Indu , Svingen Gard F. T. , Pedersen Eva R. , Ørn Stein , Svenningsson Mads M. , Tell Grethe S. , Ueland Per M. , Sulo Gerhard , Laaksonen Reijo , Nygård Ottar
Published: August 2022

Background

Trimethylamine N‐oxide (TMAO) is an amine oxide generated by gut microbial metabolism. TMAO may contribute to atherothrombosis and systemic inflammation. However, the prognostic value of circulating TMAO for risk stratification is uncertain.

Methods

We assessed prospective relationships of plasma TMAO with long‐term risk of all‐cause, cardiovascular (CV), and non‐CV mortality in the Western Norway Coronary Angiography Cohort (WECAC; 4132 patients with suspected coronary artery disease) and the Hordaland Health Study (HUSK; 6393 community‐based subjects). Risk associations were examined using Cox regression analyses.

Results

Mean follow‐up was 9.8 and 10.5 years in WECAC and HUSK, respectively. Following adjustments for established CV risk factors and indices of renal function in WECAC, the hazard ratios (HRs) (95% confidence intervals [CIs]) per one standard deviation increase in log‐transformed plasma TMAO were 1.04 (0.97–1.12), 1.06 (0.95–1.18), and 1.03 (0.93–1.13) for all‐cause, CV, and non‐CV mortality, respectively. Essentially similar results were obtained in patients with angiographically significant coronary artery disease and patients with reduced left ventricular ejection fraction. Corresponding HRs (95% CIs) in the HUSK cohort were 1.03 (0.96–1.10), 1.01 (0.89–1.13), and 1.03 (0.95–1.12) for all‐cause‐, CV, and non‐CV mortality, respectively.

Conclusions

Circulating TMAO did not predict long‐term all‐cause, CV, or non‐CV mortality in patients with coronary heart disease or in community‐based adults. This large study does not support a role of TMAO for patient risk stratification in primary or secondary prevention.
Developing National Standardized Performance Measures for School‐Based Health Centers: The National Quality Initiative*
Authors: Soleimanpour Samira , Geierstanger Sara , Goddard Anna , Cushing Katherine , Fields Paula , Love Hayley
Published: August 2022

BACKGROUND

Despite extensive literature on school‐based health center (SBHC) characteristics and outcomes, their quality of care has not been examined nationally. Standardized quality metrics can inform health care delivery and improvement.

METHODS

SBHC national performance measures (NPMs) were developed by reviewing measures from national child health quality initiatives and engaging stakeholders in a consensus‐building process. NPMs were pilot‐tested with 73 SBHCs and SBHCs nationally subsequently reported data.

RESULTS

Five NPMs were selected including the percentage of clients annually who received at least one: (1) well‐child visit, whether administered in the SBHC or elsewhere; (2) risk assessment; (3) body mass index screen with nutrition and physical activity counseling; and, if age‐appropriate, (4) depression screening with follow‐up treatment plan; and (5) chlamydia screening among sexually active clients. SBHCs experienced challenges with reporting during pilot‐testing, particularly related to extracting data from electronic health records, and identified strategies to address challenges. Approximately 20% of SBHCs nationally voluntarily reported data during the initial year.

IMPLICATIONS FOR SCHOOL HEALTH

Standardized performance measures can help SBHCs monitor and improve care delivery and demonstrate effectiveness compared to other child health delivery systems.

CONCLUSION

Ongoing data collection will help examine whether measure adoption drives quality improvement for SBHCs nationwide.
Rapid eye movement sleep parasympathetic activity predicts wake hyperarousal symptoms following a traumatic event
Authors: Daffre Carolina , Oliver Katelyn I. , Nazareno Jovi R. S. , Mäder Thomas , Seo Jeehye , Dominguez Jarrod P. , Gannon Karen , Lasko Natasha B. , Orr Scott P. , Pace‐Schott Edward F.
Published: August 2022

Heart rate variability (HRV) can be used to assess changes in output of the parasympathetic nervous system (PNS). Considering that patients with post‐traumatic stress disorder (PTSD) often experience disturbances in sleep, arousal, and autonomic functioning, we sought to explore the association of PNS activity during sleep with hyperarousal symptoms of PTSD. Because a broad literature supports the importance of rapid eye movement (REM) sleep in PTSD, REM‐sleep features were specifically examined as predictors of PTSD symptom severity. A total of 90 participants, primarily civilian and female, aged 18–40 years who had experienced a traumatic event in the last 2 years, underwent an ambulatory polysomnography (PSG) acclimation night followed by a second PSG night from which sleep physiological measures were computed. Participants underwent an ambulatory polysomnography (PSG) acclimation night followed by a second PSG night from which sleep physiological measures were computed. PTSD severity was measured using the PTSD Checklist for the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (PCL‐5). Dependent variables were total PCL‐5 score as well as its hyperarousal symptom subscore. Predictors included REM latency, percentage, density, segment length, and an index of parasympathetic tone (root mean square of the successive differences in the R–R interval or RMSSD). Hierarchical regression models were conducted to analyse the association of REM features with PCL‐5 total and hyperarousal subscales. Using hierarchical regression, REM‐sleep RMSSD accounted for a significant proportion of the variation in outcome variables, even when accounting for other REM‐sleep features. The present findings support hypothesised relationships between PTSD symptomatology and REM‐sleep physiology and, specifically, that lowered parasympathetic tone in REM may be an important associate of the hyperarousal symptom cluster in PTSD.
How representative are social partners in Europe? The role of dissimilarity
Authors: Matute Marta Martínez , Martins Pedro S.
Published: August 2022

Social partners (trade unions and employers' associations [EA]) and their representativeness can shape labour institutions and economic and social outcomes in many countries. In this paper, we argue that, when examining social partners' representativeness, it is important to consider both affiliation rates and dissimilarity measures. The latter concerns the extent to which affiliated and non‐affiliated firms or workers are distributed similarly across relevant dimensions, including firm size. In our analysis of the European Company Survey, we find that affiliation density and dissimilarity measures correlate positively across countries, particularly in the case of EA in which we focus. This result also holds across EA when we use more detailed, firm population data for Portugal. We conclude that higher affiliation densities do not necessarily correspond to more representative social partners as they can involve greater dissimilarity between affiliated and non‐affiliated firms.
The social epistemology of introspection
Authors: Unnsteinsson Elmar
Published: August 2022

I argue that introspection recruits the same mental mechanism as that which is required for the production of ordinary speech acts. In introspection, in effect, we intentionally tell ourselves that we are in some mental state, aiming thereby to produce belief about that state in ourselves. On one popular view of speech acts, however, this is precisely what speakers do when speaking to others. On this basis, I argue that every bias discovered by social epistemology applies to introspection and other forms of self‐directed representation. If so, it becomes unclear in what sense social epistemology is social.
PGC‐1 alpha regulates mitochondrial biogenesis to ameliorate hypoxia‐inhibited cementoblast mineralization
Authors: Wang Huiyi , Wang Xiaoxuan , Ma Li , Huang Xin , Peng Yan , Huang Hantao , Gao Xudong , Chen Yuan , Cao Zhengguo
Published: August 2022

Hypoxia often occurs in inflammatory tissues, such as tissues affected by periodontitis and apical periodontitis lesions. Mitochondrial biogenesis can be disrupted in hypoxia. Peroxisome proliferator‐activated receptor gamma coactivator‐1 alpha (PGC‐1α) is a core factor required for mitochondrial biogenesis. Cementoblasts are root surface lining cells that play an integral role in cementum formation. There is a dearth of research on the effect of hypoxia on cementoblasts and underlying mechanisms, particularly in relation to mitochondrial biogenesis during the hypoxic process. In this study, we found that the expression of hypoxia inducible factor‐1α was elevated in apical periodontitis tissues in vivo. In contrast, periapical lesions exhibited a reduction of PGC‐1α expression. For in vitro experiments, cobalt chloride (CoCl2) was used to induce hypoxia. We observed that CoCl2‐induced hypoxia suppressed the mineralization ability and mitochondrial biogenesis of cementoblasts, accompanied by abnormal mitochondria morphology. Furthermore, we found that CoCl2 blocked the p38 pathway, while it activated the Erk1/2 pathway, with the former upregulating the expression of PGC‐1α, while the latter reversed the effects. Overall, our findings demonstrate that mitochondrial biogenesis, especially via PGC‐1α, is impaired during cementogenesis in the context of CoCl2‐induced hypoxia, dependent on the mitogen‐activated protein kinase signaling pathway.
Cardiologic evaluation of Turkish mitochondrial fatty acid oxidation disorders
Authors: Balci Mehmet Cihan , Karaca Meryem , Ergul Yakup , Omeroglu Rukiye Eker , Demirkol Mubeccel , Gokcay Gulden Fatma
Published: August 2022

Background

Mitochondrial fatty acid oxidation disorders (FAODs) cause impairment in energy metabolism and can lead to a spectrum of cardiac pathologies including cardiomyopathy and arrhythmias. The frequency of underlying cardiac pathologies and the response to recommended treatment in FAODs was investigated.

Methods

Sixty‐eight children (35 males, 33 females) with the diagnosis of a FAOD were included in the study. Cardiac function was evaluated with 12‐lead standard electrocardiography, echocardiography, and 24 h Holter monitoring.

Results

Forty‐five patients (66%) were diagnosed after disease symptoms developed and 23 patients (34%) were diagnosed in the pre‐symptomatic period. Among symptomatic patients (n: 45), cardiovascular findings were detected in 18 (40%) patients, including cardiomyopathy in 14 (31.1%) and conduction abnormalities in 4 (8.8%) patients. Cardiac symptoms were more frequently detected in primary systemic carnitine deficiency (57.1%). Patients with multiple acyl‐CoA dehydrogenase, long‐chain 3‐hydroxyacyl‐CoA dehydrogenase, and mitochondrial trifunctional protein deficiencies also had an increased frequency of cardiac symptoms. Patients with medium‐chain acyl‐CoA dehydrogenase, very long‐chain acyl‐CoA dehydrogenase, and carnitine palmitoyltransferase I deficiencies had a lower prevalence of cardiac symptoms both during admission and during clinical follow up. Cardiomyopathy resolved completely in 8/14 (57%) patients and partially in 2/14 (14.3%) patients with treatment. Two patients with cardiomyopathy died in the newborn period; cardiomyopathy persisted in 1 (7.1%) patient with very long‐chain acyl‐CoA dehydrogenase deficiency.

Conclusion

Early diagnosis, treatment and follow up made a significant contribution to the improvement of cardiac symptoms of patients with FAODs.
Effect of rice cultivars, organic manures, and water management on methane emissions and grain yield
Authors: Win Ei Phyu , Bellingrath‐Kimura Sonoko D. , Oo Aung Zaw , Park Kyeung Il
Published: August 2022

To assess the effect of different organic manures and rice cultivars on methane emissions, a pot experiment was conducted at the Yezin Agricultural University, Nay Pyi Taw, Myanmar during the wet season of 2016. Organic manures (control, compost, and cow dung) and two rice cultivars (Manawthukha and IR 50) were tested. For both rice cultivars, high grain yield was observed in the control, and the minimum grain yield was observed in the cow dung treatment. The rate and cumulative CH4 emissions in Manawthukha were higher than those in IR 50, in accordance with the yield, because of the longer growth duration. Although not significant, the lowest methane emissions were observed in the cow dung manure treatment (0.808 g CH4 kg−1 soil) against the control (0.893 g CH4 kg−1 soil) and compost (0.951 g CH4 kg−1 soil) treatments. Based on these results, a field experiment was conducted at Madaya Township, Mandalay region, Myanmar during the dry and wet seasons of 2017 to determine the effects of water management and different rates of cow dung manure on methane emission and yield of IR 50. Higher methane emissions were recorded for continuous flooding (CF) than for alternative wetting and drying (AWD). In both seasons, higher grain yields (1.8% in dry and 7.6% in wet) were recorded for AWD than for CF. Higher methane emissions were recorded from OM3 and lower emissions from OM0 in both water management practices. In AWD, methane emissions were restricted under aerated soil conditions, although a higher amount of manure was added.
Inspection of gas bubbles in frozen Betula pendula xylem with micro‐CT: Conduit size, water status and bark permeability affect bubble characteristics
Authors: Lintunen Anna , Salmon Yann , Hölttä Teemu , Suhonen Heikki
Published: August 2022

Bubbles of gas trapped in the xylem during freezing are a major cause of damage for trees growing at high altitudes or latitudes, as the bubbles may cause embolism during thawing. Yet the factors controlling bubble formation upon freeze–thaw cycles remain poorly understood. Especially the size of the bubbles formed in the ice is crucial for winter embolism formation. We used high‐resolution X‐ray microtomography combined with freezing experiments to investigate the size and shape of 68,343 gas bubbles in frozen conduits in branches of Betula pendula. We also studied how conduit size, tree water status (−0.2 MPa vs. −0.6 MPa) and bark permeability to gases (decreased by Vaseline‐coating) affect the gas bubbles characteristics. High‐resolution X‐ray images allowed us to detect gas bubbles down to 1.0 μm in diameter and revealed that not only small spherical gas bubbles but also gaseous volumes of various shapes and sizes were found from the frozen xylem indicating that gas bubbles may have started to grow already during the freezing propagation. Most of the gas bubbles were found in fibers, but the rare gas bubbles found in the vessels were larger than those in the fibers. Bubble volume increased with conduit volume in both fibers and vessels, but conduit size alone could not explain gas bubble volume. Low water potential and restriction of gas escape from the branch seem to cause more, larger, and less spherical bubbles and thus increase the risk of embolism formation. These findings open new research avenues for further studies of winter embolism formation.
Transcriptional regulation of rice HSP101 promoter: Mitogen‐activated protein kinase‐mediated HSFA6a phosphorylation affects its stability and transactivation
Authors: Singh Garima , Banerjee Gopal , Sarkar Neelam K. , Sinha Alok Krishna , Grover Anil
Published: August 2022

Heat shock proteins (HSPs) and heat stress factors (HSFs) control the plant heat stress response to a large extent. HSP101 plays a decisive role in development of plant heat tolerance. We have previously shown that rice (Oryza sativa) cells contain 25 HSFs and among these, HSFA6a most predominantly binds to the HSP101 promoter and controls its transcript expression. This study shows that mitogen‐activated protein kinases (MAPKs), specifically MPK3, MPK4, and MPK6 phosphorylate HSFA6a. HSFA6a showed physical interaction with MPK3/MPK4, specifically in the nucleus and this interaction involved the C‐terminal end of HSFA6a. Four serine residues at positions Ser136, Ser141, Ser264, and Ser356 of HSFA6a are the putative sites of MAPK phosphorylation: we generated phospho‐mutant of HSFA6a by changing the serine residues to alanine either individually or all four together. The Hsp101 promoter binding potential of Ser136 mutant was enhanced while it declined for the other three phospho‐mutant HSFA6a forms. HSFA6a mutant lacking all the above four Ser residues exhibited reduced DNA binding and transactivation potential. We implicate the role of phosphorylation in the regulation of HSFA6a activity.
Complications and treatment errors in periodontal and implant therapy
Authors: Zucchelli Giovanni , Wang Hom‐Lay , Chambrone Leandro
Published: August 2022

The assortment of periodontal and implant‐related treatments has been continuously improved over the last 50 years. Once the decision‐making process has been established and the treatment procedure applied, the partial or complete resolution of the problem (eg, periodontal probing depth reduction, clinical attachment level gain, gingival recession reduction, dental hypersensitivity decrease) and a diagnosis change with no or minimal occurrence of adverse events (ie, complications, harms, technical errors, or adverse/side effects) can be expected. The clear identification of the potential types of adverse effects, complications, or even errors is important for contemporary decision‐making processes, as they may be related to different local, systemic, and technical aspects. This chapter focused on four core components: (a) providing periodontal definitions for errors, complications, harms, and side effects; (b) defining the types of risk and the clinical impact of adverse effects, errors, and complications in periodontal and peri‐implant therapies; (c) evaluating the influence of accidental errors versus the lack of a proper treatment planning; and (d) reporting on the importance of establishing the “net benefit ratio” between the clinical improvements promoted by the therapy and the occurrence of potential adverse events.
Impact of health and lifestyle food supplements on periodontal tissues and health
Authors: Spahr Axel , Divnic‐Resnik Tihana
Published: August 2022

According to the new classification, periodontitis is defined as a chronic multifactorial inflammatory disease associated with dysbiotic biofilms and characterized by progressive destruction of the tooth‐supporting apparatus. This definition, based on the current scientific evidence, clearly indicates and emphasizes, beside the microbial component dental biofilm, the importance of the inflammatory reaction in the progressive destruction of periodontal tissues. The idea to modulate this inflammatory reaction in order to decrease or even cease the progressive destruction was, therefore, a logical consequence. Attempts to achieve this goal involve various kinds of anti‐inflammatory drugs or medications. However, there is also an increasing effort in using food supplements or so‐called natural food ingredients to modulate patients’ immune responses and maybe even improve the healing of periodontal tissues. The aim of this chapter of Periodontology 2000 is to review the evidence of various food supplements and ingredients regarding their possible effects on periodontal inflammation and wound healing. This review may help researchers and clinicians to evaluate the current evidence and to stimulate further research in this area.
Inflammation as a link between periodontal disease and obesity
Authors: Pamuk Ferda , Kantarci Alpdogan
Published: August 2022

Nutrition plays a critical role in the homeostatic balance, maintenance of health, and longevity. There is a close link between inflammatory diseases and nutritional health. Obesity is a severe pathological process with grave implications on several organ systems and disease processes, including type 2 diabetes, cardiovascular disease, osteoarthritis, and rheumatoid arthritis. The impact of obesity on periodontal inflammation has not been fully understood; the association between nutritional balance and periodontal inflammation is much less explored. This review is focused on the potential mechanistic links between periodontal diseases and obesity and common inflammatory activity pathways that can be pharmacologically targeted.
Systematic revision, molecular phylogeny and biogeography of the antlion tribe Acanthoplectrini (Neuroptera: Myrmeleontidae: Dendroleontinae), with emphasis on the Oriental lineage
Authors: Zheng Yuchen , Badano Davide , Liu Xingyue
Published: August 2022

The tribe Acanthoplectrini (Myrmeleontidae: Dendroleontinae) includes a group of antlion genera widely distributed across the Australasian and Oriental regions. The intergeneric and interspecific relationships between or within the Australian and Oriental lineages of this tribe as well as their historical biogeography remain largely unexplored. Here, we present a molecular phylogenetic and biogeographic analyses of Acanthoplectrini to infer the diversification history of this tribe, with emphasis on the Oriental lineage. Both the Oriental and Australian lineages are monophyletic and recovered as sister groups. Ancestral area reconstruction suggests that the ancestor of Acanthoplectrini might have been once widely distributed from Indochina to Australia and then split into the Oriental and Australian lineages during the early‐Miocene. Our analyses recovered northeastern Indochina and south China as the ancestral range of the Oriental Acanthoplectrini. During the mid‐Miocene to the mid‐Pliocene, orographic events such as the rising of mountain ranges (including the Himalayas) and the formation of major islands in southeastern Asia triggered several dispersal and vicariance events in the Oriental Acanthoplectrini, driving their speciation. We revise the classification of the Oriental Acanthoplectrini, establishing the new genus Paralayahima gen. n., which is recovered sister to Layahima Navás. Moreover, we describe four new species of Layahima, Layahima aspoeckorum sp. n., Layahima monba sp. n., Layahima lhoba sp. n. and Layahima xinliae sp. n., and we reinstate two previously synonymized species, Layahima melanocoris (Yang) stat. rev. and comb. n. and Layahima nebulosa Navás stat. rev.
Discovery of the novel HLA‐B*52:109 allele in a Taiwanese individual
Authors: Yang Kuo‐Liang , Lin Py‐Yu
Published: August 2022

One nucleotide substitution in codon 141 of HLA‐B*52:01:01:01 results in a novel allele HLA‐B*52:109.
Genotyping of canine MHC gene DLA‐88 by next‐generation sequencing reveals high frequencies of new allele discovery and gene duplication
Authors: Pyo Chul‐Woo , Harkey Michael A. , Torok‐Storb Beverly , Storb Rainer , Wang Ruihan , Thomas Alexander S. , Nelson Wyatt C. , Geraghty Daniel E.
Published: August 2022

Dogs have served as one of the most reliable preclinical models for a variety of diseases and treatments, including stem/progenitor cell transplantation. At the genetic epicenter of dog transplantation models, polymorphic major histocompatibility complex (MHC) genes are most impactful on transplantation success. Among the canine class I and class II genes, DLA‐88 has been best studied in transplantation matching and outcomes, with 129 DLA‐88 alleles identified. In this study we developed and tested a next generation (NGS) sequencing protocol for rapid identification of DLA‐88 genotypes in dogs and compared the workflow and data generated with an established DLA‐88 Sanger sequencing protocol that has been in common prior use for clinical studies. By testing the NGS protocol on a random population of 382 dogs, it was possible to demonstrate superior efficacy based on laboratory execution and overall cost. In addition, NGS proved far more effective at discovering new alleles and detecting multiple alleles associated with gene duplication. A total of 51 new DLA‐88 alleles are reported here. This rate of new allele discovery indicates that a large pool of yet un‐discovered DLA‐88 alleles exists in the domestic dog population. In addition, more than 46% of dogs carried three or more copies of DLA‐88, further emphasizing the need for more sensitive and cost‐effective DLA typing methodology for the dog clinical model.
Writing goals in U.S. undergraduate data science course outlines: A textual analysis
Authors: Gooding Constance L. , Lyford Alex , Giaimo Genie N.
Published: August 2022

Instructors at postsecondary institutions have designed a myriad of data science classes to keep up with the rise of big data. Businesses and companies have become increasingly interested in hiring people with strong data acquisition, management, and communication skills. Since data science as a field of study is relatively new, though it has deep connections to statistical studies, there are few comprehensive analyses of data science classes, majors, programs, and curricular goals. Through this research, we analyze how writing and communication are taught in undergraduate data science classes in the United States. We analyze the presence of writing and communication learning goals from course descriptions and course syllabi. These results show that most data science courses emphasize technical, computing skills over writing, and communication skills. We conclude with a set of actionable heuristics that emphasize integrating writing and communication into data science courses so that students are prepared to use these skills as responsible citizens.
Longitudinal monitoring of BKPyV miRNA levels in kidney transplant recipients with BKPyV‐related pathology reflects viral DNA levels and remain high in viremia patients after clearance of viral DNA
Authors: van Doesum Willem B. , Gard Lilli , Knijff Laura W. D. , Niesters Hubert G. M. , van Son Willem J. , Stegeman Coen A. , van den Berg Anke , Groen Henk , van den Born Jacob , Riezebos‐Brilman Annelies , Sanders Jan Stephan
Published: August 2022

Introduction

It is unclear whether polyomavirus BK (BKPyV) microribonucleic acid (miRNA) measurement has additional diagnostic and predictive value in kidney transplant recipients (KTR) as compared to current methods of monitoring BKPyV DNA loads.

Patients and methods

A retrospective, longitudinal study was performed in 30 KTR with BKPyV viruria (n = 10), BKPyV viremia (n = 10), or BKPyV‐associated neuropathy (BKPyVAN) (n = 10). Bkv‐miR‐B1‐3p and 5p and BKPyV DNA load were measured in urine and plasma and compared using receiver operating characteristic (ROC) curves.

Results

Levels of Bkv‐miR‐B1‐3p and 5p and BKPyV DNA correlated strongly. Overall, mostly analog courses of urinary and plasma miRNA and DNA loads were observed. Areas under the ROC curves were not significantly different between miRNAs and DNA. Only, in contrast to BKPyV DNA load, BKPyV miRNA levels increased from 6 to 12 months in the viremia group, while in the BKPyVAN group, a decline was seen in both DNA and miRNA.

Conclusions

In this study, we could not demonstrate an additional value of BKPyV miRNA detection compared to BKPyV DNA monitoring in the early phase after kidney transplantation. We did observe significant differences between the viremia and the BKPyVAN groups during follow‐up. This study was performed with a small number of patients and therefore results should be verified in a larger patient cohort. Furthermore, future studies with larger patient groups are necessary to elucidate final clinical value of these data.

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Measurement of post‐transfusion red blood cell survival kinetics in sickle cell disease and β‐Thalassemia: A biotin label approach
Authors: Gerritsma Jorn J. , van der Bolt Nieke , van Bruggen Robin , ten Brinke Anja , van Dam John , Guerrero Guillermo , Vermeulen Christie , de Bruin Sanne , Vlaar Alexander P. J. , Biemond Bart J. , Nur Erfan , van der Schoot Ellen , Fijnvandraat Karin ,   SCORE consortium
Published: August 2022

Background

Red blood cell (RBC) transfusions are an important treatment modality for patients with sickle cell disease (SCD) and β‐thalassemia. A subgroup of these patients relies on a chronic RBC transfusion regimen. Little is known about RBC survival (RCS) of the transfused allogeneic RBCs. In this study, we aimed to study the RCS kinetics of transfused RBCs in SCD and β‐thalassemia and to investigate factors that determine RCS.

Methods and Materials

We performed a prospective cohort study on fourteen adults with SCD and β‐thalassemia disease receiving a chronic transfusion regimen. RCS and the influence of donor and patient characteristics on RCS were assessed by simultaneous transfusion of two allogeneic RBCs using RBC biotinylation. Phenotyping of well‐known RBC markers over time was performed using flow cytometry.

Results

RCS of the two transfused RBC units was similar in most patients. Although intra‐individual variation was small, inter‐individual variation in RCS kinetics was observed. Most patients demonstrated a non‐linear trend in RCS that was different from the observed linear RCS kinetics in healthy volunteers. After an initial slight increase in the proportion of biotinylated RBCs during the first 24 h, a rapid decrease within the first 10–12 days was followed by a slower clearance rate.

Conclusion

These are the first data to demonstrate that patient‐related factors largely determine post‐transfusion RCS behavior of donor RBC in SCD and β‐thalassemia, while donor factors exert a negligible effect. Further assessment and modeling of RCS kinetics and its determinants in SCD and β‐thalassemia patients may ultimately improve transfusion therapy.
Investigating different typologies for the synthesis of evidence: a scoping review protocol
Authors: Munn Zachary , Pollock Danielle , Price Carrie , Aromataris Edoardo , Stern Cindy , Stone Jennifer , Barker Timothy Hugh , Godfrey Christina M. , Clyne Barbara , Booth Andrew , Tricco Andrea C. , Jordan Zoe
Published: August 2022

Objective:

The objective of this scoping review is to identify evidence synthesis types and previously proposed classification systems, typologies, or taxonomies that have guided evidence synthesis.

Introduction:

Evidence synthesis is a constantly evolving field. There is now a plethora of evidence synthesis approaches used across many different disciplines. Historically, there have been numerous attempts to organize the types and methods of evidence synthesis in the form of classification systems, typologies, or taxonomies. This scoping review will seek to identify all the available classification systems, typologies, or taxonomies; how they were developed; their characteristics; and the types of evidence syntheses included within them.

Inclusion criteria:

This scoping review will include discussion papers, commentaries, books, editorials, manuals, handbooks, and guidance from major organizations that describe multiple approaches to evidence synthesis in any discipline.

Methods:

The Evidence Synthesis Taxonomy Initiative will support this scoping review. The search strategy will aim to locate both published and unpublished documents utilizing a three-step search strategy. An exploratory search of MEDLINE (Ovid) has identified keywords and MeSH terms. A second search of MEDLINE (Ovid), Embase (Elsevier), CINAHL with Full Text (EBSCO), ERIC (EBSCO), Scopus (Elsevier), Compendex (Elsevier), and JSTOR will be conducted. Relevant evidence synthesis organizations will be searched. Identified documents will be independently screened, selected, and extracted by two researchers, and the data will be presented in tables and summarized descriptively.

Review registration number:

OSF https://osf.io/qwc27
A Computational Fluid Dynamics Investigation Comparing the Performance of an Alternative Valvetrain Design Against a Traditional Poppet Valvetrain
Authors: Robinson Austin Clay , Garrett Norman H. , Vaseleniuck Darrick , Uddin Mesbah
Published: August 2022

The poppet valve is by far the most widely used in cylinder head design of internal combustion (IC) engines; however, poppet valves themselves create significant flow restrictions during both the intake and exhaust strokes, thus causing a reduction in volumetric efficiency that affects overall engine performance. By removing the restrictive poppet valve from the flow path of air into and out of the cylinder head and allowing air to flow unobstructed, any given IC engine can achieve greater volumetric efficiency and higher specific output. The Vaztec ECOREV rotary valve system utilizes straight-cut flow passages that reduce such restrictions. This rotary valve system is designed to be directly driven by the crankshaft, thereby replacing the camshaft and poppet valve system altogether. This paper will primarily explore the differences in flow characteristics between this rotary valve and a conventional poppet valve cylinder head using both computational fluid dynamics (CFD) and flow bench data. Both configurations will be evaluated on the same single-cylinder four-stroke internal combustion engine. CFD simulations were run at multiple valve opening positions on each cylinder head configuration for both intake and exhaust cycles to validate the CFD process against flow bench test data for both cylinder head designs. The CFD was performed in 3D using hexahedral meshing and steady-state Reynolds-averaged Navier–Stokes (RANS) turbulence models. Comparison between the two engine configurations will include both intake and exhaust airflow rates as well as discharge coefficients and overall flow field evaluation using numerous scalar and vector properties.
Discussion of  “Ghaednia, H., Wang, X., Saha, S., Xu, Y., Sharma, A., & Jackson, R. L. (2017). A Review of Elastic–Plastic Contact Mechanics. Applied Mechanics Reviews, 69(6).”
Authors: Jackson Robert L.
Published: August 2022

It has been 5 years since this review of elastic-plastic contact mechanics was published. The area still remains very active, and many advancements have been made since then. This discussion summarizes these advances and points out what might be considered the most significant ones. In some cases, experimental measurements have confirmed previous theoretical predictions. In most cases, the models of contact mechanics have increased in complexity in order to improve predictions for real applications. As a fundamental area, contact mechanics will undoubtedly remain active as its implementation is often required for new applications of technology to succeed.
Genomic Analysis Reveals Adaptation of
Vibrio campbellii
to the Hadal Ocean
Authors: Liang Jinchang , Liu Jiwen , Wang Xiaolei , Sun Hao , Zhang Yulin , Ju Feng , Thompson Fabiano , Zhang Xiao-Hua
Published: August 2022

With the development of deep-sea sampling technology, an increasing number of deep-sea
Vibrio
strains have been isolated, but the adaptation mechanism of these eutrophic
Vibrio
strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic
Vibrio
is streamlined to adapt to a long-term oligotrophic environment.
How Escherichia coli Became the Flagship Bacterium of Molecular Biology
Authors: Ruiz Natividad , Silhavy Thomas J.
Published: August 2022

Escherichia coli
is likely the most studied organism and was instrumental in developing many fundamental concepts in biology. But why
E. coli
? In the 1940s,
E. coli
was well suited for the biochemical and genetic research that blended to become the seminal field of biochemical genetics and led to the realization that processes already known to occur in complex organisms were conserved in bacteria.
Induction of Interferon-Stimulated Genes Correlates with Reduced Growth of Influenza A Virus in Lungs after RIG-I Agonist Treatment of Ferrets
Authors: Schwab Lara S. U. , Londrigan Sarah L. , Brooks Andrew G. , Hurt Aeron C. , Sahu Anshupa , Deng Yi-Mo , Moselen Jean , Coch Christoph , Zillinger Thomas , Hartmann Gunther , Reading Patrick C.
Published: August 2022

RIG-I agonists have shown potential as broad-spectrum antivirals
in vitro
and in mouse models of infection. However, their antiviral potential has not been reported in outbred animals such as ferrets, which are widely regarded as the gold standard small animal model for human IAV infections.
Complete Genome Sequences of Three Mycoplasma gallisepticum 6/85-like Isolates
Authors: Leigh Spencer A. , Evans Jeff D.
Published: August 2022

Control of
Mycoplasma gallisepticum
infection can be accomplished through vaccination. However, virulent field strains with genetic markers identical to vaccine strains have been identified. Here, we report the sequencing of three field isolates with genetic markers identical to the
M. gallisepticum
6/85 vaccine strain.
Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing
Authors: Greenberg Jonathan M. , Romero Roberto , Winters Andrew D. , Galaz Jose , Garcia-Flores Valeria , Arenas-Hernandez Marcia , Panzer Jonathan , Shaffer Zachary , Kracht David J. , Gomez-Lopez Nardhy , Theis Kevin R.
Published: August 2022

Mice are widely utilized as animal models of obstetrical complications; however, the characterization of the murine microbiota during pregnancy has been neglected. Microorganisms from the vagina, oral cavity, intestine, and lung have been found in the intra-amniotic space, where their presence threatens the progression of gestation.
AMPK Is Involved in Regulating the Utilization of Carbon Sources, Conidiation, Pathogenicity, and Stress Response of the Nematode-Trapping Fungus Arthrobotrys oligospora
Authors: Wang Wenjie , Zhao Yining , Bai Na , Zhang Ke-Qin , Yang Jinkui
Published: August 2022

NT fungi are widely distributed in various ecosystems and are important factors in the control of nematode populations in nature; their trophic mycelia can form unique infectious devices (traps) for capturing nematodes.
Arthrobotrys oligospora
is a representative NT fungi which can develop complex three-dimensional networks (adhesive networks) for nematode predation. Here, we demonstrated that AMPK plays an important role in the glycerol utilization, conidiation, trap formation, and nematode predation of
A. oligospora
, which was further confirmed by transcriptomic analysis of the wild-type and mutant strains.
Determinants of wasting among children aged 6–59 months in North-East Ethiopia: a community-based case-control study
Authors: Chekol Yeshiwas Tsehay , Arefaynie Mastewal , Kassa Assefa Andargie , Alene Tilahun Dessie , Ngusie Habtamu Setegn
Published: August 2022

Objective

Childhood acute malnutrition, in the form of wasting defined by Weight-for-Height Z-Scores, is a major public health concern. It is one of the main reasons for the death of children in developing countries like Ethiopia. Accordingly, this study aimed to assess determinants of wasting among children aged 6–59 months in Meket district, North Wollo zone, North-East Ethiopia.

Setting

The study was conducted among communities in Meket district, North Wollo zone, North-East Ethiopia.

Participants

A total of 327 (109 cases and 218 controls) children aged 6–59 months participated in the study. Children from 6 months to 59 months of age who match the definition of case/wasted/ and control/not wasted were eligible for the study. However, children who had physical deformities which make anthropometric measurements inconvenient were excluded from the study.

Primary and secondary outcome measures

The main outcome measure was wasting.

Result

The mean ages of the cases and controls were 21.77±11.41 months and 20.13±11.39 months, respectively. Factors that were significantly associated with wasting were: maternal decision making on the use of household money (adjusted odd ratio (AOR)=3.04, 95% CI 1.08 to 7.83), complementary feeding started in a month (AOR=3.02, 95% CI 1.097 to 6.97), food diversity score (AOR=2.64, 95% CI 1.64 to 5.23), frequency of complementary feeding (AOR=6.68, 95% CI 3.6 to 11.25) and history of acute respiratory infections (ARIs) 2 weeks preceding the survey (AOR=3.21, 95% CI 1.07 to 7.86).

Conclusion

Our result implies that the right time to introduce complementary foods, the frequency of feeding and also the amount of food consumed were some of the crucial factors that needed to be changed in child nutrition to reduce wasting. Furthermore, within the framework of our study, the empowerment of women in the decision-making process and the prevention of ARI should be seen as a necessary benchmark for acute malnutrition.
Healthcare workers’ perceptions on diabetic foot ulcers (DFU) and foot care in Fiji: a qualitative study
Authors: Ranuve Malakai Sovaki , Mohammadnezhad Masoud
Published: August 2022

Objectives

To explore the perception of healthcare workers (HCWs) on diabetic foot ulcers (DFU) and foot care in Rotuma, Fiji.

Design

Using a qualitative study design, two focus group discussions (FGDs) were conducted among HCWs. A semistructured open-ended questionnaire was used to guide the discussion session. Each FGD was audiorecorded and was transcribed. The transcriptions were then manually analysed using thematic analysis.

Setting

Rotuma hospital, Fiji.

Participants

HCWs who were working in Rotuma hospital for at least a year and were involved in clinical foot care of type 2 diabetes mellitus patients were included.

Results

There were five main themes, namely, depth of knowledge, quality of care in practice, factors of influence on practice, lack of resources and capacity building. Participants had superficial knowledge that showed lack of in-depth scientific knowledge. A lack of staffing in the clinics affected the delivery of service. Additionally, patients defaulting clinics, late presentations with DFU and traditional medicine also affected the quality of healthcare service in clinics. There was also a need for a multidisciplinary team to prevent and manage DFU. HCWs mostly advised on glycaemic control and ignored offering foot care advice in clinics due mainly to the lack of sound knowledge on foot care. There was also a lack of resources, infrastructure, space and professional development opportunities, which negatively impacted how HCWs deliver foot care services to patients.

Conclusion

HCWs lack significant in-depth knowledge on DFU and foot care. In addition, these are the availability of traditional medicine that delays presentations to hospital, further reducing the quality of services. HCWs need to keep their knowledge and skills updated through regular in-service training on foot care. Resources, infrastructure and supply chains need to be maintained by those in power to ensure HCWs deliver quality foot care services.