bluuebunny/crossref_metadata_2025 huggingface dataset:
Excess mortality associated with COVID-19 in Brazil: 2020–2021
Authors: Nucci L B , Enes C C , Ferraz F R , da Silva I V , Rinaldi A E M , Conde W L
Published: December 2021

Objective

To evaluate excess mortality in Brazil from January 2020 to April 2021, according to the primary causes of death registered in the Brazilian Mortality Information System (MIS).

Methods

Cross-sectional study with data extracted from the MIS. Excess deaths were examined by the primary cause of death according to 11 grouped causes. Autoregressive models used mortality data from 2015 to 2019 to predict expected deaths from January 2020 to April 2021. Excess deaths were calculated as the difference between the observed and the expected number of deaths.

Results

Total excess deaths of 370 055 were observed in the studied period, corresponding to a ratio of observed to expected of 1.14 in 2020 and 1.40 in 2021. Excess deaths were seen in three groups: symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified; other diseases of the respiratory system and coronavirus infection, unspecified site.

Conclusions

The excess mortality in Brazil in these 16 months was 1.20 times greater than the previous year. The increase in not elsewhere classified causes and causes of death associated to COVID-19 indicate caution about the negative balance for some causes. Furthermore, the inequalities of mortality reporting systems in low- and middle-income countries in relation to underestimation of mortality still need to be addressed.
Delimiting Chaucerian Obscenity in Caxton’s Second Edition of The Canterbury Tales
Authors: Flannery Mary C
Published: December 2021

This essay takes a closer look at the changes William Caxton made to his second edition of The Canterbury Tales (c. 1483), focusing in particular on the material that he deleted from his first edition (c. 1477) and did not replace. Caxton’s well-known prologue to the second edition claims that one of the printer’s key aims is to ‘satysfye thauctour’ and repair the ‘hurtyng and diffamyng’ he felt his first edition had inflicted on Chaucer’s text and reputation by accidentally omitting some of Chaucer’s text and leaving in ‘somme thynges that he neuer sayd ne made’. I show that most of what Caxton deleted consisted of bawdy spurious verse but argue that the printer was more concerned with rooting out ‘counterfeit’ Chaucerian obscenity rather than obscenity in general. By making these corrections, Caxton reveals his sense that ribaldry is a recognized element of Chaucer’s trademark style, and one whose limits must be established in order for the edition to be made according to the poet’s ‘owen makyng’.
Crypt and Villus Transcriptomic Responses in Mouse Small Intestine Following Oral Exposure to Hexavalent Chromium
Authors: Chappell Grace A , Wolf Jeffrey C , Thompson Chad M
Published: December 2021

Oral exposure to hexavalent chromium (Cr(VI)) induces tumors in the mouse duodenum. Previous microarray-based transcriptomic analyses of homogenized mouse duodenal tissue have demonstrated Cr(VI)-induced alterations in various cellular pathways and processes. However, X-ray fluorescence microscopy indicates that chromium localizes primarily to the duodenal villi following exposure to Cr(VI), suggesting that previous transcriptomic analyses of homogenized tissue provide an incomplete picture of transcriptomic responses in the duodenum. Herein, transcriptomic analyses were conducted separately on crypt and villus tissue from formalin-fixed paraffin-embedded transverse duodenal sections from the same study in which microarray-based analyses were previously conducted. A total of 28 groups (7 doses × 2 timepoints × 2 tissue compartments) were analyzed for differential gene expression, dose-response, and gene set enrichment. Tissue compartment isolation was confirmed by differences in expression of typical markers of crypt and villus compartments. Fewer than 21 genes were altered in the crypt compartment of mice exposed to 0.1-5 ppm Cr(VI) for 7 or 90 days, which increased to hundreds or thousands of genes at ≥20 ppm Cr(VI). Consistent with histological evidence for crypt proliferation, a significant, dose-dependent increase in genes that regulate mitotic cell cycle was prominent in the crypt, while subtle in the villus, when compared with samples from time-matched controls. Minimal transcriptomic evidence of DNA damage response in either the crypts or the villi is consistent with published in vivo genotoxicity data. These results are also discussed in the context of modes of action that have been proposed for Cr(VI)-induced small intestine tumors in mice.
Thyroid Storm Patients With Elevated Brain Natriuretic Peptide Levels and Associated Left Ventricular Dilatation May Require Percutaneous Mechanical Support
Authors: Arai Marina , Asaumi Yasuhide , Murata Shunsuke , Matama Hideo , Honda Satoshi , Otsuka Fumiyuki , Tahara Yoshio , Kataoka Yu , Nishimura Kunihiro , Noguchi Teruo
Published: December 2021

OBJECTIVES:

To determine the characteristics of thyroid storm patients with acute decompensated heart failure who should be candidates for temporary percutaneous mechanical circulatory support in addition to beta-blocker treatment to prevent cardiogenic shock.

DESIGN:

A single-center, retrospective review of treatment details and data collected from electronic medical records.

SETTING:

Thyrotoxicosis complicated with acute decompensated heart failure.

PATIENTS:

Eight consecutive patients who were admitted to our hospital for acute decompensated heart failure with thyroid storm between December 2011 and August 2020 were retrospectively reviewed. Of the eight patients, four were treated with percutaneous mechanical circulatory support.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

Compared with thyroid storm patients who did not require percutaneous mechanical circulatory support, those who did had a significantly higher initial plasma brain natriuretic peptide level (1,231 [911–3,387] vs 447 pg/mL [243–653 pg/mL], respectively; p = 0.015), as well as a significantly larger left ventricular end-diastolic diameter (56 [54–63] vs 48 mm [38–48 mm], respectively; p = 0.029) and end-systolic diameter (50 [49–58] vs 28 mm [28–30 mm], respectively; p = 0.029) on echocardiogram. In terms of thyroid storm severity, the Burch-Wartofsky score was higher in patients with percutaneous mechanical circulatory support than in those without, although the difference was not significant. All patients survived this index admission.

CONCLUSIONS:

In thyroid storm patients, the presence of a high brain natriuretic peptide level, “left ventricular dilatation,” or both may necessitate hemodynamic assessment to determine the indication of percutaneous mechanical circulatory support before beta-blocker administration.
Multivariable Cost Frontiers—Qualitative Financial Analyses Using Operational Metrics From the Implementation of a Surgery Fellowship
Authors: Tan Derek W. , Pandit Jaideep J. , Hudson Mark E. , Steinthorsson Georg , Tsai Mitchell H.
Published: December 2021

Objective:

We expand the application of cost frontiers and introduce a novel approach using qualitative multivariable financial analyses.

Summary Background Data:

With the creation of a 5 + 2-year fellowship program in July 2016, the Division of Vascular Surgery at the University of Vermont Medical Center altered the underlying operational structure of its inpatient services.

Method:

Using WiseOR (Palo Alto, CA), a web-based OR management data system, we extracted the operating room metrics before and after August 1, 2016 service for each 4-week period spanning from September 2015 to July 2017. The cost per minute modeled after Childers et al’s inpatient OR cost guidelines was multiplied by the after-hours utilization to determine variable cost. Zones with corresponding cutoffs were used to graphically represent cost efficiency trends.

Results:

Caseload/FTE for attending surgeons increased from 11.54 cases per month to 13.02 cases per month (P = 0.0771). Monthly variable costs/FTE increased from $540.2 to $1873 (P = 0.0138). Monthly revenue/FTE increased from $61,505 to $70,277 (P = 0.2639). Adjusted monthly reve-nue/FTE increased from $60,965 to $68,403 (P = 0.3374). Average monthly percent of adjusted revenue/FTE lost to variable costs increased from 0.85% to 2.77% (P = 0.0078). Adjusted monthly revenue/case/FTE remained the same from $5309 to $5319 (P = 0.9889).

Conclusion:

In summary, we demonstrate that multivariable cost (or performance) frontiers can track a net increase in profitability associated with fellowship implementation despite diminishing returns at higher caseloads.
Auxiliary Liver Transplantation for Cirrhosis: From APOLT to RAPID
Authors: Lim Chetana , Turco Celia , Balci Deniz , Savier Eric , Goumard Claire , Perdigao Fabiano , Rousseau Geraldine , Soubrane Olivier , Scatton Olivier
Published: December 2021

Objective:

To survey the available literature regarding the use of auxiliary liver transplantation (ALT) in the setting of cirrhosis.

Summary of background:

ALT is a type of liver transplantation (LT) procedure in which part of the cirrhotic liver is resected and part of the liver graft is transplanted. The cirrhotic liver left in situ acts as an auxiliary liver until the graft has reached sufficient volume. Recently, a 2-stage concept named RAPID (Resection and Partial Liver segment 2/3 transplantation with Delayed total hepatectomy) was developed, which combines hypertrophy of the small graft followed by delayed removal of the native liver.

Methods:

A scoping review of the literature on ALT for cirrhosis was performed, focusing on the historical background of RAPID and the status of RAPID for this indication. The new comprehensive nomenclature for hepatectomy (“New World” terminology) was used in this review.

Results:

A total of 72 cirrhotic patients underwent ALT [heterotopic (n = 34), orthotopic (Auxiliary partial orthotopic liver transplantation, n = 34 including 5 followed by resection of the native liver at the second stage) and RAPID (n = 4)]. Among the 9 2-stage LTs (APOLT, n = 5; RAPID, n = 4), portal blood flow modulation was performed in 6 patients by deportalization of the native liver (n = 4), portosystemic shunt creation (n = 1), splenic artery ligation (n = 3) or splenectomy (n = 1). The delay between the first and second stages ranged from 18 to 90 days. This procedure led to an increase in the graft-to-recipient weight ratio between 33% and 156%. Eight patients were alive at the last follow-up.

Conclusions:

Two-stage LT and, more recently, the RAPID procedure are viable options for increasing the number of transplantations for cirrhotic patients by using small grafts.
Using the Comprehensive Complication Index to Rethink the ISGLS Criteria for Post-hepatectomy Liver Failure in an International Cohort of Major Hepatectomies
Authors: Calthorpe Lucia , Rashidian Nikdokht , Cacciaguerra Andrea Benedetti , Conroy Patricia C. , Hibi Taizo , Hilal Mohammad Abu , Hoffman Daniel , Park Keon Min , Wang Jaeyun , Adam Mohamed Abdelgadir , Alseidi Adnan ,   International Post-Hepatectomy Liver Failure Study Group
Published: December 2021

Objective:

To compare different criteria for post-hepatectomy liver failure (PHLF) and evaluate the association between International Study Group of Liver Surgery (ISGLS) PHLF and the Comprehensive Complication Index (CCI)” and 90-day mortality.

Summary of Background Data:

PHLF is a serious complication following hepatic resection. Multiple criteria have been developed to characterize PHLF.

Methods:

Adults who underwent major hepatectomies at twelve international centers (2010–2020) were included. We identified patients who met criteria for PHLF based on three definitions: 1) ISGLS, 2) Balzan (INR > 1.7 and bilirubin > 2.92mg/dL) or 3) Mullen (peak bilirubin >7mg/dL). We compared the 90-day mortality and major morbidity predicted by each definition. We then used logistic regression to determine the odds of CCI>40 and 90-day mortality associated with ISGLS grades.

Results:

Among 1646 included patients, 19 (1.1%) met Balzan, 68 (4.1%) met Mullen, and 444 (27.0%) met ISGLS criteria for PHLF. Of the three definitions, the ISGLS criteria best predicted 90-day mortality (AUC = 0.72; sensitivity 69.4%). Patients with ISGLS grades B&C were at increased odds of CCI > 40 (grade B OR 4.0; 95% CI: 2.2–7.2; grade C OR 137.0; 95% CI: 59.2–317.4). Patients with ISGLS grade C were at increased odds of 90-day mortality (OR 113.6; 95% CI: 55.6–232.1). Grade A was not associated with CCI> 40 or 90-day mortality.

Conclusions:

In this diverse international cohort of major hepatectomies, ISGLS grade A was not associated with 90-day mortality or high CCI, calling into question the current classification of patients in this group as having clinically significant PHLF.
Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil
Authors: Tikhonova Ekaterina N. , Grouzdev Denis S. , Avtukh Alexander N. , Kravchenko Irina K.
Published: December 2021

A novel species is proposed for a high-affinity methanotrophic representative of the genus

Methylocystis

. Strain FST was isolated from a weakly acidic (pH 5.3) mixed forest soil of the southern Moscow area. Cells of FST are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. Only methane and methanol are used as carbon sources. FST grew at a temperature range of 4–37 °C (optimum 25–30 °C) and a pH range of 4.5 to 7.5 (optimum pH 6.0–6.5). The major fatty acids were C18  :  1ω8c, C18  :  1ω7c and C18  :  0; the major quinone as Q-8. FST displays 16S rRNA gene sequences similarity to other taxonomically recognized members of the genus Methylocystis, with

Methylocystis hirsuta

CSC1T (99.6 % similarity) and

Methylocystis rosea

SV97T (99.3 % similarity) as its closest relatives. The genome comprises 3.85 Mbp and has a DNA G+C content of 62.6 mol%. Genomic analyses and DNA–DNA relatedness with genome-sequenced members of the genus

Methylocystis

demonstrated that FST could be separated from its closest relatives. FST possesses two particulate methane monooxygenases (pMMO): low-affinity pMMO1 and high-affinity pMMO2. In laboratory experiments, it was demonstrated that FST might oxidize methane at atmospheric concentration. The genome contained various genes for nitrogen fixation, polyhydroxybutyrate synthesis, antibiotic resistance and detoxification of arsenic, cyanide and mercury. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Methylocystis silviterrae sp. nov. The type strain is FST (=KCTC 82935T=VKM B-3535T).
COVID-19 amplified racial disparities in the U.S. criminal legal system
Authors: Klein Brennan , Brandon Ogbunugafor C. , Schafer Benjamin J. , Bhadricha Zarana , Kori Preeti , Sheldon Jim , Kaza Nitish , Sharma Arush , Wang Emily A. , Eliassi-Rad Tina , Scarpino Samuel V. , Hinton Elizabeth
Published: December 2021

The criminal legal system in the United States drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features [1–3]. During the first year of the COVID-19 pandemic, the number of incarcerated people in the U.S. decreased by at least 17%—the largest, fastest reduction in prison population in American history [4]. In this study, we ask how this reduction influenced the racial com-position of U.S. prisons, and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the U.S. prison population, and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decades-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people [5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacer-bated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration.
The role of sub-genomic RNA in discordant results from RT-PCR tests for COVID-19
Authors: Toppings Noah B. , Oberding Lisa K. , Lin Yi-Chan , Evans David , Pillai Dylan R.
Published: December 2021

Reverse transcription-PCR (RT-PCR) is the standard method of diagnosing COVID-19. An inconclusive test result occurs when one RT-PCR target is positive for SARS-CoV-2 and one RT-PCR target is negative within the same sample. An inconclusive result generally requires retesting. One reason why a sample may yield an inconclusive result is that one target is at a higher concentration than another target. It was hypothesized that concentration differences across targets may be due to the transcription of sub-genomic RNA, as this would result in an increase in the concentration of gene targets near the 3’ end of the SARS-CoV-2 genome. A panel of six digital droplet (dd)PCR assays was designed to quantitate the ORF1, E-gene, and N-gene of SARS-CoV-2. This panel was used to quantify viral cultures of SARS-CoV-2 that were harvested during the eclipse phase and at peak infectivity in such a way as to maximize gene-to-gene copy ratios. Eleven clinical nasopharyngeal swabs were also tested with this panel. In culture, infected cells showed higher N-gene/ORF1 copy ratios than culture supernatants. Both the highest specific infectivity (copies/pfu) and the highest differences between gene targets were observed at 6 hours post-infection (eclipse phase) in infected cells. The same trends in the relative abundance of copies across different targets observed in infected cells was observed in clinical samples, though trends were more pronounced in infected cells. This study showed that a greater copy number of N-gene relative to E-gene and ORF1 transcripts could potentially explain inconclusive results for some RT-PCR tests on low viral load samples. The use of N-gene RT-PCR target(s) as opposed to ORF1 targets for routine testing is supported by this data.

Author Summary

This paper provides insight into a drawback of the standard method of testing for COVID-19 (RT-PCR). The results presented here propose an explanation for why inconclusive results sometimes occur with this method. These results can aid microbiologists in the interpretation of inconclusive test results. These results can also aid in decisions about which COVID-19 test a laboratory should use, as there are a plethora of options available. This is important because this standard testing method will remain a critical tool – globally – for managing the COVID-19 pandemic and any future viral pandemics and epidemics. Thus, it is important to investigate every facet of the testing method. The findings presented here are applicable to any virus which makes sub-genomic transcripts as part of its life cycle. Trends observed in viral cultures are presented alongside the same trends observed in clinical samples. Unlike similar papers in the field, this paper did not strive to develop a new methodology or tool.
A systematic literature review of individual-level psychological and behavioral responses to the health information of COVID-19 from social media and legacy media
Authors: Zhai Wei , Bian Jian , Zhang Jing , Bai Xueyin
Published: December 2021

Covid-19 has been recognized as a terrifying global health threat since its detection, with far-reaching consequences that are unprecedented in the modern era. Since the outbreak of the pandemic, social media and legacy media have collectively delivered health information related to COVID-19 to the public as a catalyst to community perception of risk. However, the existing literature exhibits different viewpoints toward the role of social media and legacy media in disseminating health information of COVID-19. In this regard, this article conducted a systematic literature review to provide an overview of the current state of research concerning individuals-level psychological and behavioral response to COVID-19 related information from different sources, as well as presents the challenges and future research directions.
The Influence of Age, Sex, and Socioeconomic Status on Glycemic Control Among People with Type 1 and Type 2 Diabetes in Canada: A Patient-Led Longitudinal Retrospective Cohort Study
Authors: Mousavi Seyedmostafa , Greenberg Dana , Ndjaboué Ruth , Greiver Michelle , Drescher Olivia , Dansokho Selma Chipenda , Boutin Denis , Chouinard Jean-Marc , Dostie Sylvie , Fenton Robert , Greenberg Marley , McGavock Jon , Najam Adhiyat , Rekik Monia , Weisz Tom , Willison Donald J. , Durand Audrey , Witteman Holly O.
Published: December 2021

Background

Clinical guidelines for most adults with diabetes recommend maintaining hemoglobin A1c (HbA1c) ≤7.0% (<53 mmol/mol) to avoid microvascular and macrovascular complications. People with diabetes of different ages, sexes, and socioeconomic statuses may differ in their ease of attaining this goal. As a team of people with diabetes, researchers, and health professionals, we aimed to explore patterns in HbA1c results among people with type 1 or type 2 diabetes in Canada. Our research question was identified by people living with diabetes.

Methods

We used generalized estimating equations to analyze the effects of age, sex and socioeconomic status in 947,543 HbA1c results measured from 2010 to 2019 among 90,770 people living with type 1 or 2 diabetes in Canada. People living with diabetes reviewed and interpreted the results.

Results

HbA1c results at or below 7.0% represented 30.5% (male people living with type 1 diabetes), 21.0% (female people living with type 1 diabetes), 55.0% (male people living with type 2 diabetes) and 59.0% (female people living with type 2 diabetes) of results in each subcategory. We observed higher HbA1c values during adolescence and, for people living with type 2 diabetes, among people living in lower income areas. Among those with type 1 diabetes, female people tended to have lower HbA1c than male people during childbearing years but higher HbA1c than male people during menopausal years. Team members living with diabetes confirmed that the patterns we observed reflected their own life courses and suggested these results be communicated to health professionals and other stakeholders to improve treatment for people living with diabetes.

Interpretation

A substantial proportion of people with diabetes in Canada are insufficiently supported to maintain guideline-recommended glycemic control goals. Blood sugar management goals may be particularly challenging for people who are going through adolescence, menopause, or living with fewer financial resources. Health professionals should be aware of the challenging nature of glycemic management and policymakers in Canada should provide more support for people with diabetes to live healthy lives.
Antibodies targeting merozoites induce natural killer cell degranulation and interferon gamma secretion and are associated with immunity against malaria
Authors: Odera Dennis O. , Tuju James , Mwai Kennedy , Nkumama Irene N. , Fürle Kristin , Chege Timothy , Kimathi Rinter , Diel Stefan , Musasia Fauzia K. , Rosenkranz Micha , Njuguna Patricia , Hamaluba Mainga , Kapulu Melissa C. , Frank Roland , Osier Faith H. A. ,   CHMI-SIKA Study Team
Published: December 2021

Natural killer cells are potent immune effectors that can be activated via antibody mediated Fc receptor engagement. Using multiparameter flow cytometry, we found that natural killer (NK) cells degranulate and release IFNγ upon stimulation with antibody-opsonized Plasmodium falciparum merozoites. Antibody-dependent NK activity (Ab-NK) was largely strain-transcending and enhanced the inhibition of invasion into erythrocytes. Ab-NK was associated with the successful control of parasitemia following experimental malaria challenge in African adults. In an independent cohort study in children, Ab-NK increased with age, was boosted by concurrent falciparum infections and associated with a lower risk of clinical episodes of malaria. Nine of 14 vaccine candidates tested induced Ab-NK including some less well-studied antigens - P41, P113, MSP11, RHOPH3, and Pf_11363200. These data highlight an important role for ab-NK in immunity against malaria and provide a new mechanism for the evaluation of vaccine candidates

One Sentence Summary

Antibody-dependent natural killer activation is induced by merozoites and associated with immunity against malaria
The association between midwifery staffing levels and the experiences of mothers on postnatal wards: cross sectional analysis of routine data
Authors: Turner Lesley , Culliford David , Ball Jane , Kitson-Reynolds Ellen , Griffiths Peter
Published: December 2021

Background

Women have consistently reported lower satisfaction with postnatal care compared with antenatal and labour care. The aim of this research was to examine whether women’s experience of inpatient postnatal care in England is associated with variation in midwifery staffing levels.

Methods

Analysis of data from the National Maternity Survey in 2018 including 17,611 women from 129 organisations. This was linked to hospital midwifery staffing numbers from the National Health Service (NHS) Workforce Statistics and the number of births from Hospital Episode Statistics. A two-level logistic regression model was created to examine the association of midwifery staffing levels and experiences in post-natal care.

Results

The median full time equivalent midwives per 100 births was 3.55 (interquartile range 3.26 to 3.78). Higher staffing levels were associated with less likelihood of women reporting delay in discharge (adjusted odds ratio [aOR] 0.849, 95% CI 0.753 to 0.959, p=0.008), increased chances of women reporting that staff always helped in a reasonable time aOR1.200 (95% CI 1.052, 1.369, p=0.007) and that they always had the information or explanations they needed aOR 1.150 (95% CI 1.040, 1.271, p=0.006). Women were more likely to report being treated with kindness and understanding with higher staffing, but the difference was small and not statistically significant aOR 1.059 (0.949, 1.181, p=0.306).

Conclusions

Negative experiences for women on postnatal wards were more likely to occur in trusts with fewer midwives. Low staffing could be contributing to discharge delays and lack of support and information, which may in turn have implications for longer term outcomes for maternal and infant wellbeing.

Explanation

While we recognise that not all gestational parents identify as women; this term was chosen as it has been used in the data source which was accessed for this study and represents most people having maternities.

Statement of significance (problem)

Women report negative experiences of postnatal care compared with antenatal care and birth. There is a recognised shortage of midwives in maternity services, and this may be impacting on the quality of postnatal care.

What is already known?

There is evidence that midwifery staffing levels are associated with birth outcomes but little empirical evidence on the impact of midwifery staffing levels in postnatal care

What this paper adds?

This analysis of survey data supports previous findings that increased midwifery staffing is associated with benefits. This is the first study to examine the effects of staffing on women’s experience of postnatal care.
Discovery and synthesis of hydroxy-L-proline based blockers of the neutral amino acid transporters SLC1A4 (ASCT1) and SLC1A5 (ASCT2)
Authors: Lyda Brent R. , Leary Gregory P. , Farnsworth Jill , Silvius Derek , Seaver Benjamin , Esslinger C. Sean , Natale Nicholas R. , Kavanaugh Michael P.
Published: December 2021

The conformationally restricted heterocycle hydroxy-L-proline is a versatile scaffold for the synthesis of diverse multi-functionalized pyrrolidines for probing the ligand binding sites of biological targets. With the goal to develop new inhibitors of the widely expressed amino acid transporters SLC1A4 and SLC1A5 (also known as ASCT1 and ASCT2), we synthesized and functionally screened a series of hydroxy-L-proline derivatives or ‘prolinols’ using electrophysiological and radio-labeled uptake assays on amino acid transporters from the SLC1, SLC7, and SLC38 solute carrier families. We identified a number of synthetic prolinols that act as selective high-affinity inhibitors of the SLC1 functional subfamily comprising the neutral amino acid transporters SLC1A4 and SLC1A5. The active and inactive prolinols were computationally docked into a threaded homology model and analyzed with respect to predicted molecular orientation and observed pharmacological activity. The series of hydroxy-L-proline derivatives identified here represents a new class of potential agents to pharmacologically modulate SLC1A4 and SLC1A5, amino acid exchangers that play important roles in a wide range of physiological and pathophysiological processes.
Using polyacrylamide hydrogels to model physiological aortic stiffness reveals that microtubules are critical regulators of isolated smooth muscle cell morphology and contractility
Authors: Ahmed Sultan , Johnson Robert. T. , Solanki Reesha , Afewerki Teclino , Wostear Finn , Warren Derek T.
Published: December 2021

Vascular smooth muscle cells (VSMCs) are the predominant cell type in the medial layer of the aortic wall and normally exist in a quiescent, contractile phenotype where actomyosin-derived contractile forces maintain vascular tone. However, VSMCs are not terminally differentiated and can dedifferentiate into a proliferative, synthetic phenotype. Actomyosin force generation is essential for the function of both phenotypes. Whilst much is already known about the mechanisms of VSMC actomyosin force generation, existing assays are either low throughput and time consuming, or qualitative and inconsistent. In this study, we use polyacrylamide hydrogels, tuned to mimic the physiological stiffness of the aortic wall, in a VSMC contractility assay. Isolated VSMC area decreases following stimulation with the contractile agonists angiotensin II or carbachol. Importantly, the angiotensin II induced reduction in cell area correlated with increased traction stress generation. Inhibition of actomyosin activity using blebbistatin or Y-27632 prevented angiotensin II mediated changes in VSMC morphology, suggesting that changes in VSMC morphology and actomyosin activity are core components of the contractile response. Furthermore, we show that microtubule stability is an essential regulator of isolated VSMC contractility. Treatment with either colchicine or paclitaxel uncoupled the morphological and/or traction stress responses of angiotensin II stimulated VSMCs. Our findings support the tensegrity model and we demonstrate that microtubules act to balance the actomyosin-derived traction stress generation and regulate the morphological responses of VSMCs.
The structural repertoire ofFusarium oxysporumf. sp.lycopersicieffectors revealed by experimental and computational studies
Authors: Yu Daniel S. , Outram Megan A. , Smith Ashley , McCombe Carl L. , Khambalkar Pravin B. , Rima Sharmin A. , Sun Xizhe , Ma Lisong , Ericsson Daniel J. , Jones David A. , Williams Simon J.
Published: December 2021

Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein x-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors fromFusarium oxysporumf. sp.lycopersici(Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of theFoldual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire ofFoland show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate thatFolsecretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding ofFol-tomato, and by extension plant-fungal interactions, which will assist the development of novel control and engineering strategies to combat plant pathogens.
Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass
Authors: Kersten Sonja , Chang Jiyang , Huber Christian D. , Voichek Yoav , Lanz Christa , Hagmaier Timo , Lang Patricia , Lutz Ulrich , Hirschberg Insa , Lerchl Jens , Porri Aimone , Van de Peer Yves , Schmid Karl , Weigel Detlef , Rabanal Fernando A.
Published: December 2021

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.
Proteome-wide cellular thermal shift assay reveals novel crosstalk between brassinosteroid and auxin signaling
Authors: Lu Qing , Zhang Yonghong , Hellner Joakim , Xu Xiangyu , Pauwels Jarne , Giannini Caterina , Ma Qian , Dejonghe Wim , Han Huibin , Van de Cotte Brigitte , Impens Francis , Gevaert Kris , Friml Jiří , De Smet Ive , Molina Daniel Martinez , Russinova Eugenia
Published: December 2021

Despite the growing interest in using chemical genetics in plant research, small-molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass-spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or post-translational modifications allows the identification of drug targets, or the study of protein-metabolite and protein-protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal- and the phospho-proteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a novel substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf thus, revealing a novel crosstalk between brassinosteroid and auxin signaling.

Significance Statement

Chemical genetics, which investigates the biological processes using small molecules, is gaining interest in plant research. However, a major challenge is to uncover the mode of action of the small molecule. Here, we applied the cellular thermal shift assay coupled with mass spectrometry (CETSA MS) to intact Arabidopsis cells and showed that bikinin, the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, changed the thermal stability of some of its direct targets and putative GSK3 interacting proteins. In combination with phosphoproteomics, we also revealed that GSK3s phosphorylate the auxin carrier PIN-FORMED1 (PIN1) and regulated its polarity that is required for the vascular patterning in the leaf.
Evolution of miRNA binding sites and regulatory networks in cichlids
Authors: Mehta Tarang K. , Penso-Dolfin Luca , Nash Will , Roy Sushmita , Di-Palma Federica , Haerty Wilfried
Published: December 2021

The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA and TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.
PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity and Sleep under Entrainment
Authors: Persons J.L. , Abhilash L. , Lopatkin A.J. , Roelofs A. , Bell E.V. , Fernandez M.P. , Shafer O.T.
Published: December 2021

The problem of entrainment is central to circadian biology. In this regard, Drosophila has been an important model system. Owing to the simplicity of its nervous system and the availability of powerful genetic tools, the system has shed significant light on the molecular and neural underpinnings of entrainment. However, much remains to be learned regarding the molecular and physiological mechanisms underlying this important phenomenon. Under cyclic light/dark conditions, Drosophila melanogaster displays crepuscular patterns of locomotor activity with one peak anticipating dawn and the other anticipating dusk. These peaks are characterized through an estimation of their phase relative to the environmental light cycle and the extent of their anticipation of light transitions. In Drosophila chronobiology, estimations of phases are often subjective, and anticipation indices vary significantly between studies. Though there is increasing interest in building flexible analysis software tools in the field, none incorporates objective measures of Drosophila activity peaks in combination with the analysis of fly activity/sleep in the same program. To this end, we have developed PHASE, a MATLAB-based program that is simple and easy to use and (i) supports the visualization and analysis of activity and sleep under entrainment, (ii) allows analysis of both activity and sleep parameters within user-defined windows within a diurnal cycle, (iii) uses a smoothing filter for the objective identification of peaks of activity (and therefore can be used to quantitatively characterize them), and (iv) offers a series of analyses for the assessment of behavioral anticipation of environmental transitions.
Clustering and visualization of single-cell RNA-seq data using path metrics
Authors: Manousidaki Andriana , Little Anna , Xie Yuying
Published: December 2021

Recent advances in single-cell technologies have enabled high-resolution characterization of tissue and cancer compositions. Although numerous tools for dimension reduction and clustering are available for single-cell data analyses, these methods often fail to simultaneously preserve local cluster structure and global data geometry. To address these challenges, we developed a novel analyses framework,Single-CellPathMetricsProfiling (scPMP), using power-weighted path metrics, which measure distances between cells in a data-driven way. Unlike Euclidean distance and other commonly used distance metrics, path metrics are density sensitive and respect the underlying data geometry. By combining path metrics with multidimensional scaling, a low dimensional embedding of the data is obtained which preserves both the global data geometry and cluster structure. We evaluate the method both for clustering quality and geometric fidelity, and it outperforms current scRNAseq clustering algorithms on a wide range of benchmarking data sets.
Selection on early survival does not explain germination rate clines in Mimulus cardinalis (Phrymaceae)
Authors: Muir Christopher D. , Van Den Elzen Courtney L. , Angert Amy L.
Published: December 2021

Premise

Many traits covary with environmental gradients to form phenotypic clines. While local adaptation to the environment can generate phenotypic clines, other nonadaptive processes may also. If local adaptation causes phenotypic clines, then the direction of genotypic selection on traits should shift from one end of the cline to the other. Traditionally genotypic selection on non-Gaussian traits like germination rate have been hampered because it is challenging to measure their genetic variance.

Methods

Here we used quantitative genetics and reciprocal transplants to test whether a previously discovered cline in germination rate showed additional signatures of adaptation in the scarlet monkeyflower (Mimulus cardinalis). We measured genotypic and population level covariation between germination rate and early survival, a component of fitness. We developed a novel discrete log-normal model to estimate genetic variance in germination rate.

Results

Contrary to our adaptive hypothesis, we found no evidence that genetic variation in germination rate contributed to variation in early survival. Across populations, southern populations in both gardens germinated earlier and survived more.

Conclusions

Southern populations have higher early survival but this is not caused by faster germination. This pattern is consistent with nonadaptive forces driving the phenotypic cline in germination rate, but future work will need to assess whether there is selection at other life stages. This statistical framework should help expand quantitative genetic analyses for other waiting-time traits.
Selective pressure on membrane proteins drives the evolution of Helicobacter pylori Colombian subpopulations
Authors: Guevara Alix A. , Torres Roberto C. , Castro-Valencia Fabian L. , Suárez John J. , Criollo-Rayo Angel , Bravo Maria Mercedes , Carmona Luis Carvajal , Polanco M. Magdalena Echeverry de , Bohórquez Mabel E. , Torres Javier
Published: December 2021

Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America H. pylori has evolved in several subpopulations specific for regions or even countries. In this study we analyzed the genome of 163 Colombian strains along with 1,113 strains that represent worldwide H. pylori populations to better discern the ancestry and adaption to Colombian people. Population structure was inferred with FineStructure and chromosome painting identifying the proportion of ancestries in Colombian isolates. Phylogenetic relationship was analyzed using the SNPs present in the core genome. Also, a Fst analysis was done to identify the gene variants with the strongest fixation in the identified Colombian subpopulations in relation to their parent population hspSWEurope. Worldwide, population structure analysis allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia. In addition, three subgroups of H. pylori were identified within hspColombia that follow their geographic origin. The Colombian H. pylori subpopulations represent an admixture of European, African and Native indigenous ancestry; although some genomes showed a high proportion of self-identity, suggesting a strong adaption to these mestizo Colombian groups. The Fst analysis identified 82 SNPs significantly fixed in 26 genes of the hspColombia subpopulation that encode mainly for outer membrane proteins and proteins involved in central metabolism. The strongest fixation indices were identified in genes encoding the membrane proteins HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations following a geographical structure, evolving to an autochthonous genetic pool, drive by a positive selective pressure especially on genes encoding for outer membrane proteins.