bluuebunny/crossref_metadata_2025 huggingface dataset:
eSCAN: scan regulatory regions for aggregate association testing using whole-genome sequencing data
Authors: Yang Yingxi , Sun Quan , Huang Le , Broome Jai G , Correa Adolfo , Reiner Alexander ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Raffield Laura M , Yang Yuchen , Li Yun
Published: November 2021

Multiple statistical methods for aggregate association testing have been developed for whole-genome sequencing (WGS) data. Many aggregate variants in a given genomic window and ignore existing knowledge to define test regions, resulting in many identified regions not clearly linked to genes, and thus, limiting biological understanding. Functional information from new technologies (such as Hi-C and its derivatives), which can help link enhancers to their effector genes, can be leveraged to predefine variant sets for aggregate testing in WGS data. Here, we propose the eSCAN (scan the enhancers) method for genome-wide assessment of enhancer regions in sequencing studies, combining the advantages of dynamic window selection in SCANG (SCAN the Genome), a previously developed method, with the advantages of incorporating putative regulatory regions from annotation. eSCAN, by searching in putative enhancers, increases statistical power and aids mechanistic interpretation, as demonstrated by extensive simulation studies. We also apply eSCAN for blood cell traits using NHLBI Trans-Omics for Precision Medicine WGS data. Results from real data analysis show that eSCAN is able to capture more significant signals, and these signals are of shorter length (indicating higher resolution fine-mapping capability) and drive association of larger regions detected by other methods.
Exploring the use of psychotropic medication in cardiac patients with and without anxiety and its association with 1-year mortality
Authors: Cromhout Pernille Fevejle , Christensen Anne Vinggaard , Jørgensen Martin Balslev , Ekholm Ola , Juel Knud , Svendsen Jesper Hastrup , Osler Merete , Rasmussen Trine Bernholdt , Borregaard Britt , Mols Rikke Elmose , Thrysoee Lars , Thorup Charlotte Brun , Berg Selina Kikkenborg
Published: November 2021

Aims

Comorbid psychiatric disorders and the use of psychotropic medication are common among cardiac patients and have been found to increase the risk of mortality. The aims of this study were: (i) to describe the use of psychotropic medication among cardiac patients with and without symptoms of anxiety, (ii) to estimate the association between use of psychotropic medication prior to hospital admission and all-cause, 1-year mortality following discharge, and (iii) to estimate the risk of mortality among users and non-users of psychotropic medication with or without self-reported symptoms of anxiety.

Methods and results

Cardiac patients from the DenHeart survey were included, providing information on self-reported symptoms of anxiety. From national registers, information on the use of psychotropic medication 6 months prior to hospitalization and mortality was obtained. By logistic regression analyses, the association between the use of psychotropic medication, anxiety, and all-cause, 1-year mortality was estimated. The risk of subsequent incident use of psychotropic medication among patients with and without anxiety was furthermore explored. All analyses were fully adjusted. A total of 12 913 patients were included, of whom 18% used psychotropic medication, and 3% died within 1 year. The use of psychotropic medication was found to be associated with increased 1-year all-cause mortality [odds ratio 1.90 (95% confidence interval, 1.46–2.46)]. Patients with symptoms of anxiety were significantly more likely to use psychotropic medication following hospital discharge [2.47 (2.25–2.72)].

Conclusion

The use of psychotropic medication was associated with 1-year mortality. Thus, the use of psychotropic medication might explain some of the association between anxiety and mortality; however, the association is probably mainly a reflection of the underlying mental illness, rather than the use of psychotropic medication.
Patient Generated Health Data Earn a Seat at the Table:Clinical Adoption During the Covid-19 Transition to Telemedicine
Authors: Rosner Benjamin I , Kvedar Joseph C , Adler-Milstein Julia
Published: November 2021

Background

Patient generated health data (PGHD) have not achieved widespread clinical adoption. However, the COVID-induced shift to telemedicine may have created opportunities for PGHD as surrogates for vital signs collected in-person. We assessed whether this shift was associated with greater ambulatory care PGHD use.

Methods

We conducted an interrupted time series analysis of physician enrollment in, and patient-initiated vital sign transmission of non-COVID associated PGHD through, a national PGHD platform (Validic).

Results

Ten health systems, 4,695 physicians, and 51,320 patients were included. We found a significant increase in physician enrollment (slope change of 0.86/week, P=.02). Platform application programming interface calls continued their pre-COVID upward trend, despite large reductions in overall encounters.

Discussion

These findings suggest significantly greater pandemic-associated clinical demand for PGHD, and patient supply disproportionate to encounter rates.

Conclusion

Increasing clinical use and ongoing efforts to reduce barriers, could help seize current adoption momentum to realize PGHD’s potential value.

Lay Summary

Patient generated health data (PGHD) - health-related data created and recorded by or from patients outside of the clinical setting to help address a health concern—have not yet achieved widespread adoption in routine clinical care. The COVID-19 pandemic precipitated a rapid transition of outpatient encounters to telemedicine in which healthcare providers lacked access to vital signs routinely collected during in-person visits. We conducted an analysis to determine whether the transition to telemedicine increased patient transmission of, and provider adoption of vital sign-related PGHD as surrogates for their in-person equivalents. We found that the number of healthcare providers enrolling on a national PGHD platform increased significantly following the transition to telemedicine, and that the amount of PGHD transmission continued the upward trajectory that it was already experiencing, substantially outpacing the dramatic decline in overall encounters that occurred early in the pandemic. While adoption challenges persist, including questions about accuracy of PGHD, liability, reimbursement, and the potential for exacerbating disparities, these findings suggest an increasing willingness of patients and healthcare providers to use vital sign-related PGHD to supplement telemedicine encounters. Increasing clinical use and ongoing efforts to reduce barriers, could help seize current adoption momentum to realize PGHD’s potential value.
Identification and Physicochemical Properties of the Novel Hemolysin(s) From Oral Secretions of Helicoverpa armigera (Lepidoptera: Noctuidae)
Authors: Wang Xiong-Ya , Cai Dong-Zhang , Li Xin , Bai Su-Fen , Yan Feng-Ming
Published: November 2021

Hemolysins cause the lysis of invading organisms, representing major humoral immunity used by invertebrates. Hemolysins have been discovered in hemolymph of Helicoverpa armigera larvae as immune factors. As oral immunity is great important to clear general pathogens, we presumed that hemolysins may be present in oral secretions (OS). To confirm this hypothesis, we conducted four testing methods to identify hemolysin(s) in larval OS of H. armigera, and analyzed physicochemical properties of the hemolysin in comparison with hemolytic melittin of Apis mellifera (L.) (Hymenoptera: Apidae) venom. We found hemolysin(s) from OS of H. armigera for the first time, and further identified in other lepidopteran herbivores. It could be precipitated by ammonium sulfate, which demonstrates that the hemolytic factor is proteinaceous. Labial gland showed significantly higher hemolytic activity than gut tissues, suggesting that hemolysin of OS is mainly derived from saliva secreted by labial glands. Physicochemical properties of hemolysin in caterpillar’s OS were different from bee venom. It was noteworthy that hemolytic activity of OS was only partially inhibited even at 100°C. Hemolytic activity of OS was not inhibited by nine tested carbohydrates contrary to bee venom melittin. Moreover, effects of metal ions on hemolytic activity were different between OS and bee venom. We conclude that there is at least a novel hemolysin in OS of herbivorous insects with proposed antibacterial function, and its hemolytic mechanism may be different from melittin. Our study enriches understanding of the potential role of hemolysins in insect immunity and provides useful data to the field of herbivorous insect-pathogen research.
Judicial Review by the People Themselves: Democracy and the Rule of Law in Ancient Athens
Authors: Carugati Federica , Calvert Randall , Weingast Barry R
Published: November 2021

Modern democratic constitutions mediate the tension between democracy and the rule of law through institutions that check unrestrained popular rule with expert judicial bodies. This paper considers the alternative arrangement that existed in ancient Athens, where checks on popular rule coexisted with strong popular control. Judicial review in Athens, however, raised two additional threats to democracy and the rule of law: unpredictability and partisanship. We combine a formal model with historical exegesis to show how the strategic incentives of Athenian institutional design, along with a strong societal consensus on the value of constitutional democracy, were necessary ingredients for dispelling both threats. In Athens, institutions responsive to citizens’ demands existed alongside a robust rule of law. This case study provides empirical evidence allowing us to reflect on the feasibility of extensive democratic input to the process of constitutional review. [JEL: H11—structure, scope, and performance of government; K40—legal procedure, the legal system, and illegal behavior (general)]
Solving the identity of the common shallow-water octopus of the Colombian Caribbean based on the analysis of mitochondrial DNA sequence data
Authors: Puentes-Sayo Alejandra , Torres-Rodríguez Javier , Lecompte Orlando
Published: November 2021

The specific identity of the common octopus fished along the Colombian Caribbean was studied based on 58 specimens collected from artisanal fishing in five localities (Providencia, San Andrés, Santa Marta, Cartagena and Isla Fuerte). A molecular systematic analysis of the mitochondrial genes 16S ribosomal RNA and cytochrome c oxidase subunit III was carried out, along with a reanalysis of data for the cytochrome c oxidase subunit I gene. These analyses revealed that the common shallow-water octopus of the Colombian Caribbean is Octopus insularis. The trees generated for the three genes and the genetic distances for each of the genes (0–0.3%) confirmed the specimens collected in this study as belonging to a single clade and the species as O. insularis. Our results confirm that the octopus described recently as O. tayrona is in fact O. insularis and this extends the known distribution of the latter species to the southwestern Caribbean (i.e. Colombian coast). We discuss our findings in the context of the species misidentification of the O. vulgaris species complex.
Multiple-Dose Dalbavancin Regimens as the Predominant Treatment of Deep-Seated or Endovascular Infections: A Scoping Review
Authors: Cooper Margaret M , Preslaski Candice R , Shihadeh Katherine C , Hawkins Kellie L , Jenkins Timothy C
Published: November 2021

Off-label use of dalbavancin for deep-seated and endovascular infections has been increasing. We performed a scoping review to evaluate the evidence for use of multiple-dose dalbavancin regimens as the predominant therapy for these indications. Predominant therapy was defined as use of dalbavancin without other concurrent antibiotics for more than half of the total treatment duration. Fifteen publications were identified; 2 were small, open-label randomized controlled trials and the remainder were retrospective observational studies or case reports. A total of 144 cases from these publications met eligibility criteria for inclusion in this review. Types of infections included osteoarticular infections, catheter-related or complicated bloodstream infections, and infective endocarditis. Overall, the evidence for use of multiple-dose regimens of dalbavancin for deep-seated and endovascular infections is limited by a paucity of data from controlled trials, heterogeneity of dosing regimens, and a lack of standardized clinical outcomes.
Wilful Blindness: Sleeping Sickness and Onchocerciasis in Colonial Northern Ghana, 1909–1957
Authors: Bannister David
Published: November 2021

As a contribution to the existing literature on deliberate or unintended neglect, concealment and ignorance regarding significant and enduring public health problems—produced by economic marginality, lack of political power and institutional failures affecting specific places and groups—this article discusses the history of epidemic sleeping sickness and endemic onchocerciasis in colonial northern Ghana from 1909 to 1957. Despite accumulating evidence of their serious impacts on the health of northern communities, and calls to action on the part of some health officials, both diseases were only officially recognised as significant risks when it was no longer politically possible to deny them. The particular histories of each disease, in the same region over the same decades, reveal two comparable and interrelated trajectories of neglect.
N6-Methyladenosine Modification of CDH1 mRNA Promotes PM2.5-Induced Pulmonary Fibrosis via Mediating Epithelial Mesenchymal Transition
Authors: Ning Jie , Du Hairong , Zhang Yaling , Liu Qingping , Jiang Tao , Pang Yaxian , Tian Xiaochen , Yan Liqun , Niu Yujie , Zhang Rong
Published: November 2021

The association between ambient airborne fine particulate matter (PM2.5) exposure and respiratory diseases has been investigated in epidemiological studies. To explore the potential mechanism of PM2.5-induced pulmonary fibrosis, 60 mice were divided into 3 groups to expose to different levels of PM2.5 for 8 and 16 weeks: filtered air, unfiltered air, and concentrated PM2.5 air, respectively. BEAS-2B cells were treated with 0, 25, 50, and 100 μg/ml PM2.5 for 24 h. The biomarkers of pulmonary fibrosis, epithelial-mesenchymal transition, N6-methyladenosine (m6A) modification, and metabolism of mRNAs were detected to characterize the effect of PM2.5 exposure. The results illustrated that PM2.5 exposure induced pathological alteration and pulmonary fibrosis in mice. The expression of E-cadherin was decreased whereas vimentin and N-cadherin expression were increased in a dose- and time-dependent manner after PM2.5 exposure. Mechanistically, PM2.5 exposure increased the levels of METTL3-mediated m6A modification of CDH1 mRNA. As a target gene of miR-494-3p, YTHDF2 was upregulated by miR-494-3p down-regulation and then recognized m6A-modified CDH1 mRNA to inhibit the E-cad expression, consequently induced the EMT progression after PM2.5 exposure. Our study indicated that PM2.5 exposure triggered EMT progression to promote the pulmonary fibrosis via miR-494-3p/YTHDF2 recognized and METTL3 mediated m6A modification.
Scientific Evidence Supporting Coronavirus Disease 2019 (COVID-19) Vaccine Efficacy and Safety in People Planning to Conceive or Who Are Pregnant or Lactating
Authors: Girardi Guillermina , Bremer Andrew A.
Published: November 2021

Three coronavirus disease 2019 (COVID-19) vaccines have been authorized for use in the United States; specifically, the Pfizer–BioNTech, Moderna, and Johnson & Johnson–Janssen COVID-19 vaccines were granted emergency use authorization by the U.S. Food and Drug Administration in late 2020 and early 2021. Vaccination coverage and intent among adults are lowest among those aged 18–39 years and among females in particular. In females of reproductive age, enthusiasm for receiving a COVID-19 vaccine may be negatively affected by claims currently circulating widely on diverse social media platforms regarding the vaccines adversely affecting fertility and pregnancy. Yet it is important to note that these claims are anecdotal in nature and not supported by the available scientific evidence. It is also imperative that the effects of COVID-19 vaccine on reproductive health are clarified. Herein, we discuss the existing scientific data supporting COVID-19 vaccine safety and efficacy in people who are planning to conceive or who are pregnant or lactating and highlight the importance of COVID-19 vaccination in females of reproductive age.
A Review of Disparities in Cardiac Rehabilitation
Authors: Mathews Lena , Brewer LaPrincess C.
Published: November 2021

Purpose:

Cardiac rehabilitation (CR) has been shown to improve functional status, quality of life, and recurrent cardiovascular disease (CVD) events. Despite its demonstrated compelling benefits and guideline recommendation, CR is underutilized, and there are significant disparities in CR utilization particularly by race, ethnicity, sex, and socioeconomic status. The purpose of this review is to summarize the evidence and drivers of these disparities and recommend potential solutions.

Methods:

In this review, key studies documenting disparities in CR referrals, enrollment, and completion are discussed. Additionally, potential mechanisms for these disparities are summarized and strategies are reviewed for addressing them.

There is a wealth of literature demonstrating disparities among racial and ethnic minorities, women, those with lower income and education attainment, and those living in rural and dense urban areas. However, there was minimal focus on how the social determinants of health contribute to the observed disparities in CR utilization in many of the studies reviewed. Interventions such as automatic referrals, inpatient liaisons, mitigation of economic barriers, novel delivery mechanisms, community partnerships, and health equity metrics to incentivize health care organizations to reduce care disparities are potential solutions.
ASSOCIATIONS BETWEEN DYSGLYCEMIA, RETINAL NEURODEGENERATION, AND MICROALBUMINURIA IN PREDIABETES AND TYPE 2 DIABETES
Authors: Kirthi Varo , Zuckerman Benjamin P. , Alam Uazman , Bunce Catey , Hopkins David , Jackson Timothy L.
Published: November 2021

Purpose:

To explore the association between retinal neurodegeneration and metabolic parameters in progressive dysglycemia.

Method:

A cross-sectional study was performed on 68 participants: normal glucose tolerance (n = 23), prediabetes (n = 25), and Type 2 diabetes without diabetic retinopathy (n = 20). Anthropometric assessment and laboratory sampling for HbA1c, fasting glucose, insulin, c-peptide, lipid profile, renal function, and albumin-to-creatinine ratio were conducted. Central and pericentral macular thicknesses on spectral domain optical coherence tomography were compared with systemic parameters.

Results:

Baseline demographic characteristics were similar across all groups. Cuzick's trend test revealed progressive full-thickness macular thinning with increasing dysglycemia across all three groups (P = 0.015). The urinary albumin-to-creatinine ratio was significantly correlated with full-thickness superior (R = −0.435; P = 0.0002), inferior (R = −0.409; P = 0.0005), temporal (R = −0.429; P = 0.003), and nasal (R = −0.493; P < 0.0001) pericentral macular thinning, after post hoc Bonferroni adjustment. There was no association between macular thinning and waist circumference, body mass index, blood pressure, lipid profile, or insulin resistance.

Conclusion:

Progressive dysglycemia is associated with macular thinning before the onset of visible retinopathy and occurs alongside microalbuminuria. Retinal neurodegenerative changes may help identify those most at risk from dysglycemic end-organ damage.
A Nurse-Navigated, Postpartum Support Text Messaging Intervention
Authors: Morris Melanie Hall , Barton Maureen , Zane Marietta , Hutson Sadie P. , Raman Rameela , Heidel R. Eric
Published: November 2021

More than 50% of maternal deaths in the United States occur during the first year following childbirth. Nearly 40% of these deaths occur between days 1 and 41 of the postpartum period. Historically, women receive less attention from healthcare providers during the postpartum period when compared with the care provided during pregnancy and childbirth. Women may not return for scheduled follow-up care until 4 to 6 weeks after birth, if they return at all. The role of postpartum nurse navigator (PPNN) was developed to deliver a novel, text messaging intervention as part of a randomized controlled trial to 43 primiparous women who experienced an unplanned cesarean birth. Through daily, interactive text messaging, the PPNN assessed study participants' general well-being, assisted with symptom navigation, offered anticipatory guidance, and provided informational support until 4 weeks postpartum. Satisfaction with the intervention was evaluated using a survey that incorporated quantitative and qualitative responses. Overwhelmingly, 93% of participants rated their overall experience with the text messaging intervention as outstanding or good. At least 95% of the participants indicated that they would likely choose to receive daily text messaging from a PPNN following a subsequent birth. Convenient access to professional nurse support for women postbirth warrants further evaluation.
Care Experiences of Persons With Perinatal Opioid Use
Authors: Blair Lisa M. , Ashford Kristin , Gentry Lauren , Bell Sarah , Fallin-Bennett Amanda
Published: November 2021

Opioid use in the perinatal period has escalated rapidly, with potentially devastating outcomes for perinatal persons and infants. Substance use treatment is effective and has the potential to greatly improve clinical outcomes; however, characteristics of care received from providers including nurses have been described as a barrier to treatment. Our purpose was to describe supportive perinatal care experiences of persons with opioid use disorder. A qualitative descriptive study design was used to examine experiences of 11 postpartum persons (ages 22-36 years) in medication-assisted treatment for opioid use disorder at an academic medical center in the southern region of the United States. Participants were interviewed about experiences with perinatal and neonatal care during the child's hospitalization for neonatal abstinence syndrome surveillance and/or treatment. Four themes of supportive care experiences emerged: informing, relating, accepting, and holistic supporting. Participants reported a range of positive and negative perinatal care experiences, with examples and counterexamples provided. This fuller understanding of perceptions and lived experiences of care can inform practice changes and educational/training priorities. Future research is needed to facilitate development of comprehensive care models geared to address perinatal care needs of persons with opioid use disorder.
Kidney in the net of acute and long-haul coronavirus disease 2019: a potential role for lipid mediators in causing renal injury and fibrosis
Authors: Chiang Kate C. , Imig John D. , Kalantar-Zadeh Kamyar , Gupta Ajay
Published: November 2021

Purpose of review

Severe COVID-19 disease is often complicated by acute kidney injury (AKI), which may transition to chronic kidney disease (CKD). Better understanding of underlying mechanisms is important in advancing therapeutic approaches.

Recent findings

SARS-CoV-2-induced endothelial injury initiates platelet activation, platelet–neutrophil partnership and release of neutrophil extracellular traps. The resulting thromboinflammation causes ischemia–reperfusion (I/R) injury to end organs. Severe COVID-19 induces a lipid-mediator storm with massive increases in thromboxane A2 (TxA2) and PGD2, which promote thromboinflammation and apoptosis of renal tubular cells, respectively, and thereby enhance renal fibrosis. COVID-19-associated AKI improves rapidly in the majority. However, 15–30% have protracted renal injury, raising the specter of transition from AKI to CKD.

In COVID-19, the lipid-mediator storm promotes thromboinflammation, ischemia–reperfusion injury and cytotoxicity. The thromboxane A2 and PGD2 signaling presents a therapeutic target with potential to mitigate AKI and transition to CKD. Ramatroban, the only dual antagonist of the thromboxane A2/TPr and PGD2/DPr2 signaling could potentially mitigate renal injury in acute and long-haul COVID. Urgent studies targeting the lipid-mediator storm are needed to potentially reduce the heavy burden of kidney disease emerging in the wake of the current pandemic.
Novel intestinal dialysis interventions and microbiome modulation to control uremia
Authors: Sumida Keiichi , Lau Wei Ling , Kalantar-Zadeh Kamyar , Kovesdy Csaba P.
Published: November 2021

Purpose of review

In patients with chronic kidney disease (CKD), the gut plays a key role in the homeostasis of fluid and electrolyte balance and the production and disposal of uremic toxins. This review summarizes the current evidence on the gut-targeted interventions to control uremia, fluid overload, hyperkalemia and hyperphosphatemia in CKD.

Recent findings

Studies have emerged that support the concept of intestinal dialysis, such as colonic perfusion with a Malone antegrade continence enema stoma or colonic irrigation with a rectal catheter, as a promising adjuvant approach to control uremia in CKD, although most findings are preliminary. The use of AST-120, an oral adsorbent, has been shown to reduce circulating levels of indoxyl sulfate and p-cresol sulfate and have potential renoprotective benefits in patients with advanced CKD. Diarrhea or inducing watery stools may modulate fluid retention and potassium and phosphorus load. Accumulating evidence indicates that plant-based diets, low-protein diets, and pre-, pro-, and synbiotic supplementation may lead to favorable alterations of the gut microbiota, contributing to reduce uremic toxin generation. The effects of these gut-targeted interventions on kidney and cardiovascular outcomes are still limited and need to be tested in future studies including clinical trials.

Interventions aimed at enhancing bowel elimination of uremic toxins, fluid and electrolytes and at modulating gut microbiota may represent novel therapeutic strategies for the management of uremia in patients with CKD.
Not all wavelengths are created equal: disinfection of SARS-CoV-2 using UVC radiation is wavelength-dependent
Authors: Mariita Richard M. , Peterson James W.
Published: November 2021

SARS-CoV-2 is mostly transmitted through close contact with infected people by infected aerosols and fomites. Ultraviolet subtype C (UVC) lamps and light-emitting diodes can be used to disrupt the transmission chain by disinfecting fomites, thus managing the disease outbreak progression. Here, we assess the ultraviolet wavelengths that are most effective in inactivation of SARS-CoV-2 on fomites. Variations in UVC wavelengths impact the dose required for disinfection of SARS-CoV-2 and alter how rapidly and effectively disruption of the virus transmission chain can be achieved. This study reveals that shorter wavelengths (254–268 nm) take a maximum of 6.25 mJ/cm2 over 5 s to obtain a target SARS-CoV-2 reduction of 99.9%. Longer wavelengths, like 280 nm, take longer irradiation time and higher dose to inactivate SARS-CoV-2. These observations emphasize that SARS-CoV-2 inactivation is wavelength-dependent.
Phaffia brasiliana sp. nov., a yeast species isolated from soil in a Cerrado–Atlantic Rain Forest ecotone site in Brazil
Authors: Santos Ana Raquel Oliveira , Aires Andreia , Pontes Ana , Silva Margarida , Brito Patricia H , Groenewald Marizeth , Melo Cidiane G. S. , Lachance Marc-André , Sampaio José Paulo , Rosa Carlos A.
Published: November 2021

During studies of yeasts associated with soil in a Cerrado–Atlantic Rain Forest ecotone site in Brazil, three orange-pigmented yeast strains were isolated from samples collected in Minas Gerais state, Brazil. Molecular analyses combining the 26S rRNA gene (D1/D2 domains) and the internal transcribed spacer (ITS) sequences as well as whole-genome sequence data showed that these strains could not be ascribed to any known species in the basidiomycetous genusPhaffia, and thus they are considered to represent a novel species for which the namePhaffia brasilianasp. nov. is proposed. The holotype is CBS 16121Tand the MycoBank number is MB 839315. The occurrence ofP. brasilianain a tropical region is unique for the genus, since all other species occur in temperate regions. Two factors appear to contribute to the distribution of the novel taxon: first, the region where it was found has relatively moderate temperature ranges and, second, an adaptation to grow or withstand temperatures higher than those of the other species in the genus seems to be in place.
Alpha oscillations are involved in localizing touch on hand-held tools
Authors: Fabio Cécile , Salemme Romeo , Koun Eric , Farnè Alessandro , Miller Luke E.
Published: November 2021

The sense of touch is not restricted to the body but can also extend to external objects. When we use a hand-held tool to contact an object, we feel the touch on the tool and not in the hand holding the tool. The ability to perceive touch on a tool actually extends along its entire surface, allowing the user to accurately localize where it is touched similarly as they would on their body. While the neural mechanisms underlying the ability to localize touch on the body have been largely investigated, those allowing to localize touch on a tool are still unknown. We aimed to fill this gap by recording the EEG signal of participants while they localized tactile stimuli on a hand-held rod. We focused on oscillatory activity in the alpha (7-14 Hz) and beta (15-30 Hz) range, as they have been previously linked to distinct spatial codes used to localize touch on the body. Beta activity reflects the mapping of touch in skin-based coordinates, whereas alpha activity reflects the mapping of touch in external space. We found that alpha activity was solely modulated by the location of tactile stimuli applied on a hand-held rod. Source reconstruction suggested that this alpha power modulation was localized in a network of fronto-parietal regions previously implicated in higher-order tactile and spatial processing. These findings are the first to implicate alpha oscillations in tool-extended sensing and suggest an important role for processing touch in external space when localizing touch on a tool.
Diversity, function and evolution of aquatic vertebrate genomes
Authors: Song Yue , Yu Mengjun , Zhang Suyu , Zhang Rui , Seim Inge , Guo Xinyu , Liu Meiru , Yu Lili , Zhang He , Li Hanbo , Liu Shanshan , Liu Xin , Xu Xun , Yang Huanming , Wang Kun , He Shunping , Wang Wen ,   Fish10K Consortium, Fan Guangyi
Published: November 2021

Aquatic vertebrates consist of jawed fish (cartilaginous fish and bony fish), aquatic mammals, reptiles and amphibians. Here, we present a comprehensive analysis of 630 aquatic vertebrate genomes to generate a standardized compendium of genomic data. We demonstrate its value by assessing their genome features as well as illuminating gene families related to the transition from water to land, such as Hox genes and olfactory receptor genes. We found that LINEs are the major transposable element (TE) type in cartilaginous fish and aquatic mammals, while DNA transposons are the dominate type in bony fish. To our surprise, TE types are not fixed in amphibians, the first group that transitioned to living on land. These results illustrate the value of a unified resource for comparative genomic analyses of aquatic vertebrates. Our data and strategy are likely to support all evolutionary and ecological research on vertebrates.
Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations
Authors: Taravella Oill Angela M. , Handley Carla , Howell Emma K. , Stone Anne C. , Mathew Sarah , Wilson Melissa A.
Published: November 2021

Objectives

The aim of this study was to characterize the genetic relationships within and among four neighboring populations in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation.

Materials and Methods

We collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals.

Results

Here we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations.

Discussion

Overall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.
A biosafety level 2 surrogate for studying SARS-CoV-2 survival in food processing environmental biofilms
Authors: Featherstone Austin B. , Dass Sapna Chitlapilly
Published: November 2021

Meat processing plants have been at the center of the SARS-CoV-2 pandemic. There are several factors that contribute to the persistence of SARS-CoV-2 in meat processing plants and one of the factors is the formation of a multi-species biofilm with virus. Biofilm can act as a reservoir in protecting, harboring, and dispersing SARS-CoV-2 from biofilm to the meat processing facility environment. We used Murine Hepatitis Virus (MHV) as a surrogate for SARS-CoV-2 virus and meat processing facility drain samples to develop mixed-species biofilms on commonly found materials in processing facilities (Stainless-Steel (SS), PVC and tiles). The results showed that MHV was able to integrate into the environmental biofilm and survived for a period of 5 days at 7°C. There was no significate difference between the viral-environmental biofilm biovolumes developed on different materials SS, PVC, and tiles. There was a 2-fold increase in the virus-environmental biofilm biovolume when compared to environmental biofilm by itself. These results indicate a complex virus-environmental biofilm interaction which is providing enhanced protection for the survival of viral particles with the environmental biofilm community.
Diverse operant control of different motor cortex populations during learning
Authors: Vendrell-Llopis Nuria , Fang Ching , Qü Albert J. , Costa Rui M. , Carmena Jose M.
Published: November 2021

During motor learning, as well as during neuroprosthetic learning, animals learn to control motor cortex activity in order to generate behavior. Two different population of motor cortex neurons, intra-telencephalic (IT) and pyramidal tract (PT) neurons, convey the resulting cortical signals within and outside the telencephalon. Although a large amount of evidence demonstrates contrasting functional organization among both populations, it is unclear whether the brain can equally learn to control the activity of either class of motor cortex neurons. To answer this question, we used a Calcium imaging based brain-machine interface (CaBMI) and trained different groups of mice to modulate the activity of either IT or PT neurons in order to receive a reward. We found that animals learn to control PT neuron activity faster and better than IT neuron activity. Moreover, our findings show that the advantage of PT neurons is the result of characteristics inherent to this population as well as their local circuitry and cortical depth location. Taken together, our results suggest that motor cortex is optimized to control the activity of pyramidal track neurons, embedded deep in cortex, and relaying motor commands outside of the telencephalon.
Ratiometric 4Pi single molecule localization with optimal resolution and color assignment
Authors: Chen Jianwei , Yao Benxi , Yang Zhichao , Shi Wei , Luo Tingdan , Xi Peng , Jin Dayong , Li Yiming
Published: November 2021

4Pi single molecule localization microscopy (4Pi-SMLM) with two opposing objectives achieves sub-10 nm isotropic 3D resolution with as few as 250 photons collected by each objective. Here, we developed a new ratiometric multi-color imaging strategy for 4Pi-SMLM which employed the intrinsic multi-phase interference intensity without increasing the complexity of the system and achieved both optimal 3D resolution and color separation. By partially linking the photon parameters between channels with interference difference of π during global fitting of the multi-channel 4Pi single molecule data, we showed on simulated data that the loss of the localization precision is minimal compared with the theoretical minimum uncertainty, the Cramer-Rao lower bound (CRLB).
The emergence of a collective sensory response threshold in ant colonies
Authors: Gal Asaf , Kronauer Daniel J. C.
Published: November 2021

The sensory response threshold is a fundamental biophysical property of biological systems that underlies many physiological and computational functions, and its systematic study has played a pivotal role in uncovering the principles of neural computation. Here, we show that ant colonies, which perform computational tasks at the group level, have emergent collective sensory response thresholds. Colonies respond collectively to step changes in temperature and evacuate the nest during severe perturbations. This response is characterized by a group-size dependent threshold, and the underlying dynamics are dominated by social feedback between the ants. Using a binary network model, we demonstrate that a balance between short-range excitatory and long-range inhibitory interactions can explain the emergence of the collective response threshold and its size dependency. Our findings illustrate how simple social dynamics allow insect colonies to integrate information about the external environment and their internal state to produce adaptive collective responses.
Bimodal Remapping of Visual Grids
Authors: Long Xiaoyang , Cai Jing , Deng Bin , Chen Zhe Sage , Zhang Sheng-Jia
Published: November 2021

Spatially modulated neurons from the rat secondary visual cortex (V2) show grid-like firing patterns during freely foraging in open-field enclosures. However, the remapping of the V2 grid cells is not well understood. Here we report two classes of V2 grid cell populations with distinct remapping properties: one regular class with invariant grid field patterns, and the other bimodal class that has remapping induced by environmental manipulations such as changes in enclosure shape, size, orientation and lighting in a familiar environment. The bimodal V2 grid cell pattern remains stable regardless of the follow-up manipulations, but restores to the original firing pattern upon animal’s re-entry into the familiar environment on the next day or from the novel environment. The bimodal V2 grid cells are modulated with theta frequency during the course of remapping and stabilize quickly. We also found conjunctive bistable V2 grid cells with invariant head directional tuning. Overall, our results suggest a new grid cell mechanism in V2 that is different from the medial entorhinal cortex (MEC) grid cells.

Highlights

Bistable V2 grid cells display bimodal or bistable remapping

V2 grid cell firing patterns are not disrupted in darkness

V2 grid cells preserve theta frequency modulation during remapping
An arachnid’s guide to be an ant: morphological and behavioural mimicry in ant-mimicking spiders
Authors: Subramaniam Nimish , Tamma Krishnapriya , Uma Divya
Published: November 2021

Batesian mimicry imposes several challenges to mimics and evokes adaptations in multiple sensory modalities. Myrmecomorphy, morphological and behavioral resemblance to ants, is seen in over 2000 arthropod species. Ant-like resemblance is observed in at least 13 spider families despite spiders having a distinct body plan compared to ants. Quantifying the extent to which spiders’ shape, size, and behavior resemble model ants will allow us to comprehend the evolutionary pressures that have facilitated myrmecomorphy. Myrmaplata plataleoides are ‘accurate’ mimics of the weaver ants, Oecophylla smaragdina. In this study, we quantify the speed of movement of model, mimic, and non-mimetic jumping spiders. We use traditional and geometric morphometrics to quantify traits such as foreleg and hindleg size, body shape between the model ant, mimic, and non-mimics. Our results suggest that while the mimics closely resemble the model ants in speed of movement, they occupy an intermediate morphological space compared to the model ants and non-mimics. We suggest that ant-mimicking spiders are better at mimicking ants’ locomotory movement than morphology and overall body shape. Our study provides a framework to understand the multimodal nature of mimicry and helps discern the relative contributions of such traits that drive mimetic accuracy in ant-mimicking spiders.
Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing
Authors: Uddin Nisar , Shinde Harshraj , Tesfamicael Kiflu , Ali Niaz , Tricker Penny J. , Rodríguez López Carlos M.
Published: November 2021

Ziziphus are economically and nutritionally important fruiting plants that were domesticated in China around 7000 years ago. We identified genetic diversity in 141 accessions of four, different species collected in Pakistan and in China, including wild species of Ziziphus mauritiana, Z. nummularia and Z. oxyphllya, and both wild and domesticated Z. jujuba Mill. Population structure, phylogenetic analysis and principal coordinates analysis based on 10,889 high-quality SNPs derived from genotyping-by-sequencing indicated that the accessions clustered into two major groups. The wild Pakistani Z. jujuba and Z. nummularia exhibited higher genetic diversity and polymorphic information content (0.37 and 0.23 respectively) than other species. We further conducted a genome-wide association study and discovered six highly significant marker-trait associations for fruit weight and plant height in this population. Our study provides important information for future breeding of Ziziphus species.
Type 1 interferon supports B cell responses to polysaccharide antigens but is not required for MPL/TDCM adjuvant effects on innate B cells
Authors: Spurrier M. Ariel , Jennings-Gee Jamie E. , Haas Karen M.
Published: November 2021

We previously described monophosphoryl lipid A (MPL) and synthetic cord factor, trehalose-6,6’-dicorynomycolate (TDCM) significantly increases antibody (Ab) responses to T cell independent type 2 antigens (TI-2 Ags) in a manner dependent on B cell-intrinsic TLR4 expression as well as MyD88 and TRIF adapter proteins. Given the requirement for TRIF in optimal MPL/TDCM adjuvant effects and the capacity of MPL to drive type I IFN production, we aimed to investigate the extent to which adjuvant effects on TI-2 Ab responses depend on type I IFN receptor (IFNAR) signaling. We found IFNAR−/−mice had impaired early TI-2 Ag-induced B cell activation and expansion and that B cell-intrinsic type I IFN signaling on B cells was essential for normal antibody responses to TI-2 Ags, including haptenated Ficoll and the pneumococcal vaccine, Pneumovax23. However, MPL/TDCM significantly increased TI-2 IgM and IgG responses in IFNAR−/−mice. MPL/TDCM enhanced TI-2 Ab production primarily by activating innate B cells (B-1b and splenic CD23−B cells) as opposed to CD23+enriched follicular B cells. In summary, our study highlights an important role for type I IFN in supporting early B cell responses to TI-2 Ags through B cell-expressed IFNAR, but nonetheless demonstrates an MPL/TDCM adjuvant significantly increases TI-2 Ab responses independently of type I IFN signaling and does so by predominantly supporting increased polysaccharide-specific Ab production by innate B cell populations.

Key points

B cell-intrinsic IFNAR expression promotes TI-2 Ab responses.

MPL/TDCM adjuvant effects are independent of type 1 IFN.

MPL/TDCM promotes TI-2 Ab responses by innate B cells.
Improving the Virtual Trichrome Assessment through Bridge Category Models
Authors: Levy Joshua , Bobak Carly , Azizgolshani Nasim , Liu Xiaoying , Ren Bing , Lisovsky Mikhail , Suriawinata Arief , Christensen Brock , O’Malley James , Vaickus Louis
Published: November 2021

Non-alcoholic steatohepatitis (NASH) is a liver disease characterized by excessive lipid accumulation and disease progression is typically assessed through inspection of a Trichrome stain for Fibrosis staging. As the public health burden of NASH worsens due to evolving lifestyle habits, pathology laboratory resources will become increasingly strained due to rising demand for specialized stains. Virtual staining processes, computational methods which can synthesize the application of chemical staining reagents, can potentially provide resource savings by obviating the need to acquire specialized stains. Virtual staining technologies are assessed by comparing virtual and real tissue stains for their realism and ability to stage. However, these assessment methods are rife with statistical mistreatment of observed phenomena that are difficult to account for. Bridge category ratings represent a phenomenon where a pathologist may assign two adjacent stages simultaneously, which may bias and/or reduce the power of research findings. Such stage assignments were frequently reported in a large-scale assessment of Virtual Trichrome technologies yet were unaccounted for since no statistical adjustment procedures existed. In this work, we provide an updated assessment of Virtual Trichrome technologies using Bridge Category Models, which account for these bridge ratings. We report that two of four pathologists tended to assign lower Fibrosis stages to virtually stained tissue while the other two pathologists assigned similar stages. These research findings differ when bridge ratings are not accounted for. While promising, these results indicate further room for algorithmic finetuning of Virtual Trichrome technologies.