bluuebunny/crossref_metadata_2025 huggingface dataset:
An Overview of Palm Oil Production Processing in Nigeria: A Case Study of Ilashe, Nigeria
Authors: Biodiin M. B. , Akinlabi E. T. , Okokpujie I. P. , Fayomi O. S. I.
Published: July 2021

Palm oil, which is extracted from the fleshy mesocarp of the palm fruit, has been a vital resource in the majority of Nigerians diet. The global need for palm oil is fast increasing because it serves as a source of income. After been refined, the oil is filtered to get a liquid fraction, which is being utilized as cooking oil. Furthermore, the Palm oil process involves the separation of the fruit from fibrous attachment, followed by the crushing of fruit, heating, and extracting the oil using an oilseed expeller, clarification in a filter press by sedimentation. This paper gives an overview of the plant layout of palm oil processing and the scheduling operation, which includes bunch reception, fruit removal, bunches sterilization, digestion of the fruit, extracting of palm oil, clarification of oil, oil storage, and recovery of the kernel. Furthermore, the survey of an area in Nigeria was also carried out to ascertain factors affecting the production of palm oil and individual view on the impact of processing. Due to the yield in oil palm enterprise, if the sector is judiciously managed, it will be a source of solution to problems that Nigeria is experiencing.
Effect of Demographic Characteristics on the choice of Paratransit Modes
Authors: Busari A.A. , Abatan O.G , Alao G.O. , Odunlami O. , Orekoya O. , Busari I.I. , Benson A.O , Moshood O.O
Published: July 2021

The absence of public transportation has led to the growth and expansion of paratransit modes. This has increased traffic congestion, traffic crashes and traffic pollution. This research assessed the effect of demographic characteristics on para transiting in Lagos with special focus on the mainland. To achieve the aim of this research, the mainland was divided into two zones based on the geographical location which are the Ikorodu and Ikeja zone. Domiciliary information techniques were used in data collection. This was backed up with an oral interview. Two hundred question (200) questionnaires were administered with 89% return rate. The information captured were demographic characteristics, the volume of trips, frequency of trips, trip types, operations of the paratransit transportation system, travel behaviour of passengers (travel time, travel cost, travel purpose). SPSS version 18 was used for the data analysis. The result of the survey revealed that paratransit modes serve as a feeder connection between neighbourhoods in the study area. Additionally, it provides a feeder connection between major arterial roads (truck A and B roads). Flexibility accounts for 41% of the reason why paratransit mode is preferred by respondents. The bivariate analysis showed a weak negative relationship for the correlation between frequency of trip and age. The outcome of this research will aid transportation planners, policymakers, and transportation experts on the appropriate strategy to adopt for effective mobility as a unimodal approach to providing effective movement may not be foreseeable in the study area.
The Atiyah–Singer index theorem
Authors: Freed Daniel
Published: July 2021

The Atiyah–Singer index theorem, a landmark achievement of the early 1960s, brings together ideas in analysis, geometry, and topology. We recount some antecedents and motivations, various forms of the theorem, and some of its implications, which extend to the present.
Challenges in Obtaining Valid Causal Effect Estimates With Machine Learning Algorithms
Authors: Naimi Ashley I , Mishler Alan E , Kennedy Edward H
Published: July 2021

Unlike parametric regression, machine learning (ML) methods do not generally require precise knowledge of the true data-generating mechanisms. As such, numerous authors have advocated for ML methods to estimate causal effects. Unfortunately, ML algorithms can perform worse than parametric regression. We demonstrate the performance of ML-based singly and doubly robust estimators. We used 100 Monte Carlo samples with sample sizes of 200, 1,200, and 5,000 to investigate bias and confidence-interval coverage under several scenarios. In a simple confounding scenario, confounders were related to the treatment and the outcome via parametric models. In a complex confounding scenario, the simple confounders were transformed to induce complicated nonlinear relationships. In the simple scenario, when ML algorithms were used, double-robust estimators were superior to singly robust estimators. In the complex scenario, single-robust estimators with ML algorithms were at least as biased as estimators using misspecified parametric models. Doubly robust estimators were less biased, but coverage was well below nominal. The use of sample splitting, inclusion of confounder interactions, reliance on a richly specified ML algorithm, and use of doubly robust estimators was the only explored approach that yielded negligible bias and nominal coverage. Our results suggest that ML-based singly robust methods should be avoided.
Aperture: alignment-free detection of structural variations and viral integrations in circulating tumor DNA
Authors: Liu Hongchao , Yin Huihui , Li Guangyu , Li Junling , Wang Xiaoyue
Published: July 2021

The identification of structural variations (SVs) and viral integrations in circulating tumor DNA (ctDNA) is a key step in precision oncology that may assist clinicians in treatment selection and monitoring. However, due to the short fragment size of ctDNA, it is challenging to accurately detect low-frequency SVs or SVs involving complex junctions in ctDNA sequencing data. Here, we describe Aperture, a new fast SV caller that applies a unique strategy of $k$-mer-based searching, binary label–based breakpoint detection and candidate clustering to detect SVs and viral integrations with high sensitivity, especially when junctions span repetitive regions. Aperture also employs a barcode-based filter to ensure specificity. Compared with existing methods, Aperture exhibits superior sensitivity and specificity in simulated, reference and real data tests, especially at low dilutions. Additionally, Aperture is able to predict sites of viral integration and identify complex SVs involving novel insertions and repetitive sequences in real patient data. Aperture is freely available at https://github.com/liuhc8/Aperture.
In Their Own Words: Nalini Nadkarni
Authors: Verdier James M
Published: July 2021

In Their Own Words chronicles the stories of scientists who have made great contributions to their fields. These short histories provide our readers a way to learn from and share their experiences. We will publish the results of these conversations in the pages of BioScience and on our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com). This history is with Nalini Nadkarni, professor of biology at the University of Utah.
Distinct cardiac-locked brain pulsations in Alzheimer’s disease
Authors: Bailes Sydney M , Lewis Laura D
Published: July 2021

This scientific commentary refers to ‘Cardiovascular brain impulses in Alzheimer’s disease’ by Rajna et al. (doi:10.1093/brain/awab144).
Three-dimensional mapping of neurofibrillary tangle burden in the human medial temporal lobe
Authors: Yushkevich Paul A , Muñoz López Mónica , Iñiguez de Onzoño Martin María Mercedes , Ittyerah Ranjit , Lim Sydney , Ravikumar Sadhana , Bedard Madigan L , Pickup Stephen , Liu Weixia , Wang Jiancong , Hung Ling Yu , Lasserve Jade , Vergnet Nicolas , Xie Long , Dong Mengjin , Cui Salena , McCollum Lauren , Robinson John L , Schuck Theresa , de Flores Robin , Grossman Murray , Tisdall M Dylan , Prabhakaran Karthik , Mizsei Gabor , Das Sandhitsu R , Artacho-Pérula Emilio , Arroyo Jiménez Marı’a del Mar , Marcos Raba Marı’a Pilar , Molina Romero Francisco Javier , Cebada Sánchez Sandra , Delgado González José Carlos , de la Rosa-Prieto Carlos , Córcoles Parada Marta , Lee Edward B , Trojanowski John Q , Ohm Daniel T , Wisse Laura E M , Wolk David A , Irwin David J , Insausti Ricardo
Published: July 2021

Tau protein neurofibrillary tangles are closely linked to neuronal/synaptic loss and cognitive decline in Alzheimer’s disease and related dementias. Our knowledge of the pattern of neurofibrillary tangle progression in the human brain, critical to the development of imaging biomarkers and interpretation of in vivo imaging studies in Alzheimer’s disease, is based on conventional two-dimensional histology studies that only sample the brain sparsely.

To address this limitation, ex vivo MRI and dense serial histological imaging in 18 human medial temporal lobe specimens (age 75.3 ± 11.4 years, range 45 to 93) were used to construct three-dimensional quantitative maps of neurofibrillary tangle burden in the medial temporal lobe at individual and group levels. Group-level maps were obtained in the space of an in vivo brain template, and neurofibrillary tangles were measured in specific anatomical regions defined in this template.

Three-dimensional maps of neurofibrillary tangle burden revealed significant variation along the anterior-posterior axis. While early neurofibrillary tangle pathology is thought to be confined to the transentorhinal region, we found similar levels of burden in this region and other medial temporal lobe subregions, including amygdala, temporopolar cortex, and subiculum/cornu ammonis 1 hippocampal subfields.

Overall, the three-dimensional maps of neurofibrillary tangle burden presented here provide more complete information about the distribution of this neurodegenerative pathology in the region of the cortex where it first emerges in Alzheimer’s disease, and may help inform the field about the patterns of pathology spread, as well as support development and validation of neuroimaging biomarkers.
CSF-resident CD4+ T-cells display a distinct gene expression profile with relevance to immune surveillance and multiple sclerosis
Authors: Hrastelj James , Andrews Robert , Loveless Samantha , Morgan Joanne , Bishop Stefan Mark , Bray Nicholas J , Williams Nigel M , Robertson Neil P
Published: July 2021

The CNS has traditionally been considered an immune privileged site, but is now understood to have a system of immune surveillance, predominantly involving CD4+ T-cells. Identifying functional differences between CNS and blood CD4+ T-cells, therefore, have relevance to CNS immune surveillance as well as to neurological conditions, such as multiple sclerosis, in which CD4+ T-cells play a central role. Here, CD4+ T-cells were purified from CSF and blood from 21 patients with newly diagnosed treatment-naïve multiple sclerosis and 20 individuals with non-inflammatory disorders using fluorescence-activated cell sorting, and their transcriptomes were profiled by RNA sequencing. Paired comparisons between CD4+ T-cells from CSF and blood identified 5156 differentially expressed genes in controls and 4263 differentially expressed in multiple sclerosis patients at false discovery rate <5%. Differential expression analysis of CD4+ T-cells collected from the CSF highlighted genes involved in migration, activation, cholesterol biosynthesis and signalling, including those with known relevance to multiple sclerosis pathogenesis and treatment. Expression of markers of CD4+ T-cell subtypes suggested an increased proportion of Th1 and Th17 cells in CSF. Gene ontology terms significant only in multiple sclerosis were predominantly those involved in cellular proliferation. A two-way comparison of CSF versus blood CD4+ T-cells in multiple sclerosis compared with non-inflammatory disorder controls identified four significant genes at false discovery rate <5% (CYP51A1, LRRD1, YES1 and PASK), further implicating cholesterol biosynthesis and migration mechanisms. Analysis of CSF CD4+ T-cells in an extended cohort of multiple sclerosis cases (total N = 41) compared with non-inflammatory disorder controls (total N = 38) identified 140 differentially expressed genes at false discovery rate < 5%, many of which have known relevance to multiple sclerosis, including XBP1, BHLHE40, CD40LG, DPP4 and ITGB1. This study provides the largest transcriptomic analysis of purified cell subpopulations in CSF to date and has relevance for the understanding of CNS immune surveillance, as well as multiple sclerosis pathogenesis and treatment discovery.
Transmission of Antimicrobial Resistant Yersinia pestis During a Pneumonic Plague Outbreak
Authors: Andrianaivoarimanana Voahangy , Wagner David M , Birdsell Dawn N , Nikolay Birgit , Rakotoarimanana Faniry , Randriantseheno Lovasoa N , Vogler Amy J , Sahl Jason W , Hall Carina M , Somprasong Nawarat , Cauchemez Simon , Schweizer Herbert P , Razafimandimby Harimahefa , Rogier Christophe , Rajerison Minoarisoa
Published: July 2021

Background

Pneumonic plague (PP), caused by Yersinia pestis, is the most feared clinical form of plague due to its rapid lethality and potential to cause outbreaks. PP outbreaks are now rare due to antimicrobial therapy.

Methods

A PP outbreak in Madagascar involving transmission of a Y. pestis strain resistant to streptomycin, the current recommended first-line treatment in Madagascar, was retrospectively characterized using epidemiology, clinical diagnostics, molecular characterization, and animal studies.

Results

The outbreak occurred in February 2013 in the Faratsiho district of Madagascar and involved 22 cases, including 3 untreated fatalities. The 19 other cases participated in funeral practices for the fatal cases and fully recovered after combination antimicrobial therapy: intramuscular streptomycin followed by oral co-trimoxazole. The Y. pestis strain that circulated during this outbreak is resistant to streptomycin resulting from a spontaneous point mutation in the 30S ribosomal protein S12 (rpsL) gene. This same mutation causes streptomycin resistance in 2 unrelated Y. pestis strains, one isolated from a fatal PP case in a different region of Madagascar in 1987 and another isolated from a fatal PP case in China in 1996, documenting this mutation has occurred independently at least 3 times in Y. pestis. Laboratory experiments revealed this mutation has no detectable impact on fitness or virulence, and revertants to wild-type are rare in other species containing it, suggesting Y. pestis strains containing it could persist in the environment.

Conclusions

Unique antimicrobial resistant (AMR) strains of Y. pestis continue to arise in Madagascar and can be transmitted during PP outbreaks.
Fecal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) RNA Is Associated With Decreased Coronavirus Disease 2019 (COVID-19) Survival
Authors: Das Adhikari Upasana , Eng George , Farcasanu Mara , Avena Laura E , Choudhary Manish C , Triant Virginia A , Flagg Meaghan , Schiff Abigail E , Gomez Isabella , Froehle Leah M , Diefenbach Thomas J , Ronsard Larance , Lingwood Daniel , Lee Grace C , Rabi Seyed Alireza , Erstad Derek , Velmahos George , Li Jonathan Z , Hodin Richard , Stone James R , Honko Anna N , Griffiths Anthony , Yilmaz Ömer H , Kwon Douglas S
Published: July 2021

The clinical significance of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) RNA in stool remains uncertain. We found that extrapulmonary dissemination of infection to the gastrointestinal tract, assessed by the presence of SARS-CoV-2 RNA in stool, is associated with decreased coronavirus disease 2019 (COVID-19) survival. Measurement of SARS-CoV-2 RNA in stool may have utility for clinical risk assessment.
Effects of force magnitude on dental arches in cervical headgear therapy
Authors: Talvitie Tuula , Helminen Mika , Karsila Susanna , Pirttiniemi Pertti , Signorelli Luca , Varho Reeta , Peltomäki Timo
Published: July 2021

Aim

To study the influence of different force magnitudes on dental arches in cervical headgear (CHG) treatment.

Material and methods

In this controlled clinical trial, patients (n = 40) were treated with CHG with light (L, 300 g, n = 22) or heavy force (H, 500 g, n = 18) magnitude. Subjects were asked to use CHG for 10 hours a day for 10 months. The outer bow of the CHG facebow was raised 10–20 degrees and the inner bow expanded 3–4 mm. Adherence to instructions and force magnitude were monitored with an electronic module (Smartgear, Swissorthodontics, Switzerland). Impressions for study models were taken before (T1) and after (T2) treatment and the study models were scanned into digital form (3Shape, R700 Scanner, Denmark). Measurements were made using the digital models (Planmeca Romexis, Model analyser, Finland).

Results

During the treatment (T1–T2) the upper inter-canine distance increased by 2.83 mm (P = 0.000) and 2.60 mm (P = 0.000) in the L and H force magnitude groups, respectively. Upper inter-molar width increased by 3.16 mm (P = 0.000) and 2.50 mm (P = 0.000) in the L and H groups, respectively. Maxillary total arch perimeter increased by 6.39 mm (P = 0.001) and 6.68 mm (P = 0.001) in the L and H groups, respectively. In the amount of change over time, T1–T2, in the upper arch measurements, no significant difference was found between the groups. Lower inter-canine width increased by 0.94 mm (P = 0.005) and 1.16 mm (P = 0.000) in the L and H groups, respectively; no difference between the groups. Lower inter-molar distance increased by 2.17 mm (P = 0.000) and 1.11 mm (P = 0.008) in the L and H groups, respectively. At the end of the study, upper and lower inter-molar width was larger in the L group than in the H group (P = 0.039 and P = 0.022, respectively).

Conclusion

CHG therapy is an effective method for expanding and releasing moderate crowding of the upper dental arch. The lower arch spontaneously follows the upper arch in widening effects, and minor expansion can also be seen on the lower arch. In the L group, larger inter-molar width was achieved on the upper and lower arch; probably due to better adherence to instructions. Light force is recommended for use in CHG therapy.
Handel’s harpsichords revisited Part II: Handel’s domestic harpsichords
Authors: Holman Peter
Published: July 2021

The harpsichords supposedly owned or played by Handel have long been the subject of scholarly enquiry, in recent years mainly to try to match their compasses and disposition to his solo music, a strategy also used, for instance, with instruments associated with J. S. Bach and Mozart. Similarly, Grant O’Brien, John Koster and others have tried to determine how Ruckers-family instruments might have been used to play early 17th-century keyboard music.

In Part I of this article (in the last Early Music) I discussed six Ruckers harpsichords associated with Handel and his followers in the 18th and 19th centuries, three of which can be identified with surviving instruments. I argued that Handel favoured them partly because they had a cachet equivalent to Amati violins, and partly because he used them for directing oratorios at Covent Garden, where a small instrument with a brilliant tone would have been an asset in a crowded performing area. In this second part I focus on five plucked instruments said to have been owned by Handel, and apparently used by him at home, for accompanying in small rehearsals, for performing solo music to his friends and for private practice. Not all the claims made for the total of eleven instruments associated with Handel stand up to scrutiny, as we shall see, but a surprising number of them can be traced back to his milieu, and I argue that the composer needed a large number of instruments for his varied activities as a composer, solo keyboard virtuoso, teacher and musical director.
Peripartum cardiomyopathy: from genetics to management
Authors: Sliwa Karen , Bauersachs Johann , Arany Zolt , Spracklen Timothy F , Hilfiker-Kleiner Denise
Published: July 2021

Peripartum cardiomyopathy (PPCM) is a disease that occurs globally in all ethnic groups and should be suspected in any peripartum women presenting with symptoms and signs of heart failure, towards the end of pregnancy or in the months following delivery, with confirmed left ventricular dysfunction. After good history taking, all women should be thoroughly assessed, and alternative causes should be excluded. Urgent cardiac investigations with electrocardiogram and natriuretic peptide measurement (if available) should be performed. Echocardiography follows as the next step in investigation. Patients with abnormal cardiac investigations should be urgently referred to a cardiology team for expert management. Referral for genetic work-up should be considered if there is a family history of cardiomyopathy or sudden death. PPCM is a disease with substantial maternal and neonatal morbidity and mortality. Maternal mortality rates range widely, from 0% to 30%, depending on the ethnic background and geographic region. Just under half of women experience myocardial recovery. Remarkable advances in the comprehension of the pathogenesis and in patient management and therapy have been achieved, largely due to team efforts and close collaboration between basic scientists, cardiologists, intensive care specialists, and obstetricians. This review summarizes current knowledge of PPCM genetics, pathophysiology, diagnostic approach, management, and outcome.
Reconstituting electrical conduction in soft tissue: the path to replace the ablationist
Authors: Post Allison D , Buchan Skylar , John Mathews , Safavi-Naeini Payam , Cosgriff-Hernández Elizabeth , Razavi Mehdi
Published: July 2021

Cardiac arrhythmias are a leading cause of morbidity and mortality in the developed world. A common mechanism underlying many of these arrhythmias is re-entry, which may occur when native conduction pathways are disrupted, often by myocardial infarction. Presently, re-entrant arrhythmias are most commonly treated with antiarrhythmic drugs and myocardial ablation, although both treatment methods are associated with adverse side effects and limited efficacy. In recent years, significant advancements in the field of biomaterials science have spurred increased interest in the development of novel therapies that enable restoration of native conduction in damaged or diseased myocardium. In this review, we assess the current landscape of materials-based approaches to eliminating re-entrant arrhythmias. These approaches potentially pave the way for the eventual replacement of myocardial ablation as a preferred therapy for such pathologies.
Has translational genomics come of age in Africa?
Authors: Kamp Michelle , Krause Amanda , Ramsay Michele
Published: July 2021

The rapid increase in genomics research in Africa and the growing promise of precision public health (PPH) begs the question of whether African genomics has come of age and is being translated into improved healthcare for Africans. An assessment of the continent’s readiness suggests that genetic service delivery remains limited and extremely fragile. The paucity of data on mutation profiles for monogenic disorders and lack of large genome-wide association cohorts for complex traits in African populations is a significant barrier, coupled with extreme genetic variation across different regions and ethnic groups. Data from many different populations are essential to developing appropriate genetic services. Of the proposed genetic service delivery models currently used in Africa—Uncharacterized, Limited, Disease-focused, Emerging and Established—the first three best describe the situation in most African countries. Implementation is fraught with difficulties related to the scarcity of an appropriately skilled medical genetic workforce, limited infrastructure and processes, insufficient health funding and lack of political support, and overstretched health systems. There is a strong nucleus of determined and optimistic clinicians and scientists with a clear vision, and there is a hope for innovative solutions and technological leapfrogging. However, a multi-dimensional approach with active interventions to stimulate genomic research, clinical genetics and overarching healthcare systems is needed to reduce genetic service inequalities and accelerate PPH on the continent. Human and infrastructure capacity development, dedicated funding, political will and supporting legislation, and public education and awareness, are critical elements for success. Africa-relevant genomic and related health economics research remains imperative with an overarching need to translate knowledge into improved healthcare. Given the limited data and genetic services across most of Africa, the continent has not yet come of ‘genomics’ age.
KCND2 variants associated with global developmental delay differentially impair Kv4.2 channel gating
Authors: Zhang Yongqiang , Tachtsidis Georgios , Schob Claudia , Koko Mahmoud , Hedrich Ulrike B S , Lerche Holger , Lemke Johannes R , van Haeringen Arie , Ruivenkamp Claudia , Prescott Trine , Tveten Kristian , Gerstner Thorsten , Pruniski Brianna , DiTroia Stephanie , VanNoy Grace E , Rehm Heidi L , McLaughlin Heather , Bolz Hanno J , Zechner Ulrich , Bryant Emily , McDonough Tiffani , Kindler Stefan , Bähring Robert
Published: July 2021

Here, we report on six unrelated individuals, all presenting with early-onset global developmental delay, associated with impaired motor, speech and cognitive development, partly with developmental epileptic encephalopathy and physical dysmorphisms. All individuals carry heterozygous missense variants of KCND2, which encodes the voltage-gated potassium (Kv) channel α-subunit Kv4.2. The amino acid substitutions associated with the variants, p.(Glu323Lys) (E323K), p.(Pro403Ala) (P403A), p.(Val404Leu) (V404L) and p.(Val404Met) (V404M), affect sites known to be critical for channel gating. To unravel their likely pathogenicity, recombinant mutant channels were studied in the absence and presence of auxiliary β-subunits under two-electrode voltage clamp in Xenopus oocytes. All channel mutants exhibited slowed and incomplete macroscopic inactivation, and the P403A variant in addition slowed activation. Co-expression of KChIP2 or DPP6 augmented the functional expression of both wild-type and mutant channels; however, the auxiliary β-subunit-mediated gating modifications differed from wild type and among mutants. To simulate the putative setting in the affected individuals, heteromeric Kv4.2 channels (wild type + mutant) were studied as ternary complexes (containing both KChIP2 and DPP6). In the heteromeric ternary configuration, the E323K variant exhibited only marginal functional alterations compared to homomeric wild-type ternary, compatible with mild loss-of-function. By contrast, the P403A, V404L and V404M variants displayed strong gating impairment in the heteromeric ternary configuration, compatible with loss-of-function or gain-of-function. Our results support the etiological involvement of Kv4.2 channel gating impairment in early-onset monogenic global developmental delay. In addition, they suggest that gain-of-function mechanisms associated with a substitution of V404 increase epileptic seizure susceptibility.
The impact of COVID-19 on the Japanese healthcare system and comparison of its mitigation measures with South Korea and Taiwan
Authors: Shin Jung-ho , Lin Huei-Ru , Imanaka Yuichi
Published: July 2021

Since the coronavirus disease 2019 (COVID-19) pandemic has begun, Asian countries/regions, such as Japan, South Korea, and Taiwan, had generally controlled the pandemic better than other countries. In this article, we showed the big impact of the pandemic on acute care hospitals in Japan, where the number of COVID-19 patients has been smaller than in other countries. We also compared the mitigation measures against the COVID-19 pandemic among Japan, South Korea, and Taiwan to study the factors affecting the differences among these relatively well-controlled countries/regions. We analyzed Diagnosis Procedure Combination data from the Quality Indicator/Improvement Project database, in which Japanese hospitals participated voluntarily. During the first declaration of emergency, which was from April 4 to May 25, the numbers of inpatients decreased roughly 20% for adults and 40% for those aged under 18 years compared to those of the same period in the previous year. In the analyses by disease, hospitalizations with acute coronary syndrome, ischemic stroke, cancer, childhood non-COVID-19 acute infections, infant and pediatric asthma decreased in number, whereas those with alcohol-related liver diseases and pancreatitis increased. Comparing selected mitigation measures against COVID-19, such as border control, enforced measures, information governance, and contact tracing, among Japan, South Korea, and Taiwan, the implementation and dissemination of measures were less strict, slower, and less comprehensive in Japan. This might explain why Japan has experienced a comparatively high incidence of COVID-19 and indicate a substantial risk of infection explosion. A change in behavioral compliance could trigger an infection explosion under poor performance in the response set. Further monitoring is warranted to promote the evolution of effective sets of countermeasures to overcome the pandemic.
Riemannian F-Manifolds, Bi-Flat F-Manifolds, and Flat Pencils of Metrics
Authors: Arsie Alessandro , Buryak Alexandr , Lorenzoni Paolo , Rossi Paolo
Published: July 2021

In this paper, we study relations between various natural structures on F-manifolds. In particular, given an arbitrary Riemannian F-manifold, we present a construction of a canonical flat F-manifold associated to it. We also describe a construction of a canonical homogeneous Riemannian F-manifold associated to an arbitrary exact homogeneous flat pencil of metrics satisfying a certain non-degeneracy assumption. In the last part of the paper, we construct Legendre transformations for Riemannian F-manifolds.
Molnupiravir Inhibits Replication of the Emerging SARS-CoV-2 Variants of Concern in a Hamster Infection Model
Authors: Abdelnabi Rana , Foo Caroline S , De Jonghe Steven , Maes Piet , Weynand Birgit , Neyts Johan
Published: July 2021

The emergence of SARS-CoV-2 variants of concern (VoCs) has exacerbated the COVID-19 pandemic. Currently available monoclonal antibodies and vaccines appear to have reduced efficacy against some of these VoCs. Antivirals targeting conserved proteins of SARS-CoV-2 are unlikely to be affected by mutations arising in VoCs and should therefore be effective against emerging variants. We here investigate the efficacy of molnupiravir, currently in phase 2 clinical trials, in hamsters infected with Wuhan strain or B.1.1.7 and B.1.351 variants. Molnupiravir proved to be effective against infections with each of the variants and therefore may have potential combating current and future emerging VoCs.
Characteristics and functions of glyceraldehyde 3-phosphate dehydrogenase S-nitrosylation during controlled aging of elm and Arabidopsis seeds
Authors: Zeng MeiYan , He YuQi , Gao Xue , Wang Yu , Deng ShiMing , Ye TianTian , Wang XiaoFeng , Xue Hua
Published: July 2021

Seed aging is the gradual decline in seed vigor, during which programmed cell death (PCD) occurs. The functions of nitric oxide (NO) are exerted through protein S-nitrosylation, a reversible post-translational modification. During seed aging, more than 80 proteins are S-nitrosylated, but the particular role of individual proteins is unknown. Here, we showed that the S-nitrosylation level of glyceraldehyde 3-phosphate dehydrogenase (UpGAPDH) in elm (Ulmus pumila L.) seeds increased after controlled deterioration treatment. UpGAPDH was S-nitrosylated at Cys154 during S-nitrosoglutathione (GSNO) treatment, and its oligomerization was triggered both in vitro and in elm seeds. Interestingly, UpGAPDH interacted with the mitochondrial voltage-dependent anion channel in an S-nitrosylation-dependent way. Some UpGAPDH–green fluorescent protein in Arabidopsis protoplasts co-localized with mitochondria during the GSNO treatment, while the S-nitrosylation-defective UpGAPDH C154S–GFP protein did not. Seeds of oxUpGAPDH lines showed cell death and lost seed vigor rapidly during controlled deterioration treatment-triggered seed aging, while those overexpressing S-nitrosylation-defective UpGAPDH-Cys154 did not. Our results suggest that S-nitrosylation of UpGAPDH may accelerate cell death and seed deterioration during controlled deterioration treatment. These results provide new insights into the effects of UpGAPDH S-nitrosylation on protein interactions and seed aging.
Superadiabaticity and the metallicity independence of the Humphreys–Davidson limit
Authors: Sabhahit Gautham N , Vink Jorick S , Higgins Erin R , Sander Andreas A C
Published: July 2021

The Humphreys–Davidson (HD) limit sets the boundary between evolutionary channels of massive stars that end their lives either as the red supergiants (RSGs) or as the hotter blue supergiants (BSGs) and Wolf–Rayet stars. Mixing in the envelopes of massive stars close to their Eddington limit is crucial for investigating the upper luminosity limit of the coolest supergiants. We study the effects of excess mixing in superadiabatic layers that are dominated by radiation pressure, and we critically investigate the effects of mixing and mass-loss on the evolution of RSGs with log (Teff/K) < 3.68 – as a function of metallicity. Using MESA, we produce grids of massive star models at three metallicities: Galactic (Z⊙), LMC $(\frac{1}{2}{\rm Z}_\odot)$, and SMC $(\frac{1}{5}{\rm Z}_\odot)$, with both high and low amounts of overshooting to study the upper luminosity limit of RSGs. We systematically study the effects of excess mixing in the superadiabatic layers of post-main-sequence massive stars, overshooting above the hydrogen core and yellow supergiant (YSG) mass-loss rates on the fraction of core helium burning time spent as a RSG. We find that the excess mixing in the superadiabatic layers is stronger at lower metallicities, as it depends on the opacities in the hydrogen bump at log (Teff/K) ≈ 4, which become more pronounced at lower metallicity. This shifts the cut-off luminosities to lower values at lower metallicities, thus balancing the first-order effect of mass-loss. The opposing effects of mass-loss and excess envelope mixing during post-main-sequence evolution of stars with higher overshooting potentially results in a metallicity-independent upper luminosity limit.
Stability analysis of the pickup ion ring-beam distributions in the outer heliosheath
Authors: Mousavi Ameneh , Liu Kaijun , Sadeghzadeh Sina
Published: July 2021

The electromagnetic instabilities driven by the pickup ions in the outer heliosheath play a crucial role in interpreting the energetic neutral atom (ENA) ribbon observed by the Interstellar Boundary EXplorer (IBEX). Previous studies on the stability of the outer heliosheath pickup ions focused on ring-like velocity distributions with pickup angles equal or close to 90°. In this study, we investigate the instabilities driven by a ring-beam velocity distribution of the pickup ions in the outer heliosheath using linear instability analysis. The modes propagating along (both parallel and antiparallel to) the background magnetic field are examined, and the emphasis is on how the instabilities change with the pickup angle, α, varying from zero to 90°. The parallel thermal spread of the pickup ions is chosen to make the plasma parameters lie in the Alfvén cyclotron ‘stability gap’ to exclude the well-studied Alfvén cyclotron instability. Our linear instability analysis reveals that the unstable modes all have left helicity but may propagate parallel or antiparallel to the background magnetic field. At small α, the parallel-propagating modes are unstable in two separate wavenumber (and frequency) ranges. The two unstable ranges merge into one when α increases to 82°. In addition, the antiparallel-propagating modes become unstable when α is above 5°, but the parallel-propagating modes have larger growth rates until α becomes larger than αc = 82.8°. The growth rates of the parallel-propagating modes quickly drop below zero when α goes beyond αc, while the antiparallel-propagating modes remain unstable until α approaches 90°.
Full-sky integrated Sachs–Wolfe maps for the MICE grand challenge lightcone simulation
Authors: Naidoo Krishna , Fosalba Pablo , Whiteway Lorne , Lahav Ofer
Published: July 2021

We present full-sky maps of the Integrated Sachs–Wolfe effect (ISW) for the MICE Grand Challenge lightcone simulation up to redshift 1.4. The maps are constructed in the linear regime using spherical Bessel transforms. We compare and contrast this procedure against analytical approximations found in the literature. By computing the ISW in the linear regime, we remove the substantial computing and storage resources required to calculate the non-linear Rees–Sciama effect. Since the linear ISW at low redshift z ≲ 1, at large angular scales, and after matter domination is ${\sim}10^{2}\, \mathrm{ times}$ larger in ΔT/T, this has a negligible impact on the maps produced and only becomes relevant on scales which are dominated by cosmic microwave background (CMB) anisotropies. The MICE simulation products have been extensively used for studies involving current and future galaxy surveys. The availability of these maps will allow MICE to be used for future galaxy and CMB cross-correlation studies, ISW reconstruction studies, and ISW void-stacking studies probed by galaxy surveys such as Dark Energy Survey, Dark Energy Spectroscopic Instrument, Euclid, and Rubin Legacy Survey of Space and Time. The pipeline developed in this study is provided as a public Python package pyGenISW. This could be used in the future studies for constructing the ISW from existing and future simulation suites probing vast sets of cosmological parameters and models.
A Gemini–NIFS view of the merger remnant NGC 34
Authors: Motter J C , Riffel R , Ricci T V , Riffel R A , Storchi-Bergmann T , Pastoriza M G , Rodriguez-Ardila A , Ruschel-Dutra D , Dahmer-Hahn L G , Dametto N Z , Diniz M R
Published: July 2021

The merger remnant NGC 34 is a local luminous infrared galaxy (LIRG) hosting a nuclear starburst and a hard X-ray source associated with a putative, obscured Seyfert 2 nucleus. In this work, we use adaptive optics assisted near-infrared (NIR) integral field unit observations of this galaxy to map the distribution and kinematics of the ionized and molecular gas in its inner $\mathrm{1.2\, kpc \times 1.2\, kpc}$, with a spatial resolution of 70 pc. The molecular and ionized gas kinematics is consistent with a disc with projected major axis along a mean PA = −9${_{.}^{\circ}}$2 ± 0${_{.}^{\circ}}$9. Our main findings are that NGC 34 hosts an AGN and that the nuclear starburst is distributed in a circumnuclear star formation ring with inner and outer radii of ≈ 60 and 180 pc, respectively, as revealed by maps of the $\mathrm{[Fe\, {\small {II}}] / Pa\,\beta }$ and H2/Br γ emission-line ratios, and corroborated by PCA tomography analysis. The spatially resolved NIR diagnostic diagram of NGC 34 also identifies a circumnuclear structure dominated by processes related to the stellar radiation field and a nuclear region where $[\rm Fe\, {\small {II}}]$ and H2 emissions are enhanced relative to the hydrogen recombination lines. We estimate that the nuclear X-ray source can account for the central H2 enhancement and conclude that $[\rm Fe\, {\small {II}}]$ and H2 emissions are due to a combination of photoionization by young stars, excitation by X-rays produced by the AGN and shocks. These emission lines show nuclear, broad, blueshifted components that can be interpreted as nuclear outflows driven by the AGN.
Diffusion as a leading dissipative mechanism in superconducting neutron stars
Authors: Kraav K Y , Gusakov M E , Kantor E M
Published: July 2021

Despite the fact that different particle species can diffuse with respect to each other in neutron star (NS) cores, the effect of particle diffusion on various phenomena associated with NS oscillations is usually ignored. Here, we demonstrate that the diffusion can be extremely powerful dissipative mechanism in superconducting NSs. In particular, it can be much more efficient than the shear and bulk viscosities. This result has important implications for the damping times of NS oscillations, development, and saturation of dynamical instabilities in NSs, and for the excitation and coupling of oscillation modes during the late inspiral of binary NSs.
Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq
Authors: Massarat Arya R , Sen Arko , Jaureguy Jeff , Tyndale Sélène T , Fu Yi , Erikson Galina , McVicker Graham
Published: July 2021

Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost ‘capture’ method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels within ATAC-seq peak regions with at least 10 reads. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.
Protected areas safeguard landbird populations in central coastal California: Evidence from long-term population trends
Authors: Dettling Mark D , Dybala Kristen E , Humple Diana L , Gardali Thomas
Published: July 2021

Many bird populations have experienced population declines across North America over the past several decades. The establishment of protected areas has been used as a conservation action to maintain or help in the recovery of these populations; however, the effectiveness of protected areas in safeguarding bird populations within their borders from negative impacts to populations in surrounding unprotected areas has rarely been evaluated. Our study aimed to evaluate the effectiveness of protected areas in the San Francisco Bay Area of California for landbirds. We conducted point count surveys along riparian corridors in coastal Marin County in protected areas, predominately national parks, and estimated the population growth rates for 14 species over 23 years. We compared these growth rates to North American Breeding Bird Survey growth rate estimates from the Coastal California and the Northern Pacific Rainforest Bird Conservation Regions, which comprise larger, regional populations. A safeguarding effect was detected for 9 of the 14 species. We expected an effect on species strongly associated with riparian vegetation, which has incurred significant loss and degradation in the region; however, we instead observed benefits to general riparian users that were at least as great as the benefits to strong riparian specialists. We also expected that populations of resident species might benefit more than migrants; however, we found strong support for a safeguarding effect for both groups. Species with increasing growth rates in coastal Marin County protected areas in comparison to regionally stable or decreasing populations demonstrate the potential for protected areas to not only maintain populations despite declines outside their boundaries but also to help them recover from current and previous losses. Continuing long-term monitoring and associated full life cycle research will help identify if and when other drivers (e.g., climate change) may weaken these safeguarding effects, or when additional conservation and management is warranted.
Co-Presentation of Posterior Reversible Encephalopathy Syndrome in a Patient with Post–Dural Puncture Headache
Authors: Sagir Afrin , Ahuja Sanchit , Soliman Loran Mounir , Farag Ehab
Published: July 2021

Introduction

Post–dural puncture headache (PDPH) is a well-known complication of neuraxial anesthesia, but the occurrence of seizures and vision loss within a few days after dural puncture could be alarming. Posterior reversible encephalopathy syndrome (PRES) is associated with reversible edema and leukoencephalopathy in the posterior parieto-occipital cortex. We report the co-presentation of PRES and PDPH after labor epidural analgesia.

Case Presentation

A 25-year-old multiparous African-American woman was admitted for evaluation of new-onset seizures and headache in the postpartum period. She had a recent history of multiple needle insertion attempts and inadvertent dural puncture during epidural analgesia for delivery. Soon after delivery, she was diagnosed with PDPH and was treated with an epidural blood patch, with no relief of symptoms. Six days later, she developed sudden-onset transient blindness, seizures, and altered sensorium, and magnetic resonance imaging of the brain revealed white matter changes suggestive of PRES.

Conclusion

PRES is an uncommon complication of cerebrospinal fluid leak and intracranial hypotension. We report the occurrence of PRES in a patient with no known risk factors except a traumatic dural tap. Is it important to expand the differentials for headache after dural puncture to encompass PRES as a possibility, especially in patients with a delayed presentation of seizures and cortical blindness.
Generational Persistence in the Nature of White Racial Attitudes
Authors: Engelhardt Andrew M
Published: July 2021

Race and racial attitudes are central to American politics. To understand these relationships, scholars often use measures developed in earlier social and political contexts. A key issue is thus whether such measures consistently capture the same construct across varied contexts. Changes in the social and political context may result in generational differences in how people interpret certain racial attitude items given different socialization experiences. Such differences make generational comparisons on these items invalid because the items capture different considerations. I build on recent work investigating this possibility and test the racial resentment measure’s equivalence between Millennial and older Whites. Despite potential generational differences, I find that the racial resentment measure operates equivalently across generations using two different analytical approaches (retrospective thought-listing and multi-group confirmatory factor analysis). The racial resentment measure offers valid insights into racial attitudes across generational cohorts. I conclude by discussing what this finding implies for emerging work on the manifestations of prejudiced attitudes among Millennial Whites and also suggest potential points of improvement for the measure.