bluuebunny/crossref_metadata_2025 huggingface dataset:
Vitamin K supplementation and arterial calcification in dialysis: results of the double-blind, randomized, placebo-controlled RenaKvit trial
Authors: Levy-Schousboe Karin , Frimodt-Møller Marie , Hansen Ditte , Peters Christian Daugaard , Kjærgaard Krista Dybtved , Jensen Jens Dam , Strandhave Charlotte , Elming Hanne , Larsen Carsten Toftager , Sandstrøm Hanne , Brasen Claus Lohman , Schmedes Anne , Madsen Jonna Skov , Jørgensen Niklas Rye , Frøkjær Jens Brøndum , Frandsen Niels Erik , Petersen Inge , Marckmann Peter
Published: January 2021

Background

Arterial calcification is associated with cardiovascular mortality in dialysis patients. Active matrix Gla protein (MGP) is a vitamin K-dependent inhibitor of arterial calcification. Elevated plasma concentrations of inactive MGP, i.e. dephosphorylated-uncarboxylated MGP (dp-ucMGP), are prevalent in dialysis patients. MGP inactivity might contribute to arterial calcification. We investigated whether vitamin K supplementation had an effect on arterial calcification in chronic dialysis patients.

Methods

In a 2-year, double-blind, placebo-controlled intervention trial, 48 dialysis patients were randomized to vitamin K [menaquinone-7 (MK-7), 360 µg daily] or placebo. MK-7 in serum and dp-ucMGP in plasma were used to assess vitamin K status. Carotid-femoral pulse wave velocity (cfPWV) and scores of coronary arterial calcification (CAC) and abdominal aortic calcification (AAC) were used to assess arterial calcification.

Results

Thirty-seven participants completed Year 1, and 21 completed Year 2. At Year 2, serum MK-7 was 40-fold higher, and plasma dp-ucMGP 40% lower after vitamin K supplementation compared with placebo {mean dp-ucMGP difference: −1380 pmol/L [95% confidence interval (CI) −2029 to −730]}. There was no significant effect of vitamin K supplementation on cfPWV [mean difference at Year 2: 1.2 m/s (95% CI −0.1 to 2.4)]. CAC Agatston score increased significantly in vitamin K supplemented participants, but was not significantly different from placebo [mean difference at Year 2: 664 (95% CI −554 to 1881)]. AAC scores increased in both groups, significantly so within the placebo group at Year 1, but with no significant between-group differences.

Conclusions

Vitamin K supplementation improved vitamin K status, but did not hinder or modify the progression of arterial calcification in dialysis patients.
Farinel’s Ground and other ‘Follyes’ in English sources of the late 17th and early 18th centuries
Authors: Schönlau Stephan
Published: January 2021

This article is the result of a comprehensive study of folia grounds—usually known as Farinel’s Ground in England—published, copied in or otherwise connected with England, a list of which is provided. A discussion of general characteristics as well as of typical melodic, harmonic and rhythmic features of folia grounds from this period is followed by a comparative analysis of all English folias. These form relatively distinct groups of sources that often share strains, suggesting patterns of transmission particular to division grounds. Lastly, the order of strains in a number of versions is discussed in conjunction with principles outlined in Christopher Simpson’s The Division-Violist (London, 1659) and Thomas Mace’s Musick’s Monument (London, 1676), shedding light on what theorists and composers at the time thought about large-scale structure in division grounds, and in ground-bass compositions in general.
Reconsidering LINE-1’s role in cancer: does LINE-1 function as a reporter detecting early cancer-associated epigenetic signatures?
Authors: Kelsey Maxfield M G
Published: January 2021

Long interspersed nuclear element-1 (LINE-1 or L1) is the only autonomously active retrotransposon in humans. While L1 has been implicated in several pathologies and the aging process, I present a model which challenges an understanding of L1 as predominantly antagonistic to human health. I hypothesize that L1 serves as a reporter in an early cancer alert system: a tripwire strung throughout the genome poised to trigger p53 and a type I interferon (IFN-1) response when the epigenetic landscape portends cancer. Cell proliferation and a shift to aerobic glycolysis cause dramatic changes in the epigenome which are permissive to L1’s escape from suppression. L1 has several properties which make it particularly apt to fulfill this hypothesized sentinel function. Being present in many copies spread throughout the genome allows it to monitor many regions for epigenetic instability and renders it robust to deactivation by mutation. This proposed cancer alert system would alter the cancer cell fitness landscape discouraging the use of growth-favoring aerobic glycolysis by threatening the activation of tumor-suppressive mechanisms. It also imposes costs on a strategy of non-specific global transcriptional derepression aimed at activating oncogenes. Erroneous activations of this system are predicted to increase the rate of aging, suggesting this represents a case of antagonistic pleiotropy trading prolonged youth for cancer prevention. More research is needed to assess this model.

Lay summary: During carcinogenesis the epigenome is remodeled by the Warburg effect and cellular proliferation. These processes globally relax chromatin. This epigenetic environment is permissive to the retrotransposon long interspersed nuclear element-1’s (LINE-1 or L1) escape from suppression. I hypothesize and present evidence for the notion that L1 has been co-opted to serve as a reporter in an early cancer alert system, poised to trigger tumor suppressive mechanisms when the epigenetic landscape portends cancer. This hypothesis describes a potentially major means by which transformation is thwarted early on.
A novel dextranase gene from the marine bacterium Bacillus aquimaris S5 and its expression and characteristics
Authors: Dong Dongxue , Wang Xuelian , Deng Tian , Ning Zhe , Tian Xiaopeng , Zu Hangtian , Ding Yanshuai , Wang Cang , Wang Shujun , Lyu Mingsheng
Published: January 2021

Dextranase specifically hydrolyzes dextran and is used to produce functional isomalto-saccharide prebiotics. Moreover, dextranase is used as an additive in mouthwash to remove dental plaque. We cloned and expressed the dextranase gene of the marine bacterium Bacillus aquimaris S5. The length of the BaDex gene was 1788 bp, encoding 573 amino acids. Using bioinformatics to predict and analyze the amino acid sequence of BaDex, we found the isoelectric point and instability coefficient to be 4.55 and 29.22, respectively. The average hydrophilicity (GRAVY) was −0.662. The secondary structure of BaDex consisted of 145 alpha helices, accounting for 25.31% of the protein; 126 extended strands, accounting for 21.99%; and 282 random coils, accounting for 49.21%. The 3D structure of the BaDex protein was predicted and simulated using SWISS-MODEL, and BaDex was classified as a Glycoside Hydrolase Family 66 protein. The optimal temperature and pH for BaDex activity were 40°C and 6.0, respectively. The hydrolysates had excellent antioxidant activity, and 8 U/mL of BaDex could remove 80% of dental plaque in MBRC experiment. This recombinant protein thus has great promise for applications in the food and pharmaceutical industries.
A Taper Equation for Loblolly Pine Using Penalized Spline Regression
Authors: Zapata-Cuartas Mauricio , Bullock Bronson P , Montes Cristian R
Published: January 2021

Stem profile needs to be modeled with an accurate taper equation to produce reliable tree volume assessments. We propose a semiparametric method where few a priori functional form assumptions or parametric specification are required. We compared the diameter and volume predictions of a penalized spline regression (P-spline), P-spline extended with an additive dbh-class variable, and six alternative parametric taper equations including single, segmented, and variable-exponent equation forms. We used taper data from 147 loblolly pine (Pinus taeda L.) trees to fit the models and make comparisons. Here we show that the extended P-spline outperforms the parametric taper equations when used to predict outside bark diameter in the lower portion of the stem, up to 40% of the tree height where the more valuable wood products (62% of the total outside bark volume) are located. For volume, both P-spline models perform equal or better than the best parametric model, with taper calibration, which could result in possible savings on inventory costs by not requiring an additional measurement. Our findings suggest that assuming a priori fixed form in taper models imposes restrictions that fail to explain the tree form adequately compared with the proposed P-spline.
Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1
Authors: Takagi Julie , Cho Christina , Duvalyan Angela , Yan Yao , Halloran Megan , Hanson-Smith Victor , Thorner Jeremy , Finnigan Gregory C
Published: January 2021

Septins are GTP-binding proteins conserved across metazoans. They can polymerize into extended filaments and, hence, are considered a component of the cytoskeleton. The number of individual septins varies across the tree of life—yeast (Saccharomyces cerevisiae) has seven distinct subunits, a nematode (Caenorhabditis elegans) has two, and humans have 13. However, the overall geometric unit (an apolar hetero-octameric protomer and filaments assembled there from) has been conserved. To understand septin evolutionary variation, we focused on a related pair of yeast subunits (Cdc11 and Shs1) that appear to have arisen from gene duplication within the fungal clade. Either Cdc11 or Shs1 occupies the terminal position within a hetero-octamer, yet Cdc11 is essential for septin function and cell viability, whereas Shs1 is not. To discern the molecular basis of this divergence, we utilized ancestral gene reconstruction to predict, synthesize, and experimentally examine the most recent common ancestor (“Anc.11-S”) of Cdc11 and Shs1. Anc.11-S was able to occupy the terminal position within an octamer, just like the modern subunits. Although Anc.11-S supplied many of the known functions of Cdc11, it was unable to replace the distinct function(s) of Shs1. To further evaluate the history of Shs1, additional intermediates along a proposed trajectory from Anc.11-S to yeast Shs1 were generated and tested. We demonstrate that multiple events contributed to the current properties of Shs1: (1) loss of Shs1–Shs1 self-association early after duplication, (2) co-evolution of heterotypic Cdc11–Shs1 interaction between neighboring hetero-octamers, and (3) eventual repurposing and acquisition of novel function(s) for its C-terminal extension domain. Thus, a pair of duplicated proteins, despite constraints imposed by assembly into a highly conserved multi-subunit structure, could evolve new functionality via a complex evolutionary pathway.
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense
Authors: Jin Shubo , Bian Chao , Jiang Sufei , Han Kai , Xiong Yiwei , Zhang Wenyi , Shi Chengcheng , Qiao Hui , Gao Zijian , Li Ruihan , Huang Yu , Gong Yongsheng , You Xinxin , Fan Guangyi , Shi Qiong , Fu Hongtuo
Published: January 2021

Background

The oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement.

Results

We sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-genome assembly of the Oriental river prawn was ∼4.5 Gb in size, with predictions of 44,086 protein-coding genes. A total of 49 chromosomes were determined, with an anchor ratio of 94.7% and a scaffold N50 of 86.8 Mb. A whole-genome duplication event was deduced to have happened 109.8 million years ago. By integration of genome and transcriptome data, 21 genes were predicted as sex-related candidate genes.

Conclusion

The first high-quality chromosome-level genome assembly of the oriental river prawn was obtained. These genomic data, along with transcriptome sequences, are essential for understanding sex-differentiation and development mechanisms in the oriental river prawn, as well as providing genetic resources for in-depth studies on developmental and evolutionary biology in arthropods.
The use of negative control outcomes in Mendelian randomization to detect potential population stratification
Authors: Sanderson Eleanor , Richardson Tom G , Hemani Gibran , Davey Smith George
Published: January 2021

A key assumption of Mendelian randomization (MR) analysis is that there is no association between the genetic variants used as instruments and the outcome other than through the exposure of interest. One way in which this assumption can be violated is through population stratification, which can introduce confounding of the relationship between the genetic variants and the outcome and so induce an association between them. Negative control outcomes are increasingly used to detect unobserved confounding in observational epidemiological studies. Here we consider the use of negative control outcomes in MR studies to detect confounding of the genetic variants and the exposure or outcome. As a negative control outcome in an MR study, we propose the use of phenotypes which are determined before the exposure and outcome but which are likely to be subject to the same confounding as the exposure or outcome of interest. We illustrate our method with a two-sample MR analysis of a preselected set of exposures on self-reported tanning ability and hair colour. Our results show that, of the 33 exposures considered, genome-wide association studies (GWAS) of adiposity and education-related traits are likely to be subject to population stratification that is not controlled for through adjustment, and so any MR study including these traits may be subject to bias that cannot be identified through standard pleiotropy robust methods. Negative control outcomes should therefore be used regularly in MR studies to detect potential population stratification in the data used.
Nonuniqueness of Solutions to the Lp Dual Minkowski Problem
Authors: Li Qi-Rui , Liu Jiakun , Lu Jian
Published: January 2021

The $L_p$ dual Minkowski problem with $p<0<q$ is investigated in this paper. By proving a new existence result of solutions and constructing an example, we obtain the nonuniqueness of solutions to this problem.
The United States, China, and the Politics of Hegemonic Ordering in East Asia
Authors: Loke Beverley
Published: January 2021

China's rise has raised important questions about the durability of US hegemony in East Asia. Much of the debate, however, has generally been cast in fairly simplistic terms, suggesting the durability or end of US regional hegemony. Such framings nevertheless fail to fully capture regional dynamics and complexity. Advancing an English School conception of hegemony, this paper examines the politics, contestation, and renegotiation of the post–Cold War US hegemonic order in East Asia. It maps out four logics of hegemonic ordering in the existing literature, outlines their shortfalls and advances a twofold argument. First, although regional order will not disintegrate into binary “order versus disorder” or “US versus Chinese hegemony” scenarios, the politics of hegemonic ordering—the interactive discourses, processes, relations, and practices that underpin hegemony—will intensify as the United States and China continue to both cooperate and compete for power, position, and influence in East Asia. Second, I argue that the East Asian regional order will evolve in ways that resemble hybrid forms of hegemony in a complex hierarchy. Specifically, I develop a new logic—“coalitional and collaborative hegemonies in a complex hierarchy”—that is anchored in assertiveness, fluidity, and compartmentalization. It demonstrates that Washington and Beijing will not only form coalitional hegemonies, seeking legitimation from multiple and often overlapping constituencies, but also engage in a collaborative hegemony on shared interests. This better reflects evolving regional dynamics and yields theoretical insights into examining hegemonic transitions less as clearly delineated transitions from one distinct hegemonic order to the next, and more as partial and hybrid ones.
Quantification of Scopoletin from the Roots of Argyreia Speciosa (Linn. F) Sweet Using HPLC Through the Concept of Design of Experiment
Authors: Patel Preksha , Raval Manan , Patel Nidhi , Patel Samir , Vyas Niraj , Patel Amit
Published: January 2021

Background

The roots of Argyreia speciosa (Linn. F) Sweet (family: Convolvulaceae) are used in Ayurveda to treat male reproductive and nervous system disorders.

Objective

Isolation of scopoletin from the roots of Argyreia speciosa, and development and validation of an analytical method using HPLC for the quantification of scopoletin from the root powder of Argyreia speciosa.

Method

Scopoletin was isolated from chloroform fraction prepared from hydrolyzed methanolic extract and identified using spectral studies. A reverse-phase HPLC-based analytical method was developed and optimized using the Design of Experiment (DoE) approach to estimate scopoletin from the roots of Argyreia speciosa. Scopoletin was separated and quantified using HPLC containing the C18 column and a PDA detector. The optimized mobile phase was methanol: water (pH∼3.2) [25: 75, %v/v].

Results

The Box–Behnken design was used to optimize chromatographic parameters and the extraction procedure. The validation studies showed a linear relationship (r2=0.998) in the range of 1–40 µg/mL. The LOD and LOQ were found to be 0.28 µg/mL and 0.84 µg/mL, respectively, and the recovery values were found to be between 91.94 and 97.86%. The developed analytical method was found to be robust as well. The amount of scopoletin was estimated to be 0.024 ± 0.0016%w/w from dried root powder.

Conclusion

The recorded chromatogram and amount of scopoletin determined would serve as one of the standardization parameters to access the quality of raw material containing Argyreia speciosa.

Highlights

Developed analytical method may be adopted as a part of the standardization procedure for Argyreia speciosa in the quality control laboratory.
Metabolic response to temperature stress in the Colombian freshwater crabNeostrengeria macropa(H. Milne Edwards, 1853) (Decapoda: Brachyura: Pseudothelphusidae)
Authors: Hudson David M
Published: January 2021

Freshwater crustaceans are distributed throughout the montane and lowland areas of Colombia, and are therefore a useful indicator group for how aquatic species will respond to climate change. As such, metabolic determination of physiological performance was evaluated for the Colombian pseudothelphusid crab, Neostrengeria macropa (H. Milne Edwards, 1853), over a temperature range inclusive of current temperatures and those predicted by future scenarios in the plateau around the city of Bogotá, namely from 8 °C to 30 °C. The performance results mostly aligned with previous exploratory behavioral determination of the ideal temperature range in the same species, although the metabolism increased at the highest temperature treatments, a point when exploratory behavior declined. These results indicate that this species of montane crab behaviorally compensates for increased thermal stress by decreasing its physical activity, which could have negative predator-prey consequences with changes to community structure as different species undergo climate-mediated geographic range shifts in the region. As this species is endemic to the plateau surrounding Bogotá, it also experiences a number of other stressors to its survival, including infrastructure development and invasive species.
CSI-based human sensing using model-based approaches: a survey
Authors: Wang Zhengjie , Huang Zehua , Zhang Chengming , Dou Wenwen , Guo Yinjing , Chen Da
Published: January 2021

Currently, human sensing draws much attention in the field of ubiquitous computing, and human sensing based on WiFi CSI (channel state information) becomes a hot research topic due to the easy deployment and availability of WiFi devices. Although various human sensing applications based on the CSI signal model are emerging, the model-based approach has not been studied thoroughly. This paper provides a comprehensive survey of the latest model-based human sensing methods and their applications. First, the CSI signal and framework of model-based human sensing methods are introduced. Then, related models and fundamental signal preprocessing techniques are described. Next, typical human sensing applications are investigated, and the crucial characteristics are summarized. Finally, the advantages, limitations, and future research trends of model-based human sensing methods are concluded in this paper.
Hidden in plain sight: on copiousness in the Kunstkammer of Emperor Rudolf II
Authors: Keating Jessica
Published: January 2021

The Kunstkammer of Holy Roman Emperor Rudolf II (1552–1612) in Prague was one of early modern Europe’s most famed princely collections. Part of this renown stemmed from the collection’s abundance of rare, exotic, costly and artfully produced objects. However, Rudolf’s Kunstkammer not only contained copious numbers of diverse objects, it also housed many objects that took copiousness (that is, sexual fertility and seasonal productivity) as their subject. This essay considers how copiousness affected the use of Rudolf’s collection. In the end, it reveals that copiousness complicated and made difficult the use of Rudolf’s collection on both a practical and an interpretative level.
Perception and Use of Economic Thresholds Among Farmers and Agricultural Professionals: A Case Study on Soybean Aphid in Minnesota
Authors: Hoidal Natalie , Koch Robert L
Published: January 2021

Economic thresholds (ETs) are a foundational principle of integrated pest management but are not always widely accepted by farmers and agricultural professionals. This article reports on a survey of Minnesota farmer and agricultural professional perceptions of the ET for soybean aphid, Aphis glycines Matsumura (Hempitera: Aphididae). We discuss insights for Extension programs on how to frame the importance of thresholds and teach stakeholders to use them effectively. Key takeaways include farmers and agricultural professionals often worry about combined effects of insect, disease, and physiological pressures, whereas effects of interactions with these other stressors are seldom discussed in educational outreach. Across groups, there is a fundamental misunderstanding about the difference between ETs and economic injury level. Many survey participants reported believing in the ET but lacked the time and capacity to fully implement it. Sales agronomists and farmers were the least likely groups to trust the university-determined soybean aphid ET, whereas commercial pesticide applicators and independent consultants were the most likely groups to trust it. Based on these results, we recommend adapting communication about ETs based on the target audience to address common misconceptions and barriers to ET use that are unique to each group.
The Global Landscape of Treatment Standards for Breast Cancer
Authors: Trapani Dario , Douillard Jean Yves , Winer Eric P , Burstein Harold , Carey Lisa Anne , Cortes Javier , Lopes Gilberto , Gralow Julie R , Gradishar William J , Magrini Nicola , Curigliano Giuseppe , Ilbawi Andrè M
Published: January 2021

Background

Breast cancer (BC) is a leading cause of morbidity, mortality, and disability for women worldwide. There is substantial variation in treatment outcomes, which is function of multiple variables, including access to treatment. Treatment standards can promote quality and improve survival; thus, their development should be a priority for the cancer-control planning.

Methods

We extracted the guidelines for the treatment of BC from a systematic review of the literature. We evaluated the development process, the methodology, and the recommendations formulated and surveyed the country resource stratification. Metrics of health-system capacity were selected to study the guidelines context appropriateness.

Results

We analyzed 49 distinct guidelines for BC, mostly in English language (n = 23), developed in upper-middle and high-income countries of the European and American regions (n = 39). A resource-stratified approach was identified in a quarter of the guidelines (n = 11), mostly from resource-constrained settings. Only one-half of the guidelines reached a gender balance of the authorship, and 10.2% were based on a multidisciplinary steering committee. A number of efforts and solutions of resource adaptations were recognized, mostly in low- and middle-income countries. Overall, the national guidelines appeared not sensitive enough of the local health-system capacity in formulating recommendations, with possible exception for the radiation therapy availability.

Conclusion

This global landscape of treatment standards for BC demonstrates that the majority is not context appropriate. Research on the formulation of cancer treatment standards is highly warranted, along with novel platforms for developing and disseminating resource-appropriate guidance.
Distinct metabonomic signatures of Polygoni Multiflori Radix Praeparata against glucolipid metabolic disorders
Authors: Yang Ya-Qin , Meng Fan-Ying , Liu Xin , Zhang Mei , Gu Wen , Yan Hong-Li , Yu Jie , Yang Xing-Xin
Published: January 2021

Objectives

Glucolipid metabolic disorders (GLMD) promote a series of major chronic diseases. Polygoni Multilori Radix Preparata (PMRP) has been widely acknowledged in the prevention and treatment of GLMD. We previously reported that water extract (WE) of PMRP and its major bioactive constituents such as polysaccharides (POL) and 2,3,5,4´-tetrahydroxy-stilbene-2-O-β-D-glucoside (TSG) could alleviate GLMD. The mitochondrial dysfunction is an important mechanism of GLMD, but the underlying mechanisms behind the regulation of mitochondria to alleviate GLMD by WE, POL from PMRP and TSG are still unknown.

Methods

In this study, we elucidated the effects of WE, POL, and TSG towards regulating the mitochondrial dysfunction and alleviating GLMD using mitochondrial metabonomics. A rat model of GLMD was established by high-sugar and high-fat (HS-HF) diet. Rats were intragastrically given WE, POL, and TSG for 12 weeks. The liver mitochondrial metabolites were analyzed by ultra-high-performance liquid chromatography/mass spectrometry followed by multivariate statistical analysis to identify the differential metabolites and metabolic pathways.

Key findings

The WE, POL, and TSG could significantly restore the level of endogenous metabolites in liver mitochondria toward normal status. In total, sixteen, seven, and fourteen differential metabolites were identified in the liver mitochondrial samples obtained from the WE, GOL, and TSG groups, respectively. These metabolites were found to be mainly involved in glycerol phospholipid, histidine, alanine, aspartic acid, glutamate metabolism, and arginine biosynthesis.

Conclusions

PMRP could improve the liver mitochondrial function by regulating the mitochondrial metabolic pathways to alleviate GLMD. Therefore, the application of PMRP might be a promising mitochondrial regulator/nutrient for alleviating GLMD-associated diseases and the mitochondrial metabonomics might provide insights into the evaluation of the efficacies and mechanisms of action of drugs.
Two plastidic glycolate/glycerate translocator 1 isoforms function together to transport photorespiratory glycolate and glycerate in rice chloroplasts
Authors: Cui Lili , Zhang Chuanling , Li Zhichao , Xian Tuxiu , Wang Limin , Zhang Zhisheng , Zhu Guohui , Peng Xinxiang
Published: January 2021

The photorespiratory pathway is highly compartmentalized. As such, metabolite shuttles between organelles are critical to ensure efficient photorespiratory carbon flux. Arabidopsis plastidic glycolate/glycerate translocator 1 (PLGG1) has been reported as a key chloroplastic glycolate/glycerate transporter. Two homologous genes, OsPLGG1a and OsPLGG1b, have been identified in the rice genome, although their distinct functions and relationships remain unknown. Herein, our analysis of exogenous expression in oocytes and yeast shows that both OsPLGG1a and OsPLGG1b have the ability to transport glycolate and glycerate. Furthermore, we demonstrate in planta that the perturbation of OsPLGG1a or OsPLGG1b expression leads to extensive accumulation of photorespiratory metabolites, especially glycolate and glycerate. Under ambient CO2 conditions, loss-of-function osplgg1a or osplgg1b mutant plants exhibited significant decreases in photosynthesis efficiency, starch accumulation, plant height, and crop productivity. These morphological defects were almost entirely recovered when the mutant plants were grown under elevated CO2 conditions. In contrast to osplgg1a, osplgg1b mutant alleles produced a mild photorespiratory phenotype and had reduced accumulation of photorespiratory metabolites. Subcellular localization analysis showed that OsPLGG1a and OsPLGG1b are located in the inner and outer membranes of the chloroplast envelope, respectively. In vitro and in vivo experiments revealed that OsPLGG1a and OsPLGG1b have a direct interaction. Our results indicate that both OsPLGG1a and OsPLGG1b are chloroplastic glycolate/glycerate transporters required for photorespiratory metabolism and plant growth, and that they may function as a singular complex.
Resurrection plants optimize photosynthesis despite very thick cell walls by means of chloroplast distribution
Authors: Nadal Miquel , Perera-Castro Alicia V , Gulías Javier , Farrant Jill M , Flexas Jaume
Published: January 2021

Resurrection plants are vascular species able to sustain extreme desiccation in their vegetative tissues. Despite its potential interest, the role of leaf anatomy in CO2 diffusion and photosynthesis under non-stressed conditions has not been explored in these species. Net CO2 assimilation (An) and its underlying diffusive, biochemical, and anatomical determinants were assessed in 10 resurrection species from diverse locations, including ferns, and homoiochlorophyllous and poikilochlorophyllous angiosperms. Data obtained were compared with previously published results in desiccation-sensitive ferns and angiosperms. An in resurrection plants was mostly driven by mesophyll conductance to CO2 (gm) and limited by CO2 diffusion. Resurrection species had a greater cell wall thickness (Tcw) than desiccation-sensitive plants, a feature associated with limited CO2 diffusion in the mesophyll, but also greater chloroplast exposure to intercellular spaces (Sc), which usually leads to higher gm. This combination enabled a higher An per Tcw compared with desiccation-sensitive species. Resurrection species possess unusual anatomical features that could confer stress tolerance (thick cell walls) without compromising the photosynthetic capacity (high chloroplast exposure). This mechanism is particularly successful in resurrection ferns, which display higher photosynthesis than their desiccation-sensitive counterparts.
Incorporation of Whipstitch Suture in Tibial Interference Fixation Improves Pullout in Anterior Cruciate Ligament Soft Tissue Grafts
Authors: Bernstein Ethan , Taniguchi Kevin , Tompane Trevor , Kirby Hannah , Ponton Ryan , McDonald Lucas S
Published: January 2021

Introduction

Interference screw fixation of soft tissue grafts is commonly used in anterior cruciate ligament (ACL) reconstruction. The purpose of this study was to determine whether including suture material at the graft–screw interface affects ultimate fixation strength of soft tissue grafts using a tibialis anterior tendon allograft model.

Materials and Methods

Forty fresh-frozen human tibialis anterior tendon allografts were fixed to rigid polyurethane foam simulating the tibial tunnel. Twenty grafts underwent fixation with interference screws and 20 with interference bolts. Within each group, 10 grafts had suture in contact with either the screw or bolt. A load-to-failure test was then performed at a rate of 200 mm/min.

Results

The group of allografts with sutures in the tibial tunnel had significantly higher load to failure than the group without sutures. Using interference screw fixation, failure load of the grafts without sutures in the tunnel (535.2 ± 73.40 N) was significantly lower (P = .001) than with sutures in the tunnel (696.3 ± 110.0 N). Using interference bolt fixation, failure load of the grafts without sutures in the tunnel (613.0 ± 83.46 N) was significantly lower (P <.0001) than with sutures in the tunnel (845.8 ± 87.23 N).

Conclusions

In a biomechanical model, suture within the tibial tunnel enhances fixation strength with both interference screw and bolt fixation for soft tissue tibialis anterior allografts. Additionally, there was no difference in load to failure when comparing failure of a screw with suture in the tunnel with an interference bolt without suture. Due to improved biomechanical properties, incorporation of suture in the bone–graft interface should be considered when performing soft tissue ACL allograft reconstructions. Failure at the tibial bone–graft interface is a known complication of ACL reconstruction, and incorporation of suture within the interface should be considered for improved biomechanical properties.
Rank Offence: The Ecological Theory of Resentment
Authors: Reis-Dennis Samuel
Published: January 2021

I argue that fitting resentment tracks unacceptable ‘ecological’ imbalances in relative social strength between victims and perpetrators that arise from violations of legitimate moral expectations. It does not respond purely, or even primarily, to offenders’ attitudes, and its proper targets need not be fully developed moral agents. It characteristically involves a wish for the restoration of social equilibrium rather than a demand for moral recognition or good will. To illuminate these contentions, I focus on cases that I believe demonstrate a corollary thesis, namely, that strength, broadly construed, is a necessary condition of resentment-worthiness. I argue that weakness can make resentment unfitting in two ways. First, weakness may prevent a wrongdoer from shifting the balance of social power. Second, a weak wrongdoer may do social damage but be so lowly that resentment, which would represent him as excessively strong, would be inapt. Finally, I consider how accepting the ecological view might affect our theorizing about moral responsibility and the ethics of blame.
maxsmooth: rapid maximally smooth function fitting with applications in Global 21-cm cosmology
Authors: Bevins H T J , Handley W J , Fialkov A , de Lera Acedo E , Greenhill L J , Price D C
Published: January 2021

Maximally Smooth Functions (MSFs) are a form of constrained functions in which there are no inflection points or zero crossings in high-order derivatives. Consequently, they have applications to signal recovery in experiments where signals of interest are expected to be non-smooth features masked by larger smooth signals or foregrounds. They can also act as a powerful tool for diagnosing the presence of systematics. The constrained nature of MSFs makes fitting these functions a non-trivial task. We introduce maxsmooth, an open-source package that uses quadratic programming to rapidly fit MSFs. We demonstrate the efficiency and reliability of maxsmooth by comparison to commonly used fitting routines and show that we can reduce the fitting time by approximately two orders of magnitude. We introduce and implement with maxsmooth Partially Smooth Functions, which are useful for describing elements of non-smooth structure in foregrounds. This work has been motivated by the problem of foreground modelling in 21-cm cosmology. We discuss applications of maxsmooth to 21-cm cosmology and highlight this with examples using data from the Experiment to Detect the Global Epoch of Reionization Signature (EDGES) and the Large-aperture Experiment to Detect the Dark Ages (LEDA) experiments. We demonstrate the presence of a sinusoidal systematic in the EDGES data with a log-evidence difference of 86.19 ± 0.12 when compared to a pure foreground fit. MSFs are applied to data from LEDA for the first time in this paper and we identify the presence of sinusoidal systematics. maxsmooth is pip installable and available for download at https://github.com/htjb/maxsmooth.
A DYRK1B-dependent pathway suppresses rDNA transcription in response to DNA damage
Authors: Dong Chao , An Liwei , Yu Cheng-han , Huen Michael S Y
Published: January 2021

DNA double-strand breaks (DSBs) at ribosomal gene loci trigger inhibition of ribosomal DNA (rDNA) transcription and extensive nucleolar reorganization, including the formation of nucleolar caps where rDNA DSBs engage with canonical DSB signaling and repair factors. While these nucleolar responses underlie maintenance of rDNA stability, the molecular components that drive each of these events remain to be defined. Here we report that full suppression of rRNA synthesis requires the DYRK1B kinase, a nucleolar DSB response that can be uncoupled from ATM-mediated DSB signaling events at the nucleolar periphery. Indeed, by targeting DSBs onto rDNA arrays, we uncovered that chemical inhibition or genetic inactivation of DYRK1B led to sustained nucleolar transcription. Not only does DYRK1B exhibit robust nucleolar accumulation following laser micro-irradiation across cell nuclei, we further showed that DYRK1B is required for rDNA DSB repair and rDNA copy number maintenance, and that DYRK1B-inactivated cells are hypersensitised to DSBs induced at the rDNA arrays. Together, our findings not only identify DYRK1B as a key signaling intermediate that coordinates DSB repair and rDNA transcriptional activities, but also support the idea of specialised DSB responses that operate within the nucleolus to preserve rDNA integrity.
Preprocedural SARS-CoV-2 Testing to Sustain Medically Needed Health Care Delivery During the COVID-19 Pandemic: A Prospective Observational Study
Authors: Haidar Ghady , Ayres Ashley , King Wendy C , McDonald Mackenzie , Wells Alan , Mitchell Stephanie L , Bilderback Andrew L , Minnier Tami , Mellors John W
Published: January 2021

Background

We implemented a preprocedural severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening initiative designed to sustain health care during a time when the extent of SARS-CoV-2 infection was unknown.

Methods

This was a prospective study of patients undergoing procedures at 3 academic hospitals in Pittsburgh, Pennsylvania (April 21–June 11), and 19 community hospitals across Middle/Western Pennsylvania and Southwestern New York (May 1–June 11). Patients at academic hospitals underwent symptom screening ≤7 days preprocedure, then SARS-CoV-2 nasopharyngeal polymerase chain reaction (PCR) testing 1–4 days preprocedure. A subset also underwent day-of-procedure testing. Community hospital patients underwent testing per local protocols. We report SARS-CoV-2 PCR positivity rates, impact, and barriers to testing encountered through June 11. PCR positivity rates of optional preprocedural SARS-CoV-2 testing for 2 consecutive periods following the screening initiative are also reported.

Results

Of 5881 eligible academic hospital patients, 2415 (41.1%) were tested (April 21–June 11). Lack of interest, distance, self-isolation, and nursing home/incarceration status were barriers. There were 11 PCR-positive patients (10 asymptomatic) among 10 539 patients tested (0.10%; 95% CI, 0.05%–0.19%): 3/2415 (0.12%; 95% CI, 0.02%–0.36%) and 8/8124 (0.10%; 95% CI, 0.04%–0.19%) at academic and community hospitals, respectively. Procedures were performed as scheduled in 40% (4/10) of asymptomatic PCR-positive patients. Positivity increased during subsequent coronavirus disease 2019 (COVID-19) surges: 54/34 948 (0.15%; 95% CI, 0.12%–0.20%) and 101/24 741 (0.41%; 95% CI, 0.33%–0.50%) PCR-positive patients from June 12–September 10 and September 11–December 15, respectively (P < .0001).

Conclusions

Implementing preprocedural PCR testing was complex and revealed low infection rates (0.24% overall), which increased during COVID-19 surges. Additional studies are needed to define the COVID-19 prevalence threshold at which universal preprocedural screening is warranted.
Metabolic control of histone demethylase activity involved in plant response to high temperature
Authors: Cui Xiaoyun , Zheng Yu , Lu Yue , Issakidis-Bourguet Emmanuelle , Zhou Dao-Xiu
Published: January 2021

Jumonji C (JmjC) domain proteins are histone lysine demethylases that require ferrous iron and alpha-ketoglutarate (or α-KG) as cofactors in the oxidative demethylation reaction. In plants, α-KG is produced by isocitrate dehydrogenases (ICDHs) in different metabolic pathways. It remains unclear whether fluctuation of α-KG levels affects JmjC demethylase activity and epigenetic regulation of plant gene expression. In this work, we studied the impact of loss of function of the cytosolic ICDH (cICDH) gene on the function of histone demethylases in Arabidopsis thaliana. Loss of cICDH resulted in increases of overall histone H3 lysine 4 trimethylation (H3K4me3) and enhanced mutation defects of the H3K4me3 demethylase gene JMJ14. Genetic analysis suggested that the cICDH mutation may affect the activity of other demethylases, including JMJ15 and JMJ18 that function redundantly with JMJ14 in the plant thermosensory response. Furthermore, we show that mutation of JMJ14 affected both the gene activation and repression programs of the plant thermosensory response and that JMJ14 and JMJ15 repressed a set of genes that are likely to play negative roles in the process. The results provide evidence that histone H3K4 demethylases are involved in the plant response to elevated ambient temperature.
The use of dried blood spots for the serological evaluation of SARS-CoV-2 antibodies
Authors: Toh Zheng Quan , Higgins Rachel A , Anderson Jeremy , Mazarakis Nadia , Do Lien Anh Ha , Rautenbacher Karin , Ramos Pedro , Dohle Kate , Tosif Shidan , Crawford Nigel , Mulholland Kim , Licciardi Paul V
Published: January 2021

Background

To determine if dried blood spot specimens (DBS) can reliably detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies, we compared the SARS-CoV-2 IgG antibody response in paired serum and eluates from DBS specimens.

Methods

A total of 95 paired DBS and serum samples were collected from 74 participants (aged 1–63 years) as part of a household cohort study in Melbourne, Australia. SARS-CoV-2 IgG antibodies specific for the receptor-binding domain (RBD) and S1 proteins between serum and eluates from DBS specimens were compared using an FDA-approved ELISA method.

Results

Among the 74 participants, 42% (31/74) were children and the rest were adults. A total of 16 children and 13 adults were SARS-CoV-2 positive by polymerase chain reaction. The IgG seropositivity rate was similar between serum and DBS specimens (18.9% (18/95) versus 16.8% (16/95)), respectively. Similar RBD and S1-specific IgG levels were detected between serum and DBS specimens. Serum IgG levels strongly correlated with DBS IgG levels (r = 0.99, P < 0.0001) for both SARS-CoV-2 proteins. Furthermore, antibodies remained stable in DBS specimens for >3 months.

Conclusions

DBS specimens can be reliably used as an alternative to serum samples for SARS-CoV-2 antibody measurement. The use of DBS specimens would facilitate serosurveillance efforts particularly in hard-to-reach populations and inform public health responses including COVID-19 vaccination strategies.
Construction of logic gates exploiting resonance phenomena in nonlinear systems
Authors: Murali K. , Rajasekar S. , Aravind Manaoj V. , Kohar Vivek , Ditto W. L. , Sinha Sudeshna
Published: January 2021

A two-state system driven by two inputs has been found to consistently produce a response mirroring a logic function of the two inputs, in an optimal window of moderate noise. This phenomenon is called logical stochastic resonance (LSR). We extend the conventional LSR paradigm to implement higher-level logic architecture or typical digital electronic structures via carefully crafted coupling schemes. Further, we examine the intriguing possibility of obtaining reliable logic outputs from a noise-free bistable system, subject only to periodic forcing, and show that this system also yields a phenomenon analogous to LSR, termed Logical Vibrational Resonance (LVR), in an appropriate window of frequency and amplitude of the periodic forcing. Lastly, this approach is extended to realize morphable logic gates through the Logical Coherence Resonance (LCR) in excitable systems under the influence of noise. The results are verified with suitable circuit experiments, demonstrating the robustness of the LSR, LVR and LCR phenomena.

This article is part of the theme issue ‘Vibrational and stochastic resonance in driven nonlinear systems (part 1)’.
The effect of high-frequency stochastic actions on the low-frequency behaviour of dynamic systems
Authors: Kremer Eugen
Published: January 2021

The dynamic system described by a finite number of first-order differential equations is considered. The right side of each equation is a sum of a slow, deterministic and, in the general case, nonlinear function of dynamic variables and a stochastic excitation. The stochastic action is a superposition of a finite number of independent random processes with coefficients depending on dynamic variables and slow time. The problem statement is oriented to applications in the field of driven systems. The analysis is based on the concept of vibration mechanics proposed by I. I. Blekhman. The modified method of direct separation of slow and fast motions uses the explicit introduction of a small parameter and some ideas of the two-scale technique. The general formulas for vibrational forces (or fluxes) are obtained. These additional terms appear in the resulting system for averaged motion instead of the stochastic terms to make the averaged system equivalent to the initial stochastic system with respect to slow motions and, in particular, to low-frequency resonances. As an example, the model of a vibration machine for bulk material processing is considered. The stochastic effect is caused by random oscillations of the bulk material mass. It is transformed into a modification of the machine's frequency characteristics leading to a specific stochastic resonance.

This article is part of the theme issue ‘Vibrational and stochastic resonance in driven nonlinear systems (part 1)’.
Mutation Rate Variations in the Human Genome are Encoded in DNA Shape
Authors: Liu Zian , Samee Md. Abul Hassan
Published: January 2021

Single nucleotide mutation rates have critical implications for human evolution and genetic diseases. Accurate modeling of these mutation rates has long remained an open problem since the rates vary substantially across the human genome. A recent model, however, explained much of the variation by considering higher order nucleotide interactions in the local (7-mer) sequence context around mutated nucleotides. Despite this model’s predictive value, we still lack a biophysically-grounded understanding of genome-wide mutation rate variations. DNA shape features are geometric measurements of DNA structural properties, such as helical twist and tilt, and are known to capture information on interactions between neighboring nucleotides within a local context. Motivated by this characteristic of DNA shape features, we used them to model mutation rates in the human genome. The DNA shape feature based models show up to 15% higher accuracy than the current nucleotide sequence-based models and pinpoint DNA structural properties predictive of mutation rates in the human genome. Further analyzing the mutation rates of individual positions of transcription factor (TF) binding sites in the human genome, we found a strong association between DNA shape and the position-specific mutation rates. The trend holds for hundreds of TFs and is even stronger in evolutionarily conserved regions. To our knowledge, this is the first attempt that demonstrates the structural underpinnings of nucleotide mutations in the human genome and lays the groundwork for future studies to incorporate DNA shape information in modeling genetic variations.