bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional plasticity of Capsicum annuum var. glabriusculum through multiple traits
Authors: Jiménez-Leyva Alberto , Orozco-Avitia Jesús , Gutiérrez Aldo , Vargas Georgina , Sánchez Esteban , Muñoz Ezequiel , Esqueda Martín
Published: May 2022

The diversity of functional traits still has not been studied enough in model plant species, even less so in little-known species. This experiment was carried out under the extreme heat of Sonoran Desert, using shading nets and under conditions where the availability of water and nutrients was not a stress factor. We evaluated how the low, intermediate and high sunlight regimes impact survival and promote multiple alterations on phenological and ecophysiological response of cultivated Capsicum annuum var. glabriusculum plants. Extremely warm temperatures promoted a high heat sum in degrees days throughout plants development. Most plants grown in high sunlight regimes did not survive; under intermediate sunlight regimes survival was high and plants developed vegetative and reproductively; but under low sunlight regimes plants survival was high; however, they developed just vegetatively. Photosynthetic response to light suggests that plants are physiologically acclimated to low and intermediate irradiance, whereas the CO2 assimilation curves suggest contrasting photosynthetic capacity traits. Under the intermediate sunlight regimes, plants strengthened their performance through multiple functional traits (e.g. CO2 and water diffusion traits, photosynthetic capacity, respiration, among others). Consequently, their biomass gain was faster and proportionally higher by 76 % with an investment of 14 % in fruits development. The principal components analysis extracted the main explanatory functional traits: photosynthetic nitrogen allocation, stomatal limitation, mesophyll conductance, Rubisco maximum carboxylation velocity, among others. In conclusion, phenological response and multiple functional traits determine plants acclimation to sunlight regimes and extremely warm temperatures in short term.
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches
Authors: Bugnon L A , Edera A A , Prochetto S , Gerard M , Raad J , Fenoy E , Rubiolo M , Chorostecki U , Gabaldón T , Ariel F , Di Persia L E , Milone D H , Stegmayer G
Published: May 2022

Motivation

In contrast to messenger RNAs, the function of the wide range of existing long noncoding RNAs (lncRNAs) largely depends on their structure, which determines interactions with partner molecules. Thus, the determination or prediction of the secondary structure of lncRNAs is critical to uncover their function. Classical approaches for predicting RNA secondary structure have been based on dynamic programming and thermodynamic calculations. In the last 4 years, a growing number of machine learning (ML)-based models, including deep learning (DL), have achieved breakthrough performance in structure prediction of biomolecules such as proteins and have outperformed classical methods in short transcripts folding. Nevertheless, the accurate prediction for lncRNA still remains far from being effectively solved. Notably, the myriad of new proposals has not been systematically and experimentally evaluated.

Results

In this work, we compare the performance of the classical methods as well as the most recently proposed approaches for secondary structure prediction of RNA sequences using a unified and consistent experimental setup. We use the publicly available structural profiles for 3023 yeast RNA sequences, and a novel benchmark of well-characterized lncRNA structures from different species. Moreover, we propose a novel metric to assess the predictive performance of methods, exclusively based on the chemical probing data commonly used for profiling RNA structures, avoiding any potential bias incorporated by computational predictions when using dot-bracket references. Our results provide a comprehensive comparative assessment of existing methodologies, and a novel and public benchmark resource to aid in the development and comparison of future approaches.

Availability

Full source code and benchmark datasets are available at: https://github.com/sinc-lab/lncRNA-folding

Contact

lbugnon@sinc.unl.edu.ar
Quantitative estimation of intracellular oxidative stress in human tissues
Authors: Bai Jun , Tan Renbo , An Zheng , Xu Ying
Published: May 2022

Oxidative stress is known to be involved in and possibly a key driver of the development of numerous chronic diseases, including cancer. It is highly desired to have a capability to reliably estimate the level of intracellular oxidative stress as it can help to identify functional changes and disease phenotypes associated with such a stress, but the problem proves to be very challenging. We present a novel computational model for quantitatively estimating the level of oxidative stress in tissues and cells based on their transcriptomic data. The model consists of (i) three sets of marker genes found to be associated with the production of oxidizing molecules, the activated antioxidation programs and the intracellular stress attributed to oxidation, respectively; (ii) three polynomial functions defined over the expression levels of the three gene sets are developed aimed to capture the total oxidizing power, the activated antioxidation capacity and the oxidative stress level, respectively, with their detailed parameters estimated by solving an optimization problem and (iii) the optimization problem is so formulated to capture the relevant known insights such as the oxidative stress level generally goes up from normal to chronic diseases and then to cancer tissues. Systematic assessments on independent datasets indicate that the trained predictor is highly reliable and numerous insights are made based on its application results to samples in the TCGA, GTEx and GEO databases.
Sufficient principal component regression for pattern discovery in transcriptomic data
Authors: Ding Lei , Zentner Gabriel E , McDonald Daniel J
Published: May 2022

Motivation

Methods for the global measurement of transcript abundance such as microarrays and RNA-Seq generate datasets in which the number of measured features far exceeds the number of observations. Extracting biologically meaningful and experimentally tractable insights from such data therefore requires high-dimensional prediction. Existing sparse linear approaches to this challenge have been stunningly successful, but some important issues remain. These methods can fail to select the correct features, predict poorly relative to non-sparse alternatives or ignore any unknown grouping structures for the features.

Results

We propose a method called SuffPCR that yields improved predictions in high-dimensional tasks including regression and classification, especially in the typical context of omics with correlated features. SuffPCR first estimates sparse principal components and then estimates a linear model on the recovered subspace. Because the estimated subspace is sparse in the features, the resulting predictions will depend on only a small subset of genes. SuffPCR works well on a variety of simulated and experimental transcriptomic data, performing nearly optimally when the model assumptions are satisfied. We also demonstrate near-optimal theoretical guarantees.

Availability and implementation

Code and raw data are freely available at https://github.com/dajmcdon/suffpcr. Package documentation may be viewed at https://dajmcdon.github.io/suffpcr.

Contact

daniel@stat.ubc.ca

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Altered SOD1 maturation and post-translational modification in amyotrophic lateral sclerosis spinal cord
Authors: Trist Benjamin G , Genoud Sian , Roudeau Stéphane , Rookyard Alexander , Abdeen Amr , Cottam Veronica , Hare Dominic J , White Melanie , Altvater Jens , Fifita Jennifer A , Hogan Alison , Grima Natalie , Blair Ian P , Kysenius Kai , Crouch Peter J , Carmona Asuncion , Rufin Yann , Claverol Stéphane , Van Malderen Stijn , Falkenberg Gerald , Paterson David J , Smith Bradley , Troakes Claire , Vance Caroline , Shaw Christopher E , Al-Sarraj Safa , Cordwell Stuart , Halliday Glenda , Ortega Richard , Double Kay L
Published: May 2022

Aberrant self-assembly and toxicity of wild-type and mutant superoxide dismutase 1 (SOD1) has been widely examined in silico, in vitro and in transgenic animal models of amyotrophic lateral sclerosis. Detailed examination of the protein in disease-affected tissues from amyotrophic lateral sclerosis patients, however, remains scarce.

We used histological, biochemical and analytical techniques to profile alterations to SOD1 protein deposition, subcellular localization, maturation and post-translational modification in post-mortem spinal cord tissues from amyotrophic lateral sclerosis cases and controls. Tissues were dissected into ventral and dorsal spinal cord grey matter to assess the specificity of alterations within regions of motor neuron degeneration.

We provide evidence of the mislocalization and accumulation of structurally disordered, immature SOD1 protein conformers in spinal cord motor neurons of SOD1-linked and non-SOD1-linked familial amyotrophic lateral sclerosis cases, and sporadic amyotrophic lateral sclerosis cases, compared with control motor neurons. These changes were collectively associated with instability and mismetallation of enzymatically active SOD1 dimers, as well as alterations to SOD1 post-translational modifications and molecular chaperones governing SOD1 maturation. Atypical changes to SOD1 protein were largely restricted to regions of neurodegeneration in amyotrophic lateral sclerosis cases, and clearly differentiated all forms of amyotrophic lateral sclerosis from controls. Substantial heterogeneity in the presence of these changes was also observed between amyotrophic lateral sclerosis cases.

Our data demonstrate that varying forms of SOD1 proteinopathy are a common feature of all forms of amyotrophic lateral sclerosis, and support the presence of one or more convergent biochemical pathways leading to SOD1 proteinopathy in amyotrophic lateral sclerosis. Most of these alterations are specific to regions of neurodegeneration, and may therefore constitute valid targets for therapeutic development.
Phonemic restoration in Alzheimer’s disease and semantic dementia: a preliminary investigation
Authors: Jiang Jessica , Johnson Jeremy C. S. , Requena-Komuro Maï-Carmen , Benhamou Elia , Sivasathiaseelan Harri , Sheppard Damion L. , Volkmer Anna , Crutch Sebastian J. , Hardy Chris J. D. , Warren Jason D
Published: May 2022

Phonemic restoration—perceiving speech sounds that are actually missing—is a fundamental perceptual process that ‘repairs’ interrupted spoken messages during noisy everyday listening. As a dynamic, integrative process, phonemic restoration is potentially affected by neurodegenerative pathologies, but this has not been clarified. Here, we studied this phenomenon in 5 patients with typical Alzheimer’s disease and 4 patients with semantic dementia, relative to 22 age-matched healthy controls. Participants heard isolated sounds, spoken real words and pseudowords in which noise bursts either overlaid a consonant or replaced it; a tendency to hear replaced (missing) speech sounds as present signified phonemic restoration. All groups perceived isolated noises normally and showed phonemic restoration of real words, most marked in Alzheimer’s patients. For pseudowords, healthy controls showed no phonemic restoration, while Alzheimer’s patients showed marked suppression of phonemic restoration and patients with semantic dementia contrastingly showed phonemic restoration comparable to real words. Our findings provide the first evidence that phonemic restoration is preserved or even enhanced in neurodegenerative diseases, with distinct syndromic profiles that may reflect the relative integrity of bottom-up phonological representation and top-down lexical disambiguation mechanisms in different diseases. This work has theoretical implications for predictive coding models of language and neurodegenerative disease and for understanding cognitive ‘repair’ processes in dementia. Future research should expand on these preliminary observations with larger cohorts.
Innovating in knowledge-intensive entrepreneurial firms: exploring the effects of a variety of internal and external knowledge sources on goods and service innovations
Authors: Gifford Ethan , Ljungberg Daniel , McKelvey Maureen
Published: May 2022

Although knowledge-intensive entrepreneurial firms experiencing high growth and generating innovations are widely acknowledged as important for economic growth, surprisingly little is known about how such firms achieve and maintain a high level of knowledge intensity through which to innovate. Our article further develops the concept of knowledge intensity by proposing that it is augmented by external and internal search activities carried out by the entrepreneurial firm and analyzes how these activities affect innovation performance. We use principal component analysis to derive formal and informal search channels from summated rating scales—measuring reliance on internal and external sources of knowledge—and then use fractional logit regression to explore how these channels relate to a firm’s innovative performance, i.e., the share of innovative goods and services sold. We find that searching via informal channels, and formal channels toward scientific and technological knowledge, improves innovation performance of both goods and services, while searching via formal channels toward market knowledge positively affects only innovative goods. Overall, informal channels matter more than formal channels. Lastly, we find substitution rather than complementarity effects between external and internal search channels in their effect on innovation performance in both goods and services. Thus, we interpret that building up knowledge intensity per se through search matters more for innovation performance than whether search is internally or externally focused. Our work contributes to the growing literature on knowledge-intensive entrepreneurship, to the related literature on new technology-based firms and young innovative firms, and to the general understanding of knowledge intensity at the firm level.
Platform competition and complementor responses: insights from combining design rules with the comparative adjustment, transaction, and opportunity cost framework
Authors: Argyres Nicholas , Nickerson Jackson , Ozalp Hakan
Published: May 2022

Platform owners regularly make decisions regarding whether, when, and how to upgrade their platforms as they compete with other platforms. These decisions must consider how platform complementors and rivals are likely to respond to various changes because a platform suffers in competition when the quantity or quality of its complementors is low. This paper analyzes such interactions in the US videogame industry. We show how a combined design rule-comparative adjustment, transaction, and opportunity cost framework can help to explain and predict these interactions in this industry.
Limited airway resection and reconstruction for paediatric tracheobronchial inflammatory myofibroblastic tumour
Authors: Dong Junguo , Gonzalez-Rivas Diego , Lv Pengcheng , Wang Zhexin , He Jiaxi , Yao Feng , Li Shuben
Published: May 2022

OBJECTIVES

The paediatric tracheobronchial inflammatory myofibroblastic tumour (IMT) is a rare disease. Whether limited surgical resection is a feasible surgical approach for these patients remains controversial. The objectives of this study were to report the long-term prognosis after limited surgical resections on paediatric tracheobronchial IMT and provide a surgical management strategy for this rare disease.

METHODS

Paediatric tracheobronchial IMT patients who underwent limited surgical resection from 2012 to 2020 were enrolled in this study. The clinical characteristics, course of treatment and long-term outcomes of all participants were collated. We presented the accumulated data and analysed the feasibility of limited surgical resection on the paediatric tracheobronchial IMT.

RESULTS

A total of 9 children with tracheobronchial IMTs were enrolled in our study. Cough and shortness of breath were the most common symptoms. All 9 participants underwent surgical treatment, including 2 tracheal reconstructions, 4 carinal reconstructions and 3 bronchial sleeve resections. Among the participants, 6/9 (66%) were positive for the anaplastic lymphoma receptor tyrosine kinase gene in terms of immunohistochemistry. None of the participants died of short-term complications. The follow-up period was 5.4 (range, 1.1–9.3) years, during which all participants remained well.

CONCLUSIONS

Limited surgical resection is preferred for paediatrics with tracheobronchial IMTs. Meanwhile, patients with complete resection have an excellent long-term prognosis.
“Groups Can Change, Therefore War is Avoidable”: How Confidence in National Identity Can Reduce Public Support for Militant Internationalism
Authors: Chung Eunbin
Published: May 2022

As a way to alleviate interstate aggression, researchers have proposed a submergence of existing national identities and promotion of universalism instead. In contrast, this study suggests that strong national identities can reduce public support for militaristic foreign policy. I examine the mechanism of this relationship, proposing that the affirmation of national identities increases beliefs that the nature of other groups is malleable rather than fixed. The belief of the malleability of group nature opens a possibility for negotiation and peacebuilding between rival states, as conflict with the other side becomes an avoidable option. Integrating theories of political psychology and conflict resolution, I conduct novel survey experiments with a sample of 944 Japanese participants. Results revealed that Japanese respondents who reflected on the positive aspects of their national identity tended to hold lower levels of support for militaristic foreign policy. These effects were transmitted via an increase in beliefs that the nature of groups is malleable and beliefs of war avoidability.
Antimicrobial resistance in commensal Escherichia coli from humans and chickens in the Mekong Delta of Vietnam is driven by antimicrobial usage and potential cross-species transmission
Authors: Nhung Nguyen Thi , Yen Nguyen Thi Phuong , Dung Nguyen Thi Thuy , Nhan Nguyen Thi Minh , Phu Doan Hoang , Kiet Bach Tuan , Thwaites Guy , Geskus Ronald B. , Baker Stephen , Carrique-Mas Juan , Choisy Marc
Published: May 2022

Objectives

To investigate phenotypic antimicrobial resistance (AMR) in relation to antimicrobial use (AMU) and potential inter-species transmission among Escherichia coli from humans and chickens located in the same households in the Mekong Delta of Vietnam.

Methods

We collected data on AMU and faecal swabs from humans (N = 426) and chickens (N = 237) from 237 small-scale farms. From each sample, one E. coli strain was isolated and tested for its susceptibility against 11 antimicrobials by Sensititre AST. The association between AMR and AMU was investigated by logistic regression modelling. Using randomization, we compared the degree of similarity in AMR patterns between human and chicken E. coli from the same farms compared with isolates from different farms.

Results

The AMU rate was ∼19 times higher in chickens (291.1 per 1000 chicken-days) than in humans (15.1 per 1000 person-days). Isolates from chickens also displayed a higher prevalence of multidrug resistance (63.3%) than those of human origin (55.1%). AMU increased the probability of resistance in isolates from human (ORs between 2.1 and 5.3) and chicken (ORs between 1.9 and 4.8). E. coli from humans and chickens living on same farms had a higher degree of similarity in their AMR patterns than isolates from humans and chicken living on different farms.

Conclusions

We demonstrated the co-influence of AMU and potential transmission on observed phenotypic AMR patterns among E. coli isolates from food-producing animals and in-contact humans. Restricting unnecessary AMU alongside limiting interspecies contact (i.e. increasing hygiene and biocontainment) are essential for reducing the burden of AMR.
Developing an integrated model for planning the delivery of construction materials to post-disaster reconstruction projects
Authors: Gharib Zahra , Yazdani Maziar , Bozorgi-Amiri Ali , Tavakkoli-Moghaddam Reza , Taghipourian Mohammad Javad
Published: May 2022

Construction material delivery to post-disaster reconstruction projects is challenging because of the resource and time limitations that follow a large-scale disaster. There is compelling evidence that inadequate planning jeopardises the success of a large number of post-disaster reconstruction projects. Thus, the current study proposes an integrated approach to facilitate the procurement planning of construction materials following a large-scale disaster. The proposed approach clustered the location of construction projects using a differential evolution (DE)-K-prototypes, a new partitional clustering algorithm based on DE and K-prototypes, method. Then, using a permanent matrix prioritises cluster points based on route reliability-affecting factors. The model’s objectives are to minimise the total travel time, maximise the reliability of the route, and minimise the total weighted undelivered materials to projects. In the case of distribution of material through land vehicles, the possibility of breakdowns in the vehicle is considered, allowing for the determination of vehicle breakdown under various scenarios and the minimisation of undelivered materials to projects. As a result of the uncertain character of the disaster, the demands of construction projects are fuzzy, and Jimenez’s method is used to handle it. Due to the complexity of the problem, two algorithms are proposed, a multi-objective evolutionary algorithm based on decomposition (MOEA/D) and a non-dominated sorting genetic algorithm-II (NSGA-II). The results confirm that the proposed MOEA/D has a higher accuracy while NSGA-II has a shorter computational time. By providing new theoretical perspectives on disaster recovery strategies in the construction sector, this study contributes to the growing body of knowledge about disaster recovery strategies in the sector. The findings of this study can be employed to develop an integrated planning system for the delivery of construction materials to post-disaster reconstruction projects in disaster-prone countries.
Escalating the 2022 Hajj during the third year of the COVID-19 pandemic
Authors: Al-Tawfiq Jaffar A , Kattan Rana F , Memish Ziad A
Published: May 2022

The escalation of the number of pilgrims for the 2022 Hajj season comes as KSA had succeeded in reaching an excellent percentage in vaccine coverage and subsequently eased the restrictions. KSA adopted an extensive surveillance, implemented risk mitigation, and maximized COVID-19 vaccines coverage.
Synthesis and signalling of strigolactone and KAI2-ligand signals in bryophytes
Authors: Bonhomme Sandrine , Guillory Ambre
Published: May 2022

Strigolactones (SLs), long known as butenolide rhizospheric signals, have been recognized since 2008 as a class of hormones regulating many aspects of plant development. Many authors also anticipate ‘KAI2-ligand’ (KL) as a novel class of phytohormones; however, this ligand remains elusive. Core genes of SL and KL pathways, first described in angiosperms, are found in all land plants and some even in green algae. This review reports current knowledge of these pathways in bryophytes. Data on the pathways mostly come from two models: the moss Physcomitrium patens and the liverwort Marchantia. Gene targeting methods have allowed functional analyses of both models. Recent work in Marchantia suggests that SLs’ ancestral role was to recruit beneficial microbes as arbuscular mycorrhizal fungi. In contrast, the hormonal role of SLs observed in P. patens is probably a result of convergent evolution. Evidence for a functional KL pathway in both bryophyte models is very recent. Nevertheless, many unknowns remain and warrant a more extensive investigation of SL and KL pathways in various land plant lineages.
ROOT PENETRATION INDEX 3, a major quantitative trait locus associated with root system penetrability in Arabidopsis
Authors: Bello Bello Elohim , Rico Cambron Thelma Y , Ortiz Ramírez Lesly Abril , Rellán Álvarez Rubén , Herrera-Estrella Luis
Published: May 2022

Soil mechanical impedance precludes root penetration, confining root system development to shallow soil horizons where mobile nutrients are scarce. Using a two-phase-agar system, we characterized Arabidopsis responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show a significant reduction in leaf area, root length, and elongation zone and an increment in root diameter, while those capable of penetrating show only minor morphological effects. Analyses using different auxin-responsive reporter lines, exogenous auxins, and inhibitor treatments suggest that auxin responsiveness and PIN-mediated auxin distribution play an important role in regulating root responses to mechanical impedance. The assessment of 21 Arabidopsis accessions revealed that primary root penetrability varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population derived from Landsberg erecta (Ler-0, with a high primary root penetrability) and Shahdara (Sha, with a low primary root penetrability) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3, ROOT PENETRATION INDEX 3 (q-RPI3), which accounted for 29.98% (logarithm of odds=8.82) of the total phenotypic variation. Employing an introgression line (IL-321) with a homozygous q-RPI3 region from Sha in the Ler-0 genetic background, we demonstrated that q-RPI3 plays a crucial role in root penetrability. This multiscale study reveals new insights into root plasticity during the penetration process in hard agar layers, natural variation, and genetic architecture behind primary root penetrability in Arabidopsis.
Orbital alignment and mass segregation in galactic nuclei via vector resonant relaxation
Authors: Magnan Nathan , Fouvry Jean-Baptiste , Pichon Christophe , Chavanis Pierre-Henri
Published: May 2022

Supermassive black holes dominate the gravitational potential in galactic nuclei. In these dense environments, stars follow nearly Keplerian orbits and see their orbital planes relax through the potential fluctuations generated by the stellar cluster itself. For typical astrophysical galactic nuclei, the most likely outcome of this vector resonant relaxation is that the orbital planes of the most massive stars spontaneously self-align within a narrow disc. We present a maximum entropy method to systematically determine this long-term distribution of orientations and use it for a wide range of stellar orbital parameters and initial conditions. The heaviest stellar objects are found to live within a thin equatorial disc. The thickness of this disk depends on the stars’ initial mass function, and on the geometry of the initial cluster. This work highlights a possible (indirect) novel method to constrain the distribution of intermediate mass black holes in galactic nuclei.
New insights in copper handling strategies in the green alga Chlamydomonas reinhardtii under low-iron condition
Authors: Kochoni Emeric , Aharchaou Imad , Ohlund Leanne , Rosabal Maikel , Sleno Lekha , Fortin Claude
Published: May 2022

Copper (Cu) is a redox-active transition element critical to various metabolic processes. These functions are accomplished in tandem with Cu-binding ligands, mainly proteins. The main goal of this work was to understand the mechanisms that govern the intracellular fate of Cu in the freshwater green alga, Chlamydomonas reinhardtii, and more specifically to understand the mechanisms underlying Cu detoxification by algal cells in low-Fe conditions. We show that Cu accumulation was up to 51-fold greater for algae exposed to Cu in low-Fe medium as compared to the replete-Fe growth medium. Using the stable isotope 65Cu as a tracer, we studied the subcellular distribution of Cu within the various cell compartments of C. reinhardtii. These data were coupled with metallomic and proteomic approaches to identify potential Cu-binding ligands in the heat-stable proteins and peptides fraction of the cytosol. Cu was mostly found in the organelles (78%), and in the heat-stable proteins and peptides (21%) fractions. The organelle fraction appeared to also be the main target compartment of Cu accumulation in Fe-depleted cells. As Fe levels in the medium were shown to influence Cu homeostasis, we found that C. reinhardtii can cope with this additional stress by utilizing different Cu-binding ligands. Indeed, in addition to expected Cu-binding ligands such as glutathione and phytochelatins, 25 proteins were detected that may also play a role in the Cu-detoxification processes in C. reinhardtii. Our results shed new light on the coping mechanisms of C. reinhardtii when exposed to environmental conditions that induce high rates of Cu accumulation.
Secondary hyperparathyroidism (CKD-MBD) treatment and the risk of dementia
Authors: Mathur Aarti , Ahn JiYoon B , Sutton Whitney , Chu Nadia M , Gross Alden L , Segev Dorry L , McAdams-DeMarco Mara
Published: May 2022

Background

Elevated parathyroid hormone (PTH) levels have been reported as a potential risk factor for cognitive impairment. Compared with the general population, older adults with end-stage renal disease (ESRD) who are frequently affected by secondary hyperparathyroidism (SHPT) are at increased risk of developing dementia. The main objective of our study was to evaluate if the risk of dementia in older (age ≥66 years) ESRD patients differed if they were treated for SHPT.

Methods

Using the United States Renal Data System and Medicare claims, we identified 189 433 older adults without a diagnosis of dementia, who initiated dialysis between 2006 and 2016. SHPT treatment was defined as the use of vitamin D analogs, phosphate binders, calcimimetics or parathyroidectomy. We quantified the association between treated SHPT and incident dementia during dialysis using a multivariable Cox proportional hazards model with inverse probability weighting, considering SHPT treatment as a time-varying exposure.

Results

Of 189 433 older ESRD adults, 92% had a claims diagnosis code of SHPT and 123 388 (65%) were treated for SHPT. The rate of incident dementia was 6 cases per 100 person-years among SHPT treated patients compared with 11 cases per 100 person-years among untreated patients. Compared with untreated SHPT patients, the risk of dementia was 42% lower [adjusted hazard ratio (aHR) = 0.58, 95% confidence interval (CI): 0.56–0.59] among SHPT treated patients. The magnitude of the beneficial effect of SHPT treatment differed by sex (Pinteraction = .02) and race (Pinteraction ≤ .01), with females (aHR = 0.56, 95% CI: 0.54–0.58) and those of Asian (aHR = 0.51, 95% CI: 0.46–0.57) or Black race (aHR = 0.51, 95% CI: 0.48–0.53) having a greatest reduction in dementia risk.

Conclusion

Receiving treatment for SHPT was associated with a lower risk of incident dementia among older patients with ESRD. This work provides additional support for the treatment of SHPT in older ESRD patients.
High temperature induces male sterility via MYB66–MYB4–Casein kinase I signaling in cotton
Authors: Li Yanlong , Li Yaoyao , Su Qian , Wu Yuanlong , Zhang Rui , Li Yawei , Ma Yizan , Ma Huanhuan , Guo Xiaoping , Zhu Longfu , Min Ling , Zhang Xianlong
Published: May 2022

High temperature (HT) causes male sterility and decreases crop yields. Our previous works have demonstrated that sugar and auxin signaling pathways, Gossypium hirsutum Casein kinase I (GhCKI), and DNA methylation are all involved in HT-induced male sterility in cotton. However, the signaling mechanisms leading to distinct GhCKI expression patterns induced by HT between HT-tolerant and HT-sensitive cotton anthers remain largely unknown. Here, we identified a GhCKI promoter (ProGhCKI) region that functions in response to HT in anthers and found the transcription factor GhMYB4 binds to this region to act as an upstream positive regulator of GhCKI. In the tapetum of early-stage cotton anthers, upregulated expression of GhMYB4 under HT and overexpressed GhMYB4 under normal temperature both led to severe male sterility phenotypes, coupled with enhanced expression of GhCKI. We also found that GhMYB4 interacts with GhMYB66 to form a heterodimer to enhance its binding to ProGhCKI. However, GhMYB66 showed an expression pattern similar to GhMYB4 under HT but did not directly bind to ProGhCKI. Furthermore, HT reduced siRNA-mediated CHH DNA methylations in the GhMYB4 promoter, which enhanced the expression of GhMYB4 in tetrad stage anthers and promoted the formation of the GhMYB4/GhMYB66 heterodimer, which in turn elevated the transcription of GhCKI in the tapetum, leading to male sterility. Overall, we shed light on the GhMYB66–GhMYB4–GhCKI regulatory pathway in response to HT in cotton anthers.
EXTRA LARGE G-PROTEIN2 mediates cell death and hyperimmunity in the chitin elicitor receptor kinase 1-4 mutant
Authors: Petutschnig Elena , Anders Julia , Stolze Marnie , Meusel Christopher , Hacke Ronja , Much Laura , Schwier Melina , Gippert Anna-Lena , Kroll Samuel , Fasshauer Patrick , Wiermer Marcel , Lipka Volker
Published: May 2022

Heterotrimeric G-proteins are signal transduction complexes that comprised three subunits, Gα, Gβ, and Gγ, and are involved in many aspects of plant life. The noncanonical Gα subunit EXTRA LARGE G-PROTEIN2 (XLG2) mediates pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species (ROS) generation and immunity downstream of pattern recognition receptors. A mutant of the chitin receptor component CHITIN ELICITOR RECEPTOR KINASE1 (CERK1), cerk1-4, maintains normal chitin signaling capacity but shows excessive cell death upon infection with powdery mildew fungi. We identified XLG2 mutants as suppressors of the cerk1-4 phenotype. Mutations in XLG2 complex partners ARABIDOPSIS Gβ1 (AGB1) and Gγ1 (AGG1) have a partial cerk1-4 suppressor effect. Contrary to its role in PAMP-induced immunity, XLG2-mediated control of ROS production by RESPIRATORY BURST OXIDASE HOMOLOGUE D (RBOHD) is not critical for cerk1-4-associated cell death and hyperimmunity. The cerk1-4 phenotype is also independent of the co-receptor/adapter kinases BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) and SUPPRESSOR OF BIR1 1 (SOBIR1), but requires the E3 ubiquitin ligase PLANT U-BOX 2 (PUB2). XLG2 localizes to both the cell periphery and nucleus, and the cerk1-4 cell death phenotype is mediated by the cell periphery pool of XLG2. Integrity of the XLG2 N-terminal domain, but not its phosphorylation, is essential for correct XLG2 localization and formation of the cerk1-4 phenotype. Our results support a model in which XLG2 acts downstream of an unknown cell surface receptor that activates an NADPH oxidase-independent cell death pathway in Arabidopsis (Arabidopsis thaliana).
Sensorimotor Relationalism and Conscious Vision
Authors: Ward Dave
Published: May 2022

I argue that the phenomenal properties of conscious visual experiences are properties of the mind-independent objects to which the subject is perceptually related, mediated by the subject's practical understanding of their sensorimotor relation to those properties. This position conjoins two existing strategies for explaining the phenomenal character of perceptual experiences: accounts appealing to perceivers’ limited, non-inferential access to the details of their sensory relation to the environment, and the relationalist conception of phenomenal properties. Bringing these two positions together by emphasizing their sensorimotor common ground allows each one to respond to damaging objections using the resources of the other. The resulting ‘sensorimotor relationalism’ about conscious vision provides a promising schema for explaining phenomenal properties of perceptual states, replacing ‘Hard’ questions with tractable ones about the perceptual relation and its sensorimotor underpinnings.
30-Day Readmission Reduction in a Skilled Facility Population Through Pharmacist-Driven Medication Reconciliation
Authors: Phillips Marc , Dillaman Megan , Matuga Rebekah , Sweet Michael , Lerfald Nathan , Krupica Troy , Briggs Frank
Published: May 2022

Background:

Transitions of care can be difficult to manage and if not performed properly, can lead to increased readmissions and poor outcomes. Transitions are more complex when patients are discharged to skilled nursing facilities.

Purpose:

We assessed the impact of pharmacist-led initiatives, including medication reconciliation, on readmission rates between an academic medical center and a local skilled nursing facility (SNF).

Methods:

We conducted a two-phase quality improvement project focusing on pharmacist-led medication reconciliation at different points in the transition process. All-cause 30-day readmission rates, medication reconciliation completion rates, and total pharmacist interventions were compared between the 2 groups.

Results:

The combined intervention and baseline cohorts resulted in a 29.8% relative reduction (14.5% vs. 20.6%) in readmission rates. Medication reconciliation was completed on 93.8% of SNF admitted patients in the first phase and 97.7% of patients in the second phase. Pharmacist interventions per reconciliation were 2.39 in the first phase compared with 1.82 in the second phase.

Conclusion:

Pharmacist-led medication reconciliation can contribute to reduction of hospital readmissions from SNFs and is an essential part of the SNF transition process.
Comparison of Laboratory and Hemodynamic Time Series Data Across Original, Alpha, and Delta Variants in Patients With Multisystem Inflammatory Syndrome in Children
Authors: Jain Parag N. , Acosta Sebastian , Annapragada Ananth , Checchia Paul A. , Moreira Axel , Muscal Eyal , Sartain Sarah E. , Tejtel S. Kristen Sexson , Vogel Tiphanie P. , Shekerdemian Lara , Rusin Craig G.
Published: May 2022

OBJECTIVES:

To compare the clinical, laboratory, and hemodynamic parameters during hospitalization for patients with multisystem inflammatory syndrome in children (MIS-C), across the Original/Alpha and the Delta variants of severe acute respiratory syndrome coronavirus 2 infection.

DESIGN:

Retrospective cohort study.

SETTING:

Single-center quaternary children’s hospital.

PATIENTS:

Children with MIS-C admitted from May 2020 to February 2021(Original and Alpha variant cohort) and August 2021 to November 2021 (Delta variant cohort).

MEASUREMENTS AND MAIN RESULTS:

Continuous vital sign measurements, laboratory results, medications data, and hospital outcomes from all subjects were evaluated. Of the 134 patients (102 with Original/Alpha and 32 with Delta), median age was 9 years, 75 (56%) were male, and 61 (46%) were Hispanics. The cohort with Original/Alpha variant had more males (61% vs 41%; p = 0.036) and more respiratory/musculoskeletal symptoms on presentation compared with the Delta variant (p < 0.05). More patients in the Original/Alpha variant cohort received mechanical ventilation (16 vs 0; p = 0.009). Median hospital length of stay (LOS) was 7 days, and ICU LOS was 3 days for the entire cohort. ICU LOS was shorter in cohort with the Delta variant compared with the Original/Alpha variant (4 vs 2 d; p = 0.001). Only one patient had cardiac arrest, two needed extracorporeal membrane oxygenation, and two needed left ventricular assist device (Impella, Danvers, MA), all in the Original/Alpha variant cohort; no mortality occurred in the entire cohort. MIS-C cohort associated with the Delta variant had lower INR, prothrombin time, WBCs, sodium, phosphorus, and potassium median values (p < 0.05) during hospitalization compared with the Original/Alpha variants. Hemodynamic assessment showed significant tachycardia in the Original/Alpha variants cohort compared with the Delta variant cohort (p < 0.05).

INTERVENTIONS:

None.

CONCLUSIONS:

Patients with MIS-C associated with the Delta variants had lower severity during hospitalization compared with the Original/Alpha variant. Analysis of distinct trends in clinical and laboratory parameters with future variants of concerns will allow for potential modification of treatment protocol.
Aerial (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots
Authors: Fukuda Kyohei , Uefune Masayoshi , Fukaki Hidehiro , Yamauchi Yasuo , Hara-Nishimura Ikuko , Ozawa Rika , Matsui Kenji , Sugimoto Koichi , Okada Kazunori , Imai Ryozo , Takahashi Kenshi , Enami Shinichi , Wurst René , Takabayashi Junji
Published: May 2022

One of the characteristic aspects of odour sensing in humans is the activation of olfactory receptors in a slightly different manner in response to different enantiomers. Here, we focused on whether plants showed enantiomer-specific response similar to that in humans. We exposed Arabidopsis seedlings to methanol (control) and (+)- or (−)-borneol, and found that only (+)-borneol reduced the root length. Furthermore, the root-tip width was more increased upon (+)-borneol exposure than upon (−)-borneol exposure. In addition, root-hair formation was observed near the root tip in response to (+)-borneol. Auxin signalling was strongly reduced in the root tip following exposure to (+)-borneol, but was detected following exposure to (−)-borneol and methanol. Similarly, in the root tip, the activity of cyclin B1:1 was detected on exposure to (−)-borneol and methanol, but not on exposure to (+)-borneol, indicating that (+)-borneol inhibits the meristematic activity in the root. These results partially explain the (+)-borneol-specific reduction in the root length of Arabidopsis. Our results indicate the presence of a sensing system specific for (+)-borneol in Arabidopsis.
Integration of visual motion and orientation signals in dyslexic children: an equivalent noise approach
Authors: Manning Catherine , Hulks Victoria , Tibber Marc S. , Dakin Steven C.
Published: May 2022

Dyslexic individuals have been reported to have reduced global motion sensitivity, which could be attributed to various causes including atypical magnocellular or dorsal stream function, impaired spatial integration, increased internal noise and/or reduced external noise exclusion. Here, we applied an equivalent noise experimental paradigm alongside a traditional motion-coherence task to determine what limits global motion processing in dyslexia. We also presented static analogues of the motion tasks (orientation tasks) to investigate whether perceptual differences in dyslexia were restricted to motion processing. We compared the performance of 48 dyslexic and 48 typically developing children aged 8 to 14 years in these tasks and used equivalent noise modelling to estimate levels of internal noise (the precision associated with estimating each element's direction/orientation) and sampling (the effective number of samples integrated to judge the overall direction/orientation). While group differences were subtle, dyslexic children had significantly higher internal noise estimates for motion discrimination, and higher orientation-coherence thresholds, than typical children. Thus, while perceptual differences in dyslexia do not appear to be restricted to motion tasks, motion and orientation processing seem to be affected differently. The pattern of results also differs from that previously reported in autistic children, suggesting perceptual processing differences are condition-specific.
Urban hierarchy and spatial diffusion over the innovation life cycle
Authors: Bokányi Eszter , Novák Martin , Jakobi Ákos , Lengyel Balázs
Published: May 2022

Successful innovations achieve large geographical coverage by spreading across settlements and distances. For decades, spatial diffusion has been argued to take place along the urban hierarchy. Yet, the role of geographical distance was difficult to identify in hierarchical diffusion due to missing data on spreading events. In this paper, we exploit spatial patterns of individual invitations sent from registered users to new users over the entire life cycle of a social media platform. We demonstrate that hierarchical diffusion overlaps with diffusion to close distances and these factors co-evolve over the life cycle. Therefore, we disentangle them in a regression framework that estimates the yearly number of invitations sent between pairs of towns. We confirm that hierarchical diffusion prevails initially across large towns only but emerges in the full spectrum of settlements in the middle of the life cycle when adoption accelerates. Unlike in previous gravity estimations, we find that after an intensifying role of distance in the middle of the life cycle a surprisingly weak distance effect characterizes the last years of diffusion. Our results stress the dominance of urban hierarchy in spatial diffusion and inform future predictions of innovation adoption at local scales.
Effect of pulsating solidification on the surface properties of conductive materials
Authors: Qin Rongshan , Bhagurkar Ashutosh
Published: May 2022

Application of pulsed electric current to solidifying conductive materials leads to a rapid and significant reduction of surface roughness. This is validated experimentally in the present work for multi-component oxides. The surface geometry of the casts without and with pulsating treatment was measured using a Leica DCM-3D Profiler. The pulsating treatment reduces the roughness of solidified materials by more than 50%. The unmeasurable points, which account for nearly 2% of total area, were interpolated using an artificial multi-layer neural network. Both the experimentally measured and neural network interpolated surface profile data were implemented to the calculation of electric current free energy. The results show that the electric current free energy can overtake surface energy and provide a significant driving force to the kinetics of surface evolution in solidification. Distortion of the electric field is noticed around the interface.
Measure of overlap between two arbitrary ellipses on a sphere
Authors: Gnidovec Andraž , Božič Anže , Jelerčič Urška , Čopar Simon
Published: May 2022

Various packing problems and simulations of hard and soft interacting particles, such as microscopic models of nematic liquid crystals, reduce to calculations of intersections and pair interactions between ellipsoids. When constrained to a spherical surface, curvature and compactness lead to non-trivial behaviour that finds uses in physics, computer science and geometry. A well-known idealized isotropic example is the Tammes problem of finding optimal non-intersecting packings of equal hard disks. The anisotropic case of elliptic particles remains, on the other hand, comparatively unexplored. We develop an algorithm to detect collisions between ellipses constrained to the two-dimensional surface of a sphere based on a solution of an eigenvalue problem. We investigate and discuss topologically distinct ways two ellipses may touch or intersect on a sphere, and define a contact function that can be used for construction of short- and long-range pair potentials.