bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated transcriptomics and metabolomics analyses reveal the molecular mechanisms of red-light on carotenoids biosynthesis in tomato fruit
Authors: Tang Jun , Li Yan , Liu Zhongliang , Wei Min , Shi Qinghua , Yang Fengjuan 
Published: February 2022

Abstract
Carotenoids are the main pigments responsible for the coloration and account for the major antioxidant activity of tomato (Solanum lycopersicum L.) fruit. Significant increments in total carotenoids and lycopene levels were observed in tomato fruit illuminated by red light relative to white light in previous studies, but the mechanism of carotenoid biosynthesis regulated by red light is still unclear. In the present study, the influence of red light on carotenoid biosynthesis in postharvest tomato fruit was conducted using targeted metabolomics and transcriptomic methods. A total of 25 differentially accumulated carotenoids and 1939 differentially expressed genes were isolated and identified. The results illustrated that the contents of phytoene and lycopene were considerably higher in fruit treated with red light than those with white light at 12 h. These differentially expressed genes are mainly enriched in plant hormone signal transduction, photosynthesis, secondary metabolite biosynthesis, and plant circadian rhythm. Moreover, from the results of coexpression network analysis, 15 transcription factors from red light-treated fruit were screened; among these, transcription factors of SlERF4, SlbHLH93 and SlIAA29, which are involved in signal transduction of light and hormones, respectively, may also play important roles in carotenoid biosynthesis regulated by red light in tomato fruit. It is concluded that red light enhanced carotenoid biosynthesis in postharvest tomato fruit and the mechanisms of enhanced carotenoid biosynthesis were not only associated with the direct regulation by red light signalling, but also with the indirect regulation by hormonal signalling.
A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome
Authors: Pootakham Wirulda , Sonthirod Chutima , Naktang Chaiwat , Kongkachana Wasitthee , U-thoomporn Sonicha , Phetchawang Phakamas , Maknual Chatree , Jiumjamrassil Darunee , Pravinvongvuthi Tamanai , Tangphatsornruang Sithichoke 
Published: February 2022

Abstract
Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves’ unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.
Optimism, Daily Stressors, and Emotional Well-Being Over Two Decades in a Cohort of Aging Men
Authors: Lee Lewina O , Grodstein Francine , Trudel-Fitzgerald Claudia , James Peter , Okuzono Sakurako S , Koga Hayami K , Schwartz Joel , Spiro Avron , Mroczek Daniel K , Kubzansky Laura D 
Published: February 2022

Abstract

Objectives
Growing evidence supports optimism as a health asset, yet how optimism influences well-being and health remains uncertain. We evaluated 1 potential pathway—the association of optimism with daily stress processes—and tested 2 hypotheses. The stressor exposure hypothesis posits that optimism would preserve emotional well-being by limiting exposure to daily stressors. The buffering hypothesis posits that higher optimism would be associated with lower emotional reactivity to daily stressors and more effective emotional recovery from them.

Methods
Participants were 233 men from the Veterans Affairs Normative Aging Study who completed the Minnesota Multiphasic Personality Inventory-2 Revised Optimism–Pessimism scale in 1986/1991 and participated in up to three 8-day daily diary bursts in 2002–2010 (age at first burst: M = 76.7, SD = 6.5). Daily stressor occurrence, positive affect (PA), and negative affect (NA) were assessed nightly. We evaluated the hypotheses using multilevel structural equation models.

Results
Optimism was unrelated to emotional reactivity to or recovery from daily stressors. Higher optimism was associated with higher average daily PA (B = 2.31, 95% Bayesian credible interval [BCI]: 1.24, 3.38) but not NA, independent of stressor exposure. Lower stressor exposure mediated the association of higher optimism with lower daily NA (indirect effect: B = −0.27, 95% BCI: −0.50, −0.09), supporting the stressor exposure hypothesis.

Discussion
Findings from a sample of older men suggest that optimism may be associated with more favorable emotional well-being in later life through differences in stressor exposure rather than emotional stress response. Optimism may preserve emotional well-being among older adults by engaging emotion regulation strategies that occur relatively early in the emotion-generative process.
Long-term outcomes of transaxillary versus video-assisted first rib resection for neurogenic thoracic outlet syndrome
Authors: Nuutinen Henrik , Kärkkäinen Jussi M , Kimmo Mäkinen , Voitto Aittola , Teemu Riekkinen , Petri Saari , Janne Pesonen 
Published: February 2022

Abstract

OBJECTIVES
This study compared the long-term outcomes in terms of clinical examinations and patient-reported outcome measures, between transaxillary and video-assisted thoracoscopic techniques for first rib resection in patients with neurogenic thoracic outlet syndrome.

METHODS
The study population comprised patients who underwent first rib resection for neurogenic thoracic outlet syndrome at our institution between 2009 and 2016. All patients were recruited in a follow-up assessment in 2019, and those who agreed to participate were included in this study. Outcomes included examinations at the outpatient clinic and patient-reported outcome measures: Disabilities of Arm Shoulder and Hand Score and Cervical Brachial Symptom Questionnaire. The completeness of the rib resection was assessed on chest X-rays.

RESULTS
:A total of 60 first rib resections (30 transaxillary + 30 video-assisted fully thoracoscopic approaches) were performed for neurogenic thoracic outlet syndrome in 47 patients between 2009 and 2016. Of these, 32 patients participated in the study including 18 who had transaxillary and 22 who had video-assisted thoracoscopic procedures. The mean follow-up was 5.9 (standard deviation: 2.2) years. The outcome was good or excellent after 15 (83.3%) and 17 (77.3%) procedures in the transaxillary and video-assisted thoracoscopic surgery groups, respectively (P = 0.709). There were no differences in patient-reported outcome measures between the 2 groups. Furthermore, the length of the residual first rib stump was similar in both groups.

CONCLUSIONS
We found no differences in the long-term outcomes between the study groups. These results indicate that both transaxillary and purely thoracoscopic approaches offer favourable long-term outcomes following first rib resection in patients with neurogenic thoracic outlet syndrome.
Numerical solution of anH(curl)-elliptic hemivariational inequality
Authors: Han Weimin , Ling Min , Wang Fei 
Published: February 2022

AbstractThis paper is concerned with the analysis and numerical solution of an $\boldsymbol {H}({\textbf {curl}})$-elliptic hemivariational inequality (HVI). One source of the HVI is through a temporal semidiscretization of a related hyperbolic Maxwell equation problem. An equivalent minimization principle is introduced, and the solution existence and uniqueness of the $\boldsymbol {H}({\textbf {curl}})$-elliptic HVI are proved. Numerical analysis of the HVI is provided with a general Galerkin approximation, including a Céa’s inequality for convergence and error estimation. When the linear edge finite element method is employed, an optimal-order error estimate is derived under a suitable solution regularity assumption. A fully discrete scheme based on the backward Euler difference in time and a mixed finite element method in space is also analyzed, and stability estimates are derived for first-order terms of the fully discrete solution. Numerical results are reported on linear edge finite element solutions of the $\boldsymbol {H}({\textbf {curl}})$-elliptic HVI for numerical evidence of the theoretically predicted convergence order.
Autophagy-independent cytoprotection by optineurin from toxicity of aggregates formed by mutant huntingtin and mutant ataxin-3
Authors: Moharir Shivranjani C , Raghawan Akhouri Kishore , Ramaswamy Rajashree , Swarup Ghanshyam 
Published: February 2022

Abstract
An important feature of several neurodegenerative diseases is the formation of pathological structures containing aggregated proteins. The autophagy receptor optineurin/OPTN is frequently observed in these structures. The role played by optineurin in these aggregates is not clear. In this study, we explored whether optineurin has a cytoprotective role in the cells having mutant protein aggregates. We overexpressed mutant huntingtin having 97 glutamine repeats (mHtt) and mutant ataxin-3 having 130 glutamine repeats (mAtax-3) in wild-type and optineurin-deficient neuronal (N2A) and non-neuronal cells (Optn−/− mouse embryonic fibroblasts) and determined the percentage of dead cells with mutant protein aggregates. Optineurin-deficient cells having mHtt or mAtax-3 aggregates showed higher cell death as compared to wild-type cells having mutant protein aggregates. Confocal microscopy revealed that optineurin formed a shell around mHtt and mAtax-3 aggregates through its C-terminal domain. The C-terminal domain of optineurin, which lacks LC3-interacting region required for autophagy, was necessary and sufficient to reduce cytotoxicity of mHtt and mAtax-3 aggregates. Our results show that in the absence of optineurin, mutant protein aggregates are highly toxic, revealing an autophagy-independent cytoprotective function of optineurin, which is mediated by its C-terminal domain.
Burn Outcomes at Extremes of Body Mass Index: Underweight Is as Problematic as Morbid Obesity
Authors: Tolley Philip D , McClellan John M , Butler Demsie , Stewart Barclay T , Pham Tam N , Sheckter Clifford C 
Published: February 2022

Abstract
Limited evidence suggests that obesity adversely affects burn outcomes. However, the impacts of body mass index (BMI) across the continuum have not been fully characterized. Therefore, we aimed to characterize outcomes after burn injury across the BMI continuum. We hypothesized that “normal” BMI (18.5–24.9) would have the lowest mortality and complication rates. The US National Trauma Data Bank (NTDB) was queried for adult burn-injured patients from 2007 to 2015. Admission BMI was calculated and grouped according to World Health Organization (WHO) classification. The primary outcome was in-hospital mortality. Secondary outcomes of time to wound closure, length of stay, and inpatient complications were similarly assessed. Of the 116,008 burn patient encounters that were identified, 7243 underwent at least one operation for wound closure. Mortality was lowest in the overweight (P = .039) and obese I cohorts (BMI 25–29.9, 30.0–34.9) at 2.9% and increased in both directions of the BMI continuum to 4.1% in the underweight (P = .032) and 5.1% in the morbidly obese (class III) group (P = .042). Time to final wound closure was longest in the two BMI extremes. BMI ≥40 was associated with increased intensive care unit days, ventilator days, renal and cardiac complications. BMI &lt;18.5 had increased hospital days and rates of sepsis. Aberrations in metabolism associated with both increases and decreases of body weight may cause pathophysiologic changes that lead to worsened outcomes in burn-injured patients. In addition to morbidly obese patients, underweight patients also experience increased burn-related death and complications. In contrast, overweight BMI patients may have greater physiologic reserves without the burden of obesity or sarcopenia.
Innovative Care for Inflammatory Bowel Disease Patients during the COVID-19 Pandemic: Use of Bedside Intestinal Ultrasound to Optimize Management
Authors: Lu Cathy , Ma Christopher , Ingram Richard J M , Chan Melissa , Kheirkhahrahimabadi Hengameh , Martin Marie-Louise , Seow Cynthia H , Kaplan Gilaad G , Heatherington Joan , Devlin Shane M , Panaccione Remo , Novak Kerri L 
Published: February 2022

Abstract

Background
The COVID-19 pandemic caused by SARS-CoV-2 has reduced access to endoscopy and imaging. Safe alternatives, available at the bedside, are needed for accurate, non-invasive strategies to evaluate disease activity. The aim of this study is to establish the impact of clinic-based bedside intestinal ultrasound (IUS) on decision making, reduction in reliance on endoscopy and short-term healthcare utilization.

Methods
We conducted a prospective observational evaluation during the COVID-19 pandemic, of the impact of a regional comprehensive care pathway to manage IBD patients consecutively recruited with acute symptoms, or suspected new diagnosis of IBD. Clinic-based access to sigmoidoscopy and bedside intestinal ultrasound were evaluated, used to direct clinical care and avoid hospitalization or hospital-based endoscopy.

Results
A total of 72 patients were seen between March 15 and June 30, 2020. Of these, 57% (41/72) were female, 64% had Crohn’s disease (46/72) with 14% (10/72) presenting with symptoms requiring investigation, of which 5 new cases of IBD were identified (50%). Immediate access to ultrasound and sigmoidoscopy led to meaningful changes in management in 80.5% (58/72) of patients. Active inflammation was detected by IUS alone (72.5%, 29/40) or in combination with in-clinic sigmoidoscopy (78%, 18/23) or sigmoidoscopy alone (78% 7/9). Six patients were referred to colorectal surgery for urgent surgical intervention including two patients admitted directly.

Conclusion
Implementation of IUS as part of a clinical care pathway during the COVID-19 pandemic is a useful strategy to enhance care delivery and improve clinical decisions, while sparing other important acute care resources.
Generative design for additive manufacturing using a biological development analogy
Authors: Price Mark , Zhang Wei , Friel Imelda , Robinson Trevor , McConnell Roisin , Nolan Declan , Kilpatrick Peter , Barbhuiya Sakil , Kyle Stephen 
Published: February 2022

Abstract
The transformation in manufacturing capability being driven by new processes, such as additive manufacturing, offers huge potential for product innovation and opportunity to create bespoke designs tailored to individual specifications or needs. However, current design systems and tools are not yet capable of fully capitalizing on these new technologies and new approaches are needed. Many current methodologies are top-down and sequential, offering limited flexibility and an overly constrained design space. Post-processing is needed to ensure that a design can be manufactured. This work presents a novel bottom-up methodology to generate designs that can be tightly integrated with the additive manufacturing environment and that can respond flexibly to changes in that environment. Focusing on overhang as an exemplar manufacturing constraint, the method engenders changes in the design either by locally adjusting the geometry to stay within limits or by adding an appropriate support structure. The method is bio-inspired, based on strategies observed in natural systems, particularly in biological growth and development. The design geometry is grown in a computer-aided design-based, bio-inspired generative design system called ‘Biohaviour’. This process is similar to plant growth, and the design’s final configuration, shape, and size are informed by both the manufacturing capability and internal design stresses. The approach is demonstrated for overhang limit and build orientation and is extensible to any general situation.
The Private and External Costs of Germany’s Nuclear Phase-Out
Authors: Jarvis Stephen , Deschenes Olivier , Jha Akshaya 
Published: February 2022

Abstract
Many countries have phased out nuclear power in response to concerns about nuclear waste and the risk of nuclear accidents. This paper examines the shutdown of more than half of the nuclear production capacity in Germany after the Fukushima accident in 2011. We use hourly data on power plant operations and a machine learning approach to estimate the impacts of the phase-out policy. We find that reductions in nuclear electricity production were offset primarily by increases in coal-fired production and net electricity imports. Our estimates of the social cost of the phase-out range from €3 to €8 billion per year. The majority of this cost comes from the increased mortality risk associated with exposure to the local air pollution emitted when burning fossil fuels. Policymakers would have to significantly overestimate the risk or cost of a nuclear accident to conclude that the benefits of the phase-out exceed its social costs. We discuss the likely role of behavioral biases in this setting, and highlight the importance of ensuring that policymakers and the public are informed about the health effects of local air pollution.
Hospital Readmissions Among Infants Diagnosed With Early-Onset Neonatal Sepsis in Connecticut
Authors: Hudon Rebecca E , Leung Vivian H , Petit Susan , Banach David B 
Published: February 2022

Abstract

Background
Early-onset neonatal sepsis, defined as sepsis within 72 hours of birth, results in significant infant morbidity and mortality. Readmissions associated with neonatal sepsis have not previously been well described. Early-onset neonatal sepsis is a mandatory reportable condition in Connecticut, allowing for expanded data collection through public health surveillance to evaluate readmissions.

Methods
Infants with early-onset neonatal sepsis born in Connecticut during 2007-2016 were identified from statewide surveillance data and matched with a statewide hospital discharge database. We describe readmission rates, causes and timing of readmissions, and demographic and clinical factors associated with readmission among this group.

Results
Among 241 infants with early-onset neonatal sepsis matched to discharge data, 203 (84.2%) infants survived their initial hospitalization at birth. During the first year of life, 47 (23.2%) infants were readmitted, most often in the first 3 months after birth (n = 29, 42.6%). The most frequent reasons for readmissions were pulmonary complications (19%), infections (17%), and gastrointestinal illness (13%). Infants with initial hospitalizations lasting longer than 30 days after birth were associated with higher rates of readmission compared with those discharged within 30 days after birth (35% vs 19%, P = .02).

Conclusions
A substantial proportion of infants diagnosed with early-onset neonatal sepsis are readmitted within the first year of life. Those with prolonged hospitalizations after birth are at the highest risk. Further efforts and intensified strategies are needed to prevent readmissions among this vulnerable patient population.
Parameterized complexity of dynamic belief updates: A complete map
Authors: Bolander Thomas , Lequen Arnaud 
Published: February 2022

Abstract
Dynamic Belief Update is a model checking problem in Dynamic Epistemic Logic concerning the effect of applying a number of epistemic actions on an initial epistemic model. It can also be considered as a plan verification problem in epistemic planning. The problem is known to be PSPACE-hard. To better understand the source of complexity of the problem, previous research has investigated the complexity of 128 parameterized versions of the problem with parameters such as number of agents and size of epistemic actions. The complexity of many parameter combinations has been determined, but previous research left 14 parameter combinations open. In this paper, we solve all of these open problems. Most of the parameter combinations turns out to be fixed-parameter intractable, except for 3 that are fixed-parameter tractable.
In Vitro Evolution Reveals Noncationic Protein–RNA Interaction Mediated by Metal Ions
Authors: Giacobelli Valerio G , Fujishima Kosuke , Lepšík Martin , Tretyachenko Vyacheslav , Kadavá Tereza , Makarov Mikhail , Bednárová Lucie , Novák Petr , Hlouchová Klára 
Published: February 2022

AbstractRNA–peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA–protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 1010 library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein–RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.