bluuebunny/crossref_metadata_2025 huggingface dataset:
Local signaling enhances output specificity of bacterial c-di-GMP signaling networks
Authors: Junkermeier Eike H , Hengge Regine
Published: May 2023

For many years the surprising multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins has intrigued researchers studying bacterial second messengers. How can several signaling pathways act in parallel to produce specific outputs despite relying on the same diffusible second messenger maintained at a certain global cellular concentration? Such high specificity and flexibility arise from combining modes of local and global c-di-GMP signaling in complex signaling networks. Local c-di-GMP signaling can be experimentally shown by three criteria being met: (i) highly specific knockout phenotypes for particular c-di-GMP-related enzymes, (ii) actual cellular c-di-GMP levels that remain unchanged by such mutations and/or below the Kd’s of the relevant c-di-GMP-binding effectors, and (iii) direct interactions between the signaling proteins involved. Here, we discuss the rationale behind these criteria and present well-studied examples of local c-di-GMP signaling in Escherichia coli and Pseudomonas. Relatively simple systems just colocalize a local source and/or a local sink for c-di-GMP, i.e. a diguanylate cyclase (DGC) and/or a specific phosphodiesterase (PDE), respectively, with a c-di-GMP-binding effector/target system. More complex systems also make use of regulatory protein interactions, e.g. when a “trigger PDE” responds to locally provided c-di-GMP, and thereby serves as a c-di-GMP-sensing effector that directly controls a target’s activity, or when a c-di-GMP-binding effector recruits and directly activates its own “private” DGC. Finally, we provide an outlook into how cells can combine local and global signaling modes of c-di-GMP and possibly integrate those into other signaling nucleotides networks.
MHC Architecture in Amphibians—Ancestral Reconstruction, Gene Rearrangements, and Duplication Patterns
Authors: He Ke , Babik Wiesław , Majda Mateusz , Minias Piotr
Published: May 2023

The hypervariable major histocompatibility complex (MHC) is a crucial component of vertebrate adaptive immunity, but large-scale studies on MHC macroevolution in nonmodel vertebrates have long been constrained by methodological limitations. Here, we used rapidly accumulating genomic data to reconstruct macroevolution of the MHC region in amphibians. We retrieved contigs containing the MHC region from genome assemblies of 32 amphibian species and examined major structural rearrangements, duplication patterns, and gene structure across the amphibian phylogeny. Based on the few available caecilian and urodele genomes, we showed that the structure of ancestral MHC region in amphibians was probably relatively simple and compact, with a close physical linkage between MHC-I and MHC-II regions. This ancestral MHC architecture was generally conserved in anurans, although the evolution of class I subregion proceeded toward more extensive duplication and rapid expansion of gene copy number, providing evidence for dynamic evolutionary trajectories. Although, in anurans, we recorded tandems of duplicated MHC-I genes outside the core subregion, our phylogenetic analyses of MHC-I sequences provided little support for an expansion of nonclassical MHC-Ib genes across amphibian families. Finally, we found that intronic regions of amphibian classical MHC genes were much longer when compared with other tetrapod lineages (birds and mammals), which could partly be driven by the expansion of genome size. Our study reveals novel evolutionary patterns of the MHC region in amphibians and provides a comprehensive framework for further studies on the MHC macroevolution across vertebrates.
Human Gene Age Dating Reveals an Early and Rapid Evolutionary Construction of the Adaptive Immune System
Authors: Zhang Li , Park Jonathan J , Dong Matthew B , Arsala Deanna , Xia Shengqian , Chen Jianhai , Sosa Dylan , Atlas Jared E , Long Manyuan , Chen Sidi
Published: May 2023

T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T cell adaptive immunity (TCAI). However, the evolution of the genes and nucleotide sequences involved in TCAI is not well understood. To investigate this, we performed comparative studies of gene annotations and genome assemblies of 28 vertebrate species and identified sets of human genes that are involved in TCAI, carcinogenesis, and aging. We found that these gene sets share interaction pathways, which may have contributed to the evolution of longevity in the vertebrate lineage leading to humans. Our human gene age dating analyses revealed that there was rapid origination of genes with TCAI-related functions prior to the Cretaceous eutherian radiation and these new genes mainly encode negative regulators. We identified no new TCAI-related genes after the divergence of placental mammals, but we did detect an extensive number of amino acid substitutions under strong positive selection in recently evolved human immunity genes suggesting they are coevolving with adaptive immunity. More specifically, we observed that antigen processing and presentation and checkpoint genes are significantly enriched among new genes evolving under positive selection. These observations reveal evolutionary processes of TCAI that were associated with rapid gene duplication in the early stages of vertebrates and subsequent sequence changes in TCAI-related genes. The analysis of vertebrate genomes provides evidence that a "big bang" of adaptive immune genes occurred 300-500 million years ago. These processes together suggest an early genetic construction of the vertebrate immune system and subsequent molecular adaptation to diverse antigens.
Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries
Authors: Laughery Marian F , Plummer Dalton A , Wilson Hannah E , Vandenberg Brittany N , Mitchell Debra , Mieczkowski Piotr A , Roberts Steven A , Wyrick John J
Published: May 2023

Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine–adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair–deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.
Detecting directional and non-directional epistasis in bi-parental populations using genomic data
Authors: Rio Simon , Charcosset Alain , Moreau Laurence , Mary-Huard Tristan
Published: May 2023

Epistasis, commonly defined as interaction effects between alleles of different loci, is an important genetic component of the variation of phenotypic traits in natural and breeding populations. In addition to its impact on variance, epistasis can also affect the expected performance of a population and is then referred to as directional epistasis. Before the advent of genomic data, the existence of epistasis (both directional and non-directional) was investigated based on complex and expensive mating schemes involving several generations evaluated for a trait of interest. In this study, we propose a methodology to detect the presence of epistasis based on simple inbred biparental populations, both genotyped and phenotyped, ideally along with their parents. Thanks to genomic data, parental proportions as well as shared parental proportions between inbred individuals can be estimated. They allow the evaluation of epistasis through a test of the expected performance for directional epistasis or the variance of genetic values. This methodology was applied to two large multiparental populations, i.e. the American maize and soybean nested association mapping populations, evaluated for different traits. Results showed significant epistasis, especially for the test of directional epistasis, e.g. the increase in anthesis to silking interval observed in most maize inbred progenies or the decrease in grain yield observed in several soybean inbred progenies. In general, the effects detected suggested that shuffling allelic associations of both elite parents had a detrimental effect on the performance of their progeny. This methodology is implemented in the EpiTest R-package and can be applied to any bi/multiparental inbred population evaluated for a trait of interest.
Frailty, an Independent Risk Factor in Progression Trajectory of Cardiometabolic Multimorbidity: A Prospective Study of UK Biobank
Authors: Ma Tianqi , He Lingfang , Luo Yi , Fu Dihan , Huang Jiaqi , Zhang Guogang , Cheng Xunjie , Bai Yongping
Published: May 2023

Background

Although frailty was associated with cardiometabolic diseases (CMDs, including coronary heart disease, stroke, and diabetes here), there was no systematic analyses estimating its role in incidence, progression, and prognosis of cardiometabolic multimorbidity (CMM).

Methods

We included 351 205 participants without CMDs at baseline in UK Biobank. Occurrences of first CMD, CMM, and death were recorded. We used multistate models to assess transition-specific role of baseline frailty measured by frailty phenotype and frailty index in CMM progression trajectory from no disease to single CMD, CMM, and death. Association between changes in frailty and outcomes was investigated among 17 264 participants.

Results

Among 351 205 participants (44.0% male, mean age 56.55 years), 8 190 (2.3%) had frail phenotype, and 13 615 (3.9%) were moderate/severe frail according to the frailty index. During median follow-up of 13.11 years, 41 558 participants experienced ≥1 CMD, 4 952 had CMM, and 20 670 died. In multistate models, frail phenotype-related hazard ratios were 1.94 and 2.69 for transitions from no CMD to single disease and death, 1.63 and 1.67 for transitions from single CMD to CMM and death, and 1.57 for transitions from CMM to death (all p < .001). Consistent results were observed for frailty index. Improvement of frailty reduced the risk of CMD progression and death.

Conclusions

Frailty is an independent risk factor for all transitions of CMM progression trajectory. Frailty-targeted management is a potential strategy for primary and secondary prevention of CMM beyond chronological age.
A multi-omics approach identifies bHLH71-like as a positive regulator of yellowing leaf pepper mutants exposed to high-intensity light
Authors: Liu Zhoubin , Mao Lianzhen , Yang Bozhi , Cui Qingzhi , Dai Yunhua , Li Xueqiao , Chen Yisong , Dai Xiongze , Zou Xuexiao , Ou Lijun , Yang Sha
Published: May 2023

Light quality and intensity can have a significant impact on plant health and crop productivity. Chlorophylls and carotenoids are classes of plant pigments that are responsible for harvesting light energy and protecting plants from the damaging effects of intense light. Our understanding of the role played by plant pigments in light sensitivity has been aided by light-sensitive mutants that change colors upon exposure to light of variable intensity. In this study, we conducted transcriptomic, metabolomic, and hormone analyses on a novel yellowing mutant of pepper (yl1) to shed light on the molecular mechanism that regulates the transition from green to yellow leaves in this mutant upon exposure to high-intensity light. Our results revealed greater accumulation of the carotenoid precursor phytoene and the carotenoids phytofluene, antheraxanthin, and zeaxanthin in yl1 compared with wild-type plants under high light intensity. A transcriptomic analysis confirmed that enzymes involved in zeaxanthin and antheraxanthin biosynthesis were upregulated in yl1 upon exposure to high-intensity light. We also identified a single basic helix–loop–helix (bHLH) transcription factor, bHLH71-like, that was differentially expressed and positively correlated with light intensity in yl1. Silencing of bHLH71-like in pepper plants suppressed the yellowing phenotype and led to reduced accumulation of zeaxanthin and antheraxanthin. We propose that the yellow phenotype of yl1 induced by high light intensity could be caused by an increase in yellow carotenoid pigments, concurrent with a decrease in chlorophyll accumulation. Our results also suggest that bHLH71-like functions as a positive regulator of carotenoid biosynthesis in pepper.
Evidence for an effective defence against ocean acidification in the key bioindicator pteropod Limacina helicina
Authors: Miller M R , Oakes R L , Covert P A , Ianson D , Dower J F
Published: May 2023

The pteropod Limacina helicina has become an important bioindicator species for the negative impacts of ocean acidification (OA) on marine ecosystems. However, pteropods diversified during earlier high CO2 periods in Earth history and currently inhabit regions that are naturally corrosive to their shells, suggesting that they possess mechanisms to survive unfavourable conditions. Recent work, which is still under considerable debate, has proposed that the periostracum, a thin organic coating on the outer shell, protects pteropods from shell dissolution. Here, we provide direct evidence that shows that damage to the L. helicina periostracum results in dissolution of the underlying shell when exposed to corrosive water for ∼8 d, while an intact periostracum protects the shell from dissolution under the same conditions. This important first line of defence suggests that pteropods are more resistant to OA-induced shell dissolution than is generally accepted.
A systematic review and physiology of pulmonary artery pulsatility index in left ventricular assist device therapy
Authors: Yim Ivan H W , Khan-Kheil Ayisha M , Drury Nigel E , Lim Hoong Sern
Published: May 2023

OBJECTIVES

Right heart failure (RHF) is a major complication following left ventricular assist device (LVAD) implantation. Pulmonary artery pulsatility index (PAPi) has been evaluated as a haemodynamic marker for RHF, but PAPi is dependent on pulmonary vascular resistance (PVR). We conducted a systematic review to assess the relationship between PAPi and RHF and death in patients undergoing LVAD implantation and examined the relationship between PAPi cut-off and PVR.

METHODS

We searched PubMed, EMBASE, CENTRAL and manually screened retrieved references to identify all clinical studies reporting PAPi in adult patients with a durable LVAD. Eligibility criteria were prespecified and 2 reviewers independently screened and extracted data; the Newcastle–Ottawa Scale was used to assess quality of non-randomized studies. This study was prospectively registered on PROSPERO (CRD42021259009).

RESULTS

From 283 unique records, we identified 16 studies reporting haemodynamic assessment in 20 634 adult patients with an implanted durable LVAD. Only 2 studies reported on mortality and in both, a lower PAPi was significantly associated with death. Fifteen studies reported RHF data and, in 10 studies, a lower PAPi was significantly associated with RHF. Six studies reported on PAPi cut-offs ranging from 0.88 to 3.3; and the cut-offs were directly related to PVR (r = 0.6613, P = 0.019).

CONCLUSIONS

Lower PAPi was associated with RHF and death following LVAD implantation, but a single PAPi cut-off cannot be defined, as it is dependent on PVR.
The effects of dietary essential fatty acid ratios and energy level on growth performance, lipid metabolism, and inflammation in grow-finish pigs
Authors: Becker Spenser L , Humphrey Dalton C , Karriker Locke A , Brown Justin T , Skoland Kristin J , Greiner Laura L
Published: May 2023

The objective of this study was to investigate the effects of dietary metabolizable energy (ME) level and the ratio of linoleic acid:α-linolenic acid (LA:ALA) on the growth performance, lipid metabolism, circulatory and joint inflammatory status, and synovial fluid proteome of grow-finish pigs. A total of 224 pigs (BW = 41.5 ± 6.1 kg; PIC Genus 337 × 1050, Hendersonville, TN) were randomly assigned to either a high (3.55 Mcal/kg; HE) or low (3.29 Mcal/kg; LE) ME dietary treatment with a high (23:1) or low (12:1) LA:ALA in a 2 × 2 factorial arrangement. Diets were fed across three 28-d phases. Pigs were housed either four barrows or four gilts per pen. Blood samples were collected on days 0, 21, 42, and 84. Synovial fluid was collected from the hock and carpus joints on days 0 and 84. Liver and adipose tissue samples were collected on day 84. Data were analyzed as repeated measures using PROC MIXED (SAS 9.4) with pen as the experimental unit and energy level, essential fatty acid ratio, sex, phase, and their interactions as fixed effects. Compared to LE, HE increased days 28, 56, and 84 body weight (BW; P = 0.005). For the overall period, HE increased average daily gain (ADG) compared to LE (P < 0.001) and improved feed efficiency (P = 0.001), while LE increased feed intake compared to HE (P < 0.001). Gilts receiving diets with low LA:ALA had similar final BW to barrows receiving a low LA:ALA at days 28, 56, and 84 (P = 0.024), resulting from improved overall days 0–84 ADG compared to gilts receiving the high LA:ALA (P = 0.031). In the liver, HE decreased the mRNA abundance of acetyl CoA carboxylase (ACACA; P = 0.004), cluster of differentiation 36 (P = 0.034), and tended to decrease fatty acid synthase (FASN; P = 0.056). In adipose tissue, HE decreased ACACA (P = 0.001) and FASN (P = 0.017). Plasma inflammatory markers C-reactive protein (CRP) and tumor necrosis factor-α (TNFα) were reduced on day 84 compared to day 0 (P ≤ 0.014). In the hock and carpus synovial fluid, LE tended to reduce CRP and TNFα (P ≤ 0.096). Hock and carpus synovial fluid CRP were also reduced on day 84 compared to day 0 (P = 0.001). Age of the pig impacted serum and hock synovial fluid protein abundance, but not energy level, LA:ALA, or their interactions (P < 0.05). To conclude, the high and low LA:ALA ratios utilized in this study can be fed at varying energy levels without impacting growth. Additionally, LA:ALA ratios can differentially impact the growth of barrows and gilts.
The Impact-based Regulatory Strategy in Environmental Law: Hallmark of Effectiveness or Pitfall for Legitimacy?
Authors: Soininen Niko , Romppanen Seita , Nieminen Mika , Soimakallio Sampo
Published: May 2023

EU environmental law increasingly adopts an impact-based regulatory strategy that places biophysical sciences in a significant role not only in designing regulation but also in interpreting and implementing the law. While crucial for the effectiveness of environmental law, such a regulatory strategy creates challenges for the legitimacy of EU environmental law. This article traces the shift from a behaviour-based to impact-based regulation in this context and analyses the latter in light of Lon L. Fuller’s eight classic criteria for the rule of law to expose the legitimacy challenges. Focusing on the EU Water Framework Directive and the Land-use Change and Forestry Regulation, this study shows that EU environmental law suffers from serious shortcomings in securing legal legitimacy and concludes by highlighting how this may be improved going forward.
Interaction behavior for multiple embedded cracks subjected to bending load in creep regimes
Authors: Gao Zhifang , Zhao Lei
Published: May 2023

Multiple cracks growing from pre-existing defects during the manufacturing/installation process or from small cracks initiated are primary concerns in evaluating the structural integrity. In this study, the interaction behavior for coplanar multiple embedded cracks subjected to bending load in creep regimes was studied using numerical simulation approach. Influences of crack configurations (crack shape, crack depth, and crack distance) and creep properties on creep interaction factor and C* distribution along the embedded cracks were evaluated based on the three-dimensional finite element solutions. Due to the interaction among the multiple cracks, the C* distribution was asymmetric along the crack front and the C* values were pronounced as the cracks approached each other. Moreover, crack depth, crack distance, and creep exponent significantly affected the creep interaction factor and crack shape had limited influence. However, the maximum creep interaction factor did not coincide with the maximum C* values occurring along the crack front. The creep interaction factor determined by the average C* values along the crack front was employed to represent the intensity effect of multiple embedded cracks on the crack growth behavior. Finally, an empirical relation was proposed for estimating crack creep interaction factors of embedded cracks.
Modelling the variable emission states of γ-ray-emitting narrow-line Seyfert 1 galaxies
Authors: Luashvili Anna , Boisson Catherine , Zech Andreas , Arrieta-Lobo Maialen , Kynoch Daniel
Published: May 2023

γ-ray-emitting narrow-line Seyfert 1 galaxies (γ-NLS1) constitute an intriguing small population of active galactic nuclei with γ-ray emission resembling low-power flat-spectrum radio quasars (FSRQ), but with differing physical properties. They are jetted, γ/radio-loud Seyfert galaxies, with relatively low black hole masses, accreting at exceptionally high, near-Eddington rates. Certain of these sources exhibit highly variable emission states on relatively short time-scales, the physical origin of which remains elusive. In this work, varying emission states of two bona fide NLS1s, 1H 0323+342 and PMN J0948+0022, and one little-studied FSRQ/intermediate object, B2 0954+25A, are examined. For each source, we analysed quasi-simultaneous multiwavelength data for different states of γ-ray activity and present the results of their broad-band emission modelling, taking into account all available physical constraints to limit the range of the model parameters. Two different scenarios are discussed, in the framework of a one-zone leptonic model, where the high-energy emission is due to the inverse Compton scattering of the disc and broad line region (BLR) or torus photons by relativistic electrons within the jet. The transition from low to high state is well described by variations of the jet parameters, leaving the external photon fields unchanged. The parameterization favours an emission scenario with particle injection on a stationary shock inside the jet. When considering all physical constraints, the disc and BLR scenario is preferred for all three sources. We use the multi-epoch modelling to characterize total jet powers and discuss the intrinsic nature of γ-NLS1 galaxies and FSRQs.
The Physics of the Accelerating Universe Survey: narrow-band image photometry
Authors: Serrano S , Gaztañaga E , Castander F J , Eriksen M , Casas R , Navarro-Gironés D , Alarcon A , Bauer A , Cabayol L , Carretero J , Fernandez E , Neissner C , Renard P , Tallada-Crespí P , Tonello N , Sevilla-Noarbe I , Crocce M , García-Bellido J , Hildebrandt H , Hoekstra H , Joachimi B , Miquel R , Padilla C , Sánchez E , de Vicente J
Published: May 2023

PAUCam is an innovative optical narrow-band imager mounted at the William Herschel Telescope built for the Physics of the Accelerating Universe Survey (PAUS). Its set of 40 filters results in images that are complex to calibrate, with specific instrumental signatures that cannot be processed with traditional data reduction techniques. In this paper, we present two pipelines developed by the PAUS data management team with the objective of producing science-ready catalogues from the uncalibrated raw images. The Nightly pipeline takes care of entire image processing, with bespoke algorithms for photometric calibration and scatter-light correction. The Multi-Epoch and Multi-Band Analysis pipeline performs forced photometry over a reference catalogue to optimize the photometric redshift (photo-z) performance. We verify against spectroscopic observations that the current approach delivers an inter-band photometric calibration of 0.8 per cent across the 40 narrow-band set. The large volume of data produced every night and the rapid survey strategy feedback constraints require operating both pipelines in the Port d’Informació Cientifica data centre with intense parallelization. While alternative algorithms for further improvements in photo-z performance are under investigation, the image calibration and photometry presented in this work already enable state-of-the-art photo-z down to iAB = 23.0.
Suicidal ideation and attempts in brain tumor patients and survivors: A systematic review
Authors: Mofatteh Mohammad , Mashayekhi Mohammad Sadegh , Arfaie Saman , Chen Yimin , Malhotra Armaan K , Alvi Mohammed Ali , Sader Nicholas , Antonick Violet , Fatehi Hassanabad Mostafa , Mansouri Alireza , Das Sunit , Liao Xuxing , McIntyre Roger S , Del Maestro Rolando , Turecki Gustavo , Cohen-Gadol Aaron A , Zadeh Gelareh , Ashkan Keyoumars
Published: May 2023

Background

Subsequent to a diagnosis of a brain tumor, psychological distress has been associated with negative effects on mental health as well as suicidality. The magnitude of such impact has been understudied in the literature. We conducted a systematic review to examine the impact of a brain tumor on suicidality (both ideation and attempts).

Methods

In accordance with the PRISMA guidelines, we searched for relevant peer-reviewed journal articles on PubMed, Scopus, and Web of Science databases from inception to October 20, 2022. Studies investigating suicide ideation and/or attempt among patients with brain tumors were included.

Results

Our search yielded 1,998 articles which were screened for eligibility. Seven studies consisting of 204,260 patients were included in the final review. Four studies comprising 203,906 patients (99.8%) reported elevated suicidal ideation and suicide attempt incidence compared with the general population. Prevalence of ideation and attempts ranged from 6.0% to 21.5% and 0.03% to 3.33%, respectively. Anxiety, depression, pain severity, physical impairment, glioblastoma diagnosis, male sex, and older age emerged as the primary risk factors associated with increased risk of suicidal ideation and attempts.

Conclusion

Suicidal ideation and attempts are increased in patients and survivors of brain tumors compared to the general population. Early identification of patients exhibiting these behaviors is crucial for providing timely psychiatric support in neuro-oncological settings to mitigate potential harm. Future research is required to understand pharmacological, neurobiological, and psychiatric mechanisms that predispose brain tumor patients to suicidality.
Pacific Barrow’s Goldeneye refine migratory phenology in response to overwintering temperatures and annual snowmelt
Authors: Kemp Jesse , Boyd W Sean , Forstner Tesia M , Esler Daniel , Bowman Timothy D , Douglas David C , Hogan Danica , McAdie Malcolm , Thompson Jonathan E , Willie Megan , Green David J
Published: May 2023

Timing of seasonal bird migrations is broadly determined by internal biological clocks, which are synchronized by photoperiod, but individuals often refine their migratory timing decisions in response to external factors. Using 11 years of satellite telemetry data, we show that Pacific Barrow’s Goldeneye (Bucephala islandica) at higher latitudes initiated spring and molt migrations later and fall migration earlier than individuals at lower latitudes. We further show that individuals refined migratory timing in response to interannual variation in environmental conditions. Individual Barrow’s Goldeneye initiated spring migration earlier in years with warmer springs at their overwintering locations and concluded spring migration earlier in years with earlier annual snowmelt on their breeding grounds. Because individuals respond to conditions both where they initiate and where they conclude spring migration, our results suggest that Barrow’s Goldeneye update their migratory decisions en route. For all 3 migrations in their annual cycle, birds delayed initiating migration if they had been captured and tagged prior to that migration. Birds that initiated migration late for their latitude were less likely to include a stopover and completed that migration faster, partially compensating for delayed departures. Our results are consistent with the hypothesis that Barrow’s Goldeneye uses a combination of endogenous cues and environmental cues in migratory decision making. Sensitivity to environmental cues suggests that Barrow’s Goldeneye may have behavioral plasticity that is adaptive when faced with ongoing climate change.
Partial Melting under Shallow-Crustal Conditions: A Study of the Pleistocene Caldera Eruption of Mendeleev Volcano, Southern Kuril Island Arc
Authors: Kotov Alexey , Smirnov Sergey , Nizametdinov Ildar , Uno Masaoki , Tsuchiya Noriyoshi , Maksimovich Ivan
Published: May 2023

The southern part of the Kuril Island Arc is one of the world’s most active modern volcanic zones, with widespread felsic caldera volcanism, but it has been less well studied compared with other arcs. The Mendeleev caldera-forming eruption (40 ka) on Kunashir Island, southern Kurils, is one of the most explosive Pleistocene eruptions to have occurred in this region. This study aimed to establish the origin and storage conditions of magma preceding the Pleistocene caldera eruption of Mendeleev volcano. Mineralogical and melt inclusion analyses reveal that the primary melts had felsic compositions and that the early stage of magmatic evolution involved amphibole breakdown into a two-pyroxene, plagioclase, and Fe–Ti oxide assemblage under pressure–temperature conditions of 107–314 MPa and 807–932°C. The caldera-forming products are represented by dacitic pumice composed of plagioclase + augite + hypersthene+ quartz + Fe–Ti oxides and melt with uniform low-K rhyolite composition. Pre-eruptive magma was stored in a reservoir at 77–195 MPa (3.0–7.6 km depth) and 830–890°C under H2O-saturated conditions. The mechanism of magmatic evolution implies the following two-step scenario: (1) generation of magma by the partial melting of an amphibole-bearing substrate accompanied by the formation of early Mg-rich clino- and orthopyroxene, plagioclase, Fe–Ti oxides, and peritectic rhyolitic melt; and (2) crystallization of late plagioclase and quartz directly from these partial melts. Local or regional extension during the Pleistocene, accompanied by increasing heat flow in the supra-subduction mantle, generated an active mafic intrusion into the upper crust. This process was accompanied by abundant subaerial eruptions of basaltic volcanoes and could have caused intense heating and partial melting of upper-crustal rocks. Our results indicate that the partial melting of amphibole-bearing substrates in island arcs may serve as a universal mechanism for the generation of silicic magmas during powerful caldera eruptions in young island arcs.
Freeze! Financial Sanctions and Bank Responses
Authors: Efing Matthias , Goldbach Stefan , Nitsch Volker
Published: May 2023

Using regulatory data, we study German bank lending in countries targeted by financial sanctions. We find that domestic banks in Germany reduce lending in sanctioned countries, whereas their foreign bank affiliates outside Germany increase lending. In some cases, this is because the bank affiliates’ host countries have not imposed sanctions themselves. However, even German bank affiliates in host countries that enact sanctions like Germany increase lending if these host countries lack strong institutions and anticrime policies. These findings suggest that even universally adopted sanctions distort bank capital flows and competition if the level of their enforcement varies across bank locations.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online
Lipidomic and comparative transcriptomic analysis of fatty acid synthesis pathway in Carya illinoinensis embryo
Authors: Lyu Yun-Zhou , Jiang Hao , Sun Hai-Nan , Yang Yong , Chao Yang , Huang Li-Bin , Dong Xiao-Yun
Published: May 2023

Pecan (Carya illinoinensis (Wagenh.) K. Koch) is an important oilseed nut and is rich in fatty acids (FAs) and flavonols. Pecan FA has significantly edible, industrial and clinical value. To investigate the dynamic patterns and compositions of FA, and the molecular mechanism that controls FA accumulation in pecan, lipidomic and transcriptomic analyses were performed to determine lipid profiles and gene expression in pecan’s FA biosynthesis pathway. In the present study, compared with cultivars ‘Caddo’ and ‘Y-01’, ‘Mahan’ formed larger and heavier embryos and accumulated higher oil content. Lipidomic analysis showed that FA and (O-acyl)-1-hydroxy FA contents were higher in ‘Mahan’ at the mature stage. Based on full-length and comparative RNA-Seq, differential expression gene enrichment analysis revealed that many functional genes participated in the pathways of ‘fatty acid biosynthesis’, ‘fatty acid metabolism’ and ‘linoleic acid metabolism’. High FA accumulation model from ‘Mahan’ demonstrated that key enzyme-encoding genes played an important role in regulating FA biosynthesis. Co-expression module analysis indicated that several transcription factors (TFs; MYB, TCP, bHLH, Dof, ERF, NAC) were involved in FA accumulation by regulating the expression of functional genes, and real-time quantitative PCR verification proved that these TFs had a high correlation with the pecan FA accumulation pattern. These findings provided an insight into the molecular mechanism of FA accumulation in C. illinoinensis embryo, which contributes to pecan oil yielding and pecan molecular breeding.
Photobiomodulation for Major Depressive Disorder: Linking Transcranial Infrared Light, Biophotons and Oxidative Stress
Authors: Vieira Willians Fernando , Gersten Maia , Caldieraro Marco Antonio Knob , Cassano Paolo
Published: May 2023

Incompletely treated major depressive disorder (MDD) poses an enormous global health burden. Conventional treatment for MDD consists of pharmacotherapy and psychotherapy, though a significant number of patients do not achieve remission with such treatments. Transcranial photobiomodulation (t-PBM) is a promising novel therapy that uses extracranial light, especially in the near-infrared (NIR) and red spectra, for biological and therapeutic effects. The aims of this Review are to evaluate the current clinical and preclinical literature on t-PBM in MDD and to discuss candidate mechanisms for effects of t-PBM in MDD, with specific attention to biophotons and oxidative stress. A search on PubMed and ClinicalTrials.gov identified clinical and preclinical studies using t-PBM for the treatment of MDD as a primary focus. After a systematic screening, only 19 studies containing original data were included in this review (9 clinical and 10 preclinical trials). Study results demonstrate consensus that t-PBM is a safe and potentially effective treatment; however, varying treatment parameters among studies complicate definitive conclusions about efficacy. Among other mechanisms of action, t-PBM stimulates the complex IV of the mitochondrial respiratory chain and induces an increase in cellular energy metabolism. We suggest that future trials include biological measures to better understand the mechanisms of action of t-PBM and to optimize treatment efficiency. Of particular interest going forward will be studying potential effects of t-PBM—an external light source on the NIR spectra—on neural circuitry implicated in depression.
Clinical Factors Impacting Outcomes From Failed Trabeculectomy Leading to Glaucoma Drainage Device Implantation and Subsequent Penetrating Keratoplasty
Authors: Chen Jessica L. , Elhusseiny Abdelrahman M. , Khodeiry Mohamed M. , Smith Michael P. , Sayed Mohamed S. , Banitt Michael , Feuer William , Yoo Sonia H. , Lee Richard K.
Published: May 2023

Précis:

We evaluated the factors that impacted time from glaucoma drainage implant (GDI) surgery to penetrating keratoplasty (PK) in eyes with previously clear corneas (ie, GDI-first sequence), and that specifically underwent a trabeculectomy before GDI surgery for intraocular pressure (IOP) control.

Purpose:

To describe through an event-triggered data collection method the clinical course and the long-term outcomes of 2 procedures that are commonly performed sequentially in complex clinical situations: GDI surgery and PK. The study investigates the clinical factors associated with the progression to PK and determines the GDI success rate and graft survival.

Methods:

A single, tertiary-care center retrospective interventional cases series including patients with a sequential history of trabeculectomy, GDI surgery, and PK from 1999 to 2009. Outcome measures included IOP, visual acuity, graft failure, GDI failure, and time from GDI to PK.

Results:

Of the eyes, 56% had primary open angle glaucoma. The time from the last trabeculectomy to GDI was 66.5 ± 66.7 months. Of the eyes, 84% received a Baerveldt GDI. Time from GDI to PK was 36.4 ± 28.4 months. IOP at the time of PK was between 5 mm Hg and 21 mm Hg in 90% of eyes. At the last follow-up, 48% of grafts were clear. At 5 years post-PK, 33% of corneal grafts remained clear, whereas 81% of tubes remained functional.

Conclusions:

Nearly half of the corneal grafts are clear at the last long-term follow-up. Graft failure occurs at a higher rate than tube failure suggesting that IOP control is only one and possibly not the most important factor in graft survival in eyes with prior glaucoma surgery.
Genetic Diseases and Invasive Infections in Infants 100 Days or Younger
Authors: Zhu Tianwen , Bei Fei , He Ruoqi , Gong Xiaohui , Chen Yan , Yin Zhanghua , Wang Jian , Sun Yu , Zhang Yongjun
Published: May 2023

Background:

Understanding the association of genetic diseases with invasive infections in neonates or infants is important, given the clinical and public health implications of genetic diseases.

Methods:

We conducted a retrospective case-control study over a 5-year period to investigate the association between genetic diseases and invasive infections in neonates or infants. The case group included 56 patients with laboratory-confirmed invasive infections and a genetic etiology identified by exome sequencing. Another 155 patients without a genetic etiology were selected as controls from the same pool of patients.

Results:

An overview of genetic diseases that predispose patients to develop invasive infections were outlined. We identified 7 independent predictors for genetic conditions, including prenatal findings [adjusted odds ratio (aOR), 38.44; 95% confidence interval (CI): 3.94–374.92], neonatal intensive care unit admission (aOR, 46.87; 95% CI: 6.30–348.93), invasive ventilation (aOR, 6.66; 95% CI: 3.07–14.46), bacterial infections (aOR, 0.21; 95% CI: 0.06–0.69), fever (aOR, 0.15; 95% CI: 0.08–0.30), anemia (aOR, 6.64; 95% CI: 3.02–14.59) and neutrophilia (aOR, 0.98; 95% CI: 0.96–0.99). The area under the curve for the predictive model was 0.921 (95% CI: 0.876–0.954). We also found that a genetic etiology [hazard ratio (HR), 7.25; 95% CI: 1.71–30.81], neurological manifestations (HR, 3.56; 95% CI: 1.29–9.88) and septic shock (HR, 13.83; 95% CI: 3.18–60.10) were associated with severe outcomes.

Conclusions:

Our study established predictive variables and risk factors for an underlying genetic etiology and its mortality in neonates or infants with invasive infections. These findings could lead to risk-directed screening and treatment strategies, which may improve patient outcomes.
Recommendations for a core outcome measurement set for clinical trials in whiplash associated disorders
Authors: Sterling Michele , Andersen Tonny , Carroll Linda , Connelly Luke , Côté Pierre , Curatolo Michele , Grant Genevieve , Jull Gwendolen , Kasch Helge , Ravn Sophie Lykkegaard , MacDermid Joy , Malmström Eva-Maj , Rebbeck Trudy , Söderlund Anne , Treleaven Julia , Walton David M. , Westergren Hans
Published: May 2023

Inconsistent reporting of outcomes in clinical trials of treatments for whiplash associated disorders (WAD) hinders effective data pooling and conclusions about treatment effectiveness. A multidisciplinary International Steering Committee recently recommended 6 core outcome domains: Physical Functioning, Perceived Recovery, Work and Social Functioning, Psychological Functioning, Quality of Life and Pain. This study aimed to reach consensus and recommend a core outcome set (COS) representing each of the 6 domains. Forty-three patient-reported outcome measures (PROMs) were identified for Physical Functioning, 2 for perceived recovery, 37 for psychological functioning, 17 for quality of life, and 2 for pain intensity. They were appraised in 5 systematic reviews following COSMIN methodology. No PROMs of Work and Social Functioning in WAD were identified. No PROMs had undergone evaluation of content validity in patients with WAD, but some had moderate-to-high-quality evidence for sufficient internal structure. Based on these results, the International Steering Committee reached 100% consensus to recommend the following COS: Neck Disability Index or Whiplash Disability Questionnaire (Physical Functioning), the Global Rating of Change Scale (Perceived Recovery), one of the Pictorial Fear of Activity Scale-Cervical, Pain Self-Efficacy Questionnaire, Pain Catastrophizing Scale, Harvard Trauma Questionnaire, or Posttraumatic Diagnostic Scale (Psychological Functioning), EQ-5D-3L or SF-6D (Quality of Life), numeric pain rating scale or visual analogue scale (Pain), and single-item questions pertaining to current work status and percent of usual work (Work and Social Functioning). These recommendations reflect the current status of research of PROMs of the 6 core outcome domains and may be modified as evidence grows.
Effects of the COVID-19 Pandemic on Emergency Department Triage Nurses' Response to Patients With Potential Acute Coronary Syndrome
Authors: Blakeman John R. , DeVon Holli A. , Stapleton Stephen J. , Kim MyoungJin , Eckhardt Ann L.
Published: May 2023

Background

The COVID-19 pandemic added challenges to patient assessment and triage in the emergency department (ED).

Objective

The aim of this study was to describe the effects of the COVID-19 pandemic on ED triage nurse decisions for patients with potential acute coronary syndrome (ACS).

Methods

This was a secondary analysis of data from a descriptive, electronic, survey-based study. Participants were asked 2 questions: whether the COVID-19 pandemic had affected their triage and/or assessment practices for patients with potential ACS and, if so, how. Descriptive statistics were used to compare the characteristics of participants. A qualitative descriptive approach was used to analyze responses to the open-ended questions about the pandemic's effect on the triage process.

Results

Participants from across the United States had a mean age of 41.7 (12.3) years; 358 (80.6%) were women. The participants had a median of 10.0 (interquartile range, 16.0) years of experience as a registered nurse, with a median of 7.0 (interquartile range, 11.0) years of ED experience. A total of 180 of 444 participants (40.5%) indicated that the COVID-19 pandemic affected their triage processes and assessment of potential ACS patients; 156 (86.7%) provided a response to the open-ended question. Responses revealed 4 themes: (1) delays in triage and treatment, (2) ambiguous patient presentation, (3) heightened awareness of COVID-19 complications and sequelae, and (4) process changes.

Conclusions

Forty percent of ED triage nurses participating reported that triage processes for patients with potential ACS were affected by the COVID-19 pandemic. Most expressed barriers that resulted in delayed assessment and treatment of patients and often resulted from overlapping cardiac symptoms and COVID-19.
Mechanism of Danggui Sini underlying the treatment of peripheral nerve injury based on network pharmacology and molecular docking: A review
Authors: Zhang Ning , Zhang Dandan , Zhang Qian , Zhang Ruisu , Wang Yan
Published: May 2023

Danggui Sini is a traditional Chinese medicine prescription for treating peripheral nerve injury (PNI). We studied the mechanisms of this decoction through network pharmacology analysis and molecular docking. Using R language and Perl software, the active components and predicted targets of Danggui Sini, as well as the related gene targets of PNI, were mined through TCMSP, GeneCards, OMIM, TTD, and DrugBank. The network diagram of active components and intersection targets was constructed using Cytoscape software and the STRING database. The CytoNCA plug-in was used to screen out the core compounds and key targets. The genes were analyzed for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment. AutoDock was used to analyze the molecular docking of key targets and core compounds of diseases. The drug component disease target regulatory network showed that the key components included quercetin, kaempferol, naringenin, and licochalcone A, which play key roles in the whole network and may be the primary compounds associated with the action of Danggui Sini against PNI. PPI network topology analysis showed high degree values for RELA, JUN, MAPK1, RB1, and FOS. Enrichment analysis showed that the core targets of Danggui Sini participated in pathways associated with neurogenesis-multiple diseases. Molecular docking showed that the active ingredients in Danggui Sini had a good binding ability with key targets. We conclude that many active components of Danggui Sini play therapeutic roles in PNI treatment by regulating RELA, JUN, MAPK1, RB1, and FOS, and multiple other targets in inflammation, immunity, and lipid metabolism.