bluuebunny/crossref_metadata_2025 huggingface dataset:
TemStaPro: protein thermostability prediction using sequence representations from protein language models
Authors: Pudžiuvelytė Ieva , Olechnovič Kliment , Godliauskaite Egle , Sermokas Kristupas , Urbaitis Tomas , Gasiunas Giedrius , Kazlauskas Darius
Published: March 2024

Motivation

Reliable prediction of protein thermostability from its sequence is valuable for both academic and industrial research. This prediction problem can be tackled using machine learning and by taking advantage of the recent blossoming of deep learning methods for sequence analysis. These methods can facilitate training on more data and, possibly, enable the development of more versatile thermostability predictors for multiple ranges of temperatures.

Results

We applied the principle of transfer learning to predict protein thermostability using embeddings generated by protein language models (pLMs) from an input protein sequence. We used large pLMs that were pre-trained on hundreds of millions of known sequences. The embeddings from such models allowed us to efficiently train and validate a high-performing prediction method using over one million sequences that we collected from organisms with annotated growth temperatures. Our method, TemStaPro (Temperatures of Stability for Proteins), was used to predict thermostability of CRISPR-Cas Class II effector proteins (C2EPs). Predictions indicated sharp differences among groups of C2EPs in terms of thermostability and were largely in tune with previously published and our newly obtained experimental data.

Availability and implementation

TemStaPro software and the related data are freely available from https://github.com/ievapudz/TemStaPro and https://doi.org/10.5281/zenodo.7743637.
Unmasked and Exposed: The Impact of COVID-19 on the Youth Custodial Estate. A Compelling Case for Ideological Change
Authors: Smithson Hannah , Jump Deborah
Published: March 2024

The impact of the COVID-19 pandemic on custodial institutions has been the subject of intense scrutiny. During the pandemic, many international jurisdictions failed to develop clear and child-focussed plans for the management of children in custody, instead relying on strategies developed for adult populations. Presenting the findings from the United Kingdom’s (England Wales) first empirical in-depth exploration of the impacts of COVID-19 on children at each stage of the Youth Justice System, this article discusses the devastating effect on incarcerated children. The pandemic exacerbated existing failures in the children’s secure estate, eradicated children’s rights and exposed children to increased vulnerabilities. We present an urgent need for a fundamental ideological reconsideration of the purpose of custody for children.
Monopolar diathermy versus a vessel-sealing device for reducing postoperative drain output after simple mastectomy: randomized clinical trial
Authors: Keelan Stephen , Dowling Gavin P , Roche Trudi , Hegarty Aisling , Davey Matthew G , Dhannoon Amenah A , O’Grady Sorcha , Downey Eithne , Bolger Jarlath , Boland Michael , Sorensen Jan , Power Colm , Butt Abeeda , Baban Chwanrow , Hill Arnold D K
Published: March 2024

Background

Electrosurgical devices are commonly used during mastectomy for simultaneous dissection and haemostasis, and can provide potential benefits regarding vessel and lymphatic ligation. The aim of this prospective RCT was to assess whether using a vessel-sealing device (LigaSure™) improves perioperative outcomes compared with monopolar diathermy when performing simple mastectomy.

Methods

Patients were recruited prospectively and randomized in a 1 : 1 manner to undergo simple mastectomy using either LigaSure™ or conventional monopolar diathermy at a single centre. The primary outcome was the number of days the drain remained in situ after surgery. Secondary outcomes of interest included operating time and complications.

Results

A total of 86 patients were recruited (42 were randomized to the monopolar diathermy group and 44 were randomized to the LigaSure™ group). There was no significant difference in the mean number of days the drain remained in situ between the monopolar diathermy group and the LigaSure™ group (7.75 days versus 8.23 days; P = 0.613) and there was no significant difference in the mean total drain output between the monopolar diathermy group and the LigaSure™ group (523.50 ml versus 572.80 ml; P = 0.694). In addition, there was no significant difference in the mean operating time between the groups, for simple mastectomy alone (88.25 min for the monopolar diathermy group versus 107.20 min for the LigaSure™ group; P = 0.078) and simple mastectomy with sentinel lymph node biopsy (107.20 min for the monopolar diathermy group versus 114.40 min for the LigaSure™ group; P = 0.440).

Conclusion

In this double-blinded single-centre RCT, there was no difference in the total drain output or the number of days the drain remained in situ between the monopolar diathermy group and the LigaSure™ group.

Registration number

EudraCT 2018-003191-13 BEAUMONT HOSPITAL REC 18/66.
O77: Invasive intraductal oncocytic papillary neoplasms (IOPN) and adenocarcinomas arising from Intraductal papillary mucinous neoplasms (IPMN): adjuvant chemotherapy, patterns of recurrence and survival
Authors: Lucocq James ,   Adeno-IPMN Collaborative, Pandanaboyana Sanjay
Published: March 2024

Introduction

Invasive intraductal oncocytic papillary neoplasms (IOPNs) are extremely rare and are increasingly being recognised as their own entity, distinct from intraductal papilliary mucinous neoplasism subtypes (IPMN). Their clinicopathologic behaviour, recurrence patterns, response to adjuvant chemotherapy and long-term survival outcomes are unknown compared to adenocarcinomas arising from IPMN but were investigated in the present study.

Methods

Patients undergoing pancreatic resection between 2010-2020 for invasive IOPNs and adenocarcinoma arising from IPMNs were identified retrospectively from 18 academic pancreatic centers worldwide. Survival analyses were conducted to compare outcome measures between IOPNs and IPMN precursor epithelial subtypes and invasive components.

Results

Of the 459 patients with invasive IOPN/IPMNs, 20 patients had an invasive IOPN (median age,69; male,n=11), the majority of which were in the pancreatic head (75%) and underwent either a Whipples procedure (40%) or PPPD (35%). After a median follow-up of 6 years, 45% of invasive IOPNs developed recurrence (1-year,30.0%; 5-year,69.2%) and 40% survived follow-up (2-year survival 55.0%, 5-year survival, 30.8%). Recurrence rates and survival of invasive IOPNs were higher than colloid IPMNs (n=64) (p=0.031 and p=0.007) and comparable with ductal IPMNs (n=331) as well as gastric (n=54) and pancreatobiliary (n=111) IPMN subtypes. Invasive IOPN had significantly lower cancer-specific survival compared to colloid carcinomas (p<0.001). Adjuvant chemotherapy did not improve rates of recurrence in invasive IOPN and IPMN subtypes (p>0.05).

Conclusions

Invasive IOPNs are more aggressive than previously suspected and should be regarded as their own entity. Adjuvant chemotherapy does not reduce rates of recurrence regardless of neoplasm type.
Dynamic nonreversibility view of intrinsic brain organization and brain dynamic analysis of repetitive transcranial magnitude stimulation
Authors: Fan Liming , Li Youjun , Zhao Xingjian , Huang Zi-gang , Liu Tian , Wang Jue
Published: March 2024

Intrinsic neural activities are characterized as endless spontaneous fluctuation over multiple time scales. However, how the intrinsic brain organization changes over time under local perturbation remains an open question. By means of statistical physics, we proposed an approach to capture whole-brain dynamics based on estimating time-varying nonreversibility and k-means clustering of dynamic varying nonreversibility patterns. We first used synthetic fMRI to investigate the effects of window parameters on the temporal variability of varying nonreversibility. Second, using real test–retest fMRI data, we examined the reproducibility, reliability, biological, and physiological correlation of the varying nonreversibility substates. Finally, using repetitive transcranial magnetic stimulation–fMRI data, we investigated the modulation effects of repetitive transcranial magnetic stimulation on varying nonreversibility substate dynamics. The results show that: (i) as window length increased, the varying nonreversibility variance decreased, while the sliding step almost did not alter it; (ii) the global high varying nonreversibility states and low varying nonreversibility states were reproducible across multiple datasets and different window lengths; and (iii) there were increased low varying nonreversibility states and decreased high varying nonreversibility states when the left frontal lobe was stimulated, but not the occipital lobe. Taken together, these results provide a thermodynamic equilibrium perspective of intrinsic brain organization and reorganization under local perturbation.
Prediction of image interpretation cognitive ability under different mental workloads: a task-state fMRI study
Authors: Li Bao , Tong Li , Zhang Chi , Chen Panpan , Wang Linyuan , Yan Bin
Published: March 2024

Visual imaging experts play an important role in multiple fields, and studies have shown that the combination of functional magnetic resonance imaging and machine learning techniques can predict cognitive abilities, which provides a possible method for selecting individuals with excellent image interpretation skills. We recorded behavioral data and neural activity of 64 participants during image interpretation tasks under different workloads. Based on the comprehensive image interpretation ability, participants were divided into two groups. general linear model analysis showed that during image interpretation tasks, the high-ability group exhibited higher activation in middle frontal gyrus (MFG), fusiform gyrus, inferior occipital gyrus, superior parietal gyrus, inferior parietal gyrus, and insula compared to the low-ability group. The radial basis function Support Vector Machine (SVM) algorithm shows the most excellent performance in predicting participants’ image interpretation abilities (Pearson correlation coefficient = 0.54, R2 = 0.31, MSE = 0.039, RMSE = 0.002). Variable importance analysis indicated that the activation features of the fusiform gyrus and MFG played an important role in predicting this ability. Our study revealed the neural basis related to image interpretation ability when exposed to different mental workloads. Additionally, our results demonstrated the efficacy of machine learning algorithms in extracting neural activation features to predict such ability.
In the face of ambiguity: intrinsic brain organization in development predicts one’s bias toward positivity or negativity
Authors: Harp Nicholas R , Nielsen Ashley N , Schultz Douglas H , Neta Maital
Published: March 2024

Exacerbated negativity bias, including in responses to ambiguity, represents a common phenotype of internalizing disorders. Individuals differ in their propensity toward positive or negative appraisals of ambiguity. This variability constitutes one’s valence bias, a stable construct linked to mental health. Evidence suggests an initial negativity in response to ambiguity that updates via regulatory processes to support a more positive bias. Previous work implicates the amygdala and prefrontal cortex, and regions of the cingulo-opercular system, in this regulatory process. Nonetheless, the neurodevelopmental origins of valence bias remain unclear. The current study tests whether intrinsic brain organization predicts valence bias among 119 children and adolescents (6 to 17 years). Using whole-brain resting-state functional connectivity, a machine-learning model predicted valence bias (r = 0.20, P = 0.03), as did a model restricted to amygdala and cingulo-opercular system features (r = 0.19, P = 0.04). Disrupting connectivity revealed additional intra-system (e.g. fronto-parietal) and inter-system (e.g. amygdala to cingulo-opercular) connectivity important for prediction. The results highlight top–down control systems and bottom–up perceptual processes that influence valence bias in development. Thus, intrinsic brain organization informs the neurodevelopmental origins of valence bias, and directs future work aimed at explicating related internalizing symptomology.
Effect of Exercise Training on Prognosis in Community-acquired Pneumonia: A Randomized Controlled Trial
Authors: Ryrsø Camilla Koch , Faurholt-Jepsen Daniel , Ritz Christian , Hegelund Maria Hein , Dungu Arnold Matovu , Pedersen Bente Klarlund , Krogh-Madsen Rikke , Lindegaard Birgitte
Published: March 2024

Objective

To investigate the effect of standard care (SoC) combined with supervised in-bed cycling (Bed-Cycle) or booklet exercises (Book-Exe) versus SoC in community-acquired pneumonia (CAP).

Methods

In this randomized controlled trial, 186 patients with CAP were assigned to SoC (n = 62), Bed-Cycle (n = 61), or Book-Exe (n = 63). Primary outcome length of stay (LOS) was analyzed with analysis of covariance. Secondary outcomes, 90-day readmission, and 180-day mortality were analyzed with Cox proportional hazard regression and readmission days with negative-binominal regression.

Results

LOS was −2% (95% CI: −24 to 25) and −1% (95% CI: −22 to 27) for Bed-Cycle and Book-Exe, compared with SoC. Ninety-day readmission was 35.6% for SoC, 27.6% for Bed-Cycle, and 21.3% for Book-Exe. Adjusted hazard ratio (aHR) for 90-day readmission was 0.63 (95% CI: .33–1.21) and 0.54 (95% CI: .27–1.08) for Bed-Cycle and Book-Exe compared with SoC. aHR for 90-day readmission for combined exercise was 0.59 (95% CI: .33–1.03) compared with SoC. aHR for 180-day mortality was 0.84 (95% CI: .27–2.60) and 0.82 (95% CI: .26–2.55) for Bed-Cycle and Book-Exe compared with SoC. Number of readmission days was 226 for SoC, 161 for Bed-Cycle, and 179 for Book-Exe. Incidence rate ratio for readmission days was 0.73 (95% CI: .48–1.10) and 0.77 (95% CI: .51–1.15) for Bed-Cycle and Book-Exe compared with SoC.

Conclusions

Although supervised exercise training during admission with CAP did not reduce LOS or mortality, this trial suggests its potential to reduce readmission risk and number of readmission days.

Clinical Trials Registration

NCT04094636.
Parental responses to children’s early health disadvantages: evidence from a British twin study
Authors: García-Sierra Alicia
Published: March 2024

Health problems experienced in the early years of life have detrimental consequences for the entire life course. However, parents can, through their child-rearing actions, alleviate or aggravate these effects. This article examines how parents respond to the early physical health disadvantages suffered by their children and whether parents from high- and low-socioeconomic backgrounds develop different responses to their children’s early health problems. Using longitudinal data from the Twins Early Development Study, I implement a series of within-twin fixed-effects models and find that, on average, parents develop more negative emotional responses and implement harsher discipline behaviours when their children experience an early health problem. Surprisingly, the effect of health problems on parental responses does not differ by the socioeconomic status of the family. With some nuances, this evidence suggests that parental responses reinforce early-in-life health disadvantages.
Seafood loss prevention and waste reduction
Authors: Conz Andrea , Davoli Enrico , Franchi Carlotta , Diomede Luisa
Published: March 2024

Despite its high demand, the seafood processing industry grapples with a substantial challenge: generating significant waste, encompassing edible and inedible by-products. This leads to considerable financial losses and raises socioecological concerns regarding managing and disposing of such waste. Urgently addressing this issue, implementing sustainable seafood preservation methods becomes crucial. This study provides a comprehensive summary of chemical and physical approaches proposed in the literature to prevent seafood loss and diminish waste. A literature search from 2000 to January 2023 yielded 49 publications meeting the inclusion criteria, revealing a fragmented landscape of studies conducted on various fish products under diverse conditions. Chemical methods include organic acids and bio-derived preservatives; physical approaches comprise cold plasma, high hydrostatic pressure, and UV-C irradiation. The advantages and disadvantages of each technique were considered and discussed. Using chitosans, derived from natural sources and Generally Recognized As Safe, has emerged as the most promising approach. However, the discourse on fish preservation methods remains an evolving topic, weaving between the complexities of food safety, consumer satisfaction, and economic and environmental impacts. Further research is needed to investigate spoilage during production and critically evaluate the waste generated at different stages of the industrial process.
Comparing HEDIS performance of Dual Eligible Special Needs Plans with other coverage types for dually eligible people
Authors: Haviland Amelia M , Mathews Megan , Martino Steven C , Overton Yvette , Dembosky Jacob W , Maksut Jessica , Elliott Marc N
Published: March 2024

People eligible for both Medicare and Medicaid coverage (“dually eligible individuals”) have lower levels of income and assets and often higher health care needs and costs than those eligible for Medicare but not Medicaid coverage. Their 3 most common Medicare coverage options are Medicare Advantage (MA) Dual Eligible Special Needs Plans (D-SNPs), non–D-SNP MA plans, and fee-for-service (FFS) Medicare with a stand-alone prescription drug plan. No prior study has examined clinical quality of care for dually eligible individuals across these 3 coverage types. To fill that void, we used logistic regression to compare these coverage types on 6 HEDIS measures of clinical quality of care that were available for both MA and FFS (constructed from claims files). D-SNPs and non–D-SNP MA plans significantly outperformed FFS for all 6 measures for dually eligible individuals, by approximately 5 percentage points for 2 measures and by 18–34 percentage points for the other 4 measures. For the 4 measures with the greatest advantage over FFS, performance was 3–8 percentage points higher in D-SNPs than in non–D-SNP MA plans.
Chest wall tuberculosis: precision surgery with indigo carmine in limited cases for safe and intuitive lesion excision
Authors: Abe Sosei , Okabayashi Kan , Tokuishi Keita , Nakashima Hiroyasu , Maekawa Shin-Ichi , Hamatake Daisuke , Sato Toshihiko
Published: March 2024

In addition to treatment with antituberculosis drugs, complete surgical excision is important for the cure of chest wall tuberculosis. However, surgery is often challenging to perform due to different factors such as the strong adhesion of tuberculous lesions to the surrounding normal tissue, growth of neovascularization and presence of fragile necrotic tissues. Firm adhesions, bleeding and fragile tissue make it difficult to determine the boundary with normal tissue and completely excide the lesion. Moreover, ingenuity is required. Herein, we report the identification of the boundary between the lesion and normal tissue by injecting indigo carmine into the abscess to completely excide the lesion, which is considered an intuitive and safe method.
Affective Polarization Between Opinion-Based Groups in a Context of Low Partisan Discord: Measuring Its Prevalence and Consequences
Authors: Schieferdecker David , Joly Philippe , Faas Thorsten
Published: March 2024

Affective polarization has been primarily studied as a phenomenon between partisans. Recently, Hobolt, Leeper, & Tilley (2021) showed in the context of Brexit that affective polarization can also materialize around opinion-based groups, that is, political identities that form around extraordinary issues and cut through partisan lines. We generalize their findings by documenting the emergence of affective polarization around a new political conflict in a national context of low partisan discord. Specifically, we study divisions around the government response to the COVID-19 pandemic in Germany, a multiparty system where all established parties supported certain freedom restrictions to contain the pandemic. Drawing on numerous indicators and a survey experiment from a representative online panel study, we explored the (a) prevalence, (b) consequences, and (c) context of affective polarization between supporters and opponents of COVID-19 containment policies. We found that the majority of supporters and a minority of opponents showed indications of affective polarization. Affectively polarized citizens showed various group biases that make productive political and social interactions less likely. Affective polarization was stable over time and different from partisan and sociostructural conflicts. We raise questions for future research and discuss what it means for democracy when deep political rifts are not captured by main parties in a party system.
Genomics in nephrology: identifying informatics opportunities to improve diagnosis of genetic kidney disorders using a human-centered design approach
Authors: Romagnoli Katrina M , Salvati Zachary M , Johnson Darren K , Ramey Heather M , Chang Alexander R , Williams Marc S
Published: March 2024

Background

Genomic kidney conditions often have a long lag between onset of symptoms and diagnosis. To design a real time genetic diagnosis process that meets the needs of nephrologists, we need to understand the current state, barriers, and facilitators nephrologists and other clinicians who treat kidney conditions experience, and identify areas of opportunity for improvement and innovation.

Methods

Qualitative in-depth interviews were conducted with nephrologists and internists from 7 health systems. Rapid analysis identified themes in the interviews. These were used to develop service blueprints and process maps depicting the current state of genetic diagnosis of kidney disease.

Results

Themes from the interviews included the importance of trustworthy resources, guidance on how to order tests, and clarity on what to do with results. Barriers included lack of knowledge, lack of access, and complexity surrounding the case and disease. Facilitators included good user experience, straightforward diagnoses, and support from colleagues.

Discussion

The current state of diagnosis of kidney diseases with genetic etiology is suboptimal, with information gaps, complexity of genetic testing processes, and heterogeneity of disease impeding efficiency and leading to poor outcomes. This study highlights opportunities for improvement and innovation to address these barriers and empower nephrologists and other clinicians who treat kidney conditions to access and use real time genetic information.
Sir Charles Eastlake, the National Gallery and Milan
Authors: Avery-Quash Susanna
Published: March 2024

The first director of the National Gallery in London, Sir Charles Eastlake (1793–1865), was an Italophile. His favourite Italian city was Venice, where he once thought of buying a second home. The city he knew best, having lived there for fourteen years from 1816, was Rome. However, between 1854 and 1864, Eastlake made twenty-three trips to Milan, meaning that during his decade as director of the National Gallery from 1855, he visited Milan more often than any other place. This article suggests that Milan became a crucial hub for Eastlake, as the place where he connected with individuals who played important roles in several interconnected areas. Milan was significant, first, as an area rich in private collections, offering fertile ground for the discovery of potential acquisitions and a place from where it was relatively easy to export paintings because German-speaking Austria, which occupied north Italy and the Veneto until 1866, was comparatively lax about imposing export restrictions; second, as a place where art-historical knowledge and connoisseurship could be developed; and third, as a leading centre of picture conservation and framing.
Digital payments
Authors: Annan Francis , Cheung Chiman , Giné Xavier
Published: March 2024

Despite the rapid growth in digital payments (DP) adoption and its positive socio-economic impacts in low-income countries, a large portion of the population remains disconnected from DP. At the same time, usage of DP conditional on adoption is low, highlighting the unexplored potential for financial inclusion and economic advancement. This paper reviews the burgeoning academic literature on DP and categorizes both macro-level adoption barriers (extensive margin) and micro-level usage challenges (intensive margin). We draw on the Transaction Cost Index, a new comprehensive database encompassing 16 low-income countries, to shed light on major themes in markets for DP. We conclude by outlining potential avenues for future research in this area.
Debottlenecking the L-DOPA 4,5-dioxygenase step with enhanced tyrosine supply boosts betalain production in Nicotiana benthamiana
Authors: Jung Soyoung , Maeda Hiroshi A
Published: March 2024

Synthetic biology provides emerging tools to produce valuable compounds in plant hosts as sustainable chemical production platforms. However, little is known about how supply and utilization of precursors is coordinated at the interface of plant primary and specialized metabolism, limiting our ability to efficiently produce high levels of target specialized metabolites in plants. L-Tyrosine is an aromatic amino acid precursor of diverse plant natural products including betalain pigments, which are used as the major natural food red colorants and more recently a visual marker for plant transformation. Here, we studied the impact of enhanced L-tyrosine supply on the production of betalain pigments by expressing arogenate dehydrogenase (TyrA) from table beet (Beta vulgaris, BvTyrAα), which has relaxed feedback inhibition by L-tyrosine. Unexpectedly, betalain levels were reduced when BvTyrAα was coexpressed with the betalain pathway genes in Nicotiana benthamiana leaves; L-tyrosine and 3,4-dihydroxy-L-phenylalanine (L-DOPA) levels were drastically elevated but not efficiently converted to betalains. An additional expression of L-DOPA 4,5-dioxygenase (DODA), but not CYP76AD1 or cyclo-DOPA 5-O-glucosyltransferase, together with BvTyrAα and the betalain pathway, drastically enhanced betalain production, indicating that DODA is a major rate-limiting step of betalain biosynthesis in this system. Learning from this initial test and further debottlenecking the DODA step maximized betalain yield to an equivalent or higher level than that in table beet. Our data suggest that balancing between enhanced supply (“push”) and effective utilization (“pull”) of precursor by alleviating a bottleneck step is critical in successful plant synthetic biology to produce high levels of target compounds.
Evaluation of a mobile COVID-19 vaccination van outreach service in an outer South London borough
Authors: Zelent Gina , Addison Kerry , King Emma , Moore James , Flowers Rachel
Published: March 2024

Background

This study aimed to explore differences in users of a COVID-19 mobile vaccine van service and users of a COVID-19 static vaccination hub, and the impact of changes in national COVID-19 vaccine policy on vaccine uptake.

Methods

The age distribution of male and female service users in each service was compared. The average number of vaccines administered per hour per week was analysed.

Results

Females aged 80–89 represented 51.9% (95% CI 49.5–54.3%) of female vaccine van users compared with 2.8% (95% CI 2.5–3.1%) of female static hub users. The static hub had significantly greater proportions of female service users in all other age brackets.

For males, the greatest difference was in those aged 70–79 who represented 29.8% (95% CI 27–32.6%) of vaccine van users and 16.6% (95% CI 16–17.2%) static hub users.

Fewer vaccines were administered 2–3 weeks before the COVID-19 autumn booster policy change compared with 2–3 weeks after; 1.92 versus 6.25 vaccines per hour, respectively (Mann–Whitney U = 7, n1 = 11, n2 = 8, P < 0.01 two-tailed).

Conclusions

These findings suggest that a mobile vaccine van service is an effective model for increasing COVID-19 vaccination uptake in elderly residents, particularly after a national policy change.
Genome-wide identification of HMT gene family explores BpHMT2 enhancing selenium accumulation and tolerance in Broussonetia papyrifera
Authors: Chen Qiangwen , Zhu Changye , Guo Longfei , Bu Xianchen , Yang Wei , Cheng Shuiyuan , Cong Xin , Xu Feng
Published: March 2024

Broussonetia papyrifera, a valuable feed resource, is known for its fast growth, wide adaptability, high protein content and strong selenium enrichment capacity. Selenomethionine (SeMet), the main selenium form in selenium fortification B. papyrifera, is safe for animals and this enhances its nutritional value as a feed resource. However, the molecular mechanisms underlying SeMet synthesis remain unclear. This study identified three homocysteine S-methyltransferase genes from the B. papyrifera genome. The phylogenetic tree demonstrated that BpHMTs were divided into two classes, and BpHMT2 in the Class 2-D subfamily evolved earlier and possesses more fundamental functions. On the basis of the correlation between gene expression levels and selenium content, BpHMT2 was identified as a key candidate gene associated with selenium tolerance. Subcellular localization experiments confirmed the targeting of BpHMT2 in nucleus, cell membrane and chloroplasts. Moreover, three BpHMT2 overexpression Arabidopsis thaliana lines were confirmed to enhance plant selenium tolerance and SeMet accumulation. Overall, our finding provides insights into the molecular mechanisms of selenium metabolism in B. papyrifera, highlighting the potential role of BpHMT2 in SeMet synthesis. This research contributes to our understanding of selenium-enriched feed resources, with increased SeMet content contributing to the improved nutritional value of B. papyrifera as a feed resource.
Integrated small RNA, transcriptome and physiological approaches provide insight into Taxodium hybrid ‘Zhongshanshan’ roots in acclimation to prolonged flooding
Authors: Lu Yan , Zhang Shuqing , Xiang Peng , Yin Yunlong , Yu Chaoguang , Hua Jianfeng , Shi Qin , Chen Tingting , Zhou Zhidong , Yu Wanwen , Creech David L , Lu Zhiguo
Published: March 2024

Although Taxodium hybrid ‘Zhongshanshan’ 406 (Taxodium mucronatum Tenore × Taxodium distichum; Taxodium 406) is an extremely flooding-tolerant woody plant, the physiological and molecular mechanisms underlying acclimation of its roots to long-term flooding remain largely unknown. Thus, we exposed saplings of Taxodium 406 to either non-flooding (control) or flooding for 2 months. Flooding resulted in reduced root biomass, which is in line with lower concentrations of citrate, α-ketoglutaric acid, fumaric acid, malic acid and adenosine triphosphate (ATP) in Taxodium 406 roots. Flooding led to elevated activities of pyruvate decarboxylase, alcohol dehydrogenase and lactate dehydrogenase, which is consistent with higher lactate concentration in the roots of Taxodium 406. Flooding brought about stimulated activities of superoxide dismutase and catalase and elevated reduced glutathione (GSH) concentration and GSH/oxidized glutathione, which is in agreement with reduced concentrations of O2− and H2O2 in Taxodium 406 roots. The levels of starch, soluble protein, indole-3-acetic acid, gibberellin A4 and jasmonate were decreased, whereas the concentrations of glucose, total non-structural carbohydrates, most amino acids and 1-aminocyclopropane-1-carboxylate (ACC) were improved in the roots of flooding-treated Taxodium 406. Underlying these changes in growth and physiological characteristics, 12,420 mRNAs and 42 miRNAs were significantly differentially expressed, and 886 miRNA–mRNA pairs were identified in the roots of flooding-exposed Taxodium 406. For instance, 1-aminocyclopropane-1-carboxylate synthase 8 (ACS8) was a target of Th-miR162-3p and 1-aminocyclopropane-1-carboxylate oxidase 4 (ACO4) was a target of Th-miR166i, and the downregulation of Th-miR162-3p and Th-miR166i results in the upregulation of ACS8 and ACO4, probably bringing about higher ACC content in flooding-treated roots. Overall, these results indicate that differentially expressed mRNA and miRNAs are involved in regulating tricarboxylic acid cycle, ATP production, fermentation, and metabolism of carbohydrates, amino acids and phytohormones, as well as reactive oxygen species detoxification of Taxodium 406 roots. These processes play pivotal roles in acclimation to flooding stress. These results will improve our understanding of the molecular and physiological bases underlying woody plant flooding acclimation and provide valuable insights into breeding-flooding tolerant trees.
MbEOMT1 regulates methyleugenol biosynthesis in Melaleuca bracteata F. Muell
Authors: Yang Chao , Lin Yongsheng , Xiang Xuwen , Shao Dandan , Qiu Ziwen , Li Yongyu , Wu Shaohua
Published: March 2024

Methyleugenol, a bioactive compound in the phenylpropene family, undergoes its final and crucial biosynthetic transformation when eugenol O-methyltransferase (EOMT) converts eugenol into methyleugenol. While Melaleuca bracteata F. Muell essential oil is particularly rich in methyleugenol, it contains only trace amounts of its precursor, eugenol. This suggests that the EOMT enzyme in M. bracteata is highly efficient, although it has not yet been characterized. In this study, we isolated and identified an EOMT gene from M. bracteata, termed MbEOMT1, which is primarily expressed in the flowers and leaves and is inducible by methyl jasmonate (MeJA). Subcellular localization of MbEOMT1 in the cytoplasm was detected. Through transient overexpression experiments, we found that MbEOMT1 significantly elevates the concentration of methyleugenol in M. bracteata leaves. Conversely, silencing of MbEOMT1 via virus-induced gene silencing led to a marked reduction in methyleugenol levels. Our in vitro enzymatic assays further confirmed that MbEOMT1 specifically catalyzes the methylation of eugenol. Collectively, these findings establish that the MbEOMT1 gene is critical for methyleugenol biosynthesis in M. bracteata. This study enriches the understanding of phenylpropene biosynthesis and suggests that MbEOMT1 could serve as a valuable catalyst for generating bioactive compounds in the future.
A new approach allows morphological recognition of cryptic diversity of the krill genus Hansarsia (formerly Nematoscelis)
Authors: Vereshchaka Alexander L , Shatravin Alexander V , Kulagin Dmitry N , Lunina Anastasiia A
Published: March 2024

Cryptic and pseudocryptic species are found on all major branches of the tree of life and probably represent a significant portion of undiscovered biodiversity, yet their identification is currently possible solely on the basis of molecular analyses. Here, we tested an alternative approach and hypothesized that all genetic clades might be identified on a morphological basis, and we analysed the morphology of nine previously detected genetic clades of Hansarsia. We made 169 sets of measurements (12 quantitative characters for each), ran multinomial logistic regression models, and showed a high ability of these models to generalize (i.e. to be able to classify correctly new specimens not included in our data matrix). The five to seven most ‘powerful’ characters provided a significant detection rate; these characters were shown to represent distinct evolutionary traits. Our findings cast some doubt on the presence of the ‘merely’ cryptic species; instead, we suggest that any genetic divergence found via traditional genetic markers is also mirrored in morphological divergence and can be detected using a combination of quantitative characters and appropriate mathematical tools. We provide a script key to genetic clades of the Atlantic Hansarsia based solely on morphological measurements and encourage other researchers to use quantitative morphological characters for detection of cryptic clades in other taxa.
Efficacy of Centers of Biomedical Research Excellence (CoBRE) grants to build research capacity in underrepresented states
Authors: Schaller Michael D.
Published: March 2024

Federal funding for research has immediate and long‐term economic impact. Since federal research funding is regionally concentrated and not geographically distributed, the benefits are not fully realized in some regions of the country. The Established (previously Experimental) Program to Stimulate Competitive Research (EPSCoR) programs at several agencies, for example, the National Science Foundation, and the Institutional Development Award (IDeA) program at the National Institutes of Health were created to increase competitiveness for funding in states with historically low levels of federal funding. The Centers of Biomedical Research Excellence (CoBRE) award program is a component of the IDeA program. The CoBRE grants support research core facilities to develop research infrastructure. These grants also support the research projects of junior investigators, under the guidance of mentoring teams of senior investigators, to develop human resources at these institutions. Few studies have assessed the effectiveness of these programs. This study examines the investment and outcomes of the CoBRE grants from 2000 through 2022. The maturation of junior investigators into independently funded principal investigators is comparable to other mentoring programs supported by NIH. The investment in research cores resulted in substantial research productivity, measured by publications. Despite the successes of individual investigators and increased research infrastructure and productivity, the geographic distribution of federal and NIH research dollars has not changed. These results will be informative in consideration of policies designed to enhance the geographic distribution of federal research dollars.
ER membrane complex (EMC): Structure, functions, and roles in diseases
Authors: Zhu Qi , Zhu Xianjun , Zhang Lin
Published: March 2024

The endoplasmic reticulum (ER) is the largest membrane system in eukaryotic cells and is the primary site for the biosynthesis of lipids and carbohydrates, as well as for the folding, assembly, modification, and transport of secreted and integrated membrane proteins. The ER membrane complex (EMC) on the ER membrane is an ER multiprotein complex that affects the quality control of membrane proteins, which is abundant and widely preserved. Its disruption has been found to affect a wide range of processes, including protein and lipid synthesis, organelle communication, endoplasmic reticulum stress, and viral maturation, and may lead to neurodevelopmental disorders and cancer. Therefore, EMC has attracted the attention of many scholars and become a hot field. In this paper, we summarized the main contributions of the research of EMC in the past nearly 15 years, and reviewed the structure and function of EMC as well as its related diseases. We hope this review will promote further progress of research on EMC.
Development of the Gerontological Nursing Competency Questionnaire
Authors: Picella David Vincent , Woods Diana Lynn
Published: March 2024

AIM

The aim of this study was to develop an instrument to measure competencies of gerontological nursing faculty.

BACKGROUND

There is no accepted instrument to assess competencies of gerontological nursing faculty.

METHOD

To develop the Gerontological Nursing Competency Questionnaire (GNCQ), we used a modified Delphi technique focused on consensus building among experts from the National Hartford Center for Gerontological Nursing Excellence. The 25-item GNCQ measures confidence in knowledge, confidence in teaching, and interest in further training in gerontological nursing. The instrument was piloted in a large nursing department at a university in southern California.

RESULTS

Low faculty competencies in knowledge and teaching and low interest in further training were observed.

CONCLUSION

The GNCQ demonstrated initial content validity and an ability to identify key areas of deficiency in knowledge and teaching among nursing faculty. It may be used for improvement initiatives in gerontological nursing programs.
Prognostic value of tumor deposits and positive lymph node ratio in stage III colorectal cancer: a retrospective cohort study
Authors: Liu Lei , Ji Jie , Ge Xianxiu , Ji Zuhong , Li Jiacong , Wu Jie , Zhu Juntao , Yao Jianan , Zhu Fangyu , Mao Boneng , Cao Zhihong , Zhou Jinyi , Miao Lin , Ji Guozhong , Hang Dong
Published: March 2024

Background:

In colorectal cancer (CRC), tumor deposits (TD) have been used to guide the N staging only in node-negative patients. It remains unknown about the prognostic value of TD in combination with positive lymph node ratio (LNR) in stage III CRC.

Patients and methods:

The authors analyzed data from 31 139 eligible patients diagnosed with stage III CRC, including 30 230 from the Surveillance, Epidemiology, and End Results (SEER) database as a training set and 909 from two Chinese hospitals as a validation set. The associations of TD and LNR with cancer-specific survival (CSS) and overall survival (OS) were evaluated using the Kaplan–Meier method and Cox regression models.

Results:

Both TD-positive and high LNR (value ≥0.4) were associated with worse CSS in the training [multivariable hazard ratio (HR), 1.50; 95% CI: 1.43–1.58 and HR, 1.74; 95% CI: 1.62–1.86, respectively] and validation sets (HR, 1.90; 95% CI: 1.41–2.54 and HR, 2.01; 95% CI: 1.29–3.15, respectively). Compared to patients with TD-negative and low LNR (value<0.4), those with TD-positive and high LNR had a 4.09-fold risk of CRC-specific death in the training set (HR, 4.09; 95% CI: 3.54–4.72) and 4.60-fold risk in the validation set (HR, 4.60; 95% CI: 2.88–7.35). Patients with TD-positive/H-LNR CRC on the right side had the worst prognosis (P<0.001). The combined variable of TD and LNR contributed the most to CSS prediction in the training (24.26%) and validation (32.31%) sets. A nomogram including TD and LNR showed satisfactory discriminative ability, and calibration curves indicated favorable consistency in both the training and validation sets.

Conclusions:

TD and LNR represent independent prognostic predictors for stage III CRC. A combination of TD and LNR could be used to identify those at high-risk of CRC deaths.
Predictive value of NT-proBNP and hs-TnT for outcomes after pediatric congenital cardiac surgery
Authors: Shen Huayan , He Qiyu , Shao Xinyang , Lin Ya-hui , Wu Dongdong , Ma Kai , Dou Zheng , Liu Yuze , Luo Fengming , Li Shoujun , Zhou Zhou
Published: March 2024

Background:

The available evidence regarding the predictive value of troponins and natriuretic peptides for early postoperative outcomes in pediatrics is limited, controversial, and based on small sample sizes. The authors aimed to investigate the association of N-terminal pro B-type natriuretic peptide (NT-proBNP) and high-sensitivity troponin T (hs-TnT) with the in-hospital adverse outcomes after congenital cardiac surgeries.

Methods:

A secondary analysis based on a prospective study of pediatric congenital heart disease (CHD) patients was conducted to investigate the association of NT-proBNP and hs-TnT tested within 6 h postoperatively with in-hospital adverse events. A multivariate logistic regression analysis with a minimum P value approach was used to identify the optimal thresholds of NT-proBNP and hs-TnT for risk stratification.

Results:

NT-proBNP and hs-TnT are positively correlated with cardiopulmonary bypass time, mechanical ventilation duration, and pediatric intensive care unit stay. The predictive performance of NT-proBNP is excellent for adverse events in both patients younger than 1 year [area under the curve (AUC): 0.771, 0.693–0.850] and those older than 1 year (AUC: 0.839, 0.757–0.922). However, hs-TnT exhibited a satisfactory predictive value solely in patients aged over 1 year. (AUC: 0.784, 0.717–0.852). NT-proBNP levels of 2000–10 000 ng/l [odds ratio (OR): 3.79, 1.47–9.76] and exceeding 10 000 ng/l (OR: 12.21, 3.66–40.80) were associated with a higher risk of postoperative adverse events in patients younger than 1 year. Patients older than 1 year, with NT-proBNP higher than 500 ng/l (OR: 15.09, 6.05–37.66) or hs-TnT higher than 1200 ng/l (OR: 5.50, 1.47–20.59), had a higher incidence of postoperative adverse events.

Conclusions:

NT-proBNP and hs-TnT tested within postoperative 6 h demonstrated significant predictive value for postoperative adverse events in CHD patients older than 1 year. However, among CHD patients younger than 1 year, only NT-proBNP exhibited commendable predictive performance for postoperative adverse events.
Minimally invasive robot-assisted and laparoscopic distal pancreatectomy in a pan-European registry a retrospective cohort study
Authors: van Bodegraven Eduard A. , van Ramshorst Tess M. E. , Bratlie Svein O. , Kokkola Arto , Sparrelid Ernesto , Björnsson Bergthor , Kleive Dyre , Burgdorf Stefan K. , Dokmak Safi , Groot Koerkamp Bas , Cabús Santiago Sánchez , Molenaar I Quintus , Boggi Ugo , Busch Olivier R. , Petrič Miha , Roeyen Geert , Hackert Thilo , Lips Daan J. , D’Hondt Mathieu , Coolsen Mariëlle M E , Ferrari Giovanni , Tingstedt Bobby , Serrablo Alejandro , Gaujoux Sebastien , Ramera Marco , Khatkov Igor , Ausania Fabio , Souche Regis , Festen Sebastiaan , Berrevoet Frederik , Keck Tobias , Sutcliffe Robert P. , Pando Elizabeth , de Wilde Roeland F. , Aussilhou Beatrice , Krohn Paul S. , Edwin Bjørn , Sandström Per , Gilg Stefan , Seppänen Hanna , Vilhav Caroline , Abu Hilal Mohammad , Besselink Marc G. ,   for the European Consortium on Minimally Invasive Pancreatic Surgery (E-MIPS)
Published: March 2024

Background:

International guidelines recommend monitoring the use and outcome of minimally invasive pancreatic surgery (MIPS). However, data from prospective international audits on minimally invasive distal pancreatectomy (MIDP) are lacking. This study examined the use and outcome of robot-assisted (RDP) and laparoscopic (LDP) distal pancreatectomy in the E-MIPS registry.

Patients and methods:

Post-hoc analysis in a prospective audit on MIPS, including consecutive patients undergoing MIDP in 83 centers from 19 European countries (01-01-2019/31-12-2021). Primary outcomes included intraoperative events (grade 1: excessive blood loss, grade 2: conversion/change in operation, grade 3: intraoperative death), major morbidity, and in-hospital/30-day mortality. Multivariable logistic regression analyses identified high-risk groups for intraoperative events. RDP and LDP were compared in the total cohort and high-risk groups.

Results:

Overall, 1672 patients undergoing MIDP were included; 606 (36.2%) RDP and 1066 (63.8%) LDP. The annual use of RDP increased from 30.5% to 42.6% (P<0.001). RDP was associated with fewer grade 2 intraoperative events compared with LDP (9.6% vs. 16.8%, P<0.001), with longer operating time (238 vs. 201 min, P<0.001). No significant differences were observed between RDP and LDP regarding major morbidity (23.4% vs. 25.9%, P=0.264) and in-hospital/30-day mortality (0.3% vs. 0.8%, P=0.344). Three high-risk groups were identified; BMI greater than 25 kg/m2, previous abdominal surgery, and vascular involvement. In each group, RDP was associated with fewer conversions and longer operative times.

Conclusion:

This European registry-based study demonstrated favorable outcomes for MIDP, with mortality rates below 1%. LDP remains the predominant approach, whereas the use of RDP is increasing. RDP was associated with fewer conversions and longer operative time, including in high-risk subgroups. Future randomized trials should confirm these findings and assess cost differences.