bluuebunny/crossref_metadata_2025 huggingface dataset:
A New Urban Greening Scheme Approach: Increasing Quantity and Quality of Urban Green Space
Authors: Dahlan M Z , Faisal B , Chaeriyah S , Hutriani I W , Amelia M
Published: December 2022

Urban green spaces are perceived as vital urban infrastructure for healing from the spread of the COVID-19 disease. Regarding the limited availability and the high price of land in urban areas, local governments are encouraged to find alternative solutions that are good, appropriate, and fast to achieve the target of 30% green open space in their area. Based on the Green City Development Roadmap by the Ministry of Public Works and Housing in 2015, several cities were creatively assessing and determining the components of green open space based on the city’s natural character and stipulated in local regulations. This causes the diversity of existing green open space data in each city which cannot be compared validly. Furthermore, along with technology development in providing more environmentally friendly elements, the term “green open space” is considered to limit improvement efforts in the quantity and quality of urban green spaces. Therefore, this descriptive-qualitative study was conducted to find a new paradigm in defining green open spaces through benchmarking methods based on selected cities’ strategic and practical policies. The study results found the term “green space” in general as a response to the spatial problem that does not limit the function and utilization of the space, such as the condition of being open or closed by a tree canopy, owned by public or private, or furnished with vegetation and/or hardscape elements. However, we consider that implementing this breakthrough idea needs to be supported by related scientific studies and best practices relevant to the environmental context, both ecological, social, and cultural aspects. Consequently, a deeper study in realizing the green space concept needs to be carried out, primarily related to proving that this concept can increase both the quantity and quality of the urban green space.
Mixed determinants, compensated integrability, and new a priori estimates in gas dynamics
Authors: Serre Denis
Published: December 2022

We extend the scope of our recent Compensated Integrability theory, by exploiting the multi-linearity of the determinant map over

S
y
m

n

(

R

)

\mathbf {Sym}_n(\mathbb {R})

. This allows us to establish new a priori estimates for inviscid gases flowing in the whole space

R

d

\mathbb {R}^d

. Notably, we estimate the defect measure (Boltzman equation) or weighted spacial correlations of the velocity field (Euler system). As usual, our bounds involve only the total mass and energy of the flow.
Hypertonic saline use in neurocritical care for treating cerebral edema: A review of optimal formulation, dosing, safety, administration and storage
Authors: Holden Devin N , Mucksavage Jeffrey J , Cokley John A , Kim Keri S , Tucker Natalie L , Esordi Molly S , Cook Aaron M
Published: December 2022

Purpose

Current Neurocritical Care Society guidelines on the management of cerebral edema recommend hypertonic saline (HTS) over mannitol in some scenarios, but practical questions remain regarding the appropriate administration method, concentration/dose, monitoring to ensure safe use, and storage. The aim of this article is to address these practical concerns based on the evidence currently available.

Many different hypertonic solutions have been studied to define the optimal hyperosmolar substance to relieve acute cerebral edema in patients with conditions such as acute ischemic stroke, intracerebral hemorrhage, subarachnoid hemorrhage, and traumatic brain injury. Mannitol and HTS are the main hyperosmolar therapies in use in contemporary neurocritical care practice. Contemporary use of HTS has followed a circuitous path in regards to the practical aspects of dosing and formulation, with evidence mainly consisting of retrospective or observational data. The effectiveness of bolus doses of HTS to lower acutely elevated intracranial pressure is well accepted. Adverse events with use of HTS are often mild and non–clinically significant if appropriate monitoring of serum sodium and chloride concentrations is performed. Available evidence shows that peripheral administration of HTS is likely safe in certain circumstances. Timely utilization of HTS is complicated by regulatory requirements for safe storage, but with appropriate safeguards HTS can be stored in patient care areas.

Conclusion

HTS formulations, methods of administration, infusion rate, and storage vary by institution, and no practice standards exist. Central intravenous administration may be preferred for HTS, but peripheral intravenous administration is safe provided measures are undertaken to detect and prevent phlebitis and extravasation. The safe use of HTS is possible with proper protocols, education, and institutional safeguards in place.
Centrally supported clinical pharmacist intervention to reduce clinical inertia in hypertension
Authors: Lowe Rachel N , Kovac Nicole , Lobo Ingrid , Billups Sarah J
Published: December 2022

Purpose

To assess the impact of a one-time hypertension (HTN)–focused clinical pharmacist intervention on the occurrence of clinical inertia and change in blood pressure (BP).

Methods

This retrospective study included patients 18 to 89 years of age with a current diagnosis of HTN and average systolic BP of ≥150 mm Hg. Centralized outreach coordinators performed telephone outreach to patients to schedule an HTN-focused visit with their primary care provider (PCP) and forwarded outreach notes for half of these patients to clinical pharmacists embedded in an internal medicine clinic. The clinical pharmacists performed a one-time focused medication review and provided evidence-based recommendations to a patient’s PCP prior to the scheduled appointment. The primary outcome was therapy intensification (medication adjustment or adherence discussion) as a measure of overcoming clinical inertia. Secondary outcomes were the mean changes in systolic and diastolic BP from preintervention values to 6-month follow-up in the intervention group versus the control group.

Results

A total of 91 patients were included, and 34 of 47 intervention patients (72%) had therapy intensification at the HTN-focused PCP appointment, compared to 20 of 44 control patients (46%) (P =0.017). The mean (SD) systolic BP reductions from baseline were 12.26 (29.04) mm Hg and 6.97 (27.05) mm Hg for the intervention and control groups, respectively (P =0.427), with diastolic BP reductions of 3.83 (13.14) mm Hg and 1.35 (10.60) mm Hg, respectively (P =0.380).

Conclusion

A collaborative model involving centralized outreach coordinators and embedded clinical pharmacists led to a significant reduction in clinical inertia. This was a small-scale pilot study, and further research is needed to determine the effect of this intervention on BP reduction.
The Accuracy of Speech and Linguistic Analysis in Early Diagnostics of Neurocognitive Disorders in a Memory Clinic Setting
Authors: ter Huurne Daphne , Ramakers Inez , Possemis Nina , Banning Leonie , Gruters Angelique , Van Asbroeck Stephanie , König Alexandra , Linz Nicklas , Tröger Johannes , Langel Kai , Verhey Frans , de Vugt Marjolein
Published: December 2022

Objective

To investigate whether automatic analysis of the Semantic Verbal Fluency test (SVF) is reliable and can extract additional information that is of value for identifying neurocognitive disorders. In addition, the associations between the automatically derived speech and linguistic features and other cognitive domains were explored.

Method

We included 135 participants from the memory clinic of the Maastricht University Medical Center+ (with Subjective Cognitive Decline [SCD; N = 69] and Mild Cognitive Impairment [MCI]/dementia [N = 66]). The SVF task (one minute, category animals) was recorded and processed via a mobile application, and speech and linguistic features were automatically extracted. The diagnostic performance of the automatically derived features was investigated by training machine learning classifiers to differentiate SCD and MCI/dementia participants.

Results

The intraclass correlation for interrater reliability between the clinical total score (golden standard) and automatically derived total word count was 0.84. The full model including the total word count and the automatically derived speech and linguistic features had an Area Under the Curve (AUC) of 0.85 for differentiating between people with SCD and MCI/dementia. The model with total word count only and the model with total word count corrected for age showed an AUC of 0.75 and 0.81, respectively. Semantic switching correlated moderately with memory as well as executive functioning.

Conclusion

The one-minute SVF task with automatically derived speech and linguistic features was as reliable as the manual scoring and differentiated well between SCD and MCI/dementia. This can be considered as a valuable addition in the screening of neurocognitive disorders and in clinical practice.
Understanding floral variation in Leiothrix (Poales: Eriocaulaceae): anatomy, development and insights into pollination
Authors: Mascarenhas Ana Angélica S , Scatena Vera L , Oriani Aline
Published: December 2022

Leiothrix differs from other genera of Eriocaulaceae by having pistillate flowers with nectariferous and stigmatic branches that diverge at different heights on the style and staminate flowers with free or fused petals. To understand the ontogenetic processes that result in these morphological variations, we studied the development and floral vasculature in six species of the genus. In pistillate flowers, the nectariferous branches, which are in a carinal position, correspond to the apex of the carpels, whereas the stigmatic branches, in a commissural position, are formed by the marginal tissues of the carpels and initiate later than the nectariferous branches. The upper margins of the carpels elongate, forming a tubular structure that raises the stigmatic branches; the greater its development, the greater the distance between the stigmatic and nectariferous branches. In staminate flowers, the fusion of the petals appears to be post-genital in the median and apical portions and congenital in the more basal portion. Despite the differences in floral development, Leiothrix shares the same pattern of floral vasculature with other genera of Eriocaulaceae, exhibiting a central vascular plexus in the receptacle from which a single trace diverges for each sepal, petal and stamen. The staminodes are not vascularized. The dorsal carpellary bundles supply the nectariferous branches, but the ventral carpel bundles are reduced and are not involved in the supply of the ovules and stigmas. The differences in the height of insertion of the nectariferous branches are probably the result of selective pressure exerted by different groups of pollinating insects. Our hypothesis is that species in which the nectariferous branches are inserted below the stigmatic branches, and are therefore less accessible, exhibit a more specialized pollination system. The absence of nectariferous branches in L. angustifolia indicates secondary loss probably associated with spontaneous geitonogamy.
No Matthew effects and stable SES gaps in math and language achievement growth throughout schooling: Evidence from Germany
Authors: Nennstiel Richard
Published: December 2022

The extent to which achievement gaps become wider or narrower over the course of schooling is a topic that is widely discussed, both publicly and in educational research. This study examines whether absolute achievement (in language and math skills) and social origin gaps grow throughout the school career. To investigate the achievement growth of three German student cohorts (N = 14,273) at different stages of their school career (primary school, lower secondary school, and upper secondary school), I use multilevel models to estimate the effects of prior achievement and social origin on achievement growth. The results consistently suggest a negative association between prior achievement and subsequent growth; hence, initially low-performing students have higher achievement gains than initially high-performing students. Additionally, I find that social origin gaps remain stable over time. However, when controlling for initial achievement, slightly growing socio-economic status gaps can be observed.
Handling high-risk patients in the catheterization laboratory
Authors: Ibrahim Karim , Tongers Jörn , Mangner Norman , Werner Nikos , Tycinska Agnieszka , Leick Jürgen , Oreglia Jacopo , Schröder Jörg
Published: December 2022

Protected percutaneous coronary intervention is considered a life-saving procedure for high-risk patients. Therefore it is important that the interventional cardiology team is prepared, the procedure is planned, and potential complications, as well as bail out strategies are considered. Throughout the procedure, it is critical to monitor the patient to identify any early signs of deterioration or changes in patient well-being to avoid any potential complications.
Short- and long-term risk of atrial fibrillation recurrence after first time ablation according to body mass index: a nationwide Danish cohort study
Authors: Tønnesen Jacob , Pallisgaard Jannik , Ruwald Martin H , Rasmussen Peter Vibe , Johannessen Arne , Hansen Jim , Worck Rene Husted , Zörner Christopher R , Riis-Vestergaard Lise , Middelfart Charlotte , Gislason Gunnar , Hansen Morten Lock
Published: December 2022

Aims

Overweight is associated with increased risk of atrial fibrillation (AF), but the impact of overweight and AF recurrence after ablation is less clear. Despite this, an increasing number of AF ablations are carried out in overweight patients. We investigated the impact of body mass index (BMI) on AF recurrence rates after ablation.

Methods and results

Through Danish nationwide registers, all patients undergoing first-time AF ablation between 2010 and 2018 were identified. Exposure of interest was BMI. The primary outcome was recurrent AF, defined from either any usage of antiarrhythmic medication, AF hospitalization, cardioversion, or re-ablation. A total of 9188 patients were included. Median age and interquartile range was 64 (60–75) in the normal-weight group and 60 (53–66) in the morbidly obese. There was an increase in comorbidity burden with increasing BMI, including a higher prevalence of heart failure, chronic obstructive pulmonary disease, diabetes, and hypertension. At 1- and 5-year follow ups, recurrence rates of AF increased incrementally by BMI categories. The hazard ratios and 95% confidence intervals of recurrent AF after ablation were 1.15 (1.07–1.23), 1.18 (1.09–1.28), and 1.26 (1.13–1.41) in overweight, obese, and morbidly obese, respectively, compared with normal-weight patients. Procedure duration and X-ray dose exposure also increased with increasing BMI.

Conclusion

Following AF ablation, recurrence rates of AF increased incrementally with increasing BMI. Therefore, aggressive weight management pre ablation in overweight patients could potentially provide substantial benefits and improve short- and long-term outcomes after ablation.
Increased incidence of overweight and obesity among preschool Swedish children during the COVID-19 pandemic
Authors: Fäldt Anna , Nejat Sahar , Edvinsson Sollander Sofia , Durbeej Natalie , Holmgren Anton
Published: December 2022

Background

The COVID-19 pandemic has had wide effects on child health globally. Increased prevalence of childhood obesity has been observed by a number of countries during the pandemic. The absence of a formal societal lockdown during the pandemic, made Sweden stand out compared to other countries. This study aims to examine changes in BMI among preschool children in Sweden before and during COVID-19 pandemic.

Methods

Retrospective population-based cross-sectional study, with longitudinal follow-up for a portion of the children. The study included 25 049 children from three Swedish regions, with growth measures at 3- (n = 16 237), 4- (n = 14 437) and 5-years of age (n = 11 711). Care Need Index was used as a socioeconomic parameter at health centre level.

Results

There was an increase in BMI in children aged three (P = 0.028) and four (P<0.001) during the COVID-19 pandemic. Obesity in 3-year-old girls increased from 2.8% to 3.9%. Four-year-olds increased in obesity, and overweight (girls) and the prevalence of underweight decreased in boys. No change in BMI was observed in 5-year-olds. Children in areas of low socioeconomic status had higher risk of obesity.

Conclusions

Overweight and obesity increased among 3- and 4-year-old children in Sweden, findings that were accentuated in children attending child health centres in areas with lower socioeconomic status. The COVID-19 pandemic is likely to have affected health behaviours negatively in Swedish preschool children. Our results expose the need for extended efforts directed to prevent childhood obesity, especially targeting lower socioeconomic areas.
High density polyethylene (HDPE) biodegradation by the fungus Cladosporium halotolerans
Authors: Di Napoli Michela , Silvestri Brigida , Castagliuolo Giusy , Carpentieri Andrea , Luciani Giuseppina , Di Maro Antimo , Sorbo Sergio , Pezzella Alessandro , Zanfardino Anna , Varcamonti Mario
Published: December 2022

Polyethylene (PE) is high molecular weight synthetic polymer, very hydrofobic and hardly biodegradable. To increase polyethylene bio-degradability it is very important to find microorganisms that improve the PE hydrophilic level and/or reduce the length of its polymeric chain by oxidation. In this study, we isolated Cladosporium halotolerans, a fungal species, from the gastric system of Galleria mellonella larvae. Here, we show that C. halotolerans grows in the presence of PE polymer, it is able to interact with plastic material through its hyphae and secretes enzymes involved in PE degradation.
The Blame Game: Public Outcry and Terrorism within and Exported from the Sanctioned State
Authors: Avdan Nazli , Early Bryan R , Liou Ryan Yu-Lin , Murdie Amanda , Peksen Dursun
Published: December 2022

What effects do economic sanctions have on the volume of domestic terrorism within target states and transnational terrorism directed toward Americans by targeted nationals? In this article, we theorize that sanctions imposed by the United States increase the likelihood of domestic and transnational terrorism, but the suggested effect is conditioned by the freedom of expression in sanctioned states. When media freedom and other information freedoms are high, we posit that citizens are more likely to direct their grievances against their own government, leading to an increase in domestic terrorism as time under economic sanction increases. When freedom of expression is low, however, leaders of sanctioned states may be able to exploit sanctions to channel hostility away from the home regime via transnational terrorism exported from the sanctioned state. Results from a time-series, cross-national data analysis lend support to our argument on domestic terrorism in the sanctioned state while showing no statistical support for the hypothesis concerning transnational terrorism.
Modeling genotype × environment interaction for single and multitrait genomic prediction in potato (Solanum tuberosum L.)
Authors: Cuevas Jaime , Reslow Fredrik , Crossa Jose , Ortiz Rodomiro
Published: December 2022

In this study, we extend research on genomic prediction (GP) to polysomic polyploid plant species with the main objective to investigate single-trait (ST) and multitrait (MT) multienvironment (ME) models using field trial data from 3 locations in Sweden [Helgegården (HEL), Mosslunda (MOS), Umeå (UM)] over 2 years (2020, 2021) of 253 potato cultivars and breeding clones for 5 tuber weight traits and 2 tuber flesh quality characteristics. This research investigated the GP of 4 genome-based prediction models with genotype × environment interactions (GEs): (1) ST reaction norm model (M1), (2) ST model considering covariances between environments (M2), (3) ST M2 extended to include a random vector that utilizes the environmental covariances (M3), and (4) MT model with GE (M4). Several prediction problems were analyzed for each of the GP accuracy of the 4 models. Results of the prediction of traits in HEL, the high yield potential testing site in 2021, show that the best-predicted traits were tuber flesh starch (%), weight of tuber above 60 or below 40 mm in size, and the total tuber weight. In terms of GP, accuracy model M4 gave the best prediction accuracy in 3 traits, namely tuber weight of 40–50 or above 60 mm in size, and total tuber weight, and very similar in the starch trait. For MOS in 2021, the best predictive traits were starch, weight of tubers above 60, 50–60, or below 40 mm in size, and the total tuber weight. MT model M4 was the best GP model based on its accuracy when some cultivars are observed in some traits. For the GP accuracy of traits in UM in 2021, the best predictive traits were the weight of tubers above 60, 50–60, or below 40 mm in size, and the best model was MT M4, followed by models ST M3 and M2.
Multimorbidity, 30-Day Readmissions, and Postdischarge Mortality Among Medicare Beneficiaries Using a New ICD-Coded Multimorbidity-Weighted Index
Authors: Wei Melissa Y
Published: December 2022

Background

Medically complex, disabled adults have high 30-day readmission rates. However, physical functioning is not routinely included in risk-adjustment models. We examined the association between multimorbidity with readmissions and mortality using a physical functioning weighted International Classification of Diseases (ICD)-coded multimorbidity-weighted index (MWI-ICD) representing 84 conditions.

Methods

We included Medicare beneficiaries with ≥1 hospitalization 2000–2015 who participated in a Health and Retirement Study interview before admission. We computed MWI-ICD by summing physical functioning weighted conditions from Medicare claims. We examined 30-, 90-, and 365-day postdischarge mortality using multivariable logistic regression and length of stay through zero-inflated negative binomials. Models adjusted for age, sex, race/ethnicity, body mass index, smoking status, physical activity, education, net worth, and marital status/living arrangement.

Results

The final sample of 10 737 participants had mean ± standard deviation (SD) age 75.9 ± 8.7 years, MWI-ICD 14.9 ± 9.0, and 20% had a 30-day readmission. Adults in the highest versus lowest quartile MWI-ICD had 92% increased odds of 30-day readmission (odds ratio [OR] = 1.92, 95% confidence interval [CI]: 1.65–2.22). A 1-point increase in MWI-ICD was associated with 24% increased odds of 30-day readmission (OR = 1.24, 95% CI: 1.18–1.31). A 1-point increase in MWI-ICD was associated with 32% increased odds of death within 365-day postdischarge (OR = 1.32, 95% CI: 1.25–1.40). Readmitted participants with the highest versus lowest quartile MWI-ICD had 37% increased number of expected hospitalized days (incidence rate ratio = 1.37, 95% CI: 1.17–1.59).

Conclusion

Among Medicare beneficiaries, multimorbidity using MWI-ICD is associated with an increased risk of readmissions, mortality, and longer length of stay. MWI-ICD appears to be a valid measure of multimorbidity that embeds physical functioning and presents an opportunity to incorporate functional status into claims-based risk-adjustment models.
Who Has Active Lifestyles? Sociodemographic and Personality Correlates of Activity Diversity in Two Samples of Adults
Authors: Lee Soomi , Ng Yee To , Charles Susan T , Almeida David M , Fingerman Karen L
Published: December 2022

Objectives

Activity diversity—an index of active lifestyles that captures variety (number) and evenness (consistency) in activity engagement—is known to support health in adulthood. However, less is known who has higher or lower activity diversity, information that helps identify individuals who may be at greater risk for poor health. This article examined sociodemographic characteristics and Big Five personality traits that may be associated with activity diversity.

Methods

We used 2 independent project samples (nsample1 = 2,699; nsample2 = 301). Sample 1 included U.S. national adults in a wide age range (25–84). Sample 2 included U.S. community-dwelling older adults (age = 65–89). Each study asked about different types of activity engagement using surveys. The activity diversity index was calculated in each sample, using Shannon’s entropy method.

Results

In Sample 1, older adults, women, non-Hispanic White individuals, married/partnered individuals, and those with higher education and fewer functional limitations had higher activity diversity. Additionally, higher conscientiousness, higher extraversion, and lower neuroticism were each associated with higher activity diversity after controlling for sociodemographic factors. Extraversion and neuroticism remained significant in the younger group (age < 65) of Sample 1, but only extraversion was a significant factor associated with activity diversity in the older group (age ≥ 65). The results in the older group were generally replicated in Sample 2, such that higher extraversion in older adults was consistently associated with higher activity diversity independent of the strong correlates of sex, education, and functional limitations.

Discussion

Findings were discussed in terms of age-specific associations between sociodemographic and personality characteristics and activity diversity.
The Quinone-Derived Small Molecule M5N32 Is an Effective Anti–Helicobacter pyloriAgent Both In Vivo and In Vitro
Authors: Wang Liyuan , Yu Yanbo , Tao Yucen , Zhao Mingzhong , Zhang Lu , Xue Junyuan , Zhao Yican , Zhan Peng , Sun Yundong
Published: December 2022

Background

Helicobacter pylori has become increasingly resistant to all commonly used clinical antibiotics. Therefore, new anti–H. pylori drugs need to be identified. Recently, quinones were found to inhibit growth of H. pylori with quinone-derived small-molecule compounds identified as having antitumor effects.

Methods

The minimum inhibitory concentrations of the compounds against H. pylori were measured by agar plate dilution method. The inhibition of biofilm formation by the compounds was assessed by SYTO9-PI double staining. The reactive oxygen species induced by the compounds were detected by DCFH-DA stain. The clearance effects of the compounds for H. pylori in mouse were evaluated by counting colony-forming units and hematoxylin and eosin staining.

Results

Our results revealed strong inhibition of M5N32 in vitro against H. pylori in both the planktonic and biofilm-forming states. Resistance to M5N32 was not developed in successive generations of the bacteria. In vivo, the combination of M5N32 and omeprazole showed enhanced effects in comparison to the standard triple therapy. M5N32 was nontoxic to normal tissues.

Conclusions

M5N32 is effective in the treatment of H. pylori infections, providing potential development of anti–H. pylori medicines in the treatment of H. pylori infections.
Evaluation of a Molecular Mosprie Assay for Detection of Helicobacter pylori and Resistance to Clarithromycin and Levofloxacin
Authors: Zhou Jiarui , Shen Yalin , Song Xiaona , Zhou Linfu , Tang Hong , Li Hong
Published: December 2022

Background

Helicobacter pylori eradication regimens should be guided by antimicrobial susceptibility testing. The objective of this study was to evaluate the molecular-based Mosprie assay for detecting H. pylori resistance to clarithromycin and levofloxacin using gastric biopsies.

Methods

A total of 185 culture-positive frozen gastric biopsies were included for Mosprie assay and also for 23S rRNA and gyrA gene sequencing. The susceptibility results by the Mosprie assay were compared with the E-test results retrospectively retrieved. The discordant results were analyzed by sequencing of the 23S rRNA and gyrA genes.

Results

Susceptibility concordance between the Mosprie assay and E-test for clarithromycin and levofloxacin was 97.30% (180/185) and 88.11% (163/185), respectively. The full agreement between clarithromycin genotypes by Mosprie assay and the 23S rRNA sequencing results was observed in the 5 samples with discordant Mosprie assay and E-test results. However, for levofloxacin, of the 16 discordant samples with resistant phenotype but a susceptible genotype by Mosprie assay, 6 were found to have levofloxacin resistance-related gyrA gene mutations.

Conclusions

The rapid and reliable Mosprie assay can be recommended for H. pylori susceptibility testing of clarithromycin and levofloxacin on gastric biopsies. Future technical improvements are needed in detecting levofloxacin resistance-associated gene mutations.
Natural history collections as a resource for conservation genomics: Understanding the past to preserve the future
Authors: Benham Phred M , Bowie Rauri C K
Published: December 2022

To avoid the worst outcomes of the current biodiversity crisis we need a deep understanding of population responses to human-induced ecological change. Rapidly expanding access to genomic resources for nonmodel taxa promises to play a unique role in meeting this goal. In particular, the increasing feasibility of sequencing DNA from historical specimens enables direct measures of population responses to the past century of anthropogenic change that will inform management strategies and refine projections of species responses to future environmental change. In this review, we discuss the methods that can be used to generate genome-scale data from the hundreds of millions of specimens housed in natural history collections around the world. We then highlight recent studies that utilize genomic data from specimens to address questions of fundamental importance to biodiversity conservation. Finally, we emphasize how traditional motivations of museum collectors, such as studies of geographic variation and community-wide inventories, provide unique opportunities for broad scale comparisons of genomic responses to anthropogenic change across time. We conclude that as sequencing technologies become increasingly accessible and more researchers take advantage of this resource, the importance of collections to the conservation of biodiversity will continue to grow.
Role of cyclooxygenase pathways in bowel fibrotic remodelling in a murine model of experimental colitis
Authors: Colucci Rocchina , Fornai Matteo , Antonioli Luca , Segnani Cristina , Ippolito Chiara , Pellegrini Carolina , Nericcio Anna , Zizzo Maria Grazia , Serio Rosa , Blandizzi Corrado , Bernardini Nunzia
Published: December 2022

Objective

Gut fibrosis occurs under chronic inflammation. This study examined the effects of different cyclooxygenase (COX) inhibitors on fibrosis in the inflamed colon.

Methods

Colitis was induced by 2,4-dinitrobenzenesulfonic acid (DNBS) in albino male Sprague–Dawley rats. After 6, 12 and 18 days, macroscopic and microscopic damage, collagen and elastic fibre content were examined. At day 6, pro-fibrotic factors (collagen I and III, hydroxyproline, fibronectin, matrix metalloproteinase-2 and -9), transforming growth factor-beta (TGF-β) signalling [TGF-β, Ras homolog gene family member A (RhoA), phosphorylated small mother against decapentaplegic (pSMAD)-2 and -6] and peristalsis were assessed, and the effects of indomethacin, SC-560 or celecoxib were tested.

Key findings

Six days after DNBS administration, significant histopathological signs of fibrotic remodelling were observed in rats. At day 6, pro-fibrotic factors were up-regulated and colonic peristalsis was altered. COX inhibitors reversed the histochemical, molecular and functional changes in the fibrotic colon. COX inhibition reduced TGF-β expression, SMAD2 phosphorylation and RhoA, and increased SMAD6 expression.

Conclusions

Colonic fibrosis is associated with altered bowel motility and induction of profibrotic factors driven by TGF-β signalling. COX-1 and COX-2 inhibition counteracts this fibrotic remodelling by the modulation of TGF-β/SMAD signalling, mainly via SMAD6 induction and reduction in SMAD2 phosphorylation.
The effect of saturated thermal conduction on clouds in a hot plasma
Authors: Sander Bastian , Hensler Gerhard
Published: December 2022

We numerically investigate the internal evolution of multiphase clouds, which are at rest with respect to an ambient, highly ionized medium (HIM) representing the hot component of the circumgalactic medium. Time-dependent saturated thermal conduction and its implications like condensation rates and mixing efficiency are assessed in multiphase clouds. Our simulations are carried out by using the adaptive mesh refinement code Flash. . The model clouds are initially in both hydrostatic and thermal equilibrium and are in pressure balance with the HIM. Thus, they have steep gradients in both temperature and density at the interface to HIM leading to non-negligible thermal conduction. Several physical processes are considered numerically or semi-analytically: thermal conduction, radiative cooling and external heating of gas, self-gravity, mass diffusion, and dissociation of molecules and ionization of atoms. It turns out that saturated thermal conduction triggers a continuous condensation irrespective of cloud mass. Dynamical interactions with ambient HIM all relate to the radial density gradient in the clouds: (1) mass flux due to condensation is the higher the more homogeneous the clouds are; (2) mixing of condensed gas with cloud gas is easier in low-mass clouds, because of their shallower radial density gradient; and thus (3) accreted gas is distributed more efficiently. A distinct and sub-structured transition zone forms at the interface between cloud and HIM, which starts at smaller radii and is much narrower as deduced from analytical theory.
Spiral arms and the angular momentum gap in Milky Way Cepheids
Authors: Semczuk Marcin , Dehnen Walter , Schönrich Ralph , Athanassoula E
Published: December 2022

The angular momentum distribution of classical Cepheids in the outer Milky Way disc is bimodal with a gap at $L_\mathrm{gap}=2950\, \rm{km\,s^{-1}}$ kpc, corresponding to $R=13\,$ kpc, while no similar feature has been found in the general population of disc stars. We show that star formation in multiple spiral arm segments at the same azimuth leads to such multimodality that quickly dissolves and only shows in young stars. Unlike other explanations, such as a 1:1 orbital resonance with the Galactic bar, this also accounts for the observed steepening of the stellar warp at Lgap, since the adjacent spiral arms represent different parts of the warped gas disc, and for the predominance of the gap at negative Galactic longitude (ℓ < 0°), since for complex spiral structure this mechanism is limited in azimuth. In this scenario, the gap is clearly present only in young stars, as observed, while most purely stellar dynamical origins would affect all disc populations, including older disc stars.
Compositional turbulence and layering in the gaseous envelopes of forming planets
Authors: Menou Kristen , Zhang Hong Tao
Published: December 2022

Differential settling and growth of dust grains impact the structure of the radiative envelopes of gaseous planets during formation. Sufficiently rapid dust growth can result in envelopes with substantially reduced opacities for radiation transport, thereby facilitating planet formation. We revisit the problem and establish that dust settling and grain growth also lead to outer planetary envelopes that are prone to compositional instabilities, by virtue of their inverted mean-molecular weight gradients. Under a variety of conditions, we find that the radiative envelopes of forming planets experience compositional turbulence driven by a semi-transparent version of the thermohaline instability (’fingering convection’). The standard double-diffusive thermohaline theory does not apply here and is replaced by a simplified first-principle treatment for the semitransparent regime of interest. The compositional turbulence seems efficient at mixing dust in the radiative envelopes of planets forming at super-au distances (say 5 au) from a Sun-like star, but not so at sub-au distances (say 0.2 au). We also address the possibility of compositional layering in this context. Distinct turbulent regimes for planetary envelopes growing at sub-au versus super-au distances could leave an imprint on the final planets formed.
Distinguishing between photoionized and collisionally ionized gas in the circumgalactic medium
Authors: Strawn Clayton , Roca-Fàbrega Santi , Primack Joel
Published: December 2022

Most studies of highly ionized plasmas have historically assumed that ions are either in photoionization equilibrium (PIE) or in collisional ionization equilibrium (CIE), sometimes including multiple phases with different relevant mechanisms. Simulation analysis packages, on the other hand, tend to use pre-computed ion fraction tables that include both mechanisms, among others. Focusing on the low-density, high-temperature phase space likely to be most relevant in the circumgalactic medium, in this work we show that most ions can be classified as ‘PI’ or ‘CI’ on an ion-by-ion basis. This means that for a cloud at a particular point in phase space, some ions will be created primarily by PI and others by CI, with other mechanisms playing only very minor roles. Specifically, we show that ions are generally CI if the thermal energy per particle is greater than ∼6 per cent of their ionization energy, and PI otherwise. We analyse the accuracy of this ansatz compared to usual PIE/CIE calculations, and show the surprisingly minor dependence of this conclusion on redshift and ionizing background.
Comparing weak lensing peak counts in baryonic correction models to hydrodynamical simulations
Authors: Lee Max E , Lu Tianhuan , Haiman Zoltán , Liu Jia , Osato Ken
Published: December 2022

Next-generation weak lensing (WL) surveys, such as by the Vera Rubin Observatory, the Roman Space Telescope, and the Euclid space mission, will supply vast amounts of data probing small, highly non-linear scales. Extracting information from these scales requires higher-order statistics and the controlling of related systematics such as baryonic effects. To account for baryonic effects in cosmological analyses at reduced computational cost, semi-analytic baryonic correction models (BCMs) have been proposed. Here, we study the accuracy of a particular BCM (the A20-BCM) for WL peak counts, a well-studied, simple, and effective higher-order statistic. We compare WL peak counts generated from the full hydrodynamical simulation IllustrisTNG and a baryon-corrected version of the corresponding dark matter-only simulation IllustrisTNG-Dark. We apply galaxy shape noise matching depths reached by DES, KiDS, HSC, LSST, Roman, and Euclid. We find that peak counts from the A20-BCM are (i) accurate at per cent level for peaks with S/N < 4, (ii) statistically indistinguishable from IllustrisTNG in most current and ongoing surveys, but (iii) insufficient for deep future surveys covering the largest solid angles, such as LSST and Euclid. We find that the BCM matches individual peaks accurately, but underpredicts the amplitude of the highest peaks. We conclude that the A20-BCM is a viable substitute for full hydrodynamical simulations in cosmological parameter estimation from beyond-Gaussian statistics for ongoing and future surveys with modest solid angles. For the largest surveys, the A20-BCM must be refined to provide a more accurate match, especially to the highest peaks.
Measuring cosmic filament spin with the kinetic Sunyaev–Zel’dovich effect
Authors: Zheng Yi , Cai Yan-Chuan , Zhu Weishan , Neyrinck Mark , Wang Peng , Li Shaohong
Published: December 2022

The spin of intergalactic filaments has been predicted from simulations, and supported by tentative evidence from redshift-space filament shapes in a galaxy redshift survey: generally, a filament is redshifted on one side of its axis, and blueshifted on the other. Here, we investigate whether filament spins could have a measurable kinetic Sunyaev–Zel’dovich (kSZ) signal, from cosmic microwave background (CMB) photons being scattered by moving ionized gas; this pure velocity information is complementary to filament redshift-space shapes. We propose to measure the kSZ dipole by combining galaxy redshift surveys with CMB experiments. We base our signal-to-noise ratio analyses first on an existing filament catalogue, and its combination with Planck data. We then investigate the detectability of the kSZ dipole using the combination of DESI or SKA-2 with next-stage CMB experiments. We find that the gas haloes of filament galaxies co-rotating with filaments induce a stronger kSZ dipole signal than that from the diffuse filamentary gas, but both signals seem too small to be detected in near-term surveys such as DESI+future CMB experiments. But the combination of SKA-2 with future CMB experiments could give a more than 10σ detection. The gain comes mainly from an increased area overlap and an increased number of filaments, but also the low noise and high resolution in future CMB experiments are important to capture signals from filaments small on the sky. Successful detection of the signals may help to find the gravitomagnetic effect in large-scale structure and advance our understanding of baryons in the cosmic web.
Secondary GeV-TeV emission from ultra-high-energy cosmic rays accelerated by GRB 221009A
Authors: Mirabal N
Published: December 2022

The origin of ultra-high-energy cosmic rays (UHECRs) remains elusive. Gamma-ray bursts (GRBs) are among the best candidates able to meet the stringent energy requirements needed for particle acceleration to such high energies. If UHECRs were accelerated by the central engine of GRB 221009A, it might be possible to detect secondary photons and neutrinos as the UHECRs travel from the source to the Earth. Here, we attempt to interpret some of the early publicly available data connected to this burst. If the reported early GeV-TeV detection was produced by secondary emission from UHECRs, it probably indicates that UHECRs reached energies >1021 eV and that GRB 221009A exploded inside a magnetic void with intergalactic magnetic field (IGMF) strength B ≤ 3 × 10−16 G. In order to understand the entire energy deposition mechanism, we propose to search existing and future Fermi-LAT data for secondary emission arriving over larger spatial scales and longer time-scales. This strategy might help clarify the origin of UHECRs, constrain the IGMF strength along this line of sight, and start to quantify the fraction of magnetic voids around GRBs.
The conserved domain database in 2023
Authors: Wang Jiyao , Chitsaz Farideh , Derbyshire Myra K , Gonzales Noreen R , Gwadz Marc , Lu Shennan , Marchler Gabriele H , Song James S , Thanki Narmada , Yamashita Roxanne A , Yang Mingzhang , Zhang Dachuan , Zheng Chanjuan , Lanczycki Christopher J , Marchler-Bauer Aron
Published: December 2022

NLM’s conserved domain database (CDD) is a collection of protein domain and protein family models constructed as multiple sequence alignments. Its main purpose is to provide annotation for protein and translated nucleotide sequences with the location of domain footprints and associated functional sites, and to define protein domain architecture as a basis for assigning gene product names and putative/predicted function. CDD has been available publicly for over 20 years and has grown substantially during that time. Maintaining an archive of pre-computed annotation continues to be a challenge and has slowed down the cadence of CDD releases. CDD curation staff builds hierarchical classifications of large protein domain families, adds models for novel domain families via surveillance of the protein ‘dark matter’ that currently lacks annotation, and now spends considerable effort on providing names and attribution for conserved domain architectures. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis
Authors: Li Rui , Wang Meihua , Gong Peng
Published: December 2022

The nucleic acid polymerase-catalyzed nucleotidyl transfer reaction associated with polymerase active site closure is a key step in the nucleotide addition cycle (NAC). Two proton transfer events can occur in such a nucleotidyl transfer: deprotonation of the priming nucleotide 3′-hydroxyl nucleophile and protonation of the pyrophosphate (PPi) leaving group. In viral RNA-dependent RNA polymerases (RdRPs), whether and how active site residues participate in this two-proton transfer reaction remained to be clarified. Here we report a 2.5 Å resolution crystal structure of enterovirus 71 (EV71) RdRP in a catalytically closed pre-chemistry conformation, with a proposed proton donor candidate K360 in close contact with the NTP γ-phosphate. Enzymology data reveal that K360 mutations not only reduce RdRP catalytic efficiency but also alter pH dependency profiles in both elongation and pre-elongation synthesis modes. Interestingly, mutations at R174, an RdRP-invariant residue in motif F, had similar effects with additional impact on the Michaelis constant of NTP (KM,NTP). However, direct participation in protonation was not evident for K360 or R174. Our data suggest that both K360 and R174 participate in nucleotidyl transfer, while their possible roles in acid–base or positional catalysis are discussed in comparison with other classes of nucleic acid polymerases.
Translation-complex profiling of fission yeast cells reveals dynamic rearrangements of scanning ribosomal subunits upon nutritional stress
Authors: Duncan Caia Deborah Suzanne , Mata Juan
Published: December 2022

Control of mRNA translation is key for stress responses. Translation initiation is usually rate-limiting and, in eukaryotes, involves mRNA scanning by the small ribosomal subunit. Despite its importance, many aspects of translation in vivo have not been explored fully, especially at the transcriptome-wide level. A recent method termed translation-complex profiling (TCP-seq) allows transcriptome-wide views of scanning ribosomal subunits. We applied TCP-seq to nutritional stress in the fission yeast Schizosaccharomyces pombe. At initiation sites, we observed multiple complexes resembling those of mammals, and consistent with queuing of scanning subunits. In 5′ UTRs, small subunit accumulations were common and may reflect impediments to scanning. A key mediator of stress responses in S. pombe is the Fil1 transcription factor, which is regulated translationally by a poorly-understood mechanism involving upstream Open Reading Frames (uORFs). TCP-seq data of fil1 shows that stress allows scanning subunits to by-pass specific uORFs and reach the fil1 coding sequence. The integration of these observations with reporter assays revealed that fil1 translational control is mediated by a combination of scanning reinitiation-repressive and permissive uORFs, and establishes fil1 as a model for uORF-mediated translational control. Altogether, our transcriptome-wide study reveals general and gene-specific features of translation in a model eukaryote.