bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated transcriptomics–functional genomics approach reveals a small RNA that modulatesBacteroides thetaiotaomicronsensitivity to tetracyclines
Authors: Ryan Daniel , Bornet Elise , Prezza Gianluca , Alampalli Shuba Varshini , Carvalho Taís Franco de , Felchle Hannah , Ebbecke Titus , Hayward Regan , Deutschbauer Adam M. , Barquist Lars , Westermann Alexander J. 
Published: February 2023

ABSTRACTGene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gutBacteroidesspp. Here, we map transcriptional units and profile their expression levels inBacteroides thetaiotaomicronover a suite of 15 defined experimental conditions that are relevantin vivo, such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. Thereby, we infer stress- and carbon source-specific transcriptional regulons, including conditional expression of capsular polysaccharides and polysaccharide utilization loci, and expand the annotation of small regulatory RNAs (sRNAs) in this organism. Integrating this comprehensive expression atlas with transposon mutant fitness data, we identify conditionally important sRNAs. One example is MasB, whose inactivation led to increased bacterial tolerance of tetracyclines. Using MS2 affinity purification coupled with RNA sequencing, we predict targets of this sRNA and discuss their potential role in the context of the MasB-associated phenotype. Together, this transcriptomic compendium in combination with functional sRNA genomics—publicly available through a new iteration of the ‘Theta-Base’ web browser (www.helmholtz-hiri.de/en/datasets/bacteroides-v2)—constitutes a valuable resource for the microbiome and sRNA research communities alike.
Ultrahigh-affinity transport proteins from ubiquitous marine bacteria reveal mechanisms and global patterns of nutrient uptake
Authors: Clifton Ben E. , Alcolombri Uria , Jackson Colin J. , Laurino Paola 
Published: February 2023

AbstractSAR11 bacteria are the most abundant members of the global ocean microbiome and have a broad impact on ocean ecosystems. To thrive in their competitive oligotrophic environments, these bacteria rely on solute-binding proteins (SBPs) that facilitate nutrient uptake through ABC transporters. Nonetheless, previous studies have been unable to access the molecular mechanisms and functions of these transporters because they rely heavily on homology-based predictions. These mechanisms and functions are essential to understand biogeochemical cycling in the ocean, including assimilation of dissolved organic matter (DOM). Here, by doing a biochemical study of the collective behavior of all SBPs in a SAR11 bacterium, we discover that these transporters have unprecedented binding affinity (Kd≥30 pM) and unexpectedly high binding specificity, revealing molecular mechanisms for oligotrophic adaptation. Our study uncovers new carbon sources for the SAR11 bacteria and provides an accurate biogeographical map of nutrient uptake in the ocean. Our results show how functional adaptation at the molecular level in ubiquitous marine bacteria impacts global patterns of DOM assimilation and provides insight into the contribution of different compounds to oceanic nutrient cycles.
Assessment of the acute effects of 2C-B vs psilocybin on subjective experience, mood and cognition
Authors: Mallaroni Pablo , Mason Natasha L. , Reckweg Johannes T. , Paci Riccardo , Ritscher Sabrina , Toennes Stefan W. , Theunissen Eef L. , Kuypers Kim P.C. , Ramaekers Johannes G. 
Published: February 2023

Abstract2,5-dimethoxy-4-bromophenethylamine (2C-B) is a hallucinogenic phenethylamine derived from mescaline. Observational and preclinical data have suggested it to be capable of producing both subjective and emotional effects on par with other classical psychedelics and entactogens. Whereas it is the most prevalently used novel serotonergic hallucinogen to date, it’s acute effects and distinctions from classical progenitors have yet to be characterised in a controlled study. We assessed for the first time the immediate acute subjective, cognitive, and cardiovascular effects of 2C-B (20 mg) in comparison to psilocybin (15mg) and placebo in a within-subjects, double-blind, placebo-controlled study of 22 healthy psychedelic-experienced participants. 2C-B elicited alterations of waking consciousness of a psychedelic nature, with dysphoria, subjective impairment, auditory alterations, and affective elements of ego dissolution largest under psilocybin. Participants demonstrated equivalent psychomotor slowing and spatial memory impairments under either compound compared to placebo, as indexed by the Digit Symbol Substitution Test (DSST), Tower of London (TOL) and Spatial Memory Task (SMT). Neither compound produced empathogenic effects on the Multifaceted Empathy Test (MET). 2C-B induced transient pressor effects to a similar degree as psilocybin. The duration of self-reported effects of 2C-B was shorter than that of psilocybin, largely resolving within 6 hours. Present findings support the categorisation of 2C-B as a subjectively “lighter” psychedelic. Tailored dose-effect studies are needed to discern the pharmacokinetic dependency of 2C-B’s experiential overlaps.
Allergic Asthma Responses Are Dependent on Macrophage Ontogeny
Authors: Tighe Robert M. , Birukova Anastasiya , Malakhau Yuryi , Kobayashi Yoshihiko , Vose Aaron T. , Chandramohan Vidya , Cyphert-Daly Jaime M. , Cumming R. Ian , Kirshner Helene Fradin , Tata Purushothama R. , Ingram Jennifer L. , Gunn Michael D. , Que Loretta G. , Yu Yen-Rei A. 
Published: February 2023

AbstractThe ontogenetic composition of tissue-resident macrophages following injury, environmental exposure, or experimental depletion can be altered upon re-establishment of homeostasis. However, the impact of altered resident macrophage ontogenetic milieu on subsequent immune responses is poorly understood. Hence, we assessed the effect of macrophage ontogeny alteration following return to homeostasis on subsequent allergic airway responses to house dust mites (HDM). Using lineage tracing, we confirmed alveolar and interstitial macrophage ontogeny and their replacement by bone marrow-derived macrophages following LPS exposure. This alteration in macrophage ontogenetic milieu reduced allergic airway responses to HDM challenge. In addition, we defined a distinct population of resident-derived interstitial macrophages expressing allergic airway disease genes, located adjacent to terminal bronchi, and reduced by prior LPS exposure. These findings support that the ontogenetic milieu of pulmonary macrophages is a central factor in allergic airway responses and has implications for how prior environmental exposures impact subsequent immune responses and the development of allergy.
Functional diversity and soil nutrients regulate the interannual variability in gross primary productivity
Authors: Yan Pu , Zhang Jiahui , He Nianpeng , Zhang Weikang , Liu CongCong , Fernández‐Martínez Marcos 
Published: February 2023

Abstract

Global change, encompassing rising temperatures and an increase in extreme precipitation events, has influenced vegetation photosynthesis; this can be seen in the gross primary productivity (GPP) of terrestrial ecosystems, which, over time affects the global carbon cycle. The impact of climate on interannual variability in GPP (GPPIAV) has been extensively explored in the literature. Other changing factors driven by global change, such as biodiversity and soil nutrient availability, are vital in predicting the future of the biosphere. However, the roles of these factors remain unclear.

We combined (i) data from 454 community plots collected using standard protocols from 2013 to 2019 across China, (ii) plant trait data and phylogenetic information of more than 2500 plant species, and (iii) soil nutrient data that we measured. Using these data from 72 “real‐world” ecosystems located across a range of environmental conditions and species pools, we investigated the role of environmental factors including temperature, precipitation and soil nutrients and multifaceted diversity (i.e. species richness, hypervolume‐based functional diversity, and phylogenetic diversity) in mediating the magnitude of GPPIAV using multi‐model averaging and structural equation modelling.

We found that soil nutrients and functional diversity are the main determinants of the magnitude of GPPIAV and that climate effects are predominantly mediated by multifaceted diversity.

Synthesis. We provide strong evidence that ecosystems with higher biodiversity have less variable annual biomass production and decrease the extent of GPPIAV through compensatory effects across diverse ecosystems. Nutrient‐rich ecosystems are likely to buffer the impact of climate variability on ecosystem carbon uptake better than nutrient‐poor ecosystems. Our results demonstrate that biodiversity plays a crucial role in buffering the effects of environmental variability on carbon uptake in terrestrial ecosystems.
Quantifying plant biomass and seed production in camelina (Camelina sativa (L.) Crantz) across a large range of plant densities: Modelling approaches
Authors: Bakhshandeh Esmaeil , Hosseini Sanehkoori Fatemeh , Ghorbani Hamidreza , Nematzadeh Ghorban Ali , Sekrafi Mansour , Abdellaoui Raoudha , Yaghoubi Khanghahi Mohammad , Crecchio Carmine 
Published: February 2023

AbstractTo date, there has been little agreement on supporting the hypothesis that how some key vegetative traits of camelina (Camelina sativa (L.) Crantz var. ‘Soheil’) are dependent on plant biomass. Therefore, the main aim of this investigation was to quantify the relationship between the size of camelina plants and seed production across a broad‐range of plant densities through modelling approaches. To make a wide range of plant densities, a fan design was used in eight replicates in an experimental field at Sari Agricultural Sciences and Natural Resources University, Iran. To quantify the relation between plant density and other plant traits, a regression analysis was carried out and the coefficient of determination (R2) was considered to evaluate the goodness of fit model. A power model (y = axb) could describe well the relationship between plant density (ranged 113–2905 plants m−2) and plant biomass, seed production, number of seeds per plant, stem diameter, and siliques number, with the coefficient of determination (R2) values of 0.85, 0.87, 0.65, 0.64, and 0.90, respectively. The harvest indexes were 13.8%–26.9%, depending on plant density. Seed production per plant was positively correlated to the siliques number (r = 0.85), the branch number (r = 0.80), and the seed number (r = 0.99) which could be key components of camelina seed production per plant. Furthermore, no significant correlation was found among plant height, thousand‐seed weight, and harvest index with seed production per plant. In conclusion, plant biomass could be considered an important trait to predict plant growth models of camelina. Also, a lower plant density of camelina can be compensated by a greater number of siliques, branches and seeds per plant.
Age‐related changes to adipose tissue and peripheral neuropathy in genetically diverse HET3 mice differ by sex and are not mitigated by rapamycin longevity treatment
Authors: Willows Jake W. , Robinson Morganne , Alshahal Zahra , Morrison Samantha K. , Mishra Gargi , Cyr Harrison , Blaszkiewicz Magdalena , Gunsch Gilian , DiPietro Sabrina , Paradie Emma , Tero Benjamin , Harrington Anne , Ryzhova Larisa , Liaw Lucy , Reifsnyder Peter C. , Harrison David E. , Townsend Kristy L. 
Published: February 2023

AbstractNeural communication between the brain and adipose tissues regulates energy expenditure and metabolism through modulation of adipose tissue functions. We have recently demonstrated that under pathophysiological conditions (obesity, diabetes, and aging), total subcutaneous white adipose tissue (scWAT) innervation is decreased (‘adipose neuropathy’). With advanced age in the C57BL/6J mouse, small fiber peripheral nerve endings in adipose tissue die back, resulting in reduced contact with adipose‐resident blood vessels and other cells. This vascular neuropathy and parenchymal neuropathy together likely pose a physiological challenge for tissue function. In the current work, we used the genetically diverse HET3 mouse model to investigate the incidence of peripheral neuropathy and adipose tissue dysregulation across several ages in both male and female mice. We also investigated the anti‐aging treatment rapamycin, an mTOR inhibitor, as a means to prevent or reduce adipose neuropathy. We found that HET3 mice displayed a reduced neuropathy phenotype compared to inbred C56BL/6 J mice, indicating genetic contributions to this aging phenotype. Compared to female HET3 mice, male HET3 mice had worse neuropathic phenotypes by 62 weeks of age. Female HET3 mice appeared to have increased protection from neuropathy until advanced age (126 weeks), after reproductive senescence. We found that rapamycin overall had little impact on neuropathy measures, and actually worsened adipose tissue inflammation and fibrosis. Despite its success as a longevity treatment in mice, higher doses and longer delivery paradigms for rapamycin may lead to a disconnect between life span and beneficial health outcomes.
Effects of environmental factors on the ecology and survival of a widespread, endemic Cerrado frog
Authors: Fiorillo Bruno F. , Faggioni Gabriel Paganini , Cerezer Felipe Osmari , Becker C. Guilherme , Díaz‐Ricaurte Juan C. , Martins Marcio 
Published: February 2023

AbstractUnderstanding the mechanisms that affect habitat use by vertebrates is critical for understanding how species are distributed across landscapes and how they cope with habitat change. The Brazilian Savanna (the Cerrado) has vegetation ranging from grassland to woodland savannas and harbors a rich and diverse amphibian fauna impacted by accelerated habitat loss. Here, we test the influence of vegetation type (from grassy scrubland to woodland) and distance from breeding sites (ephemeral water bodies) on body size, abundance, and survival of the frog Physalaemus nattereri in a natural metapopulation system of south‐central Brazil. We also test whether body size is a significant predictor of population abundance. We found that the abundance of P. nattereri varies according to the mean snout–vent length of each metapopulation (sampling unit), as well as a higher estimated mortality rate in woodlands compared with typical Cerrado. Furthermore, we found no difference in estimated mortality among sampling units located far or close to ephemeral water bodies. Thus, our results highlight variable responses of P. nattereri metapopulations to environmental factors, despite the observed high heterogeneity among sampled habitats and the importance of ephemeral water bodies for reproduction. These findings highlight that land cover and availability of breeding sites might not always interact to explain population persistence of Cerrado frogs.
Transanal irrigation is a better choice for bowel dysfunction in adults with Spina bifida: A randomised controlled trial
Authors: Brochard Charlène , Jezequel Magali , Blanchard‐Dauphin Anne , Kerdraon Jacques , Perrouin‐Verbe Brigitte , Leroi Anne‐Marie , Reymann Jean Michel , Peyronnet Benoît , Morçet Jeff , Siproudhis Laurent 
Published: February 2023

AbstractAimTo compare transanal irrigation with conservative bowel management for the treatment of bowel dysfunction in Spina bifida (SB) patients.MethodsPatients with SB and bowel dysfunction were randomly assigned to receive either transanal irrigation or conservative bowel management. The effectiveness of the treatment was defined as a decrease of 4 points in the neurogenic bowel dysfunction (NBD) score at week 10. Data on incontinence (Cleveland scores; Jorge‐Wexner [JW]) and constipation (Knowles‐Eccersley‐Scott Symptom Constipation Score [KESS]) were recorded at 10 and 24 weeks after inclusion. Data were analysed on an intention‐to‐treat basis.ResultsA total of 34 patients were randomised: 16 patients to conservative bowel management and 18 patients to transanal irrigation. A total of 19/31 (61%) patients improved at week 10, 13 (76%) in the transanal irrigation group versus six (43%) in the conservative group (p = 0.056). In the irrigation group, the decrease in NBD score was −6.9 (−9.9 to −4.02) versus −1.9 (−6.5 to −2.8) in the conservative group (p = 0.049 in univariate and p = 0.004 in multivariate analysis). The NBD, Cleveland (JW and KESS) and Rosenberg scores were significantly lower in the transanal irrigation group than in the conservative bowel management group at week 10.ConclusionsThis prospective, randomised, controlled, multicentre study in adult patients with SB suggests that transanal irrigation may be more effective than conservative bowel management.
Tax noncompliance: The role of tax morale in smokers' behavior
Authors: Prieger James E. 
Published: February 2023

AbstractMeasuring and predicting compliance with tax obligations is an important but challenging task. Survey data from California smokers show that several forms of tax avoidance and evasion were common. The analysis shows that 43% of smokers avoided taxes by purchasing cigarettes from out‐of‐state sources in the past year, 15% admitted to evading taxes through cross‐border purchases, and 26% reported purchasing likely or certainly untaxed cigarettes in the state in the past month. Attitudinal factors related to tax morale explain much more of the variance in compliance rates than demographic or law‐and‐economics factors. The implications for policy are discussed.
The long‐term impact of glucose monitoring with theFreeStyleLibre on glycaemic control and hypoglycaemia awareness in people with type 1 diabetes: Insights from the Association of British Clinical Diabetologists national audit
Authors: Shah Najeeb , Deshmukh Harshal , Wilmot Emma G. , Patmore Jane , Christian Peter , Barnes Dennis J. , Walton Chris , Ryder Robert E. J. , Sathyapalan Thozhukat 
Published: February 2023

AbstractAimsTo investigate the change in glycated haemoglobin (HbA1c), hypoglycaemia awareness and diabetes‐related distress in people with type 1 diabetes (T1D) using FreeStyle Libre (FSL) over a 2‐year follow‐up period.MethodsFSL user data from U.K wide hospitals collected during routine clinical care were analysed. People living with T1D were categorised into four groups based on the duration of follow‐up. Group I (< 1 year,n = 6940), group II (1 to 1.5 years,n = 662), group III (1.5 to 2 years,n = 385), and group IV (> 2 years,n = 642). The t‐test was used to compare the baseline and follow‐up HbA1c, GOLD score (a measure of hypoglycaemia awareness) and diabetes‐related distress scale (DDS score) (quality of life measure).ResultsThe study consisted of 16,834 people, with follow‐up data available for 8,629 participants. The change in HbA1c, GOLD and DDS score from baseline within the follow‐up sub‐groups (group I vs group II vs group III vs group IV) wasHbA1c(−6 vs −6 vs −4 vs −4 mmol/mol;p < 0.001) (−0.55 vs −0.55 vs −0.37 vs −0.37 %),GOLD score(−0.31 vs −0.45 vs −0.26 vs −0.42;p < 0.0001 group I, II, IV andp  0.07 group III), andDDS score(−0.59 vs −0.58 vs −0.63 vs −0.50;p < 0.001), respectively.ConclusionsIn people with T1D, FSL use resulted in a sustained improvement in HbA1c, hypoglycaemia awareness and diabetes‐related distress for over two years.
Trajectory of glycated haemoglobin over time, using real‐world data, in type 2 diabetes patients with obesity on a U‐100 basal‐bolus insulin regimen
Authors: Chen Jieling , Fan Ludi , Maughn Keisha , Rey Gabriel G. , Liu Yi , Nelson David R. , Hood Robert C. 
Published: February 2023

AbstractAimsTo identify patient clusters with poor glucose control among type 2 diabetes mellitus (T2DM) patients with obesity who are receiving basal‐bolus insulin and to identify the potential therapeutic inertia factors associated with poor control.MethodsGlycated haemoglobin (HbA1c) trajectories across a 3‐year period were structured at 6‐month intervals for a retrospective cohort of T2DM patients with obesity on basal‐bolus insulin from the Veterans' Health Administration database. Based on each patient's longitudinal HbA1c features, an unsupervised clustering procedure was used to determine the numbers of clusters and associated trajectory patterns. Multinomial logistic regression was used to examine the association between HbA1c trajectory clusters and patient characteristics/treatment patterns.ResultsA total of 51 273 patients were included, of whom 11.2% were in a subgroup with persistent missingness of HbA1c values. For those with sufficient HbA1c observations, cluster analysis indicated six distinct HbA1c trajectories: stable low (35.8%); stable high (20.8%); descending low (10.5%); ascending low (10.2%); descending high (5.7%); and ascending high (5.7%). Being of Black ethnicity, not initiating noninsulin antihyperglycaemic agents (sodium‐glucose cotransporter‐2 inhibitors, glucagon‐like peptide‐1 receptor agonists or thiazolidinediones) or concentrated insulin, low adherence (measured by proportion of days covered), and reduced insulin prescription refills were factors associated with poorer HbA1c clusters; similar factors were associated with persistent HbA1c missingness.ConclusionThe present study found the potential for therapeutic inertia among a significant proportion of T2DM patients with obesity on basal‐bolus insulin. Subgrouping T2DM patients based on HbA1c missingness and HbA1c trajectories can inform disease management strategies.
Subsurface fatigue crack tip strains in 7475‐T7351 aluminium alloy measured using stroboscopic neutron diffraction
Authors: Coules Harry , Probert Molly , Azuma Kisaburo , Truman Christopher , Seow Cui Er , Pirling Thilo , Cabeza Sandra 
Published: February 2023

AbstractFatigue crack growth in thick‐section metals is typically controlled by an internal plane strain region where strong triaxial constraint of the crack tip occurs. However, the crack tip stress state in this region is challenging to measure. We have used neutron diffraction to study the plane strain section of fatigue crack tips in situ. A stroboscopic form of neutron diffraction using a moving frame‐of‐reference was developed to measure crack tip strains as a function of phase in the fatigue loading cycle without interrupting the cyclic load. Using point measurements of near‐tip strain in 7475‐T7351 aluminium alloy in conjunction with finite element analysis, we can estimate the extent of the crack tip plastic zone, verifying that it is small for this material and set of loading conditions.