bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatomical insights into the vascular lay-out of the barley rachis: implications for transport and spikelet connection
Authors: Rutten Twan , Thirulogachandar Venkatasubbu , Huang Yongyu , Shanmugaraj Nandhakumar , Koppolu Ravi , Ortleb Stefan , Hensel Götz , Kumlehn Jochen , Melzer Michael , Schnurbusch Thorsten 
Published: November 2023

AbstractBackground and aimsVascular patterning is intimately related to plant form and function. However, morphologic a l studies on the vascular anatomy of cereal crops, and inflorescences in particular, are scarce despite their importance for grain yield determination. Here, using barley (Hordeum vulgare) as a model, we study the vascular anatomy of the spike-type inflorescence. Our goal is to clarify the relationship between rachis (spike axis) vasculature and spike size, the implications for transport capacity and its interaction with the spikelets.MethodsWe employed serial transversal internode sections in multiple barley lines with different spike size, and investigated the internode diameter, vascular area and vein number size along the mature barley rachis. We then modeled the vascular dynamics along the main spike axis, and analyzed their relationship with spike size.Key resultsInternode diameter and total vascular area have a clear positive correlation with spike size whereas vascular number is only weakly correlated. While the lateral periphery of the rachis contains large mature veins of constant diameter the central part is occupied by a staggered array of small immature veins. This underlines the importance of minimizing transport resistance and suggests that transport and distribution of nutrients are spatially separated. Spikelet-derived veins enter the rachis either in the central area, where they often merge with the immature rachis veins, or in the periphery where they do not merge with the large mature veins. An increase in floret fertility through the conversion of a two-rowed barley into an isogenic six-rowed line, as well a decrease in floret fertility due to enhanced pre-anthesis tip degeneration caused by the mutationtip sterile 2.b(tst2.b) significantly affected vein size, but had limited to no effects on vein number or rachis diameter. Comparative analysis of a wild barley accession suggests that the domestication of barley may have favored plants with enhanced rachis transport capacity.ConclusionsThe rachis vasculature is the result of a two-step process involving an initial lay-out followed by size adjustment according to floret fertility/spike size. The functional processes of long distance transport and local supply to spikelets are spatially separated while a vascular continuity between rachis and spikelets appears non-essential.
The Drosophila cancer-germline, head-to-head gene pairTrxTanddhdis dispensable for normal brain development but plays a major role inl(3)malignant brain tumourgrowth
Authors: Molnar Cristina , Heinen Jan Peter , Reina Jose , Llamazares Salud , Palumbo Emilio , Pollarolo Giulia , Gonzalez Cayetano 
Published: November 2023

ABSTRACTDrosophila thioredoxins Deadhead (Dhd) and Thioredoxin-T (TrxT) are encoded by a head-to-head gene pair in the X chromosome. Akin to human cancer-germline (CG) genes,dhdandTrxTexpression is normally sex and germline specific, but becomes upregulated in brain tumours of either sex caused by mutation inl(3)malignant brain tumour(l(3)mbt).Using CRISPR/Cas9-mediated knock-out alleles and RNA-seq, we show that while bothTrxTanddhdare dispensable for normal brain development, each of them has a significant but partial effect onl(3)mbtbrain tumour development as well as on tumour-linked transcriptomic signatures. Moreover, this effect is enhanced by the concomitant removal of both thioredoxins that strongly inhibitsl(3)mbtlarval brain tumour traits, reduces gene expression differences between tumour and wild-type tissue, and essentially erases all traces of gene expression differences between tumours from larvae of different sex. These results show thatTrxTanddhdplay a major synergistic role in the emergence ofl(3)mbttumour-linked transcriptomic signatures and tumour development, which is remarkable taking into account that these two genes are never expressed together under normal conditions. We have also found thatTrxTis crucial butdhdhas no effect on the growth of male-derivedl(3)mbtallografts, hence suggesting that the initial stages of tumour development and sustained, long-term tumour growth may depend upon different molecular pathways.In humans, head-to-head inverted gene pairs are abundant among the CG genes that map to the X chromosome, some of which have been shown to work as a unit cancer. Our results identify the first instance of an X-linked, head-to-head CG gene pair in Drosophila and underpin the potential of such CG genes that are dispensable for normal development and homeostasis of somatic tissue, as targets to curtail malignant growth with minimal impact on overall health.
Neuromodulator-induced Temperature Robustness in a Motor Pattern: a Comparative Study Between two Decapod Crustaceans
Authors: Stein Wolfgang , Städele Carola 
Published: November 2023

AbstractWhile temperature fluctuations pose significant challenges to the nervous system, many vital neuronal systems in poikilothermic animals function over a broad temperature range. Using the gastric mill pattern generator in the Jonah crab, we previously demonstrated that temperature-induced increases in leak conductance disrupt neuronal function and that neuropeptide modulation provides thermal protection. Here, we show that neuropeptide modulation also increases temperature robustness in Dungeness and Green crabs. Like in Jonah crabs, higher temperatures increased leak conductance in both species’ pattern-generating neuron LG and terminated rhythmic gastric mill activity. Likewise, increasing descending modulatory projection neuron activity or neuropeptide transmitter application rescued rhythms at elevated temperatures. However, decreasing input resistance using dynamic clamp only restored the rhythm in half of the experiments.Thus, neuropeptide modulation increased temperature robustness in both species, demonstrating that neuropeptide-mediated temperature compensation is not limited to one species, although the underlying cellular compensation mechanisms may be distinct.Summary statementThis study shows that the release of neuropeptide from modulatory projection neurons plays a crucial role in maintaining neuron and circuit function at elevated temperatures across crustacean species.
Evolving patterns of extreme publishing behavior across science
Authors: Ioannidis John P.A. , Collins Thomas A. , Baas Jeroen 
Published: November 2023

ABSTRACTExtreme publishing behavior may reflect a combination of some authors with genuinely high publication output and of other people who have their names listed too frequently in publications because of consortium agreements, gift authorship or other spurious practices. We aimed to evaluate the evolution of extreme publishing behavior across countries and scientific fields during 2000-2022. Extreme publishing behavior was defined as having >60 full articles (original articles, reviews, conference papers) in a single calendar year and indexed in Scopus. We identified 3,191 authors with extreme publishing behavior across science excluding Physics and 12,624 such authors in Physics. While Physics had much higher numbers of extreme publishing authors in the past, in 2022 extreme publishing authors was almost as numerous in non-Physics and Physics disciplines (1,226 vs. 1,480). Excluding Physics, China had the largest number of extreme publishing authors, followed by the USA. The largest fold-wise increases between 2016 and 2022 (5-19-fold) occurred in Thailand, Saudi Arabia, Spain, India, Italy, Russia, Pakistan, and South Korea. Excluding Physics, most extreme publishing authors were in Clinical Medicine, but from 2016 to 2022 the largest relative increases (>6-fold) were seen in Agriculture, Fisheries & Forestry, Biology, and Mathematics and Statistics. Extreme publishing authors accounted for 4,360 of the 10,000 most-cited authors (based on raw citation count) across science. While most Physics authors with extreme publishing behavior had modest citation impact in a composite citation indicator that adjusts for co-authorship and author positions, 67% of authors with extreme publishing behavior in non-Physics fields remained within the top-2% according to that indicator among all authors with >=5 full articles. Extreme publishing behavior has become worryingly common across scientific fields with rapidly increasing rates in some countries and settings and may herald a rapid depreciation of authorship standards.
Plant Phenolics Inhibit Focal Adhesion Kinase and Suppress Host Cell Invasion by UropathogenicEscherichia coli
Authors: Lewis Adam J. , Richards Amanda C. , Mendez Alejandra A. , Dhakal Bijaya K. , Jones Tiffani A. , Sundsbak Jamie L. , Eto Danelle S. , Mulvey Matthew A. 
Published: November 2023

ABSTRACTTraditional folk treatments for the prevention and management of urinary tract infections (UTIs) and other infectious diseases often include plants and plant extracts that are rich in phenolic and polyphenolic compounds. These have been ascribed a variety of activities, including inhibition of bacterial interactions with host cells. Here we tested a panel of four well-studied phenolic compounds – caffeic acid phenethyl ester (CAPE), resveratrol, catechin, and epigallocatechin gallate – for effects on host cell adherence and invasion by uropathogenicEscherichia coli(UPEC). These bacteria, which are the leading cause of UTIs, can bind and subsequently invade bladder epithelial cells via an actin-dependent process. Intracellular UPEC reservoirs within the bladder are often protected from antibiotics and host defenses, and likely contribute to the development of chronic and recurrent infections. Using cell culture-based assays, we found that only resveratrol had a notable negative effect on UPEC adherence to bladder cells. However, both CAPE and resveratrol significantly inhibited UPEC entry into the host cells, coordinate with attenuated phosphorylation of the host actin regulator Focal Adhesion Kinase (FAK, or PTK2) and marked increases in the numbers of focal adhesion structures. We further show that the intravesical delivery of resveratrol inhibits UPEC infiltration of the bladder mucosa in a murine UTI model, and that resveratrol and CAPE can disrupt the ability of other invasive pathogens to enter host cells. Together, these results highlight the therapeutic potential of molecules like CAPE and resveratrol, which could be used to augment antibiotic treatments by restricting pathogen access to protective intracellular niches.IMPORTANCEUrinary tract infections (UTIs) are exceptionally common and increasingly difficult to treat due to the ongoing rise and spread of antibiotic resistant pathogens. Furthermore, the primary cause of UTIs, uropathogenicEscherichia coli(UPEC), can avoid antibiotic exposure and many host defenses by invading the epithelial cells that line the bladder surface. Here we identified two plant-derived phenolic compounds that disrupt activation of the host machinery needed for UPEC entry into bladder cells. One of these compounds (resveratrol) effectively inhibited UPEC invasion of the bladder mucosa in a mouse UTI model, and both phenolic compounds significantly reduced host cell entry by other invasive pathogens. These findings suggest that select phenolic compounds can be used to supplement existing antibacterial therapeutics by denying uropathogens shelter within host cells and tissues, and help explain some of the benefits attributed to traditional plant-based medicines.
The Histopathology ofCephenemyia stimulator-Induced Nasopharyngeal Myiasis in Roe-Deers (Capreolus capreolus)
Authors: Ortiz-Leal Irene , Torres Mateo V. , López-Beceiro Ana , Sanchez-Quinteiro Pablo , Fidalgo Luis 
Published: November 2023

ABSTRACTNasopharyngeal myiasis in European roe deer(Capreolus capreolus)is a pathological condition caused by the larval stages ofCephenemyia stimulator, a fly from the Oestridae family. These larvae reside in the host’s upper respiratory tract for months, inducing significant tissue damage and clinical symptoms. The lifecycle ofCephenemyia stimulatoris complex, involving three larval stages before maturation into adult flies, with each stage contributing to the progressive pathology observed in the host. Despite their prevalence, the histopathological effects of these larvae in the nasopharyngeal and nasal cavities have been understudied. Our study fills this knowledge gap by providing a detailed histopathological analysis of the affected tissues, using various staining techniques to reveal the extent and nature of the damage caused by these parasitic larvae. This histopathological examination reveals significant alterations within the nasopharyngeal mucosa and nasal cavity, including erythematous changes, mucosal metaplasia, fibrosis, and tissue necrosis. Parasitic cysts and eosinophilic infiltration further characterize the infestation’s impact, compromising not only the mucosal integrity but also potentially the olfactory function of the affected animals. This research is crucial for understanding the impact of myiasis on the health of roe deer populations and could have significant implications for wildlife management and conservation.
Late onset and regional heterogeneity of synaptic deficits in cortical PV interneurons ofShank3B−/−mice
Authors: Shih Yi-Chun , Nelson Lars , Janeček Michael , Peixoto Rui T. 
Published: November 2023

AbstractEpilepsy and epileptiform patterns of cortical activity are highly prevalent in autism spectrum disorders (ASDs), but the neural substrates and pathophysiological mechanisms underlying the onset of cortical dysfunction in ASD remains elusive. Reduced cortical expression of Parvalbumin (PV) has been widely observed in ASD mouse models and human postmortem studies, suggesting a crucial role of PV interneurons (PVINs) in ASD pathogenesis.Shank3B−/−mice carrying a Δ13-16 deletion in SHANK3 exhibit cortical hyperactivity during postnatal development and reduced sensory responses in cortical GABAergic interneurons in adulthood. However, whether these phenotypes are associated with PVIN dysfunction is unknown. Using whole-cell electrophysiology and a viral-based strategy to label PVINs during postnatal development, we performed a developmental characterization of AMPAR miniature excitatory postsynaptic currents (mEPSCs) in PVINs and pyramidal (PYR) neurons of layer (L) 2/3 mPFC inShank3B−/−mice. Surprisingly, reduced mEPSC frequency was observed in both PYR and PVIN populations, but only in adulthood. At P15, when cortical hyperactivity is already observed, both neuron types exhibited normal mEPSC amplitude and frequency, suggesting that glutamatergic connectivity deficits in these neurons emerge as compensatory mechanisms. Additionally, we found normal mEPSCs in adult PVINs of L2/3 somatosensory cortex, revealing region-specific phenotypic differences of cortical PVINs inShank3B−/−mice. Together, these results demonstrate that loss of Shank3 alters PVIN function but suggest that PVIN glutamatergic synapses are a suboptimal therapeutic target for normalizing early cortical imbalances in SHANK3-associated disorders. More broadly, these findings underscore the complexity of interneuron dysfunction in ASDs, prompting further exploration of region and developmental stage specific phenotypes for understanding and developing effective interventions.
Structure of the human 80S ribosome at 1.9 Å resolution – the molecular role of chemical modifications and ions in RNA
Authors: Holvec Samuel , Barchet Charles , Lechner Antony , Fréchin Léo , Silva S. Nimali T. De , Hazemann Isabelle , Wolff Philippe , Loeffelholz Ottilie von , Klaholz Bruno P. 
Published: November 2023

SummaryThe ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. We present the 1.9 Å resolution cryo-EM structure of the 80S human ribosome resolving numerous new rRNA modifications and functionally important ions such as Zn2+, K+and Mg2+including their associated individual water molecules. 2’-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry resulting in a complete investigation of the > 230 sites many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerisation turns out to be a key mechanism for U-A base pair stabilisation in RNA in general. The structural environment of chemical modifications & ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy context and human diseases.
Influence of study characteristics, methodological rigor and publication bias on efficacy of pharmacotherapy in obsessive compulsive disorder: a systematic review and meta-analysis of randomized placebo-controlled trials
Authors: Cohen S.E. , Zantvoord J.B. , Storosum B.W.C. , Mattila T.K. , Daams J.G. , Wezenberg B.N. , De Boer A. , Denys D. 
Published: November 2023

QuestionWe examined the effect of study characteristics, risk of bias and publication bias on efficacy of pharmacotherapy in randomized controlled trials (RCT’s) for obsessive-compulsive disorder (OCD).Study selection and analysisWe conducted a systematic search for double-blinded, placebo controlled short-term RCT’s with selective serotonergic reuptake inhibitors (SSRI’s) or clomipramine. We performed a random-effect meta-analysis, using change of the Yale-Brown Obsessive-Compulsive scale (YBOCS) as primary outcome. We performed meta-regression for key study characteristics, and for risk of bias. Furthermore, we analyzed publication bias using a Bayesian selection model.FindingsWe screened 3729 articles and included 21 studies, containing 4102 participants. Meta-analysis showed an effect size of −0.59 (Hedges’ G, 95% CI −0.73 to −0.46), equaling 4.2 point reduction on the YBOCS compared to placebo. The most recent trial was performed in 2007 and most trials were at risk of bias. In our meta-regression, we found that high risk of bias was associated with a larger effect size. Clomipramine was more effective than SSRI’s, even after correcting for risk of bias. We found an indication for publication bias subsequent correction for this bias resulted in a depleted effect size.ConclusionsOur findings reveal superiority of clomipramine over SSRIs, even after adjusting for risk of bias. Effect sizes may be attenuated when considering publication bias and methodological rigor, emphasizing the importance of robust studies to guide clinical utility of OCD pharmacotherapy.
Patterns of change in regulatory modules of chemical reaction systems induced by network modification
Authors: Hishida Atsuki , Okada Takashi , Mochizuki Atsushi 
Published: November 2023

AbstractCellular functions are realized through the dynamics of chemical reaction networks formed by thousands of chemical reactions. Numerical studies have empirically demonstrated that small differences in network structures among species or tissues can cause substantial changes in dynamics. However, the existence of a general principle for behavior changes in response to network structure modifications is not known. The chemical reaction system possesses substructures called buffering structures, which are characterized by a certain topological index being zero. It was proven that the steady-state response to modulation of reaction parameters inside a buffering structure is localized in the buffering structure [1, 2, 3]. In this study, we developed a method to systematically identify the loss or creation of buffering structures induced by the addition of a single degradation reaction from network structure alone. This makes it possible to predict the qualitative and macroscopic changes in regulation that will be caused by the network modification. This method was applied to two reaction systems: the central metabolic system and the mitogen-activated protein kinases (MAPK) signal transduction system. Our method enables identification of reactions that are important for biological functions in living systems.Significance StatementDynamics of complex biological systems have been understood using mathematical models[4, 5, 6, 7]; however, various assumptions are necessary to construct models for large networks such as those found in the life sciences, and discussing the relation between the network structure and its behavior is difficult. Our study using structural sensitivity analysis [1, 2, 3] shows that directly discussing changes in the structure and behavior of a reaction network without making assumptions about kinetics is possible. This enabled the prediction of changes in behavior depending on whether a reaction is present or not and identify reactions that are essentially important for biological behavior.
Electrical impedance spectroscopy with bacterial biofilms: neuronal-like behaviour
Authors: Akabuogu Emmanuel U. , Zhang Lin , Krašovec Rok , Roberts Ian S. , Waigh Thomas A. 
Published: November 2023

AbstractNegative capacitance at low frequencies for neurons was first demonstrated in 1941 (Kenneth S. Cole) using extracellular electrodes. The phenomenon subsequently was explained by Cole using the Hodgkin-Huxley model and is due to the activity of voltage-gated potassium ion channels. We show thatE. colibiofilms exhibit significant stable negative capacitances at low frequencies when they experience a small DC bias voltage in electrical impedance spectroscopy experiments. Using a frequency domain Hodgkin-Huxley model, we characterize the conditions for the emergence of this feature and demonstrate that the negative capacitance exists only in biofilms containing living cells. Furthermore, we established the importance of the voltage-gated potassium ion channel, Kch, using knock-down mutants. The experiments provide further evidence for voltage-gated ion channels inE. coliand a new, low-cost method to probe biofilm electrophysiology e.g. to understand the efficacy of antibiotics.Abstract Figure