bluuebunny/crossref_metadata_2025_split huggingface dataset:
Warnings of declining research productivity: Does Italy buck the trend?
Authors: Abramo Giovanni , D’Angelo Ciriaco Andrea 
Published: September 2023

Abstract
The paper takes a scientometric approach to measure the change in research productivity of Italian academics before the COVID-19 pandemic outbreak. We propose a composite output/input bibliometric indicator and apply it at the field level, conducting a longitudinal analysis. Although the number of academics in the national academic system has decreased, we register very strong growth in both the number of publications and their scholarly impact. The growth in productivity, with only rare exceptions, crosses almost all fields. However, in areas that are traditionally very internationalized (Biology, Physics, and Chemistry), growth is less sustained than overall average, and also the variability of productivity across fields seems reduced. The main reason for this detail would be the smaller margins for improvement in the fields that had already reached high international standing. What emerges from the analysis goes counter to some alarms of declining scientific productivity at the global level. The Italian case is partly explained by the historic adoption of policies aimed at strengthening competitive mechanisms, in particular through the introduction of systems of performance-based research funding, and bibliometric accreditation for professorship.
Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia
Authors: Schnabel Elise , Thomas Jacklyn , El-Hawaz Rabia , Gao Yueyao , Poehlman William L. , Chavan Suchitra , Pasha Asher , Esteban Eddi , Provart Nicholas , Feltus F. Alex , Frugoli Julia 
Published: September 2023

We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Analysis of the Worldwide Diversity of Xanthomonas hortorum pv. carotae, the Agent of Bacterial Blight of Carrot, Reveals Two Distinct Populations
Authors: Dupas Enora , Durand Karine , Jacques Marie-Agnès 
Published: September 2023

Xanthomonas hortorum pv. carotae is a pathogen responsible for the bacterial blight of carrot. Although it infects carrot fields worldwide, its diversity remains unknown. Here, we validated by PCR the identification as X. hortorum pv. carotae of most of the strains isolated from symptomatic carrots. We studied their diversity by sequencing seven housekeeping genes. The analysis confirmed the identity of most of the strains previously identified as X. hortorum pv. carotae and highlighted the presence of two clusters inside the pathovar carotae. The 18 non- X. hortorum pv. carotae have been identified as Xanthomonas from other species. As the X. hortorum pv. carotae strains clustered only in two groups by this analysis, a new multilocus variable number of tandem repeats analysis scheme was developed. It allowed us to validate the subclustering in two groups and observe diversity among them. At the same time, based on this study and data from the literature, we proposed the strain CFBP 7900 as the neopathotype strain of the pathovar. The strain should replace the holopathotype strain CFBP 4997, as it is no longer available in international collections. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Genome Sequence Resource of Bacillus altitudinis KRS010, a Potential Biocontrol Agent Against Verticillium dahliae
Authors: Shan Yujia , Wang Dan , Zhang Dan-Dan , Li Ran , Li Nan-Yang , Kong Zhi-Qiang , Dai Xiao-Feng , Chen Jie-Yin , Han Dongfei , Zhang Xiao-Jun 
Published: September 2023

Bacillus altitudinis strain KRS010 was isolated from the seed of Verticillium wilt-resistant Gossypium hirsutum cultivar Zhongzhimian No. 2. An in vitro assay revealed that the isolate KRS010 exhibited significant antagonistic activity against Verticillium dahliae. Strain KRS010 could be used as a potential biocontrol agent against Verticillium wilt. The KRS010 genome consisted of a single circular chromosome 3,753,708 bp in length, with an average GC content of 41.85%. Genome annotation predicted 3,519 protein-coding genes and 128 noncoding RNA. The complete genome sequence generated in this study will provide a better understanding and application of this strain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Phyllosphere to Ferment: Site Conditions Structure Cacao Pod and Fermentation Microbiomes in Hawaiʻi
Authors: Lewis Ricky W. , Bittenbender Harry C. , Heisey Steven , Nguyen Nhu H. 
Published: September 2023

Microbial fermentation is crucial to the development of flavors in cacao-based products, but how the abiotic environment and pod surface microbiomes can contribute to these different sensory profiles is underdeveloped. To better understand the connections between environment, plant variety, associated pod phyllosphere microbiomes, and the fermentation microbiome, we characterized the fungi and bacteria on pod surfaces and early fermentations of two cacao varieties across wet and dry sites on the island of O‘ahu, Hawai‘i. We showed that site (and the environmental conditions linked to those sites) significantly influenced the microbiomes of both the pod phyllosphere and fermentations but did not significantly explain the differences between cacao varieties. Certain taxa of bacteria and fungi seemingly prefer the wet Kualoa Ranch site compared with the drier Urban Garden Center Site. Rare members of the pod phyllosphere communities became highly enriched during fermentation, where basidiomycetous yeasts ( Filobasidium sp., Hannaella zeae, Rhodotorula mucilaginosa, R. paludigena, and Sporobolomyces carnicolor) became dominant at the wet site, and both ascomycetous and basidiomycetous yeasts ( Hyphopichia burtonii, Meyerozyma sp., Yamadazyma phyllophila, Filobasidium sp., Kwoniella heveanensis, R. mucilaginosa, Sporobolomyces sp., and S. carnicolor) became dominant at the dry site. The agricultural production site where cacao plants are grown should be considered carefully because it is likely important in structuring microbes that are present on pod surfaces and the microbes (mostly yeasts) that will be carried forward into fermentation. These yeasts may contribute to the development of the unique fruity or floral flavors in chocolates produced in Hawai‘i. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Distinct SAP102 and PSD-95 nano-organization defines multiple types of synaptic scaffold protein domains at single synapses
Authors: Metzbower Sarah R. , Dharmasri Poorna A. , Levy Aaron D. , Anderson Michael C. , Blanpied Thomas A. 
Published: September 2023

AbstractThe MAGUK family of scaffold proteins plays a central role in maintaining and modulating synaptic signaling, providing a framework to retain and position receptors, signaling molecules, and other synaptic components. Of these scaffold proteins, SAP102 and PSD-95 are essential for synaptic function at distinct developmental timepoints and perform overlapping as well as unique roles. While their similar structures allow for common binding partners, SAP102 is expressed earlier in synapse development and is required for synaptogenesis, whereas PSD-95 expression peaks later in development and is associated with synapse maturation. PSD-95 and other key synaptic proteins organize into subsynaptic nanodomains that have a significant impact on synaptic transmission, but the nanoscale organization of SAP102 is unknown. How SAP102 is organized within the synapse, and how it relates spatially to PSD-95 on a nanometer scale, could impact how SAP102 clusters synaptic proteins and underlie its ability to perform its unique functions. Here we used DNA-PAINT super-resolution microscopy to measure SAP102 nano-organization and its spatial relationship to PSD-95 at individual synapses. We found that like PSD-95, SAP102 accumulates in high-density subsynaptic nanoclusters. However, SAP102 nanoclusters were smaller and denser than PSD-95 nanoclusters across development. Additionally, only a subset of SAP102 nanoclusters co-organized with PSD-95, revealing that within individual synapses there are nanodomains that contain either one or both proteins. This organization into both shared and distinct subsynaptic nanodomains may underlie the ability of SAP102 and PSD-95 to perform both common and unique synaptic functions.Significance statementSAP102 and PSD-95 are two key members of the MAGUK family of synaptic scaffold proteins that are critical for synapse development, maintenance, and modification during plasticity. Because PSD-95 has a highly complex subsynaptic nanostructure that impacts synaptic function, we asked if SAP102 is similarly organized into nanoclusters at individual synapses and how it relates to PSD-95 within synapses. We found that SAP102 forms subsynaptic nanoclusters with unique properties, and that within individual synapses proteins both concentrate into overlapping nanodomains, as well as form MAGUK-specific nanodomains. This demonstrates that organization of synaptic proteins into nanoclusters is likely to be maintained within the family of MAGUK proteins and reveals potential mechanism for specializing functions within individual synapses based on scaffold protein nanodomains.
Antibiotic ResistantCampylobacterspp Isolated from Live Broilers at an Abattoir in Lusaka, Zambia
Authors: Mukupa John , Ndashe Kunda , Kabwali Emmanuel , Mwanza Grace , Mumba Bernadette 
Published: September 2023

AbstractAntibiotic resistantCampylobacterspp causing campylobacteriosis continue to cause challenges in treatment of the infection. Poultry remains the main source of the foodborne disease. This study was undertaken to isolate and identify antibiotic resistantCampylobacterspp.A total of 160 cloacal swabs were taken from broilers at a poultry abattoir in Lusaka. The samples were analyzed using standard bacteriological test. Antimicrobial susceptibility test was conducted following Clinical and Laboratory Standard Institute guideline and three antibiotics were used ciprofloxacin, tetracycline and erythromycin.Results indicated thatCampylobacterspp was isolated from 18.75% of the sample population, furthermore the isolates were resistant to erythromycin and tetracycline and susceptible to ciprofloxacin. The results highlight the growing concern of poultry being a source of multi-drug resistant pathogenic bacteria.
Glucocorticoid receptor activation induces NK cells to produce AREG and restricts their anti-tumor activity in skin cancer
Authors: Wei Qin , Liang Guirong , zeng Rui , Li Yuancheng , Hong Anlan , Wang Hongsheng , Feng Suying , Wang Yan , Wang Yetao 
Published: September 2023

SummaryNatural killer (NK) cells are recognized as powerful anti-tumor effector cells, but their efficacy is often hindered by the tumor microenvironment (TME). In this study, we analyzed the single-cell transcriptome and cytokine production profiles of NK cells from 24 and 68 paired peri-tumor and tumor skin tissues, respectively. We found that NK cells within skin tumors downregulated anti-tumor cytokines IFN-γ and TNF-α while upregulating amphiregulin (AREG), an EGFR ligand that promotes tumor growth and immune tolerance. This cytokine shift was linked to increased activity of the glucocorticoid receptor (GR, encoded by NR3C1). We further demonstrated that glucocorticoids acting as natural ligands, specifically induced AREG production in NK cells, while NR3C1 knockout and its inhibitors abolished this effect. PGE2, prevalent in TMEs, promoted AREG production independently of glucocorticoid dosage. Moreover, GR activation induced a memory response in NK cells, enhancing AREG production upon subsequent stimuli by increasing chromatin accessibility around the AREG promoter. AREG knockout NK cells exhibited significantly enhanced tumor suppression in NCG mice inoculated with human melanoma or cutaneous squamous cell carcinoma cells. These findings highlight the therapeutic potential of targeting AREG production in NK cells for cancer treatment.Graphical abstract
Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results
Authors: Paton Victor , Gabor Attila , Flores Ricardo Omar Ramirez , Badia-i-Mompel Pau , Tanevski Jovan , Garrido-Rodriguez Martin , Saez-Rodriguez Julio 
Published: September 2023

AbstractTranscriptomics, and in particular RNA-Seq, has become a widely used approach to assess the molecular state of biological systems. To facilitate its analysis, many tools have been developed for different steps, such as filtering lowly expressed genes, normalisation, differential expression, and enrichment. While numerous studies have examined the impact of method choices on differential expression results, little attention has been paid to their effects on further downstream functional analysis using enrichment of gene sets, such as pathways, which typically provides the basis for interpretation and follow-up experiments. To address this gap, we introduce FLOP (FunctionaL Omics Processing), a comprehensive nextflow-based workflow that combines various methods for preprocessing and downstream enrichment analysis, allowing users to perform end-to-end analyses of count level transcriptomic data. We illustrate FLOP capabilities on diverse datasets comprising samples from end-stage heart failure patients and cancer cell lines in both basal and drug-perturbed states. We found that the correlation between gene set enrichment analysis results can vary significantly for alternative pipelines. Additionally, we observed that not filtering the data had the highest impact on the correlation between pipelines in the gene set space, especially in settings with limited statistical power. Overall, our results underscore the impact of carefully evaluating the consequences of the choice of preprocessing methods on downstream enrichment analyses. We envision FLOP as a valuable tool to measure the robustness of functional analyses, ultimately leading to more reliable and conclusive biological findings.Graphical abstract
Cell context-specific Synthetic lethality Prediction and Mechanism Analysis
Authors: Xing Yucui , Pu Mengchen , Cheng Kaiyang , Tian Kai , Wei Lanying , Zheng Weisheng , Peng Gongxin , Zhou Jielong , Zhang Yingsheng 
Published: September 2023

AbstractSynthetic lethality (SL) holds significant promise as a targeted cancer therapy by selectively eliminating tumor cells while sparing normal cells. However, the discovery of SL gene pairs has encountered tremendous challenges, including high costs and low efficiency of experimental methods. Current computational approaches only provide limited insights because of overlooking the crucial aspects of cellular context dependency and mechanistic understanding of SL pairs. To overcome these challenges, we have developed SLWise, a deep-learning model capable of predicting SL interactions in diverse cellular backgrounds. We evaluated SLWise using a real world ground truth standard. The evaluation demonstrated that SLWise outperformed benchmark models in SL prediction. Additionally, we proposed a novel analysis scheme called SLAD-CE (SyntheticLethalAssociated GeneDetection andCell DamageEvaluation) for the identification of abnormal essential genes induced by SL gene pairs and tracking the extent of cell damage. Leveraging the cell-line-specific input feature L1000 and employing Gene Set Enrichment Analysis (GSEA), SLAD-CE provides valuable insights into the underlying mechanisms of SLWise-predicted gene pairs. The combined utilization of SLWise and SLAD-CE offers an approach for predicting and analyzing SL interactions in specific cellular contexts. Our findings highlight the potential of SLWise and SLAD-CE in advancing SL-based therapies by improving prediction accuracy and enhancing mechanistic understanding, ultimately contributing to the development of effective precision treatments for cancer.
Altered enhancer-promoter interaction leads toMNX1expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13)
Authors: Weichenhan Dieter , Riedel Anna , Sollier Etienne , Toprak Umut H. , Hey Joschka , Breuer Kersten , Wierzbinska Justyna A. , Touzart Aurore , Lutsik Pavlo , Bähr Marion , Östlund Anders , Nilsson Tina , Jacobsson Susanna , Edler Marcel , Waraky Ahmed , Behrens Yvonne Lisa , Göhring Gudrun , Schlegelberger Brigitte , Steinek Clemens , Harz Hartmann , Leonhardt Heinrich , Dolnik Anna , Reinhard Dirk , Bullinger Lars , Palmqvist Lars , Lipka Daniel B. , Plass Christoph 
Published: September 2023

AbstractAcute myeloid leukemia (AML) with the t(7;12)(q36;p13) translocation occurs only in very young children and has a poor clinical outcome. The expected oncofusion between breakpoint partners (MNX1andETV6) has only been reported in a subset of cases. However, a universal feature is the strong transcript and protein expression of MNX1, a homeobox transcription factor that is normally not expressed in hematopoietic cells. Here, we map the translocation breakpoints on chromosomes 7 and 12 in affected patients to a region proximal toMNX1and either introns 1 or 2 ofETV6. The frequency ofMNX1overexpression in pediatric AML (n=1556, own and published data) is 2.4% and occurs predominantly in t(7;12)(q36;p13) AML. Chromatin interaction assays in a t(7;12)(q36;p13) iPSC cell line model unravel an enhancer-hijacking event that explainsMNX1overexpression in hematopoietic cells. Our data suggest that enhancer-hijacking is a more common and overlooked mechanism for structural rearrangement-mediated gene activation in AML.Key pointsExpression analysis of over 1500 pediatric AML samples demonstratesMNX1expression as a universal feature of t(7;12)(q36;p13) AML as well as in rare cases without t(7;12)(q36;p13)MNX1is activated by an enhancer-hijacking event in t(7;12)(q36;p13) AML and not, as previously postulated, by the creation of aMNX1::ETV6oncofusion gene.
Enzyme promiscuous profiles for protein sequence and reaction annotation
Authors: MohammadiPeyhani Homa , Sveshnikova Anastasia , Miskovic Ljubisa , Hatzimanikatis Vassily 
Published: September 2023

1.1AbstractNovel sequencing techniques and biochemical pathway prediction resources provide a wealth of data on novel proteins and computationally predicted enzymatic reactions. Accurate matching of protein sequences to enzymatic activities is crucial for advancing synthetic biology and metabolic engineering efforts. Here we present BridgIT+, a computational workflow that accounts for enzyme promiscuity and accurately predicts protein-reaction and reaction-protein associations. BridgIT+ builds upon the promiscuity-based method for annotating orphan and novel reactions with enzymatic activities, BridgIT, and utilizes position-specific scoring matrices (PSSM). The framework uses sequence alignment and enzyme promiscuity predictions to analyze protein sequences, identify sequence patterns, and create promiscuous protein sequence profiles for each reaction. These profiles allow us to predict the protein sequences most likely involved in the reaction. We showcase BridgIT+ by annotating (i) computationally predicted reactions with proteins and (ii) unannotated proteins ofE. coliproteome with enzymatic functions. We demonstrated the performance of BridgIT+ on several biochemical assays and compared it to three current state-of-the-art methods for matching proteins and reactions. We anticipate that the proposed conceptual framework will enhance our understanding of gene-protein-reaction relations and advance biological sequence and reaction annotation in biology and synthetic biology studies.
Measuring, visualizing and diagnosing reference bias with biastools
Authors: Lin Mao-Jan , Iyer Sheila , Chen Nae-Chyun , Langmead Ben 
Published: September 2023

AbstractMany bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it.Biastoolsanalyzes and categorizes instances of reference bias. It works in various scenarios, i.e. (a) when the donor’s variants are known and reads are simulated, (b) when donor variants are known and reads are real, and (c) when variants are unknown and reads are real. Usingbiastools, we observe that more inclusive graph genomes result in fewer biased sites. We find that end-to-end alignment reduces bias at indels relative to local aligners. Finally, we usebiastoolsto characterize how T2T references improve large-scale bias.