bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant polysaccharide degradation-related enzymes in Aspergillus oryzae
Authors: Matsuzawa Tomohiko 
Published: December 2023

ABSTRACT
Plants synthesize large amounts of stored and structural polysaccharides. Aspergillus oryzae is used in traditional Japanese fermentation and produces many types of plant polysaccharide degradation-related enzymes. The carbohydrate-active enzymes of A. oryzae are important in the fermentation process and biotechnological applications. Because plant polysaccharides have a complex structure, cooperative and synergistic actions of enzymes are crucial for the degradation of plant polysaccharides. For example, the cooperative action of isoprimeverose-producing oligoxyloglucan hydrolase, β-galactosidase, and α-xylosidase is important for the degradation of xyloglucan, and A. oryzae coordinates these enzymes at the expression level. In this review, I focus on the plant polysaccharide degradation-related enzymes identified in A. oryzae.
Wharton’s jelly and osteoarthritis of the knee
Authors: Aratikatla Adarsh , Maffulli Nicola , Gupta Manu , Potti Ishana A , Potty Anish G , Gupta Ashim 
Published: December 2023

Abstract

Introduction
The existing treatment modalities for knee osteoarthritis (OA) do not actually address the pathology. Biological therapies, including those using material derived from perinatal tissues, represent a ground-breaking approach to alleviating the symptoms of OA of the knee.

Source of data
Current scientific literature published in PubMed (MEDLINE), Embase and Scopus databases. Trials registered in various clinical trial databases.

Areas of agreement
Perinatal tissues including Wharton’s jelly (WJ) and associated mesenchymal stem cells (MSCs) can be used for the management of knee OA.

Areas of controversy
The efficacy of WJ and associated MSCs in the management of knee OA is still controversial.

Growing points
The use of WJ and associated MSCs in the management of knee OA is safe and appears to be effective.

Areas timely for developing research
The present published evidence suggests that WJ tissue and associated MSCs offer an encouraging alternative for the management of knee OA. The published in vitro, preclinical and clinical investigations demonstrate the therapeutic potential of WJ and promote further research in this field to provide symptomatic relief to patients suffering from OA, aiming also to regenerate the osteoarthritic hyaline cartilage, with disease-modifying effects. Future adequately powered randomized controlled trials should be undertaken to establish whether WJ is helpful in the management of OA of the knee.
Neural correlates of prediction error in patients with schizophrenia: evidence from an fMRI meta-analysis
Authors: Yang Xun , Song Yuan , Zou Yuhan , Li Yilin , Zeng Jianguang 
Published: December 2023

Abstract
Abnormal processes of learning from prediction errors, i.e. the discrepancies between expectations and outcomes, are thought to underlie motivational impairments in schizophrenia. Although dopaminergic abnormalities in the mesocorticolimbic reward circuit have been found in patients with schizophrenia, the pathway through which prediction error signals are processed in schizophrenia has yet to be elucidated. To determine the neural correlates of prediction error processing in schizophrenia, we conducted a meta-analysis of whole-brain neuroimaging studies that investigated prediction error signal processing in schizophrenia patients and healthy controls. A total of 14 studies (324 schizophrenia patients and 348 healthy controls) using the reinforcement learning paradigm were included. Our meta-analysis showed that, relative to healthy controls, schizophrenia patients showed increased activity in the precentral gyrus and middle frontal gyrus and reduced activity in the mesolimbic circuit, including the striatum, thalamus, amygdala, hippocampus, anterior cingulate cortex, insula, superior temporal gyrus, and cerebellum, when processing prediction errors. We also found hyperactivity in frontal areas and hypoactivity in mesolimbic areas when encoding prediction error signals in schizophrenia patients, potentially indicating abnormal dopamine signaling of reward prediction error and suggesting failure to represent the value of alternative responses during prediction error learning and decision making.
Electrical stimulation induced self-related auditory hallucinations correlate with oscillatory power change in the default mode network
Authors: Yang Jing , Shen Lu , Long Qiting , Li Wenjie , Zhang Wei , Chen Qi , Han Biao 
Published: December 2023

Abstract
Self-related information is crucial in our daily lives, which has led to the proposal that there is a specific brain mechanism for processing it. Neuroimaging studies have consistently demonstrated that the default mode network (DMN) is strongly associated with the representation and processing of self-related information. However, the precise relationship between DMN activity and self-related information, particularly in terms of neural oscillations, remains largely unknown. We electrically stimulated the superior temporal and fusiform areas, using stereo-electroencephalography to investigate neural oscillations associated with elicited self-related auditory hallucinations. Twenty-two instances of auditory hallucinations were recorded and categorized into self-related and other-related conditions. Comparing oscillatory power changes within the DMN between self-related and other-related auditory hallucinations, we discovered that self-related hallucinations are associated with significantly stronger positive power changes in both alpha and gamma bands compared to other-related hallucinations. To ensure the validity of our findings, we conducted controlled analyses for factors of familiarity and clarity, which revealed that the observed effects within the DMN remain independent of these factors. These results underscore the significance of the functional role of the DMN during the processing of self-related auditory hallucinations and shed light on the relationship between self-related perception and neural oscillatory activity.
Intermittent migration can induce pulses of speciation in a two-island system
Authors: Princepe Débora , Czarnobai Simone , Caetano Rodrigo A , Marquitti Flavia M D , de Aguiar Marcus A M , Araujo Sabrina B L 
Published: December 2023

Abstract
Geographic barriers can come and go depending on natural conditions. These fluctuations cause population cycles of expansion and contraction, introducing intermittent migrations that may not hinder speciation but rather promote diversification. Here, we study a neutral 2-island speciation model with intermittent migration driven by sea-level fluctuations. Seabed depth modulates isolation and connection periods between the islands, with migration occurring during connection periods with a certain probability. Mating is restricted to genetically compatible individuals on the same island and offspring inherit genomes from both parents through recombination. We observe speciation pulses that would not occur under strict isolation or continuous migration, with infrequent, temporary increases in species richness happening at different times depending on the combination of geographic settings and migration probability. The resulting dynamic patterns of richness exhibit contrasting behavior between connected and isolated scenarios, often including species that do not persist. Prolonged isolation can reduce richness to 1 species per island, resembling patterns commonly associated with archipelagos under sea-level fluctuations. Together with other studies, our results in out-of-equilibrium populations support the relevance of investigating the impact of variable migration on diversification, particularly in regions of high diversity.
Overlap between the Mid-Atlantic Bight Cold Pool and offshore wind lease areas
Authors: Horwitz Rebecca , Miles Travis N , Munroe Daphne , Kohut Josh 
Published: December 2023

AbstractThe Mid-Atlantic Cold Pool is a seasonal mass of cold bottom water that extends throughout the Mid-Atlantic Bight (MAB). Formed from rapid vernal surface warming, the Cold Pool dissipates in the fall due to mixing events such as storms. The Cold Pool supports a myriad of MAB coastal ecosystems and economically valuable commercial and recreational fisheries. Offshore wind energy has been rapidly developing within the MAB in recent years. Studies in Europe demonstrate that offshore wind farms can impact ocean mixing and hence seasonal stratification; there is, however, limited information on how MAB wind development will affect the Cold Pool. Seasonal overlap between the Cold Pool and pre-construction wind lease areas at varying distances from shore in the MAB was evaluated using output from a data-assimilative ocean model. Results highlight overlap periods as well as a thermal gradient that persists after bottom temperatures warm above the threshold typically used to identify the Cold Pool. These results also demonstrate cross-shelf variability in Cold Pool evolution. This work highlights the need for more focused ocean modeling studies and observations of wind farm effects on the MAB coastal environment.
Blueberry floral probiotics: nectar microbes inhibit the growth ofColletotrichumpathogens
Authors: Rering Caitlin C , Lanier Alexia M , Peres Natalia A 
Published: December 2023

AbstractAimsTo identify whether microorganisms isolated from blueberry flowers can inhibit the growth of Colletotrichum, an opportunistic plant pathogen that infects flowers and threatens yields, and to assess the impacts of floral microbes and Colletotrichum pathogens on artificial nectar sugars and honey bee consumption.Methods and resultsThe growth inhibition of Colletotrichum (Colletotrichum acutatum, Colletotrichum fioriniae, and Colletotrichum gloeosporioides) was screened using both artificial nectar co-culture and dual culture plate assays. All candidate nectar microbes were screened for antagonism against a single C. acutatum isolate. Then, the top four candidate nectar microbes showing the strongest inhibition of C. acutatum (Neokomagataea thailandica, Neokomagataea tanensis, Metschnikowia rancensis, and Symmetrospora symmetrica) were evaluated for antagonism against three additional C. acutatum isolates, and single isolates of both C. fioriniae and C. gloeosporioides. In artificial nectar assays, single and three-species cultures inhibited the growth of two of four C. acutatum isolates by ca. 60%, but growth of other Colletotrichum species was not affected. In dual culture plate assays, inhibition was observed for all Colletotrichum species for at least three of four selected microbial antagonists (13%‒53%). Neither honey bee consumption of nectar nor nectar sugar concentrations were affected by any microbe or pathogen tested.ConclusionsSelected floral microbes inhibited growth of all Colletotrichum species in vitro, although the degree of inhibition was specific to the assay and pathogen examined. In all microbial treatments, nectar sugars were preserved, and honey bee preference was not affected.
A case study of the diet-microbiota-parasite interplay in bumble bees
Authors: Gekière Antoine , Vanderplanck Maryse , Hettiarachchi Amanda , Semay Irène , Gerbaux Pascal , Michez Denis , Joossens Marie , Vandamme Peter 
Published: December 2023

Abstract

Aims
Diets and parasites influence the gut bacterial symbionts of bumble bees, but potential interactive effects remain overlooked. The main objective of this study was to assess the isolated and interactive effects of sunflower pollen, its phenolamides, and the widespread trypanosomatid Crithidia sp. on the gut bacterial symbionts of Bombus terrestris males.

Methods and results
Bumble bee males emerged in microcolonies fed on either (i) willow pollen (control), (ii) sunflower pollen, or (iii) willow pollen spiked with phenolamide extracts from sunflower pollen. These microcolonies were infected by Crithidia sp. or were pathogen-free. Using 16S rRNA amplicon sequencing (V3–V4 region), we observed a significant alteration of the beta diversity but not of the alpha diversity in the gut microbial communities of males fed on sunflower pollen compared to males fed on control pollen. Similarly, infection by the gut parasite Crithidia sp. altered the beta diversity but not the alpha diversity in the gut microbial communities of males, irrespective of the diet. By contrast, we did not observe any significant alteration of the beta or alpha diversity in the gut microbial communities of males fed on phenolamide-enriched pollen compared to males fed on control pollen. Changes in the beta diversity indicate significant dissimilarities of the bacterial taxa between the treatment groups, while the lack of difference in alpha diversity demonstrates no significant changes within each treatment group.

Conclusions
Bumble bees harbour consistent gut microbiota worldwide, but our results suggest that the gut bacterial communities of bumble bees are somewhat shaped by their diets and gut parasites as well as by the interaction of these two factors. This study confirms that bumble bees are suitable biological surrogates to assess the effect of diet and parasite infections on gut microbial communities.
Insight into the long-term impact of birth weight on intestinal development, microbial settlement, and the metabolism of weaned piglets
Authors: Trevisi Paolo , Negrini Clara , Correa Federico , Virdis Sara , Laghi Luca , Marcello Mele , Conte Giuseppe , Mazzoni Maurizio , Luise Diana 
Published: December 2023

AbstractInfant mortality of low birth body weight (LBBW) piglets can reach 10% and is mainly due to gut and immune system immaturity which can lead to a higher risk in the long term. This study aimed to assess the impact of birth body weight (BBW) on piglet metabolism, gut status, and microbial profile from weaning to 21 d postweaning. At birth, 32 piglets were selected for their BBW and inserted into the normal BBW (NBBW:1.38 ± 0.09 g) or the LBBW (0.92 ± 0.07 g) group. The piglets were weighed weekly from weaning (d0) to d21. At d9 and d21, 8 piglets/group were slaughtered to obtain the distal jejunum for morphology, immunohistochemistry, and gene expression analysis, colon content for microbiota and short-chain fatty acid (SCFA) analysis, and intestinal content for pH measurement. Blood was collected for metabolomic, haptoglobin (Hp), and reactive oxygen metabolite (ROM) analysis. The LBBW group had a lower body weight (BW) throughout the study (P &lt; 0.01), a lower average daily gain from d9-d21 (P = 0.002), and lower feed intake (P = 0.02). The LBBW piglets had lower Hp at d9 (P = 0.03), higher ROMs at d21 (P = 0.06), and a net alteration of the amino acid (AA) metabolism at d9 and d21. A higher expression of NFKB2 was observed in the LBBW piglets at d9 (P = 0.003) and d21 (P &lt; 0.001). MYD88 expression was enhanced in NBBW piglets at d9 (P &lt; 0.001). The LBBW piglets had a lower villus height, absorptive mucosal surface (P = 0.01), and villus height:crypt depth ratio (P = 0.02), and a greater number of T-lymphocytes in both the epithelium and the crypts (P &lt; 0.001) at d21. At d21, the LBBW piglets had higher lactic acid, acetate, butyrate, and valerate, and also higher SCFA in the colon (P &lt; 0.05). The LBBW piglets had a higher Shannon index (P = 0.01) at d9 and a higher abundance of SCFA-fermenting bacteria. In conclusion, the present study confirmed that LBBW could impact the gut mucosal structure, immunity, and inflammatory and oxidative status, leading to an altered AA metabolism, and delaying the recovery from weaning.
An miR164-resistant mutation in the transcription factor gene CpCUC2B enhances carpel arrest and ectopic boundary specification in Cucurbita pepo flower development
Authors: Segura María , García Alicia , Gamarra Germán , Benítez Álvaro , Iglesias-Moya Jessica , Martínez Cecilia , Jamilena Manuel 
Published: December 2023

Abstract
The sex determination process in cucurbits involves the control of stamen or carpel development during the specification of male or female flowers from a bisexual floral meristem, a function coordinated by ethylene. A gain-of-function mutation in the miR164-binding site of CpCUC2B, ortholog of the Arabidopsis transcription factor gene CUC2, not only produced ectopic floral meristems and organs, but also suppressed the development of carpels and promoted the development of stamens. The cuc2b mutation induced the transcription of CpCUC2B in the apical shoots of plants after female flowering but repressed other CUC genes regulated by miR164, suggesting a conserved functional redundancy of these genes in the development of squash flowers. The synergistic androecious phenotype of the double mutant between cuc2b and etr2b, an ethylene-insensitive mutation that enhances the production of male flowers, demonstrated that CpCUC2B arrests the development of carpels independently of ethylene and CpWIP1B. The transcriptional regulation of CpCUC1, CpCUC2, and ethylene genes in cuc2b and ethylene mutants also confirms this conclusion. However, the epistasis of cuc2b over aco1a, a mutation that suppresses stamen arrest in female flowers, and the down-regulation of CpACS27A in cuc2b female apical shoots, indicated that CpCUC2B promotes stamen development by suppressing the late ethylene production.
Bibliometric analysis and thematic review of Candida pathogenesis: Fundamental omics to applications as potential antifungal drugs and vaccines
Authors: Lim Si Jie , Muhd Noor Noor Dina , Sabri Suriana , Mohamad Ali Mohd Shukuri , Salleh Abu Bakar , Oslan Siti Nurbaya 
Published: December 2023

Abstract
Invasive candidiasis caused by the pathogenic Candida yeast species has resulted in elevating global mortality. The pathogenicity of Candida spp. is not only originated from its primary invasive yeast-to-hyphal transition; virulence factors (transcription factors, adhesins, invasins, and enzymes), biofilm, antifungal drug resistance, stress tolerance, and metabolic adaptation have also contributed to a greater clinical burden. However, the current research theme in fungal pathogenicity could hardly be delineated with the increasing research output. Therefore, our study analysed the research trends in Candida pathogenesis over the past 37 years via a bibliometric approach against the Scopus and Web of Science databases. Based on the 3993 unique documents retrieved, significant international collaborations among researchers were observed, especially between Germany (Bernhard Hube) and the UK (Julian Naglik), whose focuses are on Candida proteinases, adhesins, and candidalysin. The prominent researchers (Neils Gow, Alistair Brown, and Frank Odds) at the University of Exeter and the University of Aberdeen (second top performing affiliation) UK contribute significantly to the mechanisms of Candida adaptation, tolerance, and stress response. However, the science mapping of co-citation analysis performed herein could not identify a hub representative of subsequent work since the clusters were semi-redundant. The co-word analysis that was otherwise adopted, revealed three research clusters; the cluster-based thematic analyses indicated the severeness of Candida biofilm and antifungal resistance as well as the elevating trend on molecular mechanism elucidation for drug screening and repurposing. Importantly, the in vivo pathogen adaptation and interactions with hosts are crucial for potential vaccine development.
Saltire: a model to measure dynamical masses for high-contrast binaries and exoplanets with high-resolution spectroscopy
Authors: Sebastian D , Triaud A H M J , Brogi M 
Published: December 2023

ABSTRACT
High-resolution cross-correlation methods are widely used to discover and to characterise atomic and molecular species in exoplanet atmospheres. The characteristic cross-correlation signal is typically represented as a function of the velocity of the system, and the semi-amplitude of the planet’s orbit. We present Saltire, a fast and simple model that accurately reproduces the shape of such cross-correlation signals, allowing a direct fit to the data by using a minimum set of parameters. We show how to use this model on the detection of atmospheric carbon monoxide in archival data of the hot Jupiter $\rm \tau$ Boötis b, and how Saltire can be used to estimate the semi-amplitude and rest velocity of high brightness ratio binaries. By including the shape of the signal, we demonstrate that our model allows to robustly derive the signal position up to 10 times more accurate, compared to conventional methods. Furthermore, we discuss the impact of correlated noise and demonstrate that Saltire is a robust tool for estimating systematic uncertainties on the signal position. Saltire opens a new door to analyse high signal-to-noise data to accurately study atmospheric dynamics and to measure precise dynamical masses for exoplanets and faint stellar companions. We show that the phase-resolved shape of the atmospheric cross-correlation signal can accurately be reproduced, allowing studies of phase-dependent signal changes and to disentangle them from noise and data aliases.
The Lyman-α forest catalogue from the Dark Energy Spectroscopic Instrument Early Data Release
Authors: Ramírez-Pérez César , Pérez-Ràfols Ignasi , Font-Ribera Andreu , Karim M Abdul , Armengaud E , Bautista J , Beltran S F , Cabayol-Garcia L , Cai Z , Chabanier S , Chaussidon E , Chaves-Montero J , Cuceu A , de la Cruz R , García-Bellido J , Gonzalez-Morales A X , Gordon C , Herrera-Alcantar H K , Iršič V , Ishak M , Karaçaylı N G , Lukić Zarija , Manser C J , Montero-Camacho P , Napolitano L , Niz G , Pieri M M , Ravoux C , Sinigaglia F , Tan T , Walther M , Wang B , Aguilar J , Ahlen S , Bailey S , Brooks D , Claybaugh T , Dawson K , de la Macorra A , Dhungana G , Doel P , Fanning K , Forero-Romero J E , Gontcho S Gontcho A , Guy J , Honscheid K , Kehoe R , Kisner T , Landriau M , Le Guillou L , Levi M E , Magneville C , Martini P , Meisner A , Miquel R , Moustakas J , Mueller E , Muñoz-Gutiérrez A , Nie J , Palanque-Delabrouille N , Percival W J , Rossi G , Sanchez E , Schlafly E F , Schlegel D , Seo H , Tarlé G , Weaver B A , Yéche C , Zhou Z 
Published: December 2023

ABSTRACT
We present and validate the catalogue of Lyman-α forest fluctuations for 3D analyses using the Early Data Release (EDR) from the Dark Energy Spectroscopic Instrument (DESI) survey. We used 88 511 quasars collected from DESI Survey Validation (SV) data and the first two months of the main survey (M2). We present several improvements to the method used to extract the Lyman-α absorption fluctuations performed in previous analyses from the Sloan Digital Sky Survey (SDSS). In particular, we modify the weighting scheme and show that it can improve the precision of the correlation function measurement by more than 20 per cent. This catalogue can be downloaded from https://data.desi.lbl.gov/public/edr/vac/edr/lya/fuji/v0.3, and it will be used in the near future for the first DESI measurements of the 3D correlations in the Lyman-α forest.