bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population
Authors: Berding Kirsten , Bastiaanssen Thomaz F. S. , Moloney Gerard M. , Boscaini Serena , Strain Conall R. , Anesi Andrea , Long-Smith Caitriona , Mattivi Fulvio , Stanton Catherine , Clarke Gerard , Dinan Timothy G. , Cryan John F. 
Published: October 2022

AbstractThe impact of diet on the microbiota composition and the role of diet in supporting optimal mental health have received much attention in the last decade. However, whether whole dietary approaches can exert psychobiotic effects is largely understudied. Thus, we investigated the influence of a psychobiotic diet (high in prebiotic and fermented foods) on the microbial profile and function as well as on mental health outcomes in a healthy human population. Forty-five adults were randomized into either a psychobiotic (n = 24) or control (n = 21) diet for 4 weeks. Fecal microbiota composition and function was characterized using shotgun sequencing. Stress, overall health and diet were assessed using validated questionnaires. Metabolic profiling of plasma, urine and fecal samples was performed. Intervention with a psychobiotic diet resulted in reductions of perceived stress (32% in diet vs. 17% in control group), but not between groups. Similarly, biological marker of stress were not affected. Additionally, higher adherence to the diet resulted in stronger decreases in perceived stress. While the dietary intervention elicited only subtle changes in microbial composition and function, significant changes in the level of 40 specific fecal lipids and urinary tryptophan metabolites were observed. Lastly, microbial volatility was linked to greater changes in perceived stress scores in those on the psychobiotic diet. These results highlight that dietary approaches can be used to reduce perceived stress in a human cohort. Using microbiota-targeted diets to positively modulate gut-brain communication holds possibilities for the reduction of stress and stress-associated disorders, but additional research is warranted to investigate underlying mechanisms, including the role of the microbiota.
Visualization of BOK pores independent of BAX and BAK reveals a similar mechanism with differing regulation
Authors: Shalaby Raed , Diwan Arzoo , Flores-Romero Hector , Hertlein Vanessa , Garcia-Saez Ana J. 
Published: October 2022

AbstractBOK is a poorly understood member of the BCL-2 family of proteins that has been proposed to function as a pro-apoptotic, BAX-like effector. However, the molecular mechanism and structural properties of BOK pores remain enigmatic. Here, we show that the thermal stability and pore activity of BOK depends on the presence of its C-terminus as well as on the mitochondrial lipid cardiolipin. We directly visualized BOK pores in liposomes by electron microscopy, which appeared similar to those induced by BAX, in line with comparable oligomerization properties quantified by single molecule imaging. In addition, super-resolution STED imaging revealed that BOK organized into dots and ring-shaped assemblies in apoptotic mitochondria, also reminiscent of those found for BAX and BAK. Yet, unlike BAX and BAK, the apoptotic activity of BOK was limited by partial mitochondrial localization and was independent of and unaffected by other BCL-2 proteins. These results suggest that, while BOK activity is kept in check by subcellular localization instead of interaction with BCL-2 family members, the resulting pores are structurally similar to those of BAX and BAK.
Structural basis of actin filament assembly and aging
Authors: Oosterheert Wout , Klink Björn U. , Belyy Alexander , Pospich Sabrina , Raunser Stefan 
Published: October 2022

AbstractThe dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state1–3. It remains unclear how F-actin hydrolyses ATP and subsequently undergoes subtle conformational rearrangements that ultimately lead to filament depolymerization by actin-binding proteins. Here we present cryo-electron microscopy structures of F-actin in all nucleotide states, polymerized in the presence of Mg2+ or Ca2+ at approximately 2.2 Å resolution. The structures show that actin polymerization induces the relocation of water molecules in the nucleotide-binding pocket, activating one of them for the nucleophilic attack of ATP. Unexpectedly, the back door for the subsequent release of inorganic phosphate (Pi) is closed in all structures, indicating that Pi release occurs transiently. The small changes in the nucleotide-binding pocket after ATP hydrolysis and Pi release are sensed by a key amino acid, amplified and transmitted to the filament periphery. Furthermore, differences in the positions of water molecules in the nucleotide-binding pocket explain why Ca2+-actin shows slower polymerization rates than Mg2+-actin. Our work elucidates the solvent-driven rearrangements that govern actin filament assembly and aging and lays the foundation for the rational design of drugs and small molecules for imaging and therapeutic applications.
Phenotypic plasticity and genetic control in colorectal cancer evolution
Authors: Househam Jacob , Heide Timon , Cresswell George D. , Spiteri Inmaculada , Kimberley Chris , Zapata Luis , Lynn Claire , James Chela , Mossner Maximilian , Fernandez-Mateos Javier , Vinceti Alessandro , Baker Ann-Marie , Gabbutt Calum , Berner Alison , Schmidt Melissa , Chen Bingjie , Lakatos Eszter , Gunasri Vinaya , Nichol Daniel , Costa Helena , Mitchinson Miriam , Ramazzotti Daniele , Werner Benjamin , Iorio Francesco , Jansen Marnix , Caravagna Giulio , Barnes Chris P. , Shibata Darryl , Bridgewater John , Rodriguez-Justo Manuel , Magnani Luca , Sottoriva Andrea , Graham Trevor A. 
Published: October 2022

AbstractGenetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather ‘plastic’. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.
Functional antibodies exhibit light chain coherence
Authors: Jaffe David B. , Shahi Payam , Adams Bruce A. , Chrisman Ashley M. , Finnegan Peter M. , Raman Nandhini , Royall Ariel E. , Tsai FuNien , Vollbrecht Thomas , Reyes Daniel S. , Hepler N. Lance , McDonnell Wyatt J. 
Published: October 2022

AbstractThe vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1–CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2–22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
Clonal expansion and epigenetic inheritance of long-lasting NK cell memory
Authors: Rückert Timo , Lareau Caleb A. , Mashreghi Mir-Farzin , Ludwig Leif S. , Romagnani Chiara 
Published: October 2022

AbstractClonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV+ individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.
Detectability and parameter estimation of stellar origin black hole binaries with next generation gravitational wave detectors
Authors: Pieroni Mauro , Ricciardone Angelo , Barausse Enrico 
Published: October 2022

AbstractWe consider stellar-origin black hole binaries, which are among the main astrophysical sources for next generation gravitational wave (GW) detectors such as the Einstein Telescope (ET) and Cosmic Explorer (CE). Using population models calibrated with the most recent LIGO/Virgo results from O3b run, we show that ET and CE will be capable of detecting tens of thousands of such sources (and virtually all of those present in our past light cone up to $$z\lesssim 0.7$$

z
≲
0.7

for ET and $$z\lesssim 1$$

z
≲
1

for CE) with a signal-to-noise ratio up to several hundreds, irrespective of the detector design. When it comes to parameter estimation, we use a Fisher-matrix analysis to assess the impact of the design on the estimation of the intrinsic and extrinsic parameters. We find that the CE detector, consisting of two distinct $$L-$$

L
-

shape interferometers, has better sky localization performance compared to ET in its triangular configuration. We also find that the network is typically capable of measuring the chirp mass, symmetric mass ratio and spins of the binary at order of $$10^{-5}$$

10

-
5

, $$10^{-4}$$

10

-
4

and $$10^{-4}$$

10

-
4

fractional error respectively. While the fractional errors for the extrinsic parameters are of order $$10^{-2}$$

10

-
2

for the sky localization, luminosity distance and inclination.
Prevalence of LA-MRSA in pigsties: analysis of factors influencing the (De)colonization process
Authors: Kobusch Iris , Schröter Iris , Linnemann Sabrina , Schollenbruch Hannah , Hofmann Franka , Boelhauve Marc 
Published: October 2022

AbstractProfessional pig husbandry is often associated with a more or less high load of LA-MRSA. Possible risk factors for LA-MRSA colonization in pig herds have already been identified in studies suggesting that housing conditions may affect LA-MRSA prevalence. In Europe, pigs are kept under variety of conditions. The aim of this study is to identify husbandry and housing condition factors that affect colonization with LA-MRSA. 78 pig farms were selected and assigned to three categories according to housing conditions: conventional, alternative and organic. Animal and surface samples were taken and examined for the presence of LA-MRSA at beginning and end of one fattening period per farm. Altogether, a significant (p < 0.05) decrease in colonization with LA-MRSA from beginning to end of the fattening periods in pigs and surfaces can be observed. Alternative farms showed a higher dynamic in the colonization. In organic farms, almost no colonization was found. Influencing housing condition factors that determine LA-MRSA status at the end of the fattening period are the number of pigs in the building, LA-MRSA status at the beginning of fattening period, material of the floor (straw bedding), strictness of black–white separation and antibiotic treatment during the fattening period. For pig farming in general, knowledge and measures to reduce the colonization with LA-MRSA would be important.
Real world data on the prognostic significance of monocytopenia in myelodysplastic syndrome
Authors: Diamantopoulos Panagiotis T. , Charakopoulos Emmanouil , Symeonidis Argiris , Kotsianidis Ioannis , Viniou Nora-Athina , Pappa Vassiliki , Pontikoglou Charalampos , Tsokanas Dimitrios , Drakos Georgios , Kourakli Alexandra , Solomou Elena , Hatzimichael Eleftheria , Pouli Anastasia , Kotsopoulou Maria , Asmanis Evangelos , Dimou Maria , Panayiotidis Panayiotis , Papageorgiou Sotirios , Vassilopoulos Georgios , Anagnostopoulos Achilles , Vassilakopoulos Theodoros , Papadaki Helen , Galanopoulos Athanasios 
Published: October 2022

AbstractMonocytopenia is a common finding in patients with myelodysplastic syndrome (MDS), but although monocytes may exhibit prognostic significance in MDS due to their role in innate immunity, they have not been incorporated in any prognostic scoring system for MDS. In this study, we analyzed national registry data from 1719 adults with MDS. Monocytopenia was present in 29.5% of the patients and was correlated with the presence of excess blasts and higher revised international prognostic scoring system categories. Univariate analysis showed that monocytopenia was prognostic of a lower overall survival [(OS), 32.0 versus 65.0 months, p < 0.001], while it retained its prognostic significance in a multivariate model comprising anemia, neutropenia and thrombocytopenia [hazard ratio (HR) for OS, 1.320, p < 0.001]. Moreover, it was prognostic of a lower leukemia free survival (LFS) both in univariate analysis and in a multivariate model comprising cytopenias, bone marrow blasts, and cytogenetic risk (HR for LFS 1.27, p = 0.031). The findings regarding OS and LFR were exclusive or more pronounced in lower risk patients, respectively. Moreover, monocytopenia could divide the low and intermediate risk groups of IPSS-R in prognostically distinct subgroups. Our results redefine the prognostic role of monocytes in MDS and set the basis for further studies to validate our results and expand our knowledge on the prognostic significance of monocytopenia in MDS.
Ferritin thresholds for cardiac and liver hemosiderosis in β-thalassemia patients: a diagnostic accuracy study
Authors: Darvishi-Khezri Hadi , Aliasgharian Aily , Naderisorki Mohammad , Kosaryan Mehrnoush , Ghazaiean Mobin , Fallah Hanie , Zahedi Mohammad , Karami Hossein 
Published: October 2022

AbstractFerritin is frequently used to screen some dire consequences of iron overload in β-thalassemia patients. The study aimed to define the best cutoff point of ferritin to screen for cardiac and liver hemosiderosis in these cases. This was a registry-based study on β-thalassemia patients living throughout Mazandaran province, Iran (n = 1959). In this diagnostic research, the index test was ferritin levels measured by a chemiluminescent immunoassay. As a reference test, T2*-weighted magnetic resonance imaging (T2*-weighted MRI) was applied to determine cardiac and liver hemosiderosis. A cutoff point of 2027 ng/mL for ferritin showed a sensitivity of 50%, specificity 77.4%, PPV 42.1%, and NPV 82.5% for cardiac hemosiderosis (area under curve [AUC] 0.66, 95% CI 0.60–0.71, adjusted odds ratio [OR] 2.05, 95% CI 1.05–4.01). At an optimum cutoff point of 1090 ng/mL, sensitivity 66.7%, specificity 68%, PPV 82.9%, and NPV 46.8% for liver hemosiderosis were estimated (AUC 0.68, 95% CI 0.63–0.73, adjusted OR 3.93, 95% CI 2.02–7.64. The likelihood of cardiac hemosiderosis serum ferritin levels below 2027 ng/mL is 17.5%. Moreover, 82.9% of β-thalassemia patients with serum ferritin levels above 1090 ng/mL may suffer from liver hemosiderosis, regardless of the grades.
A quantum graph approach to metamaterial design
Authors: Lawrie Tristan , Tanner Gregor , Chronopoulos Dimitrios 
Published: October 2022

AbstractSince the turn of the century, metamaterials have gained a large amount of attention due to their potential for possessing highly nontrivial and exotic properties—such as cloaking or perfect lensing. There has been a great push to create reliable mathematical models that accurately describe the required material composition. Here, we consider a quantum graph approach to metamaterial design. An infinite square periodic quantum graph, constructed from vertices and edges, acts as a paradigm for a 2D metamaterial. Wave transport occurs along the edges with vertices acting as scatterers modelling sub-wavelength resonant elements. These resonant elements are constructed with the help of finite quantum graphs attached to each vertex of the lattice with customisable properties controlled by a unitary scattering matrix. The metamaterial properties are understood and engineered by manipulating the band diagram of the periodic structure. The engineered properties are then demonstrated in terms of the reflection and transmission behaviour of Gaussian beam solutions at an interface between two different metamaterials. We extend this treatment to N layered metamaterials using the Transfer Matrix Method. We demonstrate both positive and negative refraction and beam steering. Our proposed quantum graph modelling technique is very flexible and can be easily adjusted making it an ideal design tool for creating metamaterials with exotic band diagram properties or testing promising multi-layer set ups and wave steering effects.
The combination of ulinastatin and somatostatin reduces complication rates in acute pancreatitis: a systematic review and meta-analysis of randomized controlled trials
Authors: Horváth István László , Bunduc Stefania , Fehérvári Péter , Váncsa Szilárd , Nagy Rita , Garmaa Gantsetseg , Kleiner Dénes , Hegyi Péter , Erőss Bálint , Csupor Dezső 
Published: October 2022

AbstractCurrently, there is no specific pharmaceutical agent for treating acute pancreatitis (AP). Somatostatin and its analogues have been used to prevent the autolysis of the pancreas in AP, however, their effectiveness has not been confirmed. This investigation aimed to examine the efficacy of ulinastatin, a protease inhibitor, combined with somatostatin analogues in the treatment of AP. We conducted a systematic database search in 4 databases to identify randomized controlled trials in which the efficacy of ulinastatin in combination with somatostatin analogue was compared to somatostatin analogue alone in patients with AP. Since the patient populations of analysed papers were slightly different, we used random effect models to pool odds ratios (OR) and mean differences (MD) and the corresponding 95% confidence intervals (CI). A total of 9 articles comprising 1037 patients were included in the meta-analysis. The combination therapy significantly reduced the complication rates for acute respiratory distress syndrome, acute kidney injury, and multiple organ dysfunction. Symptoms were relieved threefold with the combination therapy compared to somatostatin alone, and combination therapy significantly shortened the length of hospital stay. The decrease in mortality was not statistically significant.﻿
Foundation plant species provide resilience and microclimatic heterogeneity in drylands
Authors: Lortie C. J. , Filazzola Alessandro , Westphal Mike , Butterfield H. Scott 
Published: October 2022

AbstractClimate change profoundly influences plants and animals in all ecosystems including drylands such as semi-arid and arid scrublands and grasslands. At the peak of an extended megadrought in the Southwestern USA, the microclimatic refuges provided by foundation plant species and through associated vegetation were examined. Shrubs and open interstitial spaces without a canopy but with annual plants were instrumented in 2016 and the wet season of 2017 in the central drylands of California. In both years and all seasons tested, vegetation significantly mediated fine-scale near-surface air temperature and relative soil moisture content—defined here as microclimate. The foundation species with other vegetation provided the most significant thermal refuge potential capacity for other plants and animals, but there was variation by growing season. Soil moisture content was frequently increased by the direct canopy effects of shrubs. This evidence suggests that the climate many plants and animals experience, even during an extended megadrought, is mediated by the local plants in highly impacted drylands with anthropogenic disturbance and significant water-induced challenges. Foundation species such as shrubs in drylands function as a potent starting point in examining the ecological relevance of climate at scales germane to many species locally. An ecological framework for climate resilience using shrubs will improve conservation and restoration planning in drylands.
Uncertainty evaluation of data acquisition and analysis system relevant to infrared flowing medium laser
Authors: Dohare Rajeev Kumar , Mainuddin  , Verma Avinash C. , Singhal Gaurav 
Published: October 2022

AbstractIn flowing medium Chemical Oxygen Iodine Laser (COIL), Singlet oxygen is produced by the exothermic reaction of basic hydrogen peroxide solution and chlorine gas. It pumps the iodine and lasing process takes place by stimulated emission. Laser power is extracted using cavity. Development of customized data acquisition system is essential for measurements and analysis of both fundamental (temperature, pressure, level) as well as derived parameters (lasing medium concentration, flow rates of gases and laser power). The focus of the present paper is to dwell on uncertainty evaluation of a complex gas laser source in terms of ascertaining influences of primary/fundamental variables and corresponding derived parameters along with manner of uncertainty propagation. The study facilitates determining the variables with most significant impact on system performance, critical form point of view from optimal functioning of large-scale systems. This enables prediction of overall system uncertainty potentially extendable to other similar laser systems involving subsystems with mutual interdependencies together being distributed over a significantly large laboratory space. The relative combined uncertainty is computed to be 8.3%. The methodology shows significant potential for true decision-making and control of realistic gas laser source operation using developed 150 channel Data Acquisition and Analysis System (DAAS).