bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Rapid Weight Loss after Bariatric Surgery in Systemic Inflammatory Response and Pulmonary Hemodynamics in Severely Obese Subjects with Pulmonary Hypertension
Authors: Valera Roberto J , Fonnegra Cristina Botero , Cogollo Vicente J , Sarmiento-Cobos Mauricio , Rivera Carlos , Lo Menzo Emanuele , Szomstein Samuel , Rosenthal Raul J 
Published: January 2023

BACKGROUND:
Pulmonary hypertension (PH) can be associated with obesity. The excessive production of proinflammatory mediators by dysfunctional adipocytes may enhance remodeling of the pulmonary vasculature and worsen pulmonary hemodynamics. This study aimed to describe the changes in pulmonary arterial pressures and systemic inflammation in patients with obesity with PH after bariatric surgery (BaS).

STUDY DESIGN:
In this retrospective cohort study, we compared patients with PH who underwent BaS from 2008 to 2018 at our institution (group 1) to a group of severely obese patients with PH (group 2). Echocardiographic right ventricular systolic pressure (RVSP) was used as an indirect measurement of pulmonary arterial pressures. Red blood cell distribution width (RDW) was used as a marker of systemic inflammation.

RESULTS:
A total of 40 patients were included, 20 per group. In group 1, the RVSP decreased from 44.69 ± 7.12 mmHg to 38.73 ± 12.81 mmHg (p = 0.041), and the RDW decreased from 15.22 ± 1.53 to 14.41 ± 1.31 (p = 0.020). In group 2, the RVSP decreased from 60.14 ± 18.08 to 59.15 ± 19.10 (0.828), and the RDW increased from 15.37 ± 1.99 to 15.38 ± 1.26 (0.983). For both groups, we found a positive correlation between RVSP and RDW changes, although the correlation was not statistically significant.

CONCLUSIONs:
Previous studies suggest BaS could be a safe and effective procedure to achieve weight loss in obese patients with PH, with an additional modest improvement in pulmonary hemodynamics. The results of this study reinforce this observation and suggest that such improvement could be related to a decrease in systemic inflammation. Further prospective studies with bigger samples are needed to better understand these findings.
Magnetic Resonance Fingerprinting based Thermometry (MRFT): application to ex vivo imaging near DBS leads
Authors: Qian Enlin , Poojar Pavan , Fung Maggie , Jin Zhezhen , Vaughan Thomas , Shrivastava Devashish , Gultekin David , Fernandes Tiago , Geethanath Sairam 
Published: January 2023

AbstractThe purpose of this study is to demonstrate the first work of T1-based magnetic resonance thermometry using magnetic resonance fingerprinting (dubbed MRFT). We compared temperature estimation of MRFT with proton resonance frequency shift (PRFS) thermometry onex vivobovine muscle. We demonstrated MRFT’s feasibility in predicting temperature onex vivobovine muscles with deep brain stimulation (DBS) lead. B0maps generated from MRFT were compared with gold standard B0maps near the DBS lead.All experiments were performed on a 3 Tesla whole-body GE Premier system equipped with a 21-channel receive head coil (GE Healthcare, Milwaukee, WI). Four fluoroptic probes were used to measure the temperature at the center of a cold muscle (probe 1), the room temperature water bottle (probe 2), and the center and periphery of the heated muscle (probes 3 and 4). We selected regions of interest (ROIs) around the location of the probes and used simple linear regression to generate the temperature sensitivity calibration equations that convert T1maps and Δs maps to temperature maps. We then repeated the same setup and compared MRFT, PRFS thermometry temperature estimation with gold standard probe measurements. For the MRFT experiment on DBS lead, we taped the probe to the tip of the DBS lead and used a turbo spin echo (TSE) sequence to induce heating near the lead. We selected ROIs around the tip of the lead to compare MRFT temperature estimation with probe measurements. Vendor-supplied B0mapping sequence was acquired to compare with MRFT-generated B0maps.We found strong linear relationships (R2>0.958) between T1and temperature and Δs and temperatures in our temperature sensitivity calibration experiment. MRFT and PRFS thermometry both accurately predict temperature (RMSE<1.55 °C) compared to probe measurements. MRFT estimated temperature near DBS lead has a similar trend as the probe temperature. Both B0maps show inhomogeneities around the lead.
Integrating physics in deep learning algorithms: A force field as a PyTorch module
Authors: Orlando Gabriele , Serrano Luis , Schymkowitz Joost , Rousseau Frederic 
Published: January 2023

AbstractDeep learning algorithms applied to structural biology often struggle to converge to meaningful solutions when limited data is available, since they are required to learn complex physical rules from examples. State-of-the-art force-fields, however, cannot interface with deep learning algorithms due to their implementation. We present MadraX, a forcefield implemented as a differentiable PyTorch module, able to interact with deep learning algorithms in an end-to-end fashion. MadraX is available at madrax.readthedocs.io
Experimentally induced drought and growing season stage modulate community-level functional traits in a temperate grassland
Authors: Fenollosa E. , Fernandes P. , Hector A. , King H. , Lawson C.S. , Jackson J. , Salguero-Gomez R. 
Published: January 2023

AbstractExtreme precipitation events are expected to become more intense and frequent with climate change. This climatic shift may impact the structure and dynamics of natural communities and the key ecosystem services they provide. Changes in species abundance under these extreme conditions are thought to be driven by functional traits, morpho-physiological characteristics of an organism that impact its fitness. Future environmental conditions may, therefore, favour different functional traits to those in present-day communities.Here, we measure functional traits on 586 vascular plants in a temperate grassland where precipitation has been experimentally manipulated for six years. We calculated community-weighted means of five functional traits (plant height, leaf dry matter content, leaf thickness, specific leaf area, and leaf phosphorus concentration) and compared community-weighted means between three levels of precipitation: drought (−50%), irrigated (+50%), and control. Additionally, we contrasted treatments at two different timings along the growing season: mid-season and late-season.We expected altered community-weighted means for traits associated with a conservative use of water that will result from increased summer stress-induced intraspecific variability in the mid-season and from community composition changes in the late-season, after the field is cut, a common management action across most European grasslands.In the drought treatment, we found significantly lower community-weighted mean plant height and leaf dry matter content. However, we only observed these differences after the mid-season cut. We also observed an increase in leaf phosphorus concentration in the drought treatment before the mid-season cut. A combination of changes in community composition and intraspecific variation contributed to these differences, with community composition being more important after the cut. Species with higher height, leaf dry matter content, and lower leaf thickness showed a more pronounced abundance decline at the drought plots. We observed no changes in functional traits community-weighted means in the irrigated treatment compared to those in control and drought treatments.Synthesis. Our results suggest how the functional trait composition of grassland communities may shift under climate change-induced drought, stressing the interacting effects with growing season stages.
Fluorescent protein lifetimes report increased local densities and phases of nuclear condensates during embryonic stem cell differentiation
Authors: Joron Khalil , Viegas Juliane Oliveira , Haas-Neill Liam , Bier Sariel , Drori Paz , Dvir Shani , Lim Patrick Siang Lin , Rauscher Sarah , Meshorer Eran , Lerner Eitan 
Published: January 2023

AbstractFluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.
An assay to reliably achieve Tar Spot symptoms on corn in a controlled environment
Authors: Breunig Mikaela , Bittner Richard , Dolezal Andrea , Ramcharan Amanda , Bunkers Greg 
Published: January 2023

AbstractTar Spot continues to threaten U.S. corn production (Telenko et al., 2022). A reliable assay under controlled conditions is needed to study the epidemiology and management of Tar Spot. Researchers have reported controlled environment infections, but incidence and severity were low and the ability to screen germplasm has not yet been reported. In this paper, we describe a controlled environment assay that reliably achieves Tar Spot symptoms on corn plants allowing differentiation of susceptible and resistant germplasm.
Integration of spatial and single-cell data across modalities with weak linkage
Authors: Chen Shuxiao , Zhu Bokai , Huang Sijia , Hickey John W. , Lin Kevin Z. , Snyder Michael , Greenleaf William J. , Nolan Garry P. , Zhang Nancy R. , Ma Zongming 
Published: January 2023

Abstractsingle-cell sequencing methods have enabled the profiling of multiple types of molecular readouts at cellular resolution, and recent developments in spatial barcoding, in situ hybridization, and in situ sequencing allow such molecular readouts to retain their spatial context. Since no technology can provide complete characterization across all layers of biological modalities within the same cell, there is pervasive need for computational cross-modal integration (also called diagonal integration) of single-cell and spatial omics data. For current methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori “linked” features. When such linked features are few or uninformative, a scenario that we call “weak linkage”, existing methods fail. We developed MaxFuse, a cross-modal data integration method that, through iterative co-embedding, data smoothing, and cell matching, leverages all information in each modality to obtain high-quality integration. MaxFuse is modality-agnostic and, through comprehensive benchmarks on single-cell and spatial ground-truth multiome datasets, demonstrates high robustness and accuracy in the weak linkage scenario. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, we demonstrate how MaxFuse enables the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
Scalable gaussian process inference of neural responses to natural images
Authors: Goldin Matías A. , Virgili Samuele , Chalk Matthew 
Published: January 2023

1AbstractPredicting the responses of sensory neurons is a long-standing neuroscience goal. However, while there has been much progress in modeling neural responses to simple and/or artificial stimuli, predicting responses to natural stimuli remains an ongoing challenge. One the one hand, deep neural networks perform very well on certain data-sets, but can fail when data is limited. On the other hand, gaussian processes (GPs) perform well on limited data, but are generally poor at predicting responses to high-dimensional stimuli, such as natural images. Here we show how structured priors, e.g. for local and smooth receptive fields, can be used to scale up GPs to high-dimensional stimuli. We show that when we do this, a GP model largely outperforms a deep neural network trained to predict retinal responses to natural images, with largest differences observed when both models are trained on a very small data-set. Further, since GPs compute the uncertainty in their predictions, they are well-suited to closed-loop experiments, where stimuli are chosen actively so as to collect ‘informative’ neural data. We show how this can be done in practice on our retinal data-set, so as to: (i) efficiently learn a model of retinal responses to natural images, using little data, and (ii) rapidly distinguish between competing models (e.g. a linear vs a non-linear model). In the future, our approach could be applied to other low-level sensory areas, beyond the retina.
Bioen-OSMOSE: A bioenergetic marine ecosystem model with physiological response to temperature and oxygen
Authors: Morell Alaia , Shin Yunne-Jai , Barrier Nicolas , Travers-Trolet Morgane , Halouani Ghassen , Ernande Bruno 
Published: January 2023

ABSTRACTMarine ecosystem models have been used to project the impacts of climate-induced changes in temperature and oxygen on biodiversity mainly through changes in species spatial distributions and primary production. However, fish populations may also respond to climatic pressures via physiological changes, leading to modifications in their life history that could either mitigate or worsen the consequences of climate change.Building on the individual-based multispecies ecosystem model OSMOSE, Bioen-OSMOSE has been developed to account for high trophic levels’ physiological responses to temperature and oxygen in future climate projections. This paper presents an overview of the Bioen-OSMOSE model, mainly detailing the new developments. These consist in the implementation of a bioenergetic sub-model that mechanistically describes somatic growth, sexual maturation and reproduction as they emerge from the energy fluxes sustained by food intake under the hypotheses of a biphasic growth model and plastic maturation age and size represented by a maturation reaction norm. These fluxes depend on temperature and oxygen concentration, thus allowing plastic physiological responses to climate change.To illustrate the capabilities of Bioen-OSMOSE to represent realistic ecosystem dynamics, the model is applied to the North Sea ecosystem. The model outputs are confronted with population biomass, catch, maturity ogive, mean size-at-age and diet data of each species of the fish community. A first exploration of current species spatial variability in response to temperature or oxygen is presented in this paper. The model succeeds in reproducing observations, with good performances for all indicators.This new model development opens the scope for new fields of research such as the exploration of seasonal or spatial variation in life history in response to biotic and abiotic factors at the individual, population and community levels. Understanding such variability is crucial to improve our knowledge on potential climate change impacts on marine ecosystems and to make more reliable projections under climate change scenarios.
Cytoplasmic Aggregation of RPB1 Predicts Failure of Neoadjuvant Chemotherapy
Authors: Nagy-Mikó Bence , Németh-Szatmári Orsolya , Faragó-Mészáros Réka , Csókási Aliz , Bognár Bence , Ördög Nóra , Borsos Barbara N. , Majoros Hajnalka , Ujfaludi Zsuzsanna , Oláh-Németh Orsolya , Nikolényi Aliz , Dobi Ágnes , Kószó Renáta , Sántha Dóra , Lázár György , Simonka Zsolt , Paszt Attila , Ormándi Katalin , Pankotai Tibor , Boros Imre M. , Villányi Zoltán , Vörös András 
Published: January 2023

AbstractWe aimed to investigate the contribution of co-translational protein aggregation to the chemotherapy resistance of tumor cells. Increased co-translational protein aggregation reflects altered translation regulation that may have the potential to buffer transcription under genotoxic stress. As an indicator for such event, we followed cytoplasmic aggregation of RPB1, the aggregation prone largest subunit of RNA polymerase II, in biopsy samples taken from patients with invasive carcinoma of no special type. RPB1 frequently aggregates co-translationally in the absence of proper HSP90 chaperone function or in ribosome mutant cells as revealed formerly in yeast. We found that cytoplasmic foci of RPB1 occur in larger sizes in tumors that showed no regression after therapy. Based on these results, we propose that monitoring the cytoplasmic aggregation of RPB1 may be suitable for determining – from biopsy samples taken before treatment – the effectiveness of neoadjuvant chemotherapy.
Top-down Modulation of Brain Responses in Spelling Error Recognition
Authors: Larionova Ekaterina , Garakh Zhanna , Martynova Olga 
Published: January 2023

AbstractThe task being undertaken can influence orthographic, phonological and semantic processes. In linguistic research, two tasks are most often used: a task requiring a decision in relation to the presented word and a passive reading task which does not require a decision regarding the presented word. The results of studies using these different tasks are not always consistent. This study aimed to explore brain responses associated with the process of recognition of spelling errors, as well as the influence of the task on this process. Event-related potentials (ERPs) were recorded in 40 adults during an orthographic decision task to determine correctly spelled words and words written with errors that did not change the phonology and during the passive reading. During spelling recognition, the early stages up to 100 ms after the stimulus were automatic and did not depend on the requirements of the task. The amplitude of the N1 component (90-160 ms) was greater in the orthographic decision task, but did not depend on the correct spelling of the word. Late word recognition after 350-500 ms was task dependent, but spelling effects were similar across the two tasks: misspelled words evoked an increase in the amplitude of the N400 component related to lexical and semantic processing regardless of the task. In addition, the orthographic decision task modulated spelling effects, this was reflected in an increase in the amplitude of the P2 component (180-260 ms) for correctly spelled words compared with misspelled words. Thus, our results show that spelling recognition involves general lexico-semantic processes independent of the task. Simultaneously, the orthographic decision task modulates the spelling-specific processes necessary to quickly detect conflicts between orthographic and phonological representations of words in memory.HighlightsThe influence of task on the recognition of correct spelling of words was studiedSublexical stages during spelling recognition are task-independentThe amplitude of the P1, N1 and P600 components is not sensitive to the spelling of wordsThe orthographic decision task modulates the spelling processes at 180–260 msSpelling recognition modulates the N400 component regardless of the task
The evolution of parthenogen fertilization rates in switching environments: from facultative cell-fusion to oogamy
Authors: Liu Xiaoyuan , Pitchford Jon , Constable George W.A. 
Published: January 2023

AbstractOrganisms with external fertilisation exhibit a broad range of reproductive modes, from simple parthenogenesis to sexual reproduction encompassing isogamy, anisogamy, and oogamy, and including environmentally-mediated facultative sex. Here we develop a unifying mathematical model which explains the emergence of these modes via the coevolution of fertilization rate and cell size. Using a minimal assumption that survival is dependent on cell mass, and by carefully accounting for biological and evolutionary time scales, we find two distinct evolutionary outcomes: high fertilization rate (obligate sexuality) is selected when costs to cell fusion are low, while zero fertilization rate (obligate asexuality) is selected for when these costs are high. Surprisingy, in high fertilization rate scenarios evolving populations can transition from isogamy to anisogamy and oogamy via evolutionary branching. Furthermore, in variable environments we show that, without phenotypic plasticity, intermediate fertilization rates and isogamy can be maintained through bet-hedging. Allowing phenotypic plasticity can give rise to facultative sex; sexual reproduction in harsh environmental conditions, and asexuality in more benign conditions. These results parsimoniously explain a large range of empirically observed parthenogen reproduction strategies, and offer an hypothesis for the origin of binary cell fusion, a key step in the evolution of syngamy and sexual reproduction itself.
Tissue-specific chromatin binding patterns ofC. elegansheterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression
Authors: de la Cruz Ruiz Patricia , Rodríguez-Palero María Jesús , Askjaer Peter , Artal-Sanz Marta 
Published: January 2023

AbstractHeterochromatin is characterized by an enrichment of repetitive elements and low gene density and is often maintained in a repressed state across cell division and differentiation. The silencing is mainly regulated by repressive histone marks, such as H3K9 and H3K27 methylated forms and the heterochromatin protein 1 (HP1) family. Here, we analyzed in a tissue-specific manner the binding profile of the two HP1 homologs inCaenorhabditis elegans, HPL-1 and HPL-2, at the L4 developmental stage. We identified the genome-wide binding profile of intestinal and hypodermal HPL-2 and intestinal HPL-1 and compared them to heterochromatin marks and other features. HPL-2 associated preferentially to the distal arms of autosomes and correlated positively with methylated forms of H3K9 and H3K27. HPL-1 was also enriched in regions containing H3K9me3 and H3K27me3 but exhibited a more even distribution between autosome arms and centers. HPL-2 showed a differential tissue-specific enrichment for repetitive elements, conversely with HPL-1 that exhibited a poor association. Finally, we found a significant intersection of genomic regions bound by the BLMP-1/PRDM1 transcription factor and intestinal HPL-1, suggesting a co-repression role during cell differentiation. Our study uncovers both shared and singular properties of conserved HP1 proteins, providing information about genomic binding preferences in relation to their role as heterochromatic markers.