bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Cataract Surgery as a Cause of Astigmatism among Patients Undergoing Phacoemulsification and Extracapsular Cataract Extraction at KCMC Hospital
Authors: Malakibungu Suzo Ambindwile , Makupa Andrew , Makupa William 
Published: April 2024

ABSTRACTBackgroundDespite the advance of cataract surgery astigmatism still occur after cataract surgery due to several reasons these include the preparation and closure of the surgical wound, the choice of suture material, and both intraoperative and postoperative manipulations in Phacoemulsification and Extracapsular cataract Etraction.ObjectivesTo evaluate cataract surgery as cause of astigmatisms among patients undergoing phacoemulsification and extracapsular cataract extraction at eye department in KCMC hospital from Sept 2022 to April 2023MethodsIt is a clinic-based, prospective cohort study. Keratometric values and demographic data were collected for eligible patients who had undergone phacoemulsification and Extracapsular Cataract Extraction using a non-contact Auto Refkeratometer BARK-80.ResultsA total of 215 patients were recruited for the study. There were 129 (60%) females and 86 (40%) males. The mean age was 67.481 (SD 10.79years). A total 110 patients had undergone phacoemulsification and 105 had undergone Extracapsular Cataract Extraction (ECCE). 189 (87.91%), had a magnitude greater or equal (≥) to 0.5 post OP astigmatism. The mean corneal astigmatism among all patients undergone ECCE were 2.29D (SD 1.41 D) and all undergone PHACO were 0.95D (SD 0.79 D). The mean astigmatism among patients who had cataract surgery done by specialist were 1.19D (SD 0.09 D) and 2.41D (SD 0.16 D) were done by residents There was no astigmatism in 7 patients (3.26%), with-the-rule (WTR) in 68 patients (31.63%), against-the-rule (ATR) in 112 patients (52.09%) and oblique astigmatism (OA) in 28 patients (13.02%). The tendency of a gradual change from with the rule (WTR) to against the rule (ATR) astigmatism was noted as the age advanced.ConclusionThe present study reveals the magnitude of astigmatism is higher in patients underwent Extra Capsular Cataract Extraction than Phacoemulsification in eye department at KCMC hospital and pre-existing astigmatism is a cause of surgical induced astigmatism if pre- operative astigmatism correction is not taken into consideration.
Spatiotemporal transcriptomic profiling reveals the dynamic immunological landscape of alveolar echinococcosis
Authors: Ou Zhihua , Li Li , Ren Peidi , Zhou Ting-Ting , He Fan , Chen Jialing , Cai Huimin , Han Xiumin , Wu Yao-Dong , Li Jiandong , Li Xiu-Rong , Tan Qiming , Li Wenhui , Chen Qi , Zhang Nian-Zhang , He Xiuju , Chen Wei-Gang , Zhao Yanping , Sun Jiwen , Zhang Qian , Wu Yan-Tao , Liang Yingan , You Jie , Hu Guohai , Tian Xue-Qi , Liao Sha , Fu Bao-Quan , Chen Ao , Cai Xue-Peng , Yang Huanming , Wang Jian , Jin Xin , Xu Xun , Jia Wan-Zhong , Li Junhua , Yan Hong-Bin 
Published: April 2024

ABSTRACTAlveolar echinococcosis (AE) is caused by the invasive growth of the metacestodes ofEchinococcus multilocularis(E. multilocularis). The early diagnosis, management, and treatment of AE remains challenging. Herein, we integrated bulk RNA-seq, scRNA-seq, and ST technologies to reveal the immune characteristics both spatially and chronologically inE. multilocularisinfected mouse liver. An unprecedented high-resolution spatial atlas of theE. multilocularisinfection foci was obtained, revealing the pivotal role of neutrophils,Spp1+monocyte-derived macrophages (MoMFs), and fibroblasts in AE progression. We observed continuous recruitment of neutrophils and macrophages into the infected tissues, indicating prolonged immune stimulation by the growing metacestodes. However, their spatial distribution patterns and functions changed during the infection cause. At the early infection stage,Il1bhineutrophils aggregated in the lesion displayed the highest pattern-recognition receptor activity and may kill the metacestodes through NETosis, but their death in the infection foci might also trigger immune suppression. Meanwhile,Spp1+MoMFs attached to the protoscoleces to clear the infection. At the late infection stage, the neutrophils failed to infiltrate into the lesion although their continuous recruitment into the infected liver. Even though theSpp1+MoMFs enclosing the microcysts ofE. multilocularismay retain their pathogen-killing ability, they may also promote fibrosis and angiogenesis through interaction with fibroblasts. The pro- and anti-inflammatory phenotype balance of these immune cells may be associated with the transition of parasite control strategy from “active killing” to “negative segregation” by the host. Our findings identify key molecular traits involved in AE development, which may benefit the treatment of echinococcosis.
Compromised actin dynamics underlie the orofacial cleft in Baraitser-Winter Cerebrofrontofacial Syndrome with a variant inACTB
Authors: Tsujimoto Takayuki , Ou Yushi , Suzuki Makoto , Murata Yuka , Inubushi Toshihiro , Nagata Miho , Ishihara Yasuki , Yonei Ayumi , Miyashita Yohei , Asano Yoshihiro , Sakai Norio , Sakata Yasushi , Ogino Hajime , Yamashiro Takashi , Kurosaka Hiroshi 
Published: April 2024

AbstractCraniofacial anomalies encompassing the orofacial cleft are associated with >30% of systemic congenital malformations. Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF) is a rare genetic disorder attributed to variants in the actin beta (ACTB) or actin gamma genes that are correlated with a range of craniofacial abnormalities, including cleft lip and/or palate. The underlying pathological mechanism of BWCFF remains elusive, and it is necessary to investigate the etiology of orofacial clefts in BWCFF.In this study, we identified a missense variant (c.1043C>T: p.S348L) in theACTBgene from a patient with BWCFF and concomitant cleft lip and palate. Furthermore, we performed functional assessments of this variant using various disease models such as the MDCK cell line andXenopus laevis. These models revealed a compromised capacity of mutated ACTB to localize at the epithelial junction, consequently affecting the behavior of epithelial cells. Additionally, we made the noteworthy discovery that mutated ACTB exhibited an impaired ability to bind PROFILIN1, a critical factor in actin polymerization. This defective ability may contribute to the molecular etiology of aberrant epithelial cell adhesion and migration, resulting in orofacial cleft formation in BWCFF.Author SummaryAdvances in clinical sequencing have rapidly elucidated the genetic basis of rare diseases affecting multiple organs. In this study, we investigate the role of a variant in theACTBgene, which is fundamental to cell structure, in causing orofacial clefts in the Baraitser-Winter Cerebrofrontofacial Syndrome (BWCFF), known for its distinctive facial anomalies. Using epithelial cell lines and frog embryo models, we investigated the effects of theACTBgene alteration on cellular functions. Our results indicate that this genetic change disrupts the normal adhesion and movement of epithelial cells, processes that are critical for facial development. This research underscores the importance of theACTBgene in shaping the face and suggests new directions for future research, potentially informing the diagnosis and treatment of BWCFF and related conditions.
Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function
Authors: Walther Nike , Anantakrishnan Sathvik , Dailey Gina M. , Tjian Robert , Darzacq Xavier 
Published: April 2024

SummaryLineage transcription factors (TFs) provide one regulatory level of differentiation crucial for the generation and maintenance of healthy tissues. To probe TF function by measuring their dynamics during adult intestinal homeostasis, we established HILO-illumination-based live-cell single-molecule tracking (SMT) in mouse small intestinal enteroid monolayers recapitulating tissue differentiation hierarchiesin vitro. To increase the throughput, capture cellular features, and correlate morphological characteristics with diffusion parameters, we developed an automated imaging and analysis pipeline, broadly applicable to 2D culture systems. Studying two absorptive lineage-determining TFs, we find an expression level-independent contrasting diffusive behavior: While Hes1, key determinant of absorptive lineage commitment, displays a large cell-to-cell variability and an average fraction of DNA-bound molecules of ∼32%, Hnf4g, conferring enterocyte identity, exhibits more uniform dynamics and a bound fraction of ∼56%. Our results suggest that TF diffusive behavior can indicate the progression of differentiation and modulate earlyversuslate differentiation within a lineage.Highlights- Automated live-cell single-molecule tracking records hundreds of cells in enteroid monolayers- Cellular diffusion clustering and morphological feature correlation reveals subpopulations- Transcription factor dynamics regulate differentiation independent of expression level- Hes1 and Hnf4g display contrasting dynamics assisting earlyvs.late absorptive differentiation
Microgliosis driven by palmitate exposure alters energy metabolism and extracellular vesicles release that impact behavior and systemic metabolism
Authors: De Paula Gabriela C. , Aldana Blanca , Battistella Roberta , Calle Rosalia Fernández , Bjure Andreas , Lundgaard Iben , Deierborg Tomas , Duarte João M. N. 
Published: April 2024

AbstractDietary patterns that include an excess of foods rich in saturated fat are associated with brain dysfunction. Although microgliosis has been proposed to play a key role in the development of brain dysfunction in diet-induced obesity (DIO), neuroinflammation with cytokine over-expression is often not always observed. Thus, mechanisms by which microglia contribute to brain impairment in DIO are uncertain. Using the BV2 cell model, we investigated the gliosis profile of microglia exposed to palmitate (200 µmol/L), a saturated fatty acid abundant in high-fat diet and in the brain of obese individuals. We observed that microglia respond to a 24-hour palmitate exposure with increased proliferation, and with a metabolic network rearrangement that favors energy production from glycolysis rather than oxidative metabolism, despite stimulated mitochondria biogenesis. In addition, while palmitate did not induce increased cytokine expression, it modified the protein cargo of released extracellular vesicles (EVs). When administered intra-cerebroventricularly to mice, EVs from palmitate-exposed microgliain vitroled to memory impairment, depression-like behavior, and glucose intolerance, when compared to mice receiving EVs from vehicle-treated microglia. We conclude that microglia exposed to palmitate can mediate brain dysfunction through the cargo of shed EVs.
Enabling Electric Field Model of Microscopically Realistic Brain
Authors: Qi Zhen , Noetscher Gregory M. , Miles Alton , Weise Konstantin , Knösche Thomas R. , Cadman Cameron R. , Potashinsky Alina R. , Liu Kelu , Wartman William A. , Nunez Ponasso Guillermo , Bikson Marom , Lu Hanbing , Deng Zhi-De , Nummenmaa Aapo R. , Makaroff Sergey N. 
Published: April 2024

AbstractModeling brain stimulation at the microscopic scale may reveal new paradigms for various stimulation modalities. We present the largest map to date of extracellular electric field distributions within a layer L2/L3 mouse primary visual cortex brain sample. This was enabled by the automated analysis of serial section electron microscopy images with improved handling of image defects, covering a volume of 250 × 140 × 90 μm3. The map was obtained by applying a uniform brain stimulation electric field at three different polarizations and accurately computing microscopic field perturbations using the boundary element fast multipole method.We used the map to identify the effect of microscopic field perturbations on the activation thresholds of individual neurons. Previous relevant studies modeled a macroscopically homogeneous cortical volume. Our result shows that the microscopic field perturbations – an ‘electric field spatial noise’ with a mean value of zero – only modestly influence the macroscopically predicted stimulation field strengths necessary for neuronal activation. The thresholds do not change by more than 10% on average. Under the stated limitations and assumptions of our method, this result justifies the conventional theory of “invisible” neurons embedded in a macroscopic brain model for transcranial magnetic and transcranial electrical stimulation.However, our result is solely sample-specific and largely neglects the effect of the microcapillary network. Furthermore, we only considered the uniform impressed field and a single- pulse stimulation time course.Significance statementThis study is arguably the first attempt to model brain stimulation at the microscopic scale, enabled by automated analysis of modern scanning electron microscopy images of the brain. It concentrates on modeling microscopic perturbations of the extracellular electric field caused by the physical cell structure and is applicable to any type of brain stimulation.Data availability statementPost-processed cell CAD models (383, stl format), microcapillary CAD models (34, stl format), post-processed neuron morphologies (267, swc format), extracellular electric field and potential distributions at different polarizations (267x3, MATLAB format), *.ses projects files for biophysical modeling with Neuron software (267x2, Neuron format), and computed neuron activating thresholds at different conditions (267x8, Excel tables, without the sample polarization correction from Section 2.8) are made available online throughBossDB, a volumetric open-source database for 3D and 4D neuroscience data.
Bacttle: a microbiology educational board game for lay public and schools
Authors: Miguel Trabajo Tania , Dorcey Eavan , van der Meer Jan Roelof 
Published: April 2024

1.AbstractInspired by the positive impact of serious games on science understanding and motivated by personal interests in scientiﬁc outreach, we developed ‘Bacttle’, an easy-to-play microbiology board game with adaptive difficulty, targeting any player from 7 years old onward. Bacttle addresses both the lay public and teachers for use in classrooms as a way of introducing microbiology concepts.The layout of the game and its mechanism are the result of multiple rounds of trial, feedback and re-design. The ﬁnal version consists of a deck of cards, a 3D-printed board and tokens (with a paper-based alternative), with all digital content open source. Players in Bacttle take on the character of a bacterial species. The aim for each species is to proliferate under the environmental conditions of the board and the interactions with the board and with other players, which vary as the play evolves. Players start with a given number of lives that will increase or decrease based on the traits they play for different environmental scenarios. Such bacterial traits come in the form of cards that can be deployed strategically.In order to assess the impact of the game on microbiological knowledge, we scored differences in the understanding of general concepts before and after playing the game. We assessed a total of 169 visitors at two different university open day science fairs. Players were asked to ﬁll a brief survey before and after the game with questions targeting conceptual advances. Results show that Bacttle increases general microbiology knowledge on players as young as 5 years old, and with the highest impact on those who have noa priorimicrobiology comprehension.
Hexokinase 2 expression in apical enterocytes correlates with inflammation severity in patients with inflammatory bowel disease
Authors: Weber-Stiehl Saskia , Taubenheim Jan , Järke Lea , Röcken Christoph , Schreiber Stefan , Aden Konrad , Kaleta Christoph , Rosenstiel Philip , Sommer Felix 
Published: April 2024

AbstractBackgroundInflammation is characterized by a metabolic switch promoting glycolysis and lactate production. Hexokinases (HK) catalyze the first reaction of glycolysis and inhibition of epithelial HK2 protected from colitis in mice. HK2 expression has been described as elevated in patients with intestinal inflammation, however there is conflicting data from few cohorts especially with severely inflamed individuals, thus systematic studies linking disease activity with HK2 levels are needed.MethodsWe examined the relationship between HK2 expression and inflammation severity using bulk transcriptome data derived from the mucosa of thoroughly phenotyped patients suffering from intestinal inflammation of two independent cohorts. Analyzing publicly available single cell RNA sequencing data and performing immunofluorescence on colonic biopsies of unrelated patients with intestinal inflammation confirmed the RNA-based findings on cellular and protein level.ResultsHK2 expression gradually increased from mild to intermediate inflammation, yet strongly declined at high inflammation scores. Expression of epithelial marker genes also declined at high inflammation scores, whereas that of candidate immune marker genes increased, indicating a cellular remodeling of the mucosa during inflammation with an infiltration of HK2-negative immune cells and a loss of the apical epithelium – the main site of HK2 expression. Normalizing for the enterocyte loss clearly identified epithelial HK2 expression as gradually increasing with disease activity and remaining elevated at high inflammation scores. HK2 protein expression was mostly restricted to brush border enterocytes and these cells along with HK2 levels vanished with increasing disease severity.ConclusionsOur findings clearly define dysregulated epithelial HK2 expression as an indicator of disease activity in intestinal inflammation and suggest targeted HK2-inhibition as a potential therapeutic avenue.
Comparative metagenomic profiling of seed-borne microbiomes in a landrace and a hybrid maize variety
Authors: Henaut-Jacobs Sarah , Cyríaco Beatriz Elisa Barcelos , Pedrosa-Silva Francisnei , Olivares Fabio Lopes , Venancio Thiago Motta 
Published: April 2024

AbstractThe plant seed-borne microbiome comprises microorganisms vertically inherited from the mother plant. This microbiome is often linked to early-life protection and seedling growth promotion. Here, we compare the seed-borne bacteriomes of a commercial hybrid and a landrace maize variety. The landrace variety displays a more diverse seed-borne microbiome, featuring a variety of taxa across samples. In contrast, the microbiome of the hybrid variety is less diverse and more uniform across samples. Although both microbiomes lack a functional nitrogen fixation apparatus, we found a remarkably distinct presence of genes associated with phytohormone production and phosphate solubilization, particularly in the landrace variety. In addition, we recovered 18 metagenome-assembled genomes (MAGs), including four from potentially novel species. Collectively, our results allow a better understanding of the contrasting diversity between maize varieties and open important perspectives for designing synthetic microbial communities for agroecosystems.
The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius
Authors: Pettrich Laura C. , King Robert , Field Linda M. , Waldvogel Ann-Marie 
Published: April 2024

AbstractGenome resolution is often constrained for non-model species. This can be challenging for population genomic studies as estimations are highly dependent on the quality of the reference genome. This is the case for population history inferences where accuracy relies on the correct detection of single-nucleotide polymorphisms (SNPs) and accurate recombination rates. Here, we utilize a novel long-read genome assembly ofChironomus ripariuswith high resolution at a chromosome-scale and reanalyse Illumina resequencing data of five European populations. With the model MSMC2, new population demographies were inferred and compared to an older study based on a fragmented genome. Assembly contiguity and completeness led to an increase in accuracy of past demography, suggesting the onset of divergence of an ancestral population between late Pleistocene and early Holocene. These estimates are additionally supported by paleotemperature data, which reveal significant climate shifts in Central Europe during these times. Recombination severely influences population history estimates. With the new reference genome, it was possible to resolve the recombination landscape on the genome-wide scale across different populations using the tool iSMC. Recombination and the dispersal of transposable elements (TEs) in the genome are suspected to influence each other. One TE, known asCla-element, is suspected to be involved in the divergence of the differentC. ripariuspopulations. As it seems to be highly dynamic in the genome, its potential impact on the recombination landscape was explored. No global pattern could be detected which demonstrated a higher resistance of the recombination landscape to the impact of repetitive elements on genome integrity.
Application of tissue-scale tension to avian epitheliain vivoto study multiscale mechanics and inter-germ layer coupling
Authors: Oikonomou Panagiotis , Calvary Lisa , Cirne Helena C. , Welch Andreas E. , Durel John F. , Powell Olivia , Kim Kwantae , Nerurkar Nandan L. 
Published: April 2024

ABSTRACTAs cross-disciplinary approaches drawing from physics and mechanics have increasingly influenced our understanding of morphogenesis, the tools available to measure and perturb physical aspects of embryonic development have expanded as well. However, it remains a challenge to measure mechanical properties and apply exogenous tissue-scale forces in vivo, particularly for epithelia. Exploiting the size and accessibility of the developing chick embryo, here we describe a simple technique to quantitatively apply exogenous forces on the order of 1-100 N to the endodermal epithelium. To demonstrate the utility of this approach, we performed a series of proof-of-concept experiments that reveal fundamental and unexpected mechanical behaviors in the early chick embryo, including mechanotype heterogeneity among cells of the midgut endoderm, complex non-cell autonomous effects of actin disruption, and a high degree of mechanical coupling between the endoderm and adjacent paraxial mesoderm. To illustrate the broader utility of this method, we determined that forces on the order of 10 N are sufficient to unzip the neural tube during primary neurulation. Together, these findings provide basic insights into the mechanics of embryonic epithelia in vivo in the early avian embryo, and provide a useful tool for future investigations of how morphogenesis is influenced by mechanical factors.Graphical AbstractSummary StatementA simple approach is devised to quantitatively apply tension to epithelia in vivo, and used to study endoderm mechanics in the deeloping chick embryo.