bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Total and Nontotal Endoscopic Transaxillary Breast Augmentation Techniques
Authors: Yan Wen-Hui , Zeng Ang , Li Gao-Feng , Liu Hui , Mang Jian-Bo , Ren Li-Li , Gao Ji-Dong 
Published: April 2023

Background
The aim of this retrospective study was to compare the clinical outcomes of total endoscopic transaxillary (TET) breast augmentation with those of non-TET (NTET) breast augmentation. For the purposes of this study, the term NTET refers to the combination of blunt dissection and endoscopic techniques, whereas TET did not involve blunt dissection.

Methods
We conducted a retrospective review of 119 consecutive cases of primary breast augmentation from May 1, 2020, to August 31, 2020. The primary outcomes were the number of drainage days and pain scores as assessed using the visual analog scale on the first postoperative day. The secondary outcomes were the daily drainage volume recorded during the postoperative drainage days, the presence of postoperative daily pain that required the administration of tramadol for relief, reoperation rate, and operative time.

Results
The number of drainage days was significantly lower in the TET group than in the NTET group (TET vs NTET: 2.56 ± 0.57 vs 3.78 ± 1.30 days, P = 0.000). The visual analog scale score on the first postoperative day was significantly lower in the TET group than in the NTET group (TET vs NTET: 4.96 ± 0.63 vs 5.93 ± 0.93, P = 0.000).

Conclusions
We observed that the major outcomes of the TET group were more favorable than those of the NTET group. Based on our results, we recommend the avoidance of blunt dissection during endoscopic transaxillary breast augmentation.

Level of Evidence
III
Research and Innovation in Organ Donation: Recommendations From an International Consensus Forum
Authors: Escoto Manuel , Issa Fadi , Cayouette Florence , Consolo Henrietta , Chaudhury Prosanto , Dhanani Sonny , Jiang Wenshi , Oniscu Gabriel C. , Murphy Nicholas , Rockell Karen , Weiss Matthew J. , Dieudé Mélanie 
Published: April 2023

Background.
This report provides recommendations from the Research and Innovation domain as part of the International Donation and Transplantation Legislative and Policy Forum (hereafter the Forum) to provide expert guidance on the structure of an ideal organ and tissue donation and transplantation system. The recommendations focus on deceased donation research and are intended for clinicians, investigators, decision-makers, and patient, family, and donor (PFD) partners involved in the field.

Methods.
We identified topics impacting donation research through consensus using nominal group technique. Members performed narrative reviews and synthesized current knowledge on each topic, which included academic articles, policy documents, and gray literature. Using the nominal group technique, committee members discussed significant findings, which provided evidence for our recommendations. The Forum’s scientific committee then vetted recommendations.

Results.
We developed 16 recommendations in 3 key areas to provide stakeholders guidance in developing a robust deceased donor research framework. These include PFD and public involvement in research; donor, surrogate, and recipient consent within a research ethics framework; and data management. We highlight the importance of PFD and public partner involvement in research, we define the minimum ethical requirements for the protection of donors and recipients of both target and nontarget organ recipients, and we recommend the creation of a centrally administered donor research oversight committee, a single specialist institutional review board, and a research oversight body to facilitate coordination and ethical oversight of organ donor intervention research.

Conclusions.
Our recommendations provide a roadmap for developing and implementing an ethical deceased donation research framework that continually builds public trust. Although these recommendations can be applied to jurisdictions developing or reforming their organ and tissue donation and transplantation system, stakeholders are encouraged to collaborate and respond to their specific jurisdictional needs related to organ and tissue shortages.
Draft Genome Sequences of 11 Xanthomonas Strains associated with bacterial spot disease in Turkey
Authors: Subedi Aastha , Kara Serhat , Aysan Yesim , Minsavage Gerald V. , Timilsina Sujan , Roberts Pamela D. , Goss Erica M. , Jones Jeffrey B. 
Published: April 2023

Bacterial spot is an economically significant disease in tomato and pepper-producing countries globally. We report the whole genome sequence of 11 Xanthomonas strains associated with bacterial spot disease on pepper, tomato, and eggplant in the Southeastern Anatolia Region, Turkey. This genomic information can be used as a reference to study the genetic diversity of these species and contribute to illuminating pathogen evolution with respect to host specificity.
On the dynamic contact angle of capillary-driven microflows in open channels
Authors: Tokihiro Jodie C. , McManamen Anika M. , Phan David N. , Thongpang Sanitta , Blake Terence D. , Theberge Ashleigh B. , Berthier Jean 
Published: April 2023

AbstractThe true value of the contact angle between a liquid and a solid is a thorny problem in capillary microfluidics. The Lucas-Washburn-Rideal (LWR) law assumes a constant contact angle during fluid penetration. However, recent experimental studies have shown lower liquid velocities than predicted by the LWR equation, which are attributed to a velocity-dependent dynamic contact angle that is larger than its static value. Inspection of fluid penetration in closed channels has confirmed that a dynamic angle is needed in the LWR equation.In this work, the dynamic contact angle in an open channel configuration is investigated using experimental data obtained with a range of liquids, aqueous and organic, and a PMMA substrate. We demonstrate that a dynamic contact angle must be used to explain the early stages of fluid penetration, i.e., at the start of the viscous regime, when flow velocities are sufficiently high. Moreover, the open channel configuration, with its free surface, enhances the effect of the dynamic contact angle, making its inclusion even more important. We found that for the liquids in our study, the molecular-kinetic theory (MKT) is the most accurate in predicting the effect of the dynamic contact angle on liquid penetration in open channels.
Leakage beyond the primary infarction: A temporal analysis of cerebrovascular dysregulation at sites of hippocampal secondary neurodegeneration following cortical photothrombotic stroke
Authors: Hood Rebecca J. , Sanchez-Bezanilla Sonia , Beard Daniel J. , Rust Ruslan , Turner Renée J. , Stuckey Shannon M. , Collins-Praino Lyndsey E. , Walker Frederick R. , Nilsson Michael , Ong Lin Kooi 
Published: April 2023

AbstractWe have previously demonstrated that a cortical stroke causes persistent impairment of hippocampal-dependent cognitive tasks concomitant with secondary neurodegenerative processes such as amyloid-β accumulation in the hippocampus, a region remote from the primary infarct. Interestingly, there is emerging evidence suggesting that deposition of amyloid-β around cerebral vessels may lead to cerebrovascular structural changes, neurovascular dysfunction, and disruption of blood-brain barrier integrity. However, there is limited knowledge about the temporal changes of hippocampal cerebrovasculature after cortical stroke. In the current study, we aimed to characterise the spatiotemporal cerebrovascular changes after cortical stroke. This was done using the photothrombotic stroke model targeting the motor and somatosensory cortices of mice. Cerebrovascular morphology as well as the colocalization of amyloid-β with vasculature and blood-brain-barrier integrity were assessed in the cortex and hippocampal regions at 7, 28 and 84 days post-stroke. Our findings showed transient cerebrovascular remodelling in the peri-infarct area up to 28 days post-stroke. Importantly, the cerebrovascular changes were extended beyond the peri-infarct region to the ipsilateral hippocampus and were sustained out to 84 days post-stroke. When investigating vessel diameter, we showed a decrease at 84 days in the peri-infarct and CA1 regions that was exacerbated in vessels with amyloid-β deposition. Lastly, we showed sustained vascular leakage in the peri-infarct and ipsilateral hippocampus, indicative of a compromised blood-brain-barrier. Our findings indicate that hippocampal vasculature may represent an important therapeutic target to mitigate the progression of post-stroke cognitive impairment.
Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics
Authors: Shao Bin , Yan Jiawei , Zhang Jing , Buskirk Allen R. 
Published: April 2023

AbstractTranslation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurement of translation at genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts and identify sequence determinant of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. It corrects experimental artifacts in previously unseen datasets, reveals subtle differences in synonymous codon translation and uncovers a bottleneck in protein synthesis. Further, we show that Riboformer can be combined within silicomutagenesis analysis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
RaptorX-Single: single-sequence protein structure prediction by integrating protein language models
Authors: Jing Xiaoyang , Wu Fandi , Luo Xiao , Xu Jinbo 
Published: April 2023

AbstractProtein structure prediction has been greatly improved by deep learning in the past few years. However, the most successful methods rely on multiple sequence alignment (MSA) of the sequence homologs of the protein under prediction. In nature a protein folds in the absence of its sequence homologs and thus, a MSA-free structure prediction method is desired. Here we develop a single sequence-based protein structure prediction method RaptorX-Single by integrating several protein language models and a structure generation module and then study its advantage over MSA-based prediction methods. Our experimental results indicate that in addition to running much faster than MSA-based methods such as AlphaFold2, RaptorX-Single outperforms AlphaFold2 and other MSA-free methods in predicting the structure of antibodies, proteins of very few sequence homologs and single mutation effects. RaptorX-Single also compares favorably to MSA-based AlphaFold2 when the protein under prediction has a large number of sequence homologs.
Cell based dATP delivery as a therapy for chronic heart failure
Authors: Mhatre Ketaki N , Mathieu Julie , Martinson Amy , Flint Galina , Blakley Leslie P. , Tabesh Arash , Reinecke Hans , Yang Xiulan , Guan Xuan , Murali Eesha , Klaiman Jordan M , Odom Guy L , Brown Mary Beth , Tian Rong , Hauschka Stephen D , Raftery Daniel , Moussavi-Harami Farid , Regnier Michael , Murry Charles E 
Published: April 2023

AbstractTransplanted human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) improve ventricular performance when delivered acutely post-myocardial infarction but are ineffective in chronic myocardial infarction/heart failure. 2’-deoxy-ATP (dATP) activates cardiac myosin and potently increases contractility. Here we engineered hPSC-CMs to overexpress ribonucleotide reductase, the enzyme controlling dATP production. In vivo, dATP-producing CMs formed new myocardium that transferred dATP to host cardiomyocytes via gap junctions, increasing their dATP levels. Strikingly, when transplanted into chronically infarcted hearts, dATP-producing grafts increased left ventricular function, whereas heart failure worsened with wild-type grafts or vehicle injections. dATP-donor cells recipients had greater voluntary exercise, improved cardiac metabolism, reduced pulmonary congestion and pathological cardiac hypertrophy, and improved survival. This combination of remuscularization plus enhanced host contractility offers a novel approach to treating the chronically failing heart.One Sentence SummaryTransplanting gene-edited dATP-donor cardiomyocytes in chronically infarcted heart restores their cardiac function, improving both exercise tolerance and survival.
Assessment of Total Oocyte Transcripts Representation through Single Ooplasm Biopsy in Bovine with High Reliability
Authors: Ambrizi Dewison Ricardo , Nociti Ricardo Perecin , De Bem Tiago Henrique Camara , Paixao Joao Vitor Puttini , Therrien Jacinthe , De Matos Elisangela Chicaroni , Ferraz Jose Bento Sterman , Chiaratti Marcos Roberto , Sangalli Juliano , Da Silveira Juliano Coelho , Perecin Felipe , Smith Lawrence Charles , Meirelles Flavio Vieira 
Published: April 2023

ABSTRACTUnderstanding the entire transcriptional and epigenetic landscape is facilitated by the application of omics in a number of ways. Today, omic instruments are more affordable and easier to implement. In human research, for instance, single-omics are a reality and are used extensively to generate vast quantities of data. This method permits the comprehensive reconstruction of transcriptome and epigenetic markers removing bias from pooled samples. In tandem with the evolution of machines and protocols, algorithms and genome annotation have undergone continuous improvement. The genome annotation of domestic animals is inferior to that of humans, rodents, and less complex organisms. In the case of heifers, the reference is incomplete, with significant gaps and only a portion of the noncoding transcripts. The purpose of this study is to validate our compartmentalized single oocyte biopsy by comparing a small fraction of bovine oocytes, 1%, to the entire oocyte at the Metaphase II stage. In addition, we examined the use of four database sources (NCBI, ENSEMBL, UCSC, and NONCODE) to produce a merged non-redundant gene alignment and counting in order to enhance gene detection and normalization, resulting in a more accurate method to comprehend the entire landscape. This study is a continuation of our research titled “Retrospective model utilizing biopsies, granulosa cells, and polar body to predict oocyte competence in bovine” in which this method was used to retrospectively compare biopsy oocytes collected during the MII phase. With the addition of NONCODE information, gene normalization was significantly enhanced. In addition, our analysis identified 4560 noncoding genes from NONCODE references. ENSEMBL and NCBI have nearly the same number of annotated genes (16,423 vs. 17,804), but using ENSEMBL as a reference, 2356 genes were able to be normalized and identified. Proceeding to biopsy x oocyte analysis, we were able to detect a greater number of genes in oocytes than in biopsy, where the preponderance was from NONCODE sources (68). Despite these minor differences, the high correlation of expression between them (89%) was consistent and proved to be a valuable instrument for studying the oocyte without destroying it.
High-throughput optical sensing of peri-cellular oxygen in cardiac cells: system characterization, calibration, and testing
Authors: Li Weizhen , McLeod David , Ketzenberger John T. , Kowalik Grant , Russo Rebekah , Li Zhenyu , Kay Matthew W. , Entcheva Emilia 
Published: April 2023

AbstractHuman-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a scalable experimental model relevant to human physiology. Oxygen consumption of hiPSC-CMs has not been studied in high-throughput (HT) format plates used in pre-clinical studies. Here, we provide comprehensive characterization and validation of a system for HT long-term optical measurements of peri-cellular oxygen in cardiac syncytia (human iPSC-CM and human cardiac fibroblasts), grown in glass-bottom 96-well plates. Laser-cut oxygen sensors having a ruthenium dye and an oxygen-insensitive reference dye were used. Ratiometric measurements (409nm excitation) reflected dynamic changes in oxygen, as validated with simultaneous Clark electrode measurements. Emission ratios (653nm vs. 510nm) were calibrated for percent oxygen using two-point calibration. Time-dependent changes in the Stern-Volmer parameter, Ksv, were observed during the initial 40 min of incubation, likely temperature-related. Effects of pH on oxygen measurements were negligible in the pH range of 4 to 8, with a small ratio reduction for pH>10. Time-dependent calibration was implemented, and light exposure time was optimized (0.6 to 0.8s) for oxygen measurements inside an incubator. Peri-cellular oxygen dropped to levels < 5% within 3 -10 hours for densely-plated hiPSC-CMs in glass-bottom 96-well plates. After the initial oxygen decrease, samples either settled to low steady-state or exhibited intermittent peri-cellular oxygen dynamics. Cardiac fibroblasts showed slower oxygen depletion and higher steady-state levels without oscillations, compared to hiPSC-CMs. Overall, the system has great utility for long-term HT monitoring of peri-cellular oxygen dynamics in vitro for tracking cellular oxygen consumption, metabolic perturbations, and characterization of the maturation of hiPSC-CMs.
Clade-Specific MPXV PCR Assays
Authors: Negrón Daniel Antonio , Tolli Nicholas , Guertin Stephanie , Wollen-Roberts Suzanne , Mitchell Shane , Haas Jared , Pratt Catherine , Jennings Katharine , Abramson Bradley , Brinkac Lauren , Ashford David 
Published: April 2023

AbstractIn an evolving infectious disease outbreak, there are two priorities: rapid and accurate detection of the causative agent and characterization of its spread. The polymerase chain reaction (PCR) assay is an effective and portable diagnostic method that can quickly provide information associated with virulence, transmissibility, and pathogenicity. Compared to genomic sequencing, PCR requires less infrastructure, funding, and training. However, the development of sensitive and specific primer sequences is costly, particularly those with subspecies resolution. The recentmpox (monkeypox) virusoutbreak underscores the need for the rapid development of clade-specific primers, particularly when there are differences in morbidity and mortality rates. Current mpox assays use primer sequences that also bind to the broaderOrthopoxvirusgenus, resulting in suspect diagnoses, delays in treatment, and poor allocation of scarce healthcare resources. Additionally, these orthopox-based primer sets cannot distinguish between different mpox clades and cannot illuminate intra-clade evolution over the course of the outbreak. Here, we present thein silicodesign andin vitrotesting of novel clade-specific mpox assays.ImportanceThere is an ongoing global outbreak of Mpox disease, an illness with a characteristic blistering rash progression. The Mpox virus clusters into two clades with differing levels of virulence and mortality rates. Thus, proper sample identification is critical for surveillance and the public health response programs that rely on such data. Accordingly, the US government specifically lists Clade I under the Federal Select Agent Program. Current diagnostics may fail to identify the virus or its clade membership as the genome mutates. In this work, we demonstrate an end-to-end workflow to quickly evaluate existing PCR assays and design new ones for clade-based identification with respect to large sequence databases in service of preventing a catastrophic fog-of-war from forming during an outbreak.
A neural model of modified excitation/inhibition and feedback levels in schizophrenia
Authors: Zhu Jiating , Zikopoulos Basilis , Yazdanbakhsh Arash 
Published: April 2023

AbstractThe strength of certain visual illusions is weakened in individuals with schizophrenia. Such phenomena have been interpreted as the impaired integration of inhibitory and excitatory neural responses, and impaired top–down feedback mechanisms. To investigate whether and how these factors influence the perceived illusions in individuals with schizophrenia, we propose a two-layer network that can model visual receptive fields (RFs), their inhibitory and excitatory subfields, and the top-down feedback. Our neural model suggests that illusion perception changes in individuals with schizophrenia can be influenced by altered top-down mechanisms and the organization of the on-center off-surround receptive fields. Alteration of the RF inhibitory surround and/or the excitatory center can replicate the difference of illusion precepts between individuals with schizophrenia and normal controls. The results show that the simulated top-down feedback modulation enlarges the difference of the model illusion representations, replicating the difference between the two groups.
Precision pharmacological reversal of genotype-specific diet-induced metabolic syndrome in mice informed by transcriptional regulation
Authors: Wulfridge Phillip , Davidovich Adam , Salvador Anna C. , Manno Gabrielle C. , Tryggvadottir Rakel , Idrizi Adrian , Huda M. Nazmul , Bennett Brian J. , Adams L. Garry , Hansen Kasper D. , Threadgill David W. , Feinberg Andrew P. 
Published: April 2023

AbstractDiet-related metabolic syndrome is the largest contributor to adverse health in the United States. However, the study of gene-environment interactions and their epigenomic and transcriptomic integration is complicated by the lack of environmental and genetic control in humans that is possible in mouse models. Here we exposed three mouse strains, C57BL/6J (BL6), A/J, and NOD/ShiLtJ (NOD), to a high-fat high-carbohydrate diet, leading to varying degrees of metabolic syndrome. We then performed transcriptomic and genomic DNA methylation analyses and found overlapping but also highly divergent changes in gene expression and methylation upstream of the discordant metabolic phenotypes. Strain-specific pathway analysis of dietary effects reveals a dysregulation of cholesterol biosynthesis common to all three strains but distinct regulatory networks driving this dysregulation. This suggests a strategy for strain-specific targeted pharmacologic intervention of these upstream regulators informed by transcriptional regulation. As a pilot study, we administered the drug GW4064 to target one of these genotype-dependent networks, the Farnesoid X receptor pathway, and found that GW4064 exerts genotype-specific protection against dietary effects in BL6, as predicted by our transcriptomic analysis, as well as increased inflammatory-related gene expression changes in NOD. This pilot study demonstrates the potential efficacy of precision therapeutics for genotype-informed dietary metabolic intervention, and a mouse platform for guiding this approach.