bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of the definition of bronchopulmonary dysplasia on neurodevelopmental outcomes
Authors: Han Yea-Seul , Kim Sung-Ha , Sung Tae-Jung 
Published: November 2021

AbstractUnderstanding the short and long-term pulmonary and neurologic outcomes of neonates with bronchopulmonary dysplasia (BPD) is important in neonatal care for low-birth-weight infants. Different criteria for BPD may have different associations with long-term outcomes. Currently, two criteria for diagnosing BPD have been proposed by the NIH (2001) and NRN (2019) for preterm infants at a postmenstrual age (PMA) of 36 weeks. We investigated which BPD definition best predicts long-term outcomes. Korean nationwide data for preterm infants born between 24+0 and < 32+0 weeks gestation from January 2013 to December 2015 were collected. For long-term outcomes, severity based on the NRN criteria was significantly related to neurodevelopmental impairment (NDI) in a univariate analysis after other risk factors were controlled. For the admission rate for respiratory disorder, grade 3 BPD of the NRN criteria had the highest specificity (96%), negative predictive value (86%), and accuracy (83%). For predicting NDI at the 18–24 month follow-up, grade 3 BPD of the NRN criteria had the best specificity (98%), positive (64%) and negative (79%) predictive values, and accuracy (78%) while NIH severe BPD had the highest sensitivity (60%). The NRN definition was more strongly associated with poor 2-year developmental outcomes. BPD diagnosed by NRN definitions might better identify infants at high risk for NDI.
Modeling optical design parameters for fine stimulation in sciatic nerve of optogenetic mice
Authors: Fritz Nicholas , Gulick Daniel , Bailly Mark , Blain Christen Jennifer M. 
Published: November 2021

AbstractOptogenetics presents an alternative method for interfacing with the nervous system over the gold-standard of electrical stimulation. While electrical stimulation requires electrodes to be surgically embedded in tissue for in vivo studies, optical stimulation offers a less-invasive approach that may yield more specific, localized stimulation. The advent of optogenetic laboratory animals—whose motor neurons can be activated when illuminated with blue light—enables research into refining optical stimulation of the mammalian nervous system where subsets of nerve fibers within a nerve may be stimulated without embedding any device directly into the nerve itself. However, optical stimulation has a major drawback in that light is readily scattered and absorbed in tissue thereby limiting the depth with which a single emission source can penetrate. We hypothesize that the use of multiple, focused light emissions deployed around the circumference of a nerve can overcome these light-scattering limitations. To understand the physical parameters necessary to produce pinpointed light stimulation within a single nerve, we employed a simplified Monte Carlo simulation to estimate the size of nerves where this technique may be successful, as well as the necessary optical lens design for emitters to be used during future in vivo studies. By modeling multiple focused beams, we find that only fascicles within a nerve diameter less than 1 mm are fully accessible to focused optical stimulation; a minimum of 4 light sources is required to generate a photon intensity at a point in a nerve over the initial contact along its surface. To elicit the same effect in larger nerves, focusing lenses would require a numerical aperture $$> 1$$

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. These simulations inform on the design of instrumentation capable of stimulating disparate motor neurons in mouse sciatic nerve to control hindlimb movement.
Beneficial effects of end-ischemic oxygenated machine perfusion preservation for split-liver transplantation in recovering graft function and reducing ischemia–reperfusion injury
Authors: Ishii Daisuke , Matsuno Naoto , Gochi Mikako , Iwata Hiroyoshi , Shonaka Tatsuya , Nishikawa Yuji , Obara Hiromichi , Yokoo Hideki , Furukawa Hiroyuki 
Published: November 2021

AbstractThis study examined the efficacy of end-ischemic hypothermic oxygenated machine perfusion preservation (HOPE) using an originally developed machine perfusion system for split-liver transplantation. Porcine split-liver grafts were created via 75% liver resection after 10 min of warm ischemia. In Group 1, grafts were preserved by simple cold storage (CS) for 8 h (CS group; n = 4). In Group 2, grafts were preserved by simple CS for 6 h and end-ischemic HOPE for 2 h (HOPE group; n = 5). All grafts were evaluated using an isolated ex vivo reperfusion model with autologous blood for 2 h. Biochemical markers (aspartate aminotransferase and lactate dehydrogenase levels) were significantly better immediately after reperfusion in the HOPE group than in the CS group. Furthermore, the HOPE group had a better histological score. The levels of inflammatory cytokines (tumor necrosis factor-α, interferon-γ, interleukin-1β, and interleukin-10) were significantly lower after reperfusion in the HOPE group. Therefore, we concluded that end-ischemic HOPE for split-liver transplantation can aid in recovering the graft function and reducing ischemia–reperfusion injury. HOPE, using our originally developed machine perfusion system, is safe and can improve graft function while attenuating liver injury due to preservation.
Exploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking
Authors: Huo Mengqi , Ma Lina , Liu Guoguo 
Published: November 2021

AbstractYixinyin, the traditional Chinese medicine, has the effects of replenishing righteous qi, and promoting blood circulation to eliminate blood stagnation. It is often used to treat patients with acute myocardial infarction (MI). The purpose of our study is to explore the key components and targets of Yixinyin in the treatment of MI. In this study, we analyzed gene expression data and clinical information from 248 samples of MI patients with the GSE34198, GSE29111 and GSE66360 data sets. By constructing a weighted gene co-expression network, gene modules related to myocardial infarction are obtained. These modules can be mapped in Yixinyin PPI network. By integrating differential genes of healthy/MI and unstable angina/MI, key targets of Yixinyin for the treatment of myocardial infarction were screened. We validated the key objectives with external data sets. GSEA analysis is used to identify the biological processes involved in key targets. Through molecular docking screening, active components that can combine with key targets in Yixinyin were obtained. In the treatment of myocardial infarction, we have obtained key targets of Yixinyin, which are ALDH2, C5AR1, FOS, IL1B, TLR2, TXNRD1. External data sets prove that they behave differently in the healthy and MI (P < 0.05). GSEA enrichment analysis revealed that they are mainly involved in pathways associated with myocardial infarction, such as viral myocarditis, VEGF signaling pathway and type I diabetes mellitus. The docking results showed that the components that can be combined with key targets in YixinYin are Supraene, Prostaglandin B1, isomucronulatol-7,2′-di-O-glucosiole, angusifolin B, Linolenic acid ethyl ester, and Mandenol. For that matter, they may be active ingredients of Yixinyin in treating MI. These findings provide a basis for the preliminary research of myocardial infarction therapy in traditional Chinese medicine and provide ideas for the design of related drugs.
Protein innovation through template switching in the Saccharomyces cerevisiae lineage
Authors: Abraham May , Hazkani-Covo Einat 
Published: November 2021

AbstractDNA polymerase template switching between short, non-identical inverted repeats (IRs) is a genetic mechanism that leads to the homogenization of IR arms and to IR spacer inversion, which cause multinucleotide mutations (MNMs). It is unknown if and how template switching affects gene evolution. In this study, we performed a phylogenetic analysis to determine the effect of template switching between IR arms on coding DNA of Saccharomyces cerevisiae. To achieve this, perfect IRs that co-occurred with MNMs between a strain and its parental node were identified in S. cerevisiae strains. We determined that template switching introduced MNMs into 39 protein-coding genes through S. cerevisiae evolution, resulting in both arm homogenization and inversion of the IR spacer. These events in turn resulted in nonsynonymous substitutions and up to five neighboring amino acid replacements in a single gene. The study demonstrates that template switching is a powerful generator of multiple substitutions within codons. Additionally, some template switching events occurred more than once during S. cerevisiae evolution. Our findings suggest that template switching constitutes a general mutagenic mechanism that results in both nonsynonymous substitutions and parallel evolution, which are traditionally considered as evidence for positive selection, without the need for adaptive explanations.
Sperm preparedness and adaptation to osmotic and pH stressors relate to functional competence of sperm in Bos taurus
Authors: Lavanya Maharajan , Archana Santhanahalli Siddalingappa , Swathi Divakar , Ramya Laxman , Arangasamy Arunachalam , Binsila Balakrishnan , Dhali Arindam , Krishnaswamy Narayanan , Singh Sanjay Kumar , Kumar Harendra , Sivaram Muniandy , Selvaraju Sellappan 
Published: November 2021

AbstractThe adaptive ability of sperm in the female reproductive tract micromilieu signifies the successful fertilization process. The study aimed to analyze the preparedness of sperm to the prevailing osmotic and pH stressors in the female reproductive tract. Fresh bovine sperm were incubated in 290 (isosmotic-control), 355 (hyperosmotic-uterus and oviduct), and 420 (hyperosmotic-control) mOsm/kg and each with pH of 6.8 (uterus) and 7.4 (oviduct). During incubation, the changes in sperm functional attributes were studied. Sperm kinematics and head area decreased significantly (p < 0.05) immediately upon exposure to hyperosmotic stress at both pH. Proportion of sperm capacitated (%) in 355 mOsm/kg at 1 and 2 h of incubation were significantly (p < 0.05) higher than those in 290 mOsm media. The magnitude and duration of recovery of sperm progressive motility in 355 mOsm with pH 7.4 was correlated with the ejaculate rejection rate (R2 = 0.7). Using this information, the bulls were divided into good (n = 5) and poor (n = 5) osmo-adapters. The osmo-responsive genes such asNFAT5, HSP90AB1, SLC9C1, ADAM1BandGAPDHwere upregulated (p < 0.05) in the sperm of good osmo-adapters. The study suggests that sperm are prepared for the osmotic and pH challenges in the female reproductive tract and the osmoadaptive ability is associated with ejaculate quality in bulls.
Functional diversity of Himalayan bat communities declines at high elevation without the loss of phylogenetic diversity
Authors: Chakravarty Rohit , Mohan Ram , Voigt Christian C. , Krishnan Anand , Radchuk Viktoriia 
Published: November 2021

AbstractSpecies richness exhibits well-known patterns across elevational gradients in various taxa, but represents only one aspect of quantifying biodiversity patterns. Functional and phylogenetic diversity have received much less attention, particularly for vertebrate taxa. There is still a limited understanding of how functional, phylogenetic and taxonomic diversity change in concert across large gradients of elevation. Here, we focused on the Himalaya—representing the largest elevational gradients in the world—to investigate the patterns of taxonomic, functional and phylogenetic diversity in a bat assemblage. Combining field data on species occurrence, relative abundance, and functional traits with measures of phylogenetic diversity, we found that bat species richness and functional diversity declined at high elevation but phylogenetic diversity remained unchanged. At the lowest elevation, we observed low functional dispersion despite high species and functional richness, suggesting a niche packing mechanism. The decline in functional richness, dispersion, and divergence at the highest elevation is consistent with patterns observed due to environmental filtering. These patterns are driven by the absence of rhinolophid bats, four congeners with extreme trait values. Our data, some of the first on mammals from the Himalayan region, suggest that in bat assemblages with relatively high species diversity, phylogenetic diversity may not be a substitute to measure functional diversity.
Cuprizone feed formulation influences the extent of demyelinating disease pathology
Authors: Toomey Lillian M. , Papini Melissa , Lins Brittney , Wright Alexander J. , Warnock Andrew , McGonigle Terence , Hellewell Sarah C. , Bartlett Carole A. , Anyaegbu Chidozie , Fitzgerald Melinda 
Published: November 2021

AbstractCuprizone is a copper-chelating agent that induces pathology similar to that within some multiple sclerosis (MS) lesions. The reliability and reproducibility of cuprizone for inducing demyelinating disease pathology depends on the animals ingesting consistent doses of cuprizone. Cuprizone-containing pelleted feed is a convenient way of delivering cuprizone, but the efficacy of these pellets at inducing demyelination has been questioned. This study compared the degree of demyelinating disease pathology between mice fed cuprizone delivered in pellets to mice fed a powdered cuprizone formulation at an early 3 week demyelinating timepoint. Within rostral corpus callosum, cuprizone pellets were more effective than cuprizone powder at increasing astrogliosis, microglial activation, DNA damage, and decreasing the density of mature oligodendrocytes. However, cuprizone powder demonstrated greater protein nitration relative to controls. Furthermore, mice fed control powder had significantly fewer mature oligodendrocytes than those fed control pellets. In caudal corpus callosum, cuprizone pellets performed better than cuprizone powder relative to controls at increasing astrogliosis, microglial activation, protein nitration, DNA damage, tissue swelling, and reducing the density of mature oligodendrocytes. Importantly, only cuprizone pellets induced detectable demyelination compared to controls. The two feeds had similar effects on oligodendrocyte precursor cell (OPC) dynamics. Taken together, these data suggest that demyelinating disease pathology is modelled more effectively with cuprizone pellets than powder at 3 weeks. Combined with the added convenience, cuprizone pellets are a suitable choice for inducing early demyelinating disease pathology.
Experimental strategies to achieve efficient targeted knock-in via tandem paired nicking
Authors: Rahman Md. Lutfur , Hyodo Toshinori , Karnan Sivasundaram , Ota Akinobu , Hasan Muhammad Nazmul , Mihara Yuko , Wahiduzzaman Md , Tsuzuki Shinobu , Hosokawa Yoshitaka , Konishi Hiroyuki 
Published: November 2021

AbstractTandem paired nicking (TPN) is a method of genome editing that enables precise and relatively efficient targeted knock-in without appreciable restraint by p53-mediated DNA damage response. TPN is initiated by introducing two site-specific nicks on the same DNA strand using Cas9 nickases in such a way that the nicks encompass the knock-in site and are located within a homologous region between a donor DNA and the genome. This nicking design results in the creation of two nicks on the donor DNA and two in the genome, leading to relatively efficient homology-directed recombination between these DNA fragments. In this study, we sought to identify the optimal design of TPN experiments that would improve the efficiency of targeted knock-in, using multiple reporter systems based on exogenous and endogenous genes. We found that efficient targeted knock-in via TPN is supported by the use of 1700–2000-bp donor DNAs, exactly 20-nt-long spacers predicted to be efficient in on-target cleavage, and tandem-paired Cas9 nickases nicking at positions close to each other. These findings will help establish a methodology for efficient and precise targeted knock-in based on TPN, which could broaden the applicability of targeted knock-in to various fields of life science.
Role of MUC1 rs4072037 polymorphism and serum KL-6 levels in patients with antisynthetase syndrome
Authors: Remuzgo-Martínez Sara , Atienza-Mateo Belén , Ocejo-Vinyals J. Gonzalo , Genre Fernanda , Pulito-Cueto Verónica , Mora-Cuesta Víctor M. , Iturbe-Fernández David , Lera-Gómez Leticia , Pérez-Fernández Raquel , Prieto-Peña Diana , Irure Juan , Romero-Bueno Fredeswinda , Sanchez-Pernaute Olga , Alonso-Moralejo Rodrigo , Nuño Laura , Bonilla Gema , Vicente-Rabaneda Esther F. , Grafia Ignacio , Prieto-González Sergio , Narvaez Javier , Trallero-Araguas Ernesto , Selva-O’Callaghan Albert ,   Spanish Biomarkers of Antisynthetase Syndrome Consortium, Ortego-Centeno Norberto , Pérez-Gómez Nair , Mera Antonio , Martínez-Barrio Julia , Moriano Clara , Díez Elvira , Calvo-Alén Jaime , Balsa Alejandro ,   Spanish Biomarkers of Interstitial Lung Disease Consortium, Ussetti María Piedad , Laporta Rosalía , Berastegui Cristina , Solé Amparo , Gualillo Oreste , Cavagna Lorenzo , Cifrián José M. , Renzoni Elisabetta A. , Castañeda Santos , López-Mejías Raquel , González-Gay Miguel A. 
Published: November 2021

AbstractMucin 1/Krebs von den Lungen-6 (KL-6) is proposed as a serum biomarker of several interstitial lung diseases (ILDs), including connective tissue disorders associated with ILD. However, it has not been studied in a large cohort of Caucasian antisynthetase syndrome (ASSD) patients. Consequently, we assessed the role of MUC1 rs4072037 and serum KL-6 levels as a potential biomarker of ASSD susceptibility and for the differential diagnosis between patients with ILD associated with ASSD (ASSD-ILD +) and idiopathic pulmonary fibrosis (IPF). 168 ASSD patients (149 ASSD-ILD +), 174 IPF patients and 523 healthy controls were genotyped for MUC1 rs4072037 T > C. Serum KL-6 levels were determined in a subgroup of individuals. A significant increase of MUC1 rs4072037 CC genotype and C allele frequencies was observed in ASSD patients compared to healthy controls. Likewise, MUC1 rs4072037 TC and CC genotypes and C allele frequencies were significantly different between ASSD-ILD+ and IPF patients. Additionally, serum KL-6 levels were significantly higher in ASSD patients compared to healthy controls. Nevertheless, no differences in serum KL-6 levels were found between ASSD-ILD+ and IPF patients. Our results suggest that the presence of MUC1 rs4072037 C allele increases the risk of ASSD and it could be a useful genetic biomarker for the differential diagnosis between ASSD-ILD+ and IPF patients.
Controlled spermatozoa–oocyte interaction improves embryo quality in sheep
Authors: Anzalone Debora Agata , Palazzese Luca , Czernik Marta , Sabatucci Annalaura , Valbonetti Luca , Capra Emanuele , Loi Pasqualino 
Published: November 2021

AbstractThe current protocols of in vitro fertilization and culture in sheep rely on paradigms established more than 25 years ago, where Metaphase II oocytes are co-incubated with capacitated spermatozoa overnight. While this approach maximizes the number of fertilized oocytes, on the other side it exposes them to high concentration of reactive oxygen species (ROS) generated by active and degenerating spermatozoa, and positively correlates with polyspermy. Here we set up to precisely define the time frame during which spermatozoa effectively penetrates and fertilizes the oocyte, in order to drastically reduce spermatozoa-oocyte interaction. To do that, in vitro matured sheep oocytes co-incubated with spermatozoa in IVF medium were sampled every 30 min (start of incubation time 0) to verify the presence of a fertilizing spermatozoon. Having defined the fertilization time frame (4 h, data from 105 oocytes), we next compared the standard IVF procedures overnight (about 16 h spermatozoa/oocyte exposure, group o/nIVF) with a short one (4 h, group shIVF). A lower polyspermic fertilization (> 2PN) was detected in shIVF (6.5%) compared to o/nIVF (17.8%), P < 0.05. The o/nIVF group resulted in a significantly lower 2-cell stage embryos, than shIVF [34.6% (81/234) vs 50.6% (122/241) respectively, P < 0.001]. Likewise, the development to blastocyst stage confirmed a better quality [29% (70/241) vs 23.5% (55/234), shIVF vs o/nIVF respectively] and an increased Total Cell Number (TCN) in shIVF embryos, compared with o/n ones. The data on ROS have confirmed that its generation is IVF time-dependent, with high levels in the o/nIVF group. Overall, the data suggest that a shorter oocyte-spermatozoa incubation results in an improved embryo production and a better embryo quality, very likely as a consequence of a shorter exposure to the free oxygen radicals and the ensuing oxidative stress imposed by overnight culture.
A novel mouse model of postpartum depression using emotional stress as evaluated by nesting behavior
Authors: Seki Tomoe , Yamagata Hirotaka , Uchida Shusaku , Kobayashi Ayumi , Watanabe Yoshifumi , Nakagawa Shin 
Published: November 2021

AbstractPostpartum depression is an important mental health issue not only for the mother but also for the child’s development, other family members, and the society. An appropriate animal model is desired to elucidate the pathogenesis of postpartum depression. However, methods for stress loading during pregnancy have not been established. Behavioral experiments to investigate postpartum depression-like behaviors should be conducted without stress because behavioral tests affect rearing behaviors such as lactation. Therefore, we developed a new mouse model of postpartum depression using a psychological stress method. Mating partners were made to witness their partners experiencing social defeat stress and then listen to their cries. Emotional stress loading during pregnancy significantly increased postpartum depression-like behaviors. Postpartum depression also affected nurturing behaviors and caused disturbances in pup care. Furthermore, nesting behavior was impaired in the stressed group, suggesting that the observation of nesting behavior may be useful for assessing social dysfunction in postpartum depression. These results demonstrate the utility of this new mouse model of postpartum depression.
In search of different categories of abstract concepts: a fMRI adaptation study
Authors: Conca Francesca , Catricalà Eleonora , Canini Matteo , Petrini Alessandro , Vigliocco Gabriella , Cappa Stefano F. , Della Rosa Pasquale Anthony 
Published: November 2021

AbstractConcrete conceptual knowledge is supported by a distributed neural network representing different semantic features according to the neuroanatomy of sensory and motor systems. If and how this framework applies to abstract knowledge is currently debated. Here we investigated the specific brain correlates of different abstract categories. After a systematic a priori selection of brain regions involved in semantic cognition, i.e. responsible of, respectively, semantic representations and cognitive control, we used a fMRI-adaptation paradigm with a passive reading task, in order to modulate the neural response to abstract (emotions, cognitions, attitudes, human actions) and concrete (biological entities, artefacts) categories. Different portions of the left anterior temporal lobe responded selectively to abstract and concrete concepts. Emotions and attitudes adapted the left middle temporal gyrus, whereas concrete items adapted the left fusiform gyrus. Our results suggest that, similarly to concrete concepts, some categories of abstract knowledge have specific brain correlates corresponding to the prevalent semantic dimensions involved in their representation.