bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breastfeeding in a COVID-19 world
Authors: Sakalidis Vanessa S. , Perrella Sharon L. , Prosser Stuart A. , Geddes Donna T. 
Published: February 2022

Purpose of review
The coronavirus disease 2019 (COVID-19) pandemic has changed the birthing and postnatal experience of women. This review highlights how policy changes have affected pregnant and breastfeeding women, the evidence for continued breastfeeding and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines, and how the pandemic's unexpected consequences have affected these women's wellbeing. Additionally, we postulate the future of lactation and perinatal support as the pandemic continues.

Recent findings
Women who have given birth during the pandemic have had restricted access to postnatal care. Although pregnant and breastfeeding women who contract SARS-CoV-2 are more vulnerable to poor health outcomes than their nonpregnant counterparts, they are also at higher risk of mental health difficulties, with limited access to support. Continued breastfeeding may be protective to the infant, offering passive immunity against SARS-CoV-2, and vaccination against COVID-19 is safe and effective for pregnant and lactating women. Innovative and adaptable lactation care, including holistic perinatal, mental health, and social support services, both digital and in-person, will help mothers continue breastfeeding during future outbreaks.

Summary
Continued breastfeeding and vaccination may confer protection to the infant against SARS-CoV-2 infection. New mothers should not be isolated in future pandemics. Prioritizing lactation and perinatal care, including in-person services, remains paramount to optimizing breastfeeding during COVID-19.
Metabolic dysfunction-associated fatty liver disease: a year in review
Authors: Alharthi Jawaher , Gastaldelli Amalia , Cua Ian Homer , Ghazinian Hasmik , Eslam Mohammed 
Published: February 2022

Purpose of review
In 2020, a novel comprehensive redefinition of fatty liver disease was proposed by an international panel of experts. This review aims to explore current evidence regarding the impact of this new definition on the current understanding of the epidemiology, pathogenesis, diagnosis, and clinical trials for fatty liver disease.

Recent findings
The effectiveness of metabolic dysfunction-associated fatty liver disease (MAFLD) was compared to the existing criteria for nonalcoholic fatty liver disease (NAFLD). Recent data robustly suggest the superior utility of MAFLD in identifying patients at high risk for metabolic dysfunction, the hepatic and extra-hepatic complications, as well as those who would benefit from genetic testing, including patients with concomitant liver diseases. This change in name and criteria also appears to have improved disease awareness among patients and physicians.

Summary
The transformation in name and definition from NAFLD to MAFLD represents an important milestone, which indicates significant tangible progress towards a more inclusive, equitable, and patient-centred approach to addressing the profound challenges of this disease. Growing evidence has illustrated the broader and specific contexts that have tremendous potential for positively influencing the diagnosis and treatment. In addition, the momentum accompanying this name change has included widespread public attention to the unique burden of this previously underappreciated disease.
Cardiovascular effects of intrauterine exposure to maternal HIV and antiretroviral therapy in Ethiopian infants followed from fetal life
Authors: García-Otero Laura , Walles John , Balcha Taye Tolera , Merga Gadissa , López Marta , Crispi Fatima , Björkman Per 
Published: February 2022

Objective:
To assess cardiovascular effects of in-utero HIV and antiretroviral treatment (ART) exposure on offspring of HIV-positive mothers in Ethiopia.

Design:
HIV-positive and HIV-negative pregnancies were identified from a prospective cohort of women recruited at their first antenatal care visit in Ethiopia, using a nested case-control design.

Methods:
Fetal standard ultrasound and echocardiography were performed at 2237 weeks of pregnancy to assess fetal biometry and cardiac structure. Postnatal cardiovascular evaluation, including echocardiography and vascular assessment, was performed at 6 months of age. Cardiovascular data were correlated to HIV serostatus, antiretroviral drug exposure and HIV-unrelated maternal characteristics.

Results:
Fetuses from 29 HIV-positive and 67 HIV-negative women paired by gestational age at scan were included. Among HIV-positive women, 25 were on ART before conception, and 4 initiated ART during pregnancy. Estimated fetal weight was similar in both groups [mean 1873 g (standard deviation; SD 569) vs. 1839 g (SD 579) P = 0.79, respectively]. Fetal cardiac morphometry was similar with regard to maternal HIV serostatus: cardiothoracic ratio mean 0.26 (SD 0.05) vs. 0.25 (SD 0.06), P = 0.48; and septal wall thickness mean 4.03 mm (SD 0.58) vs. 3.98 mm (SD 0.70), P = 0.94. No significant cardiovascular differences were detected postnatally according to maternal HIV serostatus: septal wall thickness mean 5.46 mm (SD 0.65) vs. 5.49 (SD 0.89); P = 0.896; isovolumic relaxation time 55.08 ms (SD 6.57) vs. 56.56 (SD 6.74); P = 0.359.

Conclusion:
In offspring of Ethiopian women, intrauterine exposure to HIV and ART were not associated with cardiovascular changes from fetal life up to infanthood.
Positive FAPI PET/CT in a Bilateral Mammary Angiosarcoma Patient With Less Impressive FDG PET/CT Images
Authors: Qiu Siwen , Zou Sijuan , Cheng Siyuan , Song Shuang , Zhu Xiaohua 
Published: February 2022

Abstract
Bilateral primary angiosarcoma of the breast is an extremely rare disease. We describe a case with bilateral angiosarcoma of the breast well visualized on 68Ga-FAPI PET/CT in a 30-year-old woman with a history of right breast–conserving surgery. However, the lesions are less impressive on 18F-FDG PET/CT. No additional findings including lymph node and distant metastases were noted. The patient underwent bilateral mastectomy, and histopathology revealed well-differentiated angiosarcoma that involved bilateral breast parenchyma and the left nipple. Our case illustrates that 68Ga-FAPI PET/CT can be more sensitive in detecting well-differentiated angiosarcoma of the breast.
Neuroprotective effects of N-acetylcysteine amide against oxidative injury in an aging model of organotypic hippocampal slice cultures
Authors: Kim Un Jeng , Lee Kyung Hee 
Published: February 2022

Objectives
Oxidative stress produces neurotoxicity and has been associated with disorders of the nervous system. We observed the neuroprotective effects of N-acetylcysteine amide (NACA) against kainic acid (KA)-induced oxidative stress in aging organotypic hippocampal slice cultures (OHSCs).

Materials and methods
We used 6–8-day-old rats for long-term cultured OHSCs (9 w). Cultured slices were injured by KA (5 µM) treatment for 18 h. OHSCs were treated with NACA dose-dependently in a medium for 24 h after KA treatment. The effects of NACA treatment were observed with propidium iodide (PI) uptake, western blotting, and optical imaging.

Results
Neuronal cell death, as assessed by PI uptake, was dose-dependently reduced by NACA treatment. Western blot analysis revealed that the 1 mM NACA-treated group exhibited significantly increased expression of superoxide dismutase compared with the KA-only group. In addition, NACA activated nuclear factor erythroid 2-related factor 2-dependent anti-inflammation signaling, which is well known to affect reactive oxygen species. Optical imaging revealed that NACA treatment reduced the latency and increased amplitude of the optical signals, which shows that synaptic activity and strength are associated with neuronal survival.

Conclusion
Therefore, the neurons that survived due to the neuroprotective effects of NACA also showed enhanced functional activity in long-term cultured OHSCs using electrophysiological and biochemical assays.
Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge
Authors: Kong Yan-Hui , Ren Wen-Ting , Xu Lin , Cheng Hong , Zhou Peng , Wang Chun-Sheng , Wu Yue-Hong , Xu Xue-Wei 
Published: February 2022

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1T, T40-3T and JL-62T, were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1T, growth occurred at 15–37 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0.5–5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3T could grow at 15–40 °C (optimum, 28 °C), with 0.5–11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0–9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62T were 15–40 °C (optimum, 30 °C), pH 5.5–9.0 (optimum, pH 7.5–8.0) and 0.5–9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C18 : 1
ω7c / C18 : 1
ω6c). The major polar lipids of strains T40-1T and T40-3T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62T contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1Tand T40-3T to the family

Roseobacteraceae

and formed two independent clades from other

Roseobacteraceae

genera, and those two strains had average nucleotide identities of 62.0–72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62T represents a novel species in the genus

Oricola

belonging to the family

Phyllobacteriaceae

, which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1T, T40-3T and JL-62T were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1T (=MCCC M24557T=KCTC 82975T) and T40-3T (=MCCC 1K05135T=KCTC 82976T) are classified as representing two novel genera belonging to the family

Roseobacteraceae

with the names Mesobacterium pallidum gen. nov., sp. nov. and Heliomarina baculiformis gen. nov., sp. nov. are proposed, and strain JL-62T (=MCCC M24579T=KCTC 82974T) is proposed to represent a novel species within the genus

Oricola

with the name Oricola indica sp. nov. is proposed.
Glioblastoma stem cells express non-canonical proteins and exclusive mesenchymal-like or non-mesenchymal-like protein signatures
Authors: Babačić Haris , Galardi Silvia , Umer Husen M. , Cardinali Deborah , Pellegatta Serena , Hellström Mats , Uhrbom Lene , Maturi Nagaprathyusha , Michienzi Alessandro , Trevisi Gianluca , Mangiola Annunziato , Lehtiö Janne , Ciafrè Silvia Anna , Pernemalm Maria 
Published: February 2022

AbstractGlioblastoma’s (GBM) origin, recurrence and resistance to treatment are driven by GBM cancer stem cells (GSCs). Existing transcriptomic characterisations of GBM classify the tumours to three subtypes: classical, proneural, and mesenchymal. The comprehension of how expression patterns of the GBM subtypes are reflected at global proteome level in GSCs is limited.To characterise protein expression in GSCs, we performed in-depth proteogenomic analysis of patient-derived GSCs by RNA-sequencing and mass-spectrometry proteomics. We identified and quantified over 10,000 proteins in two independent GSCs panels, and propose a GSC-associated proteomic signature (GSAPS) that defines two distinct morphological conditions; one defined by a set of proteins expressed in non-mesenchymal - proneural and classical - GSCs (GPC-like), and another expressed in mesenchymal GSCs (GM-like). The expression of GM-like protein set in GBM tissue was associated with hypoxia, necrosis, recurrence, and worse overall survival in GBM patients.In a proof-of-concept proteogenomic approach, we discovered 252 non-canonical peptides expressed in GSCs, i.e., protein sequences that are variant or derive from genome regions previously considered protein-non-coding. We report new variants of the heterogeneous ribonucleoproteins (HNRNPs), which are implicated in mRNA splicing. Furthermore, we show that per-gene mRNA-protein correlations in GSCs are moderate and vary compared to GBM tissue.
Directional Absolute Coherence: a phase-based measure of effective connectivity for neurophysiology data
Authors: Scherer Maximilian , Wang Tianlu , Guggenberger Robert , Milosevic Luka , Gharabaghi Alireza 
Published: February 2022

AbstractCommunication between neural structures is a topic of much clinical and scientific interest and has been linked to a variety of behavioural, cognitive, and psychiatric measures. Here, we introduce a novel effective connectivity measure, termed the directional absolute coherence (DAC). Combining aspects of magnitude squared coherence, imaginary coherence, and phase slope index, DAC provides an estimate of connectivity that is resistant to volume conduction, encapsulates the directionality of neural communication, and is bound to the interval of –1 and 1. To highlight the properties of this newly proposed method, we compare DAC to a number of established connectivity methods using data recorded from the subthalamic nucleus of patients with Parkinson’s disease with deep brain stimulation electrodes. By applying a combination of real and simulated data, we demonstrate that DAC provides a reliable estimate of the magnitude and direction of connectivity, independent of the phase difference between brain signals. As such, DAC facilitates a reliable investigation of inter-regional neural communication, rendering it a valuable tool for gaining a deeper understanding of the functional architecture of the brain and its relationship to behaviour and cognition. A Python implementation of DAC is freely available at https://github.com/neurophysiological-analysis/FiNN.Highlights-Volume conduction and limited interpretability affect many connectivity methods.-DAC is a combined approach to overcome these pitfalls.-DAC augments information content and interpretability in comparison to other methods.-DAC allows for reliable estimation of effective connectivity.
Omics-informed CNV calls reduce false positive rate and improve power for CNV-trait associations
Authors: Lepamets Maarja , Auwerx Chiara , Nõukas Margit , Claringbould Annique , Porcu Eleonora , Kals Mart , Jürgenson Tuuli ,   Estonian Biobank Research Team, Morris Andrew Paul , Võsa Urmo , Bochud Murielle , Stringhini Silvia , Wijmenga Cisca , Franke Lude , Peterson Hedi , Vilo Jaak , Lepik Kaido , Mägi Reedik , Kutalik Zoltán 
Published: February 2022

AbstractCopy number variations (CNV) are believed to play an important role in a wide range of complex traits but discovering such associations remains challenging. Whilst whole genome sequencing (WGS) is the gold standard approach for CNV detection, there are several orders of magnitude more samples with available genotyping microarray data. Such array data can be exploited for CNV detection using dedicated software (e.g., PennCNV), however these calls suffer from elevated false positive and negative rates. In this study, we developed a CNV quality score that weights PennCNV calls (pCNV) based on their likelihood of being true positive. First, we established a measure of pCNV reliability by leveraging evidence from multiple omics data (WGS, transcriptomics and methylomics) obtained from the same samples. Next, we built a predictor of omics-confirmed pCNVs, termed omics-informed quality score (OQS), using only PennCNV software output parameters. Promisingly, OQS assigned to pCNVs detected in close family members was up to 35% higher than the OQS of pCNVs not carried by other relatives (P < 3.0−10−90), outperforming other scores. Finally, in an association study of four anthropometric traits in 89,516 Estonian Biobank samples, the use of OQS led to a relative increase in the trait variance explained by CNVs of up to 34% compared to raw pCNVs or previous quality scores. Overall, we put forward a flexible framework to improve any CNV detection method leveraging multi-omics evidence, applied it to improve PennCNV calls and demonstrated its utility by improving the statistical power for downstream association analyses.
Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity
Authors: Shlesinger Danielle , Hong Kai-Lin , Shammas Ghazal , Page Nicolas , Sandu Ioana , Agrafiotis Andreas , Kreiner Victor , Fonta Nicolas , Vincenti Ilena , Wagner Ingrid , Piccinno Margot , Mariotte Alexandre , Klimek Bogna , Dizerens Raphael , Manero-Carranza Marcos , Kuhn Raphael , Ehling Roy , Frei Lester , Khodaverdi Keywan , Panetti Camilla , Joller Nicole , Oxenius Annette , Merkler Doron , Reddy Sai T. , Yermanos Alexander 
Published: February 2022

AbstractAdaptive immune repertoires are composed by the ensemble of B and T cell receptors (BCR, TCR) within an individual and reflect both past and current immune responses. Recent advances in single-cell sequencing enable recovery of the complete adaptive immune receptor sequences in addition to transcriptional information. Such high-dimensional datasets enable the molecular quantification of clonal selection of B and T cells across a wide variety of conditions such as infection and disease. Due to costs, time required for the analysis and current practices of academic publishing, small-scale sequencing studies are often not made publicly available, despite having informative potential to elucidate immunological principles and guide future-studies. Here, we performed single-cell sequencing of B and T cells to profile clonal selection across murine models of viral infection and autoimmune disease. Specifically, we recovered transcriptome and immune repertoire information for polyclonal T follicular helper cells following acute and chronic viral infection, CD8+ T cells with binding specificity restricted to two distinct peptides of lymphocytic choriomeningitis virus, and B and T cells isolated from the nervous system in the context of experimental autoimmune encephalomyelitis. We could relate repertoire features such as clonal expansion, germline gene usage, and clonal convergence to cell phenotypes spanning activation, memory, naive, antibody secretion, T cell inflation, and regulation. Together, this dataset provides a resource for experimental and computational immunologists that can be integrated with future single-cell immune repertoire and transcriptome sequencing datasets.
Conservative Significance Testing of Tripartite Interactions in Multivariate Neural Data
Authors: Fomins Aleksejs , Sych Yaroslav , Helmchen Fritjof 
Published: February 2022

AbstractAn important goal in systems neuroscience is to understand the structure of neuronal interactions, frequently approached by studying functional relations between recorded neuronal signals. Commonly used pairwise metrics (e.g. correlation coefficient) offer limited insight, neither addressing the specificity of estimated neuronal interactions nor potential synergistic coupling between neuronal signals. Tripartite metrics, such as partial correlation, variance partitioning, and partial information decomposition, address these questions by disentangling functional relations into interpretable information atoms (unique, redundant and synergistic). Here, we apply these tripartite metrics to simulated neuronal recordings to investigate their sensitivity to impurities (like noise or other unexplained variance) in the data. We find that all considered metrics are accurate and specific for pure signals but experience significant bias for impure signals. We show that permutation-testing of such metrics results in high false positive rates even for small impurities and large data sizes. We present a conservative null hypothesis for significance testing of tripartite metrics, which significantly decreases false positive rate at a tolerable expense of increasing false negative rate. We hope our study raises awareness about the potential pitfalls of significance testing and of interpretation of functional relations, offering both conceptual and practical advice.Author SummaryTripartite functional relation metrics enable the study of interesting effects in neural recordings, such as redundancy, functional connection specificity and synergistic coupling. However, common estimators of such relations are designed for pure (e.g. non-noisy) signals rare for such recordings. We study the performance of tripartite estimators using simulated impure neural signals. We demonstrate that permutation-testing is not a robust procedure for inferring ground truth interactions from studied estimators. We develop an adjusted conservative testing procedure, reducing false positive rate of studied estimators for impure data. Besides addressing significance testing, our results should aid in accurate interpretation of tripartite functional relations and functional connectivity.
Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought
Authors: Moyers Brook T. , Henry Amelia , Raghavan Chitra , Zaw Hein , Marrano Annarita , Leung Hei , McKay John 
Published: February 2022

AbstractCrop adaptation is required to sustainably increase the rate of yield gains to meet projected future needs under the challenging conditions of climate change and competition for resources. Future adaptation will likely need to harness both highly polygenic traits and genotype-by-environment interactions (GxE), the study of which is aided by complex recombinant populations. We used the diverse Oryza sativa Global Multiparent Advanced Generation InterCross (MAGIC) population to study the genetic architecture and contributions of seedling emergence, establishment, and development to yield components under dry-direct seeding and seedling stage drought across three growing seasons. Dry-direct seeding is an establishment practice that has the potential to reduce methane emissions, water use, and labor demands for rice farmers, but increases the possibility of early-season drought conditions. We found substantial evidence for large roles of environmental variation and GxE in controlling trait variation. Maintenance of shoot growth during seedling stage drought was positively correlated with crown root number and both directly and indirectly influenced agronomic traits. Other than the major green revolution locus sd1, most allelic effects were conditionally neutral (affecting trait values in some environments but not others) and most alleles had their strongest effect in an environmental extreme. This discovery is both a challenge and a potential opportunity: with variable genetic architecture, selection in any one environment may not result in stable trait gains across environments. However, conditionally neutral GxE is a potential route to sustainable yield stability through allele pyramiding.