bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iron Status of the Moderate and Late Preterm Infant: A Prospective Cohort Study
Authors: M.K Alok Kumar , Pournami Femitha , Prabhakar Jyothi , Nandakumar Anand , Jain Naveen 
Published: September 2021

Abstract
Guidelines on micronutrient supplementation in moderate to late preterm infants (MLP) are mostly extrapolated from those for smaller preterms, largely due to lack of systematic studies on physiological status in this special group of infants. Actual practices vary widely. We prospectively studied iron status by measurement of serum ferritin (SF) and haematological indices at 4 months corrected age in infants born between 32 and 36 weeks gestation (MLP), after they received 2 mg/kg/day oral iron from 6 weeks of postnatal age. Proportion of MLP having normal iron status (iron replete), i.e., neither iron deficiency (ID) nor iron excess was measured. ID anaemia, growth and development, risk factors for ID were also analysed. Of the 82 infants studied, 78% babies were late preterm. Seventy-four (90.3%) were iron replete (no deficiency or excess) at 4 months. High variability in SF levels (minimum of 9.8 to maximum of 252.2 μg/l) with median (IQR) of 57.45 μg/l (37.02–98.85) was noted in the entire cohort; and also within those who were iron deficient with median (IQR) of 17.50 μg/l (11.70–18.90). There was no difference in haematological indices of ID infants when compared to those with normal iron status. Inspite of oral iron supplementation with reasonable compliance, 8.5% MLP were iron deficient at 4 months corrected age. The high variability noted in SF levels could justify the need for monitoring iron status in this group of preterm infants. This could quintessentially aid individualization of iron supplementation advice.
Endophytic Fungi as a Promising Biocontrol Agent to Protect Wheat from Fusarium graminearum Head Blight
Authors: Noel Zachary A. , Roze Ludmilla V. , Breunig Mikaela , Trail Frances 
Published: September 2021

The search for beneficial endophytes that can be part of a constructed microbial community has increased in recent years. We characterized three endophytic fungi previously isolated from wheat for their in vitro and in planta antagonism toward the Fusarium head blight pathogen, Fusarium graminearum. The endophytes were phylogenetically characterized and shown to be Alternaria destruens, Fusarium commune, and Fusarium oxysporum. Individual fungal endophytes significantly increased seed weight and lowered the accumulation of the mycotoxin deoxynivalenol compared with F. graminearum-infected wheat heads without endophyte pretreatment. Investigation into the mechanism of competition in vitro showed that endophytes competitively excluded F. graminearum by preemptive colonization and possible inhibition over a distance. Investigations on the use of these endophytes in the field are in progress. Identification of these three endophytes highlights a common quandary in searching for beneficial microbes to use in agriculture: species definitions often do not separate individual isolates’ lifestyles. A greater understanding of the risks in using intraspecies variants for biocontrol is needed and should be examined in the context of the ecology of the individuals being investigated.
Nucleobindin-2 (NUCB2) gene transcription activity and nesfatin-1 levels in correlation with anthropometric and biochemical parameters in type 2 diabetes mellitus patient groups in Vietnam
Authors: Nguyen Duc Minh , Nguyen Minh Thi , Van Can Mao , Thu Trinh Huong Ngoc , Ngo Linh Bao , Bich Vo Thuy Thi , Nghiem Minh Ngoc 
Published: September 2021

AbstractIntroductionNucleobindin-2 (NUCB2) was identified as a DNA/Ca2+ binding protein with multiple functions in humans. Prohormone convertase-mediated NUCB2 processing produced nesfatin-1 - a biologically active. Nesfatin-1, an 82-amino acid peptide, was extracted from the N-terminus of nucleobindin-2. Recently, it was described as an anorexia peptide related to weight loss, malnutrition, and appetite regulation in type 2 diabetes mellitus patients.Research design and methodsIn this study, we collected samples and divided them into groups of patients with long-term type 2 diabetes and newly diagnosed type 2 diabetes group. Serum nesfatin-1 level and mRNA NUCB2 gene expression level of the groups were analyzed and compared with those of the healthy group.Biometric parameters and biochemical indices were also analyzed to determine the correlation with nesfatin-1 level.ResultsLevels of nesfatin-1 were found to be higher in the newly diagnosed group than in the other groups. Similar results were also reported in the analysis of mRNA NUCB2 gene expression by Realtime-PCR. Meanwhile, no significant difference was found in both analyzes of nesfatin-1 levels and NUCB2 mRNA expression in subjects with long-term type 2 diabetes compared with the control group. This result can be explained by the effects of long-term treatment. In the correlation of anthropometric parameters and biochemical indices, nesfatin-1 exhibited a significant correlation with BMI (r=0.569), HbA1c (r=-0.468), HDL-C (r=0.731), LDL-C (r=-0.482), Creatinine serum (r=0.525), and Creatinine urine (r=0.592), with p<0.001, in regression analysis.ConclusionsThese results indicate that the serum nesfatin-1 level and the NUCB2 mRNA gene expression level may be associated with newly diagnosed type 2 diabetes in Vietnamese patients. However, more specific studies with larger sample sizes were still needed in future studies.
Inequalities in COVID-19 inequalities research: who had the capacity to respond?
Authors: Benach Joan , Padilla Alvaro , Cash-Gibson Lucinda , Rojas-Gualdrón Diego F. , Fernández-Gracia Juan , Eguíluz Víctor M. ,   the COVID-SHINE group
Published: September 2021

AbstractThe COVID-19 pandemic has been testing countries’ capacities and scientific preparedness to actively respond, and collaborate on a common cause. It has also heightened awareness of the urgent need to empirically describe and analyse health inequalities, to be able to act effectively. What is known about the rapidly emerging COVID-19 inequalities research field? We analysed the volume of COVID-19 inequalities scientific production (2020-2021), its distribution by country income groups and world regions, and inter-country collaborations, to provide a first snapshot. COVID-19 inequalities research has been highly collaborative, however inequalities exist within this field, and new dynamics have emerged in comparison to the global health inequalities research field. To ensure preparedness for future crises, investment in health inequalities research capacities must be a priority for all.
Mutational Signatures as Sensors of Environmental Exposures: Role of Smoking in COVID-19 Vulnerabilities
Authors: Kim Yoo-Ah , Hodzic Ermin , Saslafsky Ariella , Wojtowicz Damian , Amgalan Bayarbaatar , Przytycka Teresa M. 
Published: September 2021

AbstractBackgroundEnvironmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases including lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to measure, making it challenging to understand their impacts. On the other hand, some COVID-19 patients develop ARDS in an unfavorable disease progression and smoking has been suggested as a potential risk factor among others. Yet initial studies on COVID-19 cases reported contradictory results on the effects of smoking on the disease – some suggest that smoking might have a protective effect against it while other studies report an increased risk. A better understanding of how the exposure to smoking and other environmental factors affect biological processes relevant to SARS-CoV-2 infection and unfavorable disease progression is needed.ApproachIn this study, we utilize mutational signatures associated with environmental factors as sensors of their exposure level. Many environmental factors including smoking are mutagenic and leave characteristic patterns of mutations, called mutational signatures, in affected genomes. We postulated that analyzing mutational signatures, combined with gene expression, can shed light on the impact of the mutagenic environmental factors to the biological processes. In particular, we utilized mutational signatures from lung adenocarcinoma (LUAD) data set collected in TCGA to investigate the role of environmental factors in COVID-19 vulnerabilities. Integrating mutational signatures with gene expression in normal tissues and using a pathway level analysis, we examined how the exposure to smoking and other mutagenic environmental factors affects the infectivity of the virus and disease progression.ResultsBy delineating changes associated with smoking in pathway-level gene expression and cell type proportions, our study demonstrates that mutational signatures can be utilized to study the impact of exogenous mutagenic factors on them. Consistent with previous findings, our analysis showed that smoking mutational signature (SBS4) is associated with activation of cytokine-mediated signaling pathways, leading to inflammatory responses. Smoking related changes in cell composition were also observed, including the correlation of SBS4 with the expansion of goblet cells. On the other hand, increased basal cells and decreased ciliated cells in proportion were associated with the strength of a different mutational signature (SBS5), which is present abundantly but not exclusively in smokers. In addition, we found that smoking increases the expression levels of genes that are up-regulated in severe COVID-19 cases. Jointly, these results suggest an unfavorable impact of smoking on the disease progression and also provide novel findings on how smoking impacts biological processes in lung.
Functional and Highly Crosslinkable HIV-1 Envelope Glycoproteins Enriched in a Pretriggered Conformation
Authors: Nguyen Hanh T. , Qualizza Alessandra , Anang Saumya , Zhao Meiqing , Zou Shitao , Zhou Rong , Wang Qian , Zhang Shijian , Deshpande Ashlesha , Ding Haitao , Smith Amos B. , Kappes John C. , Sodroski Joseph G. 
Published: September 2021

ABSTRACTBinding to the receptor, CD4, drives the pretriggered, “closed” (State-1) conformation of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer into more “open” conformations (States 2 and 3). Broadly neutralizing antibodies, which are elicited inefficiently, mostly recognize the State-1 Env conformation, whereas the more commonly elicited poorly neutralizing antibodies recognize States 2/3. HIV-1 Env metastability has created challenges for defining the State-1 structure and developing immunogens mimicking this labile conformation. The availability of functional State-1 Envs that can be efficiently crosslinked at lysine and/or acidic amino acid residues might assist these endeavors. To that end, we modified HIV-1AD8Env, which exhibits an intermediate level of triggerability by CD4. We introduced lysine/acidic residues at positions that exhibit such polymorphisms in natural HIV-1 strains. Env changes that were tolerated with respect to gp120-gp41 processing, subunit association and virus entry were further combined. Two common polymorphisms, Q114E and Q567K, as well as a known variant, A582T, additively rendered pseudoviruses resistant to cold, soluble CD4 and a CD4-mimetic compound, phenotypes indicative of stabilization of the pretriggered State-1 Env conformation. Combining these changes resulted in two lysine-rich HIV-1AD8Env variants (E.2 and AE.2) with neutralization- and cold-resistant phenotypes comparable to those of natural, less triggerable Tier 2/3 HIV-1 isolates. Compared with these and the parental Envs, the E.2 and AE.2 Envs were cleaved more efficiently and exhibited stronger gp120-trimer association in detergent lysates. These highly crosslinkable Envs enriched in a pretriggered conformation should assist characterization of the structure and immunogenicity of this labile state.IMPORTANCEThe development of an efficient vaccine is critical for combating HIV-1 infection worldwide. However, the instability of the pretriggered shape (State 1) of the viral envelope glycoprotein (Env) makes it difficult to raise neutralizing antibodies against HIV-1. Here, by introducing multiple changes in Env, we derived two HIV-1 Env variants that are enriched in State 1 and can be efficiently crosslinked to maintain this shape. These Env complexes are more stable in detergent, assisting their purification. Thus, our study provides a path to a better characterization of the native pretriggered Env, which should assist vaccine development.
Analysis of overdispersion in airborne transmission of Covid-19
Authors: Chaudhuri Swetaprovo , Kasibhatla Prasad , Mukherjee Arnab , Pan William , Morrison Glenn , Mishra Sharmistha , Murty Vijaya Kumar 
Published: September 2021

AbstractSuperspreading events and overdispersion are hallmarks of the Covid-19 pandemic. To gain insight into the nature and controlling factors of these superspreading events and heterogeneity in transmission, we conducted mechanistic modeling of SARS-CoV-2 transmission by infectious aerosols using real-world occupancy data from a large number of full-service restaurants in ten US metropolises. Including a large number of factors that influence disease transmission in these settings, we demonstrate the emergence of a stretched tail in the probability density function of secondary infection numbers indicating strong heterogeneity in individual infectivity. Derived analytical results further demonstrate that variability in viral loads and variability in occupancy, together, lead to overdispersion in the number of secondary infections arising from individual index cases. Our analysis, connecting mechanistic understanding of SARS-CoV-2 transmission by aerosols with observed large-scale epidemiological characteristics of Covid-19 outbreaks, adds an important dimension to the mounting body of evidence with regards to the determinants of airborne transmission of SARS-CoV-2 by aerosols in indoor settings.
Comparison of pretraining models and strategies for health-related social media text classification
Authors: Guo Yuting , Ge Yao , Yang Yuan-Chi , Al-Garadi Mohammed Ali , Sarker Abeed 
Published: September 2021

AbstractMotivationPretrained contextual language models proposed in the recent past have been reported to achieve state-of-the-art performances in many natural language processing (NLP) tasks. There is a need to benchmark such models for targeted NLP tasks, and to explore effective pretraining strategies to improve machine learning performance.ResultsIn this work, we addressed the task of health-related social media text classification. We benchmarked five models—RoBERTa, BERTweet, TwitterBERT, BioClinical_BERT, and BioBERT on 22 tasks. We attempted to boost performance for the best models by comparing distinct pretraining strategies—domain-adaptive pretraining (DAPT), source-adaptive pretraining (SAPT), and topic-specific pretraining (TSPT). RoBERTa and BERTweet performed comparably in most tasks, and better than others. For pretraining strategies, SAPT performed better or comparable to the off-the-shelf models, and significantly outperformed DAPT. SAPT+TSPT showed consistently high performance, with statistically significant improvement in one task. Our findings demonstrate that RoBERTa and BERTweet are excellent off-the-shelf models for health-related social media text classification, and extended pretraining using SAPT and TSPT can further improve performance.Availability and implementationSource code for our model and data preprocessing is available under the Github repository https://github.com/yguo0102/transformer_dapt_sapt_tapt. Datasets must be obtained from original sources, as described in supplementary material.Supplementary informationSupplementary data are available at Bioinformatics online.
No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups When Infected with SARS-CoV-2 Delta Variant
Authors: Acharya Charlotte B. , Schrom John , Mitchell Anthea M. , Coil David A. , Marquez Carina , Rojas Susana , Wang Chung Yu , Liu Jamin , Pilarowski Genay , Solis Leslie , Georgian Elizabeth , Petersen Maya , DeRisi Joseph , Michelmore Richard , Havlir Diane 
Published: September 2021

AbstractWe found no significant difference in cycle threshold values between vaccinated and unvaccinated, asymptomatic and symptomatic groups infected with SARS-CoV-2 Delta. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered for all in settings with elevated COVID-19 transmission.
Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships
Authors: Tong Xiaoling , Han Min-Jin , Lu Kunpeng , Tai Shuaishuai , Liang Shubo , Liu Yucheng , Hu Hai , Shen Jianghong , Long Anxing , Zhan Chengyu , Ding Xin , Gao Qiang , Zhang Bili , Tan Duan , Yuan Yajie , Guo Nangkuo , Li Yanhong , Wu Zhangyan , Liu Lulu , Li Chunlin , Lu Yaru , Gai Tingting , Zhang Yahui , Yang Renkui , Qian Heying , Liu Yanqun , Luo Jiangwen , Zheng Lu , Lou Jinghou , Peng Yunwu , Zuo Weidong , Song Jiangbo , He Songzhen , Wu Songyuan , Zou Yunlong , Zhou Lei , Zhou Linli , Cheng Lan , Tang Yuxia , Cheng Guotao , Yuan Lianwei , He Weiming , Xu Jiabao , Fu Tao , Xiao Yang , Lei Ting , Xu Anying , Yin Ye , Wang Jian , Monteiro Antónia , Westhof Eric , Lu Cheng , Tian Zhixi , Wang Wen , Xiang Zhonghuai , Dai Fangyin 
Published: September 2021

AbstractThe silkworm Bombyx mori is a domestic insect for silk production and a lepidopteran model. The currently available genomes limit a full understanding of its genetic and phenotypic diversity. Here we assembled long-read genomes of 545 domestic and wild silkworms and constructed a high-resolution pan-genome dataset. We found that the silkworm population harbors extremely variable genomes containing 7,308 new gene families, 4,260 (22%) core gene families, and 3,432,266 non-redundant SVs. We deciphered a series of causal genes and variants associated with domestication, breeding, and ecological adaptation traits, and experimentally validated two of those genes using CRISPR-Cas9 or RNA interference. This unprecedented large-scale genomic resource allows for high-throughput screening of interesting traits for functional genomic research and breeding improvement of silkworms and may serve as a guideline for traits decoding in other species.
Neuronal glucose metabolism sets cholinergic tone and controls thermo-regulated signaling at the neuromuscular junction
Authors: Tang Yan , Zong Haihong , Kwon Hyokjoon , Qiu Yunping , Pessin Jacob B. , Wu Licheng , Buddo Katherine A. , Boykov Ilya , Schmidt Cameron A. , Lin Chien-Te , Darrell Neufer P. , Schwartz Gary J. , Kurland Irwin J. , Pessin Jeffrey E. 
Published: September 2021

SummaryCholinergic and sympathetic counter-regulatory networks control numerous physiologic functions including learning/memory/cognition, stress responsiveness, blood pressure, heart rate and energy balance. As neurons primarily utilize glucose as their primary metabolic energy source, we generated mice with increased glycolysis in cholinergic neurons by specific deletion of the fructose-2,6-phosphatase protein TIGAR. Steady-state and stable isotope flux analyses demonstrated increased rates of glycolysis, acetyl-CoA production, acetylcholine levels and density of neuromuscular synaptic junction clusters with enhanced acetylcholine release. The increase in cholinergic signaling reduced blood pressure and heart rate with a remarkable resistance to cold-induced hypothermia. These data directly demonstrate that increased cholinergic signaling through the modulation of glycolysis has several metabolic benefits particularly to increase energy expenditure and heat production upon cold exposure.HighlightsDeficiency of a negative regulator of glycolysis (TIGAR) in cholinergic neurons increases the biosynthesis and content of the neurotransmitter acetylcholine.Increased cholinergic tone reduces blood pressure and heart rate while enhancing signaling at neuromuscular junction.Upregulation of neuromuscular junction activation provides protection against the paralytic curare and cold-induced hypothermia.Modulation of cholinergic neuron glycolysis may provide a novel therapeutic approach for treatment of diseases stemming from reduced acetylcholine signaling such as myasthenia gravis and sarcopenic pre-synaptic dysfunction.
An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury
Authors: Denans Nicolas , Tran Nhung T. T. , Swall Madeleine E. , Diaz Daniel C. , Blanck Jillian , Piotrowski Tatjana 
Published: September 2021

AbstractMacrophages are essential for tissue repair and regeneration. Yet, the molecular programs, as well as the timing of their activation during and after tissue injury are poorly defined. Using a high spatio-temporal resolution single cell analysis of macrophages coupled with live imaging after sensory hair cell death in zebrafish, we find that the same population of macrophages transitions through a sequence of three major anti-inflammatory activation states. Macrophages first show a signature of glucocorticoid activation, then IL10 signaling and finally the induction of oxidative phosphorylation by IL4/Polyamine signaling. Importantly, loss-of-function of glucocorticoid and IL10 signaling shows that each step of the sequence is independently activated. Our results provide the first evidence that macrophages, in addition to a switch from M1 to M2, sequentially and independently transition though three anti-inflammatory pathways in vivo during tissue injury in a regenerating organ.One-Sentence SummaryWe show that macrophages are sequentially activated by three different anti-inflammatory pathways during tissue injury.
The spread of the first introns in proto-eukaryotic paralogs
Authors: Vosseberg Julian , Schinkel Michelle , Gremmen Sjoerd , Snel Berend 
Published: September 2021

AbstractSpliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20-35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were widespread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established.