bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of a Prenatal Mindfulness Intervention on Infant Autonomic and Behavioral Reactivity and Regulation
Authors: Noroña-Zhou Amanda N. , Coccia Michael , Epel Elissa , Vieten Cassandra , Adler Nancy E. , Laraia Barbara , Jones-Mason Karen , Alkon Abbey , Bush Nicole R. 
Published: June 2022

ABSTRACT

Objective
Maternal health and wellness during pregnancy are associated with long-term health outcomes in children. The current study examined whether infants of women who participated in a mindfulness-based intervention during pregnancy that reduced levels of stress and depression, increased physical activity, and improved glucose tolerance differed on biobehavioral markers of psychopathological and physical health risk compared with infants of women who did not.

Methods
Participants were 135 mother-infant dyads drawn from a racially and ethnically diverse, low-income sample experiencing high stress. The women participated in an intervention trial during pregnancy that involved assignment to either mindfulness-based intervention or treatment-as-usual (TAU). Infants of women from both groups were assessed at 6 months of age on sympathetic (preejection period), parasympathetic (respiratory sinus arrhythmia), and observed behavioral (negativity and object engagement) reactivity and regulation during the still face paradigm. Linear mixed-effects and generalized linear mixed-effects models were used to examine treatment group differences in infant outcomes.

Results
Relative to those in the intervention group, infants in the TAU group showed a delay in sympathetic activation and subsequent recovery across the still face paradigm. In addition, infants in the intervention group engaged in higher proportions of self-regulatory behavior during the paradigm, compared with the TAU group. No significant effect of intervention was found for parasympathetic response or for behavioral negativity during the still face paradigm.

Conclusions
Findings provide evidence that maternal participation in a short-term, group mindfulness-based intervention during pregnancy is associated with the early development of salutary profiles of biobehavioral reactivity and regulation in their infants. Because these systems are relevant for psychopathology and physical health, prenatal behavioral interventions may benefit two generations.
Prognostic Value of Different Computed Tomography Scoring Systems in Patients With Severe Traumatic Brain Injury Undergoing Decompressive Craniectomy
Authors: Zhao Zhi-Jie , Chen Di , Zhou Lai-Yang , Sun Zhao-Liang , Wang Bo-Cheng , Feng Dong-Fu 
Published: June 2022

Objective
In this study, we investigate the preoperative and postoperative computed tomography (CT) scores in severe traumatic brain injury (TBI) patients undergoing decompressive craniectomy (DC) and compare their predictive accuracy.

Methods
Univariate and multivariate logistic regression analyses were used to determine the relationship between CT score (preoperative and postoperative) and mortality at 30 days after injury. The discriminatory power of preoperative and postoperative CT score was assessed by the area under the receiver operating characteristic curve (AUC).

Results
Multivariate logistic regression analysis adjusted for the established predictors of TBI outcomes showed that preoperative Rotterdam CT score (odds ratio [OR], 3.60; 95% confidence interval [CI], 1.13–11.50; P = 0.030), postoperative Rotterdam CT score (OR, 4.17; 95% CI, 1.63–10.66; P = 0.003), preoperative Stockholm CT score (OR, 3.41; 95% CI, 1.42–8.18; P = 0.006), postoperative Stockholm CT score (OR, 4.50; 95% CI, 1.60–12.64; P = 0.004), preoperative Helsinki CT score (OR, 1.44; 95% CI, 1.03–2.02; P = 0.031), and postoperative Helsinki CT score (OR, 2.55; 95% CI, 1.32–4.95; P = 0.005) were significantly associated with mortality. The performance of the postoperative Rotterdam CT score was superior to the preoperative Rotterdam CT score (AUC, 0.82–0.97 vs 0.71–0.91). The postoperative Stockholm CT score was superior to the preoperative Stockholm CT score (AUC, 0.76–0.94 vs 0.72–0.92). The postoperative Helsinki CT score was superior to the preoperative Helsinki CT score (AUC, 0.88–0.99 vs 0.65–0.87).

Conclusions
In conclusion, assessing the CT score before and after DC may be more precise and efficient for predicting early mortality in severe TBI patients who undergo DC.
Efficacy and Safety of Intravenous Golimumab in Ankylosing Spondylitis Patients With Early and Late Disease Through One Year of the GO-ALIVE Study
Authors: Deodhar Atul A. , Shiff Natalie J. , Gong Cinty , Hsia Elizabeth C. , Lo Kim Hung , Kim Lilliane , Xu Stephen , Reveille John D. 
Published: June 2022

Background/Objective
This post hoc analysis assessed efficacy and safety of intravenous (IV) golimumab in ankylosing spondylitis (AS) patients with early disease (ED) versus late disease (LD).

Methods
The phase 3, double-blind, GO-ALIVE study randomized patients to IV golimumab 2 mg/kg at weeks 0 and 4 and then every 8 weeks through week 52, or placebo at weeks 0, 4, and 12 with crossover to IV golimumab at week 16. Clinical efficacy was assessed by ≥20% improvement in Assessment of Spondyloarthritis International Society response criteria (ASAS20), ≥50% improvement in Bath Ankylosing Spondylitis Disease Activity Index (BASDAI 50), and Ankylosing Spondylitis Disease Activity Score (ASDAS) <1.3 (inactive disease). Using self-reported duration of inflammatory back pain (IBP), patients were grouped into quartiles: first = ED and fourth = LD. Descriptive statistics summarized efficacy and safety findings through 1 year.

Results
Early disease patients (n = 60) were ~10 years younger and had shorter median AS (IBP) symptom duration (2–3 years) versus LD patients (n = 52; 21–24 years). At week 16, numerically higher proportions of golimumab- than placebo-treated patients achieved ASAS20 (ED: 71% vs. 32%; LD: 67% vs. 21%), BASDAI 50 (ED: 40% vs. 12%; LD: 33% vs. 7%), and ASDAS <1.3 (ED: 17% vs. 4%; LD 8% vs. 0%) regardless of IBP duration. Efficacy was durable through 1 year of treatment; however, response rates were numerically higher in patients with ED versus LD. Through week 60, adverse events and serious adverse events, respectively, were reported by 46% and 3% of ED patients and 61% and 2% of LD patients.

Conclusion
Prompt diagnosis of AS and early treatment with IV golimumab may yield more robust improvements in disease activity.
Language exposure and brain myelination in early development
Authors: Fibla Laia , Forbes Samuel H. , McCarthy Jordan , Mee Kate , Magnotta Vincent , Deoni Sean , Cameron Donnie , Spencer John P. 
Published: June 2022

AbstractThe language environment to which children are exposed has an impact on later language and cognitive abilities as well as on brain development; however, it is unclear how early such impacts emerge. This study investigates the effects of children’s early language environment and socioeconomic status (SES) on brain structure in infancy at both 6 and 30 months of age. We used magnetic resonance imaging (MRI) to quantify concentrations of myelin in specific fiber tracts in the brain. Our central question was whether Language ENvironment Analysis (LENA) measures from in-home recording devices and SES measures of maternal education and family income predicted myelin concentrations over development. Results show relationships between amount of in-home adult input and myelination in the white matter tracts most associated with language. Right hemisphere regions also show an association with SES, with older children from a higher SES background who were exposed to more adult input showing greater concentrations of myelin in language-related areas. We discuss these results in relation with the current literature and implications for future language research and intervention.Significance StatementThis is the first study to look at how brain myelination is impacted by language input and socioeconomic status early in development. We find robust relationships of both factors in language-related brain areas at 30 months of age.
Prognostic value of serum MMP-9 level in acute ischemic stroke patient
Authors: Nayak Amit R. , Muley Swapnil S. , Kashyap Rajpal S. , Lande Neha H. , Kabra Dinesh P. , Singh Lokendra R. , Daginawala Hatim F. 
Published: June 2022

AbstractPurposeMMP-9 is reported to be a marker of severity and worse outcome after stroke. Despite the above information, there are very few studies based on the evaluation of role of follow-up estimation of serum MMP-9 in acute ischemic stroke (AIS) patients. The purpose of this study was to evaluate the role of follow-up estimation of serum MMP-9 in the prognosis of AIS patients. MMP-9 levels were also compared with reported biomarkers viz. Neuron-Specific Enolase (NSE), Glial specific protein (S100ββ) and Inter-α-trypsin inhibitor heavy chain 4 (ITIH4).Materials/methodsMMP-9, NSE, and S-100ββ were measured in serum samples collected at admission and expired/discharge time of AIS patients (n=48) using commercially available ELISA kits. ITIH4 was measured using Indirect ELISA protocol.ResultsMMP-9 at admission (3639 ±1471) and discharged/expired (3707 ±1268) was significantly higher (p<0.05) in AIS patients as compared to healthy control subjects (749 ±302). Expired patients showed significantly (p<0.05) higher MMP-9 as compared to survivors. Similarly, follow-up MMP-9 at discharge was higher in AIS patients who expired within one year (75%; 3/4). The observed values of MMP-9 significantly correlates (p<0.05) with NSE (r=0.452), S-100ββ (r=0.452) and ITIH4 (r=-0.2027).ConclusionsFollow-up measurement of serum MMP-9 may help to predict both short term and long term mortality in AIS patients.
COVID-19 is not an Independent Cause of Death
Authors: Castro Marcia C , Gurzenda Susie , Turra Cassio M , Kim Sun , Andrasfay Theresa , Goldman Noreen 
Published: June 2022

AbstractThe COVID-19 pandemic has had overwhelming global impacts with deleterious social, economic, and health consequences. To assess the COVID-19 death toll researchers have estimated declines in 2020 life expectancy at birth. Because data are often available only for COVID-19 deaths, the risks of dying from COVID-19 are assumed to be independent of those from other causes. We explore the soundness of this assumption based on data from the US and Brazil, the countries with the largest number of reported COVID-19 deaths. We use three methods. One estimates the difference between 2019 and 2020 life tables and therefore does not require the assumption of independence. The other two assume independence to simulate scenarios in which COVID-19 mortality is added to 2019 death rates or is eliminated from 2020 rates. Our results reveal that COVID-19 is not independent of other causes of death. The assumption of independence can lead to either an overestimate (Brazil) or an underestimate (US) of the decline in e0, depending on how the number of other reported causes of death changed in 2020.
TheGBAvariant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines
Authors: Smith Laura. J. , Bolsinger Magdalena. M. , Chau Kai-Yin. , Gegg Matthew. E. , Schapira Anthony. H. V. 
Published: June 2022

AbstractSequence variants or mutations in theGBAgene are numerically the most important risk factor for Parkinson disease (PD). TheGBAgene encodes for the lysosomal hydrolase enzyme, glucocerebrosidase (GCase).GBAmutations often reduce GCase activity and lead to impairment of the autophagy-lysosomal pathway, which is important in the turnover of alpha-synuclein, accumulation of which is a key pathological hallmark of PD. Although the E326K variant is one of the most commonGBAvariants associated with PD, there is limited understanding of its biochemical effects. We have characterised homozygous and heterozygous E326K variants in human fibroblasts. We found that E326K variants did not cause significant loss of GCase protein or activity, endoplasmic reticulum (ER) retention or ER stress, in contrast to the L444PGBAmutation. This was confirmed in human dopaminergic SH-SY5Y neuroblastoma cell lines over-expressing GCase with either E326K or L444P protein. Despite no loss of GCase activity, a significant increase of insoluble alpha-synuclein aggregates in E326K and L444P mutants was observed. Notably, SH-SY5Y over-expressing E326K demonstrated a significant increase in lipid droplet number under basal conditions, which was exacerbated following treatment with the fatty acid oleic acid. Similarly, a significant increase in lipid droplet formation following lipid loading was observed in heterozygous and homozygous E326K fibroblasts. In conclusion, the work presented here demonstrates that the E326K mutation behaves differently to common loss of functionGBAmutations, however lipid dyshomeostasis and alpha-synuclein pathology is still evident.
H4K20me1 plays a dual role in transcriptional regulation during regeneration and axis patterning ofHydra
Authors: Gungi Akhila , Pal Mrinmoy , Saha Shagnik , Galande Sanjeev 
Published: June 2022

ABSTRACTThe evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makesHydra, a Cnidarian, an excellent model system for understanding the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration due to its interaction with β-catenin to fine-tune the underlying gene regulatory network. Its target histone mark, H4K20me1, colocalizes with transcriptional activation machinery locally at the β-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. Contrastingly, genome-wide analysis of the H4K20me1 occupancy revealed a negative correlation with transcriptional activation. We propose H4K20me1 as a general repressive histone mark in Cnidaria and describe its dichotomous role in transcriptional regulation inHydra.
Single molecule studies characterize the kinetic mechanism of tetrameric p53 binding to different native response elements
Authors: Suwita Johannes P. , Voong Calvin K. , Ly Elina , Goodrich James A. , Kugel Jennifer F. 
Published: June 2022

AbstractThe transcriptional activator p53 is a tumor suppressor protein that controls cellular pathways important for cell fate decisions, including cell cycle arrest, senescence, and apoptosis. It functions as a tetramer by binding to specific DNA sequences known as response elements (REs) to control transcription via interactions with co-regulatory complexes. Critical for understanding how p53 regulates gene expression is unraveling the fundamental mechanisms by which it binds to REs. Toward this goal we have used an in vitro single molecule fluorescence approach to quantify the dynamic binding of tetrameric p53 to five native REs in real time under equilibrium conditions. We found little evidence of dimer/DNA complexes as intermediates to the formation or dissociation of p53 tetramer/DNA complexes; however, tetramer/DNA complexes can exchange dimers at some REs. Determining rate constants for association and dissociation revealed two kinetically distinguishable populations of tetrameric p53/RE complexes. For the less stable population, the rate constants for dissociation were larger at REs closest to consensus, showing the more favorable binding sequences form the least kinetically stable complexes. Together our real time measurements provide insight into mechanisms with which tetrameric p53 forms complexes on different native REs.
GWANN: Implementing deep learning in genome wide association studies
Authors: Ashkenazy Nimrod , Feder Martin , Shir Ofer M. , Hübner Sariel 
Published: June 2022

AbstractMotivationGenome wide association studies (GWAS) are extensively used across species to identify genes that underlie important traits. Most GWAS methods apply modifications and extensions to a linear regression model in order to detect significant associations between genetic variation and a trait. Despite their popularity, these statistical models tend to suffer from high false positive rates, especially when utilized on large variant datasets or complex demographic scenarios. To overcome this, aggressive statistical corrections are applied which frequently diminish true associations.ResultsHere we consider a deep learning approach, and present an implementation of a convolutional neural network (CNN) to identify genetic variation that is associated with a trait of interest. To exploit the strength of CNNs in visual recognition, the genotype information is represented as an image, which enables the model to correctly classify genetic variants with respect to the trait, even when a population structure is present. Our proposed approach was implemented in a package called GWANN which exhibited solid performance. Overall, GWANN outperformed popular GWAS tools on both simulated and real datasets, and enabled the identification of association signals with increased sensitivity and speed.Availability and implementationThe package is available at: https://github.com/hubner-lab/GWANN
Development and Application of a Novel Simple Sequence Repeat Mining Algorithm Based on Regular Expression
Authors: Jia Zhenguo , Geng Ruimei , Wu Xiuming , Chen Shuai , Tong Ying , Yang Aiguo , Luo Chenggang , Ren Min 
Published: June 2022

ABSTRACTSimple sequence repeats (SSRs) are molecular genetic markers that are powerful tools in genomics studies; SSR markers are routinely mined as a part of genetic workflows. Here, we developed a novel SSR mining algorithm based on regular expression that can reduce the complexity of commonly used SSR mining software. We used the following SSR mining regular expression: ({i, j}?) (\1) {k}, where i and j denote the minimum and maximum lengths of the motifs of the SSR sequence, respectively, and k is the minimum number of repeat motifs. From this SSR mining algorithm, we developed an SSR sequence analysis software (named “regexSSRw”) that is capable of mining eligible SSR loci from FASTA format sequences; regexSSRw can be accessed at https://github.com/renm79/rgxSSRw. This SSR mining algorithm can aid a range of applications, from being used by programmers in the development of SSR mining software to being implemented by scholars into their SSR marker workflow.
OmicSelector: automatic feature selection and deep learning modeling for omic experiments
Authors: Stawiski Konrad , Kaszkowiak Marcin , Mikulski Damian , Hogendorf Piotr , Durczyński Adam , Strzelczyk Janusz , Chowdhury Dipanjan , Fendler Wojciech 
Published: June 2022

ABSTRACTA crucial phase of modern biomarker discovery studies is selecting the most promising features from high-throughput screening assays. Here, we present the OmicSelector - Docker-based web application and R package that facilitates the analysis of such experiments. OmicSelector provides a consistent and overfitting-resilient pipeline that integrates 94 feature selection approaches based on 25 distinct variable selection methods. It identifies and then ranks the best feature sets using 11 modeling techniques with hyperparameter optimization in hold-out or cross-validation. OmicSelector provides classification performance metrics for proposed feature sets, allowing researchers to choose the overfitting-resistant biomarker set with the highest diagnostic potential. Finally, it performs GPU-accelerated development, validation, and implementation of deep learning feedforward neural networks (up to 3 hidden layers, with or without autoencoders) on selected signatures. The application performs an extensive grid search of hyperparameters, including balancing and preprocessing of next-generation sequencing (e.g. RNA-seq, miRNA-seq) oraz qPCR data. The pipeline is applicable for determining candidate circulating or tissue miRNAs, gene expression data and methylomic, metabolomic or proteomic analyses. As a case study, we use OmicSelector to develop a diagnostic test for pancreatic and biliary tract cancer based on serum small RNA next-generation sequencing (miRNA-seq) data. The tool is open-source and available at https://biostat.umed.pl/OmicSelector/
Biocompatible polymeric microparticles serve as novel and reliable vehicles for exogenous hormone manipulations in passerines
Authors: Mahr Katharina , Anzengruber Maria , Hellerschmid Anna , Slezaceck Julia , Hoi Herbert , Subbiahdoss Guruprakash , Gabor Franz , Lendvai Ádám Z. 
Published: June 2022

AbstractThe administration of exogenous hormones emerged as an essential tool for field studies in endocrinology. However, working with wild animals remains challenging because under field conditions, not every available method meets the necessary requirements. Achieving a sustained elevation in hormone levels while simultaneously minimising handling time and invasiveness of the procedure is a difficult task in field endocrinology. Facing this challenge, we have investigated the suitability of biocompatible polymeric microparticles, a novel method for drug administration, as a tool to manipulate hormones in small songbirds. We chose the insulin-like growth factor -1 (IGF-1) as the target hormone because it receives great interest from the research community due to its important role in shaping life-history traits. Moreover, its short half-life and hydrophilic properties imply a major challenge in finding a suitable method to achieve a sustained, systemic long-term release. To study the release kinetics, we injected either IGF-1 loaded polylactic-co-glycolic acid (PLGA) microparticles or dispersion medium (control group) in the skin pocket of the interscapular region of captive bearded reedlings (Panurus biarmicus). We collected blood samples for 7 consecutive days plus an additional sampling period after two weeks and complemented these with an in vitro experiment. Our results show that in vitro, PLGA microparticles allowed a stable IGF-1 release for more than 15 days, following a burst release at the beginning of the measurement. In vivo, the initial burst was followed by a drop to still elevated levels in circulating IGF-1 until the effect vanished by 16 days post-treatment. This study is the first to describe PLGA-microparticles as a novel tool for exogenous hormone administration in a small passerine. We suggest that this method is highly suitable to achieve the systemic long-term release of hydrophilic hormones with a short half-life and reduces overall handling time, as it requires only one subcutaneous injection.