bluuebunny/crossref_metadata_2025 huggingface dataset:
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
Authors: Boytsov Alexandr , Abramov Sergey , Aiusheeva Ariuna Z , Kasianova Alexandra M , Baulin Eugene , Kuznetsov Ivan A , Aulchenko Yurii S , Kolmykov Semyon , Yevshin Ivan , Kolpakov Fedor , Vorontsov Ilya E , Makeev Vsevolod J , Kulakovskiy Ivan V
Published: April 2022

We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification.
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes
Authors: Mohammadi-Arani Razieh , Javadi-Zarnaghi Fatemeh , Boccaletto Pietro , Bujnicki Janusz M , Ponce-Salvatierra Almudena
Published: April 2022

Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.
Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli
Authors: Wang Tianhe , Simmel Friedrich C
Published: April 2022

Regulatory RNA molecules have been widely investigated as components for synthetic gene circuits, complementing the use of protein-based transcription factors. Among the potential advantages of RNA-based gene regulators are their comparatively simple design, sequence-programmability, orthogonality, and their relatively low metabolic burden. In this work, we developed a set of riboswitch-inspired riboregulators in Escherichia coli that combine the concept of toehold-mediated strand displacement (TMSD) with the switching principles of naturally occurring transcriptional and translational riboswitches. Specifically, for translational activation and repression, we sequestered anti-anti-RBS or anti-RBS sequences, respectively, inside the loop of a stable hairpin domain, which is equipped with a single-stranded toehold region at its 5′ end and is followed by regulated sequences on its 3′ side. A trigger RNA binding to the toehold region can invade the hairpin, inducing a structural rearrangement that results in translational activation or deactivation. We also demonstrate that TMSD can be applied in the context of transcriptional regulation by switching RNA secondary structure involved in Rho-dependent termination. Our designs expand the repertoire of available synthetic riboregulators by a set of RNA switches with no sequence limitation, which should prove useful for the development of robust genetic sensors and circuits.
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents
Authors: Kuechler Erich R , Jacobson Matthew , Mayor Thibault , Gsponer Jörg
Published: April 2022

Phase separation-based condensate formation is a novel working paradigm in biology, helping to rationalize many important cellular phenomena including the assembly of membraneless organelles. Uncovering the functional impact of cellular condensates requires a better knowledge of these condensates’ constituents. Herein, we introduce the webserver GraPES (Granule Protein Enrichment Server), a user-friendly online interface containing the MaGS and MaGSeq predictors, which provide propensity scores for proteins’ localization into cellular condensates. Our webpage contains models trained on human (Homo sapiens) and yeast (Saccharomyces cerevisiae) stress granule proteins. MaGS utilizes experimentally-based protein features for prediction, whereas MaGSeq is an entirely protein sequence-based implementation. GraPES is implemented in HTML/CSS and Javascript and is freely available for public use at https://grapes.msl.ubc.ca/. Documentation for using the provided webtools, descriptions of their methodology, and implementation notes can be found on the webpage.
P-TEFb is degraded by Siah1/2 in quiescent cells
Authors: Huang Fang , Feng Yongmei , Peterlin B Matija , Fujinaga Koh
Published: April 2022

P-TEFb, composed of CycT1 and CDK9, regulates the elongation of transcription by RNA polymerase II. In proliferating cells, it is regulated by 7SK snRNA in the 7SK snRNP complex. In resting cells, P-TEFb is absent, because CycT1 is dephosphorylated, released from CDK9 and rapidly degraded. In this study, we identified the mechanism of this degradation. We mapped the ubiquitination and degradation of free CycT1 to its N-terminal region from positions 1 to 280. This region is ubiquitinated at six lysines, where E3 ligases Siah1 and Siah2 bind and degrade these sequences. Importantly, the inhibition of Siah1/2 rescued the expression of free CycT1 in proliferating as well as resting primary cells. We conclude that Siah1/2 are the E3 ligases that bind and degrade the dissociated CycT1 in resting, terminally differentiated, anergic and/or exhausted cells.
The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation
Authors: Yang Lei , Lee Ka-Ming , Yu Conny Wing-Heng , Imai Hirotatsu , Choi Andrew Kwok-Ho , Banfield David K , Ito Kosuke , Uchiumi Toshio , Wong Kam-Bo
Published: April 2022

Eukaryotic uL11 contains a conserved MPPKFDP motif at the N-terminus that is not found in archaeal and bacterial homologs. Here, we determined the solution structure of human uL11 by NMR spectroscopy and characterized its backbone dynamics by 15N–1H relaxation experiments. We showed that these N-terminal residues are unstructured and flexible. Structural comparison with ribosome-bound uL11 suggests that the linker region between the N-terminal domain and C-terminal domain of human uL11 is intrinsically disordered and only becomes structured when bound to the ribosomes. Mutagenesis studies show that the N-terminal conserved MPPKFDP motif is involved in interacting with the P-complex and its extended protuberant domain of uL10 in vitro. Truncation of the MPPKFDP motif also reduced the poly-phenylalanine synthesis in both hybrid ribosome and yeast mutagenesis studies. In addition, G→A/P substitutions to the conserved GPLG motif of helix-1 reduced poly-phenylalanine synthesis to 9–32% in yeast ribosomes. We propose that the flexible N-terminal residues of uL11, which could extend up to ∼25 Å from the N-terminal domain of uL11, can form transient interactions with the uL10 that help to fetch and fix it into a position ready for recruiting the incoming translation factors and facilitate protein synthesis.
Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome
Authors: Herzel Lydia , Stanley Julian A , Yao Chun-Chen , Li Gene-Wei
Published: April 2022

Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
SuperPred 3.0: drug classification and target prediction—a machine learning approach
Authors: Gallo Kathleen , Goede Andrean , Preissner Robert , Gohlke Bjoern-Oliver
Published: April 2022

Since the last published update in 2014, the SuperPred webserver has been continuously developed to offer state-of-the-art models for drug classification according to ATC classes and target prediction. For the first time, a thoroughly filtered ATC dataset, that is suitable for accurate predictions, is provided along with detailed information on the achieved predictions. This aims to overcome the challenges in comparing different published prediction methods, since performance can vary greatly depending on the training dataset used. Additionally, both ATC and target prediction have been reworked and are now based on machine learning models instead of overall structural similarity, stressing the importance of functional groups for the mechanism of action of small molecule substances. Additionally, the dataset for the target prediction has been extensively filtered and is no longer only based on confirmed binders but also includes non-binding substances to reduce false positives. Using these methods, accuracy for the ATC prediction could be increased by almost 5% to 80.5% compared to the previous version, and additionally the scoring function now offers values which are easily assessable at first glance. SuperPred 3.0 is publicly available without the need for registration at: https://prediction.charite.de/index.php.
“Pseudo-pseudogenes” in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica
Authors: Feng Ye , Wang Zeyu , Chien Kun-Yi , Chen Hsiu-Ling , Liang Yi-Hua , Hua Xiaoting , Chiu Cheng-Hsun
Published: April 2022

Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes’ mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
Novel intraoperative strategies for enhancing tumor control: Future directions
Authors: Haddad Alexander F , Aghi Manish K , Butowski Nicholas
Published: April 2022

Maximal safe surgical resection plays a key role in the care of patients with gliomas. A range of technologies have been developed to aid surgeons in distinguishing tumor from normal tissue, with the goal of increasing tumor resection and limiting postoperative neurological deficits. Technologies that are currently being investigated to aid in improving tumor control include intraoperative imaging modalities, fluorescent tumor makers, intraoperative cell and molecular profiling of tumors, improved microscopic imaging, intraoperative mapping, augmented and virtual reality, intraoperative drug and radiation delivery, and ablative technologies. In this review, we summarize the aforementioned advancements in neurosurgical oncology and implications for improving patient outcomes.
Spinal brachytherapy
Authors: Mao Gordon , Theodore Nicholas
Published: April 2022

Brachytherapy remains an underrecognized and underutilized radiation therapy modality for the treatment of spinal tumors. This article summarizes the existing body of medical literature on the usage, indications, techniques, and outcomes of brachytherapy for the treatment of spine tumors. The disease pathology most commonly treated with brachytherapy is metastatic spine cancer, rather than primary bone tumors of the spine. Brachytherapy can be used alone, as percutaneous needle injections; however, it is more often used in conjunction with open surgery or cement vertebral body augmentation. Although the data are still relatively sparse, studies show consistent benefit from brachytherapy in terms of improvements in pain, function, local recurrence rate, and overall survival. Brachytherapy is also associated with a favorable complication profile.
Evaluation of magnetic resonance imaging-based radiomics characteristics for differentiation of benign and malignant peripheral nerve sheath tumors in neurofibromatosis type 1
Authors: Ristow Inka , Madesta Frederic , Well Lennart , Shenas Farzad , Wright Felicia , Molwitz Isabel , Farschtschi Said , Bannas Peter , Adam Gerhard , Mautner Victor F , Werner René , Salamon Johannes
Published: April 2022

Background

Patients with neurofibromatosis type 1 (NF1) develop benign (BPNST), premalignant atypical (ANF), and malignant (MPNST) peripheral nerve sheath tumors. Radiological differentiation of these entities is challenging. Therefore, we aimed to evaluate the value of a magnetic resonance imaging (MRI)-based radiomics machine-learning (ML) classifier for differentiation of these three entities of internal peripheral nerve sheath tumors in NF1 patients.

Methods

MRI was performed at 3T in 36 NF1 patients (20 male; age: 31 ± 11 years). Segmentation of 117 BPNSTs, 17 MPNSTs, and 8 ANFs was manually performed using T2w spectral attenuated inversion recovery sequences. One hundred seven features per lesion were extracted using PyRadiomics and applied for BPNST versus MPNST differentiation. A 5-feature radiomics signature was defined based on the most important features and tested for signature-based BPNST versus MPNST classification (random forest [RF] classification, leave-one-patient-out evaluation). In a second step, signature feature expressions for BPNSTs, ANFs, and MPNSTs were evaluated for radiomics-based classification for these three entities.

Results

The mean area under the receiver operator characteristic curve (AUC) for the radiomics-based BPNST versus MPNST differentiation was 0.94, corresponding to correct classification of on average 16/17 MPNSTs and 114/117 BPNSTs (sensitivity: 94%, specificity: 97%). Exploratory analysis with the eight ANFs revealed intermediate radiomic feature characteristics in-between BPNST and MPNST tumor feature expression.

Conclusion

In this proof-of-principle study, ML using MRI-based radiomics characteristics allows sensitive and specific differentiation of BPNSTs and MPNSTs in NF1 patients. Feature expression of premalignant atypical tumors was distributed in-between benign and malignant tumor feature expressions, which illustrates biological plausibility of the considered radiomics characteristics.
Tobacco Use Among Gender-Varying and Gender-Stable Adolescents and Adults Living in the United States
Authors: Kcomt Luisa , Evans-Polce Rebecca J , Engstrom Curtiss W , Boyd Carol J , Veliz Philip T , West Brady T , McCabe Sean Esteban
Published: April 2022

Introduction

This study examines the proportion of the United States adolescents and adults who are variable (ie, at least one change in gender identity) versus stable in their gender identities over time, and whether they differ significantly in their nicotine/tobacco use after adjusting for key covariates.

Methods

We fit multivariable logistic regression models to data from Waves 2–4 (2014/15–2016/18) of the Population Assessment of Tobacco and Health (PATH), a nationally representative study (n = 33 197 U.S. adolescents and adults aged ≥14 years). We examined associations of gender stability/variability over three waves with tobacco use at wave 4 (2016–2018). Differences in any past 30-day tobacco, cigarette, e-cigarette, other tobacco, and poly-tobacco use were assessed among cisgender-stable, transgender-stable, and gender-varying respondents.

Results

An estimated 1.0% of adolescents and adults were classified as gender-varying. Prevalence of any past 30-day tobacco use was higher among gender-varying individuals (42.7%) than among gender-stable individuals (transgender-stable, 37.8% and cisgender-stable, 26.7%). There were no significant differences in the odds of nicotine/tobacco use between the two gender-stable groups. However, gender-varying respondents had significant increased odds of any past 30-day tobacco use (adjusted odds ratio [AOR] = 2.0, 95% confidence interval [CI] = 1.3 to 3.0), cigarette use (AOR = 1.7, 95% CI = 1.1 to 2.5), e-cigarette use (AOR = 2.2, 95% CI = 1.4-3.5), other tobacco use (AOR = 2.2, 95% CI = 1.4 to 3.4), and poly-tobacco use (AOR = 2.0, 95% CI = 1.3 to 3.1) compared with cisgender-stable individuals.

Conclusions

Gender-varying individuals are at higher risk for nicotine/tobacco use, placing them at greater risk for tobacco-related health consequences.

Implications

Despite increased knowledge about transgender health in recent years, there remains a paucity of research about gender-varying individuals. This study is the first to examine the proportion of gender-varying individuals in the United States using a longitudinal, nationally representative sample and to explore differences in nicotine/tobacco use among gender-varying and gender-stable individuals. Our findings suggest that gender-varying people have an increased risk for nicotine/tobacco use, placing them at higher risk for tobacco-related health consequences. This study increases knowledge about nicotine/tobacco use among this under-represented population in research and underscores the importance of developing an awareness of gender diversity.
Scoping Review of Existing Evaluations of Smokeless Tobacco Control Policies: What Is Known About Countries Covered, Level of Jurisdictions, Target Groups Studied, and Instruments Evaluated?
Authors: Forberger Sarah , Khan Z , Ahmad F , Ahmed F , Frense J , Kampfmann T , Ullah S , Dogar O , Siddiqi K , Zeeb H
Published: April 2022

Objective

The implementation of smokeless tobacco control policies lags behind those for smoking. This scoping review summarizes the studies that evaluated public policies on smokeless tobacco regulation (SLT) and provides an overview of the jurisdictional level, target groups, and policy instruments.

Methods

Seven databases were systematically searched for studies reporting on public policies regulating SLT. Two reviewers independently screened all studies. Data extraction was performed using a predefined extraction form. Extraction was replicated for 10% of the identified studies for quality assurance. A narrative synthesis of the included studies was used to analyze and interpret the data. The protocol was published beforehand with the Open Science Foundation (OSF).

Results

Fourty articles comprising 41 studies were included. Most of the studies reported in the articles were conducted in the United States (n = 17) or India (n = 14). Most studies reported outcomes for students (n = 8), retailers/sellers (n = 8), and users/former users (n = 5). The impact of public policies on smokeless tobacco use, in general, was most frequently assessed (n = 9), followed by the impact of taxes (n = 7), product bans (n = 6), sales/advertising bans near educational institutions (n = 4), and health warnings (n = 3) on consumer behavior.

Conclusions

There are significant gaps in the evaluation of smokeless tobacco regulation studies that need to be filled by further research to understand the observed outcomes. WHO reporting on Framework Convention on Tobacco Control (FCTC) implementation should be linked to studies evaluating smokeless tobacco control measures at all levels of jurisdictions and in countries not members of the WHO FCTC or do not provide data.

Implication

Large gaps in the evaluation of SLT control policies exist. For some countries, WHO FCTC evaluations are available for different levels of jurisdictions. In countries with a strong federal structure, there is a lack of data beyond the national level to provide a more detailed look at compliance, indirect effects, or implementation gaps. More research is needed at all levels of jurisdictions, which add to the work of the WHO to understand what works for which target group, how the different levels of jurisdiction interact, how the real-world context can be incorporated, and what indirect effects may occur.
Effects of COVID-19-Related Disruptions on Service Use in a Large Smoking Cessation Program
Authors: Veldhuizen Scott , Mahinpey Newsha , Zawertailo Laurie , Minian Nadia , Melamed Osnat , Selby Peter
Published: April 2022

Introduction

The COVID-19 pandemic caused a rapid shift to virtual care, with largely unknown consequences for accessibility. The purpose of this study is to examine pandemic-related changes in use of care for smoking cessation.

Aims and Methods

We conducted a secondary analysis 65 565 enrollments in a large smoking cessation program in Ontario, Canada. We used piecewise mixed-effects regression to examine how weeks nicotine replacement therapy (NRT) received, as well as counseling provided and visits attended, varied with date of enrollment over three time periods: more than 6 months before the pandemic began; the 6 months before the pandemic; and the pandemic period itself. We then examined changes in the associations between use of care and participant characteristics by fitting a model including a set of interactions between time and other variables. Based on an omnibus test of these interactions, we then tested individual terms, using the Holm method to control the family-wise error rate.

Results

From the start of the pandemic in March 2020, the total weeks of NRT provided rose significantly and then declined, while the amount of counseling fell. Associations between NRT use and participant characteristics changed significantly after the pandemic onset. Individual models showed that people with lower income, living in areas of higher marginalization, unable to work, and reporting higher levels of depressive symptoms all received NRT for a longer time during the pandemic period.

Conclusions

The pandemic led to small but significant changes in the amount of services used per enrollment. The transition to remote care appears to have reduced the effects of socioeconomic and health barriers.

Implications

The amount of care used by participants in tobacco cessation treatment is known to be associated with health and sociodemographic characteristics. Most of these associations did not change markedly following the pandemic-related switch to virtual care in 2020; however, the effects of some economic and health barriers seem to have lessened, perhaps because of a likely reduction in transport and time requirements of treatment.
The effect of pistachio supplementation on metabolic syndrome and its components in adults: a systematic review and meta-analysis of randomized controlled trials
Authors: Baghery Fatemeh , Mohammadifard Noushin , Khanamani Falahati-Pour Soudeh
Published: April 2022

Context

Several observational and experimental studies have been conducted to evaluate the effects of pistachio intake on metabolic syndrome (MetS); however, the results are inconsistent.

Objective

This systematic review and meta-analysis were performed on data from randomized controlled trials (RCTs) to determine the effect of pistachio consumption on MetS components.

Data sources

The PubMed, Scopus, Google Scholar and Web of Science databases were searched from 1986 to 2021.

Study selection

English-language RCTs on pistachio intake were included that provided outcomes on hypertension, hyperglycemia, hypertriglyceridemia, and high-density lipoprotein (HDL).

Data extraction

Results are presented as pooled mean differences (MDs) between intervention and control groups with 95%CI reported for each of the components.

Results

Seventeen RCTs including 940 adults met the inclusion criteria for this systematic review and meta-analysis. Pistachio supplementation significantly reduced systolic blood pressure (BP; MD, –2.89 mmHg, 95%CI: –4.11 to –1.67; P < 0.001), triglycerides (MD, –16.76 mg/dL, 95%CI: –16.89 to –16.64; P < 0.001), fasting blood glucose (MD, –3.62 mg/dL, 95%CI: –6.45 to –0.8; P < 0.001,) and increased HDL (MD, 1.43 mg/dL, 95%CI: 1.39 to 1.47; P < 0.001) levels. However, there were not observed considerable changes in waist circumference, diastolic BP, and body mass index.

Conclusion

The results of this research show that pistachio consumption could improve some MetS components, including systolic blood pressure, triglyceride, fasting blood glucose, and HDL levels, without affecting anthropometric indices and diastolic BP.
Effectiveness of nutritional interventions to prevent nonprogressive congenital and perinatal brain injuries: a systematic review and meta-analysis of randomized trials
Authors: Curioni Cintia C , Mocellin Michel C , Tavares Marina dos S , da Silva Ana C F , de Velasco Patricia C , Ribas Simone A , Lamarca Fernando , André Charles
Published: April 2022

Context

Nutritional interventions for newborns with brain injury are scarce, and there are gaps in the knowledge of their mechanisms of action in preventing the occurrence of cerebral palsy (CP) or the incidence of other developmental disabilities.

Objective

The objective of this review was to assess the effect of nutritional interventions in preventing nonprogressive congenital or perinatal brain injuries, or in improving outcomes related to neurological development.

Data Sources

Randomized trials on any nutritional intervention for pregnant women at risk of preterm delivery, or for children with low birth weight, preterm, or with confirmed or suspected microcephaly, CP, or fetal alcohol syndrome disorders (FASDs) were retrieved from MEDLINE, Embase, Scopus, Web of Science, LILACS, and CENTRAL databases from inception to September 17, 2020.

Data Extraction

Data extraction, risk of bias (Cochrane Risk of Bias tool 2), and quality of evidence (GRADE approach) were assessed by 2 authors.

Data Analysis

Pooled risk ratios (RRs) with 95% confidence intervals were calculated using a random-effects meta-analysis. Seventeen studies were included on intravenous interventions (magnesium sulfate [n = 5], amino acids [n = 4], vitamin A [n = 1], and N-acetylcysteine [n = 1]); enteral interventions (vitamin D [n = 1], prebiotic [n = 1], nutrient-enriched formula [n = 1], and speed of increasing milk feeds [n = 1]); and oral interventions (choline [n = 1] and docosahexaenoic acid, choline, and uridine monophosphate [n = 1]). All studies assessed CP, except 1 on FASDs. Eight studies were judged as having high risk of bias. Five studies (7413 babies) with high-quality evidence demonstrated decreased risk of childhood CP (RR = 0.68, 95% CI: 0.52–0.88) with magnesium sulfate. Interventions with amino acids had no effect on CP prevention or other outcomes. Except for 1 study, no other intervention decreased the risk of CP or FASDs.

Conclusion

Although different types of nutritional interventions were found, only those with antenatal magnesium sulfate were effective in decreasing CP risk in preterm infants. Well-designed, adequately powered randomized clinical trials are required.
Relaxing the “second brain”: nutrients and bioactive compounds as a therapeutic and preventive strategy to alleviate oxidative stress in the enteric nervous system
Authors: Almeida Patricia Pereira , Tavares-Gomes Ana Lúcia , Stockler-Pinto Milena Barcza
Published: April 2022

The enteric nervous system (ENS) regulates several functional and immunological processes in the gastrointestinal tract. However, some diseases can disrupt the ENS functionality, impacting the behavior of enteric neurons and enteric glial cells by increasing the accumulation of reactive oxygen species. Oxidative stress is considered to be a trigger for alterations in these cells’ morphology, density, and neurochemical patterns. In light of this, nutritional strategies are a growing field of investigation regarding their potential to modulate enteric neurons and enteric glial cells through reduced reactive oxygen species production. Moreover, several lines of evidence show that nutrients are related to counteracting oxidative stress. Some studies have evaluated the potential of nutrients with antioxidant roles (such as amino acids, polyphenols, prebiotics, vitamins, and specific extracts obtained from foods) to modulate the ENS. Thus, this review discusses how bioactive compounds and nutrients can impact the ENS by alleviating oxidative stress.
Artificial intelligence in food science and nutrition: a narrative review
Authors: Miyazawa Taiki , Hiratsuka Yoichi , Toda Masako , Hatakeyama Nozomu , Ozawa Hitoshi , Abe Chizumi , Cheng Ting-Yu , Matsushima Yuji , Miyawaki Yoshifumi , Ashida Kinya , Iimura Jun , Tsuda Tomohiro , Bushita Hiroto , Tomonobu Kazuichi , Ohta Satoshi , Chung Hsuan , Omae Yusuke , Yamamoto Takayuki , Morinaga Makoto , Ochi Hiroshi , Nakada Hajime , Otsuka Kazuhiro , Miyazawa Teruo
Published: April 2022

In the late 2010s, artificial intelligence (AI) technologies became complementary to the research areas of food science and nutrition. This review aims to summarize these technological advances by systematically describing the following: the use of AI in other fields (eg, engineering, pharmacy, and medicine); the history of AI in relation to food science and nutrition; the AI technologies currently used in the agricultural and food industries; and some of the important applications of AI in areas such as immunity-boosting foods, dietary assessment, gut microbiome profile analysis, and toxicity prediction of food ingredients. These applications are likely to be in great demand in the near future. This review can provide a starting point for brainstorming and for generating new AI applications in food science and nutrition that have yet to be imagined.
The relationship between nutritional status at the time of stroke on adverse outcomes: a systematic review and meta-analysis of prospective cohort studies
Authors: Mehta Arnav , De Paola Lorenzo , Pana Tiberiu A , Carter Ben , Soiza Roy L , Kafri Mohannad W , Potter John F , Mamas Mamas A , Myint Phyo K
Published: April 2022

Context and Objective

The impact of existing malnutrition on stroke outcomes is poorly recognised and treated. Evidence was systematically reviewed and quantified by meta-analysis.

Methods

MEDLINE, EMBASE and Web of Science were searched from inception to 11 January 2021 and updated in July. Prospective cohort studies, in English, evaluating anthropometric and biomarkers of nutrition on stroke outcomes were included. Risk of bias was assessed using the Scottish Intercollegiate Guidelines Network checklist.

Results

Twenty-six studies (n = 156 249) were eligible (follow-up: One month-14 years). Underweight patients had increased risk of long-term mortality (adjusted hazard ratio = 1.65,1.41-1.95), whilst overweight (0.80,0.74-0.86) and obese patients (0.80,0.75-0.85) had decreased risk compared to normal weight. Odds of mortality decreased in those with high serum albumin (odds ratio = 0.29,0.18-0.48) and increased with low serum albumin (odds ratio = 3.46,1.78-6.74) compared to normal serum albumin (30-35 g/L). Being malnourished compared to well-nourished, as assessed by the Subjective Global Assessment (SGA) or by a combination of anthropometric and biochemical markers increased all-cause mortality (odds ratio = 2.38,1.85-3.06) and poor functional status (adjusted odds ratio = 2.21,1.40-3.49).

Conclusion

Nutritional status at the time of stroke predicts adverse stroke outcomes.
Staff support during COVID-19 within an Acute Hospital Trust
Authors: Blighe Sabrina , Hotton Matthew , Quarmby Louise , Pollard Teresa , Neilan Natasha , Scholcz Anna , Pinckston Molly , Samuel Rosanna
Published: April 2022

Background

The COVID-19 pandemic has put immense pressure on the National Health Service (NHS) and all healthcare professionals, not only physically but also mentally and the need to fully develop and implement a strategy to protect the mental health of healthcare professionals has never been more urgent. Research has demonstrated that staff can be supported by strengthening teams and offering frequent well-being support.

Aims

To assess the feedback from delivery of a strategy to provide psychological well-being support to NHS staff during the COVID-19 pandemic and whether this ‘Support for Teams’ initiative made a positive impact on staff and in what way.

Methods

A mixed methods design was used to gain quantitative and qualitative feedback from staff. Feedback was collected from two groups: Well-being Leads and clinicians providing support and resources to Well-being Leads. Feedback was collected via online forms.

Results

Collectively, feedback responses were received from 70 staff members. The majority of staff members felt supported and benefitted from the provisions provided.

Conclusions

This evaluation showed that our healthcare system must continue to proactively implement and adapt staff support strategies to protect the mental well-being of healthcare professionals, both in the context of future health crises and in everyday practice. This study will assist and guide development and adaptations to health and psychological well-being support, ahead of future pandemics and to provide suitable support beyond the COVID-19 pandemic.
Mobilizing women voters: experimental evidence from Pakistan
Authors: Chaudhry Zain , Hussain Karrar , Ur Rehman Attique
Published: April 2022

We provide the first estimate of a door-to-door political campaign by an incumbent politician targeting women on electoral outcomes in a developing country. Women voters are informed of the public service delivery work undertaken by the incumbent in his tenure. The campaign was randomized at the precinct level, allowing us to use official electoral data on vote shares and gender-disaggregated turnout. Our results suggest that in a highly competitive campaign, the vote share of the campaigning incumbent increased by 5%age points. This increase was primarily driven by women who were campaigned independently of their male relatives. In precincts where both men and women were mobilized, the effect is not statistically significant. However, women’s turnout in the election was unaffected.
Political connections and firms: network dimensions
Authors: Bussolo Maurizio , Commander Simon , Poupakis Stavros
Published: April 2022

Business and politician interaction is commonplace. Most research has classified firms as either connected to a politician or not: a binary approach. Yet, there are almost always strong network dimensions to these connections. This article builds a unique data set to document a network of connections between politically exposed persons (PEPs), political parties, and firms in seven economies. With this novel dataset, the article examines the association between the characteristics and performance of firms and the firms’ connections with PEP, taking into account the network nature of these connections. The originality of our analysis is to identify how participation and location in a network, including the extent of links, as well as having a strategic location or centrality, is correlated with firm scale and performance. In a binary approach, such network characteristics are omitted. One consequence is that the intensity and consequences of politically connected business may be significantly mis/under-estimated.
Wage inequality and union membership at the establishment level: An econometric study using Norwegian data
Authors: Svarstad Elin , Nymoen Ragnar
Published: April 2022

We model the empirical relationship between the within-establishment union membership rate and wage inequality in Norway. The data set is a panel of 2,285 private-sector establishments observed in the period 2000–18. The statistical model represents joint feedback between wage inequality and union membership. Dynamic panel data models are estimated for different wage inequality measures, with gini as the reference measure. The results show a negative relationship between union membership and wage inequality, which is robust with respect to different inequality measures and estimation method. The strength of the relationship increases with the permanency of the shift in union membership. We find evidence that union membership is a more important explanatory variable for the lower part of the wage distribution than for the upper part. Furthermore, the impact of union density on wage inequality is conditional on the presence of a collective agreement.
The impact of ADHD genetic risk on educational achievement: a comparative cross-national study
Authors: Dannemann Bernhard C , Gören Erkan
Published: April 2022

Human capital accumulation is a key driver of economic development across countries. Although previous studies have shown that country-specific circumstances (e.g., cultural, health-related, and educational factors) are strongly related with the accumulation of human capital in society, few studies have explored the importance of innate ability factors in general and ADHD-related behavioral symptoms in particular for cognitive skill outcomes. This paper hypothesizes and empirically establishes the educational burden of the ADHD-related behavioral symptoms on aggregate cognitive achievement outcomes. We use a novel compilation of the 2- and 7-repeat allele variants of the human DRD4 exon III gene that candidate gene association studies have identified as an important biomarker in the etiology of childhood ADHD. We find that our indicator for the prevalence of ADHD genetic risk in society has a negative and statistically significant impact on educational achievement. Additional sensitivity tests and estimation methods further corroborate our main hypothesis.
Association Between Lifestyle Changes, Mammographic Breast Density, and Breast Cancer
Authors: Lester Sara P , Kaur Aparna S , Vegunta Suneela
Published: April 2022

In screening for breast cancer (BC), mammographic breast density (MBD) is a powerful risk factor that increases breast carcinogenesis and synergistically reduces the sensitivity of mammography. It also reduces specificity of lesion identification, leading to recalls, additional testing, and delayed and later-stage diagnoses, which result in increased health care costs. These findings provide the foundation for dense breast notification laws and lead to the increase in patient and provider interest in MBD. However, unlike other risk factors for BC, MBD is dynamic through a woman’s lifetime and is modifiable. Although MBD is known to change as a result of factors such as reproductive history and hormonal status, few conclusions have been reached for lifestyle factors such as alcohol, diet, physical activity, smoking, body mass index (BMI), and some commonly used medications. Our review examines the emerging evidence for the association of modifiable factors on MBD and the influence of MBD on BC risk. There are clear associations between alcohol use and menopausal hormone therapy and increased MBD. Physical activity and the Mediterranean diet lower the risk of BC without significant effect on MBD. Although high BMI and smoking are known risk factors for BC, they have been found to decrease MBD. The influence of several other factors, including caffeine intake, nonhormonal medications, and vitamins, on MBD is unclear. We recommend counseling patients on these modifiable risk factors and using this knowledge to help with informed decision making for tailored BC prevention strategies.
The State of the Sub-discipline: Mapping Parliamentary and Legislative Studies Using a Survey and Bibliometric Analysis of Three of Its Journals
Authors: Bhattacharya Caroline , Hart Gavin , Haughey Sean , Holden Bates Stephen , Meakin Alexandra
Published: April 2022

We map the current state of parliamentary and legislative studies through a survey of 218 scholars and a bibliometric analysis of 25 years of publications in three prominent sub-field journals. We identify two groupings of researchers, a quantitative methods, rational choice-favouring grouping and a qualitative methods, interpretivism-favouring grouping with a UK focus. Upon closer examination, these groupings share similar views about the challenges and future of the sub-discipline. While the sub-discipline is becoming more diverse and international, US-focused literature remains dominant and distinct from UK-focused literature, although there are emerging sub-literatures which are well placed to link them together.
Zooplankton assemblage and body size responses to severe lake eutrophication from agricultural activities near mink farms in Nova Scotia, Canada
Authors: Jones A , Labaj A , Campbell J , Libera N , Kurek J
Published: April 2022

Mink fur farming was once a widespread agricultural activity in southwestern Nova Scotia. Freshwaters near to and downstream of several mink fur farm operations have experienced severe water quality issues, including eutrophication and recurring algal blooms. Here, we use dated lake sediments to examine trends in primary producers and primary consumers from a hypereutrophic lake to assess how cladoceran assemblages have responded to extreme eutrophication. Shifts in the dominant pelagic cladoceran taxa began in the early 1900s, coinciding with an increase in sedimentary chlorophyll-a concentrations. Notably, small-bodied bosminids decreased, while taxa such as Chydorus brevilabris and Daphnia pulex spp. dominated assemblages in recent decades. Bottom-up ecological factors, such as decades of greater primary production, were the likely drivers of assemblage shifts of primary consumers. Consistent body sizes of bosminids throughout the sedimentary record suggested that pelagic cladocerans were not influenced solely by predation pressure from macroinvertebrates or fish. This study provides evidence of large-scale ecological shifts occurring at multiple trophic levels in a hypereutrophic temperate lake with mink farming operations in its catchment.
Rising rates of starch degradation during daytime and trehalose 6-phosphate optimize carbon availability
Authors: Ishihara Hirofumi , Alseekh Saleh , Feil Regina , Perera Pumi , George Gavin M , Niedźwiecki Piotr , Arrivault Stephanie , Zeeman Samuel C , Fernie Alisdair R , Lunn John E , Smith Alison M , Stitt Mark
Published: April 2022

Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the light and remobilize it to support maintenance and growth at night. Starch synthesis and degradation are usually viewed as temporally separate processes. Recently, we reported that starch is also degraded in the light. Degradation rates are generally low early in the day but rise with time. Here, we show that the rate of degradation in the light depends on time relative to dawn rather than dusk. We also show that degradation in the light is inhibited by trehalose 6-phosphate, a signal for sucrose availability. The observed responses of degradation in the light can be simulated by a skeletal model in which the rate of degradation is a function of starch content divided by time remaining until dawn. The fit is improved by extension to include feedback inhibition of starch degradation by trehalose 6-phosphate. We also investigate possible functions of simultaneous starch synthesis and degradation in the light, using empirically parameterized models and experimental approaches. The idea that this cycle buffers growth against falling rates of photosynthesis at twilight is supported by data showing that rates of protein and cell wall synthesis remain high during a simulated dusk twilight. Degradation of starch in the light may also counter over-accumulation of starch in long photoperiods and stabilize signaling around dusk. We conclude that starch degradation in the light is regulated by mechanisms similar to those that operate at night and is important for stabilizing carbon availability and signaling, thus optimizing growth in natural light conditions.
Cell wall-localized BETA-XYLOSIDASE4 contributes to immunity of Arabidopsis against Botrytis cinerea
Authors: Guzha Athanas , McGee Robert , Scholz Patricia , Hartken Denise , Lüdke Daniel , Bauer Kornelia , Wenig Marion , Zienkiewicz Krzysztof , Herrfurth Cornelia , Feussner Ivo , Vlot A Corina , Wiermer Marcel , Haughn George , Ischebeck Till
Published: April 2022

Plant cell walls constitute physical barriers that restrict access of microbial pathogens to the contents of plant cells. The primary cell wall of multicellular plants predominantly consists of cellulose, hemicellulose, and pectin, and its composition can change upon stress. BETA-XYLOSIDASE4 (BXL4) belongs to a seven-member gene family in Arabidopsis (Arabidopsis thaliana), one of which encodes a protein (BXL1) involved in cell wall remodeling. We assayed the influence of BXL4 on plant immunity and investigated the subcellular localization and enzymatic activity of BXL4, making use of mutant and overexpression lines. BXL4 localized to the apoplast and was induced upon infection with the necrotrophic fungal pathogen Botrytis cinerea in a jasmonoyl isoleucine-dependent manner. The bxl4 mutants showed a reduced resistance to B. cinerea, while resistance was increased in conditional overexpression lines. Ectopic expression of BXL4 in Arabidopsis seed coat epidermal cells rescued a bxl1 mutant phenotype, suggesting that, like BXL1, BXL4 has both xylosidase and arabinosidase activity. We conclude that BXL4 is a xylosidase/arabinosidase that is secreted to the apoplast and its expression is upregulated under pathogen attack, contributing to immunity against B. cinerea, possibly by removal of arabinose and xylose side-chains of polysaccharides in the primary cell wall.