bluuebunny/crossref_metadata_2025 huggingface dataset:
sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome
Authors: Peng Zhao , Li Jiaqiang , Jiang Xingpeng , Wan Cuihong
Published: April 2024

Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. Here, we proposed the smORF-coding-potential-predicting framework, sOCP, which provides functions to construct a model for predicting novel smORFs in some species. The sOCP model constructed in human was based on in-frame features and the nucleotide bias around the start codon, and the small feature subset was proved to be competent enough and avoid overfitting problems for complicated models. It showed more advanced prediction metrics than previous methods and could correlate closely with experimental evidence in a heterogeneous dataset. The model was applied to Rattus norvegicus and exhibited satisfactory performance. We then scanned smORFs with ATG and non-ATG start codons from the human genome and generated a database containing about a million novel smORFs with coding potential. Around 72 000 smORFs are located on the lncRNA regions of the genome. The smORF-encoded peptides may be involved in biological pathways rare for canonical proteins, including glucocorticoid catabolic process and the prokaryotic defense system. Our work provides a model and database for human smORF investigation and a convenient tool for further smORF prediction in other species.
FlexStat: combinatory differentially expressed protein extraction
Authors: De Silva Senuri , Alli-Shaik Asfa , Gunaratne Jayantha
Published: April 2024

Motivation

Mass spectrometry-based system proteomics allows identification of dysregulated protein hubs and associated disease-related features. Obtaining differentially expressed proteins (DEPs) is the most important step of downstream bioinformatics analysis. However, the extraction of statistically significant DEPs from datasets with multiple experimental conditions or disease types through currently available tools remains a laborious task. More often such an analysis requires considerable bioinformatics expertise, making it inaccessible to researchers with limited computational analytics experience.

Results

To uncover the differences among the many conditions within the data in a user-friendly manner, here we introduce FlexStat, a web-based interface that extracts DEPs through combinatory analysis. This tool accepts a protein expression matrix as input and systematically generates DEP results for every conceivable combination of various experimental conditions or disease types. FlexStat includes a suite of robust statistical tools for data preprocessing, in addition to DEP extraction, and publication-ready visualization, which are built on established R scientific libraries in an automated manner. This analytics suite was validated in diverse public proteomic datasets to showcase its high performance of rapid and simultaneous pairwise comparisons of comprehensive datasets.

Availability and implementation

FlexStat is implemented in R and is freely available at https://jglab.shinyapps.io/flexstatv1-pipeline-only/. The source code is accessible at https://github.com/kts-desilva/FlexStat/tree/main.
Prioritization of oligogenic variant combinations in whole exomes
Authors: Gravel Barbara , Renaux Alexandre , Papadimitriou Sofia , Smits Guillaume , Nowé Ann , Lenaerts Tom
Published: April 2024

Motivation

Whole exome sequencing (WES) has emerged as a powerful tool for genetic research, enabling the collection of a tremendous amount of data about human genetic variation. However, properly identifying which variants are causative of a genetic disease remains an important challenge, often due to the number of variants that need to be screened. Expanding the screening to combinations of variants in two or more genes, as would be required under the oligogenic inheritance model, simply blows this problem out of proportion.

Results

We present here the High-throughput oligogenic prioritizer (Hop), a novel prioritization method that uses direct oligogenic information at the variant, gene and gene pair level to detect digenic variant combinations in WES data. This method leverages information from a knowledge graph, together with specialized pathogenicity predictions in order to effectively rank variant combinations based on how likely they are to explain the patient’s phenotype. The performance of Hop is evaluated in cross-validation on 36 120 synthetic exomes for training and 14 280 additional synthetic exomes for independent testing. Whereas the known pathogenic variant combinations are found in the top 20 in approximately 60% of the cross-validation exomes, 71% are found in the same ranking range when considering the independent set. These results provide a significant improvement over alternative approaches that depend simply on a monogenic assessment of pathogenicity, including early attempts for digenic ranking using monogenic pathogenicity scores.

Availability and implementation

Hop is available at https://github.com/oligogenic/HOP.
pyaging: a Python-based compendium of GPU-optimized aging clocks
Authors: de Lima Camillo Lucas Paulo
Published: April 2024

Motivation

Aging is intricately linked to diseases and mortality. It is reflected in molecular changes across various tissues which can be leveraged for the development of biomarkers of aging using machine learning models, known as aging clocks. Despite advancements in the field, a significant challenge remains: the lack of robust, Python-based software tools for integrating and comparing these diverse models. This gap highlights the need for comprehensive solutions that can handle the complexity and variety of data in aging research.

Results

To address this gap, I introduce pyaging, a comprehensive open-source Python package designed to facilitate aging research. pyaging harmonizes dozens of aging clocks, covering a range of molecular data types such as DNA methylation, transcriptomics, histone mark ChIP-Seq, and ATAC-Seq. The package is not limited to traditional model types; it features a diverse array, from linear and principal component models to neural networks and automatic relevance determination models. Thanks to a PyTorch-based backend that enables GPU acceleration, pyaging is capable of rapid inference, even when dealing with large datasets and complex models. In addition, the package’s support for multi-species analysis extends its utility across various organisms, including humans, various mammals, and Caenorhabditis elegans.

Availability and implementation

pyaging is accessible on GitHub, at https://github.com/rsinghlab/pyaging, and the distribution is available on PyPi, at https://pypi.org/project/pyaging/. The software is also archived on Zenodo, at https://zenodo.org/doi/10.5281/zenodo.10335011.
Sharp symbolic nonparametric bounds for measures of benefit in observational and imperfect randomized studies with ordinal outcomes
Authors: Gabriel Erin E , Sachs Michael C , Jensen Andreas Kryger
Published: April 2024

The probability of benefit can be a valuable and meaningful measure of treatment effect. Particularly for an ordinal outcome, it can have an intuitive interpretation. Unfortunately, this measure, and variations of it, are not identifiable even in randomized trials with perfect compliance. There is, for this reason, a long literature on nonparametric bounds for unidentifiable measures of benefit. These have primarily focused on perfect randomized trial settings and one or two specific estimands. We expand these bounds to observational settings with unmeasured confounders and imperfect randomized trials for all three estimands considered in the literature: the probability of benefit, the probability of no harm and the relative treatment effect.
The Iconic Apache: Early 1900s Paris and the Making of a Criminal Bogeyman
Authors: Beauchez Jérôme
Published: April 2024

This article describes the creation of a criminal icon, the Paris Apache, brandished as a threat by the press and conservative politicians alike at the turn of the twentieth century in France. Archival analysis points to the theory that this figure of street crime was turned into a criminal ‘bogeyman’. The iconic Apache bogeyman allowed those manipulating it to focus the general public’s fears and attention on factual violence (crimes, assaults and misdemeanours) of which the structural causes (political instability and socio-economic inequalities) were masked by framing the criminal icon as solely responsible. This bogeyman role, embodied by the Apache in the past, is also examined in the present and analysed critically from the perspective of cultural criminology.
A shift between bee and wasp pollinators explains floral divergence in the Duvernoia clade of Justicia (Acanthaceae)
Authors: Adit Arjun , Johnson Steven D
Published: April 2024

Floral divergence among sister taxa can arise from pollinator shifts and play a role in speciation. We investigate a potential case of pollinator-driven divergence in the Duvernoia clade of Justicia (Acanthaceae), which includes two species with markedly divergent floral morphology. Pollinator observations and pollen load analyses showed that Justicia aconitiflora is pollinated by vespid wasps, while its sister taxon Justicia adhatodoides is confirmed to be pollinated exclusively by large carpenter bees. Reciprocal nectar-feeding experiments show that wasps and bees are not deterred by the taste of nectar of non-preferred species. Floral morphology matches body and tongue morphology of these two insect groups, and this phenotypic matching mediates pollen transfer and physical access to nectar. Controlled pollination experiments showed that both species are self-compatible, yet dependent on pollinator visits for fruit-set. Historical reconstruction of pollination system evolution in Justicia indicates that the direction of the shift in the Duvernoia clade was from bee to wasp pollinators. This study provides a compelling example of a transition between bee and wasp pollination, and highlights the effects of floral architecture on specialization in plant pollination systems.
Memory deficit in patients with cerebral small vessel disease: evidence from eye tracking technology
Authors: Huang Kailing , Zhao Tingting , Sun Weifeng , Feng Li , Wang Quan , Feng Jie
Published: April 2024

Cerebral small vessel disease is the one of the most prevalent causes of vascular cognitive impairment. We aimed to find objective and process-based indicators related to memory function to assist in the detection of memory impairment in patients with cerebral small vessel disease. Thirty-nine cerebral small vessel disease patients and 22 healthy controls were invited to complete neurological examinations, neuropsychological assessments, and eye tracking tasks. Eye tracking indicators were recorded and analyzed in combination with imaging features. The cerebral small vessel disease patients scored lower on traditional memory task and performed worse on eye tracking memory task performance compared to the healthy controls. The cerebral small vessel disease patients exhibited longer visit duration and more visit count within areas of interest and targets and decreased percentage value of total visit duration on target images to total visit duration on areas of interest during decoding stage among all levels. Our results demonstrated the cerebral small vessel disease patients performed worse in memory scale and eye tracking memory task, potentially due to their heightened attentional allocation to nontarget images during the retrieval stage. The eye tracking memory task could provide process-based indicators to be a beneficial complement to memory assessment and new insights into mechanism of memory impairment in cerebral small vessel disease patients.
Noninvasive brain stimulations modulated brain modular interactions to ameliorate working memory in community-dwelling older adults
Authors: Fan Dongqiong , Che Xianwei , Jiang Yang , He Qinghua , Yu Jing , Zhao Haichao
Published: April 2024

Non-invasive brain stimulations have drawn attention in remediating memory decline in older adults. However, it remains unclear regarding the cognitive and neural mechanisms underpinning the neurostimulation effects on memory rehabilitation. We evaluated the intervention effects of 2-weeks of neurostimulations (high-definition transcranial direct current stimulation, HD-tDCS, and electroacupuncture, EA versus controls, CN) on brain activities and functional connectivity during a working memory task in normally cognitive older adults (age 60+, n = 60). Results showed that HD-tDCS and EA significantly improved the cognitive performance, potentiated the brain activities of overlapping neural substrates (i.e. hippocampus, dlPFC, and lingual gyrus) associated with explicit and implicit memory, and modulated the nodal topological properties and brain modular interactions manifesting as increased intramodular connection of the limbic-system dominated network, decreased intramodular connection of default-mode-like network, as well as stronger intermodular connection between frontal-dominated network and limbic-system–dominated network. Predictive model further identified the neuro-behavioral association between modular connections and working memory. This preliminary study provides evidence that noninvasive neurostimulations can improve older adults’ working memory through potentiating the brain activity of working memory-related areas and mediating the modular interactions of related brain networks. These findings have important implication for remediating older adults’ working memory and cognitive declines.
Volumetric analysis of age- and sex-related changes in the corpus striatum and thalamus in the 1–18 age group: a retrospective magnetic resonance imaging study
Authors: Işıklar Sefa , Sağlam Dilek
Published: April 2024

Studies of the development and asymmetry of the corpus striatum and thalamus in early childhood are rare. Studies investigating these structures across the lifespan have not presented their changes during childhood and adolescence in detail. For these reasons, this study investigated the effect of age and sex factors on the development and asymmetry of the corpus striatum and thalamus in the 1–18 age group. In this retrospective study, we included 652 individuals [362 (56%) males] aged 1–18 years with normal brain MRI between 2012 and 2021. Absolute and relative volumes of the corpus striatum and thalamus were obtained by segmentation of three-dimensional T1-weighted MRIs with volBrain1.0. We created age-specific volume data and month-based development models with the help of SPSS (ver.28). The corpus striatum and thalamus had cubic absolute volumetric developmental models. The relative volume of the caudate and thalamus (only males) is consistent with the decreasing “growth” model, the others with the decreasing cubic model. The absolute volumes of the males’ bilateral corpus striatum and thalamus and the relative volumes of the caudate and thalamus of the females were significantly larger (P < 0.05). The caudate showed right > left lateralization; putamen, globus pallidus, and thalamus showed left > right lateralization.
Modeling refined differences of cortical folding patterns via spatial, morphological, and temporal fusion representations
Authors: Cao Chunhong , Li Yongquan , Hu Fang , Gao Xieping
Published: April 2024

The gyrus, a pivotal cortical folding pattern, is essential for integrating brain structure-function. This study focuses on 2-Hinge and 3-Hinge folds, characterized by the gyral convergence from various directions. Existing voxel-level studies may not adequately capture the precise spatial relationships within cortical folding patterns, especially when relying solely on local cortical characteristics due to their variable shapes and homogeneous frequency-specific features. To overcome these challenges, we introduced a novel model that combines spatial distribution, morphological structure, and functional magnetic resonance imaging data. We utilized spatio-morphological residual representations to enhance and extract subtle variations in cortical spatial distribution and morphological structure during blood oxygenation, integrating these with functional magnetic resonance imaging embeddings using self-attention for spatio-morphological-temporal representations. Testing these representations for identifying cortical folding patterns, including sulci, gyri, 2-Hinge, and 2-Hinge folds, and evaluating the impact of phenotypic data (e.g. stimulus) on recognition, our experimental results demonstrate the model’s superior performance, revealing significant differences in cortical folding patterns under various stimulus. These differences are also evident in the characteristics of sulci and gyri folds between genders, with 3-Hinge showing more variations. Our findings indicate that our representations of cortical folding patterns could serve as biomarkers for understanding brain structure-function correlations.
Assessing the Impact of the 2020 Council of State and Territorial Epidemiologists Case Definition for Pertussis on Reported Pertussis Cases
Authors: Rubis Amy B , Cole Matthew , Tondella M Lucia , Pawloski Lucia C , Youngkin Erin , Firmender Patricia , Aden Vanessa , Cruz Victor , Stanislawski Emma , Wester Rachel , Cieslak Paul R , Acosta Anna M , Skoff Tami H
Published: April 2024

Background

In 2020, the Council of State and Territorial Epidemiologists (CSTE) pertussis case definition was modified; the main change was classifying polymerase chain reaction (PCR)-positive cases as confirmed, regardless of cough duration. Pertussis data reported through Enhanced Pertussis Surveillance (EPS) in 7 sites and the National Notifiable Diseases Surveillance System (NNDSS) were used to evaluate the impact of the new case definition.

Methods

We compared the number of EPS cases with cough onset in 2020 to the number that would have been reported based on the prior (2014) CSTE case definition. To assess the impact of the change nationally, the proportion of EPS cases newly reportable under the 2020 CSTE case definition was applied to 2020 NNDSS data to estimate how many additional cases were captured nationally.

Results

Among 442 confirmed and probable cases reported to EPS states in 2020, 42 (9.5%) were newly reportable according to the 2020 case definition. Applying this proportion to the 6124 confirmed and probable cases reported nationally in 2020, we estimated that the new definition added 582 cases. Had the case definition not changed, reported cases in 2020 would have decreased by 70% from 2019; the observed decrease was 67%.

Conclusions

Despite a substantial decrease in reported pertussis cases in the setting of coronavirus disease 2019 (COVID-19), our data show that the 2020 pertussis case definition change resulted in additional case reporting compared with the previous case definition, providing greater opportunities for public health interventions such as prophylaxis of close contacts.
Effective corporate income taxation and its effect on capital accumulation: cross-country evidence
Authors: Goda Thomas
Published: April 2024

It is debated to what extent corporate taxation discourages capital formation, and the related empirical cross-country evidence is inconclusive. This paper provides new insights into this matter for a large sample of developed and developing countries. In the first step, national accounts data is used to calculate backward-looking effective corporate income tax rates (ECTR) for 77 countries during 1995–2018. In the second step, dynamic panel data regressions are used to estimate the effect of ECTR on aggregate corporate investment. The main findings of this exercise are that (i) statutory corporate income tax rates (SCTR), on average, are twice as high as ECTR, (ii) average ECTR has been relatively stable but show distinct dynamics across countries and (iii) no significant negative relationship exists between ECTR and investment. The latter finding is robust to different specifications and samples and when publicly available SCTR or forward-looking effective tax rate measures are used as alternative tax rate proxies.
Clinical Decision Making in Inflammatory Bowel Disease Mimics: Practice Management from Inflammatory Bowel Disease LIVE
Authors: Fiske Hannah W , Ward Christopher , Shah Samir A , Holubar Stefan D , Al-Bawardy Badr , Barnes Edward L , Binion David , Bohm Matthew , Brand Myron , Clarke Kofi , Cohen Benjamin L , Cross Raymond K , Dueker Jeffrey , Engels Michael , Farraye Francis A , Fine Sean , Forster Erin , Gaidos Jill , Ginsburg Philip , Goyal Alka , Hanson John , Herfath Hans , Hull Tracy , Kelly Colleen R , Lazarev Mark , Levy L Campbell , Melia Joanna , Philpott Jessica , Qazi Taha , Siegel Corey A , Watson Andrew , Wexner Steven D , Williams Emmanuelle D , Regueiro Miguel
Published: April 2024

Background

Since 2009, inflammatory bowel disease (IBD) specialists have utilized “IBD LIVE,” a weekly live video conference with a global audience, to discuss the multidisciplinary management of their most challenging cases. While most cases presented were confirmed IBD, a substantial number were diseases that mimic IBD. We have categorized all IBD LIVE cases and identified “IBD-mimics” with consequent clinical management implications.

Methods

Cases have been recorded/archived since May 2018; we reviewed all 371 cases from May 2018–February 2023. IBD-mimics were analyzed/categorized according to their diagnostic and therapeutic workup.

Results

Confirmed IBD cases made up 82.5% (306/371; 193 Crohn’s disease, 107 ulcerative colitis, and 6 IBD-unclassified). Sixty-five (17.5%) cases were found to be mimics, most commonly medication-induced (n = 8) or vasculitis (n = 7). The evaluations that ultimately resulted in correct diagnosis included additional endoscopic biopsies (n = 13, 21%), surgical exploration/pathology (n = 10, 16.5%), biopsies from outside the GI tract (n = 10, 16.5%), genetic/laboratory testing (n = 8, 13%), extensive review of patient history (n = 8, 13%), imaging (n = 5, 8%), balloon enteroscopy (n = 5, 8%), and capsule endoscopy (n = 2, 3%). Twenty-five patients (25/65, 38%) were treated with biologics for presumed IBD, 5 of whom subsequently experienced adverse events requiring discontinuation of the biologic. Many patients were prescribed steroids, azathioprine, mercaptopurine, or methotrexate, and 3 were trialed on tofacitinib.

Conclusions

The diverse presentation of IBD and IBD-mimics necessitates periodic consideration of the differential diagnosis, and reassessment of treatment in presumed IBD patients without appropriate clinical response. The substantial differences and often conflicting treatment approaches to IBD versus IBD-mimics directly impact the quality and cost of patient care.
Apico-aortic conduit: a readily available technical modification
Authors: Wantiez Pauline , Flecher Erwan , Heautot Jean-François , Allain Geraldine
Published: April 2024

When neither surgical valve replacement nor transcatheter aortic valve implantation is possible, performing an apico-aortic conduit remains a therapeutic option. This procedure has become rare and the rigid angled apical connectors usually used to facilitate ventricular anastomosis are no longer commercially available. We described the technique that we performed on a 60-year-old patient with readily available material.
Weather shocks and pesticide purchases
Authors: Bareille François , Chakir Raja , Keles Derya
Published: April 2024

This paper investigates whether farmers adapt their pesticide use to cope with weather shocks. Using a unique, exhaustive dataset detailing all active substance purchases per zip code in France between 2014 and 2019, we econometrically explain abnormal pesticide purchase deviations by weather shocks. We identify heterogeneous weather impacts across pesticide types, seasons and locations. Because our analyses suggest limited year-to-year pesticide storage and farmers’ adaptation along other margins, we interpret our estimates as true weather impacts on pesticide use. Our preferred estimates suggest that, ceteris paribus, farmers increase pesticide use by seven to fifteen per cent in 2050 under a RCP4.5 climate change scenario.
Introduction to the special issue on bioeconomy innovation pipelines and supply chain shocks
Authors: Drabik Dušan , Wesseler Justus
Published: April 2024

This introduction presents five articles of the virtual issue on bioeconomy innovation pipelines and supply chain shocks. The presented cases use alternative methodological approaches with their own advantages and disadvantages. The conclusion we can draw is that the specificities of individual case studies make it difficult to generalise and many more cases would be needed to perform a meta-analysis. We encourage agricultural economists to provide further research on detailed cases, which will be particularly important for gaining a better understanding of the potential effects of the EU Green Deal.
Leaf surface microbiota transplantation confers resistance to coffee leaf rust in susceptible Coffea arabica
Authors: de Sousa Leandro Pio , Mondego Jorge Maurício Costa
Published: April 2024

Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.
Powdery mildew-induced changes in phyllosphere microbial community dynamics of cucumber
Authors: Yue Cong , Du Changxia , Wang Xiaodan , Tan Yinqing , Liu Xingchen , Fan Huaifu
Published: April 2024

As an important habitat for microorganisms, the phyllosphere has a great impact on plant growth and health, and changes in phyllosphere microorganisms are closely related to the occurrence of leaf diseases. However, there remains a limited understanding regarding alterations to the microbial community in the phyllosphere resulting from pathogen infections. Here, we analyzed and compared the differences in phyllosphere microorganisms of powdery mildew cucumber from three disease severity levels (0% < L1 < 30%, 30% ≤ L2 < 50%, L3 ≥ 50%, the number represents the lesion coverage rate of powdery mildew on leaves). There were significant differences in α diversity and community structure of phyllosphere communities under different disease levels. Disease severity altered the community structure of phyllosphere microorganisms, Rosenbergiella, Rickettsia, and Cladosporium accounted for the largest proportion in the L1 disease grade, while Bacillus, Pantoea, Kocuria, and Podosphaera had the highest relative abundance in the L3 disease grade. The co-occurrence network analysis of the phyllosphere microbial community indicated that the phyllosphere bacterial community was most affected by the severity of disease. Our results suggested that with the development of cucumber powdery mildew, the symbiotic relationship between species was broken, and the entire bacterial community tended to compete.
Case reports on uniparental disomy of chromosomes 6 and 3 in paternity testing
Authors: Ren He , Liu Zhiyong , Chen Chong , Shi Yan , Zhang Jiarong , Chen Ying , Jia Li , Liu Yacheng , Yan Jiangwei
Published: April 2024

In paternity testing, when there are Mendelian errors in the alleles between the child and the parents, a slippage mutation, or silent allele may not fully explain the phenomenon. Sometimes, it is attributed to chromosomal abnormalities, such as uniparental disomy (UPD). Here, we present the investigation of two cases of suspected UPD in paternity testing based on short tandem repeat (STR) detection (capillary electrophoresis platform). Case 1 involves a trio, where all genotypes detected on chromosome 6 in the child are homozygous and found in the father. Case 2 is a duo (mother and child), where all genotypes on chromosome 3 in the child are homozygous and not always found in the mother. At the same time, Mendelian error alleles were also observed at specific loci in these two chromosomes. Furthermore, we used the MGIEasy Signature Identification Library Prep Kit for sequencing on the massively parallel sequencing platform, which included common autosomal, X and Y chromosomes, and mitochondrial genetic markers used in forensic practice. The results showed that the genotypes of shared STRs on the two platforms were consistent, and STRs and single nucleotide polymorphisms (SNPs) on these two chromosomes were homozygous. All other genetic markers followed the laws of inheritance. A comprehensive analysis supported the parent–child relationship between the child and the alleged parent, and the observed genetic anomalies can be attributed to UPD. UPD occurrences are rare, and ignoring its presence can lead to erroneous exclusions in paternity testing, particularly when multiple loci on a chromosome exhibit homozygosity.
Inequalities in Healthcare Access, Experience and Outcomes in Adults With Inflammatory Bowel Disease: A Scoping Review
Authors: Hawkins Rachel L , Zia Maryam , Hind Daniel , Lobo Alan J
Published: April 2024

Background

Inflammatory bowel diseases (IBDs) are incurable diseases that require lifelong access to health services. Accumulating evidence of inequalities in health care access, experience, and outcomes for individuals with IBD is apparent. This review aimed to describe the inequalities in healthcare access, experiences, and outcomes of care for adults with IBD, to identify research gaps, and to identify future research priorities in this area.

Methods

A scoping review was conducted to retrieve quantitative, qualitative, and mixed methods evidence from 3 databases (EMBASE, Medline, and CINAHL) published between January 1, 2000, and September 27, 2023.

Results

Fifty-one studies met the criteria for inclusion. The majority (42 of 51) focused on IBD health outcomes, followed by healthcare access (24 of 51). Significantly fewer investigated patient experiences of IBD healthcare (8 of 51). Most available studies reported on race/ethnic disparities of healthcare (33 of 51), followed by inequalities driven by socioeconomic differences (12 of 51), rurality (7 of 51), gender and sex (3 of 51), age (2 of 51), culture (2 of 51), literacy (1 of 51), and sexuality (1 of 51). Inflammatory bowel disease patients from Black, Asian, and Hispanic ethnic groups had significantly poorer health outcomes. A lack of research was found in the sexual and gender minority community (1 of 51). No research was found to investigate inequalities in IBD patients with learning disabilities or autism.

Conclusions

Further research, particularly utilizing qualitative methods, is needed to understand health experiences of underserved patient populations with IBD. Cultural humility in IBD care is required to better serve individuals with IBD of Black and Asian race/ethnicity. The lack of research amongst sexual and gender minority groups with IBD, and with learning disabilities, poses a risk of creating inequalities within inequalities.
Exoskeletal Trade-off between Claws and Carapace in Deep-sea Hydrothermal Vent Decapod Crustaceans
Authors: Cho Boongho , Seo Hyein , Hong Junyoung , Jang Sook-Jin , Kim Taewon
Published: April 2024

Synopsis

Limitations on energetic resources create evolutionary trade-offs, prompting us to investigate if investment in claw strength remains consistent across crustaceans living in diverse habitats. Decapod crustaceans living in deep-sea hydrothermal vents are ideal for this study due to their extreme environment. In this study, we investigated whether decapods (blind crab Austinograea sp. and the squat lobster Munidopsis lauensis) living in deep-sea hydrothermal vents prioritize investing in strong claws compared to the carapace, like coastal decapods. We analyzed exoskeleton morphology, mechanical properties, structures, and elemental composition in both the carapace and claws of four Decapoda species (two each from Brachyura and Anomura infraorders) in vent and coastal habitats. Coastal decapods had ∼4–9 times more teeth on their claw cutting edge than the vent species. Further, only the coastal species exhibited higher firmness in their claws than in their carapaces. Each infraorder controlled exoskeletal hardness differently: Brachyura changed the stacking height of the Bouligand structure, while Anomura regulated magnesium content in the exoskeleton. The vent decapods may prioritize strengthening their carapace over developing robust claws, allocating resources to adapt to the harsh conditions of deep-sea hydrothermal vents. This choice might enhance their survival in the extreme environment, where carapace strength is crucial for protecting internal organs from environmental factors, rather than relying on the powerful claws seen in coastal decapods for a competitive advantage.
Alternative venous access sites for dual-lumen extracorporeal membrane oxygenation cannulation
Authors: Schoeberl Armin-Kai , Staudacher Dawid , Kawashima Mitsuaki , Fischer Courtney , Cypel Marcelo , Buchtele Nina , Staudinger Thomas , Aigner Clemens , Hoetzenecker Konrad , Schweiger Thomas
Published: April 2024

OBJECTIVES

Dual-lumen cannulas for veno-venous (VV) extracorporeal membrane oxygenation (ECMO) support are typically inserted in the right internal jugular vein (RIJV); however, some scenarios can make this venous route inaccessible. This multicentre case series aims to evaluate if single-site cannulation using an alternative venous access is safe and feasible in patients with an inaccessible RIJV.

METHODS

We performed a multi-institutional retrospective analysis including high-volume ECMO centres with substantial experience in dual-lumen cannulation (DLC) (defined as >10 DLC per year). Three centres [Freiburg (Germany), Toronto (Canada) and Vienna (Austria)] agreed to share their data, including baseline characteristics, technical ECMO and cannulation data as well as complications related to ECMO cannulation and outcome.

RESULTS

A total of 20 patients received alternative DLC for respiratory failure. Cannula insertion sites included the left internal jugular vein (n = 5), the right (n = 7) or left (n = 3) subclavian vein and the right (n = 4) or left (n = 1) femoral vein. The median cannula size was 26 (19–28) French. The median initial target ECMO flow was 2.9 (1.8–3.1) l/min and corresponded with used cannula size and estimated cardiac output. No procedural complications were reported during cannulation and median ECMO runtime was 15 (9–22) days. Ten patients were successfully bridged to lung transplantation (n = 5) or lung recovery (n = 5). Ten patients died during or after ECMO support.

CONCLUSIONS

Alternative venous access sites for single-site dual-lumen catheters are a safe and feasible option to provide veno-venous ECMO support to patients with inaccessible RIJV.
Theoretical performance assessment of a multi-effect distillation system integrated with thermal vapour compression unit running on solar energy
Authors: Shahzamanian B , Varga S , Soares J , Palmero-Marrero AI , Oliveira AC
Published: April 2024

Mathematical models can be successfully applied to predict the multi-effect distillation system integrated with thermal vapour compression unit (MED-TVC) performance under different operating conditions. In this work, a one-dimensional (1-D) mathematical model was developed to perform the theoretical analysis of a small-scale parallel feed MED-TVC desalination system driven by solar heat. A parametric study was conducted allowing the ejector motive steam temperature, first effect temperature, between effects temperature difference and ejector compression ratio to vary within an expectable range.

The results showed that higher motive steam temperatures, had a positive impact on the water yield up to an optimal point. Any additional increase of driving steam temperature reduced water yield. Gain output ratio ($GOR$) was maximum at the highest considered motive temperature. It was found that the calculated specific heat transfer area does not depend on the motive temperature variation. Water yield, $GOR$ and specific heat transfer area decrease with the ejector compression ratio. The temperature difference between the evaporator effects had no effect on the water yield and $GOR$. It only decreases the specific heat transfer area. First effect temperature should be as low as possible with respect to operational constraints. Based on the parametric study, the optimal design operating conditions, corresponding to the maximum water yield is identified for a small-scale three-effect desalination system. The unit can produce up to 204 l/h drinking water with a gain output ratio of 8.6 and specific heat transfer area of 575 m2/kg/s using about 22 kW of solar heat.
Outpatient Antipsychotic Use and Severe COVID-19: Avoiding the Impact of Age in a Real-World Data Study
Authors: Pintos-Rodríguez Samuel , Visos-Varela Irene , Rodríguez-Fernández Almudena , Zapata-Cachafeiro Maruxa , Piñeiro-Lamas María , Herdeiro María Teresa , García-Álvarez Rosa María , Figueiras Adolfo , Salgado-Barreira Ángel
Published: April 2024

Background

The association between use of antipsychotics and COVID-19 outcomes is inconsistent, which may be linked to use of these drugs in age-related diseases. Furthermore, there is little evidence regarding their effect in the nongeriatric population. We aim to assess the association between antipsychotic use and risk of disease progression and hospitalization due to COVID-19 among the general population, stratifying by age.

Methods

We conducted a population-based, multiple case-control study to assess risk of hospitalization, with cases being patients with a PCR(+) test who required hospitalization and controls being individuals without a PCR(+) test; and risk of progression to hospitalization, with cases being the same as those used in the hospitalization substudy and controls being nonhospitalized PCR(+) patients. We calculated adjusted odds-ratios (aOR) and 95% confidence intervals (CI), both overall and stratified by age.

Results

Antipsychotic treatment in patients younger than 65 years was not associated with a higher risk of hospitalization due to COVID-19 (aOR 0.94 [95%CI = 0.69–1.27]) and disease progression among PCR(+) patients (aOR 0.96 [95%CI = 0.70–1.33]). For patients aged 65 years or older, however, there was a significant, increased risk of hospitalization (aOR 1.58 [95% CI = 1.38–1.80]) and disease progression (aOR 1.31 [95% CI = 1.12–1.55]).

Conclusions

The results of our large-scale real-world data study suggest that antipsychotic use is not associated with a greater risk of hospitalization due to COVID-19 and progression to hospitalization among patients younger than 65 years. The effect found in the group aged 65 years or older might be associated with off-label use of antipsychotics.
Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses
Authors: Bovio-Winkler Patricia , Cabezas Angela , Etchebehere Claudia
Published: April 2024

The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.
Conducting Care-full Research: Collaborative Research amidst Corona, a Coup, and Other Crises
Authors: Berents Helen , Mollica Caitlin , Odgers-Jewell Casey , Payne Hayley , Spalding Savannah
Published: April 2024

Feminists have long called attention to often profoundly uneven power relations in international relations research, assumptions regarding who is able to be a “knowledge producer,” and the risks of extractive research. In research “on” and with young people, these dilemmas are compounded by ageist suppositions about youth competencies. This paper reflects on efforts by the authors to design and undertake a youth-led, adult-supported research project on youth activism and peace processes in South Sudan, Afghanistan, and Myanmar through virtual interviews. It discusses how our approach to skills training, mentorship, and research design empowers youth researchers to engage in dialogue with youth peacebuilders to establish a more collaborative research agenda. Centering collaboration offers opportunities for more responsive engagement with communities traditionally marginalized within the research environment. The global pandemic has raised questions about research at a distance, the requirements of “participation,” and the ethics of reciprocity with research participants as knowledge producers. In each case, challenges raised difficult questions about the ethics of pursuing research in these complex contexts. We offer the idea of care-full research that centers a feminist, reflexive approach, is collaborative in multiple ways, and generates new possibilities for knowledge creation amidst multiple crises and beyond.
Complexities of State-Building in Somaliland
Authors: Fagioli Monica
Published: April 2024

Abstracts

Since the mid-2000s, state-building in Somaliland has emerged as a complex mixture of coexisting, competing programs, political aspirations, and foreign agendas. This article applies a dialectical approach to focus on the scalar relations among actors and models of capacity-building, from programs’ design to their implementation. Drawing on science and technology studies, I use the term “complexities” to describe the “multiplicities” of programs, actors, and different ways of ordering that coexist and overlap, sometimes in tension among them, other times in coordination. Specifically, this article examines two approaches to state-building in Somaliland: the United Nations Development Program’s institution-building and US Agency for International Development (USAID)-funded stabilization programs. Going beyond fixed binaries, such as international and local, homogenous and hybrid, state-building and state-formation, this article observes how these dichotomies are formed and how, rather than being separate, they combine together, generating techno-political arrangements. Somaliland’s complexity is made up of techno-political arrangements that are coproduced by both technical expertise and national political aspirations. Technical capacity-building programs, such as the redesign of the Somalia Institutional Development Project (SIDP), the creation of Somaliland’s National Development Plan (NDP), and the allocation of USAID’s grants, have become the terrain for political claims over the redistribution of resources and the control of state institutions.
Bisdechlorogeodin from antarctic Pseudogymnoascus sp. LAMAI 2784 for citrus canker control
Authors: Ferrarezi Juliano H , Marin Vítor R , Vieira Gabrielle , Ferreira Henrique , Sette Lara D , Sass Daiane C
Published: April 2024

Aims

Citrus canker caused by Xanthomonas citri subsp. citri (X. citri) is a disease of economic importance. Control of this disease includes the use of metallic copper, which is harmful to the environment and human health. Previous studies showed that the crude extract from the fungus Pseudogymnoascus sp. LAMAI 2784 isolated from Antarctic soil had in vitro antibacterial action against X. citri. The aim of the present study was to expand the applications of this extract.

Methods and results

In greenhouse assays, the crude extract was able to reduce bacterial infection on citrus leaves from 1.55 lesions/cm2 (untreated plants) to 0.04 lesions/cm2. Bisdechlorogeodin was identified as the main compound of the bioactive fraction produced by Pseudogymnoascus sp. LAMAI 2784, which inhibited bacterial growth in vitro (IC90 ≈ 156 µg ml−1) and permeated 80% of X. citri cells, indicating that the membrane is the primary target.

Conclusion

The present results showed that the bioactive fraction of the extract is mainly composed of the compound bisdechlorogeodin, which is likely responsible for the biological activity against X. citri, and the main mechanism of action is the targeting of the cell membrane. This study indicates that bisdechlorogeodin has valuable potential for the control of X. citri.