bluuebunny/crossref_metadata_2025_split huggingface dataset:
Web-based Tool Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis
Authors: Routray Sweta Padma , Sahoo Swayamprabha , Nayak Debasish Swapnesh Kumar , Shah Sejal , Swarnkar Tripti 
Published: December 2022

AbstractGlobal public health is seriously threatened by Antimicrobial Resistance (AMR), and there is an urgent need for quick and precise AMR diagnostic tools. The prevalence of novel Antibiotic Resistance Genes (ARGs) has increased substantially during the last decade, owing to the recent burden of microbial sequencing. The major problem is extracting vital information from the massive amounts of generated data. Even though there are many tools available to predict AMR, very few of them are accurate and can keep up with the unstoppable growth of data in the present. Here, we briefly examine a variety of AMR prediction tools that are available. We highlighted three potential tools from the perspective of the user experience that is preferable web-based AMR prediction analysis, as a web-based tool offers users accessibility across devices, device customization, system integration, eliminating the maintenance hassles, and provides enhanced flexibility and scalability. By using thePseudomonas aeruginosaComplete Plasmid Sequence (CPS), we conducted a case study in which we identified the strengths and shortcomings of the system and empirically discussed its prediction efficacy of AMR sequences, ARGs, amount of information produced and visualisation. We discovered that ResFinder delivers a great amount of information regarding the ARGS along with improved visualisation. KmerResistance is useful for identifying resistance plasmids, obtaining information about related species and the template gene, as well as predicting ARGs. ResFinderFG does not provide any information about ARGs, but it predicts AMR determinants and has a better visualisation than KmerResistance.Author summaryAMR is the capacity of microorganisms to survive or grow in the presence of drugs intended to stop them or kill them. Consequently, there is an increase in the Burden of disease, death rates, and the cost of healthcare, making it a serious global threat to both human and animal health. Next-Generation Sequencing (NGS) based molecular monitoring can be a real boon to phenotypic monitoring of AMR. Researchers face difficult challenges in terms of producing, managing, analysing, and interpreting massive amounts of sequence data. There are many tools available to predict AMR, but only a small number of them are reliable and able to keep up with the current rate of unstoppable data growth. Each tool has specific benefits and drawbacks of its own. Our research offers a comprehensive overview of the outcomes produced by three different tools, enabling users to choose the tool that best suits their requirements.
Randomised trial ofAureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: Favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation
Authors: Raghavan Kadalraja , Dedeepiya Vidyasagar Devaprasad , Yamamoto Naoki , Ikewaki Nobunao , Iwasaki Masaru , Dinassing Ashwamed , Senthilkumar Rajappa , Preethy Senthilkumar , Abraham Samuel JK 
Published: December 2022

AbstractObjectiveDuchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Following anti-inflammatory and anti-fibrotic outcomes of anAureobasidium pullulansstrain N-163-produced beta 1,3-1,6-glucan food supplement in clinical and pre-clinical studies of DMD, herein we report their implications on the gut microbiome in patients with DMD.DesignTwenty-seven patients with DMD were included in the pilot study (Control [n=9], N-163 [n=18]) which had previously reported the clinical decrease in inflammatory and fibrosis biomarkers. For the current study, whole genome metagenomic sequencing was performed in pre- and post N-163 intervention faecal samples of each of these participants.ResultsAfter N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such asRoseburiaandFaecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria andAlistipes.ConclusionBeneficial reconstitution of the gut microbiome after N-163 beta-glucan administration, in addition to their implications in anti-inflammatory and anti-fibrotic outcomes, require further in-depth exploration on their roles in epigenetic manipulation.
Ceramides as risk markers for future cardiovascular events and all-cause mortality in long-standing type 1 diabetes
Authors: Wretlind Asger , Curovic Viktor R. , Suvitaival Tommi , Theilade Simone , Tofte Nete , Winther Signe A. , Vilsbøll Tina , Vestergaard Henrik , Rossing Peter , Legido-Quigley Cristina 
Published: December 2022

AbstractBackgroundCeramides are lipid molecules involved in inflammation-related signaling. Recent studies have shown that higher amounts of specific circulating ceramides and ceramide ratios are associated with future development of cardiovascular (CV) disease (CVD). In persons with longstanding type 1 diabetes (T1D), we investigated if serum ceramide levels and ratios predicted CVD, kidney failure and all-cause mortality.MethodsWe included 662 participants with T1D from 2009-2011. Health registry data was obtained at a 6-year follow-up. Baseline serum samples were analyzed using liquid chromatography-mass spectrometry. Six predefined ceramide levels were measured and ratios calculated. Adjusted Cox regression analyses were carried out to investigate ceramide levels in relation to future CV events (CVE), kidney failure and all-cause mortality.ResultsCeramide ratio cer(d18:1/18:0)/cer(d18:1/24:0) was significantly associated with risk of CVE (HR = 1.33, P = 0.01) and all-cause mortality (HR = 1,48, P = 0.01) before and after adjustments. All five investigated ceramide ratios were associated with kidney failure, before adjusting for the kidney markers estimated glomerular filtration rate and urinary albumin excretion rate.ConclusionsSpecific ceramides and ratios associated with 6-year cardiovascular risk and all-cause mortality in a T1D cohort. The ratio of cer(d18:1/18:0)/cer(d18:1/24:0) was an especially robust indicator. This highlights the strength of ceramide association with vascular complications and presents a new potential tool for early risk assessment if validated in other cohorts.Trial RegistrationClinicalTrial.govidentifier:NCT01171248
Exploring the use of synthetic placebo populations in ALS randomized clinical trials
Authors: Bowles Harry , Opie-Martin Sarah , Shojaie Ali , Libonati Laura , Iacoangeli Alfredo , Al Khleifat Ahmad , Al-Chalabi Ammar 
Published: December 2022

ObjectivesThe use of synthetic data to supplement clinical trial placebo groups or for trial planning is rapidly gaining interest. However, there is not yet an established framework for generating synthetic data for these purposes. In this work we test two approaches to generating synthetic placebo arms for ALS trials with survival being the primary outcome variable.MethodsFor the first approach, we extracted sample subsets from the UK MND register (n = 308) using an evolutionary algorithm such that the subset baseline variables matched a target trials group, either people enrolled in LiCALS (n = 106) or people included in the PRO-ACT database (n = 171). We also applied trial specific exclusion criteria where possible or alternatively we applied a custom ‘time filter’. For the second approach, survival was predicted for LiCALS participants using the ENCALS model. Survival probabilities from each method were compared to real placebo participants using Kaplan-Meier analysis and the log rank test.ResultsWe found that the synthetic placebo groups derived from the MND register matched the target trials outcomes very well. The ENCALS model produces synthetic placebo groups that are significantly different to the real placebo groups. However, when participants are censored at 6 month intervals, the ENCALS synthetic group matches the target group very well between 24 and 48 months, indicating a possible timeframe that this method could be utilised.ConclusionBoth the register based approach and the ENCALS prognostic model generated synthetic placebo groups that matched placebo groups from historical trials. These methods need to be validated in prospective trials.
De novo designed ice-binding proteins from twist-constrained helices
Authors: de Haas R.J. , Tas R.P. , van den Broek D. , Nguyen H. , Kang A. , Bera A.K. , King N.P. , Voets I. K. , de Vries R. 
Published: December 2022

AbstractAttaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs) but these have poorly understood structure-activity relationships. We propose that reverse engineering usingde novocomputational protein design can shed light on structureactivity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein (wfAFP) uses an unusual under-twisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. We find that ice recrystallization inhibition by the designed proteins increases with the degree of designed under-twisting, thus validating our hypothesis and opening up new avenues for the computational design of icebinding proteins.Significance StatementIce-binding proteins (IBPs) modulate ice nucleation and growth in cold-adapted organisms so that they can survive in ice-laden environments at (sub)freezing temperatures. The functional repertoire of IBPs is diverse, ranging from inhibition of recrystallization and freezing point depression to shaping of ice crystals and ice nucleation. Precisely how these activities arise from the structure and ice-binding properties of IBPs is poorly understood. We demonstrate throughde novocomputational protein design that constraining the twist of an ice-binding helix is a key feature determining its ice-binding activity, opening new avenues for the design of synthetic IBPs with activities tailored to the requirements of specific applications, such as cell and tissue cryopreservation.
Urbanisation impacts the diversity, coloration, and body size of wild bees in a Mediterranean city
Authors: Badiane Arnaud , Ropars Lise , Flacher Floriane , Schurr Lucie , Zakardjian Marie , Affre Laurence , Deschamps-Cottin Magali , Gachet Sophie , Robles Christine , Geslin Benoît 
Published: December 2022

AbstractUrbanisation is a growing phenomenon causing the decline of wild bees globally. Yet, bees manage to persist in the urban matrix thanks to islands of vegetation in public parks and private gardens. While we begin to comprehend the impact of urbanisation on bees’ diversity and abundance, our understanding of its impact on the functional diversity of wild bees is limited. Here, we use an integrative approach to investigate the response of wild bees to urbanisation at the community, species, and individual levels. To do so, we sampled wild bees in 24 public parks along an urbanisation gradient in the Mediterranean city of Marseille. We found that species richness and abundance decreased in more urbanised areas, but increased in larger city parks. Moreover, larger individuals within species, but not larger species, were found in larger city parks, suggesting that park size is crucial for the persistence of bees in cities. Interestingly, we show that brighter species were found in parks surrounded by a large amount of impervious surface, highlighting the importance of colour traits in the response to environmental changes. Finally, our results revealed that larger species, but not larger individuals, were also more colourful. In summary, our study not only confirmed that urbanisation negatively impacts community-level traits, but that it also affects species’ coloration and individuals’ body size, thus improving our understanding of the functional response of wild bees to urbanisation. We suggest that increasing park size may compensate for the negative effects of urbanisation on wild bees.
A survey of proteomic variation across two ethnic groups in Nigeria and its relationship to obesity risk
Authors: Biddanda Arjun , de Arce Karen Perez , Eze-Echesi Golibe , Nwuba Chiamaka , Ibrahim Yusuf , Oyedele Olubukunola , Joshi Esha , Alalade Boladale , Ajayi Olanrewaju , Nwatu Chidimma , Yakubu Aminu , Ene-Obong Abasi , Popoola Jumi , O’Dushlaine Colm , Fekkes Peter 
Published: December 2022

ABSTRACTProteomic variation between individuals has immense potential for identifying novel drug targets and disease mechanisms. However, with high-throughput proteomic technologies still in their infancy, they have largely been applied in large majority European ancestry cohorts (e.g. the UK Biobank). An open question is the degree to which proteomic signatures seen in European and other groups mirror those seen in diverse populations, such as cohorts from Africa. Coupled with genetic information, we can also gain a better understanding of the role of genetic variants in the regulation of the proteome and subsequent disease mechanisms.To address the gap in our understanding of proteomic variation in individuals of African ancestry, we collected proteomic data from 176 individuals across two ethnic groups (Igbo and Yoruba) in Nigeria. These individuals were also stratified into high BMI (BMI > 30 kg/m2) and normal BMI (20 kg/m2< BMI < 30 kg/m2) categories. We characterized differences in plasma protein abundance using the Olink Explore 1536 panel between high and normal BMI individuals, finding strong associations consistent with previously known signals in individuals of European descent. We additionally found 73 sentinel cis-pQTL in this dataset, with 21 lead cis-pQTL not observed in catalogs of variation from European-ancestry individuals. In summary, our study highlights the value of leveraging proteomic data in cohorts of diverse ancestry for investigating trait-specific mechanisms and discovering novel genetic regulators of the plasma proteome.
Origin, evolution and diversification of plant mechanosensitive channel of small conductance-like (MSL) proteins
Authors: Zhang Zaibao , Ye Fan , Xiong Tao , Chen Jiahui , Cao Jiajia , Chen Yurui , Luo Tian , Liu Sushuang 
Published: December 2022

AbstractMechanosensitive (MS) ion channels provide efficient molecular mechanism for transducing mechanical forces into intracellular ion fluxes in all kingdoms of life. The mechanosensitive channel of small conductance (MscS) was one of the best-studied MS channels and its homologs (MSL, MscS-like) were widely distributed in cell-walled organisms. However, the origin, evolution and expansion of MSL proteins in plants are still not clear. Here, we identified more than 2100 MSL proteins from 176 plants and conducted a broad-scale phylogenetic analysis. The phylogenetic tree showed that plant MSL proteins were divided into three groups (I, II and III) prior to the emergence of chlorophytae algae, which was consistent with their specific subcellular localization. MSL proteins were distributed unevenly into each of plant species, and four parallel expansion was identified in angiosperms. In Brassicaceae, most MSL duplicates were derived by whole-genome duplication (WGD)/segmental duplications. Finally, a hypothetical evolutionary model of MSL proteins in plants was proposed based on phylogeny. Our studies illustrate the evolutionary history of the MSL proteins and provide a guide for future functional diversity analyses of these proteins in plants.
Pseudomonasisolates from ponds populated with duckweed prevent disease caused by pathogenicPseudomonasspecies
Authors: Baggs E.L , Stark F.G , Tiersma M.B , Krasileva K.V 
Published: December 2022

AbstractDuckweeds are notoriously invasive plants. They are successful in inhabiting diverse environments, despite their lack of conventional immune pathways that are essential for disease resistance in other plant species. It is unclear how duckweeds thrive in the absence of these immune pathways. In this study, we investigated the effect of bacteria from duckweeds’ natural habitat on disease progression utilizing the duckweed-Pseudomonaspathosystem. Through nanopore sequencing of 16S and ITS rDNA amplicons we identified duckweed-associated bacterial and fungal genera present at three environmental sites. The pond filtrate from one of the three environmental locations primed duckweed’s pathogen defenses leading to a reduction in disease symptoms. Furthermore, we were able to identify bacterial isolates from the filtrate that protect duckweed from disease symptoms uponPseudomonaspathogen inoculation. The isolated protective bacteria belong to thePseudomonasgenus, and we demonstrated antagonistic interactions between the pathogen and beneficial strainsin vitroandin vivo. The ability of our environmental isolates to protect againstPseudomonaspathogens appears to be plant/species specific as environmental strains showed no protective effect againstPseudomonaspathogens inArabidopsisassays. Genome sequencing of the beneficialPseudomonasstrains showed the presence of several genes involved in bacterial competition. We have thus demonstrated thatPseudomonasspecies from duckweeds natural habitat can successfully antagonize other plant pathogens.
Profile of the pregnant woman with Gestational Diabetes Mellitus in a private hospital in Joinville, Brazil
Authors: Baptista João Pedro Ribeiro , Schulz Matheus Augusto , Fleith Lehana , Kitzberger Israel , Hilário Wesley Feitosa , Neumann Dieter Alisson , da Silva Júlia Opolski Nunes , e Silva Rodrigo Ribeiro , Nascimento Iramar Baptistella do , Silva Jean Carl 
Published: December 2022

AbstractObjectiveTo analyze the maternal-fetal characteristics of patients with gestational diabetes mellitus (GDM) attended in a private service.Materials and MethodsThis is a cross-sectional study. Data collection was carried out from the medical records of patients diagnosed with GDM at Centro Hospitalar UNIMED, in Joinville city, between 2011 and 2017. Maternal-fetal characteristics, therapeutics and complications of pregnant women diagnosed with GDM were analyzed.Results515 patients with GDM were reported. Of the maternal characteristics, the mean age was (31.77), BMI (27.82). The proportion of obese pregnant women was (55.6%), normal (42.4%) and low weight (2%). The preference for cesarean section was (81.4%) and Gestational Age (GA) of GDM diagnosis (26.85), with higher diagnosis in the third trimester (65.2%) than second (29.3%) and first (5.3%). Incidences of hypertension (7.4%), preeclampsia (0.6%) and pregnant women with previous abortions (16.5%) were found. The mean glycemic profile showed HbA1C (5.26), estimated glucose (104.30) and FPG fasting (86.38), in the first hour (144.46) and in the second hour (64.15). Treatment with diet and exercise (38.3%), metformin (40%), insulin (14.5%) and combined (7.8%). Regarding newborns, the mean weight was (3.123.46) and the GA at birth (37.46). Regarding the percentile, AGP (71.8%), SGP (28.2%) and no cases of LGP. In terms of adverse outcomes, hyperbilirubinemia was evidenced in (25.6%), prematurity (10.9%) and fetal hypoglycemia (9.9%).ConclusionPregnant women diagnosed with GDM had a higher GA at diagnosis in the third trimester and more cesarean sections. Among the adverse outcomes related to newborns, there were more cases of hyperbilirubinemia, prematurity and fetal hypoglycemia.
Reduced mortality among COVID-19 ICU patients after treatment with HemoClear convalescent plasma in Suriname
Authors: Bihariesingh-Sanchit R. , Bansie R. , Ramdhani N. , Mangroo R. , Bustamente D. , Diaz E. , A Foek C. Fung , Thakoer I. , Vreden S. , Choudhry Z. , van ‘t Wout A.B. , Diavatopoulos D.A. , Nierich A.P. 
Published: December 2022

AbstractConvalescent plasma is a promising therapy for coronavirus disease 2019 (COVID-19), but its efficacy in intensive care unit (ICU) patients in a low and middle income country setting such as Suriname is unknown. Bedside plasma separation using the HemoClear device made convalescent plasma therapy accessible as treatment option in Suriname. Two hundred patients with severe SARS-CoV-2 infection requiring intensive care were recruited. Fifty eight patients (29%) received COVID-19 convalescent plasma (CCP) treatment in addition to standard of care (SOC). The CCP treatment and SOC groups were matched by age, sex, and disease severity scores. Mortality in the CCP treatment group was significantly lower than in the SOC group (21% versus 39%; Fisher’s exactP= 0.0133). Multivariate analysis using ICU days showed that CCP treatment reduced mortality (hazard ratio [HR], 0.35; 95% CI, 0.18–0.66;P= 0.001), while complication of acute renal failure (creatinine levels >110 mol/L; HR, 4.45; 95%CI, 2.54-7.80;P< 0.0001) was independently associated with death. Decrease in chest X-ray score in the CCP treatment group (median -3 points, IQR -4 to -1) was significantly greater than in the SOC group (median -1 point, IQR -3 to 1, Mann WhitneyP= 0.0004). Improvement in PaO2/FiOs ratio was also significantly greater in the CCP treatment group (median 83, IQR 8 to 140) than in the SOC group (median 35, IQR -3 to 92, Mann WhitneyP= 0.0234). Further research is needed for HemoClear-produced CCP as therapy in SARS-CoV-2 infections together with adequately powered, randomized controlled trials.ImportanceThis study compares mortality and other endpoints between intensive care unit (ICU) COVID-19 patients treated with convalescent plasma plus standard of care (CCP), and a control group of patients hospitalized in the same medical ICU facility treated with standard of care alone (SOC) in a low and middle income country (LMIC) setting using bedside donor whole blood separation by gravity (HemoClear) to produce the CCP. It demonstrates a significant 65% survival improvement in HemoClear-produced CCP recipients (HR 0.35; 95% CI, 0.19–0.66; P = 0.001). Although this is an exploratory study, it clearly shows the benefit of using the HemoClear-produced CCP in ICU patients in the Suriname LMIC setting. Additional studies can further substantiate our findings and their applicability to both LMICs and high income countries and the use of CCP as a prepared readiness method to combat new viral pandemics.