bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel gut microbiota and microbiota-metabolites signatures in gliomas and its predictive/prognosis functions
Authors: Zhou Min , Song Chong , Gu Junwei , Wang Tong , Shi Linyong , Li Chiyang , Zhu Liwen , Li Hong , Qi Songtao , Lu Yuntao 
Published: January 2023

AbstractGliomas are the most common malignant tumors in the central nervous system. Host genetic and environmental factors have been implicated as the causes and regulators of gliomas. Evidence shows that alterations of the gut microbiome play an important role in multiple diseases including central nervous system disorders. However, the influence of gut microbiome to the epigenesis of gliomas remains largely unknown. Here we profiled the gut microbiome and metabolome in fecal samples from healthy volunteers and the patients with gliomas through the 16S rRNA gene sequencing and LC-MS analyses. The fecal samples from primary glioma patients (n=51), recurrent glioma patients (n=11), patients who underwent TMZ radio-chemotherapy (n=16) and healthy volunteers (n=37) were collected. 56 discriminatory OTUs and 144 metabolites were observed in gliomas compared to those in healthy volunteers, and some species were correlated with clinical parameters, such as tumor grade, IDH-1 and MGMT status. Moreover, the gliomas group showed increased activity in pathways associated with ectoine biosynthesis, fatty acid elongation (saturated), and protocatechuate degradation. At the same time, we revealed 4 fatty-acid metabolites(palmitic acid, oleic acid, DL−beta−Hydroxypalmitic acid, 4−(Methylamino)−4−(3−pyridyl)butyric acid) as possibly interacting with glioma growth. Random forest modeling indicated that a model involving 8 genera and 10 metabolite biomarkers achieved a high accuracy in gliomas prediction (AUC=94.4%). We investigated interassociations between the microbial genera in glioblastoma multiforme (GBM) and progression-free survival (PFS) and overall survival (OS) by Spearman’s correlation analysis. Patients with high proportions of fecalFaecalibacteriumhad significantly better median PFS or OS than those with low proportions (mPFS 495 vs. 281 days, p=0.005; mOS 604 vs. 395 days, p=0.044). Moreover, animal experiments have verified the causal relationship between the structural changes of gut microbiome and glioma growth. Our current study comprehensively characterizes the perturbed interface of gut microbiome and metabolites in glioma patients, which may be used as diagnostic and prognostic biomarkers of gliomas.
Metagenomic profiling of long-read sequencing for clinical diagnosis of ocular inflammation
Authors: Koyanagi Yoshito , Sajiki Ai Fujita , Ushida Hiroaki , Kawano Kenichi , Fujita Kosuke , Okuda Daishi , Kawabe Mitsuki , Yamada Kazuhisa , Suzumura Ayana , Kachi Shu , Kaneko Hiroki , Komatsu Hiroyuki , Usui Yoshihiko , Goto Hiroshi , Nishiguchi Koji M. 
Published: January 2023

AbstractObjectiveTo establish a metagenomic profiling method using long-read sequencing for clinical diagnosis of ocular inflammation and detect the etiologic virus of herpetic uveitis.DesignA retrospective, cross-sectional study.ParticipantsThe participants were 44 uveitis patients with a suspected infectious etiology and 22 controls with cataract.MethodsThe anterior aqueous humor (10-20 µl) was subjected to DNA purification, followed by whole genome amplification. The Nanopore MinION™ using the Flongle Flow Cell was used to perform rapid long-read sequencing and the phylogenetic composition of the microorganisms in the specimen was evaluated.Main Outcomes and MeasuresThe detection of the DNA sequence reads of the etiologic virus of herpetic uveitis in the generated FASTQ files from nanopore sequencing and the evaluation of the limits of detection (LOD) of metagenomic analysis compared to multiplex polymerase chain reaction (mPCR) testing for etiologic virus detection of herpetic uveitis.ResultsThe detection rate of nanopore metagenomic analysis was approximately 59.0% as a result of validation against 22 mPCR-positive cases. The LOD was between 103.6and 106copies of virus DNA. The undetectable cases tended to have significantly lower copy numbers by mPCR, suggesting the lower metagenomic analysis sensitivity compared to mPCR. The nine pathogenic microorganisms evaluated by mPCR were also not detected by nanopore in all mPCR-negative cases and controls. The minimum time to obtain analysis results using this method was approximately 190 minutes.Conclusions and RelevanceOur established sequencing protocol from the anterior aqueous humor detected the DNA fragments of etiologic viruses in patients with herpes virus uveitis. Conversely, nanopore metagenomic results contained considerable noise and were found to be less sensitive compared to the conventional mPCR tests for ocular infections.
Comparative effectiveness of Paxlovid versus sotrovimab and molnupiravir for preventing severe COVID-19 outcomes in non-hospitalised patients: observational cohort study using the OpenSAFELY platform
Authors: Zheng Bang , Tazare John , Nab Linda , Mehrkar Amir , MacKenna Brian , Goldacre Ben , Douglas Ian J , Tomlinson Laurie A 
Published: January 2023

AbstractObjectiveTo compare the effectiveness of Paxlovid vs. sotrovimab and molnupiravir in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients.DesignWith the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform.SettingPatient-level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death within the OpenSAFELY-TPP platform, covering a period where both Paxlovid and sotrovimab were first-line treatment options in community settings.ParticipantsNon-hospitalised adult COVID-19 patients at high risk of severe outcomes treated with Paxlovid, sotrovimab or molnupiravir between February 11, 2022 and October 1, 2022.InterventionsPaxlovid, sotrovimab or molnupiravir administered in the community by COVID-19 Medicine Delivery Units.Main outcome measureCOVID-19 related hospitalisation or COVID-19 related death within 28 days after treatment initiation.ResultsA total of 7683 eligible patients treated with Paxlovid (n=4836) and sotrovimab (n=2847) were included in the main analysis. The mean age was 54.3 (SD=14.9) years; 64% were female, 93% White and 93% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 52 (0.68%) COVID-19 related hospitalisations/deaths were observed (33 (0.68%) treated with Paxlovid and 19 (0.67%) with sotrovimab). Cox proportional hazards model stratified by region showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with Paxlovid was associated with a similar risk of outcome event as treatment with sotrovimab (HR=1.14, 95% CI: 0.62 to 2.08; P=0.673). Results from propensity score weighted Cox model also showed comparable risks in these two treatment groups (HR=0.88, 95% CI: 0.45 to 1.71; P=0.700). An exploratory analysis comparing Paxlovid users with 802 molnupiravir users (11 (1.37%) COVID-19 related hospitalisations/deaths) showed some evidence in favour of Paxlovid but with variation in the effect estimates between models (HR ranging from 0.26 to 0.61).ConclusionIn routine care of non-hospitalised high-risk adult patients with COVID-19 in England, no substantial difference in the risk of severe COVID-19 outcomes was observed between those who received Paxlovid and sotrovimab between February and October 2022, when different subvariants of Omicron were dominant.
Overcrowded Housing Reduces COVID-19 Mitigation Measures and Lowers Emotional Health Among San Diego Refugees from September to November of 2020
Authors: Hassani Ashkan , Omaleki Vinton , Erikat Jeanine , Frost Elizabeth , Streuli Samantha , Sahid Ramla , Yusufi Homayra , Fielding-Miller Rebecca 
Published: January 2023

AbstractRefugee communities are vulnerable to housing insecurity, which drives numerous health disparity outcomes in a historically marginalized population. The COVID-19 pandemic has only worsened the ongoing affordable housing crisis in the United States while continuing to highlight disparities in health outcomes across populations. We conducted interviewer-administered surveys with refugee and asylum seekers in San Diego County at the height of the COVID-19 pandemic to understand the social effects and drivers of COVID-19 in one of the largest refugee communities in the United States. Staff from a community-based refugee advocacy and research organization administered the surveys from September - November 2020. 544 respondents participated in the survey, which captured the diversity of the San Diego refugee community including East African (38%), Middle Eastern (35%), Afghan (17%), and Southeast Asian (11%) participants. Nearly two-thirds of respondents (65%) reported living in overcrowded conditions (>1 individual per room) and 30% in severely crowded conditions (>1.5 individuals per room). Respondents living in affordable housing units or receiving section 8 housing vouchers had a 66% lower probability of living in severely crowded settings (aOR:0.34, 95% CI:0.19– 0.61). Refugees living in overcrowded and severely overcrowded housing had more than twice the odds to have not accessed COVID-19 testing since the pandemic began (OR: 2.28, 95% CI: 1.38 - 3.78) and had nearly 4 times the odds to report lower emotional health (OR: 3.90, 95% CI: 2.62 - 5.82). Longer United States residency was associated with a 7% reduction in the odds of living in crowded housing per additional year (aOR:0.93, 95% CI:0.90–0.97). Overcrowding housing is a structural burden that reduces COVID-19 risk mitigation behaviors. Improved access to affordable housing units or receiving vouchers could reduce overcrowded housing in vulnerable refugee communities.
A novel description of the network dynamics underpinning working memory
Authors: Rossi Chiara , Vidaurre Diego , Costers Lars , Akbarian Fahimeh , Woolrich Mark , Nagels Guy , Van Schependom Jeroen 
Published: January 2023

AbstractWorking memory (WM) plays a central role in cognition, prompting neuroscientists to investigate its functional and structural substrates. The WM dynamic recruits large-scale frequency-specific brain networks that unfold over a few milliseconds – this complexity challenges traditional neuroimaging analyses. In this study, we unravel the WM network dynamics in an unsupervised, data-driven way, applying the time delay embedded-hidden Markov model (TDE-HMM). We acquired MEG data from 38 healthy subjects performing an n-back working memory task. The TDE-HMM model inferred four task-specific states with each unique temporal (activation), spectral (phase-coherence connections), and spatial (power spectral density distribution) profiles. A theta frontoparietal state performs executive functions, an alpha temporo-occipital state maintains the information, and a broad-band and spatially complex state with an M300 temporal profile leads the retrieval process and motor response. The HMM states can be straightforwardly interpreted within the neuropsychological multi-component model of WM, significantly improving the comprehensive description of WM.HighlightsWorking memory recruits different frequency-specific brain networks that wax and wane at a millisecond scale.Through the time-delay embedded hidden (TDE-HMM) we are able to extract data-driven functional networks with unique spatial, spectral, and temporal profiles.We demonstrate the existence of four task-specific brain networks that can be interpreted within the well-known Baddeley’s multicomponent model of working memory.This novel WM description unveils new features that will lead to a more in-depth characterization of cognitive processes in MEG data.
First record of highly invasive Chinese sleeperPerccottus gleniiDybowski, 1877 (Perciformes: Odontobutidae) in the Elbe River Basin, Czechia
Authors: Šmejkal Marek , Dočkal Ondřej , Thomas Kiran , Kalous Lukáš 
Published: January 2023

AbstractThe Chinese sleeper (Perccottus glenii) has invaded European freshwaters and we present evidence of its first documented occurrence in the Elbe River basin in Czechia. The individual fish was caught by a fisherman and posted on social media. After immediately contacting the person in question, we obtained a live fish from him. The Chinese sleeper appears to have been present in interconnected ponds and streams for ten years and may have spread over a larger area. We recommend that eradication measures be implemented to prevent further spread.Statement of SignificanceThe Chinese sleeper has invaded many European countries in the last 50 years, and it is expected to invade western Europe because of the favourable conditions for its establishment. This finding indicates that it could spread in the Elbe River Basin, which could have serious impacts on floodplain and wetland ecosystems. To prevent this scenario, eradication measures should be implemented.
Comparative benchmarking of optical genome mapping and chromosomal microarray reveals high technological concordance in CNV identification and structural variant refinement
Authors: Barseghyan Hayk , Pang Andy , Clifford Ben , Serrano Moises , Chaubey Alka , Hastie Alex 
Published: January 2023

ABSTRACTPURPOSEThe recommended practice for individuals suspected of a genetic etiology for disorders including unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA) involves a genetic testing workflow including chromosomal microarray (CMA), Fragile-X testing, karyotype analysis, and/or sequencing based gene panels. Since genomic imbalances are often found to be causative, CMA is recommended as first tier testing for many indications. Optical genome mapping (OGM) is an emerging next generation cytogenomic technique that can detect not only copy number variants (CNVs), triploidy and absence of heterozygosity (AOH) like CMA, but can also define the location of duplications, and detect other structural variants (SVs), including balanced rearrangements and repeat expansions/contractions. This study compares OGM to CMA for clinically reported genomic variants, some of which have additional structural characterization with fluorescencein situhybridization (FISH).METHODSOGM was performed on IRB approved, de-identified specimen from 55 individuals with unbalanced genomic abnormalities previously identified by CMA (61 clinically reported abnormalities). SVs identified by OGM were filtered by a control database to remove polymorphic variants and against an established gene list to prioritize clinically relevant findings before comparing with CMA and FISH results.RESULTSTOGM results showed 100% concordance with CMA findings for pathogenic variants and 98% concordant for all pathogenic/likely pathogenic/variants of uncertain significance (VUS), while also providing additional insight into the genomic structure of abnormalities that CMA was unable to provide.CONCLUSIONOGM demonstrates equivalent or superior performance to CMA and adds to an increasing body of evidence on the analytical validity and ability to detect clinically relevant abnormalities identified by CMA. Moreover, OGM identifies translocations, structures of duplications and complex CNVs intractable by CMA, yielding additional clinical utility.
Test Development with Content Validity in Pediatric Hematology
Authors: Armijo Beeling M. , Abusin Ghada A. , Kreiter Clarence D. , Barlow Patrick B. , Lentz Steven R. 
Published: January 2023

AbstractContent validity is often lacking in tools for the assessment of competency in medical specialty and subspecialty trainees. The primary aim of this study was to develop a protocol for early test assessment in pediatric hematology using iterative rounds of expert evaluation in the context of explicit knowledge goals. We used the pediatric hematology content of the American Board of Pediatrics as a test case for assessment protocol development. We found that the use of expert input and three rounds of test development increased test content validity. The instrument developed here has the potential to improve assessment of competency in pediatric hematology. This approach also may be useful in the development of competency assessment tools for other medical subspecialties.
Minuteman – A versatile cloud computational platform for collaborative research
Authors: Li Xinkai , Charkaborty Joydeep , Jameson Michael , Moore Hobert , Laux-Biehlmann Alexis , Hayat Sikander , Jain Dhawal 
Published: January 2023

AbstractSecure platforms for bio-computation are critical to foster increasingly complex and data-intensive collaborations involving biomedical data. Here, we present Minuteman – an open-source cloud computing platform that can be securely used across organizations. Minuteman can be used for hosting data sources and running computational pipelines in an organized way. The platform consists of three fundamental features, 1) data operations including collaborative data processing and analytics, 2) customizable user access management for secure dissemination of the data, and 3) interactive exploration of the data through 3rdparty (e.g. shiny, dashboard etc.) applications that can be scaled using docker containers. Strict data access rules and user-specific roles are applied across the whole platform to maintain data security. Minuteman is ideal for scenarios where data security, and privileged access are critical, such as industry-academia collaborations, and multi-institution consortiums. Using single-cell transcriptomics preprocessing, analyses and visualization pipelines across labs, we showcase the utility of the Minuteman platform for biomedical data analyses. Minuteman code is available at (https://github.com/hayatlab/minuteman)
Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein
Authors: Bosnakovski Darko , Toso Erik A. , Ener Elizabeth T. , Gearhart Micah D. , Yin Lulu , Lüttmann Felipe F. , Magli Alessandro , Shi Ke , Kim Johnny , Aihara Hideki , Kyba Michael 
Published: January 2023

SUMMARYDouble homeobox (DUX) genes are unique to eutherian mammals and normally expressed transiently during zygotic genome activation. The canonical member, DUX4, is involved in facioscapulohumeral muscular dystrophy (FSHD) and cancer, when misexpressed in other contexts. We evaluate the 3 human DUX genes and the ancestral single homeobox gene sDUX from the non-eutherian mammal, platypus, and find that DUX4 activities are not shared with DUXA or DUXB, which lack transcriptional activation potential, but surprisingly are shared with platypus sDUX. In human myoblasts, platypus sDUX drives cytotoxicity, inhibits myogenesis, and induces DUX4 target genes, particularly those associated with zygotic genome activation (ZGA), by binding DNA as a homodimer in a way that overlaps the DUX4 homeodomain crystal structure. DUXA lacks transcriptional activity but has DNA-binding and chromatin accessibility overlap with DUX4 and sDUX, including on ZGA genes and LTR elements, and can actually be converted into a DUX4-like cytotoxic factor by fusion to a synthetic transactivation domain. DUXA competition antagonizes the activity of DUX4 on its target genes, including in FSHD patient cells. Since DUXA is an early DUX4 target gene, this activity potentiates feedback inhibition, constraining the window of DUX4 activity. The DUX gene family therefore comprises cross-regulating members of opposing function, with implications for their roles in ZGA, FSHD, and cancer.HIGHLIGHTSPlatypus sDUX is toxic and inhibits myogenic differentiation.DUXA targets overlap substantially with those of DUX4.DUXA fused to a synthetic transactivation domain acquires DUX4-like toxicity.DUXA behaves as a competitive inhibitor of DUX4.
Nano-computed tomography reveals repeated phenotypic divergence in parasites to escape host defense
Authors: Kolencik Stanislav , Stanley Edward L. , Punnath Aswaj , Grant Avery R. , Doña Jorge , Johnson Kevin P. , Allen Julie M. 
Published: January 2023

AbstractUnderstanding how selective pressures drive morphological change is a central question in evolutionary biology. Feather lice have repeatedly diversified into convergent ecomorphs, based on how they escape from host defenses in different microhabitats. Here, we used nano-computed tomography scan data of 89 specimens of feather lice, belonging to four ecomorph groups to quantify variation of functional traits, including mandibular muscle volume, limb length, and three-dimensional head shape data in these tiny insects. The results suggest that the shape of the head, the proportional volume of the chewing muscles, and the length of the leg segments in feather lice are all strongly associated with specific host-habitats. Further, species that co-occur on hosts have increased rates of morphological evolution, suggesting competition for host space is one of the drivers of morphology. This supports previous work indicating that the phenotypic diversity of feather lice is the result of repeated convergence resulting from resource partitioning, microhabitat specialization, and selection pressures imposed by host defense.
A publishing infrastructure for AI-assisted academic authoring
Authors: Pividori Milton , Greene Casey S. 
Published: January 2023

AbstractIn this work we investigate how models with advanced natural language processing capabilities can be used to reduce the time-consuming process of writing and revising scholarly manuscripts. To this end, we integrate large language models into the Manubot publishing ecosystem to suggest revisions for scholarly text. We tested our AI-based revision workflow in three case studies of existing manuscripts, including the present one. Our results suggest that these models can capture the concepts in the scholarly text and produce high-quality revisions that improve clarity. Given the amount of time that researchers put into crafting prose, we anticipate that this advance will revolutionize the type of knowledge work performed by academics.