bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is severe traumatic brain injury no longer a contraindication for surgical stabilization of rib fractures in patients with multiple rib fractures? A propensity-matched analysis
Authors: Lagazzi Emanuele , de Roulet Amory , Proaño-Zamudio Jefferson A. , Argandykov Dias , Romijn Anne-Sophie , Abiad May , Rafaqat Wardah , Hwabejire John O. , Velmahos George C. , Paranjape Charudutt 
Published: April 2023

BACKGROUND
Traumatic brain injury (TBI) is often considered a contraindication to surgical stabilization of rib fractures (SSRF). In this study, we hypothesized that, compared with nonoperative management, SSRF is associated with improved outcomes in TBI patients.

METHODS
Using the American College of Surgeons Trauma Quality Improvement Program 2016–2019, we performed a retrospective analysis of patients with concurrent TBI and multiple rib fractures. Following propensity score matching, we compared patients who underwent SSRF with those who were managed nonoperatively. Our primary outcome was mortality. Secondary outcomes included ventilator-associated pneumonia, hospital and intensive care unit (ICU) length of stay (LOS), ventilator days, tracheostomy rate, and hospital discharge disposition. In a subgroup analysis, we stratified patients into mild and moderate TBI (GCS score >8) and severe TBI (GCS score ≤8).

RESULTS
Of 36,088 patients included in this study, 879 (2.4%) underwent SSRF. After propensity-score matching, compared with nonoperative management, SSRF was associated with decreased mortality (5.4% vs. 14.5%,p < 0.001), increased hospital LOS (15 days vs. 9 days, p < 0.001), increased ICU LOS (12 days vs. 8 days, p < 0.001), and increased ventilator days (7 days vs. 4 days, p < 0.001). In the subgroup analyses, in mild and moderate TBI, SSRF was associated with decreased in-hospital mortality (5.0% vs. 9.9%, p = 0.006), increased hospital LOS (13 days vs. 9 days, p < 0.001), ICU LOS (10 days vs. 7 days, p < 0.001), and ventilator days (5 days vs. 2 days, p < 0.001). In patients with severe TBI, SSRF was associated with decreased mortality (6.2% vs. 18%, p < 0.001), increased hospital LOS (20 days vs. 14 days, p = 0.001), and increased ICU LOS (16 days vs. 13 days, p = 0.004).

CONCLUSION
In patients with TBI and multiple rib fractures, SSRF is associated with a significant decrease in in-hospital mortality and with longer hospital and ICU LOSs. These findings suggest that SSRF should be considered in patients with TBI and multiple rib fractures.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level III.
Long COVID and especially headache syndromes
Authors: Tana Claudio , Giamberardino Maria Adele , Martelletti Paolo 
Published: April 2023

Purpose of review
This is an expert overview on recent literature about the complex relationship between coronavirus disease 2019 (COVID-19) and headache.

Recent findings
Long COVID is a clinical syndrome characterized by the presence of persistent symptoms following the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Headache is one of the most common symptoms and is described most often as throbbing pain, associated with photo and phonofobia and worsening with physical exercise. In acute COVID-19, headache is usually described as moderate or severe, diffuse and oppressive although sometimes it has been described with a migraine-like phenotype, especially in patients with a previous history of migraine. Headache intensity during acute phase seems to be the most important predictor of duration of headache over time. Some COVID-19 cases can be associated with cerebrovascular complications, and red flags of secondary headaches (e.g. new worsening or unresponsive headache, or new onset of neurological focal signs) should be urgently investigated with imaging. Treatment goals are the reduction of number and intensity of headache crises, and the prevention of chronic forms.

Summary
This review can help clinicians to approach patients with headache and infection from SARS-CoV-2, with particular attention to persistent headache in long COVID.
Fluorescein Angiography Findings in Susac Syndrome: A Multicenter Retrospective Case Series
Authors: Cohen Devon A. , Tajfirouz Deena , Vodopivec Ivana , Kyle Kevin , Bouffard Marc A. , Bhattacharyya Shamik , Douglas Vanja C. , Rasool Nailyn , Bhatti M. Tariq , McKeon Andrew , Pittock Sean , Flanagan Eoin P. , Prasad Sashank , Nagagopal Venna , Egan Robert A. , Chen John J. , Chwalisz Bart K. 
Published: April 2023

Background:
Susac syndrome is a vasculopathy, resulting in the classic triad of branch retinal artery occlusion (BRAO), inner ear ischemia, and brain ischemia. In this retrospective chart review, we characterize fluorescein angiography (FA) findings and other ancillary studies in Susac syndrome, including the appearance of persistent disease activity and the occurrence of new subclinical disease on FA.

Methods:
This multicenter, retrospective case series was institutional review board–approved and included patients with the complete triad of Susac syndrome evaluated with FA, contrasted MRI of the brain, and audiometry from 2010 to 2020. The medical records were reviewed for these ancillary tests, along with demographics, symptoms, visual acuity, visual field defects, and findings on fundoscopy. Clinical relapse was defined as any objective evidence of disease activity during the follow-up period after initial induction of clinical quiescence. The main outcome measure was the sensitivity of ancillary testing, including FA, MRI, and audiometry, to detect relapse.

Results:
Twenty of the 31 (64%) patients had the complete triad of brain, retinal, and vestibulocochlear involvement from Susac syndrome and were included. Median age at diagnosis was 43.5 years (range 21–63), and 14 (70%) were women. Hearing loss occurred in 20 (100%), encephalopathy in 13 (65%), vertigo in 15 (75%), and headaches in 19 (95%) throughout the course of follow-up. Median visual acuity at both onset and final visit was 20/20 in both eyes. Seventeen (85%) had BRAO at baseline, and 10 (50%) experienced subsequent BRAO during follow-up. FA revealed nonspecific leakage from previous arteriolar damage in 20 (100%), including in patients who were otherwise in remission. Of the 11 episodes of disease activity in which all testing modalities were performed, visual field testing/fundoscopy was abnormal in 4 (36.4%), MRI brain in 2 (18.2%), audiogram in 8 (72.7%), and FA in 9 (81.8%).

Conclusions:
New leakage on FA is the most sensitive marker of active disease. Persistent leakage represents previous damage, whereas new areas of leakage suggest ongoing disease activity that requires consideration of modifying immunosuppressive therapy.
Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
Authors: Kim Kyeong Ryeol , Kim Jeong Min , Lee Jae Kyeong , Han Dong Min , Hao Lujiang , Jeon Che Ok 
Published: April 2023

A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10–37 °C (optimum, 25–30 °C) and pH 6.0–9.0 (optimum, pH 8.0), and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Strain U1T contained iso-C15 : 0, C16 : 0, C16 : 1 ω5c and summed feature 3 (comprising C16 : 1
ω6c and/or C16 : 1 ω7c) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus

Dyadobacter

. Strain U1T has the highest 16S rRNA sequence similarity to

Dyadobacter bucti

QTA69T (97.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain U1T and

D. bucti

QTA69T were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus

Dyadobacter

, for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).
Improvement in Delivery of Ischemic Stroke Treatments but Stagnation of Clinical Outcomes in Young Adults in South Korea
Authors: Kim Jonguk , Kim Jun Yup , Kang Jihoon , Kim Beom Joon , Han Moon-Ku , Lee Jeong-Yoon , Park Tai Hwan , Lee Ji Sung , Lee Keon-Joo , Kim Joon-Tae , Choi Kang-Ho , Park Jong-Moo , Kang Kyusik , Lee Soo Joo , Kim Jae Guk , Cha Jae-Kwan , Kim Dae-Hyun , Lee Kyungbok , Lee Jun , Hong Keun-Sik , Cho Yong-Jin , Park Hong-Kyun , Lee Byung-Chul , Yu Kyung-Ho , Oh Mi-Sun , Kim Dong-Eog , Ryu Wi-Sun , Choi Jay Chol , Kwon Jee-Hyun , Kim Wook-Joo , Shin Dong-Ick , Yum Kyu Sun , Sohn Sung Il , Hong Jeong-ho , Lee Sang-Hwa , Lee Juneyoung , Gorelick Philip B. , Bae Hee-Joon 
Published: April 2023

AbstractBackgroundThere is limited information on the delivery of acute stroke therapies and secondary preventive measures and clinical outcomes over time in young adults with acute ischemic stroke (AIS). This study investigated whether advances in these treatments improved outcomes in this population.MethodsUsing a prospective multicenter stroke registry in Korea, young adults (aged 18–50 years) with AIS hospitalized between 2008 and 2019 were identified. The observation period was divided into four epochs: 2008–2010, 2011–2013, 2014–2016, and 2017–2019. Secular trends for patient characteristics, treatments, and outcomes were analyzed.ResultsA total of 7,050 eligible patients (mean age 43.1; men 71.9%) were registered. The mean age decreased from 43.6 to 42.9 years (Ptrend=0.01). Current smoking decreased, whereas obesity increased. Other risk factors remained unchanged. Intravenous thrombolysis and mechanical thrombectomy rates increased over time from 2008–2010 to 2017–2019 (9.5% to 13.8% and 3.2% to 9.2%, respectively; Ptrend’s<0.01). Door-to-needle time improved (Ptrend<.001), but onset-to-door and door-to-puncture time remained constant. Secondary prevention including the administration of dual antiplatelets for noncardioembolic minor stroke (26.7% to 47.0%), direct oral anticoagulants for atrial fibrillation (0.0% to 56.2%), and statins for large artery atherosclerosis (76.1% to 95.3%) increased (Ptrend’s<0.01). Outcome data were available from 2011. One-year mortality (2.5% in 2011–2013 and 2.3% in 2017–2019) and 3-month modified Rankin scale scores 0–1 (68.3% to 69.1%) and 0–2 (87.6% to 86.2%) remained unchanged. The one-year stroke recurrence rate increased (4.1% to 5.5%, Ptrend=0.04), altough the differnce was not significant after adjusting for sex and age.ConclusionImprovements in the delivery of acute stroke treatments did not necessarily lead to better outcomes in young adults with AIS over the past decade, indicating a need for further progress.
Ki-67 is necessary during DNA replication for forks protection and genome stability
Authors: Stamatiou Konstantinos , Huguet Florentin , Spanos Christos , Rappsilber Juri , Vagnarelli Paola 
Published: April 2023

ABSTRACTBackgroundThe proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years but investigations on its biological functions have lagged. Recently, Ki-67 was shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromatin organisation and gene transcription. However, a role for Ki-67 in regulating cell cycle progression has never been reported. The progress towards understanding Ki-67 function have been limited by the tools available to deplete the protein coupled to its abundance and fluctuation during the cell cycle.ResultsHere we have used an auxin-inducible degron tag (AID) to achieve a rapid and homogeneous degradation of Ki-67 in HCT116 cells. This system, coupled with APEX2 proteomics and phospho-proteomics approaches, allowed us to show for the first time that Ki-67 plays a role during DNA replication. In its absence, DNA replication is severely delayed, the replication machinery is unloaded, causing DNA damage that is not sensed by the canonical pathways and dependant on HUWE1 ligase. This leads to replication and sister chromatids cohesion defects, but it also triggers an interferon response mediated by the cGAS/STING pathway in all the cell lines tested.ConclusionsWe have unveiled a new function of Ki-67 in DNA replication and genome maintenance that is independent of its previously known role in mitosis and gene regulation.
Spatial-extent inference for testing variance components in reliability and heritability studies
Authors: Pan Ruyi , Dickie Erin W. , Hawco Colin , Reid Nancy , Voineskos Aristotle N. , Park Jun Young 
Published: April 2023

AbstractClusterwise inference is a popular approach in neuroimaging to increase sensitivity, but most existing methods are currently restricted to the General Linear Model (GLM) for testing mean parameters. Statistical methods for testingvariance components, which are critical in neuroimaging studies that involve estimation of narrow-sense heritability or test-retest reliability, are underdeveloped due to methodological and computational challenges, which would potentially lead to low power. We propose a fast and powerful test for variance components called CLEAN-V (CLEANfor testingVariance components). CLEAN-V models the global spatial dependence structure of imaging data and computes a locally powerful variance component test statistic by data-adaptively pooling neighborhood information. Correction for multiple comparisons is achieved by permutations to control family-wise error rate (FWER). Through analysis of task-fMRI data from the Human Connectome Project across five tasks and comprehensive data-driven simulations, we show that CLEAN-V outperforms existing methods in detecting test-retest reliability and narrow-sense heritability with significantly improved power, with the detected areas aligning with activation maps. The computational efficiency of CLEAN-V also speaks of its practical utility, and it is available as an R package.
Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics
Authors: Wu Enhui , Mallawaarachchi Vijini , Zhao Jinzhi , Yang Yi , Liu Hebin , Wang Xiaoqing , Shen Chengpin , Lin Yu , Qiao Liang 
Published: April 2023

AbstractMicrobiota are closely associated to human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high diversity of microbiota samples. One of the main challenges is constructing a protein sequence database that best fits the microbiota sample. Herein, we proposed an accurate taxonomic annotation pipeline from metagenomic data for deep metaproteomic coverage, namely contigs directed gene annotation (ConDiGA). We mixed 12 known bacterial species to derive a synthetic microbial community to benchmark metagenomic and metaproteomic pipelines. With the optimized taxonomic annotation strategy by ConDiGA, we built a protein sequence database from the metagenomic data for metaproteomic analysis and identified about 12,000 protein groups, which was very close to the result obtained with the reference proteome protein sequence database of the 12 species. We also demonstrated the practicability of the method in real fecal samples, achieved deep proteome coverage of human gut microbiome, and compared the function and taxonomy of gut microbiota at metagenomic level and metaproteomic level. Our study can tackle the current taxonomic annotation reliability problem in metagenomics-derived protein sequence database for metaproteomics. The unique dataset of metagenomic and the metaproteomic data of the 12 bacterial species is publicly available as a standard benchmarking sample for evaluating various analysis pipelines. The code of ConDiGA is open access at GitHub for the analysis of real microbiota samples.
VibrioMARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy
Authors: Herrera Alfa , Packer Megan M. , Rosas-Lemus Monica , Minasov George , Brummel John H. , Satchell Karla J. F. 
Published: April 2023

AbstractVibrio vulnificuscauses life threatening infections dependent upon the effectors released from the Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The Makes Caterpillars Floppy-like (MCF) cysteine protease effector is activated by host ADP ribosylation factors (ARFs), although the targets of processing activity were unknown. In this study we show MCF bindsRas-related proteins inbrain (Rab) GTPases at the same interface occupied by ARFs and then cleaves and/or degrades 24 distinct members of the Rab GTPases family. The cleavage occurs in the C-terminal tails of Rabs. We determine the crystal structure of MCF as a swapped dimer revealing the open, activated state of MCF and then use structure prediction algorithms to show that structural composition, rather than sequence or localization, determine Rabs selected as MCF proteolytic targets. Once cleaved, Rabs become dispersed in cells to drive organelle damage and cell death to promote pathogenesis of these rapidly fatal infections.
Upregulated NF-κB pathway proteins may underlieAPOE44associated astrocyte phenotypes in sporadic Alzheimer’s disease
Authors: Roberts Adele Pryce , Dec Karolina , McAllister Branduff , Tyrrell Victoria , O’Donnell Valerie B , Harwood Adrian , Williams Julie 
Published: April 2023

AbstractThe Apolipoprotein-E4 allele (APOE) is the strongest genetic risk factor for sporadic Alzheimer’s disease but its role in disease pathogenesis is incompletely understood. TheAPOEgene encodes Apolipoprotein E (ApoE). Astrocytes are the main source of ApoE in the central nervous system (CNS) and are essential for homeostasis in health and disease. In response to CNS insult, a coordinated multicellular inflammatory response is triggered causing reactive astrogliosis with changes in astrocytic gene expression, cellular structure and function.Human embryonic stem-cells with the ‘neutral’APOE33genotype were edited using CRISPR Cas-9 gene-editing to create isogenicAPOElines with an APOE44 genotype. Quiescent astrocytes were differentiated then stimulated with TNF-α, IL1α and C1q inducing an astrogliotic A1 phenotype. Several potentially pathologicalAPOE44-related phenotypes were identified in both quiescent cells and reactive A1 astrocytes including significantly decreased phagocytosis, impaired glutamate and a defective immunomodulatory response.In quiescentAPOE44astrocytes there was significantly decreased secretion of IL6, IL8 and several oxylipins. In A1 astrocytes there was a pro-inflammatory phenotype in APOE44 astrocytes with increases in GRO, ENA78, IL6 and IL8, a decrease in IL10 as well as significant differences in oxylipin expression. As TNF-α induced signaling in astrocytes is driven by Nuclear factor kappa B (NF-κB) proteins of this pathway were measured. Significantly higher levels of the p50, p65 and IκBα sub-units were found in both quiescent and A1APOE44astrocytes. This suggests that perturbation of NF-κB signaling may contribute to the damagingAPOE44cell phenotypes observed providing a new direction for targeted disease therapeutics.
Wnt5a-Ror2 signaling activates p62-Nrf2 axis in reactive astrocytes after brain injury
Authors: Endo Mitsuharu , Tanaka Yuki , Fukuoka Mayo , Suzuki Hayata , Minami Yasuhiro 
Published: April 2023

AbstractIn the brains under pathological conditions, astrocytes become reactive astrocytes that exhibit various context-dependent functions through the regulation of specific signaling pathways and transcriptional mechanisms in response to environmental changes. Reactive astrocytes induced in injured brains begin proliferating and play a role in promoting protection and repair of damaged tissues, but the relationship between the proliferative characteristics and tissue-protective and repair functions of reactive astrocytes remains unclear. Here, we show that growth factor signaling elicited by bFGF and HB-EGF, whose expression is up-regulated in the injured brains, acts synergistically with inflammatory cytokine signaling in astrocytes, thereby markedly up-regulating gene expression of the Ror-family protein Ror2, a receptor for Wnt5a. Activation of Wnt5a-Ror2 signaling in astrocytes results in intracellular accumulation of phosphorylated p62, thereby activating antioxidative transcription factor Nrf2. Finally, we provide evidence demonstrating that forced activation of Wnt5a-Ror2-p62-Nrf2 signaling axis in astrocytes reduces cellular damage caused by hemin, a degradation product of hemoglobin, and promotes repair of the damaged blood brain barrier after brain hemorrhage.
A Comprehensive Benchmark Study on Biomedical Text Generation and Mining with ChatGPT
Authors: Chen Qijie , Sun Haotong , Liu Haoyang , Jiang Yinghui , Ran Ting , Jin Xurui , Xiao Xianglu , Lin Zhimin , Niu Zhangming , Chen Hongming 
Published: April 2023

AbstractIn recent years, the development of natural language process (NLP) technologies and deep learning hardware has led to significant improvement in large language models(LLMs). The ChatGPT, the state-of-the-art LLM built on GPT-3.5, shows excellent capabilities in general language understanding and reasoning. Researchers also tested the GPTs on a variety of NLP related tasks and benchmarks and got excellent results. To evaluate the performance of ChatGPT on biomedical related tasks, this paper presents a comprehensive benchmark study on the use of ChatGPT for biomedical corpus, including article abstracts, clinical trials description, biomedical questions and so on. Through a series of experiments, we demonstrated the effectiveness and versatility of Chat-GPT in biomedical text understanding, reasoning and generation.
Neural Extracellular Matrix Remodeling Signatures in Genetic and Acquired Mouse Models of Epilepsy
Authors: Blondiaux Armand , Jia Shaobo , Annamneedi Anil , Çalışkan Gürsel , Schulze Jana , Montenegro-Venegas Carolina , Wykes Robert C. , Fejtova Anna , Walker Matthew C. , Stork Oliver , Gundelfinger Eckart D. , Dityatev Alexander , Seidenbecher Constanze I. 
Published: April 2023

AbstractEpilepsies are multifaceted neurological disorders characterized by abnormal brain activity, e.g., caused by imbalanced synaptic excitation and inhibition. The neural extracellular matrix (ECM) is dynamically modulated by physiological and pathophysiological activity and critically involved in controlling the brain’s excitability. We used different epilepsy models, i.e. mice lacking the presynaptic scaffolding protein Bassoon at excitatory, inhibitory or all synapse types as genetic models for rapidly generalizing early-onset epilepsy, and intra-hippocampal kainate injection, a model for acquired temporal lobe epilepsy, to study the relationship between epileptic seizures and ECM composition. Electroencephalogram recordings revealed Bassoon deletion at excitatory or inhibitory synapses having diverse effects on epilepsy-related phenotypes. While constitutiveBsnmutants and GABAergic neuron-specific knockouts (BsnDlx5/6cKO) displayed severe epilepsy with more and stronger seizures than kainate-injected animals, mutants lacking Bassoon solely in excitatory forebrain neurons (BsnEmx1cKO) showed only mild impairments. By semiquantitative immunoblotting and immunohistochemistry we show model-specific patterns of neural ECM remodeling, and we also demonstrate significant upregulation of the ECM receptor CD44 in null andBsnDlx5/6cKOmutants. ECM-associated WFA-binding chondroitin sulfates were strongly augmented in seizure models. Strikingly, Brevican, Neurocan, Aggrecan and link protein Hapln1 levels reliably predicted seizure properties across models, suggesting a link between ECM state and epileptic phenotype.