bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxidative Stress and Neural Dysfunction in Gastrointestinal Diseases: Can Stem Cells Offer a Solution?
Authors: Stavely Rhian , Ott Leah C , Sahakian Lauren , Rashidi Niloufar , Sakkal Samy , Nurgali Kulmira 
Published: September 2023

Abstract
Oxidative stress is involved in many gastrointestinal (GI) disorders as either the primary pathogenesis (radiation, chemotherapy, toxicity, ischemia-reperfusion) or a secondary driving force of disease progression (inflammation and diabetes). The GI tract is innervated intrinsically by the enteric nervous system (ENS) with a diverse role in maintaining gut homeostasis and GI motility. Complications in the physiological functioning of the ENS results in GI dysfunction that can result in debilitating sequelae from dysmotility greatly impacting quality of life and leading to potentially fatal complications. Therapeutics to remedy either oxidative stress or enteric neuronal dysfunction are severely limited, resulting in a critical gap in clinical care for GI disease and neurointestinal complications. Stem cell therapies have shown great promise in the treatment of several gut disorders via mechanisms including cell regeneration, anti-inflammatory activity, providing trophic support, and emerging evidence of antioxidant and neuroprotective functions. The potential of mesenchymal stem cell (MSC) therapies and recent evidence of their antioxidant and neuroprotective activity in several GI conditions are discussed. Finally, future therapeutic aspects of stem cell-based tools for combatting oxidative stress and enteric neuropathies in GI disease are considered.
Association of Genetic Variants with Postsurgical Pain: A Systematic Review and Meta-analyses
Authors: Frangakis Stephan G. , MacEachern Mark , Akbar T. Adam , Bolton Christian , Lin Victor , Smith Albert V. , Brummett Chad M. , Bicket Mark C. 
Published: September 2023

Background
Postsurgical pain is a key component of surgical recovery. However, the genetic drivers of postsurgical pain remain unclear. A broad review and meta-analyses of variants of interest will help investigators understand the potential effects of genetic variation.

Methods
This article is a systematic review of genetic variants associated with postsurgical pain in humans, assessing association with postsurgical pain scores and opioid use in both acute (0 to 48 h postoperatively) and chronic (at least 3 months postoperatively) settings. PubMed, Embase, and the Cochrane Central Register of Controlled Trials were searched from 2000 to 2022 for studies using search terms related to genetic variants and postsurgical pain in humans. English-language studies in adult patients examining associations of one or more genetic variants with postsurgical pain were included. The primary outcome was association of genetic variants with either acute or chronic postsurgical pain. Pain was measured by patient-reported pain score or analgesic or opioid consumption.

Results
A total of 163 studies were included, evaluating 129 unique genes and 594 unique genetic variants. Many of the reported significant associations fail to be replicated in other studies. Meta-analyses were performed for seven variants for which there was sufficient data (OPRM1 rs1799971; COMT rs4680, rs4818, rs4633, and rs6269; and ABCB1 rs1045642 and rs2032582). Only two variants were associated with small differences in postsurgical pain: OPRM1 rs1799971 (for acute postsurgical opioid use standard mean difference = 0.25; 95% CI, 0.16 to 0.35; cohort size, 8,227; acute postsurgical pain score standard mean difference = 0.20; 95% CI, 0.09 to 0.31; cohort size, 4,619) and COMT rs4680 (chronic postsurgical pain score standard mean difference = 0.26; 95% CI, 0.08 to 0.44; cohort size, 1,726).

Conclusions
Despite much published data, only two alleles have a small association with postsurgical pain. Small sample sizes, potential confounding variables, and inconsistent findings underscore the need to examine larger cohorts with consistent outcome measures.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
A case report: A patient rescued by VA-ECMO after cardiac arrest triggered by trigeminocardiac reflex after nasal surgery
Authors: Zhang Xu , Sun Bin , Pac-Soo Chen , Ma Daqing , Wang Liwei 
Published: September 2023

Rationale:
Cardiac arrest (CA) caused by trigeminocardiac reflex (TCR) after endoscopic nasal surgery is rare. Hence, when a patient suffers from TCR induced CA in the recovery room, most doctors may not be able to find the cause in a short time, and standard cardiopulmonary resuscitation and resuscitation measures may not be effective. Providing circulatory assistance through venous-arterial extracorporeal membrane oxygenation (VA-ECMO) can help healthcare providers gain time to identify the etiology and initiate symptom-specific treatment.

Patient concerns:
We report a rare case of CA after endoscopic nasal surgery treated with VA-ECMO.

Diagnoses:
We excluded myocardial infarction, pulmonary embolism, allergies, hypoxia, and electrolyte abnormalities based on the relevant examination results. Following a multidisciplinary consultation, clinical manifestation and a review of previous literature, we reasoned that the CA was due to TCR.

Interventions:
VA-ECMO was established to resuscitate the patient successfully during effective cardiopulmonary resuscitation.

Outcomes:
ECMO was successfully evacuated a period of 190 minutes of therapy. The patient was discharged home on day 8.

Lessons:
TCR is notable during endoscopic nasal surgery. Our case indicates that CA in operating room is worth prolonged CCPR. The ideal time for ECPR implementation should not be limited within 20 minutes after CCPR.
A case of early-onset periodontitis with vitamin D deficiency: A case report and literature review
Authors: Li Chen , Zhang Jinmei , Wang Lufei , Yang Jingmei 
Published: September 2023

Rationale:
Periodontitis is an inflammatory disease with multifactorial etiology. Vitamin D, a fat-soluble vitamin, has protective effects on inflammatory response in various systemic conditions. The clinical features of vitamin D deficiency include growth failure, hypotonia, pathologic fractures, rachitic rosary, tetany and so on. Here we present a case of 12-year-old girl affected by early-onset periodontitis accompanied with vitamin D deficiency.

Patient concerns:
A 12-year-old girl with gingival redness, bleeding associated with tooth brushing, and mandibular anterior teeth movement, with difficulty in mastication for the past 2 months. There is no relevant family history or special systemic disease history. The serological microelement test showed vitamin D levels were significantly lower than normal range. Immunological test showed abnormal CD4+/CD8+(CD3+CD4+/CD3+CD8+) ratio as well.

Diagnoses:
Based on the clinical and serological findings, this patient was ultimately diagnosed with early-onset periodontitis accompanied with vitamin D deficiency.

Interventions:
The main treatments for this patient were 3-fold: periodontal therapy, vitamin D supplement and oral hygiene instructions.

Outcomes:
Following 1-year therapy, periodontal conditions recovered and became stable. And serological vitamin D levels returned to normal range.

Lessons:
The case of interest serves as an important reminder to clinicians, that the early-onset periodontitis may be associated with micronutrients abnormalities, and early-diagnosis and treatment could avoid the body heathy disorders.
Efficacy of scrambler therapy in patients with painful diabetic peripheral neuropathy: A single-arm, prospective, pilot study
Authors: Yoo Seung Hee , Kim Won-joong , Chae Ji Seon , Kang Bo Kyung , Kang Min Jeong , Beak Min Hyouk 
Published: September 2023

Background:
A variety of medications are available to manage painful diabetic peripheral neuropathy (DPN), but the proper treatment remains challenging. Accordingly, various neuromodulation modalities have been used. However, no prospective clinical trials have evaluated the use of scrambler therapy (ST) in painful DPN. This study aimed to explore the long-term effects of ST in managing painful DPN.

Methods:
The patients received 10 consecutive STs of 45 minutes every 1 to 2 days. The primary outcome was pain score. We measured the visual analog scale (VAS) pain scores at baseline, during ST, immediately after ST, and at 1, 2, 3, and 6 months after ST. The secondary outcomes were Michigan Neuropathy Screening Instrument (MNSI), Semmes-Weinstein monofilament test, and Leeds Assessment of Neuropathic Symptoms and Signs pain scores, which were measured at baseline, immediately after ST, and at 1, 2, 3, and 6 months after ST.

Results:
VAS scores showed significant improvement at the 8th, 9th, and 10th sessions during ST and 1 month after ST. The MNSI self-report component score was decreased 1 month after the ST. However, all other outcomes did not show significant differences compared to the baseline.

Conclusion:
ST may have short-term effects and limited long-term effects on painful DPN.
Successful perioperative management with damage control surgery following cardiac arrest due to massive postpartum hemorrhage: A case report
Authors: Park Chan Hee , Bae Jin Gon , Lee Jeong Woo 
Published: September 2023

Introduction:
Although declining, maternal mortality due to postpartum hemorrhage (PPH) remains significant. Here we report the case of a 31-year-old primipara patient admitted with cardiac arrest due to PPH.

Case presentation:
Labor was induced at gestational week 39, and the infant was delivered rapidly. Cardiac arrest due to PPH occurred during the transfer to our hospital, and the patient underwent cardiopulmonary resuscitation upon arrival to the emergency room. On admission, her hemoglobin level was 0.7 g/dL and she was in hypovolemic shock. Resuscitation and hysterectomy were performed immediately, including damage control surgery and gauze packing, to control the diffuse oozing bleeding due to severe disseminated intravascular coagulation. Relaparotomy for hemostasis was subsequently performed because of a decrease in hemoglobin level and blood pressure, and gauze packing was reinserted with temporary abdominal closure. Two days later, the abdominal wall was closed after confirming the absence of bleeding and the patient recovered well without further intervention.

Conclusion:
A prompt and assertive intensive response through collaborative efforts, utilizing feasible damage control surgery, can elegantly salvage uncontrolled bleeding in PPH patients with disseminated intravascular coagulation.
Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov.
Authors: Liu Wen-Li , Yang Zi-Wen , Guo Dan-Yuan , Deng Qi-Qi , Li Jia-Ling , Wang Pan-Deng , Chen Sen-Hua , Liu Lan , Nie Guo-Xing , Li Wen-Jun 
Published: September 2023

A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828T, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4–37 °C (optimum, 28 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C18 : 1
ω7c/C18 : 1
ω6c, C18 : 1
ω7c11-methyl and C18 : 0 (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828T belonged to the genus

Cereibacter

and had the highest sequences similarity to ‘Rhodobacter xinxiangensis’ TJ48T (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828T represents a novel species of the genus

Cereibacter

, for which the name Cereibacter flavus sp. nov. is proposed. The type strain is SYSU M79828T (=GDMCC 1.3803T=KCTC 92893T). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that

Rhodobacter alkalitolerans

should be reclassified as Cereibacter alkalitolerans comb. nov.
Transcriptomic gene profiles in anex vivomodel of erythropoiesis to unravel molecular pathomechanisms of Sickle Cell Disease
Authors: Tinguely Matthis , Opitz Lennart , Schaer Dominik J. , Vallelian Florence , Schmugge Markus , Franzoso Francesca D. 
Published: September 2023

AbstractWe characterized the transcriptional profiles of erythroid cells differentiated from peripheral blood mononuclear cells (PBMCs) from peripheral blood collected from patients diagnosed with Sickle Cell Disease (SCD), which have been treated with Hydroxyurea (HU) in comparison to untreated SCD patients and healthy controls (HC) using bulk RNAseq. We identified 1398 differentially expressed genes (DEGs) in SCD non-treated-derived erythroid cells and 495 DEGs in SCD HU-treated patient-derived erythroid cells compared to HC. We found biological processes such as oxidative phosphorylation pathway, proteasome, autophagy, natural killer cell (NK) cytotoxicity, adaptive immune response or inflammatory response to be significantly enriched in our patient study groups by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Our findings collectively suggest different as well as common molecular signatures between our groups. We could validate 12 of our top DEGs in treated patients by qRT-PCR. We found similar regulation patterns when comparing the mRNA levels of mutS homolog 5-Suppressor APC Domain Containing 1 (MSH5-SAPCD1), G protein subunit gamma 4 (GNG4), stabilin 1/ clever-1 (STAB1) and Fas Binding Factor 1 (FBF1) from the bone marrow cells and spleen tissue from the Berkely SCD mouse model to the expressions observed in the transcriptome of our ex-vivo patient-derived erythropoiesis model.
LEOPARD: missing view completion for multi-timepoint omics data via representation disentanglement and temporal knowledge transfer
Authors: Han Siyu , Yu Shixiang , Shi Mengya , Harada Makoto , Ge Jianhong , Lin Jiesheng , Prehn Cornelia , Petrera Agnese , Li Ying , Sam Flora , Matullo Giuseppe , Adamski Jerzy , Suhre Karsten , Gieger Christian , Hauck Stefanie M. , Herder Christian , Roden Michael , Casale Francesco Paolo , Cai Na , Peters Annette , Wang-Sattler Rui 
Published: September 2023

AbstractLongitudinal multi-view omics data offer unique insights into the temporal dynamics of individual-level physiology, which provides opportunities to advance personalized healthcare. However, the common occurrence of incomplete views makes extrapolation tasks difficult, and there is a lack of tailored methods for this critical issue. Here, we introduce LEOPARD, an innovative approach specifically designed to complete missing views in multi-timepoint omics data. By disentangling longitudinal omics data into content and temporal representations, LEOPARD transfers the temporal knowledge to the omics-specific content, thereby completing missing views. The effectiveness of LEOPARD is validated on three benchmark datasets constructed with data from the MGH COVID study and the KORA cohort, spanning periods from 3 days to 14 years. Compared to conventional imputation methods, such as missForest, PMM, GLMM, and cGAN, LEOPARD yields the most robust results across the benchmark datasets. LEOPARD-imputed data also achieve the highest agreement with observed data in our analyses for age-associated metabolites detection, estimated glomerular filtration rate-associated proteins identification, and chronic kidney disease prediction. Our work takes the first step toward a generalized treatment of missing views in longitudinal omics data, enabling comprehensive exploration of temporal dynamics and providing valuable insights into personalized healthcare.
Intrinsic disorder in flaviviral capsid proteins and their role in pathogenesis
Authors: Sundar Anirudh , Umashankar Pavithra , Sankar Priyanka , Ramasamy Kavitha , Venkataraman Sangita 
Published: September 2023

ABSTRACTA high level of disorder in many viral proteins is a direct consequence of their small genomes, which makes interaction with multiple binding partners a necessity for infection and pathogenicity. A segment of the flaviviral capsid protein, also known as the molecular recognition feature (MoRF), undergoes a disorder-to-order transition upon binding to several protein partners. In order to understand their role in pathogenesis, the MORFs were identified and their homology was studied. Despite the lack of sequence similarities, the docking studies of Cs with the host proteins indicate conserved interactions involving MORFs across members of the phylogenetic subclades. Additionally, it was observed from the protein-protein networks that some MoRFs preferentially bind proteins that are involved in specialized functions such as ribosome biogenesis. The findings point to the importance of the MoRFs in the flaviviral life cycle, with important consequences for disease progression and suppression of the host immune system. Potentially, they might have impacted the way flaviviruses evolved to infect varied hosts using multiple vectors.
Immune Cells and Inflammatory mediators cause endothelial dysfunction in a vascular microphysiological system
Authors: Rengarajan Aishwarya , Goldblatt Hannah E , Beebe David J. , Virumbrales-Muñoz María , Boeldt Derek S 
Published: September 2023

ABSTRACTFunctional assessment of endothelium serves as an important indicator of vascular health and is compromised in vascular disorders including hypertension, atherosclerosis, and preeclampsia. Endothelial dysfunction in these cases is linked to dysregulation of the immune system involving both changes to immune cells and increased secretion of inflammatory cytokines. Herein, we utilize a well-established microfluidic device to generate a 3-dimensional vascular Microphysiological System (MPS) consisting of a tubular blood vessel lined with Human Umbilical Vein Endothelial Cells (HUVECs) to evaluate endothelial function measured via endothelial permeability and Ca2+signaling. We evaluated the effect of a mixture of factors associated with inflammation and cardiovascular disease (TNFα, VEGF-A, IL-6 at 10ng/ml each) on vascular MPS and inferred that inflammatory mediators contribute to endothelial dysfunction by disrupting the endothelial barrier over a 48-hour treatment and by diminishing coordinated Ca2+activity over a 1-hour treatment.We also evaluated the effect of peripheral blood mononuclear cells (PBMCs) on endothelial permeability and Ca2+signaling in the HUVEC MPS. HUVECs were co-cultured with PBMCs either directly wherein PBMCs passed through the lumen or embedded in the supporting collagen hydrogel. We revealed that Phytohemagglutinin (PHA)-M activated PBMCs cause endothelial dysfunction in MPS both through increased permeability and decreased coordinated Ca2+activity compared to non-activated PBMCs. Our MPS has potential applications in modeling cardiovascular disorders and screening for potential treatments using measures of endothelial function.
The effects of warming on the stability of consumer-resource interactions
Authors: Synodinos Alexis D. , Sentis Arnaud , Montoya José M. , Haegeman Bart 
Published: September 2023

AbstractTemperature regulates the physiology and behaviour of organisms. Thus, changing temperatures induce dynamics in species interactions. Considering that consumer-resource interactions underpin ecological communities, the impacts of warming on the stability of consumer-resource interactions have been extensively studied. However, a consensus among empirically determined warming-stability relationships and a clear understanding thereof is lacking. To investigate these systematically, we propose a simplified theoretical framework that can incorporate empirical data in three steps. First, we constrain stability to intrinsic oscillations to avoid comparing disparate stability notions. Second, we reduce complexity by utilising a one-dimensional stability metric. Third, we enable the direct comparison of all data by converting all thermal dependence parameterisations into a single function, with two parameters in the exponent determining its shape. The empirical data generate four different warming-stability relationships: stability increases, decreases, is hump-shaped or U-shaped with temperature. The diversity of warming-stability relationships, though partly attributable to context-dependence, is fundamentally caused by sensitivity to two factors: how the processes within the functional response are defined and the thermal dependence of carrying capacity. Consistency across studies regarding the former and acquiring more data on the latter should help uncover systematic patterns in the thermal dependence of stability in consumer-resource interactions.
Synthetic Hydrogels with Entangled Neutrophil Extracellular Traps Influence Tumor Progression in MDA-MB-231 Cells
Authors: Katz Rachel R. , Shetty Shamitha , West Jennifer L. 
Published: September 2023

ABSTRACTWe incorporated neutrophil extracellular traps (NETs) in a poly(ethylene glycol)-based synthetic extracellular matrix to study their impact on tumorigenesis in triple negative breast carcinoma (TNBC) cells in a highly controlled environment. We observed that NETs helped to increase cell survival, proliferation, and pro-metastatic morphological phenotype. We also showed that the presence of NETs influenced the secretion of IL-8, a pro-NETosis factor, and that conditioned media from cells cultured in these gels influenced NETosis in an IL-8 dependent manner. The results observed in this system correlate with murine models and clinical studies in the literature and help to provide additional insight of the individual factors at play in the NET-mediated promotion of TNBC progression and metastasis.
The Integration of Proteogenomics and Ribosome Profiling Circumvents Key Limitations to Increase the Coverage and Confidence of Novel Microproteins
Authors: de Souza Eduardo V. , Bookout Angie L. , Barnes Christopher A. , Miller Brendan , Machado Pablo , Basso Luiz A. , Bizarro Cristiano V. , Saghatelian Alan 
Published: September 2023

AbstractThere has been a dramatic increase in the identification of non-conical translation and a significant expansion of the protein-coding genome and proteome. Among the strategies used to identify novel small ORFs (smORFs), Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple sites in the genome are computationally removed since they cannot unambiguously be assigned to a specific genomic location, or to a specific transcript in the case of multiple isoforms. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of ambiguous and multi-mapping alignments, such that smORFs that reside in these regions cannot be identified by Ribo-Seq. Here, we show that the inclusion of proteogenomics to create a Ribosome Profiling and Proteogenomics Pipeline (RP3) bypasses this limitation to identify a group of microprotein-encoding smORFs that are missed by current Ribo-Seq pipelines. Moreover, we show that the microproteins identified by RP3 have different sequence compositions from the ones identified by Ribo-Seq-only pipelines, which can affect proteomics identification. In aggregate, the development of RP3 maximizes the detection and confidence of protein-encoding smORFs and microproteins.