bluuebunny/crossref_metadata_2025 huggingface dataset:
An uncommon and easily overlooked case: Delayed intraperitoneal bladder rupture following blunt trauma: A case report and review of the literature
Authors: Ma Man , Wei Gongbin , Liu Chaopu , Xu Yanan
Published: February 2024

Introduction:

Delayed intraperitoneal bladder rupture is a rare clinical occurrence, frequently overlooked and misdiagnosed due to its nonspecific clinical manifestations. However, literature provides only a limited number of cases reporting delayed intraperitoneal bladder rupture resulting from blunt abdominal injury.

Patient concerns:

A 72-year-old female pedestrian was struck by a vehicle and experienced sudden, severe abdominal pain on the 8th day following the injury. Abdominal B-ultrasound revealed a significant accumulation of peritoneal effusion. The abdominal puncture retrieved serosanguinous ascites. Then the patient was promptly transferred to our hospital. Upon transfer, the physical examination revealed the patient vital signs to be stable, accompanied by mild abdominal distension, slight tenderness, tension, and an absence of rebound tenderness. Urinalysis detected microscopic hematuria, while contrast-enhanced computed tomography (CT) revealed considerable fluid accumulation in the abdominal cavity, without evidence of solid organ damage, and the bladder was adequately filled.

Diagnosis:

The diagnosis of delayed intraperitoneal bladder rupture primarily relied on intraoperative observations.

Interventions:

An emergency exploratory laparotomy was performed, revealing a linear rupture at the dome of the bladder. Subsequently, the bladder rupture was repaired.

Outcomes:

Postoperative cystography demonstrated full recovery and the patient was discharged 28 days post-surgery. The postoperative recovery was uneventful without any complications.

Conclusions:

A well-distended bladder observed in CT does not definitively rule out the potential for bladder injury. False negatives may occur due to incomplete bladder filling during CT cystography. Retrograde cystography can identify cases missed by CT cystography. In cases of substantial intra-abdominal free fluid, surgical intervention should be actively considered for patients with blunt abdominal trauma without concurrent solid organ damage.
Progress of plant polyphenol extracts in treating depression by anti-neuroinflammatory mechanism: A review
Authors: Guo Yuting , Yang Yan
Published: February 2024

There is a growing body of evidence supporting the involvement of central nervous system inflammation in the pathophysiology of depression. Polyphenols are a diverse group of compounds known for their antioxidative and anti-inflammatory properties. They offer a promising and effective supplementary approach to alleviating neuropsychiatric symptoms associated with inflammation-induced depression. This paper provides a summary of the potential anti-neuroinflammatory mechanisms of plant polyphenol extracts against depression. This includes direct interference with inflammatory regulators and inhibition of the expression of pro-inflammatory cytokines. Additionally, it covers downregulating the expression of pro-inflammatory cytokines by altering protein kinases or affecting the activity of the signaling pathways that they activate. These pathways interfere with the conduction of signaling molecules, resulting in the destruction and reduced synthesis of all inflammatory mediators and cytokines. This reduces the apoptosis of neurons and plays a neuroprotective role. This paper provides a theoretical basis for the clinical application of plant polyphenols.
Evaluation of the correlation of neutrophil/lymphocyte ratio with prognostic classification systems in papillary thyroid carcinoma patients
Authors: Yildiz Eren Ozan , Işcen Kutay , Kaya Feyza , Güney Onur Alptekin , Ulukent Suat Can
Published: February 2024

We aimed to evaluate the use of cost-effective NLR (Neutrophil Lymphocyte Ratio) in determining the prognosis and recurrence risk of thyroid papillary carcinoma patients. This retrospective, cross-sectional and single-center study was carried out in the Department of General Surgery, Istanbul Gaziosmanpaşa Training and Research Hospital. Between 2018 and 2021, who were diagnosed with papillary thyroid cancer and underwent total thyroidectomy, and patients who underwent total thyroidectomy due to multinodular goiter were analyzed. For patients in the malignancy group, the NLR cutoff value was determined as 1.73, the sensitivity was calculated as 51.77% and the specificity as 86.15%. NLR in the malignant group was found to be 9.5 times higher than the NLR in the control group (Odds Ratio: 9.5). A statistically significant difference was found between NLR and papillary thyroid carcinoma prognostic classification systems (AJCC/TNM, AMES, and MACIS). NLR medians differ according to ATA recurrence risk classification (P = .020). According to the results we obtained in our study, we believe that cost-effective NLR can be a useful indicator in terms of predicting malignancy in a patient with thyroid nodule and in determining the prognosis and risk of recurrence in patients with thyroid papillary carcinoma.
Comparison between novel zipper device and conventional methods for skin closure: a systematic review and meta-analysis
Authors: Shrestha Oshan , Basukala Sunil , Karki Sagun , Thapa Niranjan , Bhugai Nabaraj , Bohara Sujan , Joshi Niraj , Paudel Sushanta
Published: February 2024

Introduction:

The zipper device is a wound closure device that can be directly applied over the intact skin on either side of the wound edges and does not need anchoring into the skin or subcutaneous plane. The noninvasive nature of the zipper device makes it less time-consuming and less painful, but its effectiveness and related complications need to be studied.

Methods:

Prospective registration of the protocol followed in this study was done. Electronic databases were searched for relevant articles, and their screening was completed, followed by data extraction and analysis. The odds ratio, mean difference, or standardised mean difference were used as an effect measure per the nature of the variables. Surgical site infection, wound dehiscence, skin closure time, scar score, and patient satisfaction were compared in this study.

Results:

A total of 10 studies were identified, out of which eight compared zippers with sutures and two compared zippers with stapler devices. Compared to the suture, the zipper device took 4.9 min less to close the incision, and the scar scale outcome reported after one month was inferior, while other results were not significant. Staples showed a lower patient satisfaction level and no difference in complications.

Conclusion:

The zipper device is a less technically demanding and less time-consuming method of skin closure, with no significant difference in the complication rate compared to conventional methods. The zipper device is an effective measure to use in settings with less expertise or at health institutions after assessing the cost at the local level.
Understanding Factors Influencing Nursing Faculty Departure and Intentions
Authors: Anderson Matthew , Taylor Noelle , Rowley Tom , Owens Chase , Iacob Eli
Published: February 2024

Background:

There is a known shortage of nursing faculty in academia. Understanding factors influencing the shortage will help to develop strategies to reduce it.

Purpose:

The purpose was to identify the underlying factors influencing the decisions of current and former nursing faculty to leave or consider leaving their teaching roles.

Methods:

A cross-sectional state-level survey was distributed to licensed registered nurses and advanced practice registered nurses. The survey covered demographics, employment status, compensation, tenure, mentorship experiences, and significant factors affecting their decision-making.

Results:

Of 496 nursing faculty responses (221 current, 275 former), low compensation, unrealistic workload, retirement, lack of appreciation, and personal/family issues were noted as significant reasons for leaving or considering departure.

Conclusions:

The study gives voice to various factors influencing nursing faculty’s intention to leave and emphasizes the need to address issues of compensation, workload, and mentorship to mitigate faculty shortages.
Post-Intensive Care Sequelae in Pediatrics—Results of an Early Rehabilitation Implementation Study
Authors: Choong Karen , Fraser Douglas D. , Cameron Saoirse , Cuello Carlos , Debigaré Sylvie , Ewusie Joycelyne , Kho Michelle E. , Krasevich Kimberley , Martin Claudio M. , Thabane Lehana , Todt Ashley , Cupido Cynthia ,   on behalf of the Canadian Critical Care Trials Group
Published: February 2024

OBJECTIVES:

To compare post-PICU discharge functioning, health-related quality of life (HRQL), and parental stress before and after the implementation of an early rehabilitation bundle.

DESIGN AND SETTING:

Prospective cohort substudy within an early rehabilitation implementation program, conducted at the PICUs at McMaster Children’s Hospital and London Health Sciences, London, Ontario, Canada.

INTERVENTIONS:

A bundle consisting of: 1) analgesia-first sedation; 2) delirium monitoring and prevention; and 3) early mobilization. Patients with an anticipated 48-hour PICU length of stay were approached for consent to participate.

PATIENTS:

Critically ill children with an anticipated 48-hour PICU length of stay were approached for consent to participate.

MEASUREMENTS AND MAIN RESULTS:

Patient-/proxy-reported outcome measures were assessed at baseline, PICU discharge, and 1 and 3 months post-PICU discharge using: 1) Pediatric Evaluation of Disability Inventory Computer Adaptive Test to assess physical, social, cognitive, and responsibility/caregiver domains of functioning; 2) KIDSCREEN to assess HRQL; and 3) the Pediatric Inventory for Parents to assess caregiver stress. A total of 117 participants were enrolled. Patient demographic characteristics were similar in the pre- and post-intervention groups. Following bundle implementation, 30 of 47 respondents (63.8%) experienced functional decline and 18 of 45 (40%) experienced low HRQL at PICU discharge. Eighteen of 36 (50%) at 1 month and 14 of 38 (36.8%) at 3 months experienced either persistent functional decline and/or low HRQL; 2.8% and 2.6% at 1- and 3-month follow-up, respectively, experienced both persistent functional decline and low HRQL. There were no significant differences in the rates of persistent functional decline, low HRQL, or caregiver stress scores post-bundle compared with pre-rehabilitation bundle implementation.

CONCLUSIONS:

We were unable to adequately determine the efficacy of a rehabilitation bundle on patient-centered outcomes as this substudy was not powered for these outcomes. Our results did reveal that persistent low functioning is common in PICU survivors, more common than low HRQL, while experiencing both functional decline and low HRQL was uncommon.
18F-FDG PET/CT and 99mTc-MDP Bone Scintigraphy Findings of Multifocal Desmoid Fibromatosis
Authors: Filizoglu Nuh , Ozguven Salih , Ones Tunc , Dede Fuat , Erdil Tanju Yusuf
Published: February 2024

Desmoid fibromatosis, also called desmoid tumors, is a group of locally aggressive fibromatous proliferative disorders. They represent less than 3% of all soft tissue sarcoma and are multifocal in approximately 10% of cases. However, there are only a few cases in the literature describing 18F-FDG PET/CT and 99mTc-MDP bone scan features of extra-abdominal desmoid fibromas, and all were solitary bone lesions. Herein, we presented a unique case of multifocal desmoid fibromatosis of bone illustrating the prospective value of 18F-FDG PET/CT and 99mTc-MDP bone scan in the evaluation of desmoid tumors.
Histologic Heterogeneity of Chondrosarcoma Reflected on Bone SPECT/CT
Authors: Choi Woo Hee , Joo Min Wook , Park Hong-Sik
Published: February 2024

Chondrosarcomas are a heterogeneous group of cartilage-forming tumors. The tumor is graded on areas demonstrating the highest grade. A 71-year-old man underwent bone SPECT/CT to investigate a tumorous lesion on his right femur. Correlating with the pathological findings, the high-grade area showed higher uptake in bone SPECT/CT. This case suggests that bone SPECT/CT could aid in selecting an optimal biopsy site for diagnosis, and determining the proper treatment of patients with suspected chondroid tumors.
Cerebellar Ataxia With Neuropathy and Vestibular Areflexia Syndrome Due to Replication Factor C Subunit 1 Gene Repeat Expansion
Authors: Tsuchiya Mitsuteru , Bunai Tomoyasu , Watanabe Kazuki , Saitsu Hirotomo , Goshima Satoshi
Published: February 2024

A 56-year-old man was born to consanguineous parents. He experienced slow-progressing sensory disturbances in the upper extremities. T1-weighted images showed cerebellar atrophy. 123I-IMP SPECT revealed reduced cerebral blood flow in the cerebellum. 123I-FP-CIT SPECT showed low uptake of dopamine transporter in the bilateral tail of the striatum. 123I-MIBG scintigraphy shows a decreased heart-to-mediastinum ratio. Flanking polymerase chain reaction suggested biallelic repeat expansion in intron 2 of RFC1, and subsequent repeat-primed polymerase chain reaction revealed ACAGG repeat expansion. Thus, he was diagnosed as cerebellar ataxia with neuropathy and vestibular areflexia syndrome.
Identification of Antibodies to DQβ:DRα Interisotypic Heterodimers in Human Sera
Authors: Nong Thoa , Shih Nengjen Remi , Bray Robert A. , Lopez-Cepero Mayra , Murphey Cathi , Nickerson Peter W. , Lee Jar-How
Published: February 2024

Background.

HLA class II antigens, DR, DQ, and DP, comprised an α and β chains, which typically combine, within the same isotype, to form the major histocompatibility complex:peptide complex. Interisotypic pairing is not commonly observed. Although reports of DQβ:DRα heterodimers exist, the pairing was reported to be unstable and, therefore, not studied to any extent.

Methods.

DQβ:DRα single antigens were produced through transfectant cell lines and used to identify and characterize positive reactive human sera by a multiplex bead-based assay.

Results.

Stable DQβ:DRα transfectants were constructed. Cell surface staining with class II–specific monoclonal antibodies revealed that some DQB1 alleles appear to be more efficient in expressing DQβ:DRα heterodimers. Interestingly, alleles within the same serological group varied in their efficiency of forming dimers on the cell surface. For example, DQβ0601:DRα had the highest transfection and cell membrane expression efficiency among 16 common DQB1 alleles tested. In contrast, DQβ0603:DRα-positive transfectants demonstrated minimal surface expression. Assembly of DQβ0601:DRα was not affected by the presence of a DQα chain. DQβ0601:DRα and DQβ0603:DRα single-antigen beads were used to screen human sera. Positive sera were identified that reacted to the unique epitopes of DQβ0601:DRα protein on the cell surface of the transfectants.

Conclusions.

Our studies have demonstrated that unique DQβ:DRα heterodimers can be formed and are stably expressed on the cell surface. Such antigenic combinations, presented on single-antigen beads, demonstrated that patient sera can react with such heterodimers. Investigations on the potential clinical roles of antibodies against such interisotypic heterodimers are now possible.
Effects of motion type on motion-onset and steady-state visual evoked potentials: rotation vs. flicker
Authors: Yu BingBing , Sui Li
Published: February 2024

The underlying mechanisms of information processing for two basic motion types, rotation and flicker, are not fully understood. Rotational and flickering animations at four speeds – 7 frames per second (fps), 8 fps, 11 fps, and 12 fps, respectively – are presented as visual stimuli. The motion-onset visual evoked potentials (VEPs) and steady-state VEPs (SSVEP) elicited by these motion stimuli were compared between the rotation and flicker motion types at time windows of 0–500 ms and 1000–5000 ms post-stimulus, respectively. The standardized low-resolution electromagnetic tomography (sLORETA) source localization was investigated as well. Four motion speeds had no effect on the whole VEP waveform in either the rotation or the flicker groups. Significant differences in motion-onset VEPs and sLORETA source localization were found between the rotation and the flicker motion types at time windows of 200–500 ms post-stimulus. For the time windows of 1000–5000 ms post-stimulus, both the rotation and flicker groups all demonstrated the characteristics of SSVEP, with the peak spectral topographies showing at the four different frequencies, which correspond to the four motion speeds. Additionally, a higher power of spectral topography at each of the four motion speeds was found in the rotation relative to the flicker stimulation. The perceptual and cognitive processes are distinct for two types of motion: rotation and flicker. In terms of motion-onset VEPs and the characteristics of SSVEP, rotating visual stimulation is superior to flicker stimulation and may be more appropriate for clinical and engineering applications.
GSK-3β inhibitor TWS119 promotes neuronal differentiation after hypoxic-ischemic brain damage in neonatal rats
Authors: Gao Limin , Gao Shuqiang , Shan Hailei , Wu Yanqiu , Zhou Qili
Published: February 2024

Brain injury in preterm infants is a major cause of disability and mortality in children. GSK-3β is a common pathogenic factor for cognitive dysfunction and involves in neuronal proliferation and differentiation. However, GSK-3β affected neuronal differentiation and its molecular pathogenesis after hypoxic-ischemic brain damage in neonatal rats remains unclear. This study investigated the effects of GSK-3β inhibitor (TWS119) on cell cycle regulatory proteins, a neuronal differentiation factor (CEND1), maturation neurons, T-box brain transcription factor 1 (TBR1)-positive neurons to clarify the mechanisms of hypoxic-ischemic brain damage in neonatal rats. We used hypoxic-ischemic Sprague–Dawley neonatal rats with brain damage as models. These rats were used for investigating the effect of GSK-3β on cell cycle regulatory proteins, neuronal differentiation factor (CEND1), maturation neurons, TBR1-positive neurons by western blot and immunofluorescence. Cyclin D1 (a positive cell cycle regulator) expression decreased, and p21 (a negative cell cycle regulator) expression increased in the TWS119 group compared to the hypoxia-ischemia (HI) group 7 days after HI. Additionally, compared to the HI group, TWS119 treatment up-regulated CEND1 expression and promoted neuronal differentiation and cortex development based on NeuN and TBR1 expression. Our study suggests that the GSK-3β inhibitor TWS119 promotes neuronal differentiation after hypoxic-ischemic brain damage in neonatal rats by inhibiting cell cycle pathway.
Description of Chryseobacterium fluminis sp. nov., a keratinolytic bacterium isolated from a freshwater river
Authors: Kim Moonsoo , Oh Eun Tak , Kim Seung Bum
Published: February 2024

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated MMS21-Ot14T, was isolated from a freshwater river, and shown to represent a novel species of the genus Chryseobacterium on the basis of the results from a polyphasic approach. The 16S rRNA gene sequence analysis revealed that MMS21-Ot14T represented a member of the genus Chryseobacterium of the family Weeksellaceae and was closely related to Chryseobacterium hagamense RHA2-9T (97.52 % sequence similarity), Chryseobacterium gwangjuense THG A18T (97.46 %) and Chryseobacterium gregarium P 461/12T (97.27 %). The optimal growth of MMS21-Ot14T occurred at 25–30 °C, pH 6.0–7.0 and in the absence of NaCl. MMS21-Ot14T was capable of hydrolysing casein, starch, DNA, Tween 20 and tyrosine. The strain also showed keratinolytic activity with keratin azure and decolourising activity with remazol brilliant blue R (RBBR), which indicated potential ability to degrade keratin and lignin. The main polar lipids of MMS21-Ot14T were phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, an unidentified phospholipid and several unidentified lipids. The predominant fatty acids of MMS21-Ot14T were iso-C15 : 0 and iso-C17 : 0 3-OH, and the major isoprenoid quinone was menaquinone 6 (MK-6). The whole genome of MMS21-Ot14T was 5 062 016 bp in length with a DNA G+C content of 37.7 %. The average nucleotide identity and digital DNA–DNA hybridisation values between MMS21-Ot14T and phylogenetically related members of the genus Chryseobacterium were well below the threshold values for species delineation. It is evident from the results of this study that MMS21-Ot14T should be classified as representing a novel species of the genus Chryseobacterium, for which the name Chryseobacterium fluminis sp. nov. (type strain, MMS21-Ot14T = KCTC 92255T = LMG 32529T) is proposed.
Visualizing the impact of disease-associated mutations on G protein–nucleotide interactions
Authors: Anazia Kara , Koenekoop Lucien , Ferré Guillaume , Petracco Enzo , Gutiérrez-de-Teran Hugo , Eddy Matthew T.
Published: February 2024

Activation of G proteins stimulates ubiquitous intracellular signaling cascades essential for life processes. Under normal physiological conditions, nucleotide exchange is initiated upon the formation of complexes between a G protein and G protein-coupled receptor (GPCR), which facilitates exchange of bound GDP for GTP, subsequently dissociating the trimeric G protein into its Gα and Gβγ subunits. However, single point mutations in Gα circumvent nucleotide exchange regulated by GPCR–G protein interactions, leading to either loss-of-function or constitutive gain-of-function. Mutations in several Gα subtypes are closely linked to the development of multiple diseases, including several intractable cancers. We leveraged an integrative spectroscopic and computational approach to investigate the mechanisms by which seven of the most frequently observed clinically-relevant mutations in the α subunit of the stimulatory G protein result in functional changes. Variable temperature circular dichroism (CD) spectroscopy showed a bimodal distribution of thermal melting temperatures across all GαSvariants. Modeling from molecular dynamics (MD) simulations established a correlation between observed thermal melting temperatures and structural changes caused by the mutations. Concurrently, saturation-transfer difference NMR (STD– NMR) highlighted variations in the interactions of GαSvariants with bound nucleotides. MD simulations indicated that changes in local interactions within the nucleotide-binding pocket did not consistently align with global structural changes. This collective evidence suggests a multifaceted energy landscape, wherein each mutation may introduce distinct perturbations to the nucleotide-binding site and protein-protein interaction sites. Consequently, it underscores the importance of tailoring therapeutic strategies to address the unique challenges posed by individual mutations.
Cefiderocol heteroresistance associated with mutations in TonB-dependent receptor genes inPseudomonas aeruginosaof clinical origin
Authors: Egge Stephanie L. , Rizvi Samie A. , Simar Shelby R. , Alcalde Manuel , Martinez Jose R.W. , Hanson Blake M. , Dinh An Q. , Baptista Rodrigo P. , Tran Truc T. , Shelburne Samuel A. , Munita Jose M. , Arias Cesar A. , Hakki Morgan , Miller William R.
Published: February 2024

The siderophore-cephalosporin cefiderocol(FDC) presents a promising treatment option for carbapenem-resistant (CR)P. aeruginosa(PA). FDC circumvents traditional porin and efflux mediated resistance by utilizing TonB-dependent receptors (TBDRs) to access the periplasmic space. Emerging FDC resistance has been associated with loss of function mutations within TBDR genes or the regulatory genes controlling TBDR expression. Further, difficulties with antimicrobial susceptibility testing (AST) and unexpected negative clinical treatment outcomes have prompted concerns for heteroresistance, where a single lineage isolate contains resistant subpopulations not detectable by standard AST. This study aimed to evaluate the prevalence of TBDR mutations among clinical isolates ofP. aeruginosaand the phenotypic effect on FDC susceptibility and heteroresistance. We evaluated the sequence ofpirR,pirS,pirA,piuAorpiuDfrom 498 unique isolates collected before the introduction of FDC from 4 clinical sites in Portland, OR (1), Houston, TX (2), and Santiago, Chile (1). At some clinical sites, TBDR mutations were seen in up to 25% of isolates, and insertion, deletion, or frameshift mutations were predicted to impair protein function were seen in 3% of all isolates (n=15). Using population analysis profile testing, we found thatP. aeruginosawith major TBDR mutations were enriched for a heteroresistant phenotype and undergo a shift in the susceptibility distribution of the population as compared to susceptible strains with wild type TBDR genes. Our results indicate that mutations in TBDR genes predate the clinical introduction of FDC, and these mutations may predispose to the emergence of FDC resistance.
Stratification of viral shedding patterns in saliva of COVID-19 patients
Authors: Park Hyeongki , Yoshimura Raiki , Iwanami Shoya , Kim Kwang Su , Ejima Keisuke , Nakamura Naotoshi , Aihara Kazuyuki , Miyazaki Yoshitsugu , Umeyama Takashi , Miyazawa Ken , Morita Takeshi , Watashi Koichi , Brooke Christopher B. , Ke Ruian , Iwami Shingo , Miyazaki Taiga
Published: February 2024

Living with COVID-19 requires continued vigilance against the spread and emergence of variants of concern (VOCs). Rapid and accurate saliva diagnostic testing, alongside basic public health responses, is a viable option contributing to effective transmission control. Nevertheless, our knowledge regarding the dynamics of SARS-CoV-2 infection in saliva is not as advanced as our understanding of the respiratory tract. Here we analyzed longitudinal viral load data of SARS-CoV-2 in saliva samples from 144 patients with mild COVID-19 (a combination of our collected data and published data). Using a mathematical model, we successfully stratified infection dynamics into three distinct groups with clear patterns of viral shedding: viral shedding durations in the three groups were 11.5 days (95% CI: 10.6 to 12.4), 17.4 days (16.6 to 18.2), and 30.0 days (28.1 to 31.8), respectively. Surprisingly, this stratified grouping remained unexplained despite our analysis of 47 types of clinical data, including basic demographic information, clinical symptoms, results of blood tests, and vital signs. Additionally, we quantified the expression levels of 92 micro-RNAs in a subset of saliva samples, but these also failed to explain the observed stratification, although the mir-1846 level may have been weakly correlated with peak viral load. Our study provides insights into SARS-CoV-2 infection dynamics in saliva, highlighting the challenges in predicting the duration of viral shedding without indicators that directly reflect an individual’s immune response, such as antibody induction. Given the significant individual heterogeneity in the kinetics of saliva viral shedding, identifying biomarker(s) for viral shedding patterns will be crucial for improving public health interventions in the era of living with COVID-19.
Systematic characterization of protein structural features of alternative splicing isoforms using AlphaFold 2
Authors: Yang Yuntao , Xie Yuhan , Li Zhao , Diala Chiamaka , Ali Meer , Li Rongbin , Xu Yi , Wu Albon , Kim Pora , Hosseini Sayed-Rzgar , Bi Erfei , Zhao Hongyu , Zheng W. Jim
Published: February 2024

Alternative splicing is an important cellular process in eukaryotes, altering pre-mRNA to yield multiple protein isoforms from a single gene. However, our understanding of the impact of alternative splicing events on protein structures is currently constrained by a lack of sufficient protein structural data. To address this limitation, we employed AlphaFold 2, a cutting-edge protein structure prediction tool, to conduct a comprehensive analysis of alternative splicing for approximately 3,000 human genes, providing valuable insights into its impact on the protein structural. Our investigation employed state of the art high-performance computing infrastructure to systematically characterize structural features in alternatively spliced regions and identified changes in protein structure following alternative splicing events. Notably, we found that alternative splicing tends to alter the structure of residues primarily located in coils and beta-sheets. Our research highlighted a significant enrichment of loops and highly exposed residues within human alternatively spliced regions. Specifically, our examination of the Septin-9 protein revealed potential associations between loops and alternative splicing, providing insights into its evolutionary role. Furthermore, our analysis uncovered two missense mutations in the Tau protein that could influence alternative splicing, potentially contributing to the pathogenesis of Alzheimer's disease. In summary, our work, through a thorough statistical analysis of extensive protein structural data, sheds new light on the intricate relationship between alternative splicing, evolution, and human disease.
Distinct platelet interactions with soluble and immobilized von Willebrand factor modulate platelet adhesion and aggregation with differential impact on hemostasis and thrombosis
Authors: Chen Yunfeng , Ruggeri Zaverio M.
Published: February 2024

Arterial thrombosis is a prevailing and lethal pathological condition that remains difficult to treat or prevent without potentially serious side effects, mostly hemorrhagic in nature. Platelets and von Willebrand factor (VWF) have a recognized major role in the pathogenesis of arterial thrombosis. Platelets bind to surface immobilized VWF for initial adhesion to injured vascular sites, but also interact with soluble VWF to aggregate into thrombi, particularly under flow conditions creating elevated shear stress. Whether the binding of immobilized and soluble VWF to platelets is regulated by separate mechanisms and how they respectively regulate hemostasis and thrombosis remains unclear. Using targeted mutagenesis we engineered VWF to achieve modified binding kinetics with the platelet receptor glycoprotein (GP) Ibα and discovered that the interactions of immobilized and soluble VWF with platelets can be differentially regulated with distinct consequences on platelet adhesion and aggregation. Based on these results, we studied a monoclonal antibody, NMC4, known to bind to an epitope in the VWFA1 domain and to inhibit preferentially platelet aggregation under elevated shear stress conditions. We found that NMC4 was less efficient in reducing platelet adhesion to immobilized VWF than platelet aggregation mediated by soluble VWF and, surprisingly, also inhibited arterial thrombosis in a mouse model of ferric chloride-induced carotid artery occlusion at a dose that failed to prolong post-injury bleeding. Thus, our current findings help delineate interrelated biochemical and biophysical mechanisms underlying VWF function in vascular health; and suggest selective inhibition of VWF-mediated platelet aggregation as opposed to adhesion as a strategy to prevent arterial thrombosis while minimizing bleeding complications.
nanoBERT: A deep learning model for gene agnostic navigation of the nanobody mutational space
Authors: Hadsund Johannes Thorling , Satława Tadeusz , Janusz Bartosz , Shan Lu , Zhou Li , Röttger Richard , Krawczyk Konrad
Published: February 2024

Nanobodies are a subclass of immunoglobulins, whose binding site consists of only one peptide chain, bestowing favorable biophysical properties. Recently, the first nanobody therapy was approved, paving the way for further clinical applications of this antibody format. Further development of nanobody-based therapeutics could be streamlined by computational methods. One of such methods is infilling - positional prediction of biologically feasible mutations in nanobodies. Being able to identify possible positional substitutions based on sequence context, facilitates functional design of such molecules. Here we present nanoBERT, a nanobody-specific transformer to predict amino acids in a given position in a query sequence. We demonstrate the need to develop such machine-learning based protocol as opposed to gene-specific positional statistics since appropriate genetic reference is not available. We benchmark nanoBERT with respect to human-based language models and ESM-2, demonstrating the benefit for domain-specific language models. We also demonstrate the benefit of employing nanobody-specific predictions for fine-tuning on experimentally measured thermostability dataset. We hope that nanoBERT will help engineers in a range of predictive tasks for designing therapeutic nanobodies.

Availability

https://huggingface.co/NaturalAntibody/
GlycansToGraphs: visualizing and simplifying complex mass spectra
Authors: Bonner R. , Jacquet C. , Hopfgartner G.
Published: February 2024

1.

We describe a software tool, GlycansToGraphs, used to identify and visualize relationships between masses in MS or MS/MS spectra and illustrate its application to data dependent acquisition (DDA) spectra of glycopeptides. The software is written in python 3.11 and uses the ‘streamlit’ package (1.29) to generate a User Interface (UI) in a web browser. It uses simple text input files, does not require databases (glycan or protein) and the user can define any mass difference that the software searches for in an unbiased manner. Located mass differences generate graphs with edges that correspond to the relationships between nodes (masses) and collections of connected nodes, known as components, which can be analyzed to extract sequences of relationships.
EcoLiDAR: An economical LiDAR scanner for ecological research
Authors: Mendes Calebe Pereira , Lim Norman T-Lon
Published: February 2024

Despite recent popularization and widespread use in modern electronic devices, LiDAR technology remains expensive for research purposes, in part due to the very high performance offered by commercially available LiDAR scanners. However, such high performance is not always needed, and the expensive price ends up making LiDAR scanners inaccessible for research projects with reduced budget, such as those in developing countries. Here we designed and built a simple ground-based LiDAR scanner, with performance sufficient to fulfil the requirements for a variety of ecological research projects, while being cheap and easy to build. We managed to assemble a LiDAR scanner under 400 USD (as of 2021), and it is simple enough to be built by personnel with minimal engineering background. We also demonstrated the quality of the resulting point clouds by scanning a test site and producing some common LiDAR products. Although not adequate for mapping large area due to its limited range, our LiDAR design is open, customizable, and can produce adequate results while costing ∼1% of “low-cost” scanners available in the market. As such, our LiDAR scanner opens a world of new opportunities, particularly for projects in developing countries.
Impact of extended Elexacaftor/Tezacaftor/Ivacaftor therapy on the gut microbiome in cystic fibrosis
Authors: Marsh Ryan , Dos Santos Claudio , Yule Alexander , Dellschaft Neele S , Hoad Caroline L , Ng Christabella , Major Giles , Smyth Alan R , Rivett Damian , van der Gast Christopher
Published: February 2024

Background

There is a paucity of knowledge on the longer-term effects of CF transmembrane conductance regulator (CFTR) modulator therapies upon the gut microbiome and associated outcomes. In a pilot study, we investigated longitudinal Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy on the gut microbiota, metabolomic functioning, and clinical outcomes in people with CF (pwCF).

Study design

Faecal samples from 20 pwCF were acquired before and then following 3, 6, and 17+ months of ETI therapy. Samples were subjected to microbiota sequencing and targeted metabolomics to profile and quantify short-chain fatty acid composition. Ten healthy matched controls were included for comparison. Clinical data, including markers of intestinal function were integrated to investigate relationships.

Results

Extended ETI therapy increased core microbiota diversity and composition, which translated to gradual shifts in whole microbiota composition towards that observed in healthy controls. Despite becoming more similar over time, CF microbiota and functional metabolite compositions remained significantly different to healthy controls. Antibiotic treatment for pulmonary infection significantly explained a relatively large degree of variation within the whole microbiota and rarer satellite taxa. Clinical outcomes were not significantly different following ETI.

Conclusions

A positive trajectory towards the microbiota observed in healthy controls was found. However, we posit that progression was predominately impeded by pulmonary antibiotics administration. We recommend future studies use integrated omics approaches within a combination of long-term longitudinal patient studies and model experimental systems. This will deepen our understanding of the impacts of CFTR modulator therapy and respiratory antibiotic interventions upon the gut microbiome and gastrointestinal pathophysiology in CF.
Biogenesis of cytochromescandc1in the electron transport chain of malaria parasites
Authors: García-Guerrero Aldo E. , Marvin Rebecca G. , Blackwell Amanda Mixon , Sigala Paul A.
Published: February 2024

Plasmodiummalaria parasites retain an essential mitochondrional electron transport chain (ETC) that is critical for growth within humans and mosquitoes and a key antimalarial drug target. ETC function requires cytochromescandc1that are unusual among heme proteins due to their covalent binding to heme via conserved CXXCH sequence motifs. Heme attachment to these proteins in most eukaryotes requires the mitochondrial enzyme holocytochromecsynthase (HCCS) that binds heme and the apo cytochrome to facilitate biogenesis of the mature cytochromecorc1. Although humans encode a single bifunctional HCCS that attaches heme to both proteins,Plasmodiumparasites are like yeast and encode two separate HCCS homologs thought to be specific for heme attachment to cytc(HCCS) or cytc1(HCC1S). To test the function and specificity ofP. falciparumHCCS and HCC1S, we used CRISPR/Cas9 to tag both genes for conditional expression. HCC1S knockdown selectively impaired cytc1biogenesis and caused lethal ETC dysfunction that was not reversed by over-expression of HCCS. Knockdown of HCCS caused a more modest growth defect but strongly sensitized parasites to mitochondrial depolarization by proguanil, revealing key defects in ETC function. These results and prior heterologous studies inE. coliof cytchemylation byP. falciparumHCCS and HCC1S strongly suggest that both homologs are essential for mitochondrial ETC function and have distinct specificities for biogenesis of cytcandc1, respectively, in parasites. This study lays a foundation to develop novel strategies to selectively block ETC function in malaria parasites.
Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes
Authors: Chen Xi Dawn , Chen Zeyu , Wythes George , Zhang Yifan , Orr Benno C. , Sun Gary , Thao Ka , Vallurupalli Mounica , Sun Jing , Borji Mehdi , Tkacik Emre , Chen Haiqi , Bernstein Bradley E. , Chen Fei
Published: February 2024

A major challenge in human genomics is to decipher the context specific relationship of sequence to function. However, existing tools for locus specific hypermutation and evolution in the native genome context are limited. Here we present a novel programmable platform for long-range, locus-specific hypermutation called helicase-assisted continuous editing (HACE). HACE leverages CRISPR-Cas9 to target a processive helicase-deaminase fusion that incurs mutations across large (>1000 bp) genomic intervals. We applied HACE to identify mutations in MEK1 that confer kinase inhibitor resistance, to dissect the impact of individual variants in SF3B1-dependent mis-splicing, and to evaluate noncoding variants in a stimulation-dependent immune enhancer of CD69. HACE provides a powerful tool for investigating coding and noncoding variants, uncovering combinatorial sequence-to-function relationships, and evolving new biological functions.

One Sentence Summary

We developed a tool for continuous, long-range, targeted diversification of endogenous mammalian genomes and used it to explore the function of genetic variants in both coding and non-coding regions.
Loss of CLN3 in microglia leads to impaired lipid metabolism and myelin turnover
Authors: Yasa Seda , Butz Elisabeth S. , Colombo Alessio , Chandrachud Uma , Montore Luca , Sheridan Steven D. , Müller Stephan A. , Lichtenthaler Stefan F. , Tahirovic Sabina , Cotman Susan L.
Published: February 2024

Background

Microglia are the primary brain cell type regulating neuroinflammation and they are important for healthy aging. Genes regulating microglial function are associated with an increased risk of neurodegenerative disease. Loss-of-function mutations inCLN3, which encodes an endolysosomal membrane protein, lead to the most common childhood-onset form of neurodegeneration, featuring early-stage neuroinflammation that long precedes neuronal cell loss. How loss of CLN3 function leads to this early neuroinflammation is not yet understood.

Methods

Here, we have comprehensively studied microglia fromCln3Δex7/8mice, a genetically accurate CLN3 disease model. Microglia were isolated from young and oldCln3Δex7/8mice for downstream molecular and functional studies.

Results

We show that loss of CLN3 function in microglia leads to classic age-dependent CLN3-disease lysosomal storage as well as an altered morphology of the lysosome, mitochonodria and Golgi compartments. Consistent with these morphological alterations, we also discovered pathological proteomic signatures implicating defects in lysosomal function and lipid metabolism processes at an early disease stage. CLN3-deficient microglia were unable to efficiently turnover myelin and metabolize its associated lipids, showing severe defects in lipid droplet formation and significant accumulation of cholesterol, phenotypes that were corrected by treatment with autophagy inducers and cholesterol lowering drugs. Finally, we observed reduced myelination in aging homozygousCln3Δex7/8mice suggesting altered myelin turnover by microglia impacts myelination in the CLN3-deficient brain.

Conclusion

Our results implicate a cell autonomous defect in CLN3-deficient microglia that impacts the ability of these cells to support neuronal cell health. These results strongly suggest microglial targeted therapies should be considered for CLN3 disease.
A Retrospective Analysis of Career Outcomes in Neuroscience
Authors: Ullrich Lauren E. , Ogawa John R. , Jones-London Michelle D.
Published: February 2024

What factors are associated with different career outcomes among biomedical PhDs? Much of the research to-date has focused on drivers of interest in (and intention to pursue) various careers, especially during graduate school, but fewer studies have investigated the ultimate career outcomes of participants. Even less is known about what factors matter most for groups historically underrepresented in the US STEM workforce, such as for women, some racial and ethnic groups, and persons with disabilities (National Center for Science and Engineering Statistics (NCSES), 2021a). This study reports a new analysis of data from 781 PhD neuroscientists that were obtained from a retrospective survey (reported in Ullrich et al. (2021)) to investigate the factors that influence the career sector in which neuroscience PhDs are employed, and whether there were group differences according to social identity. We find evidence of academia as a “default path” for incoming PhD students, but interest in different careers changes gradually over time. Those who remained in academia had greater acceptance of the structural aspects of academic careers, such as the promotion and tenure process, and greater faculty support during their postdoctoral training. Conversely, prioritizing monetary compensation and wanting varied work were associated with not being in academia, while a strong interest in research was positively associated with being in non-academic research. Somewhat surprisingly, there were few interactions with gender, and no interactions with underrepresentation status. Our findings also underscore the role of advisors, networking, and personal relationships in securing employment in STEM.
Restricted intake of sulfur-containing amino acids reversed the hepatic injury induced by excessDesulfovibriothrough gut-liver axis
Authors: Zhou Lingxi , Lu Gexue , Nie Yawen , Ren Yilin , Shi Jin-Song , Xue Yuzheng , Xu Zheng-Hong , Geng Yan
Published: February 2024

Gut-liver axis has been a study focus for liver diseases. Diet is a key player in influencing the gut microbiota. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used mouse standard chow and purified diet to mimic two common human dietary patterns: healthy grain and planted-based diet and Western style diet, respectively and explored their impacts on the gut microbiota and liver. Gut microbiota experienced a great shift with notable increase inDesulfovibrio, gut bile acid (BA) concentration elevated significantly, and liver inflammation was observed in mice fed with the purified diet. Liver inflammation due to translocation of toxic lipopolysaccharides (LPS) and hydrophobic BAs from the damaged gut barrier was also observed in mice fed with the chow diet after receivingDesulfovibrio desulfuricansATCC 29577 (DSV). Restricted intake of sulfur-containing amino acids reversed the liver injury due to excessDesulfovibriothrough lowering the gut BA concentration and enhancing the hepatic antioxidant and detoxifying ability.Ex vivofermentation of human fecal microbiota with primary BAs also demonstrated that DSV enhanced production of secondary BAs. Germ-free mice had higher concentration of both conjugated and unconjugated primary BAs in their gut after receiving DSV.
Bio-orthogonal Glycan Imaging of Culture Cells and Whole AnimalC. eleganswith Expansion Microscopy
Authors: Kuo Joe Chin-Hun , Colville Marshall J. , Sorkin Michelle R. , Kuo Jacky Lok Ka , Huang Ling Ting , Thornlow Dana N. , Beacham Gwendolyn M. , Hollopeter Gunther , DeLisa Matthew P. , Alabi Christopher A. , Paszek Matthew J.
Published: February 2024

Complex carbohydrates called glycans play crucial roles in the regulation of cell and tissue physiology, but how glycans map to nanoscale anatomical features must still be resolved. Here, we present the first nanoscale map of mucin-typeO-glycans throughout the entirety of theCaenorhabditis elegansmodel organism. We construct a library of multifunctional linkers to probe and anchor metabolically labelled glycans in expansion microscopy (ExM), an imaging modality that overcomes the diffraction limit of conventional optical microscopes through the physical expansion of samples embedded in a polyelectrolyte gel matrix. A flexible strategy is demonstrated for the chemical synthesis of linkers with a broad inventory of bio-orthogonal functional groups, fluorophores, anchorage chemistries, and linker arms. EmployingC. elegansas a test bed, we resolve metabolically labelledO-glycans on the gut microvilli and other nanoscale anatomical features using our ExM reagents and optimized protocols. We use transmission electron microscopy images ofC. elegansnano-anatomy as ground truth data to validate the fidelity and isotropy of gel expansion. We construct whole organism maps ofC. elegans O-glycosylation in the first larval stage and identifyO-glycan “hotspots” in unexpected anatomical locations, including the body wall furrows. BeyondC. elegans, we provide validated ExM protocols for nanoscale imaging of metabolically labelled glycans on cultured mammalian cells. Together, our results suggest the broad applicability of the multifunctional reagents for imaging glycans and other metabolically labelled biomolecules at enhanced resolutions with ExM.

Graphical abstract