bluuebunny/crossref_metadata_2025 huggingface dataset:
Outcomes of Pre-Descemet Endothelial Keratoplasty for Failed Therapeutic Penetrating Keratoplasty
Authors: Narang Priya , Ashok Kumar Dhivya , Narang Rhea , Agarwal Amar
Published: September 2023

Purpose:

The aim of this study was to analyze the outcomes of pre-Descemet endothelial keratoplasty (PDEK) for failed therapeutic penetrating keratoplasty.

Methods:

This was a retrospective, interventional study that involved 12 eyes of 12 patients with failed therapeutic penetrating keratoplasty that underwent PDEK. All cases had a minimum follow-up of 12 months. The main outcome measures were best-corrected visual acuity, graft clarity, endothelial cell density loss, and graft survival. Corneal clarity was graded on a scale from 0 to 4, where grade 4 denoted an absolutely clear cornea and grade 0 denoted a totally opaque cornea. Three cases underwent PDEK, 6 cases PDEK with phacoemulsification, and 3 cases underwent PDEK with pupilloplasty.

Results:

The mean follow-up period for all cases was 18.5 ± 4.9 months. The mean preoperative and postoperative best-corrected visual acuity (in Snellen decimal equivalent) was 0.02 ± 0.01 and 0.54 ± 0.17, respectively, at the last follow-up. Postoperatively, corneal clarity grade 4 was present in 9 eyes, grade 3 in 2 eyes, and grade 2 in 1 eye. Mild subepithelial haze was noted in 2 eyes. The percentage of endothelial cell density loss was 28.2% ± 10.6%. No correlation was observed between the postoperative graft clarity and preoperative specular count (r = −0.021, P = 0.512). Rebubbling was performed for 1 eye that developed partial graft detachment in the first postoperative week. One patient had an episode of rejection that was managed with systemic and topical steroids.

Conclusions:

In patients with failed therapeutic penetrating keratoplasty, PDEK can be a useful alternative for visual rehabilitation as it demonstrates favorable visual outcomes with a good graft survival rate.
Toxidrome of an Easily Obtainable Nootropic
Authors: Martin Robin , Buffenstein Ilana , Cho Daniel , Kiyokawa Miki
Published: September 2023

Purpose/Background

Phenibut (4-amino-3-phenyl-butyric acid) is a structural analog of GABA with central nervous system depressant and anxiolytic properties, developed in the former Soviet Union for anxiety, insomnia, and alcohol withdrawal. Its primary mechanism of action is believed to be a GABA-B receptor agonist—with high affinity at the α2δ subunit-containing voltage-dependent calcium channels and therefore gabapentinoid activity—as well as, to a lesser extent, GABA-A agonist activity. While not approved or regulated by the FDA, phenibut is easily obtainable online, where it is marketed as a nootropic, or cognitive enhancer. However, phenibut can lead to problems related to intoxication, dependency, and withdrawal, similar to other sedatives.

Methods/Procedures

We present a case of phenibut intoxication and withdrawal delirium that provided diagnostic and management challenges because of a patient that was initially not forthcoming about his phenibut use which resulted in five presentations to the hospital including two admissions.

Findings/Results

Initial differential including adrenergic, serotonergic or anticholinergic toxidrome based on clinical picture and history reported at that time, however phenibut use of 50 g daily was eventually revealed, an amount exceeding the highest reported cases in our review of the English literature.

Implications/Conclusions

High-dose phenibut intoxication and withdrawal can appear as dramatic and dangerous as high-dose sedative withdrawal, however given its specified receptor affinity and binding profile we found that a pharmacotherapeutic approach targeting GABA-B, GABA-A, and gabapentenoid receptors were effective in stabilizing this patient, eventually leading to the patient's full and sustained recovery.
Comparing Longitudinal Measures of Cholinesterase as Biomarkers for Insecticide Exposure Among Latinx Children in Rural Farmworker and Urban Nonfarmworker Communities in North Carolina
Authors: Quandt Sara A. , Smith Sydney A. , Arcury Thomas A. , Chen Haiying , Hester Kirstin , Pope Carey N. , Anderson Kim A. , Laurienti Paul J.
Published: September 2023

Objective

In a 2-group prospective design, this study compared seasonal cholinesterase levels of Latinx children in rural farmworker families and comparable urban children to assess the impact of environmental exposure to cholinesterase-inhibiting insecticides.

Methods

Quarterly blood samples and passive dosimeter wristbands were collected over 2 years in 8-year-old children (74 rural, 62 urban). Laboratory analysis assessed total cholinesterase, acetylcholinesterase, and butyrylcholinesterase from blood samples, and insecticides from wristbands.

Results

In spring and summer, total cholinesterase and acetylcholinesterase levels were depressed in rural children compared with winter and fall. Butyrylcholinesterase was depressed in rural children in fall compared with spring and summer. Adjustment for insecticide exposure did not affect these associations.

Conclusions

Environmental exposures to cholinesterase-inhibiting insecticides have measurable biochemical effects on blood cholinesterases in rural children from farmworker families.
Artificial intelligence-based prediction of molecular and genetic markers for hepatitis C–related hepatocellular carcinoma
Authors: Colak Cemil , Kucukakcali Zeynep , Akbulut Sami
Published: September 2023

Background:

Hepatocellular carcinoma (HCC) is the main cause of mortality from cancer globally. This paper intends to classify public gene expression data of patients with Hepatitis C virus-related HCC (HCV+HCC) and chronic HCV without HCC (HCV alone) through the XGboost approach and to identify key genes that may be responsible for HCC.

Methods:

The current research is a retrospective case–control study. Public data from 17 patients with HCV+HCC and 35 patients with HCV-alone samples were used in this study. An XGboost model was established for the classification by 10-fold cross-validation. Accuracy (AC), balanced accuracy (BAC), sensitivity, specificity, positive predictive value, negative predictive value, and F1 score were utilized for performance assessment.

Results:

AC, BAC, sensitivity, specificity, positive predictive value, negative predictive value, and F1 scores from the XGboost model were 98.1, 97.1, 100, 94.1, 97.2, 100, and 98.6%, respectively. According to the variable importance values from the XGboost, the HAO2, TOMM20, GPC3, and PSMB4 genes can be considered potential biomarkers for HCV-related HCC.

Conclusion:

A machine learning-based prediction method discovered genes that potentially serve as biomarkers for HCV-related HCC. After clinical confirmation of the acquired genes in the following medical study, their therapeutic use can be established. Additionally, more detailed clinical works are needed to substantiate the significant conclusions in the current study.
Self-esteem and optimism in patients with major depression disorder: a cross-sectional study
Authors: Yavari Saeed , Radfar Moloud , Faraji Navid , Goli Rasoul , Bagherzadi Aynaz , Atharifar Reza , Kazemi Sahar , Dadashi Maryam
Published: September 2023

Background:

Depressive disorders are common mental illnesses characterized by persistent feelings of sadness, hopelessness, and loss of interest in activities. Self-esteem refers to the appraisal of one’s worth and personality, whereas optimism reflects a positive attitude and the expectation of positive outcomes. Therefore, the present study aims to determine the average self-esteem and optimism of patients with depression in 2022.

Methods:

The present study is a single center and prospective descriptive-analytical study in which 121 patients out of 154 participants with major depression using convenience sampling were studied. Recruitment started on 10 June 2022 and ended on 12 July 2022. Data were collected using a demographic questionnaire, the Rosenberg Self-Esteem Scale (RSES), and the Revised Life Orientation Test (LOT -R). Data analysis was performed using statistical tests and the Pearson correlation coefficient with SPSS software version 21.

Results:

The mean and SD of patients’ self-esteem scores were 14.68±1.30, and the mean and SD for optimism scores were 9.90±1.68. Pearson correlation analysis showed that educational level had a significant inverse relationship with patients’ self-esteem scores (r=−0.009,P=0.03), and sex had a significant relationship with patients’ optimism scores (r=0.175,P=0.008).

Conclusion:

Considering the importance of self-esteem and optimism in the recovery and return to society of patients with major depression, it is necessary to take measures to strengthen and increase self-esteem and optimism in these patients.
A rare case of Behcet’s disease in Nepal: multisystem manifestations and diagnostic challenges
Authors: Mahaju Satyam , Achhami Eliz , Lamichhane Seshkanta , Chalise Khem N. , Gautam Rabin
Published: September 2023

Behcet’s disease (BD) is a chronic inflammatory disorder characterized by a relapsing and remitting course and multisystem involvement. The authors present a case report of a 20-year-old male who presented with bilateral knee joint pain, oral and genital ulcers, and papulopustular skin lesions. The patient’s clinical history, physical examination, laboratory findings, and biopsy results were consistent with the diagnosis of BD. The patient tested positive for the HLA-B51 allele, confirming a genetic predisposition. The diagnosis was supported by a positive pathergy test and a skin biopsy showing vasculitis. The diagnostic criteria established by the international study group and the International Criteria for Behcet’s Disease were fulfilled. Treatment consisted of colchicine, azathioprine, and topical corticosteroids. This case highlights the importance of recognizing the varied clinical presentations of BD and the need for a multidisciplinary approach to diagnosis and management. Early and accurate diagnosis is crucial to prevent severe complications and improve patient outcomes.
Serum and Tissue Lipocalin-2 Expression in Chronic Kidney Disease Pruritic Patients
Authors: Bazid Heba A. S. , Sakr Hanaa G. , Abdallah Rania A. , Arafat Eman S. , Ragheb Ahmed , Seleit Iman
Published: September 2023

Background:

Uremic pruritus is an irritating symptom for patients with end-stage kidney disease. Lipocalin-2 (LCN2) has relevant importance in several biological cellular processes and immunity. It is also a major player in the progression of many disorders, such as renal injury.

Aim:

To evaluate LCN2 expression in chronic kidney disease (CKD) pruritic patients in serum together with immunohistochemical expression in skin samples and further correlation of their results with the studied clinicopathologic parameters.

Materials and Methods:

Serum level of LCN2 (assessed by enzyme-linked immunosorbent assay) and skin immunohistochemical expression were investigated in 25 CKD patients and 25 healthy controls. Ten patients were subjected to narrowband ultraviolet B phototherapy for 12 weeks then re-evaluated for serum and tissue LCN2 after therapy.

Results:

LCN2 expression was increased significantly in both the epidermis and dermal adnexa in CKD patients over controls. Also, serum LCN2 level was higher in patients than in healthy subjects and was significantly associated with itching severity, grades of CKD, urea, and creatinine serum level. Tissue and serum levels of LCN2 were significantly diminished in CKD patients following narrowband therapy along with improvement of the severity of pruritus.

Conclusions:

The increased serum and tissue LCN2 expression in CKD pruritic patients and its pronounced decrease, in addition to the improvement of pruritus after treatment, suggest a major pathogenic role of LCN2 in uremic pruritus.
Prepectoral Direct-to-Implant versus Staged Tissue Expander Breast Reconstruction: A Comparison of Complications
Authors: Finkelstein Emily R. , Laureano Natalia Vidal , Azizi Armina , Smartz Taylor , Zheng Caiwei , Lessard Anne-Sophie , Panthaki Zubin , Oeltjen John , Kassira Wrood
Published: September 2023

Background:

Direct-to-implant (DTI) reconstruction has multiple advantages over a staged tissue expander (TE) approach. However, its use may be limited by concerns of increased complications. This study is the largest series to date comparing postoperative outcomes for DTI versus TE reconstruction in the prepectoral plane.

Methods:

The authors retrospectively reviewed 348 patients who underwent 536 total immediate, prepectoral implant-based breast reconstructions between January of 2018 and December of 2021. The authors compared the presence of risk factors and the rate of six separate complications between patients who underwent DTI versus TE reconstruction up to 1 year after surgery.

Results:

Of 348 patients, 147 (42%) and 201 (58%) underwent TE and DTI reconstruction (P = 0.1813), respectively. The overall infection rate was 16.4% (n = 57). DTI patients had a significantly greater incidence of wounds (P < 0.0001), including minor (P < 0.0011) and major wounds (P < 0.0053). Significantly greater mastectomy resection weights were found for DTI patients who experienced any complication (P < 0.0076), postoperative wounds (P < 0.0001), and major wounds specifically (P < 0.0035). Compared with medium-thickness acellular dermal matrix (ADM), extra thick ADM was associated with significantly increased rates of infection (P < 0.0408) and wounds (P < 0.0001).

Conclusions:

Prepectoral DTI reconstruction in patients with adequate flap perfusion may have complication rates comparable to staged TE reconstruction, apart from a higher incidence of postoperative wounds. Greater mastectomy resection weights and thickness of ADM may specifically contribute to infection and wound-healing complications. Prepectoral DTI reconstruction is encouraged in the patients with adequate flap perfusion and moderate to low mastectomy resection weights who desire comparable or smaller implant volumes.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Bacterial Lipoteichoic Acid Induces Capsular Contracture by Activating Innate Immune Response
Authors: Ahmad Ikram , Xuan Tianfan , Wang Qiang , Zhang Simin , Wang Lu , Gu Jianying , Qi Fazhi , Luan Wenjie
Published: September 2023

Background:

Capsular contracture is attributed to an exaggerated fibrosis response within the capsule and is partly associated with bacterial contamination in situ. However, the cellular mechanisms that initiate this response are unclear.

Methods:

The authors developed a mouse model of capsular contracture by repeated injection of 10 μg/mL lipoteichoic acid (LTA). The histological changes in the capsule tissue were measured by hematoxylin and eosin, Masson trichrome, and immunohistochemical staining. The expression of cytokines was measured by quantitative reverse transcription polymerase chain reaction. The authors also used pharmacological methods to verify the roles of macrophages and toll-like receptor 2 (TLR2) signaling in this pathological process.

Results:

The authors discovered that repeated LTA injection, at a low concentration, could induce thickening of the capsule tissue. Macrophage infiltration and TLR2/nuclear factor-κB signaling activated in this process could be suppressed by macrophage depletion or TLR2 receptor inhibition.

Conclusion:

As TLR2 signal activation was found to cause capsular contracture by inducing macrophage infiltration as a consequence of trace amounts of LTA contamination in situ, this target is helpful for understanding that chronic or repeated subclinical infection can activate capsular contracture.

Clinical Relevance Statement:

This finding is of significant importance for understanding that chronic or repeated subclinical infection could activate a persistent immune response and capsular contracture, and provides novel strategies to interfere with the formation of capsular contracture.
Speech Outcomes and Rates of Secondary Speech Surgery from Childhood to Skeletal Maturity following Modified Furlow Palatoplasty
Authors: Salinero Lauren K. , Wagner Connor S. , Barrero Carlos E. , Valenzuela Zachary D. , McCormack Susan M. , Solot Cynthia , Cohen Marilyn , Kirschner Richard E. , Low David W. , Jackson Oksana A.
Published: September 2023

Background:

This study updates the authors’ institutional experience with modified Furlow palatoplasty, evaluating speech outcomes and incidence of secondary speech surgery throughout development and at skeletal maturity.

Methods:

Nonsyndromic patients undergoing primary modified Furlow palatoplasty between 1985 and 2005 with postoperative speech evaluations were reviewed retrospectively. Secondary speech surgery and Pittsburgh Weighted Speech Scale (PWSS) scores before secondary speech or orthognathic operations were assessed in the groups aged 5 to 7 years, 8 to 11 years, 12 to 14 years, and older than 15 years and analyzed by Veau cleft type.

Results:

A total of 551 patients with 895 total speech assessments were analyzed. Of 364 patients followed up to age 15 years or older, 19.8% underwent secondary speech surgery. Speech assessment of patients aged 15 years or older without prior secondary speech surgery showed competent velopharyngeal mechanisms in 77% of patients. PWSS nasal emission scores were worse in the 5- to 7-year age range (P = 0.02), whereas resonance scores remained stable throughout development (P = 0.2). Patients with Veau type I or II clefts had worse overall PWSS classifications in the groups aged 5 to 7 years and 8 to 11 years (P = 0.01 and P = 0.03), with greater odds of secondary speech surgery relative to those with Veau type III (OR, 2.9; P < 0.001) or IV clefts (OR, 3.6; P = 0.001).

Conclusions:

Most patients undergoing primary modified Furlow palatoplasty do not require secondary speech surgery and achieve socially acceptable speech at skeletal maturity. However, Veau type I and II clefts are associated with increased risk for early velopharyngeal dysfunction and secondary speech surgery. The incidence of secondary speech surgery was 19.8%, an increase from our previously reported rate of 8%.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Human Skeletal Muscle Fiber Heterogeneity Beyond Myosin Heavy Chains
Authors: Moreno-Justicia Roger , Van der Stede Thibaux , Stocks Ben , Laitila Jenni , Seaborne Robert A , Van de Loock Alexia , Lievens Eline , Samodova Diana , Marín-Arraiza Leyre , Dmytriyeva Oksana , Browaeys Robin , Van Vossel Kim , Moesgaard Lukas , Yigit Nurten , Anckaert Jasper , Weyns Anneleen , Van Thienen Ruud , Sahl Ronni E , Zanoteli Edmar , Lawlor Michael W , Wierer Michael , Mestdagh Pieter , Vandesompele Jo , Ochala Julien , Hostrup Morten , Derave Wim , Deshmukh Atul S
Published: September 2023

Skeletal muscle is an inherently heterogenous tissue comprised primarily of myofibers, which are historically classified into three distinct fiber types in humans: one “slow” (type 1) and two “fast” (type 2A and type 2X), delineated by the expression of myosin heavy chain isoforms (MYHs). However, heterogeneity between and within traditional fiber types remains underexplored. Indeed, whether MYHs are the main classifiers of skeletal muscle fibers has not been examined in an unbiased manner. Through the development and application of novel transcriptomic and proteomic workflows, applied to 1050 and 1038 single muscle fibers from humanvastus lateralis, respectively, we show that MYHs are not the only principal drivers of skeletal muscle fiber heterogeneity. Instead, metabolic, ribosomal, and cell junction proteins are a source of multi-dimensional variation between skeletal muscle fibers. Furthermore, whilst slow and fast fiber clusters can be identified, described by their contractile and metabolic profiles, our data suggests that type 2X fibers are not phenotypically distinct to other fast fibers at an omics level. Moreover, MYH-based classifications do not adequately describe the phenotype of skeletal muscle fibers in one of the most common genetic muscle diseases, nemaline myopathy, with fibers shifting towards a non-oxidative phenotype independently of MYH-based fiber type. We also characterize novel transcriptomic and proteomic features of slow and fast skeletal muscle fibers, including identifying several muscle fiber type-specific polypeptides, termed microproteins, encoded by transcripts annotated as non-coding RNA. Overall, our data indicates that skeletal muscle fiber heterogeneity is multi-dimensional with sources of variation beyond myosin heavy chain isoforms.
Lupus IgA1 autoantibodies synergize with IgG to enhance pDC responses to RNA-containing immune complexes
Authors: Waterman Hayley R. , Dufort Matthew J. , Posso Sylvia E. , Ni Minjian , Li Lucy Z. , Zhu Chengsong , Raj Prithvi , Smith Kelly D. , Buckner Jane H. , Hamerman Jessica A.
Published: September 2023

Autoantibodies to nuclear antigens are hallmarks of the autoimmune disease systemic lupus erythematosus (SLE) where they contribute to pathogenesis. However, there remains a gap in our knowledge regarding how different isotypes of autoantibodies contribute to disease, including the production of the critical type I interferon (IFN) cytokines by plasmacytoid dendritic cells (pDCs) in response to immune complexes (ICs). We focused on IgA, which is the second most prevalent isotype in serum, and along with IgG is deposited in glomeruli in lupus nephritis. Here, we show that individuals with SLE have IgA autoantibodies against most nuclear antigens, correlating with IgG against the same antigen. We investigated whether IgA autoantibodies against a major SLE autoantigen, Smith ribonucleoproteins (Sm/RNPs), play a role in IC activation of pDCs. We found that pDCs express the IgA-specific Fc receptor, FcαR, and there was a striking ability of IgA1 autoantibodies to synergize with IgG in RNA-containing ICs to generate robust pDC IFNα responses. pDC responses to these ICs required both FcαR and FcγRIIa, showing a potent synergy between these Fc receptors. Sm/RNP IC binding to and internalization by pDCs were greater when ICs contained both IgA1 and IgG. pDCs from individuals with SLE had higher binding of IgA1-containing ICs and higher expression of FcαR than pDCs from healthy control individuals. Whereas pDC FcαR expression correlated with blood ISG signature in SLE, TLR7 agonists, but not IFNα, upregulated pDC FcαR expression in vitro. Together, we show a new mechanism by which IgA1 autoantibodies contribute to SLE pathogenesis.

One Sentence Summary

IgA1 autoantibodies synergize with IgG in RNA-containing immune complexes to generate robust pDC IFNα responses in a FcαR receptor dependent manner.
Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition
Authors: Lai Huei-Yi , Cooper Tim F.
Published: September 2023

Antibiotic resistance genes (ARGs) is a major contributor to increasing levels of antibiotic resistance in clinical and agricultural settings. ARGs are strongly selected in environments containing corresponding antibiotics, but it is less clear how ARGs are maintained in environments where antibiotic selection might be weak or sporadic. In particular, few studies have directly estimated the effect of ARGs on host fitness in the absence of direct selection. To the extent that ARGs impose costs, it is not clear if these are fixed or might depend on the host strain, perhaps marking some ARG-host combinations as low-cost reservoirs that can act to maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in each of 11 diverseEscherichiaspp. strains in two environments. While three ARGs(blaTEM-116,cat, anddfrA5, encoding resistance to β-lactam antibiotics, chloramphenicol, and trimethoprim, respectively) imposed an overall cost, all ARGs had an effect in at least one host strain, reflecting a significant ARG effect-by-strain interaction effect. A simulation model predicts that these interactions cause the ecological success of ARGs to depend on available host strains, and, to a lesser extent, for successful host strains to depend on the ARGs present in a community. Together, these results indicate the importance of considering ARG effects over different host strains, especially the potential of reservoir strains that allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics.

Importance

Antibiotic resistance is a major and increasing public health concern. Resistance occurs through a variety of mechanisms but commonly involves bacterial strains acquiring antibiotic resistance genes (ARGs) encoded by mobile elements. It is obvious and well-documented that ARGs will be selected in bacteria that are exposed to the antibiotics they confer resistance to. ARGs can also confer costs to bacteria—in environments that do not contain antibiotics, these costs can lead to the loss of ARGs. We show that ARG costs can be significant and that they depend on the host bacterial strain and the environment in which strains are grown. This dependence creates host-environment refuges for many ARGs, allowing them to be maintained in the absence of direct selection.
Discovering biomarkers associated and predicting cardiovascular disease with high accuracy using a novel nexus of machine learning techniques for precision medicine
Authors: DeGroat William , Abdelhalim Habiba , Patel Kush , Mendhe Dinesh , Zeeshan Saman , Ahmed Zeeshan
Published: September 2023

Personalized interventions are deemed vital given the intricate characteristics, advancement, inherent genetic composition, and diversity of cardiovascular diseases (CVDs). The appropriate utilization of artificial intelligence (AI) and machine learning (ML) methodologies can yield novel understandings of CVDs, enabling improved personalized treatments through predictive analysis and deep phenotyping. In this study, we proposed and employed a novel approach combining traditional statistics and a nexus of cutting-edge AI/ML techniques to identify significant biomarkers for our predictive engine by analyzing the complete transcriptome of CVD patients. After robust gene expression data pre-processing, we utilized three statistical tests (Pearson correlation, Chi-square test, and ANOVA) to assess the differences in transcriptomic expression and clinical characteristics between healthy individuals and CVD patients. Next, the Recursive Feature Elimination (RFE) classifier assigned rankings to transcriptomic features based on their relation to the case-control variable. The top ten percent of commonly observed significant biomarkers were evaluated using four unique ML classifiers (Random Forest, Support Vector Machine, Xtreme Gradient Boosting Decision Trees, and k-Nearest Neighbors). After optimizing hyperparameters, the ensembled models, which were implemented using a soft voting classifier, accurately differentiated between patients and healthy individuals. We have uncovered 18 transcriptomic biomarkers that are highly significant in the CVD population that were used to predict disease with up to 96% accuracy. Additionally, we cross-validated our results with clinical records collected from patients in our cohort. The identified biomarkers served as potential indicators for early detection of CVDs. With its successful implementation, our newly developed predictive engine provides a valuable framework for identifying patients with CVDs based on their biomarker profiles.
Mitochondrial transplantation and its impact on infectious disease progression: a pilot study
Authors: Benson Tom , Patel Samir P. , Albensi Benedict C. , Mahajan Vinit B. , Adlimoghaddam Aida , Sikora Sergey , Saito Hiroshi
Published: September 2023

BACKGROUND

Mitochondrial transplantation has recently gained prominence as a novel technique primarily focused on addressing ischemiareperfusion injuries and rare mitochondrial mutation diseases. Platelets, abundant in the bloodstream, play a crucial role in immune function. Upon activation, platelets release mitochondria encapsulated within extracellular vesicles, here referred to as “mitlets”. These mitlets exhibit a preference for being internalized by immune cells circulating in the bloodstream, enhancing their cellular energetics. Herein, we hypothesized that the transplantation of mitlets between young animals and aged animals may exert a significant influence on the progression of infectious diseases.

STUDY DESIGN AND METHODS

In this study, murine models of Influenza H1N1 infection and sepsis were employed to investigate disease dynamics. Specifically, mitlets isolated from young and healthy mice were transplanted into cohorts of mice of the same age afflicted by H1N1 infection, or into aged mice subjected to polymicrobial infection and sepsis. Survival outcomes and the quantification of cytokine levels were assessed across experimental groups to elucidate the potential therapeutic effects of mitlet transplantation.

RESULTS

In the matched-age H1N1 infection model, as predicted, mitlet transplantation did not yield a statistically significant improvement in survival, although it did show a trend towards a reduction in the circulating inflammatory cytokine burden. In the young-to-old sepsis model, the transplantation of mitlets was associated with a significant enhancement in survival rates and a substantial reduction in bacterial loads and circulating cytokine levels.

DISCUSSION

Our findings suggest that mitochondrial transplantation may constitute a safe and promising avenue for enhancing the immune system’s capacity to counter infectious threats. This pilot investigation sets the stage for further exploration. It is plausible that in the future, immune senescence resulting from diminished mitochondrial energy production could be ameliorated through such transplantation interventions. As a consequence, this approach holds substantial potential as a novel immunotherapeutic strategy for the management of infectious diseases.
The Effect of Amniotic Fluid On Haıir Follicle Growth
Authors: Tumentemur Gamze , Aygun Elif Ganime , Yurtsever Bulut , Cakirsoy Didem , Ovali Ercument
Published: September 2023

Human amniotic fluid stem cell (hAFSC) exhibit significantly as a new treatment modality in hair loss, wound, scar and regenerative plastic surgery/dermatology. The difference of our study from previous amniotic fluid studies on the hair growth model was studied through the direct effect of human amniotic fluid (hAF). In our study, amniotic fluid was made acellular, pooled and freezed, making it more standardized in terms of its contents. Therefore, the present study is aimed at investigating the efficacy and safety of amniotic fluid in hair loss model on rat. Using the hair loss model rats, we investigated the therapeutic potential of freezing amniotic fluid (FAF) and freezing gama irradiated amniotic fluid (FAFI). Our results showed that FAF and especially FAFI increased number of total hair follicles and accelerated number of transition to anagenic hair follicle. We observed that increased rate of arginase+1(Arg+1)/CD68 activity around the hair follicles treated with hAF. Our study suggests that FAFI may represent a safe and effective tool for increasing hair follicle and accelerating to anagen stage during hair loss model.
Thermodynamic Stabilization of Human Frataxin
Authors: Núñez-Franco Reyes , Torres-Mozas Angel , Navo Claudio D. , Schedlbauer Andreas , Azkargorta Mikel , Iloro Ibon , Elortza Félix , Ortega Gabriel , Millet Oscar , Peccati Francesca , Jiménez-Osés Gonzalo
Published: September 2023

Recombinant proteins and antibodies are routinely used as drugs to treat prevalent diseases such as diabetes or cancer, while enzyme replacement and gene therapies are the main therapeutic intervention lines in rare diseases. In protein-based therapeutics, optimizedin vivostability is key as intrinsic denaturation and intracellular proteostatic degradation will limit potency, particularly in treatments requiring a sustained action, while clearance mechanisms may limit the amount of circulating protein.In vivostability is ultimately correlated with the intrinsic thermodynamic stability of the biomolecule, but this is difficult to optimize because it often goes at the expense of reducing protein activity. Here, we have usedin silicoengineering approaches to thermodynamically stabilize human frataxin, a small mitochondrial protein that acts as an allosteric activator for the biosynthesis of Fe-S clusters, whose genetically-driven impairment results in a rare disease known as Friedreich ataxia. Specifically, we developed an efficient thermostability engineering computational approach that combines information on amino acid conservation, the Rosetta energy function, and two recent artificial intelligence tools – AlphaFold and ProteinMPNN – to produce thermodynamically stabilized variants of human frataxin. Such protein variants rescued the large destabilization exerted by well-known pathological mutations, with an increase over 20 °C in the melting temperature and a thermodynamic stabilization of more than 3 kcal·mol-1at the physiological temperature. This stability surplus is translated into an enhanced resistance to proteolysis, while maintaining the protein fully functional. This case-study highlights the power of our combined computational approach to generate optimized variants, adequate for protein-based therapeutics.
Identification of cell types, states and programs by learning gene set representations
Authors: Hediyeh-zadeh Soroor , Whitfield Holly J. , Kharbanda Malvika , Curion Fabiola , Bhuva Dharmesh D. , Theis Fabian J. , Davis Melissa J.
Published: September 2023

As single cell molecular data expand, there is an increasing need for algorithms that efficiently query and prioritize gene programs, cell types and states in single-cell sequencing data, particularly in cell atlases. Here we present scDECAF, a statistical learning algorithm to identify cell types, states and programs in single-cell gene expression data using vector representation of gene sets, which improves biological interpretation by selecting a subset of most biologically relevant programs. We applied scDECAF to scRNAseq data from PBMC, Lung, Pancreas, Brain and slide-tags snRNA of human prefrontal cortex for automatic cell type annotation. We demonstrate that scDECAF can recover perturbed gene programs in Lupus PBMC cells stimulated with IFNbeta and TGFBeta-induced cells undergoing epithelial-to-mesenchymal transition. scDECAF delineates patient-specific heterogeneity in cellular programs in Ovarian Cancer data. Using a healthy PBMC reference, we apply scDECAF to a mapped query PBMC COVID-19 case-control dataset and identify multicellular programs associated with severe COVID-19. scDECAF can improve biological interpretation and complement reference mapping analysis, and provides a method for gene set and pathway analysis in single cell gene expression data.
SARS-CoV-2 Omicron infection augments the magnitude and durability of systemic and mucosal immunity in triple-dose CoronaVac recipients
Authors: Chen Yuxin , Zhao Tiantian , Chen Lin , Jiang Guozhi , Geng Yu , Li Wanting , Yin Shengxia , Tong Xin , Tao Yue , Ni Jun , Lu Qiuhan , Ning Mingzhe , Wu Chao
Published: September 2023

Background

The inactivated whole-virion vaccine, CoronaVac, is one of the most widely used coronavirus disease 2019 (COVID-19) vaccines worldwide. There is a paucity of data indicating the durability of the immune response and the impact of immune imprinting induced by CoronaVac upon Omicron breakthrough infection.

Methods

In this prospective cohort study, 41 recipients of triple-dose CoronaVac and 14 unvaccinated individuals were recruited. We comprehensively profiled adaptive immune parameters in both groups, including spike-specific immunoglobulin (Ig) G and IgA titers, neutralizing activity, B cells, follicular helper T (Tfh) cells, CD4+and CD8+T cells, and their memory subpopulations at 12 months after the third booster dose and at 4 weeks and 20 weeks after Omicron BA.5 infection.

Results

Twelve months after the third CoronaVac vaccination, spike-specific antibody and cellular responses were detectable in most vaccinated individuals. BA.5 infection significantly augmented the magnitude, cross-reactivity and durability of serum neutralization activities, Fc-mediated phagocytosis, and nasal spike-specific IgA responses, memory B cells, activated Tfh cells memory CD4+ T cells, and memory CD8+ T cells for both the ancestral strain and Omicron subvariants, compared to unvaccinated individuals. Notably, the increase in BA.5-specific immunity after breakthrough infection was consistently higher than for the ancestral strain, suggesting no evidence of immune imprinting. Immune landscape analyses showed vaccinated individuals have better synchronization of multiple immune components than unvaccinated individuals upon heterologous SARS-CoV-2 infection.

Conclusion

Our data provides detailed insight into the protective role of inactivated COVID-19 vaccine in shaping humoral and cellular immune responses to heterologous Omicron infection.

Trial registration

ClinicalTrials.govNCT05680896

Funding

This study was supported by the National Natural Science Foundation of China (92269118, 92269205), Nanjing Important Science & Technology Specific Projects (2021-11005), Scientific Research Project of Jiangsu Health Commission (M2022013), Clinical Trials from the Affiliated Drum Tower Hospital, Medical School of Nanjing University (2021-LCYJ-PY-9), and Jiangsu graduate practice innovation project (JX22013929).
Bayesian optimization of separation gradients to maximize the performance of untargeted LC-MS
Authors: Yu Huaxu , Biswas Puja , Rideout Elizabeth , Cao Yankai , Huan Tao
Published: September 2023

Liquid chromatography (LC) with gradient elution is a routine practice for separating complex chemical mixtures in mass spectrometry (MS)-based untargeted analysis. Despite its prevalence, systematic optimization of LC gradients has remained challenging. Here we develop a Bayesian optimization method, BAGO, for autonomous and efficient LC gradient optimization. BAGO is an active learning strategy that discovers the optimal gradient using limited experimental data. From over 100,000 plausible gradients, BAGO locates the optimal LC gradient within ten sample analyses. We validated BAGO on six biological studies of different sample matrices and LC columns, showing that BAGO can significantly improve quantitative performance, tandem MS spectral coverage, and spectral purity. For instance, the optimized gradient increases the count of annotated compounds meeting quantification criteria by up to 48.5%. Furthermore, applying BAGO in aDrosophilametabolomics study, an additional 57 metabolites and 126 lipids were annotated. The BAGO algorithms were implemented into user-friendly software for everyday laboratory practice and a Python package for its flexible extension.
HEART rate variability biofeedback breathing programme for LOng Covid dysautonomia (HEARTLOC): results of a feasibility study
Authors: Corrado J , Iftekhar N , Halpin SJ , Li M , Tarrant R , Grimaldi J , Simms AD , O’Connor RJ , Casson AJ , Sivan M
Published: September 2023

Introduction

Post-covid-19 syndrome, or Long covid (LC) refers to symptoms persisting 12 weeks after Covid-19 infection. LC comprises a wide range of dysautonomia symptoms, including fatigue, breathlessness, palpitations, dizziness, pain and brain fog. This study tested the feasibility and estimated the efficacy, of a Heart Rate Variability Biofeedback (HRV-B) technique via a standardised slow diaphragmatic breathing programme in individuals with LC.

Methods and Analysis

LC patients underwent a 4-week HRV-B intervention for 10 minutes twice daily for a total of 4 weeks using the Polar H10 ECG (Electrocardiogram) chest strap and Elite HRV phone application. Outcome measures C19-YRSm (Yorkshire Rehabilitation Scale modified), EQ5D-5L (EuroQol 5 Dimensions), Composite Autonomic Symptom Score (COMPASS-31), WHO Disability Assessment Schedule (WHODAS), and Root Mean Square of Successive Differences between heartbeats (RMSSD) using a Fitbit device were completed before and after the intervention. The study was pre-registered atclinicaltrials.govNCT05228665.

Results

13 participants (54% female, 46% male) completed the study with high levels of data completeness and adherence. There was a statistically significant improvement in C19YRS-m (p=0.001), EQ5D Global Health Score (p=0.009), COMPASS-31 (p=0.007), RMSSD (p=0.047) and EHODAS (p=0.02). Qualitative feedback suggested participants were able to use it independently, were satisfied with the intervention, and reported beneficial effects from the intervention.

Conclusion

This is the first study in the literature to report that HRV-B is a feasible intervention for LC and seems to be potentially improving symptoms of LC and dysautonomia.

Article summary

Strengths and limitations of the study

To our knowledge, this is the first study of HRV-B in long covid and dysautonomia and has shown the feasibility of a novel technology-based intervention in a home setting.

There was a statistically significant improvement in LC symptoms, functional ability, quality of life and dysautonomia scores.

The study provides an estimation of efficacy which will determine the sample size for a larger controlled trial in LC and dysautonomia.

The main limitation of this study is the small sample size and uncontrolled design which might not give us an accurate estimate of efficacy.

The sample was predominantly Caucasian participants, 54% of whom were female.

The take-up for HRV-B in those with a lack of experience in using digital technology and those from less privileged backgrounds is unknown.
Modelling count data with partial differential equation models in biology
Authors: Simpson Matthew J , Murphy Ryan J , Maclaren Oliver J
Published: September 2023

Partial differential equation (PDE) models are often used to study biological phenomena involving movement-birth-death processes, including ecological population dynamics and the invasion of populations of biological cells. Count data, by definition, is non-negative, and count data relating to biological populations is often bounded above by some carrying capacity that arises through biological competition for space or nutrients. Parameter estimation, parameter identifiability, and making model predictions usually involves working with a measurement error model that explicitly relating experimental measurements with the solution of a mathematical model. In many biological applications, a typical approach is to assume the data are normally distributed about the solution of the mathematical model. Despite the widespread use of the standard additive Gaussian measurement error model, the assumptions inherent in this approach are rarely explicitly considered or compared with other options. Here, we interpret scratch assay data, involving migration, proliferation and delays in a population of cancer cells using a reaction–diffusion PDE model. We consider relating experimental measurements to the PDE solution using a standard additive Gaussian measurement error model alongside a comparison to a more biologically realistic binomial measurement error model. While estimates of model parameters are relatively insensitive to the choice of measurement error model, model predictions for data realisations are very sensitive. The standard additive Gaussian measurement error model leads to biologically inconsistent predictions, such as negative counts and counts that exceed the carrying capacity across a relatively large spatial region within the experiment. Furthermore, the standard additive Gaussian measurement error model requires estimating an additional parameter compared to the binomial measurement error model. In contrast, the binomial measurement error model leads to biologically plausible predictions and is simpler to implement. We provide open source Julia software onGitHubto replicate all calculations in this work, and we explain how to generalise our approach to deal with coupled PDE models with several dependent variables through a multinomial measurement error model, as well as pointing out other potential generalisations by linking our work with established practices in the field of generalised linear models.
Rapid and cost-effective epitope mapping using PURE ribosome display coupled with next-generation sequencing and bioinformatics
Authors: Jia Beixi , Ojima-Kato Teruyo , Kojima Takaaki , Nakano Hideo
Published: September 2023

A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes anEscherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabilizes the mRNA-ribosome-peptide complex via a ribosome-arrest peptide sequence. This system was complemented by next-generation sequencing (NGS) and an algorithm for analyzing binding epitopes. To showcase the effectiveness of this method, selection conditions were refined using the anti-PA tag monoclonal antibody with the PA tag peptide as a model. Subsequently, a random peptide library was constructed using 10 NNK triplet oligonucleotides via the PURE ribosome display. The resulting random peptide library-ribosome-mRNA complex was selected using a commercially available anti-HA (YPYDVPDYA) tag monoclonal antibody, followed by NGS and bioinformatic analysis. Our approach successfully identified the “DVPDY” sequence as an epitope within the hemagglutinin amino acid sequence, which was then experimentally validated. This platform provided a valuable tool for investigating continuous epitopes in antibodies.
A key role of pectin demethylation-mediated cell wall Na+retention in regulating differential salt stress resistance in allotetraploid rapeseed genotypes
Authors: Zhou Ting , Wu Peng-jia , Chen Jun-fan , Du Xiao-qian , Feng Ying-na , Yue Cai-peng , Huang Jin-yong , Hua Ying-peng
Published: September 2023

Allotetraploid rapeseed (Brassica napusL.) is highly susceptible to salt stress, a worldwide limiting factor that causes severe losses in seed yield. Genetic variations in the resistance against salt stress found in rapeseed genotypes emphasizes the complex response architecture. Westar is ubiquitously used as a major transgenic receptor, and ZS11 is widely grown as a high production and good quality cultivar. In this study, Westar was identified to outperform than ZS11 under salt stress. Through cell component isolation, non-invasive micro-test, X-ray energy spectrum analysis, and ionomic profiling characterization, pectin demethylation was found to be a major regulator for differential salt resistance between Westar and ZS11. Integrated analyses of genome-wide DNA variations, differentially expression profiling, and gene co-expression network identifiedBnaC9.PME47, encoding pectin methyl esterase, as a positive regulator mainly responsible for salt stress resistance.BnaC9.PME47, located in two reported QTLs regions for salt resistance, was strongly induced by salt stress and localized on the cell wall. Natural variation of the promoter regions conferred higher expression ofBnaC9.PME47in Westar than in other salt-sensitive rapeseed genotypes. Loss-of-function ofAtPME47resulted in the hypersensitivity of Arabidopsis plants to salt stress. This study facilitates a more comprehensive understanding of the differential morpho-physiological and molecular responses to salt stress and abundant genetic diversity in rapeseed genotypes, and the integrated multiomics analyses provide novel insights regarding the rapid dissection of quantitative trait genes responsible for nutrient stresses in plant species with complex genomes.