bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of endometriosis on oocyte morphology in IVF-ICSI: retrospective study of a cohort of more than 6000 mature oocytes
Authors: Robin Camille , Uk Audrey , Decanter Christine , Behal Hélène , Collinet Pierre , Rubod Chrystèle , Barbotin Anne-Laure , Robin Geoffroy 
Published: October 2021

Abstract
Background
Infertility associated with endometriosis can be explained by several non-exclusive mechanisms. The oocyte plays a crucial role in determining embryonic competence and this is particularly relevant for in vitro fertilization (IVF) outcomes. According to some authors, the morphology of oocytes could also be a non-invasive marker of oocyte quality. The aim of this study was to evaluate the relationship between endometriosis and oocyte morphology after controlled ovarian stimulation for intracytoplasmic sperm injection (ICSI) on a large oocyte cohort.

Methods
Single-center comparative retrospective study in the academic In Vitro Fertilization (IVF) unit of the Lille University Hospital. A total of 596 women treated for IVF-ICSI with ejaculated spermatozoa for sperm alterations were included. They were classified as endometriosis (n = 175) or control groups (n = 401). The morphological evaluation of 2,016 mature oocytes from 348 cycles of patients with endometriosis was compared with that of 4,073 mature oocytes from 576 control cycles. The main outcome measures were Average Oocyte Quality Index (AOQI) and metaphase II oocyte morphological scoring system (MOMS). Comparison of groups was carried out by a mixed linear model and by a generalized estimation equation model with a "patient" random effect to consider that a patient might have several attempts.

Results
No difference in AOQI and MOMS scores was found between endometriosis and control women (adjusted p = 0.084 and 0.053, respectively).
In case of endometriosis, there were significantly fewer metaphase II oocytes retrieved, embryos obtained, grade 1 embryos and number of cumulative clinical pregnancies compared to controls. In the endometriosis group, endometriosis surgery was associated with a reduced number of mature oocytes retrieved, and the presence of endometrioma(s) was associated with some abnormal oocyte shapes. Nevertheless, no difference concerning the AOQI and MOMS scores was found in these subgroups.

Conclusion
Endometriosis does not have a negative impact on oocytes’ morphology in IVF-ICSI.

Trial registration
On December 16, 2019, the Institutional Review Board of the Lille University Hospital gave unrestricted approval for the anonymous use of all patients’ clinical, hormonal and ultrasound records (reference DEC20150715-0002).
Sodium phenylbutyrate inhibits Schwann cell inflammation via HDAC and NFκB to promote axonal regeneration and remyelination
Authors: Yadav Anjali , Huang Tzu-Chieh , Chen Szu-Han , Ramasamy Thamil Selvee , Hsueh Yuan-Yu , Lin Shau-Ping , Lu Fu-I , Liu Ya-Hsin , Wu Chia-Ching 
Published: October 2021

Abstract
Background
Epigenetic regulation by histone deacetylases (HDACs) in Schwann cells (SCs) after injury facilitates them to undergo de- and redifferentiation processes necessary to support various stages of nerve repair. Although de-differentiation activates the synthesis and secretion of inflammatory cytokines by SCs to initiate an immune response during nerve repair, changes in either the timing or duration of prolonged inflammation mediated by SCs can affect later processes associated with repair and regeneration. Limited studies have investigated the regulatory processes through which HDACs in SCs control inflammatory cytokines to provide a favorable environment for peripheral nerve regeneration.

Methods
We employed the HDAC inhibitor (HDACi) sodium phenylbutyrate (PBA) to address this question in an in vitro RT4 SC inflammation model and an in vivo sciatic nerve transection injury model to examine the effects of HDAC inhibition on the expression of pro-inflammatory cytokines. Furthermore, we assessed the outcomes of suppression of extended inflammation on the regenerative potential of nerves by assessing axonal regeneration, remyelination, and reinnervation.

Results
Significant reductions in lipopolysaccharide (LPS)-induced pro-inflammatory cytokine (tumor necrosis factor-α [TNFα]) expression and secretion were observed in vitro following PBA treatment. PBA treatment also affected the transient changes in nuclear factor κB (NFκB)-p65 phosphorylation and translocation in response to LPS induction in RT4 SCs. Similarly, PBA mediated long-term suppressive effects on HDAC3 expression and activity. PBA administration resulted in marked inhibition of pro-inflammatory cytokine secretion at the site of transection injury when compared with that in the hydrogel control group at 6-week post-injury. A conducive microenvironment for axonal regrowth and remyelination was generated by increasing expression levels of protein gene product 9.5 (PGP9.5) and myelin basic protein (MBP) in regenerating nerve tissues. PBA administration increased the relative gastrocnemius muscle weight percentage and maintained the intactness of muscle bundles when compared with those in the hydrogel control group.

Conclusions
Suppressing the lengthened state of inflammation using PBA treatment favors axonal regrowth and remyelination following nerve transection injury. PBA treatment also regulates pro-inflammatory cytokine expression by inhibiting the transcriptional activation of NFκB-p65 and HDAC3 in SCs in vitro.
A novel phosphoproteomic landscape evoked in response to type I interferon in the brain and in glial cells
Authors: Viengkhou Barney , White Melanie Y. , Cordwell Stuart J. , Campbell Iain L. , Hofer Markus J. 
Published: October 2021

AbstractBackgroundType I interferons (IFN-I) are key responders to central nervous system infection and injury and are also increased in common neurodegenerative diseases. Their effects are primarily mediated via transcriptional regulation of several hundred interferon-regulated genes. In addition, IFN-I activate several kinases including members of the MAPK and PI3K families. Yet, how changes to the global protein phosphoproteome contribute to the cellular response to IFN-I is unknown.MethodsThe cerebral phosphoproteome of mice with brain-targeted chronic production of the IFN-I, IFN-α, was obtained. Changes in phosphorylation were analyzed by ontology and pathway analysis and kinase enrichment predictions. These were verified by phenotypic analysis, immunohistochemistry and immunoblots. In addition, primary murine microglia and astrocytes, the brain's primary IFN-I-responding cells, were acutely treated with IFN-α and the global phosphoproteome was similarly analyzed.ResultsWe identified widespread protein phosphorylation as a novel mechanism by which IFN-I mediate their effects. In our mouse model for IFN-I-induced neurodegeneration, protein phosphorylation, rather than the proteome, aligned with the clinical hallmarks and pathological outcome, including impaired development, motor dysfunction and seizures. In vitro experiments revealed extensive and rapid IFN-I-induced protein phosphorylation in microglia and astrocytes. Response to acute IFN-I stimulation was independent of gene expression and mediated by a small number of kinase families. The changes in the phosphoproteome affected a diverse range of cellular processes and functional analysis suggested that this response induced an immediate reactive state and prepared cells for subsequent transcriptional responses.ConclusionsOur studies reveal a hitherto unappreciated role for changes in the protein phosphorylation landscape in cellular responses to IFN-I and thus provide insights for novel diagnostic and therapeutic strategies for neurological diseases caused by IFN-I.
Tocilizumab in HIV patient with severe COVID-19: case report
Authors: Bertozzi Pedro Vieira , de Oliveira Vicente Amanda , Pereira Amanda Siqueira , de Sant’Ana Joao Pedro Espinha , Mano Rafaela Braga Cabrera , Jorge Luciana Souza , da Silva Sardenberg Rodrigo Afonso 
Published: October 2021

Abstract
Background
A 73-year-old male patient who had a history of Human Immunodeficiency Virus (HIV) infection for over 20 years was diagnosed with SARS-CoV-2 infection.

Case presentation
The patient was admitted to the Intensive Care Unit (ICU), where he remained for 25 days, due to a severe condition. Intubation, hemodialysis, and tracheostomy were necessary to maintain homeostasis. In addition to regular treatment with etravirine, dolutegravir, darunavir, and ritonavir for highly active antiretroviral therapy, the patient received tocilizumab, which showed a great recovery in the patient’s condition.

Conclusion
The patient had several risk factors, such as male gender, age  >  70 years, and arterial hypertension. The use of tocilizumab was of great importance in the patient’s recovery since the drug increased his immune response, which is deficient, due to HIV infection.
The anti-diabetic effects of betanin in streptozotocin-induced diabetic rats through modulating AMPK/SIRT1/NF-κB signaling pathway
Authors: Abedimanesh Nasim , Asghari Somayyeh , Mohammadnejad Kosar , Daneshvar Zahra , Rahmani Soudeh , Shokoohi Samaneh , Farzaneh Amir Hasan , Hosseini Seyed Hojjat , Jafari Anarkooli Iraj , Noubarani Maryam , Andalib Sina , Eskandari Mohammad Reza , Motlagh Behrooz 
Published: October 2021

Abstract
Background
In the last few years, the effects of bioactive food components have received much attention because of their beneficial effects including decreasing inflammation, scavenging free radicals, and regulating cell signaling pathways. Betanin as a potent antioxidant has been previously reported to exhibit anti diabetic effects. The present study aimed to evaluate the effects of betanin on glycemic control, lipid profile, hepatic function tests, as well as the gene expression levels of 5′ adenosine monophosphate‑activated protein kinase (AMPK), sirtuin-1 (SIRT1), and nuclear factor kappa B (NF‑κB) in streptozocin (STZ) induced diabetic rats.

Methods
Diabetes was induced in male Sprague–Dawley rats by intraperitoneal administration of STZ. Different doses of betanin (10, 20 and 40 mg/kg.b.w) was administered to diabetic rats for 28 days. Fasting blood glucose and serum insulin were measured. The histopathology of liver and pancreas tissue evaluated. Real-time PCR was performed to assess gene expression levels.

Results
Treatment of diabetic rats with betanin (10 and 20 mg/kg.b.w) reduced FBG levels compared to the control diabetic rats (P < 0.001). Betanin at the dose of 20 mg/kg.b.w was most effective in increasing serum insulin levels (P < 0.001) improving glucose tolerance test (GTT) as well as improvement in lipid profile and liver enzymes levels. According to histopathologic assay, different damages induced by STZ to liver and pancreas tissues was largely eliminated by treatment with 10 and 20 mg/kg.b.w of betanin. Betanin also significantly upregulated the AMPK and SIRT1 and downregulated the NF-κB mRNA expression compared to the diabetic control rats (P < 0.05).

Conclusion
Betanin could modulate AMPK/SIRT1/NF-κB signaling pathway and this may be one of its anti-diabetic molecular mechanisms.
Selection of medicinal plants for traditional medicines in Nepal
Authors: Kutal Durga H. , Kunwar Ripu M. , Uprety Yadav , Adhikari Yagya P. , Bhattarai Shandesh , Adhikari Binaya , Kunwar Laxmi M. , Bhatt Man D. , Bussmann Rainer W. 
Published: October 2021

AbstractBackgroundThere are handful hypothesis-driven ethnobotanical studies in Nepal. In this study, we tested the non-random medicinal plant selection hypothesis using national- and community-level datasets through three different types of regression: linear model with raw data, linear model with log-transformed data and negative binomial model.MethodsFor each of these model, we identified over-utilized families as those with highest positive Studentized residuals and underutilized families with highest negative Studentized residuals. The national-level data were collected from online databases and available literature while the community-level data were collected from Baitadi and Darchula districts.ResultsBoth dataset showed larger variance (national dataset mean 6.51 < variance 156.31, community dataset mean 1.16 < variance 2.38). All three types of regression were important to determine the medicinal plant species selection and use differences among the total plant families, although negative binomial regression was most useful. The negative binomial showed a positive nonlinear relationship between total plant family size and number of medicinal species per family for the national dataset (β1 = 0.0160 ± 0.0009,Z1 = 16.59,p < 0.00001, AIC1 = 1181), and with similar slope and stronger performance for the community dataset (β2 = 0.1747 ± 0.0199,Z2 = 8.76,p < 0.00001, AIC2 = 270.78). Moraceae and Euphorbiaceae were found over-utilized while Rosaceae, Cyperaceae and Caryophyllaceae were recorded as underutilized.ConclusionsAs our datasets showed larger variance, negative binomial regression was found the most useful for testing non-random medicinal plant selection hypothesis. The predictions made by non-random selection of medicinal plants hypothesis holds true for community-level studies. The identification of over-utilized families is the first step toward sustainable conservation of plant resources and it provides a baseline for pharmacological research that might be leading to drug discovery.
Combined therapy of platelet-rich plasma and basic fibroblast growth factor using gelatin-hydrogel sheet for rotator cuff healing in rat models
Authors: Kataoka Takeshi , Mifune Yutaka , Inui Atsuyuki , Nishimoto Hanako , Kurosawa Takashi , Yamaura Kohei , Mukohara Shintaro , Matsushita Takehiko , Niikura Takahiro , Tabata Yasuhiko , Kuroda Ryosuke 
Published: October 2021

Abstract
Introduction
Excellent outcomes of arthroscopic rotator cuff repair for small and medium tears have been recently reported. However, re-tears after surgery have been a common complication after surgical repair of large and massive rotator cuff tears and often occur in early postoperative phase. It was previously reported that basic fibroblast growth factor and platelet-rich plasma enhanced rotator cuff tear healing. We hypothesized that this combined therapy could enhance rotator cuff healing after rotator cuff repair in a rat model. This study aimed to evaluate the efficacy of combined therapy of platelet-rich plasma and basic fibroblast growth factor with gelatin-hydrogel sheet.

Methods
To create a rotator cuff defect, the infraspinatus tendon of Sprague Dawley rat was resected from the greater tuberosity. The infraspinatus tendons were repaired and covered with gelatin-hydrogel sheet impregnated with PBS (control group), basic fibroblast growth factor (bFGF group), platelet-rich plasma (PRP group), or both basic fibroblast growth factor and platelet-rich plasma (combined group). Histological examinations were conducted using hematoxylin and eosin, safranin O, and immunofluorescence staining, such as Isolectin B4, type II collagen at 2 weeks postoperatively. For mechanical analysis, ultimate failure load of the tendon-humeral head complex was evaluated at 6 weeks postoperatively.

Results
In the hematoxylin and eosin staining, the tendon maturing score of the combined group was higher than that of the control group at postoperative 2 weeks. In the safranin O staining, stronger proteoglycan staining was observed in the combined group compared with the other groups at postoperative 2 weeks. Vascular staining with isolectin B4 in 3 treatment groups was significantly higher than that in the control group. Type II collagen expression in the combined group was significantly higher than those in the other groups. The ultimate failure load of the combined group was significantly higher than that of the control group.

Conclusion
Combined therapy of basic fibroblast growth factor and platelet-rich plasma promoted angiogenesis, tendon maturing and fibrocartilage regeneration at the enthesis, which could enhance the mechanical strength. It was suggested that combined basic fibroblast growth factor and platelet-rich plasma might enhance both tendon and bone–tendon junction healing, and basic fibroblast growth factor and platelet-rich plasma might be synergistic.
A double-blind, placebo-controlled, randomized trial of PXT3003 for the treatment of Charcot–Marie–Tooth type 1A
Authors: Attarian Shahram , Young Peter , Brannagan Thomas H. , Adams David , Van Damme Philip , Thomas Florian P. , Casanovas Carlos , Kafaie Jafar , Tard Céline , Walter Maggie C. , Péréon Yann , Walk David , Stino Amro , de Visser Marianne , Verhamme Camiel , Amato Anthony , Carter Gregory , Magy Laurent , Statland Jeffrey M. , Felice Kevin 
Published: October 2021

Abstract
Background
Charcot–Marie–Tooth disease type 1A (CMT1A) is a rare, orphan, hereditary neuromuscular disorder with no cure and for which only symptomatic treatment is currently available. A previous phase 2 trial has shown preliminary evidence of efficacy for PXT3003 in treating CMT1A. This phase 3, international, randomized, double-blind, placebo-controlled study further investigated the efficacy and safety of high- or low-dose PXT3003 (baclofen/naltrexone/D-sorbitol [mg]: 6/0.70/210 or 3/0.35/105) in treating subjects with mild to moderate CMT1A.

Methods
In this study, 323 subjects with mild-to-moderate CMT1A were randomly assigned in a 1:1:1 ratio to receive 5 mL of high- or low-dose PXT3003, or placebo, orally twice daily for up to 15 months. Efficacy was assessed using the change in Overall Neuropathy Limitations Scale total score from baseline to months 12 and 15 (primary endpoint). Secondary endpoints included the 10-m walk test and other assessments. The high-dose group was discontinued early due to unexpected crystal formation in the high-dose formulation, which resulted in an unanticipated high discontinuation rate, overall and especially in the high-dose group. The statistical analysis plan was adapted to account for the large amount of missing data before database lock, and a modified full analysis set was used in the main analyses. Two sensitivity analyses were performed to check the interpretation based on the use of the modified full analysis set.

Results
High-dose PXT3003 demonstrated significant improvement in the Overall Neuropathy Limitations Scale total score vs placebo (mean difference: − 0.37 points; 97.5% CI [− 0.68 to − 0.06]; p = 0.008), and consistent treatment effects were shown in the sensitivity analyses. Both PXT3003 doses were safe and well-tolerated.

Conclusion
The high-dose group demonstrated a statistically significant improvement in the primary endpoint and a good safety profile. Overall, high-dose PXT3003 is a promising treatment option for patients with Charcot–Marie–Tooth disease type 1A.
The role of the tumor microbe microenvironment in the tumor immune microenvironment: bystander, activator, or inhibitor?
Authors: Ma Jiayao , Huang Lingjuan , Hu Die , Zeng Shan , Han Ying , Shen Hong 
Published: October 2021

AbstractThe efficacy of cancer immunotherapy largely depends on the tumor microenvironment, especially the tumor immune microenvironment. Emerging studies have claimed that microbes reside within tumor cells and immune cells, suggesting that these microbes can impact the state of the tumor immune microenvironment. For the first time, this review delineates the landscape of intra-tumoral microbes and their products, herein defined as the tumor microbe microenvironment. The role of the tumor microbe microenvironment in the tumor immune microenvironment is multifaceted: either as an immune activator, inhibitor, or bystander. The underlying mechanisms include: (I) the presentation of microbial antigens by cancer cells and immune cells, (II) microbial antigens mimicry shared with tumor antigens, (III) microbe-induced immunogenic cell death, (IV) microbial adjuvanticity mediated by pattern recognition receptors, (V) microbe-derived metabolites, and (VI) microbial stimulation of inhibitory checkpoints. The review further suggests the use of potential modulation strategies of the tumor microbe microenvironment to enhance the efficacy and reduce the adverse effects of checkpoint inhibitors. Lastly, the review highlights some critical questions awaiting to be answered in this field and provides possible solutions. Overall, the tumor microbe microenvironment modulates the tumor immune microenvironment, making it a potential target for improving immunotherapy. It is a novel field facing major challenges and deserves further exploration.
Serological assessment of collagen fragments and tumor fibrosis may guide immune checkpoint inhibitor therapy
Authors: Jensen Christina , Nissen Neel I. , Von Arenstorff Claus S. , Karsdal Morten A. , Willumsen Nicholas 
Published: October 2021

AbstractDespite the overall clinical success of immune checkpoint inhibitors (ICIs) for treating patients with solid tumors, a large number of patients do not benefit from this approach. Consequently, there is a need for predictive biomarkers. The most prevalent biomarkers such as PD-L1 expression and tumor mutational burden (TMB) do not reliably predict response to ICIs across different solid tumor types suggesting that a broader view of regulating factors in the tumor microenvironment is needed. Emerging evidence indicates that one central common denominator of resistance to ICIs may be fibrotic activity characterized by extracellular matrix (ECM) and collagen production by cancer-associated fibroblasts (CAFs). A fibroblast-and collagen-rich stroma attenuates immunotherapy response by contributing to inhibition and exclusion of T cells. Here we review opportunities and limitations in the utilization of the most prevalent biomarkers for ICIs and elaborate on the unique opportunities with biomarkers originating from the activated fibroblasts producing an impermeable ECM. We propose that ECM and collagen biomarkers measured non-invasively may be a novel and practical approach to optimize treatment strategies and improve patient selection for ICI therapy.