bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vivo Thickness of the Healthy Tympanic Membrane Determined by Optical Coherence Tomography
Authors: Morgenstern Joseph , Kreusch Theodor , Golde Jonas , Steuer Svea , Ossmann Steffen , Kirsten Lars , Walther Julia , Zahnert Thomas , Koch Edmund , Neudert Marcus
Published: February 2024

Objective

Tympanic membrane (TM) thickness is an important parameter for differentiation between a healthy and a pathologic TM. Furthermore, it is needed for modeling the middle ear function. Endoscopic optical coherence tomography (eOCT) provides the opportunity to measure the TM thickness of the entire TM in vivo.

Materials and methods

A total of 27 healthy ears were examined by eOCT. The system uses a light source with a central wavelength of 1,300 nm. The endoscope with an outer diameter of 3.5 mm provides a field of view of 10 mm and a working distance of 10 mm. Thickness measurements were carried out at 8 points on the TM. Additionally, the existing literature was analyzed, and a mean TM thickness value was determined.

Results

The mean thickness of the TM over all measurement points of the pars tensa was 120.2 μm, and the pars flaccida was significantly thicker with a mean thickness of 177.9 μm. Beyond that, there were no significant differences between the single quadrants. The mean TM thickness in the literature was 88.8 μm.

Discussion

EOCT provides the possibility for in vivo thickness determination of the TM. The mean thickness seems to be higher than in the previous studies, which were mostly carried out ex vivo. Our study takes the three-dimensional refraction into account and provides a method for the refraction correction.
Exploring the mechanism of curcumin in the treatment of doxorubicin-induced cardiotoxicity based on network pharmacology and molecular docking technology
Authors: Hu Zhen
Published: February 2024

Doxorubicin (DOX) is one of the most effective chemotherapeutic agents. However, the nonselective effect leads to serious cardiotoxicity risk in clinical use. Curcumin is a well-known dietary polyphenol that showed a protective effect against the cardiotoxic effect of DOX. This study aimed to assess the role of curcumin in protection against DOX-induced cardiotoxicity. Potential compound and disease targets were obtained from relevant databases, and common targets were screened. Protein-protein interaction (PPI) was used to predict the core targets. Gene ontology (GO) bioprocess analysis and Kyoto encyclopedia of genes and genome enrichment analysis enriched the possible biological processes (BP), cellular components, molecular function, and signaling pathways involved. Finally, the binding of curcumin to target proteins was evaluated through molecular docking. The docking score verified the reliability of the prediction results. In total, 205 curcumin and 700 disease targets were identified. A topological analysis of the PPI network revealed 10 core targets including TP53, tumor necrosis factor-alpha (TNF), AKT1, vascular endothelial growth factor A (VEGFA), prostaglandin-endoperoxide synthase 2 (PTGS2), signal transducer and activator of the transcription 3 (STAT3), HIF1A, MYC, epidermal growth factor receptor (EGFR), and CASP3 (Caspase-3). Furthermore, the enrichment analyses indicated that the effects of curcumin were mediated by genes related to oxidation, inflammation, toxification, cell proliferation, migration, apoptosis, wounding, metabolism, proteolysis, and the signaling pathway of calcium (Ca2+). Molecular docking showed that curcumin could bind with the target proteins with strong molecular force, exhibiting good docking activity. Curcumin has a multi-cardioprotective effect by modulating the core targets’ expression in DOX-induced cardiotoxicity. This study elucidated the key target proteins and provided a theoretical basis for further exploring curcumin in the prevention and treatment of DOX-induced cardiotoxicity.
Serum Carbohydrate Antigen 19-9 and Metabolite Hypotaurine Are Predictive Markers for Early Recurrence of Pancreatic Ductal Adenocarcinoma
Authors: Nagao Mina , Oshima Minoru , Suto Hironobu , Sugimoto Masahiro , Enomoto Ayame , Murakami Tomomasa , Shimomura Ayaka , Wada Yukiko , Matsukawa Hiroyuki , Ando Yasuhisa , Kishino Takayoshi , Kumamoto Kensuke , Kobara Hideki , Kamada Hideki , Masaki Tsutomu , Soga Tomoyoshi , Okano Keiichi
Published: February 2024

Objective

A significant number of patients experience early recurrence after surgical resection for pancreatic ductal adenocarcinoma (PDAC), negating the benefit of surgery. The present study conducted clinicopathologic and metabolomic analyses to explore the factors associated with the early recurrence of PDAC.

Materials and Methods

Patients who underwent pancreatectomy for PDAC at Kagawa University Hospital between 2011 and 2020 were enrolled. Tissue samples of PDAC and nonneoplastic pancreas were collected and frozen immediately after resection. Charged metabolites were quantified by capillary electrophoresis-mass spectrometry. Patients who relapsed within 1 year were defined as the early recurrence group.

Results

Frozen tumor tissue and nonneoplastic pancreas were collected from 79 patients. The clinicopathologic analysis identified 11 predictive factors, including preoperative carbohydrate antigen 19-9 levels. The metabolomic analysis revealed that only hypotaurine was a significant risk factor for early recurrence. A multivariate analysis, including clinical and metabolic factors, showed that carbohydrate antigen 19-9 and hypotaurine were independent risk factors for early recurrence (P = 0.045 and P = 0.049, respectively). The recurrence-free survival rate 1 year after surgery with both risk factors was only 25%.

Conclusions

Our results suggested that tumor hypotaurine is a potential metabolite associated with early recurrence. Carbohydrate antigen 19-9 and hypotaurine showed a vital utility for predicting early recurrence.
Sex Cord–Stromal Tumors of the Ovary: An Update and Review. Part I — Pure Ovarian Stromal Tumors
Authors: Devins Kyle M. , Young Robert H. , Oliva Esther
Published: February 2024

In two separate reviews, we review the time-honored but still frequently challenging features of ovarian sex cord–stromal tumors, and also emphasize new developments including unusual morphologic appearances that, despite the relative rarity of many of the tumors, result in a disproportionate number of differential diagnostic problems, variant immunohistochemical profiles, and specific molecular and syndromic associations. These neoplasms are also of historical interest as current knowledge is still based in significant part on the contributions of 2 giants of gynecologic pathology, Dr Robert Meyer and Dr Robert E. Scully. In part I, we present the major clinical, pathologic, and genomic features of the pure ovarian stromal tumors including comments on differential diagnosis and briefly note significant historical contributions. In part II we will discuss pure sex cord and sex cord–stromal tumors.
Ki-67 Proliferation Index Is Associated With Tumor Grade and Survival in Pleural Epithelioid Mesotheliomas
Authors: Galeano Belinda , Smith Caleb J. , Yi Eunhee S. , Roden Anja C. , Jenkins Sarah , Capelle Jenna , Kittle-Francis Mary , Mansfield Aaron S. , Aubry Marie Christine
Published: February 2024

Pleural epithelioid mesothelioma (PEM) is divided into low and high grades based on nuclear atypia, mitoses, and necrosis in the tumor. Assessing mitoses and nuclear atypia tend to be labor-intensive with limited reproducibility. Ki-67 proliferation index was shown to be a prognostic factor in PEM, but its performance has not been directly correlated with tumor grade or mitotic score. This study evaluated the potential of Ki-67 index as a surrogate of tumor grade. We also compared the predictability of mitoses and Ki-67 index for overall survival (OS). Ninety-six PEM samples from 85 patients were identified from the surgical pathology file during 2000-2021 at our institution, and all glass slides were reviewed by 2 pulmonary pathologists to confirm the diagnosis and assign the tumor grade. Digital image analysis (DIA) was done for Ki-67 index. The agreement on tumor grading between 2 reviewers was moderate (kappa value = 0.47). The correlation between mitotic count (average count by 2 reviewers) and Ki-67 index was 0.65. The areas under the curve for predicting tumor grade by mitotic score and Ki-67 index were 0.84 and 0.74 (reviewer 1) and 0.85 and 0.81 (reviewer 2), respectively. High Ki-67 index and mitoses were significantly associated with poor OS (P=0.03 and 0.0005, using 30% and 10/2 mm2 as cutoffs, respectively). In conclusion, Ki-67 index by DIA was associated with tumor grade as well as mitotic count, and its predictability for OS was comparable to that of mitotic score, thus being a potential surrogate for tumor grade.
Combining Transcranial Direct Current Stimulation With Hand Robotic Rehabilitation in Chronic Stroke Patients
Authors: Bernal-Jiménez Juan J. , Dileone Michele , Mordillo-Mateos Laura , Martín-Conty José L. , Durantez-Fernández Carlos , Viñuela Antonio , Martín-Rodríguez Francisco , Lerin-Calvo Alfredo , Alcántara-Porcuna Vanesa , Polonio-López Begoña
Published: February 2024

Objective

This study aimed to assess the impact of combining transcranial direct current stimulation with end-effector robot-assisted treatment on upper limb function, spasticity, and hand dexterity in chronic stroke patients.

Design

This was a prospective, double-blind randomized trial with 20 equally allocated stroke patients. The experimental group received dual transcranial direct current stimulation (anode over affected M1, cathode over contralateral M1) alongside robot-assisted treatment, while the control group received sham transcranial direct current stimulation with the same electrode placement + robot-assisted treatment. Each patient underwent 20 combined transcranial direct current stimulation and robot-assisted treatment sessions. The primary outcome measure was the Fugl-Meyer Upper Limb motor score, with secondary outcomes including AMADEO kinematic measures, Action Research Arm Test, and Functional Independence Measure. Assessments were conducted at baseline, after rehabilitation, and 3 mos later.

Results

Combining bilateral transcranial direct current stimulation with robot-assisted treatment did not yield additional improvements in Fugl-Meyer Upper Limb motor score, Functional Independence Measure, or Action Research Arm Test scores among stroke patients. However, the real transcranial direct current stimulation group showed enhanced finger flexion in the affected hand based on AMADEO kinematic measures.

Conclusions

The addition of transcranial direct current stimulation to robot-assisted treatment did not result in significant overall functional improvements in chronic stroke patients. However, a benefit was observed in finger flexion of the affected hand.
Chronic Use of Prescription Pain Medication and Outcomes in Patients With Burn Injury
Authors: Vu Kevin , Deng Huan , Kelter Brian , Shepler Lauren , Stewart Barclay , Wolf Steven , Mandell Samuel , Bamer Alyssa , Mehta Anupam , Kazis Lewis , Ryan Colleen , Schneider Jeffrey
Published: February 2024

Objective

This study attempts to examine long-term pain medication usage after burn injury and its association with functional and psychosocial outcomes.

Design

This is a multicenter retrospective cohort study utilizing the Burn Model System National Longitudinal Database. Participants injured from 2015 to 2021 were divided into two groups, those taking and not taking prescription pain medication at 12 mos after injury. Regression analyses examined associations between pain medication use and outcomes at 12 mos, adjusting for demographics, burn size, length of hospital stay, and preinjury pain medication use and employment status. Outcomes included VR-12 Physical and Mental Component Summary scores Patient-Reported Outcomes Measurement Information System Anxiety and Depression scores, Satisfaction with Life Scale, and employment status.

Results

Of 358 participants analyzed, prescription pain medication use was associated with worse outcomes at 12 mos: Physical Component Summary (β = −7.11, P < 0.001), Mental Component Summary (β = −6.01, P < 0.001), and Patient-Reported Outcomes Measurement Information System Depression (β = 4.88, P < 0.001) and Anxiety (β = 6.16, P < 0.001). Satisfaction with Life Scale was not significantly associated with pain medication use (P = 0.069) and those taking pain medication were 52% less likely to be employed at 12 mos (P = 0.035).

Conclusions

There is a significant association between prescription pain medication use and worse physical, mental, and employment outcomes at 12 mos after burn injury.
Application and accuracy of the EAPC/IASP diagnostic algorithm for neuropathic cancer pain and quantitative sensory testing profile in patients with pain due to cancer
Authors: Shkodra Morena , Mulvey Matthew , Fallon Marie , Brunelli Cinzia , Zecca Ernesto , Bracchi Paola , Caputo Mariangela , Massa Giacomo , Lo Dico Silvia , Rolke Roman , Kaasa Stein , Caraceni Augusto
Published: February 2024

Introduction:

Better diagnosis and treatment of neuropathic cancer pain (NcP) remains an unmet clinical need. The EAPC/IASP algorithm was specifically designed for NcP diagnosis; yet, to date, there is no information on its application and accuracy.

Objectives:

Our aim was to determine the accuracy of the EAPC/IASP algorithm compared with the Neuropathic Special Interest Group grading system (gold standard) and to describe patients' sensory profile with quantitative sensory testing (QST).

Methods:

This is a cross-sectional observational study conducted in a palliative care and pain outpatient clinic. Patients with cancer pain intensity ≥3 (numerical rating scale 0–10) were eligible. The palliative care physician applied the EAPC/IASP algorithm as a grading system to diagnose probable or definite NcP, and an independent investigator applied the gold standard and performed the QST. Sensitivity and specificity of the EAPC/IASP algorithm were measured in comparison with the gold standard results. Kruskal–Wallis and unequal variance independent-samples t tests were used to compare the QST parameters in patients with and without NcP.

Results:

Ninety-eight patients were enrolled from August 2020 to March 2023. Sensitivity and specificity for the EAPC/IASP algorithm were 85% (95% CI 70.2–94.3) and 98.3% (95% CI 90.8–100), respectively. Patients with NcP in contrast to patients without NcP showed cold hypoesthesia (P = 0.0032), warm hypoesthesia (P = 0.0018), pressure hyperalgesia (P = 0.02), and the presence of allodynia (P = 0.0001).

Conclusion:

The results indicate a good performance of the EAPC/IASP algorithm in diagnosing NcP and the QST discriminated well between patients with and without NcP.
Pharmacokinetics of Single-Dose Versus Double-Dose Dolutegravir After Switching From a Failing Efavirenz-Based Regimen
Authors: Griesel Rulan , Banda Clifford G. , Zhao Ying , Omar Zaayid , Wiesner Lubbe , Meintjes Graeme , Sinxadi Phumla , Maartens Gary
Published: February 2024

Background:

Dolutegravir exposure is reduced after switching from efavirenz, which could select for dolutegravir resistance if switching occurs during virologic failure.

Methods:

We measured serial dolutegravir trough concentrations after switching from efavirenz in a clinical trial, which randomized some participants to a supplemental dolutegravir dose or placebo for the first 14 days. Changes in dolutegravir trough concentrations between days 3, 7, 14, and 28 were evaluated. The primary outcome was the geometric mean ratio of dolutegravir trough concentrations on day 7 versus day 28.

Results:

Twenty-four participants received double-dose dolutegravir (50 mg twice daily) and 11 standard dose for the first 14 days. Baseline characteristics were 77% female, median age 36 years, CD4 cell count 254 cells/mm3, and HIV-1 RNA 4.0 log10 copies/mL. The geometric mean ratio (90% CI) of dolutegravir trough concentrations on day 7 versus day 28 was 0.637 (0.485 to 0.837) in the standard-dose group and 1.654 (1.404 to 1.948) in the double-dose group. There was a prolonged induction effect at day 28 in participants with efavirenz slow metaboliser genotypes. One participant in the double-dose group had a dolutegravir trough concentration below the protein-binding adjusted concentration needed to inhibit 90% of HIV-1 (PA-IC90) at day 3.

Conclusions:

No participants on standard-dose dolutegravir had dolutegravir trough concentrations below the PA-IC90. Slow efavirenz metaboliser genotypes had higher baseline efavirenz concentrations and more pronounced and longer period of induction postswitch. These findings suggest that a 14-day lead-in supplemental dolutegravir dose may not be necessary when switching from a failing efavirenz-based first-line regimen.
The Promise of Complement Therapeutics in Solid Organ Transplantation
Authors: Steggerda Justin A. , Heeger Peter S.
Published: February 2024

Transplantation is the ideal therapy for end-stage organ failure, but outcomes for all transplant organs are suboptimal, underscoring the need to develop novel approaches to improve graft survival and function. The complement system, traditionally considered a component of innate immunity, is now known to broadly control inflammation and crucially contribute to induction and function of adaptive T-cell and B-cell immune responses, including those induced by alloantigens. Interest of pharmaceutical industries in complement therapeutics for nontransplant indications and the understanding that the complement system contributes to solid organ transplantation injury through multiple mechanisms raise the possibility that targeting specific complement components could improve transplant outcomes and patient health. Here, we provide an overview of complement biology and review the roles and mechanisms through which the complement system is pathogenically linked to solid organ transplant injury. We then discuss how this knowledge has been translated into novel therapeutic strategies to improve organ transplant outcomes and identify areas for future investigation. Although the clinical application of complement-targeted therapies in transplantation remains in its infancy, the increasing availability of new agents in this arena provides a rich environment for potentially transformative translational transplant research.
Kidney Transplantation Outcomes From Uncontrolled Donation After Circulatory Death: A Systematic Review and Meta-analysis
Authors: Vijayan Keshini , Schroder Hugh J. , Hameed Ahmer , Hitos Kerry , Lo Warren , Laurence Jerome M. , Yoon Peter D. , Nahm Christopher , Lim Wai H. , Lee Taina , Yuen Lawrence , Wong Germaine , Pleass Henry
Published: February 2024

Background.

Uncontrolled donation after circulatory death (uDCD) is a potential additional source of donor kidneys. This study reviewed uDCD kidney transplant outcomes to determine if these are comparable to controlled donation after circulatory death (cDCD).

Methods.

MEDLINE, Cochrane, and Embase databases were searched. Data on demographic information and transplant outcomes were extracted from included studies. Meta-analyses were performed, and risk ratios (RR) were estimated to compare transplant outcomes from uDCD to cDCD.

Results.

Nine cohort studies were included, from 2178 uDCD kidney transplants. There was a moderate degree of bias, as 4 studies did not account for potential confounding factors. The median incidence of primary nonfunction in uDCD was 12.3% versus 5.7% for cDCD (RR, 1.85; 95% confidence intervals, 1.06-3.23; P = 0.03, I2 = 75). The median rate of delayed graft function was 65.1% for uDCD and 52.0% for cDCD. The median 1-y graft survival for uDCD was 82.7% compared with 87.5% for cDCD (RR, 1.43; 95% confidence intervals, 1.02-2.01; P = 0.04; I2 = 71%). The median 5-y graft survival for uDCD and cDCD was 70% each. Notably, the use of normothermic regional perfusion improved primary nonfunction rates in uDCD grafts.

Conclusions.

Although uDCD outcomes may be inferior in the short-term, the long-term outcomes are comparable to cDCD.
Assessment of IgM DSAs in Transplant Recipients: Relationship to De Novo IgG DSAs and Risk for Antibody Rejection
Authors: Zhang Xiaohai , Jordan Stanley C.
Published: February 2024

Background.

The presence of anti-HLA donor-specific antibodies (DSAs) is associated with antibody-mediated rejection (AMR) and inferior graft survival. However, recent data suggest that ~50% of AMR episodes are IgG DSA negative and possibly related to non-HLA DSAs. After the initial activation of B cells to alloantigen, IgM is the first immunoglobulin produced. In addition, both IgM and IgG isotopes can activate the classic complement pathway and induce complement-dependent cytotoxicity to allograft targets. Current practices focus on the assessment of IgG DSAs with little concern for the assessment of IgM DSAs.

Methods.

Here, we examined anti-HLA IgM in a cohort of 22 patients who developed de novo IgG DSAs by a modified single-antigen bead-based test.

Results.

We found IgM HLA DSAs developed before IgG DSAs. The median time from the detection of IgM DSAs to the appearance of de novo IgG DSAs was 461 d. Most patients had IgM DSAs against the same HLA-DQ antigens, for which IgG de novo DSAs were also later detected. IgM DSAs were detected in patients with biopsies suspected of AMR.

Conclusions.

The detection of IgM DSAs could be an early indicator of alloimmune responses to allografts before IgG de novo DSAs appear.
Abdominal Wall Tension and Early Outcomes after Posterior Component Separation with Transversus Abdominis Release: Does a “Tension-Free” Closure Really Matter?
Authors: Miller Benjamin T , Ellis Ryan C , Maskal Sara M , Petro Clayton C , Krpata David M , Prabhu Ajita S , Beffa Lucas RA , Tu Chao , Rosen Michael J
Published: February 2024

BACKGROUND:

Ventral hernias result in fibrosis of the lateral abdominal wall muscles, increasing tension on fascial closure. Little is known about the effect of abdominal wall tension on outcomes after abdominal wall reconstruction. We aimed to identify an association between abdominal wall tension and early postoperative outcomes in patients who underwent posterior component separation (PCS) with transversus abdominis release (TAR).

STUDY DESIGN:

Using a proprietary, sterilizable tensiometer, the tension needed to bring the anterior fascial elements to the midline of the abdominal wall during PCS with TAR was recorded. Tensiometer measurements, in pounds (lb), were calibrated by accounting for the acceleration of Earth’s gravity. Baseline fascial tension, change in fascial tension, and fascial tension at closure were evaluated with respect to 30-day outcomes, including wound morbidity, hospital readmission, reoperation, ileus, bleeding, and pulmonary complications.

RESULTS:

A total of 100 patients underwent bilateral abdominal wall tensiometry, for a total of 200 measurements (left and right side for each patient). Mean baseline anterior fascial tension was 6.78 lb (SD 4.55) on each side. At abdominal closure, the mean anterior fascial tension was 3.12 (SD 3.21) lb on each side. Baseline fascial tension and fascial tension after PCS with TAR at abdominal closure were not associated with surgical site infection, surgical site occurrence, readmission, ileus, and bleeding requiring transfusion. The event rates for all other complications were too infrequent for statistical analysis.

CONCLUSIONS:

Baseline and residual fascial tension of the anterior abdominal wall do not correlate with early postoperative morbidity in patients undergoing PCS with TAR. Further work is needed to determine if abdominal wall tension in this context is associated with long-term outcomes, such as hernia recurrence.
Microfungal flora of Apis mellifera anatoliaca (Hymenoptera: Apidae) and Varroa destructor (Mesostigmata: Varroidae) from the Eastern Black Sea Region and fungal vector capacity in honey bee colonies
Authors: Usta Mehtap
Published: February 2024

Honey bees have a great economic importance both in Turkey and in the world due to the products they produce and their contribution to pollination. For this reason, many microflora and microbiota studies have been conducted on bees. While these research were primarily focused on pathogen isolation, the ecological roles of non-pathogenic flora members and how they may be used are now being studied more extensively. Considering the importance of pathogens, the number of studies is expected to continue to increase. This study was carried out to determine the microfungal flora of the body surfaces and digestive tracts of dead honey bee (Apis mellifera anatoliaca) and Varroa destructor samples taken from different apiaries in the Eastern Black Sea Region of Turkey (Gümüşhane, Trabzon, Artvin and Ordu) in 2022. As a result of the study, a total of 11 different fungal species belonging to the genera Penicillium, Alternaria, Mucor, Trichoderma, Fusarium, Aspergillus and Verticillium were identified and the relationships of these fungi with bees were discussed based on the literature.
CRM1 regulates androgen receptor stability and impacts DNA repair pathways in prostate cancer, independent of the androgen receptor
Authors: Kumar Rajendra , Mendonca Janet , Shetty Abhishek , Yang Yuhan , Owoyemi Olutosin , Wilson Lillian , Boyapati Kavya , Topiwala Deven , Thomas Naiju , Nguyen Huong , Luo Jun , Paller Channing J. , Denmeade Samuel , Carducci Michael A. , Kachhap Sushant K.
Published: February 2024

Among the known nuclear exportins, CRM1 is the most studied prototype. Dysregulation of CRM1 occurs in many cancers, hence, understanding the role of CRM1 in cancer can help in developing synergistic therapeutics. The study investigates how CRM1 affects prostate cancer growth and survival. It examines the role of CRM1 in regulating androgen receptor (AR) and DNA repair in prostate cancer. Our findings reveal that CRM1 influences AR mRNA and protein stability, leading to a loss of AR protein upon CRM1 inhibition. Furthermore, it highlights the involvement of HSP90 alpha, a known AR chaperone, in the CRM1-dependent regulation of AR protein stability. The combination of CRM1 inhibition with an HSP90 inhibitor demonstrates potent effects on decreasing prostate cancer cell growth and survival. The study further explores the influence of CRM1 on DNA repair proteins and proposes a strategy of combining CRM1 inhibitors with DNA repair pathway inhibitors to decrease prostate cancer growth. Overall, the findings suggest that CRM1 plays a crucial role in prostate cancer growth, and a combination of inhibitors targeting CRM1 and DNA repair pathways could be a promising therapeutic strategy.
Enhanced Fc Receptor expression and distinct immunomodulatory properties of neutrophils during HIV-1 infection and therapy
Authors: Marsile-Medun Soledad , Souchard Manon , Abba Moussa Daouda , Lorin Valérie , Mouquet Hugo , Reynaud Elisa , Dibsy Rayane , Tuaillon Edouard , Muriaux Delphine , Ngo Giang , Pugnière Martine , Naranjo-Gomez Mar , Pelegrin Mireia
Published: February 2024

Neutrophils are innate immune cells that display multiple immunomodulatory properties. Using a mouse model of retroviral infection, we previously uncovered their key immunomodulatory function in promoting protective immunity during antiviral antibody therapy, which occurs through Fc-FcγR interactions. Here, we investigated the immunomodulatory properties of neutrophils in the context of HIV-1 infection and therapy. We conducted a thorough examination of the functional activation and modulation of Fcγ receptors (FcγRs) expression on neutrophils isolated from healthy donors (HD) and people living with HIV-1 (PLWH). Upon stimulation with virions, either free or in the form of immune complexes (ICs) formed with broadly neutralizing antibodies (bNAbs), neutrophils from HD secreted cytokines and chemokines in modest quantities. Interestingly, priming HD neutrophils with pro-inflammatory cytokines augmented their chemokine production upon exposure to HIV-1 and ICs, underscoring the pivotal role of the inflammatory milieu in eliciting a functional response from neutrophils to these stimuli. Noteworthy, under inflammatory conditions, IC-activated neutrophils showed higher secretion of CXCL1 and CCL4 than HIV-1-stimulated neutrophils. Highlighting the critical influence of the inflammatory environment on their functional properties, neutrophils from PLWH displayed increased release of cytokines (IFNγ) and chemokines (CXCL1, CCL2, CCL3 and CCL4) when stimulated with danger signals associated with HIV-1 infection. In addition, PLWH’s neutrophils exhibited higher expression of two activating FcgRs (FcgRI and FcgRIII) than neutrophils from HD. Our study provides new insights into the immunomodulatory properties of neutrophils during HIV-1 infection and therapy. These findings hold potential for optimizing antiviral antibody therapies by harnessing the immunomodulatory properties of neutrophils.
SIMHYB 2: a software tool to explore and illustrate evolutionary forces in Population Genetics teaching and research. Application to Conservation Genetics
Authors: Soto Álvaro , Rodríguez-Martínez David , López de Heredia Unai
Published: February 2024

Practical approaches have become a standard in many scientific disciplines, including population genetics. By analyzing properly selected datasets, the students can calculate parameters and draw conclusions about genetic diversity, differentiation and evolution of populations with higher efficiency than if based exclusively on theoretical lessons. However, preparing the appropriate datasets is a hard task and a wrong selection can spoil a well-aimed practice. Here we present SimHyb2, a software tool specifically intended to ease the full understanding of evolutionary forces by the students and to help the teacher to prepare adequate datasets and examples for the practices. It simulates the course of a mixed population under user-defined reproductive and evolutionary conditions. Outputs can be easily adapted for downstream analysis with other popular tools as GenAlExor Structure. Thus, SimHyb2 is very suitable for project-based-learning approaches: students can produce their own datasets in different scenarios of genetic drift, migration, selective advantage, reproductive success… Additionally, SimHyb2 is the only simulation software available to date providing traceable pedigrees of individuals, being therefore very convenient for preparing datasets for parentage analysis, spatial genetic structure or conservation genetics study cases. Satisfactory results from its ongoing utilization in higher education and research are reported.
Structural enrichment attenuates colitis-associated colon cancer
Authors: Sykes Delawrence J. , Solanki Sumeet , Chukkapalli Sahiti , Williams Keyonna , Newman Erika A. , Resnicow Kenneth , Shah Yatrik M
Published: February 2024

Colorectal cancer (CRC) is a major public health concern and disproportionately impacts racial/ethnic minority populations in the US. Animal models are helpful in examining human health disparities because many stress-induced human health conditions can be recapitulated using mouse models. Azoxymethane (AOM)/ dextran sodium sulfate (DSS) treatment can be used to model colitis-associated cancers. While colitis-associated cancers account for only 2% of colon cancers, the AOM/DSS model is useful for examining links between inflammation, immunity, and colon cancer. Mice were housed in enriched and impoverished environments for 1-month prior to behavioral testing. Following behavioral testing the mice were subjected to the AOM/DSS model. While our analysis revealed no significant behavioral variances between the impoverished and enriched housing conditions, we found significant effects in tumorigenesis. Enriched mice had fewer tumors and smaller tumor volumes compared to impoverished mice. African Americans are at higher risk for early onset colorectal cancers in part due to social economic status. Furthermore, housing conditions and environment may reflect social economic status. Research aimed at understanding links between social economic status and colorectal cancer progression is important for eliminating disparities in health outcomes.
INTREPPPID - An Orthologue-Informed Quintuplet Network for Cross-Species Prediction of Protein-Protein Interaction
Authors: Szymborski Joseph , Emad Amin
Published: February 2024

An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated “wet lab” experiments.In silicoPPI inference methods are ideal tools to overcome these limitations, but often struggle with cross-species predictions. We present INTREPPPID, a method which incorporates orthology data using a new “quintuplet” neural network, which is constructed with five parallel encoders with shared parameters. INTREPPPID incorporates both a PPI classification task and an orthologous locality task. The latter learns embeddings of orthologues that have small Euclidean distances between them and large distances between embeddings of all other proteins. INTREPPPID outperforms all other leading PPI inference methods tested on both the intra-species and cross-species tasks using strict evaluation datasets. We show that INTREPPPID’s orthologous locality loss increases performance because of the biological relevance of the orthologue data, and not due to some other specious aspect of the architecture. Finally, we introduce PPI.bio and PPI Origami, a web server interface for INTREPPPID and a software tool for creating strict evaluation datasets, respectively. Together, these two initiatives aim to make both the use and development of PPI inference tools more accessible to the community.

GRAPHICAL ABSTRACT
Cell Size Controls Photosynthetic Capacity in a Mesoamerican and an Andean Genotype ofPhaseolus vulgarisL
Authors: Egesa Andrew Ogolla , Eduardo Vallejos C. , Begcy Kevin
Published: February 2024

The efficiency of CO2flux in the leaf is hindered by a several structural and biochemical barriers which affect the overall net photosynthesis. However, the dearth of information about the genetic control of these features is limiting our ability for genetic manipulation. We performed a comparative analysis between a Mesoamerican and an Andean cultivar ofPhaseolus vulgarisat variable light and CO2levels. The Mesoamerican bean had higher photosynthetic rate, maximum rate of rubisco carboxylase activity and maximum rate of photosynthetic electron transport at light saturation conditions than its Andean counterpart. Leaf anatomy comparison between genotypes showed that the Mesoamerican bean had smaller cell sizes than the Andean bean. Smaller epidermal cells in the Mesoamerican bean resulted in higher stomata density and consequently higher stomatal conductance for water vapor and CO2than in the Andean bean. Likewise, smaller palisade and spongy mesophyll cells in the Mesoamerican than in the Andean bean increased the cell surface area per unit of volume and consequently increased mesophyll conductance. Finally, smaller cells in the Mesoamerican also increased chlorophyll and protein concentration per unit of leaf area. In summary, we show that differential cell size controls the overall net photosynthesis and could be used as a target for genetic manipulation to improve photosynthesis.

Highlight

PhotosyntheUc performance comparison between a Mesoamerican and an Andean bean genotype showed higher rate at increased light and CO2levels. Differences could be explained by variaUon in cell size.
Neuroestrogens facilitate male-typical behaviors by potentiating androgen receptor signaling in medaka
Authors: Nishiike Yuji , Maki Shizuku , Miyazoe Daichi , Nakasone Kiyoshi , Kamei Yasuhiro , Todo Takeshi , Ishikawa-Fujiwara Tomoko , Ohno Kaoru , Usami Takeshi , Nagahama Yoshitaka , Okubo Kataaki
Published: February 2024

In rodents, estrogens aromatized from androgens in the brain, also known as neuroestrogens, are essential for the development of male-typical behaviors. In many other vertebrates including humans and teleost fish, however, androgens facilitate these behaviors directly via the androgen receptor without aromatization into estrogens. Here we report that male medaka fish lacking Cyp19a1b (a subtype of aromatase predominantly expressed in the brain) exhibit severely impaired male-typical mating and aggression, despite elevated brain androgen levels. These phenotypes can be rescued by estrogen administration, indicating that neuroestrogens are pivotal for male-typical behaviors even in non-rodents. Our results further suggest that neuroestrogens facilitate male-typical behaviors by potentiating androgen action in the brain via the direct stimulation of androgen receptor transcription, thereby revealing a previously unappreciated mechanism of action of neuroestrogens. We additionally show that female fish lacking Cyp19a1b are less receptive to male courtship and conversely court other females, highlighting the significance of neuroestrogens in establishing sex-typical behaviors in both sexes.
The Interaction of NF-κB Transcription Factor with Centromeric Chromatin
Authors: Filliaux Shaun , Bertelsen Chloe , Baughman Hannah , Komives Elizabeth , Lyubchenko Yuri L.
Published: February 2024

Centromeric chromatin is a subset of chromatin structure and governs chromosome segregation. The centromere is composed of both CENP-A nucleosomes (CENP-Anuc) and H3 nucleosomes (H3nuc) and is enriched with alpha-satellite (α-sat) DNA repeats. These CENP-Anuchave a different structure than H3nuc, decreasing the base pairs (bp) of wrapped DNA from 147 bp for H3nucto 121 bp for CENP-Anuc. All these factors can contribute to centromere function. We investigated the interaction of H3nucand CENP-Anucwith NF-κB, a crucial transcription factor in regulating immune response and inflammation. We utilized Atomic Force Microscopy (AFM) to characterize complexes of both types of nucleosomes with NF-κB. We found that NF-κB unravels H3nuc, removing more than 20 bp of DNA, and that NF-κB binds to the nucleosomal core. Similar results were obtained for the truncated variant of NF-κB comprised only of the Rel Homology domain and missing the transcription activation domain (TAD), suggesting the RelA TAD is not critical in unraveling H3nuc. By contrast, NF-κB did not bind to or unravel CENP- Anuc. These findings with different affinities for two types of nucleosomes to NF-κB may have implications for understanding the mechanisms of gene expression in bulk and centromere chromatin.
Indicators of a data-deficient taxa: combining bird and environmental data enhances predictive accuracy of wild bee richness
Authors: Rousseau Josée S. , Johnston Alison , Rodewald Amanda D.
Published: February 2024

Widespread declines in wild bee populations necessitate urgent action, but there remains insufficient data to guide conservation efforts. Addressing this data deficit, we investigated the relative performance of environmental and/or taxon-based indicators to predict wild bee richness in the eastern and central U.S. Our methodology leveraged publicly available data on bees (SCAN and GBIF data repository), birds (eBird participatory science project) and land cover data (USGS Cropland Data Layer). We used a Bayesian variable selection algorithm to select variables that best predicted bee richness using two datasets: a semi-structured dataset covering a wide geographical and temporal range and a structured dataset covering a focused extent with a standardized protocol. We demonstrate that an indicator based on the combination of bird and land cover data was better at predicting wild bee richness across broad geographies than indicators based on land cover or birds alone, particularly for the semi-structured dataset. In the case of wild bees specifically, we suggest that bird and land cover data serve as useful indicators to guide monitoring and conservation priorities until the quality and quantity of bee data improve.
The p300 KAT inhibitor, A-485, inhibits melanogenesis and melanin content in human melanocytes
Authors: Grbic Nicole , Waddell Aaron Richard , Leibowitz Kassidy , Wyant W. Austin , Collard Marianne , Alani Rhoda M.
Published: February 2024

Hyperpigmentation disorders are commonly diagnosed dermatologic conditions that can be cosmetically distressing for patients and cause negative psychosocial impacts. There is a need to better understand the underlying pathophysiology of pigmentary disorders as well as develop improvements in the management of these disorders. Here, we evaluated a p300 (CBP/p300) histone acetyltransferase (HAT) inhibitor, A-485, to determine if epigenetically targeting melanogenesis could be of therapeutic value. We find that A-485 treatment of primary human melanocytes and SK-MEL-30 melanoma cells drastically reduces the mRNA and protein expression of MITF and DCT, genes involved in melanin synthesis, and that this is accompanied by a reduction in melanin content. These results suggest that epigenetically targeting melanin synthesis with the A-485 p300 HAT inhibitor may be beneficial for the treatment of hyperpigmentation disorders.
Selection for later flowering time in an orchid through frost damage and pollinator activity
Authors: Wartmann Beat , Ruth Baenziger , Brigitte Gyorog-Kobi , Klaus Hess , Merz Edith , Luder Juerg , Peter Beat , Reutlinger Max , Richter Tobias , Senn Heinz , Ulrich Thomas , Waldeck Beate , Wartmann Claudia , Wuest Roland , Wuest Walter , Rusman Quint , Schiestl Florian P
Published: February 2024

Flowering time is a key trait for plant reproductive success ensuring both overlap with pollinator activity and favorable conditions for fruit development. To quantify selection on flowering time, we individually marked 1250 plants of the Small Spider Orchid, Ophrys araneola RchB., in six populations in Northern Switzerland and surveyed them during three years. We recorded the date of first flowering, frost damage, and fruiting success of individual plants. In addition, we analyzed historical records of the orchid and its only verified pollinator, the solitary bee Andrena combinata in Northern Switzerland, to estimate potential desynchronization due to climate change. We documented strong selection for later flowering driven by frost damage, with all populations showing significant selection for later flowering in at least one year. Selection for later flowering driven by pollination (fruit set) could only be analyzed in one population due to the overall low fruit set, where it was significant in one year. The historical data from between 1970 and 2019 indicated low synchronization between orchid flowering and bee occurrence, with mean flowering three weeks earlier than the mean peak of bee occurrence, corroborating selection for later flowering through fruit set. The data also showed a significant advance of flowering time and bee-occurrence in the last decades, but to a similar degree in orchids and bees, hence without an indication of increasing desynchronization through climate change. Our study shows that selection for later flowering is mostly caused by frost damage, but also by the little synchronized flowering and pollinator activity, which is however unlikely to be a consequence of climate change in this orchid.
Probing drug-target engagement of soluble Gαi1protein using the SolThermoBRET thermal shift assay
Authors: Brod Oscar , Plevako Darya , Perera Themiya , Hompluem Pattarin , Koers Eline J , Hilbert Manuel , Sykes David A , Veprintsev Dmitry
Published: February 2024

Introduction: Sensitive protein stability assays used during hit confirmation conventionally require high quantities of purified protein. Here, we describe a novel high-throughput 384-well BRET-based thermostability assay allowing for the ultrasensitive determination of Gαi1protein stability. Using this method we make use of the environmentally sensitive dye, SYPRO Red, which interacts with hydrophobic regions in the protein that become exposed upon denaturation. Assays are functional in crude cell lysates, without any requirement for protein purification.Methods: The SolThermoBRET method measures resonance energy transfer between a thermally stabilised nano-luciferase (tsNLuc) genetically engineered to the N-terminus of Gαi1, and SYPRO Red, a fluorescent dye that binds to lipophilic residues exposed upon protein unfolding in response to thermal denaturation. Samples in 384-well PCR plate were subjected to a temperature gradient (30 - 60 °C) on a PCR block and incubated for 5 minutes. Isothermal SolThermoBRET at a fixed temperature 45 °C allowed the measurement of IC50curves to various ligands. Furimazine (10 μM) was added to the samples and BRET read on the BMG Labtech PHERAstar FSX at room temperature. Melt curves were fit to a Boltzmann sigmoidal equation to obtain Tm values.Results: Ligand-induced stabilisation of Gαi1protein was demonstrated in non-purified samples. A range of Tm values were measured with increasing stabilisation observed for nucleotides/sides in the following order GDP<GTP<GppNHp<GTPγS. Correlation was observed between SolThermoBRET derived Tm's determined in the presence of high ligand concentrations and IC50determinations using Isothermal SolThermoBRET.Conclusions: SolThermoBRET represents a sensitive nanoscale method for the detection of changes in soluble protein thermostability. This method is attractive for hit conformation and the identification of novel ligands targeting soluble proteins.
Prosaposin is cleaved into saposins by multiple cathepsins in a progranulin-regulated fashion
Authors: Hodul Molly , Lane-Donovan Courtney , Mambou Edwina , Yang Zoe , Kao Aimee W.
Published: February 2024

Prosaposin (PSAP) is a lysosomal protein that plays a key role in sphingolipid metabolism. PSAP is cleaved into four bioactive disulfide-rich peptides, saposins A, B, C, and D, that catalyze sphin-golipidases to promote sphingolipid breakdown. Considering the key role of PSAP and saposins in sphingolipid metabolism and the existence of genetic mutations in PSAP associated with juve-nile-onset lysosomal storage and adult-onset neurodegenerative diseases, maintaining optimal levels of PSAP and saposins is crucial for proper lysosomal function and sphingolipid homeosta-sis. Despite this, the mechanism by which saposins are released from PSAP, and thus available to modulate sphingolipidases, sphingolipid homeostasis, and downstream lysosomal function, is not well understood. Here, we performed a comprehensive study to identify lysosomal enzymes which regulate prosaposin cleavage into saposins.In vitrocleavage assays identified multiple enzymes that can process human prosaposin into multi- and single-saposin fragments in a pH-dependent manner. We confirmed the role of cathepsins D and B in PSAP processing and showed that these and several previously unidentified lysosomal proteases (cathepsins E, K, L, S, V, G and AEP/LGMN) are able to process PSAP in distinctive, pH-dependent manners. In addition, we have demonstrated a novel role for progranulin (PGRN) in the regulation of PSAP cleavage. We found that PGRN and multi-granulin fragments (MGFs) directly regulate the cleavage of PSAP by cathepsin D. With this study, we have identified that multiple cathepsins, PGRN and MGFs work in concert to produce saposins under different conditions, which could present novel opportunities to modulate saposin levels in disease.