bluuebunny/crossref_metadata_2025 huggingface dataset:
User Needs and Factors Associated With the Acceptability of Audiovisual Feedback Devices for Chest Compression Monitoring in Cardiopulmonary Resuscitation
Authors: Kahsay Desale Tewelde , Salanterä Sanna , Tommila Miretta , Liukas Tanja , Rosio Riitta , Diji Abigail Kusi-Amponsah , Peltonen Laura-Maria
Published: March 2024

The use of audiovisual feedback devices to guide the quality of chest compressions during cardiopulmonary resuscitation has increased in recent years. Audiovisual feedback devices can be classified as integrated (eg, Zoll AED Plus defibrillator) or standalone (eg, CPRmeter). This study aimed to explore users' needs and factors affecting the acceptability of audiovisual feedback devices. Semistructured interviews were conducted with healthcare professionals involved in lifesaving activities. The Unified Theory of Acceptance and Use of Technology was used as a theoretical framework for the study. The Unified Theory of Acceptance and Use of Technology model has four constructs: performance expectancy, effort expectancy, social influence, and facilitating factors. Ten themes were identified under the four constructs. The performance expectancy constructs include three themes: perceived usefulness, outcome expectation, and applicability in diverse situations. The effort expectancy construct encompasses two themes: user-friendliness and complexity. The social influence construct has two themes: social and organizational factors. Lastly, the facilitating factors construct includes three themes: staff competence, perceived cost, and compatibility of devices. Exploring the needs and factors influencing the acceptability of audiovisual feedback devices used during cardiopulmonary resuscitation will inform healthcare providers, managers, manufacturers, and procurers on how to improve the efficiency and use of these devices.
Association between CYP2C9 and VKORC1 genetic polymorphisms and efficacy and safety of warfarin in Chinese patients
Authors: Zhang Suli , Zhao Mingzhe , Zhong Shilong , Niu Jiamin , Zhou Lijuan , Zhu Bin , Su Haili , Cao Wei , Xing Qinghe , Yan Hongli , Han Xia , Fu Qihua , Li Qiang , Chen Luan , Yang Fan , Zhang Na , Wu Hao , He Lin , Qin Shengying
Published: March 2024

Objectives

Genetic variation has been a major contributor to interindividual variability of warfarin dosage requirement. The specific genetic factors contributing to warfarin bleeding complications are largely unknown, particularly in Chinese patients. In this study, 896 Chinese patients were enrolled to explore the effect of CYP2C9 and VKORC1 genetic variations on both the efficacy and safety of warfarin therapy.

Methods and results

Univariate analyses unveiled significant associations between two specific single nucleotide polymorphisms rs1057910 in CYP2C9 and rs9923231 in VKORC1 and stable warfarin dosage (P < 0.001). Further, employing multivariate logistic regression analysis adjusted for age, sex and height, the investigation revealed that patients harboring at least one variant allele in CYP2C9 exhibited a heightened risk of bleeding events compared to those with the wild-type genotype (odds ratio = 2.16, P = 0.04). Moreover, a meta-analysis conducted to consolidate findings confirmed the associations of both CYP2C9 (rs1057910) and VKORC1 (rs9923231) with stable warfarin dosage. Notably, CYP2C9 variant genotypes were significantly linked to an increased risk of hemorrhagic complications (P < 0.00001), VKORC1 did not demonstrate a similar association.

Conclusion

The associations found between specific genetic variants and both stable warfarin dosage and bleeding risk might be the potential significance of gene detection in optimizing warfarin therapy for improving patient efficacy and safety.
Impact of clonal hematopoiesis of indeterminate potential on hepatocellular carcinoma in individuals with steatotic liver disease
Authors: Marchetti Alfredo , Pelusi Serena , Marella Alessio , Malvestiti Francesco , Ricchiuti Antony , Ronzoni Luisa , Lionetti Marta , Moretti Vittoria , Bugianesi Elisabetta , Miele Luca , Vespasiani-Gentilucci Umberto , Dongiovanni Paola , Federico Alessandro , Soardo Giorgio , D’Ambrosio Roberta , McCain Misti V. , Reeves Helen L. , La Mura Vincenzo , Prati Daniele , Bolli Niccolò , Valenti Luca ,   EPIDEMIC Study Investigators
Published: March 2024

Background and Aims:

Metabolic dysfunction–associated steatotic liver disease (MASLD) is a global epidemic and is the most rapidly rising cause of HCC. Clonal hematopoiesis of indeterminate potential (CHIP) contributes to neoplastic and cardiometabolic disorders and is considered a harbinger of tissue inflammation. CHIP was recently associated with increased risk of liver disease. The aim of this study was to examine whether CHIP is associated with HCC development in patients with SLD.

Approach and Results:

We considered individuals with MASLD-HCC (n=208) and controls with (n =414) and without (n =259) advanced fibrosis who underwent whole exome sequencing. CHIP was diagnosed when ≥2 variant callers identified a known myeloid mutation with variant allele frequency ≥2%. CHIP was observed in 116 participants (13.1%), most frequently in DNMT3A, TET2, TP53, and ASXL1, and correlated with age (p<0.0001) and advanced liver fibrosis (p=0.001). Higher aspartate aminotransferase levels predicted non-DNMT3A-CHIP, in particular with variant allele frequency ≥10% (OR: 1.14, 1.03 −1.28 and OR: 1.30, 1.12 −1.49, respectively, p<0.05). After adjustment for sex, diabetes, and a polygenic risk, a score of inherited MASLD predisposition CHIP was associated with cirrhosis (2.00, 1.30 −3.15, p=0.02), and with HCC even after further adjustment for cirrhosis (OR: 1.81, 1.11 −2.00, 1.30 −3.15, p=0.002). Despite the strong collinearity among aging and development of CHIP and HCC, non-DNTM3A-CHIP, and TET2 lesions remained associated with HCC after full correction for clinical/genetics covariates and age (OR: 2.45, 1.35 −4.53; OR: 4.8, 1.60 -17.0, p=0.02).

Conclusions:

We observed an independent association between CHIP, particularly related to non-DNTM3A and TET2 genetic lesions and MASLD-HCC.
Nonsurgical closure of full thickness macular hole under topical therapy in two eyes with pathologic myopia
Authors: Miyata Mana , Ueta Takashi , Aoki Shuichiro , Kitamoto Kohdai , Azuma Keiko , Obata Ryo
Published: March 2024

Purpose:

Non-surgical closure of a full-thickness macular hole (FTMH) with eye drops has recently been reported, but there are few similar reports in cases with pathologic myopia.

Case Presentation:

(Case 1) The right eye of a 75-year-old female with an axial length of 28.83 mm had undergone anti-vascular endothelial growth factor (VEGF) treatment for choroidal neovascularization presented with FTMH. Topical betamethasone, bromfenac, and blinzolamide treatments were started, and the FTMH was closed with visual improvement (20/32 to 20/20) after 5 weeks. (Case 2) In the right eye of a 55-year-old male with an axial length of 30.81 mm and lacquer cracks, subretinal hyperreflective material and FTMH developed. The above three drugs were started after anti-VEGF drug injection. Sixteen weeks later, the FTMH was closed with visual improvement (20/63 to 20/20).

Conclusion:

Nonoperative closure of FTMH has already been reported, but few in eyes with pathologic myopia. Our results suggest that nonoperative closure of FTMH associated with pathologic myopia under eye drops may be possible in some cases.
Management of alcohol-associated liver disease and alcohol use disorder in liver transplant candidates and recipients: Challenges and opportunities
Authors: Sharma Pratima , Shenoy Akhil , Shroff Hersh , Kwong Allison , Lim Nicholas , Pillai Anjana , Devuni Deepika , Haque Lamia Y. , Balliet Wendy , Serper Marina
Published: March 2024

Alcohol-associated liver disease poses a significant global health burden, with rising alcohol consumption and prevalence of alcohol use disorder (AUD) contributing to increased morbidity and mortality. This review examines the challenges and opportunities in the care of candidates and recipients of liver transplant (LT) with AUD. Despite advancements in posttransplant patient survival, the risk of disease recurrence and alcohol relapse remains substantial. Several challenges have been identified, including (1) rising disease burden of alcohol-associated liver disease, variable transplant practices, and systemic barriers; (2) disparities in mental health therapy access and the impact on transplant; (3) variable definitions, underdiagnosis, and stigma affecting access to care; and (4) post-LT relapse, its risk factors, and consequential harm. The review focuses on the opportunities to improve AUD care for candidates and recipients of LT through effective biochemical monitoring, behavioral and pharmacologic approaches, creating Centers of Excellence for post-LT AUD care, advocating for policy reforms, and ensuring insurance coverage for necessary services as essential steps toward improving patient outcomes. The review also highlights unmet needs, such as the scarcity of addiction specialists, and calls for further research on personalized behavioral treatments, digital health, and value-based care models to optimize AUD care in the LT setting.
Longitudinal Experience Using Pedicled Buccal Fat Pad Flaps in Cleft Palatoplasty: Mitigating Velopharyngeal Insufficiency Risk and Severity
Authors: Sheppard Nathan T. , Daniel Melissa C. , Dietze-Fiedler Megan L. , Vargo James D. , Habeshy Marissa , Wombacher Natalie R. , Vercler Christian J. , Kasten Steven J. , Buchman Steven R. , Ulma Raquel M.
Published: March 2024

Background:

Cleft palatoplasty commonly results in denuded maxillary bone in the lateral gutters and a posterior void between oral and nasal closures. Bony exposure of the anterior palate subjects the maxilla to scarring and growth restriction; scar contracture of the posterior void may result in velopharyngeal insufficiency and fistula formation. Use of the buccal fat pad flap (BFPF) at the time of palatoplasty provides vascularized tissue over these critical areas, thereby reducing the rate of secondary surgery for speech and fistula revision.

Methods:

A single-center, retrospective review identified patients who underwent palatoplasty with or without BFPF between 1995 and 2015. Data collected included cleft type, surgical technique, follow-up duration, and complications. Outcomes included rate of speech surgery and palatal fistula development. Veau phenotype index was computed on a scale of 2 to 4 as a weighted mean to reflect the frequency of cleft type (Veau II through IV) in BFPF and non-BFPF groups.

Results:

Charts of 866 patients were reviewed; 212 met inclusion criteria. Of these, 101 received a BFPF. Mean follow-up duration was 11.4 years. Despite a selection bias for more severe clefts, the BFPF group had lower incidence of speech surgery (9.9% versus 36.9%; P = 0.0072). The BFPF group had milder cases treatable with fat injection (7.9% versus 2.7%; P = 0.0346) and developed fewer fistulas (6.9% versus 18.0%; P = 0.0280).

Conclusions:

Despite the presence of more severe clefts, the BFPF group had a significantly lower rate of speech surgery. The BFPF is a valuable adjunct in primary palatoplasty, reducing velopharyngeal insufficiency and fistula formation.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Silicone Leakage from Breast Implants Is Determined by Silicone Cohesiveness: A Histologic Study of 493 Patients
Authors: Larsen Andreas , Bak Erik E. F. , Hart Liv B. , Timmermann Adam M. , Ørholt Mathias , Weltz Tim K. , Hemmingsen Mathilde , Vester-Glowinski Peter , Elberg Jens Jørgen , Trillingsgaard Jesper , Hölmich Lisbet R. , Damsgaard Tine E. , Herly Mikkel
Published: March 2024

Background:

Silicone leakage from breast implants is a concern with potential implications for patient health. This study aimed to quantify and model silicone leakage from implants to the breast implant capsule and to investigate whether silicone cohesiveness affected the silicone leakage rate.

Methods:

Silicone content in the breast implant capsule was quantified histologically by measuring the area of silicone deposits. This was used to model silicone leakage over time based on the time of implantation. The effect of cohesiveness on silicone leakage was investigated across all implant brands with declared cohesiveness and in a subanalysis comparing only Mentor cohesive I implants with cohesive II and III implants.

Results:

The study included 493 patients with 872 breasts and a median time of implantation of 13.0 years (range, 0.4 to 51 years). The modeling of silicone leakage from intact implants showed that leakage and the acceleration of the leakage rate were significantly higher in low-cohesive implants than in highly cohesive implants (P < 0.05). This was confirmed when analyzing only Mentor implants (P < 0.05) and in the case of implant rupture (P < 0.01) where low-cohesive implants also leaked significantly more than highly cohesive implants.

Conclusions:

The authors’ results suggest that highly cohesive implants are superior to low-cohesive implants in preventing silicone leakage. Because of the accelerating rate of silicone leakage especially found in low-cohesive implants, the authors propose that exchange of low-cohesive implants could be discussed with patients 10 to 15 years after implantation to minimize silicone leakage, even in the absence of implant rupture.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Cervicofacial Pediatric Tissue Expansion: Aesthetic Unit–Based Algorithm
Authors: Lopez Christopher D. , Yusuf Cynthia T. , Girard Alisa O. , Karius Alexander K. , Yang Robin , Wang Howard , Redett Richard J.
Published: March 2024

Background:

Tissue expansion is a powerful tool in reconstruction of pediatric soft-tissue pathologies, but complication rates in children have been reported to be as high as 40%. Infection and implant extrusion lead to premature removal and delays in reconstruction. Expanding the head and neck is uniquely challenging because the confluence of facial aesthetic units must be respected. These challenges prompted the senior author (R.J.R.) to create an aesthetic unit–based algorithm.

Methods:

A retrospective study of pediatric patients who underwent cervicofacial tissue expander placement over a 17-year period was performed by the senior author. Predictor variables included age, sex, race, indication, number of expanders placed at each operation, serial expansion, expander type, expander size, home versus clinic inflation, and prophylactic antibiotics. Univariate and multivariate analyses were performed to identify risk factors for complications.

Results:

An aesthetic unit–based reconstructive algorithm is proposed. Forty-eight pediatric patients had 111 cervicofacial tissue expanders placed. Twenty expanders were associated with complications (18%) for surgical site infection (12.6%), extrusion (4.5%), or expander deflation (6.3%). Expanders placed for congenital nevi (P = 0.042) and use of textured expanders (P = 0.027) were significantly associated with decreased complication levels. When controlling for covariates, serial expansion of the same site was associated with increased rate of readmission (P = 0.027) after having just 1 previous expander. Iatrogenic ectropion occurred in 13.5% of the study population; expanders with at least 1 complication during tissue expansion were significantly associated with incidence of iatrogenic ectropion (P = 0.026).

Conclusion:

By using an aesthetic unit–based algorithm, reconstructive outcomes can be optimized for pediatric cervicofacial tissue expansion.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Kaposi’s sarcoma herpesvirus viral FLICE inhibitory protein modulates A20 deubiquitinase activity
Authors: Herold Kevin , Ruffin Ayana , Chmura Jennifer C. , Dellomo Anna J. , Ehrlich ELANA
Published: March 2024

KSHV viral FLICE inhibitory protein (vFLIP) is a potent activator of NF-κB signaling and an inhibitor of apoptosis and autophagy. Inhibition of vFLIP function and NF-κB signaling promotes lytic reactivation. Here we provide evidence for a novel function of vFLIP through inhibition of the deubiquitinating (DUB) activity of the negative regulator, A20. We demonstrate direct interaction of vFLIP with Itch and A20 and provide evidence for subsequent loss of A20 DUB activity. Our results provide further insight into the function of vFLIP in the regulation of NF-κB signaling.
A comparative in silico analysis of the vlhA gene regions of Mycoplasma gallisepticum  and Myc. synoviae isolates from commercial hen farms in Mexico.

Authors: Maya Linda , Gómez-Verduzco Gabriela , Trigo-Tavera Francisco J. , Moreno-Fierros Leticia , Rojas-Trejo Verónica , Miranda-Morales Rosa Elena
Published: March 2024

Avian mycoplasmosis, caused by Mycoplasma synoviae and Myc. gallisepticum, poses significant economic challenges due to respiratory issues, reduced production, and soft eggshells. The hemagglutinin (vlhA) protein, crucial for pathogenicity, comprises conserved (MSPB) and variable (MSPA) regions. In this study, we examined vlhA sequences from field strains in Mexico's central region (Jalisco and Mexico City), revealing a close cluster relationship distinct from sequences in GeneBank. We analyzed 124 deformed eggs and 10 laying hens from nine farms with Hy-line and Bovans breeds. Using PCR targeting mgc2 and 16S RNAr genes, we characterized 24 field strains, Mycoplasma synoviae (4) and Myc. gallisepticum (20). The vlhA regions, based on AF035624.1 sequences, were analyzed with ATTC strains as positive controls. Additionally, 20 negative samples at Mycoplasma isolation, validated the sensitivity of PCR testing without the need of cultivation. Two amplification regions were identified: the 1st MSPB and 2nd MSPA. Bioanalysis revealed relationships with relatives avian Mycoplasma sequences in GenBank, alongside similarities with Acholeplasma laidlawii PG8 and Escherichia coli. Given vlhA's significance in pathogenicity and immune evasion, the identified conserved sequences hold potential as therapeutic targets and for phylogenetic studies.
A Novel, Robust, and Portable Platform for Magnetoencephalography using Optically Pumped Magnetometers
Authors: Schofield Holly , Hill Ryan M. , Feys Odile , Holmes Niall , Osborne James , Doyle Cody , Bobela David , Corvilian Pierre , Wens Vincent , Rier Lukas , Bowtell Richard , Ferez Maxime , Mullinger Karen J. , Coleman Sebastian , Rhodes Natalie , Rea Molly , Tanner Zoe , Boto Elena , de Tiège Xavier , Shah Vishal , Brookes Matthew J.
Published: March 2024

Magnetoencephalography (MEG) measures brain function via assessment of magnetic fields generated by neural currents. Conventional MEG uses superconducting sensors, which place significant limitations on performance, practicality, and deployment; however, the field has been revolutionised in recent years by the introduction of optically-pumped-magnetometers (OPMs). OPMs enable measurement of the MEG signal without cryogenics, and consequently the conception of ‘OPM-MEG’ systems which ostensibly allow increased sensitivity and resolution, lifespan compliance, free subject movement, and lower cost. However, OPM-MEG remains in its infancy with limitations on both sensor and system design. Here, we report a new OPM-MEG design with miniaturised and integrated electronic control, a high level of portability, and improved sensor dynamic range (arguably the biggest limitation of existing instrumentation). We show that this system produces equivalent measures when compared to an established instrument; specifically, when measuring task-induced beta-band, gamma-band and evoked neuro-electrical responses, source localisations from the two systems were highly comparable and temporal correlation was >0.7 at the individual level and >0.9 for groups. Using an electromagnetic phantom, we demonstrate improved dynamic range by running the system in background fields up to 8 nT. We show that the system is effective in gathering data during free movement (including a sitting-to-standing paradigm) and that it is compatible with simultaneous electroencephalography (EEG – the clinical standard). Finally, we demonstrate portability by moving the system between two laboratories. Overall, our new system is shown to be a significant step forward for OPM-MEG technology and offers an attractive platform for next generation functional medical imaging.
Principles of chromosome organization for meiotic recombination
Authors: Biot Mathilde , Toth Attila , Brun Christine , Guichard Leon , Massy Bernard de , Grey Corinne
Published: March 2024

In meiotic cells, chromosomes are organized as chromatin loop arrays anchored to a protein axis. This organization is essential to regulate meiotic recombination, from DNA double-strand break (DSB) formation to their repair1. In mammals, it is unknown how chromatin loops are organized along the genome and how proteins participating in DSB formation are tethered to the chromosome axes. Here, we identified three categories of axis-associated genomic sites: PRDM9 binding sites, where DSBs form2, binding sites of the insulator protein CTCF, and H3K4me3-enriched sites. We demonstrated that PRDM9 promotes the recruitment of MEI4 and IHO1, two proteins essential for DSB formation3,4. In turn, IHO1 anchors DSB sites to the axis components HORMAD1 and SYCP3. We discovered that IHO1, HORMAD1 and SYCP3 are associated at the DSB ends during DSB repair. Our results highlight how interactions of proteins with specific genomic elements shape the meiotic chromosome organization for recombination.
MotifScope: a multi-sample motif discovery and visualization tool for tandem repeats
Authors: Zhang Yaran , Hulsman Marc , Salazar Alex , Tesi Niccolo , Knoop Lydian , van der Lee Sven , Wijesekera Sanduni , Krizova Jana , Kamsteeg Erik-Jan , Holstege Henne
Published: March 2024

Tandem repeats (TRs) constitute a significant portion of the human genome, exhibiting high levels of polymorphism due to variations in size and motif composition. These variations have been associated with various neuropathological disorders, underscoring the clinical importance of TRs. Furthermore, the motif structure of these repeats can offer valuable insights into evolutionary dynamics and population structure. However, analysis of TRs has been hampered by the limitations of short-read sequencing technology, which lacks the ability to fully capture the complexity of these sequences. With long-read data becoming more accessible, there is now also a need for tools to explore and characterize these TRs. In this study, we introduce MotifScope, a novel algorithm for visualization of TRs in their population context based on a de novo k-mer approach for motif discovery. Comparative analysis against three established tools, uTR, TRF, and vamos, reveals that MotifScope can identify a greater number of motifs and more accurately represent the actual repeat sequence. Additionally, MotifScope enables comparison of sequencing reads within an individual and assemblies across different individuals, showing its applicability in diverse genomic contexts. We demonstrate potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.
Interleaved intersectional strategy enables genetic lineage tracing with enhanced specificity
Authors: Han Maoying , Liu Zhicong , Huang Xiuzhen , Liu Lei , Zhou Bo , Lui Kathy O. , Shu Qiang , Zhou Bin
Published: March 2024

BACKGROUND

Dual recombinases have been increasingly employed for enhanced precision in genetic targeting. A recent study utilizing an intersectional genetic approach through dual recombinases (Dre + CreER) has revealed that endocardium-derived fibroblasts (EndoFbs) play a pivotal role in cardiac fibrosis after pressure overload. However, this intersectional strategy has limitations, primarily due to ectopic genetic labeling of non-target cells within the adult heart by the constitutively active Dre recombinase.

METHODS

To address this issue, we have developed an advanced, interleaved and intersectional reporter (IIR) strategy in this study. This IIR strategy leverages an inducible CreER to prevent inadvertent Dre-rox recombination during development or disease progression by designing an interleaved reporter to allow for more specific tracing of EndoFbs. Moreover, our IIR system also incorporates Diphtheria Toxin Receptor (DTR) in targeted cells, enabling functional characterization of these cells after genetic ablation.

RESULTS

EndoFbs were regionally distributed in the heart during homeostasis and proliferated preferentially in response to pressure overload, leading to cardiac fibrosis in defined regions. The IIR strategy enables the tracing of EndoFbs with a more prominent regional pattern and facilitates genetic ablation of EndoFbs through DT injection. In addition, we have applied this IIR strategy to specifically target fibroblasts derived from the epicardium (EpiFbs). Genetic lineage tracing of EpiFb reveals that their distribution pattern is complementary to that of EndoFbs in the adult heart. When a substantial number of EpiFbs were genetically ablated, EndoFbs could replace the loss of EpiFbs in some specific regions of hearts.

CONCLUSIONS

The IIR strategy refines the precision of genetic lineage tracing while still employing the constitutively active Dre recombinase in tandem with inducible Cre. EndoFbs and EpiFbs are complementary in their distribution pattern in the heart, where EndoFbs have the potential to replace the loss of EpiFbs in some regions.
Deletion of RFX6, a Diabetes-Associated Gene, Impairs iPSC-Derived Islet Organoid Development and Survival, With No Impact on the Generation of PDX1+/NKX6.1+ Progenitors
Authors: Aldous Noura , Elsayed Ahmed K. , Memon Bushra , Ijaz Sadaf , Hayat Sikander , Abdelalim Essam M.
Published: March 2024

RFX6 is essential for pancreatic development and insulin secretion, while its role in diabetes pathogenesis is unclear. Here, RFX6 expression was detected in PDX1+ cells in the hESC-derived posterior foregut (PF). However, in the pancreatic progenitors (PPs), RFX6 did not co-localize with PDX1 and NKX6.1, but instead with NEUROG3, NKX2.2, and islet hormones in the endocrine progenitor (EPs) and islets. Single-cell analysis revealed high RFX6 expression in endocrine clusters across various hESC-derived pancreatic differentiation stages. Upon differentiating iPSCs lacking RFX6 into pancreatic islets, a significant decrease in PDX1 expression at the PF stage was observed, although it did not affect PPs co-expressing PDX1 and NKX6.1. RNA sequencing showed the downregulation of essential genes involved in pancreatic endocrine differentiation, insulin secretion, and ion transport due to RFX6 deficiency. Furthermore, RFX6 deficiency resulted in the formation of smaller islet organoids due to increased cellular apoptosis, linked to reduced Catalase (CAT) expression, implying a protective role for RFX6. Overexpression of RFX6 reversed defective phenotypes in PPs and EPs. These findings suggest that pancreatic hypoplasia and reduced islet cell formation associated with RFX6 mutations are not due to alterations in PDX1+/NKX6.1+ PPs but instead result from cellular apoptosis and downregulation of pancreatic endocrine genes.
Mechanisms underlying the loss of migratory behaviour in a long-lived bird
Authors: Andrade Pedro , Franco Aldina M. A. , Acácio Marta , Afonso Sandra , Marques Cristiana I. , Moreira Francisco , Carneiro Miguel , Catry Inês
Published: March 2024

Human-induced environmental changes are shifting the migration patterns of birds worldwide. Species are adjusting migration timings, shortening and diversifying migratory routes, or even completely disrupting migration and transitioning towards residency. Whilst the ultimate causes driving changes in migratory patterns are well established, the underlying mechanisms by which migratory species adapt to environmental change remain unclear.

Here, we studied the mechanisms driving the recent and rapid loss of migratory behaviour in Iberian white storksCiconia ciconia, a long-lived and previously fully migratory species through the African-Eurasian flyway. We combined 25 years of census data, GPS-tracking data from 213 individuals (80 adults and 133 first-year juveniles) followed for multiple years, and whole-genome sequencing, to disentangle whether within- (phenotypic flexibility) or between- (developmental plasticity or microevolution, through selection) individual shifts in migratory behaviour over time can explain the observed population-level changes towards residency.

Between 1995 and 2020, the proportion of individuals no longer migrating and remaining in Southern Europe year-round increased dramatically, from 18% to 68-83%. We demonstrate that this behavioural shift is likely explained by developmental plasticity. Within first-year birds, 98% crossed the Strait of Gibraltar towards their African wintering grounds, in Morocco or Sub-Saharan Africa. However, the majority shifted towards a non-migratory strategy as they aged - the proportion of migrants decreased to 67% and 33%, on their second and third year of life, respectively - suggesting that migratory behaviour is determined during ontogeny. Supporting these findings, only 19% of GPS-tracked adults migrated. Moreover, we did not find evidence of phenotypic flexibility, as adults were highly consistent in migratory behaviour over multiple years (only 3 individuals changed strategy between years, out of 113 yearly transitions), nor of selection acting on genetic variation, since genomes of migrants and residents are essentially undifferentiated.

Our results suggest that through developmental plasticity, traits that are plastic during specific windows of development, become fixed during adulthood. Thus, inter-generational shifts in the frequency of migratory and non-migratory young individuals could drive population changes in migratory behaviour. This can provide a fast mechanism for long-lived migratory birds to respond to rapid human-driven environmental changes.
Prediction of Aggregation Prone Regions in Proteins Using Deep Neural Networks and Their Suppression by Computational Design
Authors: Cima Vojtech , Kunka Antonin , Grakova Ekaterina , Planas-Iglesias Joan , Havlasek Martin , Subramanian Madhumalar , Beloch Michal , Marek Martin , Slaninova Katerina , Damborsky Jiri , Prokop Zbynek , Bednar David , Martinovic Jan
Published: March 2024

Protein aggregation is a hallmark of multiple neurodegenerative diseases and a great hindrance in recombinant protein production, handling, and storage. Identification of aggregation prone residues or regions (APRs) in proteins and their suppression by mutations is a powerful and straightforward strategy for improving protein solubility and yield, which significantly increases their application potential. Towards this, we developed a deep neural network based predictor that generates residue level aggregation profile for one or several input protein sequences. The model was trained on a set of hexapeptides with experimentally characterised aggregation propensities and validated on two independent sets of data including hexapeptides and full-length proteins with annotated APRs. In both cases, the model matched, or outperformed the state-of-the-art algorithms. Its performance was further verified using a set of 34 hexapeptides identified in model haloalkane dehalogenase LinB and seven proteins from AmyPro database. The experimental data from Thioflavin T fluorescence and transmission electron microscopy matched the predictions in 79% of the cases, and revealed inaccuracies in the database annotations. Finally, the utility of the algorithm was demonstrated by identifying APRs in a model enzyme (LinB) and designing aggregation-suppressing mutations in the exposed regions. The designed variants showed reduced aggregation propensity, increased solubility and improved yield, with up to a 100% enhancement compared to the wild type for the best one.
Buzz-world: Global patterns and drivers of buzzing bees and poricidal plants
Authors: Russell Avery L. , Buchmann Stephen L. , Ascher John S. , Wang Zhiheng , Kriebel Ricardo , Jolles Diana D. , Orr Michael C. , Hughes Alice C.
Published: March 2024

Foraging behavior frequently plays a major role in driving the geographic distribution of animals. Buzzing to extract protein-rich pollen from flowers is a key foraging behavior used by bee species across at least 83 genera (these genera comprise ∼58% of all bee species). Although buzzing is widely recognized to affect the ecology and evolution of bees and flowering plants (e.g., buzz-pollinated flowers), global patterns and drivers of buzzing bee biogeography remain unexplored. Here, we investigate the global species distribution patterns within each bee family and how patterns and drivers differ with respect to buzzing bee species. We found that both distributional patterns and drivers of richness typically differed for buzzing species compared to hotspots for all bee species and when grouped by family. A major predictor of the distribution, but not species richness overall for buzzing members of four of the five major bee families included in analyses (Andrenidae, Halictidae, Colletidae and to a lesser extent, Apidae) was the richness of poricidal flowering plant species, which depend on buzzing bees for pollination. As poricidal plant richness was highest in areas with low wind and high aridity, we discuss how global hotspots of buzzing bee biodiversity are likely driven by both biogeographic factors and plant host availability. Whilst we explored global patterns with State-level data, higher resolution work is needed to explore local level drivers of patterns, but from a global perspective, buzz-pollinated plants clearly play a greater role in the ecology and evolution of buzzing bees than previously predicted.
Pharmacological inhibition of macrophage triglyceride biosynthesis pathways does not improveMycobacterium tuberculosiscontrol in infected mice
Authors: Castillo Jennie Ruelas , Guerrini Valentina , Quijada Darla , Karanika Styliani , Neupane Pranita , Harris Harley , Garcia Andrew , Shenkoya Babajide , Yilma Addis , Bailey Hannah , Khan Rehan , Gopalakrishnan Mathangi , Gennaro Maria L. , Karakousis Petros C.
Published: March 2024

Triglyceride rich macrophages (foam cells) are a hallmark of necrotic granulomas in tuberculosis, and multiple antimicrobial functions are down-regulated in these cells. In this study, we assessed the ability of two different compounds to reduce triglyceride content and intracellular burden inMycobacterium tuberculosis(Mtb)-infected macrophages: A-922500 (DGATi), an inhibitor of diacylglycerol acyltransferase 1, an enzyme involved in triglyceride synthesis; and LY2584702 (p70S6Ki), an inhibitor of p70 S6 kinase, a serine/threonine kinase involved in mTORC-1dependent lipid biogenesis. Additionally, we evaluated the adjunctive activity of these inhibitors as host-directed therapies against chronic Mtb infection in C3HeB/FeJ mice. DGATi and p70S6Ki significantly reduced the lipid content and bacillary burden in Mtb-infected human monocyte-derived macrophages. In Mtb-infected mice, each inhibitor reduced the triglyceride content (P≤ 0.0001) in cells from bronchoalveolar lavage samples. Adjunctive treatment of DGATi with isoniazid and p70S6Ki monotherapy reduced the lipid droplet content (P≤ 0.05) within lung macrophages of Mtb-infected mice. However, neither inhibitor reduced the lung bacterial burden in Mtb-infected mice alone or in combination with isoniazid, and they did not alter lung inflammation. These findings provide further insights into the role of foam cells in tuberculosis pathogenesis and the utility of interventions targeting these cell populations as adjunctive host-directed therapies.
MegaLMM improves genomic predictions in new environments using environmental covariates
Authors: Hu Haixiao , Rincent Renaud , Runcie Daniel E.
Published: March 2024

Multi-environment trials (METs) are crucial for identifying varieties that perform well across a target population of environments (TPE). However, METs are typically too small to sufficiently represent all relevant environment-types, and face challenges from changing environment-types due to climate change. Statistical methods that enable prediction of variety performance for new environments beyond the METs are needed. We recently developed MegaLMM, a statistical model that can leverage hundreds of trials to significantly improve genetic value prediction accuracy within METs. Here, we extend MegaLMM to enable genomic prediction in new environments by learning regressions of latent factor loadings on Environmental Covariates (ECs) across trials. We evaluated the extended MegaLMM using the maize Genome-To-Fields dataset, consisting of 4402 varieties cultivated in 195 trials with 87.1% of phenotypic values missing, and demonstrated its high accuracy in genomic prediction under various breeding scenarios. Furthermore, we showcased MegaLMM’s superiority over univariate GBLUP in predicting trait performance of experimental genotypes in new environments. Finally, we explored the use of higher-dimensional quantitative ECs and discussed when and how detailed environmental data can be leveraged for genomic prediction from METs. We propose that MegaLMM can be applied to plant breeding of diverse crops and different fields of genetics where large-scale linear mixed models are utilized.
Reactive microglia fail to respond to environmental damage signals in a viral-induced mouse model of temporal lobe epilepsy
Authors: Wallis Glenna J. , Bell Laura A. , Wagner John N. , Buxton Lauren , Balachandar Lakshmini , Wilcox Karen S.
Published: March 2024

Microglia are highly adaptable innate immune cells that rapidly respond to damage signals in the brain through adoption of a reactive phenotype and production of defensive inflammatory cytokines. Microglia express a distinct transcriptome, encoding receptors that allow them to dynamically respond to pathogens, damage signals, and cellular debris. Expression of one such receptor, the microglia-specific purinergic receptorP2ry12, is known to be downregulated in reactive microglia. Here, we explore the microglial response to purinergic damage signals in reactive microglia in the TMEV mouse model of viral brain infection and temporal lobe epilepsy. Using two-photon calcium imaging in acute hippocampal brain slices, we found that the ability of microglia to detect damage signals, engage calcium signaling pathways, and chemoattract towards laser-induced tissue damage was dramatically reduced during the peak period of seizures, cytokine production, and infection. Using combined RNAscopein situhybridization and immunohistochemistry, we found that during this same stage of heightened infection and seizures, microglialP2ry12expression was reduced, while the pro-inflammatory cytokineTNF-aexpression was upregulated in microglia, suggesting that the depressed ability of microglia to respond to new damage signals viaP2ry12occurs during the time when local elevated cytokine production contributes to seizure generation following infection. Therefore, changes in microglial purinergic receptors during infection likely limit the ability of reactive microglia to respond to new threats in the CNS and locally contain the scale of the innate immune response in the brain.
Cell-cycle and Age-Related Modulations of Mouse Chromosome Stiffness
Authors: Liu Ning , Qiang Wenan , Jordan Philip , Marko John F , Qiao Huanyu
Published: March 2024

Chromosome structure is complex, and many aspects of its organization remain poorly understood. Measuring chromosome stiffness offers valuable insight into their structural properties. In this study, we analyzed the stiffness of chromosomes from metaphase I (MI) and metaphase II (MII) oocytes. Our results revealed a ten-fold increase in stiffness (Young’s modulus) of MI chromosomes compared to somatic chromosomes. Furthermore, the stiffness of MII chromosomes was lower than that of MI chromosomes. We examined the role of meiosis-specific cohesin complexes in regulating chromosome stiffness. Surprisingly, chromosomes from three meiosis-specific cohesin mutants exhibited stiffness comparable to that of wild-type chromosomes, indicating that these cohesins are not the primary determinants of chromosome stiffness. Additionally, our findings revealed an age-related increase in chromosome stiffness in MI oocytes. Since aging is associated with elevated levels of DNA damage, we investigated the impact of etoposide-induced DNA damage on oocyte chromosome stiffness and found that it led to a reduction in MI chromosome stiffness. Overall, our study underscores the dynamic and cyclical nature of chromosome stiffness, modulated by both the cell cycle and age-related factors.
Constitutive immune surveillance of nasal mucosa by three neutrophil subsets with distinct origin, phenotype, and function
Authors: Gonzalez Rodrigo J. , Hanč Pavel , Alvarez David , Kazer Samuel W. , Messou Marie-Angele , Mazo Irina B. , Matysiak Match Colette , Garg Rohit , Helble Jennifer D. , Pallis Paris , Ende Rachel , Basset Alan , Malley Rick , Derre Isabelle , Starnbach Michael N. , von Andrian Ulrich H.
Published: March 2024

The nasal mucosa (NM) has several critical functions, including as a chemosensory organ, as a filter and conditioning surface of inhaled air for the lower airways, and as a first line of defense against airborne infections. Owing to its constant exposure to ever-changing environments, the NM is arguably the most frequently infected tissue in mammals. Consequently, vertebrates harbor an intricate network of subepithelial immune cells that are dispersed throughout the NM. However, the origin, composition, and function of nasal immune cells and their pathophysiological role are poorly understood. Here, we show that murine steady-state NM harbors a prominent population of extravascular neutrophils (EVN) that are abundant in both conventional and germ-free mice, suggesting that their presence is not driven by microbial stimuli. Nasal EVN can be subdivided into three phenotypically distinct subsets: one population that we have termed nN1 is CD11bintLy6Gint, while the other two subsets are both CD11bhiLy6Ghiand distinguishable by the absence (nN2) or presence (nN3) of CD11c and SiglecF. nN1 EVN originate in bone marrow (BM) within osseous structures in the skull. These locally produced neutrophils appear to access the adjacent NM via conduits that connect BM cavities to the submucosal lamina propria. nN2 cells reach the NM via the blood and readily engulf infectious microbes. In the absence of infection, nN2 cells differentiate into the nN3 subset, which does not capture microbes but assumes phenotypic and functional features of antigen-presenting cells, including the capacity to cross-present exogenous antigens to CD8 T cells. These findings indicate that steady-state mammalian NM harbors a unique innate cellular immune environment that is unlike any other barrier tissue.
Modulation of pedunculopontine input to the basal ganglia relieves motor symptoms in Parkinsonian mice
Authors: Lin Caixia , Ridder Margreet , Zhong Jinhao , Albornoz Eduardo A. , Sedlak Petra , Xu Li , Woodruff Trent M. , Chen Fangyi , Sah Pankaj
Published: March 2024

Locomotion, the ability to move, is driven by central pattern generators in the spinal cord. However, its initiation, selection of gait and arrest are controlled by command centers in the brain stem of which the best understood is the mesencephalic locomotor region (MLR). Stimulation of the MLR can initiate or arrest movement, but its neural projections and the neural circuits that mediate these actions are poorly understood. Here we show that glutamatergic neurons in the pedunculopontine nucleus (PPN), a major part of the MLR, project to the substantial nigra pars reticulata (SNr) where they innervate neurons that send afferents to the ventro medial motor thalamus (VM). Stimulation of this input to the SNr in mice slows voluntary and driven movement by modifying gait, with higher frequencies arresting gait. In Parkinsons disease (PD), a neurodegenerative disorder, the cardinal symptoms are bradykinesia, tremor and rigidity. Using an mouse model of PD, we show that inhibition of PPN input to the SNr rescues bradykinesia. This is the first description of a circuit in the mammalian brain that regulates movement and gait selection. Targeting of this circuit may be a more effective modality for treating the motor symptoms of PD.
A subtle modification of modafinil-based DAT inhibitors changes conformational preference
Authors: Lee Kuo Hao , Camacho-Hernandez Gisela A. , Newman Amy Hauck , Shi Lei
Published: March 2024

Modafinil analogs with either a sulfoxide or sulfide moiety have improved binding affinities at the human dopamine transporter (hDAT) compared to modafinil, with lead sulfoxide-substituted analogs showing characteristics of atypical inhibition (e.g., JJC8-091). Interestingly, the only distinction between sulfoxide and sulfide substitution is the presence of one additional oxygen atom. To elucidate why such a subtle difference in ligand structure can result in different typical or atypical profiles, we investigated two pairs of analogs. Our quantum mechanical calculations revealed a more negatively charged distribution of electrostatic potential surface of the sulfoxide substitution. Using molecular dynamics simulations, we demonstrated that sulfoxide-substituted modafinil analogs have a propensity to attract more water into the binding pocket. They also exhibited a tendency to dissociate from Asp79 and form a new interaction with Asp421, consequently promoting an inward-facing conformation of DAT. In contrast, sulfide-substituted analogs did not display these effects. These findings deepen our understanding of the functionally relevant conformational spectrum of DAT.
Deletion of Robo4 worsens neuroinflammation and motor coordination in a mouse model of Alzheimer’s disease
Authors: Cullen Abigail E , Winder Nick R , Lee Byron , Krishna Kumaran Sahana , Arora Nayantara , Wolf Julia R , Henson Grant D , Woltjer Randy L , Walker Ashley E
Published: March 2024

Declines in vascular integrity are potential contributors to Alzheimer’s disease (AD) as these result in increased blood-brain barrier permeability and, as a consequence, accelerate neuroinflammation and cognitive impairment. Roundabout guidance receptor 4 (Robo4) is primarily expressed in endothelial cells and stabilizes the vasculature, and thus, has the potential to protect the brain in AD. To study the effect of Robo4 on neuroinflammation and cognitive function in the context of AD, we compared Robo4 knockout and wildtype mice crossed with mice with and without AD mutations (APP/tau). We found that the knockout of Robo4 led to greater astrocyte activation, as demonstrated by GFAP content, but this was dependent on the brain region studied. The knockout of Robo4 also led to greater activated microglia, as assessed by Iba1 content, but only in the presence of AD-related mutations. We found that AD mutations, but not Robo4, were associated with cognitive dysfunction measured by a nest-building test. In contrast, Robo4 deletion, but not AD mutations, was associated with impaired motor coordination. Lastly, Robo4 deletion was associated with greater arterial stiffness, but this trend did not reach statistical significance. In summary, these results demonstrate that Robo4 impacts neuroinflammation, motor coordination, and arterial stiffness, however, the impact on neuroinflammation is dependent on the presence/absence of AD-related mutations and the brain region examined.