bluuebunny/crossref_metadata_2025 huggingface dataset:
Olfactory outcomes in skull base surgery
Authors: Venkatesh Sanjena , Douglas Jennifer E.
Published: November 2024

Purpose of review

This review examines the impact of skull base surgery on olfactory function, a critical yet often overlooked aspect of postoperative quality of life. As surgical techniques continue to evolve, understanding their impact on olfaction is key to optimizing patient outcomes.

Recent findings

The relationship between skull base surgery and olfactory function continues to be debated in the literature. With the adoption of transnasal surgical approaches, a significant concern has been its impact on olfaction. Prior studies have shown evidence of olfactory dysfunction following transnasal skull base surgery, though these findings are not universal. A particular area of discussion involves the use of the pedicled nasoseptal flap, which has demonstrated potentially negative short-term olfactory impacts. Additional concerns surround flap design (olfactory strip preservation) and technique of flap harvest (cold knife versus electrocautery). Evidence suggests that olfactory strip preservation may effectively maintain postoperative olfactory performance, while cold knife techniques offer no clear advantage over electrocautery.

The inconsistencies in the literature underscore the need for standardized, large-scale studies that directly compare surgical techniques to better understand the impact of transnasal skull base surgery on olfaction. This is essential to optimizing surgical outcomes and improving patient quality of life postoperatively.
Career and lifestyle among female surgeons in Jordan
Authors: Abu-Jeyyab Mohammad , Mse’adeen Mohammad Al , Tafesh Ru’a , Zein Eddin Sadeen , Zuaiter Saja , Al-Mse’adeen Namareq , Masoud Bayan , Jariri Hala , AlKatib Malak , Alabbasi Marah , Sarhan Mohammed Y. , Akel Alaa
Published: November 2024

Background:

Female surgeons face various challenges that may affect their career and lifestyle satisfaction, such as gender bias, work-family conflict, and lack of mentorship. However, little is known about the situation of female surgeons in Jordan, a developing country with limited resources and a high demand for surgical services.

Aim:

The aim of this study was to assess the career and lifestyle satisfaction among female surgeons in Jordan, and to explore the relationship between income level, family stability, job security, and job satisfaction. The study also aimed to identify the variation of the challenges that surround female surgeons in different regions of Jordan.

Methods:

This was a cross-sectional study that used a self-administered questionnaire to collect data from 244 female surgeons working in Jordan. The questionnaire was adapted from the National Lifestyles in Surgery Today Survey, which was previously used to assess career and lifestyle satisfaction among surgeons in the United States. The questionnaire consisted of four sections: demographic and practice characteristics, career satisfaction, work-life balance, and perceived challenges and improvement areas. The data were analyzed using descriptive and inferential statistics.

Results:

The study polled 340 surgeons, the majority of whom were female, young, and general surgeons, to investigate the variables influencing their job satisfaction. Working hours were shown to be related to residence (P=0.000, X2=163.749) and to have an influence on health (4.40%), pay (64.12%), hobbies (46.76%), and family (55%). Female surgeons suffered increased sex bias (68.85%), disrespect (31.56%), inadequate mentorship (35.25%), and harassment (16.00%), according to the research. Quite similarly, 30.21% of male corespondents agreed to the presence of sex discrimination, with 10.42% and 21.88% conjoining on the evidence of lack of respect and incompetent mentoring, respectively. According to the survey, professional happiness varies by speciality, with ENTs being the most satisfied (97.10%) and OBGYNs being the least satisfied (25%). The survey also discovered that male students (36.76%) were more likely to be recommended to pursue a career in surgery than female students (31.18%). According to the survey, salary, leave, and sector are also variables impacting job happiness, with the majority of satisfied surgeons earning 1000 JOD or less, having 30 days of leave, and working in the MOH or the private sector.

Conclusions:

Female surgeons in Jordan are generally satisfied with their careers but face several challenges that affect their work-life balance and professional development. There is a need for more advocacy and support for female surgeons in Jordan to address these challenges and improve their career and lifestyle satisfaction.
Why might fears and worries persist after a pain education–grounded multimodal intervention for chronic back pain? A qualitative study
Authors: Rizzo Rodrigo R. N. , Wand Benedict M. , Leake Hayley B. , O'Hagan Edel T. , Traeger Adrian C. , Gustin Sylvia M. , Moseley G. Lorimer , Sharma Saurab , Cashin Aidan G. , Bagg Matthew K. , McAuley James H. , Bunzli Samantha
Published: November 2024

Introduction:

The effect of pain education (PE) on pain intensity and function diminishes after a few months in people with chronic low back pain (CLBP). One possible explanation is the return of underlying fears and worries related to the condition.

Objective:

To explore topics related to participants' beliefs and feelings that might explain why fears and worries persist after a PE-grounded intervention for CLBP.

Methods:

We conducted a qualitative study involving semistructured interviews with participants from the active arm of a randomised controlled trial who received an individualised PE-grounded intervention for adults with CLBP. We used reflexive thematic analysis with an inductive approach.

Results:

Twenty participants were interviewed (9 women and 11 men, median age = 54 years, median pain duration = 4 years, 13 reporting at least 30% pain reduction on the trial primary outcome). Three themes were identified: 1) “Are you implying my pain is not real?”: a few participants believed the validity of their pain was being questioned. 2) “You don't understand, my pain is different”: most participants considered the influence of an altered nervous system but did not exclude the possibility of having structural and biomechanical influences for the persistence of their back pain. 3) “I am unsure how to fit it into my daily life”: fear and worries persisted when participants could not figure out how to apply an alternative way of making sense of pain in their daily lives.

Conclusion:

Patients' perceptions about PE should be monitored and might be addressed with communication strategies, educational content that matches patients' characteristics, and reinforcements over time.
Comparative effectiveness of pre-epiglottic baton plates and mandibular distraction in infants with Robin sequence
Authors: Resnick Cory M. , de Gijsel Jens , Jindal Snigdha , Quante Mirja , Poets Christian , Katz Eliot , Wiechers Cornelia
Published: November 2024

Background:

Mandibular distraction osteogenesis (MDO) and pre-epiglottic baton plates (PEBP) are both effective for early management of upper airway obstruction (UAO) in infants with Robin sequence (RS), but have not been directly compared. The purpose of this study was to compare early airway, feeding and growth outcomes between these treatments.

Methods:

This is a bicentric retrospective cohort study from 2015-2021 including infants with RS treated with MDO or PEBP before 6 months-of-age with pre- and post-treatment sleep studies and follow-up at least through age 1-year. The primary outcome was immediate post-intervention UAO, measured as obstructive apnea-hypopnea index (oAHI) or obstructive apnea index (oAI), as available. Latest follow-up sleep studies, feeding and growth characteristics were also assessed.

Results:

114 subjects were included: MDO, n=31 and PEBP, n=83. Pre-treatment UAO was similar between groups (p=0.61). PEBP was initiated at a younger age (median [IQR] 31 [14,53] vs. 41 [28,84] days-of-life, p<0.05). Significant reduction of oAHI/oAI was achieved in both groups, but greater with MDO (98%) compared to PEBP (94%, p<0.05). PEBP demonstrated better early feeding and growth outcomes compared to MDO, with fewer surgical feeding tubes (p<0.001) and more rapid early growth (p=0.038). When stratified by pre-intervention UAO, infants starting with moderate UAO experienced similar airway outcomes with both treatments (p=0.11), while those with severe UAO had greater resolution with MDO (p<0.001).

Conclusion:

Both treatments effectively relieve moderate UAO in infants with RS, but MDO is more effective for infants with severe respiratory compromise.
The impact of transfusion kinetics on the inflammatory response following major injury
Authors: Carney Patrick R. , Zarzaur Ben L. , Holcomb John B. , Fox Erin E. , Wade Charles E. , Savage Stephanie A.
Published: November 2024

BACKGROUND

The innate immune response is activated by tissue injury and may quickly become dysregulated in the setting of major trauma. Cytokines are a key component of this response and function to activate and mobilize neutrophils, macrophages, and natural killer cells. The purpose of this study was to understand how the kinetics of blood-based resuscitation may impact the cytokine response. Specifically, we hypothesize that transfusion kinetics make a fundamental contribution to the inflammatory response, beyond the volume of transfusion and injury severity.

METHODS

The Pragmatic, Randomized Optimal Platelet and Plasma Ratio data set was used in this retrospective analysis. Transfusion kinetics were quantified by calculating the total critical administration threshold episodes in three time periods, 1 to 2 hours following injury, 3 to 4 hours, and 5 to 6 hours following injury. The longitudinal response of key cytokines over 72 hours was assessed with a multivariable linear growth model, using critical administration threshold status as a time-varying covariate.

RESULTS

A total of 522 patients were included in this analysis. Pro-inflammatory cytokines interleukin (IL)-6 (p = 0.0354) and IL-8 (p < 0.0001) were significantly increased. Anti-inflammatory cytokines IL-1ra (p = 0.0001) and IL-10 (p < 0.0001) were significantly increased. Chemokines interferon-γ-inducible protein 10 (p = 0.0433), monocyte chemoattractant protein-1 (p = 0.0064), and macrophage inflammatory protein 1β (p = 0.0003) were significantly increased, while regulated up activation, normal T-cell expressed and secreted chemokine (p = 0.0216) was significantly decreased. Growth factors showed no significant response.

CONCLUSION

The kinetics of packed red blood cell transfusion demonstrate a potential association with the expression of cytokines following injury, beyond the total transfusion requirement or the severity of injury. Because cytokines activate and mobilize neutrophils, macrophages, and natural killer cells, these alterations may have a profound effect on degree and coordination of the immune response. As the contribution of various components of major resuscitation to inflammatory activation is clarified, such as types of blood product, tempo of transfusion, and operative care, targets for intervention should become more apparent.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level III.
Percutaneous and endoscopic transpapillary cholecystoduodenal stenting in acute cholecystitis—A viable long-term option in high-risk patients?
Authors: Argandykov Dias , El Moheb Mohamad , Nzenwa Ikemsinachi C. , Kalva Sanjeeva P. , Iqbal Shams , Smolinski-Zhao Sara , Krishnan Kumar , Velmahos George C. , Paranjape Charudutt
Published: November 2024

BACKGROUND

The prolonged use of percutaneous cholecystostomy tubes (PCTs) in patients with acute cholecystitis, deemed inoperable, is fraught with complications. Transpapillary cholecystoduodenal stenting (TCDS) is an alternative technique that restores the physiologic outflow of bile, avoiding the need for an external drain. However, the long-term safety and efficacy of this approach remain unclear. We sought to prospectively assess the safety and efficacy of this procedure, performed via percutaneous or endoscopic approach, in high-risk patients presenting with acute cholecystitis.

METHODS

This prospective study included consecutive patients with acute cholecystitis and long-lasting, prohibitive surgical risk, in whom TCDS was offered at two partnering tertiary care centers between August 1, 2018, and December 31, 2022. Patients with a need for endoscopic retrograde cholangiopancreatography (ERCP) underwent ERCP-guided TCDS. In patients without a need for ERCP, a temporary PCT was followed by fluoroscopic-guided TCDS 4 weeks to 6 weeks later. Interval cholecystectomy was performed in patients who became surgical candidates later. All patients were followed up until January 1, 2023.

RESULTS

Transpapillary cholecystoduodenal stenting was successful in 67 (percutaneous in 45/50; endoscopic in 22/23) of 73 patients (92%) attempted. Over a median follow-up period of 17 months (7, 26), 10 patients (15%) developed stent blockage or migration; all but two had their stent successfully replaced. Five patients (7%) developed mild, self-limited pancreatitis. Five (7%) patients underwent interval cholecystectomy at a median time of 7 months.

CONCLUSION

Transpapillary cholecystoduodenal stenting is a safe and promising definitive alternative to chronic PCT in high-risk patients with acute cholecystitis that eliminates the discomfort and complications of long-term external drainage.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level II.
Broadening indications: A descriptive and comparative in-depth analysis of venovenous extracorporeal membrane oxygenation outcomes in trauma and nontrauma patients
Authors: Spivak Holden , Rao Appajosula , Haase Daniel , Galvagno Samuel , Kundi Rishi , O'Connor James , Stein Deborah , Scalea Thomas , Powell Elizabeth
Published: November 2024

BACKGROUND

Venovenous extracorporeal membrane oxygenation (VV ECMO) has been used for medical etiologies of acute respiratory distress syndrome refractory to conventional management. More recently, VV ECMO has been used to stabilize trauma patients with acute lung injury. We hypothesize that patients with traumatic injuries requiring VV ECMO have similar survival outcomes and describe the characteristics between the two populations.

METHODS

This single-center, retrospective cohort study included all trauma and nontrauma patients in an 8-year period who were placed on VV ECMO. Cannulation decisions were made via multidisciplinary discussions between two intensivists and a trauma surgeon. Data were analyzed with descriptive statistics and regression analysis. After testing for normality, significance was defined as a p < 0.05.

RESULTS

A total of 516 patients were identified (438 nontrauma and 78 trauma VV ECMO patients). The trauma patient, defined as undergoing cannulation during initial trauma admission, had a median age of 29 years with 81% of patients being male, while the nontrauma patient had a median age of 41 years with 64% being males. Trauma VV ECMO patients had shorter ECMO courses (216 hours vs. 372 hours, p < 0.001), earlier cannulation (8 hours vs. 120 hours, p < 0.001), higher lactic acid levels precannulation (4.2 mmol/L vs. 2.3 mmol/L, p < 0.001), higher Sequential Organ Failure Assessment scores (13 vs. 11, p = 0.001), and higher Simplified Acute Physiology Scores II (63 vs. 48, p < 0.001). There was no difference in bleeding complications. Survival to discharge rates were similar between trauma and nontrauma VV ECMO groups (69% vs. 71%, p = 0.81).

CONCLUSION

This study demonstrates that trauma VV ECMO patients have higher markers of severe illness/injury when compared with their nontrauma VV ECMO counterparts yet have similar survival rates and shorter ECMO runs. Venovenous extracorporeal membrane oxygenation in trauma patients is a useful treatment modality for refractory hypoxemia, respiratory acidosis, and stabilization because of acute lung and thoracic injury.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
Incidence and multidrug resistance of Escherichia coli pathotypes on fresh vegetables and salads.
Authors: Vázquez-Quiñones Carlos Ramón , Rincón-Guevara Monica , Natividad-Bonifacio Ivan , Vázquez-Salinas Carlos , González-Márquez Humberto
Published: November 2024

1. Abstract

Diarrheal diseases are a severe health problem and one of the leading causes of child mortality, particularly in Africa, Asia, and Latin American countries. Diarrhea is often caused by consuming contaminated meat, raw or undercooked eggs, and improperly washed fruit and vegetables that harbor norovirus, Campylobacter, non-typhoid Salmonella, and pathogenic Escherichia coli. This study analyzed 334 samples of prepared salads containing lettuce, carrots, and tomatoes and unprocessed coriander and lettuce according to the Bacteriological Analytical Manual and the NOM SSA 210 protocols. Genotyping was done by amplifying the st and lt genes for enterotoxigenic Escherichia coli (ETEC) and the uidA gene coding beta-glucuronidase. ETEC was identified in 51.56% of the confirmed isolates, representing 9.9% of the samples collected over two years. The contamination rates by ETEC were higher in coriander (78.78%), followed by lettuce (9.09%), green salad from La Vicentina Market (9.09%), and green salad from La Purísima Market (3.03%). Among samples, 12.12% showed the presence of both ETEC fragments (st/lt), 33.3% had only the lt fragment, and 54.6% just the st fragment. In salads, the lt/st genes were detected in three samples (9.09%), the st gene was detected in one sample (3.3%), and st gene was absent. In coriander samples, 21.21% were positive for lt gene, 51.51% for the st gene, and 6.06% showed amplification of both genes. ETEC was found in 9.09% of the confirmed E. coli strains for the lettuce samples, with 3.03% showing amplification of lt gene, 3.03% for st gene, and 3.03% for both genes (lt/st). There are no reported data with the same ratios for Mexico City. The presence of ETEC in products sold or consumed in markets or on the streets in some regions of Mexico City, coupled with lifestyle changes that have increased vegetable consumption, is a significant concern. These findings underscore the potential health implications and the urgent need for further investigation and preventive measures.
Combining functional annotation and multi-trait fine-mapping methods improves fine-mapping resolution at glycaemic trait loci
Authors: Soenksen Jana , Chen Ji , Varshney Arushi , Martin Susan ,   MAGIC, Parker Stephen C. J. , Morris Andrew P. , Asimit Jennifer L. , Barroso Inês
Published: November 2024

The Meta-Analysis of Glucose and Insulin-related traits Consortium (MAGIC) identified 242 loci associated with glycaemic traits fasting insulin (FI), fasting glucose (FG), 2h-Glucose (2hGlu), and glycated haemoglobin (HbA1c). However, most causal variants remain unknown. We investigated whether combining multi-trait fine-mapping with functional information would improve fine-mapping resolution.

Using single-trait fine-mapping results (FINEMAP) as input, we performed multi-trait fine-mapping (flashfm) at 50 loci significantly associated with >1 glycaemic trait. We considered 32 cell-type specific and 28 static annotations to build enrichment models with fGWAS. We performed annotation-informed fine-mapping, using FINEMAP and flashfm, with resulting prior probabilities.

Compared to annotation-agnostic single-trait fine-mapping, multi-trait fine-mapping reduced median 99% credible set sizes (99% CS) from 58 to 17.5 (p=5.75 × 10−18). Annotation information reduced 99% CS from 67 to 50.5 (p=1.57×10−7) in single-trait, and to 14.5 (p=2.69×10−18) in multi-trait fine-mapping.

In conclusion, multi-trait and annotation-informed fine-mapping narrow down likely causal variants, separately and combined.
IMMClock reveals immune aging and T cell function at single-cell resolution
Authors: Schmidt Yael Gurevich , Wu Di , Madan Sanna , Sinha Sanju , Sahni Sahil , Gopalan Vishaka , Wang Binbin , Dhruba Saugato Rahman , Schäffer Alejandro A. , Weng Nan-ping , Restifo Nicholas P. , Wang Kun , Ruppin Eytan
Published: November 2024

The aging of the immune system substantially impacts individual immune responses, yet accurately quantifying immune age remains a complex challenge. Here we developedIMMClock, a novel immune aging clock that uses gene expression data to predict the biological age of individual CD8⁺ T cells, CD4⁺ T cells, and NK cells. The accuracy of IMMClock is first validated across multiple independent datasets, demonstrating its robustness. Second, utilizing the IMMClock, we find that intrinsic cellular aging processes are more strongly altered during immune aging than differentiation processes. Thirdly, our analysis confirms the strong associations between immune aging and established processes such as cellular senescence, exhaustion, and telomere length at the single cell level. Furthermore, immune aging is accelerated under several disease conditions such as type 2 diabetes, heart disease, and cancer. Finally, we apply IMMClock to analyze a perturb-seq gene activation screen of T cell functionality. We find that the post-perturbation immune age of individual T cells is strongly correlated with their pre-perturbation immune age. Furthermore, the immune age at resting state of individual T cells is strongly predictive of their post-stimulation activation state. Overall, IMMClock advances our understanding of immune aging by providing precise, single-cell level age estimations. Its future applications hold promise for identifying interventions that concomitantly rejuvenate and activate T cells, potentially enhancing efforts to counteract age-related immune decline.
Identification of Ephrin type-B receptor 4 as a critical mediator of tissue fibrosis
Authors: Wu Brian , Lively Starlee S. , Fine Noah , Pastrello Chiara , Maglaviceanu Anca , Espin-Garcia Osvaldo , Pollock-Tahiri Evan , Nakamura Sayaka , Kaur Paramvir , Rockel Jason S. , Potla Pratibha , Gupta Himanshi , Datta Poulami , Tang Laura , Vohra Shabana , Nakamura Akihiro , Gandhi Rajiv , Wu Jiangping , Hinz Boris , Jurisica Igor , Kapoor Mohit
Published: November 2024

Pulmonary fibrosis (PF) is a pathology associated with interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF). Fibrosis promotes continual secretion of extracellular matrix (ECM), producing non-functional scar tissue and causing organ failure. This study investigated the tyrosine kinase receptor Ephrin type-B receptor 4 (EphB4) as a mediator of PF. To this end, we generated mice with conditionalCol1a2-driven deletion ofEphb4and used a preclinical mouse model of PF, total and single nuclei RNA sequencing, NanoString, publicly available single cell data, computational analysis, and functional assays of mouse and human healthy control and IPF lung fibroblasts.Col1a2-CreERT-drivenEphb4deletion, or EphB4 inhibition via NVP-BHG712, markedly protected against bleomycin-induced PF. Total RNA-sequencing of fibroblasts isolated fromEphb4-deficient fibrotic mouse lungs exhibited reduced expression of ECM, ER Cargo, and protein trafficking-related genes. NVP-BHG712 reduced expression of these identified genes in mouse lung fibroblasts under fibrotic conditionsin vitro. Single nuclei RNA sequencing of mouse lungs treated with NVP-BHG712 identified transcriptomic changes of ECM genes in specific fibroblast subpopulations. Total RNA sequencing, computational, and functional assays using mouse and human IPF fibroblasts identified elastin as a key mediator involved in EphB4 signaling. Overall, we identified EphB4 as a crucial mediator of PF.
Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues
Authors: Keller Andrew , Bakhtina Anna , Bruce James E.
Published: November 2024

Many proteins can exist in multiple conformational statesin vivoto achieve distinct functional roles. These states include alternative conformations, variable PTMs, and association with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells, organelles, or tissues together with mass spectrometry provides the relative abundance of cross-link levels formed in two or more compared samples, which depends both on the relative levels of existent protein conformational states in the compared samples as well as the relative likelihood of the cross-link originating from each. Because cross-link conformational state preferences can vary widely, one expects intra-protein cross-link levels from proteins with high conformational plasticity to display divergent quantitation among samples with differing conformational ensembles. Here we use the large volume of quantitative cross-linking data available on the public XLinkDB database to cluster intra-protein cross-links according to their quantitation in many diverse compared samples to provide the first widescale glimpse of cross-links grouped according to the protein conformational state(s) from which they predominantly originate. We further demonstrate how cluster cross-links can be aligned with any protein structure to assess the likelihood that they were derived from it.
Auto-regulation of the real-time kinetics of the human mitochondrial replicative helicase
Authors: Plaza-G.A. Ismael , Ortiz-Rodríguez María , Buchanan Seth P. , Míguez Samuel , Lemishko Kateryna M. , Moreno-Herrero Fernando , Fernandez-Leiro Rafael , Ciesielski Grzegorz L. , Ibarra Borja
Published: November 2024

The human mitochondrial replicative helicase, Twinkle, is essential for the replication and integrity of mitochondrial DNA (mtDNA). Therefore, investigating the real-time kinetics of Twinkle’s activities and their regulation is crucial for understanding mtDNA maintenance. Here, we combine biochemical and single-molecule manipulation and visualization techniques to investigate the loading of Twinkle onto the DNA fork, its real-time DNA unwinding and rewinding kinetics, and the regulation of these processes by the amino- (N) and carboxyl- (C) terminal ends of the helicase and the mitochondrial SSB protein (mtSSB). We observed that Twinkle rapidly diffuses along dsDNA scanning for the DNA fork, where it establishes specific interactions that halt further diffusion. Our results show that during DNA unwinding, the real-time kinetics of the helicase are downregulated by interactions of its N-terminal Zinc-binding domain (ZBD) with DNA and the control of the ATPase activity by the C-terminal tail. We found that binding of mtSSB to DNA likely outcompetes the ZBD-DNA interactions, alleviating the down regulatory effects of this domain. Furthermore, we show that ZBD-DNA interactions, together with the ATP binding, also control the real-time kinetics of the DNA rewinding events that follow helicase stalling. Our findings reveal that ZBD and C-terminal tail play a major role in regulation of Twinkle’s real-time kinetics. Their interplay constitutes an auto-regulatory mechanism that may be crucial for coordination of the mtDNA maintenance activities of the helicase.
Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers
Authors: Telussa Rallya , Rahayu Puji , Yunindika Thufeil , Kapsak Curtis , Rahayu Kanti Puji , Susanti Oli , Suandy Imron , Triwijayanti Nuraini , Niasono Aji B. , Ma’arif Syamsul , Wibawa Hendra , Lestari  , Utomo Gunawan B. , Zenal Farida C. , Schoonman Luuk , Voth-Gaeddert Lee E.
Published: November 2024

Antimicrobial resistance (AMR) poses significant risks to human and animal health while the environment can contribute to its spread. National AMR surveillance programs are pivotal for assessing AMR prevalence, trends, and intervention outcomes, however, integrating advanced surveillance tools can be difficult. This pilot study, conducted by FAO ECTAD Indonesia and DGLAHS, Indonesian Ministry of Agriculture, evaluated the costs and benefits of integrating the Nanopore MinION, Illumina MiSeq, and Sensititre system into a culture-based slaughterhouse-river surveillance system. Water samples were collected from six chicken slaughterhouses and adjacent rivers (pre- and post-treatment effluent, upstream, downstream). Culture-based ESBL and generalE. coliconcentrations were estimated via the WHO Tricycle Protocol, while isolates (n=42) were sequenced (MinION, MiSeq) and antimicrobial susceptibility testing conducted (Sensititre). The Tricycle Protocol results provided estimates of effluent and river concentrations of ESBL and generalE. coliidentifying ESBL-to-generalE. coliratios of 13.8% and 6.2%, respectively. Compared to hybrid sequencing assemblies, MinION had a higher concordance than MiSeq for ARG identification (98%), virulence genes (96%), and locations for both (predominately plasmids). Furthermore, MinION concordance with Sensititre AST was 91%. Cost-benefit comparisons suggest sequencing can complement culture-based methods but is dependent on the value placed on the additional information gained.

Highlights:

This study demonstrates the integration of Nanopore MinION sequencing into a national AMR surveillance program, highlighting its potential for monitoring antibiotic-resistantE. coliin slaughterhouse effluent and rivers.

Our findings show that Nanopore MinION sequencing exhibits high concordance with hybrid sequencing assemblies, validating its effectiveness for genomic surveillance in decentralized settings.

The study evaluates the cost-benefit of using Nanopore MinION, Illumina MiSeq, and Sensititre AST, comparing information gained with cost.

Graphical Abstract
Negative regulation of miRNAs sorting in EVs: the RNA-binding protein PCBP2 impairs SYNCRIP-mediated miRNAs EVs loading
Authors: Marocco Francesco , Garbo Sabrina , Montaldo Claudia , Colantoni Alessio , Quattrocchi Luca , Gaboardi Gioele , Cicchini Carla , Tartaglia Gian Gaetano , Battistelli Cecilia , Tripodi Marco
Published: November 2024

While it is accepted that Extracellular Vesicles (EVs)-mediated transfer of microRNAs contributes to intercellular communication, the knowledge about molecular mechanisms controlling the selective and dynamic miRNA-loading in EVs is still limited to few specific RNA-binding proteins interacting with sequence determinants. Moreover, although mutagenesis analysis demonstrated the presence/function of specific intracellular retention motifs, the interacting protein/s remained unknown.

Here, PCBP2 was identified as a direct interactor of an intracellular retention motif: RIP coupled to RNA pull down and proteomic analysis demonstrated that it binds to miRNAs embedding this motif and mutagenesis proved the binding specificity. Notably, PCBP2 binding requires SYNCRIP, a previously characterized miRNA EV-loader as indicated by SYNCRIP knock-down.

SYNCRIP and PCBP2 may contemporarily bind to miRNAs as demonstrated by EMSA assays and PCBP2 knock-down causes EV-loading of intracellular microRNAs.

This evidence highlights that multiple proteins/miRNA interactions govern miRNA compartmentalization and identifies PCBP2 as a dominant inhibitor of SYNCRIP function.
Multi-omic analyses of a twin pair with mirror image cleft lip identifies pathogenic variant inFGF20modified by differential methylation upstream ofZFP57
Authors: Awotoye Waheed , Machado-Paula Ligiane A , Hovey Luke , Keen Henry , Chimenti Michael , Darbro Benjamin , Dabdoub Shareef , Thomas James C , Murray Jeff , Rengasamy Venugopalan Shankar , Moreno-Uribe Lina , Petrin Aline L
Published: November 2024

Background

Disturbances in the intricate processes that control craniofacial morphogenesis can result in birth defects, most common of which are orofacial clefts (OFCs). Nonsyndromic cleft lip (nsCL), one of the phenotypic forms amongst OFCs, has a non-random laterality presentation with the left side being affected twice as often compared to the right side. This study investigates the etiology of nsCL and the factors contributing to its laterality using a pair of monozygotic twins with mirror-image cleft lip.

Methods

We conducted whole-genome sequencing (WGS) analyses in a female twin pair with mirror image nsCL, their affected mother and unaffected father to identify etiopathogenic variants. Additionally, to identify possible cleft lip laterality modifiers, DNA-methylome analysis was conducted to test for differential methylation patterns between the mirror twins. Lastly, DNA methylation patterns were also analyzed on an independent cohort of female cases with unilateral cleft lip (left=22; right=17) for replication purposes.

Results

We identified a protein-altering variant inFGF20(p.Ile79Val) within the fibroblast growth factor interacting family domain segregating with the nsCL in this family. Concurrently, DNA-methylome analysis identified differential methylation regions (DMRs) upstream of Zinc-finger transcription factorZFP57(Δβ > 5%). Replication of these results on an independent cohort, confirmed these DMRs, emphasizing their biological significance (p<0.05). Enrichment analysis indicated that these DMRs are involved in DNA methylation during early embryo development (FDR adjusted p-value = 1.3241E-13). Further bioinformatics analyses showed one of these DMRs acting as a binding site for transcription factorAP2A(TFAP2A), a key player in craniofacial development. Interactome analysis also suggested a potential role forZFP57in left/right axis specification, thus emphasizing its significance in cleft laterality.

Conclusion

This study provides novel insights into the etiology of nsCL and its laterality, suggesting an interplay between etiopathogenic variants and DNA methylation in cleft laterality. Our findings elucidate the intricate mechanisms underlying OFCs development. Understanding these factors may offer new tools for prevention and management of OFCs, alleviating the burden on affected individuals, their families and global health.
Interaction between time-of-day and oxytocin efficacy in mice and humans with and without gestational diabetes
Authors: Duong Thu Van-Quynh , Yaw Alexandra M. , Zhou Guoli , Sina Niharika , Cherukuri Aneesh Sai , Nguyen Duong , Cataldo Kylie , Ly Nicollette , Sen Aritro , Sempere Lorenzo , Detrie Cara , Seiler Robert , Nicholas Olomu I. , Cortese Rene , Long Robert , Hoffmann Hanne M.
Published: November 2024

Management of labor in women with diabetes is challenging due to the high risk of peri- and postpartum complications. To avoid cesarean section and assist with labor progression, Pitocin, a synthetic oxytocin, is frequently used to induce and augment labor. However, the efficacy of Pitocin is often compromised in diabetic pregnancies, leading to increased cesarian delivery. As diabetes deregulates the body’s circadian timekeeping system and the time-of-day of the first Pitocin administration contributes to labor duration, our objective was to determine how the time of day and the circadian clock gene,Bmal1, gates oxytocin efficacy. Our studies in mice show that, compared to the rest phase of the day (lights on), the uterotonic efficacy of oxytocin is significantly increased during the active phase (lights off). Usingin vitrostudies, a myometrium-specificBmal1conditional knockout mouse model, and a mouse model of food-induced gestational diabetes, we find thatBmal1is crucial for maintaining oxytocin receptor expression and response in the myometrium in mice. These findings also translate to humans, where oxytocin-induced human myometrial cell contraction is time-of-day dependent, and retrospective clinical data suggest that administration of Pitocin in the morning should be considered for pregnant women with gestational diabetes.
Distribution-preserved compression of single-cell atlases for privacy-protected data dissemination and novel cell type discovery
Authors: Cai Zhihan , Hu Zhibin , Sun Shuang-Rong , Wang Zexu , Yang Fan , Han Jiahuai , Zeng Feng
Published: November 2024

We introduce SUREv2, a tool for constructing lightweight, transmittable, and privacy-preserving references from single cell atlases. SUREv2 introduces a compressed data structure that maintain the distribution of cells within these atlases and develops an out-of-reference scoring method for identifying novel cell populations. This user-friendly tool shall enhance the analysis of single cell datasets by providing a consistent, privacy-focused reference framework.
Unraveling cfDNA Fragmentation Patterns: Linking Chromatin Architecture to Cancer Diagnostic Sensitivity
Authors: Johnston Andrew D , Antaw Fiach , Lu Jennifer , Stirzaker Clare , Trau Matt , Korbie Darren
Published: November 2024

Circulating cell-free DNA (cfDNA) liquid biopsies offer a powerful, non-invasive approach for cancer diagnostics, leveraging DNA fragments primarily released during apoptosis. Using droplet digital PCR on cfDNA samples from 88 breast and colorectal cancer patients, we uncovered highly consistent nucleosome breakpoints across individuals. Proximity to these cfDNA breakpoints diminishes the sensitivity of somatic mutation assays, including those targetingIDH1andNRAShotspot mutations, underscoring the importance of precise nucleosome positioning data. We introduce a probabilistic nucleosome protection scoring method that enables high-resolution mapping of nucleosome positions and cfDNA breakpoints. These maps reveal distinct nucleosome spacing patterns between heterochromatin and euchromatin, corresponding to different chromatin fiber topologies. Analysis of X-chromosome inactivation further supports the topoisomer model: heterochromatin’s 187 bp nucleosome repeat length differs from euchromatin’s 182 bp, generating wave interference patterns in nucleosome signals. Our findings suggest that loop-mediated transitions from T2 to T1 topoisomers shape chromatin accessibility and cfDNA fragmentation, advancing the diagnostic potential of liquid biopsy assays.

Highlights

Nucleosome breakpoint conservation impacts somatic mutation assay sensitivity

Probabilistic protection scoring enhances cfDNA nucleosome peak resolution

Chromatin states exhibit unique nucleosome spacing linked to distinct topologies, influencing cfDNA fragmentation

Chromosome X-inactivation phasing analyses reveal waveform interference in nucleosome positioning signals

Graphical Abstract
Integrative cardiovascular dose-response to graded lower body negative pressure
Authors: Whittle Richard S. , Keller Nathan , Hall Eric A. , Patanam Safiyya , Dunbar Bonnie J. , Diaz-Artiles Ana
Published: November 2024

Background

Lower body negative pressure (LBNP) has been posited as a potential spaceflight countermeasure to counteract the physiological deconditioning related to fluid shifts in micro-gravity. However, open questions remain as to the magnitude of LBNP that should be applied. We systematically characterized the cardiovascular effects of LBNP and quantified the effect size of varied LBNP doses across different parts of the cardiovascular system.

Methods

Twenty-four subjects (12M, 12F) were exposed to graded LBNP from 0 mmHg to −50 mmHg in 10 mmHg increments, both in supine (0°) and 15° head-down tilt postures. We measured the steady-state response in a large range of variables, including those related to the systemic circulation, cardiovascular control, and hemodynamics of the eyes and neck.

Results

Building on the experimental data, dose-response curves were constructed using a Bayesian multivariate hierarchical modeling framework to quantify the effect size of every variable considered when subjected to LBNP. The methodology allows direct comparison of the variables and the underlying structural relationships between them. Further, we demonstrated the potential for LBNP to reduce jugular venous flow stagnation, which is considered one of the major health risks during human spaceflight.

Conclusions

The Dose-response curves and effect sizes generated from this research effort establish the most comprehensive framework available to date that characterizes physiological responses to LBNP. These results directly inform the development of countermeasures to mitigate the negative effects of spaceflight, including cardiovascular deconditioning, spaceflight-associated neuro-ocular syndrome, and venous thromboembolism events.

Key Points Summary

Lower body negative pressure (LBNP) has been posited as a potential countermeasure for multiple risks associated with spaceflight, including cardiovascular deconditioning, spaceflight-associated neuro-ocular syndrome, and venous thromboembolism events. However, the specific LBNP dose needed to mitigate these risks is still unknown.

We constructed the LBNP dose-response curves in supine and 15° head-down-tilt positions to quantify the acute response of a large variety of hemodynamics, autonomic, ocular, and neck variables across a range of LBNP levels.

We also used a Bayesian multivariate modeling framework to identify significant relationships between variables and to compare their effect sizes under different levels of LBNP.

In addition, results indicate that LBNP is a promising countermeasure to reduce jugular venous flow stagnation occurring during microgravity exposure.

This study constitutes the most comprehensive analysis of cardiovascular hemodynamics, autonomic, and cephalad response to LBNP to date. This framework informs the development of countermeasures to mitigate the detrimental effects of spaceflight.
Mitochondrial genome-encoded mitomiRs regulate cellular plasticity and susceptibility to ferroptosis in triple-negative breast cancer
Authors: Kandettu Amoolya , Ghosal Joydeep , Tharayil Jesline Shaji , Kuthethur Raviprasad , Mallya Sandeep , Narasimhamurthy Rekha Koravadi , Mumbrekar Kamalesh Dattaram , Subbannayya Yashwanth , Kumar Naveena AN , Radhakrishnan Raghu , Kabekkodu Shama Prasada , Chakrabarty Sanjiban
Published: November 2024

Ferroptosis is a distinct form of regulated cell death promoted by iron-dependent lipid peroxidation. The metabolic plasticity of cancer cells determines their sensitivity to ferroptosis. Although mitochondrial dysfunction contributes to metabolic reprogramming in cancer cells, its role in ferroptosis remains to be identified. We identified that the mitochondrial genome encodes 13 miRNAs (mitomiRs) that are highly expressed in breast cancer cell lines and patient-derived tumor samples. Expression analysis revealed that mitomiRs are upregulated in basal-like triple-negative breast cancer (TNBC) cells compared to mesenchymal stem-like TNBC cells. Interestingly, 11 out of the 13 mitomiRs bind to the 3′UTR of zinc finger E-box-binding homeobox 1 (ZEB1), a transcription factor, involved in epithelial to mesenchymal transition (EMT) in breast cancer. Using mitomiR-3 mimic, inhibitor and sponges, we confirmed that mitomiR-3 indeed regulate ZEB1 expression in TNBC cells. Increased mesenchymal features in TNBC contributed to vulnerability to pro-ferroptotic metabolic reprogramming sensitizing to cell death inin vitroandin vivomodels. Some of the challenges associated with pro-ferroptotic drugs includes lack of cancer cell specificity, low targeting ability, normal tissue toxicity contributing to their limited clinical application as cancer therapeutics. Here, we identified mitomiRs which are highly expressed in TNBC subtypes with low expression in normal breast cells making them an ideal candidate for selective inhibition for targeted therapy. Further, we demonstrated that the inhibition of mitomiRs in triple-negative breast cancer cells promote pro-ferroptotic metabolic reprogramming which can be exploited as novel vulnerability for targeted ferroptotic induction in cancer cells avoiding the normal tissue toxicity. Collectively, our results indicate a novel mechanism of mitochondrial miRNA mediated ferroptosis sensitivity in TNBC subtypes which could be exploited to develop potential miRNA-based therapeutics.
Distributed coding of space and valence in the medial temporal lobe
Authors: Yang Ladan , Mikkelsen Catherine A
Published: November 2024

The hippocampus has been associated with spatial information processing (OKeefe, 1976). However, it is also not clear whether such ensemble coding of spatial information extends to other brain regions in the medial temporal lobe. Hence, this study uses various classification techniques to attempt to decode spatial and valence information utilizing publicly available rodent single-unit data (Girardeau et al., 2017). We found that the spatial information is encoded sparsely and distributed among many neurons in the hippocampus. Additionally we found that both spatial and valence information could be decoded in the hippocampus, the amygdala, and the piriform cortex. We also compared the strengths and weaknesses of four different classifiers (LDA, KNN, SVM, NB) theoretically and in practice with this dataset.
Squidiff: Predicting cellular development and responses to perturbations using a diffusion model
Authors: He Siyu , Zhu Yuefei , Tavakol Daniel Naveed , Ye Haotian , Lao Yeh-Hsing , Zhu Zixian , Xu Cong , Chauhan Sharadha , Garty Guy , Tomer Raju , Vunjak-Novakovic Gordana , Zou James , Azizi Elham , Leong Kam W.
Published: November 2024

Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and responses to environmental stimuli. However, mapping transcriptomic changes across diverse cell types in response to various stimuli and elucidating underlying disease mechanisms remains challenging. Studies involving physical stimuli, such as radiotherapy, or chemical stimuli, like drug testing, demand labor-intensive experimentation, often hindering the rapid advancement of mechanistic insight and drug discovery. To address this, we present Squidiff, a diffusion model-based generative framework designed to predict transcriptomic changes across diverse cell types in response to a wide range of environmental changes. We demonstrate Squidiff’s robustness across various scenarios, including cell differentiation, gene perturbation, and drug response prediction. Through continuous denoising and semantic feature integration, Squidiff effectively learns transient cell states and predicts high-resolution transcriptomic landscapes over time and conditions. Furthermore, we applied Squidiff to model the development of blood vessel organoids and cellular responses to neutron irradiation and growth factors. Our results demonstrate that Squidiff enablesin silicoscreening of cell molecular landscapes, facilitating rapid hypothesis generation and providing valuable insights for precision medicine.