bluuebunny/crossref_metadata_2025 huggingface dataset:
A Rare Case of Abnormal Diffuse Brain Uptake on an 123I MIBG Scan in a Patient With High-Risk Neuroblastoma
Authors: Basavalingu Deepashri , Sadic Murat , Cheeney Safia , Parisi Marguerite T.
Published: April 2024

123I-meta-iodobenzylguanidine (123I-MIBG) is extensively used for initial staging and response evaluation in children with neuroblastoma. Physiological uptake of 123I-MIBG occurs in the salivary glands, liver, adrenal gland, myocardium, bowel, and thyroid gland. 123I-MIBG cannot cross an intact blood-brain barrier. We present the rare case of a 3-year-old boy with neuroblastoma and meningeal metastases who underwent an 123I-MIBG scan for disease restaging that showed abnormal brain uptake. Abnormal MIBG uptake in the brain can occur if there is disruption of the blood-brain barrier either secondary to metastases or after damage to blood-brain barrier.
Application of 3-Step Laparoscopic Cholecystectomy in Acute Difficult Cholecystitis
Authors: Zhang Chun , Guo Dengfang , Lv Guifang , Lin Feng , Wang Qinglin , Lin Jianyuan , Xiao Dexian , Wang Ruotao , Gong Qingquan
Published: April 2024

Background:

With the aging of the global population, the incidence rate of acute cholecystitis is increasing. Laparoscopic cholecystectomy is considered as the first choice to treat acute cholecystitis. How to effectively avoid serious intraoperative complications such as bile duct and blood vessel injury is still a difficult problem that puzzles surgeons. This paper introduces the application of laparoscopic cholecystectomy, a new surgical concept, in acute difficult cholecystitis.

Methods:

This retrospective analysis was carried out from January 2019 to January 2021. A total of 36 patients with acute difficult cholecystitis underwent 3-step laparoscopic cholecystectomy. The general information, clinical features, surgical methods, surgical results, and postoperative complications of the patients were analyzed.

Results:

All patients successfully completed the surgery, one of them was converted to laparotomy, and the other 35 cases were treated with 3-step laparoscopic cholecystectomy. Postoperative bile leakage occurred in 2 cases (5.56%), secondary choledocholithiasis in 1 case (2.78%), and hepatic effusion in 1 case (2.78%). No postoperative bleeding, septal infection, and other complications occurred, and no postoperative colon injury, gastroduodenal injury, liver injury, bile duct injury, vascular injury, and other surgery-related complications occurred. All 36 patients were discharged from hospital after successful recovery. No one died 30 days after surgery, and there was no abnormality in outpatient follow-up for 3 months after surgery.

Conclusions:

Three-step laparoscopic cholecystectomy seems to be safer and more feasible for acute difficult cholecystitis patients. Compared with traditional laparoscopic cholecystectomy or partial cholecystectomy, 3-step laparoscopic cholecystectomy has the advantages of safe surgery and less complications, which is worth trying by clinicians.
Cutaneous tuberculosis an unusual localization: A case report
Authors: ZIAD Fatima , Benaissa Elmostafa , Ait sahel Omar , MAAROUFI Abdelkhaleq , Ben lahlou Yassine , Maleb Adil , Chadli Mariama , Elouennass Mostafa
Published: April 2024

Tuberculosis is a major public health concern. Morocco is a tuberculosis endemic country; nearly 30,000 cases are recorded each year. Pulmonary tuberculosis accounts for 57%, extrapulmonary tuberculosis 43%. Cutaneous localization is exceptional; it accounts for 0.5%  to 2% of cases of tuberculosis. It is very difficult to diagnose, given the variability of clinical presentation. We report a rare case of cutaneous tuberculosis in a patient with a history of pulmonary and cutaneous sarcoidosis.
Translational arrest and mRNA decay are independent activities of alphaherpesvirus virion host shutoff proteins
Authors: Eke Lucy , Tweedie Alistair , Cutts Sophie , Wise Emma L. , Elliott Gillian
Published: April 2024

The herpes simplex virus 1 (HSV1) virion host shutoff (vhs) protein is an endoribonuclease that regulates the translational environment of the infected cell, by inducing the degradation of host mRNA via cellular exonuclease activity. To further understand the relationship between translational shutoff and mRNA decay, we have used ectopic expression to compare HSV1 vhs (vhsH) to its homologues from four other alphaherpesviruses – varicella zoster virus (vhsV), bovine herpesvirus 1 (vhsB), equine herpesvirus 1 (vhsE) and Marek’s disease virus (vhsM). Only vhsH, vhsB and vhsE induced degradation of a reporter luciferase mRNA, with poly(A)+ in situ hybridization indicating a global depletion of cytoplasmic poly(A)+ RNA and a concomitant increase in nuclear poly(A)+ RNA and the polyA tail binding protein PABPC1 in cells expressing these variants. By contrast, vhsV and vhsM failed to induce reporter mRNA decay and poly(A)+ depletion, but rather, induced cytoplasmic G3BP1 and poly(A)+ mRNA- containing granules and phosphorylation of the stress response proteins eIF2α and protein kinase R. Intriguingly, regardless of their apparent endoribonuclease activity, all vhs homologues induced an equivalent general blockade to translation as measured by single-cell puromycin incorporation. Taken together, these data suggest that the activities of translational arrest and mRNA decay induced by vhs are separable and we propose that they represent sequential steps of the vhs host interaction pathway.
Exploring thermal tolerance across time and space in a tropical bivalve,Pinctada margaritifera
Authors: Lugue K. , Monaco C. J. , Vigouroux E. , Sham Koua M. , Vidal-Dupiol J. , Mitta G. , Le Luyer J.
Published: April 2024

Ectotherm’s vulnerability to climate change is predicted to increase with temperature variations. Still, translating laboratory observations of organisms’ heat stress responses to the natural fluctuating environment remains challenging. In this study, we used an integrative framework combining insights from the TDT curves and physiological reaction norms, to precisely capturePinctada margaritiferastage -specific thermal tolerance. On a second hand, this study aimed to explore applicability of the model of accumulation of thermal injury, by making in situ predictions at three contrasting sites across French Polynesia. By working with two life stages (early planktonic vs. spat), our study revealed an ontogenetic shift in lethal (CTmax) and sub-lethal (Tc) thermal limits, with higher vulnerability for early larval stages. Cumulative injury calculations resulted in thermal failure (100% injury) for larvae within 12 and 22 h, at the most ‘extreme’ site (Nuku Hiva; T°C > 38°C), and warm lagoon (Reao Atoll), respectively. While substantial damages accumulated in spats, when exposed to consecutive extreme tides (Nuku Hiva) for 8 days. Overall, our results revealed thatP. margarifierais living closer to their upper thermal limits than previously estimated, and inhabit environments where important reduction of settlement and heat stress are already occurring during warmest months.
Lipopeptide antibiotics disrupt interactions of undecaprenyl phosphate with UptA
Authors: Oluwole Abraham O. , Kalmankar Neha , Guida Michela , Bennett Jack L. , Poce Giovanna , Bolla Jani R. , Robinson Carol V.
Published: April 2024

The peptidoglycan pathway represents one of the most successful antibacterial targets with the last critical step being the flipping of carrier lipid, undecaprenyl phosphate (C55-P), across the membrane to re-enter the pathway. This translocation of C55-P is facilitated by DedA and DUF368 domain-containing family membrane proteins via unknown mechanisms. Here we employ native mass spectrometry to investigate the interactions of UptA, a member of the DedA family of membrane protein fromBacillus subtilis, with C55-P, membrane phospholipids and cell wall-targeting antibiotics. Our results show that UptA, expressed and purified inE. coli, forms monomer-dimer equilibria, and binds to C55-P in a pH-dependent fashion. Specifically, we show that UptA interacts more favourably with C55-P over shorter-chain analogues and membrane phospholipids. Moreover, we demonstrate that lipopeptide antibiotics, amphomycin and aspartocin D, can directly inhibit UptA function by out-competing the substrate for the protein binding, in addition to their propensity to form complex with free C55-P. Overall, this study shows that UptA-mediated translocation of C55-P is potentially mediated by pH and anionic phospholipids and provides insights for future development of antibiotics targeting carrier lipid recycling.
Population-level whole genome sequencing ofAscochyta rabieiidentifies genomic loci associated with isolate aggressiveness
Authors: Vaghefi Niloofar , Bar Ido , Lawley Jonathan Wanderley , Thanjavur Sambasivam Prabhakaran , Christie Melody , Ford Rebecca
Published: April 2024

Ascochyta blight caused by the ascomyceteAscochyta rabieiposes a major biotic threat to chickpea (Cicer arietinum) industries worldwide and incurs substantial costs to the Australian multimillion-dollar chickpea industry both in disease control and yield loss. The fungus was introduced to Australia in the 1970s from an unknown source population, and within a few decades, successfully established in all Australian agroecological chickpea growing regions. Although genetically highly clonal, a broad range of phenotypic variation in terms of aggressiveness exists among the AustralianA. rabieiisolates. More recently, highly aggressive isolates capable of causing severe disease symptoms on moderate to highly resistant chickpea cultivars have increased in frequency. To identify genetic loci potentially associated withA. rabieiaggressiveness on Australian chickpea cultivars, we performed deep genome sequencing of 230 isolates collected from a range of agroecological chickpea growing regions between 2013 and 2020. Population genetic analyses using genome-wide single nucleotide polymorphism data identified three main clusters of genetically closely related isolates in Australia. Phylogenetic analyses showed that highly aggressive phenotypes developed multiple times independently throughout the phylogeny. Results point to minor contribution of multiple genetic regions and most likely epigenomic variations to aggressiveness ofA. rabieiisolates on Australian chickpea cultivars.

IMPACT STATEMENT

This research introduces new knowledge on the AustralianA. rabieipopulation structure, molecular pathogenicity drivers and evolution as a clonal pathogen through comprehensive whole-genome sequencing approach. The knowledge generated on the structure and origin of the AustralianA. rabieiand existence of only one mating type continues to inform researchers, growers, breeders and the broader industry on the importance for continued tight biosecurity measures and inform development of accurate and informed disease management and resistance breeding strategies. This research provides a rare real-life example to the effect of genetic drift on a clonal pathogen population and the importance of biosecurity to protect introduction from non-endemic isolates through seed importation in the current era of international markets.

DATA SUMMARY

An online dataset containing the data and code required to reproduce the results found in this publication have been deposited at Zenodo (DOI10.5281/zenodo.12575659). Isolate aggressiveness and collection metadata are available in the Ascochyta dashboard athttp://bit.ly/asco-dashboard. Raw sequencing data used in this study was deposited to the NCBI Short Read Archive (SRA) and is available through BioProjectPRJNA1175002. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
A TALS-likeRTTNmutation impedes neural rosette formation in human cortical organoids
Authors: Guguin Justine , Chen Ting-Yu , Besson Alicia , Cuinat Silvestre , Bertiaux Eloïse , Boutaud Lucile , Ardito Nolan , Murguiondo Miren Imaz , Cabet Sara , Hamel Virginie , Thomas Sophie , Pain Bertrand , Edery Patrick , Putoux Audrey , Tang Tang K. , Mazoyer Sylvie , Delous Marion
Published: April 2024

The Taybi-Linder syndrome (TALS) is a rare genetic disorder characterized by a severe microcephaly with abnormal gyral pattern, severe growth retardation, bone abnormalities and a reduced life span for the most severe cases. It is caused by mutations inRNU4ATACwhose transcript, the small nuclear RNA U4atac, is a core component of the minor spliceosome involved in the excision of minor introns spread over ∼750 genes.

Here, we report a patient presenting with TALS features but no mutation inRNU4ATAC; instead, she carries theRTTNc.2953A>G variant at the homozygous state. This variant, already reported in patients with syndromic microcephaly, encodes the missense p.Arg985Gly amino acid change. It is also known to affectRTTNpre-mRNA splicing, with the expression of two forms lacking either exon 23 (in-frame) or exons 22-23 (out-of-frame). By using the engineeredRTTNdepleted RPE1 cellular model, we analysed independently the impact of the missense and in-frame deletion of exon 23RTTNisoforms on the localisation and function of the protein at the centrosome, and showed that the pathogenicity of the c.2953A>G variant is mostly due to the latter. In patient fibroblasts, we observed a reduction of the centriole length and an alteration of ciliary function, while the analysis of neuronal stem cells (NSC) derived from CRISPR/Cas9-edited induced pluripotent stem cells revealed major cell cycle and mitotic abnormalities, leading to aneuploidy, cell cycle arrest and increased cell death. Finally, by generating cortical organoids, we discovered a new function of RTTN in the self-organisation of NSC into neural rosettes. We observed a delayed apico-basal polarization of NSC, accompanied with decreased cell division and increased apoptosis. Altogether, these defects lead to a marked decrease of rosette number and size inRTTN-mutated organoids, thus impeding their overall growth.

To conclude, our study gives new insights on microcephaly-related pathophysiological mechanisms underlying the only recurrentRTTNmutation, that could also open a path to better understand those involved inRNU4ATAC-associated Taybi-Linder syndrome.
Paving the way for precision treatment of psychiatric symptoms with functional connectivity neurofeedback
Authors: Taylor JE , Oka T , Murakami M , Motegi T , Yamada T , Kawashima T , Kobayashi Y , Yoshihara Y , Miyata J , Murai T , Kawato M , Cortese A
Published: April 2024

Despite the prevalence of Major depressive disorder (MDD), a large proportion of patients do not respond well to its existing treatments. Patients with MDD have heterogeneous transdiagnostic subsets of symptoms with differing underlying neural aberrations. Therefore, better treatment response might be achieved using more customizable treatments. Showing promise for this, brain-machine interfaces (BMIs) can be used to directly target patient-specific underlying neural aberrations. As a major step in this direction, here we reproduce and extend, with a larger sample, our previous findings that a BMI technique called Functional Connectivity Neurofeedback (FCNef) can normalize neural aberrations related to specific MDD symptoms. For the first time, we show that normalization of the target neural activity (here, connectivity between the dorsolateral prefrontal cortex and the precuneus) corresponds meaningfully more to reductions in corresponding than non-corresponding symptoms (here, significantly more to reductions in rumination than anxiety symptoms). Furthermore, we showed for the first time that this depended on the specific parameters that FCNef was run with. Specifically, normalization of the targeted neural activity and a corresponding reduction in related symptoms was greater withmore external rewardand withconsecutive(compared to non-consecutive) days of training, but did not differ depending on whether participants were given shorter or longer time-windows to manipulate their neural activity. Overall, these findings demonstrate the promise of FCNef for precision medicine and highlight the importance of BMI parameter testing for enhancing the feasibility of actual clinical trials. Hereby, we inch closer to a future where signals from our own brains are used to guide our own individual medical interventions.
Mutational pressure drives enhanced release of proteasome-generated public CD8+T cell epitopes from SARS-CoV-2 RBD of Omicron and its current lineages
Authors: Kudriaeva Anna A. , Butenko Ivan O. , Saratov George A. , Ri Maxim , Mokrushina Yuliana A. , Bondarev Alexey A. , Evpak Alena S. , Smirnov Ivan V. , Matyushkina Daria S. , Gabibov Alexander G. , Govorun Vadim M. , Belogurov Alexey A.
Published: April 2024

The COVID-19 pandemic was the most dramatic in the newest history with nearly 7 million deaths and global impact on mankind. Here we report binding index of 305 HLA class I molecules from 18,771 unique haplotypes of 28,104 individuals to 821 peptides experimentally observed from spike protein RBD of 5 main SARS-CoV-2 strains hydrolyzed by human proteasomes with constitutive and immune catalytic phenotypes. Our data read that mutations in the hACE2-binding region RBD496-513of Omicron B.1.1.529 strain results in a dramatic increase of proteasome-mediated release of two public HLA class I epitopes. Global population analysis of HLA class I haplotypes, specific to these peptides, demonstrated decreased mortality of human populations enriched in these haplotypes from COVID-19 after but not before December, 2021, when Omicron became dominant SARS-CoV-2 strain. Noteworthy, currently circulating BA.2.86 and JN.1 lineages contain no amino acid substitutions in RBD496-513thus preserving identified core epitopes.
A Randomized, Placebo-Controlled Trial to Evaluate the Safety and Efficacy of VIR-2482 in Healthy Adults for Prevention of Influenza A Illness (PENINSULA)
Authors: Tan Susanna K. , Cebrik Deborah , Plotnik David , Agostini Maria L. , Boundy Keith , Hebner Christy M. , Yeh Wendy W. , Pang Phillip S. , Moya Jaynier , Fogarty Charles , Darani Manuchehr , Hayden Frederick G.
Published: April 2024

Background

Influenza A results in significant morbidity and mortality. VIR-2482, an engineered human monoclonal antibody with extended half-life, targets a highly conserved epitope on the stem region of influenza A hemagglutinin, and may protect against seasonal and pandemic influenza.

Methods

This double-blind, randomized, placebo-controlled, phase 2 study examined the safety and efficacy of VIR-2482 for seasonal influenza A illness prevention in unvaccinated healthy adults. Participants (N = 2977) were randomized 1:1:1 to receive VIR-2482 450 mg, VIR-2482 1200 mg, or placebo via intramuscular (IM) injection. Primary and secondary efficacy endpoints were the proportions of participants with reverse transcriptase-polymerase chain reaction (RT-PCR)–confirmed influenza A infection and either protocol-defined influenza-like illness (ILI) and Centers for Disease Control and Prevention (CDC)–defined ILI or World Health Organization (WHO)–defined ILI, respectively.

Results

VIR-2482 450 mg and 1200 mg prophylaxis did not reduce the risk of protocol-defined ILI with RT-PCR–confirmed influenza A versus placebo (relative risk reduction [RRR], 3.8% [95% CI: −67.3, 44.6] and 15.9% [95% CI: −49.3, 52.3], respectively). At the 1200 mg dose, the RRRs in influenza A illness were 57.2% [95% CI: −2.5, 82.2] using CDC-ILI and 44.1% [95% CI: −50.5, 79.3] using WHO-ILI definitions, respectively. Serum VIR-2482 levels were similar regardless of influenza status; variants with reduced VIR-2482 susceptibility were not detected. Local injection-site reactions were mild and similar across groups.

Conclusion

VIR-2482 1200 mg IM was well tolerated but did not significantly prevent protocol-defined ILI. Secondary endpoint analyses suggest this dose may have reduced influenza A illness.

Trial registration

ClinicalTrials.govidentifier,NCT05567783

Key points

Prophylactic administration of 1200 mg of VIR-2482, an engineered human monoclonal antibody targeting a highly conserved epitope on the stem region of influenza A hemagglutinin, did not significantly reduce risk of influenza-like illness from influenza A virus in healthy adults.
Reward enhances motor adaptation learning in acute stroke patients
Authors: Paul Theresa , Wiemer Valerie M. , Günther Jonas , Lehnberg Finn M. , Grafton Scott T. , Fink Gereon R. , Volz Lukas J.
Published: April 2024

The majority of motor recovery occurs within the first weeks after stroke and has been hypothesized to rely on similar mechanisms as motor learning. However, it remains unknown whether acute stroke patients are capable of error-based motor adaptation learning and, if so, whether such learning may be enhanced by reinforcement feedback. Here, we show for the first time that acute stroke patients exhibit successful error-based motor adaptation with their paretic hand by replicating well-known phenomena such as savings and retention of adaptation learning. Notably, reward and punishment feedback exerted dissociative modulatory effects on motor adaptation. Contrary to findings in healthy subjects and chronic stroke patients, punishment did not enhance learning rates during early adaptation but led to poorer performance than reward. Most importantly, reward feedback enhanced both initial learning and retention, emphasizing the potential of reward and discouraging punishment feedback in early neurorehabilitation after stroke.
Modulation of subcortical activity along the migraine cycle during cognitive executive load
Authors: Ruiz-Tagle Amparo , Caetano Gina , Fouto Ana , Esteves Inês , Cabaço Inês , Da Silva Nuno , Vilela Pedro , Alves Pedro Nascimento , Martins Isabel Pavão , Gouveia Raquel Gil , Figueiredo Patrícia
Published: April 2024

Objective

To analyze cognition and brain activation during an executive task in migraine patients studied in the different phases of the migraine cycle, compared with healthy participants.

Background

Cognitive difficulties reported during migraine attacks remain poorly understood, despite evidence that the lateral frontoparietal network undergoes reversible disturbances and decreased activation during attacks. Recent findings in resting state functional magnetic resonance imaging suggest that brain areas involved in this network interact with subcortical regions during spontaneous migraine attacks.

Methods

Patients with low-frequency episodic menstrual migraine without aura were assessed with functional magnetic resonance imaging while performing a working memory task, along the four phases of natural migraine cycles, including spontaneous attacks, namely: peri-ictal (preictal, ictal, postictal) phases and interictally (in-between attacks). Healthy controls were assessed during the corresponding phases of their menstrual cycles.

Results

The protocol was completed by 24 female participants aged 21 to 47 years: 10 with migraine (four sessions each) and 14 controls (two sessions each). Patients and controls showed similar performance on the working memory task and displayed increased brain activity in regions linked to this function, namely the middle frontal gyrus, inferior parietal lobe, and anterior cingulate cortex, during all phases of the migraine/menstrual cycle. Migraine patients exhibited a significant decrease in hypothalamic activity during the postictal phase when compared to perimenstrual controls (p= 0.007), interictal (p= 0.002) and preictal (p= 0.034) migraine phases.

Conclusion

Cognitive areas were actively recruited during a working memory task in different phases of the migraine cycle. In addition, migraine patients displayed significantly lower neural activity at the subcortical level in the peri-ictal period. These findings, combined with previous research showing activation in cortical areas, suggest subcortical-cortical interaction during the peri-ictal phases, which may act as a compensatory mechanism when the individual faces a cognitively demanding task during migraine attacks.
Molecular epidemiology of invasive Group A Streptococcal infections before and after the COVID-19 pandemic in Switzerland
Authors: Andrianaki Angeliki M. , Franz Jessica , Andreoni Federica , Bergada-Pijuan Judith , Scheier Thomas C. , Duwe Tanja , Pfister Marc , Seth-Smith Helena , Roloff Tim , Kolesnik-Goldmann Natalia , Burkhard Sara H. , Cusini Alexia , Karrer Urs , Rüegg Christian , Schibli Adrian , Schrenzel Jacques , Musumeci Stefano , Kouyos Roger D. , Egli Adrian , Brugger Silvio D. , Zinkernagel Annelies S.
Published: April 2024

Group AStreptococcus(GAS, akaStreptococcus pyogenes) poses a significant public health concern, causing a diverse spectrum of infections with high mortality rates. Following the COVID-19 pandemic, a resurgence of invasive GAS (iGAS) infections has been documented, necessitating efficient outbreak detection methods. Whole genome sequencing (WGS) serves as the gold standard for GAS molecular typing, albeit constrained by time and costs. This study aimed to characterize the post-pandemic increased prevalence of iGAS on the molecular epidemiological level in order to assess whether new, more virulent variants have emerged, as well as to assess the performance of the rapid and cost-effective Fourier-transform infrared (FT-IR) spectroscopy as an alternative to WGS for detecting and characterizing GAS transmission routes. A total of 66 iGAS strains isolated from nine Swiss hospitals during the COVID-19 post-pandemic increased GAS prevalence were evaluated and compared to 15 strains collected before and 12 during the COVID-19 pandemic. FT-IR measurements and WGS were conducted for network analysis. Demographic, clinical, and epidemiological data were collected. Skin and soft tissue infection was the most common diagnosis, followed by primary bacteremia and pneumonia. Viral co-infections were found in 25% of cases and were significantly associated with more severe disease requiring intensive care unit admission. WGS analysis did not reveal emerging GAS genetic distinct variants after the COVID-19 pandemic, indicating the absence of a pandemic-induced shift. FT-IR spectroscopy exhibited limitations in differentiating genetically distant GAS strains, yielding poor overlap with WGS-derived clusters. Theemm1/ST28 gebotype was predominant in our cohort and was associated with five of the seven deaths recorded, in accordance with the molecular epidemiological data before the pandemic. Additionally, no notable shift in antibiotic susceptibility patterns was observed. Our data suggest that mainly non-pathogen related factors contributed to the recent increased prevalence of iGAS.
Effect of Eligibility Criteria on Patients’ Survival and Serious Adverse Events in Colorectal Cancer Drug Trials
Authors: Wang Chang , Chen Aokun , He Xing , Balian Patrick , George Thomas J. , Wang Fei , Bian Jiang , Guo Yi
Published: April 2024

This study investigates the impact of clinical trial eligibility criteria on patient survival and serious adverse events (SAEs) in colorectal cancer (CRC) drug trials using real-world data. We utilized the OneFlorida+ network’s data repository, conducting a retrospective analysis of CRC patients receiving FDA-approved first-line metastatic treatments. Propensity score matching created balanced case-control groups, which were evaluated using survival analysis and machine learning algorithms to assess the effects of eligibility criteria. Our study included 68,375 patients, with matched case-control groups comprising 1,126 patients each. Survival analysis revealed ethnicity and race, along with specific medical history (eligibility criteria), as significant survival outcome predictors. Machine learning models, particularly the XgBoost regressor, were employed to analyze SAEs, indicating that age and study groups were notable factors in SAEs occurrence. The study’s findings highlight the importance of considering patient demographics and medical history in CRC trial designs.
Implementation and Assessment of the HIV Enhanced Access Testing in the Emergency Department (HEATED) Program in Nairobi, Kenya: A Quasi-Experimental Prospective Study
Authors: Aluisio Adam R. , Smith-Sreen Joshua , Offorjebe Agatha , Maina Wamutitu , Pirirei Sankei , Kinuthia John , Bukusi David , Waweru Harriet , Bosire Rose , Ojuka Daniel K. , Eastment McKenna C. , Katz David A. , Mello Michael J. , Farquhar Carey
Published: April 2024

Background

Persons seeking emergency injury care are often from underserved key populations (KPs) and priority populations (PPs) for HIV programming. While facility-based HIV Testing Services (HTS) in Kenya are effective, emergency department (ED) delivery is limited, despite the potential to reach underserved persons.

Methods

This quasi-experimental prospective study evaluated implementation of the HIV Enhanced Access Testing in Emergency Departments (HEATED) at Kenyatta National Hospital ED in Nairobi, Kenya. The HEATED program was designed using setting specific data and utilizes resource reorganization, services integration and HIV sensitization to promote ED-HTS. KPs included sex workers, gay men, men who have sex with men, transgender persons and persons who inject drugs. PPs included young persons (18-24 years), victims of interpersonal violence, persons with hazardous alcohol use and those never previously HIV tested. Data were obtained from systems-level records, enrolled injured patient participants and healthcare providers. Systems and patient-level data were collected during a pre-implementation period (6 March - 16 April 2023) and post-implementation (period 1, 1 May - 26 June 2023). Additional, systems-level data were collected during a second post-implementation (period 2, 27 June – 20 August 2023). Evaluation analyses were completed across reach, effectiveness, adoption, implementation and maintenance framework domains.

Results

All 151 clinical staff were reached through trainings and sensitizations on the HEATED program. Systems-level ED-HTS increased from 16.7% pre-implementation to 23.0% post-implementation periods 1 and 2 (RR=1.31, 95% CI:1.21-1.43; p<0.001) with a 62.9% relative increase in HIV self-test kit provision. Among 605 patient participants, facilities-based HTS increased from 5.7% pre-implementation to 62.3% post-implementation period 1 (RR=11.2, 95%CI:6.9-18.1; p<0.001). There were 440 (72.7%) patient participants identified as KPs (5.6%) and/or PPs (65.3%). For enrolled KPs/PPs, HTS increased from 4.6% pre-implementation to 72.3% post-implementation period 1 (RR=13.8, 95%CI:5.5-28.7, p<0.001). Systems and participant level data demonstrated successful adoption and implementation of the HEATED program. Through 16-weeks post-implementation a significant increase in ED-HTS delivery was maintained as compared to pre-implementation.

Conclusions

The HEATED program increased ED-HTS and augmented delivery to KPs/PPs, suggesting that broader implementation could improve HIV services for underserved persons, already in contact with health systems.
Etiologies of bloody diarrhea in children presenting with acute gastroenteritis to US emergency departments
Authors: Fonseca-Romero Paola , Ahmed Sharia M. , Brintz Ben J. , Vierkant D. Matthew , Bard Jennifer Dien , Cohen Daniel M. , Festekjian Ara , Leber Amy L. , Jackson Jami T. , Kanwar Neena , Larsen Chari , Selvarangan Rangaraj , Chapin Kimberle C. , Pavia Andrew T. , Leung Daniel T.
Published: April 2024

Among 111 children presenting with bloody diarrhea in a multicenter study of molecular testing in US emergency departments, we found viral pathogens in 18%, bacteria in 48%, protozoa in 2%, and no pathogens detected in 38%.
Dual targeting of GPX4 and TXNRD1 triggers eradication of AML cells through induction of apoptosis and ferroptosis
Authors: Favreau Cécile , Savy Coline , Bourgoin Maxence , Botton Thomas , Bailly Sarah , Granger Florence , Birck Catherine , Zerhouni Marwa , Kerreneur Emeline , Vigroux Alban , Gautheret Jade Dussart , Arcangeli Marie-Laure , Porterszman Arnaud , Cluzeau Thomas , Rocchi Stephane , Jacquel Arnaud , Benhida Rachid , Auberger Patrick , Martin Anthony R , Robert Guillaume
Published: April 2024

MyeloDysplastic Syndromes (MDS) are a group of heterogeneous hematological disorders characterized by bone marrow failure and abnormal hematopoietic cell expansion, often progressing to acute myeloid leukemia (AML). Current treatments for AML and high-risk MDS have limited efficacy, requiring the exploration of new therapeutic approaches. Recent research highlighted the potential of inducing cell death through ferroptosis, either independently or alongside traditional chemotherapy, as promising approaches for treating MDS/AML cells. We described here two novel compounds, HA344 and #231, capable of targeting both ferroptosis and apoptosis, leading to the effective eradication of cell lines and primary blasts from MDS/AML patients, while sparing normal hematopoietic cells. RNASeq analysis identified oxidation reduction and apoptotic processes as highly significant induced pathways in two different AML cell lines. Using click-chemistry approaches coupled to mass spectrometry, we identified glutathione peroxidase 4 (GPX4) and thioredoxin reductase 1 (TXNRD1) as the main targets of HA344 and #231 in a large panel of AML cells. Accordingly, both compounds inhibited GPX4 and TXNRD1 activity in the micromolar range and triggered GPX4 degradation. Moreover, using recombinant GPX4 carrying or not a selenium (GPX4-Se and GPX4-S), we confirmed by mass spectrometry that HA344 and #231 bind more efficiently GPX4-Se than GPX4-S. In conclusion, these compounds might represent a new pharmacological approach in the treatment of MDS and AML, offering a potential avenue for future therapies.
Blended Genome Exome (BGE) as a Cost Efficient Alternative to Deep Whole Genomes or Arrays
Authors: DeFelice Matthew , Grimsby Jonna L. , Howrigan Daniel , Yuan Kai , Chapman Sinéad B. , Stevens Christine , DeLuca Samuel , Townsend Megan , Buxbaum Joseph , Pericak-Vance Margaret , Qin Shengying , Stein Dan J. , Teferra Solomon , Xavier Ramnik J. , Huang Hailiang , Martin Alicia R. , Neale Benjamin M.
Published: April 2024

Genomic scientists have long been promised cheaper DNA sequencing, but deep whole genomes are still costly, especially when considered for large cohorts in population-level studies. More affordable options include microarrays + imputation, whole exome sequencing (WES), or low-pass whole genome sequencing (WGS) + imputation. WES + array + imputation has recently been shown to yield 99% of association signals detected by WGS. However, a method free from ascertainment biases of arrays or the need for merging different data types that still benefits from deeper exome coverage to enhance novel coding variant detection does not exist. We developed a new, combined, “Blended Genome Exome” (BGE) in which a whole genome library is generated, an aliquot of that genome is amplified by PCR, the exome regions are selected and enriched, and the genome and exome libraries are combined back into a single tube for sequencing (33% exome, 67% genome). This creates a single CRAM with a low-coverage whole genome (2-3x) combined with a higher coverage exome (30-40x). This BGE can be used for imputing common variants throughout the genome as well as for calling rare coding variants. We tested this new method and observed >99% r2concordance between imputed BGE data and existing 30x WGS data for exome and genome variants. BGE can serve as a useful and cost-efficient alternative sequencing product for genomic researchers, requiring ten-fold less sequencing compared to 30x WGS without the need for complicated harmonization of array and sequencing data.
Continuous monitoring of glucose levelsin vivowith a micro-organ based microfluidic biosensor
Authors: Puginier Emilie , Pirog Antoine , Poulletier de Gannes Florence , Gaitan Julien , Hurtier Annabelle , Monchablon Marie , Raoux Matthieu , Renaud Sylvie , Lang Jochen
Published: April 2024

Continuous monitoring of glucose levels has improved diabetes therapy. Current approaches rely on enzyme-linked electrochemical probes but do not allow a fully autonomous artificial pancreas. In contrast, monitoring the activity of a few electrogenic pancreatic islets in a biosensor may harness the computational power of the different endocrine cell types in the micro-organ, shaped for nutrient detection during evolution, and provide a more appropriate read-out. Extracellular electrophysiology captures slow potentials (SPs), which reflect coupled islet β-cell activity and is thus a method of choice for long-term monitoring of native islet activityin vitro.

We have now developed a microfluidic microelectrode chip containing a few islets and linked to interstitial fluids in live rats by subcutaneous microdialysis. The electrical activity in terms of slow potentials monitored by this biosensor reactsex vivoproportionally to glucose levels off-line in serum or dialysed interstitial fluid. On-line monitoringin vivoreveals an excellent correlation between islet slow potential frequency, and to a lesser degree to slow potential amplitudes, to glucose concentrations with little variation between animals. The microorgan-based biosensor harness multiple parametersin vivoand provides a read-out closer to physiology. This demonstrates the usefulness of such biosensors for sensor-based therapy of diabetes.
Possible acquisition and molecular evolution ofvpugenes inferred from comprehensive sequence analysis of human and simian immunodeficiency viruses
Authors: Naruki Miu , Saito Motofumi , Nomaguchi Masako , Kanai Akio
Published: April 2024

Vpu, an accessory protein ofHuman immunodeficiency virus 1(HIV-1), plays a crucial role in viral particle production and release, contributing to HIV virulence and its associated pandemic. Despite its significance, the acquisition and evolution of thevpugene remain poorly understood. In this study, we conducted a comprehensive computational analysis of approximately 38,000 sequences fromSimian immunodeficiency viruses(SIV) and HIV. From these, we obtained 141 representative Vpu protein sequences, while preserving their diversity by removing redundant sequences. We then created a phylogenetic tree, which revealed that SIV and HIV strains can be classified into four major types based on the Vpu proteins they express: Vpu-type 1, the putative ancestral type, which includes SIVs from Dent’s mona monkey, mona monkey, and moustached guenon; Vpu-type 2, which includes SIVgor from gorillas and HIV-1 group O; Vpu-type 3, which includes SIVcpz from chimpanzees; and Vpu-type 4, which includes HIV-1 group M, HIV-1 pandemic strain (subtype 4a), and HIV-1 group N (subtype 4b). Vpu-types 1 and 2 show variations invpulength, whereas Vpu-types 3 and 4 show less variability. Notably, the gene encoding Vpu-type 1 varies in the length of its overlap with theenvgene. To clarify the evolutionary relationship between Vpu-type 1 SIVs and SIVs lacking Vpu, we constructed a phylogenetic tree based on the nucleotide sequence between thepolandenvgenes, using 401 sequences derived from HIV-1, HIV-2, and SIVs. Vpu-type 1 (SIVden and SIVmon), SIVasc (red-tailed monkey), and SIVsyk (Sykes’ monkeys) clustered closely on the phylogenetic tree. Considering the observed similarities between thevpu, vprandenvgenes in SIVdeb and SIVsyk, we speculated that thevpugene originated within the SIV genome. A phylogenetic tree constructed with 242 Vpu-type 4a sequences from the HIV pandemic strain and 135 sequences of circulating recombinant forms of HIV-1 revealed that the viral subtypes can be further classified into 18 distinct protein subtypes, surpassing the number of previously known subtypes. Collectively, our results suggest an evolutionary model for thevpugene that sheds light on its origin and divergence, and their implications in the context of HIV-1 and SIV evolution.
Variable orthogonality of RDF – large serine integrase interactions within the ϕC31 family
Authors: MacDonald Alasdair I. , Baksh Aron , Holland Alex , Shin Heewhan , Rice Phoebe A. , Stark W. Marshall , Olorunniji Femi J.
Published: April 2024

Large serine integrases are phage- (or mobile element-) encoded enzymes that catalyse site-specific recombination reactions between a short DNA sequence on the phage genome (attP) and a corresponding host genome sequence (attB), thereby integrating the phage DNA into the host genome. Each integrase has its unique pair ofattPandattBsites, a feature that allows them to be used as orthogonal tools for genome modification applications. In the presence of a second protein, the Recombination Directionality Factor (RDF), integrase catalyses the reverse, excisive reaction, generating new recombination sites,attRandattL. In addition to promotingattRxattLreaction, the RDF inhibitsattPxattBrecombination. This feature makes the directionality of integrase reactions programmable, allowing them to be useful for building synthetic biology devices. In this report, we describe the degree of orthogonality of both integrative and excisive reactions for three related integrases (ϕC31, ϕBT1, and TG1) and their RDFs. Among these, TG1 integrase is the most active, showing near complete recombination in bothattPxattBandattRxattLreactions, and the most directional in the presence of its RDF. Our findings show that there is varying orthogonality among these three integrases – RDF pairs: ϕC31 integrase was the least selective, with all three RDFs activating it forattRxattLrecombination. Similarly, ϕC31 RDF was the least effective among the three RDFs in promoting the excisive activities of the integrases, including its cognate ϕC31 integrase. ϕBT1 and TG1 RDFs were noticeably more effective than ϕC31 RDF at inhibitingattPxattBrecombination by their respective integrases, making them more suitable for building reversible genetic switches. AlphaFold-Multimer predicts very similar structural interactions between each cognate integrase – RDF pair. The binding surface on RDF is much more conserved than the binding surface on integrase, an indication that specificity is determined more by the integrase than the RDF. Overall, the observed weak integrase/RDF orthogonality across the three enzymes emphasizes the need for identifying and characterizing more integrase – RDF pairs. Additionally, the ability of a particular integrase’s preferred reaction direction to be controlled to varying degrees by non-cognate RDFs provides a path to tunable, non-binary genetic switches.
A Tunable and Druggable Mechanism to Delay Forgetting of Olfactory Memories inC. elegans
Authors: Berliner Dana Landschaft , Goldstein Kesem , Teichman Guy , Anava Sarit , Gingold Hila , Rieger Itai , Levi Noam , Pechuk Vladyslava , Salzberg Yehuda , Agarwal Priti , Sagi Dror , Cohen Dror , Nikelshparg Evelina , Ben-Zvi Anat , Zaidel-Bar Ronen , Vizuete Antonio Miranda , Oren-Suissa Meital , Rechavi Oded
Published: April 2024

The poet W.B Yeats wrote that“All that is personal soon rots, it must be packed in ice or salt”. Here we show that inCaenorhabditis elegansnematodes, simple animals with just 302 neurons, memories are preserved on ice and in lithium salt.C. elegansnematodes can form associative memories, which are typically forgotten quickly. We discovered that when placed on ice, worms delay forgetting of specific olfactory memories by at least 8-fold. Delayed forgetting was canceled completely when the worms were gradually adapted to low temperatures, owing to a genetically-encoded program that turns acclimated worms cold-tolerant. RNA-seq, mutant analyses, and pharmacological assays revealed that regulation of membrane properties switches cold-induced delayed forgetting ON and OFF, and, remarkably, that lithium delays forgetting only in cold-sensitive but not cold-tolerant worms. We found that downregulation of the diacylglycerol pathway in the AWC sensory neurons is essential for lithium-mediated delayed forgetting, and using neuronal activity recordings located the memory trace to the downstream AIY interneurons. We suggest that the awesome genetic tractability ofC. elegansmight be harnessed to study the effects of lithium and cold temperatures on the brain, why it influences psychiatric disorders, and even more fundamentally how memory is stored and lost.
Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung
Authors: Holmes Caitlyn L. , Dailey Katherine G. , Hullahalli Karthik , Wilcox Alexis E. , Mason Sophia , Moricz Bridget S. , Unverdorben Lavinia , Waldor Matthew K. , Bachman Michael A.
Published: April 2024

Bacteremia, a leading cause of death, generally arises after bacteria establish infection in a particular tissue and transit to secondary sites. Studying dissemination from primary sites by solely measuring bacterial burdens does not capture the movement of individual clones. Here, by barcoding Klebsiella pneumoniae, a leading cause of bacteremia, we tracked pathogen dissemination following pneumonia. Variability in organ bacterial burdens was attributable to two distinct dissemination patterns distinguished by the extent of clonal expansion in the lungs. In metastatic dissemination, bacterial clones underwent heterogeneous clonal expansion within the lung and the dominant clones spread to secondary organs. In direct dissemination, bacterial clones exited the lungs without clonal expansion, leading to lower burdens in systemic sites. We uncover bacterial and host factors that govern these two modes of dissemination. Our data reveal unexpected heterogeneity in the dynamics of Klebsiella bacteremia and define a new paradigm for understanding within-host bacterial dissemination.
Extracellular vesicles isolated from frozen and fresh human melanoma tissue are similar in purity and protein composition
Authors: D’Arrigo Daniele , Lässer Cecilia , Urzì Ornella , Park Kyong-Su , Bagge Roger Olofsson , Lötvall Jan , Crescitelli Rossella
Published: April 2024

Extracellular vesicles (EVs) isolated from tumor tissues represent a precious source of EVs because they are enriched in disease-associated biomarkers and are highly concentrated. However, a fundamental question is whether freezing of tissues influences the EVs’ integrity and function and whether non-EVs are co-isolated with the EVs. In this work, we isolated EVs from metastatic melanoma tissue both immediately after tissue resection and after being frozen for at least two weeks. Specifically, the samples were divided into two parts: one was immediately processed for EV isolation (hereafter called fresh), and the other was frozen on dry ice and stored for two weeks before being processed for EV isolation (hereafter called frozen). Large and small EVs were isolated through ultracentrifugation, pooled, and further purified on an iodixanol density cushion. The EVs were analyzed by transmission electron microscopy, nanoparticle tracking analysis, and protein quantification as well as by quantitative mass spectrometry. The results did not show any significant difference between EVs isolated from fresh and frozen tissue. Importantly, there was no enrichment of either intracellular proteins or mitochondrial proteins in EVs isolated from frozen tissues vs. fresh tissues. Moreover, there were no significant differences in the quantity of proteins like MT-CO2, Cox6, SLC24A22, HLA-DR, and Erlin2, which were previously identified as potential markers of melanoma, ovarian cancer, and breast cancer. Overall, this study supports the use of frozen tissues as a source of EVs for research purposes because frozen tissue-derived EVs do not differ in purity or protein composition compared to their fresh counterparts.