bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observing picomolar protein unfolding using resonance light scattering
Authors: Alvarez Alain Bolaño , Arvesen Kristian B. , Hjuler Kasper F. , Bjerring Peter , Petersen Steffen B. 
Published: November 2024

AbstractWe here present a novel and sensitive methodology for determining the melting point (MP) of Bovine Serum Albumin (BSA) from micromolar to picomolar concentration levels under label free conditions. At 1 pM we could model the melting with a sharp gaussian. However, from the transient state observed during the melting process by using a simple exponential decay model we determined a time constant of 67 seconds. We applied this methodology by studying a 3.3 pM sample of a botulinum toxin A (BoNT-A) (stabilized with 2.8 nanomolar denatured Human Serum Albumin (HSA)). We were able to determine the Tm of BoNT-A in the presence of the approximately 1000-fold more concentrated HSA.Entry for the Table of ContentsProtein label-free melting point (MP) determination at ultralow concentrations is a huge problem which concern to the biopharmaceutical industry. Here, we present a novel method to determine the MP of bovine serum albumin (BSA) from 1μM to 1pM under label-free conditions. The benefits of this study match the purposes of stability studies in formulations, in which the protein active component is successful at very low concentrations, such as botulinum toxin A (BoNT-A). We used BOCOUTRE, a commercially available pharmaceutical product based on BoNT-A, and Human Serum Albumin (HSA) as a stabilizer. Our method can detect the MP of the stabilizer protein, even if its concentration is markedly different from that of the active component protein (1000-fold) in the case of BOCOUTRE.
Antigen flexibility supports the avidity of hemagglutinin-specific antibodies at low antigen densities
Authors: Benegal Ananya , He Yuanyuan , Ho Katilyn , Groff Giselle , Guo Zijian , Vahey Michael D. 
Published: November 2024

ABSTRACTThe receptor-binding protein of influenza A virus, hemagglutinin (HA), is the most abundant protein on the viral surface. While high densities of HA are thought to improve cellular attachment by increasing avidity for the viral receptor, they may also increase the avidity of neutralizing antibodies. The tradeoff between these two competing effects of avidity is not well understood. To better understand how features of the viral surface influence antibody avidity, we developed fluorescence-based assays to measure dissociation kinetics and steady-state binding of antibodies to intact virions. Focusing on two antibodies that bind to the HA head domain (S139/1 and C05), we confirm that binding orientations that favor bivalent attachment of antibodies to the viral surface can offset weak monovalent affinity by facilitating crosslinking. By modulating HA density in both engineered viruses and synthetic nanoparticles, we find that bivalent antibody binding remains resilient down to one-tenth the HA density on the viral surface and, in the case of C05, that antibody occupancy increases at these lowest densities. Finally, using a combination of structure-guided modeling and antibodies that lock HA in a tilted conformation, we identify flexibility of the HA ectodomain as an additional determinant of antibody avidity. Together, these results establish features of the viral surface that help support or suppress the binding of neutralizing antibodies.
Co-delivery of neurotrophic factors and a zinc chelator substantially promotes axon regeneration in the optic nerve crush model
Authors: Dieu Nguyen Huynh Quang , Nam Mi-hyun , Vigh Jozsef , Brzezinski Joseph , Duncan Lucas , Park Daewon 
Published: November 2024

ABSTRACTTraumatic optic neuropathies cause the death of retinal ganglion cells (RGCs) and axon degeneration. This is a result of the blockage of neurotrophic factor (NTF) supply from the brain and a vicious cycle of neurotoxicity, possibly mediated by increased levels of retinal Zn2+. Ciliary neurotrophic factor (CNTF) and brain-derived neurotrophic factor (BDNF) are two NTFs that are known to support RGC survival and promote axon regeneration. Dipicolylamine (DPA) has a strong affinity to Zn2+and can selectively chelate this ion. To continuously supply NTFs and reduce elevated retinal Zn2+, we developed poly(serinol hexamethylene urea)-based sulfonated nanoparticles (S-PSHU NPs), that co-delivers CNTF, BDNF, and DPA. Anin vitrorelease study was performed using the NTF-DPA-loaded S-PSHU NPs, demonstrating a sustained release of CNTF and BDNF for up to 8 weeks, while DPA was released for 4 weeks. In a rat optic nerve crush (ONC) model, DPA-loaded S-PSHU NPs exhibited dose-dependent elimination of retinal Zn2+. Similarly,in vitroprimary RGC culture demonstrated that the activity of RGCs and axon growth were dependent on the dosage of CNTF and BDNF. In addition, the NTF-DPA-loaded S-PSHU NPs significantly improved RGC survival and axon regeneration following ONC in rats, with the regenerated axons extending to the distal segment of the brain, including the suprachiasmatic nucleus, lateral geniculate nucleus, and superior colliculus.
Metabolic Adaptations To Acute Glucose Uptake Inhibition Converge Upon Mitochondrial Respiration For Leukemia Cell Survival
Authors: Komza Monika , Khatun Jesminara , Gelles Jesse D. , Trotta Andrew P. , Abraham-Enachescu Ioana , Henao Juan , Elsaadi Ahmed , Kotini Andriana G. , Clementelli Cara , Arandela JoAnn , El Ghaity-Beckley Sebastian , Barua Agneesh , Chen Yiyang , Marcellino Bridget K. , Papapetrou Eirini P. , Poyurovsky Masha V. , Chipuk Jerry Edward 
Published: November 2024

ABSTRACTOne hallmark of cancer is the upregulation and dependency on glucose metabolism to fuel macromolecule biosynthesis and rapid proliferation. Despite significant pre-clinical effort to exploit this pathway, additional mechanistic insights are necessary to prioritize the diversity of metabolic adaptations upon acute loss of glucose metabolism. Here, we investigated a potent small molecule inhibitor to Class I glucose transporters, KL-11743, using glycolytic leukemia cell lines and patient-based model systems. Our results reveal that while several metabolic adaptations occur in response to acute glucose uptake inhibition, the most critical is increased mitochondrial oxidative phosphorylation. KL-11743 treatment efficiently blocks the majority of glucose uptake and glycolysis, yet markedly increases mitochondrial respiration via enhanced Complex I function. Compared to partial glucose uptake inhibition, dependency on mitochondrial respiration is less apparent suggesting robust blockage of glucose uptake is essential to create a metabolic vulnerability. When wild-type and oncogenic RAS patient-derived induced pluripotent stem cell acute myeloid leukemia (AML) models were examined, KL-11743 mediated induction of mitochondrial respiration and dependency for survival associated with oncogenic RAS. Furthermore, we examined the therapeutic potential of these observations by treating a cohort of primary AML patient samples with KL-11743 and witnessed similar dependency on mitochondrial respiration for sustained cellular survival. Together, these data highlight conserved adaptations to acute glucose uptake inhibition in diverse leukemic models and AML patient samples, and position mitochondrial respiration as a key determinant of treatment success.
Natural killer cell dysfunction drives keloid pathogenesis
Authors: Zhao Ying , Wei Qin , Zeng Rui , Wang Yan , Yang Yong , Wang Yetao 
Published: November 2024

SummaryKeloids, characterized by excessive scar tissue resulting from abnormal wound healing, are primarily driven by hyperproliferative fibroblasts and overproduction of extracellular matrix. Although human natural killer (NK) cells are known for their role in inhibiting uncontrolled cell growth through cytokines like IFN-γ and TNF-α, they also produce amphiregulin (AREG), which paradoxically promotes cell proliferation and survival. The involvement of NK cells in keloid pathogenesis, however, remains largely unexplored. This study uncovers remarkable functional changes in NK cells within both lesional skin and the blood of keloid patients. In the skin, NK cell-produced IFN-γ plays a pivotal role in limiting keloid progression by inducing fibroblast apoptosis and curbing excessive extracellular matrix production, while NK cell-derived AREG actively opposes these protective effects. Notably, TGF-β-driven fibroblasts in keloid lesions further dampen NK cell IFN-γ production, revealing a complex and dynamic cellular interplay. In the bloodstream of keloid patients, a distinct NK cell subset emerges, marked by elevated interferon-stimulated genes (ISGs) and diminished IFN-γ production, which correlates with increased plasma IFN-β levels. This elevated IFN-β serves as a key initiating factor, driving NK cell exhaustion through impaired mitochondrial function and metabolic disruption. These findings highlight a critical mechanism underlying the functional abnormalities of keloid-associated NK cells and emphasize the influence of both local and systemic factors in shaping NK cell responses in keloid pathogenesis.Graphical abstractHighlightsIn the skin, NK cell-derived IFN-γ is crucial for suppressing keloid fibroblast proliferation and extracellular matrix production.AREG from NK cells counteracts the inhibitory effects of IFN-γ on keloid progression.In the blood, elevated IFN-β in keloid patients drives the emergence of ISG+NK cells with reduced IFN-γ production.IFN-β induces mitochondrial dysfunction and functional exhaustion in NK cells.
Study Protocol Efficacy, safety, and tolerability of ultra-high-caloric, fatty diet (UFD) in amyotrophic lateral sclerosis
Authors: Dorst Johannes , Ruckes Christian 
Published: November 2024

ABSTRACTThe LIPCAL-ALS II study investigates the efficacy, safety, and tolerability of an ultra-high-caloric, fatty diet (UFD) in amyotrophic lateral sclerosis (ALS). It is a multicenter, 1:1-randomized, prospective, stratified, parallel-group, double-blind, placebo-controlled, confirmatory study with 392 patients conducted in 25 centers of the German network for motor neuron diseases (MND Net). Patients will be randomized to receive either the experimental intervention, consisting of an ultra-high-caloric fatty dietary supplement for drinking (100% lipid, 4.5 kcal/ml) 140 ml/day (630 kcal) or matching placebo (140 ml/day, <5% fat, <50 kcal) in addition to normal food intake. The primary endpoint is survival after 18 months of intervention. Patients with possible, probable (clinically or laboratory supported) or definite ALS according to revised El Escorial criteria with a disease duration of <36 months and a loss of ALS functional rating scale revised (ALSFRS-R) ≥0.33 points/months will be included.Synopsis
FGF14repeat length and mosaic interruptions: modifiers of SCA27B?
Authors: Laß Joshua , Thomsen Mirja , Borsche Max , Lüth Theresa , Prietzsche Julia C. , Schaake Susen , Milovanović Andona , Macpherson Hannah , Gustavsson Emil K. , Awad Paula Saffie , Dragašević-Mišković Nataša , Laabs Björn-Hergen , König Inke R. , Westenberger Ana , Pearson Christopher E. , Brüggemann Norbert , Klein Christine , Trinh Joanne 
Published: November 2024

AbstractDeep intronicFGF14repeat expansions have been identified as a frequent genetic cause of late-onset cerebellar ataxias, explaining up to 30% of patients. Interruptions between repeats have previously been identified to impact the penetrance in other repeat expansion disorders. Repeat interruptions withinFGF14have yet to be characterized in detail.We utilized long-range PCR, Sanger sequencing, repeat-primed PCR, Nanopore, and PacBio sequencing to distinguish the repeat motifs, mosaicism, and number of repeat interruptions present inFGF14-related ataxia patients and unaffected individuals.A total of 304 patients with late-onset ataxia and 190 unaffected individuals were previously screened for repeat expansions in theFGF14gene by long-range PCR, identifying 37 individuals with expanded repeat lengths (≥250 repeats). These, along with three newly identified expansion carriers were included in the present study, and advanced genetic methods were applied to investigate the repeat composition in 27 patients and 13 unaffected individuals. The expansions, based on Nanopore data, ranged from 236 to 486 repeats (SD = 60), with 20 individuals showing repeat interruptions, including complex motifs such asGAG, GAAGGA, GAAGAAAGAA, GAAAAGAAGAAGGAAGAAGGAA, GAAAAGAAGAAGGAA, andGCAGAAGAAGAAGAA. We calculated the longest pure GAA length from the long-read data for all 40 individuals. When comparing the pure GAA tract between patients and unaffected individuals, clusters were apparent based on greater or less than 200 repeats. Five ataxia patients with interruptions still had a remaining pure GAA expansion >200. We observed an association of the pure GAA length with age at onset (p=0.016,R2=0.256). Somatically-incurred mosaic divergent repeat interruptions were discovered that affect motif length and sequence (mDRILS), which varied in number and mosaicism (frequency: 0.37-0.93). The mDRILS correlated with pure GAA length (p=0.022,R2=0.334), with a higher mosaic frequency of interruptions in unaffected individuals compared to patients (unaffected: 0.90; patients: 0.67;p=0.010).We demonstrate that i) long-read sequencing is required to detect complex repeat interruptions accurately; ii) repeat interruptions inFGF14are mosaic, have various lengths and start positions in the repeat tract, and can thereby be annotated as mDRILS, which iii) enabled us to establish a categorization based on remaining pure GAA repeats quantifying the impact of mDRILS on pathogenicity or age at onset, dependent on the interruption length and position, with high accuracy. Finally, we iv) provide evidence that mosaicism stabilizes pure GAA repeats in interruptedFGF14repeat expansions.
A rapid CRISPR/Cas12a-based assay for the detection of HIV-1 Indian Clade-C infections
Authors: Gaur Anjli , Bhakhri Harsh , Mishra Nitesh , Sharma Shaifali , Bansal Tanu , Kalaivani Mani , Brijwal Megha , Das Bimal Kumar , Lodha Rakesh , Sinha Subrata , Luthra Kalpana 
Published: November 2024

AbstractEarly detection of HIV-1 infection is crucial to initiate anti-retroviral therapy (ART) to suppress viremia and disease progression. Herein, we developed a CRISPR/Cas12a-based HIV-1 detection assay by optimizing components for a coupled isothermal preamplification by recombinase polymerase amplification (RPA). The HIV-1 Indian Clade-C-specific conserved pol region was targeted by crRNA designed for Clade-specific detection. The CRISPR/Cas12a cleavage of the viral cDNA input is displayed as a single visually detectable outcome due to the collateral cleavage of the ssDNA-FAM-BQ reporter, enabling the rapid detection of HIV-1. The performance of the assay was evaluated by testing sera of 41 Indian Clade C HIV-1 seropositive individuals, which included 28 HIV-1 infected infant samples, HIV-1 Indian clade C genome plasmid, viral disease control DNA/RNA samples (Influenza, RSV, Parvovirus, HPIV, CMV, and HBV), and 31 healthy donor sera samples. With 96% sensitivity and 92.65% specificity for HIV-1C detection, with fluorescence and visual readout, and a capability of detection using lateral flow dipsticks, our CRISPR/Cas12a-based HIV-1 C detection assay demonstrates the potential to be developed into a robust point-of-care molecular diagnostic test for HIV-1C. Moreover, it may serve as a potential rapid NAT alternative in detecting mother-to-child transmission (MCT) of HIV-1C in infants (<2 years of age), where rapid antibody-based serology tests are rendered ineffective due to the presence of maternal antibodies.
Deep learning classification of MRI differentiates brain changes in genetic and idiopathic Parkinson’s disease
Authors: Courtman Megan , Thurston Mark , Wang Hongrui , Banerjee Sube , Streeter Adam , McGavin Lucy , Hall Stephen , Sun Lingfen , Ifeachor Emmanuel , Mullin Stephen 
Published: November 2024

AbstractBackgroundThe prospect of neuroprotective treatments for Parkinson’s disease highlights the need for early diagnostic tests. Specialised MRI sequences suggest changes related to Parkinson’s disease may be detectable.ObjectivesWe used the Parkinson’s Progression Markers Initiative dataset to investigate whether deep learning can detect early brain MRI changes of idiopathic and GBA/LRRK2 prodromal Parkinson’s disease.MethodsPairs of matched cohorts were used to train convolutional neural networks to classify T2 axial images. Explainability methods were used to visualise drivers of model predictions.ResultsModels built to distinguish between idiopathic Parkinson’s disease scans (n=504) and matched controls exhibited good classification performance for scans taken more than four years after diagnosis, with a Receiver Operating Characteristic area-under-the-curve of 0.89 (n=98). Model performance deteriorated as time since diagnosis reduced. Models built to distinguish non-manifesting carriers ofLRRK2(area-under-the-curve 0.92, 90% accuracy,n=115) andGBA(area-under-the-curve 0.94, 92% accuracy,n=109) from controls exhibited excellent classification performance. All models demonstrated foci of interest in cerebrospinal fluid spaces surrounding the brainstem. Models usingGBAscans also identified foci of interest in occipital lobes.ConclusionsDeep learning models appear able to reproducibly detect changes in the brains of those with established but not early Parkinson’s disease. Conversely changes in at risk genetic cohorts are detectable at all stages, including in those who have not developed Parkinson’s disease. This implies a distinct pathological process ongoing within the brains of carriers of Parkinson’s disease genetic risk factors compared to those with sporadic Parkinson’s disease.
Scaling-up Cervical Cancer Services for Women Living with HIV in Mozambique, October 2018–September 2023
Authors: Correia Della , Bay Zurnaid , Wate Argentina , Nhanguiombe Herminio , Manhica Pinto , Bila Erica , Tualufo Sheila , Mate Celina , Amado Celeste , Lorenzoni Cesaltina 
Published: November 2024

AbstractBackgroundCervical cancer is the most common cancer among women in Mozambique. Women living with HIV (WLHIV) have a six times greater risk of developing cervical cancer. National guidelines call for annual screening of all HIV-positive women aged 20-49 years or below 20 years if she is sexually active and HIV-negative women aged 25-49 years, with follow-up after 1 year for HIV-positive and 3 years for HIV-negative women that screen negative. Women screened positive are referred to treatment with cryotherapy, thermal ablation, or loop electrosurgical excision procedure (LEEP). In 2021, HIV prevalence among women aged 15–49 years was estimated at 15.4%. We analyzed routine program data to describe the expansion of cervical cancer services and identify gaps in screening and treatment coverage among WLHIV since 2018.MethodsWe analyzed semi-annual, routinely collected programmatic data on cervical cancer screening and treatment services reported between 21 September 2018 to 20 March 2019 (585 sites reported) and 21 March to 20 September 2023 (610 sites reported). We verify rates of screening coverage (WLHIV screened divided by WLHIV on ART aged ≥15 years), screen positivity (WLHIV screened positive divided by number screened), and treatment (WLHIV treated for precancerous lesions divided by number screened positive).ResultsThe screening coverage improved from 1.4% (10,596 screened/731,572 WLHIV on ART) in October 2018–March 2019 to 36.2% (395,609/1,094,033) in March–September 2023. In the same period, screen positivity rates increased from 8.1% (861/10,596) to 10.9% (43,290/395,614), and treatment rates increased from 59.9% (516/861) to 94.0% (40,677/43,290).ConclusionAccess to cervical cancer services has improved dramatically for a large population of WLHIV. With increased screening, more WLHIV with pre-cancerous lesions have been found and treated, averting morbidity and mortality due to cervical cancer. Quality improvement strategies may further improve service delivery as the program expands to reach all eligible WLHIV in Mozambique.
Knowledge, attitudes and practices relating to HIV self-testing following its introduction in the Bas-Sassandra region of Côte d’Ivoire: the case of the ATLAS project
Authors: Simo Fotso Arlette , Koukobo Christian , Silhol Romain , Kra Arsène Kouassi , Boily Marie-Claude , Vautier Anthony , Larmarange Joseph 
Published: November 2024

AbstractBackgroundAwareness of HIV status is crucial for accessing HIV care and prevention but remains suboptimal in West Africa. The ATLAS initiative, launched in Côte d’Ivoire, Mali, and Senegal, addressed this gap by distributing approximately 380,000 HIV self-testing (HIVST) kits from 2019 to 2021, primarily to key populations and their social networks. This study assessed levels and correlates of Knowledge, Attitudes, and Practices (KAP) related to HIVST in the Bas-Sassandra region of Côte d’Ivoire following ATLAS’s introduction.MethodA cross-sectional population-based survey was conducted in the Bas-Sassandra region in 2021 among individuals aged 15-49. Bivariate statistics and multivariable logistic regressions were used to assess KAP levels and the associated factors.ResultsAlthough few participants reported having heard about HIVST (11%) or having used it (3%), most of them reported that if it were freely available, they would be interested/very interested in using it for themselves (76%), as well as for their sexual partners (75%). Education and wealth were positively associated with knowledge and positive attitudes towards HIVST among both men and women, whereas age was positively correlated to knowledge and use of HIVST among men only. The number of sexual partners over the last 12 months was positively associated with knowledge of HIVST and willingness to use HIVST for themselves or their sexual partners among both sexes. We also found that high HIV-related knowledge and low levels of stigma were positively associated with positive attitudes towards HIVST, while exposure to the media appeared to be correlated to knowledge of HIVST.ConclusionThe high level of positive attitudes towards HIVST calls for a scaling up of access to HIVST in the region. Specific attention to groups with the worst KAP, such as the less educated, the poor or groups that are highly stigmatised, could enhance the success of such initiatives.