bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Recovery Desalting Tip Columns for a Wide Variety of Peptides in Mass Spectrometry-based Proteomics
Authors: Kanao Eisuke , Tanaka Shunsuke , Tomioka Ayana , Tanigawa Tetsuya , Kubo Takuya , Ishihama Yasushi 
Published: July 2024

ABSTRACTIn mass spectrometry-based proteomics, loss-minimized peptide purification techniques play a key role in improving sensitivity and coverage. We have developed a desalting tip column packed with thermoplastic polymer-coated chromatographic particles, named ChocoTip, to achieve high recoveries in peptide purification by pipette-tip-based LC with centrifugation (tipLC). ChocoTip identified more than twice as many peptides from 20 ng of tryptic peptides from Hela cell lysate compared to a typical StageTip packed with chromatographic particles entangled in a Teflon mesh in tipLC. The high recovery of ChocoTip in tipLC was maintained for peptides with a wide variety of physical properties over the entire retention time range of the LC/MS/MS analysis, and was especially noteworthy for peptides with long retention times. These excellent properties are attributable to the unique morphology of ChocoTip, in which the thermoplastic polymer covers the pores, thereby inhibiting irreversible adsorption of peptides into mesopores of the chromatographic particles.ChocoTip is expected to find applications, especially in clinical proteomics and single-cell proteomics, where sample amounts are limited.
Validation of a novel, low-cost, portable MRI-compatible exercise device in healthy volunteers and patients with pulmonary hypertension
Authors: Virsinskaite Ruta , Brown James T. , Kotecha Tushar , Bower Darren , Steeden Jennifer A. , Montalt-Tordera Javier , Jaubert Olivier , Fontana Marianna , Coghlan J. Gerry , Knight Daniel S. , Muthurangu Vivek 
Published: July 2024

AbstractIntroductionThe value of exercise cardiovascular magnetic resonance (CMR) has been shown in many clinical scenarios. We have developed a MR-compatible exercise apparatus and aim to validate it against the reference standard MR-conventional ergometer.MethodsThe novel device consisted of two half-pipes fixed to a wooden base, with participants wearing knee-length socks with a 0.5kg weight in each sock. Increased workload was achieved by increasing the rate of alternating leg flexion and extension in time with a bleep sound of increasing frequency.Twenty subjects (10 healthy volunteers, 10 patients with pulmonary hypertension) performed two CMR-augmented cardiopulmonary exercise tests (CMR-CPET) using the novel exercise apparatus and a conventional ergometer in a randomised order.ResultsComparing peak metrics elicited on both exercise devices, there was a moderate correlation in peak oxygen consumption (VO2, r=0.86, P<0.001), cardiac output (CO, r=0.66, P=0.002), stroke volume (SV, r=0.75, P<0.001), peak heart rate (HR, r=0.65, P=0.002) and peak arteriovenous oxygen content gradient (ΔavO2, r=0.71, P<0.001). However, all metrics (except peak SV) were significantly lower from the novel device. Both devices were able to elicit statistically significant differences in VO2, HR and RVEF between patients and healthy subjects (P≤0.036).ConclusionsWe have created a simple, easy to use and affordable exercise apparatus for CMR environment. This may encourage greater dissemination of exercise CMR in clinical and research practice.
A scalable genetic tool for the functional analysis of the signal recognition particle
Authors: Long Lawton F. , Biskunda Shivani , Yang Ming “Peter” , Wu George C. , Simas Cassidy , Bruner Steven D. , Denard Carl A. 
Published: July 2024

AbstractMutations in theSRP54gene are linked to the pathophysiology of severe congenital neutropenia (SCN).SRP54is a key protein comprising one of the six protein subunits of the signal recognition particle responsible for co-translational targeting of proteins to the ER; mutations inSRP54disrupt this process. Crystal structures and biochemical characterization of a fewSRP54mutants provide insights into howSRP54mutations affect its function. However, to date, no scalable, flexible platform exists to study the sequence-structure-function relationships of SRP54 mutations and perform functional genomics and genome-wide association studies. In this work, we established a haploid model inSaccharomyces cerevisiaebased on inducible gene expression that allows these relationships to be studied. We employed this model to test the function of orthologous clinical mutations to demonstrate the model’s suitability for studying SCN. Lastly, we demonstrate the suspected dominant-negative phenotypes associated withSRP54mutants. In doing so, we discovered for the first time that the most common yeast orthologous clinical mutation, S125del (T117del human orthologue) displayed the least severe growth defect while the less common G234E mutant (G226E human orthologue) displayed the most severe growth defect. The ability of this haploid model to recapitulate these phenotypes while remaining amenable to high-throughput screening approaches makes it a powerful tool for studyingSRP54. Furthermore, the methodology used to create this model may also be used to study other human diseases involving essential and quasi-essential genes.TakeawayThe constitutively expressed quasi-essential nativeSRP54gene in yeast is replaced with an aldosterone-inducible version, making a yeast haploid strain, LFL001, that requires aldosterone for growth.Strains developed in this work corroborated that yeastSRP54mutations exhibit dominant-negative phenotypes.The LFL000 and LFL001 yeast strains developed here are uniquely positioned to interrogate sequence-structure-function relationships ofSRP54.
Hierarchical Bayesian modeling of multi-region brain cell count data
Authors: Dimmock Sydney , Exley Benjamin M. S. , Moore Gerald , Menage Lucy , Delogu Alessio , Schultz Simon R. , Warburton E. Clea , Houghton Conor , O’Donnell Cian 
Published: July 2024

We can now collect cell-count data across whole animal brains quantifying recent neuronal activity, gene expression, or anatomical connectivity. This is a powerful approach since it is a multi-region measurement, but because the imaging is done post-mortem, each animal only provides one set of counts. Experiments are expensive and since cells are counted by imaging and aligning a large number of brain sections, they are time-intensive. The resulting datasets tend to be under-sampled with fewer animals than brain regions. As a consequence, these data are a challenge for traditional statistical approaches. We demonstrate that hierarchical Bayesian methods are well suited to these data by presenting a ‘standard’ partially-pooled Bayesian model for multi-region cell-count data and applying it to two example datasets. For both datasets the Bayesian model outperformed standard parallel t-tests. Overall, the Bayesian approach’s ability to capture nested data and its rigorous handling of uncertainty in under-sampled data can substantially improve inference for cell-count data.Significance StatementCell-count data is important for studying neuronal activation and gene expression relating to the complex processes in the brain. However, the difficulty and expense of data collection means that such datasets often have small sample sizes. Many routine analyses are not well-suited, especially if there is high variability among animals and surprising outliers in the data. Here we describe a multilevel, mixed effects Bayesian model for these data and show that the Bayesian approach improves inferences compared to the usual approach for two different cell-count datasets with different data characteristics.
N6-methyladenosine in DNA promotes genome stability
Authors: Conti Brooke A. , Novikov Leo , Tong Deyan , Xiang Qing , Vigil Savon , McLellan Thomas J. , Nguyen Chuong , De La Cruz Nancy , Veettil Reshma T. , Pradhan Prashant , Sahasrabudhe Parag , Arroyo Jason D. , Shang Lei , Sabari Benjamin R. , Shields David J. , Oppikofer Mariano 
Published: July 2024

SummaryDNA base lesions, such as incorporation of uracil into DNA or base mismatches, can be mutagenic and toxic to replicating cells. To discover factors in repair of genomic uracil, we performed a CRISPR knockout screen in the presence of floxuridine, a chemotherapeutic agent that incorporates uracil and fluoro-uracil into DNA. We identified known factors, such as uracil DNA N-glycosylase (UNG), and unknown factors, such as the N6-adenosine methyltransferase, METTL3, as required to overcome floxuridine-driven cytotoxicity. Visualized with immunofluorescence, the product of METTL3 activity, N6-methyladenosine, formed nuclear foci in cells treated with floxuridine. The observed N6-methyladenosine was embedded in DNA, called 6mA, and these results were confirmed using an orthogonal approach, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). METTL3 and 6mA were required for repair of lesions driven by additional base damaging agents, including raltitrexed, gemcitabine, and hydroxyurea. Our results establish a role for METTL3 and 6mA in promoting genome stability in mammalian cells, especially in response to base damage.
Structural basis of long-range transcription-translation coupling
Authors: Wang Chengyuan , Molodtsov Vadim , Kaelber Jason T. , Blaha Gregor , Ebright Richard H. 
Published: July 2024

AbstractStructures recently have been reported of molecular assemblies that mediate transcription-translation coupling inEscherichia coli. In these molecular assemblies, termed “coupled transcription-translation complexes” or “TTC-B”, RNA polymerase (RNAP) interacts directly with the ribosome, the transcription elongation factor NusG or its paralog RfaH forms a bridge between RNAP and ribosome, and the transcription elongation factor NusA optionally forms a second bridge between RNAP and ribosome. Here, we have determined structures of coupled transcription-translation complexes having mRNA spacers between RNAP and ribosome longer than the maximum-length mRNA spacer compatible with formation of TTC-B. The results define a new class of coupled transcription-translation complex, termed “TTC-LC,” where “LC” denotes “long-range coupling.” TTC-LC differs from TTC-B by a ∼60° rotation and ∼70 Å translation of RNAP relative to ribosome, resulting in loss of direct interactions between RNAP and ribosome and creation of a ∼70 Å gap between RNAP and ribosome. TTC-LC accommodates long mRNA spacers by looping out mRNA from the gap between RNAP and ribosome. We propose that TTC-LC is an intermediate in assembling and disassembling TTC-B, mediating pre-TTC-B transcription-translation coupling before a ribosome catches up to RNAP, and mediating post-TTC-B transcription-translation coupling after a ribosome stops moving and RNAP continues moving.
A high-resolution model of gene expression duringGossypium hirsutum(cotton) fiber development
Authors: Grover Corrinne E , Jareczek Josef J , Swaminathan Sivakumar , Lee Youngwoo , Howell Alexander H , Rani Heena , Arick Mark A , Leach Alexis G , Miller Emma R , Yang Pengcheng , Hu Guanjing , Xiong Xianpeng , Mallery Eileen L , Peterson Daniel G , Xie Jun , Haigler Candace H , Zabotina Olga A , Szymanski Daniel B , Wendel Jonathan F 
Published: July 2024

AbstractCotton fiber development relies on complex and intricate biological processes to transform newly differentiated fiber initials into the mature, extravagantly elongated cellulosic cells that are the foundation of this economically important cash crop. Here we extend previous research into cotton fiber development by employing controlled conditions to minimize variability and utilizing time-series sampling and analyses to capture daily transcriptomic changes from early elongation through the early stages of secondary wall synthesis (6 to 24 days post anthesis; DPA). A majority of genes are expressed in fiber, largely partitioned into two major coexpression modules that represent genes whose expression generally increases or decreases during development. Differential gene expression reveals a massive transcriptomic shift between 16 and 17 DPA, corresponding to the onset of the transition phase that leads to secondary wall synthesis. Subtle gene expression changes are captured by the daily sampling, which are discussed in the context of fiber development. Coexpression and gene regulatory networks are constructed and associated with phenotypic aspects of fiber development, including turgor and cellulose production. Key genes are considered in the broader context of plant secondary wall synthesis, noting their known and putative roles in cotton fiber development. The analyses presented here highlight the importance of fine-scale temporal sampling on understanding developmental processes and offer insight into genes and regulatory networks that may be important in conferring the unique fiber phenotype.
Long-Term Outcomes of Untreated Micropenis: Growth Patterns and Predictive Factors
Authors: Amirkashani Davoud , Abdollahi Mostafa , Masoumi Mostafa 
Published: July 2024

AbstractBackgroundMicropenis, defined as a penile length more than 2.5 standard deviations below the mean for age and population, presents significant concerns for patients and parents. Despite current guidelines recommending multidisciplinary management, there is limited evidence on long-term outcomes, particularly in untreated patients.MethodsThis retrospective cohort study involved 46 male children aged 7 to 9 years presenting with micropenis at the Ali Asghar Endocrine Clinic from 2015 to 2023. Initial penile size, BMI, and other growth parameters were measured, with biannual follow-ups extending three years post-bone fusion to evaluate growth rates and influential factors.ResultsInitial mean stretched penile length (SPL) was 3.22 ± 0.21 cm. Significant increases in penile size were observed across all intervals, with the highest growth rates occurring between the first- and second-years post-fusion. BMI emerged as the most significant predictor of penile growth, while initial SPL was the least influential factor. By the third-year post-fusion, all subjects achieved penile lengths within the normal range.ConclusionOur findings indicate that most untreated micropenis patients attain normal penile size by adulthood, highlighting the importance of monitoring growth rates rather than focusing solely on initial penile size. This study provides critical insights for developing guidelines and management strategies for micropenis, emphasizing the necessity of continued follow-up to ensure optimal outcomes.
Connectivity of the Piriform Cortex and its Implications in Temporal Lobe Epilepsy
Authors: Lucas Alfredo , Jaskir Marc , Sinha Nishant , Pattnaik Akash , Mouchtaris Sofia , Josyula Mariam , Petillo Nina , Roth Rebecca W. , Dikecligil Gulce N. , Bonilha Leonardo , Gottfried Jay , Gleichgerrcht Ezequiel , Das Sandhitsu , Stein Joel M. , Gugger James J. , Davis Kathryn A. 
Published: July 2024

BackgroundThe piriform cortex has been implicated in the initiation, spread and termination of epileptic seizures. This understanding has extended to surgical management of epilepsy, where it has been shown that resection or ablation of the piriform cortex can result in better outcomes. How and why the piriform cortex may play such a crucial role in seizure networks is not well understood. To answer these questions, we investigated the functional and structural connectivity of the piriform cortex in both healthy controls and temporal lobe epilepsy (TLE) patients.MethodsWe studied a retrospective cohort of 55 drug-resistant unilateral TLE patients and 26 healthy controls who received structural and functional neuroimaging. Using seed-to-voxel connectivity we compared the normative whole-brain connectivity of the piriform to that of the hippocampus, a region commonly involved in epilepsy, to understand the differential contribution of the piriform to the epileptogenic network. We subsequently measured the inter-piriform coupling (IPC) to quantify similarities in the inter-hemispheric cortical functional connectivity profile between the two piriform cortices. We related differences in IPC in TLE back to aberrations in normative piriform connectivity, whole brain functional properties, and structural connectivity.ResultsWe find that relative to the hippocampus, the piriform is functionally connected to the anterior insula and the rest of the salience ventral attention network (SAN). We also find that low IPC is a sensitive metric of poor surgical outcome (sensitivity: 85.71%, 95% CI: [19.12%, 99.64%]); and differences in IPC within TLE were related to disconnectivity and hyperconnectivity to the anterior insula and the SAN. More globally, we find that low IPC is associated with whole-brain functional and structural segregation, marked by decreased functional small-worldness and fractional anisotropy.ConclusionsOur study presents novel insights into the functional and structural neural network alterations associated with this structure, laying the foundation for future work to carefully consider its connectivity during the presurgical management of epilepsy.
Adaptor protein 2 sigma subunit (AP2S1) variants associated with neurodevelopmental disorders
Authors: Stevenson Mark , Bayliss Asha L. , Stokes Victoria J. , English Katherine A. , Kooblall Kreepa G. , Fischer Roman , Heilig Raphael , Vendrell Iolanda , Albers Maria E. W. A. , Bartos Meghan , Begtrup Amber , Bourgois Alexia , Buchert Rebecca , Carey David J. , Carere Deanna A. , Carnevale Amanda , Claeys Kristl G. , Cogne Benjamin , Costain Gregory , de Leeuw Nicole , Denommé-Pichon Anne-Sophie , Donner Elizabeth J. , Drogouti Eftychia , Dyment David A. , Gangaram Balram , Haack Tobias B. , Haley Jeremy S. , Heide Solveig , Husain Ralf A. , Isidor Bertrand , Izatt Louise , Jacquinet Adeline , Juusola Jane , Kahle Juliette J. , Keren Boris , Klee Eric W. , Kokosali Evgenia , Lanpher Brendan C. , Macke Erica L. , Marco Elysa J. , McWalter Kirsty , Mendelsohn Bryce A. , Milunsky Aubrey , Osmond Matthew , Piton Amelie , Riess Angelika , Ruault Valentin , Rump Patrick , Schuhmann Sarah , Shillington Amelle L. , Smelser Diane T. , Snijders Blok Lot , Tran Mau-Them Frederic , Tsakalidis Christos , Turnwald Abigail , Van Gassen Koen L. I. , Van Schil Kristof , Vasileiou Georgia , Vawter-Lee Marissa , Willems Marjolaine , Willemsen Marjolein H. , Wong-Kisiel Lily C. , Wonneberger Antje , Zaganas Ioannis ,   Genomics England Research Consortium, Hannan Fadil M. , Lines Kate E. , Thakker Rajesh V. 
Published: July 2024

AbstractAdaptor-Related Protein Complex 2 Sigma-1 Subunit(AP2S1) encodes AP2σ2, which forms part of the heterotetrameric AP2 complex that is composed of α, β2, μ2, and σ2 subunits and has a pivotal role in clathrin-mediated endocytosis (CME)1–3.AP2S1variants involving the Arg15 residue are associated with familial hypocalciuric hypercalcaemia type 3 (FHH3)1,4–6. Here, we report 5 differentAP2S1variants (AP2σ2: p.Arg10Trp, p.Arg10Gln, p.Lys18Glu, p.Lys18Asn and p.Arg61His) in 26 patients with neurodevelopmental delay, of whom >70% had epilepsy, 50% had brain abnormalities, and none had hypercalcaemia. All 5 variants decreased cell viability, 4 reduced CME transferrin uptake, and 4 disrupted interactions with other AP2 complex subunits, thereby affecting AP2 formation. Furthermore, AP2σ2 p.Arg10Trp had reduced interactions with 44 human proteins including intersectin 1, a component required for clathrin-coated pit formation and synaptic vesicle dynamics in neurones. Thus, our results show that AP2σ2 variants may disrupt CME and be associated with neurodevelopmental disorders.
Brains Under Stress: Unravelling the Effects of the COVID-19 Pandemic on Brain Ageing
Authors: Mohammadi-Nejad Ali-Reza , Craig Martin , Cox Eleanor , Chen Xin , Jenkins R. Gisli , Francis Susan , Sotiropoulos Stamatios N. , Auer Dorothee P. 
Published: July 2024

AbstractThe impact of SARS-CoV-2 and the COVID-19 pandemic on cognitive and mental health is recognised, yet specific effects on brain health remain understudied. We investigated the pandemic’s impact on brain ageing using longitudinal neuroimaging data from the UK Biobank. Brain age prediction models were trained from hundreds of multi-modal imaging features using a cohort of 15,334 healthy participants. These models were then applied to an independent cohort of 1,336 participants with two MRI scans: either both collected before the pandemic (“Control” groups), or one before and one after the pandemic onset (“Pandemic” group). Our findings reveal that, even with initially matched brain age gaps (predicted brain age vs. chronological age), the pandemic significantly accelerated brain ageing. The “Pandemic” group showed on average 11-month higher deviation of brain age gap at the second time point compared with controls. Accelerated brain ageing was more pronounced in males and those from deprived socio-demographic backgrounds, with average increases of 3.3 and 7 months, respectively. These deviations existed regardless of SARS-CoV-2 infection. However, accelerated brain ageing correlated with reduced cognitive performance only in COVID-infected participants. Our study highlights the pandemic’s significant impact on brain health, beyond direct infection effects, emphasising the need to consider broader social and health inequalities.
Micronutrient-deficient diets and possible environmental enteric dysfunction in Buruli ulcer endemic communities in Ghana: lower dietary diversity and reduced serum zinc and vitamin C implicate micronutrient status a possible susceptibility factor
Authors: Loglo Aloysius Dzigbordi , Antwi Philemon Boasiako , Abass Kabiru Mohammed , Osei-Mireku Samuel , Amofa George , Ofori Elizabeth , Adjei Jonathan , Oppong Michael Ntiamoah , Phillips Richard Odame , Annan Reginald , Engel Barbara , Simmonds Rachel E. 
Published: July 2024

AbstractBackgroundThe nutritional status of communities susceptible to Buruli ulcer (BU, a skin NTD caused by infection withMycobacterium ulcerans) remains almost completely obscure. We have assessed the diets of BU patients vs. controls from the same BU-endemic communities, and compared their circulating biomarkers of nutrients and inflammation.Methods/Principal FindingsWe investigated two cohorts of BU patients and controls. The first were administered food frequency and multi-pass 24-hour recall questionnaires to determine patterns of foods consumed, nutrient intake and nutrient adequacy. The second used archived serum samples collected as baseline to measure the circulating concentration of zinc, vitamin C, CRP, IL-1β, IFN-γ, TNF-α and IL-6. Stunted growth was more prevalent than expected (31%), while 18% of participants were underweight and most had inadequate intake of all micronutrients except for carbohydrate. BU patients had a lower intake of, selenium, vitamin B12and zinc, and for selenium and vitamin B12a higher proportion had dietary insufficiency (40% vs. 15% and 80% vs. 55%, respectively). In line with this, BU patients had significantly lower levels of zinc in their serum, and more had levels below the normal range (72% vs. 43%). Despite many participants having a good intake of vitamin C, serum levels were low, and lower amongst the BU patients. As expected, there was little evidence of systemic inflammation (CRP <0.6 mg/L). Elevated IL-6 levels were present in several participants suggesting that environmental enteric dysfunction may be prevalent in these communities, however this was similar in cases vs. controls.Conclusions/SignificanceDiet and nutritional status may be a contributing factor to BU pathogenesis. Protein and the micronutrients zinc, selenium, vitamin B12and vitamin C may be of particular importance. Nutritional interventions may have potential for both prophylaxis and treatment of BU, which may be a cost-effective approach to achieving the NTD Roadmap goals.