bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal trends in the treatment and outcome of nonagenarians with acute coronary syndrome
Authors: Losin Ilya , Giladi Ela , Arow Ziad , Hilu Ranin , Ovdat Tal , Assali Abid , Pereg David
Published: September 2024

Background

Nonagenarians are a fast-growing age group among acute coronary syndrome (ACS) patients. While new therapeutic options have improved outcomes of ACS patients, data regarding very elderly ACS patients are limited. We aimed to evaluate temporal trends in the treatment and outcomes of nonagenarian ACS patients.

Methods

Included were ACS patients aged below 90 years enrolled in ACS Israeli Survey. Patients were divided into two groups according to enrolment period: early (2000–2010) and recent (2012–2021). The primary endpoints were 30-day major adverse cardiovascular events and all-cause mortality. Secondary outcomes included in-hospital and 1-year all-cause mortality.

Results

Included were 316 elderly ACS patients. Of them, 184 were enrolled in the early and 132 in recent surveys. Patients enrolled in the recent period were more commonly referred for an invasive strategy and more commonly received guideline-based medical therapy. All-cause mortality at 30 days was significantly lower in the recent group compared with the early group (12.5 and 26.1%, respectively, P = 0.005). Rates of 30-day major adverse cardiovascular events were also significantly lower in the recent group (21.9 and 35.9%, respectively, P = 0.012). Patients in the recent group received more aggressive medical therapy in discharge but at 30-day follow-up, no difference in medical treatment was observed in the two groups. There were no significant differences in 1-year mortality rates.

Conclusions

Treatment of nonagenarians with ACS has improved over the past decade. Treatment improvement was associated with a significant improvement in 30-day outcomes without any effect in 1 year. Nevertheless, even with contemporary treatment, nonagenarians with ACS remain a high-risk group with high mortality rates.
Diagnostic performance of simultaneous PET-MR versus PET-CT in oncology with an overview on clinical utility and referral pattern of PET-MR: a single institutional study
Authors: Palaniswamy Shanmuga Sundaram , Subramanyam Padma
Published: September 2024

Background

PET-Magnetic Resonance (PET-MR) imaging is an upcoming investigative modality with a few installations in Asia and only three in India. PET-Computed Tomography (PET-CT) is an established diagnostic cornerstone for oncological indications but with limited resolution for small lesions due to low soft-tissue contrast and additional radiation exposure.

Objective

Our primary objective was to evaluate the diagnostic performance of simultaneous PET-MR and PET-CT in lesion detection in oncological practice. Secondly to assess the referral pattern and study the clinical utility of PET-MR in a university hospital practice.

Materials and methods

A total of 100 consecutive biopsy-proven cancer patients (breast or lung malignancy with suspected metastases) underwent 18F Fluorodeoxyglucose (FDG) PET-MR and PET-CT for staging as a single injection, double examination protocol. Morphological lesion detection on correlative imaging/histopathology was used as the gold standard. Analysing the referral pattern, a total of 9366 patients underwent simultaneous PET-MR imaging for various indications in the past 5 years since installation.

Results

18F FDG PET-MR detected 100% of primary tumours in breast/lung carcinoma patients while PET-CT was positive in 96%. Overall accuracy of nodal metastases detection for PET-MR and PET-CT was 96 and 88%, while for distant metastases the accuracy was 100 and 93%, respectively. FDG PET-MR proved more sensitive and specific than PET-CT for regional nodal (P = 0.011 and P < 0.001) and distant metastases detection (P = 0.017 and P < 0.001, respectively). Analysing the general referral pattern for PET-MR, the majority were oncology referrals when compared to nononcological indications (66.5, 33.5%). About 66.24% were FDG based, followed by 68Ga Prostate-Specific Membrane Antigen (PSMA) and dodecane tetraacetic acid (DOTA). The general utility of PET-MR was found incremental in better delineation of small lesions especially in head, neck, liver, brain and gynaecological malignancies.

Conclusion

In our past 5 years of PET-MR practice, we found that simultaneous PET-MR is a highly recommended ideal imaging technique for oncological and nononcological indications. It has excellent diagnostic performance with high sensitivity, specificity and accuracy when compared to PET-CT in primary tumour, nodal and distant metastases (TNM) staging in specific subgroup of breast and lung malignancy patients.
Detection of Antiretroviral Drug-Resistant Mutations and HIV-1 Subtypes in Circulation Among Men Who Have Sex With Men, SEM Females, and Female Sex Workers: Results of Vietnam's HIV Sentinel Surveillance Plus System, 2018–2020
Authors: Ngo Hanh Hong Thi , Pham Tram Phuong Thi , Hoang Ha Thanh Thi , Bui Duc Hoang , Phan Huong Thu Thi , Nguyen Quoc Cuong , Duong Thanh Cong , Bui Hien Thu , Nguyen Ha Thanh Thi , Le Mai Quynh Thi , Dang Anh Duc , McFarland Willi , Truong Hong-Ha M. , Pham Thang Hong
Published: September 2024

Background:

HIV drug resistance can reduce the effectiveness of antiretroviral drugs in preventing morbidity and mortality, limit options for treatment, and prevention. Our study aimed to assess HIV-1 subtypes and HIV drug resistance among key populations in HIV Sentinel Surveillance Plus Behavior in 2018 and 2020.

Methods:

One-stage venue-based cluster sampling was used to recruit participants at hotspots identified for men who have sex with men (MSM) in 7 provinces and sexual minority females and female sex workers (FSW) in 13 provinces. Participants completed a standard questionnaire about risk and preventive behaviors, and antiretroviral therapy history, and provided intravenous blood for HIV testing. HIV drug resistance testing was conducted on HIV-positive samples with viral load >1000 copies/mL.

Results:

A total of 185 of 435 (42.5%) HIV-positive samples had viral load ≥1000 copies/mL, of which 130 of 136 from MSM and 26 of 49 from FSW were successfully sequenced. Six HIV-1 subtypes were detected (CRF01_AE, A, CRF07/08_BC, B, C, CRF25_cpx), with CRF01_AE (82.7%, 129/156) the most common. Drug resistance mutations were detected in 16.7% of participants overall (26/156), in 15.4% (20/130) of MSM, and in 23.1% (6/26) of FSW. Mutations associated with resistance to non-nucleoside reverse transcriptase inhibitor (NNRTI) were the most frequently detected (73.1%, 19/26). The high level of resistance was presented in NNRTI and nucleoside reverse transcriptase inhibitors classes. There are 10 major resistance mutations detected with nucleoside reverse transcriptase inhibitors (M184VI-25.0%, K65KR-50.0%, Y115F-25%), NNRTI (K103N-21.1%, E138A-10.5%, V106M-5.3%, K101E-5.3%, G190A-5.3%), protease inhibitors (L33F-40.0%, M46L-20.0%).

Conclusions:

Vietnam's HIV Sentinel Surveillance Plus system identified an emerging strain of HIV-1 and mutations associated with resistance to multiple drug classes among MSM and FSW.
Potential Utility of SPECT/CT for Early Detection of Scapular Stress Reaction Following Reverse Total Shoulder Arthroplasty
Authors: Cho Chul-Hyun , Kim Du-Han , Won Kyoung Sook
Published: September 2024

Scapular stress fracture (SSF) after reverse total shoulder arthroplasty is a unique and common complication that may have negative impact for long-term outcomes. Scapular stress reaction (SSR), characterized by pain and tenderness without radiographic evidence of fracture, can be precursor of SSF. We believe that early detection using SPECT/CT with proper management for SSRs including acromion, scapular spine, and coracoid process is crucial for better prognosis without additional complications by preventing SSFs. Therefore, we present 3 typical cases with SSR following reverse total shoulder arthroplasty with the findings of SPECT/CT.
Impact of Social Vulnerability, Race, and Urbanicity on Early Nutritional Outcomes in Patients With Cleft Palate
Authors: Edwards Shelley R. , Elver Ashlie A. , Frederick Keeley B. , Humphries Laura S. , Hoppe Ian C.
Published: September 2024

Patients with cleft palate experience early feeding difficulties, resulting in increased hospital utilization due to poor nutritional status. Sociodemographic factors may impact access and outcomes for cleft patients. This study investigates the association of social vulnerability, race, and urbanicity on birth encounter metrics and failure to thrive (FTT) rates for patients with cleft palate. Retrospective data from 2013 to 2023 was queried from Cosmos, a national deidentified database from Epic electronic health record. Birth metrics, the prevalence of FTT, and MyChart activation rates were compared across sociodemographic cohorts based on (1) social vulnerability index (SVI) quartiles, (2) patient race, and (3) USDA Rural-Urban Commuting Area (RUCA) codes using χ2 or Fisher exact tests. There were 92,437 patients diagnosed with cleft palate. Birth weight was lower in socially vulnerable and Black patients (SVI 75%: 101.50±1.57 oz; SVI 25%: 106.40±1.85 oz; Black: 95.3±2.63 oz; White: 104.90±1.02 oz; Other: 104.80±2.09 oz), and length of stay was longer (SVI 75%: 21±2.39 d; SVI 25%: 15±2.18 d; Black: 22±4 d). FTT related admissions increased with SVI quartile (Q25: 0.19%; Q25–50; 0.29%, Q50–75: 0.34%; Q75: 0.47%; P<0.001). An opposite trend was observed for MyChart activation rates (P<0.001). High SVI and Black patients are susceptible to unfavorable nutritional outcomes. Access disparities, such as direct-to-provider communication systems (ie, MyChart), may contribute. Awareness of social identities, geography, and community may assist in providing individualized care in early life.
Prepregnancy BMI Modified the Association Between Gestational Weight Gain and Birth Weight in Preterm Neonates
Authors: Song Qiying , Zhao Xiaoli , Zhang Jian , Ma Liya , Zhu Yuanfang
Published: September 2024

Maternal prepregnancy body mass index (BMI), gestational weight gain (GWG), and physical activity during pregnancy are associated with neonatal birth weight. This study aimed to evaluate their associations and interactions specifically among preterm neonates. Both inadequate and excessive GWG were associated with an increased risk of low birth weight (LBW) (P < .05). Inadequate GWG was associated with an increased risk of LBW only in underweight and normal weight women, while excessive GWG was related to an increased risk of LBW only in overweight/obese women (P = .001), indicating that maternal prepregnancy BMI may modify the association between GWG and preterm neonatal birth weight.
Early Electrophysiology in Suspected Acute Guillain–Barré Syndrome: A Prospective Study of Comprehensive Testing
Authors: Winkel Antony , Sanders Lauren , Seiderer Linda , Cook Mark , Roberts Leslie
Published: September 2024

Purpose:

Electrophysiologic changes in early Guillain–Barré Syndrome (GBS) can be nondiagnostic. Improved testing paradigms may improve hyperacute treatment.

Methods:

This work prospectively evaluated consecutive patients admitted to a metropolitan teaching hospital in Melbourne, Australia, with suspected acute GBS. We performed extensive neurophysiology at three different time points. Novel tests, including cutaneous silent periods, long latency reflexes, and contraction-induced H reflexes, were assessed.

Results:

Twenty-three participants were studied, including 13 cases of acute GBS. In total, 69% of acute cases of GBS were accurately diagnosed on the first nerve conduction study using published neurophysiologic criteria, with serial studies rarely altering the GBS subtype classification. Antidromic and orthodromic upper limb sensory studies were diagnostically equivalent. A sural sparing pattern was seen in 77% of cases of GBS at the first test. Long latency reflexes and contraction-induced H reflexes testing were abnormal in most participants but were limited by muscle weakness in some. Cutaneous silent periods testing was unobtainable in approximately 50% of cases because of weakness and did not discriminate from mimic disorders.

Conclusions:

Abnormalities of long latency reflexes and contraction-induced H reflexes may be helpful where initial electrophysiology is nondiagnostic but are nonspecific. Cutaneous silent periods testing seems of limited value. Comprehensive testing provides diagnostic certainty in most cases of GBS from the very first study.
Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus
Authors: Kawano Keisuke , Awano Tatsuya , Yoshinaga Arata , Sugiyama Junji , Sawayama Shigeki , Nakagawa Satoshi
Published: September 2024

Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23T and NKW57T, were isolated from a brittle star Ophioplocus japonicus collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23T represented a member of the family Paracoccaceae, with Limibaculum halophilum CAU 1123T as its closest relative (94.4% sequence identity). NKW57T was identified as representing a member of the family Microbulbiferaceae, with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23T formed a novel lineage, branching deeply prior to the divergence of the genera Limibaculum and Thermohalobaculum, with an evolutionary distance (ED) of 0.31–0.32, indicative of genus-level differentiation. NKW57T similarly formed a distinct lineage separate from the species of the genus Microbulbifer. The major respiratory quinones of NKW23T and NKW57T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23T and NKW57T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: Paralimibaculum aggregatum gen. nov., sp. nov., with strain NKW23T (=JCM 36220T=KCTC 8062T) as the type strain, and Biformimicrobium ophioploci gen. nov., sp. nov., with strain NKW57T (=JCM 36221T=KCTC 8063T) as the type strain.
Universal Receptive System as a novel regulator of transcriptomic activity ofStaphylococcus aureus
Authors: Tetz George , Kardava Kristina , Vecherkovskaya Maria , Khodadadi-Jamayran Alireza , Tsirigos Aristotelis , Tetz Victor
Published: September 2024

Our previous studies revealed the existence of a Universal Receptive System that regulates interactions between cells and their environment. This system is composed of DNA- and RNA-based Teazeled receptors (TezRs) found on the surface of prokaryotic and eukaryotic cells, as well as integrases and recombinases.. In the current study, we aimed to provide further insight into the regulatory role of TezR and its loss inStaphylococcus aureusgene transcription. To this end, transcriptomic analysis ofS. aureusMSSA VT209 was performed following the destruction of TezRs. Bacterial RNA samples were extracted from nuclease-treated and untreatedS. aureusMSSA VT209. After destruction of the DNA-based-, RNA-, or combined DNA- and RNA-based TezRs ofS. aureus, 103, 150, and 93 genes were significantly differently expressed, respectively. The analysis revealed differential clustering of gene expression following the loss of different TezRs, highlighting individual cellular responses following the loss of DNA- and RNA-based TezRs. KEGG pathway gene enrichment analysis revealed that the most upregulated pathways following TezR inactivation included those related to energy metabolism, cell wall metabolism, and secretion systems. Some of the genetic pathways were related to the inhibition of biofilm formation and increased antibiotic resistance, and we confirmed this at the phenotypic level usingin vitrostudies. The results of this study add another line of evidence that the Universal Receptive System plays an important role in cell regulation, including cell responses to the environmental factors of clinically important pathogens, and that nucleic acid-based TezRs are functionally active parts of the extrabiome.
The role of pigments in light color variation of the fireflyPhotinus pyralis
Authors: Popecki M.S. , Rogers R.L. , Archer-Hartmann S.A. , Wares J. P. , Stanger-Hall K.F.
Published: September 2024

Fireflies use bioluminescent signals to communicate with their mates. Luciferase has been thought to be the sole contributor to light color; however, populations of the Photinus pyralis firefly display variation in the color of their emitted signals yet have identical luciferase sequences. Here, we examined whether pigments could be present in the light organs of the twilight-active species P. pyralis and contribute to this variation. We detected patterns of expression that suggest ommochrome and pterin screening pigments are expressed in P. pyralis light organs and could filter light emitted by luciferase and play a role in signal tuning. There were no significant differences between the pigment gene expression of P. pyralis individuals with yellower and greener signals. Our study provides alternative mechanisms that could influence pigments in P. pyralis light organs that could also play a role in modifying signal color.
RNA-DCGen: Dual Constrained RNA Sequence Generation with LLM-Attack
Authors: Shahgir Haz Sameen , Ratul Md. Rownok Zahan , Tahmid Md Toki , Sayeed Khondker Salman , Rahman Atif
Published: September 2024

Designing RNA sequences with specific properties is critical for developing personalized medications and therapeutics. While recent diffusion and flow-matching-based generative models have made strides in conditional sequence design, they face two key limitations: specialization for fixed constraint types, such as tertiary structures, and lack of flexibility in imposing additional conditions beyond the primary property of interest. To address these challenges, we introduce RNA-DCGen, a generalized framework for RNA sequence generation that is adaptable to any structural or functional properties through straightforward finetuning with an RNA language model (RNA-LM). Additionally, RNA-DCGen can enforce conditions on the generated sequences by fixing specific conserved regions. On RNA generation conditioned on RNA distance maps, RNA-DCGen generates sequences with an averageR2score of 0.625 compared to random sequences that score only 0.118 over 250 generations as judged by a separate more capable RNA-LM. When conditioned on RNA secondary structures, RNA-DCGen achieves an average F1 score of 0.4 against a random baseline of 0.006.
Genetic analysis of the X-linked AdrenoleukodystrophyABCD1 geneinDrosophilauncovers a role in Peroxisomal dynamics
Authors: Manor Joshua , Jangam Sharayu V , Chung Hyung-lok , Bhagwat Pranjali , Andrews Jonathan , Chester Hillary , Kondo Shu , Srivastav Saurabh , Botas Juan , Moser Ann B. , Huguenin Suzette M. , Wangler Michael F
Published: September 2024

X-linked adrenoleukodystrophy (X-ALD) is a progressive neurodegenerative disorder caused by a loss-of-function (LOF) mutation in theATP-binding cassette subfamily D member 1(ABCD1)gene, leading to the accumulation of very long-chain fatty acids (VLCFAs). This disorder exhibits striking heterogeneity; some male patients develop an early childhood neuroinflammatory demyelination disorder, while other patients, including adult males and most affected female carriers, experience a chronic progressive myelopathy. Adrenocortical failure is observed in almost all male patients, with age of onset varying sometimes being the first diagnostic finding. The gene underlying this spectrum of disease encodes an ATP-binding cassette (ABC) transporter that localizes to peroxisomes and facilitates VLCFA transport. X-ALD is considered a single peroxisomal component defect and does not play a direct role in peroxisome assembly.Drosophilamodels of other peroxisomal genes have provided mechanistic insight into some of the neurodegenerative mechanisms with reduced lifespan, retinal degeneration, and VLCFA accumulation. Here, we perform a genetic analysis of the fly ABCD1 orthologAbcd1(CG2316). Knockdown or deficiency ofAbcd1leads to VLCFA accumulation, salivary gland defects, locomotor impairment and retinal lipid abnormalities. Interestingly, there is also evidence of reduced peroxisomal numbers. Flies overexpressing the human cDNA forABCD1display a wing crumpling phenotype characteristic of thepex2loss-of-function. Surprisingly, overexpression of humanABCD1appears to inhibit or overwhelm peroxisomal biogenesis to levels similar to null mutations in flypex2,pex16andpex3.Drosophila Abcd1is therefore implicated in peroxisomal number, and overexpression of the humanABCD1gene acts a potent inhibitor of peroxisomal biogenesis in flies.
Normative trajectories of extra-axial cerebrospinal fluid during childhood and adolescence defined in a clinically-acquired MRI dataset
Authors: Mandal Ayan S. , Dorfschmidt Lena , Schabdach Jenna M. , Gardner Margaret , Yerys Benjamin E. , Bethlehem Richard A. I. , Sotardi Susan , Katherine Henry M. , Wood Joanne N. , Chaiyachati Barbara H. , Alexander-Bloch Aaron , Seidlitz Jakob
Published: September 2024

Background

Extra-axial cerebrospinal fluid (eaCSF) refers to the CSF in the subarachnoid spaces that surrounds the brain parenchyma. Benign enlargement of the subarachnoid space (BESS), a condition marked by increased eaCSF thickness, has been associated with macrocephaly and may be associated with subdural collections. However, diagnosis of BESS is complicated by the lack of age-specific normative data which hinders rigorous investigation of its clinical associations. Growth charts of eaCSF could shed light on normal CSF dynamics while also providing a normative benchmark to assist the diagnosis of BESS and other associated conditions.

Methods

We accessed clinically-acquired T1w MRI scans from 1226 pediatric patients to form a clinical control cohort. Nine scans from subjects with a diagnosis of BESS from a board-certified pediatric neuroradiologist were also reviewed. SynthSeg was used to segment each T1w scan into various tissue types, including eaCSF. Growth charts of eaCSF were modeled using the clinical control cohort. The confirmed BESS cases were then benchmarked against these charts to test the performance of eaCSF growth charts.

Results

eaCSF thickness varied nonlinearly with age, steadily decreasing from birth to two years, then trending upwards in early adolescence. Seven of the nine patients with a clinical diagnosis of BESS were above the 97.5thpercentile for their age for at least one eaCSF measure. Centile scores were able to distinguish BESS cases from controls with an area under curve (AUC) greater than 0.95.

Discussion

eaCSF thickness evolves in a dynamic pattern throughout childhood and adolescence. Patients with BESS can be differentiated from clinical controls using computational measurements of eaCSF thickness paired with normative modeling. Our findings demonstrate the feasibility of computational extraction of eaCSF with a potential point of clinical relevance, delineation of BESS diagnosis. Enhanced understanding of normative eaCSF is critical in further investigations its clinical associations.
Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells
Authors: Zhao Yan , Tsuiko Olga , Jatsenko Tatjana , Peeters Greet , Souche Erika , Geysens Mathilde , Dimitriadou Eftychia , Vanhie Arne , Peeraer Karen , Debrock Sophie , Van Esch Hilde , Vermeesch Joris Robert
Published: September 2024

Long-read whole-genome sequencing (lrWGS) enhances haplotyping by providing more phasing information per read compared to short-read sequencing. However, its use for single-cell haplotype phasing remains underexplored. This proof-of-concept study examines lrWGS data from single cells for small variant (SNV and indel) calling and haplotyping using the Genome in a Bottle (GIAB) Ashkenazi trio. lrWGS was performed on single-cell (1 cell) and multi-cell (10 cells) samples from the offspring. Chromosome-length haplotypes were obtained by leveraging both long reads and pedigree information. These haplotypes were further refined by replacing them with matched parental haplotypes. In single-cell and multi-cell samples, 92% and 98% of heterozygous SNVs, and 74% and 78% of heterozygous indels were accurately haplotyped. Applied to human embryos for preimplantation genetic testing (PGT), lrWGS demonstrated 100% consistency with array-based methods for detecting monogenic disorders, without requiring phasing references. Aneuploidies were accurately detected, with insights into the mechanistic origins of chromosomal abnormalities inferred from the parental unique allele fractions. We show that lrWGS-based concurrent haplotyping and aneuploidy profiling of single cells provides an alternative to current PGT methods, with applications potential in areas such as cell-based prenatal diagnosis and animal and plant breeding.
Broad-spectrum immune suppression encoded in self-amplifying RNA enables non-cytotoxic, non-immunostimulatory, externally controllable transgene expression
Authors: Lim Tony K.Y , Ritoux Anne , Paine Luke W. , Ferguson Larissa , Abdul Tawab , John Smith Ewan St.
Published: September 2024

Self-amplifying RNA (saRNA) has the potential to provide durable, non-integrative transgene expression for transient gene therapy. However, its auto-replicative nature mimics viral infection, triggering innate immune responses that shutdown cap-dependent translation, degrade cellular mRNA, induce cell death, and release cytokines. In non-immunotherapy applications, this immune activation is undesirable as it limits transgene expression, depletes transfected cells, and induces inflammation, undermining therapeutic outcomes. Moreover, the use of exogenous immune suppressants to mitigate these effects often increases treatment complexity and the risk of unintended systemic side effects. To address these challenges, we developed a strategy to encode broad-spectrum innate immune suppression directly within saRNA. This approach leverages cap-independent translation to bypass saRNA-triggered translation shutdown, enabling the expression of multiple inhibitors targeting diverse double-stranded RNA-sensing and inflammatory signaling pathways. In mouse primary fibroblast-like synoviocytes—a cell type relevant to inflammatory joint diseases—this strategy eliminates the need for external immune inhibitors, reduces cytotoxicity and antiviral cytokine secretion, and enables sustained transgene expression that can be controlled with a small-molecule antiviral. These findings support the development of saRNA therapeutics that offer durable, non-integrative, externally controllable transgene expression without persistent immune activation or reliance on exogenous immune suppressants.

GRAPHICAL ABSTRACT
Hematological phenotypes in GATA2 deficiency syndrome arise from secondary injuries and maladaptation to proliferation
Authors: Fernandez-Orth Juncal , Koyunlar Cansu , Weiss Julia M. , Gioacchino Emanuele , de Looper Hans , Andrieux Geoffroy , Borg Mariëtte Ter , Zink Joke , Gonzalez-Menendez Irene , Hoogenboezem Remco , Yigit Baris , Gussinklo Kirsten J , Mulet-Lazaro Roger , Wantzen Charlotte , Pfeiffer Sophie , Molnar Christian , Bindels Eric , Bohler Sheila , Sanders Mathijs , Quintanilla-Martinez Leticia , Wlodarski Marcin , Boerries Melanie , Touw Ivo P. , Niemeyer Charlotte , Erlacher Miriam , de Pater Emma
Published: September 2024

The GATA2 transcription factor is a pivotal regulator of hematopoiesis. Disruptions in theGATA2gene drive severe hematologic abnormalities and are associated with an increased risk of myelodysplastic syndromes and acute myeloid leukemia; however, the mechanisms underlying the pathophysiology of GATA2 deficiency remain still unclear. We developed two different mouse models that are based on serial and limiting donor cell transplantation of (aged) GATA2 haploinsufficient cells and mirror the symptoms of GATA2 deficiency. Similar to what has been observed in patients, our models show that GATA2 haploinsufficiency leads to B lymphopenia, monocytopenia, lethal bone marrow failure (BMF), myelodysplasia and leukemia. Leukemia arises exclusively as a result of BMF, driven by somatic aberrations and accompanied by increasedMyctarget expression and genomic instability. These findings were confirmed in human GATA2+/− K562 cell lines showing defects in cytokinesis and are in line with the fact that monosomy 7 and trisomy 8 are frequent events in patients with MDS.

Key points

In a mouse model for GATA2 deficiency, leukemia emerges from bone marrow failure

Maladaptation to proliferative signals and chromosomal segregation defects contribute to the hematological phenotypes in GATA2 deficiency
Evolution of transcription factor-containing superfamilies in Eukaryotes
Authors: Dubey Akshara , Muthu Ganesh , Seshasayee Aswin Sai Narain
Published: September 2024

Regulation of gene expression helps determine various phenotypes in most cellular life forms. It is orchestrated at different levels and at the point of transcription initiation by transcription factors (TFs). TFs bind to DNA through domains that are evolutionarily related, by shared membership of the same superfamilies (TF-SFs), to those found in other nucleic acid binding and protein-binding functions (nTFs for non-TFs). Here we ask how TF DNA binding sequence families in eukaryotes have evolved in relation to their nTF relatives. TF numbers scale by power law with the total number of protein-coding genes differently in different clades, with fungi usually showing sub-linear powers whereas chordates show super-linear scaling. The LECA probably encoded a complex regulatory machinery with both TFs and nTFs, but with an excess of nTFs when compared to the relative distribution of TFs and nTFs in extant organisms. Losses drive the evolution of TFs and nTFs, with the possible exception of TFs in Animalia for some tree topologies. TFs are highly dynamic in evolution, showing higher gain and loss rates than nTFs though both are conserved to similar extents. Gains of TFs and nTFs are driven by the appearance of a large number of new sequence clusters in a small number of nodes, which determine the presence of as many as a third of extant TFs and nTFs as well as the relative presence of TFs and nTFs. Whereas nodes showing explosion of TF numbers belong to multicellular clades, those for nTFs lie among the fungi and the protists.
Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons
Authors: Hundley Frances V. , Gonzalez-Lozano Miguel A. , Gottschalk Lena M. , Cook Aslan N. K. , Zhang Jiuchun , Paulo Joao A. , Harper J. Wade
Published: September 2024

Plasma membrane protein degradation and recycling is regulated by the endolysosomal system, wherein endosomes bud from the plasma membrane into the cytosol and mature into degradative lysosomes. As such, the endolysosomal system plays a critical role in determining the abundance of proteins on the cell surface, influencing cellular identity and function. Highly polarized cells, like neurons, rely on the endolysosomal system for axonal and dendritic specialization and synaptic compartmentalization. The importance of this system to neuronal function is reflected by the prevalence of risk variants in components of the system in several neurodegenerative diseases, ranging from Parkinson’s to Alzheimer’s disease. Nevertheless, our understanding of endocytic cargo and core endolysosomal machinery in neurons is limited, in part due to technical limitations. Here, we developed a toolkit for capturing EEA1-postive endosomes (Endo-IP) and TMEM192-positive lysosomes (Lyso-IP) in stem cell-derived induced neurons (iNeurons). We demonstrated its utility by revealing the endolysosomal protein landscapes for cortical-like iNeurons and stem cells. This allowed us to globally profile endocytic cargo, identifying hundreds of transmembrane proteins, including neurogenesis and synaptic proteins, as well as endocytic cargo with predicted SNX17 or SNX27 recognition motifs. By contrast, parallel lysosome profiling reveals a simpler protein repertoire, reflecting in part temporally controlled recycling or degradation for many endocytic targets. This system will facilitate mechanistic interrogation of endolysosomal components found as risk factors in neurodegenerative disease.
Gene coexpression network analysis of galactomannan biosynthesis and endosperm maturation in species of the genusCoffea
Authors: Dussert Stéphane , Stavrinides Anna K. , Serret Julien , Vaissayre Virginie , Combes Marie-Christine , Morcillo Fabienne , Lefort Eveline , Rialle Stéphanie , Etienne Hervé , Lashermes Philippe , Joët Thierry
Published: September 2024

In a few important plant families and genera, including Arecaceae, Fabaceae and the genusCoffea, the main seed storage polysaccharide is not starch but cell wall galactomannans. Such seeds are albuminous with a persistent copious living endosperm that accumulates galactomannans. However, our understanding of the regulation of endosperm maturation, cell wall formation and galactomannan biosynthesis in albuminous seeds remains very limited. To gain insights into these processes, a large RNA-seq dataset was produced (14 coffee species × 5 endosperm developmental stages) and scrutinized using gene coexpression network analysis. The network revealed tight transcriptional coordination of the core galactomannan biosynthetic machinery for sucrose import, glycolysis, nucleotide sugar synthesis and transport, arabinogalactan protein and cellulose synthesis, and regulation of the trans-Golgi network. The orchestration of galactomannan and oil accumulation during endosperm maturation appeared to be exerted by the transcription factors FUSCA3, WRINKLED1, SHINE2 and DREB2D. The latter was the only coexpression partner of galactomannan biosynthetic genes. Numerous key genes of galactomannan biosynthesis were significantly upregulated in coffee somatic embryos overexpressing DREB2D, which showed increased production of UDP-galactose and diversion towards raffinose family oligosaccharides. Further, most genes of the galactomannan coexpression module were identified as DREB2D target genes by DAP-seq analysis.

Highlight

Gene coexpression network analysis of the maturing endosperm identified the AP2/ERF transcription factor DREB2D as a major regulator of galactomannan accumulation in the cell walls of albuminous coffee seeds.
An Atlas of Linkage Disequilibrium Across Species
Authors: Zhu Tian-Neng , Huang Xing , Yang Meng-yuan , Qi Guo-An , Zhang Qi-Xin , Lin Feng , Zhang Wenjing , Zhang Zhe , Jin Xin , Zheng Hou-Feng , Xu Hai-Ming , Yu Shizhou , Chen Guo-Bo
Published: September 2024

Linkage disequilibrium (LD) is a key metric that characterizes populations in flux. To reach a genomic scale LD illustration, which has a substantial computational cost of𝒪(nm2), we introduce a framework with two novel algorithms for LD estimation: X-LD, with a time complexity of𝒪(n2m) suitable for small sample sizes (n <104); X-LDR, a stochastic algorithm with a time complexity of𝒪(nmB) for biobank-scale data (Biterations);nthe sample size, andmthe number of SNPs. These methods can refine the entire genome into high-resolution LD grids, such as more than 9 million grids for UK Biobank samples (∼4.2 million SNPs). The efficient resolution for genome-wide LD leads to intriguing biological discoveries.I)High-resolution LD illustrations revealed how the pericentromeric regions and the HLA region lead to intense and extended LD patterns.II)Two universal LD patterns, identified as Norm I and Norm II patterns, provide insights on the evolutionary history of populations and can also highlight genomic regions of deviation, such as chromosomes 6 and 11 or ncRNA regions.III)The results of our innovative LD decay method aligned with the LD decay scores of 59.5 for Europeans, 60.2 for East Asians, and 33.2 for Africans; correspondingly, the length of the LD was approximately 2.85 Mb, 2.18 Mb, and 1.58 Mb for these three ethnicities. Rare or imputed variants universally increased LD.IV)An unprecedented LD atlas for 25 reference populations contoured interspecies diversity in terms of their Norm I and Norm II LD patterns, highlighting the impact of refined population structure, quality of reference genomes, and uncovered a profoundstatus quoof these populations. The algorithms have been implemented in C++ and are freely available (https://github.com/gc5k/gear2).
Protein Sequence Modelling with Bayesian Flow Networks
Authors: Atkinson Timothy , Barrett Thomas D. , Cameron Scott , Guloglu Bora , Greenig Matthew , Robinson Louis , Graves Alex , Copoiu Liviu , Laterre Alexandre
Published: September 2024

Exploring the vast and largely uncharted territory of amino acid sequences is crucial for understanding complex protein functions and the engineering of novel therapeutic proteins. Whilst generative machine learning has advanced protein sequence modelling, no existing approach is proficient for both unconditional and conditional generation. In this work, we propose that Bayesian Flow Networks (BFNs), a recently introduced framework for generative modelling, can address these challenges. We present ProtBFN, a 650M parameter model trained on protein sequences curated from UniProtKB, which generates natural-like, diverse, structurally coherent, and novel protein sequences, significantly outperforming leading autoregressive and discrete diffusion models. Further, we fine-tune ProtBFN on heavy chains from the Observed Antibody Space (OAS) to obtain an antibody-specific model, AbBFN, which we use to evaluate zero-shot conditional generation capabilities. AbBFN is found to be competitive with, or better than, antibody-specific BERT-style models, when applied to predicting individual framework or complimentary determining regions (CDR).
Effect of Mutations on Smlt1473 Binding to Various Substrates Using Molecular Dynamics Simulations
Authors: Mondal Kinjal , Felton Samantha , Berger Bryan W. , Klauda Jeffery B.
Published: September 2024

Smlt1473 is a polysaccharide lyase fromStenotrophomonas maltophiliawhose crystal structure was solved recently using X-ray crystallography. There was an effort to study the effect of mutations on the activity of Smlt1473 binding to various substrates like hyaluronic acid(HA), mannuronic acid(ManA), and alginate. In this study, we use molecular docking and molecular dynamics simulations to investigate the effect of binding of various substrates (HA and ManA) to Smlt1473 and two of its mutants H221F and R312L. We further studied the stability in the binding of Smlt1473 to its various substrates as well as the role of fluctuations. Machine-Learning based clustering algorithms were used to group the entire simulation trajectory into various stable states. The molecular interactions Smlt1473 to the substrates were calculated and the importance of specific residues were tested with observed activity assays due to residue mutations. Overall, we find that the R218 plays an important role in substrate binding and thus impacting the activity due to the H221F mutant and R/L312 itself plays an important role in the R312 mutation. In addition, we have also found three more residues K56, R107, and R164 important for substrate binding which we further proceed to confirm using wet lab mutagenesis studies.
Variability in proliferative and migratory defects in Hirschsprung disease-associatedRETpathogenic variants
Authors: Fries Lauren E , Dharma Sree , Chakravarti Aravinda , Chatterjee Sumantra
Published: September 2024

Despite the extensive genetic heterogeneity of Hirschsprung disease (HSCR; congenital colonic aganglionosis) 72% of patients harbor pathogenic variants in 10 genes that form a gene regulatory network (GRN) controlling the development of the enteric nervous system (ENS). Among these genes, the receptor tyrosine kinase gene RET is the most significant contributor, accounting for pathogenic variants in 12%-50% of patients depending on phenotype. RET plays a critical role in the proliferation and migration of ENS precursors, and defects in these processes lead to HSCR. However, despite the gene’s importance in HSCR, the functional consequences of RET pathogenic variants and their mechanism of disease remain poorly understood. To address this, we investigated the proliferative and migratory phenotypes in a RET-dependent neural crest-derived cell line harboring one of five missense (L56M, E178Q, Y791F, S922Y, F998L) or three nonsense (Y204X, R770X, Y981X) pathogenic heterozygous variants. Using a combination of cDNA-based and CRISPR-based PRIME editing coupled with quantitative proliferation and migration assays, we detected significant losses in cell proliferation and migration in three missense (E178Q, S922Y, F998L) and all nonsense variants. Our data suggests that the Y791F variant, whose pathogenicity has been debated, is likely not pathogenic. Importantly, the severity of migration loss did not consistently correlate with proliferation defects, and the phenotypic severity of nonsense variants was independent of their position within the RET protein. This study highlights the necessity and feasibility of targeted functional assays to accurately assess the pathogenicity of HSCR-associated variants, rather than relying solely on machine learning predictions, which could themselves be refined by incorporating such functional data.
GPR30 in spinal cholecystokinin-positive neurons modulates neuropathic pain via mediating descending facilitation
Authors: Chen Qing , Wu Hui , Xie Shulan , Zhu Fangfang , Xu Fang , Xu Qi , Sun Lihong , Yang Yue , Xie Linghua , Xie Jiaqian , Li Hua , Dai Ange , Zhang Wenxin , Wang Luyang , Jiao Cuicui , Zhang Honghai , Xu Zhen-Zhong , Chen Xinzhong
Published: September 2024

Neuropathic pain, a major health problem affecting 7 - 10% of the global population, lacks effective treatment due to its elusive mechanisms. Cholecystokinin-positive (CCK+) neurons in the spinal dorsal horn (SDH) are critical for neuropathic pain, yet the underlying molecular mechanisms remain unclear. Here we showed that the membrane estrogen receptor G-protein coupled estrogen receptor (GPER/GPR30) in spinal was significantly upregulated in chronic constriction injury (CCI) mice and that inhibition of GPR30 in CCK+neurons reversed CCI-induced neuropathic pain. Besides, GPR30 in spinal CCK+neurons was essential for the enhancement of AMPA-mediated excitatory synaptic transmission in CCI mice. Furthermore, GPR30 was expressed in the spinal CCK+neurons receiving direct projection from the primary sensory cortex (S1-SDH). Chemogenetic inhibition of S1-SDH post-synaptic neurons alleviated CCI-induced neuropathic pain. Conversely, chemogenetic activation of these neurons mimicked neuropathic pain symptoms, which were attenuated by spinal inhibition of GPR30. Finally, we confirmed that GPR30 in S1-SDH post-synaptic neurons is required for CCI-induced neuropathic pain. Taken together, our findings suggest that GPR30 in spinal CCK+neurons is pivotal for neuropathic pain and mediates descending facilitation by corticospinal direct projections, thereby representing a promising therapeutic target for neuropathic pain.
Alzheimer’s neuropathology and longitudinal change in subjective cognitive complaints
Authors: Bannerjee Alisa , Elkins Wendy , Resnick Susan M. , Bilgel Murat
Published: September 2024

INTRODUCTION

Subjective cognitive complaints often precede declines in objective measures of cognitive performance. Incipient AD neuropathology may be associated with subjective cognitive complaints prior to detectable associations with neuropsychological testing among cognitively normal individuals.

METHODS

We examined the independent associations of PET measures of amyloid-β and tau pathology with longitudinal change in subjective complaints and memory among 91 cognitively normal Baltimore Longitudinal Study of Aging participants using linear mixed effects models. Subjective complaints and memory performance were assessed with the Cognitive Failures Questionnaire and the California Verbal Learning Test, respectively.

RESULTS

Greater parahippocampal tau, independent of amyloid, was associated with higher subjective complaints (estimate=0.203, SE=0.0825,p=0.016), while greater entorhinal tau corresponded to an attenuated increase in complaints over time (estimate=-0.0629, SE=0.0299,p=0.040). Hippocampal tau was associated with steeper memory decline (estimate=-0.0279, SE=0.0135,p=0.043).

CONCLUSION

Subjective cognitive complaints may serve as early indicators of cerebral tau pathology in cognitively normal individuals.
Detection of Mpox and other Orthopoxviruses using a Lateral Flow Device as a Point of Care diagnostic
Authors: Laidlaw Stephen M. , Ulaeto David , Lonsdale Steve , Clark Graeme , Sumner Rebecca , Edwards Thomas , Adams Emily , Logist Anne-Sophie , Holm Bram Van , Maluquer de Motes Carlos , Horby Peter , Maes Piet , Carroll Miles W.
Published: September 2024

Introduction

In 2022 the WHO declared the worldwide outbreak of mpox to be a public health emergency of international concern (PHEIC). The causative monkeypox virus (MPXV) belonged to Clade IIb and transmitted through sexual contact with a low case fatality rate (0.1%), which together with underdetection, all contributed to a rapid global spread particularly within the MSM (men who have sex with men) community. As MPXV Clade II remains circulating worldwide, a new outbreak of the more fatal Clade I disease has been declared in Central and East Africa and remains uncontrolled in part due to the lack of Point of Care (POC) diagnostics for rapid decisions on treatment and self-isolation.

Aim

To address the lack of POC solutions for mpox we have designed and evaluated an orthopoxvirus-specific lateral flow device (LFD) that could be used for diagnosis of mpox.

Results

Using an LFD comprising four monoclonal antibodies against the A27 protein we demonstrate sensitivity to 3×105pfu/ml. This sensitivity is expected to be sufficient for detection of MPXV from lesion sites and may also be sufficient for other sample types such as saliva and urine. However, sample collection buffer may have a detrimental impact on sensitivity for clinical material.

Conclusion

Point of care (POC) diagnosis of mpox may be possible using a LFD to reduce delays arising from sample shipment to centralised laboratory testing facilities.