@article{14543,
  abstract     = {The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.},
  author       = {Kaiyrzhanov, Rauan and Rad, Aboulfazl and Lin, Sheng-Jia and Bertoli-Avella, Aida and Kallemeijn, Wouter W and Godwin, Annie and Zaki, Maha S and Huang, Kevin and Lau, Tracy and Petree, Cassidy and Efthymiou, Stephanie and Ghayoor Karimiani, Ehsan and Hempel, Maja and Normand, Elizabeth A and Rudnik-Schöneborn, Sabine and Schatz, Ulrich A and Baggelaar, Marc P and Ilyas, Muhammad and Sultan, Tipu and Alvi, Javeria Raza and Ganieva, Manizha and Fowler, Ben and Aanicai, Ruxandra and Akay Tayfun, Gulsen and Al Saman, Abdulaziz and Alswaid, Abdulrahman and Amiri, Nafise and Asilova, Nilufar and Shotelersuk, Vorasuk and Yeetong, Patra and Azam, Matloob and Babaei, Meisam and Bahrami Monajemi, Gholamreza and Mohammadi, Pouria and Samie, Saeed and Banu, Selina Husna and Basto, Jorge Pinto and Kortüm, Fanny and Bauer, Mislen and Bauer, Peter and Beetz, Christian and Garshasbi, Masoud and Hameed Issa, Awatif and Eyaid, Wafaa and Ahmed, Hind and Hashemi, Narges and Hassanpour, Kazem and Herman, Isabella and Ibrohimov, Sherozjon and Abdul-Majeed, Ban A and Imdad, Maria and Isrofilov, Maksudjon and Kaiyal, Qassem and Khan, Suliman and Kirmse, Brian and Koster, Janet and Lourenço, Charles Marques and Mitani, Tadahiro and Moldovan, Oana and Murphy, David and Najafi, Maryam and Pehlivan, Davut and Rocha, Maria Eugenia and Salpietro, Vincenzo and Schmidts, Miriam and Shalata, Adel and Mahroum, Mohammad and Talbeya, Jawabreh Kassem and Taylor, Robert W and Vazquez, Dayana and Vetro, Annalisa and Waterham, Hans R and Zaman, Mashaya and Schrader, Tina A and Chung, Wendy K and Guerrini, Renzo and Lupski, James R and Gleeson, Joseph and Suri, Mohnish and Jamshidi, Yalda and Bhatia, Kailash P and Vona, Barbara and Schrader, Michael and Severino, Mariasavina and Guille, Matthew and Tate, Edward W and Varshney, Gaurav K and Houlden, Henry and Maroofian, Reza},
  issn         = {1460-2156},
  journal      = {Brain},
  keywords     = {Neurology (clinical)},
  number       = {4},
  pages        = {1436--1456},
  publisher    = {Oxford University Press},
  title        = {{Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders}},
  doi          = {10.1093/brain/awad380},
  volume       = {147},
  year         = {2024},
}

@article{14726,
  abstract     = {Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.},
  author       = {Zhou, Liang-Zi and Wang, Lele and Chen, Xia and Ge, Zengxiang and Mergner, Julia and Li, Xingli and Küster, Bernhard and Längst, Gernot and Qu, Li-Jia and Dresselhaus, Thomas},
  issn         = {1532-298X},
  journal      = {The Plant Cell},
  keywords     = {Cell Biology, Plant Science},
  number       = {5},
  publisher    = {Oxford University Press},
  title        = {{The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize}},
  doi          = {10.1093/plcell/koad324},
  volume       = {36},
  year         = {2024},
}

@article{15189,
  abstract     = {Cataclysmic variables (CVs) that have evolved past the period minimum during their lifetimes are predicted to be systems with a brown dwarf donor. While population synthesis models predict that around 40–70 per cent of the Galactic CVs are post-period minimum systems referred to as ‘period bouncers’, only a few dozen confirmed systems are known. We report the study and characterization of a new eclipsing CV, SRGeJ041130.3+685350 (SRGeJ0411), discovered from a joint SRG/eROSITA and ZTF programme. The optical spectrum of SRGeJ0411 shows prominent hydrogen and helium emission lines, typical for CVs. We obtained optical high-speed photometry to confirm the eclipse of SRGeJ0411 and determine the orbital period to be Porb ≈ 97.530 min. The spectral energy distribution suggests that the donor has an effective temperature of ≲ 1800 K. We constrain the donor mass with the period–density relationship for Roche lobe-filling stars and find that Mdonor ≲ 0.04 M⊙. The binary parameters are consistent with evolutionary models for post-period minimum CVs, suggesting that SRGeJ0411 is a new period bouncer. The optical emission lines of SRGeJ0411 are single-peaked despite the system being eclipsing, which is typically only seen due to stream-fed accretion in polars. X-ray spectroscopy hints that the white dwarf in SRGeJ0411 could be magnetic, but verifying the magnetic nature of SRGeJ0411 requires further investigation. The lack of optical outbursts has made SRGeJ0411 elusive in previous surveys, and joint X-ray and optical surveys highlight the potential for discovering similar systems in the near future.},
  author       = {Galiullin, Ilkham and Rodriguez, Antonio C and Kulkarni, Shrinivas R and Sunyaev, Rashid and Gilfanov, Marat and Bikmaev, Ilfan and Yungelson, Lev and van Roestel, Jan and Gänsicke, Boris T and Khamitov, Irek and Szkody, Paula and El-Badry, Kareem and Suslikov, Mikhail and Prince, Thomas A and Buntov, Mikhail and Caiazzo, Ilaria and Gorbachev, Mark and Graham, Matthew J and Gumerov, Rustam and Irtuganov, Eldar and Laher, Russ R and Medvedev, Pavel and Riddle, Reed and Rusholme, Ben and Sakhibullin, Nail and Sklyanov, Alexander and Vanderbosch, Zachary P},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics},
  number       = {1},
  pages        = {676--692},
  publisher    = {Oxford University Press},
  title        = {{A joint SRG/eROSITA + ZTF search: Discovery of a 97-min period eclipsing cataclysmic variable with evidence of a brown dwarf secondary}},
  doi          = {10.1093/mnras/stae012},
  volume       = {528},
  year         = {2024},
}

@article{15191,
  abstract     = {Despite their shared origin, members of globular clusters display star-to-star variations in composition. The observed pattern of element abundances is unique to these stellar environments and cannot be fully explained by any proposed mechanism. It remains unclear whether stars form with chemical heterogeneity or inherit it from interactions with other members. These scenarios may be differentiated by the dependence of chemical spread on stellar mass; however, obtaining a sufficiently large mass baseline requires abundance measurements on the lower main sequence, which is too faint for spectroscopy even in the nearest globular clusters. We developed a stellar modeling method to obtain precise chemical abundances for stars near the end of the main sequence from multiband photometry, and we applied it to the globular cluster 47 Tucanae. The computational efficiency is attained by matching chemical elements to the model components that are most sensitive to their abundance. We determined [O/Fe] for ∼5000 members below the main-sequence knee at the level of accuracy, comparable to the spectroscopic measurements of evolved members in the literature. The inferred distribution disfavors stellar interactions as the origin of chemical spread; however, an accurate theory of accretion is required to draw a more definitive conclusion. We anticipate that future observations of 47 Tucanae with the James Webb Space Telescope will extend the mass baseline of our analysis into the substellar regime. Therefore, we present predicted color–magnitude diagrams and mass–magnitude relations for the brown dwarf members of 47 Tucanae.},
  author       = {Gerasimov, Roman and Burgasser, Adam J. and Caiazzo, Ilaria and Homeier, Derek and Richer, Harvey B. and Correnti, Matteo and Heyl, Jeremy},
  issn         = {1538-4357},
  journal      = {The Astrophysical Journal},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics},
  number       = {1},
  publisher    = {American Astronomical Society},
  title        = {{Exploring the chemistry and mass function of the globular cluster 47 Tucanae with new theoretical color–magnitude diagrams}},
  doi          = {10.3847/1538-4357/ad08bf},
  volume       = {961},
  year         = {2024},
}

@article{15379,
  abstract     = {Long-term potentiation (LTP) of excitatory synapses is a leading model to explain the concept of information storage in the brain. Multiple mechanisms contribute to LTP, but central amongst them is an increased sensitivity of the postsynaptic membrane to neurotransmitter release. This sensitivity is predominantly determined by the abundance and localization of AMPA-type glutamate receptors (AMPARs). A combination of AMPAR structural data, super-resolution imaging of excitatory synapses, and an abundance of electrophysiological studies are providing an ever-clearer picture of how AMPARs are recruited and organized at synaptic junctions. Here, we review the latest insights into this process, and discuss how both cytoplasmic and extracellular receptor elements cooperate to tune the AMPAR response at the hippocampal CA1 synapse.},
  author       = {Stockwell, Imogen and Watson, Jake and Greger, Ingo H.},
  issn         = {1521-1878},
  journal      = {BioEssays},
  number       = {7},
  publisher    = {Wiley},
  title        = {{Tuning synaptic strength by regulation of AMPA glutamate receptor localization}},
  doi          = {10.1002/bies.202400006},
  volume       = {46},
  year         = {2024},
}

@misc{17042,
  abstract     = {Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13C-13C and heteronuclear H-N, H-C and N-C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples. },
  author       = {Schanda, Paul},
  keywords     = {nuclear magnetic resonance, NMR, cellwall, structural biology, spectroscopy},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Raw data to "MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments"}},
  doi          = {10.15479/AT:ISTA:17042},
  year         = {2024},
}

@article{17111,
  abstract     = {Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.},
  author       = {Kamatar, Advika and Bravo, Jack Peter Kelly and Yuan, Feng and Wang, Liping and Lafer, Eileen M. and Taylor, David W. and Stachowiak, Jeanne C. and Parekh, Sapun H.},
  issn         = {0006-3495},
  journal      = {Biophysical Journal},
  number       = {11},
  pages        = {1494--1507},
  publisher    = {Elsevier},
  title        = {{Lipid droplets as substrates for protein phase separation}},
  doi          = {10.1016/j.bpj.2024.03.015},
  volume       = {123},
  year         = {2024},
}

@article{17112,
  abstract     = {The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.},
  author       = {Steens, Jurre A. and Bravo, Jack Peter Kelly and Salazar, Carl Raymund P. and Yildiz, Caglar and Amieiro, Afonso M. and Köstlbacher, Stephan and Prinsen, Stijn H.P. and Patinios, Constantinos and Bardis, Andreas and Barendregt, Arjan and Scheltema, Richard A. and Ettema, Thijs J.G. and van der Oost, John and Taylor, David W. and Staals, Raymond H.J.},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6682},
  pages        = {512--519},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Type III-B CRISPR-Cas cascade of proteolytic cleavages}},
  doi          = {10.1126/science.adk0378},
  volume       = {383},
  year         = {2024},
}

@article{17113,
  abstract     = {CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for <jats:italic>Streptococcus pyogenes</jats:italic> Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.},
  author       = {Hibshman, Grace N. and Bravo, Jack Peter Kelly and Hooper, Matthew M. and Dangerfield, Tyler L. and Zhang, Hongshan and Finkelstein, Ilya J. and Johnson, Kenneth A. and Taylor, David W.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9}},
  doi          = {10.1038/s41467-024-47830-3},
  volume       = {15},
  year         = {2024},
}

@article{17114,
  abstract     = {CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction<jats:sup>1–5</jats:sup>. Target RNA cleavage at regular intervals is characteristic of type III effector complexes<jats:sup>6–8</jats:sup>. Here, we determine the structures of the <jats:italic>Synechocystis</jats:italic> type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors<jats:sup>9,10</jats:sup>, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.},
  author       = {Schwartz, Evan A. and Bravo, Jack Peter Kelly and Ahsan, Mohd and Macias, Luis A. and McCafferty, Caitlyn L. and Dangerfield, Tyler L. and Walker, Jada N. and Brodbelt, Jennifer S. and Palermo, Giulia and Fineran, Peter C. and Fagerlund, Robert D. and Taylor, David W.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{RNA targeting and cleavage by the type III-Dv CRISPR effector complex}},
  doi          = {10.1038/s41467-024-47506-y},
  volume       = {15},
  year         = {2024},
}

@article{17122,
  abstract     = {Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.
Methods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.
Results: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).
Conclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses.},
  author       = {Ramming, Hannah and Theuerkauf, Linda and Hoos, Olaf and Lichter, Katharina and Kittel-Schneider, Sarah},
  issn         = {1471-244X},
  journal      = {BMC Psychiatry},
  publisher    = {Springer Nature},
  title        = {{The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study}},
  doi          = {10.1186/s12888-024-05849-2},
  volume       = {24},
  year         = {2024},
}

@inproceedings{17139,
  author       = {Schlögl, Alois and Khalid, Waleed and Elefante, Stefano and Stadlbauer, Stephan},
  booktitle    = {ASHPC24 - Austrian-Slovenian HPC Meeting 2024},
  isbn         = {9783200096455},
  location     = {Grundlsee, Austria},
  pages        = {46},
  publisher    = {EuroCC Austria},
  title        = {{How much memory per CPU core is requested?}},
  doi          = {10.25365/phaidra.463},
  year         = {2024},
}

@article{18451,
  abstract     = {Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials.},
  author       = {Zhou, Yu and Shaukat, Ahmed and Seitsonen, Jani and Rigoni, Carlo and Timonen, Jaakko V.I. and Kostiainen, Mauri A.},
  issn         = {2198-3844},
  journal      = {Advanced Science},
  number       = {45},
  publisher    = {Wiley},
  title        = {{Protein cage directed assembly of binary nanoparticle superlattices}},
  doi          = {10.1002/advs.202408416},
  volume       = {11},
  year         = {2024},
}

@article{18545,
  abstract     = {Clinical implementation of therapeutic genome editing relies on efficient in vivo delivery and the safety of CRISPR-Cas tools. Previously, we identified PsCas9 as a Type II-B family enzyme capable of editing mouse liver genome upon adenoviral delivery without detectable off-targets and reduced chromosomal translocations. Yet, its efficacy remains insufficient with non-viral delivery, a common challenge for many Cas9 orthologues. Here, we sought to redesign PsCas9 for in vivo editing using lipid nanoparticles. We solve the PsCas9 ribonucleoprotein structure with cryo-EM and characterize it biochemically, providing a basis for its rational engineering. Screening over numerous guide RNA and protein variants lead us to develop engineered PsCas9 (ePsCas9) with up to 20-fold increased activity across various targets and preserved safety advantages. We apply the same design principles to boost the activity of FnCas9, an enzyme phylogenetically relevant to PsCas9. Remarkably, a single administration of mRNA encoding ePsCas9 and its guide formulated with lipid nanoparticles results in high levels of editing in the Pcsk9 gene in mouse liver, a clinically relevant target for hypercholesterolemia treatment. Collectively, our findings introduce ePsCas9 as a highly efficient, and precise tool for therapeutic genome editing, in addition to the engineering strategy applicable to other Cas9 orthologues.},
  author       = {Degtev, Dmitrii and Bravo, Jack Peter Kelly and Emmanouilidi, Aikaterini and Zdravković, Aleksandar and Choong, Oi Kuan and Liz Touza, Julia and Selfjord, Niklas and Weisheit, Isabel and Francescatto, Margherita and Akcakaya, Pinar and Porritt, Michelle and Maresca, Marcello and Taylor, David and Sienski, Grzegorz},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles}},
  doi          = {10.1038/s41467-024-53418-8},
  volume       = {15},
  year         = {2024},
}

@misc{18579,
  abstract     = {Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. },
  author       = {Vega Zuniga, Tomas A and Sumser, Anton L and Symonova, Olga and Koppensteiner, Peter and Schmidt, Florian and Jösch, Maximilian A},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics}},
  doi          = {10.15479/AT:ISTA:18579},
  year         = {2024},
}

@article{18645,
  abstract     = {Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA ‘unwrapping’. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming.},
  author       = {Kobayashi, Wataru and Sappler, Anna H. and Bollschweiler, Daniel and Kümmecke, Maximilian and Basquin, Jérôme and Arslantas, Eda Nur and Ruangroengkulrith, Siwat and Hornberger, Renate and Duderstadt, Karl and Tachibana, Kikuë},
  issn         = {1545-9985},
  journal      = {Nature Structural & Molecular Biology},
  pages        = {757--766},
  publisher    = {Springer Nature},
  title        = {{Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition}},
  doi          = {10.1038/s41594-024-01239-0},
  volume       = {31},
  year         = {2024},
}

@inproceedings{18756,
  abstract     = {The evasive LWE assumption, proposed by Wee [Eurocrypt’22 Wee] for constructing a lattice-based optimal broadcast encryption, has shown to be a powerful assumption, adopted by subsequent works to construct advanced primitives ranging from ABE variants to obfuscation for null circuits. However, a closer look reveals significant differences among the precise assumption statements involved in different works, leading to the fundamental question of how these assumptions compare to each other. In this work, we initiate a more systematic study on evasive LWE assumptions:
(i) Based on the standard LWE assumption, we construct simple counterexamples against three private-coin evasive LWE variants, used in [Crypto’22 Tsabary, Asiacrypt’22 VWW, Crypto’23 ARYY] respectively, showing that these assumptions are unlikely to hold.

(ii) Based on existing evasive LWE variants and our counterexamples, we propose and define three classes of plausible evasive LWE assumptions, suitably capturing all existing variants for which we are not aware of non-obfuscation-based counterexamples.

(iii) We show that under our assumption formulations, the security proofs of [Asiacrypt’22 VWW] and [Crypto’23 ARYY] can be recovered, and we reason why the security proof of [Crypto’22 Tsabary] is also plausibly repairable using an appropriate evasive LWE assumption.},
  author       = {Brzuska, Chris and Ünal, Akin and Woo, Ivy K.Y.},
  booktitle    = {30th International Conference on the Theory and Application of Cryptology and Information Security},
  isbn         = {9789819608935},
  issn         = {1611-3349},
  location     = {Kolkata, India},
  pages        = {418--449},
  publisher    = {Springer Nature},
  title        = {{Evasive LWE assumptions: Definitions, classes, and counterexamples}},
  doi          = {10.1007/978-981-96-0894-2_14},
  volume       = {15487},
  year         = {2024},
}

@article{18867,
  abstract     = {In an accreting X-ray pulsar, a neutron star accretes matter from a companion star through an accretion disk. The magnetic field of the rotating neutron star disrupts the inner edge of the disk, funnelling the gas to flow onto the poles on its surface. Hercules X-1 is a prototypical persistent X-ray pulsar about 7 kpc from Earth. Its emission varies on three distinct timescales: the neutron star rotates every 1.2 s, it is eclipsed by its companion each 1.7 d, and the system exhibits a superorbital period of 35 d, which has remained stable since its discovery. Several lines of evidence point to the source of this variation as the precession of the accretion disk or that of the neutron star. Despite the many hints over the past 50 yr, the precession of the neutron star itself has yet not been confirmed or refuted. X-ray polarization measurements (probing the spin geometry of Her X-1) with the Imaging X-ray Polarimetry Explorer suggest that free precession of the neutron star crust sets the 35 d period; this has the important implication that its crust is somewhat asymmetric by a few parts per ten million.},
  author       = {Heyl, Jeremy and Doroshenko, Victor and González-Caniulef, Denis and Caiazzo, Ilaria and Poutanen, Juri and Mushtukov, Alexander and Tsygankov, Sergey S. and Kirmizibayrak, Demet and Bachetti, Matteo and Pavlov, George G. and Forsblom, Sofia V. and Malacaria, Christian and Suleimanov, Valery F. and Agudo, Iván and Antonelli, Lucio Angelo and Baldini, Luca and Baumgartner, Wayne H. and Bellazzini, Ronaldo and Bianchi, Stefano and Bongiorno, Stephen D. and Bonino, Raffaella and Brez, Alessandro and Bucciantini, Niccolò and Capitanio, Fiamma and Castellano, Simone and Cavazzuti, Elisabetta and Chen, Chien-Ting and Ciprini, Stefano and Costa, Enrico and De Rosa, Alessandra and Del Monte, Ettore and Di Gesu, Laura and Di Lalla, Niccolò and Di Marco, Alessandro and Donnarumma, Immacolata and Dovčiak, Michal and Ehlert, Steven R. and Enoto, Teruaki and Evangelista, Yuri and Fabiani, Sergio and Ferrazzoli, Riccardo and Garcia, Javier A. and Gunji, Shuichi and Hayashida, Kiyoshi and Iwakiri, Wataru and Jorstad, Svetlana G. and Kaaret, Philip and Karas, Vladimir and Kislat, Fabian and Kitaguchi, Takao and Kolodziejczak, Jeffery J. and Krawczynski, Henric and La Monaca, Fabio and Latronico, Luca and Liodakis, Ioannis and Maldera, Simone and Manfreda, Alberto and Marin, Frédéric and Marinucci, Andrea and Marscher, Alan P. and Marshall, Herman L. and Massaro, Francesco and Matt, Giorgio and Mitsuishi, Ikuyuki and Mizuno, Tsunefumi and Muleri, Fabio and Negro, Michela and Ng, C.-Y. and O’Dell, Stephen L. and Omodei, Nicola and Oppedisano, Chiara and Papitto, Alessandro and Peirson, Abel Lawrence and Perri, Matteo and Pesce-Rollins, Melissa and Petrucci, Pierre-Olivier and Pilia, Maura and Possenti, Andrea and Puccetti, Simonetta and Ramsey, Brian D. and Rankin, John and Ratheesh, Ajay and Roberts, Oliver J. and Romani, Roger W. and Sgrò, Carmelo and Slane, Patrick and Soffitta, Paolo and Spandre, Gloria and Swartz, Douglas A. and Tamagawa, Toru and Tavecchio, Fabrizio and Taverna, Roberto and Tawara, Yuzuru and Tennant, Allyn F. and Thomas, Nicholas E. and Tombesi, Francesco and Trois, Alessio and Turolla, Roberto and Vink, Jacco and Weisskopf, Martin C. and Wu, Kinwah and Xie, Fei and Zane, Silvia},
  issn         = {2397-3366},
  journal      = {Nature Astronomy},
  pages        = {1047--1053},
  publisher    = {Springer Nature},
  title        = {{Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization}},
  doi          = {10.1038/s41550-024-02295-8},
  volume       = {8},
  year         = {2024},
}

@article{18868,
  abstract     = {We develop two new highly efficient estimators to measure the polarization (Stokes parameters) in experiments that constrain the position angle of individual photons such as scattering and gas-pixel-detector polarimeters, and analyse in detail a previously proposed estimator. All three of these estimators are at least fifty percent more efficient on typical datasets than the standard estimator used in the field. We present analytic estimates of the variance of these estimators and numerical experiments to verify these estimates. Two of the three estimators can be calculated quickly and directly through summations over the measurements of individual photons.},
  author       = {Heyl, Jeremy and González-Caniulef, Denis and Caiazzo, Ilaria},
  issn         = {2565-6120},
  journal      = {The Open Journal of Astrophysics},
  publisher    = {Maynooth Academic Publishing},
  title        = {{Optimal summary statistics for X-ray polarization}},
  doi          = {10.33232/001c.117476},
  volume       = {7},
  year         = {2024},
}

@inproceedings{18998,
  abstract     = {Word embeddings represent language vocabularies as clouds of d-dimensional points. We investigate how information is conveyed by the general shape of these clouds, instead of representing the semantic meaning of each token. Specifically, we use the notion of persistent homology from topological data analysis (TDA) to measure the distances between language pairs from the shape of their unlabeled embeddings. These distances quantify the degree of non-isometry of the embeddings. To distinguish whether these differences are random training errors or capture real information about the languages, we use the computed distance matrices to construct language phylogenetic trees over 81 Indo-European languages. Careful evaluation shows that our reconstructed trees exhibit strong and statistically-significant similarities to the reference.},
  author       = {Draganov, Ondrej and Skiena, Steven},
  booktitle    = {Findings of the Association for Computational Linguistics: EMNLP 2024},
  location     = {Miami, FL, United States},
  pages        = {12080--12099},
  publisher    = {Association for Computational Linguistics},
  title        = {{The shape of word embeddings: Quantifying non-isometry with topological data analysis}},
  doi          = {10.18653/v1/2024.findings-emnlp.705},
  year         = {2024},
}