bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics
Authors: Choi Sam B. , Muñoz-LLancao Pablo , Chiara Manzini M. , Nemes Peter 
Published: August 2021

ABSTRACTMeasurement of broad types of proteins from a small number of cells to single cells would help to better understand the nervous system but requires significant leaps in high-resolution mass spectrometry (HRMS) sensitivity. Microanalytical capillary electrophoresis electrospray ionization (μCE-ESI) offers a path to ultrasensitive proteomics by integrating scalability with sensitivity. We report here a data acquisition strategy that expands the detectable and quantifiable proteome in trace amounts of digests using μCE-ESI-HRMS. Data-dependent acquisition (DDA) was programmed to progressively exclude high-intensity peptide signals during repeated measurements. These nested experiments formed rungs of our “DDA ladder.” The method was tested for replicates analyzing ~500 pg of protein digest from cultured hippocampal (primary) neurons (mouse), which estimates to the total amount of protein from a single neuron. Analysis of net amounts approximating to ~10 neurons identified 428 nonredundant proteins (415 quantified), an ~35% increase over traditional DDA. The identified proteins were enriched in neuronal marker genes and molecular pathways of neurobiological importance. The DDA ladder deepens the detectable proteome from trace amounts of proteins, expanding the analytical toolbox of neuroscience.
Bi-modal Variational Autoencoders for Metabolite Identification Using Tandem Mass Spectrometry
Authors: Kutuzova Svetlana , Igel Christian , Nielsen Mads , McCloskey Douglas 
Published: August 2021

AbstractA grand challenge of analytical chemistry is the identification of unknown molecules based on tandem mass spectrometry (MS/MS) spectra. Current metabolite annotation approaches are often manual or partially automated, and commonly rely on a spectral database to search from or train machine learning classifiers on. Unfortunately, spectral databases are often instrument specific and incomplete due to the limited availability of compound standards or a molecular database, which limits the ability of methods utilizing them to predict novel molecule structures. We describe a generative modeling approach that can leverage the vast amount of unpaired and/or unlabeled molecule structures and MS/MS spectra to learn general rules for synthesizing molecule structures and MS/MS spectra. The approach is based on recent work using semi-supervised deep variational autoencoders to learn joint latent representations of multiple and complex modalities. We show that adding molecule structures with no spectra to the training set improves the prediction quality on spectra from a structure disjoint dataset of new molecules, which is not possible using bi-modal supervised approaches. The described methodology provides a demonstration and framework for how recent advances in semi-supervised machine learning can be applied to overcome bottlenecks in missing annotations and noisy data to tackle unaddressed problems in the life sciences where large volumes of data are available.
Principles of sensor-effector organization in six-transmembrane ion channels
Authors: Dou Alex , Kang Po Wei , Hou Panpan , Zaydman Mark A. , Zheng Jie , Jegla Timothy , Cui Jianmin 
Published: August 2021

AbstractReceptor proteins sense stimuli and generate downstream signals via sensor and effector domains. Presently, the structural constraints on sensor-effector organization across receptor protein superfamilies are not clear. Here, we perform statistical coupling analysis (SCA) on the transient receptor potential (TRP) and voltage-gated potassium (Kv) ion channel superfamilies to characterize the networks of coevolving residues, or protein sectors, that mediate their receptor functions. Comparisons to structural and functional studies reveal a conserved “core” sector that extends from the pore and mediates effector functions, including pore gating and sensor-pore coupling, while sensors correspond to family-specific “accessory” sectors and localize according to three principles: Sensors (1) may emerge in any region with access to the core, (2) must maintain contact with the core, and (3) must preserve the integrity of the core. This sensor-core architecture may represent a conserved and generalizable paradigm for the structure-function relationships underlying the evolution of receptor proteins.
A generic hidden Markov model for multi-parent populations
Authors: Broman Karl W. 
Published: August 2021

AbstractA common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a probability model for the pattern of founder alleles along chromosomes, including the relative frequency of founder alleles and the probability of exchanges among them, which depend on a model for meiotic recombination and on the mating design for the population. While the precise experimental design used to generate the population may be used to derive a precise characterization of the model for exchanges among founder alleles, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly-available data on Diversity Outbred and Collaborative Cross mice
Influence of internal seiche dynamics on vertical movement of fish
Authors: Jarić Ivan , Říha Milan , Souza Allan T. , Rabaneda-Bueno Rubén , Děd Vilem , Gjelland Karl Ø. , Baktoft Henrik , Čech Martin , Blabolil Petr , Holubová Michaela , Jůza Tomáš , Muška Milan , Sajdlová Zuzana , Šmejkal Marek , Vejřík Lukáš , Vejříková Ivana , Peterka Jiří 
Published: August 2021

AbstractInternal seiches are common in stratified lakes, with significant effects on stratification patterns, hydrodynamics and vertical nutrient transport. In particular, seiche can change the vertical distribution of the thermocline and the cold hypolimnetic and warm epilimnetic water masses by several meters on a timescale of a few hours. The results are rapid and strong changes in temperature profiles and oxygen availability that can have profound effects on vagrant and sessile organisms. Internal seiche dynamics could therefore affect fish communities directly through physiological stress and elevated mortality, and indirectly through prey distribution.The aim of this study was to analyze the effects of internal seiche dynamics on lacustrine fish behaviour, and to characterize fish reaction patterns, with the main focus on vertical movement of fish in the vicinity of a shifting thermocline, and avoidance of cold hypolimnetic water.The analysis was based on acoustic telemetry data from Lake Milada, a post-mining lake in the Czech Republic, with a total of 55 tracked individuals of four species: northern pike (Esox lucius), wels catfish (Silurus glanis), tench (Tinca tinca) and rudd (Scardinius erythropthalmus).The effects of seiche dynamics on the four species studied were weak but significant during the day, but only on rudd during the night. Upward seiche produced stronger reactions in fish than downward seiche, and the effects were manifested only during the strongest seiche events.Thermocline shifting during seiche events may induce a transient reduction in habitat for seiche-reacting species, thus potentially affecting predation and other inter- and intra-specific interactions, and probably affecting fish community dynamics.Graphical abstract
IL-13 promotes recovery fromC. difficileinfection
Authors: Donlan A.N. , Leslie J.L. , Simpson M.E. , Petri W.A. , Allen J.E. , Petri W.A. 
Published: August 2021

AbstractClostridioides difficileinfection (CDI) is the leading hospital-acquired infection in North America. We have previously discovered that antibiotic disruption of the gut microbiota decreases intestinal IL-33 and IL-25 and increases susceptibility to CDI. We further found that IL-33 promotes protection through type 2 Innate Lymphoid Cells (ILC2s), which produce IL-13. However, the contribution of IL-13 to disease has never been explored. We found that administration of IL-13 protected, and anti-IL-13 exacerbated CDI as measured by weight loss and clinical score, particularly during disease resolution. Additionally, concordant with IL-13 being important for M2 macrophage polarization, we saw a decrease in M2 macrophages (CD11B+CD64+CD206+) cells following neutralization of IL-13. We also observed monocyte accumulation as early as day three post-infection following IL-13 neutralization, suggesting IL-13 may be directly or indirectly important for their recruitment or transition into macrophages. Neutralization of the decoy receptor IL-13Rα2 resulted in protection from disease, likely through increased available endogenous IL-13. Our data highlight the protective role of IL-13 in promoting recovery from CDI and the association of poor responses with a dysregulated monocytemacrophage compartment. These results increase our understanding of type 2 immunity in CDI and may have implications for treating disease in patients.
Endothelial Semaphorin 3fb regulates Vegf pathway-mediated angiogenic sprouting
Authors: Watterston Charlene , Halabi Rami , McFarlane Sarah , Childs Sarah J 
Published: August 2021

AbstractVessel growth integrates diverse extrinsic signals with intrinsic signaling cascades to coordinate cell migration and sprouting morphogenesis. The pro-angiogenic effects of Vascular Endothelial Growth Factor (VEGF) are carefully controlled during sprouting to generate an efficiently patterned vascular network. We identify crosstalk between VEGF signaling and that of the secreted ligand Semaphorin 3fb (Sema3fb), one of two zebrafish paralogs of mammalian Sema3F. Thesema3fbgene is expressed by endothelial cells in actively sprouting vessels. Loss ofsema3fbresults in abnormally wide and stunted intersegmental vessel artery sprouts. Although the sprouts initiate at the correct developmental time, they have a reduced migration speed. These sprouts have persistent filopodia and abnormally spaced nuclei suggesting dysregulated control of actin assembly. sema3fbmutants show simultaneously higher expression of pro-angiogenic (VEGF receptor 2(vegfr2)anddelta-like 4(dll4))and anti-angiogenic (solubleVEGF receptor 1 (svegfr1)/soluble Fms Related Receptor Tyrosine Kinase 1 (sflt1))pathway components. We show increased phospho-ERK staining in migrating angioblasts, consistent with enhanced Vegf activity. Reducing Vegfr2 kinase activity insema3fbmutants rescues angiogenic sprouting. Our data suggest that Sema3fb plays a critical role in promoting endothelial sprouting through modulating the VEGF signaling pathway, acting as an autocrine cue that modulates intrinsic growth factor signaling.Author summaryTo supply tissues with essential oxygen and nutrients, blood vessel development is carefully orchestrated by positive ‘go’ and negative ‘stop’ growth signals as well as directional cues to shape patterning. Semaphorin proteins are named after the ‘Semaphore’ railway signaling system that directed trains along the appropriate tracks. Our work highlights the role of the Semaphorin 3fb protein in providing a pro-growth signal to developing vessels. Semaphorin 3fb is both produced by, and acts on the precursors of blood vessels as they migrate, a process known as autocrine control. We find that losing Semaphorin 3fb leads to stalled blood vessel growth, indicating it normally acts as a positive signal. It acts via modulating the VEGF growth factor signaling pathway that in turn, controls the migration process. We propose that Semaphorin3b fine-tunes vessel growth, thus ensuring a properly patterned network develops.
De novoevolution of macroscopic multicellularity
Authors: Bozdag G. Ozan , Zamani-Dahaj Seyed Alireza , Day Thomas C. , Kahn Penelope C. , Burnetti Anthony J. , Lac Dung T. , Tong Kai , Conlin Peter L. , Balwani Aishwarya H. , Dyer Eva L. , Yunker Peter J. , Ratcliff William C. 
Published: August 2021

AbstractWhile early multicellular lineages necessarily started out as relatively simple groups of cells, little is known about how they became Darwinian entities capable of open-ended multicellular adaptation1,2. To explore this, we initiated the Multicellularity Long Term Evolution Experiment (MuLTEE), selecting for larger group size in the snowflake yeast (Saccharomyces cerevisiae) model system. Given the historical importance of oxygen limitation3, our ongoing experiment consists of three metabolic treatments4: anaerobic, obligately aerobic, and mixotrophic yeast. After 600 rounds of selection, snowflake yeast in the anaerobic treatment evolved to be macroscopic, becoming ~2·104times larger (~mm scale) and ~104-fold more biophysically tough, while retaining a clonal multicellular life cycle. They accomplished this through sustained biophysical adaptation, evolving increasingly elongate cells that initially reduced the strain of cellular packing, then facilitated branch entanglements that enabled groups of cells to stay together even after many cellular bonds fracture. In contrast, snowflake yeast competing for low oxygen remained microscopic, evolving to be just ~6-fold larger, underscoring the critical role of oxygen levels in the evolution of multicellular size. Taken together, this work provides unique insight into an ongoing evolutionary transition in individuality, showing how simple groups of cells overcome fundamental biophysical limitations via gradual, yet sustained, multicellular adaptation.
Loss of BCL-3 sensitises colorectal cancer cells to DNA damage, revealing a role for BCL-3 in double strand break repair by homologous recombination
Authors: Parker Christopher , Chambers Adam C , Flanagan Dustin , Collard Tracey J , Ngo Greg , Baird Duncan M , Timms Penny , Morgan Rhys G , Sansom Owen , Williams Ann C 
Published: August 2021

AbstractObjectiveThe proto-oncogene BCL-3 is upregulated in a subset of colorectal cancers (CRC) and increased expression of the gene correlates with poor patient prognosis. The aim is to investigate whether inhibiting BCL-3 can increase the response to DNA damage in CRC.DesignThe function of BCL-3 in DNA damage response was studied in vitro using siRNA and CRISPR-Cas9 genome editing and in vivo using Bcl3-/- mice. DNA damage induced by γ-irradiation and/or cisplatin was quantified using H2AX and RAD51 foci, repair pathways investigated using HR/NHEJ assays and treatment with the PARP inhibitor olaparib.ResultSuppression of BCL-3 increases double strand break number and decreases homologous recombination in CRC cells, supported by reduced RAD51 foci number and increased sensitivity to PARP inhibition. Importantly, a similar phenotype is seen in Bcl3-/- mice, where the intestinal crypts of these mice exhibit sensitivity to DNA damage and a greater number of double strand breaks compared to wild type mice. Furthermore Apc.Krasmutant x Bcl3-/- mice exhibit increased DNA damage and reduced RAD51+ cells compared to their wild type counterparts when treated with cisplatin.ConclusionThis work identifies BCL-3 as a regulator of the cellular response to DNA damage and suggests that elevated BCL-3 expression could increase resistance of tumour cells to DNA damaging agents including radiotherapy. These findings offer a rationale for targeting BCL-3 in CRC as an adjuvant to conventional therapies and suggest that BCL-3 expression in tumours could be a useful biomarker in stratification of rectal cancer patients for neo-adjuvant chemoradiotherapy.
Single particle cryo-EM structure of the outer hair cell motor protein prestin
Authors: Butan Carmen , Song Qiang , Bai Jun-Ping , Tan Winston J. T. , Navaratnam Dhasakumar , Santos-Sacchi Joseph 
Published: August 2021

AbstractThe mammalian outer hair cell (OHC) protein prestin (Slc26a5), a member of the solute carrier 26 (Slc26) family of membrane proteins, differs from other members of the family owing to its unique piezoelectric-like property that drives OHC electromotility. OHCs require prestin for cochlear amplification, a process that enhances mammalian hearing. Despite substantial biophysical characterization, the mechanistic basis for the prestin’s electro-mechanical behavior is not fully understood. To gain insight into such behavior, we have used cryo-electron microscopy at subnanometer resolution (overall resolution of 4.0 Å) to investigate the three-dimensional structure of prestin from gerbil (Meriones unguiculatus). Our studies show that prestin dimerizes with a 3D architecture strikingly similar to the dimeric conformation observed in the Slc26a9 anion transporter in an inside open/intermediate state, which we infer, based on patch-clamp recordings, to reflect the contracted state of prestin. The structure shows two well-separated transmembrane (TM) subunits and two cytoplasmic sulfate transporter and anti-sigma factor antagonist (STAS) domains forming a swapped dimer. The dimerization interface is defined by interactions between the domain-swapped STAS dimer and the transmembrane domains of the opposing half unit, further strengthened by an antiparallel beta-strand at its N terminus. The structure also shows that each one of its two transmembrane subunits consists of 14 transmembrane segments organized in two inverted 7-segment repeats with a topology that was first observed in the structure of bacterial symporter UraA (Lu F, et al., Nature 472, 2011). Finally, the solved anion binding site structural features of prestin are quite similar to that of SLC26a9 and other family members. Despite this similarity, we find that SLC26a9 lacks the characteristic displacement currents (or NonLinear Capacitance(NLC)) found with prestin, and we show that mutation of prestin’s Cl- binding site removes salicylate competition with anions in the face of normal NLC, thus refuting the yet accepted extrinsic voltage sensor hypothesis and any associated transport-like requirements for voltage-driven electromotility.
The CD8+ T cell landscape of human brain metastases
Authors: Sudmeier Lisa J. , Hoang Kimberly B. , Nduom Edjah K. , Wieland Andreas , Neill Stewart G. , Schniederjan Matthew J. , Ramalingam Suresh S. , Olson Jeffrey J. , Ahmed Rafi , Hudson William H. 
Published: August 2021

AbstractDespite improved outcomes with checkpoint blockade immunotherapy, patients with brain metastases have the worst prognosis among patients with metastatic cancer. Immune checkpoint blockade agents target inhibitory receptors, such as PD-1, on exhausted CD8+ T cells to restore their anti-cancer function. Many patients, however, either do not respond or progress after an initial response to immune checkpoint blockade, and distant intracranial failure is common despite excellent options for local treatment of brain metastasis. To develop more effective therapeutic strategies for the treatment of brain metastases, an understanding of the phenotype of brain metastasis-infiltrating CD8+ T cells is essential. Here we performed a detailed characterization of the CD8+ T cells contained in brain metastases. Brain metastases were densely infiltrated by CD8+ T cells; blood contamination of tumor samples was rare. Compared to patient-matched circulating cells, brain metastasis-infiltrating CD8+ T cells had a distinct phenotype characterized by more frequent expression of PD-1, with subpopulations defined by expression of additional co-inhibitory molecules and the residence marker CD69. Single cell RNA-sequencing identified four phenotypic subpopulations within brain metastasis-infiltrating PD-1+ CD8+ T cells. Two of these populations — a terminally-differentiated and a dividing population — were characterized by high expression of co-inhibitory molecules and lacked expression of progenitor markers such as TCF-1. There was significant T cell receptor (TCR) overlap between the terminally-differentiated and dividing populations, suggesting that the dividing cells give rise to the terminally-differentiated cells. There was minimal TCR overlap between these two populations and other brain metastasis-infiltrating PD-1+ CD8+ T cells. T cell clones from brain metastasis-infiltrating CD8+ T cells were rare in circulation, particularly clones from the terminally-differentiated and dividing populations. We systematically identified bystander CD8+ T cells specific for microbial antigens; these cells infiltrated brain metastases and expressed genes shared with exhausted progenitor CD8+ T cells, such as TCF7 and IL7R. We performed spatial transcriptomics on brain metastases and used a novel method to obtain TCR sequences from spatial transcriptomics data. These data revealed distinct niches within the TME defined by their gene expression patterns and cytokine profiles. Terminally-differentiated CD8+ T cells preferentially occupied niches within the tumor parenchyma. Together, our results show that antigen-specificity restricts the spatial localization, phenotypic states, and differentiation pathways available to CD8+ T cells within the brain metastasis TME.
Flexible recruitments of fundamental muscle synergies in the trunk and lower limbs for highly variable movements and postures
Authors: Saito Hiroki , Yokoyama Hikaru , Sasaki Atsushi , Kato Tatsuya , Nakazawa Kimitaka 
Published: August 2021

AbstractThe extent to which muscle synergies represent the neural control of human behavior remains unknown. Here, we tested whether certain sets of muscle synergies that are fundamentally necessary across behaviors exist. We measured the electromyographic activities of 26 muscles including bilateral trunk and lower limb muscles during 24 locomotion, dynamic and static stability tasks, and extracted the muscle synergies using non-negative matrix factorization. Our results showed that 13 muscle synergies that may have unique functional roles accounted for almost all 24 tasks by combinations of single and/or merging of synergies. Therefore, our results may support the notion of the low dimensionality in motor outputs, in which the central nervous system flexibly recruits fundamental muscle synergies to execute diverse human behaviors. Further studies using manipulations of the central nervous system and/or neural recording are required the neural representation with such fundamental components of muscle synergies.