A key task in single-cell RNA-seq (scRNA-seq) data analysis is to accurately detect the number of cell types in the sample, which can be critical for downstream analyses such as cell type ...identification. Various scRNA-seq data clustering algorithms have been specifically designed to automatically estimate the number of cell types through optimising the number of clusters in a dataset. The lack of benchmark studies, however, complicates the choice of the methods.
We systematically benchmark a range of popular clustering algorithms on estimating the number of cell types in a variety of settings by sampling from the Tabula Muris data to create scRNA-seq datasets with a varying number of cell types, varying number of cells in each cell type, and different cell type proportions. The large number of datasets enables us to assess the performance of the algorithms, covering four broad categories of approaches, from various aspects using a panel of criteria. We further cross-compared the performance on datasets with high cell numbers using Tabula Muris and Tabula Sapiens data.
We identify the strengths and weaknesses of each method on multiple criteria including the deviation of estimation from the true number of cell types, variability of estimation, clustering concordance of cells to their predefined cell types, and running time and peak memory usage. We then summarise these results into a multi-aspect recommendation to the users. The proposed stability-based approach for estimating the number of cell types is implemented in an R package and is freely available from ( https://github.com/PYangLab/scCCESS ).
The effect of transport stress on blood metabolism, glycolytic potential, and meat quality in broilers was investigated. Arbor Acres chicks (n = 360, 1 d old, males) were randomly allotted to 1 of 5 ...treatments: unstressed control, 45-min (short-term) transport with 45-min (short-term) recovery, 45-min transport with 3-h (long-term) recovery; 3 h (long-term) transport with 45-min recovery, and 3-h transport with 3-h recovery. Each treatment consisted of 6 replicates with 12 birds each. On d 46, all birds (except the control group) were transported according to a designed protocol. Transport time affected plasma glucose level (P < 0.05) and glycogen level (P = 0.06) in breast muscle as well as the area (P < 0.01) and density (P < 0.01) of IIa fibers. Glucose concentration increased slightly during the first 45 min of transport and then decreased dramatically in the long-term transported broilers (P < 0.05). Long-term transport decreased the concentration of breast glycogen (P = 0.06) and affected the size of IIa fibers in tibialis anterior by decreasing the area (P < 0.01) with an increase in density (P < 0.01). However, a long-term recovery after transport contributed to the homeostasis of blood corticosterone (CORT, P = 0.05) and low levels of glycogen (P < 0.05), lactate (P < 0.01), and glycolytic potential (P < 0.01) in thigh muscles. Interactions existed between transport and recovery time on area (P < 0.05) and density (P < 0.01) of IIa fibers. Furthermore, plasma nonesterified fatty acids increased significantly in the 3-h transport with 3-h recovery group (P < 0.05) in comparison with the control. These results suggested that transport induced the release of plasma CORT and glycopenia, which affected the contractive status of muscle fibers by changing their area and density, and enhanced glycolysis and even lipolysis. A long-term recovery after transport was beneficial in lowering plasma CORT levels and reducing muscle glycolysis, which might improve broiler meat quality.
Abstract
A recent focus of quantum spin liquid (QSL) studies is how disorder/randomness in a QSL candidate affects its true magnetic ground state. The ultimate question is whether the QSL survives ...disorder or the disorder leads to a “spin-liquid-like” state, such as the proposed random-singlet (RS) state. Since disorder is a standard feature of most QSL candidates, this question represents a major challenge for QSL candidates. YbMgGaO
4
, a triangular lattice antiferromagnet with effective spin-1/2 Yb
3+
ions, is an ideal system to address this question, since it shows no long-range magnetic ordering with Mg/Ga site disorder. Despite the intensive study, it remains unresolved as to whether YbMgGaO
4
is a QSL or in the RS state. Here, through ultralow-temperature thermal conductivity and magnetic torque measurements, plus specific heat and DC magnetization data, we observed a residual
κ
0
/
T
term and series of quantum spin state transitions in the zero temperature limit for YbMgGaO
4
. These observations strongly suggest that a QSL state with itinerant excitations and quantum spin fluctuations survives disorder in YbMgGaO
4
.
Skeletal muscle stem cells, also called Satellite Cells (SCs), are actively maintained in quiescence but can activate quickly upon extrinsic stimuli. However, the mechanisms of how quiescent SCs ...(QSCs) activate swiftly remain elusive. Here, using a whole mouse perfusion fixation approach to obtain bona fide QSCs, we identify massive proteomic changes during the quiescence-to-activation transition in pathways such as chromatin maintenance, metabolism, transcription, and translation. Discordant correlation of transcriptomic and proteomic changes reveals potential translational regulation upon SC activation. Importantly, we show Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1), post-transcriptionally affects protein translation during SC activation by binding to the 3' UTRs of different transcripts. We demonstrate phosphorylation-dependent CPEB1 promoted Myod1 protein synthesis by binding to the cytoplasmic polyadenylation elements (CPEs) within its 3' UTRs to regulate SC activation and muscle regeneration. Our study characterizes CPEB1 as a key regulator to reprogram the translational landscape directing SC activation and subsequent proliferation.
Numerous historical works have mentioned that trade routes were to blame for the spread of plague in European history, yet this relationship has never been tested by quantitative evidence. Here, we ...resolve the hypothetical role of trade routes through statistical analysis on the geo-referenced major trade routes in the early modern period and the 6,656 geo-referenced plague outbreak records in AD1347-1760. Ordinary Least Square (OLS) estimation results show that major trade routes played a dominant role in spreading plague in pre-industrial Europe. Furthermore, the negative correlation between plague outbreaks and their distance from major trade ports indicates the absence of a permanent plague focus in the inland areas of Europe. Major trade routes decided the major plague outbreak hotspots, while navigable rivers determined the geographic pattern of sporadic plague cases. A case study in Germany indicates that plague penetrated further into Europe through the local trade route network. Based on our findings, we propose the mechanism of plague transmission in historical Europe, which is imperative in demonstrating how pandemics were spread in recent human history.
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