Miracle-dz/UniFAR-FTUs huggingface dataset:
Explorations and Exploitation for Parity-based RAIDs with Ultra-fast SSDs

Following a conventional design principle that pays more fast-CPU-cycles for fewer slow-I/Os, popular software storage architecture Linux Multiple-Disk (MD) for parity-based RAID (e.g., RAID5 and RAID6) assigns one or more centralized worker threads to efficiently process all user requests based on multi-stage asynchronous control and global data structures, successfully exploiting characteristics of slow devices, e.g., Hard Disk Drives (HDDs). However, we observe that, with high-performance NVMe-based Solid State Drives (SSDs), even the recently added multi-worker processing mode in MD achieves only limited performance gain because of the severe lock contentions under intensive write workloads. In this paper, we propose a novel stripe-threaded RAID architecture, StRAID, assigning a dedicated worker thread for each stripe-write (one-for-one model) to sufficiently exploit high parallelism inherent among RAID stripes, multi-core processors, and SSDs. For the notoriously performance-punishing partial-stripe writes that induce extra read and write I/Os, StRAID presents a two-stage stripe write mechanism and a two-dimensional multi-log SSD buffer. All writes first are opportunistically batched in memory, and then are written into the primary RAID for aggregated full-stripe writes or conditionally redirected to the buffer for partial-stripe writes. These buffered data are strategically reclaimed to the primary RAID. We evaluate a StRAID prototype with a variety of benchmarks and real-world traces. StRAID is demonstrated to outperform MD by up to 5.8 times in write throughput.
MemPerf: Profiling Allocator-Induced Performance Slowdowns

The memory allocator plays a key role in the performance of applications, but none of the existing profilers can pinpoint performance slowdowns caused by a memory allocator. Consequently, programmers may spend time improving application code incorrectly or unnecessarily, achieving low or no performance improvement. This paper designs the first profiler—MemPerf—to identify allocator-induced performance slowdowns without comparing against another allocator. Based on the key observation that an allocator may impact the whole life-cycle of heap objects, including the accesses (or uses) of these objects, MemPerf proposes a life-cycle based detection to identify slowdowns caused by slow memory management operations and slow accesses separately. For the prior one, MemPerf proposes a thread-aware and type-aware performance modeling to identify slow management operations. For slow memory accesses, MemPerf utilizes a top-down approach to identify all possible reasons for slow memory accesses introduced by the allocator, mainly due to cache and TLB misses, and further proposes a unified method to identify them correctly and efficiently. Based on our extensive evaluation, MemPerf reports 98% medium and large allocator-reduced slowdowns (larger than 5%) correctly without reporting any false positives. MemPerf also pinpoints multiple known and unknown design issues in widely-used allocators.
A Calculus of Delayed Reductions

We introduce the Calculus of Delayed Reduction (cdr), that expresses that redexes can only be contracted when brought to the right position in a term, and will show that Call by Name or Value (cbn, cbv) reduction for the λ -calculus can be modelled through reduction in cdr, and that the cbn fragment of the -calculus can model reduction in cdr. cdr is a Call by Push Value calculus (cbpv) in that it separates terms in computations and values, with their corresponding types. Some simulation results were already achieved by others for cbpv, but only up to equality for cbv; for cbn past results are rather weak. In order to achieve a single-step reduction respecting mapping for the cbn λ -calculus, we allow forcing only for variables, thunking only for computations that are not forced variables, and change the nature of term substitution, and abolish the U-reduction rule. We will show that, by changing the standard interpretation, we can achieve a reduction-respecting mapping for the cbv λ -calculus as well. Moreover, these changes make it possible to establish a strong relation between cdr and , allowing to simulate cdr reduction in , and preserving assignable types.
Message Chains for Distributed System Verification

Verification of asynchronous distributed programs is challenging due to the need to reason about numerous control paths resulting from the myriad interleaving of messages and failures. In this paper, we propose an automated bookkeeping method based on message chains. Message chains reveal structure in asynchronous distributed system executions and can help programmers verify their systems at the message passing level of abstraction. To evaluate our contributions empirically we build a verification prototype for the P programming language that integrates message chains. We use it to verify 16 benchmarks from related work, one new benchmark that exemplifies the kinds of systems our method focuses on, and two industrial benchmarks. We find that message chains are able to simplify existing proofs and our prototype performs comparably to existing work in terms of runtime. We extend our work with support for specification mining and find that message chains provide enough structure to allow existing learning and program synthesis tools to automatically infer meaningful specifications using only execution examples.
Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists

Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in-situ expression maps of hundreds of genes. We exploit direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high throughput and large multiplexing. We validate the method across a number of species, and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to highthroughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands

With the great progress on determining protein structures over the last decade comes a renewed appreciation that structures must be combined with dynamics and energetics to understand function. Fluorescence spectroscopy, specifically Förster resonance energy transfer (FRET), provides a great window into dynamics and energetics due to its application at physiological temperatures and ability to measure dynamics on the ångström scale. We have recently advanced transition metal FRET (tmFRET) to study allosteric regulation of maltose binding protein and have reported measurements of maltose- dependent distance changes with an accuracy of ∼1.5 Å. When paired with the noncanonical amino acid Acd as a donor, our previous tmFRET acceptors were useful over a working distance of 10 Å to 20 Å. Here, we use cysteine-reactive bipyridyl and phenanthroline compounds as chelators for Fe2+ and Ru2+ to produce novel tmFRET acceptors to expand the working distance to as long as 50 Å, while preserving our ability to resolve even small maltose-dependent changes in distance. We compare our measured FRET efficiencies to predictions based on models using rotameric ensembles of the donors and acceptors to demonstrate that steady-state measurements of tmFRET with our new probes have unprecedented ability to measure conformational rearrangements under physiological conditions. STATEMENT OF SIGNIFICANCE In this work, we expand the working distance of transition metal ion Förster Resonance Energy Transfer (tmFRET) to allow the measurement of donor-acceptor distances from 10 Å to 50 Å. We develop new cysteine-reactive bipyridyl- and phenanthroline-based ligands for Cu2+, Fe2+, and Ru2+ and examine their ability to resolve small ligand-dependent distance changes in maltose binding protein. We extend these studies using pulsed electron paramagnetic resonance spectroscopy to demonstrate the high accuracy of tmFRET for studying protein allostery.
Interaction of GAT1 with sodium ions: from efficient recruitment to stabilisation of substrate and conformation

The human GABA transporter (GAT1) is a membrane transporter that mediates the reuptake of the neurotransmitter GABA from the synaptic cleft into neurons and glial cells. Dysregulation of the transport cycle has been associated with epilepsy and neuropsychiatric disorders, highlighting the crucial role of the transporter in maintaining homeostasis of brain GABA levels. GAT1 is a secondary active transporter that couples the movement of substrate to the simultaneous transport of sodium and chloride ions along their electrochemical gradients. Using MD simulations, we identified a novel sodium recruiting site at the entrance to the outer vestibule, which attracts positively charged ions and increases the local sodium concentration, thereby indirectly increasing sodium affinity. Mutations of negatively charged residues at the recruiting site slowed the binding kinetics, while experimental data revealed a change in sodium dependency of GABA uptake and a reduction of sodium affinity. Simulation showed that sodium displays a higher affinity for the sodium binding site NA2, which plays a role in the stabilisation of the outward-open conformation. We directly show that the presence of a sodium ion bound to NA2 increases the stability of the closed inner gate and restrains motions of TM5. We find that sodium is only weakly bound to NA1 in the absence of GABA, while the presence of the substrate strengthens the interaction due to the completed ion coordinating shell, explaining cooperativity of between GABA and sodium.
NBS-SNI, an extension of the network-based statistic: Abnormal functional connections between important structural actors

Elucidating the coupling between the structure and the function of the brain and its development across maturation has attracted a lot of interest in the field of network neuroscience in the last fifteen years. Mounting evidence support the hypothesis that the onset of certain brain disorders is linked with the interplay between the structural architecture of the brain and its functional processes, often accompanied with unusual connectivity features. This paper introduces a method called the Network-based statistic–simultaneous node investigation (NBS-SNI) that integrates both representations into a single framework, and identifies connectivity abnormalities in case-control studies. With this method, significance is given to the properties of the nodes, as well as to their connections. This approach builds on the well-established Network-based statistic (NBS) proposed in 2010. We uncover and identify the regimes in which NBS-SNI offers a gain in statistical resolution to identify a contrast of interest using synthetic data. We also apply our method on two real case-control studies, one consisting of individuals diagnosed with autism and the other consisting of individuals diagnosed with early-psychosis. Using NBS-SNI and node properties such as the closeness centrality and local information dimension, we found hypo and hyperconnected subnetworks and show that our method can offer a 9 percentage points gain in prediction power over the standard NBS. AUTHOR SUMMARY We propose an extension to the well-known Network-based statistic (NBS) dubbed NBS-SNI, where the extension SNI stands for simultaneous node investigation. The goal of this approach is to integrate nodal properties such as centrality measures into the statistical network-based framework of NBS to probe for abnormal connectivity between important nodes in case-control studies. We expose the regimes where NBS-SNI offers greater statistical resolution for identifying a contrast of interest using synthetic data and test the approach with a real autism-healthy dataset which contains both the structural (DTI) and functional (fMRI) brain networks of each individual. We also tested our approach on a second dataset of individuals diagnosed with early-psychosis. In the second case, our framework is supplemented by incorporating the anatomically derived measures of intrinsic curvature index and gray matter volume directly as a node property, rather than the structural networks, thereby illustrating the versatility of our approach.
A methoxylated flavone from Artemisia afra kills Mycobacterium tuberculosis

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), is a deadly and debilitating disease globally affecting millions annually. Emerging drug-resistant Mtb strains endanger the efficacy of the current combination therapies employed to treat tuberculosis; therefore, there is an urgent need to develop novel drugs to combat this disease. Artemisia afra is used traditionally in southern Africa to treat malaria and recently has shown anti tuberculosis activity. This genus synthesizes a prodigious number of phytochemicals, many of which have demonstrated human health effects. Transcriptomic analysis revealed that A. afra exerts different effects on Mtb compared to A. annua or the well-known antimalarial artemisinin, suggesting other phytochemicals present in A. afra with unique modes of action. A biochemometric study of A. afra resulted in the isolation of a methoxylated flavone (1), which displayed considerable activity against Mtb strain mc26230. Compound 1 had an MIC of 312.5 μg/mL and yielded no viable colonies after 6 days of treatment. In addition, 1 was effective in killing hypoxic Mtb cultures, with no viable cultures after 2 days of treatment. This suggested that A. afra is a source of potentially powerful anti-Mtb phytochemicals with novel mechanisms of action.
Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity

The defining characteristic of ductal carcinoma in situ (DCIS) is neoplastic epithelial growth within a duct surrounded by an intact basement membrane (BM) whereas invasive breast cancer (IBC) is defined by tumor cell extravasation associated with loss of the intact BM. To understand mechanisms underlying the development of DCIS, we performed single-cell RNA-sequencing (scRNA-seq) on DCIS and synchronous normal tissue. We identified neoplastic epithelial cells by inferring copy number variations from RNA expression and then classified cells using previously defined phenotypes from normal human breast epithelium. We identify an increase in luminal cells in DCIS and a concomitant decrease in basal cells, which are a significant source of BM gene expression. We hypothesize that the reduction of the relative abundance of basal cells reduces the integrity of the BM that can result in the invasive phenotype.
Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples

Data independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be easily optimised to minimise the occurrence of false positives across different samples. Using an immunological infection model system to demonstrate the impact of adjusting search settings we analysed mouse macrophages and compared their proteome to macrophages spiked with Candida albicans. This experimental system enabled the identification of ‘false positives’ since Candida albicans peptides and proteins should not be present in the mouse only samples. We show that adjusting the search parameters reduced ‘false positive’ identifications by 89% at the peptide and protein level, thereby considerably increasing the quality of the data. We also show that these optimised parameters incur a moderate cost, only reducing the overall number of ‘true positive’ identifications across each biological replicate by <6.7% at both the peptide and protein level. We believe the value of our updated search parameters extends beyond a two-organism analysis and would be of great value to any DIA experiment analysing heterogenous populations of cell types or tissues.
Rapid generation of single-insertion transgenics by Tol2 transposition in zebrafish

The Tol2 transposable element is the most widely used transgenesis tool in zebrafish. However, its high activity almost always leads to multiple unlinked integrations of the transgenic cassette in F1 fish. Each of these transgenes is susceptible to position effects from surrounding regulatory landscape, which can lead to altered expression and, consequently, activity. Scientists therefore must strike a balance between the need to maximize reproducibility by establishing single-insertion transgenic lines and the need to complete experiments within a reasonable timeframe. In this article, we introduce a simple competitive dilution strategy for rapid generation of single-insertion transgenics. By using cry:BFP reporter plasmid as a competitor, we achieved a nearly fourfold reduction in the number of the transgene of interest (TgOI) integrations while simultaneously increasing the proportion of single-insertion F1 generation transgenics to over 50%. We also observed variations in TgOI expression among independent single-insertion transgenics, highlighting that the commonly used ubiquitous ubb promoter is susceptible to position effects. Wide application of our competitive dilution strategy will save time, reduce animal usage, and improve reproducibility of zebrafish research. Summary Competitive dilution of Tol2 transgenesis vectors facilitates isolation of single-insertion transgenic zebrafish lines in the F1 generation, reducing animal usage, improving reproducibility, and saving time.
Defining the mechanism of galectin-3-mediated TGF-β1 activation and its role in lung fibrosis

Integrin-mediated activation of the pro-fibrotic mediator transforming growth factor-β1 (TGF-β1), plays a critical role in idiopathic pulmonary fibrosis (IPF) pathogenesis. Galectin-3 is believed to contribute to the pathological wound healing seen in IPF individuals, although its mechanism of action is not precisely defined. We hypothesised that galectin-3 potentiates TGF-β1 activation and/or signaling in the lung to promote fibrogenesis. We show that galectin-3 induces TGF-β1 activation in human lung fibroblasts (HLFs) and specifically that extracellular galectin-3 promotes oleoyl-L-α-lysophosphatidic acid sodium salt (LPA)-induced integrin-mediated TGF-β1 activation. Surface plasmon resonance (SPR) analysis confirmed that galectin-3 binds to the αv integrins, αvβ1, αvβS and αvβ6 and also to the TGFβRII subunit in a glycosylation-dependent manner. This galectin-3 binding is heterogeneous and not a 1:1 binding stoichiometry. These binding interactions were blocked by small molecule inhibitors of galectin-3 which target the carbohydrate recognition domain. Binding of galectin-3 to the β1 integrin was validated in vitro by co-immunoprecipitation (Co-IP) in HLFs. In addition, proximity ligation assay (PLA) data indicates that galectin-3 and the β1 integrin colocalize closely (40 nm) on the cell surface of HLFs, that colocalization is increased by TGF-β1 treatment and galectin-3 inhibitors prevented this colocalization. In the absence of TGF-β1 stimulation, such colocalization was detectable only in HLFs isolated from IPF patients suggesting that the proteins are inherently more closely associated in the disease state. Taken together, this data suggests that galectin-3 promotes TGF-β1 signaling and may induce fibrogenesis by interacting directly with components of the TGF-β1 signaling cascade. Declaration of Interests RGJ reports grants or contracts from AstraZeneca, Biogen, Galecto Biotech, GlaxoSmithKline, Nordic Biosciences, RedX, Plaint, consulting fees from Bristol Myers Squibb, Chiesi, Daewoong Veracyre, Resolution Therapeutics and Pliant, honoraria from Boehringer Ingelheim, Chiesi, Roche, PatientMPower, AstraZeneca, advisory roles with Boehringer Ingelheim, Galapagos and Vicore, non-financial support from NuMedii, and is a Trustee for Action for Pulmonary Fibrosis. AEJ reports grant funding from Galecto Biotech. BG reports CASE student project partnership with Galecto Biotech, honoraria from GlaxoSmithKline and Vertex and grants and fellowships from UKRI MRC and BBSRC, Alpha-1 Foundation, BLF/A+LUK, Wellcome Trust. RJS, ACM, FRZ, JFC are Galecto employees with shares/options in the company. NRP is a Roche employee. GH, RML, PS, SBC, DJS declare no competing interests.
Data-driven optimization yielded a highly-efficient CRISPR/Cas9 system for gene editing in Arabidopsis

The CRISPR/Cas9 technology is widely used for plant gene editing. In Arabidopsis, the early CRISPR/Cas9 systems using constitutive promoters to drive Cas9 expression usually have low heritable mutation efficiencies in the T1 generation. Germ cell-specific or cell division-specific promoters, like EC1.2en-EC1.1p fusion, YAO and CDC45, have been used as alternatives to direct Cas9 expression, but the efficiency of getting nonchimeric mutations is still not high. To further improve gene editing efficiency, we used gene co-expression network analysis to identify NUC1 as a candidate promoter for driving Cas9 expression. NUC1 has expression patterns similar to YAO, but expresses at a much higher level. We constructed a CRISPR/Cas9 system pHY07 that uses the NUC1 promoter to drive Cas9 and carries the mCherry protein as a fluorescent marker for selecting transgenic seeds. Using this system to edit the GL2 gene, we obtained apparently nonchimeric mutations in 55% of the T1 transgenic plants. Among the Cas9-free T2 plants 99% harbored mutations that are stably inherited from the previous generation. Therefore, our system exhibited extremely high editing efficiency, and through fluorescent screening of transgenic seeds, it become easy to obtain Cas9-free and stable genetic mutants in the T2 generation.
Remotely controlled drug release in deep brain regions of non-human primates

Many areas of science and medicine would benefit from selective release of drugs in specific regions of interest. Nanoparticle drug carriers activated by focused ultrasound—remotely applied, depth-penetrating energy—may provide such selective interventions. Here, we developed stable, ultrasound-responsive nanoparticles that can be used to release drugs effectively and safely in non-human primates. The nanoparticles were used to release propofol in deep brain visual regions. The release reversibly modulated the subjects’ visual choice behavior and was specific to the targeted region and to the released drug. Gadolinium-enhanced MRI imaging suggested an intact blood-brain barrier. Blood draws showed normal clinical chemistry and hematology. In summary, this study provides a safe and effective approach to release drugs on demand in selected deep brain regions at levels sufficient to modulate behavior.