Miracle-dz/UniFAR-FTUs huggingface dataset:
ListDB: Union of Write-Ahead Logs and Persistent SkipLists for Incremental Checkpointing on Persistent Memory

Due to the latency difference between DRAM and non-volatile main memory (NVMM) and the limited capacity of DRAM, incoming writes are often stalled in LSM tree-based key-value stores. This paper presents ListDB , a write-optimized key-value store for NVMM to overcome the gap between DRAM and NVMM write latencies and thereby, resolve the write stall problem. The contribution of ListDB consists of three novel techniques: (i) byte-addressable Index-Uniﬁed Logging , which incrementally converts write-ahead logs into SkipLists, (ii) Braided SkipList , a simple NUMA-aware SkipList that effectively reduces the NUMA effects of NVMM, and (iii) Zipper Compaction , which moves down the LSM-tree levels without copying key-value objects, but by merging SkipLists in place without blocking concurrent reads. Using the three techniques, ListDB makes background compaction fast enough to resolve the infamous write stall problem and shows 1.6x and 25x higher write throughputs than PACTree and Intel Pmem-RocksDB, respectively.
Enhanced photoelectric properties of ZnO nanorods arrays synthesized by controlled sol-gel-assisted hydrothermal method

Abstract ZnO nanorods arrays were synthesized by sol-gel-assisted hydrothermal method adjusting hydrothermal [Zn2+]/[(CH2)6N4] concentration ratio and study their photoelectric properties. When the concentration ratio of [Zn2+]/[(CH2)6N4] is 1:2.5, ZnO nanorods arrays have the best crystal quality, and the photoelectric performance of that is relatively good with a dark current of 3.98 µA, photocurrent of 1045.77 µA. and photoelectric sensitivity of 262.8. In addition, the photoelectric response rise and fall time of that are 53.6 s and 139.8 s. This research has further improved the photoelectric properties of ZnO nanomaterials and is expected to be applied to various ZnO high-performance photodetectors.
Neural representational geometries correlate with behavioral differences in monkeys and recurrent neural networks

Animals likely use a variety of strategies to solve laboratory tasks. Traditionally, combined analysis of behavioral and neural recording data across subjects employing different strategies may obscure important signals and give confusing results. Hence, it is essential to develop techniques that can infer strategy at the single-subject level. We analyzed an experiment in which two monkeys performed a visually cued rule-based task. The analysis of their performance shows no indication that they used a different strategy. However, when we examined the geometry of stimulus representations in the state space of the neural activities recorded in dorsolateral prefrontal cortex, we found striking differences between the two monkeys. Our purely neural results induced us to reanalyze the behavior. The new analysis showed that the differences in representational geometry correlate with differences in the reaction times, revealing behavioral differences we were unaware of. All these analyses indicate that the monkeys are using different strategies. Finally, using recurrent neural network models trained to perform the same task, we show that these strategies correlate with the amount of training, suggesting a possible explanation for the observed neural and behavioral differences.
Discovery of deep-sea coral symbionts from a novel family of marine bacteria, Oceanoplasmataceae, with severely reduced genomes

Microbes perform critical functions in corals yet most knowledge is derived from the photic zone. Here, we discovered two mollicutes that dominate the microbiome of the deep-sea octocoral, Callogorgia delta, and reside in the mesoglea. These symbionts were abundant across the host’s range, absent in the water, and rare in sediments. The symbionts lack all known fermentative capabilities including glycolysis and can only generate energy from arginine provided by the coral host. Their genomes feature extensive mechanisms to interact with foreign DNA which may be indicative of their role in symbiosis. We erect the novel family Oceanoplasmataceae which includes these symbionts and others associated with four marine invertebrate phyla. Its exceptionally broad host range suggests that the diversity of this enigmatic family remains largely undiscovered. Oceanoplasmataceae genomes are the most highly reduced among mollicutes providing new insight into their reductive evolution and the roles of coral symbionts.
Novel triplex nucleic acid lateral flow immuno-assay (NALFIA) for rapid detection of Nipah virus, Middle East respiratory syndrome coronavirus and Reston ebolavirus

We report the development of the first triplex Nucleic Acid Lateral Flow Assay (NALFIA) for detection of genomes of Nipah virus (NiV), Middle East respiratory syndrome coronavirus (MERS-CoV) and Reston ebolavirus (REBOV), intended for screening of bats as well as other hosts and reservoirs of these three viruses. Our triplex NALFIA is a two-step assay format wherein the target nucleic acid in sample is first amplified using tagged primers, and the tagged ds DNA amplicons are captured by immobilized antibodies on NALFIA device resulting to signal development from binding of streptavidin-colloidal gold conjugate to biotin tag on the captured amplicons. Triplex amplification of N gene of NiV, UpE gene of MERS-CoV, and Vp40 gene of REBOV was optimized using primers adapted from validated real-time RT-PCR assays of previous studies and the compatible combinations of hapten-labels and antibodies for triplex NALFIA device were identified. Digoxigenin, rhodamine red and alexa fluor 488 were identified as suitable 5’ labels on forward primers. The lowest copy number detected by the triplex NALFIA with 2 μl of triplex RT-PCR product were up to 8.21e4 for NiV N target, 7.09e1 for MERS-CoV UpE target, and 1.83e4 for REBOV Vp40 target. Using simulated samples and Taqman real-time RT-PCR as standard, the sensitivity and positive predictive values were found to be 100% for MERS-CoV UpE and REBOV Vp40 targets and 91% for NiV N target while the specificity and negative predictive values were 100% for MERS-CoV UpE targets and REBOV Vp40, and 93.3% for NiV N target.
Efficiency of heterogenous functional connectomes explains variance in callous-unemotional traits after computational lesioning of cortical midline and salience regions

Callous-unemotional (CU) traits are a youth antisocial phenotype hypothesized to be a result of differences in the integration of multiple brain systems. However, mechanistic insights into these brain systems are a continued challenge. Where prior work describes activation and connectivity of the connectome in relation to these systems, new mechanistic insights can be derived by removing nodes and characterizing changes in network properties (hereafter referred to as computational lesioning) to characterize the resilience and vulnerability of the brain’s functional connectome. Here, we study the resilience of connectome integration in CU traits by estimating changes in efficiency after computationally lesioning individual-level connectomes. From resting-state data of 86 participants (48% female, age 14.52±1.31) drawn from the Nathan Kline institute’s Rockland study, individual-level connectomes were estimated using graphical lasso. Computational lesioning was conducted both sequentially and by targeting global and local hubs. We calculated changes in network efficiency after each lesion. Then, elastic net regression was applied to determine how these changes explained variance in CU traits. Follow-up analyses characterized modeled node hubs, examined moderation, determined impact of targeting, and decoded the brain mask by comparing regions to meta-analytic maps. Elastic net regression revealed that computational lesioning of 23 nodes, network modularity, and Tanner stage explained variance in CU traits. Hub assignment of selected hubs differed at higher CU traits. No evidence for moderation between simulated lesioning and CU traits was found. Targeting global hubs increased efficiency and targeting local hubs had no effect at higher CU traits. Identified brain mask meta-analytically associated with more emotion and cognitive terms. Although reliable patterns were found across participants, adolescent brains were heterogeneous even for those with a similar CU traits score. Adolescent brain response to simulated lesioning revealed a pattern of connectome resiliency and vulnerability that explains variance in CU traits, which can aid prediction of youth at greater risk for higher CU traits.
A Homology Guide for Pacific Salmon Genus Oncorhynchus resolves patterns of Duplicate Retention, Rediploidization and Local Adaptation Following the Salmonid Specific Whole Genome Duplication Event

Salmonid fishes have emerged as a tractable model to study whole genome duplications (WGD) as this group has undergone four rounds of WGD, with a significant proportion of the genome yet to rediploidize. The fact that much of modern salmonid genomes retain duplicates from the most recent WGD while other regions have rediploidized creates complications for genetic studies by obscuring homology relationships and the necessity of filtering duplicate regions from many analyses. The difficulty this creates is particularly prominent in Pacific salmonids genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural role these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of duplicate retention and rediploidization. Overall, we find that retained duplicates comprise over half of modern gene repertoires and that retained duplicate genes are enriched for genes involved in nuclear stability, while rediploidized genes which represent a smaller proportion of genes are heavily enriched in dosage sensitive processes such as mitochondria. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss we demonstrate that retained duplicates are more likely to be associated with adaptive divergence than rediploidized genes, highlighting the potential of WGDs to promote adaptation. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life history traits or gene editing targets.
THE POLARIZATION SIGNATURE OF LOCAL BULK FLOWS

A large peculiar velocity of the intergalactic medium produces a Doppler shift of the cosmic microwave background with a frequency-dependent quadrupole term. This quadrupole will act as a source for polarization of the cosmic microwave background, creating a large-scale polarization anisotropy if the bulk flow is local and coherent on large scales. In the case where we are near the center of the moving region, the polarization signal is a pure quadrupole. We show that the signal is small, but detectable with future experiments for bulk flows as large as some recent reports.
Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis

Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M. brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (∼ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. We show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment.
National Institutes of Health research project grant inflation 1998 to 2021

We analyzed changes in total costs for National Institutes of Health (NIH) awarded Research Project Grants issued from 1998 to 2003. The NIH uses a data-driven price index – the Biomedical Research and Development Price Index (BRDPI) – to account for inflation based increases in grant costs. The BRDPI was higher than the general rate of inflation from 1998 until 2012; since then, the rate of inflation for NIH-funded research has been similar to the general rate of inflation. Despite increases in nominal costs, recent years have seen increases in the absolute numbers of RPG and R01 awards. Real (BRDPI-adjusted) average and median RPG costs increased during the NIH-doubling (1998 to 2003), but have remained relatively stable since. Of note, though, the degree of variation of RPG costs has changed over time, with more marked extremes observed on both higher and lower levels of cost. On both ends of the cost spectrum, the agency is funding a greater proportion of solicited projects, with nearly half of RPG money going towards solicited projects. After adjusting for potential confounders in a wholly non-parametric machine learning regression, we find no independent association of time with BRDPI-adjusted costs.
Structures of human cytoplasmic dynein in complex with the lissencephaly 1 protein, LIS1

The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by relieving its autoinhibited form. We recently reported a 3. 1Å structure of yeast dynein bound to Pac1, the yeast homologue of LIS1, which revealed the details of their interactions (Gillies et al., 2022). Based on this structure, we made mutations that disrupted these interactions and showed that they were required for dynein’s function in vivo in yeast. We also used our yeast dynein-Pac1 structure to design mutations in human dynein to probe the role of LIS1 in promoting the assembly of active dynein complexes. These mutations had relatively mild effects on dynein activation, suggesting that there may be differences in how dynein and Pac1/LIS1 interact between yeast and humans. Here, we report cryo-EM structures of human dynein-LIS1 complexes. Our new structures reveal the differences between the yeast and human systems and provide a blueprint to disrupt the human dynein-LIS1 interaction more accurately. Our new structures also allow us to map type-1 lissencephaly disease mutations, as well as mutations in dynein linked to malformations of cortical development/ intellectual disability, in the context of the human dynein-LIS1 complex.
Detecting clonemates in multicellular clonal species based on 1 "Shared Heterozygosity (SH)” and technical replicates

11 Clonal reproduction, the formation of new individuals that are genetically nearly identical to 12 the parent via mitosis in the absence of genetic recombination, is a very common reproductive 13 mode across plants, fungi, and animals. Current genetic marker based methods fail to detect 14 clonal structure when all collected samples belong to one single clone, which seems to be 15 more common than previously thought. Here we propose a new similarity index, “Shared 16 Heterozygosity (SH)” based on the number of genetic markers (typically SNPs, single- 17 nucleotide polymorphisms) that are identically heterozygous among two or more genomes 18 (i.e., N SH ). Ideally N SH should be on the order of approximately >=3,000, which can be easily 19 achieved nowadays via Restriction-site Associated DNA (RAD) sequencing or whole-genome 20 resequencing. One should be careful when N SH is small (roughly <1,000). We analyze two 21 large seagrass clones ( Posidonia australis , Zostera marina ) along with two Z. marina clones 22 of known age (17-yrs), and show that SH can potentially extend the detection of clonemates 23 to any pair of samples with the aid of technical replicates. Another potential application of SH 24 is to detect possible parent-descendant pairs under selfing, because the heterozygous loci in 25 the selfing-produced descendants represent a subset of those in the parent. Our proposed 26 workflow takes advantage of the availability of the larger number of genetic markers in the 27 genomic era, and fills a gap in detecting clonemates in the growing number of cases where 28 many or all samples at a location belong to one single clone.
Hybrid reconstruction of the physical model with the deep learning that improves structured illumination microscopy

Abstract. Structured illumination microscopy (SIM) has been widely used in live-cell superresolution (SR) imaging. However, conventional physical model-based SIM SR reconstruction algorithms are prone to artifacts in handling raw images with low signal-to-noise ratios (SNRs). Deep-learning (DL)-based methods can address this challenge but may lead to degradation and hallucinations. By combining the physical inversion model with a total deep variation (TDV) regularization, we propose a hybrid restoration method (TDV-SIM) that outperforms conventional or DL methods in suppressing artifacts and hallucinations while maintaining resolutions. We demonstrate the performance superiority of TDV-SIM in restoring actin filaments, endoplasmic reticulum, and mitochondrial cristae from extremely low SNR raw images. Thus TDV-SIM represents the ideal method for prolonged live-cell SR imaging with minimal exposure and photodamage. Overall, TDV-SIM proves the power of integrating model-based reconstruction methods with DL ones, possibly leading to the rapid exploration of similar strategies in high-fidelity reconstructions of other microscopy methods.
A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0.1]

We present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensemble (WE) path sampling strategy to even larger systems and/or slower processes. The tutorials demonstrate the use of the following key features: (i) a generalized resampler module for the creation of “binless” schemes, (ii) a minimal adaptive binning scheme for more efficient surmounting of free energy barriers, (iii) streamlined handling of large simulation datasets using an HDF5 framework, (iv) two different schemes for more efficient rate-constant estimation, (v) a Python API for simplified analysis of WE simulations, and (vi) plugins/extensions for Markovian Weighted Ensemble Milestoning and WE rule-based modeling at the system biology level. Applications of the tutorials range from atomistic to residue-level to non-spatial models, and include complex processes such as protein folding and the membrane permeability of a drug-like molecule. Users are expected to already have significant experience with running conventional molecular dynamics simulations and completed the previous suite of WESTPA tutorials.
Alignment, calibration, and validation of an 1 adaptive optics scanning laser 2 ophthalmoscope optimized for resolving 3 human cones in the central fovea 4

: Advances in adaptive optics scanning laser ophthalmoscope (AOSLO) technology 16 have enabled cones in the human fovea to be reliably resolved, providing new insight into 17 human foveal anatomy, visual perception, and retinal degenerative diseases. These high-18 resolution ophthalmoscopes require careful alignment of each optical subsystem to ensure 19 diffraction-limited imaging performance, which is necessary for resolving the smallest foveal 20 cones. We present a systematic and rigorous methodology for building, aligning, calibrating, 21 and testing an AOSLO optimized for imaging the cone mosaic of the central fovea in humans. 22 This methodology uses a two-stage alignment procedure and thorough system testing to achieve 23 an AOSLO with diffraction-limited performance. Human retinal imaging of two healthy 24 subjects demonstrates that the system can reliably resolve the smallest foveal cones. 25
Investigating the attentional focus to workplace-related soundscapes in a complex audio-visual-motor task using EEG

In demanding work situations (e.g., during a surgery) the processing of complex soundscapes varies over time and can be a burden for medical personnel. Here we study, using mobile electroencephalography (EEG), how humans process workplace-related soundscapes while performing a complex audio-visual-motor task (3D Tetris). Specifically, we wanted to know how the attentional focus changes the processing of the soundscape as a whole. Participants played a game of 3D Tetris in which they had to use both hands to control falling blocks. At the same time, participants listened to a complex soundscape, similar to what is found in an operating room (i.e., sound of machinery, people talking in the background, alarm sounds, and instructions). In this within-subject design, participants had to react to instructions (e.g., “place the next Block in the upper left corner”) and to sounds depending on the experimental condition, either to a specific alarm sound originating from a fixed location or to a beep sound that originated from varying locations. Attention to the alarm reflected a narrow attentional focus, as it was easy to detect and most of the soundscape could be ignored. Attention to the beep reflected a wide attentional focus, as it required the participants to monitor multiple different sound streams. Results show the robustness of the N1 and P3 event related potential response during this dynamic task with a complex auditory soundscape. Furthermore, we used temporal response functions to study auditory processing to the whole soundscape. This work is a step towards studying workplace-related sound processing in the operating room using mobile EEG.
Free-water volume fraction increases non-linearly with age in the white matter of the healthy human brain

The term free-water volume fraction (FWVF) refers to the cerebrospinal and interstitial fluids in the extracellular space of the white matter (WM) of the brain, which has been demonstrated as a sensitive biomarker that correlates with the cognitive performance and the neuropathological processes modifying the interstitial extracellular spaces. It can be quantified by properly fitting the isotropic compartment of the magnetic resonance (MR) signal in diffusion-sensitized sequences. Using N = 287 healthy subjects aged 25-94, this study examines in detail the evolution of the FWVF in the human brain WM across the adult lifespan, which has been previously reported to exhibit a positive trend. We found evidence of a noticeably non-linear gain after the sixth decade of life, with a region-specific variate and varying change rate of the FWVF parameter with age, at the same time a heteroskedastic pattern across the adult lifespan is suggested. On the other hand, the FW-compensated MR signal leads to a region-dependent flattened age-related evolution of the mean diffusivity (MD) and fractional anisotropy (FA), along with a considerable reduction in their variability, as compared to standard studies conducted over the raw MR signal. This way, our study provides a new perspective on the trajectory-based assessment of the brain and explains the source of the variations observed in FA and MD parameters across the lifespan with previous studies with the standard diffusion tensor imaging.