Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA and protein expression analysis of HLA‐DQB1*03:01:01:21Q allele: A null allele renamed as HLA‐DQB1*03:01:01:21N

The characterization of the expression profile of HLA questionable alleles (Q) is clinically relevant in allogeneic hematopoietic stem cell transplantation (HSTC) because an aberrant expression of these alleles could lead to transplantation‐related complications. HLA‐DQB1*03:01:01:21Q shows a substitution at the donor splice site of intron 3 that potentially could affect the expression of this allele. In order to determine their expression profile at RNA and protein level, we analyzed the presence of the HLA‐DQ7 molecule by complement‐dependent cytotoxicity test (CDC) and flow cytometry, and their RNA processing by cDNA analyses and sequencing by Sanger methods. Our results reveal that HLA‐DQ7 is not detectable by serological methods, this is confirmed by cDNA methods demonstrating the absence of specific HLA‐DQB1*03:01:01:21Q mRNA, probably due to an intron 3 retention that creates a premature TGA stop codon, leading to mRNA degradation via nonsense‐mediated decay (NMD). These findings demonstrate that the HLA‐DQB1*03:01:01:21Q allele is nonexpressed, thus it has been renamed as DQB1*03:01:01:21N.
How bad is the state of occupational fatalities in New Zealand

The Pike River disaster has increased attention on safety in the New Zealand mining industry. While mining is a dangerous occupation, its fatality rate does not appear to have increased. Furthermore, most workplace fatalities do not occur in mining. This paper explores the data on occupational fatalities and finds the following. First, occupational fatalities are concentrated in just a few industries. Second, these industries are noticeably riskier than others. Third, the gap between New Zealand's occupational fatality rate and those of countries it compares itself with has increased. Fourth, work-related fatalities are only a small proportion of all accidental deaths in New Zealand. Possible reasons for these facts are discussed.
Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 µM and 66 µM. In addition, eight compounds inhibited PLpro with IC50 ranging from 1.7 µM to 46 µM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
Neural correlate of reduced respiratory chemosensitivity during chronic epilepsy

Central autonomic cardiorespiratory dysfunction underlies sudden unexpected death in epilepsy (SUDEP). Here we used single cell neuronal Ca2+ imaging and intrahippocampal kainic acid (KA)-induced chronic epilepsy in mice to investigate progressive changes in key cardiorespiratory brainstem circuits during chronic epilepsy. Following induction of status epilepticus (SE), adaptive ventilatory responses to hypercapnia were reduced in mice with chronic epilepsy for 5 weeks post-SE with partial recovery at week 7. These changes were paralleled by post-SE alterations in the chemosensory responses of neurons in the retrotrapezoid nucleus (RTN). Neurons that displayed adapting responses to hypercapnia were less prevalent and exhibited smaller responses over weeks 3-5, whereas neurons that displayed graded responses to hypercapnia became more prevalent by week 7. Over the same period, chemosensory responses of the presympathetic rostral ventrolateral medullary neurons showed no change. Mice with chronic epilepsy showed enhanced sensitivity to seizures, which can invade the RTN and possibly impair further the chemosensory circuits. Our work suggests that assessment of respiratory chemosensitivity may have potential for identifying people at risk of SUDEP.
Metabolic alterations in skeletal muscle following eccentric exercise induced damage : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy, Massey University, Palmerston North, New Zealand

The contents of chapter 4 form the basis of the following publication: Hughes, J. D. , Johnson, N. A. , Brown, S. J., Sachinwalla, T. , Walton, D. W. , & Stannard, S. R. (2010). Effects of eccentric exercise-induced muscle damage on intramyocellular lipid concentration and high energy phosphates. European Journal of Applied Physiology, 110(6), 1135-1141. doi: 10.1007/s00421-010-1605-5 (The original publication is available at www.springerlink.com)
Nanometer-Resolution Long-term Tracking of Single Cargos Reveals Dynein Motor Mechanisms

Cytoplasmic dynein is essential for intracellular transport, but because of its complexity, we still do not fully understand how this 1.5 megadalton protein works. Here, we used novel optical probes that enable single-particle tracking (SPT) of individual cargos transported by dynein motors in live neurons over 900 μm. Analyses using the Fluctuation Theorem (FT) showed that the number of dynein molecules switches between 1-5 motors during the transport. Clearly resolved single-molecular steps revealed that the dwell times between individual steps were accurately described by an enzymatic cycle dominated by two equal and thermally-activated rate constants. Based on these data, we propose a new molecular model whereby each step requires the hydrolysis of 2 ATPs. The model is consistent with extensive structural, single-molecule and biochemical measurements.
Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS

In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence and live-cell imaging revealed that lamin C but not the other lamin isoforms rapidly accumulated at sites of NE rupture induced by laser microirradiation in mouse embryonic fibroblasts. The immunoglobulin-like fold domain and the NLS were required for the recruitment from the nucleoplasm to the rupture sites with the Barrier-to-autointegration factor (BAF). The accumulation of nuclear BAF and cytoplasmic cyclic GMP-AMP synthase (cGAS) at the rupture sites was in part dependent on lamin A/C. These results suggest that nucleoplasmic lamin C, BAF and cGAS concertedly accumulate at sites of NE rupture for repair. Summary Kono et al. show the rapid recruitment of nucleoplasmic lamin C to sites of nuclear envelope rupture with Barrier-to-autointegration factor. Lamin A/C is also involved in nuclear DNA sensing with cytoplasmic cGAS at the ruptured sites.
Investigating the NRAS 5’ UTR as a Target for Small Molecules

Neuroblastoma RAS (NRAS) is an oncogene that is deregulated and highly mutated in cancers including melanomas and acute myeloid leukemias. Constitutively activated NRAS induces the MAPK and AKT signaling pathways and leads to uncontrolled proliferation and cell growth, making it an attractive target for small molecule inhibition. Like all RAS-family proteins, it has proven difficult to identify small molecules that directly inhibit the protein. An alternative approach would involve targeting the NRAS mRNA. The 5′ untranslated region (5′ UTR) of the NRAS mRNA is reported to contain a G-quadruplex (G4) that regulates translation of NRAS mRNA. Stabilizing the G4 structure with small molecules could reduce NRAS protein expression in cancer cells by impacting translation. Here we report a novel class of small molecule that binds to the G4 structure located in the 5′ UTR of the NRAS mRNA. We used a small molecule microarray (SMM) screen to identify molecules that selectively bind to the NRAS-G4. Biophysical studies demonstrated that compound 18 binds reversibly to the NRAS-G4 structure with submicromolar affinity. A Luciferase based reporter assay indicated that 18 inhibits the translation of NRAS via stabilizing the NRAS-G4 in vitro but showed only moderate effects on the NRAS levels in cellulo. Rapid Amplification of cDNA Ends (RACE), RT-PCR analysis on 14 different NRAS-expressing cell lines, coupled with analysis of publicly available CAGE seq experiments, revealed that predominant NRAS transcript does not possess the G4 structure. Further analysis of published rG4 and G4 sequencing data indicated the presence of G4 structure in the promoter region of NRAS gene (DNA) but not in the mRNA. Thus, although many NRAS transcripts lack a G4 in many cell lines the broader concept of targeting folded regions within 5’ UTRs to control translation remains a highly attractive strategy and this work represents an intriguing example of transcript heterogeneity impacting targetability.
Fast event-related mapping of fingertip population receptive fields in human somatosensory and motor cortex

The majority of fMRI studies investigating somatotopic body representations in the human cortex have used either block or phase-encoding stimulation designs. Event-related (ER) designs allow for more natural and flexible stimulation sequences, while enabling the independent estimation of responses to different body parts in the same cortical location. Here we compared an efficiency-optimized fast ER design (2s inter stimulus interval, ISI) to a slow ER design (8s ISI) for mapping fingertip voxelwise tuning properties in the sensorimotor cortex of 6 participants at 7 Tesla. The fast ER design resulted in similar, but more robust, estimates compared to the slow ER design. Concatenating the fast and slow ER data, we demonstrate in each individual brain the existence of two separate somatotopically-organized representations of the fingertips, one in S1 on the post-central gyrus and the other at the border of the motor and pre-motor cortices on the pre-central gyrus. In both post-central and pre-central representations, fingertip tuning width increases progressively, from narrowly-tuned Brodmann areas 3b and 4a respectively, towards parietal and frontal regions responding equally to all fingertips.
The NF-κB pathway controls H3K9me3 levels at intronic LINE-1 elements and hematopoietic stem cell gene expression in cis

Ionizing radiations (IR) alter hematopoietic stem cell (HSC) function on the long-term, but the mechanisms underlying these effects are still poorly understood. We recently showed that IR induces the derepression of L1Md, the mouse young subfamilies of LINE-1/L1 retroelements. L1 contribute to gene regulatory networks. However, how L1Md are derepressed and impact HSC gene expression are not known. Here we show that IR triggers genome-wide H3K9me3 decrease that occurs mainly at L1Md. Loss of H3K9me3 at intronic L1Md harboring NF-κB binding sites motifs but not at promoters is associated with the repression of HSC specific genes. This is correlated with reduced NFKB1 repressor expression. TNF-α-treatment before IR rescued all these effects and prevented IR-induced HSC loss of function in vivo. This TNF-α/NF-κB/H3K9me3/L1Md axis might be important to maintain of HSCs while allowing expression of immune genes during myeloid regeneration or damage-induced bone marrow ablation.
Non-Canonical Odor Coding in the Mosquito

Female Aedes aegypti mosquitoes are a persistent human foe, transmitting arboviruses including dengue and yellow fever when they bite us to obtain a blood meal. Mosquitoes are intensely attracted to human-emitted body odor, heat, and carbon dioxide, which they detect using three different large multi-gene families encoding odor-gated ion channels. Genetic mutations that cause profound disruptions to the olfactory system have modest effects on human attraction, suggesting significant redundancy in odor coding. The canonical view is that olfactory sensory neurons each express a single chemosensory receptor that defines its ligand selectivity. Using immunostaining, RNA in situ hybridization, and single nucleus RNA sequencing, we discovered that Aedes aegypti uses an entirely different organizational principle, with many neurons co-expressing multiple chemosensory receptor genes. In vivo electrophysiology demonstrates that the broad ligand-sensitivity of mosquito olfactory neurons is due to this non-canonical co-expression. The redundancy afforded by an olfactory system in which many neurons co-express multiple receptors with different chemical sensitivity may greatly increase the robustness of the mosquito olfactory system and explain our longstanding inability to engineer new compounds that disrupt the detection of human body odor by mosquitoes.
bMSI-CAST: a systematic method for next generation sequencing-based microsatellite instability detection in plasma cell-free DNA

Microsatellite instability (MSI) is a well-established prognostic and predictive biomarker in certain types of cancers. MSI detection using tumour tissue is often limited by the availability of specimens. Next generation sequencing (NGS)-based MSI detection in plasma cell-free DNA (cfDNA) is challenged by a much lower signal-to-noise ratio. We developed a highly accurate cfDNA MSI detection method called bMSI-CAST (blood MSI Caller Adjusted with Sequence duplicaTes), with improvement on three features including a set of locus selection principles ensuring loci with high robustness and compatibility across sequencing platforms, an MSI-specific duplicate removal strategy, and a calling algorithm that dynamically matches baselines with a broad range of duplication levels. Analytical validation via MSI-high (MSI-H) cell gDNA showed an LOD of 0.15%. Furthermore, in an analysis of 95 evaluable cfDNA samples from patients with gastrointestinal cancers, bMSI-CAST exhibited a positive predictive agreement (PPA) of 92.9% (39/42) and negative predictive agreement (NPA) of 100% (53/53) with tissue MSI-PCR. In conclusion, bMSI-CAST provides novel and advanced solutions to key aspects fundamental to cfDNA MSI calling but not sufficiently addressed by existing methods, and it is a validated method ready to be applied to aid clinical decisions for cancer patients.
Feasibility of Using Wearable EMG Armbands combined with Unsupervised Transfer Learning for Seamless Myoelectric Control

Myoelectric control uses electromyography (EMG) signals as human-originated input to enable intuitive interfaces with machines. As such, recent rehabilitation robotics employs myoelectric control to autonomously classify user intent or operation mode using machine learning. However, performance in such applications inherently suffers from the non-stationarity of EMG signals across measurement conditions. Current laboratory-based solutions rely on careful, time-consuming control of the recordings or periodic recalibration, impeding real-world deployment. We propose that robust yet seamless myoelectric control can be achieved using a low-end, easy-to-“don” and “doff” wearable EMG sensor combined with unsupervised transfer learning. Here, we test the feasibility of one such application using a consumer-grade sensor (Myo armband, 8 EMG channels @ 200 Hz) for gesture classification across measurement conditions using an existing dataset: 5 users x 10 days x 3 sensor locations. Specifically, we first train a deep neural network using Temporal-Spatial Descriptors (TSD) with labeled source data from any particular user, day, or location. We then apply the Self-Calibrating Asynchronous Domain Adversarial Neural Network (SCADANN), which automatically adjusts the trained TSD to improve classification performance for unlabeled target data from a different user, day, or sensor location. Compared to the original TSD, SCADANN improves accuracy by 12±5.2% (avg±sd), 9.6±5.0%, and 8.6±3.3% across all possible user-to-user, day-to-day, and location-to-location cases, respectively. In one best-case scenario, accuracy improves by 26% (from 67% to 93%), whereas sometimes the gain is modest (e.g., from 76% to 78%). We also show that the performance of transfer learning can be improved by using a “better” model trained with “good” (e.g., incremental) source data. We postulate that the proposed approach is feasible and promising and can be further tailored for seamless myoelectric control of powered prosthetics or exoskeletons.
Texture-like representation of objects in human visual cortex

The human visual ability to recognize objects and scenes is widely thought to rely on representations in category-selective regions of visual cortex. These representations could support object vision by specifically representing objects, or, more simply, by representing complex visual features regardless of the particular spatial arrangement needed to constitute real world objects. That is, by representing visual textures. To discriminate between these hypotheses, we leveraged an image synthesis approach that, unlike previous methods, provides independent control over the complexity and spatial arrangement of visual features. We found that human observers could easily detect a natural object among synthetic images with similar complex features that were spatially scrambled. However, observer models built from BOLD responses from category-selective regions, as well as a model of macaque inferotemporal cortex and Imagenet-trained deep convolutional neural networks, were all unable to identify the real object. This inability was not due to a lack of signal-to-noise, as all of these observer models could predict human performance in image categorization tasks. How then might these texture-like representations in category-selective regions support object perception? An image-specific readout from category-selective cortex yielded a representation that was more selective for natural feature arrangement, showing that the information necessary for object discrimination is available. Thus, our results suggest that the role of human category-selective visual cortex is not to explicitly encode objects but rather to provide a basis set of texture-like features that can be infinitely reconfigured to flexibly learn and identify new object categories. Significance Statement Virtually indistinguishable metamers of visual textures, such as wood grain, can be synthesized by matching complex features regardless of their spatial arrangement (1–3). However, humans are not fooled by such synthetic images of scrambled objects. Thus, category-selective regions of human visual cortex might be expected to exhibit representational geometry preferentially sensitive to natural objects. Contrarily, we demonstrate that observer models based on category-selective regions, models of macaque inferotemporal cortex and Imagenet-trained deep convolutional neural networks do not preferentially represent natural images, even while they are able to discriminate image categories. This suggests the need to reconceptualize the role of category-selective cortex as representing a basis set of complex texture-like features, useful for a myriad of visual behaviors.
360 ◦ real‑time and power‑efficient 3D DAMOT for autonomous driving applications

Autonomous Driving (AD) promises an efficient, comfortable and safe driving experience. Nevertheless, fatalities involving vehicles equipped with Automated Driving Systems (ADSs) are on the rise, especially those related to the perception module of the vehicle. This paper presents a real-time and power-efficient 3D Multi-Object Detection and Tracking (DAMOT) method proposed for Intelligent Vehicles (IV) applications, allowing the vehicle to track 360 ◦ surrounding objects as a preliminary stage to perform trajectory forecasting to prevent collisions and anticipate the ego-vehicle to future traffic scenarios. First, we present our DAMOT pipeline based on Fast Encoders for object detection and a combination of a 3D Kalman Filter and Hungarian Algorithm, used for state estimation and data association respectively. We extend our previous work ellaborating a preliminary version of sensor fusion based DAMOT, merging the extracted features by a Convolutional Neural Network (CNN) using camera information for long-term re-identification and obstacles retrieved by the 3D object detector. Both pipelines exploit the concepts of lightweight Linux containers using the Docker approach to provide the system with isolation, flexibility and portability, and standard communication in robotics using the Robot Operating System (ROS). Second, both pipelines are validated using the recently proposed KITTI-3DMOT evaluation tool that demonstrates the full strength of 3D localization and tracking of a MOT system. Finally, the most efficient architecture is validated in some interesting traffic scenarios implemented in the CARLA (Car Learning to Act) open-source driving simulator and in our real-world autonomous electric car using the NVIDIA AGX Xavier, an AI embedded system for autonomous machines, studying its performance in a controlled but realistic urban environment with real-time execution (results).
RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA

Small RNAs are known to mediate silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. Post-zygotic development of the Paramecium somatic genome requires elimination of thousands of transposon remnants (IESs) and transposable elements that are scattered throughout the germline genome (Garnier et al. 2004). The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries (Bouhouche et al. 2011; Furrer et al. 2017). Previous research suggests that small RNAs induce heterochromatin formation within IESs, which, in turn, is required for DNA elimination (Liu et al. 2007). Here we show that IES recognition and precise excision is facilitated by recruitment of a homolog of a chromatin remodeler ISWI, which depletes target genomic regions of nucleosomes, making the chromatin accessible for DNA cleavage. ISWI knockdown in Paramecium leads to pronounced inhibition of DNA elimination. Furthermore, nucleosome profiling indicates that ISWI is required for IES elimination in nucleosome-dense genomic regions, while other IESs do not require small RNAs or ISWI for excision. ISWI silencing notably also reduces DNA elimination precision, resulting in aberrant excision at alternative IES boundaries. In summary, we demonstrate that chromatin remodeling that increases DNA accessibility together with small RNAs are necessary for efficient and precise DNA elimination in Paramecium.
Application of the CAD/CAM System in the Production of the Anatomic Insole

CAD technology has introduced a turning point in the way of design. In the period before the introduction of computer systems, drafts were traditionally made by pen and each mistake meant erasing, whereas bigger mistakes often required re-creation of the anatomical documentation. The closely linked development of CAD/CAM technology marked the upturn in obtaining the anatomic shape and its creation. This article gives a brief insight into 3D digitization in the field of making the anatomic insole.