Miracle-dz/UniFAR-FTUs huggingface dataset:
Familial clustering of primary lateral sclerosis and amyotrophic lateral sclerosis: Supplementary evidence for a continuum

Primary lateral sclerosis (PLS) is a motor neuron disorder characterized by a pure upper motor neuron degeneration in the bulbar and spinal regions. The key difference with amyotrophic lateral sclerosis (ALS) is the lower motor neuron system integrity. Despite important literature on this disease, the pathophysiology of PLS remains unknown, and the link with ALS still balances between a continuum and a separate entity from ALS.
European automotive technological innovation systems in the age of disruption: The suppliers’ view

Abstract Although empirical studies show that suppliers’ innovativeness enhances original equipment manufacturers’ (OEM) total innovation performance, some evidence reveals that suppliers’ innovation affects OEM in quantitatively and qualitatively limited ways. This study aims to explore innovation systems of European automobile producers, i.e., OEM. Technological innovation systems (TIS) remain relatively underexplored, but the approach is especially valuable for explaining why and how sustainable and circular innovation develop and spread. We applied a mixed-method approach and conducted patent analyses and interviews with 20 respondents from Slovenia, Austria, and Hungary, which are representatives of suppliers for the automotive industry and automotive clusters. We confirm that the European OEMs build innovation ecosystems that are more closed than their Asian counterparts. Furthermore, we define three paths of how inventions of suppliers can reach the OEMs, with developmental suppliers (large companies) having the highest probability of influencing the innovation activity of OEMs. The entry of small and medium-sized enterprises (SME) and start-ups with their inventions is difficult. However, it is not impossible, especially if they develop new solutions connected to current disruptive trends in the automotive industry: electric cars, autonomous driving and digitalisation.
Modelling, characterization of data-dependent and process-dependent errors in DNA data storage

Motivation Using DNA as the medium to store information has recently been recognized as a promising solution for long-term data storage. While several system prototypes have been demonstrated, the error characteristics in DNA data storage are discussed with limited content. Due to the data and process variations from experiment to experiment, the error variation and its effect on data recovery remain to be uncovered. To close the gap, we systematically investigate the storage channel, i.e., error characteristics in the storage process. Results We first propose a new concept named sequence corruption to unify the error characteristics into the sequence level, easing the channel analysis. Then we derived the formulations of the data imperfection at the decoder including both sequence loss and sequence corruption, revealing the decoding demand and monitoring the data recovery. Furthermore, we extensively explored several data-dependent unevenness observed in the base error patterns and studied a few potential factors and their impacts on the data imperfection at the decoder both theoretically and experimentally. The results presented here introduce a more comprehensive channel model and offer a new angle towards the data recovery issue in DNA data storage by further elucidating the error characteristics of the storage process. Contact poh.chuehloo@nus.edu. sg
Gene regulation is commonly selected for high plasticity and low noise

Bacteria often respond to dynamically changing environments by regulating gene expression. Despite this regulation being critically important for growth and survival, little is known about how selection shapes gene regulation in natural populations. To better understand the role natural selection plays in shaping bacterial gene regulation, here we compare differences in the regulatory behaviour of naturally segregating promoter variants from Escherichia coli (which have been subject to natural selection) to randomly mutated promoter variants (which have never been exposed to natural selection). We quantify gene expression phenotypes (expression level, plasticity, and noise) for hundreds of promoter variants across multiple environments, and show that segregating promoter variants are enriched for mutations with minimal effects on expression level. In many promoters, we infer that there is strong selection to maintain high levels of plasticity, and direct selection to decrease or increase cell-to-cell variability in expression. Finally, taking an integrated view, we show that across all phenotypes combined, segregating promoter variants are far more phenotypically similar than would be expected given their genetic divergence. This is the consequence of both stabilizing and directional selection acting on individual phenotypes to minimize differences among segregating variants. Taken together, these results expand our knowledge of how gene regulation is affected by natural selection and highlight the power of comparing naturally segregating polymorphisms to de novo random mutations to quantify the action of selection.
A mosaic adeno-associated virus vector as a versatile tool that exhibits high levels of transgene expression and neuron specificity in primate brain

Recent emphasis has been placed on gene transduction mediated through recombinant adeno-associated virus (AAV) vector to manipulate activity of neurons and their circuitry in the primate brain. In the present study, we created a novel AAV vector of which capsid was composed of capsid proteins derived from the serotypes 1 and 2 (AAV1 and AAV2). Following the injection into the frontal cortex of macaque monkeys, this mosaic vector, termed AAV2.1 vector, was found to exhibit the excellence in transgene expression (for the AAV1 vector) and neuron specificity (for the AAV2 vector) simultaneously. To explore its applicability to chemogenetic manipulation and in vivo calcium imaging, the AAV2.1 vector expressing excitatory DREADDs or GCaMP was injected into the striatum or the visual cortex of macaque monkeys, respectively. Our results have defined that such vectors secure intense and stable expression of the target proteins and yield conspicuous modulation and imaging of neuronal activity.
CUT&Tag-BS: an efficient and low-cost method for simultaneous profiling of histone modification and DNA methylation

It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic localization of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS shows similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further reveals that H3K4me1-marked regions are mostly CpG-poor, lack methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenarios with precious biological samples.
The effect of oxalic acid activation on the bleaching properties of a bentonite from Milos Island, Greece

Abstract A bentonite from Milos, Greece, was activated with oxalic acid and the effect of acid activation conditions on bleaching of sunflower oil was investigated. The activation parameters studied were temperature, retention time and oxalic acid to bentonite mass ratio. The activated materials produced had good bleaching properties and were suitable for industrial use as bleaching earths. Optimum bleaching properties could be achieved using a variety of combinations of acid to bentonite ratios and activation times. Bleaching efficiency tests indicated that 24 h activation at 100°C with 1m oxalic acid and 25% pulp density (w/v) gave results equivalent to that of a commercial bleaching earth (Tonsil Optimum 210 FF). The combination that is likely to be more preferable on an industrial scale was 100ºC, 25% pulp density (w/v), 1m initial oxalic acid concentration, 60% recycling of the oxalate solution (making up an acid to bentonite ratio 0.2 w/w) and 6 h activation time. The materials produced under these conditions have acceptable bleaching properties, corresponding to bleaching capacity greater than 78% compared to commercial Tonsil, and colour index (in red and yellow units) equal or even better than Tonsil.
Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics across a river catchment

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network through time using environmental DNA. We find contrasting biodiversity patterns, with richness (α-diversity) of fish increasing towards downstream positions within the catchment, while freshwater bacteria and invertebrates having an invariant and minimal decrease in richness, respectively, with downstream position. Food-web characteristics, such as link density and nestedness, however, were relatively conserved across space, but varied over season. Patterns of biodiversity across major taxonomic groups are thus not directly scalable to food-web structures at the same spatial and temporal scales, indicating that effective conservation measures must consider them jointly.
The Long Non-Coding RNA H19 Drives the Proliferation of Diffuse Intrinsic Pontine Glioma with H3K27 Mutation

Diffuse intrinsic pontine glioma (DIPG) is an incurable paediatric malignancy. Identifying molecular drivers of DIPG progression is of utmost importance. Long non-coding RNAs (lncRNAs) represent a large family of disease- and tissue-specific transcripts, whose functions have not been yet elucidated in DIPG. Here, we study the oncogenic role of the development-associated H19 lncRNA in DIPG. Bioinformatic analyses of clinical datasets were used to measure the expression of H19 lncRNA in paediatric high-grade gliomas (pedHGG). Expression and sub-cellular location of H19 lncRNA was validated in DIPG cell lines. Locked nucleic acid antisense oligonucleotides were designed to test the function of H19 in DIPG cells. We found that H19 expression was higher in DIPG vs normal brain tissue and other pedHGGs. H19 knockdown resulted in decreased cell proliferation and survival in DIPG cells. Mechanistically, H19 buffers let-7 microRNAs, resulting in up-regulation of oncogenic let-7 target (e.g SULF2, OSMR). H19 is the first functionally characterized lncRNA in DIPG and a promising therapeutic candidate to treat this incurable cancer.
Interferon-Induced Transmembrane Proteins Inhibit Infection by the Kaposi’s Sarcoma-Associated Herpesvirus and the Related Rhesus Monkey Rhadinovirus in a Cell Type-Specific Manner

The interferon-induced transmembrane proteins (IFITMs) are broad-spectrum antiviral proteins that inhibit the entry of enveloped viruses. We analyzed the effect of IFITMs on the gamma2-herpesviruses Kaposi’s sarcoma-associated herpesvirus (KSHV) and the closely related rhesus monkey rhadinovirus (RRV). We used CRISPR/Cas9-mediated gene knockout to generate A549, human foreskin fibroblast (HFF) and human umbilical vein endothelial cells (HUVEC) with combined IFITM1/2/3 knockout and identified IFITMs as cell type-dependent inhibitors of KSHV and RRV infection in A549 and HFF but not HUVEC. IFITM overexpression revealed IFITM1 as the relevant IFITM that inhibits KSHV and RRV infection. Fluorescent KSHV particles did not pronouncedly colocalize with IFITM-positive compartments. However, we found that KSHV and RRV glycoprotein-mediated cell-cell fusion is enhanced upon IFITM1/2/3 knockout. Taken together, we identified IFITM1 as a cell type-dependent restriction factor of KSHV and RRV that acts at the level of membrane fusion. Strikingly, we observed that the endotheliotropic KSHV circumvents IFITM-mediated restriction in HUVEC despite high IFITM expression, while influenza A virus (IAV) glycoprotein-driven entry into HUVEC is potently restricted by IFITMs even in the absence of interferon. IMPORTANCE IFITM proteins are the first line of defense against infection by many pathogens, which may also have therapeutic importance, as they, among other effectors, mediate the antiviral effect of interferons. Neither their function against herpesviruses nor their mechanism of action are well understood. We report here that in some cells, but not in, for example, primary umbilical vein endothelial cells, IFITM1 restricts KSHV and RRV, and that, mechanistically, this is likely effected by reducing the fusogenicity of the cell membrane. Further, we demonstrate potent inhibition of IAV glycoprotein-driven infection of cells of extrapulmonary origin by high constitutive IFITM expression.
Vaccinia Virus Arrests and Shifts the Cell Cycle

Modulation of the host cell cycle is a common strategy used by viruses to create a pro-replicative environment. To facilitate viral genome replication, vaccinia virus (VACV) has been reported to alter cell cycle regulation and trigger the host cell DNA damage response. However, the cellular factors and viral effectors that mediate these changes remain unknown. Here, we set out to investigate the effect of VACV infection on cell proliferation and host cell cycle progression. Using a subset of VACV mutants we characterize the stage of infection required for inhibition of cell proliferation and define the viral effectors required to dysregulate the host cell cycle. Consistent with previous studies, we show that VACV inhibits, and subsequently shifts the host cell cycle. We demonstrate that these two phenomena are independent of one another, with viral early genes being responsible for cell cycle inhibition, and post-replicative viral gene(s) responsible for the cell cycle shift. Extending previous findings, we show that the viral kinase F10 is required to activate the DNA damage checkpoint and that the viral B1/B12 (pseudo) kinases mediate degradation of checkpoint effectors p53 and p21 during infection. We conclude that VACV modulates host cell proliferation and host cell cycle progression through temporal expression of multiple VACV effector proteins.
The Pathological Features of Common Hereditary Mitochondrial Dynamics Neuropathy

Objectives Mitofusin 2 and ganglioside-induced differentiation-associated protein 1 are two main mitochondrial dynamics-related proteins. Dysfunction of these two proteins leads to different subtypes of Charcot–Marie–Tooth disease type 2A (CMT2A) and CMT2K. This study aims to report the pathological difference between CMT2A and CMT2K in a large cohort. Methods Thirty patients with molecularly confirmed CMT2A and nine with CMT2K were identified by next-generation sequencing. Sural nerve biopsies were performed in 29 patients. Results The patients with both diseases showed length-dependent neuropathy with distal weakness, sensory loss, and no deep tendon reflex. Optic neuropathy appeared in 3/30 (10%) patients with CMT2A. Tendon contracture appeared in 4/9 (50.0%) patients with CMT2K. Sural biopsy revealed the loss of both myelinated and unmyelinated nerve fibers. Closely packed, irregularly oriented neurofilaments were observed in axons of unmyelinated nerve fibers in both diseases. Another important finding was the ubiquitous presence of smaller, rounded, and fragmented mitochondria in CMT2A and elongated mitochondria in CMT2K in the myelinated and unmyelinated axons. Conclusion This study confirmed large diversity in phenotypes between CMT2A and CMT2K. Mitochondrial dynamics-related variations can induce different mitochondrial morphological changes and neurofilament accumulation in axons.
Acute Hemodynamic Effect of Acetazolamide in Patients With Pulmonary Hypertension Whilst Breathing Normoxic and Hypoxic Gas: A Randomized Cross-Over Trial

Aims: To test the acute hemodynamic effect of acetazolamide in patients with pulmonary hypertension (PH) under ambient air and hypoxia. Methods: Patients with pulmonary arterial or chronic thromboembolic PH (PAH/CTEPH) undergoing right heart catheterization were included in this randomized, placebo-controlled, double-blinded, crossover trial. The main outcome, pulmonary vascular resistance (PVR), further hemodynamics, blood- and cerebral oxygenation were measured 1 h after intravenous administration of 500 mg acetazolamide or placebo-saline on ambient air (normoxia) and at the end of breathing hypoxic gas (FIO2 0.15, hypoxia) for 15 min. Results: 24 PH-patients, 71% men, mean ± SD age 59 ± 14 years, BMI 28 ± 5 kg/m2, PVR 4.7 ± 2.1 WU participated. Mean PVR after acetazolamide vs. placebo was 5.5 ± 3.0 vs. 5.3 ± 3.0 WU; mean difference (95% CI) 0.2 (−0.2–0.6, p = 0.341). Heart rate was higher after acetazolamide (79 ± 12 vs. 77 ± 11 bpm, p = 0.026), pH was lower (7.40 ± 0.02 vs. 7.42 ± 0.03, p = 0.002) but PaCO2 and PaO2 remained unchanged while cerebral tissue oxygenation increased (71 ± 6 vs. 69 ± 6%, p = 0.017). In acute hypoxia, acetazolamide decreased PVR by 0.4 WU (0.0–0.9, p = 0.046) while PaO2 and PaCO2 were not changed. No adverse effects occurred. Conclusions: In patients with PAH/CTEPH, i.v. acetazolamide did not change pulmonary hemodynamics compared to placebo after 1 hour in normoxia but it reduced PVR after subsequent acute exposure to hypoxia. Our findings in normoxia do not suggest a direct acute pulmonary vasodilator effect of acetazolamide. The reduction of PVR during hypoxia requires further corroboration. Whether acetazolamide improves PH when given over a prolonged period by stimulating ventilation, increasing oxygenation, and/or altering vascular inflammation and remodeling remains to be investigated.
Systematic Review of the Effect of a Zero-Markup Policy for Essential Drugs on Healthcare Costs and Utilization in China, 2015–2021

Objective: This systematic review aimed to discuss the effects of a zero-markup policy for essential drugs (ZPED) on healthcare costs and utilization in China in the years 2015–2021. Methods: We searched the PubMed, Embase, Scopus, and CINAHL databases for all associated studies carried out from January 1, 2015, to May 31, 2021, without any limitations regarding the language the studies were written in. To prevent selection bias, gray documents were tackled by other means. The methodological approaches were assessed by applying the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and the Newcastle-Ottawa Scale (NOS) collaboration tool. Results: Forty studies were selected at first and then 15 studies that met the inclusion criterion. Most of the studies showed a considerable decrease in total medical spending and drug spending in both outpatient and inpatient services. After the implementation of ZPED, studies showed that the medical services increased and total hospital income sustained, despite a decrease in drug revenue. Minimal or no government subsidy is required from a financial perspective. Conclusions: Although, the government could implement ZEPD with lower medical cost and drug cost to patients, and sustained income for health facilities, we have limited understanding of whether the increase in medical services was induced by the provider or was a response to unmet needs in the population. Further, studies using rigorous and advanced methods to study health policy, patient behaviors, provider behaviors, and government decisions are warranted.
The Dynamic Motor Control Index as a Marker of Age-Related Neuromuscular Impairment

Biomarkers that can identify age-related decline in walking function have potential to promote healthier aging by triggering timely interventions that can mitigate or reverse impairments. Recent evidence suggests that changes in neuromuscular control precede changes in walking function; however, it is unclear which measures are best suited for identifying age-related changes. In this study, non-negative matrix factorization of electromyography data collected during treadmill walking was used to calculate two measures of the complexity of muscle co-activations during walking for 36 adults: (1) the number of muscle synergies and (2) the dynamic motor control index. Study participants were grouped into young (18–35 years old), young-old (65–74 years old), and old–old (75+ years old) subsets. We found that the dynamic motor control index [χ2(2) = 9.41, p = 0.009], and not the number of muscle synergies [χ2(2) = 5.42, p = 0.067], differentiates between age groups [χ2(4) = 10.62, p = 0.031, Nagelkerke R2 = 0.297]. Moreover, an impairment threshold set at a dynamic motor control index of 90 (i.e., one standard deviation below the young adults) was able to differentiate between age groups [χ2(2) = 9.351, p = 0.009]. The dynamic motor control index identifies age-related differences in neuromuscular complexity not measured by the number of muscle synergies and may have clinical utility as a marker of neuromotor impairment.