Miracle-dz/UniFAR-FTUs huggingface dataset:
Br Ief Definitive Repor T

IntroductIon Severe myeloid cytopenia is a serious complication of radiation or chemotherapy and leads to profound susceptibility to a variety of opportunistic infections. Myeloablative treatments are also required for autologous or allogeneic hematopoietic cell transplantation (HCT), a common medical procedure to treat hematological disorders. Hematopoiesis from the transplanted hematopoietic stem cells (HSCs) and progenitor cells (HS/PCs) occurs with a significant lag phase, in which the patient shows severe myeloid cytopenia and is vulnerable to severe and potentially lethal infections, for example by the clinically important gram-negative bacterium Pseudomo-nas aeruginosa or the fungus Aspergillus fumigatus. Despite improved conditioning regimens, better supportive care, and new antimicrobial and antifungal agents, infection remains a cause of death in 8% of autologous HCT and 17–20% of allogeneic HCT recipients (Tomblyn et al., 2009). Antibiotic and antifungal prophylaxis during HCT can also be asso
across the of

The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp. , we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted en-zymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest asso-ciations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages. false SNP calling a truth set, simulated 670,000 random mutations in the reference genome of mutations sequenced strains. aligned the raw reads to the random-mutated reference, called SNPs, and compared the known truth set of simulated mutations to the accuracy of our data and process. Both the number of true positives (658,566; precision, 99.8%, and sensitivity, 98.3%) and the number of false positives (386; 0.06%) show the high accuracy of the overall process, including read quality, alignment accuracy, and the SNP calls. the chromosomal copy number variation (CCNV) and the distribution of SNPs across the genome, calculated the alignment density (depth of read coverage) and SNP density (frequency of SNPs per site), respectively. All VCF ﬁles were summarized in 10-kb nonoverlapping windows. The alignment density was normalized by the average genomic coverage and the window length. The SNP density was normalized by the window length. The genome assembly of Pb18 is anchored to chromosomes (12); we used this reference to map the alignment density and SNP density into chromosomes. PbCnh, Pb300, Pb01 model, relaxed clock/uncorrelated lognormal clock model. For nonpartitioned variant sites, we used the strict clock model, with the constant pattern model, general time reversible (GTR) (G (cid:5) I) substitution model, and 20,000,000 Markov chain Monte Carlo (MCMC) chains. Tracer v1.6. 0 (http://beast.bio.ed.ac.uk/Tracer) was used to visualize traces and inspect the effective sample size and MCMC. We determined the relationship of the sequenced isolates using the NeighborNet algorithm with SplitsTree4 (40). and annotated Paracoccidioides
Pathogenic mutation hotspots in protein kinase domain structure

Control of eukaryotic cellular function is heavily reliant on the phosphorylation of proteins at specific amino acid residues, such as serine, threonine, tyrosine, and histidine. Protein kinases that are responsible for this process comprise one of the largest families of evolutionarily related proteins. Dysregulation of protein kinase signaling pathways is a frequent cause of a large variety of human diseases including cancer, autoimmune, neurodegenerative, and cardiovascular disorders. In this study, we mapped all pathogenic mutations in 497 human protein kinase domains from the ClinVar database to the reference structure of Aurora kinase A (AURKA) and grouped them by the relevance to the disease type. Our study revealed that the majority of mutation hotspots associated with cancer are situated within the catalytic and activation loops of the kinase domain, whereas non‐cancer‐related hotspots tend to be located outside of these regions. Additionally, we identified a hotspot at residue R371 of the AURKA structure that has the highest number of exclusively non‐cancer‐related pathogenic mutations (21) and has not been previously discussed.
Cross-Species Metabolomic Analyses in the Brassicaceae Reveals Common Responses to Ultraviolet-B Exposure

Abstract Exposure to UV-B radiation, an intrinsic component of solar light, is detrimental to all living organisms as chromophore units of DNA, RNA and proteins readily absorb high-energy photons. Indirect damage to the same molecules and lipids is mediated by elevated reactive oxygen species (ROS) levels, a side effect of exposure to UV-B stress. To protect themselves from UV-B radiation, plants produce phytochemical sunscreens, among which flavonoids have shown to be particularly effective. The core aglycone of flavonoid molecules is subjected to chemical decoration, such as glycosylation and acylation, further improving sunscreen properties. In particular, acylation, which adds a phenolic ring to flavonoid molecules, enhances the spectral absorption of UV-A and UV-B rays, providing to this class of compounds exceptional shielding power. In this study, we comprehensively analyzed the responses to UV-B radiation in four Brassicaceae species, including Arabidopsis thaliana, Brassica napus, Brassica oleracea, and Brassica rapa. Our study revealed a complete reprogramming of the central metabolic pathway in response to UV-B radiation characterized by increased production of functional precursors of specialized metabolites with UV-B shielding properties, indicating a targeted effort of plant metabolism to provide increased protection. The analysis of specialized metabolites and transcripts revealed the activation of the phenylpropanoid–acetate pathway, leading to the production of specific classes of flavonoids and a cross-species increase in phenylacylated-flavonoid glucosides with synapoyl glycoside decorations. Interestingly, our analysis also revealed that acyltransferase genes of the class of serine carboxypeptidase-like (SCPLs) proteins are costitutively expressed, but downregulated in response to UV-B radiation, possibly independently of the ELONGATED HYPOCOTYL 5 (HY5) signaling pathway.
Combined proteomics and transcriptomics identifies serpin family C member 1 associated protein as a biomarker of endometriosis

Abstract Objective To explore potential biomarkers indicating endometriosis (EM). Materials and methods A proteomics method and combined quantitative transcriptomics were adopted to highlight markers in the EM. Venn analysis was used to integrate the ribonucleic acid sequencing (RNA-seq) and protein profiles. Promising candidate markers were tested by enzyme-related immunosorbent assay. Results A sum of 979 mRNAs and 39 proteins were tested to be significantly differentially expression in the standard cluster compared with the EM cluster. Venn analysis showed a filtered signature of only two down-regulated molecules in the EM group, i.e. fetuin B (FETUB) and serpin family C member 1 (SERPINC1); the latter showed a big variance between the control category and the EM set in the authentication test. Conclusion SERPINC1 may be a useful possible biomarker for the analysis of EM.
The state of the coast (Toestand van de kust). Case study: North Holland

Over more than a thousand years, the Dutch coast has been eroding for large stretches. Coastal retreat puts coastal functions (e.g. safety against flooding) under pressure. Since 1990, the Dutch policy aims at preventing further retreat of the coastline, but in the meantime taking the valuable dynamical behaviour of the coast into account. Therefore, sand nourishments have been preferred over hard structures to counteract the systematic erosion. The Dutch Government is responsible for the planning and realization of the nourishments. Deltares has been commissioned to develop the knowledge needed to carry out an effective nourishment strategy. Due to its strategic importance, the Dutch coastal area is also one of the most extensive studied areas in the world. However, most of the morphological research so far has focussed into the understanding of just part of the Dutch coastal system (e.g. dune area, foreshore). Hardly any attempt has been made to describe in a quantitative way the complete morphodynamic development of the system from the dunes to deep water and the cumulative effect of the past nourishment strategy at various time- and spatial scales. The aim of this study is the assessment of the functioning of the complete coastal system through a number of indicators describing the morphological system at different time scales. In particular, the relations between anthropogenic intervention (e.g. sediment management over the past 40 years, construction of hard structures), natural yearly variation in storminess and time variation of the indicators are assessed. As a case study, the North Holland coast has been analyzed. The study shows that the current nourishment strategy has lead to a clear shift in indicators related to safety, nature and recreation towards a "safer" coastline, with larger space suitable for nature and tourism . Hard structures also play a primary role into the morphological development of the coastline. The effect of the yearly variation in storminess appears to be correlated to a number of indicators (e.g. dune foot position). However, nourishments have contributed to damp the effect of these natural forcings. The results of different nourishment strategies applied in different areas have been intercom pared with the aim of assessing the most cost-effective management strategy. The present study is part of the project (KPP - Beheer en Onderhoud van de kust; Coastal Management and Maintenance). We would like to acknowledge comments and remarks from Gemma Ramaekers (Waterdienst) which have resulted into an improved manuscript. We would also like to thank the photo raph Jurriaan Brobbel for the picture on the cover.
Viltolarsen: a treatment option for Duchenne muscular dystrophy patients who are amenable to exon 53 skipping therapy

ABSTRACT Introduction Duchenne muscular dystrophy (DMD) is a progressive genetic disease leading to muscular weakness. DMD is caused by mutations of the dystrophin gene on the X chromosome that is responsible for production of dystrophin protein. Dystrophin contributes to structural support in muscle cells and mutations result in dystrophin protein deficiency which causes muscle damage and the associated clinical presentation. Exon skipping medications, including the exon 53 targeting viltolarsen, are the first agents with the ability to partially restore dystrophin protein. Areas covered Herein, the authors profile viltolarsen for the DMD patients who are amenable to exon 53 skipping therapy and provide their expert perspectives on this subject. Expert opinion Current findings suggest that viltolarsen could play a role in the current and possible future treatment of DMD. Viltolarsen seems to be safe and restores dystrophin protein to around 6% of the normal level. Due to orphan drug status, after the completion of the phase 2 clinical trial, viltolarsen was granted accelerated approval in Japan and in the US. A phase 3 trial is currently in progress and needs to earn full approval. Although a multidisciplinary approach continues to be critical, the addition of exon skipping agents like viltolarsen may improve the quality of patients’ lives. However, data on the long-term safety and efficacy of this medication are not yet available due to its recent accelerated approval.
Rice‐produced classical swine fever virus glycoprotein E2 with herringbone‐dimer design to enhance immune responses

Summary Pestiviruses, including classical swine fever virus, remain a concern for global animal health and are responsible for major economic losses of livestock worldwide. Despite high levels of vaccination, currently available commercial vaccines are limited by safety concerns, moderate efficacy, and required high doses. The development of new vaccines is therefore essential. Vaccine efforts should focus on optimizing antigen presentation to enhance immune responses. Here, we describe a simple herringbone‐dimer strategy for efficient vaccine design, using the classical swine fever virus E2 expressed in a rice endosperm as an example. The expression of rE2 protein was identified, with the rE2 antigen accumulating to 480 mg/kg. Immunological assays in mice, rabbits, and pigs showed high antigenicity of rE2. Two immunizations with 284 ng of the rE2 vaccine or one shot with 5.12 μg provided effective protection in pigs without interference from pre‐existing antibodies. Crystal structure and small‐angle X‐ray scattering results confirmed the stable herringbone dimeric conformation, which had two fully exposed duplex receptor binding domains. Our results demonstrated that rice endosperm is a promising platform for precise vaccine design, and this strategy can be universally applied to other Flaviviridae virus vaccines.
Spatio-temporal correlation super-resolution optical fluctuation imaging

We describe a new concept of multimodal super-resolution imaging which combines the cumulant analysis from Super-resolution Optical Fluctuation Imaging (SOFI) with the imprinting of three-dimensional, spectral or other information into peculiar Point-Spread Function (PSF) patterns. This concept allows for encoding multidimensional or multimodal information into a single image plane and to extract this information by an appropriate spatio-temporal correlation analysis of emitter fluctuations. Here, we develop the general theory of this concept, and present proof-of-principle experiments of three-dimensional super-resolution imaging.
Epidemiology and identification of Eimeria species affecting poultry in East Gojjam Zone, North West Ethiopia

Abstract Background Despite the expansion of modernized poultry farming in Ethiopia, the presence of high prevalence of Eimeria species is the bottleneck in the sector causing high morbidity and mortality rate in poultry. Objectives The objectives of this study were to estimate the prevalence and identify Eimeria species and investigate the major risk factors. Method A cross‐sectional study was conducted from November 2019 to April 2020 in East Gojjam Zone, North West Ethiopia. A total of 384 chickens were used. Both floatation and McMaster coprological techniques were employed. Univariate and multinomial logistic regression was used to calculate the odds ratio for the associated risk factors. Analysis of variance was used to analyse differences in Eimeria oocyst counts among the groups. Results Overall prevalence of Eimeria species in poultry from the study area was 26.5%. Age (OR = 0.25, p = 0.001), management system (OR = 12.44, p = 0.001) and production system (OR = 0.37, p = 0.001) were found significantly (p < 0.05) associated with the risk of Eimeria species in poultry. The mean Eimeria oocyst count was significantly different by age and management system (F = 6.526, p = 0.002), (F = 5.369, p = 0.005), respectively. The mean Eimeria oocyst count was significantly greater in 6–12 weeks (p = 0.004) and <6 weeks of age (p = 0.025). A total of 6 Eimeria species were identified. Eimeria tenella (46.07%), Eimeria necatrix (24.5%) and Eimeria acervulina (8.82%) were the most common Eimeria species encountered. Conclusion The prevalence of Eimeria species was higher in poultry in North West Ethiopia. Therefore, tailor‐made intervention is required to mitigate risk factors and reduce the prevalence of Eimeria species in poultry from the study area.
Nuclear Fusion: Holy Grail of Energy

The declining reserves of fossil fuels and their detrimental effects on the environment have thrust nuclear power based on fission reaction into the limelight as a promising option to energy-starved economies around the world. However, the 1986 Chernobyl and 2011 Fukushima accidents have heightened our fears about nuclear technology ’ s ability to provide a safe way of generating clean power. There is another kind of nuclear energy that has been powering the Sun and stars since their formation. It is nuclear fusion — a process in which two lighter nuclei, typically isotopes of hydrogen, combine together under conditions of extreme pressure and temperature to form a heavier nucleus. In this chapter, harnessing the energy produced in nuclear fusion reaction in a laboratory environment is discussed. Various research programs dedicated to building fusion reactors are also discussed. Emphasis is given on over-coming some of the technological challenges, such as surmounting the Coulomb barrier, confining the plasma, and achieving the “ ignition ” temperature for fusion.
Underwater archaeology and coastal management : focus on Alexandria

The knowledge that indigenous, artisanal and commercial fishers and marine hunters accumulate over the course of their fishing careers can be invaluable to marine researchers despite its low scientific repute among methodological purists. Over the past several decades, and in tropical, temperate and Arctic fisheries, it has cast considerable light on important subjects such as stock structure, interannual variability in stock abundance, migrations, the behaviour of larval/post-larval fish, currents and the nature of island wakes, nesting site fidelity in sea turtles, spawning aggregations and locations, local trends in abundance and local extinctions. It has also cast light on the dynamics of fisheries and their relationship to scientific understanding. This chapter draws on a series of examples from indigenous, artisanal and commercial fisheries to explore ways in which the knowledge of fishers and fisheries scientists can complement each other and, in the process, drive forward not only our knowledge about fisheries’ resources but also our capacity to manage our degraded marine ecosystems to recovery.
Log-periodic gravitational-wave background beyond Einstein gravity

Periodic patterns of logarithmic oscillations can arise in primordial curvature perturbation spectra and in the associated gravitational-wave background via different mechanisms. We show that, in the presence of log oscillations, the spectral shape of the stochastic background has a unique parametrization independent of its physical origin. We also show that this log-periodic modulation can be generated in any scenario beyond Einstein gravity endowed with an approximate discrete scale invariance, a symmetry typical of deterministic fractal spacetimes that could emerge in quantum gravity under certain conditions. We discuss how a log-oscillatory spectral shape arises from concrete inflationary models beyond Einstein gravity and the prospects for detection in Einstein Telescope and other next-generation gravitational-wave observatories. We find that these instruments will be sensitive to log-periodic features if the detection is made with a high signal-to-noise ratio (SNR) and that the error scales as 1/SNR .
Optical Script Identification for multi-lingual Indic-script

Script identification and text recognition are some of the major domains in the application of Artificial Intelligence. In this era of digitalization, the use of digital note-taking has become a common practice. Still, conventional methods of using pen and paper is a prominent way of writing. This leads to the classification of scripts based on the method they are obtained. A survey on the current methodologies and state-of-art methods used for processing and identification would prove beneficial for researchers. The aim of this article is to discuss the advancement in the techniques for script pre-processing and text recognition. In India there are twelve prominent Indic scripts, unlike the English language, these scripts have layers of characteristics. Complex characteristics such as similarity in text shape make them difficult to recognize and analyze, thus this requires advance preprocessing methods for their accurate recognition. A sincere attempt is made in this survey to provide a comparison between all algorithms. We hope that this survey would provide insight to a researcher working not only on Indic scripts but also other languages.
Semantics2Hands: Transferring Hand Motion Semantics between Avatars

Human hands, the primary means of non-verbal communication, convey intricate semantics in various scenarios. Due to the high sensitivity of individuals to hand motions, even minor errors in hand motions can significantly impact the user experience. Real applications often involve multiple avatars with varying hand shapes, highlighting the importance of maintaining the intricate semantics of hand motions across the avatars. Therefore, this paper aims to transfer the hand motion semantics between diverse avatars based on their respective hand models. To address this problem, we introduce a novel anatomy-based semantic matrix (ASM) that encodes the semantics of hand motions. The ASM quantifies the positions of the palm and other joints relative to the local frame of the corresponding joint, enabling precise retargeting of hand motions. Subsequently, we obtain a mapping function from the source ASM to the target hand joint rotations by employing an anatomy-based semantics reconstruction network (ASRN). We train the ASRN using a semi-supervised learning strategy on the Mixamo and InterHand2.6M datasets. We evaluate our method in intra-domain and cross-domain hand motion retargeting tasks. The qualitative and quantitative results demonstrate the significant superiority of our ASRN over the state-of-the-arts. Code available at https://github.com/abcyzj/Semantics2Hand
Embracing Errors is More Efficient than Avoiding Them through Constrained Coding for DNA Data Storage

DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the number of errors, a common technique is to include constraints that avoid homopolymers (consecutive repeated nucleotides) and balance the GC content, as sequences with homopolymers and unbalanced GC contents are often associated with larger error rates. However, constrained coding comes at the cost of an increase in redundancy. An alternative (unconstrained coding) is to control the errors by randomizing the sequences, embracing errors, and paying for them with additional coding redundancy. In this paper, we determine the error regimes in which embracing errors is more efficient than constrained coding. We find that constrained coding is inefficient in most common error regimes for DNA data storage. Specifically, the error probabilities for nucleotides in homopolymers and in sequences with unbalanced GC contents must be very large for constrained coding to achieve a higher code rate than unconstrained coding.