bluuebunny/crossref_metadata_2025_split huggingface dataset:
The N764K and N856K mutations in SARS-CoV-2 Omicron BA.1 S protein generate potential cleavage sites for SKI-1/S1P protease
Authors: Maaroufi Halim 
Published: January 2022

AbstractSpike (S) protein is a key protein in coronaviruses life cycle. SARS-CoV-2 Omicron BA.1 variant of concern (VoC) presents an exceptionally high number of 30 substitutions, 6 deletions and 3 insertions in the S protein. Recent works revealed major changes in the SARS-CoV-2 Omicron biological properties compared to earlier variants of concern (VoCs). Here, these major changes could be explained, at least in part, by the mutations N764K and/or N856K in S2 subunit. These mutations were not previously detected in other VoCs. N764K and N856K generate two potential cleavage sites for SKI-1/S1P serine protease, known to cleave viral envelope glycoproteins. The new sites where SKI-1/S1P could cleave S protein might impede the exposition of the internal fusion peptide for membrane fusion and syncytia formation. Based on the human protein atlas, SKI-1/S1P protease is not found in lung tissues (alveolar cells type I/II and endothelial cells), but present in bronchus and nasopharynx. This may explain why Omicron has change of tissue tropism. Viruses have evolved to use several host proteases for cleavage/activation of envelope glycoproteins. Mutations that allow viruses to change of protease may have a strong impact in host range, cell and tissue tropism, and pathogenesis.
Evaluation of gonadal function in transfusion-dependent β-thalassemia patients of Bangladesh
Authors: Chowdhury Romana , Hasan Mohammad Mehedi , Ahmed Mushfiq Newaz , Iktidar Mohammad Azmain , Hoque Tapan Md. Mazharul , Islam Shaheen Sheikh Saiful , Rahman Atiar , Khatun Ayesha 
Published: January 2022

AbstractBackgroundHypogonadism is one of the most frequent complications in transfusion-dependent thalassemia patients, and early recognition and treatment is the core element to restore impaired gonadal function. Despite the high burden of disease, relevant studies are scarcely addressing the gonadal function of such patients. The pattern of gonadal function in transfusion-dependent thalassemia patients must be picturized before planning a generalized management plan; therefore, this study was conducted.MethodsThis cross-sectional study was conducted at the Department of Transfusion Medicine of Bangabandhu Sheikh Mujib Medical University. According to inclusion and exclusion criteria, a total of 94 patients were enrolled in this study. A detailed history and thorough clinical examination were carried out in each patient and recorded using a pretested structured questionnaire. In addition, laboratory assessment of LH, FSH, testosterone and estradiol in serum were also done. Data were analyzed using STATA (v.16).ResultsThe mean age of the patients with transfusion-dependent thalassemia was 18.81±4.65 (SD), with 53.3% of the patients being male. The most common symptoms of gonadal dysfunction among males were loss of body hair (6%) followed by fatigue (4%), and among females were slow or absent breast growth, hot flashes and amenorrhea (6.82% each).ConclusionThe overall prevalence of hypogonadism was 35.11%, 18.1% being normogonadotropic, 11.7% being hypogonadotropic, and 5.3% being hypergonadotropic. Therefore, gonadal hormone analysis of transfusion-dependent thalassemia patients can be considered a screening tool for assessing gonadal function and early detection and prevention of hypogonadism.
Death review caused by Covid 19 in Bangladesh
Authors: Roy Biswas Rajat Sanker , Nath Jishu Deb , Nisha Fatema Emrose 
Published: January 2022

ABSTRACTIntroductionCOVID-19 pandemic had taken away lots of human life prematurely worldwide and death laid its icy hands also on Bangladesh. So, objectives of this study were to explore the monthly distributions, age, sex, co-morbidities, localities and duration of hospital stay among the COVID death cases.MethodsIn this observational study six months hospital death files were collected and explored for monthly distributions, age, sex, co-morbidities, localities and hospital stay. RT-PCR positive confirmed 113 COVID deaths were enrolled and suspected COVID deaths were excluded. Ethical clearance from the hospital authority was taken before hand. Data was compiled and analyzed by SPSS-20.ResultsThere was a low frequency of death in May-2021 and October-2021(7.1% and 2.7% respectively) but more during June -2021 to September 2021 (12.4%, 16.8%, 42.5% and 18.6% respectively). Female deaths were little more than male deaths(53.1% vs 46.9%). Age more than 51 years were the most vulnerable where 26(23%) deaths were at age group 51-60 years, 39(34.5%) deaths were at 61-70 years and 22(19.4%) deaths were more than 71 years. Mean age of death was found 60.66 years and mean duration of hospital stay was found 9.45 days. Maximum duration of hospital stay was 45 days for one patient. Co-morbidities of death cases revealed 52(46.00%) patients had DM and HTN both, 17(15.0%) patients had HTN, 16(14.1%) had DM, 3(2.6%) had BA and COPD, 4(3.5%) had CKD, 2(1.7%) had cancer, 3(2.6%) had CVD, 19(16.8%) had IHD and 16(14.1%) patients had no co-morbidities. Locality of the death cases revealed 44(38.9%) came from rural areas and 69(61.1%) came from urban areas.ConclusionHigher age group and multiple co-morbidities specially DM, HTN and IHD were related with COVID deaths mostly found in our study.
Super-Resolution of Magnetic Resonance Images Acquired Under Clinical Protocols using Deep Attention-based Method
Authors: Li Bryan M. , Castorina Leonardo V. , Valdés-Hernández Maria del C. , Clancy Una , Wiseman Stewart J. , Sakka Eleni , Storkey Amos J. , Garcia Daniela Jaime , Cheng Yajun , Doubal Fergus , Thrippleton Michael T. , Stringer Michael , Wardlaw Joanna M. 
Published: January 2022

AbstractVast quantities of Magnetic Resonance Images (MRI) are routinely acquired in clinical practice but, to speed up acquisition, these scans are typically of a quality that is sufficient for clinical diagnosis but sub-optimal for large-scale precision medicine, computational diagnostics, and large-scale neuroimaging research. Here, we present a critic-guided framework to upsample low-resolution (often 2D) MRI scans. In addition, we incorporated feature-importance and self-attention methods into our model to improve the interpretability of this work. We evaluate our framework on paired low- and high-resolution brain MRI structural full scans (i.e. T1-, T2-weighted and FLAIR sequences are simultaneously input) obtained in clinical and research settings from scanners manufactured by Siemens, Phillips and GE. We showed that the upsampled MRIs are qualitatively faithful to the ground-truth high-quality scans (PSNR = 35.39; MAE = 3.78E −3; NMSE = 4.32E −10; SSIM = 0.9852; mean normal-appearing grey/white matter ratio intensity differences ranging from 0.0363 to 0.0784 for FLAIR, from 0.0010 to 0.0138 for T1-weighted and from 0.0156 to 0.074 for T2-weighted sequences). The automatic raw segmentations of tissues and lesions using the super-resolved images have fewer false positives and higher accuracy than those obtained from interpolated images in protocols represented with more than three sets in the training sample, making our approach a strong candidate for practical application in clinical research.
Sex differences in the influence of toxoplasmosis on stress and perceived anxiety: Evidence for the stress-coping hypothesis
Authors: Flegr Jaroslav , Kaňková Šárka 
Published: January 2022

AbstractLife-long infection with Toxoplasma, which affects 30% of the human population, has specific behavioral effects. The stress-coping hypothesis explains why the toxoplasmosis-associated behavioral changes go in opposite directions in men and women. It suggests that toxoplasmosis impairs the health of humans, which results in chronic stress. Men and women are known to cope with stress in opposite ways. The first presumption of the hypothesis, impaired health, was confirmed in many studies. The second, higher level of stress, was tested only rarely. Levels of stress and anxiety, measured with the Perceived Stress Scale, and the State-Trait Anxiety Inventory X-2, respectively, were compared in a population of 614 Toxoplasma-free and 162 Toxoplasma-infected subjects. Higher stress was detected in the infected men, but not women. We also found that physical health had a positive rather than negative effect on stress when mental health is controlled, which seems to contradict the prediction of the stress-coping hypothesis. No differences were found in the anxiety of infected and noninfected subjects. Subjects who have objective reasons for stress (those with worse physical health) are less stressed than those without such reasons.
Mathematical Modeling of Thyroid Homeostasis: Implications for the Allan-Herndon-Dudley Syndrome
Authors: Wolff Tobias M. , Veil Carina , Dietrich Johannes W. , Müller Matthias A. 
Published: January 2022

AbstractObjectiveA mathematical model of the pituitary-thyroid feedback loop is extended to deepen the understanding of the Allan-Herndon-Dudley syndrome (AHDS).BackgroundThe AHDS is characterized by unusual thyroid hormone concentrations and a mutation in theSLC16A2gene encoding for the monocarboxylate transporter 8 (MCT8). This mutation leads to a loss of thyroid hormone transport activity. One hypothesis to explain the unusual hormone concentrations of AHDS patients is that due to the loss of thyroid hormone transport activity, thyroxine (T4) is partially retained in thyroid cells.MethodsThis hypothesis is investigated by extending a mathematical model of the pituitary-thyroid feedback loop to include a model of the net effects of membrane transporters such that the thyroid hormone transport activity can be considered. Two modeling approaches of the membrane transporters are employed: on the one hand a nonlinear approach based on the Michaelis-Menten kinetics and on the other hand its linear approximation. The unknown parameters are identified through a constrained parameter optimization.ResultsIn dynamic simulations, damaged membrane transporters result in a retention ofT4in thyroid cells and ultimately in the unusual hormone concentrations of AHDS patients. The two different modeling approaches lead to similar results.ConclusionThe results support the hypothesis that a partial retention ofT4in thyroid cells represents one mechanism responsible for the unusual hormone concentrations of AHDS patients. Moreover, our results suggest that the retention ofT4in thyroid cells could be the main reason for the unusual hormone concentrations of AHDS patients.
The sowing date changed the temperature and light conditions in the field modified the cadmium content of brown rice (Oryza sativa L.) by regulating the expression of Cd-related genes
Authors: Rang Zhongwen , Xiao Huan , Yi Zhenxie , Wang Xuehua , Chen Qiaomao , Kuang Yu , Ao Hejun 
Published: January 2022

AbstractCadmium (Cd) contamination in rice is a potential health hazard when ingested through the food chain worldwide. Reducing the Cd content in rice through agronomic measures is an effective way to reduce the risk of Cd contamination to human health. In order to clarify the correlation between temperature and light conditions and Cd accumulation (Cd-A) and Cd content of brown rice (CdBR) during the field growth period (FGP) of rice, consequently provide a theoretical basis for the selection of sowing date (SD) for “Low-Cd-Rice” production, field experiment with different SDs was carried out by using two rice varieties with different Cd accumulation characteristics (Luliangyou 996, V1, a high Cd accumulation variety; Zhuliangyou 819, V2, a low Cd accumulation variety). The results showed that the temperature and light factors such as mean soil temperature (ST), mean air temperature (AT), soil accumulation temperature (SAT), air accumulation temperature (AAT), ultraviolet radiation accumulation (UR), photosynthetic radiation accumulation (PR), light intensity accumulation (I) and sunshine hours accumulation (SH) varied to different degrees under different SDs; The difference in CdBR in two varieties could be up to 2.82 and 8.48 times respectively among SDs, with the CdBR of S4 and S5 of V2 being lower than the national standard of 0.2 mg/kg. The relative expression of OsIRT1 in the root system was significantly positively correlated with ST, SAT, AT, AAT, and SH, while OsNramp5, OsNramp1, and OsHMA3 showed significant negative correlations with ST, SAT, AT, AAT, and SH in relative expression in the root system; OsIRT1 expressed in the roots of V1 was significantly negatively correlated with CdBR, while OsHMA3 expression was significantly positively correlated with CdBR; OsLCD, OsNramp1, and OsHMA3 expression in the roots of V2 were significantly positively correlated with Cd-A and CdBR, while OsIRT1 in the roots of V2 and OsLCT1 in the leaves were significantly negatively correlated with Cd-A; The expression of OsNramp5 in roots was significantly negatively correlated with Cd-A and CdBR in both V1 and V2. Bias correlation analysis showed that ST, SAT, AT, and AAT were significantly negatively correlated with both Cd-A and CdBR; SH was significantly negatively correlated with CdBR in V1. Summarily, the temperature and light conditions during the FGP of rice and their regulation of the expression levels of related genes could be changed by sowing selection, so as to achieve safe production of rice under Cd-contaminated fields.
Self-rectifying magnetoelectric metamaterials enable precisely timed remote neural stimulation and restoration of sensory motor functions
Authors: Chen Joshua C. , Bhave Gauri , Alrashdan Fatima , Dhuliyawalla Abdeali , Robinson Jacob T. 
Published: January 2022

AbstractMagnetoelectric materials convert magnetic fields to electric fields and have applications in wireless data and power transmission, electronics, sensing, data storage, and biomedical technology. For example, magnetoelectrics could enable precisely timed remote stimulation of neural tissue, but the resonance frequencies where magnetoelectric effects are maximized are typically too high to stimulate neural activity. To overcome this challenge, we created the first self-rectifying magnetoelectric “metamaterial.” This metamaterial relies on nonlinear charge transport across semiconductor layers that allow the material to generate a steady bias voltage in the presence of an alternating magnetic field. This “self-rectification” allows us to generate arbitrary electrical pulse sequences that have a time-averaged voltage in excess of 1 V. As a result, we can use magnetoelectric nonlinear metamaterials (MNMs) to remotely stimulate peripheral nerves with repeatable latencies of less than 5 ms, which is more than 120 times faster than previous neural stimulation approaches based on magnetic materials. These short latencies enable this metamaterial to be used in applications where fast neural signal transduction is necessary such as in sensory or motor neuroprosthetics. As a proof of principle, we show wireless stimulation to restore a sensory reflex in an anesthetized rat model as well as using the MNM to restore signal propagation in a severed nerve. The rational design of nonlinearities in the magnetic-to-electric transduction pathway as described here opens the door to many potential designs of MNMs tailored to applications spanning electronics, biotechnology, and sensing.
A system-wide quantitative map of RNA and protein subcellular localisation dynamics
Authors: Villanueva Eneko , Smith Tom , Pizzinga Mariavittoria , Elzek Mohamed , Queiroz Rayner M. L. , Harvey Robert F. , Breckels Lisa M , Crook Oliver M. , Monti Mie , Dezi Veronica , Willis Anne E. , Lilley Kathryn S. 
Published: January 2022

AbstractExisting methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and mitochondria) and membraneless compartments (cytosol, nucleolus and phase-separated granules). Simultaneous interrogation of all RNA locations allows the system-wide quantification of RNA proportional distribution and the comprehensive analysis of RNA subcellular dynamics. Moreover, we have re-engineered the LOPIT (Localisation Of Proteins by Isotope Tagging) method, enabling integration with LoRNA, to jointly map RNA and protein subcellular localisation. Applying this framework, we obtain a global re-localisation map for 31839 transcripts and 5314 proteins during the unfolded protein response, uncovering that ER-localised transcripts are more efficiently recruited to stress granules than cytosolic RNAs, and revealing eIF3d is key to sustain cytoskeletal function. Overall, we provide the most exhaustive map to date of RNA and protein subcellular dynamics.
Does the impact of cultivar mixtures on virulence dynamics in Zymoseptoria tritici populations persist after interseason sexual reproduction?
Authors: Orellana-Torrejon Carolina , Vidal Tiphaine , Saint-Jean Sébastien , Suffert Frédéric 
Published: January 2022

AbstractThis study follows on from a previous study showing that binary mixtures of wheat cultivars affect the evolution of Zymoseptoria tritici populations within a field epidemic from the beginning (t1) to the end (t2) of a growing season. Here, we focused on the impact of interseason sexual reproduction on this evolution. We studied mixtures of susceptible and resistant cultivars (carrying Stb16q, a recently broken-down resistance gene) in proportions of 0.25, 0.5 and 0.75, and their pure stands. We determined the virulence status of 1440 ascospore-derived strains collected from residues of each cultivar by phenotyping on seedlings. Virulence frequencies were lower in mixtures than in pure stands of the resistant cultivar, as at t2, revealing that the impact of mixtures persisted until the beginning of the next epidemic (t3). The frequency of virulence was lower in the offspring population on the susceptible cultivar and, more surprisingly, the frequency of avirulence on the resistant cultivar increased after sexual reproduction. Our findings highlight two epidemiological processes in mixtures: selection within the local pathogen population between t1 and t2 driven by asexual cross-contamination between cultivars (previous study) and sexual crosses between avirulent and virulent strains between t2 and t3 driven by changes in the probabilities of physical encounters (this study). Mixtures therefore appear to be a promising strategy for the deployment of qualitative resistances, not only to limit the intensity of Septoria tritici blotch epidemics, but also to reduce the erosion of resistances by managing evolution of the pathogen population at a pluriannual scale.
Types of cis- and trans-gene regulation of expression quantitative trait loci across human tissues
Authors: Kvamme Jarred , Badsha MD Bahadur , Martin Evan A. , Wu Jiayu , Wang Xiaoyue , Fu Audrey Qiuyan 
Published: January 2022

AbstractExpression quantitative trait loci (eQTLs) have been identified for most genes in the human genome across tissues and cell types. While most of the eQTLs are near the associated genes, some can be far away or on different chromosomes, with the regulatory mechanisms largely unknown. Here, we study cis- and trans-regulation by eQTLs on protein-coding genes and long noncoding RNAs (lncRNAs) across nearly 50 tissues and cell types. Specifically, we constructed trios consisting of an eQTL, its cis-gene and trans-gene and inferred the regulatory relationships with causal network inference. We identify multiple types of regulatory networks for trios: across all the tissues, more than half of the trios are inferred to be conditionally independent, where the two genes are conditionally independent given the genotype of the eQTL (gene 1 ← eQTL → gene 2). Around 1.5% of the trios are inferred to be mediation (eQTL → mediator → target), around 1.3% fully connected among the three nodes, and just a handful v-structures (eQTL → gene 1 ← gene 2). Unexpectedly, across the tissues, on average more than half of the mediation trios have the trans-gene as the mediator. Most of the mediators (cis and trans) are tissue specific, and cis-gene mediators are significantly enriched for protein-coding genes, whereas trans-gene mediators have a similar distribution of protein-coding genes and lncRNAs to the whole genome.
Light-controlled phosphorylation in the TrkA-Y785 site by photosensitive UAAs activates the MAPK/ERK signaling pathway
Authors: Zhao Shu , Liu Dong 
Published: January 2022

AbstractTrkA is a membrane receptor that upon ligand binding, induces autophosphorylation of tyrosine residues in the intracellular domain, and this process includes sites in the kinase activation loop (Y670, Y674, Y675) and two direct sites involved in downstream signaling pathways (Y490, Y785). At present, researchers cannot fully elucidate the regulatory mechanism of TrkA phosphorylation because TrkA signaling is a highly dynamic process, and a strategy with high temporal and spatial resolution will be beneficial to the mechanism research. Our previous study proposed a design scheme for photosensitive TrkA, which utilizes a new molecular light control technology to target TrkA-Y490 and three kinase domain sites (Y670, Y674, and Y675) through Genetic Code Expansion (GCE) technology combined with site-directed mutagenesis. We chose two light-controllable unnatural amino acids (UAAs) to introduce at the specific phosphorylation sites of the target protein TrkA. We focused on the regulation mechanism of these sites on the MAPK/ERK pathway downstream of TrkA. However, this method has not yet been validated for the TrkA-Y785 site. Therefore, this paper will continue to test the light-controlled method we established earlier in the Y785 site. We aim to improve further the experimental model of light-controlled phosphorylation of TrkA that we have established and finally lay the foundation for the comprehensive analysis of kinase-related pathways.
Integrated fault detection for industrial process monitoring based on multi-dimensional Taylor network
Authors: Li Chen-Long , Yuan Chang-Shun , Ma Xiao-Shuang , Chen Wen-Liang , Wang Jun 
Published: January 2022

Purpose
This paper aims to provide a novel integrated fault detection method for industrial process monitoring.

Design/methodology/approach
A novel integrated fault detection method based on the combination of Mallat (MA) algorithm, weight-elimination (WE) algorithm, conjugate gradient (CG) algorithm and multi-dimensional Taylor network (MTN) dynamic model, namely, MA-WE-CG-MTN, is proposed in this paper. First, MA algorithm is taken as data pre-processing. Second, in virtue of approximation ability and low computation complexity owing to the simple structure of MTN, MTN dynamic models are constructed for each frequency band. Furthermore, the CG algorithm is used to discipline the model parameters and the outputs of MTN model of each frequency band are gained. Third, the authors introduce the WE algorithm to cut down the number of middle layer nodes of MTN, reducing the complexity of the network. Finally, the outputs of MTN model for each frequency band are superimposed to achieve outputs of MTN model, and fault detection is proceeded by the residual error generator based on the difference between the output of MTN model and the actual output.

Findings
The novel proposed method is used to perform fault detection for industrial process monitoring effectively, such as the Benchmark Simulation Model 1 wastewater treatment process.

Originality/value
The novel proposed method has generality and provides considerably improved performance and effectiveness, which is used to perform fault detection for industrial process monitoring. The proposed method has good robustness, low complexity and easy implementation.