Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Identification and Expression Analysis of OsbZIP09 Target Genes in Rice Reveal Its Mechanism of Controlling Seed Germination

Seed dormancy and germination are key events in plant development and are critical for crop production, and defects in seed germination or the inappropriate release of seed dormancy cause substantial losses in crop yields. Rice is the staple food for more than half of the world’s population, and preharvest sprouting (PHS) is one of the most severe problems in rice production, due to a low level of seed dormancy, especially under warm and damp conditions. Therefore, PHS leads to yield loss and a decrease in rice quality and vitality. We reveal that mutation of OsbZIP09 inhibited rice PHS. Analysis of the expression of OsbZIP09 and its encoded protein sequence and structure indicated that OsbZIP09 is a typical bZIP transcription factor that contains conserved bZIP domains, and its expression is induced by ABA. Moreover, RNA sequencing (RNA-seq) and DNA affinity purification sequencing (DAP-seq) analyses were performed and 52 key direct targets of OsbZIP09 were identified, including OsLOX2 and Late Embryogenesis Abundant (LEA) family genes, which are involved in controlling seed germination. Most of these key targets showed consistent changes in expression in response to abscisic acid (ABA) treatment and OsbZIP09 mutation. The data characterize a number of key target genes that are directly regulated by OsbZIP09 and contribute to revealing the molecular mechanism that underlies how OsbZIP09 controls rice seed germination.
Disturbance of myocardial metabolism participates in autoantibodies against β1‐adrenoceptor‐induced cardiac dysfunction

Cardiac dysfunction is involved in disorders of energy metabolism. High‐titre autoantibodies against the β1‐adrenoceptor (β1‐AAs) have been reported to exist in patients with cardiac dysfunction; however, the mechanism by which β1‐AAs affect cardiac function is unknown. This study aimed to determine whether β1‐AAs disturb myocardium energy metabolism and cause cardiac dysfunction. β1‐AA monoclonal antibodies (β1‐AAmAbs) were successfully pre‐synthesized by hybridoma clones and used in all experiments. β1‐AAmAbs impaired cardiac function and induced a myocardial metabolic disturbance, as evidenced by decreased left ventricular ejection fraction and fractional shortening. In addition, β1‐AAmAbs decreased the adenosine triphosphate level and increased cardiac energy consumption (rate–pressure product). We further showed that the effects of β1‐AAmAbs on heart tissue might involve the mitochondria and metabolic pathways via the β1‐adrenoceptor based on an immunoprecipitation and mass spectrometry. Additionally, we found that β1‐AAmAbs impaired myocardial mitochondrial structure, decreased the membrane potential, and induced insufficient mitophagy. In conclusion, β1‐AAmAb‐induced cardiac dysfunction is partly due to a disturbance in myocardial energy metabolism.
ALMI—A Generic Active Learning System for Computational Object Classification in Marine Observation Images

In recent years, an increasing number of cabled Fixed Underwater Observatories (FUOs) have been deployed, many of them equipped with digital cameras recording high-resolution digital image time series for a given period. The manual extraction of quantitative information from these data regarding resident species is necessary to link the image time series information to data from other sensors but requires computational support to overcome the bottleneck problem in manual analysis. As a priori knowledge about the objects of interest in the images is almost never available, computational methods are required that are not dependent on the posterior availability of a large training data set of annotated images. In this paper, we propose a new strategy for collecting and using training data for machine learning-based observatory image interpretation much more efficiently. The method combines the training efficiency of a special active learning procedure with the advantages of deep learning feature representations. The method is tested on two highly disparate data sets. In our experiments, we can show that the proposed method ALMI achieves on one data set a classification accuracy A > 90% with less than N = 258 data samples and A > 80% after N = 150 iterations, i.e., training samples, on the other data set outperforming the reference method regarding accuracy and training data required.
The Polybasic Cleavage Site in SARS-CoV-2 Spike Modulates Viral Sensitivity to Type I Interferon and IFITM2

The furin cleavage site in the spike protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals, compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. ABSTRACT The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein. The presence of a polybasic cleavage site in SARS-CoV-2 spike at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-CoV-2 compared to SARS-CoV-1 by facilitating maturation of the spike precursor by furin-like proteases in the producer cells rather than endosomal cathepsins in the target. We investigate the relevance of the polybasic cleavage site in the route of entry of SARS-CoV-2 and the consequences this has for sensitivity to interferons (IFNs) and, more specifically, the IFN-induced transmembrane (IFITM) protein family that inhibit entry of diverse enveloped viruses. We found that SARS-CoV-2 is restricted predominantly by IFITM2, rather than IFITM3, and the degree of this restriction is governed by route of viral entry. Importantly, removal of the cleavage site in the spike protein renders SARS-CoV-2 entry highly pH and cathepsin dependent in late endosomes, where, like SARS-CoV-1 spike, it is more sensitive to IFITM2 restriction. Furthermore, we found that potent inhibition of SARS-CoV-2 replication by type I but not type II IFNs is alleviated by targeted depletion of IFITM2 expression. We propose that the polybasic cleavage site allows SARS-CoV-2 to mediate viral entry in a pH-independent manner, in part to mitigate against IFITM-mediated restriction and promote replication and transmission. This suggests that therapeutic strategies that target furin-mediated cleavage of SARS-CoV-2 spike may reduce viral replication through the activity of type I IFNs. IMPORTANCE The furin cleavage site in the spike protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals, compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. Here, we show that SARS-CoV-2 is inhibited by antiviral membrane protein IFITM2 and that the sensitivity is exacerbated by deletion of the furin cleavage site, which restricts viral entry to low pH compartments. Furthermore, we find that IFITM2 is a significant effector of the antiviral activity of type I interferons against SARS-CoV-2 replication. We suggest that one role of the furin cleavage site is to reduce SARS-CoV-2 sensitivity to innate immune restriction, and thus, it may represent a potential therapeutic target for COVID-19 treatment development.
An RNA-interference screen in Drosophila to identify ZAD-containing C2H2 zinc finger genes that function in female germ cells

Abstract The zinc finger-associated domain (ZAD) is present in over 90 C2H2 zinc finger (ZNF) proteins. Despite their abundance, only a few ZAD-ZNF genes have been characterized to date. Here, we systematically analyze the function of 68 ZAD-ZNF genes in Drosophila female germ cells by performing an in vivo RNA-interference screen. We identified eight ZAD-ZNF genes required for oogenesis, and based on further characterization of the knockdown phenotypes, we uncovered defects broadly consistent with functions in germ cell specification and/or survival, early differentiation, and egg chamber maturation. These results provide a candidate pool for future studies aimed at functionalization of this large but poorly characterized gene family.
Influence of Electric Field on Microstructures of Pentacene Thin‐Films in Field‐Effect Transistors

We report on electric‐field‐induced irreversible structural modifications in pentacene thin films after long‐term operation of organic field‐effect transistor (OFET) devices. Micro‐Raman spectroscopy allows for the analysis of the microstructural modifications of pentacene in the small active channel of OFET during device operation. The results suggest that the herringbone packing of pentacene molecules in a solid film is affected by an external electric field, particularly the source‐to‐drain field that parallels the a–b lattice plane. The analysis of vibrational frequency and Davydov splitting in the Raman spectra reveals a singular behavior suggesting a reduced separation distance between pentacene molecules after long‐term operations and, thus, large intermolecular interactions. These results provide evidence for improved OFET performance after long‐term operation, related to the microstructures of organic semiconductors. It is known that the application of large electric fields alters the semiconductor properties of the material owing to the generation of defects and the trapping of charges. However, we first suggest that large electric fields may alter the molecular geometry and further induce structural phase transitions in the pentacene films. These results provide a basis for understanding the improved electronic properties in test devices after long‐term operations, including enhanced field‐effect mobility, improved on/off current ratio, sharp sub‐threshold swing, and a slower decay rate in the output drain current. In addition, the effects of source‐to‐drain electric field, gate electric field, current and charge carriers, and thermal annealing on the pentacene films during OFET operations are discussed.
Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance

Abstract Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.
Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets

Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments are typically performed with well-mixed cultures and large effective population sizes, while pathogenic microbes typically experience strong bottlenecks during infection or drug treatment. Yet, our knowledge about adaptation in very small populations, where selection strength and mutation supplies are limited, is scant. In this study, wild-type and mutator strains of the bacterium Escherichia coli were evolved for about 100 generations towards increased resistance to the β-lactam antibiotic cefotaxime in millifluidic droplets of 0.5 µL and effective population size of approximately 27,000 cells. The small effective population size limited the adaptive potential of wild-type populations, where adaptation was limited to inactivating mutations, which caused the increased production of outer-membrane vesicles, leading to modest fitness increases. In contrast, mutator clones with an average of ~30-fold higher mutation rate adapted much faster by acquiring both inactivating mutations of an outer-membrane porin and particularly inactivating and gain-of-function mutations, causing the upregulation or activation of a common efflux pump, respectively. Our results demonstrate how in very small populations, clonal interference and mutation bias together affect the choice of adaptive trajectories by mediating the balance between high-rate and large-benefit mutations.
Noncanonical functions of the serine‐arginine‐rich splicing factor (SR) family of proteins in development and disease

Members of the serine/arginine (SR)‐rich protein family of splicing factors play versatile roles in RNA processing steps and are often essential for normal development. Dynamic changes in RNA processing and turnover allow fast cellular adaptions to a changing microenvironment and thereby closely cooperate with transcription factor networks that establish cell identity within tissues. SR proteins play fundamental roles in the processing of pre‐mRNAs by regulating constitutive and alternative splicing. More recently, SR proteins have also been implicated in other aspects of RNA metabolism such as mRNA stability, transport and translation. The‐ emerging noncanonical functions highlight the multifaceted functions of these SR proteins and identify them as important coordinators of gene expression programmes. Accordingly, most SR proteins are essential for normal cell function and their misregulation contributes to human diseases such as cancer.
Atomic displacement parameters for Ni(ND3)4(NO2)2 from 9 K X-ray and 13 K time-of-flight neutron diffraction data

Structural parameters derived from 9(1)K X-ray diffraction data and 13(1)K time-of-flight neutron diffraction data on perdeuterated tetraamminedinitro-nickel(II), Ni(ND 3 ) 4 (NO 2 ) 2 , are compared. It is shown that excellent agreement can be obtained for both positional and thermal parameters derived separately from the two experiments, provided that great care is taken in all steps of the process, including data collection, data reduction, and nuclear and electronic structure refinement. The mean difference in the thermal parameters, , is as low as 0.00034 A 2 and 1/2 = 1.92, showing that, even without any form of scaling between the parameters, the same values can be obtained. This, compared with other such studies, indicates that time-of-flight neutron diffraction data can give structural information of a quality comparable to monochromatic neutron diffraction. The excellent correspondence between the thermal parameters derived separately from X-ray and neutron diffraction data gives confidence in the deconvolution of the thermal motion from the X-ray diffraction data, which is necessary for any study of a static electron density distribution.
Focal Adhesion Kinase Fine Tunes Multifaced Signals toward Breast Cancer Progression

Simple Summary Breast cancer is the most common diagnosed malignancy and the main leading cause of tumor-related death among women worldwide. Thus, several studies have been carried out in order to identify valuable molecular biomarkers for the prognosis and prediction of therapeutic responses in breast tumor patients. Focal adhesion kinase (FAK) is a cytoplasmic non-receptor protein tyrosine kinase overexpressed in diverse tumors, including breast cancer. Here, we review previous evidence dealing with the role of FAK in the growth and metastatic features of breast tumors, its action as a driver of cancer stem cell phenotype and function as a mechanotransducer, and FAK activity within the breast tumor microenvironment and critical prognostic value of FAK expression in breast malignancy. In addition, we recapitulated the usefulness of FAK inhibitors in breast cancer treatment. Abstract Breast cancer represents the most common diagnosed malignancy and the main leading cause of tumor-related death among women worldwide. Therefore, several efforts have been made in order to identify valuable molecular biomarkers for the prognosis and prediction of therapeutic responses in breast tumor patients. In this context, emerging discoveries have indicated that focal adhesion kinase (FAK), a non-receptor tyrosine kinase, might represent a promising target involved in breast tumorigenesis. Of note, high FAK expression and activity have been tightly correlated with a poor clinical outcome and metastatic features in several tumors, including breast cancer. Recently, a role for the integrin-FAK signaling in mechanotransduction has been suggested and the function of FAK within the breast tumor microenvironment has been ascertained toward tumor angiogenesis and vascular permeability. FAK has been also involved in cancer stem cells (CSCs)-mediated initiation, maintenance and therapeutic responses of breast tumors. In addition, the potential of FAK to elicit breast tumor-promoting effects has been even associated with the capability to modulate immune responses. On the basis of these findings, several agents targeting FAK have been exploited in diverse preclinical tumor models. Here, we recapitulate the multifaceted action exerted by FAK and its prognostic significance in breast cancer. Moreover, we highlight the recent clinical evidence regarding the usefulness of FAK inhibitors in the treatment of breast tumors.
The cerebellum could serve as a potential imaging biomarker of dementia conversion in patients with amyloid‐negative amnestic mild cognitive impairment

As part of network‐specific neurodegeneration, changes in cerebellar gray matter (GM) volume and impaired cerebello–cerebral functional networks have been reported in Alzheimer disease (AD). Compared with healthy controls, a volume loss in the cerebellum has been observed in patients with continuum of AD. However, little is known about the anatomical or functional changes in patients with clinical AD but no brain amyloidosis. We aimed to identify the relationship between cerebellar volume and dementia conversion of amyloid‐negative mild cognitive impairment (MCI).
Effect of Short-Term Metro-Rhythmic Stimulations on Gait Variability

The aim of the study was to define the effect of different short-term metro-rhythmic stimulations on the time and spatial parameters of gait. The secondary goal was to test whether prior instructions on how to respond to stimulations played a significant role in the stimulation by sound stimuli. Experimental tests of gait were conducted on a group of 36 healthy participants: group 1—subjects who were not informed how to react after hearing sound stimuli, group 2—subjects who received a clear instruction before the test to adjust the frequency of taking steps to the rhythm of the music. The gait research was carried out on a Zebris FDM-S (zebris Medical Gmbh, Isny, Germany) treadmill for various sound stimuli (arrhythmic stimulus, rhythmic stimuli at different rate). It was shown that a short-term influence of metro-rhythmic stimulations changes the time and spatial parameters of gait, i.e., gait frequency, length and duration of the gait cycle. The greatest impact on the modification of the time–space parameters of walking is exerted by rhythmic stimuli at a pace different from the frequency of gait at a preferred velocity. Providing information on how to respond to sounds heard may be important in gait therapy with RAS (rhythmic auditory stimulation).
Migration history and risk of psychosis: results from the multinational EU-GEI study

Abstract Background Psychosis rates are higher among some migrant groups. We hypothesized that psychosis in migrants is associated with cumulative social disadvantage during different phases of migration. Methods We used data from the EUropean Network of National Schizophrenia Networks studying Gene-Environment Interactions (EU-GEI) case–control study. We defined a set of three indicators of social disadvantage for each phase: pre-migration, migration and post-migration. We examined whether social disadvantage in the pre- and post-migration phases, migration adversities, and mismatch between achievements and expectations differed between first-generation migrants with first-episode psychosis and healthy first-generation migrants, and tested whether this accounted for differences in odds of psychosis in multivariable logistic regression models. Results In total, 249 cases and 219 controls were assessed. Pre-migration (OR 1.61, 95% CI 1.06–2.44, p = 0.027) and post-migration social disadvantages (OR 1.89, 95% CI 1.02–3.51, p = 0.044), along with expectations/achievements mismatch (OR 1.14, 95% CI 1.03–1.26, p = 0.014) were all significantly associated with psychosis. Migration adversities (OR 1.18, 95% CI 0.672–2.06, p = 0.568) were not significantly related to the outcome. Finally, we found a dose–response effect between the number of adversities across all phases and odds of psychosis (⩾6: OR 14.09, 95% CI 2.06–96.47, p = 0.007). Conclusions The cumulative effect of social disadvantages before, during and after migration was associated with increased odds of psychosis in migrants, independently of ethnicity or length of stay in the country of arrival. Public health initiatives that address the social disadvantages that many migrants face during the whole migration process and post-migration psychological support may reduce the excess of psychosis in migrants.
MnO Nanocrystals: A Platform for Integration of MRI and Genuine Autophagy Induction for Chemotherapy

Herein, a kind of novel monocomponent hydrophilic and paramagnetic manganese(II) oxide nanocrystal is prepared in polar solution by a one‐pot microwave‐assisted synthesis. This kind of nanocrystal can be taken up efficiently to serve as an excellent T1 magnetic resonance imaging (MRI) contrast agent with an enhanced r1 value of 0.81 mM−1 s−1. The key to the success of this method is that no additional capping agents are required for coating onto the surface via ligand exchange, facilitating research of their intrinsic biological activities. Furthermore, multiple lines of convincing evidence are presented to prove that MnO nanocrystals (NCs) elicit p53‐activation‐independent and authentic functional autophagy via inducing autophagosome formation. Notably, there are very few reports so far of the autophagy phenomenon induced by magnetic nanocrystals. Moreover, these results offer an indication for cancer therapy that MnO NCs combined with doxorubicin at a nontoxic concentration can have a definite synergistic effect, which is mediated through the genuine autophagy induction, on killing cancer cells in vitro and in vivo.