Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteria-induced mineral precipitation: a mechanistic review

Micro-organisms contribute to Earth’s mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.
Fullerene Derivatives for the Applications as Acceptor and Cathode Buffer Layer Materials for Organic and Perovskite Solar Cells

Organic solar cells (OSCs) and organic‐inorganic metal halide perovskite solar cells (pero‐SCs) have been regarded as two promising photovoltaic technologies. The recent advances with power conversion efficiency over 10% and 20% have been realized in OSCs and pero‐SCs, respectively. The fullerene derivatives play important role as acceptor materials in OSCs and cathode buffer layer (CBL) materials in OSCs and pero‐SCs. Here, we provide a comprehensive overview of recent progresses and perspectives of the functional fullerene derivatives as acceptor materials and CBLs for OSCs and pero‐SCs.
A CNN identified by reinforcement learning-based optimization framework for EEG-based state evaluation

Objective. Electroencephalogram (EEG) data, as a kind of complex time-series, is one of the most widely-used information measurements for evaluating human psychophysiological states. Recently, numerous works applied deep learning techniques, especially the convolutional neural network (CNN), into EEG-based research. The design of the hyper-parameters of the CNN model has a great influence on the performance of the model. Therefore, automatically designing these hyper-parameters can save the time and labor of experts. This leads to the appearance of the neural architecture search technique. In this paper, we propose a reinforcement learning (RL)-based step-by-step framework to efficiently search for CNN models. Approach. Specifically, the deep Q network in RL is first used to determine the depth of convolutional layers and the connection modes among layers. Then particle swarm optimization algorithm is used to fine-tune the number and size of convolution kernels. Through this step-by-step strategy, the search space can be narrowed in each step for saving the overall time cost. This framework is employed for both EEG-based sleep stage classification and driver drowsiness evaluation tasks. Main results. The results show that compared with state-of-the-art methods, the high-performance CNN models identified by the proposed optimization framework, can achieve high overall accuracy and better root mean squared error in the two tasks. Significance. Therefore, the proposed optimization framework has a great potential to provide high-performance results for other kinds of classification and prediction tasks. In this way, it can greatly save researchers’ time cost and promote broader applications of CNNs.
Onset of Nut Allergy in a Pediatric Cohort: Clinical and Molecular Patterns in the AFRUSEN Study

Background: Nut allergy is a growing problem, yet little is known about its onset in children. Objective: To characterize the onset of nut allergy in children in southern Europe. Methods: The study population comprised consecutive patients up to 14 years of age who visited allergy departments with an initial allergic reaction to peanut, tree nut, or seed. The allergy work-up included a clinical history, food challenge, skin prick testing, determination of whole-extract sIgE, and ImmunoCAP ISAC-112 assay. Results: Of the 271 children included, 260 were first diagnosed with nut allergy at a mean age of 6.5 years and at a mean (SD) of 11.8 (21.2) months after the index reaction. The most common culprit nuts at onset were walnut (36.5%), peanut (28.5%), cashew (10.4%), hazelnut (8.5%), pistachio (5.4%), and almond (5%). Onset of peanut allergy was more frequent in children ≤6 years and walnut in those aged >6 years (P=.032). In 65% of cases, the allergic reaction occurred the first time the patient consumed the nut, and 35% of reactions were anaphylactic. Overall, polysensitization to nuts was detected by skin prick testing in 64.9% of patients, although this rate was lower among walnut-allergic children (54.7%) and peanut-allergic children (54.1%) (P<.0001). Sensitization to 2S albumins was predominant (75%), especially Jug r 1 (52.8%), whereas sensitization to lipid transfer proteins was less relevant (37%). Conclusion: In the population we assessed, the onset of nut allergy occurred around 6 years of age, slightly later than that reported in English-speaking countries. Walnut was the main trigger, followed by peanut. 2S albumin storage proteins, especially Jug r 1, were the most relevant allergens. This study will help guide management and may contribute to preventive strategies in pediatric nut allergy.
Youth and Provider Perspectives on Behavior-Tracking Mobile Apps: Qualitative Analysis

Background Mobile health apps stand as one possible means of improving evidence-based mental health interventions for youth. However, a better understanding of youth and provider perspectives is necessary to support widespread implementation. Objective The objective of this research was to explore both youth and provider perspectives on using mobile apps to enhance evidence-based clinical care, with an emphasis on gathering perspectives on behavior-tracking apps. Methods Inductive qualitative analysis was conducted on data obtained from semistructured interviews held with 10 youths who received psychotherapy and 12 mental health care providers who conducted therapy with youths aged 13-26 years. Interviews were independently coded by multiple coders and consensus meetings were held to establish reliability. Results During the interviews, the youths and providers broadly agreed on the benefits of behavior tracking and believed that tracking via app could be more enjoyable and accessible. Providers and youths also shared similar concerns that negative emotions and user burden could limit app usage. Participants also suggested potential app features that, if implemented, would help meet the clinical needs of providers and support long-term use among youth. Such features included having a pleasant user interface, reminders for clients, and graphical output of data to clients and providers. Conclusions Youths and providers explained that the integration of mobile health into psychotherapy has the potential to make treatment, particularly behavior tracking, easy and more accessible. However, both groups had concerns about the increased burden that could be placed on the clients and providers.
CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice1

CRISPR-based assessment reveals nonredundant functions and diversified evolution of enzymes in the gibberellin metabolic pathway in rice. Gibberellin (GA) functions as an essential natural regulator of growth and development in plants. For each step of the GA metabolic pathway, different copy numbers can be found in different species, as is the case with the 13 genes across four enzymatic steps in rice (Oryza sativa). A common view is that such gene duplication creates homologs that buffer organisms against loss-of-function (LOF) mutations. Therefore, knockouts of any single homolog might be expected to have little effect. To test this question, we generated clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) knockouts for these homologs and measured effects on growth and reproduction. Surprisingly, we report here that there is consistently one or more essential gene at each enzymatic step, for which LOF mutation induces death or sterility—suggesting that the GA pathway does not have a redundancy route and that each gene family is essential for GA metabolism. In most of these genes from the same gene family, we observed defects in plant height and infertility, suggesting that the duplicated members retain functions related to GA synthesis or degradation. We identified both subfunctionalization of the three recently diversified homologs OsKO1, OsKO2, and OsKO5 and neofunctionalization in OsKO3 and OsKO4. Thus, although the function of each step is conserved, the evolution of duplicates in that step is diversified. Interestingly, the CRISPR/Cas9 lines at the SD1 locus were typically sterile, whereas the natural sd1 mutants, related to the “Green Revolution” in rice, show normal setting rates. Collectively, our results identify candidates for control of GA production and provide insight into the evolution of four critical gene families in plants.
Heterozygous missense variant in TRPC6 in a boy with rapidly progressive infantile nephrotic syndrome associated with diffuse mesangial sclerosis

Transient receptor potential channel C6 encoded by TRPC6 is involved in slit diaphragm formation in podocytes, and abnormalities of the TRPC6 protein cause various glomerular diseases. The first identified pathogenic variant of TRPC6 was found to cause steroid‐resistant nephrotic syndrome that typically developed in adulthood and then slowly led to end‐stage renal disease, along with a renal pathology of focal segmental glomerulosclerosis. Here, we report a patient with rapidly progressing infantile nephrotic syndrome and a heterozygous missense TRPC6 variant. The patient, a 2‐year‐old Japanese boy, developed steroid‐resistant nephrotic syndrome at age 11 months. His renal function deteriorated rapidly, and peritoneal dialysis was introduced at age 1 year and 6 months. His renal pathology, obtained at age 1 year and 1 month, was consistent with diffuse mesangial sclerosis (DMS). Clinical exome analysis and custom panel analysis for hereditary renal diseases revealed a reported heterozygous missense variant in TRPC6 (NM_004621.5:c.523C > T:p.Arg175Trp). This is the first report of a patient with a TRPC6‐related renal disorder associated with DMS.
Erastin synergizes with cisplatin via ferroptosis to inhibit ovarian cancer growth in vitro and in vivo

Cisplatin‐based chemotherapy is the first‐line treatment for ovarian cancer. However, acquired resistance to cisplatin treatment or serious side effects often occurs in ovarian cancer, and thus, there is an urgent need for effective and combined therapies to overcome such obstacles. In the present study, we aimed to uncover synergistic effects between erastin and cisplatin (CDDP) in inhibiting ovarian cancer cell growth by inducing ferroptosis in vitro and in vivo.
Mycorrhizal symbiosis primes the accumulation of antiherbivore compounds and enhances herbivore mortality in tomato

Abstract Plant association with arbuscular mycorrhizal fungi (AMF) can increase their ability to overcome multiple stresses, but their impact on plant interactions with herbivorous insects is controversial. Here we show higher mortality of the leaf-chewer Spodoptera exigua when fed on tomato plants colonized by the AMF Funneliformis mosseae, evidencing mycorrhiza-induced resistance. In search of the underlying mechanisms, an untargeted metabolomic analysis through ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS) was performed. The results showed that mycorrhizal symbiosis had a very limited impact on the leaf metabolome in the absence of stress, but significantly modulated the response to herbivory in the damaged area. A cluster of over accumulated metabolites was identified in those leaflets damaged by S. exigua feeding in mycorrhizal plants, while unwounded distal leaflets responded similar to those from non-mycorrhizal plants. These primed-compounds were mostly related to alkaloids, fatty acid derivatives and phenylpropanoid-polyamine conjugates. The deleterious effect on larval survival of some of these compounds, including the alkaloid physostigmine, the fatty acid derivatives 4-oxododecanedioic acid and azelaic acid, was confirmed. Thus, our results evidence the impact of AMF on metabolic reprograming upon herbivory that leads to a primed accumulation of defensive compounds.
Improved low-dose positron emission tomography image reconstruction using deep learned prior

Positron emission tomography (PET) is a promising medical imaging technology that provides non-invasive and quantitative measurement of biochemical process in the human bodies. PET image reconstruction is challenging due to the ill-poseness of the inverse problem. With lower statistics caused by the limited detected photons, low-dose PET imaging leads to noisy reconstructed images with much quality degradation. Recently, deep neural networks (DNN) have been widely used in computer vision tasks and attracted growing interests in medical imaging. In this paper, we proposed a maximum a posteriori (MAP) reconstruction algorithm incorporating a convolutional neural network (CNN) representation in the formation of the prior. Rather than using the CNN in post-processing, we embedded the neural network in the reconstruction framework for image representation. Using the simulated data, we first quantitatively evaluated our proposed method in terms of the noise-bias tradeoff, and compared with the filtered maximum likelihood (ML), the conventional MAP, and the CNN post-processing methods. In addition to the simulation experiments, the proposed method was further quantitatively validated on the acquired patient brain and body data with the tradeoff between noise and contrast. The results demonstrated that the proposed CNN-MAP method improved noise-bias tradeoff compared with the filtered ML, the conventional MAP, and the CNN post-processing methods in the simulation study. For the patient study, the CNN-MAP method achieved better noise-contrast tradeoff over the other three methods. The quantitative enhancements indicate the potential value of the proposed CNN-MAP method in low-dose PET imaging.
Pressurized hot water extraction and chemometric fingerprinting of flavonoids from Bidens pilosa by UPLC-tandem mass spectrometry

ABSTRACT The need for greener extraction procedures that are quick and efficient has prompted the evolution of pressurized hot water extraction (PHWE). Here, the extraction of flavonoids from Bidens pilosa was demonstrated using PHWE at 50°C, 100°C and 150°C. The extracts were analyzed on UPLC-qTOF-MS/MS and 28 flavonoids of different classes were identified. Further analysis of the data using principal component analysis revealed differential distribution patterns of the identified molecules. In overall, the extraction yield increased proportionately with increasing temperature. It can thus be deduced that PHWE is an excellent extraction method of flavonoids from plant tissues. Again, this study reiterates B. pilosa as a rich source of flavonoids.
Primary and secondary non-response: in need of operational definitions in observational studies

© Author(s) (or their employer(s)) 2021. Reuse permitted under CC BYNC. No commercial reuse. See rights and permissions. Published by BMJ. INTRODUCTION Treatment response to biologics and targeted synthetic diseasemodifying antirheumatic drugs in rheumatoid arthritis (RA) patients can be classified as primary or secondary nonresponse, based on evidence of an initial response. Conceptually, primary nonresponse is generally considered if the drug was ineffective, with no clinical response within the initial treatment period, while secondary nonresponse would be considered if, after an initial response, the effectiveness is lost over time. Despite these generally accepted definitions, there is no consensus on how to operationalise these concepts. Consequently, the current observational evidence is highly heterogeneous and the prevalence of primary versus secondary failure remains largely unknown. The underlying mechanisms for primary and secondary nonresponse may differ, 5 thus, we believe that defining the type of nonresponse is key to improving patient care. While primary nonresponse may be due to a mechanistic failure, secondary nonresponse may be driven by immunogenicity. Previous studies have shown that both the type of nonresponse and the development of antidrug antibodies (ADAbs) are important factors when predicting the success of the second biologic. 7 Thus, developing clear definitions of how to operationalise primary and secondary nonresponse is essential to accelerate research that aims to predict the optimal therapy for a given patient, which will, in turn, improve clinical practice recommendations. For example, if a patient is a primary nonresponder to a tumour necrosis factor inhibitor (antiTNF), the best practice would likely be to switch to a biologic with different mechanism of action. However, if the patient was able to achieve clinical response prior to failure (secondary nonresponder), it would be reasonable to proceed with another antiTNF. Additionally, following the growing postmarketing research targeting comparative effectiveness of treatments in RA, agreement on operational definitions would improve crossstudy comparisons. Thus, we believe that unifying this terminology would benefit the clinical practice, clinical trials and postmarketing research, and a unique operational procedure for those three scenarios would be ideal. However, since translating clinical concepts into studies in realworld data represents extra challenges, we drive our discussion in the context of observational research. In this viewpoint, we discuss the concepts of primary and secondary nonresponse, with special attention to its implementation in observational data, and we suggest recommendations for future research. Ultimately, we hope this discussion will trigger expert committees to develop standard terminology for these concepts as a step towards harmonising study results.
Plasma Metabolic Profiling in Patients With Silicosis and Asbestosis

Supplemental Digital Content is available in the text Objectives: To explore the circulating metabolites and related pathways in silicosis and asbestosis exposure to different mineral dust. Methods: Plasma of 30 silicosis, 30 asbestosis, and 20 healthy controls was analyzed using liquid chromatography-mass spectrometry. Metabolic networks and the relevance of the identified metabolic derangements were explored. Results: Compared with healthy controls, 37 and 39 dysregulated plasma metabolites were found in silicosis and asbestosis, respectively, of which the levels of 22 metabolites differed. Three major pathways were identified, among which arginine and proline metabolism was identified as the most closely related metabolic pathway. Conclusions: The types and quantities of up-regulated metabolites including lipids, amino acids, and carnitines differed between silicosis and asbestosis. Pathways inducing lung fibrosis were common to mineral dust exposure, while pathways related to oxidative stress and tumorigenesis differed between silicosis and asbestosis.
A Family of Toxoplasma gondii Genes Related to GRA12 Regulate Cyst Burdens and Cyst Reactivation

If host immunity weakens, Toxoplasma gondii cysts recrudesce in the central nervous system and cause a severe toxoplasmic encephalitis. Current therapies target acute stage infection but do not eliminate chronic cysts. ABSTRACT Toxoplasma gondii causes a chronic infection that renders the immunocompromised human host susceptible to toxoplasmic encephalitis triggered by cyst reactivation in the central nervous system. The dense granule protein GRA12 is a major parasite virulence factor required for parasite survival during acute infection. Here, we characterized the role of four GRA12-related genes in acute and chronic stages of infection. While GRA12A, GRA12B, and GRA12D were highly expressed in asexual stage tachyzoites and bradyzoites, expression of GRA12C appeared to be restricted to the sexual stages. In contrast to deletion of GRA12 (Δgra12), no major defects in acute virulence were observed in Δgra12A, Δgra12B, or Δgra12D parasites, though Δgra12B parasites exhibited an increased tachyzoite replication rate. Bradyzoites secreted GRA12A, GRA12B, and GRA12D and incorporated these molecules into the developing cyst wall, as well as the cyst matrix in distinct patterns. Similar to GRA12, GRA12A, GRA12B, and GRA12D colocalized with the dense granules in extracellular tachyzoites, with GRA2 and the intravacuolar network in the tachyzoite stage parasitophorous vacuole and with GRA2 in the cyst matrix and cyst wall. Chronic stage cyst burdens were decreased in mice infected with Δgra12A parasites and were increased in mice infected with Δgra12B parasites. However, Δgra12B cysts were not efficiently maintained in vivo. Δgra12A, Δgra12B, and Δgra12D in vitro cysts displayed a reduced reactivation efficiency, and reactivation of Δgra12A cysts was delayed. Collectively, our results suggest that a family of genes related to GRA12 play significant roles in the formation, maintenance, and reactivation of chronic stage cysts. IMPORTANCE If host immunity weakens, Toxoplasma gondii cysts recrudesce in the central nervous system and cause a severe toxoplasmic encephalitis. Current therapies target acute stage infection but do not eliminate chronic cysts. Parasite molecules that mediate the development and persistence of chronic infection are poorly characterized. Dense granule (GRA) proteins such as GRA12 are key virulence factors during acute infection. Here, we investigated four GRA12-related genes. GRA12-related genes were not major virulence factors during acute infection. Instead, GRA12-related proteins localized at the cyst wall and cyst matrix and played significant roles in cyst development, persistence, and reactivation during chronic infection. Similar to GRA12, the GRA12-related proteins selectively associated with the intravacuolar network of membranes inside the vacuole. Collectively, our results support the hypothesis that GRA12 proteins associated with the intravacuolar membrane system support parasite virulence during acute infection and cyst development, persistence, and reactivation during chronic infection.