Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic aging in adult neurogenesis

Neural stem cells (NSCs) in the hippocampus generate new neurons throughout life, which functionally contribute to cognitive flexibility and mood regulation. Yet adult hippocampal neurogenesis substantially declines with age and age‐related impairments in NSC activity underlie this reduction. Particularly, increased NSC quiescence and consequently reduced NSC proliferation are considered to be major drivers of the low neurogenesis levels in the aged brain. Epigenetic regulators control the gene expression programs underlying NSC quiescence, proliferation and differentiation and are hence critical to the regulation of adult neurogenesis. Epigenetic alterations have also emerged as central hallmarks of aging, and recent studies suggest the deterioration of the NSC‐specific epigenetic landscape as a driver of the age‐dependent decline in adult neurogenesis. In this review, we summarize the recently accumulating evidence for a role of epigenetic dysregulation in NSC aging and propose perspectives for future research directions.
Controlling therapeutic protein expression via inhalation of a butter flavor molecule

Abstract Precise control of the delivery of therapeutic proteins is critical for gene- and cell-based therapies, and expression should only be switched on in the presence of a specific trigger signal of appropriate magnitude. Focusing on the advantages of delivering the trigger by inhalation, we have developed a mammalian synthetic gene switch that enables regulation of transgene expression by exposure to the semi-volatile small molecule acetoin, a widely used, FDA-approved food flavor additive. The gene switch capitalizes on the bacterial regulatory protein AcoR fused to a mammalian transactivation domain, which binds to promoter regions with specific DNA sequences in the presence of acetoin and dose-dependently activates expression of downstream transgenes. Wild-type mice implanted with alginate-encapsulated cells transgenic for the acetoin gene switch showed a dose-dependent increase in blood levels of reporter protein in response to either administration of acetoin solution via oral gavage or longer exposure to acetoin aerosol generated by a commercial portable inhaler. Intake of typical acetoin-containing foods, such as butter, lychees and cheese, did not activate transgene expression. As a proof of concept, we show that blood glucose levels were normalized by acetoin aerosol inhalation in type-I diabetic mice implanted with acetoin-responsive insulin-producing cells. Delivery of trigger molecules using portable inhalers may facilitate regular administration of therapeutic proteins via next-generation cell-based therapies to treat chronic diseases for which frequent dosing is required.
Automatic Cervical Cell Classification Using Features Extracted by Convolutional Neural Network

Based on World Health Organization (WHO), cervical cancer is one of deadliest disease in human life. There are some researches related to this issues, but the need of improvement is still needed in order to help doctors in making a decision to the patients. This paper aims to provide a better method in cervical cell classification case indicated by giving better results compared to the previous researches. The proposed method mainly consists of three stages, features extraction, features reduction, and the last is classification. Convolutional Neural Network (CNN) algorithm which has been proven as a good algorithm in image domain was implemented in feature extraction stage. As CNN results high numbers of features, this research proposes a feature reduction stage consist of Linear Discriminant Analysis (LDA) followed by Principal Component Analysis (PCA). Those features were eventually classified by using robust kernel based classifier, Support Vector Machine (SVM) and softmax classifier. The results show that the proposed method has better performance than the previous researches.
Regulation of Helicobacter pylori Urease and Acetone Carboxylase Genes by Nitric Oxide and the CrdRS Two-Component System

The molecular strategies used by Helicobacter pylori to colonize and persist in the harsh environment of the human stomach are a critical area of study. Our study identified several genes in this gastric pathogen, including ureA, a gene encoding a protein essential to the survival of H. pylori, that are regulated via the CrdRS two-component system (TCS) in response to nitric oxide (NO). ABSTRACT Helicobacter pylori colonizes the human gastric mucosa and causes various gastroduodenal diseases, including peptic ulceration and gastric cancer. Colonization requires the actions of two-component systems (TCSs) to sense and respond to changes in the host environment. In this study, we evaluated gene regulation mediated by the CrdRS TCS. Few studies have evaluated this TCS, leaving the signal(s) yet to be exhaustively determined and a need for a more complete regulon to be delineated. We performed RNA sequencing (RNA-Seq) on three isogenic H. pylori 26695 mutants: a control, a mutant with deletion of the sensory histidine kinase, ΔcrdS, and a mutant with deletion of the response regulator, ΔcrdR. Comparison of the RNA-Seq results from these mutants established a 40-gene regulon putatively controlled by the CrdRS TCS. Quantitative reverse transcriptase PCR (RT-qPCR) was used to validate 7 of 11 putative regulon members selected for analysis. We further investigated 6 confirmed CrdRS regulon genes by using phospho-incompetent H. pylori 26695 CrdR D53A and CrdS H173A mutants. These experiments further confirmed the role of CrdRS in regulation of urease, acetone carboxylase, hofD, and HP1440. Expression of these CrdRS regulon genes was also evaluated under 10 μM nitric oxide (NO) conditions. This revealed that ureA, acxA, hofD, and HP1440 expression is affected by NO in a CrdRS-dependent manner. Importantly, three of these genes (ureA, acxA, and hofD) are known to play important roles in H. pylori colonization of the stomach. IMPORTANCE The molecular strategies used by Helicobacter pylori to colonize and persist in the harsh environment of the human stomach are a critical area of study. Our study identified several genes in this gastric pathogen, including ureA, a gene encoding a protein essential to the survival of H. pylori, that are regulated via the CrdRS two-component system (TCS) in response to nitric oxide (NO). NO is a product of the innate immune system of the human host. The identification of these genes whose expression is regulated by this molecule may give insights to novel therapeutics. Two genes (ureA and acxA) determined in this study to be regulated by NO via CrdRS have been previously determined to be regulated by other TCSs, indicating that the expression of these genes may be of critical importance to H. pylori.
Phase-conjugate mirror for water waves driven by the Faraday instability

Significance Nonlinear and parametric processes are central in mastering wave propagation. They are at the core of numerous applications in optics and acoustics. In the case of water waves, the Faraday instability is the archetype of a parametric excitation. A periodic vertical excitation results in the destabilization of a liquid interface. However, it has always been interpreted as an instability, completely overshadowing its potential to control water-wave propagation. In this paper, we unveil the ability of this temporal modulation to act as a phase-conjugate mirror. We show that waves refocus to any initial emitting source position, whatever the shape of the mirror. This paper thus revisits this historical instability and opens up exciting perspectives in water-wave manipulation. The Faraday instability appears on liquid baths submitted to vertical oscillations above a critical value. The pattern of standing ripples at half the vibrating frequency that results from this parametric forcing is usually shaped by the boundary conditions imposed by the enclosing receptacle. Here, we show that the time modulation of the medium involved in the Faraday instability can act as a phase-conjugate mirror––a fact which is hidden in the extensively studied case of the boundary-driven regime. We first demonstrate the complete analogy with the equations governing its optical counterpart. We then use water baths combining shallow and deep areas of arbitrary shapes to spatially localize the Faraday instability. We give experimental evidence of the ability of the Faraday instability to generate counterpropagating phase-conjugated waves for any propagating signal wave. The canonical geometries of a point and plane source are implemented. We also verify that Faraday-based phase-conjugate mirrors hold the genuine property of being shape independent. These results show that a periodic modulation of the effective gravity can perform time-reversal operations on monochromatic propagating water waves, with a remarkable efficiency compared with wave manipulation in other fields of physics.
Impact of pre‐analytical sample handling factors on plasma biomarkers of Alzheimer's disease

An unmet need exists for reliable plasma biomarkers of amyloid pathology, in the clinical laboratory setting, to streamline diagnosis of Alzheimer's disease (AD). For routine clinical use, a biomarker must provide robust and reliable results under pre‐analytical sample handling conditions. We investigated the impact of different pre‐analytical sample handling procedures on the levels of seven plasma biomarkers in development for potential routine use in AD. Using (1) fresh (never frozen) and (2) previously frozen plasma, we evaluated the effects of (A) storage time and temperature, (B) freeze/thaw (F/T) cycles, (C) anticoagulants, (D) tube transfer, and (E) plastic tube types. Blood samples were prospectively collected from patients with cognitive impairment undergoing investigation in a memory clinic. β‐amyloid 1–40 (Aβ40), β‐amyloid 1–42 (Aβ42), apolipoprotein E4, glial fibrillary acidic protein, neurofilament light chain, phosphorylated‐tau (phospho‐tau) 181, and phospho‐tau‐217 were measured using Elecsys® plasma prototype immunoassays. Recovery signals for each plasma biomarker and sample handling parameter were calculated. For all plasma biomarkers measured, pre‐analytical effects were comparable between fresh (never frozen) and previously frozen samples. All plasma biomarkers tested were stable for ≤24 h at 4°C when stored as whole blood and ethylenediaminetetraacetic acid (EDTA) plasma. Recovery signals were acceptable for up to five tube transfers, or two F/T cycles, and in both polypropylene and low‐density polyethylene tubes. For all plasma biomarkers except Aβ42 and Aβ40, analyte levels were largely comparable between EDTA, lithium heparin, and sodium citrate tubes. Aβ42 and Aβ40 were most sensitive to pre‐analytical handling, and the effects could only be partially compensated by the Aβ42/Aβ40 ratio. We provide recommendations for an optimal sample handling protocol for analysis of plasma biomarkers for amyloid pathology AD, to improve the reproducibility of future studies on plasma biomarkers assays and for potential use in routine clinical practice.
High conductivity carbon nanotube wires from radial densification and ionic doping

Application of drawing dies to radially densify sheets of carbon nanotubes (CNTs) into bulk wires has shown the ability to control electrical conductivity and wire density. Simultaneous use of KAuBr4 doping solution, during wire drawing, has led to an electrical conductivity in the CNT wire of 1.3×106 S/m. Temperature-dependent electrical measurements show that conduction is dominated by fluctuation-assisted tunneling, and introduction of KAuBr4 significantly reduces the tunneling barrier between individual nanotubes. Ultimately, the concomitant doping and densification process leads to closer packed CNTs and a reduced charge transfer barrier, resulting in enhanced bulk electrical conductivity.
SARS-CoV-2-infection in the setting of autotransplants for multiple sclerosis

ABSTRACT The severe adult respiratory syndrome virus type 2 (SARS-CoV-2) related acute respiratory distress syndrome (ARDS) has a strong immunological and inflammatory component; accordingly investigators are employing monoclonal antibodies to ameliorate the virus-induced cytokine storm such as antibodies against interleukin 6 (IL-6), tumor necrosis factors alpha (TNF-alpha) and CC chemokine receptor 5 (CCR5) (1). Cyclophosphamide (Cy) has proven its role in various settings including autoimmune diseases, and in the post-haploidentical stem cell transplant setting; Cy depletes cytotoxic and effector T cell populations while relatively sparing the regulatory T cells (Tregs) and could tip the balance away from the overtly pro-inflammatory setting (1). We present here the cases of three persons who were infected by the SARS-CoV-2 virus during the Cy-induced pancytopenia of an autologous hematopoietic stem cell transplantation (HSCT), aimed to down-regulate the immune response in multiple sclerosis (MS) (2). The surprisingly benign course of the COVID-19 in the three cases suggest that the Cy could have had a role in abrogating the inflammatory response in these persons.
On the effectiveness of random walks for modeling epidemics on networks

Random walks on graphs are often used to analyse and predict epidemic spreads and to investigate possible control actions to mitigate them. In this study, we first show that models based on random walks with a single stochastic agent (such as Google’s popular PageRank) may provide a poor description of certain features of epidemic spread: most notably, spreading times. Then, we discuss another Markov chain based method that does reflect the correct mean infection times for the disease to spread between individuals in a network, and we determine a procedure that allows one to compute them efficiently via a sampling strategy. Finally, we present a novel centrality measure based on infection times, and we compare its node ranking properties with other centrality measures based on random walks. Our results are provided for a simple SI model for epidemic spreading.
The flagellar length control system: exploring the physical biology of organelle size

How cells build and maintain dynamic structures of defined size is currently an important unsolved problem in quantitative cell biology. The flagella of the unicellular green alga Chlamydomonas provide a highly tractable model system to investigate this general question, but while the powerful genetics of this organism have revealed numerous genes required for proper flagellar length, in most cases we do not understand their mechanistic role in length control. Flagellar length can be viewed as the steady state solution of a dynamical system involving assembly and disassembly of axonemal microtubules, with assembly depending on an active transport process known as intraflagellar transport (IFT). The inherent length dependence of IFT gives rise to a family of simple models for length regulation that can account for many previously described phenomena such as the ability of flagella to maintain equal lengths. But these models requires that the cell has a way to measure flagellar length in order to adjust IFT rates accordingly. Several models for length sensing have been modeled theoretically and evaluated experimentally, allowing them to be ruled out. Current data support a model in which the diffusive return of the kinesin motor driving IFT provides a length dependence that ultimately is the basis for length regulation. By combining models of length sensing with a more detailed representation of cargo transport and availability, it is now becoming possible to formulate concrete hypotheses to explain length altering mutants.
Memory Versus Expectation: Processing Relative Clauses in a Flexible Word Order Language

Abstract Memory limitations and probabilistic expectations are two key factors that have been posited to play a role in the incremental processing of natural language. Relative clauses (RCs) have long served as a key proving ground for such theories of language processing. Across three self‐paced reading experiments, we test the online comprehension of Hungarian subject‐ and object‐extracted RCs (SRCs and ORCs, respectively). We capitalize on the syntactic properties of Hungarian that allow for a variety of word orders within RCs, which helps us to delineate the processing costs associated with memory demand and violated expectations. Results showed a processing cost at the RC verb for structures that have longer verb‐argument distances, despite those structures being more frequent in the corpus. These findings thus support theories that attribute processing difficulty to memory limitations, rather than theories that attribute difficulty to less expected structures.
Evaluation of a stepped, fixed-height magnification marker stand for use with a 100-mm marker in implant sizing prediction in 52 total hip replacement procedures in dogs

Objective To describe the use of a 100-millimeter marker placed on a stepped, fixed-height magnification marker stand to measure radiographic magnification on accuracy of implant size prediction when used for canine total hip replacement (THR) implant size selection. Study design Retrospective study. Animals Fifty-two hips in 45 dogs. Methods This study evaluated 52 consecutive canine total hip replacement surgery pre-planning procedures involving 45 dogs with 7 undergoing staged bilateral THRs. Data collected included demographic information, measured radiographic magnification for magnification recalibration, implant size prediction of the cups (52) and the stems (52) based on digital templates superimposed on digital radiographs, and the actual implant sizes used during surgery. Results Use of the magnification marker stand (MMS) and template application system resulted in an accurate prediction of implant size of 98/104 implants (94.2%) implants. Conclusion A 100-mm marker placed on a magnification marker stand was a viable method to measure and recalibrate for magnification on digital radiographs during the template process to predict the THR implant sizes that should be available when the surgery begins. Clinical significance This stepped calibration marker stand is helpful in determination of an accurate preoperative THR implant size prediction, lowering implant stock thresholds, operating time, and associated complications. Additionally, the radiographic documentation of the marker’s step height allows for indefinite confirmation of the magnification marker height used and for accurate repeatability for all follow-up imaging examinations and contralateral procedure planning.
Characterization of a glycan-binding complex of minor pilins completes the analysis of Streptococcus sanguinis type 4 pili subunits

Significance Type 4 pili (T4P)—important in bacterial pathogens—are filaments composed of one well-characterized major pilin, and several minor pilins whose roles are often poorly understood. Streptococcus sanguinis T4P are composed of five pilins, which makes it a good model to determine the role of each pilin subunit in detail. Here, we characterize PilA and PilC, showing how they interact and how they function. Together with our previous findings, this provides an integrated view of the role of the five pilin subunits in S. sanguinis T4P. PilE1/PilE2 are the major pilins forming the backbone of the filament, while the three minor pilins (PilA, PilB, and PilC) form a tip-located complex promoting adhesion to various host receptors.
Dynamic and informational rock bolting design method for coal roadway and its application

The contents and characteristics of dynamic and informational rock bolting design method for coal roadway are introduced ,including geomechanics measurements and evaluation for rock surrounding roadways,numerical computation design, monitoring in -situ,information feedback and design modification.The application and technical effect in Lu'an Coal Area are expounded .
Microbiome Signature of Endophytes in Wheat Seed Response to Wheat Dwarf Bunt Caused by Tilletia controversa Kühn

This is the first study on the microbiome signature of endophytes in wheat seed response to wheat dwarf bunt caused by Tilletia controversa Kühn. Some antagonistic microbes suppressed the germination of teliospores of the pathogen significantly, which will provide clues for future studies against wheat dwarf bunt. Collectively, this research first advances the understanding of the microbial assembly of wheat seed upon exposure to the fungal pathogen (T. controversa) infection. ABSTRACT Wheat dwarf bunt leads to the replacement of seeds with fungal galls containing millions of teliospores of the pathogen Tilletia controversa Kühn. As one of the most devastating internationally quarantined wheat diseases, wheat dwarf bunt spreads to cause distant outbreaks by seeds containing teliospores. In this study, based on a combination of amplicon sequencing and isolation approaches, we analyzed the seed microbiome signatures of endophytes between resistant and susceptible cultivars after infection with T. controversa. Among 310 bacterial species obtained only by amplicon sequencing and 51 species obtained only by isolation, we found 14 overlapping species by both methods; we detected 128 fungal species only by amplicon sequencing, 56 only by isolation, and 5 species by both methods. The results indicated that resistant uninfected cultivars hosted endophytic communities that were much more stable and beneficial to plant health than those in susceptible infected cultivars. The susceptible group showed higher diversity than the resistant group, the infected group showed more diversity than the uninfected group, and the microbial communities in seeds were related to infection or resistance to the pathogen. Some antagonistic microbes significantly suppressed the germination rate of the pathogen’s teliospores, providing clues for future studies aimed at developing strategies against wheat dwarf bunt. Collectively, this research advances the understanding of the microbial assembly of wheat seeds upon exposure to fungal pathogen (T. controversa) infection. IMPORTANCE This is the first study on the microbiome signature of endophytes in wheat seed response to wheat dwarf bunt caused by Tilletia controversa Kühn. Some antagonistic microbes suppressed the germination of teliospores of the pathogen significantly, which will provide clues for future studies against wheat dwarf bunt. Collectively, this research first advances the understanding of the microbial assembly of wheat seed upon exposure to the fungal pathogen (T. controversa) infection.