Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the sister cells of embryo sac: developmental and functional attributes.

Synergids are metabolically dynamic cells of the egg apparatus and represent an important component of the female gametophyte. Besides directing the growth of the pollen tube towards the micropylar end of the embryo sac, these ephemeral structures make room for the pollen tube cytoplasm. Nature of chemotrophic substances that direct the growth of the pollen tube, the mechanism of degeneration of one of the synergids before fertilization and the molecular aspects of synergid morphogenesis have been studied in detail. Research carried out on model systems such as Arabidopsis, Brassica, Capsella, Triticum and Torenia has bettered our understanding of the molecular regulation of the pollen tube journey, its guidance and navigation in the pistil. Recently, the critical role of the central cell in fertilization and prevention of polytuby has also been thoroughly investigated. Interesting aspects that lead to degeneration of synergids, and the factors governing degeneration including molecular aspects have brought a paradigm shift in understanding of these intriguing units. Sophisticated confocal microscopy, live cell imaging, and molecular tools have helped in furthering our knowledge in the functioning of synergids. Recent research using the high throughput techniques have deciphered the role of various genes that regulate and govern the release of chemotropic substances, cell to cell interaction and synergid cell degeneration. Also, with the diversity displayed in form and function of organs in the angiosperms, and the switching over of roles of the cells of egg apparatus many new insights have been provided on the involvement of synergids both pre- and post-fertilization. Present review provides a comprehensive account of synergids, their role in fertilization and the post fertilization events that have emerged using interdisciplinary approaches in recent years. We also discuss the variations observed in degeneration of synergids and the mechanisms that have been unravelled lately. Looking at the dynamism synergids display, newer roles of these are emerging in fertilization. It is still unknown how synergids in angiosperm taxa where genetic transformation/alteration is carried out, will respond to pollen stimuli. Considering the environmental factors also a role to play in synergid functions, there is lack of experimental studies in this direction. Further research in developing adequate protocols for manipulating synergid functions is much desired. This research has enormous potential in advancement of basic science and can find applications in agriculture, horticulture, and bioprospecting.
A synthetic biology approach reveals diverse and dynamic CDK response profiles via multisite phosphorylation of NLS-NES modules

The complexity of multisite phosphorylation mechanisms in regulating nuclear localization signals (NLSs) and nuclear export signals (NESs) is not understood, and its potential has not been used in synthetic biology. The nucleocytoplasmic shuttling of many proteins is regulated by cyclin-dependent kinases (CDKs) that rely on multisite phosphorylation patterns and short linear motifs (SLiMs) to dynamically control proteins in the cell cycle. We studied the role of motif patterns in nucleocytoplasmic shuttling using sensors based on the CDK targets Dna2, Psy4, and Mcm2/3 of Saccharomyces cerevisiae. We designed multisite phosphorylation modules by rearranging phosphorylation sites, cyclin-specific SLiMs, phospho-priming, phosphatase specificity, and NLS/NES phospho-regulation and obtained very different substrate localization dynamics. These included ultrasensitive responses with and without a delay, graded responses, and different homeostatic plateaus. Thus, CDK can do much more than trigger sequential switches during the cell cycle as it can drive complex patterns of protein localization and activity by using multisite phosphorylation networks.
B cell‐intrinsic changes with age do not impact antibody‐secreting cell formation but delay B cell participation in the germinal centre reaction

Vaccines typically protect against (re)infections by generating pathogen‐neutralising antibodies. However, as we age, antibody‐secreting cell formation and vaccine‐induced antibody titres are reduced. Antibody‐secreting plasma cells differentiate from B cells either early post‐vaccination through the extrafollicular response or from the germinal centre (GC) reaction, which generates long‐lived antibody‐secreting cells. As the formation of both the extrafollicular antibody response and the GC requires the interaction of multiple cell types, the impaired antibody response in ageing could be caused by B cell intrinsic or extrinsic factors, or a combination of the two. Here, we show that B cells from older people do not have intrinsic defects in their proliferation and differentiation into antibody‐secreting cells in vitro compared to those from the younger donors. However, adoptive transfer of B cells from aged mice to young recipient mice showed that differentiation into extrafollicular plasma cells was favoured at the expense of B cells entering the GC during the early stages of GC formation. In contrast, by the peak of the GC response, GC B cells derived from the donor cells of aged mice had expanded to the same extent as those from the younger donors. This indicates that age‐related intrinsic B cell changes delay the GC response but are not responsible for the impaired antibody‐secreting response or smaller peak GC response in ageing. Collectively, this study shows that B cells from aged individuals are not intrinsically defective in responding to stimulation and becoming antibody‐secreting cells, implicating B cell‐extrinsic factors as the primary cause of age‐associated impairment in the humoral immunity.
The effect of soda taxes beyond beverages in Philadelphia

Abstract Soda taxes are implemented in several cities across the United States (US) with the aim of reducing sugar intake from sugar sweetened beverages (SSBs). Sugar is linked to obesity and to higher risk of diabetes and cardiovascular conditions. Sodas are targeted with these taxes since they are the main source of sugar for consumers in the US. In presence of potential substitutes, the policy can be undermined by consumers changing their sources of sugar. We examine the heterogeneous effects of the 2017 Philadelphia soda tax on purchases of other items containing sugar. We present an empirical evaluation focusing on the potential substitution toward additional sugary foods in Philadelphia and counties bordering Philadelphia. We find an increase in sugar from purchases of sweetened foods of about 4.3% following the introduction of the tax in Philadelphia and of 3.7% in the neighboring localities. The substitution to sugary foods in Philadelphia offsets 19% of the decrease of sugar from SSBs. Additionally, we find that the substitution offsets 37% of the decrease of sugar from SSBs when including counties bordering Philadelphia. These results suggest that while SSB taxes might be effective at lowering consumption of SSBs, substitution patterns may limit the effectiveness of the tax to reduce overall sugar intake.
Intraspecies variation of the mitochondrial genome: An evaluation for phylogenetic approaches based on the conventional choices of genes and segments on mitogenome

Intraspecies nucleotide sequence variation is a key to understanding the evolutionary history of a species, such as the geographic distribution and population structure. To date, numerous phylogenetic and population genetics studies have been conducted based on the sequences of a gene or an intergenic region on the mitochondrial genome (mtDNA), such as cytochrome c oxidase subunits or the D-loop. To evaluate the credibility of the usage of such ‘classic’ markers, we compared the phylogenetic inferences based on the analyses of the partial and entire mtDNA sequences. Importantly, the phylogenetic reconstruction based on the short marker sequences did not necessarily reproduce the tree topologies based on the analyses of the entire mtDNA. In addition, analyses on the datasets of various organisms revealed that the analyses based on the classic markers yielded phylogenetic trees with poor confidence in all tested cases compared to the results based on full-length mtDNA. These results demonstrated that phylogenetic analyses based on complete mtDNA sequences yield more insightful results compared to those based on mitochondrial genes and segments. To ameliorate the shortcomings of the classic markers, we identified a segment of mtDNA that may be used as an ‘approximate marker’ to closely reproduce the phylogenetic inference obtained from the entire mtDNA in the case of mammalian species, which can be utilized to design amplicon-seq-based studies. Our study demonstrates the importance of the choice of mitochondrial markers for phylogenetic analyses and proposes a novel approach to choosing appropriate markers for mammalian mtDNA that reproduces the phylogenetic inferences obtained from full-length mtDNA.
Optimization of stochastic planning models.

Abstract: "In order to solve the production planning problem given in 'Part I', a successive disaggregation algorithm is developed based on extensive sensitivity analysis for guiding the decisions on how to repartition the aggregate probability space. The partitioning algorithm is guaranteed to converge to the exact solution in a finite number of iterations, and has a highly parallel decomposition and computer implementation. Example problems are presented to demonstrate the solution technique. Results are compared with the alternative solution methods, variants of Benders decomposition schemes tailored to the dynamic staircase LP structure. "
Advances and challenges in intravital imaging of craniofacial and dental progenitor cells

Craniofacial and appendicular bone homeostasis is dynamically regulated by a balance between bone formation and resorption by osteoblasts and osteoclasts, respectively. Despite the developments in multiple imaging techniques in bone biology, there are still technical challenges and limitations in the investigation of spatial/anatomical location of rare stem/progenitor cells and their molecular regulation in tooth and craniofacial bones of living animals. Recent advances in live animal imaging techniques for the craniofacial and dental apparatus can provide new insights in real time into bone stem/progenitor cell dynamics and function in vivo. Here, we review the current inventions and applications of the noninvasive intravital imaging technique and its practical uses and limitations in the analysis of stem/progenitor cells in craniofacial and dental apparatus in vivo. Furthermore, we also explore the potential applications of intravital microscopy in the dental field.
Nitric oxide-inhibited chloride transport in cortical thick ascending limbs is reversed by 8-iso-prostaglandin-F2α

Background Sodium chloride (NaCl) reabsorption in the cortical thick ascending limb (cTAL) is regulated by opposing effects. Nitric oxide (NO) inhibits NaCl reabsorption while 8-iso-prostaglandin-F2α (8-iso-PGF2α) stimulates it. Their interaction has not been evaluated in the cTAL. Because 8-iso-PGF2α has considerable stability while NO is a free radical with a short half-life, we hypothesized that, in the cTAL, the inhibition of NaCl absorption will be reversed by 8-iso-PGF2α. Methods Chloride absorption (JCl) was measured in isolated perfused cTALs and whether the activation of protein kinase A (PKA) is required for this interaction. Since cyclic adenosine monophosphate (cAMP) is a major messenger for the 8-iso-PGF2α signaling cascade, and NO inhibits JCl by decreasing cAMP bioavailability, we measured 8-iso-PGF2α–stimulated cAMP in the presence of sodium nitroprusside (SNP). Results The NO donor, SNP (10–6 M), decreased JCl by 41%, while luminal 8-iso-PGF2α (100 μM) increased JCl to 315 ± 46 pmol/min/mm (p < 0.003), reversing the effects of the NO donor. SNP inhibited JCl, 8-iso-PGF2α failed to increase JCl in the presence of H89. Basal cAMP was 56 ± 13 fmol/min/mm, in the presence of SNP 57 ± 6 fmol/min/mm, and 8-iso-PGF2α increased it to 92 ± 2 fmol/min/mm (p < 0.04). Conclusion We concluded that 1) NO-induced inhibition of JCl in the cTAL can be reversed by 8-iso-PGF2α, 2) 8-iso-PGF2α and NO interaction requires PKA to control JCl, and 3) in the presence of NO, 8-iso-PGF2α continues to stimulate JCl because NO cannot reverse 8-iso-PGF2α-stimulated cAMP level.
Evaluating open-note exams: Student perceptions and preparation methods in an undergraduate biology class

Although closed-note exams have traditionally been used to evaluate students in undergraduate biology classes, open-note exams are becoming increasingly common, though little is known about how students prepare for these types of exams. We investigated student perceptions of and their preparation habits for online open-note exams in an undergraduate biology class, as compared to their previous experiences with closed-note exams in other classes. Specifically, we explored the following research questions: (1a) How do students perceive open-note exams impact their exam scores, their anxiety, the amount they studied, and the amount their peers studied? (1b) How do these perceptions impact performance outcomes? (2a) How do students prepare for open-note exams? (2b) How do these preparation methods impact performance outcomes? Results demonstrate students perceived increased exam scores, decreased exam-anxiety, decreased study time spent personally, and decreased study time spent by their peers for open-note exams, as compared to past experiences with closed-note exams. Open-ended survey responses analyzed through first- and second-cycle analyses showed students adapted their study habits by focusing on note preparation and broad conceptual understanding rather than rote memorization. Using linear mixed effects models to assess student performance, we found students who focused on understanding, note preparation and using external resources outperformed students who did not report those study habits. As institutions shift towards flexible and scalable assessments that can be used in face-to-face or online environments, the use of open-note exams can promote effective study habits and reward higher-order thinking with intentional guidance from the instructor.
Flux qubits shed a new light on BCS theory and high-$T_c$ superconductivity

A simple microscopic model of a small superconducting loop interrupted by Josephson junction (flux qubit) allows to compute from the experimental data of Wal et.al \cite{Wal} an important parameter - the density of Cooper pairs at zero temperature. This density is determined by the cut-off energy in the BCS model and agrees with the original BCS suggestion but is lower by two orders of magnitude than the value accepted in the modern literature. The immediate consequences of this result are: the validity of the strong coupling BCS model, a plausible picture of electrons recombination into Cooper pairs, and a much weaker condition for the appearance of high-temperature superconductivity. Another consequence is that the popular interpretation of Josephson qubits as macroscopic quantum systems is replaced by a picture of qubit states being superpositions of the ground state and the state containing only a single excited Cooper pair.
Adaptive Dynamic Surface Control with Guaranteed L∞ Tracking Performance for a Class of Uncertain Nonlinear Systems with Unknown Time Delays

This paper is aimed at exploring dynamic surface control (DSC) for a class of uncertain nonlinear systems in strict‐feedback form with time delays. Combining the Finite Covering Lemma (Heine‐Borel Theorem) with neural networks, a novel method is proposed to approximate time delay terms, which leads to the abandonment of traditional Lyapunov‐Krasovskii functionals. Then, a surface error modification and an initialization technique are proposed to guarantee the ℒ ∞ tracking performance. Moreover, by applying a newly‐developed neural network based adaptive control technique, it is shown that the update law for the proposed DSC scheme is needed only at the last design step with only one parameter being estimated online, which significantly reduces the computational burden, compared with current DSC schemes. Simulation results are presented to illustrate the efficiency of the proposed scheme.
Time Reversal of Lamb Waves for Damage Detection in Thermoplastic Composites

The objective of this study is to evaluate the use of correlation methods as a damage detection criterion in the application of the Time Reversal of Lamb Waves (TRLW) approach. The dispersion and attenuation characteristics of the waves are used for determining the maximum area to be inspected in a two transducers configuration. The Finite Element (FE) Model and experimental data are compared for verification of the method. The experimental setup consisted of a pair of piezoelectric transducers, working both as actuator and sensors, separated by a predetermined distance. Different defect sizes and positions with respect to the transducers were introduced on both aluminum and thermoplastic composite plates. A waveform generator was used to excite the piezoelectric actuators. An oscilloscope was used for acquiring the signals from the transducers. Those signals were processed in Matlab TM for the application of time reversal and a correlation analysis. The damage consisted of a hole through the thickness varying its diameter and location. The FEM simulates the propagation of Lamb waves in aluminum plates in order to analyze TRLW for damage detection. Lamb waves were generated using a 5 cycle Hanning window at different frequencies. The FEM consisted of standard 3D elements (C3D8I) for the plates and PZT elements (C3D8E) for the transducers. In order to simplify the model the PZTs were assumed to be perfectly bonded to the plates. The FEM analysis was mainly focused on the S 0 -wave. The indication of the presence of damage is performed using the correlation between the original actuation and the time reversed signal.
Leadership, work environment and caries prevention – what is good for the staff, is also good for the patients

Abstract Objectives Dental caries is a health problem that can be prevented. The aim of this study is to analyse if the quality of leadership, in Swedish Public Dental Health clinics, influences the extent to which patients with caries receive preventive care, and if any such effect is mediated through a collaborative work climate, clear role expectations and a low average level of burnout among staff. Methods The multilevel cross-sectional design includes work environment data from surveys of 75 general public dental clinics, register-based data on preventive measures provided to 5398 patients who received a dental filling due to a caries diagnosis, and patient demographics. Using a multilevel path analysis with logistic regression, we tested a model with one direct and three indirect pathways, controlling for the potential confounding effect of patient demographic factors. Results Leadership quality, as assessed by the staff at the clinic, was associated with increased odds of patients with caries receiving prevention, controlling for patient demographic factors. Leadership quality was also positively related to a collaborative work climate, clear role expectations and a low average level of burnout among staff. Against expectations, however, no indirect effect from leadership quality on prevention through the other work environment factors was found. Conclusions In conclusion, the quality of leadership in Swedish Public Dental Health clinics was positively related to a good work environment for staff and to delivery of preventive care to patients experiencing caries.
Mask-constrained power synthesis of maximally sparse linear arrays through a compressive-sensing-driven strategy

We propose a new deterministic approach to the synthesis of linear arrays having the least possible number of elements while radiating shaped beams lying in completely arbitrary power masks. The approach takes joint advantage from compressive sensing (CS), from the multiplicity of power patterns lying in a given mask, and from the multiplicity of field solutions corresponding to each of these power patterns. Care is taken in order to exploit the available degrees of freedom in an effective fashion, and in optimizing parameters that affect the CS performance. An extensive numerical comparison against state-of-the-art procedures proves the effectiveness of the approach.
A holistic security approach for protecting government eServices against denial-of-service attack

Security is one of the most important factors in providing eServices. This is particularly the case for organizations, including government departments, that provide critical systems. Denial-of-service (DoS) attacks are a threat to systems, individuals, organizations and society because they cause damage that is far-reaching. Protecting systems against DoS attack is a priority. To provide an acceptable level of protection for eServices against DoS attack, requirements need to be met in four key areas: functionality, security, decision accuracy and performance. A review of current models revealed that not one of the existing solutions for DoS attack satisfies all requirements. Our search for a solution to the DoS-attack problem began with an analysis of government eService business flows. We then designed a formal-analysis model to understand and describe the critical government systems. Following this, we built a comprehensive model (DoS-PIF) that integrates the three required protection tasks – packet filtering, attack detection and attack prevention – and that includes communication controls. In order to demonstrate the practical value of the model, a security approach, called the Holistic Approach for Securing and Protecting Critical Government eService Systems (HASP-CGeSS), was derived and realized. In order to implement the communication control in HASP-CGeSS, we proposed a Token-Filtering Technique (TFT) to provide an authentication and filtration layer for packet filtering. TFT offers fast packet filtering through the use of packet headers. We then designed the Token-Filtering-Technique Protocol (TFTP) to prevent DoS attack. Our subsequent evaluation indicated that the TFTP enhances packet-filtering rates, prevents the spoofing of communication sources, filters packets without needing to decrypt them, protects systems from modified and malformed packets, can manage communication timing and free the client from unproductive processing, provides stateful features in a stateless connection and provides efficient communication control between comparative communication controls. In addition, the results show that the proposed protocol is efficient and DoS-resistant for legitimate users and under seven types of DoS-attack scenarios. Furthermore, the results show that (unlike other solutions) the size of the proposed repeat-communications list does not limit the number of clients. Finally, the protocol filters DoS attacks faster than existing protocols and consequently creates greater resource availability in a system because of the reduced time required to filter DoS attacks. This research has proposed a number of innovative security advances to protect critical government systems. The outcomes of the research justify continuing investigation in this domain for the betterment of citizens, organisations, government and society.