Miracle-dz/UniFAR-FTUs huggingface dataset:
Immune Evasion Mechanisms of Staphylococcus epidermidis Biofilm Infection

The primary virulence factor of the skin commensal and opportunistic pathogen, Staphylococcus epidermidis, is the ability to form biofilms on surfaces of implanted materials. Much of this microorganism’s pathogenic success has been attributed to its ability to evade the innate immune system. The primary defense against S. epidermidis biofilm infection consists of complement activation, recruitment and subsequent killing of the pathogen by effector cells. Among pathogen-derived factors, the biofilm exopolysaccharide polysaccharide intercellular adhesion (PIA), as well as the accumulation-associated protein (Aap), and the extracellular matrix binding protein (Embp) have been shown to modulate effector cell-mediated killing of S. epidermidis. Phenol-soluble modulins (PSMs) constitute the only class of secreted toxins by S. epidermidis, at least one type of which (PSMδ) possesses strong cytolytic properties toward leukocytes. However, through selective production of non-cytolytic subtypes of PSMs, S. epidermidis is able to maintain a low inflammatory infection profile and avoid eradication by the host immune system. Taken together, our emerging understanding of the mechanisms behind immune modulation by S. epidermidis elucidates the microorganism’s success in the initial colonization of device surfaces as well as the maintenance of a chronic and indolent course of biofilm infection.
Pre- and post-pollination interaction between six co-flowering Pedicularis species via heterospecific pollen transfer.

It remains unclear how related co-flowering species with shared pollinators minimize reproductive interference, given that the degree of interspecific pollen flow and its consequences are little known in natural communities. Differences in pollen size in six Pedicularis species with different style lengths permit us to measure heterospecific pollen transfer (HPT) between species pairs in sympatry. The role of pollen-pistil interactions in mitigating the effects of HPT was examined. Field observations over 2 yr showed that bumblebee pollinators visiting one species rarely moved to another. Heterospecific pollen (HP) comprised < 10% of total stigmatic pollen loads for each species over 2 yr, and was not related to conspecific pollen deposition. Species with longer styles generally received more HP per stigma. The pollen tube study showed that pollen from short-styled species could not grow the full length of the style of long-styled species. Pollen from long-styled species could grow through the short style of P. densispica, but P. densispica rarely received HP in nature. Flower constancy is a key pre-pollination barrier to HPT between co-flowering Pedicularis species. Post-pollination pollen-pistil interactions may further mitigate the effects of HPT because HP transferred to long styles could generally be effectively filtered.
Single-Stage Amplifier Biased by Voltage Combiners With Gain and Energy-Efficiency Enhancement

This brief presents the design of a single-stage amplifier with enhanced gain and speed, without the need for using any cascode devices, positive feedback, or feed forward technique. Instead, two voltage-combiners replace the traditional tail current source, commonly employed to bias the differential pair. The resultant topology shows both additional dc gain and a gain bandwidth product enhancement. Simulation results of a properly optimized circuit, using AIDA-C, a state-of-the-art multi-objective multi-constraint IC sizing and optimization tool, demonstrate that a dc gain above 47 dB and a figure-of-merit better than 960 MHz*pF/mA, in corner conditions, can be achieved with this topology, in the UMC 130-nm technology. The circuit was fabricated and experimentally measured, showing an energy-efficiency figure-of-merit of 1023.6 MHz*pF/mA.
A new nine-level boost PWM rectifier based on stacked multilevel concepts

In this paper a new AC/DC unidirectional switching cell with nine voltage levels is proposed. It is called Stacked-Flying-Capacitors-Coupled-Inductors (SFC2I) and can be connected between an AC current source and a DC voltage source. The novelty of 9L-SFC2I topology is based on two cascaded stages that work at different currents, different voltage and different switching frequency. The first stage contains two diodes that operate at high-current, high-voltage and low-frequency. The second stage works at low-current, low-voltage and high-frequency. It combines the advantages of two stacked multilevel concepts, named Stacked-Flying-Capacitors (SFC) and Stacked-Coupled-Inductors (SCI). The SFC principle reduces the energy stored in flying-capacitors, while the SCI concept naturally sets to zero any difference between the winding currents of the coupled-inductors after each cycle. The operation principle of the 9L-SFC2I cell is verified both for single- and for three-phase unity-power-factor PWM rectifiers.
A Compact Multiple Notched Ultra-Wide Band Antenna with an Analysis of the CSRR-TO-CSRR Coupling for Portable UWB Applications

We present a compact ultra-wideband (UWB) antenna integrated with sharp notches with a detailed analysis of the mutual coupling of the multiple notch resonators. By utilizing complementary split ring resonators (CSRR) on the radiating semi-circular patch, we achieve the sharp notch-filtering of various bands within the UWB band without increasing the antenna size. The notched frequency bands include WiMAX, INSAT, and lower and upper WLAN. In order to estimate the frequency shifts of the notch due to the coupling of the nearby CSRRs, an analysis of the coupling among the multiple notch resonators is carried out and we construct the lumped-circuit equivalent model. The time domain analysis of the proposed antenna is performed to show its validity on the UWB application. The measured frequency response of the input port corresponds quite well with the calculations and simulations. The radiation pattern of the implemented quad-notched UWB antenna is nearly omnidirectional in the passband.
Relationship between PTEN and Livin expression and malignancy of renal cell carcinomas.

OBJECTIVES This study focused on PTEN and Livin expression and associations with malignancy in human renal clear cell carcinomas (RCCC). METHODS PTEN and Livin expression was assessed in 100 RCCC tissue samples, 50 paracarcinoma cases, and 20 normal renal tissue samples using the immunohistochemical Streptavidin proxidase (SP) method. The relationships between binding and corresponding biological characteristics, such as histological grade, lymph node metastases, and clinical stages were analyzed. RESULTS Positive PTEN expression in RCCC was significantly lower than in renal tissue adjacent to carcinoma tissue and normal renal tissue (P<0.01). Livin expression in the renal tissue adjacent to the carcinoma and normal renal tissues exhibited only low levels, whereas overall Livin expression in RCCC was statistically significant (P<0.01). In RCCC, PTEN expression rate gradually decreased with an increase in clinical stage, whereas that of Livin increased to statistically significant levels (P<0.01), PTEN and Livin levels being negatively correlated (r=-0.395, P<0.01). CONCLUSIONS PTEN and Livin are important in RCCC development. The two factors combined are expected to provide indices for estimating RCCC malignancy and progression levels, as well as references for RCCC diagnosis and treatment.
Cellular Plasticity–Targeted Therapy in Head and Neck Cancers

Head and neck cancer is one of the most frequent human malignancies worldwide, with a high rate of recurrence and metastasis. Head and neck squamous cell carcinoma (HNSCC) is cellularly and molecularly heterogeneous, with subsets of undifferentiated cancer cells exhibiting stem cell-like properties, called cancer stem cells (CSCs). Epithelial-mesenchymal transition, gene mutation, and epigenetic modification are associated with the formation of cellular plasticity of tumor cells in HNSCC, contributing to the acquisition of invasive, recurrent, and metastatic properties and therapeutic resistance. Tumor microenvironment (TME) plays a supportive role in the initiation, progression, and metastasis of head and neck cancer. Stromal fibroblasts, vasculature, immune cells, cytokines, and hypoxia constitute the main components of TME in HNSCC, which contributes not only to the acquisition of CSC properties but also to the recurrence and therapeutic resistance of the malignancies. In this review, we discuss the potential mechanisms underlying the development of cellular plasticity, especially the emergence of CSCs, in HNSCC. We also highlight recent studies implicating the complex interplays among TME components, plastic CSCs, tumorigenesis, recurrence, and therapeutic resistance of HNSCC. Finally, we summarize the treatment modalities of HNSCC and reinforce the novel concept of therapeutic targeting CSCs in HNSCC.
Influence of curing protocol and ceramic composition on the degree of conversion of resin cement

Abstract Due to increasing of aesthetic demand, ceramic crowns are widely used in different situations. However, to obtain long-term prognosis of restorations, a good conversion of resin cement is necessary. Objective: To evaluate the degree of conversion (DC) of one light-cure and two dual-cure resin cements under a simulated clinical cementation of ceramic crowns. Material and Methods: Prepared teeth were randomly split according to the ceramic's material, resin cement and curing protocol. The crowns were cemented as per manufacturer's directions and photoactivated either from occlusal suface only for 60 s; or from the buccal, occlusal and lingual surfaces, with an exposure time of 20 s on each aspect. After cementation, the specimens were stored in deionized water at 37°C for 7 days. Specimens were transversally sectioned from occlusal to cervical surfaces and the DC was determined along the cement line with three measurements taken and averaged from the buccal, lingual and approximal aspects using micro-Raman spectroscopy (Alpha 300R/WITec®). Data were analyzed by 3-way ANOVA and Tukey test at =5%. Results: Statistical analysis showed significant differences among cements, curing protocols and ceramic type (p<0.001). The curing protocol 3x20 resulted in higher DC for all tested conditions; lower DC was observed for Zr ceramic crowns; Duolink resin cement culminated in higher DC regardless ceramic composition and curing protocol. Conclusion: The DC of resin cement layers was dependent on the curing protocol and type of ceramic.
Clusterisasi Dokumen Web (Berita) Bahasa Indonesia Menggunakan Algoritma K-Means

Abstrak Informasi yang tersedia pada halaman-halaman web trunojoyo.ac. id semakin besar, belum tertata dengan baik, belum terstruktur atau terkategori mengikuti kaidah tertentu dan tersebar pada banyak sub-domain. Sejauh ini, tidak ada gerbangatau portal web yang menyediakan akses ke berbagai situs webyang dihosting oleh data center PTIK Universitas Trunojoyo. Salah satu masalah yang telah diselesaikan adalah pengelompokan informasi atau berita web tersebut secara otomatis menggunakan algoritma clustering K-Means. Search engine RISE yang telah berjalan menghimpun semua halaman web yang ditulis dalam bahasa Indonesia di bawah domain trunojoyo.ac. id menggunakan teknik crawling. Halaman-halaman tersebut kemudian dipre-processing menggunakan teknik standar dalam text minig (informationm retrieval). Proses utamanya adalah penerapan teknik k-menas sehingga terbentuk kelompok berita otonom. Pengujian yang telah dilakukan menunjukkan bahwa teknik clustering yang diterapkan mampu bekerja dengan baik dan memberikan akurasi yang memuaskan. Ada sekitar 300 halaman web yang dilibatkan dalam proses clustering dimana diperoleh ukuran rata-rata F-Measure sebesar 0.6129192 dan Purity bernilai 0.67294195. Faktor yang cukup berpengaruh dalam clustering dan klasifikasi teks bahasa Indonesia adalah fase pre-processing, terutama pada pendekatan stemming. Perbaikan terhadap teknik stemming diyakini akan meningkatkan akurasi pengelompokan dokumen. Kata Kunci : Clustering, K-Means, F-Measure, Purity Abstract The information available on the web pages trunojoyo.ac. id getting bigger, not well ordered, yet structured or terkategori follow certain rules and scattered in many subdomains. So far, no gerbangatau web portal that provides access to a variety of sites hosted by the data center webyang PTIK Trunojoyo University. One problem that has been solved is the grouping of information or news Web site automatically using the KMeans clustering algorithm. RISE search engines that have been running together all the web pages are written in Indonesian under trunojoyo.ac. id domain using crawling techniques. The pages are then dipre-processing using standard techniques in text Minig (informationm retrieval). The main process is the application of K-menas technique to form groups of autonomous news. Tests have shown that the clustering technique applied is able to work well and give satisfactory accuracy. There are about 300 web pages that are involved in the process of clustering which gained an average size of F-Measure 0.67294195 and Purity 0.6129192. Factors influential in clustering and classification Indonesian text is pre-processing phase, especially on the stemming approach. Repairs to stemming technique is believed to improve the accuracy of the document grouping. Keywords : Clustering, K-Means, F-Measure, Purity
Pacing behaviour of players in team sports: Influence of match status manipulation and task duration knowledge

The study aimed to identify the influence of prior knowledge of exercise duration associated with initial information about momentary match status (losing or winning) on the pacing behaviour displayed during soccer game-based activities. Twenty semi-professional male players participated in four game scenarios divided in two sessions. In the first game scenario, players were not informed about the time duration or initial match status. In the second, players were only informed they would be required to play a small-sided game for 12 minutes. In the third, players were told they would play a small-sided game for 12 minutes and that one of the teams was winning 2 to 0. Finally, in the fourth game scenario, players were instructed they would play a small-sided game for 12 minutes and the score lines used at the start of the previous game scenario were reversed. The results showed a tendency for the unknown task duration to elicit greater physical responses in all studied variables, compared with knowing the task duration. Knowing the task duration and starting the game winning or losing did not affect the players’ activity profile between the two conditions. Thus, during small-sided soccer games, knowledge (or not) about the exercise duration alters the pacing behaviour of the players. Moreover, short and undisclosed-length exercise durations resulted in the adoption of more aggressive pacing strategies, characterised by higher initial exercise intensities. Furthermore, previous information on match status does not seem to interfere with pacing patterns if the players are aware of the exercise duration. Coaches may use knowledge of exercise duration to manipulate the small-sided games’ demands.
Depletion of Regulatory T Cells in Visceral Adipose Tissues Contributes to Insulin Resistance in Hashimoto's Thyroiditis

Hashimoto's Thyroiditis (HT) is a common organ-specific autoimmune disorder associated with a high incidence, and insulin resistance is highly related to autoimmune. Here, we examined the insulin sensitivity in HT patients and found decreased insulin sensitivity occurred in HT patients. To explore the relationship between impaired insulin sensitivity and immune status, we established HT model mice which showed similar pathological features and immune features to HT patients. In HT model mice, reinfusion of regulatory T cells (Tregs) from peripheral blood of normal mice could improve insulin sensitivity and decrease the inflammation. Anti-CD25 antibodies blocked beneficial effects from reinfusion of Tregs, but delayed administration of anti-CD25 antibodies could not abolished the effect from Tregs. Delayed administration of anti-CD25 antibodies abolished exogenous Tregs in peripheral blood, but there were increased exogenous Tregs located to visceral adipose tissues (VATs) which modulated the expression of cytokines in VATs. These findings suggest that insulin resistance exists in HT patients and it associates with the decreased Tregs and increased inflammation in the VATs.
GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis

ABSTRACT How plants determine the final size of growing cells is an important, yet unresolved, issue. Root hairs provide an excellent model system with which to study this as their final cell size is remarkably constant under constant environmental conditions. Previous studies have demonstrated that a basic helix-loop helix transcription factor ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4) promotes root hair growth, but how hair growth is terminated is not known. In this study, we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin-binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. Our data further show that GTL1 and RSL4 regulate each other, as well as a set of common downstream genes, many of which have previously been implicated in root hair growth. This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by the orchestrated actions of opposing transcription factors. Summary: Arabidopsis gtl1 df1 double mutants and tissue-specific overexpression of GTL1 and DF1 demonstrate that both GTL1 and DF1 negatively regulate root hair growth by directly repressing RSL4.
A Flexible Approach Towards Security Validation

Validating security properties of complex distributed systems is a challenging problem by itself, let alone when the work needs to be performed under tight budget and time constraints on prototype systems with components at various maturity levels. This paper described a tailored approach to security evaluations involving a strategic combination of model-based quantification, emulation, and logical argumentation. By customizing the evaluation to fit existing budget and timelines, validators can achieve the most appropriate validation process, trading off fidelity with coverage across a number of different defense components and different maturity levels. We successfully applied this process to the validation of an overlay proxy network, analyzing the impact of five different defense attributes (together with combinations thereof) on access path establishment and anonymity.
Validation of surface‐to‐volume ratio measurements derived from oscillating gradient spin echo on a clinical scanner using anisotropic fiber phantoms

A diffusion measurement in the short‐time surface‐to‐volume ratio (S/V) limit (Mitra et al., Phys Rev Lett. 1992;68:3555) can disentangle the free diffusion coefficient from geometric restrictions to diffusion. Biophysical parameters, such as the S/V of tissue membranes, can be used to estimate microscopic length scales non‐invasively. However, due to gradient strength limitations on clinical MRI scanners, pulsed gradient spin echo (PGSE) measurements are impractical for probing the S/V limit. To achieve this limit on clinical systems, an oscillating gradient spin echo (OGSE) sequence was developed. Two phantoms containing 10 fiber bundles, each consisting of impermeable aligned fibers with different packing densities, were constructed to achieve a range of S/V values. The frequency‐dependent diffusion coefficient, D(ω), was measured in each fiber bundle using OGSE with different gradient waveforms (cosine, stretched cosine, and trapezoidal), while D(t) was measured from PGSE and stimulated‐echo measurements. The S/V values derived from the universal high‐frequency behavior of D(ω) were compared against those derived from quantitative proton density measurements using single spin echo (SE) with varying echo times, and from magnetic resonance fingerprinting (MRF). S/V estimates derived from different OGSE waveforms were similar and demonstrated excellent correlation with both SE‐ and MRF‐derived S/V measures (ρ ≥ 0.99). Furthermore, there was a smoother transition between OGSE frequency f and PGSE diffusion time when using teffS/V=9/64f , rather than the commonly used teff = 1/(4f), validating the specific frequency/diffusion time conversion for this regime. Our well‐characterized fiber phantom can be used for the calibration of OGSE and diffusion modeling techniques, as the S/V ratio can be measured independently using other MR modalities. Moreover, our calibration experiment offers an exciting perspective of mapping tissue S/V on clinical systems.
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

Abstract Background Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Conclusions Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.
Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column

Marinimicrobia bacteria are widespread in subeuphotic areas of the oceans and particularly abundant in oxygen minimum zones (OMZs). Information on Marinimicrobia metabolism is sparse, making the biogeochemical influence of this group challenging to predict. Here, metagenome-assembled genomes representing Marinimicrobia subgroups PN262000N21 and ARCTIC96B-7 were retrieved to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in ARCTIC96B-7. Genes for aerobic carbon monoxide (CO) oxidation, polysulfide metabolism and hydrogen utilization were identified only in PN262000N21, while genes for partial denitrification occurred in both genomes. Transcripts mapping to these genomes increased from <0.3% of total mRNA from the oxic zone to a max of 22% under anoxia. ARCTIC96B-7 transcript representation decreased an order of magnitude from non-sulfidic to sulfidic depths. In contrast, PN262000N21 representation was relatively constant throughout the OMZ, although transcripts encoding sulfur-utilizing proteins, including sulfur transferases, were enriched at sulfidic depths. PN262000N21 transcripts encoding a protein with fibronectin domains similar to those in cellulosome-producing bacteria were also abundant, suggesting a potential for high molecular weight carbon cycling. These data provide omic-level descriptions of metabolic potential and activity in OMZ-associated Marinimicrobia, suggesting differentiation between subgroups with roles in carbon and dissimilatory inorganic nitrogen and sulfur cycling.