Miracle-dz/UniFAR-FTUs huggingface dataset:
The Serine Phosphatase SerB of Porphyromonas gingivalis Suppresses IL-8 Production by Dephosphorylation of NF-κB RelA/p65

Porphyromonas gingivalis is a major pathogen in severe and chronic manifestations of periodontal disease, which is one of the most common infections of humans. A central feature of P. gingivalis pathogenicity is dysregulation of innate immunity at the gingival epithelial interface, including suppression of IL-8 production by epithelial cells. NF-κB is a transcriptional regulator that controls important aspects of innate immune responses, and NF-κB RelA/p65 homodimers regulate transcription of IL8. Phosphorylation of the NF-κB p65 subunit protein on the serine 536 residue affects nuclear translocation and transcription of target genes. Here we show that SerB, a haloacid dehalogenase (HAD) family serine phosphatase secreted by P. gingivalis, is produced intracellularly and can specifically dephosphorylate S536 of p65 in gingival epithelial cells. A P. gingivalis mutant lacking SerB was impaired in dephosphorylation of p65 S536, and ectopically expressed SerB bound to p65 and co-localized with p65 in the cytoplasm. Ectopic expression of SerB also resulted in dephosphorylation of p65 with reduced nuclear translocation in TNF-α-stimulated epithelial cells. In contrast, the p105/50 subunit of NF-κB was unaffected by SerB. Co-expression of a constitutively active p65 mutant (S536D) relieved inhibition of nuclear translocation. Both the activity of the IL8 promoter and production of IL-8 were diminished by SerB. Deletion and truncation mutants of SerB lacking the HAD-family enzyme motifs of SerB were unable to dephosphorylate p65, inhibit nuclear translocation or abrogate IL8 transcription. Specific dephosphorylation of NF-κB p65 S536 by SerB, and consequent inhibition of nuclear translocation, provides the molecular basis for a bacterial strategy to manipulate host inflammatory pathways and repress innate immunity at mucosal surfaces.
Removing N-Terminal Sequences in Pre-S1 Domain Enhanced Antibody and B-Cell Responses by an HBV Large Surface Antigen DNA Vaccine

Although the use of recombinant hepatitis B virus surface (HBsAg) protein vaccine has successfully reduced global hepatitis B infection, there are still a number of vaccine recipients who do not develop detectable antibody responses. Various novel vaccination approaches, including DNA vaccines, have been used to further improve the coverage of vaccine protection. Our previous studies demonstrated that HBsAg-based DNA vaccines could induce both humoral and CMI responses in experimental animal models. However, one form of the the HBsAg antigen, the large S antigen (HBs-L), expressed by DNA vaccine, was not sufficiently immunogenic in eliciting antibody responses. In the current study, we produced a modified large S antigen DNA vaccine, HBs-L(T), which has a truncated N-terminal sequence in the pre-S1 region. Compared to the original HBs-L DNA vaccine, the HBs-L(T) DNA vaccine improved secretion in cultured mammalian cells and generated significantly enhanced HBsAg-specific antibody and B cell responses. Furthermore, this improved HBsL DNA vaccine, along with other HBsAg-expressing DNA vaccines, was able to maintain predominantly Th1 type antibody responses while recombinant HBsAg protein vaccines produced in either yeast or CHO cells elicited mostly Th2 type antibody responses. Our data indicate that HBsAg DNA vaccines with improved immunogenicity offer a useful alternative choice to recombinant protein-based HBV vaccines, particularly for therapeutic purposes against chronic hepatitis infection where immune tolerance led to poor antibody responses to S antigens.
EGFR Exon 18 Mutations in Lung Cancer: Molecular Predictors of Augmented Sensitivity to Afatinib or Neratinib as Compared with First- or Third-Generation TKIs

Purpose: Lung cancers harboring common EGFR mutations respond to EGFR tyrosine kinase inhibitors (TKI), whereas exon 20 insertions (Ins20) are resistant to them. However, little is known about mutations in exon 18. Experimental Design: Mutational status of lung cancers between 2001 and 2015 was reviewed. Three representative mutations in exon 18, G719A, E709K, and exon 18 deletion (Del18: delE709_T710insD) were retrovirally introduced into Ba/F3 and NIH/3T3 cells. The 90% inhibitory concentrations (IC90s) of first-generation (1G; gefitinib and erlotinib), second-generation (2G; afatinib, dacomitinib, and neratinib), and third-generation TKIs (3G; AZD9291 and CO1686) were determined. Results: Among 1,402 EGFR mutations, Del19, L858R, and Ins20 were detected in 40%, 47%, and 4%, respectively. Exon 18 mutations, including G719X, E709X, and Del18, were present in 3.2%. Transfected Ba/F3 cells grew in the absence of IL3, and NIH/3T3 cells formed foci with marked pile-up, indicating their oncogenic abilities. IC90s of 1G and 3G TKIs in G719A, E709K, and Del18 were much higher than those in Del19 (by >11–50-fold), whereas IC90s of afatinib were only 3- to 7-fold greater than those for Del19. Notably, cells transfected with G719A and E709K exhibited higher sensitivity to neratinib (by 5–25-fold) than those expressing Del19. Patients with lung cancers harboring G719X exhibited higher response rate to afatinib or neratinib (∼80%) than to 1G TKIs (35%–56%) by compilation of data in the literature. Conclusions: Lung cancers harboring exon 18 mutations should not be overlooked in clinical practice. These cases can be best treated with afatinib or neratinib, although the currently available in vitro diagnostic kits cannot detect all exon 18 mutations. Clin Cancer Res; 21(23); 5305–13. ©2015 AACR.
Role of dual specificity tyrosine-phosphorylation-regulated kinase 1B (Dyrk1B) in S-phase entry of HPV E7 expressing cells from quiescence

The high-risk human papillomavirus (HPV) is the causative agent for cervical cancer. The HPV E7 oncogene promotes S-phase entry from quiescent state in the presence of elevated cell cycle inhibitor p27Kip1, a function that may contribute to carcinogenesis. However, the mechanism by which HPV E7 induces quiescent cells to entry into S-phase is not fully understood. Interestingly, we found that Dyrk1B, a dual-specificity kinase and negative regulator of cell proliferation in quiescent cells, was upregulated in E7 expressing cells. Surprisingly and in contrast to what was previously reported, Dyrk1B played a positive role in S-phase entry of quiescent HPV E7 expressing cells. Mechanistically, Dyrk1B contributed to p27 phosphorylation (at serine 10 and threonine 198), which was important for the proliferation of HPV E7 expressing cells. Moreover, Dyrk1B up-regulated HPV E7. Taken together, our studies uncovered a novel function of Dyrk1B in high-risk HPV E7-mediated cell proliferation. Dyrk1B may serve as a target for therapy in HPV-associated cancers.
Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region

In the yeast Saccharomyces cerevisiae that lacks lamins, the nuclear pore complex (NPC) has been proposed to serve a role in chromatin organization. Here, using fluorescence microscopy in living cells, we show that nuclear pore proteins of the Nup84 core complex, Nup84p, Nup145Cp, Nup120p, and Nup133p, serve to anchor telomere XI-L at the nuclear periphery. The integrity of this complex is shown to be required for repression of a URA3 gene inserted in the subtelomeric region of this chromosome end. Furthermore, altering the integrity of this complex decreases the efficiency of repair of a DNA double-strand break (DSB) only when it is generated in the subtelomeric region, even though the repair machinery is functional. These effects are specific to the Nup84 complex. Our observations thus confirm and extend the role played by the NPC, through the Nup84 complex, in the functional organization of chromatin. They also indicate that anchoring of telomeres is essential for efficient repair of DSBs occurring therein and is important for preserving genome integrity.
Analisis Psikometrik Skala Pengukuran Pengurusan Privasi Komunikasi Facebook

Facebook merupakan platform komunikasi maya yang paling popular dalam kalangan pengguna media sosial di seluruh dunia. Kajian ini bertujuan mengenalpasti analisis psikometrik S kala Pengukuran Pengurusan Privasi Komunikasi Facebook versi terjemahan Bahasa Melayu. Kajian pertama melibatkan 145 pemilik akaun Facebook dalam kalangan penjawat awam di negeri Kedah yang ditentukan melalui kaedah persampelan rawak. Borang soal selidik mengandungi maklumat demografi dan 18 item Skala Pengukuran Pengurusan Privasi Komunikasi Facebook diadaptasi daripada Skala Pengurusan Privasi Blog (Child, Pearson & Petronio, 2009). Kesemua item asal skala dinilai menggunakan Analisis Faktor Penerokaan (EFA). Empat model hipotesis diuji bagi menilai susunan struktur skala terbaik berdasarkan Analisis Faktor Pengesahan (CFA). Dapatan EFA menunjukkan komponen Sempadan Pemilikan, Sempadan Hubungan dan Sempadan Kebolehtelapan dalam skala ini terbentuk berdasarkan 12 item yang masih menepati konsep asal Teori Pengurusan Privasi Komunikasi. Analisis CFA menunjukkan model multidimensi yang dibentuk mencapai kesahan konvergen dan ketepatan padanan yang baik. Kajian kedua melibatkan 138 orang pelajar Universiti Awam untuk menentukan kekukuhan skala kajian. Borang soal selidik secara dalam talian telah disebarkan yang mengandungi maklumat demografi, S kala Pengukuran Pengurusan Privasi Komunikasi Facebook dan Kesedaran Kendiri. Analisis Faktor Pengesahan (CFA) dalam kajian kedua menunjukkan model multidimensi tiga faktor Skala Pengukuran Pengurusan Privasi Komunikasi Facebook mencapai kesahan konvergen, kesahan diskriminan, kesahan prediktif dan kebolehpercayaan yang baik. Kesimpulannya, Skala Pengukuran Pengurusan Privasi Komunikasi Facebook yang diterjemah ke Bahasa Melayu ini sesuai digunakan dalam kajian berkaitan pengurusan privasi komunikasi Facebook dan media seumpamanya di Malaysia.
Sleep well—be well study: improving school transition by improving child sleep: a translational randomised trial

Introduction The transition to primary school appears crucial for a child's future academic and psychological well-being. Addressing conditions which negatively affect children during this period, such as poor sleep, may improve these outcomes. Sleep problems are common and in a previous efficacy randomised controlled trial, we demonstrated that sleep problems can be identified and improved using school-based screening followed by a brief behavioural intervention. This trial will determine whether the same intervention is beneficial and cost-effective when delivered by an existing school-based health workforce. Methods/design We will recruit 334 children with sleep problems from approximately 40 schools after screening for behavioural sleep problems in the first year of formal education (Grade Prep). Schools in Melbourne, Australia will be invited to participate from a randomly ordered list of eligible schools and we will approach all caregivers of Grade Prep children. Children who have a parent-reported moderate or severe sleep problem will be randomised into either ‘usual care’ or ‘intervention’ groups. Trained nurses from the Primary School Nursing programme will deliver the sleep intervention programme. Intervention: Two to three contacts between the nurse and the parent; initial 45 min face-to-face meeting or phone call, 15 min phone call 2 weeks later and an optional second 30 min face-to-face meeting. Follow-up: 6 and 12 months postrandomisation using parent and teacher surveys and child face-to-face assessments. Primary outcome: child psychosocial functioning at 6 months. Secondary outcomes: child psychosocial functioning at 12 months and child sleep, behaviour, working memory, academic achievement and parent mental health at 6 and 12 months. Cost-effectiveness analysis will compare incremental costs to difference in child psychosocial functioning at 6 months. Registration International Standard Randomised Controlled Trial Number Register (ISRCTN92448857).
Multistrategy Constructive Induction: AQ17-MCI

This paper presents a method for multistrategy constructive induction that integrates two inferential learning strategies—empirical induction and deduction, and two computational methods—data-driven and hypothesis-driven. The method generates inductive hypotheses in an iteratively modified representation space. The operators modifying the representation space are classified into "constructors," which expand the space (by generating additional attributes) and "destructors" which contract the space (by removing low relevance attributes or
Talking the Talk is Like Walking the Walk : A Computational Model of Verbal Aspect

I describe an implemented computational model of verbal aspect that supports the proposition that the semantics of aspect is grounded in sensory-motor primitives. In this theory, aspectual expressions refer to schematized processes that recur in sensory-motor control (such as goal, periodicity, iteration, nal state, duration, and parameters such as force and e ort). This active model of aspect grounded in sensory-motor primitives is able to model cross-linguistic variation in aspectual expressions while avoiding some paradoxes and problems in model-theoretic and other traditional accounts.
Mothering after child removal: Living under the rule of Greek gods

Child & Family Social Work. 2018;23:417–426. Abstract Many women who experience mental illness are mothers. Evidence suggests that the role of mother is of great importance and value to these women, yet they are more likely than other women to have their children removed from their care. Little is known about the experiences of these mothers after their children are removed. This paper presents a phenomenological analysis of in‐depth interviews with 8 women to answer the following question: How do mothers living with severe mental illness experience mothering after removal of their children by child protection services? The analysis showed that mothering continued to be a major life role for these women, but the way they enacted this role was transformed. Their mothering was now constrained and prescribed by external agents, likened to Greek gods, which imposed both boundaries to what they could do and an obligation to prove themselves worthy. Like Greek gods, these external agents were seen as all powerful, unpredictable, and flawed. The study highlights the need for child protection services and support services to recognize and support noncustodial mothering activities.
Tentative Evidence for Striatal Hyperactivity in Adolescent Cannabis-Using Boys: A Cross-Sectional Multicenter fMRI Study

Abstract Adolescents' risk-taking behavior has been linked to a maturational imbalance between reward (“go”) and inhibitory-control (“stop”)-related brain circuitry. This may drive adolescent drug-taking, such as cannabis use. In this study, we assessed the non-acute effects of adolescent cannabis use on reward-related brain function. We performed a two-site (United States and Netherlands; pooled data) functional magnetic resonance imaging (fMRI) study with a cross-sectional design. Twenty-one abstinent but frequent cannabis-using boys were compared with 24 non-using peers on reward-related brain function, using a monetary incentive delay task with fMRI. Focus was on anticipatory and response stages of reward and brain areas critically involved in reward processing like the striatum. Performance in users was normal. Region-of-interest analysis indicated striatal hyperactivity during anticipatory stages of reward in users. Intriguingly, this effect was most pronounced during non-rewarding events. Striatal hyperactivity in adolescent cannabis users may signify an overly sensitive motivational brain circuitry. Frequent cannabis use during adolescence may induce diminished ability to disengage the motivational circuit when no reward can be obtained. This could strengthen the search for reinforcements like drugs of abuse, even when facing the negative (non-rewarding) consequences.
LSIFT—An improved SIFT algorithm with a new matching method

In terms of the high frequency of mis-match of SIFT method under the strong disturb and complex background, this paper proposes a new matching method based on comparing modulus. According to this method, the eigenvector limit is required at first before the normalization processing, and then, accurate matching pairs between two pictures can be found according to the difference between the modulus of the relative matching pair and that of the most similar one. The result of simulation indicates that the new matching method is of high stability and its matching time is much shorter.
Significance of HTML Tags for Document Indexing and Retrieval

Indexing quality has an overwhelming effect on retrieval effectiveness of search engines. In the past few years it has become one of the major challenges in the search engines area, particularly the task of automatically assigning highquality terms to Web documents, which remains elusive. High indexing and retrieval quality requires work on term selection algorithms. This paper investigates the feasibility of HTML tags to represent the contents of Web documents. Experiments were performed on the WT10g collection of a 1.69-million page corpus using many different combinations of term selection and information retrieval algorithms.
Spatio-temporal synchronization of periodic movements by style-phase adaptation: Application to biped walking

In this paper, we propose a framework for generating coordinated periodic movements of robotic systems with external inputs. We developed an adaptive pattern generator model that is composed of a two-factor observation model with a style parameter and phase dynamics with a phase variable. The style parameter controls the spatial patterns of the generated trajectories, and the phase variable controls its temporal profiles. To validate the effectiveness of our proposed method, we applied it to a simulated humanoid model to perform biped walking behaviors coordinated with observed walking patterns and the environment. The robot successfully performed stable biped walking behaviors even when the style of the observed walking pattern and the period were suddenly changed.
Vague Content and Structure (VCAS) Retrieval for Document-centric XML Collections

document-centric XML collections with structure conditions improves retrieval precisions. The structures of such XML collections, however, are often too complex for users to fully grasp. Thus, for queries regarding such collections, it is more appropriate to retrieve answers that approximately match the structure and content conditions in these queries, a process also known as vague content and structure (VCAS) retrieval. Most existing XML engines, however, only support content-only (CO) retrieval and/or strict content and structure (SCAS) retrieval. To remedy these shortcomings, we propose an approach for VCAS retrieval using existing XML engines. Our approach first decomposes a VCAS query into a SCAS sub-query and a CO sub- query, then uses existing XML engines to retrieve SCAS results and CO results for the decomposed sub-queries, and finally combines results from both retrievals to produce approximate results for the original query. Further, to improve retrieval precision, we propose two similarity metrics to adjust the scores of CO retrieval results by their relevancies to the path condition for the original query target. We evaluate our VCAS retrieval approach through extensive experiments with the INEX 04 XML collection and VCAS query sets. The experimental results demonstrate the effectiveness of our VCAS retrieval approach.
Measuring change in fuzzy concept lattices

The quantity of unstructured and semi-structured data available is growing rapidly. Adding structure to such data (by means of ontologies and tag-based taxonomic classifications) is potentially a very productive approach, which can lead to additional knowledge (e.g. by monitoring association and other relations between classes) as well as enabling more effective use and re-use of online knowledge. Formal concept analysis (and fuzzy formal concept analysis) enables us to identify hierarchical structure arising from similarities in attribute values, giving a starting point for an ontology. However, it is often difficult to determine the “best” attributes to use. Furthermore, in an environment where source data is updated, this data-driven approach may lead to concept lattices which vary in structure. In this paper, we describe a novel way of measuring the distance between concept lattices. The method can be applied to comparison of lattices derived from the same set of objects using different attributes or to different sets of objects categorised by the same attributes. Simple examples are used to illustrate the idea.
Palatal click allophony in Mangetti Dune !Xung: Implications for sound change

Click consonants are well known for lacking allophonic variation. This lack of variation has been attributed to the existence of articulatory constraints on the coronal constrictions that are imposed by the existence of a second dorsal constriction. The current study investigates temporal acoustic differences among the four contrastive coronal click types in the /i/ and /u/ contexts in Mangetti Dune ! Xung. Clicks have been described as being either non-affricated or affricated. However, when vowel context is taken into consideration, the typology is more complex. The alveolar click is non-affricated in both vowel contexts. The dental and lateral clicks are fricated in both contexts. The palatal click in the /i/ context has two clear anterior and posterior transients, followed by palatal frication, while in the /u/ context it is non-affricated. Results are consistent with an analysis of the palatal click in the /i/ context as involving allophonic secondary palatalization. There are trading relations between the duration of the click burst, frication noise and aspiration noise phases. Results have implications for understanding the synchronic and diachronic phonology of click consonants.
An Analysis of Crowdsourced Text Simplifications

We present a study on the text simplification operations undertaken collaboratively by Simple English Wikipedia contributors. The aim is to understand whether a complex-simple parallel corpus involving this version of Wikipedia is appropriate as data source to induce simplification rules, and whether we can automatically categorise the different operations performed by humans. A subset of the corpus was first manually analysed to identify its transformation operations. We then built machine learning models to attempt to automatically classify segments based on such transformations. This classification could be used, e.g., to filter out potentially noisy transformations. Our results show that the most common transformation operations performed by humans are paraphrasing (39.80%) and drop of information (26.76%), which are some of the most difficult operations to generalise from data. They are also the most difficult operations to identify automatically, with the lowest overall classifier accuracy among all operations (73% and 59%, respectively).
An iterative approach to comprehensive performance evaluation of integrated services networks

Future networks are expected to integrate diverse services. For this purpose, new algorithms and protocols have been proposed for link scheduling, admission control, and routing. The interaction between these three components is crucial to the performance of the network. However, this interaction is difficult to model realistically using available techniques. We present an iterative discrete-time approach that yields a realistic model which takes into account this interaction. The model applies to connection-oriented networks with different types of real-time connections. It allows the investigation of various control schemes for both transient and steady-state performances. Preliminary results indicate that our approach is computationally much cheaper than discrete-event simulation, and yields sufficiently accurate performance measures. <<ETX>>