Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis B mother-to-child transmission and infants immunization: we have not come to the end of the story yet

In this issue of Infectious Diseases, Wang and colleagues offer an interesting insight into the mechanisms underlying the lack of immunological response to hepatitis B virus (HBV) vaccination in newborns of HBsAg(þ) mothers [1], who, without proper prophylaxis measures, have a remarkable likelihood to vertically acquire the infection [2]. Mother-to-child transmission (MTCT) of HBV is associated with the highest risk of chronicity (around 95%), when compared with the chronicity rate of horizontally acquired infection acquired in subsequent ages [3]. Therefore, the implementation of adequate preventive measures in this setting is mandatory [4]. As a matter of fact, World Health Organization recommends universal HBV vaccination for all infants, by administering the first dose (of the three scheduled) shortly after birth, possibly within 24 hours [5]. The vaccine is safe and effective, but at least 5% of immunocompetent subjects are classified as ‘non-responders’, being their titers of anti-HBs lower than 10 mIU/ml [6]. How to manage these individuals is matter of debate, because an evidence on the efficacy of booster dosing is lacking [7]. In addition, the majority of studies on the failure of HBV vaccination involve adult subjects [6], often focusing on special categories such as drug users [8], HIV-infected persons [9], patients on haemodialysis [10] or with celiac disease [11]. Studies on immunological response to HBV vaccine among infants are quite heterogeneous. For instance, Chen and colleagues, in a multicentre study conducted in China involving 1063 mother-and-infant pairs, found that infants’ immune response rate as well as their antibody titres were negatively correlated with maternal anti-HBs levels, being lower among newborns of mothers with a titre of neutralizing antibodies 500 IU/L [12]. Another unanswered question in the paediatric setting concerns preterm and low-birth-weight (LBW) infants: what is, for these peculiar subjects, the best schedule as to active immunization against HBV? Although robust studies are lacking, a recent review of literature suggests a 4-dose schedule in order to overcome the unsatisfactory immunological response to current vaccination schemes by preterm and LBW infants [13]. However, the most intriguing issue is the HBV vaccination immunological response among infants born to HBsAg(þ) mothers. In a large American series enrolling 8654 HBsAg( ) newborns of HBsAg(þ) mothers, in the framework of the Enhanced Perinatal Hepatitis B Prevention Program (EPHBPP) conducted from 2008 to 2013, about 8199 (94.7%) infants showed vaccine response after a 3or 4-dose schedule [14]. At the multivariate analysis, risk factors for vaccination non-response (anti-HBs titer
Emergent minimalism : / R / in a stratal grammar

Optimality Theory (OT, Prince & Smolensky 1993) provides that the source of language specificity is a ranking of violable constraints and, according to the Richness of the Base (ROTB), denies that linguistic idiosyncrasies may be attributed to the lexicon. Segments like the French dorsal /R/ are particularly interesting, given apparent featural minimalism and sensitivity to phonetically based constraints (Tranel 1987: 141-143, Russell Webb 2004 & in press). The present work reexamines this segment, questioning base richness, the nature of input and the learning of phonological representations. A stratal grammatical model is proposed, incorporating a restrictive interpretation of ROTB. The paper proceeds as follows. Preliminary sections survey French /R/ data, ROTB and the status of input in OT. A third section reviews featural emergence, the nature of phonological inputs and the learning of underlying representations (UR) and licensing implications. A fourth section articulates the proposed model, accounting for French /R/ in learning, declarative and productive sub-modules. A final section provides synthesis and draws preliminary conclusions.
Belief Propagation approach to epidemics prediction on networks

In my thesis I study the problem of predicting the evolution of the epidemic spreading on networks when incomplete information, in form of a partial observation, is available. I focus on the irreversible process described by the discrete time version of the Susceptible-Infected-Recovered (SIR) model on networks. Because of its intrinsic stochasticity, forecasting the SIR process is very difficult, even if the structure of individuals contact pattern is known. In today's interconnected and interdependent society, infectious diseases pose the threat of a worldwide epidemic spreading, hence governments and public health systems maintain surveillance programs to report and control the emergence of new disease event ranging from the seasonal influenza to the more severe HIV or Ebola. When new infection cases are discovered in the population it is necessary to provide real-time forecasting of the epidemic evolution. However the incompleteness of accessible data and the intrinsic stochasticity of the contagion pose a major challenge. The idea behind the work of my thesis is that the correct inference of the contagion process before the detection of the disease permits to use all the available information and, consequently, to obtain reliable predictions. I use the Belief Propagation approach for the prediction of SIR epidemics when a partial observation is available. In this case the reconstruction of the past dynamics can be efficiently performed by this method and exploited to analyze the evolution of the disease. Although the Belief Propagation provides exact results on trees, it turns out that is still a good approximation on general graphs. In this cases Belief Propagation may present convergence related issues, especially on dense networks. Moreover, since this approach is based on a very general principle, it can be adapted to study a wide range of issues, some of which I analyze in the thesis.
Cleft lip with or without cleft palate: associations with transforming growth factor alpha and retinoic acid receptor loci.

The first association study of cleft lip with or without cleft palate (CL/P), with candidate genes, found an association with the transforming growth-factor alpha (TGFA) locus. This finding has since been replicated, in whole or in part, in three independent studies. Here we extend our original analysis of the TGFA TaqI RFLP to two other TGFA RFLPs and seven other RFLPs at five candidate genes in 117 nonsyndromic cases of CL/P and 113 controls. The other candidate genes were the retinoic acid receptor (RARA), the bcl-2 oncogene, and the homeobox genes 2F, 2G, and EN2. Significant associations with the TGFA TaqI and BamHI RFLPs were confirmed, although associations of clefting with previously reported haplotypes did not reach significance. Of particular interest, in view of the known teratogenic role of retinoic acid, was a significant association with the RARA PstI RFLP (P = .016; not corrected for multiple testing). The effect on risk of the A2 allele appears to be additive, and although the A2A2 homozygote only has an odds ratio of about 2 and recurrence risk to first-degree relatives (lambda 1) of 1.06, because it is so common it may account for as much as a third of the attributable risk of clefting. There is no evidence of interaction between the TGFA and RARA polymorphisms on risk, and jointly they appear to account for almost half the attributable risk of clefting.
San Diego Zoo Institute for Conservation Research

The San Diego Zoo Institute for Conservation Research (SDZICR) in San Diego, California, is a research organization [3] that works to generate, use, and share information for the conservation of wildlife and their habitats. In 1975, Kurt Benirschke, a researcher at the University of California, San Diego (UCSD) who studied human and animal reproduction, and Charles Bieler, the director of the San Diego Zoo, collaborated to form the Center for Reproduction of Endangered Species (CRES). In 2009, the San Diego Zoo announced the creation of SDZICR, which expanded and replaced CRES, to provide central organization [3] and management of scientific programs at the San Diego Zoo. By 2004, Allison Alberts was the director of research and for more than a decade oversaw the SDZICR ́s many research initiatives, including the collection and storage of genetic and reproductive information of rare and endangered animal and plant species.
Inheritance of an Epigenetic Mark: The CpG DNA Methyltransferase 1 Is Required for De Novo Establishment of a Complex Pattern of Non-CpG Methylation

Site-specific methylation of cytosines is a key epigenetic mark of vertebrate DNA. While a majority of the methylated residues are in the symmetrical (meC)pG:Gp(meC) configuration, a smaller, but significant fraction is found in the CpA, CpT and CpC asymmetric (non-CpG) dinucleotides. CpG methylation is reproducibly maintained by the activity of the DNA methyltransferase 1 (Dnmt1) on the newly replicated hemimethylated substrates (meC)pG:GpC. On the other hand, establishment and hereditary maintenance of non-CpG methylation patterns have not been analyzed in detail. We previously reported the occurrence of site- and allele-specific methylation at both CpG and non-CpG sites. Here we characterize a hereditary complex of non-CpG methylation, with the transgenerational maintenance of three distinct profiles in a constant ratio, associated with extensive CpG methylation. These observations raised the question of the signal leading to the maintenance of the pattern of asymmetric methylation. The complete non-CpG pattern was reinstated at each generation in spite of the fact that the majority of the sperm genomes contained either none or only one methylated non-CpG site. This observation led us to the hypothesis that the stable CpG patterns might act as blueprints for the maintenance of non-CpG DNA methylation. As predicted, non-CpG DNA methylation profiles were abrogated in a mutant lacking Dnmt1, the enzymes responsible for CpG methylation, but not in mutants defective for either Dnmt3a or Dnmt2.
Explorer Mechanised Verification Patterns for Dafny

In Dafny, the program text is used to both specify and implement programs in the same language [24]. It then uses a fully automated theorem prover to verify that the implementation satisfies the specification. However, the prover often needs further guidance from the user, and another role of the language is to provide such necessary hints and guidance. In this paper, we present a set of verification patterns to support this process. In previous work, we have developed a tactic language for Dafny, where users can encode their verification patterns and re-apply them for several proof tasks [16]. We extend this language with new features, implement our patterns in this tactic language and show, through experiments, generality of the patterns, and applicability of the tactic language.
Augmented RFID Tags

This paper discusses the evolution of UHF RFID tags towards Augmented Tags. Such an evolution must be compliant with the huge advantages that the tags encompass, in particular full passive feature, compact size, usage flexibility and cost effectiveness. The discussed evolutions are based on the exploitation of some of the properties of the tag antennas or the RFID chips. Indeed, it is well established that any modification introduced in the near field region of antenna will generate significant change in its parameters such as impedance and directivity. Therefore it could be used as an environment sensor. Besides, the non-linear behavior of RFID chip could be used to implement new functions such as energy harvesting and communication channel diversity. Moreover, the design of RFID chip can evolve to allow the integration of external sensor.
Race, Depressive Symptoms, and All-Cause Mortality in the United States

Purpose Despite the well-established association between baseline depressive symptoms and risk of all cause-mortality, limited information exists on racial differences in the residual effects of baseline depressive symptoms above and beyond socioeconomic status (SES) and physical health on this link. The current study compared Blacks and Whites for the residual effects of depressive symptoms over SES and health on risk of long-term all-cause mortality in the U.S. Methods Data were obtained from the Americans’ Changing Lives Study, a nationally representative longitudinal cohort of U.S. adults with up to 25 years of follow-up. The study followed 3,361 Blacks and Whites for all-cause mortality between 1986 and 2011. The main predictor of interest was baseline depressive symptoms measured at 1986 using an 11-item Center for Epidemiological Studies-Depression scale. Covariates included baseline demographics (age and gender), SES (education and income), and health [chronic medical conditions (CMCs), self-rated health (SRH), and body mass index (BMI)] measured at 1986. Race (Black versus White) was the focal moderator. We ran a series of Cox proportional hazard models in the pooled sample and also stratified by race. Results In the pooled sample, higher depressive symptoms at baseline were associated with higher risk of all-cause mortality except when the CMC, SRH, and BMI were added to the model. In this later model, race interacted with baseline depressive symptoms, suggesting a larger effect of depressive symptoms on mortality among Whites compared to Blacks. Among Whites, depressive symptoms were associated with increased risk of mortality, after controlling for SES but not after controlling for health (CMC, SRH, and BMI). Among Blacks, depressive symptoms were not associated with mortality before health was introduced to the model. After controlling for health, baseline depressive symptoms showed an inverse association with all-cause mortality among Blacks. Although the effect of baseline depressive symptoms on mortality disappeared after controlling for health among Whites, SRH did not interfere (confound) with the effect of depressive symptoms on mortality among Blacks. Conclusion The effect of depressive symptoms on increased risk of all-cause mortality, which existed among Whites, could not be found for Blacks. In addition, race may modify the roles that SES and health play regarding the link between depressive symptoms and mortality over a long period of time.
Efficacy of Giving Lactobacillus sp. As a Probiotic In Childhood Acute Diarrhea : Systematic Review

Diare merupakan penyebab kematian nomor satu pada balita di Indonesia. Menurut Organisasi Gastroenterologi Dunia, penatalaksanaan diare akut pada anak terdiri dari terapi rehidrasi oral, terapi suplementasi zinc, pola makan, probiotik, dan antibiotik yang diberikan secara selektif. Tinjauan sistematik ini bertujuan untuk mengetahui efikasi Lactobacillus sp. untuk mengobati diare akut pada anak. Dalam melakukan identifikasi literatur, peneliti menggunakan kriteria kelayakan (eligibilitas) PICOS (population, intervention, comparison, outcome, studies). Jumlah data dari penelitian ini ditampilkan menggunakan pedoman standar yaitu flowchartpreferred reporting items for systematical review and meta-analysis (PRISMA) untuk dievaluasi dengan checklist PRISMA. Kriteria yang memadai diperlukan agar tinjauansistematis ini dapat memberikan data yang representatif dan menggambarkan kualitas pemberian probiotik sebagai terapi tambahan pada anak dengan diare akut. Sumber yang digunakan dalam menyusun tinjauan sistematis ini adalah artikel yang diambil dari database Pubmed, Springer, dan Science Direct untuk mengidentifikasi artikel yang diterbitkan pada tahun 2013 hingga 2023. Kata kunci disusun menggunakan metode boolean operator. Persamaan dari kata kunci yang diinginkan, dicari dengan menggunakan medical subject heading (MeSH). Boolean operator pada penelitian ini adalah: (Probiotic) AND (Lactobacillus) AND (“Acute Diarrhea”) AND (Child OR Children OR Pediatric). Enam artikel dari total penemuan 1755 artikel pada proses seleksi studi digunakan dalam menyusun tinjauan sistematis ini, setelah melalui penilaian kritis studi RCT menggunakan JBI critical appraisal tools dan diperoleh nilai rata-rata sebesar 71,76%. Hasil penelitian ini menunjukkan bahwa pemberian Lactobacillus sp. pada penderita diare akut anak mampu memperpendek durasi diare akut dan mampu mempercepat kembalinya konsistensi tinja ke kondisi normal.
Detection and Classification of Lung Nodule in CT Scan Images Using CNN

The Identification of lung malignant cells at premature stage remain as remarkable research area for researchers. Lung nodules are account as a normal reason for death in people all over the world. Identification of lung nodules at the initial stage can build the pace of endurance of patients. In this article computed tomography (CT) scan images as input to classify lung malignant cells of non-small cell lung cancer and categories according to subtypes of cancer by using the image processing technique with a convolutional neural network (CNN). The segmentation of the CT scan is performed to simplify the representation for meaningful and easier analysis. The feature extraction technique is used which is independent from the size and rotation of the image. These extracted features will use as an input to convolutional neural network (CNN), it pass through different layer of neural network at the end output layer classifies the affected and non-affected areas of the lung nodule with respect to subtypes (adenocarcinoma, squamous cell carcinoma, and large cell carcinoma). The deep learning algorithms VGG 16 show accuracy 85.01% while another deep learning algorithms VGG 19 show best accuracy 98.74% to correctly classify the nodules and subtypes.
Alignment of Multiple DNA Sequences by Using Improved GA Operators

One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). It is a critical tool for biologists to identify the relationships between species and also possibly predict the structure and functionality of biological sequences. The general multiple sequence alignment problem is known to be NP-hard, and hence the problem of finding the best possible multiple sequence alignment is intractable. Therefore, a genetic algorithm based approach has been designed to solve the multiple DNA sequence alignment problem by using different genetic operators. Experimental results with different lengths of DNA sequences has been detailed in this paper . It has also shown that how the increase in length will affect the overall quality of the alignment. The extensive experiment on wide range of datasets and the obtained results has shown the effectiveness of the proposed approach in solving multiple DNA sequences.
Microtubule-Associated Protein Tau, α-Tubulin and βIII-Tubulin Expression in Breast Cancer

Background The microtubule-associated protein Tau binds to both inner and outer surfaces of microtubules, leading to tubulin assembly and microtubule stabilization. The aim of this study was to evaluate the significance of Tau, α-tubulin, and βIII-tubulin expression in breast carcinoma and to assess their relationships with disease progression in the context of taxane treatment. Methods Immunohistochemical expressions of Tau, α-tubulin, and βIII-tubulin were assessed in 183 breast cancer cases. Expression was correlated with clinicopathologic parameters, disease progression and overall survival. Results Tau expression was correlated with lymph node metastasis and estrogen receptor (ER) positivity (p=.003 and p<.001, respectively). Loss of α-tubulin was significantly correlated with distant metastasis (p=.034). Loss of βIII-tubulin was correlated with lymph node metastasis and ER positivity (p=.004 and p<.001, respectively). In taxane-treated cases, Tau expression and loss of α-tubulin and βIII-tubulin expression were related to disease progression (p=.001, p=.028, and p=.030, respectively). Tau expression was associated with a worse survival rate in taxane-treated patients (p=.049). Conclusions Tau expression and loss of α-tubulin and βIII-tubulin expression were correlated with aggressive behavior in taxane-treated breast cancer. Further evaluation of Tau, α-tubulin and βIII-tubulin may be useful in predicting clinical behavior and seeking therapeutic measures in taxane-based chemotherapy for breast cancer.
Effectiveness of Vegetation Surrogates for Parasitoid Wasps in Reserve Selection

Abstract: Selecting suitable nature reserves is a continuing challenge in conservation, particularly for target groups that are time‐consuming to survey, species rich, and extinction prone. One such group is the parasitoid Hymenoptera, which have been excluded from conservation planning. If basic characteristics of habitats or vegetation could be used as reliable surrogates of specific target taxa, this would greatly facilitate appropriate reserve selection. We identified a range of potential habitat indicators of the species richness of pimpline parasitoid communities (Hymenoptera: Ichneumonidae: Pimplinae, Diacritinae, Poemeniinae) and tested their efficiency at capturing the observed diversity in a group of small woodlands in the agricultural landscape of the Vale of York (United Kingdom). Eight of the 18 vegetation‐based reserve‐selection strategies were significantly better at parasitoid species inclusion than random selection of areas. The best strategy maximized richness of tree species over the entire reserve network through complementarity. This strategy omitted only 2–3 species more (out of 38 captured in the landscape as a whole) than selections derived from the parasitoid survey data. In general, strategies worked equally well at capturing species richness and rarity. Our results suggest that vegetation data as a surrogate for species richness could prove an informative tool in parasitoid conservation, but further work is needed to test how broadly applicable these indicators may be.
Ectopic Pax6 expression disturbs lens fiber cell differentiation.

PURPOSE Pax6 is a transcription factor necessary for the specification and subsequent formation of the ocular lens. It is expressed in all lens cells at early stages of development. After lens formation, Pax6 expression is maintained in the lens epithelium, whereas its level abruptly decreases in differentiated fiber cells. This study is to test the hypothesis that normal fiber cell differentiation would be perturbed by sustained Pax6 expression. METHODS Transgenic mice expressing the canonical form of mouse Pax6 were created under the control of a modified mouse alphaA-crystallin promoter. The phenotypic changes in the transgenic lens were analyzed by light and electron microscopy. The effect of ectopic Pax6 expression on the lens fiber cells was investigated by in situ hybridization, immunohistochemical staining, real-time reverse transcriptase-polymerase chain reaction (RT-PCR), and two-dimensional (2-D) gel electrophoresis. RESULTS Transgenic mice from seven different lines all had cataracts with severity that correlated with the transgene expression level in lens fiber cells. In severely affected lines, a lumen was present between the apical surfaces of the epithelial and fiber cells, suggesting that secondary fiber cell elongation is incomplete. Electron microscopy analysis showed that the ball-and-socket interdigitations between neighboring fiber cells were underdeveloped or attenuated in the transgenic lens. Most interesting, elevated levels of Pax6 in fiber cells reduced the protein levels of transcription factor cMaf, which is known to be essential in fiber cell differentiation. Furthermore, the total amount of lens proteins was 60% less than normal in the Pax6 transgenic lens. Among the crystallins examined, the relative ratio of intact betaB1-crystallin protein to total lens protein was significantly reduced. Real-time reverse transcriptase PCR showed that the ratio of betaB1-crystallin transcript levels to total mRNA levels were reduced by 87%. CONCLUSIONS The data demonstrate that high levels of Pax6 expression disrupt normal fiber cell differentiation and maturation.