Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Key Micronutrients from Nutrigenetic and Nutrigenomic Perspectives in Cancer Prevention

Regarding cancer as a genetic multi-factorial disease, a number of aspects need to be investigated and analyzed in terms of cancer’s predisposition, development and prognosis. One of these multi-dimensional factors, which has gained increased attention in the oncological field due to its unelucidated role in risk assessment for cancer, is diet. Moreover, as studies advance, a clearer connection between diet and the molecular alteration of patients is becoming identifiable and quantifiable, thereby replacing the old general view associating specific phenotypical changes with the differential intake of nutrients. Respectively, there are two major fields concentrated on the interrelation between genome and diet: nutrigenetics and nutrigenomics. Nutrigenetics studies the effects of nutrition at the gene level, whereas nutrigenomics studies the effect of nutrients on genome and transcriptome patterns. By precisely evaluating the interaction between the genomic profile of patients and their nutrient intake, it is possible to envision a concept of personalized medicine encompassing nutrition and health care. The list of nutrients that could have an inhibitory effect on cancer development is quite extensive, with evidence in the scientific literature. The administration of these nutrients showed significant results in vitro and in vivo regarding cancer inhibition, although more studies regarding administration in effective doses in actual patients need to be done.
Software platform for parallel image processing and computer vision

We describe a general purpose environment for the development of parallel image processing/computer vision algorithms: PRIME (parallel image media processing environment). 'General purpose' here means that the environment is designed so as to be used on a variety of multi-processor systems ranging from tightly-coupled computers to loosely-coupled computers. The key point of the system is that it provides an architecture- independent programming environment for image processing and computer vision. We show the outline of PRIME, its implementation, and its preliminary performance evaluation.
HNF4α and CDX2 Regulate Intestinal YAP1 Promoter Activity

The Hippo pathway is important for tissue homeostasis, regulation of organ size and growth in most tissues. The co-transcription factor yes-associated protein 1 (YAP1) serves as a main downstream effector of the Hippo pathway and its dysregulation increases cancer development and blocks colonic tissue repair. Nevertheless, little is known about the transcriptional regulation of YAP1 in intestinal cells. The aim of this study to identify gene control regions in the YAP1 gene and transcription factors important for intestinal expression. Bioinformatic analysis of caudal type homeobox 2 (CDX2) and hepatocyte nuclear factor 4 alpha (HNF4α) chromatin immunoprecipitated DNA from differentiated Caco-2 cells revealed potential intragenic enhancers in the YAP1 gene. Transfection of luciferase-expressing YAP1 promoter-reporter constructs containing the potential enhancer regions validated one potent enhancer of the YAP1 promoter activity in Caco-2 and T84 cells. Two potential CDX2 and one HNF4α binding sites were identified in the enhancer by in silico transcription factor binding site analysis and protein-DNA binding was confirmed in vitro using electrophoretic mobility shift assay. It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. Additionally, CDX2 and HNF4α binding are important for the YAP1 enhancer activity in intestinal epithelial cells.
A systematic review of clinical guidelines on choice, dose, and duration of antipsychotics treatment in first- and multi-episode schizophrenia

Abstract Clinical guidelines provide evidence-based recommendations to regulate pharmacological treatment of psychotic disorders. However, the quality of evidence, country of origin, and publication dates of such guidelines vary, which leads to discrepancies between recommendations. This systematic review aimed to examine consensus and disparities between clinical recommendations on the choice, dose, and duration of antipsychotic treatment for first- and multi-episode schizophrenia patients. A literature search through The Cochrane Library, Embase, Medline, PsycINFO, PubMed, Scopus, Web of Sciences, and relevant bibliographies revealed 24 guidelines that met the inclusion criteria. The guidelines indicated mostly consistent recommendations regarding the optimal dose range of antipsychotics, while guidance with regards to the choice and duration of treatment remains somewhat controversial. Current trends in guidelines emphasize that there is simply no ‘one-size-fits-all’ method to manage schizophrenia patients. Further research is needed not only to address discrepancies between guidelines, but also to justify the gap between theory and practice.
Intrinsic Replication Competences of HIV Strains After Zidovudine/Lamivudine/Nevirapine Treatment in the Philippines

Although drug-resistant HIV variants are considered to be less fit than drug-susceptible viruses, replication competence of these variants harbored by patients has not yet been elucidated in detail. We herein assessed the replication competence of strains obtained from individuals receiving antiretroviral therapy. Among 11 306 participants in a drug resistance surveillance in the Philippines, 2629 plasma samples were obtained from individuals after a 12-month treatment with zidovudine (ZDV)/lamivudine (3TC)/nevirapine (NVP). The replication competence of HIV isolates was then assessed by reinoculation into seronegative peripheral blood mononuclear cells in the absence of drugs in vitro. The drug resistance rate was estimated to be 9.2%. Drug-resistant strains were still a minority of closely related strains in a phylogenetic cluster. Among the available 295 samples, 37 HIV strains were successfully isolated. Progeny viruses were produced at a wide range (5.1 × 106 to 3.4 × 109 copies/mL) in primary culture of peripheral blood mononuclear cells. The viral yields were higher than the corresponding plasma viral load (1300 to 3.4 × 106 copies/mL) but correlated with those (r = 0.4). These results suggest that strains with higher intrinsic replication competence are one of the primary targets of newly selected drugs at the increasing phase of the plasma viral load during antiretroviral therapy.
Management of psoriasis as a systemic disease: what is the evidence?

Psoriasis is a chronic, systemic immune‐mediated disease characterized by development of erythematous, indurated, scaly, pruritic and often painful skin plaques. Psoriasis pathogenesis is driven by proinflammatory cytokines and psoriasis is associated with increased risk for comorbidities, including, but not limited to, psoriatic arthritis, cardiovascular disease, diabetes mellitus, obesity, inflammatory bowel disease and nonalcoholic fatty liver disease compared with the general population.
Considering the Links Between Nonalcoholic Fatty Liver Disease and Insulin Resistance: Revisiting the Role of Protein Kinase C ε

Nonalcoholic fatty liver disease (NAFLD) and insulin resistance often coincide. These twin epidemics are both sequelae of ectopic lipid accumulation, but the mechanistic links between them are debated. The protein kinase C family of serine/threonine kinases has been implicated in altered insulin action in liver, muscle and fat cells for over three decades and provides a putative link between NAFLD and insulin resistance. This article is protected by copyright. All rights reserved.
Functionally Equivalent Clone Detection Using IOT-Behavior Algorithm

This paper presents an algorithm for the detection of functionally equivalent code clones in C code. The functionally equivalent code clones is the forth type of clones, which means that two or more code fragments that do the same calculation but with different syntax. Thus, we can detect the functionally equivalent clones by observing the input-output behavior. We propose the definition of input-output behavior by including not only the values of input-output, but also the number and types of input sets and output sets. We call this as the IOT (input, output and types)-Behavior of C code fragment. Our algorithm has been tested in open source code.
Ginkgolide B promotes osteoblast differentiation via activation of canonical Wnt signalling and alleviates osteoporosis through a bone anabolic way

Osteoporosis has become a worldwide problem as the population ages. Although many advances have been made in the treatment of osteoporosis in the past few years, the outcome are sometimes disturbing because of the adverse effects of these treatments. Further studies are still needed to identify novel alternate agents to improve the therapeutic effect. Ginkgolide B (GB), a derivative of Ginkgo biloba leaves, has numerous pharmacological effects, including anticancer and anti‐inflammation activities. However, the effect of GB on the regulation of osteoblast activity and bone formation effect has not yet been investigated. In this study, we showed the in vitro and in vivo effects of GB on osteoblast differentiation and bone formation. We found that GB promotes osteoblast differentiation of Bone Mesenchymal Stem Cells (BMSCs) and MC3T3‐E1 cells in vitro in a Wnt/β‐catenin‐dependent manner. In an in vivo study, we constructed a cranial defect model in rats and treated with GB. Histomorphometric and histological analyses confirmed that the usage of GB significantly promotes bone formation. Further study on ovariectomy (OVX) rats demonstrated that GB is capable of alleviating ovariectomy‐induced bone loss by enhancing osteoblast activity. Our findings indicate that GB is a potential therapeutic agent of osteoporosis through an anabolic way in bone.
Multi-rate adaptive beamforming (MRABF)

An important trend in underwater acoustics is the use of large arrays with many elements and small resolution cells in an effort to detect weak signals. Frequently, the background noise is dominated by multiple moving surface ships that act like discrete interferers. These interferers may move through many spatial resolution cells in the time required to obtain sufficient "snapshots" for covariance matrix estimation. The non-stationarity of the background limits the performance of adaptive algorithms. Reduced degree-of-freedom approaches that can track and rapidly null interferers before they move too far are of great interest. The paper presents a new class of algorithms in which a low-rank, dynamically changing interference sub-space is estimated and tracked using a short-term average. An orthogonal projection is then applied to the data to null components in the interference sub-space. A second stage of adaptive beamforming that uses a longer averaging time is then applied to the projected data. Unlike most sub-space approaches that work for strong signals, there is no requirement that the signal be contained in the interference sub-space. It is shown how multiple interferers moving rapidly across beams can be tracked and nulled to reveal the presence of a weak target not visible with conventional, adaptive, or usual sub-space methods. The effectiveness of multi-rate adaptive beamforming is illustrated by examples. It is shown that moving interferers are effectively nulled to allow detection of weak signals when other methods including MVDR, conventional, and signal subspace fail.
Memory consistency models for shared memory multiprocessors and DSM systems

The use of systems with multiple processors that support shared memory programming paradigm is rapidly increasing nowadays. Possible buffering, pipelining, and optimization of shared memory accesses, as well as the existence of multiple copies of shared variables in these systems, may cause specific implications that can not be understood just as an intuitive extension of an uniprocessor memory model. Therefore, the memory consistency model formally specifies the memory system behavior to be expected by the programmer. This paper reveals the essence of several memory consistency models: sequential, processor, weak, release (with eager and lazy implementation), and entry. It also provides definitions and a set of examples that underline differences between particular models. Results of several performance evaluation studies are also discussed.
GLI1‐induced mammary gland tumours are transplantable and maintain major molecular features

Increased expression of GLI1, the main Hedgehog signalling pathway effector, is related to unfavourable prognosis and progressive disease of certain breast cancer subtypes. We used conditional transgenic mice induced to overexpress GLI1 in the mammary epithelium either alone or in combination with deletion of one Trp53 allele to address the role of elevated GLI1 expression in breast tumour initiation and progression. Induced GLI1 expression facilitates mammary gland tumour formation and this was further increased upon heterozygous deletion of Trp53. The GLI1‐induced primary tumours were of different murine molecular subtypes, including Normal‐likeEx, Class8Ex, Claudin‐LowEx and Erbb2‐likeEx. The gene expression profiles of some of the tumours correlated well with the PAM50 subtypes for human breast cancer. Whole‐exome sequencing revealed somatic mutation profiles with only little overlap between the primary tumours. Orthotopically serially transplanted GLI1‐induced tumours maintained the main morphological characteristics of the primary tumours for ≥10 generations. Independent of Trp53 status and molecular subtype, the serially transplanted GLI1‐induced tumours were able to grow both in the absence of transgenic GLI1 expression and in the presence of the GLI1 inhibitor GANT61. These data suggest that elevated GLI1 expression has a determinant role in tumour initiation; however, additional genetic events are required for tumour progression.
Vagal tone in infants of depressed mothers

Abstract Emotional reactivity and expressivity in infants have been previously correlated with vagal tone. This study investigated vagal tone of 3- and 6-month-old infants of depressed mothers. Vagal tone did not differ for infants of depressed versus nondepressed mothers at 3 months, but lower vagal tone was noted in infants of depressed versus nondepressed mothers at 6 months. The developmental increase in vagal tone that occurred between 3 and 6 months for infants of nondepressed mothers did not occur for infants of depressed mothers. Correlation analyses suggested that higher vagal tone at 6 months was related to more vocalizations and more optimal neurological scores.
Characterizing Eckol as a Therapeutic Aid: A Systematic Review

The marine biosphere is a treasure trove of natural bioactive secondary metabolites and the richest source of structurally diverse and unique compounds, such as phlorotannins and halo-compounds, with high therapeutic potential. Eckol is a precursor compound representing the dibenzo-1,4-dioxin class of phlorotannins abundant in the Ecklonia species, which are marine brown algae having a ubiquitous distribution. In search of compounds having biological activity from macro algae during the past three decades, this particular compound has attracted massive attention for its multiple therapeutic properties and health benefits. Although several varieties of marine algae, seaweed, and phlorotannins have already been well scrutinized, eckol deserves a place of its own because of the therapeutic properties it possesses. The relevant information about this particular compound has not yet been collected in one place; therefore, this review focuses on its biological applications, including its potential health benefits and possible applications to restrain diseases leading to good health. The facts compiled in this review could contribute to novel insights into the functions of eckol and potentially enable its use in different uninvestigated fields.
Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
Comparing the Readability of Text Displays on Paper, E-Book Readers, and Small Screen Devices

Science fiction has long promised the digitalization of books. Characters in films and television routinely check their palm-sized (or smaller) electronic displays for fast-scrolling information. However, this very technology, increasingly prevalent in today's world, has not been embraced universally. While the convenience of pocket-sized information pieces has the techno-savvy entranced, the general public still greets the advent of the e-book with a curious reluctance. This lack of enthusiasm seems strange in the face of the many advantages offered by the new medium - vastly superior storage capacity, searchability, portability, lower cost, and instantaneous access. This dissertation addresses the need for research examining the reading comprehension and the role emotional response plays in the perceived performance on e-document formats as compared to traditional paper format. This study compares the relative reading comprehension on three formats (Kindle, iTouch, and paper) and examines the relationship of subject's emotional response and relative technology exposure as factors that affect how the subject perceives they have performed on those formats. This study demonstrates that, for basic reading comprehension, the medium does not matter. Furthermore, it shows that, the more uncomfortable a person is with technology and expertise in the requested task (in this case, reading), the more they cling to the belief that they will do better on traditional (paper) media - regardless of how well they actually do.
Antenna selection diversity for framed digital signal transmission in mobile radio channel

An antenna selection diversity method is proposed in which received signal levels from the antennas are measured in a time-division manner and a switching operation is performed in the preamble or postamble portion of a framed digital signal. Hence the switching noise problem is avoided. Deterioration in diversity performance, compared with the case of a post-detection diversity, can be kept within 1 dB if a frame length, normalized by the maximum Doppler frequency, is less than 1/16. With the use of this technique, base station diversity systems, where no diversity facility is required in mobile stations for both upward and downward direction of transmission, are proposed. For single-frequency time-duplexed communication, the base station uses the proposed diversity method for reception, and an antenna selected last in the reception period is used for transmission. For dual-frequency duplex communication, the base station sends a postamble signal from the antennas in a time-division manner, and then the result determined from the comparison of the received levels that correspond to the postamble signal at the mobile station is sent back to the base station and used for antenna selection for the next transmission of the information signal. The performance of the proposed diversity for a digital FM system in the Rayleigh fading channel is investigated by computer simulation. <<ETX>>
Simultaneous Analysis in S-PLUS: The SimultAn Package

In this paper we describe the SimultAn package dedicated to simultaneous analysis. Simultaneous analysis is a new factorial methodology developed for the joint treatment of a set of several data tables. Since the first stage of simultaneous analysis requires a correspondence analysis of each table the package comprises two parts, one for correspondence analysis and one for simultaneous analysis. The package can be used to perform classical correspondence analysis of frequency/contingency tables as well as to perform simultaneous analysis of a set of frequency/contingency tables. In this package, functions for computation, summaries and graphical visualization in two dimensions are provided, including options to display partial rows and supplementary points.
The histone lysine demethylase KDM7A is required for normal development and first cell lineage specification in porcine embryos

ABSTRACT There is growing evidence that histone lysine demethylases (KDMs) play critical roles in the regulation of embryo development. This study investigated if KDM7A, a lysine demethylase known to act on mono-(me1) and di-(me2) methylation of H3K9 and H3K27, participates in the regulation of early embryo development. Knockdown of KDM7A mRNA reduced blastocyst formation by 69.2% in in vitro fertilized (IVF), 48.4% in parthenogenetically activated (PA), and 48.1% in somatic cell nuclear transfer (SCNT) embryos compared to controls. Global immunofluorescence (IF) signal in KDM7A knockdown compared to control embryos was increased for H3K27me1 on D7, for H3K27me2 on D3 and D5, for H3K9me1 on D5 and D7, and for H3K9me2 on D5 embryos, but decreased for H3K9me1, me2 and me3 on D3. Moreover, KDM7A knockdown altered mRNA expression, including the downregulation of KDM3C on D3, NANOG on D5 and D7, and OCT4 on D7 embryos, and the upregulation of CDX2, KDM4B and KDM6B on D5 embryos. On D3 and D5 embryos, total cell number and mRNA expression of embryo genome activation (EGA) markers (EIF1AX and PPP1R15B) were not affected by KDM7A knockdown. However, the ratio of inner cell mass (ICM)/total number of cells in D7 blastocysts was reduced by 45.5% in KDM7A knockdown compared to control embryos. These findings support a critical role for KDM7A in the regulation of early development and cell lineage specification in porcine embryos, which is likely mediated through the modulation of H3K9me1/me2 and H3K27me1/me2 levels, and changes in the expression of other KDMs and pluripotency genes.
Psychological pain responses in athletes and non‐athletes with low back pain: Avoidance and endurance matter

Dysfunctional psychological pain responses, namely fear‐avoidance (FAR), including catastrophizing and helplessness, as well as endurance‐related responses (ER), including thought suppression and overactivity, have been shown to be risk factors for persistent low back pain (LBP). Literature suggests that athletes may differ from non‐athletes regarding psychological responses to pain.