Miracle-dz/UniFAR-FTUs huggingface dataset:
Nearshore Wave Modeling with High-Order Boussinesq-Type Equations

The accuracy of using high-order Boussinesq-type models as compared to the typical order models is examined in this paper. The high-order model used is the two-layer model of Lynett and Liu in 2004, which captures both linear and nonlinear wave evolution up to kh≈6 . The physical situations examined all involve nearshore breaking, and an eddy-viscosity type breaking model is adopted for the two-layer model. One-horizontal dimension setups are the focus of this paper. It is shown that high-order models show significant benefit very near to the breaker line. For regular incident waves, the overshoaling seen in the one-layer (“fully nonlinear” extended Boussinesq) model is due to rapid increase of energy in the fifth and higher harmonics. These high-order nonlinear components are captured well in the two-layer model. The two-layer model also exhibits a noticeable accuracy increase for cnoidal waves breaking on a slope. For regular wave evolution over a bar, the high-order models are in good agreement with ex.
Probiotic for the Treatment of Minimal Hepatic Encephalopathy : Preliminary Report Issariyakulkarn

Objectives: Minimal hepatic encephalopathy (MHE) is a preclinical stage of overt hepatic encephalopathy (OHE). All MHE therapies modify gut microflora but consensus regarding MHE treatment is lacking. The aim of this study is to determine the effect of probiotic is reversing MHE in cirrhotic patients. Patients and Methods: A total of 58 cirrhotic patients were enrolled (44 males, 14 females) aged 4260, 87.7% in Child-Pugh class A. The diagnosis of MHE was based on the number connection test-A (NCT-A), line-tracing test (LTT) and critical flicker frequency analysis (CFF). Diagnostic criteria for MHE were met when abnormalities in at least two out of the three tests were present. Results: MHE was diagnosed in 16 patients (27.6%). Non-detectable ascites and Child A were the only significant differences between the MHE positive and MHE negative groups (p <0.01). Of the 16 patients, only 10 were recruited in the study, and were randomized, 5 patients in the probiotic group and 5 in the non-treatment group. Probiotic (Infloran) was prescribed for 8 weeks in the probiotic group. Psychometric test and CFF were performed in both groups after 4 and 8 weeks of treatment. MHE was reversed in none. No significant improvement in NCT was seen in both groups. Improvement of LTT was seen in 2 patients (40%) in the probiotic group and 3 (60%) in the non-treatment group. CFF <39 Hz was found in 4 patients (80%) before treatment and in none after
Language context modulates reading route: an electrical neuroimaging study

Introduction: The orthographic depth hypothesis (Katz and Feldman, 1983) posits that different reading routes are engaged depending on the type of grapheme/phoneme correspondence of the language being read. Shallow orthographies with consistent grapheme/phoneme correspondences favor encoding via non-lexical pathways, where each grapheme is sequentially mapped to its corresponding phoneme. In contrast, deep orthographies with inconsistent grapheme/phoneme correspondences favor lexical pathways, where phonemes are retrieved from specialized memory structures. This hypothesis, however, lacks compelling empirical support. The aim of the present study was to investigate the impact of orthographic depth on reading route selection using a within-subject design. Method: We presented the same pseudowords (PWs) to highly proficient bilinguals and manipulated the orthographic depth of PW reading by embedding them among two separated German or French language contexts, implicating respectively, shallow or deep orthography. High density electroencephalography was recorded during the task. Results: The topography of the ERPs to identical PWs differed 300–360 ms post-stimulus onset when the PWs were read in different orthographic depth context, indicating distinct brain networks engaged in reading during this time window. The brain sources underlying these topographic effects were located within left inferior frontal (German > French), parietal (French > German) and cingular areas (German > French). Conclusion: Reading in a shallow context favors non-lexical pathways, reflected in a stronger engagement of frontal phonological areas in the shallow versus the deep orthographic context. In contrast, reading PW in a deep orthographic context recruits less routine non-lexical pathways, reflected in a stronger engagement of visuo-attentional parietal areas in the deep versus shallow orthographic context. These collective results support a modulation of reading route by orthographic depth.
Aberrant methylation and silencing of IRF8 expression in non-small cell lung cancer

The aim of the present study was to investigate the aberrant methylation and altered expression of the interferon regulatory factor 8 (IRF8) gene in non-small cell lung cancer (NSCLC). Pyrosequencing assays were performed on 191 tumor specimens from NSCLC patients. The changes in IRF8 mRNA expression, prior to and following treatment with a demethylating agent and methylation itself, were examined in 13 lung cancer cell lines by quantitative polymerase chain reaction (qPCR) and pyrosequencing. IRF8 protein expression was examined in 94 of the 191 NSCLC specimens by immunohistochemical analysis. The IRF8 methylation level was significantly higher in the tumor tissues than in matched non-malignant lung tissues (P<0.0001). IRF8 was more frequently methylated in tumor tissues compared with matched non-malignant lung tissues, as defined by a predetermined cut-off value (P<0.0001). The IRF8 methylation level was strongly correlated with the change in mRNA expression in lung cancer cell lines and with the protein expression level in primary tumors. The IRF8 gene was more frequently methylated in patients without an epidermal growth factor receptor (EGFR) mutation than in patients with an EGFR mutation (P=0.015). IRF8 methylation correlated with recurrent prognosis in adenocarcinomas (log-rank test, P=0.048). IRF8 protein expression was frequently silenced in males, smokers, patients with non-adenocarcinoma or with wild-type EGFR, or in an advanced stage. IRF8 is often silenced by its methylation, which is a frequent event in NSCLC and, therefore, methylation of IRF8 may act as a prognostic marker for recurrence. Analysis of IRF8 methylation status may provide novel opportunities for improved prognosis and therapy of resected NSCLC.
Sirolimus can reverse resistance to gemcitabine, capecitabine and docetaxel combination therapy in pancreatic cancer.

CONTEXT Treating patients with metastatic carcinoma of the pancreas can lead to regression of disease, but the tumor becomes resistant to therapy within a few months. If resistance can be reversed or prevented, the chemotherapeutic benefit may be prolonged. CASE REPORTS Two patients with metastatic pancreatic cancer progressed on gemcitabine, capecitabine and docetaxel (GTX). When sirolimus was added to this regimen at a dosage to achieve a serum level of at least 10 ng/dL at the time of the gemcitabine and docetaxel infusion, their tumors regressed. CONCLUSION This demonstrates that the addition of sirolimus to a gemcitabine/docetaxel containing regimen can reverse tumor resistance in the clinical setting.
Idiotypic Multireactivity of ‘Natural’ Antibodies

One hundred and twenty IgM‐secreting hybridomas derived from unmanipulated 6‐day‐old BALB/c mice were screened for reactivity with the prototype idiotypic and anti‐idiotypic monoclonal antibodies, defining three well established systems, namely TEPC 15:10/13–15, J558:CD3.2, and MOPC 460:F6(51). Up to 25% of all IgM antibodies reacted with at least one of the six specific ligands, half of the latter being ‘monospecific’, the others reacting with two or more aniibodies. A detailed analysis of the four most multi‐reactive clones showed individually specific patterns of reactivity and revealed reactions of the same IgM molecule in idiotypic systems previously studied independently. Furthermore, when tested for functional interactions with syngeneic helper T cells expressing MOPC 460‐like clonotypes, one of these antibodies was found to inhibit effector helper activity. The results show the existence of ‘natural antibodies’ with idiotypic reactivities related to recurrent clonotypes in the strain. They may be either ‘specific’ or ‘mullireactive’, and might connect idiotypes on T and B cells and on antigenic systems so far studied independently.
Adalimumab in the treatment of rheumatoid arthritis

Introduction: Rheumatoid arthritis (RA) is a systemic inflammatory disease that causes increased morbidity and mortality. The treatment of the disease has considerably advanced with the addition of biological agents targeting pro-inflammatory cytokines such as tumor necrosis factor (TNF). Adalimumab (ADA) is one of the currently available five TNF inhibitors for clinical use in RA. It is a fully humanized monoclonal antibody which may be prescribed as monotherapy or in combination with methotrexate or other disease-modifying antirheumatic drugs. Areas covered: This review summarizes the recent available data on efficacy and safety of ADA in patients with early and established RA as well as improvement of quality of life and finally we provide data on biologic drug comparison. Expert opinion: ADA has been evaluated in various randomized placebo-controlled trials in RA, prospective observational studies as well as open-label extensions of the original double-blind trials providing experience and data about the long-term efficacy and safety of the drug. Effectiveness of the drug is sustained, while in most cases RA patients treated with ADA experienced a slower radiographic progression and consequently less disability and improved health-related quality of life outcomes. Clinical trials demonstrated no new safety signals and a safety profile consistent with that of the anti-TNF class.
Criteria for Nonlinear Time Series Models ∗

In this paper the performance of different information criteria for simultaneous model class and lag order selection is evaluated using simulation studies. We focus on the ability of the criteria to distinguish linear and nonlinear models. In the simulation studies, we consider three different versions of the commonly known criteria AIC, SIC and AICc. In addition, we also assess the performance of WIC and evaluate the impact of the error term variance estimator. Our results confirm the findings of different authors that AIC and AICc favor nonlinear over linear models, whereas weighted versions of WIC and all versions of SIC are able to successfully distinguish linear and nonlinear models. However, the discrimination between different nonlinear model classes is more difficult. Nevertheless, the lag order selection is reliable. In general, information criteria involving the unbiased error term variance estimator overfit less and should be preferred to using the usual ML estimator of the error term variance. JEL-Numbers: C15, C22
Testing Intermediate-Age Stellar Evolution Models with VLT Photometry of Large Magellanic Cloud Clusters. III. Padova Results

The color-magnitude diagrams (CMDs) of three intermediate-age Large Megallanic Cloud clusters, NGC 2173, SL 556, and NGC 2155, are analyzed to determine their age and metallicity based on Padova stellar models. Synthetic CMDs are compared with cluster data. The best match is obtained using two fitting functions based on star counts in the different bins of the cluster CMD. Two different criteria are used. One of them takes into account the uncertainties in the color of the red clump stars. Given the uncertainties on the experimental values of the clusters metallicity, we provide a set of acceptable solutions. They define the corresponding values of metallicity, age, reddening and distance modulus (for the assumed initial mass function). The comparison with Padova models suggests for NGC 2173 a prolonged star formation (spanning a period of about 0.3 Gyr), beginning 1.7 Gyr and ending 1.4 Gyr ago. The metallicity Z is in the range 0.0016–0.003. For SL 556 an age of 2.0 Gyr is obtained. The metallicity value is in the range 0.002–0.004, depending on the adopted comparison criterion. The derived age for NGC 2155 is 2.8 Gyr, and its metallicity Z is in the range 0.002–0.003. The CMD features of this cluster suggest that a more efficient overshoot should be adopted in the evolutionary models. A period of extended star formation is not required to fit the SL 556 and NGC 2155 observations.
CPMAS 13C NMR Characterization of Leaves and Litters from the Reafforestated Area of Mustigarufi in Sicily (Italy)

Reafforestation is generally based on the planting of exotic fast growing tree species suitable for adapting to even harsh environments. Once the introduced plants ameliorate soil conditions, they can be progressively replaced by au- tochthonous plant species. Reafforestation is applied worldwide. However, only few studies on the effect of reafforesta- tion on lands from Mediterranean regions are available. This paper reports the characterization by cross polarization 13 C NMR spectroscopy of fresh leaves and superficial litters from a reafforestated area in central Sicily (Italy). NMR assign- ment is attempted. A differentiation among the molecular systems within leaves and litters is also done on the basis of NMR assessment. Results showed that the main differences among the leaves of four forest trees (two eucalyptus spp., one cypress sp. and one pine sp.) occur in the distribution of the aromatic and alkyl carbons. In particular, the alkyl moie- ties in the eucalyptus spp. leaves were attributed to branched structures belonging to the eucalyptus oil, whereas linear fatty acids were more representetive in the NMR spectra of pine and cypress leaves. In addition, the aromatic carbons of the conifer leaves were assigned not only to lignin- and tannin-like structures, but also to common olefin carbons in un- saturated fatty acids and abietic acid-like systems. The spectra of the litters resembled, as expected, those of the leaves. However, the presence of very large carbohydrate NMR signals suggested that degradation processes were still ongoing in litters. A comparative evaluation of CPMAS 13 C NMR spectra was done by applying principal component analysis. This paper confirmed the suitability of CPMAS 13 C NMR spectroscopy in evaluating the differences among natural bio-masses
Excitatory Amino Acid Receptors Mediate Asymmetry and Lateralization in the Descending Cardiovascular Pathways from the Dorsomedial Hypothalamus

The dorsomedial hypothalamus (DMH) and lateral/dorsolateral periaqueductal gray (PAG) are anatomically and functionally connected. Both the DMH and PAG depend on glutamatergic inputs for activation. We recently reported that removal of GABA-ergic tone in the unilateral DMH produces: asymmetry, that is, a right- (R-) sided predominance in cardiac chronotropism, and lateralization, that is, a greater increase in ipsilateral renal sympathetic activity (RSNA). In the current study, we investigated whether excitatory amino acid (EAA) receptors in the DMH–PAG pathway contribute to the functional interhemispheric difference. In urethane (1.2 to 1.4 g/kg, i.p.) anesthetized rats, we observed that: (i) nanoinjections of N-methyl D-aspartate (NMDA 100 pmol/100 nl) into the unilateral DMH produced the same right-sided predominance in the control of cardiac chronotropy, (ii) nanoinjections of NMDA into the ipsilateral DMH or PAG evoked lateralized RSNA responses, and (iii) blockade of EAA receptors in the unilateral DMH attenuated the cardiovascular responses evoked by injection of NMDA into either the R- or left- (L-) PAG. In awake rats, nanoinjection of kynurenic acid (1 nmol/100 nL) into the L-DMH or R- or L-PAG attenuated the tachycardia evoked by air stress. However, the magnitude of stress-evoked tachycardia was smallest when the EAA receptors of the R-DMH were blocked. We conclude that EAA receptors contribute to the right-sided predominance in cardiac chronotropism. This interhemispheric difference that involves EAA receptors was observed in the DMH but not in the PAG.
Definitely maybe: can unconscious processes perform the same functions as conscious processes?

Hassin recently proposed the “Yes It Can” (YIC) principle to describe the division of labor between conscious and unconscious processes in human cognition. According to this principle, unconscious processes can carry out every fundamental high-level cognitive function that conscious processes can perform. In our commentary, we argue that the author presents an overly idealized review of the literature in support of the YIC principle. Furthermore, we point out that the dissimilar trends observed in social and cognitive psychology, with respect to published evidence of strong unconscious effects, can better be explained by the way how awareness is defined and measured in both research fields. Finally, we show that the experimental paradigm chosen by Hassin to rule out remaining objections against the YIC principle is unsuited to verify the new default notion that all high-level cognitive functions can unfold unconsciously.
Factors influence consumers' adoption of mobile payment devices in Qatar

This research examines the factors that influence the customers' intention in adapting Mobile Payment Device MPD technology in an emerging economy Qatar. Unified Theory of Acceptance and Use of Technology Model UTAUT is employed as the basis for the proposed research model. A questionnaire survey is used as a tool to collect the data. Research results reveal that performance expectancy, social influence, and perceived information security have direct significant effects on consumer's behavioural intention to adapt the MPD. It is also found that effort expectancy has indirect effect on intention through performance expectancy. Demographic factors such as gender, age, and self-reported knowledge about MPD moderate the relationship between behavioural intention to adopt MPD and the predicting variables. Implications for practitioners and researchers are discussed.
Prey Capture Behavior Evoked by Simple Visual Stimuli in Larval Zebrafish

Understanding how the nervous system recognizes salient stimuli in the environment and selects and executes the appropriate behavioral responses is a fundamental question in systems neuroscience. To facilitate the neuroethological study of visually guided behavior in larval zebrafish, we developed “virtual reality” assays in which precisely controlled visual cues can be presented to larvae whilst their behavior is automatically monitored using machine vision algorithms. Freely swimming larvae responded to moving stimuli in a size-dependent manner: they directed multiple low amplitude orienting turns (∼20°) toward small moving spots (1°) but reacted to larger spots (10°) with high-amplitude aversive turns (∼60°). The tracking of small spots led us to examine how larvae respond to prey during hunting routines. By analyzing movie sequences of larvae hunting paramecia, we discovered that all prey capture routines commence with eye convergence and larvae maintain their eyes in a highly converged position for the duration of the prey-tracking and capture swim phases. We adapted our virtual reality assay to deliver artificial visual cues to partially restrained larvae and found that small moving spots evoked convergent eye movements and J-turns of the tail, which are defining features of natural hunting. We propose that eye convergence represents the engagement of a predatory mode of behavior in larval fish and serves to increase the region of binocular visual space to enable stereoscopic targeting of prey.
Regulation of polyphenic caste differentiation in the termite Reticulitermes flavipes by interaction of intrinsic and extrinsic factors

SUMMARY Polyphenism is a key strategy used by solitary insects to adapt to changing environmental conditions and by eusocial insects for existing collaboratively in a social environment. In social insects, the morphogenetic juvenile hormone (JH) is often involved in directing the differentiation of polyphenic behavioral castes. The present study examines the effects of JH, environment and feeding on caste polyphenism in a eusocial insect, the termite Reticulitermes flavipes (Kollar). Our approach included a combination of model JH bioassays, SDS-PAGE and western blotting. Our findings revealed significant temperature-dependent effects on (1) JH-induced soldier caste differentiation, (2) abundance of soldier-inhibitory hexamerin proteins and (3) JH-sequestration by hexamerin proteins. Additionally, although it appears to be dependent on a complex interaction of factors, feeding apparently plays a significant upstream role in enhancing hexamerin accumulation under normal colony conditions. These findings offer important new information on termite eusocial polyphenism by providing the first mechanistic evidence linking an intrinsic caste regulatory factor (hexamerin proteins) to an upstream extrinsic factor (environment) and a downstream response (caste differentiation). These observations are consistent with the hypothesis that the hexamerins serve as an environmentally and nutritionally responsive switching mechanism that regulates termite caste polyphenism.
Bioinformatics for personal genome interpretation

An international consortium released the first draft sequence of the human genome 10 years ago. Although the analysis of this data has suggested the genetic underpinnings of many diseases, we have not yet been able to fully quantify the relationship between genotype and phenotype. Thus, a major current effort of the scientific community focuses on evaluating individual predispositions to specific phenotypic traits given their genetic backgrounds. Many resources aim to identify and annotate the specific genes responsible for the observed phenotypes. Some of these use intra-species genetic variability as a means for better understanding this relationship. In addition, several online resources are now dedicated to collecting single nucleotide variants and other types of variants, and annotating their functional effects and associations with phenotypic traits. This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants. In this work, we review the most important developments in the field--the databases and bioinformatics tools that will be of utmost importance in our concerted effort to interpret the human variome.
Thinking Like a Vertex

The vertex-centric programming model is an established computational paradigm recently incorporated into distributed processing frameworks to address challenges in large-scale graph processing. Billion-node graphs that exceed the memory capacity of commodity machines are not well supported by popular Big Data tools like MapReduce, which are notoriously poor performing for iterative graph algorithms such as PageRank. In response, a new type of framework challenges one to “think like a vertex” (TLAV) and implements user-defined programs from the perspective of a vertex rather than a graph. Such an approach improves locality, demonstrates linear scalability, and provides a natural way to express and compute many iterative graph algorithms. These frameworks are simple to program and widely applicable but, like an operating system, are composed of several intricate, interdependent components, of which a thorough understanding is necessary in order to elicit top performance at scale. To this end, the first comprehensive survey of TLAV frameworks is presented. In this survey, the vertex-centric approach to graph processing is overviewed, TLAV frameworks are deconstructed into four main components and respectively analyzed, and TLAV implementations are reviewed and categorized.