Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential gene expression of chemokines in KRAS and BRAF mutated colorectal cell lines: role of cytokines.

AIM To study KRAS/BRAF mutations in colorectal-cancer (CRC) that influences the efficacy of treatment. To develop strategies for overcoming combination of treatment. METHODS Five colonic cell-lines were investigated: DLD-1 with KRAS (G13D) mutation, HT 29 and Colo 205 with BRAF (V600E) mutation as well as the wild type (Wt) cell-lines Caco2 and Colo-320. DLD-1 (KRAS), HT-29 (BRAF) and Caco2 (Wt) cell lines were treated with cytokines (TNFα 50 ng, IL-1β 1 ng and IFNγ 50 ng) and harvested at different time points (1-24 h). KRAS inhibition was performed by the siRNA-approach. Two colorectal cancer cells DLD-1 and Caco2 were used for KRAS inhibition. About 70% confluency were confirmed before transfection with small interferring RNA (siRNA) oligonucleotides. All the synthetic siRNA sequences were designed in our laboratory. Total RNA and protein was isolated from the cells for RT-PCR and Western blotting. Densitometry of the Western blotting was analyzed with the Image J software (NIH). Results are shown as mean ± SD. RESULTS RT-PCR analysis in non-stimulated cells showed a low basal expression of TNFα and IL-1β in the DLD-1 KRAS-mutated cell-line, compared to Caco2 wild type. No detection was found for IL-6 and IFNγ in any of the studied cell lines. In contrast, pro-angiogenic chemokines (CXCL1, CXCL8) showed a high constitutive expression in the mutated cell-lines DLD-1 (KRAS), HT-29 and Colo205 (BRAF), compared to wild type (Caco2). The anti-angiogenic chemokine (CXCL10) showed a high basal expression in wild-type, compared to mutated cell-lines. KRAS down-regulation by siRNA showed a significant decrease in CXCL1 and CXCL10 gene expression in the DLD-1 (KRAS) cell-line in comparison to wild type (Caco2) at 72 h after KRAS silencing. In contrast, the specific KRAS inhibition resulted in an up-regulation of CXCL1 and CXCL10. The results of our study show a higher expression of pro-angiogenic chemokines at basal level in mutated cell-lines, which was further increased by cytokine treatment. CONCLUSION To summarize, basal chemokine gene expression for pro-angiogenic chemokines was high in mutated as compared to wild type cell-lines. This reflects the likely existence of a different microenvironment in tumours consistent of wild type or mutated cells. This may help to rationalize the choice of molecular targets for suitable therapeutic investigation in clinical studies.
Rumen Manipulation to Increase the Efficient Use of Local Feed Resources and Productivity of Ruminants in the Tropics

Local feed resources, particularly low-quality roughages and agricultural crop-residues, are of prime importance for ruminants raised in the tropics. These feeds exhibit close relationships with rumen ecology, microbes and rumen fermentation patterns. A number of dietary factors could influence rumen fermentation especially the basal roughage source, its physical form and fermentation end-products. Diurnal fermentation patterns in ruminants fed on rice straw were consistently maintained in terms of pH and temperature, but for for NH3-N or VFAs. Manipulating rumen fermentation through treatment of roughage and strategic supplementation with high quality feed block, tannin-containing plants, especially cassava hay and other local feed resources, could improve rumen efficiency by maintaining higher pH, optinum NH3-N and increasing microbial protein synthesis and essential VFAs, and thus enhance ruminant productivity in the tropics. However, further research on the specific roles of these feeds in rumen fermentation and practical applications both by farmers and industries, is warranted.
Repair-specific Functions of Replication Protein A*

Background: The single-strand DNA-binding protein, replication protein A (RPA), is essential for replication, repair, and recombination. Results: This study elucidates the molecular defects of RPA mutants that cause cell cycle arrest. Conclusion: These mutants are active in DNA replication but not in DNA repair because of altered binding to short ssDNA intermediates. Significance: This study indicates that DNA repair and replication require different RPA-DNA interactions. Replication protein A (RPA), the major eukaryotic single-strand DNA (ssDNA)-binding protein, is essential for replication, repair, recombination, and checkpoint activation. Defects in RPA-associated cellular activities lead to genomic instability, a major factor in the pathogenesis of cancer and other diseases. ssDNA binding activity is primarily mediated by two domains in the 70-kDa subunit of the RPA complex. These ssDNA interactions are mediated by a combination of polar residues and four conserved aromatic residues. Mutation of the aromatic residues causes a modest decrease in binding to long (30-nucleotide) ssDNA fragments but results in checkpoint activation and cell cycle arrest in cells. We have used a combination of biochemical analysis and knockdown replacement studies in cells to determine the contribution of these aromatic residues to RPA function. Cells containing the aromatic residue mutants were able to progress normally through S-phase but were defective in DNA repair. Biochemical characterization revealed that mutation of the aromatic residues severely decreased binding to short ssDNA fragments less than 20 nucleotides long. These data indicate that altered binding of RPA to short ssDNA intermediates causes a defect in DNA repair but not in DNA replication. These studies show that cells require different RPA functions in DNA replication and DNA repair.
Electrolyte Effects on Attachment of an Estuarine Bacterium

The effect of electrolyte concentration on attachment of Vibrio alginolyticus to hydroxyapatite was determined. Bacterial affinity for attachment to the surface and surface capacity were derived from linearization of bacterial adsorption isotherms. At low concentrations (<0.1 M) the affinity of the bacteria for the surface increased with increasing ionic strength, in agreement with the D.L. V.O. theory of colloid interaction. At higher concentrations, bacterial affinity for the surface decreased with increasing concentration of cations and was not related to ionic strength changes in the medium. These results demonstrate a change in the mechanism by which salts affect bacterial attachment at salt concentrations above 0.1 M. The results are consistent with the relationship between the proportion of attached bacteria and salinity observed in previously published field studies. The results may also resolve differences between various attachment studies carried out in different ionic strength media, utilizing different bacteria, surfaces, and experimental methods.
Phanerozoic evolution of atmospheric methane

A simple geochemical box model for the global cycle of methane (CH4) has been developed and applied to reconstruct the evolution of atmospheric CH4 over the entire Phanerozoic. According to the model, the partial pressure of atmospheric CH4 (pCH4) increased up to approximately 10 ppmv during the Carboniferous coal swamp era. This implies a maximum radiative forcing of about 3.5 W m−2 via CH4. Through its radiative forcing, CH4 heated the average global surface temperature by up to 1°C. The elevated pCH4 values during the Permian‐Carboniferous cold period may have moderated the temperature decline caused by the coeval drawdown of atmospheric CO2. Additional runs with a global carbon model indicate that the heating induced by elevated pCH4 favored the drawdown of atmospheric pCO2 via enhanced rates of silicate weathering. Simulations with a state‐of‐the‐art climate model reveal that the effects of atmospheric CH4 on average global surface temperature also depend on the partial pressures of CO2. The CH4 climate effect is amplified by high background levels of atmospheric CO2 such that a coeval increase in the partial pressure of both greenhouse gases has a much stronger climate effect than previously anticipated.
Cellular and Molecular Neuropathology of the Parahippocampal Region in Schizophrenia

Abstract: The entorhinal cortex, subiculum, and hippocampus have been regions of great interest in both clinical and neuropathological investigations of schizophrenia. Postmortem studies have identified numerous abnormalities, although many remain controversial or unconfirmed. Among the cellular and molecular neuropathological findings are (1) abnormal cytoarchitecture of the entorhinal cortex characterized by poorly formed layer II neuron clusters and laminar disorganization; (2) normal neuron density but smaller neuron size in the superficial lamina of the entorhinal cortex and subiculum; (3) abnormal expression of the microtubule‐associated protein MAP2 in the entorhinal cortex and subiculum; (4) aberrant glutamatergic and catecholaminergic innervation of the entorhinal cortex; (5) abnormal mRNA expression of various transcription factors, ion channels, and neurosecretory pathway‐related proteins in entorhinal stellate neurons; and (6) an absence of any neurodegeneration. Altogether, these findings suggest that aberrant neurodevelopmental processes play a key role in the pathobiology of schizophrenia and provide a neuroanatomic basis for understanding many of the clinical and neuropsychological abnormalities in the disorder.
Insights into the Rrf2 repressor family – the structure of CymR, the global cysteine regulator of Bacillus subtilis

The global regulator CymR represses the transcription of a large set of genes involved in cystine uptake and cysteine biosynthesis in Bacillus subtilis and Staphylococcus aureus. This repressor belongs to the widespread and poorly characterized Rrf2 family of regulators. The crystal structure of CymR from B. subtilis reveals a biologically active dimer, where each monomer folds into two tightly packed domains: a DNA‐binding domain, which houses a winged helix–turn–helix (wHTH) motif; and a long dimerization domain, which places the wHTH motifs at the extremes. This architecture explains how these small regulators can span 23–27‐bp DNA targets. The wHTH motif of CymR resembles those of the GntR superfamily of regulators, such as FadR and HutC. Superimposing the FadR wHTH motifs bound to their DNA fragments onto the wHTH motifs of the CymR dimer structure suggests that the DNA target and/or the protein must undergo some conformational changes upon binding. The CymR structure also hints at a possible location of the Fe–S centre associated with several Rrf2‐type regulators.
Battery efficiency of mobile devices through computational offloading: A review

Smart Internet Devices (SIDs) particularly Smartphones are soon turned to be super computers, while the restricted battery timing is a focused issue which hinders the steady meeting expectations yield of these devices. In addition, various sensors, high resolution LCDs, wireless interfaces, GPS and other advanced features drain battery quickly, thus, shrinking the operational time. Subsequently, increasing battery life of SIDs has happened to dire investigation significance at hardware and programming levels, both alike. The intention of our work is to evaluate computational offloading; sending power-intensive processing to remote servers in cloud and accepting the outcome back on device's screen. Furthermore, this paper gives a review of previous research work on computational offloading. We then summarize distinct research work with their respective findings and limitations. In addition, a short critical analysis of the review works following the summarized data.
Compact, Wideband Antennas Enabled by Interdigitated Capacitor-Loaded Metasurfaces

In this paper, a class of integrated metasurface (MS)-based planar antennas are proposed, which are fed by monopoles operating below their fundamental modes. Various interdigitated capacitor (IC) loading schemes for a metallic sheet backed MS are investigated, which provide footprint miniaturization and bandwidth enhancement. A linearly polarized (LP) MS-based antenna, loaded by ICs, provides a 15% impedance bandwidth and a gain higher than 6.67 dBi. The radiation mechanism and resonant frequency dependence were revealed via a dispersion analysis, which serves to explain the working principle of the proposed antenna. Next, a miniaturized antenna with doubly loaded ICs was introduced, achieving an impedance bandwidth of 10%, a gain above 6 dBi, and a more than 30% footprint reduction. A more advanced compact, circularly polarized (CP) MS-based antenna with a compact footprint, and improved 3-dB axial ratio (AR) bandwidth were also presented, by introducing triangular IC and diagonal slot loadings to the MS. It is demonstrated that this antenna achieves an impedance bandwidth of 16%, a gain above 5.5 dBi, and an AR <;3 dB bandwidth of 10%. Three antenna prototypes were fabricated and measured, with good correspondence between the experimental results and simulation predictions, confirming the proposed design methodologies. These compact and well-performing MS-based antennas have promising potential for applications in modern wideband wireless systems.
Accounting for Genotyping Errors in Tagging SNP Selection

One limitation of the existing tagging SNP selection algorithms is that they assume the reported genotypes are error free. However, genotyping errors are often unavoidable in practice. Many tagging SNP selection methods depend heavily on the estimated haplotype frequencies. Recent studies have demonstrated that even slight genotyping errors can lead to serious consequences with regard to haplotype reconstruction and frequency estimation. Here we present a tagging SNP selection method that allows for genotyping errors. Our method is a modification of the pair‐wise r2 tagging SNP selection algorithm proposed by Carlson et al. (2004) . We have replaced the standard EM algorithm in Carlson's method with an EM that accounts for genotyping errors, in an attempt to obtain better estimates of the haplotype frequencies and r2 measure. Through simulation studies we compared the performance of our modified algorithm with that of the original algorithm. We found that the number of tags selected by both methods increased with increasing genotyping errors, though our method led to smaller increase. The power of haplotype association tests using the selected tags decreased dramatically with increasing genotyping errors. The power of single marker tests also decreased, but the reduction was not as much as the reduction in power of haplotype tests. When restricting the mean number of tags selected by both methods to be similar to the baseline number, Carlson's method and our method led to similar power for the subsequent haplotype and single marker tests. Our results showed that, by accounting for random genotyping errors, our method can select tagging SNPs more efficiently than Carlson's method. The computer program that implements our modified tagging SNP selection algorithm is available at our web site: http://www.personal. psu.edu/tuy104/.
Metaheuristic Optimization Methods Applied to Power Converters: A Review

Power converters systems aimed at renewable energy applications have become a common option for sustainable electricity and distributed generation, since their performance has improved, and prices have steadily been reduced in the last years. However, there are still several drawbacks that hinder their widespread installation, such as the simultaneous minimization of cost and volume, efficiency maximization, size reduction, etc. Quite often, accomplishing these goals requires dealing with complicated optimization problems, which are difficult to solve by classical methods. Metaheuristic techniques provide a viable alternative to solve complex intricate optimization problems, such as those encountered in the development of power electronics converters. This paper presents a comprehensive coverage of metaheuristic methodologies applied in the area of power converters. The review includes a classification of the methodologies and main objective functions in each paper surveyed. An aim for this paper is to highlight the importance of the optimization tools, and the many benefits they provide to tackle the challenges encountered in the design, operation, and control of power converters.
Changing ecology of bacterial infections as related to antibacterial therapy.

The subject of this paper is one I dealt with more than a decade ago at a meeting of the Association of American Physicians [1]. At that time, I reviewed some of the changes in the occurrence and mortality from the major serious bacterial infections as observed at the Boston City Hospital between 1935 and 1957, a period during which we were witnessing the introduction and increasingly widespread use of a succession of new and highly effective antibacterial agents.
TinyCO – A Middleware Model for Heterogeneous Nodes in Wireless Sensor Networks

Wireless sensor networks (WSNs) contain multiple nodes of the same configuration and type. The biggest challenge nowadays is to communicate with heterogeneous nodes of different WSNs. To communicate with distinct networks, an application requires generic middleware. This middleware should be able to translate the requests for contrary WSNs. Most of the wireless nodes use the TinyOS or Contiki operating systems. These operating systems vary in their architecture, configuration and programming model. An application cannot communicate with heterogeneous networks because of their divergent nature. In this paper, we design and implement TinyCO (a generic middleware model for WSNs), which overcomes these challenges. TinyCO is a general-purpose service-oriented middleware model. This middleware model can identify the heterogeneous networks based on TinyOS and Contiki. It allows applications to communicate with these networks using a generic request. This middleware interprets the given input into signatures of the underlying networks. This proposed middleware is implemented in Java and tested on TelosB motes.
Vanadium‐induced apoptosis and pulmonary inflammation in mice: Role of reactive oxygen species

Pulmonary exposure to metals and metal‐containing compounds is associated with pulmonary inflammation, cell death, and tissue injury. The present study uses a mouse model to investigate vanadium‐induced apoptosis and lung inflammation, and the role of reactive oxygen species (ROS) in this process. Aspiration of the pentavalent form of vanadium, V (V), caused a rapid influx of polymorphonuclear leukocytes into the pulmonary airspace with a peak inflammatory response at 6 h post‐exposure and resolution by 72 h. During this period, the number of apoptotic lung cells which were predominantly neutrophils increased considerably with a peak response at 24 h accompanied by no or minimum necrosis. After 24 h when the V (V)‐induced inflammation was in the resolution phase, an increased influx of macrophages and engulfment of apoptotic bodies by these phagocytes was observed, supporting the role of macrophages in apoptotic cell clearance and resolution of V (V)‐induced lung inflammation. Electron spin resonance (ESR) studies using lavaged alveolar macrophages showed the formation of ROS, including O2·−, H2O2, and ·OH radicals which were confirmed by inhibition with free radical scavengers. The mechanism of ROS generation induced by V (V) involved the activation of an NADPH oxidase complex and the mitochondrial electron transport chain. The ROS scavenger, catalase (H2O2 scavenger), effectively inhibited both lung cell apoptosis and the inflammatory response, whereas superoxide dismutase (SOD) (O2·− scavenger) and the metal chelator, deferoxamine (inhibitor of ·OH generation by Fenton‐like reactions) had lesser effects. These results indicate that multiple oxidative species are involved in V (V)‐induced lung inflammation and apoptosis, and that H2O2 plays a major role in this process. Published 2003 Wiley‐Liss, Inc.
Gestational age estimation in Kari sheep using non-conventional ultrasonographic parameters.

The present study was designed to determine gestational age in Kari ewes measuring of non-conventional foetal growth parameters i.e., Abdominal Circumference (AC), Foetal Heart Beat Rate (FHBR) and Femur Length (FL). The experiment conducted at different gestational age in Kari sheep with a B-mode ultrasonograph and a 3.5 MHz transducer. The ewes were scanned in dorsal recumbency over a restraining chute with post-scanning shaving of the inguinal regions.Data were collected from 49 ewes. Based on varying length of gestation, Kari ewes were divided into seven categories A, B, C, D, E, F and G representing gestation length of 150 days, respectively. Abdominal Circumference (AC), Femur Length (FL) and Foetal Heart Beat Rate (HBR) were observed at weekly interval throughout gestation. Regression equations for each parameter against the Gestational age of the foetus presented in trend lines using bi-nomial regression analysis. Mean Abdominal Circumference for all categories in week 4 was 54 mm whereas the same for B was 66 mm. The correlation between gestational age and AC was 0.68 which was significant (P< 0.05. Mean Femur Length for all categories in week 3 was 17 mm whereas the same for D was 17 mm. The correlation between gestational age and FL was 0.58 which was very highly significant (P< 0.001). Mean Foetal Heart Beat Rate was 155.5 throughout the gestational life. The earliest Heart Beat was observed in the third week of gestation in category A. Early Heart Beat Rate detection indicated life when bestowed into the embryo / foetal viability. The higher coefficients of determination (R 2 ) and correlations for AC and FL with gestational age (wk) suggest its reliability to
Spatial and Temporal Patterns in the Recovery of Aedes aegypti (Diptera: Culicidae) Populations After Insecticide Treatment

Abstract Given that tools for dengue emergency control are limited, continuous evaluation of the effectiveness of insecticide applications in the field is of utmost importance. Such studies will provide a sound basis for defining spraying schemes for public health authorities in dengue-affected countries. In this article, we address the following research questions: How do different space spraying strategies affect Aedes aegypti (L.) (Diptera: Culicidae) populations in both space and time? More specifically, how well are these mosquitoes killed, and how quickly do their populations recover and from where? Field trials were carried out with ultralow volume sprayers in Kamphaeng Phet province, Thailand, with a pyrethrin mixture that was applied 1) indoors only, 2) indoors plus outdoors, 3) indoors with a doubled spraying time, and 4) indoors with doubled spraying time plus outdoors. We found that within 7 d, Ae. aegypti populations recovered to ≈50% of their original numbers. Spraying the outdoor area and doubling the time sprayed per room only had a significant impact on mosquito numbers 1 d after spraying. Two and 7 d after spraying, these effects were no longer detected. By investigating the spatial arrangement of Ae. aegypti numbers, we found that during the first 2 d after spraying immigration from untreated areas extended ≈15 m into the sprayed area, whereas after 7 d this effect extended up to 50 m. Results are discussed in relation to ongoing dengue control efforts in Thailand.