Miracle-dz/UniFAR-FTUs huggingface dataset:
The Tumor Suppressor Gene TP53: Implications for Cancer Management and Therapy

ABSTRACT The p53 protein is an inducible transcription factor with multiple anti-proliferative roles in response to genotoxic damage; unprogrammed proliferative stimuli; and deprivation of oxygen, nutrients, or ribonucleotides. Inactivation of the TP53 gene by mutation or deletion is the most common event in human cancer. Loss of p53 function compromises genetic homeostasis in cells exposed to mutagens and prevents normal cytotoxic responses to cancer therapies. Genetic and pharmacological approaches are being developed with the ultimate goal of restoring or controlling p53 functions in cancer patients. Genetic interventions aiming at expressing wild-type TP53 in cancer cells, either by retroviral or adenoviral transfer, have met limited clinical success. However, recently, the use of a defective adenovirus (ONYX-015) that selectively kills p53-incompetent cells has shown promising effects in pre-clinical and clinical studies. Pharmacological methods are under development to either stimulate wild-type p53 protein function or induce p53 mutant proteins to resume wild-type functions. These methods are based on small chemicals (CP-31388, PRIMA-1), peptides (CDB3), or single-chain Fv antibody fragments corresponding to defined p53 domains. In addition, detection of mutant TP53 may also serve as a marker for early cancer detection, prediction, and prognosis. In this review, we discuss the mechanisms underlying these approaches and their perspectives for cancer therapy.
Hydraulic modelling of drinking water treatment plant operations

The flow through a unit of a drinking water treatment plant is one of the most important parameters in terms of a unit's effectiveness. In the present paper, a new EPAnet library is presented with the typical hydraulic elements for drinking water treatment processes well abstraction, rapid sand filtration and cascade and tower aeration. Using this treatment step library, a hydraulic model was set up, calibrated and validated for the drinking water treatment plant Harderbroek. With the actual valve position and pump speeds, the flows were calculated through the several treatment steps. A case shows the use of the model to calculate the new setpoints for the current frequency converters of the effluent pumps during a filter backwash.
So Much Writing, So Little Science: A Review of 37 Years of Literature on Edetate Sodium Chelation Therapy

OBJECTIVE: To determine the safety and efficacy of edetate sodium (ethylenediamine tetraacetic acid; EDTA) chelation therapy for atherosclerosis. METHODS: Literature search using MEDLINE, encompassing 1966 through May 1993. Further references were obtained from articles and books, and from citations obtained from the American Academy of Medical Preventics. RESULTS: 16 case reports or case series, 2 longitudinal studies, and 3 clinical trials were reviewed, along with testimonials cited in 19 books. CONCLUSIONS: Little valid scientific evidence is available. Although the postulated mechanisms of action for EDTA are biologically plausible and EDTA appears to be safe, it has not been proven effective. Indeed, the best evidence shows it to be ineffective. Therefore, EDTA chelation therapy should not be used in clinical practice to treat atherosclerosis.
An exploratory study of the follow-up care needs of patients treated for colorectal cancer.

AIMS AND OBJECTIVES To explore patient perceptions of their experiences of follow-up care after treatment for colorectal cancer. BACKGROUND The optimal follow-up strategy for colorectal cancer is not known, and although patients are seen in traditional outpatient follow-up clinics, this system may not meet psycho-social and information needs. DESIGN An exploratory qualitative study. METHOD In-depth interviews were conducted with 27 patients who had completed treatment for colorectal cancer. The data were analysed using thematic analysis. RESULTS One dominant theme emerged from the data with several sub-themes. The dominant theme was 'knowing what to expect' after bowel surgery. The subthemes related to 'living with altered bowel function', the ways patients gathered information about their condition through 'trial and error' and 'information and support from specialist nurses'. Patients who did not have a stoma were particularly vulnerable and expressed a need for more information on knowing what to expect after surgery. The role of the colorectal nurse specialist was vital in providing information and support; in particular, nurse-led clinics provided continuity of care and information that was tailored to individual need. CONCLUSIONS Traditional hospital follow-up does not always address patients' psycho-social and information needs. Nurse-led services were commented on favourably in terms of providing information that was tailored to individual need as well as being responsive to urgent patient concerns; future innovative strategies for providing follow-up care for patients with colorectal cancer should draw on the specialist knowledge and skills of these nurses. RELEVANCE TO CLINICAL PRACTICE Nurse-led clinics and/or telephone follow-up by specialist nurses may be effective models of care for this particular patient group, providing appropriate access for meeting clinical, psycho-social and information needs.
THE ORIGIN OF ECOLOGICAL DIVERGENCE IN HELIANTHUS PARADOXUS (ASTERACEAE): SELECTION ON TRANSGRESSIVE CHARACTERS IN A NOVEL HYBRID HABITAT

Abstract Diploid hybrid speciation in plants is often accompanied by rapid ecological divergence between incipient neospecies and their parental taxa. One plausible means by which novel adaptation in hybrid lineages may arise is transgressive segregation, that is, the generation of extreme phenotypes that exceed those of the parental lines. Early generation (BC2) hybrids between two wild, annual sunflowers, Helianthus annuus and Helianthus petiolaris, were used to study directional selection on transgressive characters associated with the origin of Helianthus paradoxus, a diploid hybrid species adapted to extremely saline marshes. The BC2 plants descended from a single F1 hybrid backcrossed toward H. petiolaris. The strength of selection on candidate adaptive traits in the interspecific BC2 was measured in natural H. paradoxus salt marsh habitat. Positive directional selection was detected for leaf succulence and Ca uptake, two traits that are known to be important in salt stress response in plants. Strong negative directional selection operated on uptake of Na and correlated elements. A significant decrease in trait correlations over time was observed in the BC2 population for Na and Ca content, suggesting an adaptive role for increased Ca uptake coupled with increased net exclusion of Na from leaves. Patterns of directional selection in BC2 hybrids were concordant with character expression in the natural hybrid species, H. paradoxus, transplanted into the wild. Moreover, the necessary variation for generating the H. paradoxus phenotype existed only in the BC2 population, but not in samples of the two parental species, H. annuus and H. petiolaris. These results are consistent with the hypothesis that transgressive segregation of elemental uptake and leaf succulence contributed to the origin of salt adaptation in the diploid hybrid species H. paradoxus.
Implementation of Message Authentication Scheme for Elliptic Curve Cryptography in Wireless Sensor Networks

: Message authentication is one of the most effective ways to thwart unauthorized and corrupted messages from being forwarded in wireless sensor networks (WSNs). For this reason, many message authentication schemes have been developed, based on either symmetric-key cryptosystems or public-key cryptosystems. Most of them, however, have the limitations of high computational and communication overhead in addition to lack of scalability and resilience to node compromise attacks. To address these issues, a polynomial-based scheme was recently introduced. However, this scheme and its extensions all have the weakness of a built-in threshold determined by the degree of the polynomial: when the number of messages transmitted is larger than this threshold, the adversary can fully recover the polynomial. In this paper, we propose a scalable authentication scheme based on elliptic curve cryptography (ECC). While enabling intermediate nodes authentication, our proposed scheme allows any node to transmit an unlimited number of messages without suffering the threshold problem. In addition, our scheme can also provide message source privacy.
Assessment of salivary elements (Zinc, Copper and Magnesium) among groups of patients with rheumatoid arthritis and chronic periodontitis and its correlation to periodontal health status

Periodontal diseases are common in the society and some researchers suggestedan association between rheumatoid arthritis (RA) and periodontal diseases. The aims of study were to determine the periodontal health status in patient with RA and chronic periodontitis and compare it with those having chronic periodontitis without RA anddetermine the level of salivary elements Copper(Cu),Zinc( Zn) and Magnesium( Mg) in patients with rheumatoid arthritis and patients have no rheumatoid arthritis (RA) and compare with the control group.And correlate between these salivary elements with the periodontal parameters Plaque index (PLI), gingival index (GI), bleeding on probing (BOP), probing pocketdepth (PPD) and clinical attachment level (CAL). Materials and Methods: In this study, the samples were recruited from patientsreferred todepartment of Rheumatology at Baghdad hospital. Seventy five female patients participated in this study, twenty five of them rheumatoid arthritis patient andhad chronic periodontitis; twenty five were with chronicperiodontitis and have no arthritis; Twenty five patients wereperiodontally and systemically healthy (control group). Patients were with age range 40-50 yearswith no other systemic diseases. The smokers and patients taking medication affecting periodontium status were excluded from the study.Also the patients had normal weight and length. Periodontal parameters were measuredin all groups at four surfaces.Salivary elements (Zn, Cu and Mg) also measured in this study. Results: Patients with RA had higher prevalence of sites presenting dental plaque, a higher rate of gingival inflammation and bleeding on probing,greater probing depth, and greater attachment loss compared with control and high level of Copper and low level of Zinc and Magnesium. Conclusion: The results suggest higher potentiality for moderate to severe periodontitis involvement among RA patients, with higher levels of Copper (Cu), and low level of Zinc (Zn) and Magnesium (Mg).
Nucleotide sequence of the gene for cytochrome b558 of the Bacillus subtilis succinate dehydrogenase complex

The nucleotide sequence was determined for the first part of the Bacillus subtilis sdh operon. An open reading frame corresponding to the structural gene, sdhA, for cytochrome b558 was identified. The predicted molecular weight of the cytochrome (excluding the N-terminal methionine) is 22,770. It is a very hydrophobic protein with five probable membrane-spanning segments. There is little homology between the B. subtilis cytochrome b558 and cytochrome b of mitochondrial complex III from different organisms or between cytochrome b558 and the hydrophobic sdhC and sdhD peptides of the Escherichia coli sdh operon. About 30 bases downstream of the sdhA stop codon, a new open reading frame starts. The nucleotide sequence predicts the presence of a typical flavin-binding peptide which identifies this reading frame as part of the sdhB gene. Seven bases upstream of the sdhA initiation codon ATG there is a typical B. subtilis ribosome binding site (free energy of interaction, -63 kJ), and further upstream, tentative sigma 55 and sigma 32 promoter sequences were found. The upstream region also contains two 12-base-long direct repeats; their significance is unknown.
Performance of a 200‐MHz cryogenic RF probe designed for MRI and MRS of the murine brain

A cryogenic 200‐MHz RF transmit/receive probe (CryoProbe) made of copper and designed for murine brain studies is described. The probe operates at 30K and its performance was compared to a home‐made surface coil of equal dimensions and a mouse head volume resonator, both operating at room temperature (RT). Since for small volumes of tissue interrogated (<5 mL) sample noise and thermal noise of the receiver are of comparable magnitude, considerable noise reduction can be achieved by cooling of the receiver system, e.g., using cold helium gas. The effect of temperature lowering on the signal‐to‐noise ratio (SNR) was assessed in phantom and in vivo murine brain studies using conventional MRI sequences (spin and gradient echo) and single voxel MR spectroscopy. Consistent sensitivity increases were observed for the CryoProbe. SNR increases by a factor ≥2 for the phantom experiments and by factors of 1.8 to 1.9 for in vivo experiments when compared to the RT surface coil for both MRI and MRS experiments. These results are in good agreement with estimated SNR gains for a circular surface coil probe cooled to 30K. The use of a cryogenic probe represents an economically attractive option to enhance the sensitivity in small animal MRI/MRS. Magn Reson Med, 2008. © 2008 Wiley‐Liss, Inc.
Ventral Capsule / Ventral Striatum Deep Brain Correspondence BP Stimulation Does Not Consistently Diminish Occipital Cross-Frequency Coupling

Bahramisharif et al. (1) reported that deep brain stimulation (DBS) delivered to the ventral capsule/ventral striatum (VC/VS) target for obsessive-compulsive disorder (OCD) decreased beta-gamma cross-frequency coupling (CFC) in electroencephalographic (EEG) recordings from the occipital cortex. They suggested that this may represent changes in bottom-up visual processing that may make disorder-related stimuli exceptionally salient. They further noted a recent report of DBS-induced changes in motor cortex beta-gamma coupling during DBS for Parkinson’s disease (PD) (2) as potentially supporting that hypothesis. OCD, however, is different from PD in several respects. First, although there is a basal-ganglia-linked hypothesis of OCD (3), there is no clear degenerative lesion as there is in PD. Second, multiple groups have identified abnormal cortical and subcortical beta rhythms in PD (4), whereas there is no robust or well-replicated EEG signature of OCD in any frequency band. Finally, psychiatric diagnoses have profound internal heterogeneity, and this may be specifically worse in DBS cases given how rare and treatment-resistant these patients are (5,6). The observed effect of Bahramisharif et al. (1) may be driven by specific DBS settings or by unmodeled patient characteristics, including patients’ level of occipital CFC before surgery. Alternately, it may be specific to OCD or a clinical subphenotype that is more frequently selected for DBS at the authors’ center. Those alternatives are difficult to assess because few centers are able to accumulate sufficient DBS patients to conduct replication studies. We have a similar ongoing EEG study in VC/VS DBS, offering an opportunity to replicate the Bahramisharif et al. (1) analysis.
Crystal structure of an RtcB homolog protein (PH1602‐extein protein) from Pyrococcus horikoshii reveals a novel fold

Introduction. The hypothetical extein, PH1602-extein (53.5 kDa, 481 residues) from the hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3, shows sequence similarity to Escherichia coli RtcB (33% identity). RtcB homologs are conserved in all archaebacteria, in most eukaryotes, including metazoa, and in a wide variety of eubacteria. In E. coli, the rtcB gene, together with rtcA and rtcR, comprise the 54-dependent operon termed the RNA 3 -terminal phosphate cyclase operon. The functions of the gene products RtcA and RtcR have been characterized previously as RNA 3 -terminal phosphate cyclase and 54-specific regulator, respectively. On the other hand, although RtcB is highly conserved among many organisms, there have been few studies of RtcB and its homologs. In a previous study, it was suggested that human RtcB homolog may form a heterotrimer with DDX1 (putative RNA helicase) and CGI-99 (ninein-interaction protein). These three proteins were pulled down by double-stranded DNA fragments. The artificial DNA sequences included an 11-bp inverted repeat, thus enabling formation of a cruciform structure. The manner of interaction between the presumptive trimer and double-stranded DNA has not been clarified. Sequence analysis indicated that the ph1602 gene encodes an RtcB homolog with an intervening intein. Thus, translation products of ph1602 are considered to generate two mature proteins, PH1602-intein and PH1602-extein, because of the protein-splicing activity of the intein. We cloned the extein sequence of PH1602 and successfully overexpressed, purified, and crystallized the PH1602extein. Here, we report the crystal structure of PH1602extein at 2.15 Å resolution, determined by the singlewavelength anomalous diffraction (SAD) method.
PRSS3/Mesotrypsin Is a Therapeutic Target for Metastatic Prostate Cancer

PRSS3/mesotrypsin is an atypical isoform of trypsin that has been associated with breast, lung, and pancreatic cancer cell malignancy. In analyses of open source transcriptional microarray data, we find that PRSS3 expression is upregulated in metastatic prostate cancer tissue, and that expression of PRSS3 in primary prostate tumors is prognostic of systemic progression following prostatectomy. Using a mouse orthotopic model with bioluminescent imaging, we show that PRSS3/mesotrypsin is critical for prostate cancer metastasis. Silencing of PRSS3 inhibits anchorage-independent growth of prostate cancer cells in soft agar assays, and suppresses invasiveness in Matrigel transwell assays and three-dimensional (3D) cell culture models. We further show that treatment with recombinant mesotrypsin directly promotes an invasive cellular phenotype in prostate cancer cells and find that these effects are specific and require the proteolytic activity of mesotrypsin, because neither cationic trypsin nor a mesotrypsin mutant lacking activity can drive the invasive phenotype. Finally, we show that a newly developed, potent inhibitor of mesotrypsin activity can suppress prostate cancer cell invasion to a similar extent as PRSS3 gene silencing. This study defines mesotrypsin as an important mediator of prostate cancer progression and metastasis, and suggests that inhibition of mesotrypsin activity may provide a novel modality for prostate cancer treatment. Mol Cancer Res; 10(12); 1555–66. ©2012 AACR.
Supplementing Rhodobacter sphaeroides in the diet of lactating Holstein cows may naturally produce coenzyme Q10-enriched milk

Objective To examine the effects of Rhodobacter sphaeroides (R. sphaeroides) supplementation as a direct-fed microbial (DFM) on rumen fermentation in dairy cows and on coenzyme Q10 (CoQ10) transition into milk, an in vitro rumen simulation batch culture and an in vivo dairy cow experiment were conducted. Methods The characteristics of in vitro ruminal fermentation were investigated using rumen fluids from six cannulated Holstein dairy cows at 2 h post-afternoon feeding. A control treatment was included in the experiments based on a typified total mixed ration (TMR) for lactating dairy cows, which was identical to the one used in the in vivo study, plus R. sphaeroides at 0.1%, 0.3%, and 0.5% TMR dry matter. The in vivo study employed six ruminally cannulated lactating Holstein cows randomly allotted to either the control TMR (C-TMR) treatment or to a diet supplemented with a 0.5% R. sphaeroides culture (S-TMR, dry matter basis) ad libitum. The presence of R. sphaeroides was verified using denaturing gradient gel electrophoresis (DGGE) applied to the bacterial samples obtained from the in vivo study. The concentration of CoQ10 in milk and in the supernatant from the in vitro study was determined using high performance liquid chromatography. Results The results of the in vitro batch culture and DGGE showed that the concentration of CoQ10 significantly increased after 2 h of R. sphaeroides supplementation above 0.1%. When supplemented to the diet of lactating cows at the level of 0.5%, R. sphaeroides did not present any adverse effect on dry matter intake and milk yield. However, the concentration of CoQ10 in milk dramatically increased, with treated cows producing 70.9% more CoQ10 than control cows. Conclusion The CoQ10 concentration in milk increased via the use of a novel DFM, and R. sphaeroides might be used for producing value-added milk and dairy products in the future.
Optimal design of the rotor structure for interior permanent magnet synchronous motor

The permanent magnet synchronous motors are widely used in various industrial applications due to many advantages such as high power density, high efficiency, low manufacturing cost and so on, but cogging torque and moment of inertia are the most important factors affecting the performance and control precision. In this paper, firstly, the cogging torque can be effectively reduced by taking the auxiliary notches, which was obtained through the analysis of the mathematical model of cogging torque and no-load magnetic field of yoke. After that, the rotor iron core was holed to reduce the moment of inertia, which had no effect on the performance. Finally, an interior permanent magnet synchronous motor whose power is 7.5kW was taken as example. Optimization was done to the rotor structure by using the method mentioned above, which was feasibility verifying by analysis of finite element using Ansoft.
Exploiting different levels of parallelism in the biological sequence comparison problem

In the last years the fast growth of bioinformatics field has atracted the attention of computer scientists. At the same time, de exponential growth of databases that contains biological information (such as protein and DNA data) demands great efforts to improve the performance of computational platforms. In this work, we investigate how bioinformatics applications benefit from parallel architectures that combine different alternatives to exploit coarse- and fine-grain parallelism. As a case of analysis, we study the performance behavior of the Ssearch application that implements the Smith-Waterman algorithm (SW), which is a dynamic programing approach that explores the similarity between a pair of sequences. The inherent large parallelism of the application makes it ideal for architectures supporting multiple dimensions of parallelism (thread-level parallelism, TLP; data-level parallelism, DLP; instruction-level parallelism, ILP). We study how this algorithm can take advantage of different parallel machines like the SGI Altix, IBM Power6, IBM Cell BE and MareNostrum machines. Our study includes a qualitative analysis of the parallelization opportunities and also the quantification of the performance in terms of speedup and execution time. These measures are collected taking into account the specific characteristics of each architecture. As an example, our results show that a share memory multiprocessor architecture (SMP) like the PowerPC 970MP of Marenostrum machine can surpasses a heterogeneous multi- processor machine like the current IBM Cell BE.
Ninth International Conference on Ecological Vehicles and Renewable Energies ( EVER ) Robust Control of the Photovoltaic System with Improved Maximum Power Point Tracking

A robust voltage control intended for a photovoltaic system is considered. An improved maximum power points tracking (MPPT) is presented without Photovoltaic array characteristics known. In order to cope with large parameter variations and load disturbances, second order sliding mode controller, based on super twisting algorithm for DC-DC Boost converter is proposed. The designed control shows fast MPPT and good robustness with respect to parameter variations, measurement errors and unmodeled dynamics. The experimental results confirm the effectiveness of the proposed control. Keywords— DC-DC Boost converter, Photovoltaic Array Emulator, second order sliding-mode control, MPPT, voltage control.