DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches.

Motivation: Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. Results: We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using 5-repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs. Availability and implementation: The data and code are provided at https://bitbucket.org/RSO24/ddr/. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online

DAMAGE DETECTION AND LOCATION FOR IN AND OUT-OFPLANE CURVED BEAMS USING FUZZY LOGIC BASED ON FREQUENCY DIFFERENCE

In this study, structures damage identification method based on changes in the dynamic characteristics (frequencies) of the structure are examined, stiffness as well as mass matrices of the curved (in and out-of-plane vibration) beam elements is formulated using Hamilton's principle. Each node of both of them possesses seven degrees of freedom including the warping degree of freedom. The curved beam element had been derived based on the Kang and Yoo’s thin-walled curved beam theory in 1994. A computer program was developing to carry out free vibration analyses of the curved beam as well as straight beam. Comparing with the frequencies for other researchers using the general purpose program MATLAB. Fuzzy logic system (FLS) applied in two stages to calculate the damage extent and location in simply in and out-of- plane curved beam, the damage deduce by reduction in stiffness for three levels (20%, 40%, 60%). At the first stage the output faults of the fuzzy system represented by four levels of damage in curved beam (undamaged, slight, moderate, and severe), and at second stage indicate damage location at element with two defuzzification methods (centroid and middle of maximum). The results show that the frequency difference method is efficient to indicate and quantify damage with accuracy about (99.5%) for slight and moderate damage about (100%) for severe damage. Consequently fuzzy logic performs well for detecting, locating and quantifying damage in curved beam

Evaluation of the Magnetized Magnitudes of the Flowing Nuclear Spins Using Solving Bloch Equations by Finite Difference Method in MRI

The distribution of the magnetized magnitudes of the flowing nuclear spins has a key role to evaluate the radiofrequency pulses used in the magnetic resonance angiography (MRA). In this study, a finite difference method is used to solve Bloch equations for the flowing nuclear spins during and after a 90° rectangular selective pulse which is important for optimization of the pulse sequence. The results of the simulation indicate that the magnitudes are deformed due to the flowing nuclear spins, while their velocity is increased. The maximum variations are created on the transverse magnitudes namely, Mx and My. The symmetry on these profiles disappear by increasing the velocity. In contrast, no variation on the longitudinal magnitude namely Mz is observed, except a shift on the velocity direction. The sensitivity of these profiles at low velocities for the rectangular selective pulse is more than that of the sinc type, which probably it may be used for characterizing the capillary space. In general, one may obtain the distribution of magnitudes for pulses with various flip angles, as well as, the combination of different pulses. The results may be employed to improve mapping indices in the MRA as well as assessment pulse sequences on the flowing nuclear spins

Response of seedling barley (Hurdeom vulgar, L.) to foliar fertilization of nano-oxides (Fe, Cu, Mg)

Background. An experiment was conducted at the Grain Technology Laboratory, Crop Department, Faculty of Agriculture, Omar Al-Mukhtar University, during the 2023 season. The experiment utilized a completely randomized design to study the response of barley to foliar application of fine nanoscale iron, manganese, and copper fertilizers. The application was carried out as foliar spray at two different doses, two weeks and one month after sowing, using 3 kg capacity pots with 20 seeds per pot. The experiment included three observations for each treatment, with the nanoscale iron, manganese, and copper oxides applied at a concentration of 1 cmol/L. The data revealed the following: Significant positive response of barley shoots to foliar application of nanoscale iron, manganese, and copper fertilizers in various growth indicators, including shoot weight, shoot length, leaf area, crop growth rate, and specific leaf weight. High significant differences were observed in the effect of nanoscale iron, manganese, and copper oxides on the average shoot weight, crop growth rate, and leaf area. Copper oxide and manganese oxide showed the highest means, followed by iron oxide, compared to the control. Iron oxide exhibited the highest specific leaf weight for barley shoots, followed by copper oxide and then manganese oxide, compared to the control treatment

Low-Dose Antithymocyte Globulin Has No Disadvantages to Standard Higher Dose in Pediatric Kidney Transplant Recipients: Report from the Pediatric Nephrology Research Consortium

Introduction Rabbit antithymocyte globulin (rATG) dosing strategies for induction in pediatric kidney transplantation vary between centers. It is not known whether a lower rATG induction dose provides safe and effective immunosuppression compared with a “standard” higher dose. Methods We performed a retrospective multicenter study of all isolated first-time kidney transplant recipients \u3c 21 years old who received rATG induction between 1 January 2010 and 31 December 2014 at 9 pediatric centers. An a priori cutoff of a 4.5-mg/kg cumulative rATG dose was used to identify low (≤ 4.5 mg/kg) and standard (\u3e 4.5 mg/kg) exposure groups. Outcomes examined included 12 months posttransplant graft function (estimated glomerular filtration rate [eGFR]); the occurrence of acute rejection, donor-specific antibody (DSA), neutropenia, and viral infection (cytomegalovirus [CMV], Epstein-Barr virus [EBV], and BK virus); and 24-month outcomes of posttransplant lymphoproliferative disorder (PTLD) occurrence and patient and graft survival. Results Two hundred thirty-five patients were included. Baseline features of the low and standard rATG dose groups were similar. By 12 months, the rATG dose group had no significant impact on the occurrence of neutropenia, positive DSA, or viral polymerase chain reaction (PCR). Graft function was similar. Acute rejection rates were similar at 17% (low dose) versus 19% (standard dose) (P = 0.13). By 24 months, graft survival (96.4% vs. 94.6%) and patient survival (100% vs. 99.3%) were similar between the low- and standard-dose groups (P = 0.54 and 0.46), whereas the occurrence of PTLD trended higher in the standard-dose group (0% vs. 2.6%, P = 0.07). Conclusion A low rATG induction dose ≤ 4.5 mg/kg provided safe and effective outcomes in this multicenter low immunologic risk pediatric cohort. Prospective studies are warranted to define the optimal rATG induction dose in pediatric kidney transplantation

Integration of transcriptome and metabolome provides unique insights to pathways associated with obese breast cancer patients

Information regarding transcriptome and metabolome has significantly contributed to identifying potential therapeutic targets for the management of a variety of cancers. Obesity has profound effects on both cancer cell transcriptome and metabolome that can affect the outcome of cancer therapy. The information regarding the potential effects of obesity on breast cancer (BC) transcriptome, metabolome, and its integration to identify novel pathways related to disease progression are still elusive. We assessed the whole blood transcriptome and serum metabolome, as circulating metabolites, of obese BC patients compared them with non-obese BC patients. In these patients' samples, 186 significant differentially expressed genes (DEGs) were identified, comprising 156 upregulated and 30 downregulated. The expressions of these gene were confirmed by qRT-PCR. Furthermore, 96 deregulated metabolites were identified as untargeted metabolomics in the same group of patients. These detected DEGs and deregulated metabolites enriched in many cellular pathways. Further investigation, by integration analysis between transcriptomics and metabolomics data at the pathway levels, revealed seven unique enriched pathways in obese BC patients when compared with non-obese BC patients, which may provide resistance for BC cells to dodge the circulating immune cells in the blood. In conclusion, this study provides information on the unique pathways altered at transcriptome and metabolome levels in obese BC patients that could provide an important tool for researchers and contribute further to knowledge on the molecular interaction between obesity and BC. Further studies are needed to confirm this and to elucidate the exact underlying mechanism for the effects of obesity on the BC initiation or/and progression

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.

Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium

Pediatric Immunization Practices in Nephrotic Syndrome: An Assessment of Provider and Parental Knowledge

Background: Children with nephrotic syndrome (NS) are at high risk for vaccine-preventable infections due to the immunological effects from the disease and concurrent treatment with immunosuppressive medications. Immunizations in these patients may be deferred due to their immunosuppressive treatment which may increase the risk for vaccine-preventable infections. Immunization practices in children with NS continue to vary among pediatric nephrologists. This raises the question of whether children with NS are receiving the recommended vaccinations at appropriate times. Therefore, it is critical to understand the practices and patient education provided by physicians to patients on the topic of vaccinations. Methods: After informed consent, parents/guardians of 153 pediatric patients (\u3c18 years old) diagnosed with NS from 2005 to 2018 and 50 pediatric nephrologists from 11 participating centers completed anonymous surveys to evaluate immunization practices among pediatric nephrologists, assess the vaccine education provided to families of children with NS, assess the parental knowledge of immunization recommendations, and assess predictors of polysaccharide pneumococcal vaccine adherence. The Advisory Committee on Immunization Practices (ACIP) Immunization 2019 Guideline for those with altered immunocompetence was used to determine accuracy of vaccine knowledge and practices. Results: Forty-four percent of providers self-reported adherence to the ACIP guidelines for inactive vaccines and 22% to the guidelines for live vaccines. Thirty-two percent of parents/guardians reported knowledge that aligned with the ACIP guidelines for inactive vaccines and 1% for live vaccines. Subjects residing in the Midwest and provider recommendations for vaccines were positive predictors of vaccine adherence (p \u3c 0.001 and p 0.02, respectively). Conclusions: Vaccine recommendation by medical providers is paramount in vaccine adherence among pediatric patients with NS. This study identifies potential educational opportunities for medical subspecialty providers and family caregivers about immunization recommendations for immunosuppressed patients

Comparison of two high-throughput semiconductor chip sequencing platforms in noninvasive prenatal testing for Down syndrome in early pregnancy

Background: Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA reads for NIPT. However, the approval criteria vary among platforms and countries. This can delay the introduction of such devices and systems to clinics. A comparison of the sensitivity and specificity of two different platforms using the same sequencing chemistry could be useful in NIPT for fetal chromosomal aneuploidies. This would improve healthcare authorities' confidence in decision-making on sequencing-based tests. Methods: One hundred and one pregnant women who were predicted at high risk of fetal defects using conventional prenatal screening tests, and who underwent definitive diagnosis by full karyotyping, were enrolled from three hospitals in Korea. Most of the pregnant women (69.79 %) received NIPT during weeks 11-13 of gestation and 30.21 % during weeks 14-18. We used Ion Torrent PGM and Proton semi-conductor-based sequencers with 0.3x sequencing coverage depth. The average total reads of 101 samples were approximately 4.5 and 7.6 M for PGM and Proton, respectively. A Burrows-Wheeler Aligner (BWA) algorithm was used for the alignment, and a z-score was used to decide fetal trisomy 21. Interactive dot diagrams from the sequencing data showed minimal z-score values of 2.07 and 2.10 to discriminate negative versus positive cases of fetal trisomy 21 for the two different sequencing systems. Results: Our z-score-based discrimination method resulted in 100 % positive and negative prediction values for both ion semiconductor PGM and Proton sequencers, regardless of their sequencing chip and chemistry differences. Both platforms performed well at an early stage (11-13 weeks of gestation) compared with previous studies. Conclusions: These results suggested that, using two different sequencers, NIPT to detect fetal trisomy 21 in early pregnancy is accurate and platform-independent. The data suggested that the amount of sequencing and the application of common, simple, and robust statistical analyses are more important than sequencing chemistry and platform types. This result has practical implications in countries where PGM is approved for NIPT but the Proton system is not.ope