Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteriolytic Activity of Coliphages on Diarrhea Associated E. coli

There has been an alarming increase in drug-resistant strains of diarrheagenic Escherichia coli (DEC) in developing as well as developed countries. Several cases of antimicrobial resistance in DEC have been observed in different parts of the world as a result, there has been a renewed interest in alternative antimicrobial treatments, including bacteriophages. This study was conducted to isolation and characterization of a lytic coliphage from sewage water capable to infect a variety of multidrug resistance DEC strains isolated from children suffering diarrhea, as first step to further usage a lytic coliphage in future.in this study, a coliphage was isolated using spotting method and titrated, using agar overlay technique. The host range of coliphages was assessed on a lawn of E coli bacteria. This study included determination of the latent periods and burst size of coli phage then determines the stability of coliphages to physical and chemical condition (temperature, pH and sunlight exposure). The results shown that, five phages isolate (A, B, C, D and E) were exhibiting a potent lytic activity with clear plaques (1-4mm in diameter). Fifty percent of the E coli strains were infected by phage isolates. It seems, very likely, that the coliphages belonging to 3 different groups (1, 2 and3). The phage growth cycle with a detected latent period of 20 min, a burst size of 160 plaque forming units per infected cell, it was found that the phage could survive at varied pH conditions with reduction in its numbers. A temperature of above 60°C and direct sunlight beyond 8 days was found to be deleterious for survival of the phage. Keywords: key words, coliphages, E. coli , diarrhea
Neural network-based image quality comparator without collecting the human score for training

Emulating human behaviours in automated image quality assessment (IQA) enables a comparator framework to remove the differences in human bias naturally. Based on the observation of the practical applications of IQA, this study focuses on similar-content image quality comparison based on a new image quality comparator (IQC). Outstanding proven IQAs can be utilised in this comparator to achieve a new non-linear combination strategy to boost the IQAs' performance in image quality comparison. For both input images to be compared, proven IQAs are utilised to obtain nine features from each image, yielding 18 total features. Then, a four-layer comparison network conducts a classification task to indicate which input image has better quality. In the training phase, the commonly used human scores as training labels are replaced with pairwise comparison results that are automatically generated from assigned distortion level differences. By not utilising human score in training phase, this IQC shows two advantages: (i) it removes huge labor and time cost to collect the human scores and (ii) it solves the problem of over-fitting benefiting from simplicity of creating a large image training dataset. Furthermore, the experimental tests and cross-dataset validation comparison tests demonstrate its impressive performance.
microRNAs control the function of telomeres in cancer

Telomeres are located at the end of chromosomes and consist of DNA tandem repeats that recruit the specialized protein complex “shelterin”. Shelterin has a crucial role in controlling chromosome end protection, telomere recombination and telomere length. Telomeres shorten with every cell division, finally leading to telomere-dysfunction and the induction of senescence or apoptosis. Cancer formation is paralleled by a change in telomere regulation. Re-activation of telomerase ensures the maintenance of telomere function to facilitate unlimited proliferative potential. Importantly, aberrant function of the shelterin complex contributes to tumor formation and genomic instability in human cancer. miRNAs are important regulators of central cancer pathways and are of high clinical relevance. We recently showed that the onco-microRNA miR-155 controls the expression of TRF1 in human breast cancer to promote increased telomere fragility and genomic instability. Importantly, low TRF1 expression correlates with poor prognosis in estrogen receptor positive cancer patients, underlining the clinical relevance of miR-155 dependent regulation of TRF1 in human breast cancer. Our work suggests that multiple miRNAs exist that control telomere function in telomere related pathologies. Identification and functional validation of “telo-miRNAs” is expected to open new avenues in the understanding of telomere related maladies such as cancer and aging.
The Effect of UV Aging on the Structure of PVC in the Presence of Organotin(IV) Compounds

New photostabilizers of poly(vinyl chloride) (PVC) were synthesized and investigated the photostabilizing efficiency of the polymer films by ultraviolet (UV) experiment. The rate of photodecomposition constant have been calculated for PVC films as a method for evaluating the efficiency of the organotin(IV) complexes that used as a photostabilizers after 300 hour of irradiation. The results have showed that the additives had reduced the rate of photodecomposition constant of PVC films significantly with comparison to PVC (blank). The (kd) value for PVC films was the highest in the absence of any additives, and the lowest value in the presence of triphenyltin (IV) complex.
Heterogeneous Nucleation and Growth of CaCO3 on Calcite (104) and Aragonite (110) Surfaces: Implications for the Formation of Abiogenic Carbonate Cements in the Ocean

Although near-surface seawater is supersaturated with CaCO3, only a minor part of it is abiogenic (e.g., carbonate cements). The possible reason for such a phenomenon has attracted much attention in the past decades. Substrate effects on the heterogeneous nucleation and growth of CaCO3 at various Mg2+/Ca2+ ratios may contribute to the understanding of the origin of abiogenic CaCO3 cements. Here, we used in situ atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray diffraction (XRD) and Raman spectroscopy to study the heterogeneous nucleation and growth of CaCO3 on both calcite (104) and aragonite (110) surfaces. The results show that (1) calcite spiral growth occurs on calcite (104) surfaces by monomer-by-monomer addition; (2) the aggregative growth of aragonite appears on aragonite (110) surfaces through a substrate-controlled oriented attachment (OA) along the [001] direction, followed by the formation of elongated columnar aragonite; and (3) Mg2+ inhibits the crystallization of both calcite and aragonite without impacting on crystallization pathways. These findings disclose that calcite and aragonite substrates determine the crystallization pathways, while the Mg2+/Ca2+ ratios control the growth rate of CaCO3, indicating that both types of CaCO3 substrate in shallow sediments and aqueous Mg2+/Ca2+ ratios constrain the deposition of abiogenic CaCO3 cements in the ocean.
Changes in platelet and leukocyte parameters during pregnancy in women with spontaneous pre-term delivery

This study analyzed, retrospectively, the changes of platelet and leukocyte parameters in pregnant women with spontaneous preterm birth. A group of 1050 single embryo pregnant women, who underwent regular obstetric examination and in-patient delivery, were divided into three groups: a preterm birth group, a threatened preterm birth group (at admission) and a full-term group. The platelet parameters [platelet count (PLT), mean platelet volume (MPV), plateletcrit (PCT), platelet distribution width (PDW)] and leukocyte parameters [white blood cell count (WBC), neutrophil to lymphocyte ratio (NLR), lymphocyte to monocyte ratio (LMR), platelet to lymphocyte ratio (PLR)] were compared in each group. PLT and MPV in preterm birth women were higher than those in the full-term and threatened preterm birth group. Throughout pregnancy, the platelet count showed the lowest level at delivery. The NLR in the preterm group was higher than in the full-term and threatened preterm groups at admission, and the PLR was higher than in the full-term group. The NLR increased gradually during pregnancy, and reached its peak in the full-term group one week before delivery. NLR in the threatened preterm group and preterm group reached their peak in late pregnancy. A BP (back propagation) artificial neural network model was constructed with significant PLT, MPV, NLR and PLR as input values in a univariate analysis. The AUC for predicting the risk of preterm birth using the ROC curve evaluation model was 0.819. In conclusion, the elevation of PLT, MPV, NLR and PLR in pregnant women is related to spontaneous preterm birth. The BP artificial neural network model has certain predictive value for spontaneous preterm birth.
"Lesion-habitat" radiomics to distinguish radiation necrosis from tumor recurrence on post-treatment MRI in metastatic brain tumors

About a third of all cancer patients develop brain metastases. Stereotactic radiosurgery (SRS) is a common treatment for patients with brain metastases and offers excellent tumor control rates. However, the most significant clinical challenge for patients after SRS is reliably differentiating tumor progression from radiation necrosis, a side effect of SRS, which occurs in about 20% of all metastatic brain tumor patients. The current diagnostic accuracy in distinguishing radiation necrosis from tumor recurrence via visual inspection by expert radiologists on routine MRI scans is 50-60%. Invasive surgical intervention provides the only definitive means of diagnosis. Therefore, finding non-invasive markers to reliably differentiate between these diagnoses are urgently needed. In this work, we present a radiomic-pipeline that involves capturing texture features (Laws, Haralick, Gabor) from not just the lesion but also the peri-lesion environment (defined as “lesion habitat”) to distinguish radiation necrosis and tumor recurrence. We obtained a discovery dataset (n=37 studies) from Cleveland Clinic with post-Gd T1w, T2w, and FLAIR volumes. Patients were confirmed via histopathology (biopsy or resection) as having a recurrent tumor (n=17) or radiation necrosis (n=20). A separate set of 12 patients was kept blinded as the hold-out" set. Each patient's T2 and FLAIR volumes were co-registered onto Gd-T1w. Lesion habitat sub-compartments were annotated by an expert as enhancing tumor, necrosis, and perilesional edema. Following pre-processing, a total of 4,740 texture features (including Haralick, Gabor, Laws, CoLlAGe) were extracted from each sub-compartment of the lesion habitat across all three available MRI sequences. To identify the most discriminatory features, we used Wilcoxon rank-sum test to remove correlated features (correlation 0.75). This was followed by a 3-fold cross-validation scheme, within a random forest classifier using the training cohort. The most discriminatory features were then evaluated on the hold out test set. Within our discovery set, we obtained an average AUC of . 9781 with a sensitivity of . 91 and a specificity of . 92. On the blinded hold out set, we obtained an accuracy of 91% in distinguishing radiation necrosis from tumor recurrence. Laws features (capturing edges, waves, ripple patterns) from the enhancing tumor region on Gd-T1w MRI were identified as being the most discriminatory in distinguishing radiation necrosis and tumor recurrence in METs patients.
Antiepileptic Drugs Usage in Pregnant Women with Epilepsy in Saudi Arabia

Background and Purpose Epilepsy is one of the most common neurological disorders requiring continuous treatment during pregnancy. In Saudi Arabia, there is only one publication that studied the outcome of pregnancies in women with epilepsy, published in 1999. The aim of the study is to determine the major congenital malformations in infants resulting from exposure to antiepileptic drugs in pregnant women with epilepsy. Methods This is a retrospective observational study that was conducted at King Abdulaziz Medical City, Jeddah, Saudi Arabia, involving pregnant women with epilepsy using antiepileptic drugs during pregnancy. We also studied babies born to those mothers. The study period was 5 years from 2014 to 2018. Results Six hundred babies were included in the study, born to 154 mothers with epilepsy using antiepileptic drugs during pregnancy. In addition, there were 111 losses of fetuses before 20 weeks of gestation. The only malformation detected was a ventricular septal defect in one child, whose mother was using polytherapy (valproic acid and levetiracetam). Three babies were born with epilepsy, and four babies had other associated disorders (Down syndrome, osteoporosis, esotropia, and hearing impairment). Conclusions The results of this small study are an urgent call for the establishment of congenital malformations registry in Saudi Arabia. In addition, specialized epilepsy clinics utilizing multidisciplinary care are highly recommended. A specific group of interest for such clinics are married women, who have epilepsy and are using antiepileptic drugs since planning of pregnancy is not part of the culture in Saudi Arabia.
Deep Cross-Modal Image–Voice Retrieval in Remote Sensing

With the rapid progress of satellite and aircraft technologies, cross-modal remote sensing image–voice retrieval has been studied in geography recently. However, there still exist some bottlenecks: how to consider the characteristics of remote sensing data adequately and how to reduce the memory and improve the retrieval efficiency in large-scale remote sensing data. In this article, we propose a novel deep cross-modal remote sensing image–voice retrieval approach, namely, deep image–voice retrieval (DIVR), to capture more information of remote sensing data to generate hash codes with low memory and fast retrieval properties. Especially, the DIVR approach proposes inception dilated convolution module to capture multiscale contextual information of remote sensing images and voices. Moreover, in order to enhance cross-modal similarity, the deep features’ similarity term is designed to make paired similar deep features as close as possible and paired dissimilar deep features as mutually far as possible. In addition, the quantization error term is designed to drive hash-like codes to approximate hash codes, which can effectively reduce the quantization error for hash codes’ learning. Extensive experimental results on three remote sensing image–voice data sets show that the proposed DIVR approach can outperform other cross-modal retrieval approaches.
Multi-Head Attention for Speech Emotion Recognition with Auxiliary Learning of Gender Recognition

The paper presents a Multi-Head Attention deep learning network for Speech Emotion Recognition (SER) using Log mel-Filter Bank Energies (LFBE) spectral features as the input. The multi-head attention along with the position embedding jointly attends to information from different representations of the same LFBE input sequence. The position embedding helps in attending to the dominant emotion features by identifying positions of the features in the sequence. In addition to Multi-Head Attention and position embedding, we apply multi-task learning with gender recognition as an auxiliary task. The auxiliary task helps in learning the gender specific features that influence the emotion characteristics in speech and results in improved accuracy of Speech Emotion Recognition, the primary task. We conducted all our experiments on IEMOCAP dataset. We are able to achieve an overall accuracy of 76.4% and average class accuracy of 70.1%, which are 5.3% and 6.2% higher respectively than the state-of-the-art models available on SER for four emotion classes.
A Low-Cost, Open-Source, Robotic Airship for Education and Research

Miniature indoor robotic airship platforms offer high mobility, safety, and extended flight times. This paper focuses on the feasibility, design, development, and evaluation of such a platform for robotics education and research. Selected commercially available envelope materials were considered and tested in terms of their helium retention capability and mechanical properties. The obtained envelope properties were used in a feasibility study, demonstrating that indoor airships are environmentally and financially viable, given an appropriate material choice. The platform’s mechanical design was studied in terms of gondola placement and rotor angle positioning, resulting in an unconventional, asymmetric arrangement. The developed system was finally tested in a simple path following experiment for proof-of-concept purposes, proving its efficiency in attaining the desired heading and altitude configuration. The proposed robotic airship platform can be used for a variety of education and research oriented applications. Its design is open-source, facilitating replication by others.
An On-Chip Micromachined Test Structure to Study the Tribological Behavior of Deep-RIE MEMS Sidewall Surfaces

An on-chip micro-mechanical test structure is presented to investigate the tribological behavior of deep reactive ion etching (DRIE) sidewall surfaces of microelectromechanical systems (MEMS) devices. The proposed test structure is fabricated on silicon on insulator (SOI) wafer using a standard surface micromachine process. Test structure consists of two orthogonally placed electrostatic comb-drive actuators, one is used to align a contact with the friction surfaces under a certain normal load, and another one is used to generate the tangential motion on contacted sidewall surfaces. To assess the frictional behavior of DRIE sidewall surfaces, both static and dynamic friction coefficients were studied for different DRIE process parameters. Wear analysis was carried out to extract the performance and reliability of MEMS sidewall surfaces during their operation. From the experiment results, it is found that with the increment of normal load, the static friction coefficient exhibits a nonlinear dependence, and however, it has less effect on the dynamic friction coefficient. DRIE process parameters have a significant influence on static and dynamic friction coefficients, i.e., variation in asperity size changes the real contact area between the contact pairs during their operation. From the wear analysis, it is found that the friction coefficient was very high initial value, then it drops with each subsequent cycle for a few cycles and finally reaches steady-state value.
A time-domain ultrasonic approach for oil film thickness measurement with improved resolution and range

The ultrasonic-based method has been proved to be a practical technique for measuring oil film thickness in the enclosed tribo-pair of a supporting bearing and under dynamic conditions. To cope with the large-scale variations of oil film thickness in engineering applications, frequency-domain based models, being adaptive for different measurement ranges, are widely used. As an improvement, the time-domain approach can further expand the effective range, but suffers from decreased resolution in oil thickness measurement. To address these issues, this paper proposes a unified time-domain model for full-range measurement. First, a cluster of standard echoes with definite film thicknesses in a wide range are pre-constructed, and they are matched with measured echoes to find the most suitable oil film thickness. Further, an optimized interpolation is applied to both the constructed and the measured echoes for better resolution. Aiming for the lowest interpolation error, the windowed sinc function was employed optimally. Using a precision calibration rig, the proposed model was compared to the traditional frequency-domain and the time-domain models. The comparison demonstrates that the proposed model has a larger effective measurement range, covering those of all traditional frequency-domain models and with equal accuracies. In addition, the proposed model shows both a wider effective range and a higher resolution than that of the reference time-domain model. This work contributes to the development of on-line continuous measurement of oil film thickness variation at a large scale.
Functional analysis of an alternative Replication Protein A complex containing RPA4

Replication Protein A (RPA), the eukaryotic single-stranded DNA-binding complex, is essential for multiple processes in cellular DNA metabolism including, but not limited to, DNA replication, DNA repair and recombination. The ‘canonical’ RPA is composed of three subunits (RPA1, RPA2, and RPA3). In addition to the three canonical subunits, there is a human homolog to the RPA2 subunit, termed RPA4, which can substitute for RPA2 in complex formation. The resulting RPA complex has been termed ‘alternative’ RPA (aRPA). The normal function of aRPA is not known; however, previous studies have shown that it does not support S-phase progression in vivo. The goal of this thesis was to characterize the function of aRPA in DNA replication, DNA repair and recombination and profile its expression in human tissues. The studies presented in this thesis show that the aRPA complex has solution and DNA binding properties indistinguishable from the canonical RPA complex as determined by gel mobility shift assays. However, aRPA was unable to support DNA replication and inhibited canonical RPA function in a cell-free simian virus 40 system. aRPA inhibited both initiation and elongation of DNA synthesis in the SV40 system. Two regions of RPA4, the putative L34 loop and the C-terminal winged helix domain, were responsible for inhibiting SV40 DNA replication. The mechanism of SV40 DNA replication inhibition during initiation and elongation was characterized using assays for DNA polymerase α and DNA polymerase δ. aRPA was shown to have reduced interaction with DNA polymerase α and was not able to efficiently stimulate DNA synthesis by DNA polymerase α on aRPA coated single-stranded DNA. However, aRPA stimulated DNA synthesis by DNA polymerase δ in the presence of PCNA and RFC even though a reduced interaction was observed between aRPA and polymerase δ.
R&D internationalisation and knowledge transfer : impact on MNEs and their home countries

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