Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge representation approach to closed loop control system - a tank system case-study

Control engineering problems are dealt within a plethora of methods and approaches depending on the a priori knowledge, the description of the process to control, and the main control goal. Classical control theory is mainly based on properties of numerical models. This paper presents an approach that applies to a class of processes described by numerical and logical relations using inference and a knowledge base system. To attain this goal an ontology for control systems is constructed. The work presented in this paper is based in a three tank system benchmark.
Heterologous Production of a Novel Cyclic Peptide Compound, KK-1, in Aspergillus oryzae

A novel cyclic peptide compound, KK-1, was originally isolated from the plant-pathogenic fungus Curvularia clavata. It consists of 10 amino acid residues, including five N-methylated amino acid residues, and has potent antifungal activity. Recently, the genome-sequencing analysis of C. clavata was completed, and the biosynthetic genes involved in KK-1 production were predicted by using a novel gene cluster mining tool, MIDDAS-M. These genes form an approximately 75-kb cluster, which includes nine open reading frames, containing a non-ribosomal peptide synthetase (NRPS) gene. To determine whether the predicted genes were responsible for the biosynthesis of KK-1, we performed heterologous production of KK-1 in Aspergillus oryzae by introduction of the cluster genes into the genome of A. oryzae. The NRPS gene was split in two fragments and then reconstructed in the A. oryzae genome, because the gene was quite large (approximately 40 kb). The remaining seven genes in the cluster, excluding the regulatory gene kkR, were simultaneously introduced into the strain of A. oryzae in which NRPS had already been incorporated. To evaluate the heterologous production of KK-1 in A. oryzae, gene expression was analyzed by RT-PCR and KK-1 productivity was quantified by HPLC. KK-1 was produced in variable quantities by a number of transformed strains, along with expression of the cluster genes. The amount of KK-1 produced by the strain with the greatest expression of all genes was lower than that produced by the original producer, C. clavata. Therefore, expression of the cluster genes is necessary and sufficient for the heterologous production of KK-1 in A. oryzae, although there may be unknown factors limiting productivity in this species.
Cooperation of LPA3 and LPA2 Is Essential for Photosystem II Assembly in Arabidopsis1[W][OA]

Photosystem II (PSII) is a multisubunit membrane protein complex that is assembled in a sequence of steps. However, the molecular mechanisms responsible for the assembly of the individual subunits into functional PSII complexes are still largely unknown. Here, we report the identification of a chloroplast protein, Low PSII Accumulation3 (LPA3), which is required for the assembly of the CP43 subunit in PSII complexes in Arabidopsis (Arabidopsis thaliana). LPA3 interacts with LPA2, a previously identified PSII CP43 assembly factor, and a double mutation of LPA2 and LPA3 is more deleterious for assembly than either single mutation, resulting in a seedling-lethal phenotype. Our results indicate that LPA3 and LPA2 have overlapping functions in assisting CP43 assembly and that cooperation between LPA2 and LPA3 is essential for PSII assembly. In addition, we provide evidence that LPA2 and LPA3 interact with Albino3 (Alb3), which is essential for thylakoid protein biogenesis. Thus, the function of Alb3 in some PSII assembly processes is probably mediated through interactions with LPA2 and LPA3.
Differential effects of dietary whey, casein and soya on colonic DNA damage and large bowel SCFA in rats fed diets low and high in resistant starch

Feeding higher levels of dietary animal protein (as casein or red meat) increases colonic DNA damage and thins the colonic mucus barrier in rats. Feeding resistant starch (RS) reverses these changes and increases large bowel SCFA. The present study examined whether high dietary dairy (casein or whey) or plant (soya) proteins had similar adverse effects and whether dietary RS was protective. Adult male rats were fed diets containing 15 or 25 % casein, whey or soya protein with or without 48 % high amylose starch (as a source of RS) for 4 weeks. DNA damage was measured in isolated colonocytes using the comet assay. Higher dietary casein and soya (but not whey) increased colonocyte DNA damage. DNA damage was highest with soya when fed at 15 or 25 % protein without RS. Dietary RS attenuated protein-induced colonocyte DNA damage in all groups but it remained significantly higher in rats fed 25 % soya compared with those fed 15 % protein. Dietary protein level did not affect colonic mucus thickness overall but the barrier was thinner in rats fed high dietary casein. This effect was reversed by feeding RS. Caecal total SCFA and butyrate pools were higher in rats fed RS compared with digestible starch. Caecal and faecal SCFA were unrelated to genetic damage but correlated with mucus thickness. The present data confirm that higher dietary protein affected colonocyte DNA and colonic mucus thickness adversely but that proteins differ in their effects on these indices of colon health. The data show also that these changes were reversed by RS.
Search for weakly decaying $b$-flavored pentaquarks

Investigations of the existence of pentaquark states containing a single b (anti)quark decaying weakly into four specific final states J/ψK+π-p, J/ψK-π-p, J/ψK-π+p, and J/ψϕ(1020)p are reported. The data sample corresponds to an integrated luminosity of 3.0 fb-1 in 7 and 8 TeV pp collisions acquired with the LHCb detector. Signals are not observed and upper limits are set on the product of the production cross section times branching fraction with respect to that of the Λb0.
Prevalence of Cigarette Smoking and Its Associated Risk Factors among Students of Hawassa University, College of Medicine and Health Sciences, 2016

Background: Cigarette smoking is a global health risk, causing increased health-care costs and loss of productivity among a number of age groups. Tobacco use in Africa, including Ethiopia, has attracted little attention, including among students. The aim of this study was to determine the prevalence of cigarette smoking and its associated risk factors among students of Hawassa University College of Medicine and Health Science. Methods: An institutional based cross sectional study was conducted to determine the prevalence of cigarette smoking and its associated risk factors among students of Hawassa University College of Medicine and Health Science. The team used systematic random sampling by determining the k value jumping some of the students from source population based on k intervals. The data was cleaned, coded and analyzed using SPSS version 20 and STATA version 12. Multiple logistic regressions were used to identify factors associated with cigarette smoking. Presence of confounders and interaction effects was investigated by computing relative changes on s coefficients at a cut-off point of 15%. Results and conclusion: The prevalence of cigarette smoking among students was 20.6% (95%CI: 0.61, 0.25). Cigarette smoking was significantly associated with students year of education (AOR=6.02; 95% CI: 2.09, 7.35), ever chewing Khat (AOR=20.99; 95% CI: 1.84, 4.3), age at start of smoking (AOR=2.21; 95% CI: 1.23, 6.12), ever drink alcohol (AOR=4.99; 95% CI: 1.02, 2.43) and receiving information about harmful effects of smoking cigarettes (AOR=4.99; 95% CI: 1.02, 2.43). Year of education, health education information, ever chewing Khat, ever drinking alcohol and age at start of smoking were significant factors for cigarette smoking. We recommend that students >20 years old be targeted with health education campaign focused on harmful effects of smoking tobacco.
Staging of digestive endocrine tumours using helical computed tomography and somatostatin receptor scintigraphy.

BACKGROUND In patients with digestive endocrine tumours, complete pre-operative staging is essential in planning proper management and evaluating treatment efficacy. To date, somatostatin receptor scintigraphy (SRS) is considered the 'gold standard' imaging procedure, and very few data are available concerning the use of helical computed tomography (hCT). This study aimed to determine the diagnostic accuracy and the ability to modify the surgical management of hCT, alone or combined with SRS. PATIENTS AND METHODS Sixty patients were staged before surgery by hCT, SRS and tumour markers, and included in group 1 if suitable for radical surgery, otherwise in group 2. All patients underwent laparotomy followed by subsequent re-staging. RESULTS SRS sensitivity was 77%, 48% and 67% for primary, lymph-node and liver lesions, respectively. hCT sensitivity was 94%, 69% and 94% for primary, lymph-node and liver lesions, respectively (P = 0.02 versus SRS, for liver lesions). During pre-operative evaluation, hCT correctly staged 92% and SRS 75% of patients (P = 0.02). hCT provided additional information in 17% of patients. CONCLUSIONS Since hCT has been shown to be extremely accurate, providing essential information for the planning of surgical treatment compared with that of SRS, both techniques should be used in the pre-operative work-up of digestive endocrine tumours.
Consequences of genetic selection for environmental impact traits on economically important traits in dairy cows

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits and the prediction of their selection response. In this study, test-day CH4 emissions were predicted from milk mid-infrared spectra of Holstein cows. Predicted CH4 emissions (PME) and log-transformed CH4 intensity (LMI) computed as the natural logarithm of PME divided by milk yield (MY). Genetic correlations of PME and LMI with traits used currently were approximated from correlations between estimated breeding values of sires. Values were for PME with MY 0.06, fat yield (FY) 0.09, protein yield (PY) 0.13, fertility 0.17; body condition score (BCS) –0.02; udder health (UDH) 0.22; and longevity 0.22. As expected by its definition, values were negative for LMI with production traits (MY –0.61; FY –0.15 and PY –0.40) and positive with fertility (0.36); BCS (0.20); UDH (0.08) and longevity (0.06). The genetic correlations of 33 type traits with PME ranged from –0.12 to 0.25 and for LMI ranged from –0.22 to 0.18. Without selecting PME and LMI (status quo) the relative genetic change through correlated responses of other traits were in PME by 2% and in LMI by –15%, but only due to the correlated response to MY. Results showed for PME that direct selection of this environmental trait would reduce milk carbon foot print but would also affect negatively fertility. Therefore, more profound changes in current indexes will be required than simply adding environmental traits as these traits also affect the expected progress of other traits.
Incidence and predictors of ovarian function recovery (OFR) in breast cancer (BC) patients with chemotherapy-induced amenorrhea (CIA) who switched from tamoxifen to exemestane.

BACKGROUND Aromatase inhibitors (AIs) may promote ovarian function recovery (OFR). True incidence, predictors and impact on the outcome of OFR are unknown. PATIENTS AND METHODS We carried out a prospective study to assess ovarian function in estrogen receptor (ER)-positive BC patients on tamoxifen who had at least 2 years of chemotherapy-induced amenorrhea (CIA) and postmenopausal E2 levels. Patients switched to exemestane and underwent a series of investigations including vaginal ultrasound, antimullerian hormone, follicle stimulating hormone (FSH), and E2. E2 measurements were made using a clinical assay (direct) and a highly sensitive (indirect) immunoassay for comparison. RESULTS Both E2 assays (indirect versus direct) showed a similar incidence of OFR 32% (95% CI 19.5-44.5) versus 30% (95% CI 17.7-42.3) and median time to OFR 5.4 months (95% CI 1.2-9.6) versus 6.0 months (95% CI 4.8-7.1). On multivariate analysis, the mean age at the start of exemestane treatment was the only marker associated with probability of OFR (OR: 0.44, 0.24-0.78; P = 0.006). According to a receiver operating characteristic (ROC) analysis, age <48 years predicted for OFR (sensitivity: 59%; 1-specificity: 17%; AUC: 0.796; P = 0.001). Patients with OFR had higher mean E2 levels (43.6 versus 5.76 pmol/l; P = 0.001) and a reduced disease-free survival [DFS; HR 9.3 (95% CI 3.3-48.0; P = 0.04)] than those without it. CONCLUSION Even with a clinical and biochemical profile compatible with menopause, switching from tamoxifen to an AI should be avoided in patients <48 with CIA.
Reconstitution of full-round uridine-deletion RNA editing with three recombinant proteins

Uridine (U)-insertion/deletion RNA editing in trypanosome mitochondria involves an initial cleavage of the preedited mRNA at specific sites determined by the annealing of partially complementary guide RNAs. An involvement of two RNase III-containing core editing complex (L-complex) proteins, MP90 (KREPB1) and MP61 (KREPB3) in, respectively, U-deletion and U-insertion editing, has been suggested, but these putative enzymes have not been characterized or expressed in active form. Recombinant MP90 proteins from Trypanosoma brucei and Leishmania major were expressed in insect cells and cytosol of Leishmania tarentolae, respectively. These proteins were active in specifically cleaving a model U-deletion site and not a U-insertion site. Deletion or mutation of the RNase III motif abolished this activity. Full-round guide RNA (gRNA)-mediated in vitro U-deletion editing was reconstituted by a mixture of recombinant MP90 and recombinant RNA editing exonuclease I from L. major, and recombinant RNA editing RNA ligase 1 from L. tarentolae. MP90 is designated REN1, for RNA-editing nuclease 1.
Population-based de novo molecule generation, using grammatical evolution

Automatic design with machine learning and molecular simulations has shown a remarkable ability to generate new and promising drug candidates. Current models, however, still have problems in simulation concurrency and molecular diversity. Most methods generate one molecule at a time and do not allow multiple simulators to run simultaneously. Additionally, better molecular diversity could boost the success rate in the subsequent drug discovery process. We propose a new population-based approach using grammatical evolution named ChemGE. In our method, a large population of molecules are updated concurrently and evaluated by multiple simulators in parallel. In docking experiments with thymidine kinase, ChemGE succeeded in generating hundreds of high-affinity molecules whose diversity is better than that of known inding molecules in DUD-E.
Validation and Search of the Ideal Cut-Off of the Sysmex UF-1000i® Flow Cytometer for the Diagnosis of Urinary Tract Infection in a Tertiary Hospital in Spain

Urinary tract infections (UTI) are one of the most prevalent infections. A rapid and reliable screening method is useful to screen out negative samples. The objective of this study was to validate the Sysmex flow cytometer UF-1000i by evaluating its accuracy, linearity and carry-over; and define an optimal cut-off value to be used in routine practice in our hospital. For the validation of the UF-1000i cytometer, precision, linearity and carry-over were studied in samples with different counts of bacteria, leukocytes and erythrocytes. Between March and June 2016, urine samples were tested in the Clinical Microbiology Laboratory at University Miguel Servet Hospital, in Spain. Samples were analyzed with the Sysmex UF-1000i cytometer, and cultured. Growth of ≥105 CFUs/mL was considered positive. The validation study reveals that the precision in all the variables is acceptable; that there is a good linearity in the dilutions performed, obtaining values almost identical to those theoretically expected; and for the carry-over has practically null values. A total of 1,220 urine specimens were included, of which 213 (17.4%) were culture positive. The optimal cut-off point of the bacteria–leukocyte combination was 138.8 bacteria or 119.8 leukocytes with an S and E of 95.3 and 70.4%, respectively. The UF-1000i cytometer is a valuable method to screen urine samples to effectively rule out UTI and, may contribute to the reduction of unnecessary urine cultures.
Absence of Fluoride Varnish–Related Adverse Events in Caries Prevention Trials in Young Children, United States

Introduction Fluoride varnish is an effective prevention intervention for caries in young children. Its routine use in clinical care is supported by meta-analyses and recommended by clinical guidelines, including the US Preventive Services Task Force (B rating). This report is the first prospective systematic assessment of adverse events related to fluoride varnish treatment in young children. Methods We determined the incidence of adverse events related to fluoride varnish treatment in 3 clinical trials on the prevention of early childhood caries, conducted under the auspices of the Early Childhood Caries Collaborating Centers, an initiative sponsored by the National Institute of Dental and Craniofacial Research. Each trial incorporated use of fluoride varnish in its protocol and systematically queried all children’s parents or legal guardians about the occurrence of acute adverse events after each fluoride varnish treatment. Results A total of 2,424 community-dwelling, dentate children aged 0 to 5 years were enrolled and followed for up to 3 years. These children received a cumulative total of 10,249 fluoride varnish treatments. On average, each child received 4.2 fluoride varnish treatments. We found zero fluoride varnish–related adverse events. Conclusion Fluoride varnish was not associated with treatment-related adverse events in young children. Our findings support its safety as an effective prevention intervention for caries in young children.
Genotyping‐by‐Sequencing for Plant Breeding and Genetics

Rapid advances in “next‐generation” DNA sequencing technology have brought the US$1000 human (Homo sapiens) genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotyping‐by‐sequencing (GBS) has been developed as a rapid and robust approach for reduced‐representation sequencing of multiplexed samples that combines genome‐wide molecular marker discovery and genotyping. The flexibility and low cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. Here we address some of the new research opportunities that are becoming more feasible with GBS. Furthermore, we highlight areas in which GBS will become more powerful with the continued increase of sequencing output, development of reference genomes, and improvement of bioinformatics. The ultimate goal of plant biology scientists is to connect phenotype to genotype. In plant breeding, the genotype can then be used to predict phenotypes and select improved cultivars. Furthering our understanding of the connection between heritable genetic factors and the resulting phenotypes will enable genomics‐assisted breeding to exist on the scale needed to increase global food supplies in the face of decreasing arable land and climate change.
Camera Motion Style Transfer

When depicting both virtual and physical worlds, the viewer's impression of presence in these worlds is strongly linked to camera motion. Plausible and artist-controlled camera movement can substantially increase scene immersion. While physical camera motion exhibits subtle details of position, rotation, and acceleration, these details are often missing for virtual camera motion. In this work, we analyze camera movement using signal theory. Our system allows us to stylize a smooth user-defined virtual base camera motion by enriching it with plausible details. A key component of our system is a database of videos filmed by physical cameras. These videos are analyzed with a camera-motion estimation algorithm (structure-from-motion) and labeled manually with a specific style. By considering spectral properties of location, orientation and acceleration, our solution learns camera motion details. Consequently, an arbitrary virtual base motion, defined in any conventional animation package, can be automatically modified according to a user-selected style. As shown in our experiments, the resulting shots are still fully artist-controlled, but appear richer and more physically plausible.
Ordered Micro-/Nanostructure Based Humidity Sensor for Fuel Cell Application

Humidity sensors are one of the most widely used sensors in commercial and industrial applications for environmental monitoring and controlling. Although related technology have been studied intensively, humidity sensing in harsh environments still remains a challenge. The inability of current humidity sensors to operate in high temperature environments is generally due to the degradation of the sensing films caused by high temperature, high humidity level, and/or contaminations. Our goal is the design and fabrication of a humidity sensor that is capable of working under high temperatures and in a condensing environment. The targeted application of this sensor is in the polymer electrolyte membrane (PEM) fuel cell, where humidity control is crucial for performance optimization. In this work, ordered macroporous silicon is thoroughly studied as a humidity sensing layer. In addition to the advantages of traditional porous silicon for gas sensing (high resistance to high temperature and good compatibility with current IC fabrication process), the ordered macroporous silicon used in these experiment has uniform pore size, pore shape and distribution. All the vertical aligned pores can be opened to the environment at both ends, which can significantly increase the efficiency of gas diffusion and adsorption. Moreover, this special structure opens the door to uniform surface modifications for sensing enhancement. Both ordered macroporous silicon based heterostructure and self-supporting membrane are fabricated and investigated as a humidity sensor. Heterostructure sensors with different thin film surface coatings including bare Si, thermally grown SiO2, atom layer deposited ZnO, HfO2, and Ta2O5 are characterized. Post micro-fabrication is achieved on this ordered porous structure without affecting the material and its sensing properties. It has been proven that the ordered macroporous silicon with Ta2O5 surface coating shows the best
Gradient-based solution for hybrid precoding in MIMO systems

The combination of baseband and analog precoding for multiple-input multiple-output (MIMO) systems is considered in this paper which is referred to as hybrid precoding. The system capacity, as a design criterion, is maximized subject to unit modulus constraints on the elements of the analog precoder (phase shifters), and a total power constraint. This is a non-convex problem due to the product of the analog and baseband precoder variables. The proposed technique suggests computing non-trivial complex derivatives of the objective and constraints, analytically, in order to develop an iterative gradient-based sequential optimization algorithm to solve the non-convex problem. Promising simulation results show that the solution of the proposed algorithm is sufficiently close to the optimal (full-baseband) precoder solution, regardless of the channel characteristics.