Miracle-dz/UniFAR-FTUs huggingface dataset:
BPIFA1 Interactions with Bacteria and Their Importance for Airway Host Defence

Bactericidal/permeability-increasing protein fold-containing family member A1 (BPIFA1) is abundantly secreted protein of the upper airways that plays a pleiotropic role in airway defence, including antimicrobial and bacteriostatic functions. The mechanisms by which BPIFA1 exhibits these diverse functions is not fully resolved. I investigated the regions of BPIFA1 predicted to be functionally important by using BPIFA1-tagged proteins to visualise their ability to bind to bacteria. The ability of mouse and human BPIFA1 to bind to bacteria were compared. I also used in vitro differentiated mouse tracheal epithelial cells (mTECs) from wild-type (WT) and Bpifa1-/- mouse tracheas to investigate if BPIFA1 plays a role in host response to nontypeable Haemophilus influenzae (NTHi). Human full-length and disulphide-bond mutant BPIFA1 proteins bound to both Gram-negative and Gram-positive bacteria. However, human BPIFA1 lacking residues 22-42 was not able to bind to bacteria, implying that this region may be important for BPIFA1’s binding. Mouse BPIFA1 also bound to both Gram-negative and Gram-positive bacteria. No apparent differences in the bacterial binding of human and mouse BPIFA1 proteins were observed. In vitro studies with WT and Bpifa1-/- mTECs showed the trend towards an increased NTHi colonisation in Bpifa1-/- mTEC cultures compared to WT. NTHi caused patchy infection of mTECs, suggesting that they exhibit resistance to NTHi. No clear differential infection between WT and Bpifa1-/- cells was detected. NTHi was capable of associating with the multiple cell types of tracheal epithelium, but not with BPIFA1-positive cells. NTHi infection disrupted cellular tight-junctions, suggesting that epithelial barrier function was impaired. This, in turn, allowed NTHi to cross through the mTECs. Differences in the BPIFA1 secretion by NTHi-exposed WT mTECs was observed compared to WT MOCK-exposed mTECs but no clear difference between WT and Bpifa1-/- mTECs inflammatory responses was detected. Overall, the data from this study suggest that human and mouse BPIFA1 proteins play a role in airway defence by binding to Gram-negative and Gram-positive bacteria. The S18 region (G22-L42) of human BPIFA1, but not the disulphide bond, appears to be important for the binding activity of protein but further research is required to determine the true biological functions of this region. Mouse BPIFA1 binds to NTHi and appears to initially protect BPIFA1-positive cells from NTHi invasion, however BPIFA1 deficiency does not lead to significantly increased NTHi infection in mTECs. These findings imply that BPIFA1 is mucosal defence molecule that functions to modulate bacterial infection of the airways.
Translational Studies of Equine Infectious Anemia Virus RNA and Analysis of the Viral Regulatory Proteins.

vii CHAPTER 1 LITERATURE REVIEW Retroviruses. 1 Retroviral Gene Expression. 7 Equine Infectious Anemia Virus. 48 Research Objectives. 72 2 IN VITRO TRANSLATION OF EIAV MULTICISTRONIC RNAS Introduction. 73 Materials and Methods. 76 Results. 82 Discussion.116 3 IN VIVO EXPRESSION OF THE EIAV ORF PROTEINS Introduction.125 Materials and Methods. 128 Results and Discussion.133 4 SUMMARY, CONCLUSIONS, AND FUTURE STUDIES Summary and Conclusions.166 Future Studies.172 REFERENCES. 178 VITA.200 LIST OF FIGURES Figure Page 1. Genome and virion structure of a typical retrovirus. 5 2. The structure of HIV-1 proviral D N A . 8 3. The HIV-1 LTR.11 4. The structure of HIV-1 TAR RN A . 17 5. The structure of the HIV-1 Rev response elem ent. 23 6. The 4.0-kb size class of HIV-1 RNAs. 37 7. The 1.8-kb size class of HIV-1 RNAs. 39 8. Schematic representation of EIAV disease course. 50 9. Schematic representation of the EIAV proviral genome.52 10. A comparison of the HIV-1 and EIAV TAR RNAs. 60 11. Schematic representation of the EIAV open reading frames and transcripts.70 12. Schematic representation of the EIAV 3.5-kb R N A . 75 13. Schematic diagram of the pSP720 in vitro transcription vector and nucleotide sequence of the corresponding in vitro transcrip t.84 14. Translation of the pSP720 and pSP585 RNAs in wheat germ extracts and identification of the protein products by im m unoprecipitation. 87 15. Predicted amino acid sequences of the tat and S2 ORFs and location of the synthetic peptides used for antisera preparation.88 16. Microsequence analysis of the [3H]-glycine labeled S2 protein.90 17. Microsequence analysis of the [3H]-glycine labeled SI protein and SDS-PAGE of purified SI and S2 p ro te ins.92 18. Microsequence analysis of the [3H]-arginine labeled SI p ro te in . 95 19. Quantitation of the SI, S2, and Agp90 proteins produced from the pSP720 RNA in wheat germ extracts. 97 20. Effect of m 7GpppG cap analog on the pSP720 RNA translation.99 21. Effect of potassium ion concentration on the translation of pSP720 RNA in wheat germ extracts. 103
Upotreba algoritma Naive Bayes u procesu donošenja poslovnih odluka

Rezime: Postoji značajan broj sistema za pomoć u poslovnom odlučivanju koji kao osnovu koriste Bajesovu teoremu. U ovom radu, prikazuje se jedna od primena ove teoreme korišćenjem algoritma Naive Bayes koji svoju upotrebnu vrednost dokazuje u mnogobrojnim praktičnim primenama upravo zbog jednostavnosti u fazama učenja i klasifikacije, kao i zbog činjenice da se može obučavati na izuzetno malim skupovima podataka i postići prilično veliku brzinu rada u poređenju sa drugim algoritmima mašinskog učenja. U ovom radu, prikazuju se matematičke osnove i način rada algoritma Naive Bayes, uz osvrt na skupove podataka sa kojima se pogodno koristi. Takođe, predstavlja se i praktično softversko rešenje koje su autori razvili za rad sa ovim algoritmom i kao pomoć u donošenju poslovnih odluka.
Local Surface Electric Field’s Effect on Adsorbed Proteins’ Orientation

Hydrogenated nanocrystalline silicon, while being non-charged and non-polar, could be an ideal candidate for the non-covalent and orientation-controlled immobilization of biomolecules thanks to local electric fields around nanocrystals. To that effect, the adsorption of bovine serum albumin on substrates with different densities of nanocrystals, revealed by Raman spectroscopy and X-ray diffraction, was studied using infrared spectroscopy and atomic force microscopy. It was found that the protein–surface interactions followed different mechanisms depending on the nanostructure at the surface: hydrophobic on the non-crystalline part of the surface and electrostatic around the crystalline part. These electrostatic interactions were driven by the electric fields that arose at the junction between crystalline and amorphous structures. These electric fields were found to be strong enough to interact with the amide dipoles, thereby reorienting the adsorbed protein molecules on this part of the surface. Nevertheless, the adsorbed proteins were found to be denatured, which was due to the surface chemistry, and not affected by the nanostructure.
Cloud Computing Cryptography "State-of-the-Art"

Cloud computing technology is very useful in present day to day life, it uses the internet and the central remote servers to provide and maintain data as well as applications. Such applications in turn can be used by the end users via the cloud communications without any installation. Moreover, the end users’ data files can be accessed and manipulated from any other computer using the internet services. Despite the flexibility of data and application accessing and usage that cloud computing environments provide, there are many questions still coming up on how to gain a trusted environment that protect data and applications in clouds from hackers and intruders. This paper surveys the “keys generation and management” mechanism and encryption/decryption algorithms used in cloud computing environments, We proposed new security architecture for cloud computing environment that considers the various security gaps as much as possible. A new cryptographic environment that implements quantum mechanics in order to gain more trusted with less computation cloud communications is given. Keywords—Cloud Computing, Cloud Encryption Model, Quantum Key Distribution.
Decentralised primary and secondary control strategies for islanded microgrids considering energy storage systems characteristics

One of the main subjects of Microgrid (MG) islanded operation is its stability. Using the Energy Storage Systems (ESSs) in MGs, the stability can be improved. To ensure the proper operation of the ESSs, their State of Charge (SoC) should be monitored and controlled. In this paper, a new decentralized control method based on the conventional droop method is proposed which considers different types of ESSs used in islanded MG, i.e. ESSs with high power density and high energy density. In the proposed method, the ESS units are divided into two main categories. The master ESS is the main primary frequency control unit and the other ESSs respond to active and reactive power variations of the load and participate in the secondary control of frequency. For each of these categories, a new control method is proposed. The proposed method, including the primary and secondary control, is decentralized, and based on local measurements. Moreover, in the proposed method, a SoC equalization of ESSs is considered. To assess the stability of the MG, a small signal stability model is developed. Three scenarios are simulated to verify the effectiveness of the proposed method in MG frequency control and ESSs SoC balancing.
La sucesión de la empresa familiar; una aproximación teórica

La sucesión en la empresa familiar es considerada como una etapa decisiva para su continuidad. Aunque es uno de los tópicos más estudiados, solo una pequeña proporción de ellas sobrevive a cada transferencia generacional. En las economías en desarrollo como las latinoamericanas, la generación de conocimiento sobre el tema es significativa dada la importante proporción de empresas familiares en cada país, y en consecuencia su contribución económica y social. El presente trabajo es una revisión bibliográfica sobre el proceso de sucesión de la empresa familiar. Tiene por objetivo la reconstrucción de su campo de estudio para propiciar el desarrollo de nuevos trabajos. Entre los principales resultados destaca la relación entre la sucesión y la planeación estratégica, la influencia familiar y la gestión integral.
The BRCA 2 gene is a potential molecular target during 5-fluorouracil therapy in human oral cancer cells

5-Fluorouracil (5-FU) is widely used in clinical cancer therapy. It is commonly used either alone or in combination with other drugs and/or radiation for head and neck, and other types of cancers. 5-FU induces DNA double-strand breaks (DSBs). Inhibition of the repair of 5-FU-induced DSBs may improve the therapeutic response in many tumors to this anticancer agent. The aim of the present study was to further our understanding of the pathways which are involved in the repair of 5-FU-induced DSBs. Cell survival after drug treatment was examined with colony forming assays using Chinese hamster lung fibroblast cells or Chinese hamster ovary cell lines which are deficient in DSB repair pathways involving the homologous recombination repair-related genes BRCA2 and XRCC2, and the non-homologous end joining repair-related genes DNA-PKcs and Ku80. It was found that BRCA2 was involved in such repair, and may be effectively targeted to inhibit the repair of 5-FU-induced damage. Observations showed that knockdown of BRCA2 using small interference RNA suppression increased the sensitivity to 5-FU of human oral cancer cell lines (SAS and HSC3). These findings suggest that downregulation of BRCA2 may be useful for sensitizing tumor cells during 5-FU chemotherapy.
Plant disease and pest detection using deep learning-based features

The timely and accurate diagnosis of plant diseases plays an important role in preventing the loss of productivity and loss or reduced quantity of agricultural products. In order to solve such problems, methods based on machine learning can be used. In recent years, deep learning, which is especially widely used in image processing, offers many new applications related to precision agriculture. In this study, we evaluated the performance results using different approaches of nine powerful architectures of deep neural networks for plant disease detection. Transfer learning and deep feature extraction methods are used, which adapt these deep learning models to the problem at hand. The utilized pretrained deep models are considered in the presented work for feature extraction and for further fine-tuning. The obtained features using deep feature extraction are then classified by support vector machine (SVM), extreme learning machine (ELM), and K-nearest neighbor (KNN) methods. The experiments are carried out using data consisting of real disease and pest images from Turkey. The accuracy, sensitivity, specificity, and F1-score are all calculated for performance evaluation. The evaluation results show that deep feature extraction and SVM/ELM classification produced better results than transfer learning. In addition, the fc6 layers of the AlexNet, VGG16, and VGG19 models produced better accuracy scores when compared to the other layers.
ARGONAUTE5 Mediates Fine-Tuning of Vegetative-to-Reproductive Phase Transition Through Its Interaction with miR156 in Arabidopsis

Vegetative-to-reproductive phase change is a finely tuned process in plants, largely controlled by the age-regulated microRNA156 (miR156), which functions by suppressing the transcripts of SQUAMOSA-PROMOTER BINDING LIKE (SPL) transcription factors. ARGONAUTE proteins (AGO) are essential effectors of miRNA-mediated gene regulation. However, which AGO(s) mediate(s) the control of flowering time remains unclear. Here, we demonstrate a role for AGO5 in vegetative-to-reproductive phase transition through the modulation of SPL transcription factors. We show that AGO5 interacts physically and functionally with miR156 and that ago5 mutants present an early flowering phenotype in Arabidopsis. Furthermore, in ago5 mutants, the repression of flowering caused by miR156 overexpression is largely reversed, whereas leaf morphology remains unaffected. Our results thus indicate a specific role for AGO5 in mediating miR156 activity in meristematic, but not vegetative, tissue. As such, our data suggest a spatiotemporal regulation of the miR156 aging pathway, mediated through different AGO proteins in different tissues.
Strategi Personal Branding Pustakawan di Perpustakaan Universitas Muhammadiyah Purwokerto

Tujuan penelitian ini adalah untuk mengetahui strategi personal branding pustakawan Perpustakaan di Universitas Muhammadiyah Purwokerto (UMP). Penelitian ini menggunakam metode penelitian kualitatif dengan pendekatan analisis deskriftif. Penelitian kualitatif ini menekankan pada kedalaman data serta detail data yang didapatkan oleh peneliti. Peneliti melakukan penelitian dengan menggunakan pendekatan teori Peter Montoya tentang the eight laws of personal branding. Dari hasil penelitian ini menunjukan ada kesamaan dan perbedaan komponen strategi dalam membangun personal branding dengan teori yang dikemukanan Peter Montoya. Kesamaan tersebut peneliti temukan pada komponen kompetensi, spesifikasi, kepemimpinan, kepribadian, perbedaan, dan good will. Sementara itu, temuan lain di lapangan terdapat komponen kompetensi dan brand image yang menjadi salah satu strategi personal branding pustakawan UMP. Kesimpulan penelitian menunjukan bahwa ada tujuh strategi personal branding pustakawan Perpustakan UMP. Ke tujuh strategi personal branding pustakawan tersebut merupakan alat untuk membentuk persepsi publik bahwa pustakawan Perpustakaan UMP adalah seorang yang ramah, jujur, sopan, santun, bertanggungjawab, disiplin, dan penuh profesionalitas.
Multi-Factor Competitiveness Analysis of the Chemical and Pharmaceutical Industry in Eueu Member States

This paper aims to assess the degree of influence of various factors on the competitiveness of the chemical and pharmaceutical industry in EAEU member states. The analysis results made it possible to determine the level of competitiveness in pharmaceutical markets in individual EAEU member states, and to assess how much their competitiveness is impacted by such factors as the ratio between pharmaceutical imports and exports in the external market; prices offered by pharmaceutical manufacturers and output of pharmaceutical products. Upon completion of the research, the authors defined main development trends for the unified pharmaceutical market in EAEU member states, including how to harmonize laws, elaborate measures of price regulation and introduce new pricing approaches towards pharmaceutical products. Moreover, to improve competitiveness and strengthen the export potential of the EAEU pharmaceutical industry it is necessary to tighten regulatory requirements for the production of safe and high-quality pharmaceuticals in accordance with the unified EAEU GMP standards.
FOUNDATIONS OF CRYPTOGRAPHY

In this lecture we discuss the problem of constructing a protocol for computing a function whose input is divided among a number of parties. This protocol must retain the privacy of data of each of the participants, even when some of the other parties try to get this data. We define the notion of a protocol that privately computesa function. We show a protocol that privately computesany function, according to the given definition, when more than half of the parties are honest . The time complexity of the protocol is polynomial in the complexity of the function.
Effect of Operating Conditions on the Liquid Water Content Flowing Out of the Cathode Side and the Stability of PEM Fuel Cell Performance

Management of the water in the stack is a major problem in achieving optimal performance of a Proton Exchange Membrane (PEM) fuel cell. One of the problems caused by water imbalance in the PEM system is the formation of liquid water on the side of the cathode. High water content in the PEM fuel cell stack causes liquid water and flooding, and decreases its performance. The presence of liquid water on the cathode side of the fuel cell leads to a decrease in the amount of oxygen reacting in the catalyst layer. The results of this study indicate that a general increase in water content results in a decrease in the performance of PEM fuel cell systems. The highest water content occurs at a current density of 0.9, with Rha and RHc of 90%. In this condition, system performance is relatively stable at 0.67 volts, with 0.00016 gr/cm 2 of liquid water content produced. Above this water content, system performance decreases significantly. system. Their results show that optimal system performance occurs between 70% and 90% Rhc and 70% Rha.
A CASE OF NEAR-HANGING

Hanging is the suspension of a person by a noose or ligature around the neck and has been a common method of capital punishmentsince medieval times. Hanging is also a common method of suicide/homicide worldwide as also in India. We report a case ofattempted suicidal hanging admitted in our intensive care unit. The patient, a 32-year old male, presented with poor clinical status,in gasping condition, hypoxemic and required immediate intubation, resuscitation, assisted ventilation and intensive care treatment.He received standard supportive intensive care and made a full clinical recovery without any neurological deficit. The purpose of thecase report is to emphasize that the cases of near-hanging need to be aggressively resuscitated and managed irrespective of dismalinitial presentation.
A CMOS Receiver–TDC Chip Set for Accurate Pulsed TOF Laser Ranging

An integrated receiver–time-to-digital converter (TDC) chip set is developed for pulsed time-of-flight (TOF) laser rangefinding. The receiver detects the current pulse from the optical detector and produces a timing mark for the TDC. The receiver uses time mode walk error compensation scheme achieving <±2.5-mm residual timing-walk error within a dynamic range of ~1:40 000. The multichannel TDC measures the time position, width, and rise time of the echo pulses simultaneously with ~10-ps precision. Both chips are manufactured in 0.35- $\mu \text{m}$ complementary metal–oxide–semiconductor (CMOS) technology. The functionality of the chip set was demonstrated in a laser radar platform using 12 W and 3-ns optical pulses produced by a laser diode (LD). Measurement accuracy of ~ ±3 mm was achieved with noncooperative targets at a distance range of a few tens of meters within an amplitude range of received echoes of 1:40 000.
Biochemical Characterisation and Sensory Evaluation of Differently Coloured and Shaped Tomato Cultivars

Antioxidant capacity, total phenolic content, colour, sugar, volatiles, ascorbic acid and carotenoid (β-carotene and lycopene) contents of differently coloured and shaped tomato cultivars (cvs) grown in the Eastern Mediterranean region, Turkey were determined, along with a sensory evaluation. Tomato cultivars of two different types (cherry and beefsteak) and four different colours (red, yellow, orange and brown) were analysed. All plants were simultaneously grown in the same field and subjected to identical horticultural practices to minimise the effects of environmental conditions and to maximise those related to genotype. The red cherry cultivar had the highest lycopene content, while the orange beefsteak cultivar had the highest β-carotene content. The highest antioxidant capacity, total phenolic content and hardness scores were found in cherry-type tomatoes, except the yellow one. The red cherry cultivar had the highest sugar content. Red and brown cherry cultivars were also significant in terms of their high carotenoid and sugar contents, along with a high antioxidant activity. The brown cherry cultivar had the highest total phenol content. The highest quantities of 2-hexenal, 3-hexen-1-ol, and 6-methyl-5-hepten-2-one were detected in red cultivars. The brown cherry cultivar had the highest sweetness, typical aroma and hardness scores, while the yellow beefsteak cultivars the lowest sweetness typical aroma scores. In terms of sensory parameters, red and brown cultivars scored higher than yellow and orange ones. ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********
Dynamical Tunneling in the Systems of Double Quantum Dots and Rings

Semiconductor heterostructures as quantum dots (QD) or quantum rings (QR) demonstrate discrete atom-like energy level structure. In the case of double QD (DQD) or double concentric QR (DCQR), a single electron spectrum is composed as a set of quasi-doublets. We study influence of these specific spectrum properties on electron tunneling which is related to the electron transport through DQD (DCQR). The double InAs/GaAs QDs (QRs) are considered within the single sub-band effective approach. The whole spectrum of the single electron is calculated for two and three dimensional quantum objects. We considered two type of dynamical tunneling in DQD. The first is related to tunneling in the system of two identical QDs; the second one occurs in the system of non-identical QDs. We study the effect of symmetry violation of DQD (DQR), the shape geometry on tunneling and show that violation of symmetry creates difficulties for tunneling.