Miracle-dz/UniFAR-FTUs huggingface dataset:
Role Of The Charges Of Lysine Side Chains In The Interaction Of Bovine Carbonic Anhydrase With Sodium Dodecyl Sulfate

In this work, the molecular dynamics (MD) method was used for the study of the interaction of bovine carbonic anhydrase with sodium dodecyl sulfate (SDS), with emphasis on the role of the charges of lysine side chains. For this purpose, bovine carbonic anhydrase was considered in two forms, namely BCA (with eighteen lysine-NH2 groups) and BCA-H (with eighteen lysine- + 3 NH groups). Simulation of each of these proteins was performed in two different concentrations of SDS. The following parameters: root mean square deviation of C-alpha of backbone, radius of gyration, hydrophobic solvent accessible surface area and the number of protein hydrogen bonds were calculated for BCA and BCA-H in the two concentrations of SDS. With regard to these parameters, no considerable differences were observed between BCA and BCA-H. In spite of the noted similar behavior, it was specified that these two structures were different concerning residues flexibility. Also, the number of SDS molecules bonded to these two structures was different.
Development of a new polymorphic genetic marker in "Araucaria araucana" (Mol) K. Koch

Seed storage proteins have been used as genetic marker in forest species to evaluate genetic variability, demonstrating its effectiveness both in conifers and broad-leaved. In conifers, megagametophyte storage proteins are particularly useful because of their haploid nature. The aim of this study was to determine whether these proteins could be used as a new marker of genetic diversity in Araucaria araucana, one of the oldest conifers of South America and a representative symbol of Chilean forest biodiversity. For this, megagametophytes from two A. araucana populations were assessed to identify polymorphic bands and to obtain a preliminary estimation of the genetic diversity. The results revealed that globulin is the best fraction for measuring the variability in the species, due to their high level of variation (20 identified bands, eleven of them polymorphic). Both populations showed high genetic diversity, with more than 92% of the variation within populations. The study highlighted that these proteins can be used to measure the genetic diversity in A. araucana, providing good information to ensure the preservation of the species genetic resources.
The Three-Dimensional Structure of the Cystic Fibrosis Locus: A Dissertation

The three dimensional structure of the human genome is known to play a critical role in gene function and expression. I used chromosome conformation capture (3C) and 3C-carbon copy (5C) techniques to investigate the three-dimensional structure of the cystic fibrosis transmembrane conductance regulator (CFTR) locus. This is an important disease gene that, when mutated, causes cystic fibrosis. 3C experiments identified four distinct looping elements that contact the CFTR gene promoter only in CFTR-expressing cells. Using 5C, I expanded the region of study to a 2.8 Mb region surrounding the CFTR gene. The 5C study shows 7 clear topologically associating domains (TADs) present at the locus, identical in all five cell lines tested, regardless of gene expression status. CFTR and all its known regulatory elements are contained within one TAD, suggesting TADs play a role in constraining promoters to a local search space. The four looping elements identified in the 3C experiment and confirmed in the 5C experiment were then tested for enhancer activity using a luciferase assay, which showed that elements III and IV could act as enhancers. These elements were tested against a library of human transcription factors in a yeast one-hybrid assay to identify potential binding proteins. Element III gave two strong candidates, TCF4 and LEF1. A literature search supported these transcription factors as playing a role in CFTR gene expression. Overall, this work represents a model locus that can be used to test important questions regarding the role of three dimensional looping on gene expression.
Is Problem-Based Learning Momentous in Augmenting the Industrial Capabilities of Graduates? A Literature Based Study

Educational management studies are now established as a way to infuse students with various pedagogic as well as didactic principles. The approaches are now switching from reading and lecture-based modes to analytical case-studies and problem-oriented learning methodologies. These inclusive development procedures are undertaken by educational institutions jointly in partnership with industry associates. This research paper highlights the consequences of learning practices in reducing the gap between corporate and academic entities through involvement in the problem-based learning methodology which is frequently utilized in business and medical studies at the Higher Educational Institutions (HEIs) of Pakistan. The paper investigates how the pedagogical method of problem-based learning is significant in meeting the changing needs of industry through enhancing the proficiency of graduates to manage corporate challenges in volatile external environments. The results lead us to conclude that problem-based learning at HEIs plays a substantial role in upgrading the potential of graduates to serve competitively in corporate sectors, thus realizing the inherent existence of strong ties between commercial and educational management sectors. Hence, PBL serves to be a more effective approach than the traditional teaching methodologies for producing better knowledge outcomes in terms of capable alumnae to serve at commercial levels.
Protein Engineering of Avidin by Rational Design and DNA Family Shuffling

Avidins represent an interesting group of proteins showing high structural similarity and ligand-binding properties but low similarity in primary structure. In this study, we show that it is possible to create functional chimeric proteins from the avidin protein family when applying DNA family shuffling to the genes of the avidin protein family: avidin, avidin related gene 2 and biotin-binding protein A. The novel chimeric proteins were selected by phage display biopanning against biotin, and the selected enriched proteins vailable online 11 November 2011 eywords: NA shuffling irected evolution vidin were characterized, displaying diverse features distinct from the parental genes, including binding to cysteine. © 2011 Elsevier B.V. All rights reserved.
Diseases of Amphibians and Reptiles

KRIEGER PUBLISHING COMPANY 1-800-724-0025 Preface and Acknowledgments 1. Animal Rights and Species Protection 2. Diagnostic Procedures 2.1 Case History and General External Examination 2.2 Parasitological Examinations 2.3 Bacteriological Examinations 2.4 Mycological Examinations 2.5 Virological Examinations 2.6 Imaging Techniques 2.6. 1 X-Rays 2.6. 2 Ultrasound 2.6. 3 Endoscopy 2.7 Blood Samples and Tests 2.8 Autopsy 3. Treatment 3.1 Preventive Measures 3.2 First Aid 3.3 Housing and Care of Patients 3.4 Administering Medications 3.4. 1 External Application of Medications 3.4. 2 Internal Adminstration of Medications 3.5 Four Basics of Treating Important Diseases 3.5. 1 Parasitic Diseases 3.5. 2 Bacterial Infections 3.5. 3 Mycotic Diseases 3.5. 4 Viral Infections 3.5. 5 Refusal to Eat, Vomiting, Diarrhea, Bloating, and Constipation 3.5. 6 Bites, Burns, Shedding Problems, and Abscesses 3.5. 7 Diseases of the Kidneys and Bladder Stones 3.5. 8 Egg Binding 3.5. 9 Prolapses of the Intestine and Hemipenes 3.5. 10 Joint Inflammation 3.6 Anesthesia 3.6. 1 Anesthesia in Reptiles 3.6. 2 Anesthesia in Amphibians 3.7 Surgical Methods 3.7. 1 Surgical Removal of Subcutaneous Abscesses, Tumors, and Parasite Stages 3.7. 2 Shell Injuries in Chelonians 3.7. 3 Opening of the Abdominal Cavity in Crocodilians, Lizards, and Snakes 3.7. 4 Opening of the Abdominal Cavity in Chelonians 3.7. 5 Surgical Treatment of Egg Binding in Reptiles 3.7. 6 Surgical Treatment of Follicle Retention in Lizards 3.7. 7 Surgical Interventions to the Stomach and Intestines 3.7. 8 Bladder Stone Surgery 3.7. 9 Surgical Treatment of Cloacal and Intestinal Prolapses 3.7. 10 Surgical Treatment of Hemipenis Prolapses 3.7. 11 Surgical Treatment of Oviduct Prolapses 3.7. 12 Surgical Treatment of Fractures 4. Congenital Defects 5. Tumors 6. Euthanasia 7. Amphibians and Reptiles As Transmitters of Zoonotic Diseases CONTENTS Dr. Kohler presents clear, basic information on how to care for amphibians and reptiles, and he draws extensively on his experience as a veterinarian. He describes general diagnostic techniques—parasitological, bacteriological, mycological, and virological—as well as x-ray, ultrasonics and endoscopy. There is a section on proper care and housing for these animals, and the author stresses the importance of providing the right conditions for them, which will contribute greatly toward keeping them healthy. Dr. Kohler also supplies detailed descriptions of the major diseases that affect these animals, making diagnosis and decisions about the correct therapy easier. Tips on how to handle emergencies and give first aid are also provided. The book is a valuable guide for both veterinarians and hobbyists.
Event-triggered control with robust communication and guaranteed performance

In this chapter we study fundamental properties of minimum inter-event times for several event-triggered control setups, both in the absence and presence of external disturbances and/or measurement noise. This analysis reveals, amongst others, that for several popular event-generators no positive minimum inter-event time can be guaranteed in the presence of arbitrary small external disturbances or measurement noise. This clearly shows that it is essential to include the effects of external disturbances and measurement noise in the analysis of the computation/communication properties of event-triggered control systems. In fact, this chapter also identifies event-generators that do exhibit these important event-separation properties.
Transcription regulation in eukaryotes

The HFSP workshops were initiated by Michel Cuénod (Secretary-General, HFSPO) with the support of the Board of Trustees and the Council of Scientists. The workshops, held in English, are organized at the HFSPO office in Strasbourg on specific scientific topics of particular timeliness in the two fields of research covered by HFSP: brain functions and biological functions at the molecular level. The guiding principles are general significance and novelty of the topic, treatment by leading experts, emphasis on discussion, and broad international, inter-continental and interdisciplinary representation. There is no general audience but the reports, edited by the organizers, present the issues discussed in a format attractive to specialists, post-doctoral trainees and students. The present report is based on a meeting held in Strasbourg from December 3–5, 1998. Acknowledgements The proposal for the workshop came from Pierre Chambon (Strasbourg), Toshio Fukasawa (Tokyo) and Roger Kornberg (Stanford) and the meeting was organized by them with the help of the HFSP staff. Our thanks go to the five rapporteurs who wrote the initial reports of the talks given at the meeting: These reports were edited and the book produced by Chris Coath (Norwich) and Jennifer Altman (London). We thank Valérie Dupé (London) and Olivia Wendling (Strasbourg) for technical support at the meeting, Stuart Molloy (Resolution Design Ltd, London) for the artwork, Alissa Surges (Ann Arbor) for compiling the bibliography and Solange Metzger (HFSPO, Strasbourg) for her unfailing support in administration and production. We acknowledge the following publishers for their permission to reproduce copy
Automatic Construction of the Finnish Parliament Speech Corpus

Automatic speech recognition (ASR) systems require large amounts of transcribed speech data, for training state-of-theart deep neural network (DNN) acoustic models. Transcribed speech is a scarce and expensive resource, and ASR systems are prone to underperform in domains where there is not a lot of training data available. In this work, we open up a vast and previously unused resource of transcribed speech for Finnish, by retrieving and aligning all the recordings and meeting transcripts from the web portal of the Parliament of Finland. Short speech-text segment pairs are retrieved from the audio and text material, by using the Levenshtein algorithm to align the firstpass ASR hypotheses with the corresponding meeting transcripts. DNN acoustic models are trained on the automatically constructed corpus, and performance is compared to other models trained on a commercially available speech corpus. Model performance is evaluated on Finnish parliament speech, by dividing the testing set into seen and unseen speakers. Performance is also evaluated on broadcast speech to test the general applicability of the parliament speech corpus. We also study the use of meeting transcripts in language model adaptation, to achieve additional gains in speech recognition accuracy of Finnish parliament speech.
Heavy metals content in degraded agricultural soils of a mountain region related to soil properties

(1) Department of Agrochemistry and the Environment, Miguel Hernández University of Elche, Av. de la Universidad, s/n, 03202 Elche (Alicante), Spain, (2) Soil Science Laboratory, Faculty of Biology, University of Barcelona, Barcelona (Spain), (3) Cyprus Open University, Faculty of Pure and Applied Sciences, Environmental Conservation and Management, Lab of Chemical Engineering and Engineering Sustainability, P.O. Box 12794, 2252, Latsia, Nicosia, Cyprus.
Deux Ravageurs nouveaux du Cocotier (Cocos nucifera L.) pour la faune des Comores : Aleurotrachelus atratus Hempel, 1922, et Paraleyrodes bondari Peracchi, 1971 (Hemiptera, Aleyrodidae)

Aleurotrachelus atratus Hempel, 1922, et Paraleyrodes bondari Peracchi, 1971, sont signales pour la premiere fois des Comores. Les degâts occasionnes sont tres importants sur Cocotier (Cocos nucifera). A. atratus est de loin l'espece la plus abondante. Les degâts sont decrits, leur importance et leur repartition dans l'archipel sont donnees. L'introduction remonte probablement a quelques annees. Quelques auxiliaires ont ete observes.
DETECTION OF EXTENDED SPECTRUM AND AMBLER CLASS C BETA LACTAMASES AMONG BETA-LACTAM RESISTANT KLEBSIELLA SPECIES: GENETIC ASPECTS -

Background and objective: It is well recognized that life infections due to variety of β-lactamases producing isolates of Klebsiella spp. are the major problematic in the treatment of these types of infections due to their expression high level of resistance to the most effective antimicrobial agents. This study has been undertaken for detecting the ability of Klebsiella species to produce extended-spectrum β-lactamases (ESBLs) and Ambler class C (AmpC). Further, for determining the genetic elements encoding for such enzymes whether chromosomally or conjugated plasmid mediated. The study was performed on 110 wound patients admitted to Department of Surgery, Ramadi Teaching Hospital.Rapid iodometric β-lactamase production test, double disk synergy test, and phenotypic and confirmatory tests for production of extended spectrum and AmpCβ- lactamases were performed. Plasmid DNA extraction, conjugation and curing experiments were performed. Fifty isolates were bacteriologically identified as Klebsiellae spp. including 36 (72%) Klebsiellae pneumoniae and 14 (28%) Klebsiellae oxytoca. In double disk synergy test, out of the 25 β-lactamase producer isolates, 12 (48%) and 7 (70%) isolates of K. pneumonia and K. oxytoca respectively demonstrated a clavulanic acid effect with cefotaxime or ceftazidime.In the plasmid profile analysis, the results revealed that 7 (87.5%) of Eight ESBLproducer isolates of Klebsiella spp. respectively were conjugative plasmid mediated. The result of curing experiments showed successful curing for all the study isolates by both methods. The study suggested that the production of β-lactamases of type ESBLs and Amp C, appeared to be the major mechanisms ofresistance of Klebsiellae spp. to β-lactams. In addition, conjugative plasmids were found to be the main genetic elements encoding for ESBLs produced by Klebsiellae spp. Finally, the study suggested that sodium dodecyl sulphate was of higher potency than elevated growth temperature in the curing of plasmid DNA.
A Comparison Study for Agrobacterium-mediated transformation Method in Sugarcane (Saccharum spp L.)

In order to compare transient expression of gus gene driven by CaMV 35S or rice ubiquitin RUBQ2 promoter, Agrobacterium-mediated transformation was conducted using embryogenic callus and suspension cultures of sugarcane. Histochemical observation of GUS activity after co-cultivation showed that rice ubiquitin promoter produced high level of clear blue spots both in embryogenic callus and suspension cultures, while the CaMV35S promoter was not detected. Regenerated shoots from the infected materials were found higher in suspension cultures than embryogenic callus. The results showed that the rice ubiquitin promoter as well as suspension cultures are more efficient for the Agrobacterium-mediated transformation. However, PCR analysis found there was no amplification of DNA neither for CaMV35 nor rice ubiquitin in genome DNA of regenerated shoot. Lacking of integration of the DNA into the genome showed that the regenerated shoots were not truly transformants might due to the presence of somaclonal variation that was common phenomenon in the regeneration from callus. To avoid the presence of somaclonal variation the transformation was then conduced using in vitro plant without intervening callus phase. Basal segment of in vitro plants prepared from axillary buds of sugarcane were used as the explants for the transformation. The histochemical observation of GUS activity showed that almost all of the infected materials partially exhibited blue color on the basal region. Infected in vitro plants showed rapidly grow and multiplied in theselection medium. Further investigation of the transformation using in vitro plants and Agrobacterium harboring SoSUT1 DNA construct driven by rice actin promoter resulted in development of antibiotic resistant sugarcane shoots. Interestingly the PCR analysis found an insertion of the antibiotic DNA fragment into the sugarcane genome DNA. This result suggests that in vitro plant is an effective target tissue for Agrobacterium-mediated transformation in sugarcane.
Plant cell line selection : procedures and applications

Culture systems and selection procedures in vitro mutagenesis flow cytometry for selection of plant cells in vitro micromanipulation of higher plant cells in vitro selection for disease resistance herbicide resistance environmental stress resistance screening and selection of cultured plant cells for increased yields of secondary metabolites selection and choice of genetic markers auxotrophic temperature-sensitive and hormone mutants isolated in vitro selection of somatic hybrids selection and analysis of cytoplasmic hybrids selection of transformed cells.
Composition of the Essential Oil of Spontaneous Rosmarinus officinalis from Greece and Antifungal Activity Against Phytopathogenic Fungi

Abstract The chemical composition of the essential oil of spontaneous Rosmarinus officinalis from Greece was analyzed by GC and GC/MS and tested for its antifungal activity against five phytopathogenic fungi (Sclerotinia sclerotiorum, Phytophthora nicotianae, Sclerotium cepivorum, Fusarium oxysporum f. sp. dianthi and Fusarium proliferatum). Thirty-seven components compounds representing 97.3% of the total oil were identified. The major constituents were α-pinene (24.1%), camphor (14.9%), 1,8-cineole (9.3%), camphene (8.9%), α-terpineol (8.8%) and borneol (8.0%). The most sensitive fungus was Ph. nicotianae, followed by S. sclerotiorum, S. cepivorum, F. proliferatum and F. oxysporum f. sp. dianthi.
Effect of feeding time on rumen microbial protein synthesis in cattle fed with sugarcane tops as staple roughage.

*Corresponding Author C. Bandeswaran bandeswaran@gmail.com A survey followed by in vitro and in vivo experiments were carried out to enhance rumen microbial protein synthesis in low milk yielding cattle under sugarcane tops based feeding system without altering the quantity of forage / feed ingredients. The survey revealed that majority of farmers fed the sugarcane tops twice daily during morning and evening and supplemented with groundnut cake at forenoon and evening along with de-oiled rice bran in drinking water. The half time (t1/2) of organic matter and nitrogen determined by in vitro for sugarcane tops were 29 ± 2 and 40 ± 6 hour, respectively. The respective t1/2 time of organic matter and nitrogen for the commonly fed supplemental feeds viz., groundnut cake and de-oiled rice bran were 7 ± 1 and 9 ± 1 and 8 ± 0 and 7 ± 1 hour, respectively. Altering the feeding strategy based on t1/2 value of organic matter and nitrogen sources did not increased the rumen microbial protein yield by in vitro / in vivo experiments. Hence, it was recommended to adopt farmers feeding strategy in sugarcane tops based feeding system.
Spatial organization of bacterial flora in normal and inflamed intestine： A fluorescence in situ hybridization study in mice

AIM: To studythe role of intestinal flora in inflammatory bowel disease (IBD). METHODS: The spatial organization of intestinal flora was investigated in normal mice and in two models of murine colitis using fluorescence in situ hybridization.RESULTS: The murine small intestine was nearly bacteriafree. The normal colonic flora was organized in three distinct compartments (crypt, interlaced, and fecal), each with different bacterial compositions. Crypt bacteria were present in the cecum and proximal colon. The fecal compartment was composed of homogeneously mixed bacterial groups that directly contacted the colonic wall in the cecum but were separated from the proximal colonic wall by a dense interlaced layer. Beginning in the middle colon, a mucus gap of growing thickness physically separated all intestinal bacteria from contact with the epithelium. Colonic inflammation was accompanied with a depletion of bacteria within the fecal compartment, a reduced surface area in which feces had direct contact with the colonic wall, increased thickness and spread of the mucus gap, and massive increases of bacterial concentrations in the crypt and interlaced compartments. Adhesive and infiltrative bacteria were observed in inflamed colon only, with dominant Bacteroides species.CONCLUSION: The proximal and distal colons are functionally different organs with respect to the intestinal flora, representing a bioreactor and a Segregation device.The highly organized structure of the colonic flora, its specific arrangement in different colonic segments, and its specialized response to inflammatory stimuli indicate that the intestinal flora is an innate part of host immunity that is under complex control.