Miracle-dz/UniFAR-FTUs huggingface dataset:
BIMBOT-(Artificial intelligence applied to BIM design)

BIMBOT es un asistente de diseño inteligente para la industria AEC. Sus herramientas se ejecutan sobre un software de modelado BIM y producen varias soluciones de diseño con modelos BIM optimizados. Funciona con el uso de métodos avanzados de Inteligencia Artificial (optimización soft computing y Machine Learning) y es compatible con bases de datos NoSQL. Contempla varias etapas: La definición por el usuario de restricciones / prioridades establecidas ejecuta un proceso de diseño generativo impulsado por varios métodos de IA. Éste crea diferentes soluciones en modelos BIM almacenados y refinados a partir de un catálogo de objetos inteligentes. Con ello, los usuarios pueden interactuar importando modelos BIM con diseños propuestos, crearlos o editarlos in situ y recibir asistencia de una serie de métricas configurables que dan calidad al diseño de acuerdo con las preferencias iniciales. Así, obtenemos un Modelo BIM completo como resultado del proceso iterativo. Finalmente, el entrenamiento continuo de los algoritmos mejorará la eficiencia en futuros diseños. BIMBOT está concebido para extender las habilidades de los diseñadores a través del desarrollo de software BIM, permitiéndoles ser más productivos en tareas complejas del proceso de diseño. BIMBOT está financiado por el programa europeo Eureka / Eurostars (E! 12863).
Protein Turnover in Broiler, Layers, and Broiler Breeders

Protein turnover in skeletal tissue for broiler breeders has shown to increase at sexual maturity and then decline with increased egg production. Regarding broiler chickens the industry is facing two situations that need to be clarified: the appearance of white stripes in birds over 56 days of age and the positive effect in breast meat yield that supplementation of 25OH-D3 is causing. A series of studies were conducted to determine the effect of sexual maturity in protein turnover in broiler breeders and laying hens and to understand the effect of 25OHD3 in breast meat yield in broiler chickens and why white striping occurs in birds older than 56 days of age. In the first trial, a 4x6 factorial study was conducted to determine the effect of sexual maturity on protein turnover in broiler breeder pure line (4 lines x 6 ages). Results showed that as the birds enter sexual maturity the degradation rate significantly increased and then it decreased as they pass peak egg production, suggesting that they might be relying on their muscle protein reserves for egg formation. In the second trial, a 4x10 factorial study was conducted to evaluate the effect of four different programs and sexual maturity in broiler breeder pullets and hens. Results showed no difference regarding protein turnover between feeding programs. Fractional breakdown rate showed the same pattern as the first trial. In the third trial, a study was conducted to evaluate the effect of sexual maturity on protein turnover in laying hens. Results showed that also in this birds, as they reach peak egg production, the fractional breakdown rate significantly increased. In the fourth trial, a study was conducted to track labeled leucine from the breast of the hens to the egg. Results showed, that hens are using their skeletal muscle for egg formation, since we were able to find labeled leucine in the egg. The last two trials were conducted in broiler chickens to understand the white striping issue and how 25OHD3 enhances muscle growth. We were able to conclude, that birds with severe white striping have a higher protein fractional breakdown rate than the birds with no white stripes. Results regarding 25OHD3 showed that this supplement is enhancing muscle growth through the mTOR pathway. ACKNOWLEDGEMENTS I would like to thank all the wonderful people who was supporting and helping me during this journey: My family, my friends and research group: Judy England, Justina Caldas, Nirun Boonsinchai, Phiphob Sodsee, Ethan Holt, Monticha Putsakum and my partner Erik Pollock. I would also like to thank Linda Kirby, Eric Vaught and the staff of the University of Arkansas Poultry Research farm for all their help. Finally I would like to thank my advisor Dr. Craig Coon for the support and for all the advice he gave me and my committee members: David Kreider, Sami Dridi, and Charles Maxwell.
The microbiological context of HIV resistance

ii ACKNOWLEDGEMENTS . iv LIST OF TABLES . vi LIST OF FIGURES. viii ABBREVIATIONS USED . x LIST OF PUBLICATIONS . xii SEQUENCE ACCESSIONS. xiii A. INTRODUCTION. 1 1. Review. 1 2. Hypotheses, Goals & Objectives. 37 B. MATERIALS & METHODS. 40 C. RESULTS. 68 1. Description of study groups in Winnipeg and Nairobi . 68 2. Diagnosis of BV by microscopy and assessment of vaginal pH. 81 3. Flow cytometric quantification of bacteria in vaginal specimens. 96 4. Culture-based quantification and functional analysis of vaginal specimens. 106 5. Determination of acid and H2O2 production by vaginal isolates . 119 6. Phylogenetic profiling of isolates by RISA and cpn60 UT sequencing. 136 7. Ultra-deep molecular characterization of vaginal microbiota. 157 8. Enumeration of bacterial genomes for five cpn60 phylotypes by qPCR . 193 D. DISCUSSION . 201 E. CONCLUSION . 223 REFERENCES. 225
The Evaluation of RS1805086 and RS1805065 Polymorphisms in Mstn Gene and Anthropometric Properties of National and Amateur Arm Wrestlers

The evaluation of rs1805086 and rs1805065 polymorphisms in mstn gene and anthropometric properties of national and amateur arm wrestlers. Int. J. 38(4) :1148-1154, 2020. SUMMARY: The aim of this study is to investigate rs1805086 and rs1805065 polymorphisms of MSTN gene of national and amateur Turkish arm wrestlers and people leading a sedentary lifestyle, and the anthropometric properties such as hand, wrist, and forearm circumferences of national and amateur Turkish arm wrestlers are aimed to be explored. In this study, a total of 79 volunteers who were 24 national (7 females, 17 males) Turkish arm wrestlers, 21 amateur (7 females, 14 males) Turkish arm wrestlers and 34 sedentary people (12 females, 22 males) participated. To analyse the data, Statistical Package for the Social Sciences, SPSS 22 (SPSS Inc., Chicago, IL, USA) was used. As a result of the study, when data on rs1805086 and rs1805065 polymorphisms of MSTN gene were examined respectively, it was found out that MSTN 153KK genotype was 100.0% dominant in both national (n=24) and amateur (n=21) arm wrestlers, and it was 94.12 % dominant in sedentary people. KR genotype was observed in 5.88 % of the sedentary people. The data from the other rs1805065 polymorphism of MSTN gene showed that all participants (n = 45, 100.0 %) were carriers of normal homozygous genotype. Furthermore, for both female group and male group, there found to be statistically significant difference in terms of anthropometric properties. It can be concluded that though there was no significant difference between national and amateur Turkish arm wrestlers in terms of their MSTN gene characteristics; in terms of anthropometric properties, significant differences were discovered. It was found out that on these athletes, not MSTN gene polymorphisms but anthropometric properties were effective.
The lipid droplet protein Pgc1 controls the subcellular distribution of phosphatidylglycerol

The biosynthesis of yeast phosphatidylglycerol (PG) takes place in the inner mitochondrial membrane. Outside mitochondria, the abundance of PG is low. Here we present evidence that the subcellular distribution of PG is maintained by locally controlled enzymatic activity of the PG-specific phospholipase, Pgc1. We document that the Pgc1 absence leads to spreading of PG over various cellular membranes. Fluorescently labeled Pgc1 protein strongly accumulates at the surface of lipid droplets (LD). We show, however, that LD are not only dispensable for Pgc1-mediated PG degradation, but even host no phospholipase activity of Pgc1. Our in vitro assays document the capability of LD-accumulated Pgc1 to degrade PG upon entry to membranes of the endoplasmic reticulum, mitochondria, and even of artificial phospholipid vesicles. FRAP analysis confirms continuous exchange of GFP-Pgc1 within individual LD in situ, suggesting that a steady-state equilibrium exists between LD and membranes to regulate immediate phospholipase activity of Pgc1. In this model, LD serve as storage place and shelter Pgc1 preventing untimely degradation, while both phospholipase activity and degradation of the enzyme occur in membranes.
The Genomic Prediction of Disease: Example of type 2 diabetes (T2D)

Application of concepts from information theory have revealed new features of Single Nucleotide Polymorphism (SNP) organization. These features lead to effective classifiers by which to distinguish genomic sequences of contrasting phenotypes; as in case/control cohorts. When applied to a disease/control database, a disease classifier results; a parallel analysis leads to the determination of a wellness classifier. The classifiers have non-intersecting loci, and each involves roughly 100 alleles. The effectiveness of this framework is illustrated by application to adult onset, type 2, diabetes (T2D), as represented in the Wellcome Trust ((WT) Case/Control database. Simultaneous use of the two classifiers on the WT database leads to successful prediction of disease versus wellness; to the extent that near certain genomic forecasting is achieved. This framework gives a resolution to the oft posed uncertainty: “Where is the missing heritability? ” Application of both classifiers on two additional T2D databases produced informative consequences. A fully independent, compelling, confirmation of the present results is obtained by means of the machine learning algorithm, Random Forests. The analytical model presented here is generalizable to other diseases. One Sentence Summary Discovery of intrinsic chromosomal SNP organizations leads to near certain genomic disease prediction.
Ventricular chamber-specific Pitx2 insufficiency leads to cardiac hypertrophy and arrhythmias

Genome-wide association studies (GWAS) have identified genetic risk variant adjacent to the homeobox transcription factor PITX2 in atrial fibrillation (AF) patients. Experimental studies demonstrated that Pitx2 insufficiency leads to cellular and molecular substrates that increased atrial arrhythmias susceptibility. Pitx2 expression is present not only in the atrial but also in the ventricular myocytes. This study aims to investigate if insufficiency of Pitx2 in the developing and adult ventricular chambers increased susceptibility to ventricular arrhythmias. Conditional Pitx2 loss-offunction ventricular chamber-specific (Mlc2v-Cre) mouse mutants were generated using Cre/loxP technology. Pitx2 insufficiency in the ventricular myocardium leads interventricular septal thickening during cardiogenesis but else mice are viable until adulthood. Adult Mlc2vCre+Pitx2-/- hearts display hypertrophic and dilated ventricular chambers. ECG recordings demonstrated that Mlc2vCre+Pitx2-/- mice display increased QT and QRS intervals. Molecular analyses demonstrate that repolarization but not depolarization is severely impaired in these mutants. Microarrays analysis identified mRNAs and microRNAs altered in Pitx2 ventricular-specific mutants and provide evidences for miR-1 and miR-148 deregulation which in turn modulate Klf4 and distinct ion channel expression linked to cardiac hypertrophy and long QT-like defects. Our data demonstrate that Pitx2 insufficiency play leads to cellular and molecular ventricular remodeling which results in hypertrophic and dilated ventricular chambers and electrophysiological defects resembling long QT syndrome.
Ethylene causes transcriptomic changes in Synechocystis during phototaxis

Abstract Ethylene is well known as a plant hormone, but its role in bacteria is poorly studied. We recently showed that Synechocystis sp. Strain PCC 6803 has a functional receptor for ethylene, ethylene response 1 (Etr1), that is involved in various processes such as phototaxis in response to directional light and biofilm formation. Here, we use RNA sequencing to examine the changes in gene transcripts caused by ethylene under phototaxis conditions. Over 500 gene transcripts across many functional categories, of approximately 3700 protein‐encoding genes, were altered by application of ethylene. In general, ethylene caused both up‐ and downregulation of genes within a functional category. However, the transcript levels of amino acid metabolism genes were mainly upregulated and cell envelope genes were mostly downregulated by ethylene. The changes in cell envelope genes correlate with our prior observation that ethylene affects cell surface properties to alter cell motility. Ethylene caused a twofold or more change in 62 transcripts with the largest category of upregulated genes annotated as transporters and the largest category of downregulated genes annotated as glycosyltransferases which sometimes are involved in changing the composition of sugars on the cell surface. Consistent with changes in cell envelope, glycosyltransferase, and transporter gene transcripts, application of ethylene altered the levels of specific sugar moieties on the surface of cells. Light signaling from Etr1 involves two proteins (Slr1213 and Slr1214) and a small, noncoding RNA, carbon stress‐induced RNA1 (csiR1). Application of ethylene caused a rapid, but transient, decrease in the transcript levels of etr1, slr1213, and slr1214 and a rapid and prolonged decrease in csiR1 transcript. Deletion of Slr1214 caused a large increase in csiR1 transcript levels and ethylene lowered csiR1 transcript. These data combined with prior reports indicate that ethylene functions as a signal to affect a variety of processes altering the physiology of Synechocystis cells.
The influence of small hydroelectric power plants on the richness and composition of Odonata species in the Brazilian Savanna

Regardless of the economic and social development that damming processes related to hydroelectric power plants bring to a region, they represent a wide range of disturbances to the physical, chemical, and biological characteristics of rivers. We evaluated the effects of dams on Odonata communities from the southeastern region of Goiás, Brazil. Thirteen streams connected to three dams were studied: seven were used as reference samples (located upstream from the damming site, therefore not directly affected by damming) and six were used as affected area samples (located downstream from the dam). A total of 1128 odonates from six families, 22 genera, and 39 species were captured and identified. The results showed that Odonata richness was affected by the presence of dams, with different effects on Anisoptera and Zygoptera suborders. We discuss that these effects are related mostly to the physical and chemical variables in waterbodies directly affected by small hydroelectric power plants (SHPs). It is possible that negative effects on the Odonata community in SHP areas are related to changes in waterflow, pH and turbidity.
Restoration potential of Asian oysters on heavily developed coastlines

Reef‐building oysters historically provided the main structural and ecological component of temperate and subtropical coastal waters globally. While the loss of oyster reefs is documented in most regions globally, assessments of the status of Asian oyster reefs are limited. The feasibility of restoration within the regional biological and societal contexts needs to be assessed before implementation. Here, we quantified the current distribution of natural oyster reefs (Crassostrea spp.) in the shallow coastal waters of Hong Kong, assessed the biological feasibility of reestablishing reefs using natural recruitment, and examined their current and potential water filtration capacity as a key ecosystem service provided by restoration. We found natural low‐relief oyster beds in the low intertidal coastal areas at a subset of the locations surveyed. These areas are, however, degraded and have sparse densities of oysters generally <2 years old. Recruitment was high in some areas (>500,000 indiv./m2) and while survival to maturity varied across sites there was adequate larval supply and survival for restoration. Filtration rates for a 1‐year‐old recruit (90 mm length, approximately 30 L/hour per individual) at summer temperatures (30°C) meant that even the small remnant populations are able to provide some filtration services (up to 31.7 ML/hour). High natural recruitment means that oyster reef restoration can be achieved with the addition of hard substrate for recruitment, increased protection of restoration sites, and would not only increase the ecological value of reefs regionally but also serve as a model for future restoration in Asia.
Impact of perceived value on behavior intention of parent-child runners in a marathon event

Abstract In China, there has been a rapid growth of marathon events in recent years. With more events being staged, an opportunity has arisen for parents to attend with their children as a way of family time together. Due to the swift pace of industrialization, urbanization, and work commitment, parenting time and family interaction have become a major challenge for Chinese residents today. Building on previous research indications that individual value beliefs and perceptions would affect one’s behavior, this study was designed to examine the impact of perceived value parents placed on marathons as an opportunity to bond with their children. Through a comprehensive review of literature and test of content validity, the Scale of Parenting Value Perception was developed. The survey form also contained items assessing consumption behavior. A total of 384 marathon runners who were parents to one or more children participating in a marathon event responded to the survey. Perceived value of parents and children fell into five factors, including functional value, social value, sentiment value, experiential value, and personal value, which were significantly (p < .001) predictive of behavioral intentions. The findings highlight the benefits parents perceive and children receive through joint participation in sports and also indicate the necessity for sport managers to build family friendly events and promote the family value of these events through educational programs, publicity mechanism, and most importantly, high-quality family services to accommodate the needs and wants of parents and their children.
Derin Sinir Ağları Kullanarak Histopatolojik Görüntülerde Meme Kanseri Tespiti

Bu calismada cagimizin en tehlikeli hastaliklarindan birisi olan ve gec teshis durumunda tedavisi oldukca zor bir hal alan meme kanserinin histopatolojik goruntulerde tespiti icin derin sinir aglari kullanilarak bir model onerilmistir. Calisma ile bilgisayar destekli teshis sistemlerinin yuksek dogruluk degerlerine ulasarak meme kanserinin tespitinde yardimci bir teshis metodu kullanilmasi saglanmistir. Kullanilan veriseti 40X, 100X, 200X ve 400X yakinlastirma oranlarina sahip ve toplamda 7909 adet histopatolojik goruntu icermektedir. Onerilen derin sinir agi modelinde DenseNet201, Inception V3, ResNet50 ve Xception olmak uzere dort farkli on-egitimli (pre-trained) ag kullanilarak daha basarili sonuclar elde edilmistir. Modellerin basarimlarini daha da artirmak amaciyla birakma (dropout) ve veri artirma (data augmentation) yontemleri kullanilmistir. Kullanilan bu aglar kendi arasinda karsilastirilmis ve Xception agi ile elde edilen sonuclarin diger aglara oranla daha basarili oldugu gorulmustur. Xception agi ile 200X yakinlastirma oraninda gerceklestirilen deneysel calismalarda, hem diger aglara gore hem de diger yakinlastirma oranlarina gore en basarili sonuclara ulasilmis ve 98.01’lik bir dogruluk (Accuracy) skoru, 97.89’luk bir hassasiyet (Precision) degeri ve 97.47’lik bir hatirlama (Recall) degeri elde edilmistir. Xception aginin 200X yakinlastirma oranindaki ROC egrisi altindaki alan degeri ise 0.975 olarak hesaplanmistir.
ISOLATION, IDENTIFICATION AND PRODUCTION OF LIPASE PRODUCING BACTERIA FROM OIL CONTAMINATED SOIL

The production of commercial enzymes, including lipase from bacteria has always been the industrial choice due to its economical and commercial feasibility. Lipases are produced by microorganisms such as bacteria and fungi. However, we have focused on bacterial microbial lipases were economically importance of several properties. The present studies of the goals of this paper were isolation and identification of lipase producing bacteria from Oil contaminated soil. Screening and isolation of lipase producing strains of bacteria was carried out from different soil samples collected from various area in Surat, Gujarat, India. Tributyrin agar, selective media for isolation of lipase producing bacteria was used. Out of 41 isolates,20 were showing lipolytic activity. Agar well diffusion method used for further screening of best isolate for lipase production. The isolate AD1 with maximum zone of 27mm on Phenol red agar plate produce the lipase with the activity of 4.27U/ml obtained after 96hrs of incubation period at 37°C and 120 rpm at pH 7.0.
Application of the alternative variational iteration method to solve delay differential equations

In this paper, alternative variational iteration method (AVIM) is presented to solve linear and nonlinear delay differential equations (DDEs). A general lagrange multiplier is used to construct a correction functional. The proposed series solutions are found to converge to exact solution rapidly. The computation of three test examples of DDEs was presented to confirm the efficacy and validity of AVIM. The results obtained show that the AVIM is very simple and efficient. Key words: Alternative variational iteration method (AVIM), Lagrange multiplier, Delay differential equations (DDEs).
Savannas after afforestation: Assessment of herbaceous community responses to wildfire versus native tree planting

Afforestation and fire exclusion are pervasive threats to tropical savannas. In Brazil, laws limiting prescribed burning hinder the study of fire in the restoration of Cerrado plant communities. We took advantage of a 2017 wildfire to evaluate the potential for tree cutting and fire to promote the passive restoration of savanna herbaceous plant communities after destruction by exotic tree plantations. We sampled a burned pine plantation (Burned Plantation); a former plantation that was harvested and burned (Harvested & Burned); an unburned former plantation that was harvested, planted with native trees, and treated with herbicide to control invasive grasses (Native Tree Planting); and two old‐growth savannas which served as reference communities. Our results confirm that herbaceous plant communities on post‐afforestation sites are very different from old‐growth savannas. Among post‐afforestation sites, Harvested & Burned herbaceous communities were modestly more similar in composition to old‐growth savannas, had slightly higher richness of savanna plants (3.8 species per 50‐m2), and supported the greatest cover of native herbaceous plants (56%). These positive trends in herbaceous community recovery would be missed in assessments of tree cover: whereas canopy cover in the Harvested & Burned site was 6% (less than typical of savannas of the Cerrado), the Burned Plantation and Native Tree Planting supported 34% and 19% cover, respectively. By focusing on savanna herbaceous plants, these results highlight that tree cutting and fire, not simply tree planting and fire exclusion, should receive greater attention in efforts to restore savannas of the Cerrado.