Miracle-dz/UniFAR-FTUs huggingface dataset:
A mathematical model of Chagas disease transmission

Chagas disease is a parasitic infection caused by protozoan Trypanosoma cruzi which is transmitted to human by insects of the subfamily Triatominae, including Rhodnius prolixus. This disease is a major problem in several countries of Latin America. A mathematical model of Chagas disease with separate vector reservoir and a neighboring human resident is constructed. The basic reproductive ratio is obtained and stability analysis of the equilibria is shown. We also performed sensitivity populations dynamics of infected humans and infected insects based on migration rate, carrying capacity, and infection rate parameters. Our findings showed that the dynamics of the infected human and insect is mostly affected by carrying capacity insect in the settlement.Chagas disease is a parasitic infection caused by protozoan Trypanosoma cruzi which is transmitted to human by insects of the subfamily Triatominae, including Rhodnius prolixus. This disease is a major problem in several countries of Latin America. A mathematical model of Chagas disease with separate vector reservoir and a neighboring human resident is constructed. The basic reproductive ratio is obtained and stability analysis of the equilibria is shown. We also performed sensitivity populations dynamics of infected humans and infected insects based on migration rate, carrying capacity, and infection rate parameters. Our findings showed that the dynamics of the infected human and insect is mostly affected by carrying capacity insect in the settlement.
Fitness status and myocardial morphology in youth

Wyatt FB, Baker JS, Buchan DS. Fitness Status and Myocardial Morphology in Youth. JEPonline 2015;18(2):1-12. The purpose of this study was to determine if fit adolescent males and females indicate myocardial morphology changes outside normal values. Twenty-two young adults 15 to 18 yrs of age acted as subjects. Resting measures included: age (yrs), height (ht, cm), weight (wt, kg), systolic blood pressure (SBP, mmHg), diastolic blood pressure (DBP, mmHg), percentage body fat (%BF), body mass index (BMI, kg·m-2), waist circumference (WC, cm), waist/hip (W/H, ratio). A resting echocardiogram was used to determine the subjects’ myocardial morphology, which included left ventricular mass (LVM, gm), left ventricular internal diameter end-diastolic (LVIDd, cm), left ventricular internal diameter end-systolic (LVIDs, cm), septal wall thickness (SWT, cm), and posterior wall thickness (PWT, cm). The subjects ran the Aerobic Fitness Shuttle Test and took the Physical Activity Questionnaire (PAQ). Statistical procedures included mean (±SD) for group measures. A Pearson Product R Correlation Coefficient determined bi-variate associations. Post hoc regression analyses established prediction equations between associated variables. The statistical significance was set at P≤0.05. Left ventricular internal diameter end-diastolic significantly associated with ht, wt, WC, LVIDs, LVM, and PWT. Posterior wall thickness, LM, and ST showed significant predictive qualities to the Aerobic Shuttle Test through regression analyses. Linear regression analyses determined specific myocardial morphologies can be determined through weight and fitness status. These include LVIDd, PWT, SWT, and LVM.
Next-generation genetically engineered mouse models to study PI3K/3-phosphoinositide-dependent protein kinase 1 (Pdk1) signaling in pancreatic cancer

In this study, the role of Craf and Pdk1 in a KrasG12D-driven mouse model of pancreatic cancer (PDAC) was analyzed. In contrast to Craf, loss of Pdk1 completely blocked pancreatic carcinogenesis. To delete potential therapeutic targets like Pdk1 in autochthonous tumors, a novel inducible dual-recombinase system by combining the Flp/frt and Cre/loxP recombination system was generated. As a proof-of-concept, we validated genetic tumor therapy using a latent diphtheria-toxin A allele in established PDAC in vivo.
DNA methylation profile of the DKK2 gene as a biomarker in patients with colorectal cancer

Purpose: Epigenetic changes can be detected in precancerous lesions, suggesting that may be involved in the early stages of carcinogenesis. The methylation of specifics genes has been correlated with the outcome of many different types of cancers. This study compared the levels of DNA methylation between normal and tumor tissues from patients with colorectal cancer (CRC). Methods: Candidate genes were screened using the Methyl-Profiler™ PCR Array System and the Dickkopf-related protein 2 (DKK2) genes were selected for study. DNA methylation of these genes was assessed by polymerase chain reaction–high-resolution melting (PCR–HRM) analysis. Results: Out of the 112 patients studied, 68 were controls with a mean age (SD) of 59.9 years (13.4) and 45 were patients with CRC with a mean age (SD) of 64.6 years (13.6). Among the patients with CRC, 25 were women, 28 were diagnosed with colon cancer and 18 were diagnosed with rectal cancer. The number of patients with Stage I, II, III, and IV of the disease, as per the TNM classification, were 2 (4.3%), 20 (43.4%), 18 (39.1%), and 2 (4.3%), respectively. Furthermore, the DKK2 gene had a higher methylation profile in the CRC tissues when compared to normal mucosa (p < 0.001), whereas the methylation profile analysis was not statistically significant when comparing the stages of the disease (p = 0.078). Conclusion: The presence of differentially methylated sequences of the DKK2 gene between the groups showed that the methylation changes of these genes could potentially be prognostic and predictive markers in CRC.
Charakterisierung der Funktion von DENEDDYLASE 1 in Arabidopsis thaliana

In dieser Dissertation wurde die Funktion des Enzyms DENEDDYLASE 1 in dem pflanzlichen Modellorganismus Arabidopsis thaliana untersucht. Ich konnte zeigen, dass DEN1 ein Bestandteil des essentiellen Neddylierungssystems ist und die Isopeptidbindung zwischen der posttranslationalen Peptidmodifikation NEDD8 und ihren Proteinsubstraten hydrolysiert. Des Weiteren wurde mit dem Protein AXR1 das erste DEN1-spezifische NEDD8-Substrat aus Arabidopsis identifiziert und die biologische Funktion der AXR1-Neddylierung naher untersucht.
Reduced Proximal Tubular Expression of Megalin and Neonatal Fc Receptor in Proteinuria: The Role of Matrix Metalloproteinases

Proteinuria is clearly associated with the progression of chronic kidney disease (CKD) but the mechanisms underlying this relationship remain unclear. Recent evidence suggests that altered proximal tubular (PT) handling of filtered proteins may significantly modulate urine protein excretion and progressive renal disease. Megalin and neonatal Fc receptor (FcRn) are endocytic receptors responsible for the PT reabsorption of glomerular ultrafiltered proteins by receptor-mediated endocytosis (RME) and transcytosis, and are expressed on the luminal surface of the PT. This study aimed to investigate the expression and turnover of megalin and FcRn in proteinuria, and the possible mechanisms underlying down-regulation of expression of these receptors. In protein overload proteinuria (POP), the PT expression of megalin and FcRn were both downregulated compared to control animals. In addition, significant amount of both receptor were detected in the urine of proteinuric animals. This reduction in megalin and FcRn protein expression was accompanied by a significant increase in the urinary excretion of plasma proteins including the most abundant albumin. Increased expression and activity of both matrix metalloproteinase (MMP) and gamma secretase (γ-secretase) was evident in proteinuric animals and was paralleled with the urinary excretion of both megalin and FcRn. Megalin was previously identified to undergo regulated intramembrane proteolysis (RIP). RIP includes the MMP-mediated cleavage of the extracellular domain of megalin which in turn excreted into the urine, and the subsequent cleavage of the intracellular domain by γ-secretase. A synthetic inhibitor of MMPs, batimastat (BB-94) significantly reduced urinary excretion and also preserved the PT expression of megalin. In addition, inhibition of MMPs appeared to be antiproteinuric by markedly reducing urinary excretion of albumin and plasma proteins. The urinary excretion of FcRn was also reduced in BB-94 treated animals but the mechanism of this reduction was not clear. Further, BB-94 treatment preserved PT expression of FcRn in proteinuric animals. The POP model was developed to investigate the degree of tubulointerstitial damage in experimental animals. Injury was detected in the interstitium of proteinuric animals with significant increases in inflammatory markers including tumour necrosis factor alpha (TNF-α), interleukin-6 (IL-6) and the transforming growth factor-beta (TGF-β) as well as interstitial collagen deposition and marked interstitial infiltration of macrophages (F4/80). Blockade of MMP in proteinuric animals significantly reduced the expression of these markers in the kidney and abrogated the progression of interstitial inflammation and fibrosis.
Age, growth, and natural mortality of cubera snapper, Lutjanus cyanopterus, from the southeastern United States

Ages of cubera snapper, Lutjanus cyanopterus (Cuvier, 1828) (n = 106), collected from the southeastern United States coast from 2001 to 2015, were determined using sectioned sagittal otoliths. We determined that opaque zones were annular, forming April–August (peaking in May–June). Cubera snapper ranged from 4 to 55 yrs, and the largest fish measured 1422 mm total length (TL). Body-size relationships for cubera snapper were: TL = 1.02 FL + 12.76 (n = 28, r 2 = 0.99), FL = 0.97 TL – 9.65 (n = 28, r 2 = 0.99), and W = 4.9 × 10–9 TL3.16, where W is total weight (kg) and FL is fork length (mm). The von Bertalanffy growth equation for cubera snapper was Lt = 1495 (1 – e–0.05(t + 3.33)) (n = 106). Point estimate of natural mortality was M = 0.08, while age-specific estimates of M ranged 0.50–0.05 yr–1 for ages 1–55. Here, we present the first published findings of life history parameters for cubera snapper from the Atlantic waters off the southeastern United States. These data contribute to filling in gaps of basic biological information for data-limited reef fish species in the southeastern United States.
Physico-chemical and quality characterization of pulp oil from two varieties of pili (Canarium ovatum Engl.) from Bicol, Philippines

Tugay, M.M.D.R. , Mopera, L.E. , Esguerra, E.B. and Castillo-Israel, K.A. T. Institute of Food Science and Technology, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, 4031 College of Industrial Technology, Catanduanes State University, Calatagan, Virac, Catanduanes, 4800 Postharvest Horticulture Training and Research Center, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, 4031
Signaler and receiver boldness influence response to alarm calls in eastern chipmunks

&NA; Using social information can benefit individuals in many ways. Responding to alarm signals can, for instance, maximize survival under predation risk. However, foraging individuals should consider the reliability of such risk‐based information to balance antipredator behavior and resource acquisition. Receiver decisions could depend on personality effects, as individual variation in risk‐taking tendencies (i.e., boldness) could not only affect receiver perception of the signaled threat but also signaler reliability. Recent theoretical models support the possibility of coevolution between personality and communication strategies. Using a playback experiment, we show that wild eastern chipmunks (Tamias striatus) respond to alarm calls according to their own boldness level (measured as consistent individual differences in basal vigilance) and that they increase their vigilance response to bolder callers potentially considered as more reliable. Further, receivers respond to the callers' boldness regardless of their own boldness and independently of their familiarity level with callers, therefore decoding this information from vocalizations. Such effects of individual behavioral variation on the perception and interpretation of social information could apply to signals used in a variety of ecological contexts.
N:P supply ratio-dependent growth, cellular chemical composition and toxicity in Alexandrium tamarense

The dinoflagellate Alexandrium tamarense forms one of the most harmfu1 a1ga1 b1ooms around the world and produces a potent neurotoxin that causes paralytic shellfish poisoning (PSP; HALLEGRAEFF 1995). Variability in the physio1ogical characteristics of A. tamarense is controlled by different environmental conditions such as salinity, temperature and nutrient (WHITE 1978, BOYER et al. 1987, MACINTYRE et al. 1997). eoastal environments are increasingly influenced by phosphorus (P) in addition to nitrogen (N), which are supplied by riverine inputs (MIDDELBURG & NIEUWENHUIZE 2000) and atrnospheric deposition (HowARTH et al. 1996). The ratio of N to P varies widely around global coastal waters and this N:P ratio can affect physiological characteristics and production ofphytoplankton (FoNG et al. 1993). eoastal dinoflagellates such as Alexandrium species often encounter various N:P supply ratios (FLYNN et al. 1994) due to vertical migration and horizontal dispersion, although cellular N:P ratio of 16:1 in phytoplankton is noted by REDFIELD (1958). Variability in physiological status is observed at various combinations ofN and P. The effect onA. tamarense o f N without adjusting the P concentration has been investigated by LEONG et al. (2004); however, the impact of P on the physiological status has been less studied. When A. tamarense is exposed to a variable N:P supply ratio, physiological changes including growth characteristics, cellular chemical composition and toxicity could be expected to occur within the cells. Those changes seem to be dependent on the cell volume as long as the cells are growing logarithmically (MONTAGNES et al. 1994). The aim o f the present study was to determine the effect of N:P supply ratio on the toxicity of A. tamarense based on cell volume in relation to growth rate, and cellular carbon, nitrogen and phosphorus under most favorable condition.
Aurora B-mediated exclusion of HP1a from latesegregating chromatin prevents formation of micronuclei

Late-segregating acentric chromosomes pose a serious risk to genomic integrity when they are excluded from dividing daughter nuclei and form damage-prone micronuclei. Insight into the cellular mechanisms that prevent the formation of micronuclei from acentrics come from studies demonstrating that acentrics reincorporate into daughter telophase nuclei by passing through Aurora B kinase-dependent channels in the nuclear envelope of Drosophila neuroblasts. Here, we uncover a mechanism of nuclear envelope channel formation in which localized concentrations of Aurora B preferentially phosphorylate H3(S10) on heterochromatic acentrics and their associated DNA tethers. This phosphorylation event prevents HP1a from associating with heterochromatin and results in localized inhibition of nuclear envelope reassembly on endonuclease- and X-irradiation-induced acentrics and the main daughter nuclei at the sites of acentric entry to promote the formation of channels. Finally, we find that HP1a also specifies initiation sites of nuclear envelope reassembly on undamaged chromatin. Taken together, these results demonstrate that Aurora B-mediated regulation of HP1a-chromatin interactions plays a key role maintaining genome integrity by locally preventing nuclear envelope assembly and facilitating incorporation of late-segregating acentrics into daughter nuclei.
Responses of broiler chickens under hot humid tropical climate as affected by Azadirachta indica leaf

Environmental temperature is the most critical variable influencing the performance of broiler chickens in the hot humid tropical climate. Neem (Azadirachta indica) has been reported to possess several benefits including antioxidants which may be able to alleviate the effects of heat stress on broiler chickens during hot dry season. A study was carried out to evaluate the effect of Azadirachta indica leaf powder (NLP) on the growth, haematology and serum biochemistry parameters of broiler chicks. Two hundred and forty day-old broiler chicks were randomly assigned to four treatments which contained 0, 5, 10 and 15g/Kg diets in a Completely Randomized Design experiment. Each treatment was replicated four times with fifteen birds in each replicate. Feed and water were provided ad libitum. The results showed that the levels of creatine kinase of the birds fed 0 and 5g NLP were similar but higher than those of the birds 10 and 15g NLP. The final body weights of the broiler chickens fed 10 and 15% NLP were similar but significantly higher than those of the birds fed 0 and 10g NLP. The weights gains and feed conversion ratios of the birds followed a similar trend to that of the final body weights. The feed conversion ratios of the birds fed 10 and 15g NLP were similar but significantly lower (P < 0.05) than those fed 0 and 5g NLP. It was concluded that broiler chickens exposed to heat stress in the hot–humid climate responded favorably to inclusion of neem leaf in their diets up to 10g/Kg diet. Keywords : Chicken, physiology, performance, antioxidant, hot-dry season.
Notch Signaling in Tumor Angiogenesis

Notch Signaling in Tumor Angiogenesis Thaned Kangsamaksin Notch signaling plays an important role in developmental and pathological angiogenesis. Notch ligands, Dll4 and Jag1, have been implicated in tumor angiogenesis. Inhibition of Dll4-mediated Notch signaling results in hypersprouting of non-functional vasculature in tumors. We have constructed and analyzed pan-Notch ligand inhibitors, Notch1 decoys 1-24 and 1-36, which are based on the extracellular EGF-like repeats of Notch1. Both Notch1 decoys block angiogenesis in in vitro endothelial cell-based assays and in the mouse retina. We also show that they similarly inhibit Dll4and Jag1-induced Notch signaling in vitro and result in a significant decrease in tumor growth and tumor vasculature in mouse and human tumor xenograft models. Interestingly, truncated Notch1 decoy variants, Notch1 decoys 1-13 and 10-24, act as ligand-specific Notch inhibitors. Notch1 decoy 1-13 is Dll4-specific whereas Notch1 decoy 10-24 is Jag1-specific. Ligand-specific Notch1 decoys effectively reduce tumor growth in tumor xenograft models in the mouse, including Mm5MT-FGF4, KP1-VEGF, LLC, and B16-F10. Notch1 decoy 1-13 has been demonstrated to increase tumor vasculature by increasing endothelial sprouting and number of tip cells. However, similar to the previously reported effects of Dll4 blockade, the tumor vessels are poorly perfused and hardly functional. On the other hand, Jag1-specific Notch1 decoy 10-24 significantly reduces tumor vessel density and disrupting endothelialpericyte interactions, causing the impaired vascular structure and attenuated vascular perfusion. In addition, Notch1 decoys 1-13, 10-24, and 1-24 show an anti-metastatic potential in causing a delay of lung metastasis in the B16-F10 tumor model. Unlike ! -secretase inhibitors and Dll4-blocking agents, Notch1 decoys do not cause GI-associated toxicity or vascular neoplasms. Therefore, our Notch1 decoys may represent a novel alternative and may hold future promise for Notch-targeted cancer therapy.
FOLIC ACID, VITAMIN B12, AND DNA METHYLATION: AN UPDATE.

Epigenetics is one of the exciting and fastest expanding fields of biology; this is above genetics. Methylation is the process involved in the transfer of methyl group to amino acids, proteins, enzymes and DNA of all the cells, and tissues of the body. During cell-division low folate availability may result in decreased production of thymidine wherein uracil may be substituted in the place of thymidine in the DNA sequence. It was reported that folate and Vitamin B12 restricted diet resulted in aberrant methylation patterns. The current review was undertaken to explore the role of folic acid and Vitamin B12 in DNA methylation.
Awakening the sleeping giant: methods for reactivating the inactive X chromosome as clinical treatment for X-linked disorders

© The Author(s) 2018. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing, adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Awakening the sleeping giant: methods for reactivating the inactive X chromosome as clinical treatment for X-linked disorders
Glikoz İzomeraz Üreticisi Dört Geobacillus Suşunun İzolasyonu ve Moleküler Metotlar Kullanarak Tanımlanması

Turkiye'nin batisindaki iki kaplica, termofilik mikroorganizmalarin mevcudiyetine gore arastirildi ve iki termal kaplicadan,23 termofilik bakteri izole edildi. Izolatlardan, 4 tanesinin glikoz izomeraz uretimi acisindan pozitif oldugu belirlendi. BT5, CT6SARI ve CT1.2 izolatlarinin glikoz izomerazlari, pH 6.5'te optimum buyume gosterdi; buna karsilik izolat BT1 enzimi, pH 7.5'te optimal aktivite gosterdi. Bu enzimler arasinda BT1 izolatinin optimal buyume sicakligi 75 °C olarak belirlenirken, diger uc izolatin enzimleri ise 80 °C'de optimal buyume gosterdi. 16S rRNA gen dizi analizleri ile 4 izolatin, Geobacillus cinsine ait turler olduklari belirlendi. recN dizisi benzerlik analizine dayanarak, izolat CT6SARI ’nin, G. termodenitficans ’a; izolat BT1 ’in de, G. stearothermophilus ’a ait suslar olduklari belirlendi. BT5 ve CT1.2 izolatlarinin kesin tur tayinleri yapilamadi.
Elucidating the metabolic activities of SUP05, an abundant group of marine sulfur oxidizing gamma-proteobacteria

Elucidating the metabolic activities of SUP05, an abundant group of marine sulfur oxidizing gamma-proteobacteria Katharine Marshall Lalish Chair of the Supervisory Committee: Professor Robert M. Morris School of Oceanography Chemoautotrophic bacteria that oxidize sulfur and reduce nitrogen in low oxygen zones carry out chemical transformations of molecules containing the key elements: carbon, nitrogen and sulfur. Members of the SUP05 clade of marine gamma-proteobacterial sulfur oxidizers (GSOs) are abundant and cosmopolitan in the oceans, consisting of metabolically diverse bacteria that have been found throughout the water column in oxic and anoxic marine environments and as symbionts in the gill tissues of deep sea clams and mussels. Environmental studies suggest that the SUP05 clade is comprised of diverse members with autotrophic, heterotrophic or mixotrophic capabilities. Although there are indications that these physiologies correspond to differing ecological niches, the lack of cultivated representatives has limited studies to elucidate patterns of metabolic diversity within the clade. In chapter one, I obtain the first isolate from the SUP05 clade (Thioglobus singularis GSO-PS1) and show that energy from sulfur oxidation enhances heterotrophic biosynthesis in controlled growth experiments. In chapter two, I demonstrate that despite having a streamlined genome, T. singularis GSO-PS1 has the genetic potential for carbon mixotrophy and confirm that autotrophic and heterotrophic functions are expressed in the environment. In chapter three, I use the complete genome sequences of two SUP05 isolates, T. singularis GSO-PS1 and T. autotrophica SUP05-EF1 (Shah et al., in prep) to identify co-occurring subclades in diverse OMZs. Results from these analyses indicate that members of the T. singularis subclade are aerobic mixotrophs with the metabolic potential to produce energy and to biosynthesize using organic and inorganic substrates, and that members of the T. autotrophica subclade are chemoautotrophic facultative anaerobes with the metabolic potential for denitrification. This suggests that T. singularis and T. autotrophica represent SUP05 subclades with distinct ecological niches and with different roles in carbon, nitrogen, and sulfur cycling.