Miracle-dz/UniFAR-FTUs huggingface dataset:
A molecular cytogenetic investigation of secondary abnormalities and clonal evolution in ETV6-RUNX1 positive acute lymphoblastic leukaemia

©2013 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2013. 085175 The online version of this article has a Supplementary Appendix. Manuscript received on January 25, 2013. Manuscript accepted on March 8, 2013. Correspondence: christine.harrison@newcastle.ac. uk Introduction The cytogenetics of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is well documented, with specific chromosomal abnormalities used in risk stratification of patients for treatment. Genomic studies have shown that copy number abnormalities (CNA) of genes involved in B-lymphocyte development and differentiation, cell cycle control and those of significance in hematopoiesis are common in BCPALL. Notable deletions include PAX5, IKZF1 (Ikaros), and genes within the pseudoautosomal region (PAR1) of the sex chromosomes, resulting in the P2RY8-CRLF2 gene fusion and overexpression of CRLF2. Here there is particular interest in IKZF1 and CRLF2 in relation to outcome and their role as molecular targets for therapy. IKZF1 deletions have been associated with a poor prognosis in BCP-ALL, while the risk relating to CRLF2 has been variable and dependent on other features. Nevertheless, thus far these diverse findings have not led to any treatment changes. Studies have focused on small or selected cohorts and analyses have often been carried out independently from other genetic changes. Thus their accurate incidence, relationship to each other, and the major cytogenetic subgroups still have to be determined in order to understand their true clinical relevance. Recently, we demonstrated that multiplex ligation-dependent probe amplification (MLPA) provided an accurate and reliable high throughput method to screen for CNA of the significant genes in BCP-ALL. In this study, we screened a cohort of 1427 childhood BCP-ALL patients from two consecutive treatment trials using the same MLPA approach. We report the frequency and type of CNA involving these genes, their associations with established chromosomal abnormalities, and other clinical features.
Genetic diversification of local onion populations under different production systems in Uruguay

In Uruguay, onion (Allium cepa L.) germplasm is mainly derived from the genetic material introduced by several waves of European immigrants and subsequently multiplied by household farmers, resulting in a wealth of locally adapted populations. This study examined the genetic diversity in a collection of 27 local onion populations and two cultivars derived from them. A total of 843 onion plants were fingerprinted, and 83 inter-simple sequence repeat polymorphic bands were generated. Analysis of molecular variance showed high diversity within the populations (66% of the total variation). Some short-day populations from different geographical origins were grouped together by the unweighted pair-group method using arithmetic averages, principal coordinate analysis and cluster analysis, while the more extensively sampled long- and intermediate-day populations showed a widespread distribution, with no significant subgrouping among them. This weakly structured gene pool is probably the consequence of seed and bulb exchange between farmers and natural inter-pollination. Nevertheless, a Bayesian analysis allowed the distinction of four genetic backgrounds of alleles in the whole collection, and populations were predominately assigned to each genetic background. In addition, mitochondrial variants determining normal (N) pollen fertility or the sterile S or T types were analysed for the same set of plants using specific primers. Most accessions showed a proportion of male-sterile individuals. Cytoplasm type T was the most represented (26 out of 29 accessions), and cytoplasm type S was found in a low proportion of individuals in seven populations. Uruguayan onion germplasm maintains a low degree of genetic differentiation despite the small cultivated area and intense seed exchange, probably due in part to different market purposes based on the growing cycle.
Ination Targeting and Exchange Rate Pass-through

This paper analyzes how endogenous imperfect exchange rate pass-through a¤ects ination targeting optimal monetary policies in a New Keynesian small open economy. The paper shows that an inverse relation exists between the passthrough and the insulation of the economy from foreign and monetary policy shocks, and that imperfect pass-through tends to decrease the variability of the terms of trade. Furthermore, with CPI ination targeting, in the short run, delayed pass-through constrains monetary policy more than incomplete passthrough and interest rate smoothing ampli es this e¤ect. When the pass-through decreases, the variability in economic activity tends to raise and the trade-o¤ between the stabilization of CPI ination and output worsens in direct relation to how strictly the central bank is targeting CPI ination. In contrast, with domestic ination targeting, optimal monetary policy is not constrained and opposite results occur. Consequently, imperfect pass-through favors the choice of domestic to CPI ination targeting. JEL Classi cation: E52, E58, F41.
A STUDY ON ANTIMICROBIAL EFFECTS OF PLANTAGO PSYLLIUM

شور و داوم اه : لاس رد هك يبرجت هعلاطم نيا رد ۱۳۸۸ جوـساي يكشزپ مولع هاگشناد رد ،دش ماجنا عمج زا دعب روآ ي هت و ي ه هراصع ه ي لکلاورد ي گ ي ها نآ رـثا ،هزرفـسا ور رـب ي ۱۰ م ي ناگراورک ي مس يسررب فلتخم دش . مه نچ ي گدـننک راـهم تـظلغ لقادـح ن ي لقادـح و دـشر گدنشک تظلغ ي ا ي ور هراصع ن ي رتکاب ي هزادنا اه گ ي ر ي ا دشر مدع هلاه رطق سپس و دش ي ن تن آ اب هراصع ي ب ي تو ي ک اه ي اقم درادناتسا ي دش هس . هداد عمج ياه زا هدافتـسا اـب هدـش يروآ مرن رازفا SPSS مزآ و نو ياه دندش ليلحت و هيزجت ود ياك و سنايراو زيلانآ يرامآ .
Determining the cell surface receptors on macrophages that mediate biological activity of the POVPC-peptide, an oxidized phospholipid analogue

OF THE THESIS Determining the Cell Surface Receptors on Macrophages That Mediate Biological Activity of the POVPC-Peptide, an Oxidized Phospholipid Analogue by Erica Noemi Montano Master of Science in Biology with a Concentration in Molecular Biology San Diego State University, 2015 Atherosclerosis is a chronic inflammatory disease that is a leading cause of death and illness worldwide. Growing evidence suggests that oxidized low-density lipoprotein (OxLDL), particularly oxidized phospholipids (OxPL), plays a critical role in the pathogenesis of atherosclerosis. Mounting evidence has implicated toll-like receptors (TLRs) and scavenger receptor CD36 in playing a role in the progression of many inflammatory diseases, including atherosclerosis. POVPC (1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3phosphocholine) is an oxidized phospholipid found in OxLDL. It has pro-inflammatory effects on macrophages (MAC) that promote inflammatory diseases. However, the mechanism by which it does this is not well understood. OxPLs include a heterogeneous group of oxidation products and many of them are unstable. In order to study inflammatory effects on MAC, we developed a synthetic POVPC-peptide adduct at the sn-2 side chain, which is water soluble, stable, not prone to further oxidation and highly bioactive. We show that the POVPC-peptide mediates inflammatory gene expression of IL-1, TNF-, MIP-2, in MACs via TLRs 2/1 and co-receptor CD36. Understanding the mechanisms and role of POVPC in mediating MAC inflammation could provide insights into the role of OxPLs in inflammation and atherosclerosis, and could lead to novel therapies to inhibit these effects.
Experimental Hypothalamico-Hypophyseal Obesity in the Rat.∗

Smith 1 produced obesity in rats by injecting chromic acid into the hypophysis via a subtemporal approach. Because hypophysectomy did not bring about the same result, Smith reasoned that hypophyseal deficiency could not be responsible for the adiposity—and that hypothalamic damage incurred during the chromic acid operation must have been the cause. Ranson, Fisher, and Ingram 2 have reported the effect of hypothalamic lesions on fat deposition in a large number of cats and monkeys observed in our laboratory, and lately the guinea pig has been added to this list. In all 3 species the results have been negative. In an effort to discover the reason for this divergence of findings we have repeated, with modifications, Smith's chromic acid injections on rats. About 0.01 cc of 5% chromic acid was injected through a needle with a curved tip into the hypophyses of albino rats via a parapharyngeal approach. Using this method we hoped to minimize the danger of simultaneous hypothalamic damage. We have also placed lesions in the hypothalami of rats with the Horsley-Clarke instrument. Two electrolytic lesions were placed on each side in the lateral hypothalamic areas between the levels of the optic chiasma rostrally and the infundibulum caudally. All rats were operated at about the time of sexual maturity. They had litter mate controls, and were allowed to survive well over the maximum time elapsing before any obese rat showed definite signs of its disorder. They were weighed at weekly intervals. At autopsy the brains were fixed in formalin, and the hypophyses in either Zenker-formol or Champy fluid. Serial sections of the hypothalami and neighboring areas were cut and stained with cresyl violet; the hypophyses were stained by either the Haterius modification of the Masson stain, or by the Severinghaus technic.
A Biomechanical Perspective on Beeswax

American Entomologist • Volume 51, Number 1 We are interested in how structural materials used by bees relate to the evolution of complex social communication. In particular, we explored how fatty acids affect the mechanical function of beeswax (Fig. 1). This interest led us to compare the mechanical properties of the waxes of a wide variety of social bees. These fatty acids are major components in beeswax (Aichholz and Lorbeer 1999) and are also used by bees in social recognition (Breed 1998, Breed et al. 2004). Although the nature of beeswax has been explored in detail in the Western honey bee, Apis mellifera (Hepburn 1986), little is known of the waxes of other apid bees. Bees in the family Apidae exhibit different levels of sociality, ranging from solitary to primitively eusocial to highly eusocial. In addition to differences in social organization, apids also display differences in nest construction. The three most highly derived subfamilies in the family Apidae are the Bombinae (bumble bees), Meliponinae (stingless bees), and Apinae (honey bees). Aside from parasitic species, the bumblebees are primitively eusocial. The queens and workers are only slightly different morphologically, and reproductive dominance is maintained via aggressive behavior of the queen. The relatively small colonies dwell in annual nests (Michener 1974). These nests are constructed by the foundress, usually in an abandoned rodent’s nest, and consist of several ovular wax cells roughly stacked on one another. All stingless bees and honey bees are highly eusocial. The queens and workers are morphologically very different; and at least in Apis, reproductive dominance is maintained through pheromones. The relatively large perennial nests of these bees are most often found in cavities such as hollow trees. Stingless bees construct their nests with highly organized, horizontal combs where brood are raised; ovular storage pots are roughly stacked separately from the brood comb. In addition to endogenously produced wax, stingless bees incorporate large amounts of plant material in their nests. Conversely, honey bee nests comprise one or many vertically hanging combs. In honey bees, the combs are constructed almost exclusively from endogenously produced wax containing primarily esters, straight-chained hydrocarbons, and fatty acids (Tulloch 1980). These beeswax structures gain their mechanical properties from two distinct sources. For a structure to function properly, it must possess the right combination of material and geometry. The mechanical properties of the building materials have a great influence on the properties such as A Biomechanical Perspective on Beeswax
Agent-Based Modelling: A Methodology for Neo-Schumpeterian Economics

Modellers have had to wrestle with an unavoidable trade-off between the demand of a general theoretical approach and the descriptive accuracy required to model a particular phenomenon. A new class of simulation models has shown to be well adapted to this challenge, basically by shifting outwards this trade-off: So-called agent-based models (ABMs henceforth) are increasingly used for the modelling of socio-economic developments. Our paper deals with the new requirements for modelling entailed by the necessity to focus on qualitative developments, pattern formation, etc. which is generally highlighted within Neo-Schumpeterian Economics and the possibilities given by ABMs.
Transmissão congênita em cabras reinfectadas com Toxoplasma gondii

This study evaluated the potential of congenital transmission in goats experimentally infected and reinfected with Toxoplasma gondii , in three gestational stages (initial, intermediate and final). Of the 25 non-pregnant females negative for T. gondii , 20 were orally inoculated with 2.5 x 103 T. gondii ME49 oocysts. Of these, 15 pregnant females chronically infected were reinoculated, via oral, with 2.5 x 103 T. gondii VEG oocysts. Five experimental groups were formed (n=5): I, II and III (reinoculations in the initial, intermediate and final gestational stage, respectively), IV (inoculation) and V (no inoculation). Clinical and serological exams (IgG IFAT [indirect immunofluorescence antibody test]) in different days of evaluation, and bioassay and PCR were performed in all goats. In the infected goats with T. gondii a peak of 40.2°C (IV) at nine, seroconversion (IgG≥64) at 21 and stabilization (IgG<1024) at 119 days postinoculation were observed. In the reinfected goats with T. gondii occurred an increase in IgG titers (≥1,024) at 28 (I), 7 (II) and 3 (III) days post-reinoculation. During kidding were observed only in the reinfected groups: dystocia, malformation body, stillbirth and weakness, and IgG anti- Toxoplasma were detected in all and in some offsprings of the reinfected and infected goats, respectively. Tissue parasitism by T. gondii was diagnosed by bioassay and PCR in infected and reinfected goats and in their offspring. The congenital toxoplasmosis was possible in goats chronically infected and reinfected with T. gondii . The primary infection with T. gondii did not protect the pregnant goats against congenital disease resulting from toxoplasmic reinfection, in different gestational stages (initial, intermediate and final).
Nitrogen content and biomass: scaling from the tree to the forest level

Nitrogen is an essential nutrient for plant growth. Although much has been learned about its utilization and distribution within the plant body, little is known about the relationship between nitrogen content and standing biomass at the level of entire forests. Data for nitrogen content (N) and biomass (M) of 10 deciduous species in USA at the individual trees level and 37 species grown in three forest biomes (i.e. tropic, subtropics, and temperate) in China at stands level were gathered to determine the N versus M scaling relationships for different tissueand organ-types (e.g. bark and leaves). Model Type II regression protocols were used to calculate scaling exponents and allometric constants (i.e. slopes and y-intercepts of log-log bivariate plots, respectively) between N and M to. At the level of individual plants, N scaled nearly isometrically with M for the different tissueand organ-types (i.e. N α M 0.97–1.04). At the stand-level, N scaled similarly with respect to leaf, branch, and bark M, despite differences in stand size-frequency distributions and species composition. However, total stand N scaled allometrically with respect to total stem or root M and thus to total stand mass (i.e. N α MT 0.77–0.87). This was attributed to the accumulation of wood (and other ‘necromass’ tissue components that have lower N content than physiologically active tissues) in progressively older (and thus more massive) tree stands. When coupled to the scaling of N with respect to annual plant growth rates, these exponents provide important boundary conditions with which to model forest nutrient cycling.
In vitro propagation and flavonoid contents in local justicia gendarussa Burm. F

Justicia gendarussa or locally known as Gandarussa have been reported to contain naringenin and kaempferol that possess biological activities such as strong antioxidant and cytotoxicity. This paper present plant regeneration studies of J. gendarussa using different type of explants (young leaf and nodal segment) and media (B5 or MS basal media) supplemented with different concentration of plant growth regulators. The results indicated a maximum of callus fresh weight gains was obtained (1.21 g  0.11) when young leaf explants were cultured on MS medium supplemented with Kn (3.0 mgL -1) + 2,4-D (1.0 mgL -1). For shoot induction, high percentage of shoot regeneration (100 %) and number of shoots produced per explants (5.33  0.33) was recorded when nodal explants were cultured on MSB5 plates supplemented with 2.0 mgL -1 BAP. Then, the shooted explants were rooted in medium-free hormone. Determination of flavonoids (naringenin and kaempferol) content in methanolic organ extracts of in vitro plantlets was analyzed using Gas Chromatography-Flame Ionization Detector [GC-FID]. Green calli (701.27 mgkg -1 ± 7.69) contained significant higher naringenin content than in vitro leaves (419.99 mgkg -1 ± 133.39). However, there was no significant difference in kaempferol content between green calli (214.19 mgkg -1 ± 8.28) and in vitro leaves (242.03 mgkg -1 ± 41.13). In conclusion, accumulation of flavonoids in vitro plants offers potential of manipulating culture parameters such as medium composition and hormone concentration for enhancement of flavonoids content in plant tissues.
Effects of Different Doses of Pentoxifylline on CA1 Pyramidal Cells of Hippocampus following Brain Ischemia in Rats

دوش یم ،پماكوپيه CA1 ةيحان هب هژيو هب ،ديدش یاه بيسآ ندمآ دراو ثعاب یزغم یمكسيا :فده ريظن یقورع یاه هدننكدا��شگ رثا یور یدا��يز تاعلاطم ،ی��بصع تفاب تظفاحم ر��ظن زا هزور��ما نآ بسانم رادقم و وراد نيا یكيرحت رثا یبرجت یاه لدم رد زونه یلو ،ت��سا هدش نيليف ی��سكوتنپ یسررب ارذگ ريگارف نژويفرپير/یمك��سيا یپرد پماكوپيه CA1 ةيحان یمره یاه نورون ظفح رب یشيامزآ یاه هورگ رد )رات��سيو( گرزب ديف��س شوم ددع 30 ،قيقحت نيا رد :شور .ت��سا هد��شن نيليف یسكوتنپ mg/kg 600و 400و 200 بيترت هب ،یمكسيا زا دعب تعاس كي و لبق تعاس كي،3و2و1 لماح و م��ش ،دها��ش هورگ زا دندوب ترابع اه هورگ ريا��س .دندرك تفايرد یقافص لخاد تروص هب اب عطاقم نيا سپس و دش هيهت یتفاب عطاقم اه شوم زغم زا ،یمكسيا زا دعب زور راهچ .)نيلاس لامرن( پماكوپيه CA1 یمره یاه لولس دادعت هك دنداد ناشن جياتن :اه هتفاي .دندش یزيمآ گنر لسين شور دهاش هورگ اب یرادانعم توافت )نيليف یسكوتنپ mg/kg 200 ةدننك تفايرد ( لوا ی��شيامزآ هورگ رد mg/ 600و 400 ريداقم هك یياه هورگ ملا��س یمره یاه لول��س دادعت هك یلاح رد ،)P>0.05( درادن . دوب هدرك دها��ش هورگ اب یرادانعم توافت و هتفاي ش��هاك دندوب هدرك تفايرد نيليف ی��سكوتنپ kg زا یتظافح رثا داجيا اب دناوتب نيليف ی��سكوتنپ mg/kg 200زا هدافتسا د��سر یم رظن هب :یريگ هجيتن ديفس شوم یزغم یارذگريگارف نژويفرپير /یمكسيا لابند هب ،پماكوپيه CA1 ةيحان تاعياض تدش . دهاكب گرزب پماكوپيه ،نيليف یسكوتنپ ،نژويفرپير ،یمكسيا :اه هژاوديلک
Estudo molecular de teschovírus suíno, sapelovírus suíno e enterovírus G em javalis (Sus scrofa scrofa) de cativeiro no Paraná

Teschovirus suino (PTV), sapelovirus suino (PSV) e enterovirus G(EV-G) sao agentes infecciosos especificos da especie suina que estao endemicamente disseminados em todo o mundo. O objetivo deste estudo foi investigar a infeccao natural por estes picornavirus entericos suinos em javalis (Sus scrofa scrofa) do estado do Parana, Brasil e avaliar pecaris (Pecari tajacu e Tayassu pecari) como hospedeiros alternativos para estes virus. Amostras fecais (n=36) de javalis assintomaticos (n=22) com idades de 2 a 7 meses (jovens, n=14) e 2 a 4 anos (adultos, n=8) e de pecaris (6 a 8 meses de idade, n=14) foram coletadas em um cativeiro e zoologico, respectivamente, ambos localizados no estado do Parana. A transcricao reversa seguida por reacoes da polimerase em cadeia (RT-PCR) e nested-PCR com alvo na regiao 5'-nao traduzida do genoma viral foram utilizadas para a identificacao dos virus. Picornavirus entericos suinos foram detectados em 12 das 22 amostras fecais de javalis. De acordo com cada um dos virus, EV-G foi mais frequentemente (11/22, 50%) detectado, seguido pelo PTV (10/22; 45,5%) e PSV (4/22; 18,2%). Considerando os grupos de idade, javalis jovens foram mais frequentemente (9/14; 64,3%) infectados com PTV, PSV e EV-G do que os javalis adultos (3/8; 37,4%). Um produto amplificado na nested-PCR para cada um dos virus foi submetido a analise de sequenciamento e as sequencias de nucleotideos foram comparadas com virus relacionados, o que mostrou que as similaridades variaram entre 97,7% a 100% para o PTV, 92,4% a 96,2% para o PSV e 87,1% a 100% para o EV-G. Os pecaris foram negativos para as viroses investigadas e neste estudo nao se apresentaram como hospedeiros alternativos para as infeccoes. Este estudo e o primeiro a relatar a deteccao molecular de PTV, PSV e EV-G em javalis de cativeiro de um pais da America Latina e o primeiro a avaliar pecaris como especie hospedeira alternativa para picornavirus entericos suinos.
Synthesis and In Vitro Evaluation of New Thiosemicarbazone Derivatives as Potential Antimicrobial Agents

In an effort to develop potent antimicrobial agents, new thiosemicarbazone derivatives were synthesized via the reaction of 4-[4-(trifluoromethyl)phenyl]thiosemicarbazide with aromatic aldehydes. The compounds were evaluated for their inhibitory effects on pathogenic bacteria and yeasts using the CLSI broth microdilution method. Microplate Alamar Blue Assay was also carried out to determine the antimycobacterial activities of the compounds against Mycobacterium tuberculosis H37Rv. Among these derivatives, compounds 5 and 11 were more effective against Enterococcus faecalis (ATCC 29212) than chloramphenicol, whereas compounds 1, 2, and 12 and chloramphenicol showed the same level of antibacterial activity against E. faecalis. Moreover, compound 2 and chloramphenicol exhibited the same level of antibacterial activity against Staphylococcus aureus. On the other hand, the most potent anticandidal derivatives were found as compounds 2 and 5. These derivatives and ketoconazole exhibited the same level of antifungal activity against Candida glabrata. According to the Microplate Alamar Blue Assay, the tested compounds showed weak to moderate antitubercular activity.
Heterologous expression and enzymatic characterisation of exopolygalacturonase PGX1

Fusarium oxysporum f. sp radicis lycopersi (FORL) is a tomato pathogen which produces several cell wall degrading enzymes during the process of colonisation. Among these enzymes, polygalacturonases (PGs) are important because of their role in deconstruction the plant cell wall during host plant infection. Production of PGs in heterologous systems is an alternative approach to characterize individual enzymes, a difficult task, since complex patterns of PG isoforms, arising from different genes and patterns of postraductional modifications are generally present in in vitro cultures. In this work, we have successfully performed the heterologous expression of one exopolygalacturonase of FORL for the first time in the methylotrophic yeast Pichia pastoris. The enzyme produced showed an exo mode of action as predicted, and optimal pH and temperature values of 5 and 55 oC, respectively. Heterologous PGX1 showed higher affinity for trigalacturonic acid than for digalacturonic or polygalacturonic acid. The enzymatic features analyzed are discussed in relation to the other exopolygalacturonase (PGX2) described in F. oxysporum f.sp. radicis lycopersici.