Miracle-dz/UniFAR-FTUs huggingface dataset:
Regression from pathological hypertrophy is sexually dimorphic and stimulus-specific

Aims Pathological cardiac hypertrophy is the result of increased cardiomyocyte size, leading to thickening of the left ventricular walls and a decrease in the left ventricular chamber. With early treatment of the underlying cause, cardiac hypertrophy can be reversed in some individuals, while it persists in others. Here, we investigate mechanisms leading to regression of pathological cardiac hypertrophy in two mouse models, in addition to defining the sex differences associated with hypertrophy and regression. Methods and Results Two pathological hypertrophic stimuli were used in male and female mice (Isoproterenol or Angiotensin II). The stimulus was removed after 7 days of treatment, then the left ventricle was studied at intervals up to 7 days following the removal of the stimulus. Following Isoproterenol removal, male hearts returned to baseline sizes in 4 days while it took 7 days for female hearts to regress. After Angiotensin II removal, the left ventricular masses of males and females did not regress. ERK1/2 was activated in response to both Isoproterenol and Angiotensin II in males, then decreased back to baseline one day after stimulus removal. Expression of ECM genes was greater in response to Angiotensin II and remained elevated longer after Angiotensin II removal, compared to Isoproterenol. Further, collagen content may be playing a role in the irreversible state of Angiotensin II induced hypertrophy as hydroxyproline content was increased following the removal of Angiotensin II in both males and females. Conclusions Regression of pathological cardiac hypertrophy is possible in some people and in some mouse models; however, the ability for the heart to regress is dependent on the stimulus and biological sex. Further, molecular changes including cellular signaling, protein degradation pathways and the formation of a fibrotic network may contribute to the ability to reverse pathological cardiac hypertrophy and are stimulus- and sex-dependent. Translational Perspective Pathological cardiac hypertrophy is a major risk factor for mortality. If cardiac hypertrophy persists for an extended time, there can be many maladaptive changes to the myocardium. With early treatment of the underlying cause, cardiac hypertrophy can be reversed in some individuals, but not in others. While cardiac hypertrophy has been studied extensively, very little is understood about regression of cardiac hypertrophy. It is important that we have a better understanding of mechanisms leading to regression and why this process might not be reversible in some individuals.
Normalizations and selection of speech segments for speaker recognition scoring

Normalization and selection techniques are described which improve speaker recognition accuracy using very short uncontrolled speech samples. The first normalization depends on the means and variances of scores for a short, unknown sample matched to different models for many speakers. The selection procedure discards portions of a speech sample with poor speaker-discrimination ability. A second normalization is based on the range of matching scores of the supposed speaker's model against other speaker's models. It facilitates setting acceptance thresholds for speaker verification against an open population. <<ETX>>
Designing gene drives to limit spillover to non-target populations

The prospect of utilizing CRISPR-based gene-drive technology for controlling populations, such as invasive and disease-vector species, has generated much excitement. However, the potential for spillovers of gene drive alleles from the target population to non-target populations — events that may be ecologically catastrophic — has raised concerns. Here, using two-population mathematical models, we investigate the possibility of limiting spillovers and impact on non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene drive parameters. Most of these configurations ensure differential targeting only under relatively low migration rates between target and non-target populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. When migration is increased, differential-targeting states can sharply transition to states of global fixation or global loss of the gene drive. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. Our results emphasize that, although gene drive technology is promising, understanding the potential consequences for populations other than the targets requires detailed analysis of gene-drive spillovers, and that ways to limit the unintended effects of gene drives to non-target populations should be explored prior to the application of gene drives in natural settings.
The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

Background Pathway-centric approaches are widely used to interpret and contextualize -omics data. However, databases contain different representations of the same biological pathway, which may lead to different results of statistical enrichment analysis and predictive models in the context of precision medicine. Results We have performed an in-depth benchmarking of the impact of pathway database choice on statistical enrichment analysis and predictive modeling. We analyzed five cancer datasets using three major pathway databases and developed an approach to merge several databases into a single integrative database: MPath. Our results show that equivalent pathways from different databases yield disparate results in statistical enrichment analysis. Moreover, we observed a significant dataset-dependent impact on performance of machine learning models on different prediction tasks. Further, MPath significantly improved prediction performance and reduced the variance of prediction performances in some cases. At the same time, MPath yielded more consistent and biologically plausible results in the statistical enrichment analyses. Finally, we implemented a software package designed to make our comparative analysis with these and additional databases fully reproducible and to facilitate the update of our integrative pathway resource in the future. Conclusion This benchmarking study demonstrates that pathway database choice can influence the results of statistical enrichment analysis and prediction modeling. Therefore, we recommend the use of multiple pathway databases or the use of integrative databases.
Pathogen Evasion of Chemokine Response Through Suppression of CXCL10

Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on an immune response with well-regulated cytokine signaling. Here we describe a pathogen-mediated mechanism of evading CXCL10, a chemokine with diverse antimicrobial functions, including T cell recruitment. Infection with L. major in a human monocyte cell line induced robust CXCL10 transcription without increasing extracellular CXCL10 protein concentrations. We found that this transcriptionally independent suppression of CXCL10 is mediated by the virulence factor and protease, glycoprotein-63 (gp63). Specifically, GP63 cleaves CXCL10 after amino acid A81 at the base of a C-terminal alpha-helix. Cytokine cleavage by GP63 demonstrated specificity, as GP63 cleaved CXCL10 and its homologues, which all bind the CXCR3 receptor, but not distantly related chemokines, such as CXCL8 and CCL22. Further characterization demonstrated that CXCL10 cleavage activity by GP63 was produced by both extracellular promastigotes and intracellular amastigotes. Crucially, CXCL10 cleavage impaired T cell chemotaxis in vitro, indicating that cleaved CXCL10 cannot signal through CXCR3. Ultimately, we propose CXCL10 suppression is a convergent mechanism of immune evasion, as Salmonella enterica and Chlamydia trachomatis also suppress CXCL10. This commonality suggests that counteracting CXCL10 suppression may provide a generalizable therapeutic strategy against intracellular pathogens. Importance Leishmaniasis, an infectious disease that annually affects over one million people, is caused by intracellular parasites that have evolved to evade the host’s attempts to eliminate the parasite. Cutaneous leishmaniasis results in disfiguring skin lesions if the host immune system does not appropriately respond to infection. A family of molecules called chemokines coordinate recruitment of the immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that Leishmania (L.) major employs to suppress host chemokines: an L. major protease cleaves chemokines known to recruit T cells that fight off infection. We observe that other common human intracellular pathogens, including Chlamydia trachomatis and Salmonella enterica, reduce levels of the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival.
Determination of the Species of Tephritidae family (Diptera) on Cherry Orchards in Adana Province and Surroundings in Turkey

Bu calisma, Kiraz yetistiriciligi yapilan Adana ili ve cevresinde Tephritidae (Diptera) familyasina bagli turlerin belirlenmesi amaciyla yurutulmustur. Ornekler 2015 – 2018 yillari boyunca kiraz bahcesinde bulunan tum konukcu bitkilerden periyodik ve periyodik olmayan arazi cikislari ile toplanmistir. Calismada, Tephritidae familyasina ait dokuz tur tespit edilmistir. Bu turler; Rhagoletis cerasi (Linnaeus, 1758), Ceratitis capitata (Wiedemann, 1824), Rhagoletis batava (Hering, 1958), Carpomya schineri (Loew, 1856), Tephritis nigricauda (Loew, 1856), Tephritis fallax (Loew, 1844) , Tephritis dioscurea (Loew, 1856), Tephritis hurvitzi (Freidberg, 1981) ve Tephritis divisa (Rondani, 1871)’ dir.
Cymbidium mosaic virus y Odontoglossum ringspot virus en diversos generos de orquideas cultivadas en Mexico

En el Orquideario de Miguel Ángel Soto Arenas, de la Facultad de Ciencias UNAM, se han detectado plantas con síntomas consistentes en clorosis, variegado, necrosis y mosaico. Varias de estas plantas son especies endémicas de México y a la fecha no existe información sobre su manejo fitosanitario. Por lo tanto, el objetivo del presente estudio fue conocer a los virus asociados a estos síntomas mediante pruebas de ELISA, RT-PCR, plantas diferenciales y análisis filogenéticos. Se detectó al <em>Odontoglossum ringspot virus</em> (ORSV) y al <em>Cymbidium mosaic virus</em> (CymMV) en el 89% de las plantas con síntomas muestreadas. Las plantas diferenciales <em>Nicotiana tabacum</em> var. xhanti <em>N. glutinosa</em>, <em>Chenopodium quinoa</em>, <em>C. amaranthicolor</em> y<em> Datura stramonium</em> inoculadas mecánicamente con tejido foliar positivo a ambos virus mostraron lesiones locales seis días después de la inoculación y sólo CymMV infectó sistémicamente a <em>N. benthamiana</em>. El análisis filogenético mostró que estos virus se agruparon con aislamientos de países asiáticos lo que sugiere que la infección se originó probablemente por el intercambio de material vegetal entre productores. Este es el primer reporte del CymMV y ORSV infectando a <em>Barkeria</em>, <em>Lycaste</em>, <em>Rossioglossum</em>, <em>Masdevallia</em>, <em>Leochilus</em>, <em>Stanhopea</em>, <em>Maxillaria</em>, <em>Epidendrum</em> sec. <em>Oerstedella</em>, <em>Dendrobium</em>, <em>Sobralia</em> y <em>Cuitlauzina</em> en México.
Gene action and combining ability studies for protein content and grain quality traits in rice (Oryza sativa L.)

Combining ability analysis was carried out with ten parents and twenty four F1’ s in Line × Tester mating design for the grain quality and nutritional traits viz., protein content, iron content and zinc content. The results showed that the dominance genetic variance is higher than that of additive genetic variance which indicated the predominance of non additive gene action for protein content, iron content, zinc content, hulling percentage, milling percentage, head rice recovery, kernel length, kernel breadth, kernel L/B ratio, linear elongation ratio, amylose content, gel consistency and gelatinization temperature whereas additive gene action was observed for kernel length after cooking. Among the lines, NLR 34449 was the best parent as it exhibited significant per se and gca effects for iron content, zinc content and important quality traits. In testers, CR Dhan 310 was found to be the best general combiner for protein content and Kodai for iron and zinc content which recorded highly significant positive gca effects. The hybrid ASD 16/ Kodai showed significant and desirable per se performance and sca effects for the nutritional traits viz., protein content, iron and zinc content. The hybrid RNR 15048/CB 14740 was adjudged as the best for the characters viz., kernel length, kernel L/B ratio, kernel length after cooking. These hybrids could be recommended for heterosis breeding to improve the nutritional and grain quality traits.
The influence of user experience and presentation medium on strategies of viewing algorithms

Two empirical studies of the interaction between presentation medium and users' experience are reported. Subjects were presented with sets of algorithms that either showed their textual definition or demonstrated their behavior using graphics as an alternative presentation medium. Results of the first experiment showed an interaction between experience, presentation medium, and the algorithm itself. In particular, the presentation order plays a significant role. Textural presentations prior to graphical ones seem to provide the necessary framework for later assimilation of detailed information. A wide range of scan patterns was found. The findings suggest that textual and graphical presentation media differ in the way they facilitate understanding of algorithms. Furthermore, the great variety of viewing styles could be categorized according to the user's programming experience. <<ETX>>
Assessment of grain quality in terms of functional group response to elevated [CO2], water, and nitrogen using a meta‐analysis: Grain protein, zinc, and iron under future climate

Abstract The increasing [CO2] in the atmosphere increases crop productivity. However, grain quality of cereals and pulses are substantially decreased and consequently compromise human health. Meta‐analysis techniques were employed to investigate the effect of elevated [CO2] (e[CO2]) on protein, zinc (Zn), and iron (Fe) concentrations of major food crops (542 experimental observations from 135 studies) including wheat, rice, soybean, field peas, and corn considering different levels of water and nitrogen (N). Each crop, except soybean, had decreased protein, Zn, and Fe concentrations when grown at e[CO2] concentration (≥550 μmol/mol) compared to ambient [CO2] (a[CO2]) concentration (≤380 μmol/mol). Grain protein, Zn, and Fe concentrations were reduced under e[CO2]; however, the responses of protein, Zn, and Fe concentrations to e[CO2] were modified by water stress and N. There was an increase in Fe concentration in soybean under medium N and wet conditions but nonsignificant. The reductions in protein concentrations for wheat and rice were ~5%–10%, and the reductions in Zn and Fe concentrations were ~3%–12%. For soybean, there was a small and nonsignificant increase of 0.37% in its protein concentration under medium N and dry water, while Zn and Fe concentrations were reduced by ~2%–5%. The protein concentration of field peas decreased by 1.7%, and the reductions in Zn and Fe concentrations were ~4%–10%. The reductions in protein, Zn, and Fe concentrations of corn were ~5%–10%. Bias in the dataset was assessed using a regression test and rank correlation. The analysis indicated that there are medium levels of bias within published meta‐analysis studies of crops responses to free‐air [CO2] enrichment (FACE). However, the integration of the influence of reporting bias did not affect the significance or the direction of the [CO2] effects.
The Effects of Cultural Medium and Cultivars on Some Qualitative Characteristic of Cucumber Transplant (Cucumis Sativus)

Cucumber produced by transplanting cause to seed saving, reduce the risk of cold, pest and disease control. In order to investigate the effects of cultural medium and cultivars on characteristic of cucumber transplants, an experiment was conducted based on a randomized complete design with 5 replications at the Applied Science in Agricultural Education Center Shahrood (Iran) during 2011. Treatments included 6 levels of cultural medium (a1= 50% peat + 25% coco peat + 25% sand, a2= 50% peat + 25% coco peat + 25% + 25% vermicompost, a3= 50% peat + 25% coco peat + 25% perlit, a4= 50% coco peat + 25% peat+25% sand, a5= 50% coco peat + 25% peat + 25% vermicompost, a6= 50% coco peat + 25% peat + 25% perlit) and 2 types of cultivars (Vilmorin and Royal, 24189). The results indicated that the effects of substrate were significant in all of treats (leaf area, stem diameter, height of transplant, root dry weight, shoot dry weight, root wet weight, and shoot wet weight). A2 and A5 have better performance than others in all of treats. There is not any significant effect between cultivars and an interaction between substrate and cultivar wasn't significant.
Disentangling sources of selection on exonic transcriptional enhancers

In addition to coding for proteins, exons can also impact transcription by encoding regulatory elements such as enhancers. It has been debated whether such features confer heightened selective constraint, or evolve neutrally. We have addressed this question by developing a new approach to disentangle the sources of selection acting on exonic enhancers, in which we model the evolutionary rates of every possible substitution as a function of their effects on both protein sequence and enhancer activity. In three exonic enhancers, we found no significant association between evolutionary rates and effects on enhancer activity. This suggests that despite having biochemical activity, these exonic enhancers have no detectable selective constraint, and thus are unlikely to play a major role in protein evolution.
Influence of a Foliar Endophyte and Budburst Phenology on Survival of Wild and Laboratory-Reared Eastern Spruce Budworm, Choristoneura fumiferana on White Spruce (Picea glauca)

A manipulative field study was carried out to determine whether the foliar endophyte fungus, Phialocephala scopiformis DAOM 229536, decreased the performance of eastern spruce budworm, Choristoneura fumiferana larvae developing on white spruce trees. Overwintered second-instar budworm larvae from a laboratory colony or from a wild population were placed on endophyte positive or negative trees one or two weeks before budburst. The presence of the endophyte in the needles reduced the survival of C. fumiferana from both a wild population and a laboratory colony. Survival for budworm juveniles up to pupation and to adult emergence was 13% and 17% lower, respectively, on endophyte positive trees. The endophyte did not influence the size or sex of survivors and budworm survival was not influenced by any two- or three-way interactions. Budworm survival was higher for wild than for laboratory-reared budworm and for budworm placed on trees a week before budburst. This may be the first field study to demonstrate the efficacy of an endophytic fungus against wild individuals of a major forest insect pest. The efficacy of the endophyte at low larval densities suggests that it could be a useful tactic to limit spruce budworm population growth in the context of an early intervention strategy.
Teak (Tectona grandis) silviculture and research: applications for smallholders in Lao PDR

ABSTRACT Teak is an important forest plantation species in Lao PDR (Laos), that has been planted extensively by smallholders, supplying domestic industries and international markets. There have been significant advances in the intensive silvicultural management of teak focused on the production of high-quality timber. Laos is not an exception. With support from the Australian Centre for International Agricultural Research, there have been advances in the understanding and knowledge of appropriate management practices for smallholder teak, as well as development of supporting technologies (i.e. ex situ conservation, genetic improvement, growth models, thinning and pruning prescriptions, and agroforestry systems). This paper summarises published information on the silviculture and management of teak, including improvement of genetic resources, stocking rate, thinning and agroforestry systems used in Asia, Africa, Latin America and Oceania, and relates this to the current situation in northern Laos. The challenge is to now transfer this knowledge to the teak smallholders, professionals, educators and policy decision makers of Laos.
Feature Design for Protein Interface hotspots using KFC2 and Rosetta

Protein-protein interactions regulate many essential biological processes and play an important role in health and disease. The process of experimentally charac-terizing protein residues that contribute the most to protein-protein interaction affin-ity and specificity is laborious. Thus, developing models that accurately characterize hotspots at protein-protein interfaces provides important information about how to inhibit therapeutically relevant protein-protein interactions. During the course of the ICERM WiSDM workshop 2017, we combined the KFC2a protein-protein interaction hotspot prediction features with Rosetta scoring function terms and interface filter metrics. A 2-way and 3-way forward selection strategy was employed to train support vector machine classifiers, as was a reverse feature elimination strategy. From these results, we identified subsets of KFC2a and Rosetta combined features that show improved performance over KFC2a features alone.
Evaluation of heavy metals in some selected medicinal plants growing within the University of Ibadan Campus

Background: Medicinal plants are a potent source of therapeutic molecules that heal various diseases in the world.Aim: The aim of this study was to evaluate heavy metal concentrations in the leaves of some selected medicinal plants in selected locations.Setting: The leaves of Azadirachta indica, Magnifera indica and Newbouldia laevis were collected from the botanical garden, roadside and residential area in the University of Ibadan and were authenticated at the Forest Herbarium Ibadan. The samples were thoroughly washed with deionised water and air-dried at room temperature for about three weeks, then ground into powder with a mechanical grinder. The samples were subsequently stored in air-tight bottles for further work.Methods: The milled samples were subjected to wet digestion, and then lead (Pb), chromium (Cr), cadmium (Cd) and nickel (Ni) were analysed using standard methods.Results: The results obtained show that the highest concentrations of Pb, Cr and Cd in the medicinal plants studied were found in N. laevis (23.93 ppm; road side), N. laevis (4.79 ppm; road side) and M. indica (0.36 ppm; road side), respectively, while the lowest concentrations of Pb, Cr and Cd were found in A. indica (7.10 ppm; botanical garden), N. laevis (0.73 ppm; residential) and N. laevis (0.05 ppm; residential), respectively. Ni was totally undetected in all three medicinal plants studied in all the locations.Conclusion: The concentrations of heavy metals at the roadside and residential area were higher than permissible limits set for medicinal plants, but the botanical garden was the lowest and safest in terms of heavy metals accumulation in the medicinal plants studied in the three locations.