Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Analysis of Real-Time PCR Expression Production by REST and 2~((-ΔΔCT))

Objective To develop a simple and accurate method for the quantification of real-time RT-PCR gene products.Method Standard curves of POLK and GAPDH genes were made from 5-fold serially diluted cDNA samples from the normal 16HBE cells.The levels of POLK mRNA in the malignant transformed 16HBE cells and human lung cancer cells(H1299) treated with various concentrations of BPDE were determined.GAPDH gene was used as the reference gene.The relative expression levels were analyzed by REST and 2(-ΔΔCT) method.Result A good linear relationship(Rsq 0.997) was obtained from the standard curves.The efficiency of amplification of POLK and GAPDH genes was 117.5% and 103.5%,respectively.The expression ratios calculated by using 2(-ΔΔCT) method were higher than the rations obtained from the REST. Conclusion Real-time RT-PCR in combination with REST is a simple and accurate method for relative quantification of gene expression.
Effect of pH on functional properties of corn steep water protein hydrolysates

Corn steep water protein hydrolysates was got by hydrolyzing corn steep water protein with protamex,the functional properties variation of corn steep water protein hydrolysates were investigated,such as the variation of solubility,viscosity,emulsifying capacity and stability and foaming capacity and stability in different pH condition.The result showed that the solubility of hydrolysates changed slightly with pH,the hydrolysates have better solubility;the viscosity of hydrolysates changed slightly with pH in the researchful pH range;the hydrolysates have good foaming capacity at both sides of pI 6.9 and kept steadily in the other pH;the foaming stability,the emulsifying capacity and stability of hydrolysates changed slightly with pH.Corn steep water hydrolysates with the good functional properties were propitious to application in the food industry.
Heterosis and Combining Ability in African Marigold

The present study was undertaken on a 7 × 7 diallel cross excluding reciprocals. In the F1 hybrids there was appreciable heterosis in all the eight characters, namely plant height, days for first flowering, duration of flowering, flower size, flower weight, flowers at peak flowering, total number of flowers and seed weight. The maximum heterosis was observed in total number of flowers. The crosses P1 × P5, P1 × P6 and P4 × P6 showed the highest heterosis percentage in flower size and flower weight, early flowering and total number of flowers respectively. The highest flower yield was recorded in the hybrid P5 × P6. The mean squares for g.c. a. were greater than those for s.c. a. in all cases except in total number of flowers. In all the hybrids which showed best s.c. a. effects the parental lines involved were at least one of the three most outstanding parental lines namely Spun Gold, Sun Giant and Hawaii which also had high g.c. a. effects for one or more of the characters contributing towards yield.
Agriculture creates subtle genetic structure among migratory and nonmigratory populations of burrowing owls throughout North America

Abstract Population structure across a species distribution primarily reflects historical, ecological, and evolutionary processes. However, large‐scale contemporaneous changes in land use have the potential to create changes in habitat quality and thereby cause changes in gene flow, population structure, and distributions. As such, land‐use changes in one portion of a species range may explain declines in other portions of their range. For example, many burrowing owl populations have declined or become extirpated near the northern edge of the species' breeding distribution during the second half of the 20th century. In the same period, large extensions of thornscrub were converted to irrigated agriculture in northwestern Mexico. These irrigated areas may now support the highest densities of burrowing owls in North America. We tested the hypothesis that burrowing owls that colonized this recently created owl habitat in northwestern Mexico originated from declining migratory populations from the northern portion of the species' range (migration‐driven breeding dispersal whereby long‐distance migrants from Canada and the United States became year‐round residents in the newly created irrigated agriculture areas in Mexico). We used 10 novel microsatellite markers to genotype 1,560 owls from 36 study locations in Canada, Mexico, and the United States. We found that burrowing owl populations are practically panmictic throughout the entire North American breeding range. However, an analysis of molecular variance provided some evidence that burrowing owl populations in northwestern Mexico and Canada together are more genetically differentiated from the rest of the populations in the breeding range, lending some support to our migration‐driven breeding dispersal hypothesis. We found evidence of subtle genetic differentiation associated with irrigated agricultural areas in southern Sonora and Sinaloa in northwestern Mexico. Our results suggest that land use can produce location‐specific population dynamics leading to subtle genetic structure even in the absence of dispersal barriers.
Psychological symptoms, family functioning, and religious coping in second- and third- generation Holocaust survivors

Research has examined psychological symptoms, communication patterns from parent to child, parenting style, and protective and resiliency factors in descendants of Holocaust survivors. The current study explored intergenerational trauma and resilience in secondand third-generation Holocaust survivors as compared to a matched comparison group. Four groups were studied based on the participants’ Holocaust background and demographics: second generation (2GH; n=47) and third generation survivors (3GH; n=45) who self-identified as having at least one parent or grandparent, respectively, who is/was a Holocaust survivor interned during the war, and a matched comparison group (2GM; n=22, 3GM; n=13) for each generation consisting of non-Jewish descent who had one parent or grandparent who emigrated from the same European countries between 1945-1952. Ten 2GH and 3GH participants opted to complete the additional qualitative interview in which they were asked questions about their experiences as a descendant of a Holocaust survivor. Results showed that third-generation survivors endorsed more symptomatology than the matched comparison group; however, second generation survivors did not endorse more symptomatology than second generation match comparisons. Additionally, when descendants reported less adaptive family communication, affect responsiveness, and family cohesion, they reported higher levels of symptomatology. Lastly, we found that descendants who reported turning toward religion during times of stress (positive religious coping) endorsed higher levels of obsessive-compulsive and anxiety symptoms and those who endorsed turning away from religion in times of stress (negative religious coping) reported more depressive symptoms. A conceptual model is presented that includes vulnerability and resilience factors related to the intergenerational effects of Holocaust exposure. xiii !
Optical counterparts of two candidate ultraluminous X-ray sources in NGC 4536

Archival XMM-Newton, Chandra and Hubble Space Telescope (HST) data have been used to study the X-ray and optical properties of two candidate ultraluminous X-ray sources (ULXs) in NGC 4536. In order to search for potential optical counterparts, relative astrometry between Chandra and HST was improved, and as a result, optical counterparts were detected for both X-ray sources. To complement our findings (based on the archival data), ground-based optical spectra of the counterparts were obtained with the 6m BTA Telescope located at the Special Astrophysical Observatory (SAO). The calculated redshift (z = 0.4391±0.0010) for one of the sources (X-3) indicates that the source is, in fact, a background active galactic nucleus (AGN). Two possible optical counterparts (s1 and s2) were found for X-2. Whether s1 is point-like or an extended source is unclear: If it is point-like and the emission is dominated by the donor its spectral type indicates O-B star. The second source (s2) is point-like and is consistent with the colors and absolute magnitudes of a red supergiant.
Plasmid mediated Naphthalene Degradation in Pseudomonas sp. strain NGK 1

A large indigenous plasmid was found in the naphthalene degrading Pseudomonas sp. (NGK1). This plasmid, pND15 appears to contain complete genetic information for the degradation of naphthalene as the plasmid cured strain failed to utilize naphthalene as source of carbon. The E. coli transformed with pND15 showed ability to degrade naphthalene and growth pattern similar to that of wild type Pseudomonas sp. (NGK1).
Gentisyl alcohol inhibits apoptosis by suppressing caspase activity induced by etoposide

In the course of our screening for small molecules to inhibit apoptosis of U937 human leukemia cells induced by etoposide (10 μg/ml), Penicillium sp. F020150 with potent inhibitory activity was selected. The active compound was purified from ethyl acetate extract of the microorganism by Sephadex LH-20 column chromatography and HPLC, and was identified as gentisyl alcohol (2,5-dihydroxybenzyl alcohol) by spectroscopic methods. The compound inhibited caspase-3 induction with IC 50 value of 3.0 μg/ml after 8 h of etoposide treatment. The expression levels of caspase-3 and PARP were dose-dependently inhibited by the compound, suggesting that gentisyl alcohol inhibits etoposide-induced apoptosis via downregulation of caspases.
A New Method for Estimating of Patient Effective Dose in Computed Tomography Based on Body Mass Index: Performance of the Method in Abdomen-Pelvic Examination

Introduction: The CT Provide high quality images, especially in low-contrast soft tissue, are another advantage. Along with all the benefits that the CT scans which have, the patient dose of this modality is much greater than other methods. As a result, medical imaging community must ensure that the benefits of radiological examination for each patient are higher than related risks. Although the CT has a small percentage of radiological examination, but it has a large contribution on the exposure to the community. the purpose of the present study was to investigate how the introduction of MDCT scanners and patient-size-dependent imaging protocols have affected patient doses and propose a simple method to predict an estimation of the organ and effective doses by using BMI and mAeff. The nobility of the present scientific study was to investigate how the introduction of MDCT scanners and patient-size-dependent imaging protocols have affected patient doses. Materials and Methods: Demographic data of each patient were recorded as well as data from a CT scan of the abdomen and pelvic of 52 patients were studied. For assessment of patient and effective doses, the information related to the scan in ImPACT software was applied. The results are analyzed and regression was used in order to examine the relation between the results of the scan data in MATLAB environment. Results: The research findings showed that the received dose to the most patients is the same as determined by the ICRP103. An average of the effective dose(6mSv) was less than predicted amount by ICRP103. To estimate the effective dose of the body, according to the patient’s BMI, an equation was obtained [Effective Dose (mSv) = 0.257 BMI - 0.637]. The results from this equation are corresponded to the calculated dose by Impact (R2>0.95). In addition, the method was proposed to predict the parameters of mAeff and DLP resulted from the related scan. [mAeff (mGy.cm) = 4.73 BMI -19.81 , DLP(mGy.cm) = 17.17 BMI -56.36]. Conclusion: According to the results of this study, authors proposed a good alternative to estimate the effective dose according to BMI instead of ImPACT calculations for scanners and scanning conditions as well as a method to predict the effective dose by using the parameters of the CT system and BMI without being radiated on the patients.
Surprisingly Low Levels of Measles Immunity in Persons With HIV: A Seroprevalence Survey in a United States HIV Clinic

Abstract Background Measles outbreaks have become increasingly common due to deteriorating vaccination rates, fluctuating herd immunity, and varying antibody decline. Limited knowledge exists regarding prevalence and risk factors associated with measles seronegativity among persons with HIV (PWH). Methods This was a cross-sectional study conducted at an academic HIV clinic in Omaha, Nebraska. Participants were screened for the presence of measles IgG antibody. Demographic and clinical information was obtained through electronic medical record review. Simple and multivariable logistic regressions were performed to identify risk factors for measles seronegativity. Results Three hundred fifty-one participants were enrolled, with a measles seroprevalence rate of 70.3%. The mean age (range) was 48 (20–74) years, 77% were male, and 53% were Caucasian. The mean CD4 nadir (range) was 334 (1–1675) cells/mm3. At the time of testing, 86% and 87% of the seronegative and seropositive participants had an HIV RNA <50 copies/mL, respectively. Younger age was significantly associated with measles seronegativity (P = .003), as was birth year after 1957 (P = .021). Prior history of measles infection was associated with seropositivity (P = .011). All other risk factors evaluated, including written documentation of adequate vaccination, were not associated with seronegativity. Conclusions Our study demonstrates a measles seroprevalence rate that is remarkably lower than previously reported in PWH (92%), and, more importantly, is considerably lower than the rate needed to maintain herd immunity (95%). With higher than expected seronegativity and absence of notable risk factors aside from age, our findings support expanded measles immunity screening for PWH who are at risk of measles exposure.
Bergmann's rule is followed at multiple stages of postembryonic development in a long‐distance migratory songbird

Abstract Bergmann’s rule is a well‐established, ecogeographical principle that states that body size varies positively with latitude, reflecting the thermoregulatory benefits of larger bodies as temperatures decline. However, this principle does not seem to easily apply to migratory species that are able to avoid the extreme temperatures during winter at higher latitudes. Further, little is known about the ontogeny of this relationship across life stages or how it is influenced by ongoing global climate change. To address these knowledge gaps, we assessed the contemporary relationship between latitude and body size in a long‐distance migratory species, the prothonotary warbler (Protonotaria citrea) across life stages (egg to adult) on their breeding grounds. We also measured historic eggs (1865‐1961) to assess if the relationship between latitude and size during this life stage has changed over time. In accordance with Bergmann’s rule, we found a positive relationship between latitude and body mass during all post‐embryonic life stages, from early nestling stage through adulthood. We observed this same predicted pattern with historic eggs, but contemporary eggs exhibited the reverse (negative) relationship. We suggest that these results indicate a genetic component to this pattern and speculate that selection for larger body size in altricial nestlings as latitude increases may possibly drive the pattern in migratory species as even rare extreme cold weather events may cause mortality during early life stages. Furthermore, the opposite relationships observed in eggs, dependent on time period, may be related to the rapidly warming environments of higher latitudes that is associated with climate change. Although it is unclear what mechanism(s) would allow for this recent reversal in eggs (but still allow for its maintenance in later life stages). This evidence of a reversal suggests that anthropogenic climate change may be in the process of altering one of the longest‐standing principles in ecology.
How do less‐expensive nitrogen alternatives affect legume sanctions on rhizobia?

Abstract The evolutionary stability of mutualistic interactions involving multiple partners requires “sanctioning”–the ability to influence the fitness of each partner based on its respective contribution. Sanctions must be sensitive to even small differences if even slightly less‐beneficial partners could gain a fitness advantage by diverting resources away from the mutualistic service toward their own reproductive fitness. Here, we test whether legume hosts sanction even mediocre N2‐fixing rhizobial strains by influencing either nodule growth (which limits rhizobial cell numbers) or carbon accumulation (polyhydroxybutryate or PHB) per rhizobial cell. We also test whether sanctions depend on the availability of less‐expensive nitrogen alternatives, either as nitrate or coinoculation with a more‐efficient isogenic strain. We found that nitrate eliminated differences in nodule size between the mediocre and more‐efficient strains, suggesting that host sanctions were compromised. However, nitrate additions also decreased PHB accumulation by the mediocre strain, which may eliminate any fitness advantages of diverting resources from N2 fixation. Coinoculation with a more‐efficient strain could also compromise host sanctions if reduction in fitness from smaller nodules does not offset the potential fitness gain from greater PHB accumulation that we observed in the mediocre strain. Hence, a host's ability to sanction mediocre strains depends not only on alternative sources of nitrogen but also the relative importance of different components of rhizobial fitness.
Nearly unbiased estimator of contemporary Ne/N based on kinship relationships

Abstract This study develops a nearly unbiased estimator of the ratio of the contemporary effective mother size to the census size in a population, as a proxy of the ratio of contemporary effective size (or effective breeding size) to census size (Ne/N or Nb/N). The proposed estimator is based on both known mother–offspring (MO) and maternal‐sibling (MS) relationships observed within the same cohort, in which sampled individuals in the cohort probably share MO relationships with sampled mothers. The rationale is that the frequency of MO and MS pairs contains information regarding the contemporary effective mother size and the (mature) census size, respectively. Therefore, the estimator can be obtained only from genetic data. We also evaluate the performance of the estimator by running an individual‐based model. The results of this study provide the following: (a) parameter range for satisfying the unbiasedness, and (b) guidance for sample sizes to ensure the required accuracy and precision, especially when the order of the ratio is available. Furthermore, the results demonstrate the usefulness of a sibship assignment method for genetic monitoring, providing insights for interpreting environmental and/or anthropological factors fluctuating Ne/N (or Nb/N), especially in the context of conservation biology and wildlife management.
An integrated molecular cell biology and agent-based simulation approach to dissecting microRNA regulatory networks

Discoveries in the world of non-coding RNAs made during the turn of the last century challenge the flow of information described by Francis Crick in his description of the central dogma of molecular biology – the information encoded by the DNA no longer solely requires a protein intermediate to control the fate of a living cell. Dozens of mechanisms involving RNA-protein, protein-protein and RNA-RNA interactions have been described that govern regulation of information controlled at the level of replication, transcription and translation. The networks that emerge from these interactions support unique, context dependent regulation of gene expression, are dynamic in nature, and provide multiple layers of complexity underlying the biological system. Advancements in molecular biology allow researchers to dissect complex interactions between components of gene regulatory networks, interpretation of which is only feasible using automated computer-aided approaches. Inevitably, uncovering novel mechanisms involved in biological systems benefits from an integrated approach between experimental biology and computational modelling. This thesis investigates the function of a group of non coding RNAs, microRNAs, that regulate gene expression at a post-transcriptional level. Firstly, Argonaute-2, the crucial effector of microRNA function, is revealed as a novel direct target of microRNA-132. The functional role of this regulation is explored in primary lymphatic endothelial cells during cell activation. Secondly, the regulation of two microRNA-132 targets – Argonaute-2, required for microRNA-mediated gene regulation, and E1A associated Protein p300, necessary for microRNA-132 transcription – are incorporated into an agent-based model. Following the CoSMoS process, a rigorous methodology for model development, the documented regulatory network is captured in a model that is able to simulate the expected behaviour of the real-world problem domain. Finally, using the gathered data on microRNA-132 regulation and cell activation, the model is used to evaluate the domain knowledge of microRNA mediated gene silencing in silico, proposing testable hypothesis for in vitro experimentation.
Hemodynamic Response Function in Brain White Matter in a Resting State

Abstract The hemodynamic response function (HRF) characterizes temporal variations of blood oxygenation level-dependent (BOLD) signals. Although a variety of HRF models have been proposed for gray matter responses to functional demands, few studies have investigated HRF profiles in white matter particularly under resting conditions. In the present work we quantified the nature of the HRFs that are embedded in resting state BOLD signals in white matter, and which modulate the temporal fluctuations of baseline signals. We demonstrate that resting state HRFs in white matter could be derived by referencing to intrinsic avalanches in gray matter activities, and the derived white matter HRFs had reduced peak amplitudes and delayed peak times as compared with those in gray matter. Distributions of the time delays and correlation profiles in white matter depend on gray matter activities as well as white matter tract distributions, indicating that resting state BOLD signals in white matter encode neural activities associated with those of gray matter. This is the first investigation of derivations and characterizations of resting state HRFs in white matter and their relations to gray matter activities. Findings from this work have important implications for analysis of BOLD signals in the brain.
Live Long and Prosper: a health promotion group treatment for reducing health risk behaviors in veterans diagnosed with Posttraumatic Stress Disorder: assessment strategy

xiv INTRODUCTION.1 METHODS.6 Purpose of the Resource.6 Live Long and Prosper Group Development History.7 Target Audience.9 Development of the Resource.9 Division of the Literature.10 Purpose and Content of the Assessment Strategy.11 Development Process.13 Measures of Behavioral Frequency.16 Stages of Change Measures.22 Facilitator’s Adherence Checklist.24 DISCUSSION.24 Current Applications.24 Clinical Applications.26 Limitations.27 Future Research.29 REFERENCES.31 APPENDIX A: NARRATIVE OF THE EMPIRICAL LITERATURE.41 APPENDIX B: TABLES OF THE EMPIRICAL LITERATURE . 63 APPENDIX C: LIVE LONG AND PROSPER: ASSESSMENT STRATEGY.88