Miracle-dz/UniFAR-FTUs huggingface dataset:
Th1/Th2 cell dichotomy in acquired immunity to Bordetella pertussis: variables in the in vivo priming and in vitro cytokine detection techniques affect the classification of T‐cell subsets as Th1, Th2 or Th0

In studies of the mechanism of immunity to Bordetella pertussis in a murine respiratory infection model, we have previously demonstrated that natural infection of immunization with a whole cell vaccine induces a potent protective immune response, which is mediated by T‐helper type‐1 (Th1) cells. In contrast an acellular vaccine generates Th2 cells and is associated with delayed bacterial clearance following respiratory challenge. In the present study we have investigated the apparent Th1/Th2 cell dichotomy in acquired immunity and have examined the factors that affect their induction or detection. The cytokine profiles of B. pertussis‐specific T cells in immune animals were determined using antigen‐stimulated ex vivo spleen cells or CD4+ T‐cell lines and clones established in the presence of interleukin‐2 (IL‐2) or IL‐4. Antigen‐specific T cells derived from mice immunized with the acellular vaccine were almost exclusively of the Th2 cell type. In contrast, T‐cell lines and clones established following respiratory infection or immunization with the whole cell vaccine were predominantly of the Th1 type. However, a proportion of T cells from convalescent mice, especially when cultured in the presence of IL‐4, secreted IL‐4 and IL‐5 with or without detectable IL‐2 and interferon‐γ (IFN‐γ), suggesting that Th0 or Th2 cells were also primed during natural infection in vivo. Furthermore, when mice were assessed 6 months after infection, spleen cells produced significant levels of IL‐4 and IL‐5, which were not evident at 6 weeks. The route of immunization and the genetic background of the mice were also found to influence the preferential priming of Th1 cells, and this was directly related to the level of protection against respiratory or intracerebral (i.c.) challenge. Our findings underline the critical role of CD4+ Th1 cells in immunity to B. pertussis, but also demonstrate that a number of factors in the in vivo priming and in vitro restimulation can skew the apparent dominance of one Th cell type over another.
Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus

The imprinted SNRPN locus is a complex transcriptional unit that encodes the SNURF and SmN polypeptides as well as multiple non-coding RNAs. SNRPN is located within the Prader-Willi and Angelman syndrome (PWS/AS) region that contains multiple imprinted genes, which are coordinately regulated by a bipartite imprinting center (IC). The SNRPN 5′ region co-localizes with the PWS-IC and contains two DNase I hypersensitive sites, DHS1 at the SNRPN promoter, and DHS2 within intron 1, exclusively on the paternally inherited chromosome. We have examined DHS1 and DHS2 to identify cis- and trans-acting regulatory elements within the endogenous SNRPN 5′ region. Analysis of DHS1 by in vivo footprinting and chromatin immunoprecipitation identified allele-specific interaction with multiple regulatory proteins, including NRF-1, which regulates genes involved in mitochondrial and metabolic functions. DHS2 acted as an enhancer of the SNRPN promoter and contained a highly conserved region that showed allele-specific interaction with unphosphorylated RNA polymerase II, YY1, Sp1 and NRF-1, further suggesting a key role for NRF-1 in regulation of the SNRPN locus. We propose that one or more of the regulatory elements identified in this study may also contribute to PWS-IC function.
The Acute Effect of Direct Vibration on Muscular Power Performance in Master Athletes

Abstract This study examined the acute effect of direct vibration on biceps brachii muscular power in master athletes. 10 healthy male national representative master field-hockey players were randomly assigned to receive 10 min of pulsing sinusoidal vibration or no vibration (control) to the right and left biceps brachii. Pre- and post-testing included lifting 2 repetitions of standing dumbbell (DB) biceps curl at 50% 1 RM (repetition maximum). Mechanical peak power (PP), mean concentric power (MCP) and normalised electromyography (EMG) was assessed during the concentric phase of the biceps curl. Following vibration PP increased 44.3±23.6 W (difference pre-post; p=0.013) compared to control (5.9±9.5 W; p=0.334). Similarly, MCP increased 12.0±4.5 W (p=0.002) compared to control (1.5±0.8 W; p=0.397). However, there was no significant difference in normalised EMG between vibration and control (p>0.05). The increase in PP and MCP did not coincide with an increase in EMG and suggests that other mechanisms may be contributing to changes in muscle performance. Given its ease of use and portability the vibratory device may be considered as an alternative warm-up modality immediately prior to explosive activities.
Exploring the Optimal Strategy to Predict Essential Genes in Microbes

Accurately predicting essential genes is important in many aspects of biology, medicine and bioengineering. In previous research, we have developed a machine learning based integrative algorithm to predict essential genes in bacterial species. This algorithm lends itself to two approaches for predicting essential genes: learning the traits from known essential genes in the target organism, or transferring essential gene annotations from a closely related model organism. However, for an understudied microbe, each approach has its potential limitations. The first is constricted by the often small number of known essential genes. The second is limited by the availability of model organisms and by evolutionary distance. In this study, we aim to determine the optimal strategy for predicting essential genes by examining four microbes with well-characterized essential genes. Our results suggest that, unless the known essential genes are few, learning from the known essential genes in the target organism usually outperforms transferring essential gene annotations from a related model organism. In fact, the required number of known essential genes is surprisingly small to make accurate predictions. In prokaryotes, when the number of known essential genes is greater than 2% of total genes, this approach already comes close to its optimal performance. In eukaryotes, achieving the same best performance requires over 4% of total genes, reflecting the increased complexity of eukaryotic organisms. Combining the two approaches resulted in an increased performance when the known essential genes are few. Our investigation thus provides key information on accurately predicting essential genes and will greatly facilitate annotations of microbial genomes.
Cloning of Porcine Pituitary Tumor Transforming Gene 1 and Its Expression in Porcine Oocytes and Embryos

The maternal-to-embryonic transition (MET) is a complex process that occurs during early mammalian embryogenesis and is characterized by activation of the zygotic genome, initiation of embryonic transcription, and replacement of maternal mRNA with embryonic mRNA. The objective of this study was to reveal the temporal expression and localization patterns of PTTG1 during early porcine embryonic development and to establish a relationship between PTTG1 and the MET. To achieve this goal, reverse transcription-polymerase chain reaction (RT-PCR) was performed to clone porcine PTTG1. Subsequently, germinal vesicle (GV)- and metaphase II (MII)-stage oocytes, zygotes, 2-, 4-, and 8-cell-stage embryos, morulas, and blastocysts were produced in vitro and their gene expression was analyzed. The results revealed that the coding sequence of porcine PTTG1 is 609-bp in length and that it encodes a 202-aa polypeptide. Using qRT-PCR, PTTG1 mRNA expression was observed to be maintained at high levels in GV- and MII-stage oocytes. The transcript levels in oocytes were also significantly higher than those in embryos from the zygote to blastocyst stages. Immunohistochemical analyses revealed that porcine PTTG1 was primarily localized to the cytoplasm and partially localized to the nucleus. Furthermore, the PTTG1 protein levels in MII-stage oocytes and zygotes were significantly higher than those in embryos from the 2-cell to blastocyst stage. After fertilization, the level of this protein began to decrease gradually until the blastocyst stage. The results of our study suggest that porcine PTTG1 is a new candidate maternal effect gene (MEG) that may participate in the processes of oocyte maturation and zygotic genome activation during porcine embryogenesis.
Semen quality among Danish and Finnish men attempting to conceive. The Danish First Pregnancy Planner Study Team.

OBJECTIVE To assess differences in semen quality between similar populations from Denmark and Finland. DESIGN Comparison of semen quality between 221 Finnish men (of whom 115 had no proven fertility) and 411 Danish men with no proven fertility in two follow-up studies among normal couples trying to conceive. METHODS In Finland male partners of couples without experienced infertility attempting to conceive were recruited through advertisements in local newspapers from 1984 to 1986. From 1992 to 1995 Danish men who lived with a partner and who had not attempted to achieve a pregnancy previously were recruited through their union when they discontinued birth control. All semen analyses were performed in accordance with the World Health Organization guidelines. RESULTS Median sperm concentration, total sperm count and the percentage of morphologically normal spermatozoa were significantly higher among the Finnish men without proven fertility (104.0 million/ml, 304.0 million and 58% respectively) compared with the Danish men (53.0 million/ml, 140.8 million, and 41% respectively). Sperm concentration was 105.7% (95% confidence interval (CI) 58.1%-167.6%) and total sperm count was 127.4% (95% CI 71.4%-201.6%) higher among Finnish men without proven fertility than among Danish men after control for confounders. CONCLUSIONS Some, but hardly all, of the observed difference in semen quality may be explained by differences in recruitment procedures, selection of the men and by methodological differences in semen analysis between the two countries. Also a birth cohort effect may explain some of the differences between countries as the Finnish men were recruited 11 years before the Danish men. Therefore, follow-up studies with identical recruitment and selection of men from the two countries are needed.
Assessment of Band-Based Similarity Coefficients for Automatic Type and Subtype Classification of Microbial Isolates Analyzed by Pulsed-Field Gel Electrophoresis

ABSTRACT Pulsed-field gel electrophoresis (PFGE) has been the typing method of choice for strain identification in epidemiological studies of several bacterial species of medical importance. The usual procedure for the comparison of strains and assignment of strain type and subtype relies on visual assessment of band difference number, followed by an incremental assignment to the group hosting the most similar type previously seen. Band-based similarity coefficients, such as the Dice or the Jaccard coefficient, are then used for dendrogram construction, which provides a quantitative assessment of strain similarity. PFGE type assignment is based on the definition of a threshold linkage value, below which strains are assigned to the same group. This is typically performed empirically by inspecting the hierarchical cluster analysis dendrogram containing the strains of interest. This approach has the problem that the threshold value selected is dependent on the linkage method used for dendrogram construction. Furthermore, the use of a linkage method skews the original similarity values between strains. In this paper we assess the goodness of classification of several band-based similarity coefficients by comparing it with the band difference number for PFGE type and subtype classification using receiver operating characteristic curves. The procedure described was applied to a collection of PFGE results for 1,798 isolates of Streptococcus pneumoniae, which documented 96 types and 396 subtypes. The band-based similarity coefficients were found to perform equally well for type classification, but with different proportions of false-positive and false-negative classifications in their minimal false discovery rate when they were used for subtype classification.
Botryane Sesquiterpenoids, Cyclopentadepsipeptides, Xanthones, and Trichothecenes from Trichoderma oligosporum

Abstract Five new botryane sesquiterpenes (1–5), one new cyclopentadepsipeptide (9), and two new xanthones (11 – 12), together with 11 known compounds, were isolated from Trichoderma oligosporum. The structures of the new compounds were identified by comprehensive spectroscopic methods including nuclear magnetic resonance and mass spectrometry. The cytotoxicity of 1–19 was evaluated against K562, A549, and ASPC cell lines. Compounds 5, 8, 11, 17, and 18 showed cytotoxicity against the K562 cell line with more than 50% inhibition at 12.5 µM. As to A549 cell line, compound 8 showed the strongest cytotoxicity with approximately 50% inhibition at 25.0 µM. No compounds showed cytotoxicity against the ASPC cell line.
In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)

Plant genomes are now sequenced rapidly and inexpensively. In silico approaches allow efficient development of simple sequence repeat markers, also known as microsatellite markers, from these sequences. A search of the genome sequence of 'Jefferson' hazelnut (Corylus avellana L.) identified 8,708 tri-nucleotide simple sequence repeats with at least five repeat units, and stepwise removal of the less promising sequences led to the development of 150 polymorphic markers. Fragments in the 'Jefferson' sequence containing tri-nucleotide repeats were used as references and aligned with genomic sequences from seven other cultivars. Following in silico alignment, sequences that showed variation in number of repeat units were selected and primer pairs were designed for 243 of them. Screening on agarose gels identified 173 as polymorphic. Removal of duplicate and previously published sequences reduced the number to 150, for which fluorescent primers and capillary electrophoresis were used for amplicon sizing. These were characterized using 50 diverse hazelnut accessions. Of the 150, 132 generated the expected one or two alleles per accession while 18 amplified more than two amplicons in at least one accession. Diversity parameters of the 132 marker loci averaged 4.73 for number of alleles, 0.51 for expected heterozygosity (He), 0.49 for observed heterozygosity (Ho), 0.46 for polymorphism information content (PIC), and 0.04 for frequency of null alleles. The clustering of the 50 accessions in a dendrogram constructed from the 150 markers confirmed the wide genetic diversity and presence of three of the four major geographic groups: Central European, Black Sea, and Spanish-Italian. In the mapping population, 105 loci segregated, of which 101 were assigned to a linkage group (LG), with positions well-dispersed across all 11 LGs. These new markers will be useful for cultivar fingerprinting, diversity studies, genome comparisons, mapping, and alignment of the linkage map with the genome sequence and physical map.
Stop interfering: Stroop task conflict independence from informational conflict and interference

Performance of the Stroop task reflects two conflicts—informational (between the incongruent word and ink colour) and task (between relevant colour naming and irrelevant word reading). This is supported by findings showing that the anterior cingulate cortex is more activated by congruent and incongruent stimuli than by nonword neutral stimuli. Previously, researchers demonstrated behavioural evidence for task conflict—a reverse facilitation effect under a reduced task conflict control condition. The boundary conditions of this Stroop reverse facilitation effect are not yet clear. The current study aimed to investigate whether task conflict arises, and task control is needed, whenever there are two possible tasks, even if the irrelevant task cannot mislead one to give erroneous responses (i.e., stimuli do not contain an informational conflict). To this end, in both experiments no incongruent stimuli were presented. In Experiment 1, participants conducted a Stroop task with a high proportion of nonword neutrals and with a neutral/congruent cue in 50% of the trials. In Experiment 2, the nonword neutral was replaced by a real non-colour-word. We found the reverse facilitation effect in the noncued trials of Experiment 1. Moreover, as expected, this effect was eliminated when a noncolour neutral word that induced task conflict was used (Experiment 2). We conclude that task conflict control is reactively activated whenever there are at least two possible tasks, even in the absence of any possibility of informational conflict.
Estonian Children’s Perceptions Of Rights: Implications For Societies In Transition

Analysis of social reform in the twentieth century has identified the scale and purposes of intervention into childhood. Children and childhood have become the object of massive interventions. Re-thinking children and re-thinking childhood is difficult. First, because there is a large and powerful body of knowledge on child development and socialisation. The sociology of childhood has begun to shift adult understandings of what it is to be a child, and how this varies across time and across societies. In this chapter the author reports on data from his recent study with nineyear-olds in London. He have been doing two things: discussing with them how they understand the social status of childhood, motherhood and fatherhood; and asking them to reflect on their daily lives. The 57 children were situated in two school classes, one from each of two schools. Keywords:Childhood; London; re-thinking children; socialisation
Mitofusin2 Mutations Disrupt Axonal Mitochondrial Positioning and Promote Axon Degeneration

Alterations in mitochondrial dynamics (fission, fusion, and movement) are implicated in many neurodegenerative diseases, from rare genetic disorders such as Charcot-Marie-Tooth disease, to common conditions including Alzheimer's disease. However, the relationship between altered mitochondrial dynamics and neurodegeneration is incompletely understood. Here we show that disease associated MFN2 proteins suppressed both mitochondrial fusion and transport, and produced classic features of segmental axonal degeneration without cell body death, including neurofilament filled swellings, loss of calcium homeostasis, and accumulation of reactive oxygen species. By contrast, depletion of Opa1 suppressed mitochondrial fusion while sparing transport, and did not induce axonal degeneration. Axon degeneration induced by mutant MFN2 proteins correlated with the disruption of the proper mitochondrial positioning within axons, rather than loss of overall mitochondrial movement, or global mitochondrial dysfunction. We also found that augmenting expression of MFN1 rescued the axonal degeneration caused by MFN2 mutants, suggesting a possible therapeutic strategy for Charcot-Marie-Tooth disease. These experiments provide evidence that the ability of mitochondria to sense energy requirements and localize properly within axons is key to maintaining axonal integrity, and may be a common pathway by which disruptions in axonal transport contribute to neurodegeneration.
Morphological growth of Han boys and girls born and raised near sea level and at high altitude in western China

This study compares the morphological characteristics of Han children, adolescents, and young adults who were born at 250 m near Beijing and at three high altitudes in Qinghai Province, Peoples Republic of China (3,200 m, 3,800 m, and 4,300 m). From ages 6 through 15, Han children growing up at high altitudes are significantly shorter, lighter, have less fat, and are less muscular than Han children growing up at low altitude. However, older adolescents and young adults show no such altitude differences. Younger adolescents and children in this study were all born after the government economic reforms of 1978. These reforms had a greater impact on the growth of children in and around large cities than on those in more remote areas. Therefore, the altitude differences in size among Han children ages 15 and younger may be a consequence of regional variation in health and nutrition, rather than due to the influence of hypoxia. There are no altitude‐related differences in thorax dimensions among Han children, adolescents, or young adults. This suggests that hypoxia does not affect the thorax growth of Han children. Am. J. Hum. Biol. 12:665–681, 2000. © 2000 Wiley‐Liss, Inc.
Response Latency in Survey Research: A Strategy for Detection and Avoidance of Satisficing Behaviors.

WANICH, WIPADA, Ph.D., August 2010, Educational Research and Evaluation Response Latency in Survey Research: A Strategy for Detection and Avoidance of Satisficing Behaviors (177 pp.) Director of Dissertation: George A. Johanson Response latency has been widely used as a cognitive method to investigate how respondents answer survey questions and also as a method to identify problems with survey questions (e.g., flawed or poorly worded questions) or errors associated with respondents‘ behaviors (e.g., faking). However, little attention has been paid to using response latency to investigate respondents‘ motivations, in particular to detect responding behaviors that are less than optimal. Marginal responding behavior where reduced cognitive effort is expended is referred to as satisficing. The present study used response latency to identify satisficers and also used a forced time survey structure to encourage participants to optimally respond. In addition, the study was designed to test the assumption that the construct validity (factor structure and model fit) of an instrument would improve if the researcher could encourage participants to optimally respond by discouraging them from satisficing. It also was designed to test a second assumption that construct validity would improve if the responses from satisficers were removed from the data set. To test the first assumption, a sample of 1,180 undergraduate students (sophomore, junior, and senior) was assigned to one of two groups: a not-forced-time group and a forced-time group. In the not-forced-time group, satisficing behavior was identified by capturing the response
The Induction and Transfer of Declarative Bias

People constantly apply acquired knowledge to new learning tasks, but machines almost never do. Research on transfer learning attempts to address this dissimilarity. Working within this area, we report on a procedure that learns and transfers constraints in the context of inductive process modeling, which we review. After discussing the role of constraints in model induction, we describe the learning method, MISC, and introduce our metrics for assessing the cost and benefit of transferred knowledge. The reported results suggest that cross-domain transfer is beneficial in the scenarios that we investigated, lending further evidence that this strategy is a broadly effective means for increasing the efficiency of learning systems. We conclude by discussing the aspects of inductive process modeling that encourage effective transfer, by reviewing related strategies, and by describing future research plans for constraint induction and transfer learning.