Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map

An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in “skeleton bin maps,” which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in “bins. ” A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).
Job stress and other working conditions: Relationships with smoking behaviors in a representative sample of working Australians.

OBJECTIVES To assess the relationships between current smoking status and psychosocial working conditions. METHODS A cross-sectional population-based telephone survey was conducted (66% response rate, N = 1,101). Job stress was measured using the demand/control, effort/reward imbalance (ERI), and job pressure models. Multiple regression modelling was conducted for smoking status (current versus non-smokers, and a more restricted analysis of current versus former-smokers) and daily smoking intensity outcomes in relation to job stress measures, working hours, shift work, and other independent variables. RESULTS After adjustment for age, education, martial status, and hostility, high job strain was positively associated with current smoking in men only. Employment in active jobs was associated with decreased odds of smoking among women only. High strain jobs were associated with decreased odds of current smoking compared to former smoking in women. In men, extreme and moderate job pressure were related to current smoking compared to current non-smoking, and moderate job pressure was associated with current smoking compared with former smokers. Other working conditions associated with smoking were excessive working hours in men and physical demand in women. Daily smoking intensity in current smokers was associated with high psychological demand and with ERI in women. CONCLUSIONS These results suggest that job stress is related to smoking status at the population level, with different patterns in men and women.
Police legitimacy among immigrants in Europe: Institutional frames and group position

Recent research has begun to explore the extent to which factors beyond behaviour and performance shape the empirical legitimacy of the police. In this paper, data from the European Social Survey are used to explore the association between immigration and legitimacy. Starting from the assumption that police legitimacy will vary between immigrant and non-immigrant populations, we consider three distinct sets of variable that might explain such variation: contact with the police, group position and the change in frames of reference that the act of migration engenders. Findings suggest, first, that variables from all three groups predict legitimacy, with police contact emerging as the most important. Second, conditional on these factors there is no difference in the views of recent immigrants and their non-immigrant peers. However, other groups of immigrants – particularly those who migrated as children – tend to grant the police somewhat less legitimacy.
Fixation based event‐related fmri analysis: Using eye fixations as events in functional magnetic resonance imaging to reveal cortical processing during the free exploration of visual images

Eye movements, comprising predominantly fixations and saccades, are known to reveal information about perception and cognition, and they provide an explicit measure of attention. Nevertheless, fixations have not been considered as events in the analyses of data obtained during functional magnetic resonance imaging (fMRI) experiments. Most likely, this is due to their brevity and statistical properties. Despite these limitations, we used fixations as events to model brain activation in a free viewing experiment with standard fMRI scanning parameters. First, we found that fixations on different objects in different task contexts resulted in distinct cortical patterns of activation. Second, using multivariate pattern analysis, we showed that the BOLD signal revealed meaningful information about the task context of individual fixations and about the object being inspected during these fixations. We conclude that fixation‐based event‐related (FIBER) fMRI analysis creates new pathways for studying human brain function by enabling researchers to explore natural viewing behavior. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.
Variables affecting survival after second primary lung cancer: A population-based study of 187 Hodgkin's lymphoma patients.

BACKGROUND Patients successfully treated for Hodgkin's lymphoma (HL) are at known risk for subsequent malignancies, the most common of which is lung cancer. To date, no population-based study has analyzed prognostic variables for overall survival (OS) among HL survivors who developed non-small cell lung cancer (NSCLC). METHODS For 187 HL patients who developed NSCLC (among 22,648 HL survivors), we examined the impact of the following variables on OS after NSCLC diagnosis: gender, race, sociodemographic status (based upon county of residence), calendar year and age at NSCLC diagnosis, NSCLC histology and grade, HL stage and subtype, radiation for HL and latency between HL and NSCLC. Patients were grouped by NSCLC stage as follows: localized, regional or distant. All patients were reported to the population-based Surveillance, Epidemiology, and End Results program. For those variables significant on univariate analyses, hazard ratios (HR) were derived from Cox proportional hazards model. RESULTS Sociodemogaphic status, gender and latency between NSCLC and HL did not significantly affect OS of any NSCLC stage group. For patients with localized NSCLC, a history of mixed celluarlity HL was associated with a 3-fold improved OS (P=0.006). For patients with regional NSCLC, prior radiotherapy for HL was associated with a 2-fold worse OS (P=0.025). CONCLUSIONS A history of mixed cellularity HL subtype and a history of no radiotherapy for HL are favorable prognostic factors among patients who develop NSCLC. Further research into clinicopathologic and treatment-associated variables potentially affecting OS after second primary NSCLC among HL survivors is warranted.
Assessment of prenatal tobacco smoke exposure by determining nicotine and its metabolites in meconium

Meconium samples collected from 115 neonates were analysed for nicotine, cotinine and trans -3-hydroxycotinine (OH-cotinine) by means of high-performance liquid chromatography (HPLC) to identify prenatal smoke exposure. The self-reported maternal smoking status during pregnancy was determined by means of a questionnaire and verified by measurements in urine prior to childbirth. The total sum of nicotine and its metabolites (Sumtot) of the first passed meconium samples was 1560 ± 1024 pmol/g in newborns of smoking mothers. Smoking of less than five cigarettes was clearly detected. Sumtot remained constant in all meconium samples passed by a neonate in succession. However, the proportion of nicotine decreased with the time of passage after birth and the OH-cotinine proportion increased, whereas cotinine hardly changed. Nicotine or its metabolites were not detectable in meconium (detection limit < 20 pmol/g), when the mothers were only exposed to environmental tobacco smoke (ETS) using the HPLC method. The hypothesis that the content of nicotine metabolites in meconium reflects long-term smoke exposure could not be confirmed in newborns whose mothers had quit smoking during the latter half of pregnancy. Determining Sumtot enables the intensity of continuous smoking during pregnancy to be estimated in all meconium samples passed by a newborn. Human & Experimental Toxicology (2007) 26 : 535—544
Tract-Based Analysis of Callosal, Projection, and Association Pathways in Pediatric Patients with Multiple Sclerosis: A Preliminary Study

BACKGROUND AND PURPOSE: Region-of-interest (ROI) and tract-based diffusion tensor imaging (DTI) analyses have detected increased apparent diffusion coefficients (ADCs) and decreased fractional anisotropy (FA) in callosal and projection systems of adult patients with multiple sclerosis (MS). We explored whether similar changes occur in pediatric patients with MS, assessing 3 major white matter pathways (interhemispheric, projection, and intrahemispheric) in both visibly involved and normal-appearing white matter (NAWM). MATERIALS AND METHODS: DTI datasets from 10 patients with established pediatric MS and 10 age- sex-, and imaging technique−matched controls were analyzed. Tracts were reconstructed by using a fiber assignment by continuous tracking algorithm with a diffusion-weighted imaging mask and a 35° angular threshold. Tracts were selected by using standard ROI placements on color FA maps cross-referenced to b = 0 T2-weighted images for studying white matter pathways. Ten identical ROIs were placed in NAWM on b = 0 T2-weighted images to ensure that both ROIs and resulting tracts passed through NAWM. RESULTS: In pediatric MS, all tracts had higher mean ADC values (P = .002 to P < .04) and lower mean FA (P = .009 to P < .02) than those in healthy controls. Even when the tracts were confined to NAWM, the mean ADC was higher (P < .004 to P < .05) and the mean FA was lower (P = .002 to P < .02). T2 lesion burden correlated with tract-based mean ADC. ROI mean ADC increased, and both tract and ROI mean FA decreased with increasing T2 lesion burden, however with a statistically nonsignificant correlation. CONCLUSIONS: Increased mean ADC and decreased mean FA occur in all 3 major white matter pathways, both in visibly involved white matter and NAWM in pediatric MS.
Plasticity in gene transcription explains the differential performance of two invasive fish species

Phenotypic plasticity buffers organisms from environmental change and is hypothesized to aid the initial establishment of nonindigenous species in novel environments and postestablishment range expansion. The genetic mechanisms that underpin phenotypically plastic traits are generally poorly characterized; however, there is strong evidence that modulation of gene transcription is an important component of these responses. Here, we use RNA sequencing to examine the transcriptional basis of temperature tolerance for round and tubenose goby, two nonindigenous fish species that differ dramatically in the extent of their Great Lakes invasions despite similar invasion dates. We used generalized linear models of read count data to compare gene transcription responses of organisms exposed to increased and decreased water temperature from those at ambient conditions. We identify greater response in the magnitude of transcriptional changes for the more successful round goby compared with the less successful tubenose goby. Round goby transcriptional responses reflect alteration of biological function consistent with adaptive responses to maintain or regain homeostatic function in other species. In contrast, tubenose goby transcription patterns indicate a response to stressful conditions, but the pattern of change in biological functions does not match those expected for a return to homeostatic status. Transcriptional plasticity plays an important role in the acute thermal tolerance for these species; however, the impaired response to stress we demonstrate in the tubenose goby may contribute to their limited invasion success relative to the round goby. Transcriptional profiling allows the simultaneous assessment of the magnitude of transcriptional response as well as the biological functions involved in the response to environmental stress and is thus a valuable approach for evaluating invasion potential.
Extent of smoking and age at initiation of smoking among adult survivors of childhood cancer in Britain.

BACKGROUND Smoking should be particularly discouraged among survivors of childhood cancer, who are at increased risk of adverse effects of the cancer and its treatment. We examined the extent of cigarette smoking, factors associated with being a current smoker, and age at initiation of regular smoking among adult survivors of childhood cancer and compared the survivors' smoking habits with those of the general population. METHODS We used data from the British Childhood Cancer Survivor Study (BCCSS), a population-based cohort of 17 981 individuals who were diagnosed with childhood cancer between 1940 and 1991 in Britain and had survived for at least 5 years after diagnosis. The 14 836 cohort members who were alive and aged 16 years or older up to September 2006 were eligible to receive a mailed questionnaire that ascertained smoking status and other factors. The general population data were from the 2002 General Household Survey in Britain. Logistic regression was used to investigate factors associated with being a current regular smoker and to compare the prevalence of current regular smoking in the study cohort with that in the general population. Cox regression was used to examine associations between explanatory factors and age at smoking initiation. All statistical tests were two-sided. RESULTS Of the 10 326 childhood cancer survivors who returned completed questionnaires, 20.0% were current regular smokers and 29.8% were ever regular smokers, whereas in the comparable general population 28.1% were current regular smokers and 48.8% were ever regular smokers. Current regular smoking was more prevalent among survivors of Wilms tumor or Hodgkin lymphoma than survivors of a central nervous system (CNS) neoplasm; in those aged 10-14 years at diagnosis than 0-4 years; in those not treated with radiotherapy; in those in manual occupations; in those who were separated, widowed, or divorced; in those with lower educational attainment; and in those not currently on long-term regular hospital follow-up. Rates of smoking initiation were lower in women; in those treated with chemotherapy or radiotherapy; and in those with a third party-completed questionnaire. The rate of smoking initiation was highest among those diagnosed at 10-14 years of age. The odds ratio for being a current regular smoker among the survivors compared with the general population was 0.51 (99% confidence interval [CI] = 0.46 to 0.57). Survivors who smoked, smoked fewer cigarettes per day than smokers in the general population; the difference in the multivariable model was 1.5 fewer cigarettes per day (95% CI = 1.03 to 1.99). CONCLUSION The prevalence of smoking varies by subgroup among adult survivors of childhood cancer in the BCCSS but is substantially less overall than that in the general population.
The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80°C, -20°C for 1 week, at +4°C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80°C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80°C versus the other methods and -80°C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80°C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4°C or room temperature) or freezing at -20°C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.
SCG10 is a JNK target in the axonal degeneration pathway

Axons actively self-destruct following genetic, mechanical, metabolic, and toxic insults, but the mechanism of axonal degeneration is poorly understood. The JNK pathway promotes axonal degeneration shortly after axonal injury, hours before irreversible axon fragmentation ensues. Inhibition of JNK activity during this period delays axonal degeneration, but critical JNK substrates that facilitate axon degeneration are unknown. Here we show that superior cervical ganglion 10 (SCG10), an axonal JNK substrate, is lost rapidly from mouse dorsal root ganglion axons following axotomy. SCG10 loss precedes axon fragmentation and occurs selectively in the axon segments distal to transection that are destined to degenerate. Rapid SCG10 loss after injury requires JNK activity. The JNK phosphorylation sites on SCG10 are required for its rapid degradation, suggesting that direct JNK phosphorylation targets SCG10 for degradation. We present a mechanism for the selective loss of SCG10 distal to the injury site. In healthy axons, SCG10 undergoes rapid JNK-dependent degradation and is replenished by fast axonal transport. Injury blocks axonal transport and the delivery of SCG10, leading to the selective loss of the labile SCG10 distal to the injury site. SCG10 loss is functionally important: Knocking down SCG10 accelerates axon fragmentation, whereas experimentally maintaining SCG10 after injury promotes mitochondrial movement and delays axonal degeneration. Taken together, these data support the model that SCG10 is an axonal-maintenance factor whose loss is permissive for execution of the injury-induced axonal degeneration program.
Reliability of Side‐to‐Side Sonographic Cross‐sectional Area Measurements of Upper Extremity Nerves in Healthy Volunteers

In sonographic evaluations of peripheral nerves, the healthy, contralateral side may be used as an internal control for the pathologic one. Therefore, the inherent side‐to‐side differences must be minimal. The goal of this study was to determine the reliability of side‐to‐side measurements of upper extremity nerves in healthy volunteers.
Semitic Languages

The Semitic languages are a family of languages spoken by more that 370 million people across much of the Middle East and North and East Africa. This is the first general survey of those languages, including the Arab and Aramaic dialects and various languages of Ethiopia. Containing twenty-two chapters that present a comprehensive survey of this language family from its origins in antiquity to the present day, The Semitic Languages is an essential source of reference for the specialist and the lay reader.
Cold Weather Training: A Risk Factor for Achilles Paratendinitis among Recruits

In a prospective study of risk factors for Achilles tendinopathy among four induction cycles of infantry recruits, 95 out of 1405 recruits, (6.8%) were found to suffer from Achilles tendinopathy. In more than 94% of the cases, the tendinopathy was considered to be paratendinitis. Training season had a statistically significant effect on the incidence of Achilles paratendinitis with 3.6% suffering in the summer and 9.4% in the winter (p = .001). This increased risk for Achilles paratendinitis in cold weather outdoor training can be explained by a fall in temperature of the Achilles paratenon whose membranes are rich in mucopolysaccharides and serve as a lubricant for gliding of the tendon and epitenon. Decreased temperature may increase the viscosity of the lubricant and thereby increases friction and risk for Achilles paratendinitis. This same relationship illustrates why “warming up” before exercising may be important in lowering the incidence of Achilles paratendinitis.
Clonal polymorphisms of outer membrane protein OspB of Borrelia burgdorferi

The outer membrane protein OspB of Borrelia burgdorferi, the Lyme borreliosis agent, differs in relative molecular weight (Mr) among strains. To determine whether antigenic variation occurs in B. burgdorferi, a cell population of the human isolate HB19 was cloned first by being diluted in broth and then by being plated on agar medium. Several clones were obtained and characterized by polyacrylamide gel electrophoresis, in situ protease treatment, and Western (immunoblot), Southern, and Northern (RNA) blot analyses. Variants featuring OspB proteins that differed in Mrs and in reactivities with monoclonal antibodies were found. One variant made increased amounts of a 21,000-molecular-weight protein (21K protein) in addition to normal amounts of a 33K OspB protein. Another variant did not produce an OspB protein at all but did express an 18.5K protein. Both the 18.5K and 21K proteins were susceptible in situ to trypsin and were bound by a monoclonal antibody directed against the OspB of strain HB19. There were no differences in the Southern and Northern blot analyses of the different variants. The results led to the following conclusions. (i) Clonal polymorphisms in the surface protein OspB occurred in B. burgdorferi. (ii) Hitherto uncharacterized 18.5K and 21K proteins were protease susceptible, antigenically related to OspB, and apparently produced in greater amounts when an OspB either was not produced or was altered in structure. (iii) The OspB variations, including its absence from cells, were not accounted for by major DNA rearrangements or failure of transcription of the ospB gene.