Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing the Human Past using Ancient and Modern Genomes

Skoglund, P. 2013. Reconstructing the Human Past using Ancient and Modern Genomes. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1069. 68 pp. Uppsala. ISBN 978-91-554-8744-7. The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modernday contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farmingand hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.
Muslim views on mental health and psychotherapy.

OBJECTIVES The aim of this research was to explore with a heterogeneous Muslim population their understanding of the concept of mental health and how any mental distress experienced by an individual can best be addressed. DESIGN A qualitative approach was taken. Participants were interviewed, and data analysed thematically. METHODS A sample of 14 Muslims was interviewed according to a semi-structured interview schedule. Participants were recruited via electronic mailing lists, and communications with local Muslim organizations. Interviews were transcribed verbatim, and data were analysed using thematic analysis. RESULTS Thematic analysis identified seven operationalizing themes that were given the labels 'causes', 'problem management', 'relevance of services', 'barriers', 'service delivery', 'therapy content', and 'therapist characteristics'. CONCLUSIONS The results highlight the interweaving of religious and secular perspectives on mental distress and responses to it. Potential barriers are discussed, as are the important characteristics of therapy, therapists, and service provision. Clinical implications are presented along with the limitations of this study and suggestions for future research.
Community Computing: Comparisons between Rural and Urban Societies Using Mobile Phone Data

We present a comparative analysis of the behavioral dynamics of rural and urban societies using four years of mobile phone data from all 1.4M subscribers within a small country. We use information from communication logs and top up denominations to characterize attributes such as socioeconomic status and region. We show that rural and urban communities differ dramatically not only in terms of personal network topologies, but also in terms of inferred behavioral characteristics such as travel. We confirm the hypothesis for behavioral adaptation, demonstrating that individuals change their patterns of communication to increase the similarity with their new social environment. To our knowledge, this is the first comprehensive comparison between regional groups of this size.
The detection of temporally defined objects does not require focused attention

Perceptual grouping is crucial to distinguish objects from their background. Recent studies have shown that observers can detect an object that does not have any unique qualities other than unique temporal properties. A crucial question is whether focused attention is needed for this type of grouping. In two visual search experiments, we show that searching for an object defined by temporal grouping can occur in parallel. These findings suggest that focused attention is not needed for temporal grouping to occur. It is proposed that temporal grouping may occur because the neurons representing the changing object elements adopt firing frequencies that cause the visual system to bind these elements together without the need for focused attention.
Correlation between Dopamine Transporter Degradation and Striatocortical Network Alteration in Parkinson’s Disease

The association between dopamine neuron loss and functional change in the striatocortical network was analyzed in 31 patients with Parkinson’s disease (PD) [mean disease duration 4.03 ± 4.20 years; Hoehn and Yahr (HY) stage 2.2 ± 1.2] and 37 age-matched normal control subjects. We performed 99mTc-TRODAT-1 SPECT/CT imaging to detect neuron losses and resting-state functional magnetic resonance imaging to detect functional changes. Mean striatal dopamine transporter binding ratios were determined by region of interest analysis. The functional connectivity correlation coefficient (fc-cc) was determined in six striatal subregions, and interactions between these binding ratios and the striatocortical fc-cc values were analyzed. The PD patients had significant functional network alterations in all striatal subregions. Lower striatal dopamine transporter binding correlated significantly with lower fc-cc values in the superior medial frontal (SMF) lobe and superior frontal lobe and higher fc-cc values in the cerebellum and parahippocampus. The difference in fc-cc between the ventral inferior striatum and SMF lobe was significantly correlated with increased disease duration (r = –0.533, P = 0.004), higher HY stage (r = –0.431, P = 0.020), and lower activities of daily living score (r = 0.369, P = 0.049). The correlation of frontostriatal network changes with clinical manifestations suggests that fc-cc may serve as a surrogate marker of disease progression.
Assessment of predictions submitted for the CASP7 domain prediction category

This paper details the assessment process and evaluation results for the Critical Assessment of Protein Structure Prediction (CASP7) domain prediction category. Domain predictions were assessed using the Normalized Domain Overlap score introduced in CASP6 and the accuracy of prediction of domain break points. The results of the analysis clearly demonstrate that the best methods are able to make consistently reliable predictions when the target has a structural template, although they are less good when the domain break occurs in a region not covered by a template. The conditions of the experiment meant that it was impossible to draw any conclusions about domain prediction for free modeling targets and it was also difficult to draw many distinctions between the best groups. Two thirds of the targets submitted were single domains and hence regarded as easy to predict. Even those targets defined as having multiple domains always had at least one domain with a similar template structure. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Earlier finishing of Xp21.2 subband replication of the inactive X chromosome in Rett syndrome girl but not in her 47,XXX mother

X‐inactivation mosaicism has been proposed to explain the origin of Rett syndrome. We present the results of the cytogenetic analysis, including RBG dynamic replication pattern, in a girl with Rett syndrome. The late replicating X chromosome (LRX) showed the earlier replication of subband Xp21.2 in 36% of analysed cells. Unexpectedly the maternal karyotype 47,XXX was found. Replication timing of both maternal LRX chromosomes was normal. The critical region of Xp essential for RS is proposed.
Probabilistic Reverse Annotation for Large Scale Image Retrieval

Automatic annotation is an elegant alternative to explicit recognition in images. In annotation, the image is matched with keyword models, and the most relevant keywords are assigned to the image. Using existing techniques, the annotation time for large collections is very high, while the annotation performance degrades with increase in number of keywords. Towards the goal of large scale annotation, we present an approach called "Reverse Annotation ". Unlike traditional annotation where keywords are identified for a given image, in Reverse Annotation, the relevant images are identified for each keyword. With this seemingly simple shift in perspective, the annotation time is reduced significantly. To be able to rank relevant images, the approach is extended to Probabilistic Reverse Annotation. Our framework is applicable to a wide variety of multimedia documents, and scalable to large collections. Here, we demonstrate the framework over a large collection of 75,000 document images, containing 21 million word segments, annotated by 35000 keywords. Our image retrieval system replicates text-based search engines, in response time.
Identification and Characterization of the Multidrug Resistance Gene cfr in a Panton-Valentine Leukocidin-Positive Sequence Type 8 Methicillin-Resistant Staphylococcus aureus IVa (USA300) Isolate

ABSTRACT The staphylococcal cfr gene mediates resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A, a phenotype that has been termed PhLOPSA. The cfr gene has mainly been associated with coagulase-negative staphylococcal isolates from animals, and only a few cfr-positive methicillin-resistant Staphylococcus aureus (MRSA) isolates have been described so far. This study reports the first description of a cfr-positive MRSA isolate (M05/0060) belonging to the pandemic Panton-Valentine leukocidin (PVL)-positive sequence type 8 MRSA IVa/USA300 (ST8-MRSA-IVa/USA300) clone. The cfr gene was detected in M05/0060 using a DNA microarray which was used to screen PVL-positive MRSA isolates for the presence of virulence genes, typing markers, and antimicrobial resistance genes. Antimicrobial susceptibility testing revealed that M05/0060 exhibited the cfr-associated resistance phenotype. Molecular analysis identified the presence of cfr and a second phenicol resistance gene, fexA, on a novel 45-kb conjugative plasmid, which was designated pSCFS7. Within pSCFS7, a DNA segment consisting of cfr, a truncated copy of insertion sequence IS21-558, and a region with homology to the DNA invertase gene bin3 of transposon Tn552 from Bacillus mycoides was integrated into the transposase gene tnpB of the fexA-carrying transposon Tn558. The emergence of a multidrug-resistant cfr-positive variant of ST8-MRSA-IVa/USA300 is alarming and requires ongoing surveillance. Moreover, the identification of a novel conjugative plasmid carrying the cfr gene indicates the ability of cfr to spread to other MRSA strains.
Age, Intelligence, and Socioeconomic Status Variance in Preposition Acquisition by Children

This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. For more information, please contact pdxscholar@pdx.edu. Recommended Citation Hustead, Georgie, "Age, Intelligence, and Socioeconomic Status Variance in Preposition Acquisition by Children" (1974). Dissertations and Theses. Paper 2175.
Men's places literature review

This literature review examines the prevention of and response to family violence, focusing on the engagement of Indigenous men in remote communities. This report includes information on: engagement barriers to engaging men service paradigms social exclusion changing the orientation of services to engage and support men exploring the potential role of a men’s space. The report highlights the: need to work with Indigenous men limitations of mainstream law and order approaches to family violence lack of an evidence base for community-based approaches to family violence need to use models which represent men’s attitudes to violence, health, service delivery and changes to behavior.
Contractility of the cell rear drives invasion of breast tumor cells in 3D Matrigel

Cancer cells use different modes of migration, including integrin-dependent mesenchymal migration of elongated cells along elements of the 3D matrix as opposed to low-adhesion-, contraction-based amoeboid motility of rounded cells. We report that MDA-MB-231 human breast adenocarcinoma cells invade 3D Matrigel with a characteristic rounded morphology and with F-actin and myosin-IIa accumulating at the cell rear in a uropod-like structure. MDA-MB-231 cells display neither lamellipodia nor bleb extensions at the leading edge and do not require Arp2/3 complex activity for 3D invasion in Matrigel. Accumulation of phospho-MLC and blebbing activity were restricted to the uropod as reporters of actomyosin contractility, and velocimetric analysis of fluorescent beads embedded within the 3D matrix showed that pulling forces exerted to the matrix are restricted to the side and rear of cells. Inhibition of actomyosin contractility or β1 integrin function interferes with uropod formation, matrix deformation, and invasion through Matrigel. These findings support a model whereby actomyosin-based uropod contractility generates traction forces on the β1 integrin adhesion system to drive cell propulsion within the 3D matrix, with no contribution of lamellipodia extension or blebbing to movement.
The comparative study of diabetic specific formula and standard formula on postprandial plasma glucose control in type 2 DM patients.

OBJECTIVE To compare the postprandial plasma glucose level after diabetic specific formula (DSF) and standard formula (SF) administration in type 2 diabetic patients. MATERIAL AND METHOD Thirty type 2 diabetic patients were included in the present randomized, controlled, double-blind, cross-over study. Subjects received DSF and isocaloric SF as a bolus administration of 400 mL while continuing their anti-diabetic medications. Venous blood samples were collected and analyzed to assess plasma glucose levels at pre- and at 30, 60, 90, 120, and 180 min post-administration of the formulas. RESULTS Postprandial glucose profiles were significantly lower with DSF compared to SF administration determined as a mean glucose concentration at 2-hour post-administration. The glucose area under the curve (AUC) after DSF consumption was 33% lower than the AUC after SF consumption, p < 0.001. CONCLUSION Use of DSF resulted in a significantly lower postprandial rise in plasma glucose concentrations than using SF. It should be the preferred option in diabetic patients who need nutritional support.
Bilateral four‐headed biceps brachii muscles: The median nerve and brachial artery passing through a tunnel formed by a muscle slip from the accessory head

Bilateral four‐headed biceps brachii muscles were observed in the dissected cadaver of a 95‐year‐old Japanese woman. The third head on both sides originated from the humerus at the insertion of the coracobrachialis and inserted into the distal part of the biceps brachii and the proximal part of the common biceps tendon on the ipsilateral side. The fourth head on both sides arose from a thin fibrous origin from the intertubercular sulcus and the insertion of the pectoralis major, and inserted into the confluence of the biceps brachii and the third head. This anomaly is relatively rare. Moreover, the left third head gave off a muscle slip into the posterior fascia of the pronator teres, forming a tunnel. The median nerve and the brachial artery passed through the tunnel, where the nerve and artery seemed to be compressed. The possible production of clinical symptoms, given the anatomy, is discussed. Clin. Anat. 11:209–212, 1998. © 1998 Wiley‐Liss, Inc.
Experimental Characterization of an Atmospheric Environment With a Stratospheric Balloon

We report a stratospheric flight with a CNES balloon for which we developed a silicon detector in order to obtain data on the atmospheric radiation environment. The number of detected protons is shown to be directly correlated with the altitude. Simulations with the MC-ORACLE code, which uses pre-calculated fluxes with QARM, are in good agreement with our experimental results.
Becoming Heidegger: On the Trail of His Early Occasional Writings, 1910-1927

An Editor's Introduction Introductory Chronological Overview Heldegger's Academic Career 1909-1930 Part I: Student Years Part II: Early Freiburg Period Part III: The Marburg Period Supplements by Heidegger's Contemporaries Appendix I: Academic Evaluations of Heidegger by His Teachers and Peers Appendix II: Heidegger and Husserl in Correspondence Appendix III: Karl Lowith's impressions of Heidegger and Husserl.
Tissue microarrays for comparing molecular features with proliferation activity in breast cancer

Tissue microarrays (TMAs) are potentially suited to find associations between molecular features and clinical outcome. Enhanced cell proliferation, as measured by Ki67 immunohistochemistry, is related to poor patient prognosis in many different tumor types. Ki67 expression shows considerable intratumoral heterogeneity. It is unclear if the TMA format is suitable for the analysis of potentially heterogeneous markers because of the small size of TMA spots. We have analyzed a breast cancer TMA containing 2,517 breast tissues, including 2,222 neoplastic and 295 normal or premalignant samples, for Ki67 labeling index (Ki67 LI) and additional markers with a known relationship to Ki67 LI by immunohistochemistry (ER, PR, Bcl‐2, Egfr, p16, p53) and Fluorescence in situ hybridization (HER2, MDM2, CCND1, MYC). A high Ki67 LI was linked to tumor phenotype including grade (p < 0.0001), stage (p < 0.0001), nodal stage (p = 0.0018), and patient prognosis (p < 0.0001), elevated protein levels of p53, p16 and Egfr, reduced levels of Bcl2, ER, and PR (p < 0.0001 each), as well as amplifications of HER2, MYC, CCND1 and MDM2 (p < 0.0001 each). In summary, all expected associations between Ki67 and the analyzed molecular markers could be reproduced with high statistical significance using a TMA containing only one tissue sample per tumor, measuring 0.6 mm in diameter. We conclude that associations with cell proliferation can be reliably analyzed in a TMA format. © 2005 Wiley‐Liss, Inc.
Learning Through a Smokescreen: Earnings Management and CEO Compensation over Tenure

We investigate how boards set a CEO’s compensation over her tenure in the presence of performance distortions by the CEO that may confuse the signal that the board gets from reported performance. Career concerns suggest that CEOs have an incentive to distort performance to extend their tenure (Fudenberg and Tirole (1995)), particularly in the early years when there is greater uncertainty about their ability. But managerial discretion in the use of accruals may also be informative about underlying business conditions (Teoh, Welch, and Wong, 1998). Over the CEO’s tenure, as more information is revealed about her ability, boards will place less weight on distorted performance in determining compensation. Consistent with this argument, we find that compensation is positively associated with earnings distortion in the early years of a CEO’s tenure, when less is known about ability, and the relationship becomes weaker and negative over tenure. We show that the relationship between reporting distortions and compensation varies based on CEO characteristics that capture uncertainty about ability and career concerns: earnings management is more strongly correlated with the compensation of younger CEOs; and, CEOs without a fixed-term employment contract. These results are robust to treating tenure and earnings management as endogenous and imply that boards adjust compensation in response to potential earnings distortions in the early years of a CEO’s tenure.
The individual zones of optimal functioning (IZOF) model (1978–2014): Historical overview of its development and use

The individual zones of optimal functioning (IZOF) model is a sport-specific framework that describes the relationship between emotional experiences and relative success in sporting tasks on the basis of individual rather than group-based patterns. Initially developed by the psychologist Juri Hanin in the 1970s, the number of published studies using the model has since significantly grown and diversified. In an effort to create a comprehensive database of IZOF research and reviews, a literature search was conducted using several databases and existing reference lists. This analysis yielded a total of 183 IZOF-based publications (from 380 compiled). The list of publications was subdivided into several categories including general reviews (N = 25), assessment and methodology (N = 13), peer-reviewed and research papers involving samples ranging from elite athletes to physical education students (N = 120). Twenty-five studies were related to communication or interpersonal relationships, coaching and optimisation of performance. Future IZOF research directions will focus on multimodal profiling of athletes’ performance-related emotional and non-emotional experiences, and assessment of individually optimal performance.
A Functional Analysis of Televised U.S. Senate and Gubernatorial Campaign Debates

This study extended previous research on the Functional Theory of Political Campaign Discourse to investigate the nature of 21 U.S. Senate campaign debates and 15 gubernatorial debates from 1994 to 2006. Acclaims were more common than attacks or defenses in Senate (56%, 30%, 14%) and gubernatorial (68%, 30%, 2%) debates. Challengers attacked more and acclaimed less than incumbents in both groups of debates. Senate and gubernatorial incumbents used past deeds much more to acclaim than attack; challengers were prone to use past deeds to attack more than acclaim. There was no consistent effect of political party on functions of debates. The candidates focused more attention on policy than character in Senate (70%, 30%) and gubernatorial debates (73%, 27%). There was no difference in topics stressed by Democrats and Republicans, or incumbents and challengers, in either set of debates. These results are generally consistent with the findings from prior analyses of presidential debates.