Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian identification of admixture events using multilocus molecular markers

Bayesian statistical methods for the estimation of hidden genetic structure of populations have gained considerable popularity in the recent years. Utilizing molecular marker data, Bayesian mixture models attempt to identify a hidden population structure by clustering individuals into genetically divergent groups, whereas admixture models target at separating the ancestral sources of the alleles observed in different individuals. We discuss the difficulties involved in the simultaneous estimation of the number of ancestral populations and the levels of admixture in studied individuals’ genomes. To resolve this issue, we introduce a computationally efficient method for the identification of admixture events in the population history. Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at http://www.rni. helsinki.fi/~jic/bapspage.html.
Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis.

OBJECTIVE To profile the abundance and diversity of subgingival oral microbiota in patients with never-treated, new-onset rheumatoid arthritis (RA). METHODS Periodontal disease (PD) status, clinical activity, and sociodemographic factors were determined in patients with new-onset RA, patients with chronic RA, and healthy subjects. Multiplexed-454 pyrosequencing was used to compare the composition of subgingival microbiota and establish correlations between the presence/abundance of bacteria and disease phenotypes. Anti-Porphyromonas gingivalis antibody testing was performed to assess prior exposure to the bacterial pathogen P gingivalis. RESULTS The more advanced forms of periodontitis were already present at disease onset in patients with new-onset RA. The subgingival microbiota observed in patients with new-onset RA was distinct from that found in healthy controls. In most cases, however, these microbial differences could be attributed to the severity of PD and were not inherent to RA. The presence and abundance of P gingivalis were also directly associated with the severity of PD and were not unique to RA. The presence of P gingivalis was not correlated with anti-citrullinated protein antibody (ACPA) titers. Overall exposure to P gingivalis was similar between patients with new-onset RA and controls, observed in 78% of patients and 83% of controls. The presence and abundance of Anaeroglobus geminatus correlated with the presence of ACPAs/rheumatoid factor. Prevotella and Leptotrichia species were the only characteristic taxa observed in patients with new-onset RA irrespective of PD status. CONCLUSION Patients with new-onset RA exhibited a high prevalence of PD at disease onset, despite their young age and paucity of smoking history. The subgingival microbiota profile in patients with new-onset RA was similar to that in patients with chronic RA and healthy subjects whose PD was of comparable severity. Although colonization with P gingivalis correlated with the severity of PD, overall exposure to P gingivalis was similar among the groups. The role of A geminatus and Prevotella/Leptotrichia species in this process merits further study.
Development of acute hydrocephalus does not change brain tissue mechanical properties in adult rats, but in juvenile rats

Introduction Regional changes in brain stiffness were previously demonstrated in an experimental obstructive hydrocephalus juvenile rat model. The open cranial sutures in the juvenile rats have influenced brain compression and mechanical properties during hydrocephalus development and the extent by which closed cranial sutures in adult hydrocephalic rat models affect brain stiffness in-vivo remains unclear. The aims of this study were to determine changes in brain tissue mechanical properties and brain structure size during hydrocephalus development in adult rat with fixed cranial volume and how these changes were related to brain tissue deformation. Methods Hydrocephalus was induced in 9 female ten weeks old Sprague-Dawley rats by injecting 60 μL of a kaolin suspension (25%) into the cisterna magna under anaesthesia. 6 sham-injected age-matched female SD rats were used as controls. MR imaging (9.4T, Bruker) was performed 1 day before and then at 3 days post injection. T2-weighted anatomical MR images were collected to quantify ventricle and brain tissue cross-sectional areas. MR elastography (800 Hz) was used to measure the brain stiffness (G*, shear modulus). Results Brain tissue in the adult hydrocephalic rats was more compressed than the juvenile hydrocephalic rats because the skulls of the adult hydrocephalic rats were unable to expand like the juvenile rats. In the adult hydrocephalic rats, the cortical gray matter thickness and the caudate-putamen cross-sectional area decreased (Spearman, P < 0.001 for both) but there were no significant changes in cranial cross-sectional area (Spearman, P = 0.35), cortical gray matter stiffness (Spearman, P = 0.24) and caudate-putamen (Spearman, P = 0.11) stiffness. No significant changes in the size of brain structures were observed in the controls. Conclusions This study showed that although brain tissue in the adult hydrocephalic rats was severely compressed, their brain tissue stiffness did not change significantly. These results are in contrast with our previous findings in juvenile hydrocephalic rats which had significantly less brain compression (as the brain circumference was able to stretch with the cranium due to the open skull sutures) and had a significant increase in caudate putamen stiffness. These results suggest that change in brain mechanical properties in hydrocephalus is complex and is not solely dependent on brain tissue deformation. Further studies on the interactions between brain tissue stiffness, deformation, tissue oedema and neural damage are necessary before MRE can be used as a tool to track changes in brain biomechanics in hydrocephalus.
Quality of life in patients after minimally invasive endoscopic atraumatic coronary artery bypass grafting: a long-term follow-up.

BACKGROUND Quality of life (QoL) is an acknowledged parameter that subjectively describes treatment effectiveness and is used also in cardiac surgery. Minimally-invasive totally endoscopic atraumatic coronary artery bypass grafting (EACAB) does not require the use of cardiopulmonary bypass, reduces hospital stay and facilitates early rehabilitation. Therefore, this procedure should significantly improve QoL in patients with coronary artery disease. AIM To assess QoL during a 12-year follow-up in patients who underwent EACAB. METHODS The study group comprised 706 consecutive patients who underwent EACAB between April 1998 and December 2010. Median duration of follow-up was 1918 days. QoL was assessed by either telephone interview or letter correspondence. Complete data were obtained from 413 persons aged 59 ± 6 years. We evaluated the effect of pre- and postoperative variables on QoL. RESULTS Compared with the preoperative period, a marked improvement in QoL after EACAB was reported by 38.6%, and improvement by 37.2% of patients. No change in QoL was noted by 18.8% of subjects, and 5.4% of responders reported deterioration of QoL. The following parameters were found to have no impact on QoL: gender (p = 0.3), myocardial infarction (MI) before EACAB (p = 0.3), diabetes mellitus (p = 0.7), and baseline angina severity by the Canadian Cardiovascular Society (CCS) classification (p = 0.8). Time delay between the surgery and QoL assessment had no impact on the results. During the follow-up, reported QoL was related to the severity of angina symptoms (p = 0.006), need for rehospitalisation (p = 0.02), MI (p = 0.04) and repeated revascularisation (p = 0.02). In multivariate analysis, only MI had a significant impact on QoL (p = 0.04). Current drug therapy had no impact on QoL. CONCLUSIONS EACAB significantly improved QoL in coronary patients. MI during follow-up was associated with deterioration of QoL.
The mitochondrial gene tree comes of age.

Mitochondrial DNA (mtDNA) has been illuminating human evolution for almost 20 years, but it is only now that complete mtDNA sequences are finally being published in substantial numbers. One of the great virtues of mtDNA—arising from its cytoplasmic inheritance, lack of recombination, and high mutation rate—is the opportunity it provides for detailed estimation of the human maternal genealogy. With the arrival of complete sequences, it is timely to make explicit the issue of genealogical resolution, since these data will give us as much information as we can expect ever to obtain on the shape of the mitochondrial gene tree. The issue of genealogical resolution has been a major, often unacknowledged factor from the very beginning, and has underlain many of the debates about demographic history that mtDNA has provoked
From Competitive Regions to Competitive City-Regions: A New Orthodoxy, But Some Old Mistakes

Under the titles of ‘global city-regions’ and the new ‘city regionalism’ there has been a growing support for a resurgence of city-regions within economic geography. While sympathetic to the general tenor of the new city-regionalism, this paper argues for a more synthetic approach to understanding the significance of the city-region. It is argued that the same inherent weaknesses that undermined the previous new regionalist orthodoxy within economic geography, have been collapsed into the present focus upon the scale of the city-region. The paper concludes by looking at the broader implications of this for the future of economic geography.
Salmonella typhi entry into intestinal epithelial cells.

INTRODUCTION Salmonella typhi triggers a microfilament-dependent entry into cultured cells. Kinetic studies have revealed a strict physical limitation on S. typhi Ty2W invation into INT407 human epithelial cells at MOIs•†40. Analyses of time course-infected monolayers showed that all host cells were susceptible to S. typhi entry and that internalized bacteria were typically located in 2-3 foci of infection per host cell. Scanning EM/TEM revealed that the host cell apical surface contained 2-3 focal aggregates containing 1 or few bacteria bound to shortened microvilli. At 10-30 min postinfection, the host cell undergoes surface-detectable, cytoskeletal rearrangements resulting in the macropinocytosis of bound bacteria. These data indicate that S. typhi are internalized at 2-3 entry sites/receptors on infected INT407 cells, after which further entry is limited. Competitive inhibition assays showed that a KmR Ty2W strain was inhibited 2-3 logs in entry efficiency by monolayer pretreatment for 30 min with Ty2W, but did not reduce the microfilament-dependent, Yersinia invasin-mediated entry pathway. S. typhimurium entry was efficiently and competitively inhibited by Ty2W, indicating that these two serovars recognize the same major INT407 cell receptors. Preincubation of INT407 monolayers with mouse monoclonal antibodies to the ƒÀ1 integrin reduced invasion ability of E. coli HB 101
Feeding activity and swimming patterns of Acartia grani and Oithona davisae nauplii in the presence of motile and non-motile prey

The feeding behaviour of the nauplii of the copepods Acartia grani (calanoid) and Oithona davisae (cyclopoid) was investigated in relation to the different motility capabilities of their prey. The prey were the motile dinoflagellate Heterocapsa sp. (equivalent spherical diameter, ESD = 12.8 µm) and the non-motile diatom Thalassiosira weissflogii (ESD = 14.4 µm). Functional response feeding experiments showed that A. grani nauplii exhibited higher ingestion rates on the motile than on the non-motile prey, with maximum daily rations of, respectively, 299 and 185% body C d -1 . O. davisae nauplii showed lower ingestion rates (121% body C d -1 ) and were unable to feed on the non-motile prey. Video observations showed that A. grani nauplii moved with a continuous hopping behaviour, either in a straight or helical pattern; feeding events were observed mainly while swim- ming in helicoids. O. davisae nauplii exhibited a jump and sink behaviour, typical of ambush feeding. Both species showed changes in their behaviour when presented with the motile prey Heterocapsa sp. This indicates that the nauplii are capable of adjusting their feeding behaviour to the different prey characteristics, thereby optimising ingestion rates.
Smartphone Addiction among University Undergraduates: A Literature Review

ABSTRACT Purpose : This paper reviews the growing literature on Smartphone addiction among university undergraduates to identify trends. Design/Methodological Approach: It is based on literature published during the period 1996-2013. Only original research papers have been included in this literature review. The thematic structure has been adopted. In the beginning, such concepts as the symptoms and levels of this addiction will be clarified. Afterwards, the underlying problems and methodological issues raised in the literature will be touched upon. The paper also reviews the relationship between Smartphone addiction among undergraduates and their academic achievement. Finally, significant differences in addiction among undergraduates according to their gender, field of study, parents educational level and family income level will be examined. Findings: While some studies have shown gender differences in Smartphone addictive use, others have proved that gender and Smartphone use are not significantly related. A few studies have examined the relationship between addiction and students' field of study. Some of these Review Article
PREVALENCE OF MENINGEAL WORM (Parelaphostrongylus tenuis) IN WHITE-TAILED DEER FROM NEW HAMPSHIRE1

Parelaphostrongylus tenuis was found in 79 (62.2%) of 127 white-tailed deer heads (Odocoileus virginianus) collected in New Hampshire. Prevalence of infection was higher in fawns and male deer, but older female deer (5.0 + years) had a higher intensity of infection (3.1) than any other age or sex class. Male deer in forest cover type 2 (northern hardwoods-hemlock-white pine) had a significantly greater prevalence of infection than the females in the same habitat (P < .05). Adult females had a higher prevalence of infection (67.0%) than female fawns (20%) in forest cover type 1 (spruce-fir-northern hardwoods). In the craniums examined, P. tenuis was found most frequently in the tentorium cerebelli (23.6%) while the falx cerebri, the most prevalent site of infection in fawns, was a significantly less frequent site of infection in older deer (P < .02). Male deer of age class 3.5 years had a significantly higher rate of infection in the dura mater-olfactory lobe than any other age or sex group (P <.02). The cavernous sinus was the most frequent site of parasitism in male fawns (25.0%) and was the second most common location in all deer (13.4%).
Mouse cone arrestin expression pattern: light induced translocation in cone photoreceptors.

PURPOSE Arrestins are a superfamily of regulatory proteins that down-regulate activated and phosphorylated G-protein coupled receptors (GPCRs). Cone arrestin (CAR) is expressed in cone photoreceptors and pinealocytes and may contribute to the shutoff mechanisms associtated with high acuity color vision. To initiate a study of CAR's function in cone phototransduction, the mouse CAR (mCAR) transcript and protein expression patterns are examined and in vitro binding assays are also presented. METHODS Tissue distribution of mCAR was determined by Northern and immunoblot analyses and its cellular localization identified by In situ hybridization and immunohistochemistry. The protein expression pattern of mCAR in the postnatal developmental and adult mouse retina was analyzed by immunoblotting in normal C57 and rd/rd mouse retinas. In vitro binding assays with in vitro translated arrestins were used to study the interaction of mCAR and mouse S-antigen (mSAG) with embryonic chicken outer segment (OS) membranes containing both rod and cone opsins. RESULTS MCAR has a high level of amino acid sequence identity with orthologous sequences reported for other species except the C-terminal region, which is highly conserved between mouse and rat but divergent in other species. MCAR is expressed exclusively in the retina and the pineal gland, and unique isoforms are expressed during postnatal development of the retina and the pineal gland. The postnatal developmental expression pattern of mCAR and mSAG in the rd/rd mouse retina parallels the generation and degeneration of the cone and rod photoreceptors in these mice. In situ and immunohistochemistry both reveal cone-specific expression of mCAR in the retina. Immunofluorescent staining of retinal sections from dark-adapted or light-exposed mice suggests a light-dependent translocation of mCAR immunoreactivity from the cone inner segments (CIS) and other parts of the cell body to the cone outer segments (COS), similar to but not as dramatic as rod arrestin. In vitro binding assays show a small yet significant increase in binding of the full-length mCAR (mCARFL) to embryonic chicken OS membranes following light activation and phosphorylation of the opsins in the membranes. CONCLUSIONS MCAR is expressed in retinal cone photoreceptors and the pineal gland. The light-dependent translocation of mCAR immunoreactivity and the increase of mCAR binding to light-activated, phosphorylated embryonic chicken OS membranes, compared to its binding to dark, unphosphorylated membranes, suggest the possibility that mCAR is involved in shutting off the phototransduction cascade in cone photoreceptors as rod arrestin does in rod photoreceptors. However, prominent differences exist between rod arrestin and CAR, suggesting other functions for CAR.
Influence of Cochlear Function on Auditory Temporal Resolution in Tinnitus Patients

Our aim was to analyze the influence of subtle cochlear damage on temporal auditory resolution in tinnitus patients. Forty-eight subjects (hearing threshold ≤25 dB HL) were assigned to one of two experimental groups: 28 without auditory complaints (mean age, 28.8 years) and 20 with tinnitus (mean age, 33.5 years). We analyzed distortion product otoacoustic emission growth functions (by threshold, slope, and estimated amplitude), extended high-frequency thresholds, and the Gaps-in-Noise test. There were differences between the groups, principally in the extended high-frequency thresholds and the Gaps-in-Noise test results. Our findings suggest that subtle peripheral hearing impairment affects temporal resolution in tinnitus, even when pure-tone thresholds as conventionally measured appear normal.
Spatial Distributions of Trapping Centers in $ \hbox{HfO}_{2}/\hbox{SiO}_{2}$ Gate Stack

An analysis methodology for charge pumping (CP) measurements was developed and applied to extract spatial distributions of traps in SiO 2/HfO2 gate stacks. This analysis indicates that the traps accessible by CP measurements in the frequency range down to a few kilohertz are located primarily within the SiO2 layer and HfO2/SiO2 interface region. The trap density in the SiO2 layer increases closer to the high-kappa dielectric, while the trap spatial profile as a function of the distance from the high-kappa film was found to be dependent on high-kappa film characteristics. These results point to interactions with the high-kappa dielectric as a cause of trap generation in the interfacial SiO2 layer
A Large-Scale Evaluation of a Model for the Evaluation of Games for Teaching Software Engineering

In order to adopt games for Software Engineering (SE) education effectively it is essential to obtain sound evidence on their quality. A prominent evaluation model is MEEGA (Model for the Evaluation of Educational Games), which provides a systematic support to evaluate the game's quality in terms of motivation, user experience and learning. To facilitate its application, the model provides a questionnaire for collecting data on the perception of the students after they played an educational game in a case study with a one-shot post-test design. However, in order to assure a valid feedback on the game's quality an important issue is the reliability and validity of the questionnaire. In this respect, this article presents a large-scale evaluation of the MEEGA questionnaire in terms of reliability and construct validity. The analysis is based on data collected in 43 case studies, evaluating 20 different SE games, involving a population of 723 students. Our analysis indicates that the MEEGA questionnaire can be considered reliable (Cronbach's alpha α=.915). In terms of construct validity, there exists evidence of convergent validity through an acceptable degree of correlation of almost all item pairs within each dimension. Yet, we identified a need for the re-grouping of items based on the results of a factor analysis, mainly with respect to items related to motivation and user experience. These results allow SE researchers and instructors to rely on the MEEGA questionnaire in order to evaluate SE games and, thus, contribute to their improvement and to direct an effective and efficient adoption for SE education.
Cell surface protease PRT1 identified in the fungal pathogen Pneumocystis carinii

The subtelomeric regions of the chromosomes of many organisms contain gene families that allow adaptation to a changing environment. In a number of parasites, these subtelomeric gene families encode cell surface proteins that undergo antigenic variation. Proteases are another important virulence determinant in pathogenic microorganisms. We report the localization of the PRT1 protease of the pathogenic fungus Pneumocystis carinii sp. f. carinii, encoded by a subtelomeric gene family, to the cell surface of both the trophozoite and the cyst phase of the organism. Using anti‐PRT1 antiserum, we demonstrated specificity to P. carinii sp. f. carinii in sections of infected rat lungs and, using immunofluorescence, we showed that the PRT1 protease has the characteristic distribution of a surface protein. The anti‐PRT1 antiserum showed cross‐reactivity with a number of P. carinii sp. f. carinii proteins migrating between 185 kDa and 28 kDa, the majority migrating between 42 kDa and 52 kDa, a region that has been shown by serological studies to contain important immunodominant P. carinii proteins. Cross‐reactivity was also observed with P. carinii sp. f. hominis proteins. We have also cloned a portion of the catalytic domain of PRT1 from P. carinii sp. f. hominis, P. carinii sp. f. muris and P. carinii sp. f. rattus. Our data suggest that the PRT1 protease plays an important role in the pathogenicity of P. carinii.
Results in Optimal Discrimination

We study the problem of discriminating between non‐orthogonal quantum states with least probability of error. We demonstrate that this problem can be simplified if we solve for the error itself rather than solving directly for the optimal measurement. This method enables us to derive solutions directly and thus make definite statements about the uniqueness of an optimal strategy. This approach immediately leads us to a state‐discrimination analogue of Davies Theorem.In the course of this, a complete solution for distinguishing equally likely pure qubit states is presented.