Miracle-dz/UniFAR-FTUs huggingface dataset:
Population genomic analyses of early-phase Atlantic Salmon (Salmo salar) domestication/captive breeding

Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild Atlantic salmon (Salmo salar L.) populations are threatened by anthropogenic influences, and they are supplemented with captively bred fish. The Atlantic salmon is also widely used in selective breeding programs to increase the mean trait values for desired phenotypic traits. We analyzed a genomewide set of SNPs in three domesticated Atlantic salmon strains and their wild conspecifics to identify loci underlying domestication. The genetic differentiation between domesticated strains and wild populations was low (FST < 0.03), and domesticated strains harbored similar levels of genetic diversity compared to their wild conspecifics. Only a few loci showed footprints of selection, and these loci were located in different linkage groups among the different wild population/hatchery strain comparisons. Simulated scenarios indicated that differentiation in quantitative trait loci exceeded that in neutral markers during the early phases of divergence only when the difference in the phenotypic optimum between populations was large. This study indicates that detecting selection using standard approaches in the early phases of domestication might be challenging unless selection is strong and the traits under selection show simple inheritance patterns.
Comparison of Basic Visual Servoing Methods

In this paper, comparison of the position-based and image-based robot visual servoing methods is investigated, with an emphasis on the system stability, robustness, sensitivity, and dynamic performance in the Cartesian and image spaces. A common comparison framework using both predefined and taught references is defined in the context of the sensory task space robot control approach. The camera, target, and robot modeling errors in the system are considered in the comparison. Both methods are shown to be locally asymptotically stable and locally robust with respect to modeling errors. While the two methods are shown to be comparable and sensitive to the camera and target modeling errors when using predefined references, they are insensitive to these errors when using taught references. However, the system Cartesian and image trajectories and time-to-converge are affected by the camera, target, and robot modeling errors regardless of the type of references. Finally, other fundamental characteristics of the two methods including sensory task space singularity and local minima, motion coupling, and implementation issues are also compared. The comparison results are verified in simulations.
Intraabdominal complications secondary to ventriculoperitoneal shunts: CT findings and review of the literature.

OBJECTIVE The purpose of our study was to evaluate the abdominopelvic CT findings of various intraabdominal complications secondary to ventriculoperitoneal shunts for hydrocephalus and to review the literature. MATERIALS AND METHODS The CT images of 70 patients (33 men and 37 women; mean age, 48.5 years) who underwent ventriculoperitoneal shunt placement and abdominopelvic CT because of shunt-related abdominal symptoms were reviewed retrospectively. CT images were analyzed with regard to the location of the shunting catheter tip; site, size, wall, and septa of localized fluid collection; peritoneal thickening; omentomesentery infiltration; abscess; bowel perforation; abdominal wall infiltration; and thickening of the catheter track wall. RESULTS The mean period between the last ventriculoperitoneal shunting operation and CT was 11 months (range, 1 week to 115 months), and the mean number of ventriculoperitoneal shunting operations undergone was 1.4 (range, 1-6). A total of 76 ventriculoperitoneal shunting catheters were introduced in 70 patients: 64 patients had a unilateral catheter inserted and six patients had bilateral catheters inserted. Sixteen patients (22.9%) were pathologically diagnosed with ventriculoperitoneal shunt-related complications: 11 cases (15.7%) of shunt infection, six cases (8.6%) of CSF pseudocyst, four cases (5.7%) of abdominal abscess, three cases (4.3%) of infected fluid collection, and one case (1.4%) of bowel perforation. Microorganisms were cultured from the tip of the shunting catheter or peritoneal fluid in 11 patients (15.7%). CONCLUSION On abdominopelvic CT, various intraabdominal complications secondary to ventriculoperitoneal shunt were shown, of which, shunt infection was the most common, followed by CSF pseudocyst, abscess, and infected fluid collection.
Risk Factors for Postoperative Bleeding in Endoscopic Submucosal Dissection of Colorectal Tumors

Background: Colonoscopic removal of adenomatous polyps or early cancer prevents death from colorectal cancer. Endoscopic submucosal dissection (ESD), which enables endoscopists to perform en bloc resection of flat or depressed colorectal tumors >20 mm, has recently been introduced and become a standard procedure in Japan. Although postoperative bleeding (POB) is a major complication associated with ESD, risk factors for POB have not been fully identified. Methods: A total of 451 patients (509 lesions) who underwent colorectal ESD were retrospectively analyzed to identify clinical parameters associated with POB. Results: POB occurred in 14 patients, and 7 of them had received antithrombotic therapy before ESD. Uni- and multivariate analyses revealed that antithrombotic therapy and rectal tumor location were strongly associated with POB following colorectal ESD. The incidence of POB was higher in patients on heparin bridge therapy (HBT) for the replacement of antithrombotic therapy than in patients with no HBT. Four of 7 patients (57.1%) on antithrombotic therapy experienced POB from the rectal lesions. Conclusion: Antithrombotic therapy and rectal lesions result in a higher POB incidence after colorectal ESD.
Prevalence of significant carotid artery stenosis in patients with transient ischaemic attack.

BACKGROUND Carotid artery stenosis is one of the risk factors for transient ischaemic attack (TIA) and stroke. The purpose of this study was to investigate the prevalence of carotid artery stenosis and the prevalence of candidates for carotid endarterectomy in a hospital-based cohort of TIA patients under 71 years of age. MATERIAL/METHODS This retrospective study included 205 patients with TIA admitted to an acute stroke unit. A carotid Doppler sonography was performed in 114 patients with TIAs in the internal carotid artery territory and a mean age of 60 years. Based on Doppler examinations, the patients were divided into 4 groups according to the following degrees of stenosis: 40-59%, 60-79%, 80-99% stenosis, and occlusion. RESULTS Doppler examinations showed that 5% had a 40-59% stenosis, 5% had stenosis >60% and 4% had occlusion of the relevant internal carotid artery. Carotid endarterectomy was done in 2% of the patients. Carotid artery stenosis was associated with a history of angina pectoris and myocardial infarction in univariate analysis, but not in multivariate analysis. CONCLUSIONS The prevalence of significant carotid artery stenosis on the relevant side in patients with TIA was quite low: only 5% had a degree of stenosis where carotid endarterectomy should be considered. Only 2% eventually had carotid endarterectomy.
The Impact of Durable Relationship with Banks when Crisis Hits

ABSTRACT Firms develop relationships with their banks in order to ensure access to financing when credit conditions deteriorate in time of crisis. I investigate the effect of bank-firm relationships in Turkey where 90 percent of a firm’s financial debt is obtained through bank loans. I find that adjusted for loan terms and firm-fixed effects, borrowers with past relationships with incumbent banks have lower risk-adjusted financing costs. Furthermore, lower financing costs associated with relationship are even more pronounced during the 2008–2009 financial crisis.
DIAGNOSIS AND TREATMENT OF PRIMARY VAGINAL CARCINOMA IN SITU AND DYSPLASIA

Abstract. Fifteen cases of primary carcinoma in situ or severe or moderate dysplasia of the vagina have been diagnosed and treated during the period 1966–75 at the Department of Obstetrics and Gynecology, Turku University Central Hospital. Because of abnormal vaginal cytology the lesion was localized by means of colposcopy and iodine staining. For 6 patients local estrogen treatment was applied to increase the thickness of the epidermal layer. For 6 patients, treatment consisted of simple excision. Nine patients, including both those with carcinoma in situ, were treated with intravaginal radiation therapy. The radiation dosage was 2000 to 2600 rad at a distance of 1 cm from the surface of the epithelium. None of the patients showed any complications, and all are now symptom‐free.
Circulating ghrelin levels in patients with inflammatory bowel disease

Ghrelin, the gut-brain peptide recently identified as the natural endogenous ligand for growth hormone secretagogue receptors, exerts various endocrine and non-endocrine effects, including control of food intake and energy homeostasis.1 It could also play a role in modulating immune responses and inflammatory processes.1 Indeed, ghrelin exerts potent anti-inflammatory effects in vitro and in vivo,1–5 and high circulating ghrelin levels have been found in rats with septic shock, cysteamine induced duodenal ulcers, and adjuvant induced arthritis.4–6 Also, we have recently demonstrated that in patients with newly diagnosed coeliac disease, circulating ghrelin levels are abnormally high, correlate positively with intestinal mucosal lesion severity, and normalise in successfully gluten free diet treated patients.7 However, normal or even decreased ghrelin levels have been found in other inflammatory diseases, including rheumatoid arthritis and Helicobacter pylori associated …
Differential effects of retinoic acid and growth factors on osteoblastic markers and CD10/NEP activity in stromal‐derived osteoblasts

The effects of retinoic acid (RA) on the expression of osteoblastic‐related cell makers was examined. A marrow and osteogenic cell line, MBA‐15, was analyzed by Northern blotting for the expression of bone matrix proteins. These cells constituentively express mRNA encoding for procolllagen a2 (1), osteonectin, osteopontin, biglycan and alkaline phosphatase (ALK‐P). Gene expression was unchanged in response to RA triggering for 24hr. Furthermore, cell growth and enzymatic activities of ALK‐P and neutral endopeptidase (CD10/NEP) were studied. These parameters were examined in MBA‐15 and clonal populations representing different stages of differentiation. The cell's growth rate was unchanged, while ALK‐P activity was greatly increased during the culture period under RA treatment in MBA‐15 and in the clonal cell lines examined while CD10/NEP activity dispalyed a different pattern. MBA‐15.4, a presosteoblast cell ine, exhibited an inhibition in CD10/NEP activity at the beginning of the culture period, reaching basal level with time. This activity was greatly increased over control level in MBA‐15.6, a mature stage of osteoblasts. Furthermore, the response of cell lines to various growth factors was tested subsequent to priming the cultures with RA. A synergistic effect was monitored for ALK‐P activity in MBA‐15.4 and MBA‐15.6 cells under rh‐bone morphogenic protein (BMP‐2) and purified osteogenin (BMP‐3), and an antagonist effect was measured when cells were exposed to transforming growth factor β (TGFβ). Contrarily, BMP‐2 and BMP‐3 inhibited the CD10/NEP activity that had remained unchanged following priming of the cell with RA. Insulin‐like growth factor 1 (IGF‐1) and basic fibroblast growth factors (bFGF) did not affect either ALK‐P nor CD10/NEP activities in both cloned cells. Cellular response to bone‐seeking hormone, parathyroid hormone (PTH), and prostaglandin E2 (PGE2) was monitored by activation of intracellular cAMP. Treatment with RA caused a dramatic increase in MBA‐15.6 cell responses to PTH and PGE2 but no significant effects could be observed in other clonal lines.
Positional Stability of Damaged Chromatin Domains along Radiation Tracks in Mammalian Cells

Abstract Jakob, B. , Splinter, J. and Taucher-Scholz, G. Positional Stability of Damaged Chromatin Domains along Radiation Tracks in Mammalian Cells. Radiat. Res. 171, 405–418 (2009). Irradiation of cell nuclei with charged particles leads to the spatially defined production of DNA damage along the particle trajectories, thus facilitating studies on the dynamics of radiation-induced protein foci associated with lesion processing. Here we used visual inspection and computational analysis of the track morphology after immunodetection to describe the patterns of formation of γ-H2AX foci and the repair-related proteins 53BP1 and RPA. We addressed the influence of lesion density on γ-H2AX formation and the mobility of damaged chromatin sites by using low-angle irradiation of cell monolayers with low-energy carbon or uranium ions. We show the discrete formation of γ-H2AX foci and the recruitment of repair-related proteins along ion trajectories over an LET range from 200 to 14300 keV/μm in human fibroblasts and in HeLa cells. The marked DSBs exhibited a limited mobility that was independent of the LET. The moderate extent of mobility in human fibroblasts pointed to a relatively stable positioning of the damaged chromatin domains during repair, in contrast to HeLa cells, which showed significant changes in the streak patterns in a fraction of cells, suggesting greater mobility in the local processing of DSBs. Our data indicate that the presence of single or multiple DSBs is not associated with an altered potential for movement of damaged chromatin. We infer that the repair of high-LET radiation-induced DSBs in mammalian cells is not coupled to an increased motional activity of lesions enhancing the probability of translocations.
Establishment of a human cell line (mono mac 6) with characteristics of mature monocytes

A monocytic cell line, termed Mono Mac, was established from peripheral blood of a patient with monoblastic leukemia. Two clones, designated Mono Mac I and Mono Mac 6, were isolated and both were assigned to the monocyte lineage on the basis of morphological, cytochemical and immunological criteria. Most importantly, the clones express NaF‐sensitive non‐specific‐esterase, produce reactive oxygen and stain with MAb My4. Mono Mac 6, in addition, constitutively exhibits phagocytosis of antibody‐coated erythrocytes in 80% of the cells and reacts with a panel of MAbs that are specific for mature monocytes, i.e., M42, LeuM3, 63D3, Mo2 and UCHMI. By contrast, the monoblastic cell lines U937 and THP‐I are negative for all these markers. Only expression of My4 could be detected after differentiation induced by interferon‐γ (IFN‐γ). Similar treatment of Mono Mac I, however, resulted in staining with all the monocyte‐specific MAbs mentioned above, while IFN‐γ treatment of Mono Mac 6 enhanced antigen expression. In addition, the cells showed an increased frequency of multinucleated cells with a rise from 4.8% to 21.9%. Mono Mac 6 appears to be the only one of the cell lines studied to constitutively express phenotypic and functional features of mature monocytes.
Dynamics of international negotiations : a simulation of EU intergovernmental conferences

Complex negotiations seem indeterminate. In constellations with many negotiation parties, each consisting of internal factions, varying internal decision rules and more or less defined organizational boundaries, bargaining over multiple issues over more than one sequence, make outcomes unpredictable. Despite providing useful abstract representations of such processes, game theory is often limited to highly stylized set-ups. Relying on the behavioral assumptions of the Zeuthen-Harsanyi process model we propose a dynamic simulation model. We explicitly take into account of preferential and informational determinants of governments' risk attitudes. We empirically confront predicted outcomes with actual negotiation outcomes, using quantitative data for the complex multi-lateral, multi-level, multi-issue negotiation system of the EU intergovernmental conference of 1996, which resulted in the Amsterdam treaty.
Comparison of two α1‐adrenoceptor antagonists, naftopidil and tamsulosin hydrochloride, in the treatment of lower urinary tract symptoms with benign prostatic hyperplasia: a randomized crossover study

To compare the efficacy of two α1‐adrenoceptor antagonists, α1A‐adrenoceptor‐selective tamsulosin hydrochloride and α1D‐adrenoceptor‐selective naftopidil, in the treatment of lower urinary tract symptoms (LUTS) with benign prostatic hyperplasia (BPH).
Skeletal muscle fibre type and capillary density in college-aged blacks and whites.

The purpose of this study was to compare muscle fibre type proportions and capillary density in untrained, college-aged blacks (n = 14) and whites (n = 14). Both groups were similar in terms of peak oxygen uptake (VO2peak), measured during cycle ergometry (blacks: 42.6 +/- 4, whites: 44.3 +/- 4 ml.kg-1 min-1, mean +/- SD). Muscle samples were obtained from the quadriceps femoris (vastus lateralis) by the needle biopsy technique. Fibre type was determined by myosin ATPase stain (pH = 4.54) and capillaries were identified by amylase-periodic acid Schiff (PAS) stain. The percentage of type I, IIa, and IIb fibres in the blacks was 39.5 +/- 11.5, 40.0 +/- 8.4, and 22.8 +/- 9.8, respectively. In whites the percentage of type I, IIa, and IIb fibres was 44.9 +/- 8.5, 36.6 +/- 6.9, and 18.3 +/- 9.6, respectively. No significant differences were noted between the two racial groups for type I, IIa, or IIb fibres. Capillary density was 277 +/- 39/mm2 in the blacks compared to 289 +/- 32/mm2 in the whites. Capillary density was positively correlated to percentage of type I fibres (r = 0.497) and negatively correlated to percentage of type IIa fibres (r = -0.389), in the overall study population. These data suggest that if racial differences in fibre type do exist, such differences are small compared to the variability in this measure.
The simian immunodeficiency virus mnd(GB-1) strain uses CXCR4, not CCR5, as coreceptor for entry in human cells.

The simian immunodeficiency virus (SIV) mnd(GB-1) strain, isolated from a mandrill, replicates in a human T cell line, CEM cells, and is inhibited by the CXC-chemokines, stromal cell-derived factor 1alpha and 1beta (SDF-1alpha/SDF-1beta), the natural ligands for CXCR4. The IC50 was around 70-80 ng/ml, which corresponds to the IC50 of SDF-1alpha/SDF-1beta for T-tropic human immunodeficiency virus type 1 (HIV-1) and HIV-2. The specific anti-CXCR4 MAb 12G5 inhibited replication of SIVmnd at an IC50 of 1 microg/ml. Also, the IC50 of 8 ng/ml for SIVmnd of the bicyclam AMD3100, a specific CXCR4 antagonist, is comparable with its IC50 for T-tropic HIV-1 and HIV-2 strains. Two other SIV strains, SIVagm3 and SIVmac251, were insensitive to SDF-1alpha/SDF-1beta, anti-CXCR4 MAb and AMD3100. SIVmnd replicates only in HOS.CD4 cells expressing CXCR4 and not in HOS.CD4 transfectants expressing CCR1, CCR2b, CCR3, CCR4 or CCR5. This is, to our knowledge, the first SIV strain found to use CXCR4 and not CCR5 as a main coreceptor for entering human cells.
CEO Turnover in Large Banks: Does Tail Risk Matter?

In a cross-country setting we show the probability of a forced CEO turnover in large banks is positively associated with idiosyncratic tail risk. This finding is strengthened the greater the competition in the banking industry and when stakeholders have more to lose in the case of distress. Overall, the exposure to idiosyncratic tail risk offers valuable signals to bank boards on the quality of the choices made by CEOs. In contrast, systematic tail risk becomes important for forced CEO turnovers only in the presence of a major variation in the costs this risk generates for shareholders and the organization.
The Effect Of Earnings Quality On The Predictbaility Of Accruals And Cash Flow Models In Forcasting Future Cash Flows

Earnings management affects negatively the quality of earnings which affect the predictability of earnings. The main questions this paper answer are: (1) is the superiority of aggregate earnings over aggregate cash flows affected by the level of earnings quality? (2) Is the superiority of aggregate earnings over the main components of earnings (i.e. operating cash flows, accounts receivable, inventory, accounts payable, and depreciation) affected by the level of earnings quality? The methodology used in this study is a development of the study of Barth et al (2001). We provide replication of their main analysis, and then extend this to deal with the effect of earnings quality. Three main measures for earnings quality used (i.e. the modified Jones model (MJ, the modified Jones model with return on assets (MJROA) and the accruals quality (AQ). To provide answers on the questions of this study, the whole sample of the study is divided into two groups according to the level of earnings quality: high earnings quality and low earnings quality. The study covers the case of Jordan and employs data on a sample of industrial and services firms. The time horizon of this study includes the period of 2000-2014. The main conclusions of this study is derived from comparing the adjusted R2 of the models employed using Vuong's test. The results of the analysis reveal that the quality of earnings affect the predictability of both cash flow and earnings in that earnings outperform cash flows in predicting one-year a head future cash flow when earning quality is high. On the other hand, the main component earnings reveal incremental information content beyond that exist in earnings or cash flow regardless of the quality of earnings. These findings suggest that operating cash flow is appreciated by the market when earnings quality is low. In addition, the finding of this study provide more evidence on the importance of using all the accounting data provided in the financial statement to predict future cash flow to avoid the effect of earnings management on the predictability of the accounting data. This paper contribute to the existence literature in different ways: (i) provide more evidence on the superiority of cash flows over earnings based on developing countries as most the evidence were based on developed countries. (ii) the results shed light on the role of earnings management in destroying the reliability of earnings as a tool to predict future cash flows.