Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Ascertainment Bias on Recovering Human Demographic History

In recent years multilocus data sets have been used to study the demographic history of human populations. In this paper (1) analyses previously done on 60 short tandem repeat (STR) loci are repeated on 30 restriction site polymorphism (RSP) markers; (2) relative population weights are estimated from the RSP data set and compared to previously published estimates from STR and craniometric data sets; and (3) computer simulations are performed to show the effects of ascertainment bias on relative population weight estimates. Not surprisingly, given that the RSP markers were originally identified in a small panel of Caucasians, estimates of relative population weights are biased and the European population weight is artificially inflated. However, the effects of ascertainment bias are not apparent in a principal components plot or estimates of FST. Ascertainment bias can have a large effect in other genetic systems with inherently low heterozygosity such as Alus or single nucleotide polymorphisms (SNPs), and care must be taken to have prior knowledge of how polymorphic markers in a given data set were originally identified. Otherwise, results can be skewed and interpretations faulty.
Inheritance Taxation and Wealth Effects on the Labor Supply of Heirs

The taxation of bequests can have a positive impact on the labor supply of heirs through wealth effects. This leads to an increase in future labor income tax revenue on top of direct bequest tax revenue. We first show in a theoretical model that a simple back-of-the envelope calculation, based on existing estimates for the reduction in earnings after wealth transfers, fails: the marginal propensity to earn out of unearned income is not a sufficient statistic for the calculation of this effect because (i) heirs anticipate the reduction in net bequests and adjust their labor supply already prior to inheriting, and (ii) when bequest receipt is stochastic, even those who ex post end up not inheriting anything respond ex ante to the implied change in their distribution of net bequests. We quantitatively elaborate the size of the overall revenue effect due to labor supply changes of heirs by using a state of the art life-cycle model that we calibrate to the German economy. Besides the joint distribution of income and inheritances, quasi-experimental evidence regarding the size of wealth effects on labor supply is a key target for this calibration. We find that for each Euro of bequest tax revenue the government mechanically generates, it obtains an additional 9 Cents of labor income tax revenue (in net present value) through higher labor supply of (non-)heirs.
Barriers to dog rabies vaccination during an urban rabies outbreak: Qualitative findings from Arequipa, Peru

Background Canine rabies was reintroduced to the city of Arequipa, Peru in March 2015. The Ministry of Health has conducted a series of mass dog vaccination campaigns to contain the outbreak, but canine rabies virus transmission continues in Arequipa’s complex urban environment, putting the city’s 1 million inhabitants at risk of infection. The proximate driver of canine rabies in Arequipa is low dog vaccination coverage. Our objectives were to qualitatively assess barriers to and facilitators of rabies vaccination during mass campaigns, and to explore strategies to increase participation in future efforts. Methodology/Principal findings We conducted 8 focus groups (FG) in urban and peri-urban communities of Mariano Melgar district; each FG included both sexes, and campaign participants and non-participants. All FG were transcribed and then coded independently by two coders. Results were summarized using the Social Ecological Model. At the individual level, participants described not knowing enough about rabies and vaccination campaigns, mistrusting the campaign, and being unable to handle their dogs, particularly in peri-urban vs. urban areas. At the interpersonal level, we detected some social pressure to vaccinate dogs, as well as some disparaging of those who invest time and money in pet dogs. At the organizational level, participants found the campaign information to be insufficient and ill-timed, and campaign locations and personnel inadequate. At the community level, the influence of landscape and topography on accessibility to vaccination points was reported differently between participants from the urban and peri-urban areas. Poor security and impermanent housing materials in the peri-urban areas also drives higher prevalence of guard dog ownership for home protection; these dogs usually roam freely on the streets and are more difficult to handle and bring to the vaccination points. Conclusions A well-designed communication campaign could improve knowledge about canine rabies. Timely messages on where and when vaccination is occurring could increase dog owners’ perception of their own ability to bring their dogs to the vaccination points and be part of the campaign. Small changes in the implementation of the campaign at the vaccination points could increase the public’s trust and motivation. Location of vaccination points should take into account landscape and community concerns.
Does research and development (R&D) investment lead to economic growth? Evidence from the South African peach and nectarine industry

Agricultural research programmes in Africa have experienced waning state financial allocations. Efforts to change these funding trends have been fettered by the limited evidence of research investment benefits and the long lags associated with these returns. In a bid to provide such information, this article seeks to calculate the benefits of investments in the Agricultural Research Council’s peach and nectarine research programme – one of Africa’s successful and oldest research programmes. It uses the supply response function to model South Africa’s peach and nectarine industry and estimates the effect of deciduous fruit prices, production costs, research investment and weather on production. A lag distribution of research and development (R&D) investment is estimated using the polynomial distribution function and the derived elasticities are used to calculate the marginal internal rate of return. The study’s results reveal that investment in the peach and nectarine programme is associated with a marginal internal rate of return of 55.9%. This means that every R100 invested yields a R55.9 increase in value in the peach and nectarine industry. In light of these findings, it is concluded that R&D investment is worthwhile and recommends that the funding allocated to this programme be increased.
Cyclooxygenase-2 Expression Is Related With Localization, Proliferation, and Overall Survival in Canine Melanocytic Neoplasms

A direct relationship has been firmly established between cyclooxygenase-2 (COX-2) expression and malignant behavior in human melanoma. This report examines the relationship between COX-2 expression and tumor location, mitotic and proliferative indices, degree of T CD3+ lymphocyte infiltration, overall survival, and frequency of recurrence and metastasis of 57 melanocytic tumors (25 oral and 32 cutaneous). COX-2 was highly or moderately expressed in 88% of oral neoplasms (22 of 25), whereas for their cutaneous counterparts, COX-2 expression was low or insignificant in 75% of cases (24 of 32). High and moderate COX-2 expression levels were observed in 73% of melanocytic tumors with a mitotic index ≥ 3 per 10 high-power fields (26 of 36), whereas in 81% of tumors with a mitotic index < 3 (17 of 21), expression was mild or absent. There were 41 cases with known clinical outcomes; of those showing high, moderate, and mild COX-2 expression, 83.3% (10 of 12), 37.5% (3 of 8), and 25% (2 of 8) died, respectively, whereas 100% of animals showing no COX-2 expression (13 of 13) were still alive at the last follow-up. COX-2 expression was statistically correlated with tumor location, mitotic and percentage Ki-67 proliferative indices, and overall survival, frequency of neoplastic recurrence and metastasis. Regression analysis also showed disease-specific predictive value for COX-2 expression for subjects with melanocytic neoplasms. Additionally, only high COX-2 expression showed significant differences in overall survival, in comparison with moderate, mild, or absent expression. These results suggest that high COX-2 expression may be considered a prognostic biomarker and potentially as a target for therapeutic and preventive strategies in canine melanocytic neoplasms.
Epidermal Growth Factor Receptor Mutation Testing in the Care of Lung Cancer Patients

As the literature about epidermal growth factor receptor (EGFR) mutations grows and screening for mutations becomes increasingly integrated into clinical care, it is important to examine how best to do somatic mutational analyses and how best to use the test results in clinical decision making. We began offering mutation screening by comprehensive direct sequence analysis of exons 18 to 24 of the tyrosine kinase domain of EGFR in August 2004 as part of clinical cancer care and protocol therapy at our institutions. All identified potential mutations are confirmed with three to five independent PCRs of the original genomic DNA sample and, if not previously noted in the literature, are compared with the patient's germ-line DNA to ensure the finding is somatic. We formally analyzed the first 100 patients to undergo EGFR sequence analysis and found that testing was feasible and significantly affected the treatment of patients with non–small cell lung cancer (NSCLC). Patients harboring EGFR mutations were significantly more likely to receive recommendations for therapy with EGFR tyrosine kinase inhibitors (i.e., gefitinib or erlotinib) than patients without mutations. However, negative EGFR test results did not prevent physicians from administering these agents to selected patients. Ideally, a standardized technique for mutation testing could be developed, with demonstrated reproducibility and validity. Clinical trials incorporating molecular diagnostics are ongoing to assess the efficacy of EGFR tyrosine kinase inhibitors as first-line therapy for metastatic NSCLC and as adjuvant therapy for early-stage resected NSCLC. It is likely that mutation testing and other molecular analyses will be most useful in these two clinical situations.
Reduction of Foxp3+ T cell subsets involved in incidence of chronic graft‐versus‐host disease after allogeneic hematopoietic stem cell transplantation

Foxp3+ T cells (CD4+ Tregs and CD8+ Treg) have been demonstrated to play roles in the maintenance of tolerance after allogeneic hematopoietic stem cell transplantation (Allo‐HSCT). We have found that Foxp3+ γδTCR+ Treg cells (γδTregs) exerted regulatory functions. In the current study, patients were recruited and divided as non‐cGVHD, limited cGVHD and extensive cGVHD groups. Healthy volunteers were recruited as healthy group. Treg cells were evaluated by flow cytometry. Serum cytokine levels of IL‐2, tumour necrosis factor‐α, interferon‐γ and transforming growth factor‐β1 (TGF‐β1) were evaluated by ELISA. The results showed that percentages of CD4+ Tregs, CD8+ Tregs and γδTregs were all significantly increased in non‐cGVHD group compared with those in healthy group, limited cGVHD group and extensive cGVHD group. Moreover, compared with extensive cGVHD group, percentages of these three types of Tregs were significantly increased in limited cGVHD group. The levels of TGF‐β1 increased dramatically in non‐cGVHD group compared with other groups. Spearman's correlation analysis revealed that the increased levels of TGF‐β1 and IL‐2 were positively associated with increased Treg subsets, indicating that TGF‐β1 and IL‐2 participated in the expansion process of Foxp3+ Tregs in vivo. Our findings support that increasing the number of Tregs following allo‐HSCT would be a preferential strategy for controlling cGVHD. Copyright © 2015 John Wiley & Sons, Ltd.
Insertion of the 34-kDa Chloroplast Protein Import Component, IAP34, into the Chloroplast Outer Membrane Is Dependent on Its Intrinsic GTP-binding Capacity*

IAP34 is a 34-kDa component of the outer membrane complex that mediates the initial stages of protein import into chloroplasts (Seedorf, M., Waegemann, K., and Soll, J. (1995) Plant J. 7, 401-411; Kessler, F. , Blobel, G. , Patel, H. A. , and Schnell, D. J. (1994) Science 266, 1035-1039). We have investigated the targeting and insertion of IAP34 at the outer envelope membrane. The analyses of IAP34 deletion mutants and hybrid proteins (consisting of regions of IAP34 fused to the soluble IgG-binding domain of staphylococcal protein A) suggest that the transmembrane domain and C-terminal tail of IAP34 contain information essential but not sufficient for targeting to the outer membrane. Treatment of chloroplasts with exogenous proteases does not affect IAP34 insertion, indicating that targeting does not require surface-exposed receptors at the envelope. GTP or GDP is required for maximal integration of IAP34 into the outer membrane. The GTP/GDP requirement is attributed to the intrinsic GTP binding activity of IAP34 because GTP/GDP binding-deficient mutants are defective in outer membrane insertion. On the basis of these observations, we propose that IAP34 is targeted to the chloroplast by a C-terminal signal and efficiently integrated into the outer membrane by conformation-induced insertion upon GTP/GDP binding.
Biologic correlates of intratumoral heterogeneity in 18F-FDG distribution with regional expression of glucose transporters and hexokinase-II in experimental tumor.

UNLABELLED The biologic mechanisms involved in the intratumoral heterogeneous distribution of 18F-FDG have not been fully investigated. To clarify factors inducing heterogeneous 18F-FDG distribution, we determined the intratumoral distribution of 18F-FDG by autoradiography (ARG) and compared it with the regional expression levels of glucose transporters Glut-1 and Glut-3 and hexokinase-II (HK-II) in a rat model of malignant tumor. METHODS Rats were inoculated with allogenic hepatoma cells (KDH-8) into the left calf muscle (n = 7). Tumor tissues were excised 1 h after the intravenous injection of 18F-FDG and sectioned to obtain 2 adjacent slices for ARG and histochemical studies. The regions of interest (ROIs) were placed on ARG images to cover mainly the central (CT) and peripheral (PT) regions of viable tumor tissues and necrotic/apoptotic (NA) regions. The radioactivity in each ROI was analyzed quantitatively using a computerized imaging analysis system. The expression levels of Glut-1, Glut-3, and HK-II were determined by immunostaining and semiquantitative evaluation. The hypoxia-inducible factor 1 (HIF-1) was also immunostained. RESULTS ARG images showed that intratumoral 18F-FDG distribution was heterogeneous. The accumulation of 18F-FDG in the CT region was the highest, which was 1.6 and 2.3 times higher than those in the PT and NA regions, respectively (P < 0.001). The expression levels of Glut-1, Glut-3, and HK-II were markedly higher in the CT region (P < 0.001) compared with those in the PT region. The intratumoral distribution of 18F-FDG significantly correlated with the expression levels of Glut-1, Glut-3, and HK-II (r = 0.923, P < 0.001 for Glut-1; r = 0.829, P < 0.001 for Glut-3; and r = 0.764, P < 0.01 for HK-II). The positive staining of HIF-1 was observed in the CT region. CONCLUSION These results demonstrate that intratumoral 18F-FDG distribution corresponds well to the expression levels of Glut-1, Glut-3, and HK-II. The elevated expression levels of Glut-1, Glut-3, and HK-II, induced by hypoxia (HIF-1), may be contributing factors to the higher 18F-FDG accumulation in the CT region.
Population-response model for vibrotactile spatial summation

A computational model based on previous physiological and psychophysical data is presented for the human Pacinian (P) psychophysical channel. The model can predict the probability of detection in simple psychophysical tasks, and hence psychometric functions and thresholds. The model simulates stimulating variable and fixed glabrous skin sites with different-sized contactors and includes spatial variation of monkey P-fiber sensitivities. Therefore, it is especially suitable for studying spatial summation, i.e. the improvement of threshold with increasing contactor area. Selective contributions of neural integration (n.i.) and probability summation (p.s.) are also incorporated into the model. Model predictions are compared to psychophysical results of Gescheider et al. (). The performance of the model regarding the effects of contactor size is very good. In addition to predicting approximately 3 dB improvement of thresholds when the contactor area is doubled, the model also reveals nonlinear contributions of p.s. and n.i. Furthermore, the model asserts that thresholds are largely governed by neural integration when small contactors are used. These and other findings discussed in the article show that the presented model is a helpful tool for formulating testable hypotheses. Although the model can also simulate some temporal summation effects, simulation results do not conform well to previous data on temporal response properties. Thus, the model needs to be refined in that respect.
Interactions between broiler chickens, soil parameters and short rotation coppice willow in a free-range system

ABSTRACT Planting short rotation coppice willows (SRCW) in chickens’ free-range areas could have several advantages for the chickens, environment and farmer. Our aim was to test the effects of combining SRCW and chickens on free-range use, soil conditions and SRCW growth. A free-range chicken area was partially planted with a grass/clover mixture, and partially with SRCW. Chickens preferred to range in SRCW compared to grassland. No effects of periodical chicken presence on SRCW growth were observed. Total mineral N (Nmin) was affected by interactions between vegetation type, location, and soil depth; it was generally higher in SRCW than in grassland and in areas close to the chicken houses. Nmin did not appear to accumulate in the soil over the years, but there were strong indications for higher risk of N leaching to deeper soil layers and possibly to groundwater close to the houses and in SRCW. SRCW was beneficial for the chickens, but the combination needs to be studied further with a focus on strategies for preventing nutrient leaching to groundwater.
Early teleostean basal ganglia development visualized by Zebrafish Dlx2a, Lhx6, Lhx7, Tbr2 (eomesa), and GAD67 gene expression

We examined the brain expression patterns of zebrafish genes Lhx6, Lhx7, Dlx2a, GAD67, and Tbr2/eomesa; except for GAD67, expression domains are restricted to the forebrain. In particular, a distribution of transcripts in the early zebrafish telencephalon comparable to that of tetrapods is revealed. Expression domains of Lhx6 and Lhx7 are restricted to a ventral subdivision (Sdv) of the precommissural dorsal subpallium, interpreted here as the homologue of the mammalian medial ganglionic eminence (the adult pallidum in mammals). In contrast, there is no such expression in the dorsal subdivision (Sdd) of the dorsal subpallium, interpreted here as the homologue of the mammalian lateral ganglionic eminence (the adult caudatoputamen in mammals). The Lhx6 and Lhx7 genes are furthermore expressed in the zebrafish ventral subpallium (Sv, septum), and in the supra‐/postcommissurally lying posterior subdivision of the dorsal subpallium (Sdp; possible homologue of the subpallial amygdala). Also in support of this comparative interpretation, Dlx2a is generally expressed in all of the subpallium, including the ventricular zones of (all three subvidisions of) the dorsal as well as of the ventral subpallium. In contrast, Tbr2 is expressed in all of the zebrafish pallium and in a restricted zone of the ventral subpallium, comparable to the known restricted septal expression in mammals. The telencephalic expression of GAD67 largely coincides with that of Dlx2a. However, GAD67‐positive cells migrate (radially) into postmitotic zones of the peripheral subpallium (as does Dlx2a and Lhx6) as well as (tangentially) into pallial zones (as does Dlx2a, but not Lhx6). J. Comp. Neurol. 507:1245–1257, 2008. © 2008 Wiley‐Liss, Inc.
Secondary Students’ Perceptions of Open Science Textbooks

In an attempt to align instructional resources with new state standards and to increase teacher awareness of these standards, one large suburban public school district piloted the development and adoption of open secondary science textbooks. Open textbooks created by teachers in grades six through nine replaced conventional science textbooks provided by mainstream publishing companies. Therefore, grade nine students were not included in this study. At the end of the first quarter, middle school students (grades six through eight) who used the open textbooks were surveyed. Survey responses required respondents to consider their learning before and during the use of the open textbook. The survey included quality and presentation of content questions, as well as an opportunity for students to explain their responses. There were qualitative and quantitative indications that students’ perceptions of an open textbook in place of a standard textbook are improving students’ attitudes and behaviors toward learning.
Comparison of the Framingham risk score, UK Prospective Diabetes Study (UKPDS) Risk Engine, Japanese Atherosclerosis Longitudinal Study-Existing Cohorts Combine (JALS-ECC) and maximum carotid intima-media thickness for predicting coronary artery stenosis in patients with asymptomatic type 2 diabetes

AIMS To compare the efficacy of Framingham Risk Score (FRS), UK Prospective Diabetes Study (UKPDS) risk engine, a risk score based on the Japanese Atherosclerosis Longitudinal Study-Existing Cohorts Combine (JALS-ECC), the maximum intima-media thickness (max-IMT) determined on coronary computed tomography angiography (CCTA) and their combination in asymptomatic patients with type 2 diabetes. METHODS A total of 116 Japanese patients with type 2 diabetes underwent CCTA. The risk of coronary heart disease was calculated according to the FRS, UKPDS and JALS-ECC. We evaluated the reclassification of coronary artery stenosis (CAS) based on the risk score categories after adding each IMT related variable. RESULTS Sixty-eight patients had CAS. The areas under the curves (AUCs) in the receiver operating characteristic curve analyses of FRS, UKPDS and JALS-ECC were 0.763 (95% confidence interval [CI]: 0.674-0.853), 0.785 (95% CI: 0.703-0.868) and 0.767 (95% CI: 0.681-0.853), respectively. The AUCs for FRS, UKPDS and JALS-ECC combined with the max-IMT were 0.788 (95% CI: 0.705-0.872), 0.800 (95% CI: 0.720-0.879) and 0.786 (95% CI: 0.703-0.869), respectively. Combining the max-IMT with the risk scores improved the identification of subjects with stenotic lesions, in particular, those in the first, second and third tertiles of the FRS, first and second tertiles of the UKPDS and first and second tertiles of the JALS-ECC (P=0.054, P=0.056, P=0.015, P=0.082, P=0.060, P=0.007, and P=0.080, respectively). The net reclassification improvement increased following the addition of a max-IMT of ≥ 1.9 mm (32.4% in FRS, 19.9% in UKPDS and 51.7% in JALS-ECC). CONCLUSIONS These data suggest that combining a risk score with the max-IMT improves the prediction of CAS in comparison with the risk score alone.