Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.
Hierarchy in directed random networks: analytical and numerical results

In recent years, the theory and application of complex networks have been quickly developing in a markable way due to the increasing amount of data from real systems and the fruitful application of powerful methods used in statistical physics. Many important characteristics of social or biological systems can be described by the study of their underlying structure of interactions. Hierarchy is one of these features that can be formulated in the language of networks. In this paper we present some (qualitative) analytic results on the hierarchical properties of random network models with zero correlations and also investigate, mainly numerically, the effects of different types of correlations. The behavior of the hierarchy is different in the absence and the presence of giant components. We show that the hierarchical structure can be drastically different if there are one-point correlations in the network. We also show numerical results suggesting that the hierarchy does not change monotonically with the correlations and there is an optimal level of nonzero correlations maximizing the level of hierarchy.
Functional Characterization and Cellular Dynamics of the CDC-42 – RAC – CDC-24 Module in Neurospora crassa

Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 – RAC – CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.
Correction: Clonal CD8+ T Cell Persistence and Variable Gene Usage Bias in a Human Transplanted Hand

There is an error in the first sentence under the subheading Study Subject, in the Materials and Methods section. The correct sentence is: A 27 year-old woman (HLA A1, B8, B72, DR8, DR17, DQ2, and DQ4) was the recipient of a right hand from a male donor (HLA A2, A11, B35, B51, DR4, DR7, DQ2, and DQ8).
Effect of bright light and melatonin on cognitive and noncognitive function in elderly residents of group care facilities: a randomized controlled trial.

CONTEXT Cognitive decline, mood, behavioral and sleep disturbances, and limitations of activities of daily living commonly burden elderly patients with dementia and their caregivers. Circadian rhythm disturbances have been associated with these symptoms. OBJECTIVE To determine whether the progression of cognitive and noncognitive symptoms may be ameliorated by individual or combined long-term application of the 2 major synchronizers of the circadian timing system: bright light and melatonin. DESIGN, SETTING, AND PARTICIPANTS A long-term, double-blind, placebo-controlled, 2 x 2 factorial randomized trial performed from 1999 to 2004 with 189 residents of 12 group care facilities in the Netherlands; mean (SD) age, 85.8 (5.5) years; 90% were female and 87% had dementia. INTERVENTIONS Random assignment by facility to long-term daily treatment with whole-day bright (+/- 1000 lux) or dim (+/- 300 lux) light and by participant to evening melatonin (2.5 mg) or placebo for a mean (SD) of 15 (12) months (maximum period of 3.5 years). MAIN OUTCOME MEASURES Standardized scales for cognitive and noncognitive symptoms, limitations of activities of daily living, and adverse effects assessed every 6 months. RESULTS Light attenuated cognitive deterioration by a mean of 0.9 points (95% confidence interval [CI], 0.04-1.71) on the Mini-Mental State Examination or a relative 5%. Light also ameliorated depressive symptoms by 1.5 points (95% CI, 0.24-2.70) on the Cornell Scale for Depression in Dementia or a relative 19%, and attenuated the increase in functional limitations over time by 1.8 points per year (95% CI, 0.61-2.92) on the nurse-informant activities of daily living scale or a relative 53% difference. Melatonin shortened sleep onset latency by 8.2 minutes (95% CI, 1.08-15.38) or 19% and increased sleep duration by 27 minutes (95% CI, 9-46) or 6%. However, melatonin adversely affected scores on the Philadelphia Geriatric Centre Affect Rating Scale, both for positive affect (-0.5 points; 95% CI, -0.10 to -1.00) and negative affect (0.8 points; 95% CI, 0.20-1.44). Melatonin also increased withdrawn behavior by 1.02 points (95% CI, 0.18-1.86) on the Multi Observational Scale for Elderly Subjects scale, although this effect was not seen if given in combination with light. Combined treatment also attenuated aggressive behavior by 3.9 points (95% CI, 0.88-6.92) on the Cohen-Mansfield Agitation Index or 9%, increased sleep efficiency by 3.5% (95% CI, 0.8%-6.1%), and improved nocturnal restlessness by 1.00 minute per hour each year (95% CI, 0.26-1.78) or 9% (treatment x time effect). CONCLUSIONS Light has a modest benefit in improving some cognitive and noncognitive symptoms of dementia. To counteract the adverse effect of melatonin on mood, it is recommended only in combination with light. TRIAL REGISTRATION controlled-trials.com/isrctn Identifier: ISRCTN93133646.
Quantification of IgA and IgG and specificities of antibodies to viral proteins in parotid saliva at different stages of HIV‐1 infection

Paired sera and parotid saliva from 75 HIV‐1‐infected patients, divided in three equal groups with CD4+ cell counts > 500, 200–500 and < 200/mm3, respectively, were analysed for IgG, IgA and secretory IgA (sIgA) concentrations and for IgG and IgA antibody directed to HIV‐1. Twenty‐nine age‐matched HIV− subjects were used as controls. In serum the concentrations of immunoglobulins were significantly increased in HIV‐infected subjects compared with controls, and a progressive increase of IgA and sIgA was noticed while the CD4+ cell count decreased. In contrast, concentrations of IgA and sIgA were not different in parotid saliva between the four subject groups. By an ELISA test directed towards HIV‐1 proteins, 73 of the 75 serum specimens from the HIV‐infected subjects (97%) and 43 of the corresponding saliva (57%) were found positive for specific IgA antibodies to HIV‐1, with an even distribution among the three groups of patients. By Western blotting multiple specificities of IgA to HIV‐1 proteins were not frequently found in patients. By contrast, in spite of an IgG concentration in saliva about 100 times lower than that of IgA, reactivities were significantly higher for IgG than for IgA antibodies, especially to env and to pol HIV‐1 products. Altogether, these data suggest that the regulation of IgA production in HIV‐infected subjects is independent in serum and in parotid saliva. This imbalance of IgA/IgG antibodies to HIV‐1 at the mucosal level appears to be a specific feature of HIV‐1 infection, and may raise important issues in terms of local protection after immunization.
The Impact of Windstorm Damage in the Assessment of the Carbon Balance in Even-Aged Fagus sylvatica L. Stands

Due to the fact that forest ecosystems can potentially mitigate the impact of climate change, the carbon balance of managed forests has caught the attention of a large scientific community. Some authors conclude that extending rotation lengths would actually favour the climate change mitigation effect since more carbon would be stored in the biomass on the average. However, when the occurrence of catastrophic disturbances such as windstorms is not considered, the advantage of extending the rotation length might be overestimated for some species. In this study, we addressed this issue by coupling a growth model, a windstorm damage model and a carbon assessment tool. The evolution of an even-aged European beech (Fagus sylvatica L.) stand was simulated under three different rotation lengths. Simulations including stochastic windstorm events were run and compared with deterministic simulations with no catastrophic disturbance. Our results indicate that when disturbances caused by storms were not taken into account, the carbon balance was actually overestimated in some cases and that this overestimation increased with the rotation length. In our case study, omitting windstorm damage resulted in an overestimation as large as 8% for the longer rotation length. Nevertheless, when windstorm damage was taken into account in the simulation, the longer rotation length still stored more carbon on the average than shorter rotation lengths. However, the marginal gain in carbon storage induced by the increase of the rotation length was reduced.
FTO Genotype and 2-Year Change in Body Composition and Fat Distribution in Response to Weight-Loss Diets

Recent evidence suggests that the fat mass and obesity-associated gene (FTO) genotype may interact with dietary intakes in relation to adiposity. We tested the effect of FTO variant on weight loss in response to 2-year diet interventions. FTO rs1558902 was genotyped in 742 obese adults who were randomly assigned to one of four diets differing in the proportions of fat, protein, and carbohydrate. Body composition and fat distribution were measured by dual-energy x-ray absorptiometry and computed tomography. We found significant modification effects for intervention varying in dietary protein on 2-year changes in fat-free mass, whole body total percentage of fat mass, total adipose tissue mass, visceral adipose tissue mass, and superficial adipose tissue mass (for all interactions, P < 0.05). Carriers of the risk allele had a greater reduction in weight, body composition, and fat distribution in response to a high-protein diet, whereas an opposite genetic effect was observed on changes in fat distribution in response to a low-protein diet. Likewise, significant interaction patterns also were observed at 6 months. Our data suggest that a high-protein diet may be beneficial for weight loss and improvement of body composition and fat distribution in individuals with the risk allele of the FTO variant rs1558902.
Seasonal Streamflow Forecasting Using Snow Budget and El Nino-Southern Oscillation Climate Signals: Application to the Salt River Basin in Arizona

In this paper, a method for streamflow forecasting in arid and semiarid regions is presented. The proposed methodology consists of three steps. In the first step, hydrologic seasons are defined to capture coupled effects of climatic and hydrologic characteristics of a basin. For this purpose, the correlation between average snow water equivalent (SWE), the similarity in basic statistical characteristics of the streamflows in different months, and the general characteristics of the study area are considered for defining hydrologic seasons. In the second step, a seasonal streamflow forecast time series is developed using autoregressive integrated moving average (ARIMA) models. In the third step, the fuzzy rules are developed to modify the statistical forecasts, utilizing average snow budget over a watershed, El Nino–Southern Oscillation (ENSO) climate signals, historical streamflow data, and time series of forecasted streamflows. Application of the proposed algorithm to the Salt River Basin in Arizona has s.
Large Conductance Voltage- and Ca2+-gated Potassium (BK) Channel β4 Subunit Influences Sensitivity and Tolerance to Alcohol by Altering Its Response to Kinases*

Background: Large conductance voltage- and Ca2+-gated potassium channel (BK) β4 subunit profoundly influences BK acute ethanol tolerance with both physiological and behavioral consequences. Results: PKA, CaMKII, and phosphatases modulate BK, and influence its response to ethanol. The presence of β4 strongly regulates these responses. Conclusion: The control of BK β4 of kinase modulation is critical to ethanol response. Significance: The influence of β4 on kinase-mediated alcohol action provides insight into the molecular basis for alcohol tolerance. Tolerance is a well described component of alcohol abuse and addiction. The large conductance voltage- and Ca2+-gated potassium channel (BK) has been very useful for studying molecular tolerance. The influence of association with the β4 subunit can be observed at the level of individual channels, action potentials in brain slices, and finally, drinking behavior in the mouse. Previously, we showed that 50 mm alcohol increases both α and αβ4 BK channel open probability, but only α BK develops acute tolerance to this effect. Currently, we explore the possibility that the influence of the β4 subunit on tolerance may result from a striking effect of β4 on kinase modulation of the BK channel. We examine the influence of the β4 subunit on PKA, CaMKII, and phosphatase modulation of channel activity, and on molecular tolerance to alcohol. We record from human BK channels heterologously expressed in HEK 293 cells composed of its core subunit, α alone (Insertless), or co-expressed with the β4 BK auxiliary subunit, as well as, acutely dissociated nucleus accumbens neurons using the cell-attached patch clamp configuration. Our results indicate that BK channels are strongly modulated by activation of specific kinases (PKA and CaMKII) and phosphatases. The presence of the β4 subunit greatly influences this modulation, allowing a variety of outcomes for BK channel activity in response to acute alcohol.
Transvaginal sonography, saline contrast sonohysterography and hysteroscopy for the investigation of women with postmenopausal bleeding and endometrium > 5 mm

To determine the ability of transvaginal ultrasound, with or without saline infusion, to detect focally growing lesions in the uterine cavity in women with postmenopausal bleeding and endometrium > 5 mm, and to determine the accuracy of conventional ultrasound, saline contrast sonohysterography and diagnostic hysteroscopy under general anesthesia to diagnose endometrial polyps, submucous myomas and uterine malignancy.
Studies on isolation and nitrogen fixation ability of Azospirillum spp.isolated from Thanjavur district

stimulate plant growth. Azospirillum is a microaerophilic, plant growth. Promoting bacterium, grow well in semi-solid medium. In this study, Azospirillum strains were isolated from paddy rhizosphere soil of Thanjavur district. All 30 isolates were analyzed for its nitrogen fixing ability by using Microkjeldhal method. Thus the present study is focused on to identify the highest N2 fixing of Azospirillum strain and compared to each other
A New Suffix Tree Similarity Measure and Labeling for Web Search Results Clustering

Due to the enormous size of the web and low precision of user queries, finding the right information from the web can be difficult if not impossible. One approach that tries to solve this problem is using clustering techniques for grouping similar documents together in order to facilitate presentation of results in more compact form and enable thematic browsing of the results set. Web Search Results Clustering is an attempt to apply the idea of clustering to document references (snippets) returned by a search engine in response to a query. Thus, it can be perceived as a way of organizing the snippets into set of meaningful thematic groups. This paper introduces a new similarity criterion for merging which is evaluated for search results returned from actual web search engines.
Uncertainty Analysis With High Dimensional Dependence Modelling

of it means — however, if the reader has previously failed to understand these terms, I doubt that the discussion will help. It may help newcomers. On the other hand, some things are misstated here including “[t]he closer to ±1, the closer to a perfect linear relationship. ” However, it is easy to obtain a high correlation (over .8) with a nonlinear relationship (Anscombe 1973; Analytical Methods Committee 1988). Finally, Chapter 7 provides help on searching for information. Each chapter ends with an “on your own” section of exercises—I found many of these confusing. The author’s website for this book, checked on 10/11/06, is still in the very early stages; most of the material was written before the book. There is no section on correction of errors. The author states that “I plan to add resources when I have time, such as answers to On your Own exercises and a bibliography with live links to the free full text when available. ” Notwithstanding my negative comments and tone above, there are valuable points here; they are, however, generally too hard to find and some of them are undercut by the author’s misguided attempt to be “fair. ” If the author were to clean up the typographical errors and omissions and highlight the main points, the result would be a much better book.
The influence of chromosome density variations on the increase in nuclear disorder strength in carcinogenesis

Microscopic structural changes have long been observed in cancer cells and used as a marker in cancer diagnosis. Recent development of an optical technique, partial-wave spectroscopy (PWS), enabled more sensitive detection of nanoscale structural changes in early carcinogenesis in terms of the disorder strength related to density variations. These nanoscale alterations precede the well-known microscopic morphological changes. We investigate the influence of nuclear density variations due to chromosome condensation on changes of disorder strength by computer simulations of model chromosomes. Nuclear configurations with different degrees of chromosome condensation are realized from simulations of decondensing chromosomes and the disorder strength is calculated for these nuclear configurations. We found that the disorder strength increases significantly for configurations with slightly more condensed chromosomes. Coupled with PWS measurements, the simulation results suggest that the chromosome condensation and the resulting spatial density inhomogeneity may represent one of the earliest events in carcinogenesis.
Nps1/Sth1p, a component of an essential chromatin‐remodeling complex of Saccharomyces cerevisiae, is required for the maximal expression of early meiotic genes

The NPS1/STH1 gene of Saccharomyces cerevisiae is essential for mitotic growth, especially for the progression through the G2/M phase. It encodes a major component of the chromatin‐remodelling complex, RSC, of unknown function. We attempted to address the function of NPS1 in meiosis.
Hematopoietic mobilization in mice increases the presence of bone marrow–derived hepatocytes via in vivo cell fusion

The mechanisms for in vivo production of bone marrow–derived hepatocytes (BMDHs) remain largely unclear. We investigated whether granulocyte colony–stimulating factor (G‐CSF)–mediated mobilization of hematopoietic cells increases the phenomenon. Recurrent liver injury in mice expressing green fluorescent protein (EGFP) in all hematopoietic‐derived cells was produced by 3 months of carbon tetrachloride (CCL4) injections. Histologically, there were necrotic foci with histiocyte‐rich infiltrates, but little oval cell proliferation. Subsequently, some animals were mobilized with G‐CSF for 1, 2, or 3 weeks. Animals were sacrificed 1 month after growth factor treatment. BMDH percentages were lower than previously reported, though G‐CSF mobilization significantly augmented BMDH production in injured livers. BMDHs originating from in vivo fusion were evaluated by transplanting female EGFP+ cells into male mice. Binucleated, EGFP+ hepatocytes with one Y chromosome, indicating fusion, were identified. In conclusion, (1) mobilization of hematopoietic cells increases BMDH production and (2) as with the FAH‐null model, the first model demonstrating hematopoietic/hepatocyte fusion, recurring CCl4‐induced injury has macrophage‐rich infiltrates, a blunted oval cell response, and a predominantly in vivo fusion process for circulating cell engraftment into the liver. These findings open the possibility of using hematopoietic growth factors to treat nonhematopoietic degenerative diseases. (HEPATOLOGY 2006;43:108–116.)
Large Contests

We consider contests with many, possibly heterogeneous, players and prizes that include many existing contest models as special cases. We show that the equilibria of such contests are approximated by an appropriately defined set of incentive-compatible individually-rational single-agent mechanisms. This approach makes it possible to approximate the equilibria of contests whose exact equilibrium characterization is complicated, as well as the equilibria of contests for which there is no existing equilibrium characterization. This facilitates contest design, welfare analysis, and comparative statics.