julilili42/papers huggingface dataset:
Paleoamerican morphology in the context of European and East Asian late Pleistocene variation: Implications for human dispersion into the new world
2010-11-29

Abstract Early American crania show a different morphological pattern from the one shared by late Native Americans. Although the origin of the diachronic morphological diversity seen on the continents is still debated, the distinct morphology of early Americans is well documented and widely dispersed. This morphology has been described extensively for South America, where larger samples are available. Here we test the hypotheses that the morphology of Early Americans results from retention of the morphological pattern of Late Pleistocene modern humans and that the occupation of the New World precedes the morphological differentiation that gave rise to recent Eurasian and American morphology. We compare Early American samples with European Upper Paleolithic skulls, the East Asian Zhoukoudian Upper Cave specimens and a series of 20 modern human reference crania. Canonical Analysis and Minimum Spanning Tree were used to assess the morphological affinities among the series, while Mantel and Dow‐Cheverud tests based on Mahalanobis Squared Distances were used to test different evolutionary scenarios. Our results show strong morphological affinities among the early series irrespective of geographical origin, which together with the matrix analyses results favor the scenario of a late morphological differentiation of modern humans. We conclude that the geographic differentiation of modern human morphology is a late phenomenon that occurred after the initial settlement of the Americas. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.
Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors
2010-11-30

Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most intensively studied eukaryotic organisms (i.e., human, rat and mouse), roughly one-sixth of all proteins with annotated DNA-binding domain have been characterized experimentally. Here, we present a new method based on support vector regression for predicting quantitative DNA-binding specificities of TFs in different eukaryotic species. This approach estimates a quantitative measure for the PFM similarity of two proteins, based on various features derived from their protein sequences. The method is trained and tested on a dataset containing 1 239 TFs with known DNA-binding specificity, and used to predict specific DNA target motifs for 645 TFs with high accuracy.
NAT traversal for LISP mobile node
2010-11-30

The Locator/ID Separation Protocol (LISP) is currently being developed and standardized in the IETF aiming to solve the Internet's routing scaling problem. It separates global routing in the Internet from local routing in end-user networks (so-called LISP-domains). It also provides additional benefits like simplified multihoming or the avoidance of network renumbering. The basic LISP architecture does not support mobility. Recently, the mobility extension LISP Mobile Node (LISP-MN) was presented. It describes a mechanism that enables LISP mobile nodes to roam into LISP and non-LISP networks while being reachable under the same identifier address. Currently, LISP-MN does not support networks that use network address translation (NAT). In this paper, we present a NAT traversal mechanism for LISP mobile nodes and a slight adaptation which is also applicable to stationary LISP domains behind a NAT.
Timing of India‐Asia collision: Geological, biostratigraphic, and palaeomagnetic constraints
2010-12-01

A range of ages have been proposed for the timing of India‐Asia collision; the range to some extent reflects different definitions of collision and methods used to date it. In this paper we discuss three approaches that have been used to constrain the time of collision: the time of cessation of marine facies, the time of the first arrival of Asian detritus on the Indian plate, and the determination of the relative positions of India and Asia through time. In the Qumiba sedimentary section located south of the Yarlung Tsangpo suture in Tibet, a previous work has dated marine facies at middle to late Eocene, by far the youngest marine sediments recorded in the region. By contrast, our biostratigraphic data indicate the youngest marine facies preserved at this locality are 50.6–52.8 Ma, in broad agreement with the timing of cessation of marine facies elsewhere throughout the region. Double dating of detrital zircons from this formation, by U‐Pb and fission track methods, indicates an Asian contribution to the rocks thus documenting the time of arrival of Asian material onto the Indian plate at this time and hence constraining the time of India‐Asia collision. Our reconstruction of the positions of India and Asia by using a compilation of published palaeomagnetic data indicates initial contact between the continents in the early Eocene. We conclude the paper with a discussion on the viability of a recent assertion that collision between India and Asia could not have occurred prior to ∼35 Ma.
Regulation of Peptidoglycan Synthesis by Outer-Membrane Proteins
2010-12-01

Growth of the mesh-like peptidoglycan (PG) sacculus located between the bacterial inner and outer membranes (OM) is tightly regulated to ensure cellular integrity, maintain cell shape, and orchestrate division. Cytoskeletal elements direct placement and activity of PG synthases from inside the cell, but precise spatiotemporal control over this process is poorly understood. We demonstrate that PG synthases are also controlled from outside of the sacculus. Two OM lipoproteins, LpoA and LpoB, are essential for the function, respectively, of PBP1A and PBP1B, the major E. coli bifunctional PG synthases. Each Lpo protein binds specifically to its cognate PBP and stimulates its transpeptidase activity, thereby facilitating attachment of new PG to the sacculus. LpoB shows partial septal localization, and our data suggest that the LpoB-PBP1B complex contributes to OM constriction during cell division. LpoA/LpoB and their PBP-docking regions are restricted to γ-proteobacteria, providing models for niche-specific regulation of sacculus growth.
False teeth: conodont-vertebrate phylogenetic relationships revisited
2010-12-01

Turner, Susan, Burrow, Carole J., Schultze, Hans-Peter, Blieck, Alain, Reif, Wolf-Ernst, Rexroad, Carl B., Bultynck, Pierre, Nowlan, Godfrey S. (2010): False teeth: conodont-vertebrate phylogenetic relationships revisited. Geodiversitas 32 (4): 545-594, DOI: 10.5252/g2010n4a1, URL: http://www.bioone.org/doi/abs/10.5252/g2010n4a1
The Brustkrebs-Studien.de website for breast cancer patients: User acceptance of a German internet portal offering information on the disease and treatment options, and a clinical trials matching service
2010-12-01

BKS is an established and trusted breast cancer information platform offering up-to-date resources and protocols to the growing physician and patient community to encourage participation in clinical trials. Further studies are needed to assess potential increases in trial enrolment by eligibility matching services.
JuSt &ndash; a multimodal program for treatment of insomnia in adolescents: a pilot study
2010-12-01

Insomnia is the most prevalent sleep disorder in adolescents. A number of studies have evaluated the efficacy of the management of chronic insomnia in adults. Behavioral therapy for insomnia is the treatment of first choice, encompassing education about sleep and sleep hygiene, stimulus control, relaxation techniques, and cognitive strategies to combat nocturnal ruminations. Special programs for adolescents are lacking. In this study an age-oriented treatment program for adolescents (JuSt) was developed and evaluated. Eighteen adolescents and their parents participated in a psychological short-term treatment comprising six sessions. First results show that the treatment was well accepted by the adolescents and their parents and led to a significant reduction in sleep problems, such as sleep onset, sleep efficacy, sleep duration, and feeling rested as well as in cognitive parameters, such as ruminations and mental health. Randomized controlled studies are needed to evaluate the efficacy of this new approach to treat insomnia in adolescents.
The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana
2010-12-01

Abstract Background Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA (CLV) proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars. Results Here we show that a family of four plant-specific proteins, encoded by the FANTASTIC FOUR ( FAF ) genes, has the potential to regulate shoot meristem size in Arabidopsis thaliana . FAF2 and FAF4 are expressed in the centre of the shoot meristem, overlapping with the site of WUS expression. Consistent with a regulatory interaction between the FAF gene family and WUS , our experiments indicate that the FAFs can repress WUS , which ultimately leads to an arrest of meristem activity in FAF overexpressing lines. The finding that meristematic expression of FAF2 and FAF4 is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem. Conclusion This study reports the initial characterization of the Arabidopsis thaliana FAF gene family. Our data indicate that the FAF genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.
miRNA: Small Molecules as Potential Novel Biomarkers in Cancer
2010-12-01

Four different types of small RNAs functionally associated with gene silencing have been discovered in animals including small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs). Experimental evidence suggests that miRNAs regulate the expression of more than 30% of protein-coding genes. These molecules can also act as oncogenes or tumor suppressors. Expression profiling has revealed characteristic miRNA signatures not only in human cancers but also in serum and blood cells of cancer patients. Numerous human miRNA genes map to chromosomal regions which are susceptible to amplification, deletion or translocation in the process of tumor development. Despite the pivotal role of miRNA in cancer precise mechanisms of action are yet to be elucidated. This review is focused on recent findings related to the emerging field of miRNA serving as novel potential biomarkers in cancer diagnosis, prognosis and possibly, therapies.
Spatial characterization of the hydraulic conductivity using direct‐push injection logging
2010-12-01

Detailed information on the spatial structure of hydraulic conductivity ( K ) is important for understanding and predicting groundwater flow and transport. Direct‐push injection logging (DPIL) is a promising technology for rapid measurement of K in unconsolidated formations. This technology was used to gain information on the highly heterogeneous aquifer at the Lauswiesen test site in Germany. Using a large body of DPIL and direct‐push slug testing measurements, we characterize the structure of K on scales not previously possible. Two new applications of DPIL are put forward: (1) use of raw DPIL measurements of relative conductivity K r to characterize the spatial distribution of K and (2) transformation of K r measurements to K values based on their statistical moments. The DPIL results are compatible to those obtained using more conventional methodologies. The main achievement of the methodology is the possibility to delineate deterministic aquifer subunits as well as the identification of the statistical parameters of the log conductivity for each subunit. In particular, the horizontal integral scale I , a parameter affecting solute transport, is difficult and costly to identify using other approaches. Nevertheless, further studies are needed to clarify questions on low K r measurements and the nature of the relationship between K r and K .
Plant Species Classification Using a 3D LIDAR Sensor and Machine Learning
2010-12-01

In the domain of agricultural robotics, one major application is crop scouting, e.g., for the task of weed control. For this task a key enabler is a robust detection and classification of the plant and species. Automatically distinguishing between plant species is a challenging task, because some species look very similar. It is also difficult to translate the symbolic high level description of the appearances and the differences between the plants used by humans, into a formal, computer understandable form. Also it is not possible to reliably detect structures, like leaves and branches in 3D data provided by our sensor. One approach to solve this problem is to learn how to classify the species by using a set of example plants and machine learning methods. In this paper we are introducing a method for distinguishing plant species using a 3D LIDAR sensor and supervised learning. For that we have developed a set of size and rotation invariant features and evaluated experimentally which are the most descriptive ones. Besides these features we have also compared different learning methods using the toolbox Weka. It turned out that the best methods for our application are simple logistic regression functions, support vector machines and neural networks. In our experiments we used six different plant species, typically available at common nurseries, and about 20 examples of each species. In the laboratory we were able to identify over 98% of these plants correctly.
Metabolites Indicate Hot Spots of Biodegradation and Biogeochemical Gradients in a High-Resolution Monitoring Well
2010-12-01

Anaerobic degradation processes play an important role in contaminated aquifers. To indicate active biodegradation processes signature metabolites can be used. In this study field samples from a high-resolution multilevel well in a tar oil-contaminated, anoxic aquifer were analyzed for metabolites by liquid chromatography-tandem mass spectrometry and time-of-flight mass spectrometry. In addition to already known specific degradation products of toluene, xylenes, and naphthalenes, the seldom reported degradation products benzothiophenemethylsuccinic acid (BTMS), benzofuranmethylsuccinic acid (BFMS), methylnaphthyl-2-methylsuccinic acid (MNMS), and acenaphthene-5-carboxylic acid (AC) could be identified (BFMS, AC) and tentatively identified (BTMS, MNMS). The occurrence of BTMS and BFMS clearly show that the fumarate addition pathway, known for toluene and methylnaphthalene, is also important for the anaerobic degradation of heterocyclic contaminants in aquifers. The molar concentration ratios of metabolites and their related parent compounds differ over a wide range which shows that there is no simple and consistent quantitative relation. However, generally higher ratios were found for the more recalcitrant compounds, which are putatively cometabolically degraded (e.g., 2-carboxybenzothiophene and acenaphthene-5-carboxylic acid), indicating an accumulation of these metabolites. Vertical concentration profiles of benzylsuccinic acid (BS) and methyl-benzylsuccinic acid (MBS) showed distinct peaks at the fringes of the toluene and xylene plume indicating hot spots of biodegradation activity and supporting the plume fringe concept. However, there are some compounds which show a different vertical distribution with the most prominent concentrations where also the precursor compounds peaked.
Pituitary insufficiency as a side effect after radiosurgery for pituitary adenomas: the role of the hypothalamus
2010-12-01

Object Causes of pituitary insufficiencies as a side effect of Gamma Knife surgery (GKS) following irradiation of the hypothalamopituitary axis are still under debate. In an investigation of pituitary insufficiencies after GKS, the authors' main focus is on what role can be attributed to the hypothalamus with regard to endocrinological changes in hypothalamopituitary function following GKS. Methods A total of 108 patients consecutively treated between April 1992 and July 2003 were included in this retrospective study. All patients had undergone either transsphenoidal or transcranial surgery prior to GKS. The spot dosimetry method was used to determine doses delivered to structures of the hypothalamopituitary axis. For statistical analyses, endocrine insufficiency and deterioration in pituitary function were defined as a decrease in hormonal blood levels below the normal range for 1 or more anterior pituitary lobe hormones. Additionally, an analysis of the rate of patients requiring hormone replacement therapy after GKS due to new endocrinopathies was performed. Results Complete patient records of 61 male and 47 female patients with a mean age of 51.9 years (range 9.1–81.2 years) were available for our investigation. The overall tumor control rate was 97% and the endocrinological cure rate was 61.2%. Mean treatment doses in patients with and without new endocrine insufficiencies (shown as with/without insufficiencies and followed by probability values) were as follows: 1.3/0.8 Gy to the hypothalamus (p = 0.2); 2.2/1.6 Gy to the median eminence (p = 0.1); 6.5/4.1 Gy to the pituitary stalk (p = 0.004); and 12.4/9.5 Gy to the pituitary gland (p = 0.05). The median overall duration of follow-up after GKS was 6.7 years, with 84 patients (77.7%) whose follow-up was longer than 12 months. The median follow-up time after GKS in patients who developed a new pituitary dysfunction was 79.5 months (6.6 years, SD 3.8 years), and the median follow-up time in patients with no new insufficiencies was 78.4 months (6.5 years, SD 4 years). Conclusions Gamma Knife surgery is a safe and effective treatment for patients with residual and recurrent pituitary adenomas. The rate of pituitary insufficiencies after GKS is still lower than that after conventional radiotherapy. Very low radiation doses are directed to the hypothalamus, and thus this structure does not play a major role in the development of pituitary insufficiencies after GKS. The results of this study show that patients in whom the pituitary stalk and pituitary gland receive a high mean point dose are more likely to develop pituitary insufficiencies after GKS than those who receive a lower dose.
First effects of a multicomponent treatment for sleep disorders in children
2010-12-01

Insomnia in children is a common disorder, yet only few child-specific treatment modalities exist so far. The goal of this study was to investigate the effectiveness of a multicomponent intervention program for children with insomnia at 5-10 years of age and their parents. The program was a structured six-session behavioral and hypnotherapeutic group treatment with three sessions for the children and three for their parents. Thirty-eight children (5.1-10.9 years) were randomly assigned to the specific treatment condition or waiting list plus sleep diary control condition. Twenty-two children participated in the treatment group and 16 in the control group. All children suffered from insomnia according to the International Classification of Sleep Disorders criteria. Sleep symptoms were assessed with a sleep diary and the German version of the Children Sleep Habit Questionnaire (CSHQ) and the Sleep Disturbance Scale for Children (SDSC). Although both conditions showed a significant decrease in several sleep symptoms, the treatment group exhibited a significantly greater improvement with regard to CSHQ and SDSC total scores as well as in several sleep parameters, reflecting the most important features of the intervention program, such as bedtime, sleep-related anxiety, night waking, and sleeping in parents' bed. By contrast, the control group's data revealed only unspecific effects. These pilot data suggest that insomnia in childhood can be treated effectively with this child-specific multicomponent group treatment.
Pituitary insufficiency as a side effect after radiosurgery for pituitary adenomas: the role of the hypothalamus.
2010-12-01

Gamma Knife surgery is a safe and effective treatment for patients with residual and recurrent pituitary adenomas. The rate of pituitary insufficiencies after GKS is still lower than that after conventional radiotherapy.Very low radiation doses are directed to the hypothalamus, and thus this structure does not play a major role in the development of pituitary insufficiencies after GKS. The results of this study show that patients in whom the pituitary stalk and pituitary gland receive a high mean point dose are more likely to develop pituitary insufficiencies after GKS than those who receive a lower dose. (DOI: 10.3171/2010.8.GKS10959).
Organotypic Cultures as Tools for Testing Neuroactive Drugs – Link Between In-Vitro and In-Vivo Experiments
2010-12-01

The development of neuroactive drugs is a time consuming procedure. Candidate drugs must be run through a battery of tests, including receptor studies and behavioural tests on animals. As a rule, numerous substances with promising properties as assessed in receptor studies must be eliminated from the development pipeline in advanced test phases because of unforeseen problems like intolerable side-effects or unsatisfactory performance in the whole organism. Clearly, test systems of intermediate complexity would alleviate this inefficiency. In this review, we propose cultured organotypic brain slices as model systems that could bridge the 'interpolation gap' between receptors and the brain, with a focus on the development of new general anaesthetics with lesser side effects. General anaesthesia is based on the modulation of neurotransmitter receptors and other conductances located on neurons in diverse brain regions, including cerebral cortex and spinal cord. It is well known that different components of general anaesthesia, e.g. hypnosis and immobility, are produced by the depression of neuronal activity in distinct brain regions. The ventral horn of the spinal cord is an important structure for the induction of immobility. Thus, the potentially immobilizing effects of a newly designed drug can be estimated from its depressant effect on neuronal network activity in cultured spinal slices. A drug's sedative and hypnotic potential can be examined in cortical cultures. Combined with genetically engineered mice, this approach can point to receptor subtypes most relevant to the drug's intended net effect and in return can help in the design of more selective drugs. In conclusion, the use of organotypic cultures permits predictions of neuroactive properties of newly designed drugs on an intermediate level, and should therefore open up avenues for a more creative and economic drug development process.
IGR J16547-1916/1RXS J165443.5-191620—a new intermediate polar from the INTEGRAL galactic survey
2010-12-01

We present the results of our optical identification of the X-ray source IGR J16547-1916 detected by the INTEGRAL observatory during a deep all-sky survey. Analysis of the spectroscopic data from the SWIFT and INTEGRAL observatories in the X-ray energy band and from the BTA (Special Astrophysical Observatory) telescope in the optical band has shown that the source is most likely an intermediate polar -- an accreting white dwarf with the mass of M~0.85 M_Sun in a low-mass binary system. Subsequent studies of the object's rapid variability with the RTT-150 telescope have confirmed this conclusion by revealing periodic pulsations of its optical emission with a period of ~550 s.