julilili42/papers huggingface dataset:
Identification of gene expression profile during fertilization in Brassica campestris subsp. chinensis
2012-11-01

Fertilization is controlled by a complex gene regulatory network. To study the fertilization mechanism, we determined time courses of the four developmental stages of fertilization in Chinese cabbage pak-choi (Brassica campestris subsp. chinensis) by cytological observation. We then used the Arabidopsis ATH1 microarray to characterize the gene expression profiles of pollinated and unpollinated pistils in B. campestris subsp. chinensis. The result showed 44 up-regulated genes and 33 down-regulated genes in pollinated pistils compared with unpollinated pistils. Gene ontology analysis identified 20% of the up-regulated genes as belonging to the category of cell wall metabolism. We compared the up-regulated genes in pollinated pistils with previously identified pollen development related genes. Ten genes were found to be in common, which were termed as continuously expressed genes, in the two processes in the present article. Their expression patterns during pollen development and fertilization processes were then verified by RT–PCR. One of the continuously expressed genes, the homologous gene of At3g01270 in B. campestris subsp. chinensis, was confirmed as specifically expressed in microspores and pollinated pistils by using in situ hybridization. The potential biological functions of the other continuously expressed genes were also discussed.
A brain-computer interface for chronic pain patients using epidural ECoG and visual feedback
2012-11-01

Electrocorticography (ECoG) offers the possibility of decoding movement intention even in the absence of motor control, making it a powerful signal source for brain-computer interfaces (BCI). We designed a BCI that translates attempts to move the hand into movements of a video of an opening hand to investigate its use for pain therapy and stroke rehabilitation. One patient with phantom limb pain after amputation of the arm and one patient suffering from chronic pain and paralysis after a stroke trained with this BCI for several sessions. Signals were acquired with epidural ECoG grids placed over the motor cortex contralateral to the affected or missing hand. The analysis of data obtained in screening sessions with cued attempted movements showed highly significant (p <; 0.01, permutation test) r <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> values for the discrimination between movement and rest conditions for most frequencies up to 200 Hz. Both patients acquired control of the BCI system which was verified by the evaluation of three measures of the ability to start and stop the video application. In particular, both patients learned to reliably start the video application in all trials. This demonstrates that it is feasible for patients with phantom limb pain and chronic pain as well as paralysis after stroke to operate a BCI that targets their missing or impaired limb, making it a potentially useful tool for new approaches in pain therapy and stroke rehabilitation.
Comparing sperm swimming speed
2012-11-01

Question: Do current methods correctly compare sperm swimming speed (SSS) between males, species or species groups? Data incorporated: Thirty-four studies published since 2009. Method of analysis: Logical and statistical examination of several assumptions behind comparisons of SSS measurements. Conclusions: If sperm swimming speed is measured with a time lag from sperm activation, false-positive correlations can arise between sperm swimming speed and sperm longevity, and between initial and later sperm swimming speed. Comparing the mean, rather than the maximum, sperm swimming speed per ejaculate across subjects may also mask trade-off effects. Environmental and genotype × environment interaction effects can complicate, or invalidate, comparisons of sperm swimming speed. Unlike a previous study, we found that sperm swimming speed and sperm longevity in Tanganyikan cichlids were related to mouthbrooding, not to sperm competition.
Reevaluation of the Reliability and Usefulness of the Somatic Homologous Recombination Reporter Lines
2012-11-01

A widely used approach for assessing genome instability in plants makes use of somatic homologous recombination (SHR) reporter lines. Here, we review the published characteristics and uses of SHR lines. We found a lack of detailed information on these lines and a lack of sufficient evidence that they report only homologous recombination. We postulate that instead of SHR, these lines might be reporting a number of alternative stress-induced stochastic events known to occur at transcriptional, posttranscriptional, and posttranslational levels. We conclude that the reliability and usefulness of the somatic homologous recombination reporter lines requires revision. Thus, more detailed information about these reporter lines is needed before they can be used with confidence to measure genome instability, including the complete sequences of SHR constructs, the genomic location of reporter genes and, importantly, molecular evidence that reconstituted gene expression in these lines is indeed a result of somatic recombination.
Like Father(s), like Son(s): Does the Relation between Advisor and Student Productivity Persist on Group Level?
2012-11-01

In light of the trend towards the Anglo-Saxon model of structured PhD education we analyze whether the positive relation between supervisor research productivity and young researcher productivity does persist in research groups where several PhD and postdoctoral students are supervised by a team of cooperating senior researchers. Our empirical analysis is based on a data set of 86 research training groups from different disciplinary fields funded by the German Research Foundation. We find that the positive relation between supervisor and student productivity also holds on group level. Controlling for group composition with respect to students' study background and demographics (age, gender and cultural background), we find evidence for age and gender diversity effects. Our results prove to be robust to a whole set of additional control variables such as group size, disciplinary field and advisor-student ratio.
Automated odometry self-calibration for car-like robots with four-wheel-steering
2012-11-01

This paper addresses the task of calibrating the kinematic parameters and odometry of car-like robots with dual-axis steering. To achieve this goal only the robots builtin laser rangers and no external tracking systems are employed. We introduce a method to actively calibrate the steering angles of both front and rear steering angles with a multi-input multi-output (MIMO) controller. Using the determined function between steering servo input and steering angle the effective wheelbase and wheel diameters are estimated. We present an automated self-calibration procedure for car-like robots with dual-axis steering. The results are verified using our self-developed outdoor robot platform.
SYSCILIA, “A systems biology approach to dissect cilia function and its disruption in human genetic disease”
2012-11-01

Primary cilia are basically signaling hubs, harboring amongst others the noncanonical WNT, Hedgehog,and PDGF signaling systems, and their disruption leads to striking developmental defects. Some ciliopathy-associated proteins have recently been revealed to be physically or functionally associated in several distinct groupings, with limited connections to other crucial biological processes. Early proteomics studies have also suggested a discrete repertoire of about 1000 proteins within the organelle (i.e. <5% of the proteome) that are still in need of organisation into pathways and networks. Small, relatively isolated systems are often targeted by systems biology approaches under the assumption that a limited set of molecules and interactions will be more tractable for modelling systems. Cilia are thus ideal organelles for systems biology as they can be regarded as semi-closed systems being both largely spatially and biologically separated from many other cellular structures and processes.
Differential requirements of ciliogenic/ciliopathy module components in restricting Joubert syndrome-associated Arl13b to a C. elegans Inv-like ciliary compartment
2012-11-01

Cilium dysfunction causes disorders such as Meckel syndrome (MKS), Bardet-Biedl syndrome (BBS), Nephronophthisis (NPHP) and Joubert syndrome (JS).Most ciliopathy proteins localize to cilia where they regulate developmental signaling and transport.Previously we showed that JS-associated Arl13b localises at proximal ciliary membranes, where it regulates transport in C. elegans.Now we employ C. elegans to investigate the molecular basis of Arl13b ciliary compartmentalisation. First we find that the localisation of C. elegans Arl13b (ARL-13) to proximal ciliary regions does not include transition zones.This localisation, reminiscent of the mammalian Inversin (Inv) ciliary compartment, requires an RVxP motif.Using quantitative imaging, ciliopathy and ciliary transport genes were found to differentially restrict ARL-13 to cilia, with IFT, BBS and MKS gene mutants displaying varying ARL-13 accumulations explicitly at periciliary membranes.Specifically, we observed strong accumulations in IFT-B complex mutants, moderate accumulations in IFT-A, BBS and MKS mutants, and no accumulations in NPHP, septin or kinesin-2 mutants.Interestingly, within IFT/BBS/MKS mutant cilia, ARL-13 distributions were unaffected, as was ARL-13 ciliary mobility.Finally, using a TAP-tag immunoprecipitation approach from mammalian HEK293T cells and state-of-the-art mass spectrometry, we identified components of mammalian Arl13b-associated complexes, including the IFT-B subcomplex.These data show that ARL-13 localisation to an Inv-like ciliary compartment requires an RVxP motif and differential contributions by ciliary transport and ciliopathy modules.Our data also suggest that IFT/BBS/MKS modules are not required for ARL-13 distribution and mobility within cilia, but rather its entry into cilia, perhaps by overcoming a transport barrier at the ciliary base.
Scrutinizing ciliopathies by unravelling the ciliary interactome
2012-11-01

Recent (affinity) proteomics studies have focused on the composition and dynamics of ciliary protein interaction networks. This has unveiled important knowledge about the highly ordered, interconnected but very dynamic nature of the cilium as a molecular machine in the cell. Disruption of members of functional modules of this machine leads to overlapping phenotypes. Detailed analyses of the binding repertoire, the biochemical properties and the biological functions of such modules have yielded the identification of new ciliopathy genes as well as new insights into the pathogenic mechanisms underlying ciliopathies. To gain better insights into the molecular disease mechanisms that underlie ciliopathies and to acquire knowledge about the general importance of the cilium for cellular homeostasis, we are conducting ciliary interactome studies and will combine this information with subcellular localization data, and functional data derived from gene knockdown in ciliated cells or knockout/mutant vertebrate models. This integrated dataset enables us to generate models of interacting functional modules associated with cell signalling cascades, developmental events or specific ciliary functions such as intraflagellar transport. To date, we have performed affinity proteomics for the majority of known ciliopathy-associated proteins and many other ciliary proteins. In addition, yeast two-hybrid experiments have been performed to study the physical interaction between ciliary proteins in more detail. Our current dataset shows high interconnectivity between many of the ciliopathy-associated proteins. These may be part of functional ciliary modules as many are associated with clinically overlapping phenotypes. In addition, new members of these modules are excellent novel candidate ciliopathy proteins.
Electronically Generated Death Reports Improve Collaboration Between Donor-Hospitals and OPO
2012-11-01

Introduction: In order to analyze deaths of potential organ donors, all hospitals with intensive care units in Baden-Württemberg (n=136) are requested to send paper-based questionaires to the German organ procurement organisation (DSO). In view of a poor participation in this practice we implemented the form into our electronic patient record (ISH-med). The form appears automatically on the screen in case of a documented death, asking for contraindications to donation, brain death diagnostics, consent of relatives and the final realization of the donation. A second hospital also implemented the questionaire, the rest (n=134) continued with hand-written reports. Methods: Over a period of 4 years we evaluated the number of completed electronic questionaires in two hospitals with neurosurgery vs. the number of hand-written questionaires in 14 hospitals with and 120 hospitals without neurosurgery. We also registered the number of prospective contacts to the OPO and of finally realized donations. Results: 2008-2011 the two hospitals with neurosurgery reporting electronically sent an average of 103 questionaires per hospital plus 101 direct communications, resulting in 44 realized donors per hospital. The remaining 14 hospitals with neurosurgery reported manually an average of 10 questionaires per hospital, plus 45 direct communications, resulting in 22 realized donors per hospital. Finally the hospitals without neurosurgery produced an average of 1,5 reports and 2,5 direct contacts resulting in only one donor per hospital in 4 years. Conclusion: The implementation of a short questionaire into the electronical patient record improves the communication between donor hospital and organ procurement organization and facilitates retrospective analyses of deaths. Whether higher donation rates are due to this fact has to be analyzed when more hospitals participate. The possible implementation of our system in all hospitals of Baden-Württemberg is currently examined by the Ministry of Health, supported by a German health insurance company.
Reperfusion of the Transplanted Liver: Heterogeneous Techniques in European Transplantation Centres
2012-11-01

Introduction: Liver transplantation is the standard treatment for end-stage liver cirrhosis as well as for certain primary and secondary tumours. However, the reperfusion technique of the liver graft after transplantation has not been standardized. It is still unclear from the literature which method of revascularization is the best in terms of the development of complications and quality of liver graft function. Aim: To compare the experience of different European transplantation centres concerning the sequence of reperfusion of the liver graft at transplantation. Methods: An online survey was sent to 37 European transplantation centres in order to collect information about the centre-specific technique of liver reperfusion and the reason for the adopted technique. Results: By the end of January 2012, 28 European transplantation centres (75,7%) had responded to our survey, which was sent per e-mail in November 2011. 26 of the 28 responses could be included in this study. 10 centres from 26 (38,5%) perform simultaneous reperfusion; 16 centres (61,5%) perform sequential reperfusion, 13 (81,25%) of which are anterograde and 3 (18,75%) retrograde. 12 of the 13 (92,3%) centres performing the sequential anterograde reperfusion first revascularize the portal vein, one centre (7,7%) first revascularizes first the hepatic artery. One (8,3%) of the centres performing the sequential anterograde reperfusion first using the portal vein does not use this technique on children; in this case simultaneous reperfusion is performed. In 20 of the 26 (77%) centres, the technique and order of reperfusion is standardized. In 19 (95%) of these centres, this standard is based on personal/institutional experience; only in 1 (5%) centre the technique used is based on available literature. In 6 (23%) centres, the technique is not standardized and is left at the discretion of the surgeon performing the procedure. Most of the 26 (73%) centres agree on the need for randomized controlled trials (RCT) in this field and would participate in a multicenter RCT. Conclusion: The most frequently used reperfusion technique (46,1%) in European transplantation centres is the anterograde sequential reperfusion via the portal vein first. In 20 of the 26 centres (77 %), the procedure used is standard. Only 1 (3,8%) centre based the decision of how to reperfuse on available literature. These results confirm a lack of evidence-based data and therefore a lack of consensus on the optimal reperfusion techniques. Almost all European transplantation centres base their decision on personal/institutional experience. These results demonstrate the need for RCTs, which most of the centres would support.
Treatment Satisfaction and Goal Attainment With OnabotulinumtoxinA in Patients With Incontinence Due to Idiopathic OAB
2012-11-01

Previous studies have demonstrated the efficacy of onabotulinumtoxinA injection (botulinum toxin type A) in patients with overactive bladder (OAB) syndrome. Patient satisfaction with botulinum toxin A therapy for this syndrome has been reported in a large number of studies. Clinically meaningful relief of symptoms of OAB is associated with patient satisfaction. The present study used data from a previous published multicenter, double-blind, randomized, placebo-controlled trial to investigate the effect of treatment with onabotulinumtoxinA on patient satisfaction and patient goal and expectation attainment. That study had demonstrated that a single dose of onabotulinumtoxinA was efficacious and well tolerated over 36 weeks in patients with OAB with urinary urgency incontinence not adequately managed with anticholinergic therapy. The study population was composed of 313 participants with OAB and urinary urgency incontinence who had been randomized to either placebo or 1 of 5 onabotulinumtoxinA doses. Satisfaction with treatment was evaluated for the 5 onabotulinumtoxinA doses. At baseline and various times after injection of the drug, patient satisfaction was assessed using the modified version of the OAB–Patient Satisfaction With Treatment Questionnaire. Satisfaction was also assessed using Patient Global Assessment, which included questions on changes in symptoms, quality of life, activity limitations, and emotions. There was significant improvement from baseline in mean main module OAB–Patient Satisfaction With Treatment Questionnaire scores (Q2–Q13) at week 12 for each onabotulinumtoxinA dose group (mean improvement range with treatment: −31.5% to −48.9% vs mean improvement with placebo: −17.6%). A higher proportion of patients in the onabotulinumtoxinA dose groups attained their primary goal (range, 34.5%–65.3%) compared with placebo (23.7%). These findings show that patients with OAB treated with onabotulinumtoxinA are more likely to be satisfied and/or achieve their primary treatment goal compared with placebo, consistent with relief of symptoms.
Sequential Step-Down Preconditioning - A Solution for Very High Isoagglutinin Titers in AB0-Incompatible Kidney Transplantation
2012-11-01

Rationale: AB0-incompatible living donor kidney transplantation after recipient preconditioning has become standard practice in Europe with long-term results comparable to blood group compatible transplantation. Intensity of pre-transplant immunoadsorption required varies upon blood group constellation and isoagglutinin titers. Titers ≥ 1:128 are considered high titers which may preclude effective preconditioning. Here we present sequential step-down preconditioning for patients with very high isoagglutinine titers, enabling successful living donor kidney transplantation in these patients. Methods: Two patients with blood group 0 and anti-A1 isoagglutinine titers of 1:2048 and 1:8192 against their respective living kidney donor presented to our transplant center. With no creditable waitlist time or alternative kidney donor, we used a sequential step-down protocol for preconditioning, accounting for magnitude and kinetics of isoagglutinin antibodies. Results: For initial B-cell therapy, standard rituximab (375 mg/m2) was used and effective depletion verified by FACS analysis. Immunoadsorption was initiated using regenerable unselective protein A columns with monitoring of isoagglutinin titers, immunoglobulin (Ig)G levels and fibrinogen. This allowed reduction to pre-treatment isoagglutinin titers ≤ 1:128. To target antibody producing plasma cells, thymoglobulin (1.5 mg/kg) was adminstered, followed by a 10 day interval allowing for reequilibration of isoagglutinins. A second series of immunoadsorption was subsequently performed using unselective and selective anti-A columns, also binding IgM isoagglutinins. Patients were eligible for transplantation with post-treatment isoagglutinin titers of ≤ 1:4. No immunoadsorption was required after transplantation and outcome in both patients is excellent. Conclusion: In patients with very high isoagglutinine titers, sequential step-down preconditioning is cost-sensitive and enables adequate titer reduction and successful transplantation.
The Medically Complex Donor - An Increasing Challenge in Living Donor Kidney Transplantation
2012-11-01

Rationale: Living kidney donation is associated with better patient and graft survival. The long-term risk for the healthy donor is not substantially increased. However, with demographic, social and health changes, we face an increasing number of medically complex living donors. Despite the growing number of living kidney donations, few data is published on criteria of donor evaluation. The 2004 Amsterdam Forum consensus statement provides a framework, yet huge differences exist in clinical practice among transplant centers. We provide data from our university hospital kidney donor evaluation program. Methods: Follow-up of 90 donor-recipient pairs, presenting to our transplant center between 03/2007 and 08/2011 was included in the analysis. Outcomes of donor-recipient evaluation were assessed and declinations stratified into donor- or recipient reasons and underlying conditions. Results: 49% of presenting donor-recipient pairs were accepted for transplantation, among them one-fourth in an AB0 or HLA-incompatible setting. 51% of presenting donor-recipient pairs were declined at first assessment, 26% for recipient reasons and 74% for donor reasons. Almost half of donor declinations were due to increased cardiovascular risk with the presence of diabetes mellitus or prediabetes (IFT, IGT) as the largest single cause of declination. In selected patients, lifestyle intervention allowed donation at a later timepoint. Long-term outcome of accepted donors is excellent. Conclusion: We demonstrate a declination rate of about 50 % of donor-recipient pairs upon first evaluation, reflecting the increasingly complex and comorbid patients presenting to our transplant center. The large majority of declinations is for donor reasons. The prevalence of metabolic disorders (i.e. (pre)diabetes, obesity) emphasizes the need for lifestyle intervention and prevention. We suggest structured programs for living donor preconditioning. This may increase the number of persons eligible for kidney donation.