julilili42/papers huggingface dataset:
Contributions of Primate Prefrontal and Posterior Parietal Cortices to Length and Numerosity Representation
2009-03-26

The ability to understand and manipulate quantities ensures the survival of animals and humans alike. The frontoparietal network in primates has been implicated in representing, along with other cognitive abilities, abstract quantity. The respective roles of the prefrontal and parietal areas and the way continuous quantities, as opposed to discrete ones, are represented in this network, however, are unknown. We investigated this issue by simultaneously analyzing recorded single-unit activity in the prefrontal cortex (PFC) and the fundus of the intraparietal sulcus (IPS) of two macaque monkeys while they were engaged in delayed match-to-sample tasks discriminating line length and numerosity. In both areas, we found anatomically intermingled neurons encoding either length, numerosity, or both types of quantities. Even though different sets of neurons coded these quantities, the representation of length and numerosity was similar within the IPS and PFC. Both length and numerosity were coded by tuning functions peaking at the preferred quantity, thus supporting a labeled-line code for continuous and discrete quantity. A comparison of the response characteristics between parietal and frontal areas revealed a larger proportion of IPS neurons representing each quantity type in the early sample phase, in addition to shorter response latencies to quantity for IPS neurons. Moreover, IPS neurons discriminated quantities during the sample phase better than PFC neurons, as quantified by the receiver operating characteristic area. In the memory period, the discharge properties of PFC and IPS neurons were comparable. These single-cell results are in good agreement with functional imaging data from humans and support the notion that representations of continuous and discrete quantities share a frontoparietal substrate, with IPS neurons constituting the putative entry stage of the processing hierarchy.
LFERs for Soil Organic Carbon−Water Distribution Coefficients (KOC) at Environmentally Relevant Sorbate Concentrations
2009-03-26

Organic carbon-water distribution coefficients, Koc, for organic compounds at environmentally relevant, low sorbate concentrations may substantially differ from those at higher concentrations due to nonlinear sorption to soil organic matter. However, prediction methods for Koc such as linear free energy relationships (LFERs) are currently only available for high sorbate concentrations (i.e., near solubility limits), reflecting the lack of a set of consistent experimental data in an environmentally more relevant concentration range (i.e., orders of magnitude lower than solubilities). In this study, we determined Koc for two model sorbents of soil organic matter, peat and lignite, at sorbate concentrations of 4.3 and 19 mg/kg-organic-carbon, respectively, in batch suspensions. The measured Koc values for organic sorbates (51 for peat, 58 for lignite) of varying sizes and polarities were modeled successfully with polyparameter linear free energy relationships (PP-LFERs). The resulting PP-LFER for peat was significantly different from the PP-LFERs in the literature determined at near aqueous solubility limits of sorbates. The literature PP-LFERs were found to underestimate the measured Koc values for peat at the low concentration by up to 1 order of magnitude. The extent of underestimation highly depends on the sorbate properties and can be explained by differing sorption nonlinearities of the sorbates as predicted by a reported empirical relationship between the nonlinearity in peat and the sorbate dipolarity/polarizability parameter S. Lignite appearsto be a stronger sorbent toward many sorbates than typical soil organic matter irrespective of the concentration range and thus may not be representative for organic matter with regard to the magnitude of Koc. The present study offers the first PP-LFER equation for log Koc in soil organic matter at typical environmental sorbate concentrations.
MRI assessment of cardiac amyloidosis: experience of six cases with review of the current literature
2009-03-26

Cardiac MRI is known to be diagnostically valuable in cardiac amyloidosis. Several features are frequently found, including myocardial hypertrophy, diastolic dysfunction, a faster gadolinium blood wash out, pleural and pericardial effusions, and diffuse myocardial delayed enhancement. Cardiac MR facilitates the detection of cardiac amyloidosis and allows longitudinal assessment of myocardial function. This pictorial review focuses on cases with histologically proven systemic amyloidosis and cardiac involvement in order to illustrate typical findings.
Factors affecting postoperative cerebrospinal fluid leaks after retrosigmoidal craniotomy for vestibular schwannomas
2009-03-30

Object The aim of this study was to identify patients likely to develop CSF leaks after vestibular schwannoma surgery using a retrospective analysis for the identification of risk factors. Methods Between January 2001 and December 2006, 420 patients underwent retrosigmoidal microsurgical tumor removal in a standardized procedure. Of these 420 patients, 363 underwent treatment for the first time, and 27 suffered from recurrent tumors. Twenty-six patients had bilateral tumors due to neurofibromatosis Type 2, and 4 patients had previously undergone radiosurgical treatment. An analysis was performed to examine the incidence of postoperative CSF fistulas in all 4 groups. Results The incidence of CSF leakage was higher in the tumor recurrence group (11.1%) than in patients undergoing surgery for the first time (4.4%). There were no CSF fistulas in the neurofibromatosis Type 2 group or in patients with preoperative radiosurgical treatment. Tumor size was identified as a possible risk factor in a previous study. Conclusions Surgery for recurrent tumors is a significant risk factor for the development of CSF leaks.
Stellar oscillations in tensor-vector-scalar theory
2009-03-30

An alternative theory of gravity has recently been proposed by Bekenstein, named Tensor-Vector-Scalar (TeVeS) theory, which can explain many galactic and cosmological observations without the need for dark matter. Whilst this theory passes basic solar system tests, and has been scrutinized with considerable detail in other weak-field regimes, comparatively little has been done in the strong-field limit of the theory. In this article, with Cowling approximation, we examine the oscillation spectra of neutron stars in TeVeS. As a result, we find that the frequencies of fundamental modes in TeVeS could become lager than those expected in general relativity, while the dependence of frequency of higher overtone on gravitational theory is stronger than that of lower modes. These imprints of TeVeS make it possible to distinguish the gravitational theory in strong-field regime via the observations of gravitational waves, which can provide unique confirmation of the existence of scalar field.
Proteomic analysis of the bacterial pathogen Bartonella henselae and identification of immunogenic proteins for serodiagnosis
2009-03-30

Abstract Bartonella henselae is a slow growing, fastidious and facultative intracellular pathogen causing cat scratch disease and vasculoproliferative disorders. To date, knowledge about the pathogenicity of this human pathogenic bacterium is limited and, additionally, serodiagnosis still needs further improvement. Here, we investigated the proteome of B. henselae using 2‐D SDS‐PAGE and MALDI‐TOF‐MS. We provide a comprehensive 2‐D proteome reference map of the whole cell lysate of B. henselae with 431 identified protein spots representing 191 different proteins of which 16 were formerly assigned as hypothetical proteins. To unravel immunoreactive antigens, we applied 2‐D SDS‐PAGE and subsequent immunoblotting using 33 sera of patients suffering from B. henselae infections. The analysis revealed 79 immunoreactive proteins of which 71 were identified. Setting a threshold of 20% seroreactivity, 11 proteins turned out to be immunodominant antigens potentially useful for an improved Bartonella ‐specific serodiagnosis. Therefore, we provide for the first time (i) a comprehensive 2‐D proteome map of B. henselae for further proteome‐based studies focussed on the pathogenicity of B. henselae and (ii) an integrated view into the humoral immune responses targeted against this newly emerged human pathogenic bacterium.
Detection of novel non-M2-related antimitochondrial antibodies in patients with anti-M2 negative primary biliary cirrhosis
2009-03-30

Objective: In 95% of patients with primary biliary cirrhosis (PBC) antimitochondrial antibodies (AMAs) can be detected reacting with at least one of the five components of the M2 antigen identified as the 2-oxoacid dehydrogenase complex (OADC). However, among our PBC sera 15–20% are anti-M2 negative by ELISA and western blotting but in the immunofluorescence test (IFT) they show the typical AMA staining. The aim of the present study was to characterise the target antigen(s) of these non-M2-related AMAs. Patients and methods: We analysed sera from 27 patients with clinically and histologically proven PBC being AMA positive by the IFT but anti-M2 negative by ELISA and western blotting. They were tested by western blotting against various 100 000 g supernatants obtained after sonication of mitochondria from rat liver, bovine heart and pig kidney. These were further separated by isopycnic sucrose density centrifugation using different sucrose density fractions. Results: Fourteen of the 27 AMA positive/anti-M2 negative sera (52%) reacted in the western blotting with a 60 kDa protein and eight (29%) with an 80 kDa protein, both present in the 100 000 g supernatant from bovine heart mitochondria accumulating at sucrose densities of 1.14–1.16. An identity of these determinants with any of the M2-related antigens could be excluded. In the 60 kDa band components of the mitochondrial enzymes F 1 F 0 -ATPase, ubiquinone cytochrome c reductase and acyl CoA dehydrogenase were detected by MALDI–TOF analysis; the 80 kDa protein could not be further characterised. Conclusions: AMA positive/anti-M2 negative PBC sera contain antibodies to further mitochondrial antigens at 60 and 80 kDa which do not correspond to any of the M2 determinants. Those antibodies can be detected to a lesser extent in sera from patients with classical anti-M2 positive PBC but not in patients with other hepatic and non-hepatic disorders and may, therefore, represent additional marker antibodies for the serological diagnosis of PBC.
G‐DRG Version 2009: New Developments
2009-03-30

Summary The update of the G‐DRG system for the year 2009 has been successfully negotiated. Like in the past years, changes are minimal and not dramatic, but they significantly enhance the quality of the DRG system. Once again, the German DRG system demonstrates its versatility and reliability for clinical reimbursement purposes. In the field of dermatology, several improvements or enhancements can be identified; the average case mix index that declined in the past years should now rise by 0.5 percent for 2009. Oncology cases are affected especially by this increase. Some refinements advanced for several years by the German Dermatologic Society (DDG) have been recognized –complex therapies like vacuum wound therapy, isolation due to multi‐resistant infections and multiple primary tumors now have better cost weights. Although there still remain some minor problems like reimbursement of cost‐intensive treatments, German dermatology is in summary very well prepared for the year 2009.
Imaging findings in relapsing multiple myeloma
2009-03-30

We present the case of a 59-year-old woman with Bence Jones (kappa type) multiple myeloma, first diagnosed in October 2005. After initial induction treatment followed by single high-dose chemotherapy with melphalan, a very good partial remission was reached and lasted for more than 2 years. At this stage (October 2007), residual medullary involvement of the right humeral diaphysis was documented on a computed tomography (CT) scan (left). Three months later in January 2008, serum levels of free kappa light chains had increased, from 286 to 1770 mg/l. At this time the CT scan identified relapsing myeloma with infiltration of the medulla of the humeral diaphysis (centre). As disease progression was not clinically relevant at this point, the patient remained under close follow-up. Six months later, further disease progression was documented with progressive proteinuria, impaired renal function and a free kappa light chain level of 17 240 mg/l. CT scan revealed an increase in extent and attenuation of the medullary myelomatous infiltrate, which correlated with the clinical course (right). Consequently, treatment with bortezomib and dexamethasone was initiated.
Phenomenological description of the states 0+and 2+in some even–even nuclei
2009-03-30

A sixth-order quadrupole boson Hamiltonian is used to describe the states and identified in several nuclei by various types of experiments. Two alternative descriptions of energy levels are proposed. One corresponds to a semi-classical approach of the model Hamiltonian while the other one provides the exact eigenvalues. Both procedures yield close formulas for energies. The first procedure involves four parameters, while the second involves a compact formula with five parameters. In each case the parameters are fixed by a least-square fit procedure. Applications are performed for eight even-even nuclei. Both methods yield results which are in a surprisingly good agreement with the experimental data. We give also our predicted reduced transition probabilities within the two approaches, although the corresponding experimental data are not yet available.
Ductus venosus Doppler in screening for trisomies 21, 18 and 13 and Turner syndrome at 11–13 weeks of gestation
2009-03-31

Abstract Objectives To investigate the performance of first‐trimester screening for aneuploidies by including assessment of ductus venosus flow in the combined test of maternal age, fetal nuchal translucency thickness, fetal heart rate, and serum free β‐human chorionic gonadotropin and pregnancy‐associated plasma protein‐A. Methods Screening by the combined test was performed in singleton pregnancies, including 19 614 with euploid fetuses, 122 with trisomy 21, 36 with trisomy 18, 20 with trisomy 13 and eight with Turner syndrome. In all cases the a‐wave in the fetal ductus venosus flow was assessed. We examined the performance of two screening strategies: first, assessment of the a‐wave in all patients and, second, first‐stage screening using the combined test in all patients followed by second‐stage assessment of the a‐wave only in those with an intermediate risk of one in 51 to one in 1000 after the first stage Results Reversed a‐wave was observed in 3.2% of the euploid fetuses, and in 66.4%, 58.3%, 55.0% and 75.0% of fetuses with trisomies 21, 18 and 13 and Turner syndrome, respectively. Inclusion of ductus venosus flow in all pregnancies would detect 96%, 92%, 100% and 100% of trisomies 21, 18 and 13 and Turner syndrome, respectively, at a false‐positive rate of 3%. The same detection rates were achieved with the two‐stage strategy at a false‐positive rate of 2.6%, in which it was necessary to assess the ductus venosus in only 15% of the total population. Conclusions Assessment of ductus venosus flow improves the performance of first‐trimester screening for aneuploidies. Copyright © 2009 ISUOG. Published by John Wiley &amp; Sons, Ltd.
The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis
2009-03-31

Mycobacterium tuberculosis can utilize various nutrients including nitrate as a source of nitrogen. Assimilation of nitrate requires the reduction of nitrate via nitrite to ammonium, which is then incorporated into metabolic pathways. This study was undertaken to define the molecular mechanism of nitrate assimilation in M. tuberculosis . Homologues to a narGHJI -encoded nitrate reductase and a nirBD -encoded nitrite reductase have been found on the chromosome of M. tuberculosis . Previous studies have implied a role for NarGHJI in nitrate respiration rather than nitrate assimilation. Here, we show that a narG mutant of M. tuberculosis failed to grow on nitrate. A nirB mutant of M. tuberculosis failed to grow on both nitrate and nitrite. Mutant strains of Mycobacterium smegmatis mc 2 155 that are unable to grow on nitrate were isolated. The mutants were rescued by screening a cosmid library from M. tuberculosis , and a gene with homology to the response regulator gene glnR of Streptomyces coelicolor was identified. A Δ glnR mutant of M. tuberculosis was generated, which also failed to grow on nitrate, but regained its ability to utilize nitrate when nirBD was expressed from a plasmid, suggesting a role of GlnR in regulating nirBD expression. A specific binding site for GlnR within the nirB promoter was identified and confirmed by electrophoretic mobility shift assay using purified recombinant GlnR. Semiquantitative reverse transcription PCR, as well as microarray analysis, demonstrated upregulation of nirBD expression in response to GlnR under nitrogen-limiting conditions. In summary, we conclude that NarGHJI and NirBD of M. tuberculosis mediate the assimilatory reduction of nitrate and nitrite, respectively, and that GlnR acts as a transcriptional activator of nirBD .
Pharmacogenetic Analyses of a Phase III Trial in Metastatic Gastroesophageal Adenocarcinoma With Fluorouracil and Leucovorin Plus Either Oxaliplatin or Cisplatin: A Study of the Arbeitsgemeinschaft Internistische Onkologie
2009-03-31

Purpose To evaluate the association of germ-line polymorphisms of genes that may impact treatment outcome of platinum and fluorouracil combination chemotherapy in advanced gastric cancer (AGC). Patients and Methods Blood samples of 156 patients enrolled onto a phase III study comparing fluorouracil, leucovorin, and oxaliplatin with fluorouracil, leucovorin, and cisplatin were collected. Polymorphisms within genes of TS, MTHFR, MTR, OPRT, XPD, ERCC1, XRCC1, XPA, GSTP1, GSTT1, and GSTM1 were genotyped using polymerase chain reaction–based techniques. Results Median overall survival (OS) was 11.8 months (95% CI, 9.75 to 13.79 months) and median progression-free survival (PFS) was 5.8 months (95% CI, 4.99 to 6.61 months). The TS-3R/+6 haplotype (P = .004), the GSTT1 deletion polymorphism (P = .015), and genotypes of OPRT-Gly213Ala (P = .003) and XRCC1-Arg399Gln (P = .023) could be identified as independent predictors of OS. For PFS analyses, the TS-3R/+6 haplotye (P = .003) and MTR-A2756G (P = .01) were identified as independent positive predictors. The association between the GSTT1 deletion polymorphism and PFS showed only borderline significance (P = .053). Treatment related hematotoxicity in terms of grade 3/4 leukopenia was lowest among TS-3R/+6 haplotype carriers (P = .037). Grade 3/4 neutropenia was directly associated with the MTR-2756G/G genotype (P = .011), GSTP1-105Ile/Ile genotype (P = .02), and with the ERCC1-118T/8092C-haplotype (P = .042). In addition, significant associations between GSTP1-105Ile/Ile genotype and neurotoxicity and between the XPD-Asn312/751Gln haplotype and nephrotoxicity could be identified (P = .028 and P = .005, respectively). Conclusion These findings underline the hypothesis that germ-line polymorphisms may play an important role in individualizing chemotherapy in AGC and deserve further prospective evaluation in AGC patients.
Role of p38 and Early Growth Response Factor 1 in the Macrophage Response to Group B Streptococcus
2009-03-31

ABSTRACT Group B streptococcus (GBS), the most frequent single isolate in neonatal sepsis and meningitis, potently activates inflammatory macrophage genes via myeloid differentiation antigen 88 (MyD88). However, events parallel to and downstream of MyD88 that instruct the macrophage response are incompletely understood. In this study, we found that only MyD88, not the Toll-like receptor (TLR) adapter proteins MAL/TIRAP, TRIF, and TRAM, essentially mediates the cytokine (tumor necrosis factor [TNF] and interleukin-6) and chemokine (RANTES) responses to whole GBS organisms, although MAL, TRIF, and TRAM have been shown to mediate the responses to substructures in other gram-positive and gram-negative bacteria. GBS-induced, MyD88-dependent phosphorylation of the mitogen-activated protein kinase p38 activated the transcription factor AP-1 and early growth response factor 1 (Egr-1) but not NF-κB. Furthermore, phosphorylation of Ets-like molecule 1 (Elk-1) was mediated by p38. However, in contrast to Egr-1 and AP-1, Elk-1 was dispensable for transcriptional activation of TNF by GBS organisms. Studies of macrophages from Elk-1-deficient mice revealed that Elk-1 was furthermore nonessential for the TNF responses to purified TLR2 and TLR4 agonists, which was in notable contrast to what was revealed in studies employing in vitro expression systems. In conclusion, MyD88, p38, and Egr-1, but not Elk-1, essentially mediate the inflammatory cytokine response to GBS organisms.
Pausing of Golgi Bodies on Microtubules Regulates Secretion of Cellulose Synthase Complexes in Arabidopsis
2009-04-01

Abstract Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by plasma membrane–bound complexes containing cellulose synthase proteins (CESAs). Here, we establish a role for the cytoskeleton in intracellular trafficking of cellulose synthase complexes (CSCs) through the in vivo study of the green fluorescent protein (GFP)-CESA3 fusion protein in Arabidopsis thaliana hypocotyls. GFP-CESA3 localizes to the plasma membrane, Golgi apparatus, a compartment identified by the VHA-a1 marker, and, surprisingly, a novel microtubule-associated cellulose synthase compartment (MASC) whose formation and movement depend on the dynamic cortical microtubule array. Osmotic stress or treatment with the cellulose synthesis inhibitor CGA 325'615 induces internalization of CSCs in MASCs, mimicking the intracellular distribution of CSCs in nongrowing cells. Our results indicate that cellulose synthesis is coordinated with growth status and regulated in part through CSC internalization. We find that CSC insertion in the plasma membrane is regulated by pauses of the Golgi apparatus along cortical microtubules. Our data support a model in which cortical microtubules not only guide the trajectories of CSCs in the plasma membrane, but also regulate the insertion and internalization of CSCs, thus allowing dynamic remodeling of CSC secretion during cell expansion and differentiation.
Efficient reconstruction of nonrigid shape and motion from real-time 3D scanner data
2009-04-01

We present a new technique for reconstructing a single shape and its nonrigid motion from 3D scanning data. Our algorithm takes a set of time-varying unstructured sample points that capture partial views of a deforming object as input and reconstructs a single shape and a deformation field that fit the data. This representation yields dense correspondences for the whole sequence, as well as a completed 3D shape in every frame. In addition, the algorithm automatically removes spatial and temporal noise artifacts and outliers from the raw input data. Unlike previous methods, the algorithm does not require any shape template but computes a fitting shape automatically from the input data. Our reconstruction framework is based upon a novel topology-aware adaptive subspace deformation technique that allows handling long sequences with complex geometry efficiently. The algorithm accesses data in multiple sequential passes, so that long sequences can be streamed from hard disk, not being limited by main memory. We apply the technique to several benchmark datasets, significantly increasing the complexity of the data that can be handled efficiently in comparison to previous work.