julilili42/papers huggingface dataset:
Gene Expression Profiling of the Retina after Transcorneal Electrical Stimulation in Wild-type Brown Norway Rats
2011-08-28

These results demonstrate that TES applied to the retina of the wild-type BN rats induces distinct transcriptome level changes and may help in the understanding of the mechanisms underlying TES. In addition, TES treatment indicates no negative effect on structure and function of the wild-type BN retina up to 35 hours after application.
Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death
2011-08-29

Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348–1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.
Multiconfigurational time-dependent Hartree method to describe particle loss due to absorbing boundary conditions
2011-08-29

Absorbing boundary conditions in the form of a complex absorbing potential\\nare routinely introduced in the Schr\\\\"odinger equation to limit the\\ncomputational domain or to study reactive scattering events using the\\nmulti-configurational time-dependent Hartree method (MCTDH). However, it is\\nknown that a pure wave-function description does not allow the modeling and\\npropagation of the remnants of a system of which some parts are removed by the\\nabsorbing boundary. It was recently shown [S. Selst{\\\\o} and S. Kvaal, J. Phys.\\nB: At. Mol. Opt. Phys. {\\\\bfseries 43} (2010), 065004] that a master equation of\\nLindblad form was necessary for such a description. We formulate a\\nmulticonfigurational time-dependent Hartree method for this master equation,\\nusable for any quantum system composed of any mixture of species. The\\nformulation is a strict generalization of pure-state propagation using standard\\nMCTDH. We demonstrate the formulation with a numerical experiment.\\n
The Body Adiposity Index and the Sexual Dimorphism in Body Fat
2011-08-29

TO THE EDITOR: Bergman et al. in article titled “A Better Index of Body Adiposity (1)” introduce the body adiposity index (BAI) as a measure of body adiposity being superior to the commonly used BMI. The BAI correlated more strongly with percentage body fat (PBF) determined by dual-energy X-ray absorptiometry (DXA). Although the authors need to be commended for their attempt to find an easily calculated alternative to the BMI, we would like to point out some difficulties. The correlation between body height and PBF in the study of Bergman et al. (1) may largely be driven by sex differences in both, height and PBF. This raises the question whether one could use sex instead of height besides hip circumference to calculate the BAI. It furthermore makes a comparison to BMI somewhat unfair: BMI is largely independent of height while BAI attempts to reflect both, relative body fatness and differences in body composition between males and females. Although in the total population BMI may not be highly correlated with PBF from DXA, the correlation was quite high considering women and men separately, a finding supported by NHANES data (2). BMI together with sex can be used to predict PBF from densitometry quite accurately (r2 ∼0.67) (3). Whether the BAI is superior here still needs to be demonstrated. The particularly strong correlation between hip circumference and PBF from DXA compared to other measures in the study of Bergman et al. (1) may in part be due to the over-representation of women. Unfortunately, Bergman et al. (1) do not report whether BAI predicts PBF among males and females similarly well. Figures 3 and 4 indicate that the relation between BAI and PBF from DXA may be nonlinear with different slopes for men and women and that BAI may overestimate PBF at the lower end of body fatness (thus, more frequently among males). Furthermore, while hip circumference might be more informative compared to waist circumference to predict PBF among women, the correlation between waist circumference and PBF is considerably stronger among men (2). Thus, it seems possible that waist circumference among men and hip circumference among women outperform BAI. Taken together, the added value of the BAI beyond BMI seems that it captures the well-established difference in body composition between males and females (4). However, using hip and waist circumferences as gender-specific correlates of body fatness could be more accurate and easier options for this task. No matter how PBF is estimated from easily obtained anthropometric measurements—based on single circumferences, ratios like the BAI, or more comprehensive prediction models—the superiority of PBF over BMI to predict obesity related markers or endpoints has not clearly been demonstrated so far (5). Furthermore, future studies are needed to determine cutoffs of PBF in relation to type 2 diabetes, cardiovascular morbidity, and mortality. Such cutoffs will likely need to be sex-specific given the large sexual dimorphism related to body composition (4). The authors declared no conflict of interest.
Postinfectious irritable bowel syndrome: follow-up of a patient cohort of confirmed cases of bacterial infection with Salmonella or Campylobacter
2011-08-30

Nearly 10% of patients with an intestinal bacterial infection report postinfectious symptoms up to 10 years after the infectious event. They represent a clinically important population with high psychiatric comorbidity and somatic symptom burden.
How the serotonin transporter 5-HTTLPR polymorphism influences amygdala function: the roles of in vivo serotonin transporter expression and amygdala structure
2011-08-30

The serotonin transporter-linked promoter region (5-HTTLPR) polymorphism of the serotonin transporter gene is associated with amygdala response during negative emotion. The aim of this study was to investigate whether this genotype effect on amygdala function is mediated by current serotonin transporter (5-HTT) levels or rather by genetically induced influences during neurodevelopment, shaping brain structure. A total of 54 healthy subjects underwent functional and structural magnetic resonance imaging, [(11)C]DASB positron emission tomography and 5-HTTLPR genotyping to analyze the interrelationships between amygdala activation during processing of unpleasant stimuli, 5-HTTLPR genotype, amygdala volumes and 5-HTT levels in the midbrain and in other brain regions. In line with previous research, carriers of the short allele (S) showed increased amygdala activation. Path analysis demonstrated that this genotype effect was not procured by current 5-HTT availability but by amygdala structure, with smaller amygdala volumes in the S than in the LL genotype, as well as smaller volumes being associated with increased amygdala activation. Our findings stress the role of genetic effects during neurodevelopment.
Sensitivity of Red Sea circulation to sea level and insolation forcing during the last interglacial
2011-08-30

Abstract. This study investigates the response of Red Sea circulation to sea level and insolation changes during termination II and across the last interglacial, in comparison with termination I and the Holocene. Sediment cores from the central and northern part of the Red Sea were investigated by micropaleontological and geochemical proxies. The recovery of the planktic foraminiferal fauna following high salinities during marine isotopic stage (MIS) 6 took place at similar sea-level stand (~50 m below present day), and with a similar species succession, as during termination I. This indicates a consistent sensitivity of the basin oceanography and the plankton ecology to sea-level forcing. Based on planktic foraminifera, we find that increased water exchange with the Gulf of Aden especially occurred during the sea-level highstand of interglacial MIS 5e. From MIS 6 to the peak of MIS 5e, northern Red Sea sea surface temperature (SST) increased from 21 °C to 25 °C, with about 3 °C of this increase taking place during termination II. Changes in planktic foraminiferal assemblages indicate that the development of the Red Sea oceanography during MIS 5 was strongly determined by insolation and monsoon strength. The SW Monsoon summer circulation mode was enhanced during the termination, causing low productivity in northern central Red Sea core KL9, marked by high abundance of G. sacculifer, which – as in the Holocene – followed summer insolation. Core KL11 records the northern tip of the intruding intermediate water layer from the Gulf of Aden and its planktic foraminifera fauna shows evidence for elevated productivity during the sea-level highstand in the southern central Red Sea. By the time of MIS 5 sea-level regression, elevated organic biomarker BIT values suggest denudation of soil organic matter into the Red Sea and high abundances of G. glutinata, and high reconstructed chlorophyll-a values, indicate an intensified NE Monsoon winter circulation mode. Our results imply that the amplitude of insolation fluctuations, and the resulting monsoon strength, strongly influence the Red Sea oceanography during sea-level highstands by regulating the intensity of water exchange with the Gulf of Aden. These processes are responsible for the observation that MIS 5e/d is characterized by higher primary productivity than the Holocene.
Room temperature excitation spectroscopy of single quantum dots
2011-08-30

We report a single molecule detection scheme to investigate excitation spectra of single emitters at room temperature. We demonstrate the potential of single emitter photoluminescence excitation spectroscopy by recording excitation spectra of single CdSe nanocrystals over a wide spectral range of 100 nm. The spectra exhibit emission intermittency, characteristic of single emitters. We observe large variations in the spectra close to the band edge, which represent the individual heterogeneity of the observed quantum dots. We also find specific excitation wavelengths for which the single quantum dots analyzed show an increased propensity for a transition to a long-lived dark state. We expect that the additional capability of recording excitation spectra at room temperature from single emitters will enable insights into the photophysics of emitters that so far have remained inaccessible.
Optical trapping of gold nanoparticles using a radially polarized laser beam
2011-08-30

In this work we present new results regarding the optical trapping of single gold nanoparticles with a radially polarized laser beam. Since a radially polarized laser beam possesses a strong longitudinal component of the electric field in the center of the focal area, it opens up new advantages for optical manipulation. We describe a procedure of coating the experimental chamber with a charged polymer and the gold nanoparticles with ligands carrying the same charge as the polymer, thus generating electrostatic repulsion which prevents the nanoparticles from depositing on the bottom surface of the experimental chamber. Our experimental results show that a radially polarized laser beam focused with a high numerical aperture objective lens forms a stable trap of a single gold nanoparticle in aqueous solution. By comparing the duration of the interaction of particles with the trapping laser, we found that the average duration of the interactions with a radial beam is two times longer than with a Gaussian beam. Thus, we demonstrate that a radially polarized laser beam exerts stronger forces on the nanoparticles than the Gaussian beam. These findings provide a new insight into the complex interaction of a nanoparticle with the electromagnetic field of optical tweezers.
Nanophotonics, nano-optics and nanospectroscopy
2011-08-30

This Thematic Series of the Beilstein Journal of Nanotechnology is devoted to nanophotonics, nano-optics and nanospectroscopy, and covers the field where nanoscience meets photonics, optics and spectroscopy. Since the pioneering days of scanning near-field optical microscopy [1–2], one of the main goals has been to combine scanning probe microscopy techniques with the spectroscopic means to characterize the chemical structure of materials with nanometer spatial resolution [3–6]. This has turned out to be a demanding but, at the same time, rewarding endeavor. The scaling down of optics and spectroscopy to the length scale of molecules is not simply a matter of making things smaller; the optical phenomena and spectroscopic behavior at the nanoscale are indeed markedly different from those at the macroscopic scale. This challenge continues to fascinate researchers all around the world and has led to many new discoveries concerning the interaction between light and matter at dimensions much smaller than the wavelength of electromagnetic radiation [7–9]. Well-known examples are the negative refractive index created by metamaterials [10–11], the quantum confinement observed in the absorption and luminescence spectra of semiconductor nanoparticles [12], and the plasmon resonances of silver and gold nanoparticles. The concept of plasmon resonance has led to broad applications, such as optical antennas made from noble metals, which have been used to locally focus light into volumes with dimensions far below the diffraction limit and to enhance the emission of locally excited states into the far field [13]. Equally important are fundamental studies of the optical properties of individual quantum systems, such as single atoms, single molecules [14] or single quantum dots, with high spectral resolution and high time resolution. A single molecule is the smallest chemical unit and can be regarded as a single-photon source; its optical properties demonstrate most naturally the quantum characteristics of light and reveal details of intermolecular interactions that would be otherwise hidden in an ensemble. Nanophotonics and nanospectroscopy shine light into this intriguing new world. The study of the interaction between light and matter at the nanometer scale is motivated by the rapid progress in nanoscience and nanotechnology and requires the close cooperation of researchers from a number of different disciplines, including physics, chemistry and biology. Widespread applications can be imagined, e.g., in materials sciences in the pursuit of efficient photovoltaic energy conversion; in the engineering sciences as quantum devices functioning as switches that truly operate at the quantum limit with single photons; or in the life sciences as local optical sensors to observe chemical processes in living cells. Tubingen, August 2011 Alfred J. Meixner
Imaging of photoinduced tautomerism in single porphyrin molecules
2011-08-30

In this work we present our new experimental and theoretical results upon investigations of the photoinduced tautomerism processes of single metal-free porphyrin-type molecules. During tautomerization a molecule changes its structure, therefore the excitation transition dipole moment (TDM) of the molecule changes its orientation. Using confocal microscopy in combination with azimuthally and radially polarized laser beams we are able to determine the orientation of the TDM as well as the orientation of a single molecule itself. In the case of tautomerism we are able to visualize this process and even the involved isomers separately. The study first focuses on two symmetrical compounds: a phthalocyanine and a porphyrin. Additionally, differences of the single molecules embedded in a polymer matrix or just spin-coated on a glass cover slide and under nitrogen flow are investigated. In the latter case we observe a higher frequency of the change of the TDM orientation. The experimental studies are supplemented by quantum chemical calculations. Variations of the molecular substituents, the environment and excitation wavelength can give new insights into the excited-state tautomerism process of a single molecule. We also introduce some suggestions for future experiments to support the understanding of the photoinduced tautomerism.
Intranasal administration of insulin to the brain impacts cognitive function and peripheral metabolism
2011-08-31

In recent years, the central nervous system (CNS) has emerged as a principle site of insulin action. This notion is supported by studies in animals relying on intracerebroventricular insulin infusion and by experiments in humans that make use of the intranasal pathway of insulin administration to the brain. Employing neurobehavioural and metabolic measurements as well as functional imaging techniques, these studies have provided insight into a broad range of central and peripheral effects of brain insulin. The present review focusses on CNS effects of insulin administered via the intranasal route on cognition, in particular memory function, and whole‐body energy homeostasis including glucose metabolism. Furthermore, evidence is reviewed that suggests a pathophysiological role of impaired brain insulin signaling in obesity and type 2 diabetes, which are hallmarked by peripheral and possibly central nervous insulin resistance, as well as in conditions such as Alzheimer's disease where CNS insulin resistance might contribute to cognitive dysfunction.
Activation of steroid‐sensitive TRPM3 channels potentiates glutamatergic transmission at cerebellar Purkinje neurons from developing rats
2011-08-31

J. Neurochem. (2011) 119 , 474–485. Abstract The functional implications of transient receptor potential melastatin 3 (TRPM3) activation, the most recently described member of the melastatin subfamily of cation permeable TRP channels, have begun to be elucidated in recent years. The discovery of TRPM3 activation by the steroid pregnenolone sulfate (PregS) has shed new light on the physiological role of this channel. For example, TRPM3 activation enhances insulin secretion from β pancreatic cells, induces contraction of vascular smooth muscle, and is also involved in the detection of noxious heat. Although TRPM3 expression has been detected in several regions of the developing and mature brain, little is known about the roles of TRPM3 in brain physiology. In this study, we demonstrate the abundant expression of TRPM3 steroid‐sensitive channels in the developing cerebellar cortex. We also show that TRPM3‐like channels are expressed at glutamatergic synapses in neonatal Purkinje cells. We recently showed that PregS potentiates spontaneous glutamate release onto neonatal Purkinje cells during a period of active glutamatergic synapse formation; we now show that this effect of PregS is mediated by TRPM3‐like channels. Mefenamic acid, a recently discovered TRPM3 antagonist, blocked the effect of PregS on glutamate release. The PregS effect on glutamate release was mimicked by other TRPM3 agonists (nifedipine and epipregnanolone sulfate) but not by a TRMP3‐inactive steroid (progesterone). Our findings identify TRPM3 channels as novel modulators of glutamatergic transmission in the developing brain.
Vaccination in the elderly
2011-08-31

Summary There is a general consensus that the elderly do not respond as well to vaccination as the young, but robust studies are few and far between. Most refer to influenza vaccination, but even here, adequate immunological and clinical data are surprisingly thin on the ground. The meta‐analysis by Goodwin et al . from 2006 is still the most comprehensive that we have. They reviewed 31 antibody response studies comparing influenza vaccination efficacy in groups of elderly and younger adults. They reported that the adjusted odds ratio (OR) of responses in elderly versus young adults ranged from 0.24 to 0.59 for the three influenza antigens used in the vaccines. They concluded that rather than the estimated 70–90% clinical vaccine efficacy in younger adults, this figure was only 17–53% in the elderly, depending on which viruses were prevalent that year. They stated that ‘this highlights the need for more immunogenic vaccine formulations for the elderly’. How to achieve this? There are three areas where we may consider alterations to increase vaccine efficacy: (i) make the vaccine more potent; (ii) use adjuvants to enhance immunity; and (iii) apply immune modulators or other interventions to alter host immunity generally. We will consider these three options, focusing on influenza vaccination, in this mini‐review.
Increased responsiveness in feeding behaviour ofCaenorhabditis elegansafter experimental coevolution with its microparasiteBacillus thuringiensis
2011-08-31

Immune responses, either constitutive or induced, are costly. An alternative defence strategy may be based on behavioural responses. For example, avoidance behaviour reduces contact with pathogens and thus the risk of infection as well as the requirement of immune system activation. Similarly, if pathogens are taken up orally, preferential feeding of pathogen-free food may be advantageous. Behavioural defences have been found in many animals, including the nematode Caenorhabditis elegans . We here tested nematodes from a laboratory based evolution experiment which had either coevolved with their microparasite Bacillus thuringiensis (BT) or evolved under control conditions. After 48 generations, coevolved populations were more sensitive to food conditions: in comparison with the controls, they reduced feeding activity in the presence of pathogenic BT strains while at the same time increasing it in the presence of non-pathogenic strains. We conclude that host–parasite coevolution can drive changes in the behavioural responsiveness to bacterial microbes, potentially leading to an increased defence against pathogens.
Modern imaging techniques during therapy in patients with multiple myeloma
2011-08-31

Imaging modalities used in the diagnosis of multiple myeloma have evolved and most of them are also suitable for either early or mid-term monitoring of response to novel antimyeloma therapy. This pictorial essay focuses on modern imaging techniques for diagnosis and follow-up of patients with multiple myeloma in order to highlight their individual strengths and limitations. Also, the impact of recently established modern pharmaceutical therapy, like anti-angiogenic medication, on the tumor is addressed.
Do antidiabetic medications play a specific role in differentiated thyroid cancer compared to other cancer types?
2011-08-31

The risk for differentiated thyroid cancer, like for many other types of cancer, is increased in obese individuals and people with intermediate hyperglycaemia. The incidence of all cancers, with the exception of thyroid cancer, is also increased in type 2 diabetes mellitus patients. The review compares the prevalence of thyroid carcinoma and other cancers in obese, people with intermediate hyperglycaemia and patients with diabetes and summarizes mode of action and anti‐tumourigenic effect of common antidiabetic medications. The over‐expression of dipeptidyl peptidase IV in the tumours, not seen in the other cancer types, is suggested as a potential reason for the unique situation in thyroid cancer.