julilili42/papers huggingface dataset:
FROM DUST TO PLANETESIMALS: AN IMPROVED MODEL FOR COLLISIONAL GROWTH IN PROTOPLANETARY DISKS
2013-02-01

Planet formation occurs within the gas and dust rich environments of\\nprotoplanetary disks. Observations of these objects show that the growth of\\nprimordial sub micron sized particles into larger aggregates occurs at the\\nearliest stages of the disks. However, theoretical models of particle growth\\nthat use the Smoluchowski equation to describe collisional coagulation and\\nfragmentation have so far failed to produce large particles while maintaining a\\nsignificant populations of small grains. This has been generally attributed to\\nthe existence of two barriers impeding growth due to bouncing and fragmentation\\nof colliding particles. In this paper, we demonstrate that the importance of\\nthese barriers has been artificially inflated through the use of simplified\\nmodels that do not take into account the stochastic nature of the particle\\nmotions within the gas disk. We present a new approach in which the relative\\nvelocities between two particles is described by a probability distribution\\nfunction that models both deterministic motion and stochastic motion. Taking\\nboth into account can give quite different results to what has been considered\\nrecently in other studies. We demonstrate the vital effect of two "ingredients"\\nfor particle growth: the proper implementation of a velocity distribution\\nfunction that overcomes the bouncing barrier and, in combination with mass\\ntransfer in high-mass-ratio collisions, boosts the growth of larger particles\\nbeyond the fragmentation barrier. A robust result of our simulations is the\\nemergence of two particle populations (small and large), potentially explaining\\nsimultaneously a number of long-standing problems in protoplanetary disks,\\nincluding planetesimal formation close to the central star, the presence of mm\\nto cm size particles far out in the disk, and the persistence of micron-size\\ngrains for millions of years.\\n
Psychosocial and Ethical Aspects in Non-Invasive EEG-Based BCI Research—A Survey Among BCI Users and BCI Professionals
2013-02-01

In this paper, the results of a pilot interview study with 19 subjects participating in an EEG-based non-invasive brain–computer interface (BCI) research study on stroke rehabilitation and assistive technology and of a survey among 17 BCI professionals are presented and discussed in the light of ethical, legal, and social issues in research with human subjects. Most of the users were content with study participation and felt well informed. Negative aspects reported include the long and cumbersome preparation procedure, discomfort with the cap and the wet electrodes, problems concerning BCI control, and strains during the training sessions. In addition, some users reflected on issues concerning system security. When asked for morally problematic issues in this field of non-invasive BCI research, the BCI professionals stressed the need for correct information transfer, the obligation to avoid unrealistic expectations in study participants, the selection of study participants, benefits and strains of participation, BCI illiteracy, the possibility of detrimental brain modifications induced by BCI use, and problems that may arise at the end of the trials. Furthermore, privacy issues were raised. Based on the results obtained, psychosocial and ethical aspects of EEG-based non-invasive BCI research are discussed and possible implications for future research addressed.
Iodide-Catalyzed Halocyclization/Cycloaddition/Elimination Cascade Reaction
2013-02-01

An iodocyclization reaction of o-alkynylphenyl carboxaldehydes is reported that is truly catalytic with respect to the electrophilic iodine source. With a combination of tetrabutylammonium iodide (TBAI), Oxone as non-nucleophilic and easy to handle co-oxidant, and fluorinated protic solvents, highly substituted 1-naphthalenones could be prepared in high yields of up to 91%.
Characterization of the novelTrypanosoma bruceiinosine 5′-monophosphate dehydrogenase
2013-02-01

SUMMARY There is an alarming rate of human African trypanosomiasis recrudescence in many parts of sub-Saharan Africa. Yet, the disease has no successful chemotherapy. Trypanosoma lacks the enzymatic machinery for the de novo synthesis of purine nucleotides, and is critically dependent on salvage mechanisms. Inosine 5′-monophosphate dehydrogenase (IMPDH) is responsible for the rate-limiting step in guanine nucleotide metabolism. Here, we characterize recombinant Trypanosoma brucei IMPDH (TbIMPDH) to investigate the enzymatic differences between TbIMPDH and host IMPDH. Size-exclusion chromatography and analytical ultracentrifugation sedimentation velocity experiments reveal that TbIMPDH forms a heptamer, different from type 1 and 2 mammalian tetrameric IMPDHs. Kinetic analysis reveals calculated K m values of 30 and 1300 μ m for IMP and NAD, respectively. The obtained K m value of TbIMPDH for NAD is approximately 20–200-fold higher than that of mammalian enzymes and indicative of a different NAD binding mode between trypanosomal and mammalian IMPDHs. Inhibition studies show K i values of 3·2 μ m , 21 nM and 3·3 nM for ribavirin 5′-monophosphate, mycophenolic acid and mizoribine 5′-monophosphate, respectively. Our results show that TbIMPDH is different from its mammalian counterpart and thus may be a good target for further studies on anti-trypanosomal drugs.
Different surgical approaches for stress urinary incontinence in women.
2013-02-01

Stress urinary incontinence (SUI) constitutes involuntary voiding as a consequence of rising intra-abdominal pressure caused by sphincter weakness. In recent years studies were published according to surgical SUI management evaluating and comparing therapy options and outcomes. Therapy options were evaluated using a Medline search, including only publications in English between 2000-2012. Key words used were: SUI, conservative and surgical treatment, midurethral sling, colposuspension. Surgical treatment options demonstrate significantly better results than conservative treatment. MUS demonstrate better subjective and objective cure rates than colposuspension; it is less invasive and more cost-effective. First line SUI therapy such as RP MUS and TVT seem to be favored when compared to transobturator techniques. Retropubic and transobturator MUS showed equivalent objective and subjective success rates. Open colposuspension is an effective treatment possibility for recurrent SUI after failed MUS. TVT, compared with other MUS, seems to show slightly better cure rates. but perioperative complications appear to be similar. Long-term results (>10 years) of repeated SUI surgery showed that the Burch procedure had the lowest 9-year cumulative incidence of repeat SUI surgery. Mini-sling techniques may be underestimated but long-time results are pending and closer monitoring of the adverse event profile must be carried out. MUS are first choice in the treatment of SUI, of which TVT, has the best cure rate. Colpussupension continues to have its place in recurrent SUI. The new mini-MUS needs a longer follow-up for final evaluation.
Characterizing Disturbed Desert Soils Using Multiobjective Parameter Optimization
2013-02-01

Simulating soil moisture dynamics in coarse‐textured alluvial soils under high evaporative demand and infrequent rainfall challenges both characterization and numerical methods. For this study, three geomorphically young disturbed soils in the central Mojave Desert were characterized using direct, indirect, and inverse parameter estimation methods for numerical simulations using HYDRUS. Observations of soil water content (θ) and matric head ( h ) were used to formulate our multiobjective framework optimized using the AMALGAM algorithm. Both the direct and indirect parameterization methods reproduced θ but proved inadequate for h data. Sensitivity analysis found the parameters related to the dry end of the soil hydraulic function—including residual water content (θ r ) and pore‐size distribution ( n) —most sensitive but often conflicting between the two criteria while soil temperature was effectively simulated but insensitive. At the sites, a large dynamic range of h (1–400 m) was accompanied by a relatively small range of θ (0.04–0.10 m 3 m −3 ), limiting our ability to resolve the wet‐end of the hydraulic functions. Direct parameterization from infiltrometer data and indirect pedotransfer functions had good agreement with θ but largely underestimated h . Pareto analysis determined the trade‐off between fitting both criteria and revealed model structure inadequacies as well as bifurcations into parameter populations, favoring either θ or h error minimization. The Pareto solutions compensated for the underestimation of h by forcing the α and n parameters to uncharacteristically low values for such coarse textures. This compensation kept the water capacity sufficiently high at lower θ to maintain conductivity toward the surface. These results are likely a consequence of either the disturbed soil system or hysteresis between measurements of θ and h .
Comparative analysis of photometric variability of TT ARI in the years 1994–1995 and 2001, 2004
2013-02-01

We present the results of photometric observations of a bright cataclysmic variable TT Ari with an orbital period of 0.13755 days. CCD observations were carried out with the Russian-Turkish RTT 150 telescope in 2001 and 2004 (13 nights). Multi-color photoelectric observations of the system were obtained with the Zeiss 600 telescope of SAO RAS in 1994–1995 (6 nights). In 1994–1995, the photometric period of the system was smaller than the orbital one (0 . d 132 and 0 . d 134), whereas it exceeded the latter (0 . d 150 and 0 . d 148) in 2001, 2004. An additional period exceeding the orbital one (0 . d 144) is detected in 1995 modulations. We interpret it as indicating the elliptic disc precession in the direction of the orbital motion. In 1994, the variability in colors shows periods close to the orbital one (0 . d 136, b-v), as well as to the period indicating the elliptic disk precession (0 . d 146, w-b). We confirm that during the epochs characterized by photometric periods shorter than the orbital one, the quasi-periodic variability of TT Ari at time scales about 20 min is stronger than during epochs with long photometric periods. In general, the variability of the system can be described as a “red” noise with increased amplitudes of modulations at characteristic time scales of 10–40 min.
Abnormal cytology during pregnancy--a retrospective analysis of patients in a dysplasia clinic.
2013-02-01

The distinctive feature of the present study is the high number of follow-up examinations, which showed that even women with highly dysplastic changes in pregnancy, who are regularly monitored can be advised to continue pregnancy. Vaginal delivery is possible in most cases.
Small Interfering RNA Transfection Against Serum Response Factor Mediates Growth Inhibition of Benign Prostatic Hyperplasia Fibroblasts
2013-02-01

To treat urethral strictures of the lower urinary tract, urethrotomy is the method of choice. But this minimally invasive method suffers from poor outcome rates and leads often to restenosis of the urinary tract because of hyper-proliferating fibroblasts. Our aim is to minimize the proliferation of excessive tissue due to a new minimal invasive therapeutic approach. As an appropriate model, we isolated fibroblasts from different benign prostatic hyperplasia patients and transfected them with small interfering RNA (siRNA) against the transcription factor serum response factor (SRF), a key factor for cell cycle regulation and apoptosis. The resulting knockdown of SRF was examined on the messenger RNA level by quantitative real-time polymerase chain reaction and on the protein level by western blot. The correlation of SRF silencing and impact on cell proliferation was examined by xCELLigence, 5-bromo-2′-deoxiuridine proliferation assay, total cell counts, and senescence assay. The transfection of primary prostatic fibroblasts with SRFsiRNA revealed specific and significant knockdown of SRF, leading to significant inhibition of proliferation after the second transfection, which was revealed by proliferation assay and total cell number. The results of this study indicate a substantial role of SRF in prostatic fibroblasts and we suggest that SRF silencing might be used for the treatment of urethral strictures to achieve a durably patent urethra.
Efficient Majority-Logic Decoding of Short-Length Reed-Muller Codes at Information Positions
2013-02-01

Short-length Reed--Muller codes under majority-logic decoding are of\\nparticular importance for efficient hardware implementations in real-time and\\nembedded systems. This paper significantly improves Chen's two-step\\nmajority-logic decoding method for binary Reed--Muller codes ,\\n , if --- systematic encoding assumed --- only errors at information\\npositions are to be corrected. Some general results on the minimal number of\\nmajority gates are presented that are particularly good for short codes.\\nSpecifically, with its importance in applications as a 3-error-correcting,\\nself-dual code, the smallest non-trivial example, of dimension\\n16 and length 32, is investigated in detail. Further, the decoding complexity\\nof our procedure is compared with that of Chen's decoding algorithm for various\\nReed--Muller codes up to length .\\n
Longitudinal Melatonin Production in Female Laboratory Rats During 1997-2006: Possible Modulatory Effects of Changing Solar Activity
2013-02-01

Earlier we reported that the urinary excretion of 6-sulfatoxymelatonin (aMT6s) displayed seasonal rhythms in laboratory rats and hypothesized that the horizontal intensity H of the geomagnetic field may act as seasonal zeitgeber. To test this, long-term experiments were performed with female Sprague-Dawley rats. In experiment I (n=12: 1997-1999) nocturnal aMT6s displayed a winter-summer increase by 30% and a rhythm with a phase-length of 24 months peaking in July 1998. In experiment II (n=12; 1999-2000) the winter-summer increase amounted to 40%. The estimated rhythm had a phase-length of 18 months with a peak in September 2000. Compared to experiment I both the rhythm-adjusted mean (MESOR, + 28%) and amplitude (+68%) were elevated. In experiment III (n=30; 2003-2004) the winter-summer increment was just 20%. A circannual rhythm with a peak in April/May was found. The MESOR was 13% higher than in experiment I but the amplitude was depleted ( -14%). In experiment IV (n=15; 2005-2006) a slight winter-summer increase (+15%) was found and a low-amplitude rhythm of 24 months phase-length peaking in June 2006. The MESOR was similar to experiment I but the amplitude was depressed (-36%). These results demonstrate that female rats within two years of age show elevated aMT6s during summer/spring which supports our initial hypothesis. The apparent inter-experimental amplitude variation indicates the involvement of additional variables. Based on our initial hypothesis, we postulate an involvement of the solar cycle affecting H leading to year to year variations and present supportive analyses.
Heterocycles [h]-Fused onto 4-Oxoquinoline-3-carboxylic Acid. Part X [1]. Synthesis and X-Ray Structure of a Model 4- Oxo[1,4]benzoxazepino[2,3-h]quinoline-3-carboxylic Ester
2013-02-01

Direct interaction of salicylaldehyde oxyanion with ethyl 7-chloro-8-nitro-4-oxoquinoline-3- carboxylate (2) delivered the respective 7-(2-formyl-phenoxy)-8-nitro-4-oxoquinoline-3-carboxylic ester 3. Reductive cyclization of 3 furnished the corresponding 4-oxo-[1,4]benzoxazepino[2,3- h]quinoline-3-carboxylic ester 5. Acid-catalyzed hydrolysis of the esters 3/5 produced the respective acids 4/6. Structural assignments for the new compounds 3 - 6 are supported by microanalytical and spectral (IR, HRMS, NMR) data and confirmed by X-ray structure determination for compound 5. Interestingly, compound 6 exhibited good antifungal activity against C. albicans.
Genetic Variants Associated With Glycine Metabolism and Their Role in Insulin Sensitivity and Type 2 Diabetes
2013-02-02

Circulating metabolites associated with insulin sensitivity may represent useful biomarkers, but their causal role in insulin sensitivity and diabetes is less certain. We previously identified novel metabolites correlated with insulin sensitivity measured by the hyperinsulinemic-euglycemic clamp. The top-ranking metabolites were in the glutathione and glycine biosynthesis pathways. We aimed to identify common genetic variants associated with metabolites in these pathways and test their role in insulin sensitivity and type 2 diabetes. With 1,004 nondiabetic individuals from the RISC study, we performed a genome-wide association study (GWAS) of 14 insulin sensitivity–related metabolites and one metabolite ratio. We replicated our results in the Botnia study (n = 342). We assessed the association of these variants with diabetes-related traits in GWAS meta-analyses (GENESIS [including RISC, EUGENE2, and Stanford], MAGIC, and DIAGRAM). We identified four associations with three metabolites—glycine (rs715 at CPS1), serine (rs478093 at PHGDH), and betaine (rs499368 at SLC6A12; rs17823642 at BHMT)—and one association signal with glycine-to-serine ratio (rs1107366 at ALDH1L1). There was no robust evidence for association between these variants and insulin resistance or diabetes. Genetic variants associated with genes in the glycine biosynthesis pathways do not provide consistent evidence for a role of glycine in diabetes-related traits.
Reevaluation of Fatty Acid Receptor 1 as a Drug Target for the Stimulation of Insulin Secretion in Humans
2013-02-02

The role of free fatty acid receptor 1 (FFAR1/GPR40) in glucose homeostasis is still incompletely understood. Small receptor agonists stimulating insulin secretion are undergoing investigation for the treatment of type 2 diabetes. Surprisingly, genome-wide association studies did not discover diabetes risk variants in FFAR1. We reevaluated the role of FFAR1 in insulin secretion using a specific agonist, FFAR1-knockout mice and human islets. Nondiabetic individuals were metabolically phenotyped and genotyped. In vitro experiments indicated that palmitate and a specific FFAR1 agonist, TUG-469, stimulate glucose-induced insulin secretion through FFAR1. The proapoptotic effect of chronic exposure of β-cells to palmitate was independent of FFAR1. TUG-469 was protective, whereas inhibition of FFAR1 promoted apoptosis. In accordance with the proapoptotic effect of palmitate, in vivo cross-sectional observations demonstrated a negative association between fasting free fatty acids (NEFAs) and insulin secretion. Because NEFAs stimulate secretion through FFAR1, we examined the interaction of genetic variation in FFAR1 with NEFA and insulin secretion. The inverse association of NEFA and secretion was modulated by rs1573611 and became steeper for carriers of the minor allele. In conclusion, FFAR1 agonists support β-cell function, but variation in FFAR1 influences NEFA effects on insulin secretion and therefore could affect therapeutic efficacy of FFAR1 agonists.
An update on the molecular genetics toolbox for staphylococci
2013-02-02

Staphylococci are Gram-positive spherical bacteria of enormous clinical and biotechnological relevance. Staphylococcus aureus has been extensively studied as a model pathogen. A plethora of methods and molecular tools has been developed for genetic modification of at least ten different staphylococcal species to date. Here we review recent developments of various genetic tools and molecular methods for staphylococcal research, which include reporter systems and vectors for controllable gene expression, gene inactivation, gene essentiality testing, chromosomal integration and transposon delivery. It is furthermore illustrated how mutant strain construction by homologous or site-specific recombination benefits from sophisticated counterselection methods. The underlying genetic components have been shown to operate in wild-type staphylococci or modified chassis strains. Finally, possible future developments in the field of applied Staphylococcus genetics are highlighted.
Is the SNARC Effect Related to the Level of Mathematics? No Systematic Relationship Observed despite More Power, More Repetitions, and More Direct Assessment of Arithmetic Skill
2013-02-04

The SNARC (spatial–numerical association of response codes) described that larger numbers are responded faster with the right hand and smaller numbers with the left hand. It is held in the literature that arithmetically skilled and nonskilled adults differ in the SNARC. However, the respective data are descriptive, and the decisive tests are nonsignificant. Possible reasons for this nonsignificance could be that in previous studies (a) very small samples were used, (b) there were too few repetitions producing too little power and, consequently, reliabilities that were too small to reach conventional significance levels for the descriptive skill differences in the SNARC, and (c) general mathematical ability was assessed by the field of study of students, while individual arithmetic skills were not examined. Therefore we used a much bigger sample, a lot more repetitions, and direct assessment of arithmetic skills to explore relations between the SNARC effect and arithmetic skills. Nevertheless, a difference in SNARC effect between arithmetically skilled and nonskilled participants was not obtained. Bayesian analysis showed positive evidence of a true null effect, not just a power problem. Hence we conclude that the idea that arithmetically skilled and nonskilled participants generally differ in the SNARC effect is not warranted by our data.
I Can't Keep Your Face and Voice Out of My Head: Neural Correlates of an Attentional Bias Toward Nonverbal Emotional Cues
2013-02-04

Emotional information can be conveyed by verbal and nonverbal cues with the latter often suggested to exert a greater influence in shaping our perceptions of others. The present functional magnetic resonance imaging study sought to explore attentional biases toward nonverbal signals by investigating the interaction of verbal and nonverbal cues. Results obtained in this study underline the previous suggestions of a "nonverbal dominance" in emotion communication by evidencing implicit effects of nonverbal cues on emotion judgements even when attention is directed away from nonverbal signals and focused on verbal cues. Attentional biases toward nonverbal signals appeared to be reflected in increasing activation of the dorsolateral prefrontal cortex (DLPFC) assumed to reflect increasing difficulties to suppress nonverbal cues during task conditions that asked to shift attention away from nonverbal signals. Aside the DLPFC, results suggest the right amygdala to play a role in attention control mechanisms related to the processing of emotional cues. Analyses conducted to determine the cerebral correlates of the individual ability to shift attention between verbal and nonverbal sources of information indicated that higher task-switching abilities seem to be associated with the up-regulation of right amygdala activation during explicit judgments of nonverbal cues, whereas difficulties in task-switching seem to be related to a down-regulation.