julilili42/papers huggingface dataset:
Association of a Functional Variant in the Wnt Co-Receptor LRP6 with Early Onset Ileal Crohn's Disease
2012-02-23

Ileal Crohn's Disease (CD), a chronic small intestinal inflammatory disorder, is characterized by reduced levels of the antimicrobial peptides DEFA5 (HD-5) and DEFA6 (HD-6). Both of these α-defensins are exclusively produced in Paneth cells (PCs) at small intestinal crypt bases. Different ileal CD-associated genes including NOD2, ATG16L1, and recently the β-catenin-dependant Wnt transcription factor TCF7L2 have been linked to impaired PC antimicrobial function. The Wnt pathway influences gut mucosal homeostasis and PC maturation, besides directly controlling HD-5/6 gene expression. The herein reported candidate gene study focuses on another crucial Wnt factor, the co-receptor low density lipoprotein receptor-related protein 6 (LRP6). We analysed exonic single nucleotide polymorphisms (SNPs) in a large cohort (Oxford: n = 1,893) and prospectively tested 2 additional European sample sets (Leuven: n = 688, Vienna: n = 1,628). We revealed an association of a non-synonymous SNP (rs2302685; Ile1062Val) with early onset ileal CD (OR 1.8; p = 0.00034; for homozygous carriers: OR 4.1; p = 0.00004) and additionally with penetrating ileal CD behaviour (OR 1.3; p = 0.00917). In contrast, it was not linked to adult onset ileal CD, colonic CD, or ulcerative colitis. Since the rare variant is known to impair LRP6 activity, we investigated its role in patient mucosa. Overall, LRP6 mRNA was diminished in patients independently from the genotype. Analysing the mRNA levels of PC product in biopsies from genotyped individuals (15 controls, 32 ileal, and 12 exclusively colonic CD), we found particularly low defensin levels in ileal CD patients who were carrying the variant. In addition, we confirmed a direct relationship between LRP6 activity and the transcriptional expression of HD-5 using transient transfection. Taken together, we identified LRP6 as a new candidate gene in ileal CD. Impairments in Wnt signalling and Paneth cell biology seem to represent pathophysiological hallmarks in small intestinal inflammation and should therefore be considered as interesting targets for new therapeutic approaches.
Uveitis Treatment Trials—A Cross-study Perspective
2012-02-23

The previous issue of Ocular Immunology and Inflammation (OII) contains an important and timely report by Martel and colleagues on the 10-year experience of the Francis I. Proctor Foundation with t...
Efficacy of Cut-and-Sew Box Isolation of the Posterior Left Atrium for Treatment of Atrial Fibrillation�Long-term Follow-up after a Modified Maze Procedure
2012-02-23

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Box isolation of the posterior left atrium is one surgical or catheter ablative approach for treating atrial fibrillation (AF). In such cases, incomplete transmurality or recovery of pulmonary vein conduction after the application of various ablative techniques is considered the main reason for the recurrence of postprocedural arrhythmia. The use of solely cut-and-sew box isolation does not have these disadvantages and therefore demonstrates maximum efficacy for this therapeutic approach.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We treated 15 patients with both an indication for open heart surgery and AF (2 paroxysmal, 6 short persistent [&lt;12 months], and 7 long persistent [&gt;12 months] cases) with a solely cut-and-sew box lesion. These patients were then retrospectively followed up over the long term with respect to the end point of freedom of atrial tachyarrhythmias &gt;30 seconds.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The median follow-up duration was 42 months (range, 32-84 months). Five (63%) of 8 patients with preoperative paroxysmal or short persistent AF had no arrhythmia recurrence, whereas arrhythmia recurrence was documented in all 7 patients with preoperative long persistent AF.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Despite reliable transmural isolation with cut-and-sew lesions, we observed long-term arrhythmia recurrence in patients who had preoperative paroxysmal or short persistent AF, suggesting that therapy approaches that are more complex than box isolation might be needed for selected patients to achieve long-term stable sinus rhythm, despite the initially paroxysmal or short persistent character of the arrhythmia. A high rate of recurrence in patients with severe structural heart disease and preoperative long persistent AF might indicate that, in general, isolation of the left posterior atrium alone is not an adequate therapeutic approach for these patients.&lt;/p&gt;
Functionally specific oscillatory activity correlates between visual and auditory cortex in the blind
2012-02-24

Many studies have shown that the visual cortex of blind humans is activated in non-visual tasks. However, the electrophysiological signals underlying this cross-modal plasticity are largely unknown. Here, we characterize the neuronal population activity in the visual and auditory cortex of congenitally blind humans and sighted controls in a complex cognitive task. We recorded magnetoencephalographic responses from participants performing semantic categorization of meaningful sounds that followed the presentation of a semantically related or unrelated haptic object. Source analysis of the spectrally resolved magnetoencephalography data revealed that: (i) neuronal responses to sounds were stronger and longer lasting in the auditory cortex of blind subjects; (ii) auditory stimulation elicited strong oscillatory responses in the visual cortex of blind subjects that closely resembled responses to visual stimulation in sighted humans; (iii) the signal in the gamma frequency range was modulated by semantic congruency between the sounds and the preceding haptic objects; and (iv) signal power in the gamma range was correlated on a trial-by-trial basis between auditory and visual cortex in blind subjects, and the strength of this correlation was modulated by semantic congruency. Our results suggest that specifically oscillatory activity in the gamma range reflects non-visual processing in the visual cortex of blind individuals. Moreover, our results provide evidence that the deprived visual cortex is functionally integrated into a larger network that serves non-visual functions.
Sun of Righteousness, Arise! The Freedom of a Christian—Then and Now—for the Perpetrators and for the Victims of Sin
2012-02-27

The following is a lecture, which Prof. Dr. Jürgen Moltmann gave for the Reformation Day Celebration at Emory University, Atlanta, Georgia. It has an ecumenical direction, beginning with Martin Luther and ending with Charles Wesley’s verse “Sun of Righteousness, Arise!” The lecture moves from Martin Luther in the sixteenth century and his treatise on “The Freedom of a Christian” to Martin Luther King Jr. in the twentieth century, and the inscription on his grave: “Free at last. At last free!”
New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
2012-02-28

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.
The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
2012-02-28

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.
NIPA1 polyalanine repeat expansions are associated with amyotrophic lateral sclerosis
2012-02-28

Mutations in NIPA1 cause Hereditary Spastic Paraplegia type 6, a neurodegenerative disease characterized by an (upper) motor neuron phenotype. Deletions of NIPA1 have been associated with a higher susceptibility to amyotrophic lateral sclerosis (ALS). The exact role of genetic variation in NIPA1 in ALS susceptibility and disease course is, however, not known. We sequenced the entire coding sequence of NIPA1 and genotyped a polyalanine repeat located in the first exon of NIPA1. A total of 2292 ALS patients and 2777 controls from three independent European populations were included. We identified two sequence variants that have a potentially damaging effect on NIPA1 protein function. Both variants were identified in ALS patients; no damaging variants were found in controls. Secondly, we found a significant effect of 'long' polyalanine repeat alleles on disease susceptibility: odds ratio = 1.71, P = 1.6 × 10(-4). Our analyses also revealed a significant effect of 'long' alleles on patient survival [hazard ratio (HR) = 1.60, P = 4.2 × 10(-4)] and on the age at onset of symptoms (HR = 1.37, P = 4.6 × 10(-3)). In patients carrying 'long' alleles, median survival was 3 months shorter than patients with 'normal' genotypes and onset of symptoms occurred 3.6 years earlier. Our data show that NIPA1 polyalanine repeat expansions are a common risk factor for ALS and modulate disease course.
Ethyl 5-amino-3-(pyridin-4-yl)-1-(2,4,6-trichlorophenyl)-1H-pyrazole-4-carboxylate dimethyl sulfoxide hemisolvate
2012-02-28

The asymmetric unit of the title compound, C(17)H(13)Cl(3)N(4)O(2)·0.5C(2)H(6)OS, contains two almost identical mol-ecules and one dimethyl sulfoxide (DMSO-d(6)) solvent mol-ecule. The pyrazole ring forms dihedral angles of 54.6 (4) and 80.0 (4)° in one mol-ecule, and dihedral angles of 54.2 (4) and 81.2 (4)° in the other mol-ecule, with the directly attached pyridine and trichloro-phenyl rings, respectively. The dihedral angles of the pyridine and trichloro-phenyl rings are 51.2 (4) and 52.0 (4)°, respectively. The crystal packing is characterized by intra- and inter-molecular hydrogen bonds. The crystal is a nonmerohedral twin with a contribution of 0.488 (1) for the minor twin component. The terminal ethyl group of one mol-ecule and the S atom of DMSO are disordered over two sites.
A Review of “Lingua franca English: the role of simplification and transfer”
2012-02-28

For the last two decades, research on situations of language use in which the English language occupies the role of a lingua franca has been highly productive. The debates it spurned have led to a ...
IR TrueFISP with a golden‐ratio‐based radial readout: Fast quantification of T1, T2, and proton density
2012-02-29

Abstract A promising approach for the simultaneous quantification of relative proton density ( M 0 ), T 1 , and T 2 is the inversion‐recovery TrueFISP sequence, consisting of an inversion pulse followed by a series of balanced steady‐state free precession acquisitions. Parameters can then be obtained from a mono‐exponential fit to the series of images. However, a segmented acquisition is usually necessary, which increases the total acquisition time considerably. The goal of this study is to obtain M 0 , T 1 , and T 2 maps using a single‐shot acquisition, with T 1 and T 2 measurements in brain that are consistent with the published literature, with a 20‐fold speed improvement over the segmented approach, and at a clinically relevant spatial resolution. To this end, a single‐shot inversion‐recovery TrueFISP sequence was combined with a radial view‐sharing technique. The parameters M 0 , T 1 , and T 2 were then obtained on a pixel‐wise basis from a three fit parameter to the signal evolution. The accuracy of this method for quantifying these parameters is demonstrated in vivo. In addition, further corrections to the quantification necessary owing to other experimental factors, namely magnetization transfer and imperfect slice profiles, were developed. Including additional scans necessary for these corrections in the measurement protocol, the required scan time is increased from approximately 6 to 18‐28 s per slice. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Polarization‐Dependent SERS at Differently Oriented Single Gold Nanorods
2012-02-29

Abstract We investigated the influence of the orientation of individual gold nanorods on the polarization‐dependent single‐particle surface‐enhanced Raman spectroscopy (SERS) of adenine. Higher‐order laser beams (radial and azimuthal polarizations) have been used in combination with a parabolic mirror‐assisted confocal optical microscope. Based on the photoluminescence (PL) patterns of the single gold nanorods and the simulated electric‐field distribution in the focus, we distinguished between isolated gold rods and clusters as well as single nanorods with different orientations. We found that for single gold nanorods lying flat on the substrate, the longitudinal particle plasmon resonance (PPR) mode can be excited more efficiently with the in‐plane field component in the focus of an azimuthally polarized laser beam, which enables the observation of stronger enhanced adenine Raman spectra from the single gold nanorods compared to the case of a radially polarized beam.
On Moral Enhancement from a Habermasian Perspective
2012-02-29

The human being’s mastery of itself, on which the self is founded, practically always involves the annihilation of the subject in whose service that mastery is maintained, because the substance which is mastered, suppressed, and disintegrated by self-preservation is nothing other than the living entity.
Role of Intracellular Hydrogen Peroxide as Signalling Molecule for Plant Senescence
2012-02-29

Mitochondria are an important origin of ROS.During respiration, the ubiquinone pool is the main source for superoxide production.The alternative oxidase (AOX) could be identified in plants and protists, e.g.Trypanosoma, fungi, like Neurospora crassa and Hansenula anomala and in green algae, e.g. in Chlamydomonas (McIntosh, 1994).It acts as a quinoloxidase by transferring electrons from the reduced ubiquinone directly to molecular oxygen forming water (Siedow & Moore, 1993).AOX mediates an energy-wasteful form of respiration, but its physiological significance is still a matter of intense debate (Rasmusson et al., 2009;Vanlerberghe et al., 2009;Millar et al., 2011).The plant alternative oxidases form homodimers (Moore et al., 2002) and are encoded by a small gene family.In Arabidopsis thaliana five genes are known, AOX1a, AOX1b, AOX1c, AOX1d and AOX2, each exhibiting organ specific expression (Saisho et al., 1997; https:/www.genevestigator.com).Among these five AOX genes in Arabidopsis thaliana, AOX1a is the major isoform expressed in leaves (Clifton et al., 2006).One important function of the alternative oxidase is to prevent the formation of excess of reactive oxygen molecules (Maxwell et al., 1999).AOX ensures a low reduction status of the ubiquinone pool by oxidizing ubiquinol.Thus, the electron flow is guaranteed (Millenaar & Lambers, 2003).This reaction is necessary, if the cytochrome c dependent pathway is restricted by naturally occurring cyanide, NO, sulphide, high concentrations of CO 2 , low temperatures or phosphorus deprivation (Millenaar & Lambers, 2003) as well as wounding, drought, osmotic stress, ripening and pathogen infection www.intechopen.com
Invariance, Structure, Measurement – Eino Kaila and the History of Logical Empiricism
2012-02-29

Abstract Eino Kaila's thought occupies a curious position within the logical empiricist movement. Along with Hans Reichenbach, Herbert Feigl, and the early Moritz Schlick, Kaila advocates a realist approach towards science and the project of a “scientific world conception”. This realist approach was chiefly directed at both Kantianism and Poincaréan conventionalism. The case in point was the theory of measurement. According to Kaila, the foundations of physical reality are characterized by the existence of invariant systems of relations, which he called structures. In a certain sense, these invariant structures, he maintained, are constituted in the act of measuring. By “constitution”, however, Kaila meant neither the dependency of the objects of measurement on a priori concepts (or Kantian categories) nor their being effected by conventional stipulations in a Poincaréan sense. He held that invariant structures are, quite literally, real: they exist prior to and independently of our theoretical capacity. By executing measurements, invariant structures are detected and objectively determinable by laws of nature.
Initial India-Asia Continental Collision and Foreland Basin Evolution in the Tethyan Himalaya of Tibet: Evidence from Stratigraphy and Paleontology
2012-03-01

The onset of the India-Asia continent-continent collision in Tibet was accompanied by the elimination of oceanic crust and the development of a peripheral foreland basin on the subducting continental crust. However, owing to the progressively southward migration of this foreland basin, the appearance of flexural uplift (forebulge) predated flexural subsidence (foredeep) at the distal location, such as at Gamba and Tingri in the southern Tethyan Himalaya. Consequently, to trace and date this forebulge may provide a better constraint on the India-Asia collision. At Gamba and Tingri, our studies on the stratigraphy, paleontology, and paleoenvironment show that depositional cessation of the limestones occurred at Shallow Benthic Zone 7 (SBZ 7, ∼54–55 Ma) in the Gamba area and at the base of SBZ 10 (∼52.8 Ma) in the Tingri area. At Gamba, a conglomerate layer within the upper Zongpu Formation is suggested to represent the formation of the forebulge at the onset of the foreland basin, and the coincidence of the conglomerate layer with the Carbon Isotope Excursion (CIE) provides a precise age of ∼56 Ma (the Paleocene/Eocene boundary) for the possible initial India-Asia continental collision. Our results not only provide a reliable and precise age for the India-Asia collision but, for the first time, report time equivalence between the India-Asia collision and the CIE in Tibet.
Query strategies for evading convex-inducing classifiers
2012-03-01

Classifiers are often used to detect miscreant activities. We study how an adversary can systematically query a classifier to elicit information that allows the attacker to evade detection while incurring a near-minimal cost of modifying their intended malfeasance. We generalize the theory of Lowd and Meek (2005) to the family of convex-inducing classifiers that partition their feature space into two sets, one of which is convex. We present query algorithms for this family that construct undetected instances of approximately minimal cost using only polynomially-many queries in the dimension of the space and in the level of approximation. Our results demonstrate that nearoptimal evasion can be accomplished for this family without reverse engineering the classifier's decision boundary. We also consider general lp costs and show that near-optimal evasion on the family of convex-inducing classifiers is generally efficient for both positive and negative convexity for all levels of approximation if p = 1.
Asymmetry and dynamics of a narrow sonar beam in an echolocating harbor porpoise
2012-03-01

A key component in the operation of a biosonar system is the radiation of sound energy from the sound producing head structures of toothed whales and microbats. The current view involves a fixed transmission aperture by which the beam width can only change via changes in the frequency of radiated clicks. To test that for a porpoise, echolocation clicks were recorded with high angular resolution using a 16 hydrophone array. The beam is narrower than previously reported (DI = 24 dB) and slightly dorso-ventrally compressed (horizontal −3 dB beam width: 13°, vertical −3 dB beam width: 11°). The narrow beam indicates that all smaller toothed whales investigated so far have surprisingly similar beam widths across taxa and habitats. Obtaining high directionality may thus be at least in part an evolutionary factor that led to high centroid frequencies in a group of smaller toothed whales emitting narrow band high frequency clicks. Despite the production of stereotyped narrow band high frequency clicks, changes in the directionality by a few degrees were observed, showing that porpoises can obtain changes in sound radiation.
Can we prevent incontinence?: ICI‐RS 2011
2012-03-01

Abstract Aims A review of the current state of research with regard to prevention of incontinence. Methods The search was limited to English language publications on the topic of incontinence prevention. Results Incontinence is associated with a range of risk factors, most of which are modifiable. Lifestyle changes with behavioral modifications that can prevent urinary incontinence (UI) need to be adopted from an early phase of life. Pregnancy per se for the woman , independent of labor and delivery practice, is a risk factor for UI. The influence of estrogen is still under discussion as to its direct influence to UI. For both men and women, there is a correlation between pelvic‐floor related surgery and UI and fecal incontinence (FI). With further improvement in surgical techniques, UI is often only a transient symptom for most patients. Psychological illnesses and their treatment can induce or worsen incontinence and therefore should be evaluated especially with other necessary co‐medications. Conclusions The evidence would suggest that in some cases incontinence can be prevented. Although the evidence base for UI is greater than that for FI, the conditions share many similarities with respect to risk and treatment, suggesting that similar benefits may derive from population‐based prevention strategies. With primary prevention, actions taken early, even in the absence of incontinence, may avoid or delay its onset. There is also evidence that some risk factors for incontinence are modifiable, although not type specific, and can be reduced through preventive measures. Neurourol. Urodynam. 31:390–399, 2012. © 2012 Wiley Periodicals, Inc.