julilili42/papers huggingface dataset:
Deletion of myosin VI causes slow retinal optic neuropathy and age-related macular degeneration (AMD)-relevant retinal phenotype
2015-05-05

The unconventional myosin VI, a member of the actin-based motor protein family of myosins, is expressed in the retina. Its deletion was previously shown to reduce amplitudes of the a- and b-waves of the electroretinogram. Analyzing wild-type and myosin VI-deficient Snell's Waltzer mice in more detail, the expression pattern of myosin VI in retinal pigment epithelium, outer limiting membrane, and outer plexiform layer could be linked with differential progressing ocular deficits. These encompassed reduced a-waves and b-waves and disturbed oscillatory potentials in the electroretinogram, photoreceptor cell death, retinal microglia infiltration, and formation of basal laminar deposits. A phenotype comprising features of glaucoma (neurodegeneration) and age-related macular degeneration could thus be uncovered that suggests dysfunction of myosin VI and its variable cargo adaptor proteins for membrane sorting and autophagy, as possible candidate mediators for both disease forms.
Otoacoustic emission testing in Ghanaian children with sickle‐cell disease
2015-05-05

Abstract Objective To evaluate hearing loss in children as a complication of sickle‐cell disease. Methods In Kumasi, Ghana, 35 children with SCD aged 6 months to 10 years underwent transient‐evoked otoacoustic emissions testing ( TEOAE ) to investigate the function of the inner ear. Healthy Ghanaian children recruited in school and kindergarten served as controls. Results One of 35 children with SCD and 13 of 115 control children failed the otoacoustic emissions testing. This difference between the control group and the children with SCD was not statistically significant. Conclusion Early hearing impairment does not regularly occur in sickle‐cell disease, and in children, it is not a likely cause of delayed or impaired language development.
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
2015-05-06

Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
Imaging Ca<sup>2+</sup> Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina
2015-05-06

Retinal cone photoreceptors (cones) serve daylight vision and are the basis of color discrimination. They are subject to degeneration, often leading to blindness in many retinal diseases. Calcium (Ca(2+)), a key second messenger in photoreceptor signaling and metabolism, has been proposed to be indirectly linked with photoreceptor degeneration in various animal models. Systematically studying these aspects of cone physiology and pathophysiology has been hampered by the difficulties of electrically recording from these small cells, in particular in the mouse where the retina is dominated by rod photoreceptors. To circumvent this issue, we established a two-photon Ca(2+) imaging protocol using a transgenic mouse line that expresses the genetically encoded Ca(2+) biosensor TN-XL exclusively in cones and can be crossbred with mouse models for photoreceptor degeneration. The protocol described here involves preparing vertical sections ("slices") of retinas from mice and optical imaging of light stimulus-evoked changes in cone Ca(2+) level. The protocol also allows "in-slice measurement" of absolute Ca(2+) concentrations; as the recordings can be followed by calibration. This protocol enables studies into functional cone properties and is expected to contribute to the understanding of cone Ca(2+) signaling as well as the potential involvement of Ca(2+) in photoreceptor death and retinal degeneration.
Audio-Vocal Interaction in Single Neurons of the Monkey Ventrolateral Prefrontal Cortex
2015-05-06

Complex audio-vocal integration systems depend on a strong interconnection between the auditory and the vocal motor system. To gain cognitive control over audio-vocal interaction during vocal motor control, the PFC needs to be involved. Neurons in the ventrolateral PFC (VLPFC) have been shown to separately encode the sensory perceptions and motor production of vocalizations. It is unknown, however, whether single neurons in the PFC reflect audio-vocal interactions. We therefore recorded single-unit activity in the VLPFC of rhesus monkeys ( Macaca mulatta ) while they produced vocalizations on command or passively listened to monkey calls. We found that 12% of randomly selected neurons in VLPFC modulated their discharge rate in response to acoustic stimulation with species-specific calls. Almost three-fourths of these auditory neurons showed an additional modulation of their discharge rates either before and/or during the monkeys' motor production of vocalization. Based on these audio-vocal interactions, the VLPFC might be well positioned to combine higher order auditory processing with cognitive control of the vocal motor output. Such audio-vocal integration processes in the VLPFC might constitute a precursor for the evolution of complex learned audio-vocal integration systems, ultimately giving rise to human speech.
Measurement and numerical calculation of Rubidium Rydberg Stark spectra
2015-05-06

We report on the measurement of Stark shifted energy levels of Rb\\nRydberg atoms in static electric fields by means of electromagnetically induced\\ntransparency (EIT). Electric field strengths of up to 500V/cm, ranging beyond\\nthe classical ionisation threshold, were applied using electrodes inside a\\nglass cell with rubidium vapour. Stark maps for principal quantum numbers\\n and have been obtained with high signal-to-noise ratio for\\ncomparison with results from ab initio calculations following the method\\ndescribed in [M. L. Zimmerman et al., Phys. Rev. A 20, 2251 (1979)], which was\\noriginally only verified for states around . We also calculate the dipole\\nmatrix elements between low-lying states and Stark shifted Rydberg states to\\ngive a theoretical estimate of the relative strength of the EIT signal. The\\npresent work significantly extends the experimental verification of this\\nnumerical method in the range of both high principal quantum numbers and high\\nelectric fields with an accuracy of up to 2MHz.\\n
Addressing spontaneous signal voids in repetitive single‐shot DWI of musculature: spatial and temporal patterns in the calves of healthy volunteers and consideration of unintended muscle activities as underlying mechanism
2015-05-06

Single‐shot diffusion‐weighted MRI sensitive to different types of incoherent motion inside tissue shows sporadic signal voids with a considerable size (&gt;1 cm) in calf musculature at rest. Spatial and temporal patterns of these signal voids and their dependence on measurement conditions were tested systematically in order to obtain more insight into the underlying mechanism. Lower leg muscles of 10 healthy subjects were examined by recording series of 1000 echo‐planar single‐shot scans with repetition time 500 ms and b ‐value 100 s/mm 2 . Effects of strength and orientation of motion sensitization gradients and of repetition times were analysed. Potential influences of arterial blood pulsations and positioning of the subject were studied. Comparison of calf muscle groups showed more frequent signal voids in gastrocnemius and soleus muscle compared with tibialis muscles. Large inter‐individual variance in the total number of signal voids visible in a transverse slice of the lower leg was observed (minimum 40/1000 scans; maximum &gt;550/1000 scans). Typical sizes of the affected muscular areas ranged from 1.5 to 2.5 cm in the transverse and from 1.5 to 7 cm in the head–feet direction. Signal voids occurred nearly independent of the cardiac phase and with similar frequencies for supine and prone positions. Resting calf muscles show spontaneous signal voids in single‐shot DWI at low b ‐values with an irregular temporal and spatial pattern. Values of mean diffusivity, diffusion tensor parameters, and IVIM‐derived perfusion are expected to be clearly distorted by such signal voids if no rejection of affected data is applied. Several potential causes for the signal voids are discussed. The most probable explanation for the phenomenon is seen in the occurrence of spontaneous incoherent mechanical activity in musculature based on weak muscle fibre contractions. If this is the case it opens up a new field for studies on the physiological role and regulation of these unintended muscle activities. Copyright © 2015 John Wiley &amp; Sons, Ltd.
A Comparison of Two Methods for Quantifying Soil Organic Carbon of Alpine Grasslands on the Tibetan Plateau
2015-05-06

As CO2 concentrations continue to rise and drive global climate change, much effort has been put into estimating soil carbon (C) stocks and dynamics over time. However, the inconsistent methods employed by researchers hamper the comparability of such works, creating a pressing need to standardize the methods for soil organic C (SOC) quantification by the various methods. Here, we collected 712 soil samples from 36 sites of alpine grasslands on the Tibetan Plateau covering different soil depths and vegetation and soil types. We used an elemental analyzer for soil total C (STC) and an inorganic carbon analyzer for soil inorganic C (SIC), and then defined the difference between STC and SIC as SOCCNS. In addition, we employed the modified Walkley-Black (MWB) method, hereafter SOCMWB. Our results showed that there was a strong correlation between SOCCNS and SOCMWB across the data set, given the application of a correction factor of 1.103. Soil depth and soil type significantly influenced on the recovery, defined as the ratio of SOCMWB to SOCCNS, and the recovery was closely associated with soil carbonate content and pH value as well. The differences of recovery between alpine meadow and steppe were largely driven by soil pH. In addition, statistically, a relatively strong correlation between SOCCNS and STC was also found, suggesting that it is feasible to estimate SOCCNS stocks through the STC data across the Tibetan grasslands. Therefore, our results suggest that in order to accurately estimate the absolute SOC stocks and its change in the Tibetan alpine grasslands, adequate correction of the modified WB measurements is essential with correct consideration of the effects of soil types, vegetation, soil pH and soil depth.
Alternative Pathway to a Glycopeptide-Resistant Cell Wall in the Balhimycin Producer Amycolatopsis balhimycina
2015-05-06

Balhimycin, a vancomycin-type glycopeptide, is a lipid II targeting antibiotic produced by Amycolatopsis balhimycina. A. balhimycina has developed a self-resistance mechanism based on the synergistic action of different enzymes resulting in modified peptidoglycan. The canonical resistance mechanism against glycopeptides is the synthesis of peptidoglycan precursors ending with acyl-d-alanyl-d-lactate (d-Ala-d-Lac) rather than acyl-d-alanyl-d-alanine (d-Ala-d-Ala). This reprogramming is the result of the enzymes VanH, VanA, and VanX. VanH and VanA are required to produce d-Ala-d-Lac; VanX cleaves cytosolic pools of d-Ala-d-Ala, thereby ensuring that peptidoglycan is enriched in d-Ala-d-Lac. In A. balhimycina, the ΔvanHAXAb mutant showed a reduced glycopeptide resistance in comparison to the wild type. Nevertheless, ΔvanHAXAb was paradoxically still able to produce d-Ala-d-Lac containing resistant cell wall precursors suggesting the presence of a novel alternative glycopeptide resistance mechanism. In silico analysis, inactivation studies, and biochemical assays led to the characterization of an enzyme, Ddl1Ab, as a paraloguous chromosomal d-Ala-d-Lac ligase able to complement the function of VanAAb in the ΔvanHAXAb mutant. Furthermore, A. balhimycina harbors a vanYAb gene encoding a d,d-carboxypeptidase. Transcriptional analysis revealed an upregulated expression of vanYAb in the ΔvanHAXAb mutant. VanYAb cleaves the endstanding d-Ala from the pentapeptide precursors, reducing the quantity of sensitive cell wall precursors in the absence of VanXAb. These findings represent an unprecedented coordinated layer of resistance mechanisms in a glycopeptide antibiotic producing bacterium.
Imaging Ca<sup>2+</sup> Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina
2015-05-06

Retinal cone photoreceptors (cones) serve daylight vision and are the basis of color discrimination. They are subject to degeneration, often leading to blindness in many retinal diseases. Calcium (Ca2+), a key second messenger in photoreceptor signaling and metabolism, has been proposed to be indirectly linked with photoreceptor degeneration in various animal models. Systematically studying these aspects of cone physiology and pathophysiology has been hampered by the difficulties of electrically recording from these small cells, in particular in the mouse where the retina is dominated by rod photoreceptors. To circumvent this issue, we established a two-photon Ca2+ imaging protocol using a transgenic mouse line that expresses the genetically encoded Ca2+ biosensor TN-XL exclusively in cones and can be crossbred with mouse models for photoreceptor degeneration. The protocol described here involves preparing vertical sections ("slices") of retinas from mice and optical imaging of light stimulus-evoked changes in cone Ca2+ level. The protocol also allows "in-slice measurement" of absolute Ca2+ concentrations; as the recordings can be followed by calibration. This protocol enables studies into functional cone properties and is expected to contribute to the understanding of cone Ca2+ signaling as well as the potential involvement of Ca2+ in photoreceptor death and retinal degeneration.
Misspellings in responses to listening comprehension questions:Prospects for scoring based on phonetic normalization
2015-05-06

Automated scoring systems which evaluate content require robust ways of dealing with form errors. The work presented in this paper is set in the context of scoring learners’ responses to listening comprehension items included in a placement test of German as a foreign language. Based on a corpus of over 3000 responses to 17 questions, by test takers of different language proficiencies, we perform a quantitative analysis of the diversity in misspellings. We evaluate the performance of an off-the-shelf open source spell-checker on our data showing that around 45% of the reported non-word errors are not correctly accounted for, that is, they are either falsely identified as misspelt or the spell-checker is unable to identify the intended word. We propose to address misspellings in computer-based scoring of constructed response items by means of phonetic normalization. Learner responses transcribed into Soundex codes and into two encodings borrowed from historical linguistics (ASJP and Dolgopolsky’s sound classes) are compared to transcribed reference answers using string distance measures. We show that reliable correlation with teachers’ scores can be obtained, however, similarity thresholds are item-specific.
Burden Analysis of Rare Microdeletions Suggests a Strong Impact of Neurodevelopmental Genes in Genetic Generalised Epilepsies
2015-05-07

Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
NK Cells are Activated in Amnestic Mild Cognitive Impairment but not in Mild Alzheimer’s Disease Patients
2015-05-07

Alzheimerś disease (AD) is a progressive irreversible neurological brain disorder characterized by accumulation of amyloid-β, amyloid plaques, and neurofibrillary tangles. Inflammation and immune alterations have been linked to AD, suggesting that the peripheral immune system plays a role during the asymptomatic period of AD. NK cells participate in innate immune surveillance against intracellular pathogens and malignancy but their role in AD remains controversial. We have investigated changes in peripheral NK cell phenotypes and functions in amnestic mild cognitive impairment (aMCI, n = 10), patients with mild AD (mAD, n = 11), and healthy elderly controls (n = 10). Patients selected according to NINCDS-ADRDA criteria were classified using neuropsychological assessment tests. Phenotype analysis revealed differences in expression of CD16 (increased in mAD), NKG2A (decreased in aMCI), and TLR2 and TLR9 (both decreased in mAD). Functional assays revealed that NK cell killing activity and degranulation (CD107 expression) were unchanged in the three groups. In contrast, expression of the CD95 receptor was increased in aMCI and mAD. Granzyme B expression and cytokine production (TNFα, IFNγ) were increased in aMCI but not in mAD. CCL19- but not CCL21-dependent chemotaxis was decreased in aMCI and mAD, despite the fact that CCR7 expression was increased in aMCI. Our data suggest that the number of alterations observed in peripheral NK cells in aMCI represent an activation state compared to mAD patients and that may reflect an active immune response against a still to be defined aggression.
Quantitative Evaluation of Segmentation- and Atlas-Based Attenuation Correction for PET/MR on Pediatric Patients
2015-05-07

The use of a dedicated atlas for the pediatric patient collective resulted in improved attenuation map prediction in osseous regions and reduced interpatient bias variation in femur-adjacent VOIs. For the lungs, in which intrapatient variation was higher for the pediatric collective, a patient- or group-specific attenuation coefficient might improve attenuation map accuracy. Mean errors of -14% and -23% in bone marrow and femur-adjacent VOIs can affect PET quantification in these regions when bone tissue is ignored.
TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASE-Mediated Generation and Metabolic Analysis of Camalexin-Deficient cyp71a12 cyp71a13 Double Knockout Lines
2015-05-07

Abstract In Arabidopsis (Arabidopsis thaliana), a number of defense-related metabolites are synthesized via indole-3-acetonitrile (IAN), including camalexin and indole-3-carboxylic acid (ICOOH) derivatives. Cytochrome P450 71A13 (CYP71A13) is a key enzyme for camalexin biosynthesis and catalyzes the conversion of indole-3-acetaldoxime (IAOx) to IAN. The CYP71A13 gene is located in tandem with its close homolog CYP71A12, also encoding an IAOx dehydratase. However, for CYP71A12, indole-3-carbaldehyde and cyanide were identified as major reaction products. To clarify CYP71A12 function in vivo and to better understand IAN metabolism, we generated two cyp71a12 cyp71a13 double knockout mutant lines. CYP71A12-specific transcription activator-like effector nucleases were introduced into the cyp71a13 background, and very efficient somatic mutagenesis was achieved. We observed stable transmission of the cyp71a12 mutation to the following generations, which is a major challenge for targeted mutagenesis in Arabidopsis. In contrast to cyp71a13 plants, in which camalexin accumulation is partially reduced, double mutants synthesized only traces of camalexin, demonstrating that CYP71A12 contributes to camalexin biosynthesis in leaf tissue. A major role of CYP71A12 was identified for the inducible biosynthesis of ICOOH. Specifically, the ICOOH methyl ester was reduced to 12% of the wild-type level in AgNO3-challenged cyp71a12 leaves. In contrast, indole-3-carbaldehyde derivatives apparently are synthesized via alternative pathways, such as the degradation of indole glucosinolates. Based on these results, we present a model for this surprisingly complex metabolic network with multiple IAN sources and channeling of IAOx-derived IAN into camalexin biosynthesis. In conclusion, transcription activator-like effector nuclease-mediated mutation is a powerful tool for functional analysis of tandem genes in secondary metabolism.