Chromatin Preparation and Chromatin Immuno-precipitation from Drosophila Embryos

This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq)

The type of Aplosmilia vidali Angelis d’Ossat, 1905 (Scleractinia; Early Cretaceous)

Se revisa la especie de coral escleractinio Aplosmilia vidali Angelis d’Ossat, 1905 del Cretácico inferior y se le asigna un lectotipo. La forma solitaria pertenece al género Tiarasmilia y es probablemente un sinónimo anterior a la especie-tipo de este género, Tiarasmilia casteri Wells, 1932.Se revisa la especie de coral escleractinio Aplosmilia vidali Angelis d’Ossat, 1905 del Cretácico inferior y se le asigna un lectotipo. La forma solitaria pertenece al género Tiarasmilia y es probablemente un sinónimo anterior a la especie-tipo de este género, Tiarasmilia casteri Wells, 1932.The Early Cretaceous Scleractinian coral species Aplosmilia vidali Angelis d’Ossat, 1905 is revised and a lectotype is designated. The solitary coral belongs to the genus Tiarasmilia and is probably a senior synonym of the type species of this genus, Tiarasmilia casteri Wells, 1932

Remarks on the Scleractinian coral genus Anisoria Vidal, 1917

Precisiones sobre el género de coral escleractinio AnisoriaVidal, 1917. El coral escleractinio Anisoria Vidal, 1917 es un coral del Cretácico terminal (Campaniense superior – Maastrichtiense) endémico del norte de la península Ibérica. Aquí se reconsidera a partir de láminas delgadas obtenidas de uno de los sintipos de la especie tipo Anisoria vidali y de material adicional de la especie tipo procedente de la localidad tipo. Ello posibilita definir la estructura fina de este coral con mayor detalle así como fijar con mayor precisión su posición sistemática. El género es comparable a otros géneros denominados Meandrínidos tales como Meandroria, Pachygyra y Orbignygyra. La mayor afinidad se da con Pachygyra que posee una columela lamelar, ausente en Anisoria. Palabras clave: Scleractinia, corales, España, Cretácico.Precisiones sobre el género de coral escleractinio AnisoriaVidal, 1917. El coral escleractinio Anisoria Vidal, 1917 es un coral del Cretácico terminal (Campaniense superior – Maastrichtiense) endémico del norte de la península Ibérica. Aquí se reconsidera a partir de láminas delgadas obtenidas de uno de los sintipos de la especie tipo Anisoria vidali y de material adicional de la especie tipo procedente de la localidad tipo. Ello posibilita definir la estructura fina de este coral con mayor detalle así como fijar con mayor precisión su posición sistemática. El género es comparable a otros géneros denominados Meandrínidos tales como Meandroria, Pachygyra y Orbignygyra. La mayor afinidad se da con Pachygyra que posee una columela lamelar, ausente en Anisoria. Palabras clave: Scleractinia, corales, España, Cretácico.The Scleractinian coral genus Anisoria Vidal, 1917 is a Late Cretaceous (Upper Campanian – Maastrichtian) coral endemic to the north of the Iberian Peninsula. Herein it is reconsidered on the basis of thin sections obtained from one of the syntypes of the type species Anisoria vidali and additional material of the type species from its type locality. This makes possible to define the fine structure of this coral in greater detail and to state more precisely its systematic position. The genus is comparable to other so-called Meandrininid genera such as Meandroria, Pachygyra and Orbignygyra. The closest relationship exists with Pachygyra, which has a lamellar columella that is lacking in Anisoria. Key words: Scleractinia, corals, Spain, Cretaceou

Remarks on the genus Angelismilia Reig, 1988 (Scleractinia, Early Cretaceous)

Puntualizaciones sobre el género Angelismilia Reig. 1988 (Scleractinia, Cretácico temprano). Se revisa el género AngelismiliaReig, 1988, un coral del Albiense temprano, en base a un sintipo y a material adicional procedentedel área de los tipos. Angelismilia, anteriormente considerado un coral con septos perforados y establecido sin una posición sistemática, tiene septos compactos y palios, siendo asignado a la familia Caryophylliidae.The Early Albian coral genus AngelismiliaReig, 1988 is revised using a syntype of the type species as well as topotypical material from the type area. Angelismilia, formerly considered a coral with perforated septa that was created without indicating its systematic position, has compact septa and pali. For this reason it is placed in the family Caryophylliidae.Puntualizaciones sobre el género Angelismilia Reig. 1988 (Scleractinia, Cretácico temprano). Se revisa el género AngelismiliaReig, 1988, un coral del Albiense temprano, en base a un sintipo y a material adicional procedentedel área de los tipos. Angelismilia, anteriormente considerado un coral con septos perforados y establecido sin una posición sistemática, tiene septos compactos y palios, siendo asignado a la familia Caryophylliidae

Analysing Errors of Open Information Extraction Systems

We report results on benchmarking Open Information Extraction (OIE) systems using RelVis, a toolkit for benchmarking Open Information Extraction systems. Our comprehensive benchmark contains three data sets from the news domain and one data set from Wikipedia with overall 4522 labeled sentences and 11243 binary or n-ary OIE relations. In our analysis on these data sets we compared the performance of four popular OIE systems, ClausIE, OpenIE 4.2, Stanford OpenIE and PredPatt. In addition, we evaluated the impact of five common error classes on a subset of 749 n-ary tuples. From our deep analysis we unreveal important research directions for a next generation of OIE systems.Comment: Accepted at Building Linguistically Generalizable NLP Systems at EMNLP 201

Striatal dopamine transporter availability and individual clinical course within the 1-year follow-up of deep brain stimulation of the subthalamic nucleus in patients with Parkinson’s disease

Objective: Degeneration of dopaminergic neurons in the substantia nigra projecting to the striatum is responsible for the motor symptoms in Parkinson’s disease (PD). Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a well-established procedure to alleviate these symptoms in advanced PD. Yet the mechanism of action, especially the effects of STN-DBS on the availability of striatal dopamine transporter (DAT) as a marker of nigrostriatal nerve cell function, remains largely unknown. The aim of our study was therefore to evaluate whether 1) DAT availability changes within one year of STN-DBS and whether 2) the clinical outcome is predictable by DAT availability before surgical procedure (pre-op). Methods: Twenty-seven PD patients (age: 62.7 ± 8.9 years (y); duration of illness: 13.0 ± 4.9y; PD subtypes: akinetic-rigid n=11, equivalence n=13, tremor-dominant n=3) underwent [123I]FP-CIT single-photon emission computed tomography (SPECT) pre-op and one year after STN-DBS (post-op). DAT availability (specific-to-unspecific binding ratio, SBR) was assessed by volume of interest (VOI) analysis of the caudate nucleus and the putamen ipsilateral and contralateral to the clinically more affected side. Results: 1) Unified Parkinson’s Disease Rating Scale (UPDRS) III (pre-op on: on medication; pre-op off: off medication; post-op on/on: on medication/on stimulation; post-op on/off: on medication/off stimulation) improved significantly (pre-op on: 25.6 ± 12.3, pre-op off: 42.3 ± 15.2, post-op on/off: 41.4 ± 13.2; post-op on/on: 16.1 ± 9.4; pre-op on vs. post-op on/on: p = 0.006) while L-dopa equivalent daily dose (LEDD) was reduced (pre-op 957 ± 440 mg, post-op 313 ± 189 mg; p < 0.001). SBR did not differ significantly before and one year after DBS, regardless of PD subtypes. 2) Pre-op DAT availability was not related to the change in UPDRS III but the change in DAT availability was significantly correlated with the change in UPDRS III (contralateral head of the caudate VOI: p=0.014, contralateral putamen VOI: p=0.018). Conclusion Overall, DAT availability did not change significantly after one-year of STN-DBS. However, on an individual base, the improvement in UPDRS III was associated with an increase of DAT availability while DAT availability before STN-DBS surgery did not predict the clinical outcome. Whether a subtype-specific pattern of pre-op DAT availability can become a reliable predictor for successful STN-DBS has to be evaluated in larger study cohorts.:Introduction 2 1.1 Parkinson’s Disease Pathophysiology 2 1.2 Parkinson’s Disease Clinical Manifestation 4 1.2.1 Parkinson’s Disease Diagnosis 5 1.2.1.1 Unified Parkinson’s Disease Rating Scale 5 1.2.1.2 Imaging 6 1.2.2 Parkinson’s Disease Subtypes 6 1.3 Parkinson’s Disease Therapy 7 1.3.1 Pharmacologic Therapy 7 1.3.2 Surgical Therapy – Deep Brain Stimulation 9 1.3.2.1 Patient Selection 9 1.3.2.2 Operative Technique 9 1.3.2.3 Efficacy 10 1.3.2.4 Complications 11 1.3.2.5 Mechanism of action 11 2 Publication 15 3 Summary of Work 23 3.1 Background 23 3.2 DAT availability changes after STN-DBS 24 3.3 Pre-op DAT availability predicts the clinical outcome 25 3.4 DBS has a neuroprotective effect 25 3.5 Limitations and future direction 26 3.6 Conclusion 26 4 References 27 5 Attachments 35 5.1 Index of Abbreviations 35 5.2 List of figures 36 5.3 Academic Contribution 37 5.4 Declaration of the independent writing of this thesis 39 5.5 Declaration of Submission 40 5.6 Curriculum Vitae 41 5.7 Acknowledgements 4