gebhart/patrepeval huggingface dataset:
New Methodological Approach for the Vanadium K-Edge X-ray Absorption Near-Edge Structure Interpretation:  Application to the Speciation of Vanadium in Oxide Phases from Steel Slag (2007)

This paper presents a comparison between several methods dedicated to the interpretation of V K-edge X-ray absorption near-edge structure (XANES) features. V K-edge XANES spectra of several V-bearing standard compounds were measured in an effort to evaluate advantages and limits of each method. The standard compounds include natural minerals and synthetic compounds containing vanadium at various oxidation state (from +3 to +5) and in different symmetry (octahedral, tetrahedral, and square pyramidal). Correlations between normalized pre-edge peak area and its centroid position have been identified as the most reliable method for determining quantitative and accurate redox and symmetry information for vanadium. This methodology has been previously developed for the Fe K edge. It is also well adapted for the V K edge and is less influenced by the standard choice than other methods. This methodology was applied on an "environmental sample," i.e., a well-crystallized leached steel slag containing vanadium as traces. Micro-XANES measurements allowed elucidating the microdistribution of vanadium speciation in leached steel slag. The vanadium exhibits an important evolution from the unaltered to the altered phases. Its oxidation state increases from +3 to +5 together with the decrease of its symmetry (from octahedral to tetrahedral).
Regulation of endoplasmic reticulum cholesterol by plasma membrane cholesterol (1999)

The abundance of cell cholesterol is governed by multiple regulatory proteins in the endoplasmic reticulum (ER) which, in turn, are under the control of the cholesterol in that organelle. But how does ER cholesterol reflect cell (mostly plasma membrane) cholesterol? We have systematically quantitated this relationship for the first time. We found that ER cholesterol in resting human fibroblasts comprised approximately 0.5% of the cell total. The ER pool rose by more than 10-fold in less than 1 h as cell cholesterol was increased by approximately 50% from below to above its physiological value. The curve describing the dependence of ER on plasma membrane cholesterol had a J shape. Its vertex was at the ambient level of cell cholesterol and thus could correspond to a threshold. A variety of class 2 amphiphiles (e.g., U18666A) rapidly reduced ER cholesterol but caused only minor alterations in the J-curve. In contrast, brief exposure of cells to the oxysterol, 25-hydroxycholesterol, elevated and linearized the J-curve, increasing ER cholesterol at all values of cell cholesterol. This finding can explain the rapid action of oxysterols on cholesterol homeostasis. Other functions have also been observed to depend acutely on the level of plasma membrane cholesterol near its physiological level, perhaps reflecting a cholesterol-dependent structural or organizational transition in the bilayer. Such a physical transition could serve as a set-point above which excess plasma membrane cholesterol is transported to the ER where it would signal regulatory proteins to down-regulate its further accumulation.
Complexities of Rett Syndrome and MeCP2: Figure 1. (2011)

### Introduction 1Rett syndrome (RTT, MIM 312750), originally described by the Austrian pediatrician Andreas Rett, is an X-linked neurodevelopmental disorder that primarily affects girls at a frequency of 1:10,000 live female births ([Rett, 1966][1]; [Hagberg, 1985][2]; [Laurvick et al., 2006][3
The beta 2-agonist controversy revisited. (1995)

beta-Agonists have been used for more than 30 years to treat and prevent asthma, yet the controversy over the safety of these drugs has surfaced only occasionally during this period. A careful review of the data should result in the conclusion that beta 2-agonists remain an appropriate and reliable treatment option for patients with asthma.
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids (1983)

Etude des differents elements helicoidaux. Structures d'ordre superieur a la structure secondaire
Small-molecule direct thrombin inhibitors (1997)

Because of its central role in the control of thrombus formation, the trypsin-like serine protease thrombin is an important target for therapeutic intervention in thrombotic disease. The patent literature from the past several years illustrates that the design of low molecular weight, active-site thrombin inhibitors has followed several major themes. These include tripeptides and peptide mimimics of the cleavage site of fibrinogen, analogues of tertiary arginine amides, and non-peptide inhibitors derived from screening and rational design. This report reviews the concurrent development of these approaches.
EdgeConnect: Structure Guided Image Inpainting using Edge Prediction (2019)

In recent years, many deep learning techniques have been applied to the image inpainting problem: the task of filling incomplete regions of an image. However, these models struggle to recover and/or preserve image structure especially when significant portions of the image are missing. We propose a two-stage model that separates the inpainting problem into structure prediction and image completion. Similar to sketch art, our model first predicts the image structure of the missing region in the form of edge maps. Predicted edge maps are passed to the second stage to guide the inpainting process. We evaluate our model end-to-end over publicly available datasets CelebA, CelebHQ, Places2, and Paris StreetView on images up to a resolution of 512 × 512. We demonstrate that this approach outperforms current state-of-the-art techniques quantitatively and qualitatively.
A study on automatically extracted keywords in text categorization (2006)

This paper presents a study on if and how automatically extracted keywords can be used to improve text categorization. In summary we show that a higher performance --- as measured by micro-averaged F-measure on a standard text categorization collection --- is achieved when the full-text representation is combined with the automatically extracted keywords. The combination is obtained by giving higher weights to words in the full-texts that are also extracted as keywords. We also present results for experiments in which the keywords are the only input to the categorizer, either represented as unigrams or intact. Of these two experiments, the unigrams have the best performance, although neither performs as well as headlines only.
Thermodynamic phase transitions in a frustrated magnetic metamaterial (2015)

Materials with interacting magnetic degrees of freedom display a rich variety of magnetic behaviour that can lead to novel collective equilibrium and out-of-equilibrium phenomena. In equilibrium, thermodynamic phases appear with the associated phase transitions providing a characteristic signature of the underlying collective behaviour. Here we create a thermally active artificial kagome spin ice that is made up of a large array of dipolar interacting nanomagnets and undergoes phase transitions predicted by microscopic theory. We use low energy muon spectroscopy to probe the dynamic behaviour of the interacting nanomagnets and observe peaks in the muon relaxation rate that can be identified with the critical temperatures of the predicted phase transitions. This provides experimental evidence that a frustrated magnetic metamaterial can be engineered to admit thermodynamic phases.
XXXII. Magnetic behaviour of thin single-crystal nickel films (1954)

Summary The coercivity of monocrystalline films of nickel, grown epitaxially on the (100) face of rocksalt, has been studied as a function of thickness over the range 200Å to 1000 Å. Films grown in this way do not exhibit the granularity characteristic of films deposited on cold, inactive substrates; electron micrographs show continuity over distances of the order several microns. The behaviour of such a film is expected to be simpler than that of a polycrystalline film, in which the magnetic properties depend on crystallite boundaries, crystallite size distribution, orientation, etc. Spontaneous magnetization of the films is observed, with the magnetization vector in the plane of the film. The high coercivity characteristic of a single domain structure is observed and the maximum value agrees roughly with that calculated from the anisotropy constants. As is expected, the behaviour of monoerystalline films differs markedly from that of polycrystalline specimens.
Updated guidelines for managing fungal diseases in hematology patients (2010)

Many prospective open or comparative studies have been published over the last few years on antifungals. As invasive fungal disease remains an important cause of morbidity and mortality in high-risk hematology patients, the correct use of antifungal drugs, either as prophylaxis, empirical treatment in neutropenic patients or for therapy of overt disease, is of the utmost importance. Several international or national groups, including the Infectious Diseases Society of America and the European Conference on Infections in Leukaemia, have elaborated practice guidelines to improve the correct usage of antifungals. This article summarizes these guidelines, which have very similar recommendations, and comments on their evidence base.
Meningeal inflammation is widespread and linked to cortical pathology in multiple sclerosis (2011)

Meningeal inflammation in the form of ectopic lymphoid-like structures has been suggested to play a prominent role in the development of cerebral cortical grey matter pathology in multiple sclerosis. The aim of this study was to analyse the incidence and distribution of B cell follicle-like structures in an extensive collection of cases with secondary progressive multiple sclerosis with a wide age range and to determine their relationship to diffuse meningeal inflammation, white matter perivascular infiltrates and microglial activation. One hundred and twenty three cases with secondary progressive multiple sclerosis were examined for the presence of meningeal and perivascular immune cell infiltrates in tissue blocks and/or whole coronal macrosections encompassing a wide array of brain areas. Large, dense, B cell-rich lymphocytic aggregates were screened for the presence of follicular dendritic cells, proliferating B cells and plasma cells. Ectopic B cell follicle-like structures were found, with variable frequency, in 49 cases (40%) and were distributed throughout the forebrain, where they were most frequently located in the deep sulci of the temporal, cingulate, insula and frontal cortex. Subpial grey matter demyelinated lesions were located both adjacent to, and some distance from such structures. The presence of B cell follicle-like structures was associated with an accompanying quantitative increase in diffuse meningeal inflammation that correlated with the degree of microglial activation and grey matter cortical demyelination. The median age of disease onset, time to disease progression, time to wheelchair dependence and age at death all differed significantly in these cases when compared with those without B cell follicle-like structures. Our findings suggest that meningeal infiltrates may play a contributory role in the underlying subpial grey matter pathology and accelerated clinical course, which is exacerbated in a significant proportion of cases by the presence of B cell follicle-like structures.
Particles (2012)

Chapter 10 examines particles, the Kayardild word class which escapes all inflection. True particles are distinguished from semantically similar DPs which do inflect under the right conditions. Evidence is provided to establish the status of particles as ‘special clitics’, which align with the left or right edges of clauses or DPs. A small set of roots is identified which alternates between particle and normal nominal behaviour.
Construction and Validation of a RET TK Catalytic Domain by Homology Modeling (2007)

RET tyrosine kinase (TK) oncoproteins are potential targets for anticancer therapy. However, the search for novel RET inhibitors has been hampered by the lack of a 3D structure of the receptor. In this study, the "open" and the "closed" structure of the RET TK catalytic domain have been built by homology modeling techniques. The structures were validated by extensive docking studies with practically all the inhibitors reported in the literature and through molecular dynamics simulations of the resulting complexes. All the expected major interactions between the active domain amino acids and the inhibitors have been reproduced in their details. Furthermore, the proposed 3D models are in agreement with the results of available mutation studies. Therefore, these models could be profitably used to filter off from large libraries new potential hit compounds able to target this enzyme.
Assessing single-stranded oligonucleotide drug-induced effects in vitro reveals key risk factors for thrombocytopenia (2017)

Single-stranded oligonucleotides (ON) comprise a promising therapeutic platform that enables selective modulation of currently undruggable targets. The development of novel ON drug candidates has demonstrated excellent efficacy, but in certain cases also some safety liabilities were reported. Among them are events of thrombocytopenia, which have recently been evident in late stage trials with ON drugs. The underlying mechanisms are poorly understood and the risk for ON candidates causing such events cannot be sufficiently assessed pre-clinically. We investigated potential thrombocytopenia risk factors of ONs and implemented a set of in vitro assays to assess these risks. Our findings support previous observations that phosphorothioate (PS)-ONs can bind to platelet proteins such as platelet collagen receptor glycoprotein VI (GPVI) and activate human platelets in vitro to various extents. We also show that these PS-ONs can bind to platelet factor 4 (PF4). Binding to platelet proteins and subsequent activation correlates with ON length and connected to this, the number of PS in the backbone of the molecule. Moreover, we demonstrate that locked nucleic acid (LNA) ribosyl modifications in the wings of the PS-ONs strongly suppress binding to GPVI and PF4, paralleled by markedly reduced platelet activation. In addition, we provide evidence that PS-ONs do not directly affect hematopoietic cell differentiation in culture but at higher concentrations show a pro-inflammatory potential, which might contribute to platelet activation. Overall, our data confirm that certain molecular attributes of ONs are associated with a higher risk for thrombocytopenia. We propose that applying the in vitro assays discussed here during the lead optimization phase may aid in deprioritizing ONs with a potential to induce thrombocytopenia.
Benchmarking a highly selective USP30 inhibitor for enhancement of mitophagy and pexophagy (2021)

Abstract The deubiquitylase USP30 is an actionable target considered for treatment of conditions associated with defects in the PINK1/Parkin pathway leading to mitophagy. These include Parkinson’s disease and pulmonary fibrosis. We provide a detailed cell biological characterisation of a benzenesulphonamide molecule, compound 39, that has previously been reported to inhibit USP30 in an in vitro enzymatic assay. The current compound offers increased selectivity over previously described inhibitors. It enhances mitophagy and generates a signature response for USP30 inhibition following mitochondrial depolarisation. This includes enhancement of TOM20 and SYNJ2BP ubiquitylation and phosphoubiquitin accumulation, alongside increased mitophagy. In dopaminergic neurons, generated from Parkinson’s disease patients carrying loss of function Parkin mutations, compound 39 could significantly restore mitophagy to a level approaching control values. USP30 is located on both mitochondria and peroxisomes and has also been linked to the PINK1 independent pexophagy pathway. Using a fluorescence reporter of pexophagy expressed in U20S cells, we observe increased pexophagy upon application of compound 39 that recapitulates the previously described effect for USP30 depletion. This provides the first pharmacological intervention with a synthetic molecule to enhance peroxisome turnover.
Performance of the Helical Screw Rheometer for Fluid Food Suspensions (1993)

ABSTRACT The Helical Screw Rheometer (HSR) consists of a helical screw enclosed in a tight fitting cylinder. When the screw is rotated with the system closed it generates a linearly increasing pressure differential along the axis of the screw. The pressure is proportional to the viscosity of a Newtonian fluid. Viscosity of standard Newtonian fluids measured using the HSR correlated well with measurements on a rotational rheometer with cone and plate fixtures. HSR data on non‐Newtonian suspensions analyzed with a power law model (σ= mγ a ) did not agree as well with results from cone and plate fiiures on the rotational rheometer.
Requirement for NF-kappaB signalling in a mouse model of lung adenocarcinoma. (2009)

NF-kappaB transcription factors function as crucial regulators of inflammatory and immune responses as well as of cell survival. They have also been implicated in cellular transformation and tumorigenesis. However, despite extensive biochemical characterization of NF-kappaB signalling during the past twenty years, the requirement for NF-kappaB in tumour development in vivo, particularly in solid tumours, is not completely understood. Here we show that the NF-kappaB pathway is required for the development of tumours in a mouse model of lung adenocarcinoma. Concomitant loss of p53 (also known as Trp53) and expression of oncogenic Kras(G12D) resulted in NF-kappaB activation in primary mouse embryonic fibroblasts. Conversely, in lung tumour cell lines expressing Kras(G12D) and lacking p53, p53 restoration led to NF-kappaB inhibition. Furthermore, the inhibition of NF-kappaB signalling induced apoptosis in p53-null lung cancer cell lines. Inhibition of the pathway in lung tumours in vivo, from the time of tumour initiation or after tumour progression, resulted in significantly reduced tumour development. Together, these results indicate a critical function for NF-kappaB signalling in lung tumour development and, further, that this requirement depends on p53 status. These findings also provide support for the development of NF-kappaB inhibitory drugs as targeted therapies for the treatment of patients with defined mutations in Kras and p53.
An algorithm for distributed groupware applications (2002)

Computer supported cooperative work (CSCW) is a rapidly growing field. Real-time groupware systems are addressed that allow a group of users to edit a shared document. The architecture and concurrency control algorithm used in this system are described. The algorithm is based on the semantics of the application and can be used by the developers of other groupware systems. The authors begin by introducing the notion of a purely replicated architecture and then present GroupDesign, a shared drawing tool implemented with this architecture. They then present the main parts of the algorithm that implement the distribution. The algorithm gives the best response time for the interface and reduces the number of undo and redo operations when conflicts occur.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Role of Phonons in the Oscillatory Photoconductivity Spectrum of Semiconducting Diamond (1969)

The oscillatory photoconductivity spectrum associated with the acceptor center in semiconducting diamond has been measured over the spectral energy range 0.35-2.6 eV (3.5-0.47 \ensuremath{\mu}). The energy separation between the acceptor ground state and the top of the valence band is more than twice the longitudinal optical (LO) phonon energy, and the spectrum is interpreted in terms of hole capture from the valence band to excited states of the acceptor center together with the cascade emission of one or more optical phonons. Transitions involving the emission of up to 14 phonons have been detected. The mean phonon energy in the cascade process is not constant, as has been generally assumed, but decreases gradually as the number of phonons involved increases. This is shown to be consistent with the curvature of the valence band and the dispersion curves for LO phonons. In addition, features have been observed in the photoconductivity spectrum which are considered to be due to the phonon-assisted hole capture to excited states of the acceptor center for which transitions from the ground state are forbidden, and which therefore have not previously been observed in absorption measurements on natural semiconducting diamond.
Presenting directions with a vibrotactile torso display (2005)

Vibrotactile displays covering the torso present spatial information in an intuitive way since the stimuli are directly mapped to the body coordinates; left is left, front is front, etc. The present study investigated the direction in the horizontal plane to which a specific torso location is mapped using a 15 tactor linear display. Participants indicated the observed external direction of a localized vibration by positioning a remotely controlled cursor. The results show that the observed direction is toward the midsagittal plane (i.e. the navel or the spine) compared to the tactor direction. This bias is consistent over the observers tested, and up to 10 degrees for the oblique directions. Inspection of the response patterns revealed that observers did not use the body midaxis as the origin for the observed direction, but used two spatially separated internal reference points, one for each body half. Therefore, the use of a torso-related transfer function in applications that require a high level of precision is suggested. The variability of the responses also depends on the tactor direction. It is higher for the left - right direction and lower for the fore - aft direction, which may be caused by the spine and navel acting as anchor points. The present results are relevant for tactile navigation displays for visually handicapped individuals or for jet pilots.
Pulmonary arterial hypertension: an autoimmune disease? (2005)

Pulmonary arterial hypertension (PAH) is a rare condition that occurs as a consequence of chronic obstruction of small pulmonary arteries due to endothelial cell, vascular smooth muscle cell and fibroblast dysfunction and proliferation 1. In recent years, major advances have been achieved in the understanding of PAH pathophysiology 1–7. It has been firmly demonstrated that pulmonary artery endothelial dysfunction leads to chronically impaired production of vasodilators, such as nitric oxide and prostacyclin, along with overexpression of vasoconstrictors such as endothelin-1 8–10. Moreover, genetic studies have shown that germline mutations in the gene coding for bone morphogenetic protein receptor type II (BMPR2) certainly play a critical role in a proportion of patients with familial and idiopathic PAH 2, 3. Immune disturbances are also believed to contribute to PAH 5. This is particularly clear in PAH related to connective tissue diseases 5, 11. In addition, there is a long standing association between autoimmunity and PAH of various origins including idiopathic PAH. However, it remains uncertain how autoimmune mechanisms contribute to the pathogenesis of PAH. In the current issue of the European Respiratory Journal , Nicolls et al. 7 review available data documenting the association of autoimmunity and PAH and speculate on the possible role of autoimmune injury in the pathogenesis of the disease.

PAH is a common …