gebhart/patrepeval huggingface dataset:
IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA–target interactions (2017)

Web repositories for almost all 'omics' types have been generated-detailing the repertoire of representatives across different tissues or cell types. A logical next step is the combination of these valuable sources. With IMOTA (interactive multi omics tissue atlas), we developed a database that includes 23 725 relations between miRNAs and 23 tissues, 310 932 relations between mRNAs and the same tissues as well as 63 043 relations between proteins and the 23 tissues in Homo sapiens. IMOTA also contains data on tissue-specific interactions, e.g. information on 331 413 miRNAs and target gene pairs that are jointly expressed in the considered tissues. By using intuitive filter and visualization techniques, it is with minimal effort possible to answer various questions. These include rather general questions but also requests specific for genes, miRNAs or proteins. An example for a general task could be 'identify all miRNAs, genes and proteins in the lung that are highly expressed and where experimental evidence proves that the miRNAs target the genes'. An example for a specific request for a gene and a miRNA could for example be 'In which tissues is miR-34c and its target gene BCL2 expressed?'. The IMOTA repository is freely available online at https://ccb-web.cs.uni-saarland.de/imota/.
Paper # 225: Linear Wear of Mobile Unicompartmental Bearings: A 20 Year In‐Vivo Study (2011)

In-vivo assessment of linear wear of the Oxford UKA mobile bearing device reveals very low linear penetration at 20-years, where impingment is avoided.
Novel applications of plasmonic metamaterials (2016)

Metamaterials are the artificial materials composed of multiple individual elements in specially designed periodic subwavelength patterns. The properties of these metamaterials strongly depend on the featured shape or size of the unit of metamaterials rather than the original properties of the composition of materials. Their precise shape, geometry, size, orientation and arrangement can affect the light in an unconventional manner, creating material properties which are unachievable with conventional materials, such as negative refractive index, abnormal reflection, and so on. Due to these fascinating properties, we have designed and fabricated various plasmonic metamaterials with localized energy, electromagnetic field enhancement, and nonlinearity by the state of the art methods, such as e-beam lithography with multi-exposure technique, focus ion beam drilling, ultrafast laser direct writing, phase-change materials etching process, etc… This talk will discuss about the diverse novel applications for the plasmonic metamaterials in the green energy, environment, and better life, respectively. As for the applications in the green energy, it will cover environmentally friendly green energy sources, high-efficiency solar energy conversion over entire spectrum, and nonlinear plasmonic nano-laser. The metamaterials could also be used for the high efficiency photo-catalyst water treatments, high-efficiency broad-band gradient meta-surface, three-dimensional full color plasmonic holograph, three-dimensional split ring resonators based biosensor, hyperbolic metamaterials for subwavelength resolution, and so on. These novel applications pave new ways to apply the fundamental physics of plasmonic metamaterials to achieve clean environment with high-efficiency energy sources, as well as the bright future of human being life.
Propriétés électroniques quasi-bidimensionnelles de couches épitaxiales de GaAs à dopage δ (1989)

Nous présentons ici une étude des propriétés de transport électronique de structures à dopage planaire Si dans GaAs. Nous utilisons des forts champs magnétiques continus et des basses températures pour caractériser la couche d'accumulation. Nous montrons le caractère bidimensionnel de la conduction et la présence de plusieurs sous-bandes.
Anomalous reactivity of benzopinacolone towards 4-phenylthiosemicarbazide, a nucleophile endowed with alpha-effect (2018)

In a medicinal chemistry-driven drug discovery program aimed at synthesizing new topically-acting trypanocidal chemotherapeutic agents to treat the African trypanosomiasis, our research group became interested in new chemical entities bearing in their center a thiohydrazide (C=S) NHNH or thiosemicarbazide NH(C=S) NHNH central template flanked on both sides by lipophilic aryl moieties. In this context, benzopinacolone was found to react as a rather unusual acylating agent via a mechanism (addition/elimination) involving addition of the nucleophile (a thiosemicarbazide derivative), formation of a resulting tetrahedral adduct, and expulsion of a trityl anion moiety as leaving group, presumably through an anchimeric assistance effect by intram-olecular participation of the thioureido side-chain via hydrogen bond formation. The present incidental discovery should be considered at this level as a first inception and further work is now being directed at closely examining the detailed mechanism of this exceptional chemical pathway; in a reaction involving the unusual breaking of a carbon-carbon bond (carbon acid as leaving group) in the rate-determining step and involving the decomposition of the intermediate tetrahedral adduct to get the final unexpected N-thiobenzoyl-thiosemicarbazide.
The Crystal Structure of 1-D-myo-Inosityl 2-Acetamido-2-deoxy-α-D-glucopyranoside Deacetylase (MshB) from Mycobacterium tuberculosis Reveals a Zinc Hydrolase with a Lactate Dehydrogenase Fold (2003)

Mycothiol (1-D-myo-inosityl 2-(N-acetyl-L-cysteinyl)amido-2-deoxy-alpha-D-glucopyranoside, MSH or AcCys-GlcN-inositol (Ins)) is the major reducing agent in actinomycetes, including Mycobacterium tuberculosis. The biosynthesis of MSH involves a deacetylase that removes the acetyl group from the precursor GlcNAc-Ins to yield GlcN-Ins. The deacetylase (MshB) corresponds to Rv1170 of M. tuberculosis with a molecular mass of 33,400 Da. MshB is a Zn2+ metalloprotein, and the deacetylase activity is completely dependent on the presence of a divalent metal cation. We have determined the x-ray crystallographic structure of MshB, which reveals a protein that folds in a manner resembling lactate dehydrogenase in the N-terminal domain and a C-terminal domain consisting of two beta-sheets and two alpha-helices. The zinc binding site is in the N-terminal domain occupying a position equivalent to that of the NAD+ co-factor of lactate dehydrogenase. The Zn2+ is 5 coordinate with 3 residues from MshB (His-13, Asp-16, His-147) and two water molecules. One water would be displaced upon binding of substrate (GlcNAc-Ins); the other is proposed as the nucleophilic water assisted by the general base carboxylate of Asp-15. In addition to the Zn2+ providing electrophilic assistance in the hydrolysis, His-144 imidazole could form a hydrogen bond to the oxyanion of the tetrahedral intermediate. The extensive sequence identity of MshB, the deacetylase, with mycothiol S-conjugate amidase, an amide hydrolase that mediates detoxification of mycothiol S-conjugate xenobiotics, has allowed us to construct a faithful model of the catalytic domain of mycothiol S-conjugate amidase based on the structure of MshB.
3D copper TSV integration, testing and reliability (2011)

Node-agnostic Cu TSVs integrated with high-K/metal gate and embedded DRAM were used in functional 3D modules. Thermal cycling and stress results show no degradation of TSV or BEOL structures, and device and functional data indicate that there is no significant impact from TSV processing and/or proximity.
Anthrax surrogate spores are destroyed by PDT mediated by phenothiazinium dyes (2005)

Some Gram-positive bacteria (including the causative agent of anthrax - <i>Bacillus anthracis</i>) survive conditions of stress and starvation by producing dormant stage spores. The spore’s multilayered capsule consists of inner and outer membranes, cortex, proteinaceous spore coat, and in some species an exosporium. These outer layers enclose dehydrated and condensed DNA, saturated with small, acid-soluble proteins. These protective structures make spores highly resistant to damage by heat, radiation, and commonly employed anti-bacterial agents. Previously Bacillus spores have been shown to be resistant to photodynamic inactivation (PDI) using dyes and light that easily destroy the corresponding vegetative bacteria, but recently we have discovered that they are susceptible to PDI. Photoinactivation, however, is only possible if phenothiazinium dyes are used. Dimethylmethylene blue, methylene blue, new methylene blue and toluidine blue O are all effective photosensitizers. Alternative photosensitizers such as Rose Bengal, polylysine chlorin(e6) conjugate, a tricationic porphyrin and benzoporphyrin derivative are ineffective against spores even though they can easily kill vegetative cells. Spores of <i>B. cereus </i>and <i>B. thuringien</i>sis are most susceptible, <i>B. subtilis </i>and <i>B. atrophaeus </i>are also killed, while <i>B. megaterium </i>is resistant. Photoinactivation is most effective when excess dye is washed from the spores showing that the dye binds to the spores and that excess dye in solution can quench light delivery. The relatively mild conditions needed for spore killing could have applications for treating wounds contaminated by anthrax spores and for which conventional sporicides would have unacceptable tissue toxicity.
Simple suppression technique for higher-order mode amplification in bent large mode area triple-cladding fibers (2010)

A novel technique to suppress the higher-order mode in bent LMA triple-cladding fibers is proposed. It is shown that the higher-order mode can be coupled to a cladding mode with only an adjustment of the bending diameter.
Novel Adhesion Promoter for Metal–Plastic Composites (2014)

This work presents a novel bonding agent for metal–plastic composites produced by twin polymerization. During twin polymerization, an interpenetrated network of organic and inorganic homopolymers is formed from one twin monomer. The mixtures of two twin monomers with various mixing ratios are studied. The suitability of a twin polymer as adhesion promoter is evaluated by axial loading tensile tests.
Field modulated wavelength converters (2006)

We demonstrate 10Gbit/s operation of two different types of monolithic photocurrent driven wavelength converters (PD-WC). These photonic integrated circuits use a Semiconductor Optical Amplifier (SOA)-PIN photodetector receiver to drive an Electro-absorption (EA), or Mach-Zehnder (MZ) modulator that is integrated with a SGDBR tunable laser. We demonstrate improvements in optical bandwidth, insertion losses, device gain, and modulation efficiency.
Influence of equipment changes on MRI measures of brain atrophy and brain microstructure in a placebo-controlled trial of ibudilast in progressive multiple sclerosis (2021)

The results suggest that differences among hardware types should be considered when planning and analyzing brain atrophy and diffusivity in a longitudinal clinical trial.
Reduced Differentiation Potential of Primary MyoD−/− Myogenic Cells Derived from Adult Skeletal Muscle (1999)

To gain insight into the regeneration deficit of MyoD-/- muscle, we investigated the growth and differentiation of cultured MyoD-/- myogenic cells. Primary MyoD-/- myogenic cells exhibited a stellate morphology distinct from the compact morphology of wild-type myoblasts, and expressed c-met, a receptor tyrosine kinase expressed in satellite cells. However, MyoD-/- myogenic cells did not express desmin, an intermediate filament protein typically expressed in cultured myoblasts in vitro and myogenic precursor cells in vivo. Northern analysis indicated that proliferating MyoD-/- myogenic cells expressed fourfold higher levels of Myf-5 and sixfold higher levels of PEA3, an ETS-domain transcription factor expressed in newly activated satellite cells. Under conditions that normally induce differentiation, MyoD-/- cells continued to proliferate and with delayed kinetics yielded reduced numbers of predominantly mononuclear myocytes. Northern analysis revealed delayed induction of myogenin, MRF4, and other differentiation-specific markers although p21 was upregulated normally. Expression of M-cadherin mRNA was severely decreased whereas expression of IGF-1 was markedly increased in MyoD-/- myogenic cells. Mixing of lacZ-labeled MyoD-/- cells and wild-type myoblasts revealed a strict autonomy in differentiation potential. Transfection of a MyoD-expression cassette restored cytomorphology and rescued the differentiation deficit. We interpret these data to suggest that MyoD-/- myogenic cells represent an intermediate stage between a quiescent satellite cell and a myogenic precursor cell.
Source–detector calibration in three-dimensional Bayesian optical diffusion tomography (2002)

Optical diffusion tomography is a method for reconstructing three-dimensional optical properties from light that passes through a highly scattering medium. Computing reconstructions from such data requires the solution of a nonlinear inverse problem. The situation is further complicated by the fact that while reconstruction algorithms typically assume exact knowledge of the optical source and detector coupling coefficients, these coupling coefficients are generally not available in practical measurement systems. A new method for estimating these unknown coupling coefficients in the three-dimensional reconstruction process is described. The joint problem of coefficient estimation and three-dimensional reconstruction is formulated in a Bayesian framework, and the resulting estimates are computed by using a variation of iterative coordinate descent optimization that is adapted for this problem. Simulations show that this approach is an accurate and efficient method for simultaneous reconstruction of absorption and diffusion coefficients as well as the coupling coefficients. A simple experimental result validates the approach.
Lithium Ion Battery Graphite Solid Electrolyte Interphase Revealed by Microscopy and Spectroscopy (2013)

The surface reactions of electrolytes with the graphitic anode of lithium ion batteries have been investigated. The investigation utilizes two novel techniques, which are enabled by the use of binder-free graphite anodes. The first method, transmission electron microscopy (TEM) with energy dispersive X-ray spectroscopy, allows straightforward analysis of the graphite solid electrolyte interphase (SEI). The second method utilizes multi-nuclear magnetic resonance (NMR) spectroscopy of D2O extracts from the cycled anodes. The TEM and NMR data are complemented by XPS and FTIR data, which are routinely used for SEI studies. Cells were cycled with LiPF6 and ethylene carbonate (EC), ethyl methyl carbonate (EMC), and EC/EMC blends. This unique combination of techniques establishes that for EC/LiPF6 electrolytes, the graphite SEI is ∼50 nm thick after the first full lithiation cycle, and predominantly contains lithium ethylene dicarbonate (LEDC) and LiF. In cells containing EMC/LiPF6 electrolytes, the graphite SEI is nonuniform, ∼10–20 nm thick, and contains lithium ethyl carbonate (LEC), lithium methyl carbonate (LMC), and LiF. In cells containing EC/EMC/LiPF6 electrolytes, the graphite SEI is ∼50 nm thick, and predominantly contains LEDC, LMC, and LiF.
Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles (2007)

We have analyzed gene expression in different normal human tissues and different types of solid cancers derived from these tissues. The cancers analyzed include brain (astrocytoma and glioblastoma), breast, colon, endometrium, kidney, liver, lung, ovary, prostate, skin, and thyroid cancers. Comparing gene expression in each normal tissue to 12 other normal tissues, we identified 4,917 tissue-selective genes that were selectively expressed in different normal tissues. We also identified 2,929 genes that are overexpressed at least 4-fold in the cancers compared with the normal tissue from which these cancers were derived. The overlap between these two gene groups identified 1,340 tissue-selective genes that are overexpressed in cancers. Different types of cancers, including different brain cancers arising from the same lineage, showed differences in the tissue-selective genes they overexpressed. Melanomas overexpressed the highest number of brain-selective genes and this may contribute to melanoma metastasis to the brain. Of all of the genes with tissue-selective expression, those selectively expressed in testis showed the highest frequency of genes that are overexpressed in at least two types of cancer. However, colon and prostate cancers did not overexpress any testis-selective gene. Nearly all of the genes with tissue-selective expression that are overexpressed in cancers showed selective expression in tissues different from the cancers' tissue of origin. Cancers aberrantly expressing such genes may acquire phenotypic alterations that contribute to cancer cell viability, growth, and metastasis.
Macular microcirculation in hypertensive patients with and without branch retinal vein occlusion (2008)

Perifoveal capillary BFV is reduced in hypertensive patients with and without BRVO. It is possible that a decrease in BFV may be involved in the occurrence of BRVO. Measurement of perifoveal capillary BFV may be useful for investigating the pathogenesis and progression of BRVO.
Spectrally Efficient Compatible Single-Sideband Modulation for OFDM Transmission With Direct Detection (2008)

A combination of orthogonal frequency-division multiplexing (OFDM) and compatible single-sideband modulation (CompSSB) using a standard direct-detection scheme is suggested to overcome chromatic dispersion without explicit compensation. Since the proposed type of SSB modulation does not require a spectral gap between optical carrier and subcarriers, it is highly spectrally efficient and the complexity in the analogue part is reduced compared to known direct-detection schemes for OFDM.
Energy performance of 5G-NX radio access at country level (2016)

In this paper, we evaluate the technology potential of a new 5G radio access technology (RAT), here denoted 5G-NX, in terms of energy performance at the country level, in order to show what can be expected in the future when networks are being modernized and new technology is rolled out. To this end, per deployment area we calculate the daily energy consumption via system level simulations considering a typical European country categorized by six deployment areas, and extend the results to country scale according to a large-scale deployment model. The results show that 55% energy saving is achievable at the country level with 5G-NX networks while providing up to 15 times more capacity and 9 times higher peak rate compared to a baseline LTE network using the same site grid.
Treatment of Osteonecrosis of the Femoral Head with Free Vascularized Fibular Transfer (1998)

Thirty-one free vascularized fibular bone grafts were performed for treatment of osteonecrosis of the femoral head in 26 patients. Twenty-four men and 2 women ranged in age from 16 to 48 years (mean, 32 years). Twenty-one patients had unilateral disease. Five patients had bilateral disease and underwent staged bilateral free vascularized fibular grafts 3 months apart. Associated etiological factors included alcohol (9 patients), steroid use (7 patients), and trauma (1 patient). The condition was considered idiopathic in the remaining 9 patients. Radiological staging by Ficat included stage I in 1 hip, stage II in 15 hips, stage III in 14 hips, and stage IV in 1 hip. A skin island flap was used for monitoring purposes to check the patency of blood flow to the grafted fibula. One flap failed by venous occlusion and was left as a nonvascularized bone graft. Thirty hips were followed. Pain was relieved in 28 hips (93.3%) and aggravated in 2 hips (6.7%). On radiographic evaluation, 26 hips (86.7%) demonstrated excellent preservation of the femoral head contour. Progressive collapse of the femoral head (>1-2 mm) occurred in two hips, with 1-mm depression in one hip with stage III disease and 2-mm collapse in one hip with stage IV disease. Follow-up ranged from 12 to 40 months (mean, 21 months). In conclusion, even in this relatively short follow-up period, the free vascularized fibular bone graft is an excellent treatment modality for preserving the femoral head and relieving symptoms in patients with osteonecrosis of the femoral head.
A Blocker of N- and T-type Voltage-Gated Calcium Channels Attenuates Ethanol-Induced Intoxication, Place Preference, Self-Administration, and Reinstatement (2008)

There is a clear need for new therapeutics to treat alcoholism. Here, we test our hypothesis that selective inhibitors of neuronal calcium channels will reduce ethanol consumption and intoxication, based on our previous studies using knock-out mice and cell culture systems. We demonstrate that pretreatment with the novel mixed N-type and T-type calcium channel antagonist 1-(6,6-bis(4-fluorophenyl)hexyl)-4-(3,4,5-trimethoxybenzyl)piperazine (NP078585) reduced ethanol intoxication. NP078585 also attenuated the reinforcing and rewarding properties of ethanol, measured by operant self-administration and the expression of an ethanol conditioned place preference, and abolished stress-induced reinstatement of ethanol seeking. NP078585 did not affect alcohol responses in mice lacking N-type calcium channels. These results suggest that selective calcium channel inhibitors may be useful in reducing acute ethanol intoxication and alcohol consumption by human alcoholics.
Mycoplasma lipophilum sp. nov. (1974)

Two Mycoplasma strains isolated from the human oral cavity exhibit cultural and serological properties distinguishing them from the known human Mycoplasma species. Further, a variety of cultural and serological procedures fail to identify the strains with any of a wide range of Mycoplasmatales tested. The strains are described as a new species under the name Mycoplasma lipophilum previously referred to as (M. lipophilia) of the family Mycoplasmataceae. The type strain is MaBy (=ATCC 27104).
BacTregulators: a database of transcriptional regulators in bacteria and archaea (2004)

The BacTregulators is available at www.bactregulators.org
Integrative Oncology: A Paradigm Shift in Cancer Care (2020)

How important is an integrative approach in the field of oncology today? Is there a need for a paradigm shift in the way that we, as clinicians, view people with cancer?
Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions (2020)

Genetic diseases are driven by aberrations of the human genome. Identification of such aberrations including structural variations (SVs) is key to our understanding. Conventional short-reads whole genome sequencing (cWGS) can identify SVs to base-pair resolution, but utilizes only short-range information and suffers from high false discovery rate (FDR). Linked-reads sequencing (10XWGS) utilizes long-range information by linkage of short-reads originating from the same large DNA molecule. This can mitigate alignment-based artefacts especially in repetitive regions and should enable better prediction of SVs. However, an unbiased evaluation of this technology is not available. In this study, we performed a comprehensive analysis of different types and sizes of SVs predicted by both the technologies and validated with an independent PCR based approach. The SVs commonly identified by both the technologies were highly specific, while validation rate dropped for uncommon events. A particularly high FDR was observed for SVs only found by 10XWGS. To improve FDR and sensitivity, statistical models for both the technologies were trained. Using our approach, we characterized SVs from the MCF7 cell line and a primary breast cancer tumor with high precision. This approach improves SV prediction and can therefore help in understanding the underlying genetics in various diseases.