gebhart/patrepeval huggingface dataset:
Epistasis Detection in Genome-Wide Screening for Complex Human Diseases in Structured Populations (2019)

Over the years, a more prominent role has been given to gene–gene interaction (epistasis) detection, in view of precision medicine and the hunt for novel drug targets and biomarkers for complex diseases. Acknowledging data complexity as embodied by epistasis potentially increases the power of genome-wide association studies (GWAS) and may reveal relevant biological and biochemical pathways previously undetected. Although confounding of GWAS due to shared genetic ancestry has been well recognized, the extent and impact of such confounding in gene–gene interaction association epistasis studies is much less understood. In the same spirit, the role of population substructure in epistasis detection is largely under-investigated, especially outside a regression framework. This is surprising as inadequate handling of such confounding is likely to lead to spurious epistatic associations, hampering replication and the identification of causal loci in synergy. To improve interpretability and replicability of epistasis results, we introduce “MB-MDR for Structured Populations” (Model-Based Multifactor Dimensionality Reduction-Principal Component [MBMDR-PC]). It extends classic MBMDR that was developed for samples sharing the same genetic ancestry, by replacing the original phenotypes with new phenotypes that have been adjusted for population structure as captured by PCs. The method is applied on International Inflammatory Bowel Disease Genetics Consortium Crohn's disease (CD) data from 15 countries. Significant interacting single nucleotide polymorphisms are found within NOD2 and CYLD genes among others that suggest a potential synergetic effect of NOD2 and CYLD on CD. The study highlights the value of examining epistasis effects and indicates the need for further studies to understand the epistasis effects on CD.
[Expression of the human extracellular domain of high density lipoprotein receptor in methylotropic yeast]. (2003)

HDL receptor plays a very important role in reverse cholesterol transport, and it represents a novel therapeutic target for atherosclerosis. For construction of an in vitro high-throughput drug screening model based on competitive receptor--ligand binding, the extracellular domain of HDL receptor was expressed in the methylotropic yeast Pichia pastoris. The DNA fragment encoding for extracellular domain of HDL receptor was cloned by RT-PCR from Hepatoma Bel-7402 total RNA and the nucleotide sequence of the cloned cDNA was verified by inserting it into pGEM-T vector. Then the cDNA was subcloned into pPIC9K, the integrative secretory expression plasmid of Pichia pastoris was constructed, with the methanol-inducible alcohol oxidase promoter and alpha-signal peptide. The recombinant plasmid was transformed into Pichia pastoris GS115 (His- strain) by electroporation. PCR was used to confirm the insertion of HDLR gene into the genome of Mut+ transformants. During cultivation the recombinant strain was induced by 1% methanol and supernatant was analyzed by SDS-PAGE and Western blot. The result showed a specific protein band at approximately 64.5 kDa after 5 days of induction. Then the ligand binding activity was confirmed using the DiI-AcLDL as ligand.
Ad35.CS.01 - RTS,S/AS01 Heterologous Prime Boost Vaccine Efficacy against Sporozoite Challenge in Healthy Malaria-Naïve Adults (2015)

ClinicalTrials.gov NCT01366534.
clearScience: Infrastructure for Communicating Data-Intensive Science. (2013)

Progress in biomedical research requires effective scientific communication to one's peers and to the public. Current research routinely encompasses large datasets and complex analytic processes, and the constraints of traditional journal formats limit useful transmission of these elements. We are constructing a framework through which authors can not only provide the narrative of what was done, but the primary and derivative data, the source code, the compute environment, and web-accessible virtual machines. This infrastructure allows authors to "hand their machine"- prepopulated with libraries, data, and code-to those interested in reviewing or building off of their work. This project, "clearScience," seeks to provide an integrated system that accommodates the ad hoc nature of discovery in the data-intensive sciences and seamless transitions from working to reporting. We demonstrate that rather than merely describing the science being reported, one can deliver the science itself.
CramÉr–Rao Bounds for Multiple Poles and Coefficients of Quasi-Polynomials in Colored Noise (2008)

In this paper, we provide analytical expressions of the Cramer-Rao bounds for the frequencies, damping factors, amplitudes, and phases of complex exponentials in colored noise. These expressions show the explicit dependence of the bounds of each distinct parameter with respect to the amplitudes and phases, leading to readily interpretable formulae, which are then simplified in an asymptotic context. The results are presented in the general framework of the polynomial amplitude complex exponentials (PACE) model, also referred to as the quasi-polynomial model in the literature, which accounts for systems involving multiple poles and represents a signal as a mixture of complex exponentials modulated by polynomials. This work looks further and generalizes the studies previously undertaken on the exponential and the quasi-polynomial models.
Aminopyrrolic Synthetic Receptors for Monosaccharides: A Class of Carbohydrate‐Binding Agents Endowed with Antibiotic Activity versus Pathogenic Yeasts (2012)

The biological activity of a set of structurally related aminopyrrolic synthetic receptors for monosaccharides has been tested versus yeast and yeast-like microorganisms and compared to their binding affinity toward mannosides. Antibiotic activity comparable to that of well-known polyene (amphotericin B) or azole (ketoconazole) drugs has been found for some members of the family, along with a general correlation with binding abilities. A systematic structure-activity-affinity investigation shed light on the structural and functional requirements necessary for antibiotic activity and identified the tripodal compound 1 as the most potent compound of the set. Together with toxicity tests and inhibitor localization experiments performed through fluorescence microscopy, these studies led to the characterization of a new class of carbohydrate binding agents possessing antibiotic activity, in which pyrrolic groups precisely structured on a tripodal architecture appear to be responsible for permeability through the cell wall of pathogens, as well as for antibiotic activity inside the cytoplasm.
Vitamin D and Allergy Susceptibility during Gestation and Early Life (2021)

Worldwide, the prevalence of allergies in young children, but also vitamin D deficiency during pregnancy and in newborns is rising. Vitamin D modulates the development and activity of the immune system and a low vitamin D status during pregnancy and in early life might be associated with an increased risk to develop an allergy during early childhood. This review studies the effects of vitamin D during gestation and early life, on allergy susceptibility in infants. The bioactive form of vitamin D, 1,25(OH)2D, inhibits maturation and results in immature dendritic cells that cause a decreased differentiation of naive T cells into effector T cells. Nevertheless, the development of regulatory T cells and the production of interleukin-10 was increased. Consequently, a more tolerogenic immune response developed against antigens. Secondly, binding of 1,25(OH)2D to epithelial cells induces the expression of tight junction proteins resulting in enhanced epithelial barrier function. Thirdly, 1,25(OH)2D increased the expression of anti-microbial peptides by epithelial cells that also promoted the defense mechanism against pathogens, by preventing an invasive penetration of pathogens. Immune intervention by vitamin D supplementation can mitigate the disease burden from asthma and allergy. In conclusion, our review indicates that a sufficient vitamin D status during gestation and early life can lower the susceptibility to develop an allergy in infants although there remains a need for more causal evidence.
A New Prenylated Flavonoid from Propolis Collected in Okinawa, Japan (2004)

The new prenylflavonoid, isonymphaeol-B (1), together with three known compounds, nymphaeol-A (2), nymphaeol-B (3), and nymphaeol-C (4), were isolated from propolis collected in Okinawa, the southern-most prefecture of Japan. The structure of each compound was determined by spectral methods, including mass spectrometry and 2D NMR. Each compound had 1,1-diphenyl-2-picryl-hydrazyl radical-scavenging activity.
The Anti-adhesive Activity of Thrombospondin Is Mediated by the N-terminal Domain of Cell Surface Calreticulin (2002)

Thrombospondin (TSP) induces reorganization of the actin cytoskeleton and restructuring of focal adhesions through binding of amino acids (aa) 17-35 (hep I peptide) of thrombospondin to a cell surface form of calreticulin (CRT). In this report we provide further evidence for the involvement of calreticulin in thrombospondin signaling and characterize thrombospondin-calreticulin interactions. Wild type but not crt(-/-) cells respond to hep I/TSP. Responsiveness can be restored by incubation of cells with exogenous calreticulin or by transfection with calreticulin. Thrombospondin forms complexes with the CRT-N-domain that are enhanced by physiologic levels of calcium and zinc. Consistent with thrombospondin/CRT-N-domain binding, only the CRT-N-domain blocks hep I- and thrombospondin-stimulated focal adhesion disassembly. A series of glutathione S-transferase-N-domain mutants were used to map the sequence within the N-domain that interacts with TSP/hep I. A construct containing aa 1-43 but not a construct of aa 1-31 supported thrombospondin binding and focal adhesion disassembly. A series of overlapping peptides were used to further map the thrombospondin-binding site. Peptides spanning aa 19-36 (RWIESKHKSDFGKFVLSS) blocked hep I-stimulated focal adhesion disassembly, indicating that the TSP/hep I-binding site is located to this sequence in calreticulin. A mutant fusion protein lacking aa 19-36 (glutathione S-transferase-CRTDeltahep I) failed to restore responsiveness to hep I in crt(-/-) cells, bind thrombospondin, or competitively block focal adhesion disassembly, providing evidence for the role of this calreticulin sequence in mediating thrombospondin signaling.
Low-power digital systems based on adiabatic-switching principles (1994)

Adiabatic switching is an approach to low-power digital circuits that differs fundamentally from other practical low-power techniques. When adiabatic switching is used, the signal energies stored on circuit capacitances may be recycled instead of dissipated as heat. We describe the fundamental adiabatic amplifier circuit and analyze its performance. The dissipation of the adiabatic amplifier is compared to that of conventional switching circuits, both for the case of a fixed voltage swing and the case when the voltage swing can be scaled to reduce power dissipation. We show how combinational and sequential adiabatic-switching logic circuits may be constructed and describe the timing restrictions required for adiabatic operation. Small chip-building experiments have been performed to validate the techniques and to analyse the associated circuit overhead.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Airway Basal Cells show a dedifferentiated KRT17 high Phenotype and promote Fibrosis in Idiopathic Pulmonary Fibrosis (2020)

ABSTRACT Idiopathic pulmonary fibrosis (IPF) is a fatal disease with limited treatment options. In this study we focus on the profibrotic properties of airway basal cells (ABC) obtained from patients with IPF (IPF-ABC). Single cell RNA sequencing of bronchial brushes revealed extensive reprogramming of IPF-ABC towards a KRT17 high PTEN low dedifferentiated cell type. In the 3D organoid model, compared to ABC obtained from healthy volunteers, IPF-ABC give rise to more bronchospheres, de novo bronchial structures resembling lung developmental processes, induce fibroblast proliferation and extracellular matrix deposition in co-culture. Intratracheal application of IPF-ABC into minimally injured lungs of Rag2 -/- or NRG mice causes severe fibrosis, remodeling of the alveolar compartment, and formation of honeycomb cyst-like structures. Connectivity MAP analysis of scRNA seq of bronchial brushings suggested that gene expression changes in IPF-ABC can be reversed by SRC inhibition. After demonstrating enhanced SRC expression and activity in these cells, and in IPF lungs, we tested the effects of saracatinib, a potent SRC inhibitor previously studied in humans. We demonstrated that saracatinib modified in-vitro and in-vivo the profibrotic changes observed in our 3D culture system and novel mouse xenograft model.
Study on Relationship of the Material Removal Amount and the Increase in Abrasive Nanoparticle Size during Si-CMP (2018)

Chemical Mechanical Polishing (CMP) of silicon wafer is indispensable for providing the substrate used in manufacturing of semiconductor device. However, the CMP process has many parameters, such as polishing pressure, platen/carrier rotational speed, polishing pad characteristics, chemical solution/abrasive in polishing slurry. In these parameters, abrasive particles in the slurry have both mechanical and chemical actions. To enhance the CMP process efficiency, we have been studied the relationship between the Material Removal Amount (MRA) and the increase of abrasive particle size during CMP. In this report, the colloidal silica abrasive nanoparticle sizes of 20 nm and 55 nm were used for polishing the Silicon wafers by a CMP machine, which is installed a slurry pool. A dynamic light scattering (DLS) spectra measures the increase in abrasive nanoparticle sizes. The silicon particle size after CMP process were direct proportion with MRA of Si-wafer was polished.
Controlled Vocabularies, Indexing and Medical Language Processing. Medical Language Processing: Database Capture of Natural Language Echocardiographic Reports: A Unified Medical Language System Approach (1989)

We describe a prototype system for semi-automatic database capture of free-text echocardiography reports. The system is very simple and uses a Unified Medical Language System compatible architecture. We use this system and a large body of texts to create a patient database and develop a comprehensive hierarchical dictionary for echocardiography.
A hybrid approach to pedestrian clothing color attribute extraction (2015)

Clothing attributes, of which color plays an important role, are receiving more and more interests in machine vision researches and applications because of their uses and effectiveness in tasks like pedestrian analysis. However, color description is a challenging problem due to complex environments such as illumination variations. Most prior works describe color attributes using only low-level features or mid-level descriptors, which results in a marked drop of the discriminative power or photometric invariance. In this paper we introduce a new efficient joint representation that aims to overcome the shortcomings of using low-level features or mid-level descriptors alone and present a novel hybrid approach to pedestrian clothing color attribute extraction. As a necessary preprocessing step, a novel processing pipeline is also proposed. We evaluate our approach on the task of color classification on both the public dataset VIPeR and our own newly-built pedestrian dataset. Experimental results have demonstrated the effectiveness of our approach and have shown its great potential for further researches and applications.
Tetrahedral Distortion and Energetic Packing Penalty in “Zeolite” Frameworks:  Linked Phenomena? (2005)

We report a computational study on the distortion of SiO4 tetrahedra in zeolite frameworks. For all previously observed frameworks, the tetrahedral mismatch was found to span a narrow range (1.0 x 10(-3) to 2.5 x 10(-2) angstroms2) of values, in contrast to the hypothetical frameworks, which were calculated to have a much wider range of mismatch values. The energy of the frameworks was not found to be a function of the tetrahedral distortion for the previously observed and moderately distorted (tetrahedral mismatch <2.5 x 10(-2) angstroms2) hypothetical frameworks. In contrast, the energy of the bulk of the hypothetical frameworks was shown to be a strong function of the tetrahedral distortion. The fact that the framework energies of some hypothetical frameworks lie much higher than both those of the observed frameworks and the values we would expect from our previously developed topological method (the so-called energetic packing penalty) is explained in terms of the tetrahedral distortion contribution to the framework energy which is negligible for the observed frameworks. Finally, it is hypothesized that the absence of tetrahedral distortion is pivotal for a framework to be experimentally realized, in which case a large fraction of hypothetical frameworks are unrealizable and will forever remain in the realms of the abstract.
Selectivity and Residual Damage of Colloidal Silica Chemi-Mechanical Polishing of Silicon Carbide (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
DNA nanotechnology: a future perspective (2013)

In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology.
Esterification and hydrolysis of cellulose using oxalic acid dihydrate in a solvent-free reaction suitable for preparation of surface-functionalised cellulose nanocrystals with high yield (2017)

A quick and simple process to prepare surface-functionalised cellulose nanocrystals.
The Expansion of the PRAME Gene Family in Eutheria (2011)

The PRAME gene family belongs to the group of cancer/testis genes whose expression is restricted primarily to the testis and a variety of cancers. The expansion of this gene family as a result of gene duplication has been observed in primates and rodents. We analyzed the PRAME gene family in Eutheria and discovered a novel Y-linked PRAME gene family in bovine, PRAMEY, which underwent amplification after a lineage-specific, autosome-to-Y transposition. Phylogenetic analyses revealed two major evolutionary clades. Clade I containing the amplified PRAMEYs and the unamplified autosomal homologs in cattle and other eutherians is under stronger functional constraints; whereas, Clade II containing the amplified autosomal PRAMEs is under positive selection. Deep-sequencing analysis indicated that eight of the identified 16 PRAMEY loci are active transcriptionally. Compared to the bovine autosomal PRAME that is expressed predominantly in testis, the PRAMEY gene family is expressed exclusively in testis and is up-regulated during testicular maturation. Furthermore, the sense RNA of PRAMEY is expressed specifically whereas the antisense RNA is expressed predominantly in spermatids. This study revealed that the expansion of the PRAME family occurred in both autosomes and sex chromosomes in a lineage-dependent manner. Differential selection forces have shaped the evolution and function of the PRAME family. The positive selection observed on the autosomal PRAMEs (Clade II) may result in their functional diversification in immunity and reproduction. Conversely, selective constraints have operated on the expanded PRAMEYs to preserve their essential function in spermatogenesis.
Regioselective C–H amination of free base porphyrins via electrogenerated pyridinium-porphyrins and stabilization of easily oxidized amino-porphyrins by protonation (2019)

Four free base aminoporphyrins were synthesized in two steps via regioselective anodic nucleophilic substitution with pyridine followed by ring opening of the electrogenerated pyridinium with piperidine. The X-ray crystallographic structure of the unstable 2-aminotetraphenylporphyrin was solved. Protonation of this latter compound leads to the stable diiminium porphyrin salt.
Self6D: Self-Supervised Monocular 6D Object Pose Estimation (2020)

6D object pose estimation is a fundamental problem in computer vision. Convolutional Neural Networks (CNNs) have recently proven to be capable of predicting reliable 6D pose estimates even from monocular images. Nonetheless, CNNs are identified as being extremely data-driven, and acquiring adequate annotations is oftentimes very time-consuming and labor intensive. To overcome this shortcoming, we propose the idea of monocular 6D pose estimation by means of self-supervised learning, removing the need for real annotations. After training our proposed network fully supervised with synthetic RGB data, we leverage recent advances in neural rendering to further self-supervise the model on unannotated real RGB-D data, seeking for a visually and geometrically optimal alignment. Extensive evaluations demonstrate that our proposed self-supervision is able to significantly enhance the model's original performance, outperforming all other methods relying on synthetic data or employing elaborate techniques from the domain adaptation realm.
Reaping the benefits of open science in scholarly communication (2021)

Regardless of multiple efforts carried out across many countries to disseminate the ideas and the practice of open science, most scholars in the early 2020s do not self-archive their research articles and do not publish research papers in preprint form. Having received no education and training on open science, researchers are often puzzled on what to do, in practice, to start reaping the benefits of open science. This study offers a succinct vademecum on how to benefit from the open science approach to scholarly communication, no matter whether in natural or in humanistic and social sciences.