gebhart/patrepeval huggingface dataset:
Identification of metastasis driver genes by massive parallel sequencing of successive steps of breast cancer progression (2018)

Cancer results from alterations at essential genomic sites and is characterized by uncontrolled cell proliferation, invasion and metastasis. Identification of driver genes of metastatic progression is essential, as metastases, not primary tumors, are fatal. To gain insight into the mutational concordance between different steps of malignant progression we performed exome sequencing and validation with targeted deep sequencing of successive steps of malignant progression from pre-invasive stages to asynchronous distant metastases in six breast cancer patients. Using the ratio of non-synonymous to synonymous mutations, a surprisingly large number of cancer driver genes, ranging between 3 and 145, were estimated to confer a selective advantage in the studied primary tumors. We report a substantial amount of metastasis specific mutations and a number of novel putative metastasis driver genes. Most notable are the DCC, ABCA13, TIAM2, CREBBP, BCL6B and ZNF185 genes, mainly mutated exclusively in metastases and highly likely driver genes of metastatic progression. We find different genes and pathways to be affected at different steps of malignant progression. The Adherens junction pathway is affected in four of the six studied patients and this pathway most likely plays a vital role in the metastatic process.
Pushing the Limits of Fast Acquisition in TEM Tomography and 4D-STEM (2016)

JEOL ARM200-CF in order to investigate different samples with the ptychographic phase reconstruction technique.
Isolated Hypervariable Regions Derived from Streptococcal M Proteins Specifically Bind Human C4b-Binding Protein: Implications for Antigenic Variation (2001)

Antigenic variation in microbial surface proteins represents an apparent paradox, because the variable region must retain an important function, while exhibiting extensive immunological variability. We studied this problem for a group of streptococcal M proteins in which the approximately 50-residue hypervariable regions (HVRs) show essentially no residue identity but nevertheless bind the same ligand, the human complement regulator C4b-binding protein (C4BP). Synthetic peptides derived from different HVRs were found to retain the ability to bind C4BP, implying that the HVR corresponds to a distinct ligand-binding domain that can be studied in isolated form. This finding allowed direct characterization of the ligand-binding properties of isolated HVRs and permitted comparisons between different HVRs in the absence of conserved parts of the M proteins. Affinity chromatography of human serum on immobilized peptides showed that they bound C4BP with high specificity and inhibition experiments indicated that different peptides bound to the same site in C4BP. Different C4BP-binding peptides did not exhibit any immunological cross-reactivity, but structural analysis suggested that they have similar folds. These data show that the HVR of streptococcal M protein can exhibit extreme variability in sequence and immunological properties while retaining a highly specific ligand-binding function.
Geodesic Discrete Global Grid Systems (2003)

In recent years, a number of data structures for global geo-referenced data sets have been proposed based on regular, multi-resolution partitions of polyhedra. We present a survey of the most promising of such systems, which we call Geodesic Discrete Global Grid Systems (Geodesic DGGSs). We show that Geodesic DGGS alternatives can be constructed by specifying five substantially independent design choices: a base regular polyhedron, a fixed orientation of the base regular polyhedron relative to the Earth, a hierarchical spatial partitioning method defined symmetrically on a face (or set of faces) of the base regular polyhedron, a method for transforming that planar partition to the corresponding spherical/ellipsoidal surface, and a method for assigning point representations to grid cells. The majority of systems surveyed are based on the icosahedron, use an aperture 4 triangle or hexagon partition, and are either created directly on the surface of the sphere or by using an equal-area transformation. An examination of the design choice options leads us to the construction of the Icosahedral Snyder Equal Area aperture 3 Hexagon (ISEA3H) Geodesic DGGS.
Modulation of p210BCR-ABL activity in transduced primary human hematopoietic cells controls lineage programming (2002)

Retroviral transduction of primary hematopoietic cells with human oncogenes provides a powerful approach to investigating the molecular mechanisms controlling the normal proliferation and differentiation of these cells. Here we show that primitive human CD34(+) cord blood cells, including multipotent as well as granulopoietic- and erythroid-restricted progenitors, can be efficiently transduced with a MSCV-BCR-ABL-IRES-GFP retrovirus, resulting in the sustained expression by their progeny of very high levels of tyrosine phosphorylated p210(BCR-ABL). Interestingly, even in the presence of growth factors that supported the exclusive production of granulopoietic cells from green fluorescent protein (GFP)-transduced control cells, BCR-ABL-transduced progenitor subpopulations generated large numbers of erythropoietin-independent terminally differentiating erythroid cells and reduced numbers of granulopoietic cells. Analyses of individual clones generated by single transduced cells in both semisolid and liquid cultures showed this BCR-ABL-induced erythroid differentiation response to be elicited at a high frequency from all types of transduced CD34(+) cells independent of their apparent prior lineage commitment status. Additional experiments showed that this erythroid differentiation response was largely prevented when the cells were transduced and maintained in the presence of the BCR-ABL-specific tyrosine kinase inhibitor, STI-571. These findings indicate that overexpression of BCR-ABL in primary human hematopoietic cells can activate an erythroid differentiation program in apparently granulopoietic-restricted cells through a BCR-ABL kinase-dependent mechanism, thus providing a new molecular tool for elucidating mechanisms underlying lineage fate determination in human hematopoietic cells and infidelity in human leukemia.
Aged Carbonate Cores Wettability Verification (2016)

Abstract With the question of reliability on the results of standard and SCAL tests on carbonate cores of the Central Khoreiver Uplift (CKU) reservoirs, a study was carried out to develop appropriate core preparation techniques for the rock. Several tests were carried out on core plugs with cleaning agents like: alcohol-benzene, toluene, chloroform, carbon tetrachloride in the Soxhlet apparatus, cold kerosene in centrifuge and hot kerosene in coreholder. Cleaning effects on porosity, gas permeability, wettability, irreducible water saturation were studied. The influence of each agent on basic core properties is shown. Based on the various cleaning techniques available and the results achieved, the most suitable cleaning method for CKU carbonates was recommended. Core aging techniques with dead oil at reservoir temperature and set pressure were carried out. Single aging and sequential multi aging at different aging periods and their effects on core properties were shown. Core preparation techniques, uncleaned core tests evaluation, aging methods and further studies were also recommended.
Coupled thermal-mechanical-hydrologic processes near a deep borehole and potential impacts on hydrologic testing. (2011)

Abstract not provided.
Phosphorylation of the catalytic subunit of Na+,K(+)-ATPase inhibits the activity of the enzyme. (1991)

We have examined two distinct protein kinases, cAMP-dependent protein kinase and protein kinase C, for their ability to phosphorylate and regulate the activity of three different types of Na+,K(+)-ATPase preparation. cAMP-dependent protein kinase phosphorylated purified shark rectal gland Na+,K(+)-ATPase to a stoichiometry of approximately 1 mol of phosphate per mol of alpha subunit. Protein kinase C phosphorylated purified shark rectal gland Na+,K(+)-ATPase to a stoichiometry of approximately 2 mol of phosphate per mol of alpha subunit. The phosphorylation by each of the kinases was associated with an inhibition of Na+,K(+)-ATPase activity of about 40-50%. These two protein kinases also inhibited the activity of a partially purified preparation of Na+,K(+)-ATPase from rat renal cortex and the activity of Na+,K(+)-ATPase present in preparations of basolateral membrane vesicles from rat renal cortex.
Overproduction, purification, crystallization and preliminary X-ray diffraction studies of the human spliceosomal protein TXNL4B (2005)

The human gene coding for the spliceosomal protein thioredoxin-like 4B (TXNL4B) was overexpressed in Escherichia coli and the encoded protein was purified and crystallized. Well diffracting single crystals were obtained by the vapor-diffusion method in hanging drops. The crystals belong to the primitive monoclinic space group P2, with unit-cell parameters a = 39.0, b = 63.6, c = 51.0 A, beta = 92.484 degrees,, and diffract to at least 1.50 A. A SeMet derivative of the protein was prepared and crystallized for MAD phasing.
AICP: Augmented Informative Cooperative Perception (2022)

Connected vehicles, whether equipped with advanced driver-assistance systems or fully autonomous, require human driver supervision and are currently constrained to visual information in their line-of-sight. A cooperative perception system among vehicles increases their situational awareness by extending their perception range. Existing solutions focus on improving perspective transformation and fast information collection. However, such solutions fail to filter out large amounts of less relevant data and thus impose significant network and computation load. Moreover, presenting all this less relevant data can overwhelm the driver and thus actually hinder them. To address such issues, we present Augmented Informative Cooperative Perception (AICP), the first fast-filtering system which optimizes the informativeness of shared data at vehicles to improve the fused presentation. To this end, an informativeness maximization problem is presented for vehicles to select a subset of data to display to their drivers. Specifically, we propose (i) a dedicated system design with custom data structure and lightweight routing protocol for convenient data encapsulation, fast interpretation and transmission, and (ii) a comprehensive problem formulation and efficient fitness-based sorting algorithm to select the most valuable data to display at the application layer. We implement a proof-of-concept prototype of AICP with a bandwidth-hungry, latency-constrained real-life augmented reality application. The prototype adds only 12.6 milliseconds of latency to a current informativeness-unaware system. Next, we test the networking performance of AICP at scale and show that AICP effectively filters out less relevant packets and decreases the channel busy time.
3D sensor zoo – Species and natural habitats (2006)

Abstract Optical 3D Sensors provide a fast non‐destructive possibility to obtain the three‐dimensional shape of a huge variety of objects. In this paper we will give an overview of some important sensor principles and their limits as well as some critical points to pay attention to when choosing a sensor.
Transport properties in dilute gases: an approach using time-correlation functions. Part 1.—Viscosity and thermal conductivity of gases and gas mixtures in which the exchange of molecular internal energy is slow (1980)

Equations for the viscosity and thermal conductivity are derived, using the method of time-correlation functions, for dilute single gases and gas mixtures which may contain polyatomic molecules, but in which the rate of exchange of internal molecular energy is slow. The treatment follows that of H. Mori, who showed that the assumption of an exponential form for the time-correlation functions leads to expressions for the viscosity and thermal conductivity of a single monatomic gas that are identical with those of the Chapman–Enskog first approximations. In the present analysis, time-correlation functions have to be considered in general to be sums of exponential decays which are justified on the basis of the first-collision approximation of Reissner and Steele. For many systems considered, familiar equations are obtained, e.g., Chapman–Enskog first approximations and the modified Eucken and Hirschfelder–Eucken equations. For viscosity and for the translational contribution to thermal conductivity in mixtures, however, simpler (though less correct) equations than the Chapman–Enskog approximations are obtained: in the case of thermal conductivity a new equation is derived and tested. Though less rigorous than the traditional methods, the derivations are simpler and more easily understood in physical terms (provided the expressions for the transport properties in terms of time-correlation functions are accepted as a starting point) and therefore the approach offers some advantages.
Archaea and the human gut: New beginning of an old story (2014)

Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.
Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder (2016)

These findings suggest that there may be shared susceptibility genes for DCD and other neurodevelopmental disorders and highlight the need for thorough phenotyping when investigating the genetics of neurodevelopmental disorders. Furthermore, these data provide compelling evidence supporting a genetic basis for DCD, and further implicate rare CNVs in the aetiology of neurodevelopmental disorders.
Smartphone-Based Assistance for Blind People to Stand in Lines (2020)

We present a system to allow blind people to stand in line in public spaces by using an off-the-shelf smartphone only. The technologies to navigate blind pedestrians in public spaces are rapidly improving, but tasks which require to understand surrounding people's behavior are still difficult to assist. Standing in line at shops, stations, and other crowded places is one of such tasks. Therefore, we developed a system to detect and notify the distance to a person in front continuously by using a smartphone with a RGB camera and an infrared depth sensor. The system alerts three levels of distance via vibration patterns to allow users to start/stop moving forward to the right position at the right timing. To evaluate the effectiveness of the system, we performed a study with six blind people. We observed that the system enables blind participants to stand in line successfully, while also gaining more confidence.
Sensitive identification of neoantigens and cognate TCRs in human solid tumors (2021)

The identification of patient-specific tumor antigens is complicated by the low frequency of T cells specific for each tumor antigen. Here we describe NeoScreen, a method that enables the sensitive identification of rare tumor (neo)antigens and of cognate T cell receptors (TCRs) expressed by tumor-infiltrating lymphocytes. T cells transduced with tumor antigen-specific TCRs identified by NeoScreen mediate regression of established tumors in patient-derived xenograft mice.
Sensors and haptics technologies for user interface design in wearables (2016)

In this paper, a summary of various sensory technologies and interactions within them in wearable platforms is presented. In the first part of the paper, we discuss the way humans perceive various sensory inputs. Then, we review today's state of art sensor technologies for user interfaces, followed by discussions on opportunities uniquely enabled by the wearable form factor.
Histidine Residue at Position 234 of Oxidosqualene‐Lanosterol Cyclase from <i>Saccharomyces cerevisiae</i> Simultaneously Influences Cyclization, Rearrangement, and Deprotonation Reactions (2005)

Multiple triterpenes, including achilleol A (1), protosta-12,24-dien-3β-ol (2), lanosterol (3), and parkeol (4; 14:26:51:9) were isolated from an ERG7 oxidosqualene-lanosterol cyclase-deficient Saccharomyces cerevisiae TKW14 strain that expresses the ERG7H234Y mutation. The results indicate a role for H234 in modulating multiple aspects of the oxidosqualene cyclization/rearrangement reaction, including cyclization, rearrangement, and deprotonation. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2005/z500084_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Sandwich enzyme-linked immunosorbent assay for detection of excretory secretory antigens in humans with fascioliasis (1994)

A sandwich enzyme-linked immunosorbent assay has been developed for the detection of Fasciola hepatica excretory secretory (ES) antigens in stool specimens of infected humans. The assay uses antibodies against F. hepatica ES antigens. A monoclonal antibody (ES78, mouse immunoglobulin G2a) was used to capture ES antigens, and a rabbit polyclonal antibody, peroxidase conjugate, was used to identify ES antigens. Thirteen of 14 patients with parasitological evidence of fascioliasis had a detectable concentration of ES antigens (more than 15 ng/ml). None of the stool specimens from controls and from patients with parasites other than F. hepatica showed a positive reaction, suggesting the absence of cross-reactions in this assay. When the 14 patients were retested 2 months after treatment, all of the specimens from the 11 parasitologically cured patients were negative by the antigen detection assay while the specimens from the 3 patients with persisting F. hepatica eggs in their stools remained positive.
Microcrystalline silicon thin films studied using spectroscopic ellipsometry (2002)

We used spectroscopic ellipsometry to characterize four different microcrystalline silicon (μc-Si) films, which were fabricated by crystallizing a-Si:H films predeposited on glass substrates using solid phase crystallization (SPC), excimer laser annealing (ELA), Ni induced silicide-mediated crystallization (Ni-SMC), and field enhanced silicide-mediated crystallization (FESMC) method, respectively. A linear regression analysis, which took the effective dielectric function of μc-Si layer into account using effective medium approximation, showed that all these films were homogeneous throughout their thickness except the oxide overlayers, and completely crystallized regardless of the crystallization method. In our linear regression analysis, the complex dielectric function of silicon microcrystallites was represented by the Adachi model dielectric function (MDF) [T. Suzuki and S. Adachi, Jpn. J. Appl. Phys., Part1 32, 4900 (1993)], and the broadening parameters of the critical points (CPs) in MDF were allowed to vary. The dielectric function of silicon microcrystallites showed systematic broadening and shrinking of the peak features corresponding to the E1 and E2 CPs, from which we concluded that the average microcrystallite size increased in the order of SPC, ELA, Ni-SMC, and FESMC μc-Si. The Raman spectra and the transmission-electron-microscopy images of these films also supported the idea of systematic variation in the microcrystallite size.
Near Net–Shape Si02–TiO2–Glass Compacts with Reduced Thermal Expansion (2008)

ULE™ glasses show negligible thermal expansion in the useful temperature range. In this paper, colloidal sol-gel alternative to costly flame hydrolysis is presented. Colloidal gel processing of pure silica powders leads to greenbodies with open pores. Near net-shape SiO2–TiO2–glass production can base on this technique as it can be combined with penetration of the fluid titanium compound. After removing organic compounds by calcination, purely anorganic greenbodies can be sintered to dense glassbodies. The transparent samples show a smaller coefficient of thermal expansion (CTE) than fused silica.
Fabrication of refractive freeform array masters for artificial compound eye cameras (2014)

There is a huge demand on miniaturized cameras in the field of mobile consumer electronics. These cameras are currently based on miniaturized single aperture optics. In order to further decrease the thickness of miniaturized camera systems, a multichannel imaging principle needs to be used. These artificial compound eye cameras permit a further decrease in thickness by a factor of two in comparison to miniaturized single aperture optics with same resolution and pixel size. Their fabrication process is currently based on the reflow of photoresist. Due to physical limitations of this technique, only spherical and ellipsoidal surface profiles of the single lenslets are achievable. Consequently, the potential for correcting optical aberrations is restricted leading to limited image quality and resolution. This can be improved significantly by the use of refractive freeform arrays. Due to the non-symmetrical and aspherical surface shapes of the single lenslets, the fabrication by the reflow of photoresist is no longer possible. Therefore, we propose an approach for the fabrication of these structures based on the combination of an ultra-precision machining process together with a microimprinting approach.