gebhart/patrepeval huggingface dataset:
Regenerative potential of induced pluripotent stem cells derived from patients undergoing haemodialysis in kidney regeneration (2018)

Kidney regeneration from pluripotent stem cells is receiving a lot of attention because limited treatments are currently available for chronic kidney disease (CKD). It has been shown that uremic state in CKD is toxic to somatic stem/progenitor cells, such as endothelial progenitor and mesenchymal stem cells, affecting their differentiation and angiogenic potential. Recent studies reported that specific abnormalities caused by the non-inherited disease are often retained in induced pluripotent stem cell (iPSC)-derived products obtained from patients. Thus, it is indispensable to first assess whether iPSCs derived from patients with CKD due to non-inherited disease (CKD-iPSCs) have the ability to generate kidneys. In this study, we generated iPSCs from patients undergoing haemodialysis due to diabetes nephropathy and glomerulonephritis (HD-iPSCs) as representatives of CKD-iPSCs or from healthy controls (HC-iPSCs). HD-iPSCs differentiated into nephron progenitor cells (NPCs) with similar efficiency to HC-iPSCs. Additionally, HD-iPSC-derived NPCs expressed comparable levels of NPC markers and differentiated into vascularised glomeruli upon transplantation into mice, as HC-iPSC-derived NPCs. Our results indicate the potential of HD-iPSCs as a feasible cell source for kidney regeneration. This is the first study paving the way for CKD patient-stem cell-derived kidney regeneration, emphasising the potential of CKD-iPSCs.
Hierarchical ranking of facial attributes (2011)

We propose a novel hierarchical structured prediction approach for ranking images of faces based on attributes. We view ranking as a bipartite graph matching problem; learning to rank under this setting can be achieved through structured prediction techniques that directly optimize the matching measures. Our key contribution is a novel model that combines structured predictors for different feature descriptors in a hierarchical fashion, enabling accurate ranking. We demonstrate our method on an important application which consists of searching for people over short intervals of time based on facial attributes. Given queries containing physical traits of a person (e.g., red hat, beard, and sunglasses), and an input database of face images, our system ranks the images in the database according to the query. Experiments show that our proposed hierarchical ranking approach poses significant enhancements in terms of accuracy over the non-hierarchical baseline.
Heteroaryl‐Substituted 4‐(1<i>H</i>‐pyrazol‐1‐yl)‐5,6‐dihydro‐1<i>H</i>‐pyrrolo[2,3‐<i>d</i>]pyrimidine Derivatives as Potent and Selective Corticotropin‐Releasing Factor Receptor‐1 Antagonists (2007)

Potent and selective CRF1 receptor antagonists based on the 5,6-dihydro-1H-pyrrolo[2,3-d]pyrimidines 2 were discovered and characterized. Identification of two complementary synthetic pathways allowed an efficient SAR exploration, which was facilitated by computational methods that allowed the rational design of target compounds within a defined drug-like physicochemical space.
Optical-fibre waveguide with a single-crystal core (1974)

Some properties of a new single-crystal optical fibre are described. The fibre is constructed with the nonlinear optical crystal meta-nitroaniline as its core. In its present configuration, the fibre acts as an effective polariser. Alternative configurations may yield a number of electro-optic fibre devices.
Pulsed laser interferometry with sub-picometer resolution using quadrature detection (2016)

Femtosecond pulsed laser interferometry has important applications in measuring picometer-level displacements on sub-nanosecond time scales. In this paper, we experimentally examine its achievable displacement resolution, as well as the relationship between the laser's optical spectrum and the interferometer's effective wavelength. The resulting broadband displacement noise and noise floor of the pulsed laser Michelson interferometer are equivalent to that achieved with a stabilized continuous wave HeNe laser, where values of 1.01 nm RMS and 27.75 fm/√Hz have been demonstrated. It is also shown that a single effective wavelength can accurately describe the fringes of the pulsed laser interferometer but the effective wavelength value can only be determined from the optical spectrum under certain conditions. These results will be used for time-resolved displacement metrology with picosecond temporal resolution in the future.
Uncovering rumen microbiome components shaping feed efficiency in dairy cows (2015)

Ruminants provide human society with high quality food from non-human-edible resources, but their emissions negatively impact the environment via greenhouse gas production. The rumen and its resident microorganisms dictate both processes. The overall goal of this project was to determine whether a causal relationship exists between the rumen microbiome and the host animal's physiology, and if so, to isolate and examine the specific determinants that enable this causality. To this end, we divided the project into three specific parts: (1) determining the feed efficiency of 200 milking cows, (2) determining whether the feed- efficiency phenotype can be transferred by transplantation and (3) isolating and examining microbial consortia that can affect the feed-efficiency phenotype by their transplantation into germ-free ruminants. We finally included 1000 dairy cow metadata in our study that revealed a global core microbiome present in the rumen whose composition and abundance predicted many of the cows’ production phenotypes, including methane emission. Certain members of the core microbiome are heritable and have strong associations to cardinal rumen metabolites and fermentation products that govern the efficiency of milk production. These heritable core microbes therefore present primary targets for rumen manipulation towards sustainable and environmentally friendly agriculture. We then went beyond examining the metagenomic content, and asked whether microbes behave differently with relation to the host efficiency state. We sampled twelve animals with two extreme efficiency phenotypes, high efficiency and low efficiency where the first represents animals that maximize energy utilization from their feed whilst the later represents animals with very low utilization of the energy from their feed. Our analysis revealed differences in two host efficiency states in terms of the microbial expression profiles both with regards to protein identities and quantities. Another aim of the proposal was the cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of the cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort. In the context of the grant, the establishment of ruminant germ-free facility was possible and preliminary experiments were successful, which open up the way for direct applications of the new concepts discovered here, prior to the larger scale implementation at the agricultural level.
Inhibition and Reversal of Microbial Attachment by an Antibody with Parasteric Activity against the FimH Adhesin of Uropathogenic E. coli (2015)

Attachment proteins from the surface of eukaryotic cells, bacteria and viruses are critical receptors in cell adhesion or signaling and are primary targets for the development of vaccines and therapeutic antibodies. It is proposed that the ligand-binding pocket in receptor proteins can shift between inactive and active conformations with weak and strong ligand-binding capability, respectively. Here, using monoclonal antibodies against a vaccine target protein - fimbrial adhesin FimH of uropathogenic Escherichia coli, we demonstrate that unusually strong receptor inhibition can be achieved by antibody that binds within the binding pocket and displaces the ligand in a non-competitive way. The non-competitive antibody binds to a loop that interacts with the ligand in the active conformation of the pocket but is shifted away from ligand in the inactive conformation. We refer to this as a parasteric inhibition, where the inhibitor binds adjacent to the ligand in the binding pocket. We showed that the receptor-blocking mechanism of parasteric antibody differs from that of orthosteric inhibition, where the inhibitor replaces the ligand or allosteric inhibition where the inhibitor binds at a site distant from the ligand, and is very potent in blocking bacterial adhesion, dissolving surface-adherent biofilms and protecting mice from urinary bladder infection.
Enhanced carrier phase tracking in fading environments using frequency diversity (2016)

This research focuses on improving GNSS carrier phase tracking performance in multipath fading environments. A new approach based on frequency diversity combining at correlator level is proposed to enhance carrier phase estimation robustness. The proposed method works on the fact that in a multipath environment the fading observed in different frequency bands is independent of each other. The uncorrelated nature of signal power fluctuations can be exploited to combine their correlator outputs to eventually enhance carrier phase estimation. The proposed method is tested on different data sets collected in static and kinematic scenarios. The Phase Lock Indicator enhancement and the carrier Doppler error reduction obtained are analyzed and compared with those from single frequency tracking. Results show that the number of carrier phase cycle slip events decrease when employing the proposed method.
Binding of uropathogenic Escherichia coli R45 to glycolipids extracted from vaginal epithelial cells is dependent on histo-blood group secretor status. (1992)

Women with a history of recurrent Escherichia coli urinary tract infections (UTIs) are two to three times more likely to be nonsecretors of histo-blood group antigens than are women without such a history. Further, uroepithelial cells from women who are nonsecretors show enhanced adherence of uropathogenic E. coli compared with cells from secretors. To investigate the hypothesis that nonsecretors express unique receptors for uropathogenic E. coli related to their genetic background, we extracted glycosphingolipids (GSLs) from vaginal epithelial cells collected from nonsecretors and secretors and used an assay in which radiolabeled uropathogenic E. coli were bound to these GSLs separated on TLC plates. An E. coli strain (R45) expressing both P and F adhesins, which was isolated from one of these patients' UTIs, was metabolically labeled with 35S for the TLC binding assay. The radiolabeled E. coli R45 bound to two extended globo-series GSLs, sialosyl gal-globoside (SGG) and disialosyl gal-globoside (DSGG), found in the GSL extracts from nonsecretors but not from secretors. The identity of SGG in the nonsecretor GSL extracts was con- firmed in radioimmunoassays using an mAb to SGG and in immunofluorescence assays with this mAb and native vaginal epithelial cells. We show that SGG and DSGG are selectively expressed by epithelial cells of nonsecretors, presumably as a result of sialylation of the gal-globoside precursor glycolipid, which in secretors is fucosylated and processed to ABH anti- gens. The presence of SGG and DSGG may account for the increased binding of E. coli to uroepithelial cells from nonse- cretors and for their increased susceptibility to recurrent UTI.
Highly Efficient Peptide Synthesis: Automated Simultaneous Multiple Solid-Phase Synthesis and Peptide Library. (1994)

The need for high-quality synthetic peptides has been greatly increased due to the expansion of life-science research. Production of polypeptides by genetic engineering has been more and more popular. However, chemical synthesis is still indispensable for production of peptides containing unusual amino acids or peptides with a C-terminal amide. At the present time chemical synthesis is definitely preferable for the preparation of peptides with up to 30 amino acid residues. This article will focus on highly efficient synthesis, which involves rapid synthesis using automated simultaneous multiple solid-phase synthesis with high yield and high homogeneity of synthetic products, safe operation with a small amount of waste, low cost hardware and low running cost. Reagents, solid-supports, a novel synthesizer without cross-contamination, simultaneous cleavage for highly efficient synthesis and characterization of synthetic peptides, and additionally the construction of peptide library are reviewed.
Bases of the obligate biotrophy of arbuscular mycorrhizal fungi (2002)

The obligate biotrophic nature of arbuscular mycorrhizal fungi (AMF) has long been accepted (Azcón-Aguilar et al. 1999), although its absolute occurrence under natural conditions has never been proved. Saprophytic capabilities of AMF have been suspected based on observations of prolonged independent growth of these fungi in vitro (Hepper 1983; Mosse 1988; Strullu et al. 1997; reviewed by Azcón-Aguilar et al. 1999), but all efforts of culturing these organisms continuously under axenic conditions have failed up to now.
Finite-length MIMO decision feedback equalization for space-time block-coded signals over multipath-fading channels (2001)

A finite-length optimized-delay multi-input-multi-output (MIMO) mean-square-error decision-feedback equalizer for space-time block-coded transmissions over multipath-fading channels is presented. Alamouti's (see IEEE J. Select. Areas Commun., p.1451-58, 1998) space-time block code with two transmit and two receive antennas on a typical urban EDGE channel is taken as a case study. We propose a combined equalization and decoding scheme under the constraint of linear processing complexity (no trellis search) at the receiver. Performance comparisons are made with the single-transmit/single-receive antenna case and the case of MIMO feedforward linear equalization only with no decision feedback.
Improved crossover and mutation operators for Genetic-Algorithm project scheduling (2009)

In Genetic Algorithms (GAs) technique, offspring chromosomes are created by merging two parent chromosomes using a crossover operator or modifying an existing chromosome using a mutation operator. However, in scheduling problems in which the genes represent activities' start times, the crossover and mutation operators may cause violation of the precedence relationships in the offspring chromosomes. This paper proposes improved crossover and mutation algorithms to directly devise feasible offspring chromosomes. The proposed algorithms employed the traditional Free Float (FF) and a newly-introduced Backward Free Float (BFF). The obtained results exhibited robustness of the proposed algorithms to reduce the computational costs, and high effectiveness to search for optimal solutions. Moreover, validation was performed by comparing the results against the exact solutions obtained by the Integer Programming (IP) technique.
Iron Oxide Mesoporous Magnetic Nanostructures with High Surface Area for Enhanced and Selective Drug Delivery to Metastatic Cancer Cells (2021)

This work reports the fabrication of iron oxide mesoporous magnetic nanostructures (IO-MMNs) via the nano-replication method using acid-prepared mesoporous spheres (APMS) as the rigid silica host and iron (III) nitrate as the iron precursor. The obtained nanosized mesostructures were fully characterized by SEM, TEM, DLS, FTIR, XRD, VSM, and nitrogen physisorption. IO-MMNs exhibited relatively high surface areas and large pore volumes (<i>S<sub>BET</sub></i> = 70-120 m<sup>2</sup>/g and <i>V<sub>pore</sub></i> = 0.25-0.45 cm<sup>3</sup>/g), small sizes (~300 nm), good crystallinity and magnetization, and excellent biocompatibility. With their intrinsic porosities, high drug loading efficiencies (up to 70%) were achieved and the drug release rates were found to be pH-dependent. Cytotoxicity, confocal microscopy, and flow cytometry experiments against different types of cancerous cells indicated that Dox-loaded IO-MMNs reduced the viability of metastatic MCF-7 and KAIMRC-1 breast as well as HT-29 colon cancer cells, with the least uptake and toxicity towards normal primary cells (up to 4-fold enhancement). These results strongly suggest the potential use of IO-MMNs as promising agents for enhanced and effective drug delivery in cancer theranostics.
On composite channel estimation in wireless massive MIMO systems (2013)

A multiuser MIMO (MU-MIMO) TDD system in which the base station (BS) uses a large scale antenna array to communicate with single-antenna mobile users is considered. We present novel schemes to estimate both large-scale and small-scale fading coefficients by uplink pilot sequences. The large-scale fading coefficients (LSFCs) are usually ignored or assumed perfectly known and almost all MIMO channel state information (CSI) estimation studies deal solely with small-scale fading coefficients (SSFCs). We propose low complexity algorithms that give reliable estimates for both FCs. The LSFC estimator takes advantage of the excess spatial samples received and the channel hardening effect while the SSFC estimator is based on a rank-reduction approach. Our estimators require a low training overhead and both analysis and numerical experiments prove that they offer superior mean-squared error performance.
The midpoint method for parallelization of particle simulations (2006)

The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.
The Expression of Plasminogen Activator System in a Rat Model of Periodontal Wound Healing (2001)

These findings indicate that the plasminogen activator system is involved in the entire process of periodontal wound healing, in particular with the formation of fibrin matrix on the root surface and its replacement by granulation tissue, as well as the subsequent formation of the attachment of soft tissue to the root surface during the later stages of wound repair.
Efficient Cooling of Multiple Components in a Shielded Circuit Pack (2006)

Abstract We describe a technology in which multiple components inside a circuit pack shielded from electromagnetic interference (EMI) are efficiently cooled by individual heat sinks that protrude into an external airflow through openings in the lid of the shield. Compliant, electrically conductive gaskets are used to form perimeter seals between the bases of the heat sinks and the lid of the enclosure. The gaskets accommodate variations in the heights of the components and allow solid-to-solid contact in the thermal-grease-filled interface between the components and their heat sinks without compromising EMI shielding. This technology provides efficient cooling because the heat sinks can be tailored to the thermal loads of the individual components. Moreover, a set of small heat sinks presents a lower flow resistance to the cooling airflow than the conventional configuration of fins covering the entire lid of an EMI shield. We have examined the implementation of this solution by numerical modeling and by experiment. It leads to acceptable thermal performance, and lower flow resistance relative to the conventional approach. It may reduce cost and weight and it eases rework.
Low-cost thin-film absorber/evaporator for an absorption chiller. Final report, May 1992-April 1993 (1993)

The feasibility of making the absorber and evaporator of a small lithium-bromide absorption chiller from thin plastic films was studied. Tests were performed to measure (1) pressure limitations for a plastic thin-film heat exchanger, (2) flow pressure-drop characteristics, (3) air permeation rates across the plastic films, and (4) creep characteristics of the plastic films. Initial tests were performed on heat exchangers made of either low-density polyethylene (LDPE), high-density polyethylene (HDPE), or a LDPE/HDPE blend. While initial designs for the heat exchanger failed at internal pressures of only 5 to 6 psi, the final design could withstand pressures of 34 psi.
Principles of surface-phase-resolved shearography (2019)

There is a need to remotely measure the full phase and amplitude information of small-scale acoustoseismic vibrations in order to detect the presence of buried objects (e.g., tunnels, etc.), or for other purposes. This remote sensing information may need to be collected with a large area coverage rate and at a safe standoff distance. To accomplish this, we have implemented a shearographic imaging system that incorporates phase stepping in a novel way, automatically separating random speckle noise from surface motion, without requiring an intermediate unwrapping step. This method, which we call surface-phase-resolved shearography, is especially effective for very low-amplitude motions that generate less than one light-wavelength of phase change.
Slowing Down DNA Translocation through Solid-State Nanopores by Edge-Field Leakage (2020)

Abstract Solid-state nanopores allow high-throughput single-molecule detection but identifying and even registering all translocating small molecules remain key challenges due to their high translocation speeds. We show here the same electric field that drives the molecules into the pore can selectively pin and delay their transport. A thin high-permittivity dielectric coating on slender bullet-shaped polymer nanopores permits electric field leakage at the pore tip to produce a voltage-dependent surface field on the upper periphery of the pore that can reversibly edge-pin entering molecules that can absorb conformally to the tip corner. This localized tip field renders molecular entry an activated process with sensitive exponential dependence on the bias voltage and molecular rigidity. The exponential sensitivity allows us to selectively prolong the translocation time of short single-stranded DNA molecules by up to 5 orders of magnitude, allowing discrimination against their double-stranded duplexes with 97% confidence. We show evidence that the leak-field pinned single-stranded DNA actually absorbs onto the edge before entering the pore, yielding translocation times as long as minutes.