gebhart/patrepeval huggingface dataset:
A proposed framework for an appropriate evaluation scheme for microorganisms as novel foods with a health claim in Europe (2015)

This paper concerns the procedure and the scientific approach to obtain market authorization for a microorganism to be recognized as a novel food with a health claim. Microorganisms that have not been traditionally used during food production in Europe prior to 1997 are considered as novel foods, which should undergo an in-depth characterization and safety assessment before being authorized on the European market. If a novel food bacterium is claimed to provide a beneficial effect on health, these claims must also be investigated before they can be authorized. Some requirements to obtain novel food certification are shared with those required to obtain a health claim. Although regulation exists that deals with these issues for foods in general, bacteria in food raise a specific set of questions that are only minimally addressed in official documentation. We propose a framework and suggest a list of criteria that should be assessed to obtain marketing authorization and health claim for a bacterium in accordance with European health policy.
Navigation Among Movable Obstacles in unknown environments (2010)

This paper explores the Navigation Among Movable Obstacles (NAMO) problem in an unknown environment. We consider the realistic scenario in which the robot has to navigate to a goal position in an unknown environment consisting of static and movable objects. The robot may move objects if the goal can not be reached otherwise or if moving the object may significantly shorten the path to the goal. We consider real situations in which the robot only has limited sensing information and where the action selection can therefore only be based on partial knowledge learned from the environment at that point. This paper introduces an algorithm that significantly reduces the necessary calculations to accomplish this task compared to a direct approach. We present an efficient implementation for the case of planar, axis-aligned environments and report experimental results on challenging scenarios with more than 50 objects.
Micro-photonic cylindrical waveguide based protein biosensor (2006)

In this paper we experimentally demonstrate the fabrication and operation of a rapidly prototyped optical cylindrical micro-waveguide based biosensor. This device works on the principle of variation to the light intensity and path of coupled input light due to the binding of protein bio-molecules onto the micro-waveguide surface as a method of physical transduction. The variation to the coupled light intensity and path is dependent on the nature of the bio-molecule and the density of the bio-molecules. This technique has been used to identify protein biomarkers for inflammation and thrombosis, namely myeloperoxidase (MPO) and C-reactive protein (CRP). The detection limit that has been demonstrated is pg?ml?1. The detection speed is of the order of seconds from the time of injection of the bio-molecule. The optical signature that is obtained to identify a protein bio-molecule is entirely dependent on the nature of adsorption of the bio-molecule on to the cylindrical cavity surfaces. This in turn is dependent on the protein conformation and the surface charge of the bio-molecules. Hence a specific protein bio-molecule generates a unique optical identifier based on the nature of binding/adsorption to the cavity surface. This physical phenomenon is exploited to identify individual proteins. This technique is a demonstration of detection of nano-scale protein bio-molecules using the optical biosensor technique with unprecedented sensitivity.
Experimental demonstration of error recovery in an integrated cyberphysical digital-microfluidic platform (2015)

Digital (droplet-based) microfluidics enables the integration of fluid-handling operations and reaction-outcome detection. Despite these benefits, defects and erroneous fluidic operations continue to be major barriers to the adoption and deployment of these devices. We describe the first practical and fully integrated cyberphysical error-recovery system that can be implemented in real time on a field-programmable gate array (FPGA). The hardware-assisted solution is based on an error dictionary containing the error-recovery plans for various anticipated errors. The dictionary is computed and stored in FPGA memory before the start of the biochemical experiment. Errors in droplet operations on the digital microfluidic platform are detected using capacitive sensors, the test outcome is interpreted by control hardware, and corresponding error-recovery plans are triggered in real-time. Experimental results are reported for a fabricated silicon device, and links to videos are provided for the first-ever experimental demonstration of real-time error recovery in cyberphysical digital-microfluidic biochips using a hardware-implemented dictionary.
Modulation of integrin expression in endometrial stromal cells in vitro. (1996)

Integrins, a class of cell adhesion molecules found on virtually all cells, display dynamic temporal and spatial patterns of expression in the endometrium during the menstrual cycle and in early pregnancy. To study integrin regulation, we measured the expression of eight different integrin subunits on cultured human endometrial stromal cells obtained from proliferative phase endometrium, using immunofluorescence and flow cytometry. Treatment with estrogen and progesterone induced hormonal changes of decidualization but did not alter the expression of any of the integrins. It is presently unknown whether steroid hormones other than estrogen or progesterone affect integrin expression. In contrast, treatment with several growth factors and cytokines resulted in specific alterations of integrin levels. Epidermal growth factor, transforming growth factor-alpha, and transforming growth factor-beta 1 induced expression of the alpha 1 beta 1 collagen/laminin receptor. There also was a trend towards decreased expression of the alpha 6 subunit in response to interleukin-1 alpha, interleukin-1 beta, and tumor necrosis factor-alpha. The expression of alpha 1 beta 1 was accompanied by increased adhesion to collagen but there was no change in the binding to fibronectin and vitronectin. Our findings suggest that some aspects of decidualization may be regulated by steroid hormones, whereas others, such as integrin expression, are regulated by cytokines or growth factors, possibly of trophoblast origin. Integrins are likely to play a role in the interaction between trophoblast and endometrium.
A New Paradigm for Anion Trapping in High Capacity and Selectivity: Crystal-to-Crystal Transformation of Cationic Materials (2011)

We describe a new methodology to the selective trapping of priority pollutants that occur inherently as oxo-anions (e.g., perchlorate, chromate, arsenate, pertechnetate, etc.) or organic anions (e.g., salicylate, pharmaceuticals, and their metabolites, which are often chlorinated into potentially more harmful compounds). The typical approach to trapping anions is exchange into cationic hosts such as resins or layered double hydroxides. Both capacity and selectivity are limited by the equilibrium of the process and moreover are often subject to interference, e.g. by carbonate that is always present in water from atmospheric CO(2). Our approach takes advantage of the metastability of our cationically charged materials to instead trap by recrystallization to a new structure. Exceptionally high adsorption capacities for permanganate and perrhenate--studied as models for pertechnetate--were found for a Ag(I)-based cationic extended framework. The exchange capacity reached 292 and 602 mg/g, respectively, over five times the exchange capacity compared to conventional layered double hydroxides. Our cationic material can also selectively trap these and other toxic oxo-anions when nontoxic anions (e.g., nitrate, carbonate) were present in an over 100-fold excess concentration.
8.6 A 6.5-to-23.3fJ/b/mm balanced charge-recycling bus in 16nm FinFET CMOS at 1.7-to-2.6Gb/s/wire with clock forwarding and low-crosstalk contraflow wiring (2016)

Signaling over chip-scale global interconnect is consuming a larger fraction of total power in large processor chips, as processes continue to shrink. Solving this growing crisis requires simple, low-energy and area-efficient signaling for high-bandwidth data buses. This paper describes a balanced charge-recycling bus (BCRB) that achieves quadratic power savings, relative to signaling with full-swing CMOS repeaters. The scheme stacks two CMOS repeated wire links, one operating in the Vtop domain, between Vdd and Vmid=Vdd/2, the other, Vbot, between Vmid and GND. Unlike previous work [1], we require no voltage regulator to maintain the Vmid voltage at Vdd/2, to compensate for differences in data activity in Vtop and Vbot domains. The BCRB also uses simple single-ended signaling, to achieve higher bandwidth per unit bus width than differential buses [2] and lower signaling energy than precharging schemes [3], since we take full advantage of low switching activity and bus-invert coding.
In vivo and in vitro stem cell function of c-kit- and Sca-1-positive murine hematopoietic cells (1992)

c-kit is expressed on hematopoietic stem cells and progenitor cells, but not on lymphohematopoietic differentiated cells. Lineage marker- negative, c-kit-positive (Lin-c-kit+) bone marrow cells were fractionated by means of Ly6A/E or Sca-1 expression. Lin-c-kit+Sca-1+ cells, which consisted of 0.08% of bone marrow nucleated cells, did not contain day-8 colony-forming units-spleen (CFU-S), but 80% were day-12 CFU-S. One hundred cells rescued the lethally irradiated mice and reconstituted hematopoiesis. On the other hand, 2 x 10(3) of Lin-c- kit+Sca-1- cells formed 20 day-8 and 11 day-12 spleen colonies, but they could not rescue the lethally irradiated mice. These data indicate that Lin-c-kit+Sca-1+ cells are primitive hematopoietic stem cells and that Sca-1-cells do not contain stem cells that reconstitute hematopoiesis. Lin-c-kit+Sca-1+ cells formed no colonies in the presence of stem cell factor (SCF) or interleukin-6 (IL-6), and only 10% of them formed colonies in the presence of IL-3. However, approximately 50% of them formed large colonies in the presence of IL-3, IL-6, and SCF. Moreover, when single cells were deposited into culture medium by fluorescence-activated cell sorter clone sorting system, 40% of them proliferated on a stromal cell line (PA-6) and proliferated for more than 2 weeks. In contrast, 15% of the Lin-c- kit+Sca-1-cells formed colonies in the presence of IL-3, but no synergistic effects were observed in combination with SCF plus IL-6 and/or IL-3. Approximately 10% proliferated on PA-6, but most of them degenerated within 2 weeks. The population ratio of c-kit+Sca-1+ to c-kit+Sca-1- increased 2 and 4 days after exposure to 5-fluorouracil (5-FU). These results are consistent with the relative enrichment of highly proliferative colony-forming cells by 5-FU. These data show that, although c-kit is found both on the primitive hematopoietic stem cells and progenitors, Sca-1+ cells are more primitive and respond better than Sca-1- cells to a combination of hematopoietic factors, including SCF and stromal cells.
A162 Fundamental research on Drop-wise condensation heat transfer on a vertical tube of PCCS (2005)

After TMI and Chernobyl accidents, many efforts have been made to enhance the nuclear safety with passive features. Among such passive features, the passive containment cooling system has been suggested. In case of a Loss of Coolant Accident (LOCA) occurred, Passive Containment Cooling System (PCCS) cools the core decay heat. The objective of this experimental study is to clarify the heat transfer characteristics of PCCS on a vertical pipe. In order to calculate overall heat transfer coefficient between the cooling water and atmosphere, cooling water flow rate, cooling water temperature and gas temperature are measured. The influence of the system pressure is clarified in the range of 0.1 to 0.4MPa(abs) of the system pressure at 0% of the air fraction. It is confirmed that increasing of the heat transfer coefficient is affected by increasing of the system pressure.
Site-Selective Hydrogenation of Electron-Poor Alkenes and Dienes Enabled by a Rh-Catalyzed Hydride Addition/Protonolysis Mechanism (2022)

The transition metal catalyzed hydrogenation of alkenes is a well-developed technology used on a lab scale as well as on large scales in the chemical industry. Site- and chemoselective mono-hydrogenations of polarized conjugated dienes remain challenging. Instead, stoichiometric main-group hydrides are used rather than H2. As part of an effort to develop a scalable route to prepare geranylacetone, we discovered that Rh(CO)2acac/xantphos based catalysts enable the selective monohydrogenation of electron-poor 1,3-dienes, enones, and other polyunsaturated substrates. D-labeling and DFT studies support a mechanism where a nucleophilic Rh(I)-hydride selectively adds to electron-poor alkenes and the resulting Rh-enolate undergoes subsequent inner-sphere protonation by alcohol solvent. The finding that (Ln)Rh(H)(CO) type catalysts can enable selective mono-hydrogenation of electron-poor (poly)enes provides a valuable tool in the design of related chemoselective reduction processes of unsaturated substrates.
Analytic expression of fluorescence ratio detection correlates with depth in multi-spectral sub-surface imaging (2011)

Here we derived analytical solutions to diffuse light transport in biological tissue based on spectral deformation of diffused near-infrared measurements. These solutions provide a closed-form mathematical expression which predicts that the depth of a fluorescent molecule distribution is linearly related to the logarithm of the ratio of fluorescence at two different wavelengths. The slope and intercept values of the equation depend on the intrinsic values of absorption and reduced scattering of tissue. This linear behavior occurs if the following two conditions are satisfied: the depth is beyond a few millimeters and the tissue is relatively homogeneous. We present experimental measurements acquired with a broad-beam non-contact multi-spectral fluorescence imaging system using a hemoglobin-containing diffusive phantom. Preliminary results confirm that a significant correlation exists between the predicted depth of a distribution of protoporphyrin IX molecules and the measured ratio of fluorescence at two different wavelengths. These results suggest that depth assessment of fluorescence contrast can be achieved in fluorescence-guided surgery to allow improved intra-operative delineation of tumor margins.
Association of allergic patients’ phenotypes with IgE reactivity to recombinant pollen marker allergens (2009)

IgE reactivity to recombinant marker allergens is associated with clinical phenotypes of allergic sensitization and may be useful for the selection of treatment strategies.
Identification of an allosteric binding site for RORγt inhibition (2015)

RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of small-molecule antagonists demonstrates occupancy of a previously unreported allosteric binding pocket. Binding at this non-canonical site induces an unprecedented conformational reorientation of helix 12 in the RORγt LBD, which blocks cofactor binding. The functional consequence of this allosteric ligand-mediated conformation is inhibition of function as evidenced by both biochemical and cellular studies. RORγt function is thus antagonized in a manner molecularly distinct from that of previously described orthosteric RORγt ligands. This brings forward an approach to target RORγt for the treatment of Th17-mediated autoimmune diseases. The elucidation of an unprecedented modality of pharmacological antagonism establishes a mechanism for modulation of nuclear receptors.
Signature of n→π* interactions in α‐helices (2011)

The oxygen of a peptide bond has two lone pairs of electrons. One of these lone pairs is poised to interact with the electron-deficient carbon of the subsequent peptide bond in the chain. Any partial covalency that results from this n→π* interaction should induce pyramidalization of the carbon (C'(i)) toward the oxygen (O(i-1)). We searched for such pyramidalization in 14 peptides that contain both α- and β-amino acid residues and that assume a helical structure. We found that the α-amino acid residues, which adopt the main chain dihedral angles of an α-helix, display dramatic pyramidalization but the β-amino acid residues do not. Thus, we conclude that O(i-1) and C'(i) are linked by a partial covalent bond in α-helices. This finding has important ramifications for the folding and conformational stability of α-helices in isolation and in proteins.
Gaussian proposal density using moment matching in SMC methods (2008)

In this article we introduce a new Gaussian proposal distribution to be used in conjunction with the sequential Monte Carlo (SMC) method for solving non-linear filtering problems. The proposal, in line with the recent trend, incorporates the current observation. The introduced proposal is characterized by the exact moments obtained from the dynamical system. This is in contrast with recent works where the moments are approximated either numerically or by linearizing the observation model. We show further that the newly introduced proposal performs better than other similar proposal functions which also incorporate both state and observations.
PMSM Control System Based on Digital Signal Processor (2013)

For the high power density of PMSM, designed the corresponding drive controller to improve the servo efficiency of PMSM servo system. According to the theory of math model of PMSM under the dq coordinate system, applied i d = 0 vector control method as a PMSM control strategy, established PMSM controller model based on vector control. Taking DSP TMS320F2812 as controller core, built a power-driven circuit, control circuit and the main detection protection circuit. The algorithm of control program was completed on the hardware platform to present its software processes. The simulation results show that: the control system response is fast, can track the given speed and position quickly and accurately. The speed fluctuation, overshoot and steady state error are very small. The designed controller is reasonable, which has better dynamic and static characteristics, and be benefit to improve the efficiency of PMSM servo system.
A novel µ‐conopeptide, CnIIIC, exerts potent and preferential inhibition of NaV1.2/1.4 channels and blocks neuronal nicotinic acetylcholine receptors (2012)

µ-CnIIIC potently blocked VGSCs in skeletal muscle and nerve, and hence is applicable to myorelaxation. Its atypical pharmacological profile suggests some common structural features between VGSCs and nAChR channels.
Label-free interferometric scattering imaging of molecular fluctuation predicts fluorescence nuclear microscope images (2021)

We demonstrate a computational method to map the nuclear organization of live cells based on a deep-learning approach where the time-varying scattering signal is used to estimate the density of chromatin in the fluorescence image.
Organ Repair, Hemostasis, and In Vivo Bonding of Medical Devices by Aqueous Solutions of Nanoparticles (2014)

Sutures are traumatic to soft connective tissues, such as liver or lungs. Polymer tissue adhesives require complex in vivo control of polymerization or cross-linking reactions and currently suffer from being toxic, weak, or inefficient within the wet conditions of the body. Herein, we demonstrate using Stöber silica or iron oxide nanoparticles that nanobridging, that is, adhesion by aqueous nanoparticle solutions, can be used in vivo in rats to achieve rapid and strong closure and healing of deep wounds in skin and liver. Nanoparticles were also used to fix polymer membranes to tissues even in the presence of blood flow, such as occurring after liver resection, yielding permanent hemostasis within a minute. Furthermore, medical devices and tissue engineering constructs were fixed to organs such as a beating heart. The simplicity, rapidity, and robustness of nanobridging bode well for clinical applications, surgery, and regenerative medicine.
Observation based analysis on the use of mobile applications for visually impaired users (2016)

The current efforts to specify an usability guideline for accessible mobile applications are sparse and they are still far to present a concrete pattern. Our previous work carried out a broad survey to consolidate the findings of these efforts in a unique list with 36 requirements, 13 of them focused on vision impairments. In this paper we show the results of an observation-based analysis involving visually impaired volunteers, whose aim was to complement this review and confirm if the lack of these requirements in fact affects the use of mobile applications.
P09-21 LB. Deep sequencing of HIV-1 from acute infection: low initial diversity, and rapid but variable CTL escape (2009)

Address: 1Los Alamos National Laboratory, Los Alamos, NM, USA, 2Dept. of Medicine, Univ. of Alabama at Birmingham, Birmingham, AL, USA, 3Group T-2, Los Alamos National Laboratory, Los Alamos, NM, USA, 4Group B-6, Los Alamos National Laboratory, Los Alamos, NM, USA, 5Depts. of Medicine and Microbiology, Univ. of Alabama at Birmingham, Birmingham, AL, USA, 6Division of Hematology/Oncology, Univ. of Alabama at Birmingham, Birmingham, AL, USA and 7Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA * Corresponding author
Single cell biology—a Keystone Symposia report (2021)

Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
Implementation of deadbeat-direct torque and flux control for synchronous reluctance machines to minimize loss each switching period (2016)

Deadbeat-direct torque and flux control (DB-DTFC) has been emerged as a high performance digital control law for induction machines and permanent magnet machines. Its key attributes are excellent dynamic performance, the use of only one single control law over a wide torque/speed range and direct applicability to overmodulation strategies. This paper extends prior research by presenting the implementation of DB-DTFC for synchronous reluctance machines (SynRMs). In addition, a control law for minimizing SynRM losses each switching period is proposed. Real-time implementation on a 5.5kW test bench is demonstrated.