gebhart/patrepeval huggingface dataset:
Failure to detect infectious hepatitis b virus using high dose safety test for hepatitis b vaccine (1980)

One hundred milliliters of an inactivated hepatitis B vaccine (20 microgram/ml) were inoculated intravenously into two colony-born infant chimpanzees. Immediately thereafter each received hepatitis B virus from a documented infectious inoculum intravenously at a separate site. Neither chimpanzee developed elevation of aminotransferase levels, hepatitis B surface antigen (HBsAg), or antibody to hepatitis B core antigen during six months of evaluation, the duration of the currently recommended safety test. Both chimpanzees developed antibody to HBsAg beginning 8 and 9 weeks, respectively, after inoculation. The administration of a large intravenous quantity of vaccine antigen thus appeared capable of masking or preventing infection by simultaneously administered hepatitis B virus. This study suggests that a chimpanzee safety test for hepatitis B vaccine should not employ large quantities of vaccine antigen, since such a safety test may fail to detect small amounts of residual infectious hepatitis B virus.
Ion flux asymmetry in radiofrequency capacitively-coupled plasmas excited by sawtooth-like waveforms (2014)

International audience
Reversal of mitochondrial defects with CSB-dependent serine protease inhibitors in patient cells of the progeroid Cockayne syndrome (2015)

UV-sensitive syndrome (UV(S)S) and Cockayne syndrome (CS) are human disorders caused by CSA or CSB gene mutations; both conditions cause defective transcription-coupled repair and photosensitivity. Patients with CS also display neurological and developmental abnormalities and dramatic premature aging, and their cells are hypersensitive to oxidative stress. We report CSA/CSB-dependent depletion of the mitochondrial DNA polymerase-γ catalytic subunit (POLG1), due to HTRA3 serine protease accumulation in CS, but not in UV(s)S or control fibroblasts. Inhibition of serine proteases restored physiological POLG1 levels in either CS fibroblasts and in CSB-silenced cells. Moreover, patient-derived CS cells displayed greater nitroso-redox imbalance than UV(S)S cells. Scavengers of reactive oxygen species and peroxynitrite normalized HTRA3 and POLG1 levels in CS cells, and notably, increased mitochondrial oxidative phosphorylation, which was altered in CS cells. These data reveal critical deregulation of proteases potentially linked to progeroid phenotypes in CS, and our results suggest rescue strategies as a therapeutic option.
Radiolabeled Fucoidan as a P-Selectin Targeting Agent for In Vivo Imaging of Platelet-Rich Thrombus and Endothelial Activation (2011)

This study supports (99m)Tc-fucoidan as a relevant imaging agent for in vivo detection of biologic activities associated with P-selectin overexpression, such as arterial thrombus and ischemic memory. Given the reported wide availability at a low cost, and its low toxicity, fucoidan seems to overcome some of the limitations of previous P-selectin-targeted imaging agents.
Association of the Autoimmune Disease Scleroderma with an Immunologic Response to Cancer (2013)

Autoimmune diseases are thought to be initiated by exposures to foreign antigens that cross-react with endogenous molecules. Scleroderma is an autoimmune connective tissue disease in which patients make antibodies to a limited group of autoantigens, including RPC1, encoded by the POLR3A gene. As patients with scleroderma and antibodies against RPC1 are at increased risk for cancer, we hypothesized that the "foreign" antigens in this autoimmune disease are encoded by somatically mutated genes in the patients' incipient cancers. Studying cancers from scleroderma patients, we found genetic alterations of the POLR3A locus in six of eight patients with antibodies to RPC1 but not in eight patients without antibodies to RPC1. Analyses of peripheral blood lymphocytes and serum suggested that POLR3A mutations triggered cellular immunity and cross-reactive humoral immune responses. These results offer insight into the pathogenesis of scleroderma and provide support for the idea that acquired immunity helps to control naturally occurring cancers.
A Real-Time Data Center Airflow and Energy Assessment Tool (2009)

A tool has been created to provide a simple assessment of airflow and energy management in an existing data center. Calculations are based on a well-mixed model of the data equivalent to the assumption that there is one effective rack and one effective cooling unit. The Air Distribution Effectiveness (ADE) index is proposed as a performance metric. For a given facility layout, ADE is a fixed number and is independent of IT load and cooler airflow. Therefore, ADE may be used as a performance metric and also to estimate rack inlet temperatures under various alternative cooler-airflow and rack-load scenarios. The tool described here may be used to determine how cooler airflow may be reduced or the chilled-water temperature may be increased to reduce data center energy consumption. The total net savings includes possible IT server fan speed (power) increases in response to inlet temperatures reaching a critical threshold value. This paper details the methods used in the software tool and shows example applications.
Heterogeneous Integration of Molecules in Nonvolatile Memory (2008)

In this paper, we present a much simpler implementation of the double tunnel junction by utilizing the monodisperse nature of these nanoscale entities. C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> molecules instead of Si NCs are embedded inside the oxide barrier to overcome the limitation on the NC size control. We will further show improved tR I tPE ratio in a metal NC memory integrated with this barrier.
Peptidyl <i>N</i>,<i>N</i>-Bis(2-mercaptoethyl)-amides as Thioester Precursors for Native Chemical Ligation (2010)

With two β-mercaptoethyl groups on the N, a tertiary amide of structure 1 is always poised for intramolecular thioesterification however it flips about the C-N bond. It is shown that a peptide with such a C-terminal N,N-bis(2-mercaptoethyl)-amide (BMEA) can be used directly for native chemical ligation (NCL). These BMEA peptides are easily prepared with standard Fmoc-solid phase peptide synthesis protocols, thus giving a very convenient access to the thioester components for NCL.
Froid (2017)

For decades, RDBMSs have supported declarative SQL as well as imperative functions and procedures as ways for users to express data processing tasks. While the evaluation of declarative SQL has received a lot of attention resulting in highly sophisticated techniques, the evaluation of imperative programs has remained naïve and highly inefficient. Imperative programs offer several benefits over SQL and hence are often preferred and widely used. But unfortunately, their abysmal performance discourages, and even prohibits their use in many situations. We address this important problem that has hitherto received little attention. We present Froid, an extensible framework for optimizing imperative programs in relational databases. Froid's novel approach automatically transforms entire User Defined Functions (UDFs) into relational algebraic expressions, and embeds them into the calling SQL query. This form is now amenable to cost-based optimization and results in efficient, set-oriented, parallel plans as opposed to inefficient, iterative, serial execution of UDFs. Froid's approach additionally brings the benefits of many compiler optimizations to UDFs with no additional implementation effort. We describe the design of Froid and present our experimental evaluation that demonstrates performance improvements of up to multiple orders of magnitude on real workloads.
Shallow Water Demultiple Using Hybrid Multichannel Prediction (2013)

In this paper, we present a hybrid approach combining the strengths of Shallow Water Demultiple (SWD) and model-based methods. We show that the multichannel prediction operator estimated by SWD can be used as an accurate kinematic representation of the seafloor reflection with a higher signal-to-noise (S/N) ratio, allowing the travel time of the seafloor to be automatically estimated. With this information the Green’s function of water-layer primary reflections can be modeled, and form a hybrid operator such that it compensates the missing high dips of the multichannel prediction operator and contains more than the seafloor event as represented by the Green’s function only. The hybrid operator is then used for multiple prediction and removal. We first present the theory of the method and then demonstrate its effectiveness on synthetics and field data acquired offshore Australia.
Differentiation of Human Induced Pluripotent Stem Cells into Functional Enterocyte-like Cells Using a Simple Method (2013)

Human induced pluripotent stem (iPS) cells were differentiated into the endoderm using activin A and were then treated with fibroblast growth factor 2 (FGF2) for differentiation into intestinal stem cell-like cells. These immature cells were then differentiated into enterocyte-like cells using epidermal growth factor (EGF) in 2% fetal bovine serum (FBS). At the early stage of differentiation, mRNA expression of caudal type homeobox 2 (CDX2), a major transcription factor related to intestinal development and differentiation, and leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5), an intestinal stem cell marker, was markedly increased by treatment with FGF2. When cells were cultured in medium containing EGF and a low concentration of FBS, mRNAs of specific markers of intestinal epithelial cells, including sucrase-isomaltase, the intestinal oligopeptide transporter SLC15A1/peptide transporter 1 (PEPT1), and the major metabolizing enzyme CYP3A4, were expressed. In addition, sucrase-isomaltase protein expression and uptake of β-Ala-Lys-N-7-amino-4-methylcoumarin-3-acetic acid (β-Ala-Lys-AMCA), a fluorescence-labeled substrate of the oligopeptide transporter, were detected. These results demonstrate a simple and direct method for differentiating human iPS cells into functional enterocyte-like cells.
Mycoplasma pneumoniae proteins that selectively bind to host cells (1982)

Mycoplasma pneumoniae proteins that bind to hamster trachea epithelial cells were identified by incubating 125I-labeled, detergent-solubilized mycoplasmas with glutaraldehyde-fixed host cells. Analysis of the bound fraction by gel electrophoresis and autoradiography revealed that proteins P1, P2, and HMW3 (molecular weights, 165,000, 110,000, and 140,000, respectively), previously implicated in attachment, were among the predominant species. Unlabeled mycoplasma preparations competed with the binding of radiolabeled proteins, suggesting the involvement of a limited number of receptor sites on the host cells.
Optoelectronic devices based on type II polytype tunnel heterostructures (1992)

We describe a new family of optoelectronic devices based on the unique properties of combinations of semiconductor tunnel junctions with type II polytype heterostructures. A typical light-emitting device structure consists of AlSb (thin barrier)/InAs(quantum well)/AlSb(thin barrier) structure clad by AlInAsSb emitter and GaSb collector. The emission source is the intersubband radiative transition between the first two subbands in the InAs well. Since the conduction-bank minimum of InAs is energetically lower than the valence-band maximum of GaSb, the device can be designed in such a way that electrons are injected only into the higher subband and extracted out only from the lower subband, both via tunneling, leading to an intraband population inversion and highly efficient radiative transitions. The same operation principle can be applied to design detector structures.
DIFFERENTIAL OPTICAL DISPERSION SPECTROSCOPY FOR COMPARATIVE MOLECULAR QUANTIFICATION (2013)

Author Institution: Department of Electrical Engineering, Princeton University, Princeton, NJ, 08544, USA
Dynamic Cloud Network Control Under Reconfiguration Delay and Cost (2019)

Network virtualization and programmability allow operators to deploy a wide range of services over a common physical infrastructure and elastically allocate cloud and network resources according to changing requirements. While the elastic reconfiguration of virtual resources enables dynamically scaling capacity in order to support service demands with minimal operational cost, reconfiguration operations make resources unavailable during a given time period and may incur additional cost. In this paper, we address the dynamic cloud network control problem under non-negligible reconfiguration delay and cost. We show that while the capacity region remains unchanged regardless of the reconfiguration delay/cost values, a reconfiguration-agnostic policy may fail to guarantee throughput-optimality and minimum cost under nonzero reconfiguration delay/cost. We then present an adaptive dynamic cloud network control policy that allows network nodes to make local flow scheduling and resource allocation decisions while controlling the frequency of reconfiguration in order to support any input rate in the capacity region and achieve arbitrarily close to minimum cost for any finite reconfiguration delay/cost values.
Low-Complexity Time-Domain ICI Equalization for OFDM Communications Over Rapidly Varying Channels (2006)

We consider wireless OFDM communications over rapidly varying channels as occurring e.g. in high-mobility scenarios. Here, intercarrier interference (ICI) is the major source of impairment that limits the transmission quality. In this paper, we propose novel equalizers to combat ICI and enable reliable communications even at high Doppler frequencies. In contrast to existing frequency-domain approaches, our schemes operate in the time domain. This allows a low-complexity implementation without introducing any systematic channel approximation errors. Numerical simulations illustrate the effectiveness of our approach and show that in conjunction with channel coding our methods achieve significant Doppler diversity.
Mass filtered plasma focused ion beam system (2012)

The authors describe an inductively coupled plasma ion source combined with a mass tunable Wien (E × B) filter that is capable of delivering single or mixed gas plasma generated ions. Gases for the RF powered ion source can be premixed or of variable stoichiometry by mixing individual gases. The gas mixtures can contain a variety of elements providing light to heavy gaseous ions which can be selected by mass filtering. Optimization of the plasma source consists of varying parameters such as the RF power, pressure, and gas stoichiometry. Subsequently, the mass filter/plasma-gas ion column can be optimized for a wide range of applications. For example, high resolution imaging using high reduced brightness light ions (e.g., for subsurface imaging) or fast material removal using heavy ions may be accomplished across a wide range of beam currents, typically 10 pA to 10 μA, with the same gas mixture. The authors have examined several candidate species (He+, Ne+, Ar+, Xe+, O2+, O+, O−, N+, N2+, H+, H2+, H3+) and present a subset of these recent results involving production of H+ from H2 and O2/H2O mixtures.
A Perspective on Symmetric Lateral Bipolar Transistors on SOI as a Complementary Bipolar Logic Technology (2014)

Recently published reports suggest that symmetric lateral bipolar transistors on semiconductor-on-insulator (SOI) is CMOS compatible in fabrication process, and can be much denser than CMOS due to their much larger (5-10× larger) drive-current capability. When used in traditional bipolar circuits, SOI bipolar offers much lower power dissipation and/or much higher maximum speed. With both NPN and PNP devices of comparable characteristics, SOI lateral bipolar suggests the possibility of complementary bipolar (CBipolar) circuits in configurations analogous to CMOS. In this paper, the performance versus power dissipation of CBipolar circuits is examined using analytic equations. It is shown that for CBipolar to be superior to CMOS in both performance and power dissipation, narrow-gap-base heterojunction structures, such as Si emitter with Ge base or Si emitter with SiGe base, are required.
Introducing hierarchy-awareness in replacement and bypass algorithms for last-level caches (2012)

The replacement policies for the last-level caches (LLCs) are usually designed based on the access information available locally at the LLC. These policies are inherently sub-optimal due to lack of information about the activities in the inner-levels of the hierarchy. This paper introduces cache hierarchy-aware replacement (CHAR) algorithms for inclusive LLCs (or L3 caches) and applies the same algorithms to implement efficient bypass techniques for exclusive LLCs in a three-level hierarchy. In a hierarchy with an inclusive LLC, these algorithms mine the L2 cache eviction stream and decide if a block evicted from the L2 cache should be made a victim candidate in the LLC based on the access pattern of the evicted block. Ours is the first proposal that explores the possibility of using a subset of L2 cache eviction hints to improve the replacement algorithms of an inclusive LLC. The CHAR algorithm classifies the blocks residing in the L2 cache based on their reuse patterns and dynamically estimates the reuse probability of each class of blocks to generate selective replacement hints to the LLC. Compared to the static re-reference interval prediction (SRRIP) policy, our proposal offers an average reduction of 10.9% in LLC misses and an average improvement of 3.8% in instructions retired per cycle (IPC) for twelve single-threaded applications. The corresponding reduction in LLC misses for one hundred 4-way multi-programmed workloads is 6.8% leading to an average improvement of 3.9% in throughput. Finally, our proposal achieves an 11.1% reduction in LLC misses and a 4.2% reduction in parallel execution cycles for six 8-way threaded shared memory applications compared to the SRRIP policy.
Recent advancements in real-world microbial fuel cell applications (2018)

This short review focuses on the recent developments of the Microbial Fuel Cell (MFC) technology, its scale-up and implementation in real world applications. Microbial Fuel Cells produce (bio)energy from waste streams, which can reduce environmental pollution, but also decrease the cost of the treatment. Although the technology is still considered "new", it has a long history since its discovery, but it is only now that recent developments have allowed its implementation in real world settings, as a precursor to commercialisation.
Virtual Impedance-Based Selective Harmonic Compensation (VI-SHC) PWM for Current Source Rectifiers (2013)

To mitigate the line current harmonics of a high-power current source rectifier (CSR) system, the selective harmonic elimination (SHE) scheme is frequently used due to its low switching frequency and superior harmonic performance. However, the SHE scheme only focuses on the harmonics generated by the converter itself. It cannot cope with the line current harmonics caused by the background grid voltage harmonics. In this paper, a selective harmonic compensation scheme using the virtual impedance concept (VI-SHC) is presented. This method compensates for the preexisting grid background harmonics using only the line current measurement, and provides superior line current harmonic performance. The proposed method does not require measuring the grid voltage harmonics (which are typically low), does not rely on an accurate CSR system model, and therefore is very robust for practical implementation. Thi s PWM control scheme has been verified by real-time experiments on a CSR prototype.
A statistical wisp model and pseudophysical approaches for interactive hairstyle generation (2005)

This paper presents an interactive technique that produces static hairstyles by generating individual hair strands of the desired shape and color, subject to the presence of gravity and collisions. A variety of hairstyles can be generated by adjusting the wisp parameters, while the deformation is solved efficiently, accounting for the effects of gravity and collisions. Wisps are generated employing statistical approaches. As for hair deformation, we propose a method which is based on physical simulation concepts, but is simplified to efficiently solve the static shape of hair. On top of the statistical wisp model and the deformation solver, a constraint-based styler is proposed to model artificial features that oppose the natural flow of hair under gravity and hair elasticity, such as a hairpin. Our technique spans a wider range of human hairstyles than previously proposed methods and the styles generated by this technique are fairly realistic.
Genome Editing-Based Engineering of CESA3 Dual Cellulose-Inhibitor-Resistant Plants (2019)

The rapid appearance of herbicide-resistant weeds combined with a lack of novel herbicides being brought to market reduces crop production, thereby threatening food security worldwide. Here, we report on the use of the previously identified cellulose biosynthesis-inhibiting chemical compound C17 as a potential herbicide. Toxicity tests showed that C17 efficiently inhibits the growth of various weeds and widely cultivated dicotyledonous crops, whereas only slight or no growth inhibition was observed for monocotyledonous crops. Surprisingly, when exposed to a mixture of C17 and one of two well-known cellulose biosynthesis inhibitors (CBIs), isoxaben and indaziflam, an additive growth inhibition was observed, demonstrating that C17 has a different mode of action that can be used to sensitize plants toward known CBIs. Moreover, we demonstrate that a C17-resistant <i>CESA3</i> allele can be used as a positive transformation selection marker and that C17 resistance can be obtained through genome engineering of the wild-type <i>CESA3</i> allele using clustered regularly interspaced short palindromic repeats-mediated base editing. This editing system allowed us to engineer C17 tolerance in an isoxaben-resistant line, resulting in double herbicide-resistant plants.
A human oncogene of the RAS superfamily unmasked by expression cDNA cloning. (1994)

As an approach to identify human oncogenes, we generated an expression cDNA library from an ovarian carcinoma line. A potent transforming gene was detected by transfection analysis and identified as TC21, a recently cloned member of the RAS gene superfamily. A single point mutation substituting glutamine for leucine at position 72 was shown to be responsible for activation of transforming properties. While the cDNA clone possessed high transforming activity, the ovarian tumor genomic DNA, which contained the mutated TC21 allele, failed to induce transformed foci. Thus, expression cDNA cloning made it possible to identify and isolate a human oncogene that has evaded detection by conventional approaches.