gebhart/patrepeval huggingface dataset:
Cre/loxP-mediated excision of a neomycin resistance expression unit from an integrated retroviral vector increases long terminal repeat-driven transcription in human hematopoietic cells (1997)

Recombinant retroviruses are currently the most attractive vehicles for gene transfer into hematopoietic cells. Retroviral vectors often contain an easily selectable marker gene in addition to the gene of interest. However, the presence and selection for expression of the selectable gene often result in a significant reduction of the expression of the gene of interest in the transduced cells. In order to circumvent this problem, we have developed a Cre/loxP recombination system for specific excision of the selectable expression unit from integrated retroviruses. A retroviral vector, containing both a neomycin resistance expression unit flanked by loxP sites and granulocyte-macrophage colony-stimulating factor cDNA, was used to transduce the human hematopoietic K-562 cell line. Four transduced cell clones were then superinfected with a retrovirus containing a Cre recombinase expression unit. Molecular analyses of 30 doubly transduced subclones showed a strict correlation between cre expression and loxP-flanked selectable cassette excision, thus implying that Cre recombinase activity is very efficient in a retroviral context. Moreover, the excision of the selectable cassette results in a significant increase of granulocyte-macrophage colony-stimulating factor transcription driven by the retroviral promoter.
Bi-Level Rare Temporal Pattern Detection (2016)

Nowadays, temporal data is generated at an unprecedented speed from a variety of applications, such as wearable devices, sensor networks, wireless networks and etc. In contrast to such large amount of temporal data, it is usually the case that only a small portion of them contains information of interest. For example, for the ECG signals collected by wearable devices, most of them collected from healthy people are normal, and only a small number of them collected from people with certain heart diseases are abnormal. Furthermore, even for the abnormal temporal sequences, the abnormal patterns may only be present in a few time segments and are similar among themselves, forming a rare category of temporal patterns. For example, the ECG signal collected from an individual with a certain heart disease may be normal in most time segments, and abnormal in only a few time segments, exhibiting similar patterns. What is even more challenging is that such rare temporal patterns are often non-separable from the normal ones. Existing works on outlier detection for temporal data focus on detecting either the abnormal sequences as a whole, or the abnormal time segments directly, ignoring the relationship between abnormal sequences and abnormal time segments. Moreover, the abnormal patterns are typically treated as isolated outliers instead of a rare category with self-similarity. In this paper, for the first time, we propose a bi-level (sequence-level/ segment-level) model for rare temporal pattern detection. It is based on an optimization framework that fully exploits the bi-level structure in the data, i.e., the relationship between abnormal sequences and abnormal time segments. Furthermore, it uses sequence-specific simple hidden Markov models to obtain segment-level labels, and leverages the similarity among abnormal time segments to estimate the model parameters. To solve the optimization framework, we propose the unsupervised algorithm BIRAD, and also the semi-supervised version BIRAD-K which learns from a single labeled example. Experimental results on both synthetic and real data sets demonstrate the performance of the proposed algorithms from multiple aspects, outperforming state-of-the-art techniques on both temporal outlier detection and rare category analysis.
Redox Targeting of Prussian Blue: Toward Low-Cost and High Energy Density Redox Flow Battery and Solar Rechargeable Battery (2017)

The ever-increasing penetration of solar energy demands high energy density, safe and affordable energy storage systems. We demonstrated a redox flow battery on the basis of the redox targeting reactions of a bifunctional redox mediator – ethyl viologen diiodide (EVI2) with a low-cost pigment material – Prussian blue (PB). Sharing the same I–/I3– based electrolyte, this new battery system can be feasibly integrated with a dye-sensitized TiO2 photoelectrode for photoassisted charging process. The introduction of PB not only increases the energy density up to 117 Wh/L with good cycling performance and capacity retention, also instantaneously regenerates I– ensuring a stable I–/I3– concentration which is crucial to the operation of the photoelectrode. We anticipate that the work presented here may open an intriguing and credible way for the development of integrated all-in-one solar energy conversion and storage devices for large-scale applications.
Xylitol synthesis mutant of xylose-utilizing zymomonas for ethanol production (2023)

A strain of xylose-utilizing Zymomonas was engineered with a genetic modification to the glucose-fructose oxidoreductase gene resulting in reduced expression of GFOR enzyme activity. The engineered strain exhibits reduced production of xylitol, a detrimental by-product of xylose metabolism. It also consumes more xylose and produces more ethanol during mixed sugar fermentation under process-relevant conditions.
Energy analysis of PV cladding systems (1996)

This paper presents an energy analysis of three rainscreen cladding designs based on demonstration PV power systems installed in the UK, including a discussion of the effect of different module types. The potential for reduction of energy requirement through recycling is considered. Energy payback times of 6 years or less have been derived for these systems.
An allosteric model for heterogeneous receptor complexes: Understanding bacterial chemotaxis responses to multiple stimuli (2005)

The classical Monod-Wyman-Changeux model for homogeneous allosteric protein complex is generalized in this article to model the responses of heterogeneous receptor complexes to multiple types of ligand stimulus. We show that the recent in vivo experimental data of Escherichia coli chemotaxis responses for mutant strains with different expression levels of the chemo-receptors to different types of stimulus [Sourjik, V. & Berg, H. C. (2004) Nature 428, 437-441] all can be explained consistently within this generalized Monod-Wyman-Changeux model. Based on the model and the existing data, responses of all of the strains (studied in this article) to the presence of any combinations of ligand (Ser and MeAsp) concentrations are predicted quantitatively for future experimental verification. Through modeling the in vivo response data, our study reveals important information about the properties of different types of individual receptors, as well as the composition of the cluster. The energetic contribution of the nonligand binding, cytoplasmic parts of the cluster, such as CheA and CheW, is also discussed. The generalized allosteric model provides a consistent framework in understanding signal integration and differentiation in bacterial chemotaxis. It should also be useful for studying the functions of other heterogeneous receptor complexes.
The Fallopian tubes in domestic mammals: how vital is their physiological activity? (2005)

Set in an historical perspective, this essay examines diverse physiological aspects of Fallopian tube function in domestic animals and man. Microsurgical experiments are described that established the role of the isthmus in imposing a sperm gradient up to the site of fertilisation. Resection of the isthmus followed by reanastomosis of the remaining portions of the tube generated a high incidence of polyspermy in mated animals. Scanning electron microscopy and surgical studies revealed that spermatozoa were arrested and stored in the caudal portion of the isthmus before ovulation, the so-called functional sperm reservoir. There were specific adhesion contacts between the sperm head and endosalpingeal microvilli or cilia. Further experiments indicated that very large numbers of competent spermatozoa could be released from pre-ovulatory binding by microinjections of a solution of progesterone in oil under the serosal layer of the tube: when suitably timed, such treatment led to a high incidence of polyspermic fertilisation. Avid sperm binding in the caudal isthmus before ovulation prevents myosalpingeal activity leading to abnormal fertilisation, as might occur with multiple mating. Temperatures in the reproductive system were assessed and the caudal isthmus was found to be cooler than the ampulla during the pre-ovulatory phase of sperm storage. Finally, the existence of fluid microenvironments within the Fallopian tubes was reported, and the role of suspended cumulus-corona cells in amplifying signals from the zygote examined. An impact of Fallopian tube fluids on embryonic gene expression was also considered--an influence that may be further imposed if such fluids have access to the uterine lumen.
Role of anti-C1q autoantibodies in the pathogenesis of lupus nephritis (2005)

Anti-C1q autoantibodies can be found in the sera of patients with several autoimmune diseases, but also in healthy individuals. Although these anti-C1q autoantibodies were already identified several decades ago, they still puzzle both immunologists and nephrologists. The main reason for this puzzling effect are observations that seemed to indicate quite clearly that anti-C1q should be pathogenic to the kidney and the observation on the other hand that anti-C1q autoantibodies can be found in several disease conditions, as well as in healthy individuals, and are then unrelated to overt renal inflammation. This puzzle is the focus of the current review, which will provide an overview of the historical data, define the clinical interests and, importantly, will try to put several aspects in perspective based on recent observations in patients and in murine models. In addition, the paper will discuss therapeutic intervention possibilities regarding anti-C1q-mediated damage in systemic lupus erythematosus, as well as the therapeutic potential of anti-C1q antibodies in other conditions.
Method of achieving phase delay with wide optical bandwidth in multimode interference devices (1998)

A completely passive method of achieving phase delays inside multimode interference devices is presented. The desired relative phase is obtained by adjustment of the width of the waveguides in conjunction with the tapers to avoid interference inside the multimode section. One can generally apply the delay lines to avoid the use of active elements, and they are less sensitive to changes in wavelength than the traditional method with bends. Using this method, we have designed and analyzed a zero-to-one mode converter. The converter exhibits minimum excess loss of 0.100 and 0.102 for TE and TM polarization, respectively. A very large 1-dB bandwidth exceeding 350 nm is achieved.
Transient increase in systemic interferences in the superficial layer and its influence on event-related motor tasks: a functional near-infrared spectroscopy study (2017)

Functional near-infrared spectroscopy (fNIRS) is a widely utilized neuroimaging tool in fundamental neuroscience research and clinical investigation. Previous research has revealed that task-evoked systemic artifacts mainly originating from the superficial-tissue may preclude the identification of cerebral activation during a given task. We examined the influence of such artifacts on event-related brain activity during a brisk squeezing movement. We estimated task-evoked superficial-tissue hemodynamics from short source–detector distance channels (15 mm) by applying principal component analysis. The estimated superficial-tissue hemodynamics exhibited temporal profiles similar to the canonical cerebral hemodynamic model. Importantly, this task-evoked profile was also observed in data from a block design motor experiment, suggesting a transient increase in superficial-tissue hemodynamics occurs following motor behavior, irrespective of task design. We also confirmed that estimation of event-related cerebral hemodynamics was improved by a simple superficial-tissue hemodynamic artifact removal process using 15-mm short distance channels, compared to the results when no artifact removal was applied. Thus, our results elucidate task design-independent characteristics of superficial-tissue hemodynamics and highlight the need for the application of superficial-tissue hemodynamic artifact removal methods when analyzing fNIRS data obtained during event-related motor tasks.
System-Theoretic Analysis of a Class of Battery Equalization Systems: Mathematical Modeling and Performance Evaluation (2014)

Battery equalizers are widely used in multi-battery systems to maintain balanced charge among individual battery cells. While the research on the hardware realization of battery equalizers has received significant attention, rigorous analysis of the battery equalization process at the system level remains largely unexplored. In this paper, we study three types of battery equalization system structures: series-based, layer-based, and module-based. Specifically, we derive mathematical models that describe the system-level behavior of the battery equalization processes under these equalization structures. Then, based on the mathematical models, analytical methods are developed to evaluate the performance of the equalization processes. In addition, we carry out statistical analysis to compare the performance of the three equalization structures considered.
Phone Rate and the Effective Planning Time Hypothesis of Stuttering (1979)

Effects on syllable disfluency and phone rate (duration of phones spoken per minute) were compared in 19 adult stutterers under three reading rate conditions: control; slow normally-spoken-word-syllable timed (WS); and phone-prolongation (PP) matched to WS in syllable rate. Both phone rate and syllable disfluency were progressively reduced from control to WS to PP conditions. These results strongly support the discoordination hypothesis that any condition which facilitates initiation of phonation in coordination with articulation and respiration will reduce stuttering. A broader hypothesis is that effective planning time for voice onset coordinations is the common element that explains the power of retarded phone rate, reduction of phonatory complexity, and rhythm virtually to eliminate stuttering.
Dispersion relations for cylindrical waveguides with metamaterial linings (2008)

The dispersion relations for waves in a cylindrical waveguide with a lining of DNG material are examined for the case where both the permittivity and the permeability of the material are frequency dependent. Comparisons are made with the simpler configuration of a parallel-plate waveguide with a similar lining.
Development and Integration of Automated Systems Aimed to the Comfort of Seniors and People with Disabilities (2012)

This paper discusses the proposed methodology for developing a doctoral research project named "Development and integration of automated systems aimed to the comfort of seniors and people with disabilities". The main idea is to design an audio signal acquisition system using ambient microphones to permit older and disabilities persons to control the home devices using speech commands.
Novel helper phage design: intergenic region affects the assembly of bacteriophages and the size of antibody libraries (1995)

Phagemid vectors for display of proteins/peptides on the surface of filamentous phage utilize a plasmid genome carrying the phage origin of replication, along with the gene fused to a fragment of gene III. Generation of phage particles displaying the fusion protein also requires superinfection of the host bacterium with a helper virus. We describe here the construction of a new gene III mutant of M13 KO7 bacteriophage and compare its ability to act as helper phage with two mutants derived from Fd tet (fKN 16 and fCA 55). Furthermore, we investigate their capability to act as helper phages in SAP selection, where non-infectious helper phage, expressing antibody fragments but not protein 3, can still infect by first reacting with a soluble antigen-protein 3 fusion protein. Gene III mutants were found to be non-infectious, and high titers of infective particles were obtained only when the helper phage was grown in cells harbouring a gene III-containing plasmid. An amplification of the phage titer of 106 × was achieved in M13-derived phages, when used for the selection of specific antibody fragments.
Aggregation of blood platelets in static magnetic fields (2000)

We investigated the effects of intense magnetic fields on the blood platelet aggregation process with and without static magnetic fields of up to 14 T. A rabbit plasma and collagen mixture was used as the model system for a wounded blood vessel. Platelet aggregation was activated by the stimulation of acid soluble collagen. The platelet aggregates in strong magnetic fields were larger than the aggregates in an ambient field. An optical transmission of blood plasma during platelet aggregation also indicated that strong magnetic fields enhanced blood platelet aggregation in plasma.
Buffer-Aware and Traffic-Dependent Packet Scheduling in Wireless OFDM Networks (2007)

Most current research on wireless packet scheduling assumes infinite buffer space and fixed packet length, which is impractical for real systems. In this paper, the authors propose a practical packet scheduling algorithm for wireless packet-switched OFDM systems, called buffer-aware and traffic-dependent (BATD) scheduler, which consists of two interactive parts: PHY-layer adaptive modulation and coding (AMC) technology on each subcarrier and MAC-layer opportunistic scheduling. Aiming at decreasing the buffer overflow probability while keeping the system throughput as large as possible, the scheduling decision is made based on the information of not only channel conditions but also buffer status as well as traffic characteristics. In addition, the scheduler is able to guarantee certain fairness among users by introducing the so-called "history service function". Simulation results show that under practical constraints of finite buffer space and variable packet length, the proposed algorithm outperforms traditional packet scheduling schemes significantly in terms of packet loss rate due to buffer overflow and the total system throughput.
Synthesis and Photoluminescence of Nanocrystalline ZnS:Mn<sup>2+</sup> (2001)

The influence of the synthesis conditions on the properties of nanocrystalline ZnS:Mn2+ is discussed. Different Mn2+ precursors and different ratios of the precursor concentrations [S2-]/[Zn2+] were used. The type of Mn2+ precursor does not have an effect on the luminescence properties in the synthesis method described. On going from an excess of [Zn2+] to an excess of [S2-] during the synthesis, the particle diameter increases from 3.7 to 5.1 nm, which is reflected by a change in the luminescence properties. Photoluminescence measurements also showed the absence of the ZnS defect luminescence around 450 nm when an excess [S2-] is used during the synthesis. This effect is explained by the filling of sulfur vacancies. The ZnS luminescence is quenched with an activation energy of 62 meV, which is assigned to the detrapping of a bound hole from such a vacancy.
C−X···H Contacts in Biomolecular Systems: How They Contribute to Protein−Ligand Binding Affinity (2009)

The hydrogen bond acceptor capability of halogens has long been underappreciated in the field of biology. In this work, we have surveyed structures of protein complexes with halogenated ligands to characterize geometrical preferences of C−X···H contacts and contributions of such interactions to protein−ligand binding affinity. Notably, F···H interactions in biomolecules exhibit a remarkably different behavior as compared to three other kinds of X···H (X = Cl, Br, I) interactions, which has been rationalized by means of ab initio calculations using simple model systems. The C−X···H contacts in biological systems are characterized as weak hydrogen bonding interactions. Furthermore, the electrophile “head on” and nucleophile “side on” interactions of halogens have been extensively investigated through the examination of interactions in protein structures and a two-layer ONIOM-based QM/MM method. In biomolecular systems, C−X···H contacts are recognized as secondary interaction contributions to C−X···O halogen bonds that play important roles in conferring specificity and affinity for halogenated ligands. The results presented here are within the context of their potential applications in drug design, including relevance to the development of accurate force fields for halogens.
An electrochemical study of pentlandite leaching in sulfuric acid (1999)

The electrochemical characteristics of pentlandite leaching in acidic solutions were studied using carbon paste electrodes. At high overpotentials, pentlandite is readily oxidised to form nickel, iron and sulfate ions. This is the reaction which occurs during a highly oxidative process, such as the pressure leaching stage of the Outokumpu process. However at low overpotentials, pentlandite is oxidised to form nickel and iron ions and elemental sulfur. This is the basis of atmospheric oxygen leaching processes. Under these conditions, the formation of a coherent layer of sulfur can block the surface, and thus stop the leaching process. The addition of chloride ions can partially overcome this problem, and it is believed that the role of the chloride is to modify the morphology of the elemental sulfur.
Solubilization of Native Actin Monomers from Human Erythrocyte Membranes (1986)

Up to 50% of the actin in erythrocyte membranes can be solubilized at low ionic strength in a form capable of inhibiting DNAse I, in the presence of 0.4 mM ATP and 0.05 mM calcium. In the absence of calcium and ATP, actin is released but is apparently rapidly denatured. Solubilization of G-actin increases with temperature up to 37 degrees C. At higher temperatures, actin is released rapidly but quickly loses its ability to inhibit DNAse I.
Antioxidative factors in milk (2000)

Lipid auto-oxidation in milk is affected by a complex interplay of pro- and antioxidants. Several of these compounds are also important nutrients in the human diet and may have other physiological effects in the gastrointestinal tract and other tissues. Among antioxidative enzymes superoxide dismutase catalyses the dismutation of superoxide anion to hydrogen peroxide. The degradation of hydrogen peroxide can be catalysed by catalase and the selenoprotein glutathione peroxidase. The latter enzyme can also degrade lipid peroxides. Lactoferrin may have an important role by binding pro-oxidative iron ions. The occurrence of different forms of these antioxidative proteins in milk and available data on their functional role are reviewed. More remains to be learnt of individual compounds and as an example the potential role of seleno compounds in milk is virtually unknown. Antioxidative vitamins in milk can provide an important contribution to the daily dietary intake. Moreover vitamin E and carotenoids act as fat-soluble antioxidants, e.g. in the milk fat globule membrane, which is regarded as a major site of auto-oxidation. Vitamin C is an important water-soluble antioxidant and interacts in a complex manner with iron and fat-soluble antioxidants. The concentrations of these compounds in milk are affected by cow feeding rations and milk storage conditions. Since milk contains a number of antioxidants many reactions are possible and the specific function of each antioxidant cannot easily be defined. There are indications that other compounds may have antioxidative function and measurement of total antioxidative capacity should be a useful tool in evaluating their relative roles.