gebhart/patrepeval huggingface dataset:
Molecular Similarity in Medicinal Chemistry (2013)

Similarity is a subjective and multifaceted concept, regardless of whether compounds or any other objects are considered. Despite its intrinsically subjective nature, attempts to quantify the similarity of compounds have a long history in chemical informatics and drug discovery. Many computational methods employ similarity measures to identify new compounds for pharmaceutical research. However, chemoinformaticians and medicinal chemists typically perceive similarity in different ways. Similarity methods and numerical readouts of similarity calculations are probably among the most misunderstood computational approaches in medicinal chemistry. Herein, we evaluate different similarity concepts, highlight key aspects of molecular similarity analysis, and address some potential misunderstandings. In addition, a number of practical aspects concerning similarity calculations are discussed.
Electron velocity in Si and GaAs at very high electric fields (1980)

A microwave time-of-flight technique was used to measure the drift velocity of electrons in thin Si and GaAs epitaxial layers at very high electric fields. The room-temperature velocity-field characteristic is reported for silicon at fields up to 130 kV/cm, and for GaAs at fields up to 215 kV/cm.
Hybrid structure of zinc oxide nanorods and three dimensional graphene foam for supercapacitor and electrochemical sensor applications (2012)

A hybrid structure of zinc oxide (ZnO) on three dimensional (3D) graphene foam has been synthesized by chemical vapor deposition (CVD) growth of graphene followed by a facial in situ precipitation of ZnO nanorods under hydrothermal conditions. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) are used to characterize the morphology and structure of graphene/ZnO hybrids. The results show that the ZnO nanorods have high crystallinity and cluster uniformly on graphene skeleton to form flower-like nanostructures. Serving as a free-standing electrode, the electrochemical and biosensing performance of graphene/ZnO hybrids are studied by cyclic voltammetry, electrochemical impedance spectroscopy, galvanostatic charge–discharge and amperometric measurements. It is found that the graphene/ZnO hybrids display superior capacitive performance with high specific capacitance (∼400 F g−1) as well as excellent cycle life, making them suitable for high-performance energy storage applications. Furthermore, the graphene/ZnO hybrids exhibit high sensitivity for detection of [Fe(CN)6]3+ and dopamine, with the extrapolated lower detection limits of ∼1.0 μM and ∼10.0 nM respectively. These results demonstrate the potential of free-standing graphene/ZnO hybrid electrodes for the development of highly sensitive electrochemical sensors.
Plant Fiber Formation: State of the Art, Recent and Expected Progress, and Open Questions (2012)

Plant fibers are one of the most important renewable resources, used as raw material in the paper industry, and for various textiles and for composites. Fibers are structural components in timber and an energy-rich component of fuel-wood. For the plant itself, fibers are important in establishing plant architecture, as a source of mechanical support, in defence from herbivory, and in some cases as elements with contractile properties, resembling those of muscles. In addition, fibers may store ergastic carbon resources and water. Here, we review various aspects of fiber development such as initiation, elongation, cell wall formation and multinuclearity, discuss open questions and propose directions for further research. Most of the recent progress in fiber formation biology, especially in cell wall structure and chemistry, emerged from studies of only a few model plants including flax, Populus spp., Eucalyptus spp., Arabidopsis thaliana and hemp. Considering the enormous importance of fibers to humanity, it is surprising how little is known about the biology of fiber formation.
Inhibiting histone deacetylases suppresses glucose metabolism and hepatocellular carcinoma growth by restoring FBP1 expression (2017)

Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers in the world. Elevated glucose metabolism in the availability of oxygen, a phenomenon called the Warburg effect, is important for cancer cell growth. Fructose-1,6-bisphosphatase (FBP1) is a rate-limiting enzyme in gluconeogenesis and is frequently lost in various types of cancer. Here, we demonstrated that expression of FBP1 was downregulated in HCC patient specimens and decreased expression of FBP1 associated with poor prognosis. Low expression of FBP1 correlated with high levels of histone deacetylase 1 (HDAC1) and HDAC2 proteins in HCC patient tissues. Treatment of HCC cells with HDAC inhibitors or knockdown of HDAC1 and/or HDAC2 restored FBP1 expression and inhibited HCC cell growth. HDAC-mediated suppression of FBP1 expression correlated with decreased histone H3 lysine 27 acetylation (H3K27Ac) in the FBP1 enhancer. Restored expression of FBP1 decreased glucose reduction and lactate secretion and inhibited HCC cell growth in vitro and tumor growth in mice. Our data reveal that loss of FBP1 due to histone deacetylation associates with poor prognosis of HCC and restored FBP1 expression by HDAC inhibitors suppresses HCC growth. Our findings suggest that repression of FBP1 by HDACs has important implications for HCC prognosis and treatment.
On the expressive power of the bounded iteration construct (1989)

The bounded-iteration construct foreach x in Rjp do t od is very commonly used in database programming, due to the fact that database programs are dominated by data retrieval and manipulation tasks rather than by complex computations. Hence in database programming language design, it is important to understand the expressive power of the bounded-iteration construct and its relationship with other language constructs. We study the boundediteration construct within the context of a simple database programming language called the iterative transaction language. The language is shown to have NPTIME expressive power, and the deterministic subclass of it has PTIME expressive power, without any extra machineries or restrictions. We show that the bounded-iteration construct is essential for achieving this expressiveness, by characterizing its relationship with other constructs in the language. We also identify another natural subclass of iterative transactions called first-order transactions w...
The Novel Approach to the Protein Design: Active Truncated Forms of Human 1-CYS Peroxiredoxin (2007)

The object of the present study is the verification of a new approach to the design of the active truncated forms of enzymes. The method is based on a new way of investigating the protein sequences--the ANalysis of Informational Structure (ANIS). The analysis of informational structure allows to determine the hierarchically organized structures (IDIC-trees) formed by the sites with the Increased Degree of Informational Coordination between residues. The proposed approach involves the consequent removal of the fragments corresponding to the individual IDIC-trees from the wild-type enzyme sequences. The described procedure was applied to the design of the active truncated form of human 1-CYS peroxiredoxin (PrxVI). Two variants of the PrxVI truncated sequences were proposed according to ANIS method. These truncated forms of the enzyme were expressed in E. coli and purified. The respective antioxidant activities were measured. It was shown that one of the truncated recombinant proteins retains more than 90% of the wild-type PrxVI enzymatic activity. According to the results of our study we can assume that ANIS method can be an effective tool for the design of the active truncated forms of the enzymes or the chimeric proteins which combine the enzymatic activities of their wild-type prototypes.
Multiferroic<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>M</mml:mi></mml:math>-Type Hexaferrites with a Room-Temperature Conical State and Magnetically Controllable Spin Helicity (2010)

Magnetic and magnetoelectric (ME) properties have been studied for single crystals of Sc-doped M-type barium hexaferrites. Magnetization (M) and neutron diffraction measurements revealed that by tuning Sc concentration a longitudinal conical state is stabilized up to above room temperatures. ME measurements have shown that a transverse magnetic field (H) can induce electric polarization (P) at lower temperatures and that the spin helicity is nonvolatile and endurable up to near the conical magnetic transition temperature. It was also revealed that the response (reversal or retention) of the P vector upon the reversal of M varies with temperature. In turn, this feature allows us to control the relation between the spin helicity and the M vectors with H and temperature.
A Synthetic Binder of Breast Cancer Stem Cells (2018)

Cancer stem cells (CSCs) are associated with drug resistance, metastasis and recurrence of cancer. A synthetic binder of CSCs can provide a valuable tool to study the biology of CSCs and a lead to develop imaging, diagnostic and therapeutic agents targeting CSCs. Herein, a synthetic ligand (1) that specifically binds to CSCs over non-CSCs of breast cancer cells was identified for the first time via a cell-binding screening of a chemical library. The ligand 1 showed specific binding to CD24<sup>-</sup> /CD44<sup>+</sup> /ALDH<sup>+</sup> CSC population of MCF-7 and MDA-MB-231. We have demonstrated that 1-immobilized beads can be used as matrices for affinity isolation of 1-binding CSC population from breast cancer cells. The 1-binding population showed significantly increased expressions of stemness-associated transcription factors. Importantly, the 1-binding population demonstrated accelerated tumor growth in vivo, and the resulting tumor displayed an increased migratory activity and high expressions of CSC markers.
Spinal cord compression and dorsal root injury cause up‐regulation of activating transcription factor‐3 in large‐diameter dorsal root ganglion neurons (2005)

Spinal cord injury causes damage to ascending and descending tracts, as well as to local circuits, but relatively little is known about the effect of such injury on sensory neurons located within adjoining ganglia. We have therefore used immunocytochemistry for activating transcription factor-3 (ATF3), a sensitive marker of axonal damage, in order to examine the effects of spinal cord injury in rats on dorsal root ganglion (DRG) neurons. A 50-g static compression injury applied to the dorsal surface of the T12 thoracic spinal cord led to an up-regulation of ATF3 that was maximal at 1 day and affected 12-14% of DRG neurons in ganglia caudal to the injury (T13-L3). A similar response was seen after a T12 hemisection that transected the dorsal columns except that compression injury, but not hemisection, also evoked ATF3 expression in ganglia just rostral to the injury (T10, T11). ATF3 was up-regulated exclusively in DRG neurons that were of large diameter and immunoreactive for heavy neurofilament. Small-diameter cells, including the population that binds the lectin Grifffonia simplicifolia IB4, did not express ATF3 immunoreactivity. A similar pattern of ATF3 expression was induced by dorsal rhizotomy. The data show for the first time that ATF3 is up-regulated after spinal cord and dorsal root injury, but that this up-regulation is confined to the large-diameter cell population.
Vitamin B2 (riboflavin) and a mixture of vitamin B2 and C affects MMC efficiency in aerated media under irradiation. (2005)

Vitamin B2 (Riboflavin) acts as a strong radiation protecting agent in Escherichia coli bacteria (AB1157) in aerated media. This ability is reinforced by the addition of vitamin C. Under the influence of gamma-radiation, vitamin B2 completely suppresses the cytostatic activity of mitomycin C (MMC). In the presence of both vitamins, B2 and C, MMC is converted from an efficient cytostatic to a rather strong radiation protecting agent. This effect opens a new pathway for specific protection of normal mammalian cells (with a high O2-content) under treatment with ionizing radiation.
Bilateral Dorsal Cochlear Nucleus Lesions Prevent Acoustic-Trauma Induced Tinnitus in an Animal Model (2011)

Animal experiments suggest that chronic tinnitus ("ringing in the ears") may result from processes that overcompensate for lost afferent input. Abnormally elevated spontaneous neural activity has been found in the dorsal cochlear nucleus (DCN) of animals with psychophysical evidence of tinnitus. However, it has also been reported that DCN ablation fails to reduce established tinnitus. Since other auditory areas have been implicated in tinnitus, the role of the DCN is unresolved. The apparently conflicting electrophysiological and lesion data can be reconciled if the DCN serves as a necessary trigger zone rather than a chronic generator of tinnitus. The present experiment used lesion procedures identical to those that failed to decrease pre-existing tinnitus. The exception was that lesions were done prior to tinnitus induction. Young adult rats were trained and tested using a psychophysical procedure shown to detect tinnitus. Tinnitus was induced by a single unilateral high-level noise exposure. Consistent with the trigger hypothesis, bilateral dorsal DCN lesions made before high-level noise exposure prevented the development of tinnitus. A protective effect stemming from disruption of the afferent pathway could not explain the outcome because unilateral lesions ipsilateral to the noise exposure did not prevent tinnitus and unilateral lesions contralateral to the noise exposure actually exacerbated the tinnitus. The DCN trigger mechanism may involve plastic circuits that, through loss of inhibition, or upregulation of excitation, increase spontaneous neural output to rostral areas such as the inferior colliculus. The increased drive could produce persistent pathological changes in the rostral areas, such as high-frequency bursting and decreased interspike variance, that comprise the chronic tinnitus signal.
Effects of histamine and related compounds on regional cerebralblood flow in rats (1999)

The effects of histamine and related compounds on regional cerebral blood flow (rCBF) in the hippocampus of conscious rats were studied. Intracerebroventricular injection of histamine caused a dose-dependent increase in rCBF in the hippocampus, and similar findings were observed with not only the H1 agonist, 2-thiazolylethylamine, but also the H2 agonist, dimaprit. Intraperitoneal injection of L-histidine also resulted in an increase in rCBF in the hippocampus, in parallel with elevation of histamine content in the brain. The increase in rCBF in the hippocampus induced by L-histidine was antagonized by both H1 and H2 antagonists (diphenhydramine, pyrilamine and zolantidine). In addition, when both antagonists were injected simultaneously, an additive effect was observed in antagonism of the L-histidine-induced increase in rCBF. L-Histidine caused no marked changes in blood pressure even at a dose of 1,500 mg/kg, which showed an increase in rCBF in the hippocampus. These results indicate that histamine elicited an increase in rCBF via both H1 and H2 receptors.
The Combined Effect of Chemical reaction, Radiation, MHD on Mixed Convection Heat and Mass Transfer Along a Vertical Moving Surface (2010)

This paper discusses the effect of Chemical reaction, Radiation and MHD on laminar mixed convection boundary layer flow and heat and mass transfer on continuously moving vertical surface. The fluid viscosity is assumed to vary as an inverse linear function of temperature and local similarity solutions are obtained for the boundary layer equations subject to isothermally moving vertical surface with uniform speed. The system of non-linear partial differential equations developed in the process is finally transformed into a set of ordinary differential equations with the help of similarity transformations involved in the problem. This set of equations is for different values of the various parameters. The results showing the effect of physical parameters on velocity, temperature and concentration have been computed and presented graphically to discuss their in details.
Variation in Positive Selection in Termite GNBPs and Relish (2005)

Social insects are model organisms for investigating molecular evolution in the innate immune system. Their diversity affords comparative analysis among closely related species, and group living is likely to contribute to the pathogen stress imposed on the immune system. We used different models of nucleotide substitution at nonsynonymous (amino acid altering) and synonymous (silent) sites to compare the different levels and type of selection among three immunity genes in 13 Australian termite species (Nasutitermes). The immunity genes include two encoding pathogen recognition proteins (gram-negative bacterial-binding proteins) that duplicated and diverged before or soon after the evolution of the termites and a transcription factor (Relish), which induces the production of antimicrobial peptides. A comparison of evolutionary models that assign four unrestricted classes of dN/dS (the ratio of the nonsynonymous to synonymous substitution rate) to different Nasutitermes lineages revealed that the occurrence of positive selection (dN/dS > 1) varies among lineages and the three genes. Positive selection appears to have driven the evolution of all three genes in an ancestral lineage of three subterranean termites. It had previously been suggested that there was a transition along this ancestral lineage to termite morphology and ecology associated with a diet of decayed wood, a diet that may expose termites to elevated levels of fungal and bacterial pathogens. Relish appears to have experienced the highest levels of selective pressure for change among all three genes. Positively selected sites in the molecule are located in regions that are important for its activation, which suggests that amino acid substitutions at these sites are a counter response to pathogen mechanisms that disrupt the activation of Relish.
Detection of antibodies to Cowdria ruminantium in the serum of domestic ruminants by indirect ELISA. (1993)

A solid phase enzyme immunoassay for the detection of antibodies to Cowdria ruminantium in the serum of domestic ruminants was developed by using microorganisms cultivated on bovine umbilical endothelial cells as antigen. When the culture showed 90% lysis, the supernatant was centrifuged, sonicated and coated on polystyrene microtiter plates. Antibodies were detected as early as 9 days after experimental immunization of goats. The sensitivity of the ELISA calculated with 73 ruminant sera ranged between 97.3% and 98.6%. The overall specificity of the test was 97% (N = 2925). However, the specificity was far lower for sheep (94.4%, N = 881) than for goats (98.6%, N = 651) and cattle (97.8%, N = 1393). Crossreactivity which could explain some of the false positive reactions, was found between Cowdria antigen and sera raised against Ehrlichia bovis (1 bovine positive out of 2 inoculated) or E. ovina (2 sheep out of 2 inoculated became positive) but not with E. phagocytophila. The intra-assay and inter-assay variability were 7.5% and 7.8% respectively, indicating a good reproducibility of the ELISA.
Sensors and analytical chemistry (2003)

Instrumental analytical chemistry and chemical sensors, especially biosensors have made remarkable progress in the last decade. With respect to the analytical chemical performance characteristics the sensitivities could be increased drastically. However, the very important comparability of trace and ultra-trace analytical data produced in different laboratories has not been improved to the same degree. The analytical chemical performance characteristics of chemical and biochemical sensors must be judged with those facts in mind when they are validated using such traditional instrumental reference methods. Biosensors based on immune-chemical principles are more versatile in allowing nearly every analyte to be determined and are therefore chosen for this progress report. A recently developed calibration free optical single-use “immuno-chip” is described. This low-cost chip is based on an evanescence field fluorescence detection. The same technique and can also be used for a real-time recording of DNA hybridisation and dissociation events. Multi-analyte devices and DNA-arrays based on this technological platform were developed using a fast kinetic evaluation method. This offers certain advantages to methods detecting only the endpoint of a molecular association reaction especially concerning the detection of mismatches (SNP detection). Finally, a novel and relatively simple micro-electrochemical method based on a microelectrode array in combination with receptor-functionalized magnetic latex beads and an indicating redox system is described which bears in it an alternative to atomic force microscope binding forces measurements. Depending of the numer of individually addressable microelectrodes this method allows the simultaneous study of several hundred to thousands of molecule–molecule interactions within seconds. In addition, a single molecule detection and nearly unlimited multi-analyte, ultra-trace immuno-chemical sensing capabilities seem possible.
Construction of weighted finite state transducers for very wide context-dependent acoustic models (2005)

A previous paper by the authors described an algorithm for efficient construction of weighted finite state transducers for speech recognition when high-order context-dependent models of order K > 3 (triphones) with tied state observation distributions are used, and showed practical application of the algorithm up to K = 5 (quinphones). In this paper we give additional details of the improved implementation and analyze the algorithm's practical runtime requirements and memory footprint for context-orders up to K = 13 (+/-6 phones context) when building fully cross-word capable WFSTs for large vocabulary speech recognition tasks. We show that for typical systems it is possible to use any practical context-order K les 13 without having to fear an exponential explosion of the search space, since the necessary state ID to phone transducer (resembling a phone-loop observing all possible K-phone constraints) can be built in a few minutes at most. The paper also gives some implementation details of how we efficiently collect context statistics and build phonetic decision trees for very wide context-dependent acoustic models
A parallel and area-efficient architecture for deblocking filter and Adaptive Loop Filter (2011)

Adaptive Loop Filter (ALF) has been developed lately to improve the video coding performance. It is inserted between deblocking and inter-prediction, which makes deblocking and ALF very time-critical because they are conducted sequentially. In this paper, we propose an efficient architecture integrating deblocking and ALF for the decoder. The architecture not only implements deblocking and ALF in parallel but also reduces area cost as much as possible. These are achieved by shared hybrid organized memory architecture and one-block-two-edge parallel strategy using a novel filter order. The proposed architecture is implemented in verilog HDL and can achieve real-time decoding for 1080p @ 30 fps applications by working at 211MHz in a Xilinx Virtex-5 FPGA.