gebhart/patrepeval huggingface dataset:
Improving Gil-Werman algorithm for running min and max filters (1997)

The current best bound on the number of comparison operations needed to compute the running maximum or minimum over a p-element sliding data window is approximately three comparisons per output sample. This bound is probabilistic for some algorithms and is derived for their complexities on the average for independent, identically distributed (i.i.d.) input signals. The worst-case complexities of these algorithms are O(p). The worst-case complexity C/sub r/=3 -4/p comparisons per output sample for 1D signals is achieved in the Gil-Werman algorithm (1993). In this correspondence we propose a modification of the Gil-Werman algorithm with the same worst-case complexity but with a lower average complexity. A theoretical analysis shows that using the proposed modification the complexities of sliding max or min 1D and 2D filters over i.i.d. signals are reduced to C/sub 1/=2.5-3.5/p+1/p/sup 2/ and C/sub 2/=5-7/p+2/p/sup 2/ comparisons per output sample on the average, respectively. Simulations confirm the theoretical results. Moreover, experiments show that even for highly correlated data, namely, for real images the behavior of the algorithm remains the same as for i.i.d. signals.
Recombinant soluble human tissue factor secreted by Saccharomyces cerevisiae and refolded from Escherichia coli inclusion bodies: glycosylation of mutants, activity and physical characterization (1995)

Tissue factor (TF) is the cell-surface transmembrane receptor that initiates both the extrinsic and intrinsic blood coagulation cascades. The abilities of TF to associate with Factor VIIa and Factor X in a ternary complex and to enable proteolytic activation of Factor X by Factor VIIa reside in the extracellular domain of TF. We describe the expression of the surface domain of TF (truncated TF, tTF) in both Saccharomyces cerevisiae and Escherichia coli and the biochemical and physical characterization of the recombinant proteins. Wild-type tTF and several glycosylation-site mutants were secreted efficiently by S. cerevisiae under the control of the yeast prepro-alpha-signal sequence; the T13A,N137D double mutant was the most homogeneous variant expressed in milligram quantities. Wild-type tTF was expressed in a non-native state in E. coli inclusion bodies as a fusion protein with a poly(His) leader. The fusion protein could be fully renatured and the leader removed by proteolysis with thrombin; the correct molecular mass (24,729 Da) of the purified protein was confirmed by electrospray mass spectrometry. Recombinant tTFs from yeast, E. coli and Chinese hamster ovary cells were identical in their abilities to bind Factor VIIa, to enhance the catalytic activity of Factor VIIa and to enhance the proteolytic activation of Factor X by Factor VIIa. Furthermore, CD, fluorescence emission and NMR spectra of the yeast and E. coli proteins indicated that these proteins are essentially identical structurally.
Diagnosis of lung cancer in primary care: a structured review (2004)

The UK Guidelines for referral of suspected lung cancer have a weak evidence base.
Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing (2013)

Next-generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next-generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.
eIF4 Initiation Factors: Effectors of mRNA Recruitment to Ribosomes and Regulators of Translation (1999)

Eukaryotic translation initiation factor 4F (eIF4F) is a protein complex that mediates recruitment of ribosomes to mRNA. This event is the rate-limiting step for translation under most circumstances and a primary target for translational control. Functions of the constituent proteins of eIF4F include recognition of the mRNA 5' cap structure (eIF4E), delivery of an RNA helicase to the 5' region (eIF4A), bridging of the mRNA and the ribosome (eIF4G), and circularization of the mRNA via interaction with poly(A)-binding protein (eIF4G). eIF4 activity is regulated by transcription, phosphorylation, inhibitory proteins, and proteolytic cleavage. Extracellular stimuli evoke changes in phosphorylation that influence eIF4F activity, especially through the phosphoinositide 3-kinase (PI3K) and Ras signaling pathways. Viral infection and cellular stresses also affect eIF4F function. The recent determination of the structure of eIF4E at atomic resolution has provided insight about how translation is initiated and regulated. Evidence suggests that eIF4F is also implicated in malignancy and apoptosis.
Probing the Structure of DNA−Carbon Nanotube Hybrids with Molecular Dynamics (2007)

DNA-carbon nanotube hybrids (DNA-CN) are novel nanoscale materials that consist of single-wall carbon nanotubes (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments on DNA-CN have shown that this material offers a remarkable set of technologically useful properties such as facilitation of SWCN sorting, chemical sensing, and detection of DNA hybridization. Despite the importance of DNA-CN, a detailed understanding of its microscopic structure and physical properties is lacking. To address this, we have performed classical all-atom molecular dynamics (MD) simulations exploring the self-assembly mechanisms, structure, and energetic properties of this nanomaterial. MD reveals that SWCN induces ssDNA to undergo a spontaneous conformational change that enables the hybrid to self-assemble via the pi-pi stacking interaction between ssDNA bases and SWCN sidewall. ssDNA is observed to spontaneously wrap about SWCN into compact right- or left-handed helices within a few nanoseconds. Helical wrapping is driven by electrostatic and torsional interactions within the sugar-phosphate backbone that result in ssDNA wrapping from the 3' end to the 5' end.
Identification of a novel bifunctional Δ12/Δ15 fatty acid desaturase from a basidiomycete, Coprinus cinereus TD#822‐2 (2007)

A new gene encoding a delta12 fatty acid desaturase-related protein was cloned from a multicellular basidiomycete Coprinus cinereus TD#822-2. The 1326 bp full-length gene, designated as Cop-odeA, codes for a putative protein of 442 amino acids with a MW of 49224. The Cop-odeA yeast transformant accumulated four new fatty acids identified as 9,12-hexadecadienoic acid, 9,12,15-hexadecatrienoic acid, linoleic acid, and alpha-linolenic acid, which comprised 8.8%, 1.0%, 29.0%, and 0.6% of the total fatty acids, respectively. The Cop-odeA protein was confirmed to be a novel bifunctional fatty acid desaturase with both high delta12 desaturase activity and unusual delta15 desaturase activity.
Image-based view synthesis by combining trilinear tensors and learning techniques (1997)

We present a new method for rendering novel images of flexible 3D objects from a small number of example images in correspondence. The strength of the method is the ability to synthesize images whose viewing position is significantly far away from the viewing cone of the example images ("view extrapolation"), yet without ever modeling the 3D structure of the scene. The method relies on synthesizing a chain of "trilinear tensors" that govems the warping function from the example images to the novel image, together with a multi-dimensional interpolation function that synthesizes the non-rigidmotions of the viewed object from the virtual camera position. We show that two closely spaced example images alone are sufficient in practice to synthesize a significant viewing cone, thus demonstrating the ability of representing an object by a relatively small number of model images -for the purpose of cheap and fast viewers that can run on standard hardware.
An evaluation of closed-loop control options for continuum manipulators (2012)

Continuum manipulators are gaining widespread acceptance in commercial robotics, particularly in the medical field, where their compliance allows a large benefit for patient safety. However, this compliance also makes precise position control of these manipulators quite difficult. This paper presents two closed-loop control implementations applied to a small scale continuum manipulator. These implementations are both based on manipulator tip position feedback from an electromagnetic sensor. The command tracking and disturbance rejection properties of the two control implementations are shown to be approximately equivalent, and provide improved position control when compared to open-loop control, without sacrificing system stability.
Six Networks on a Universal Neuromorphic Computing Substrate (2013)

In this study, we present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks. At the heart of this system lies a mixed-signal chip, with analog implementations of neurons and synapses and digital transmission of action potentials. Major advantages of this emulation device, which has been explicitly designed as a universal neural network emulator, are its inherent parallelism and high acceleration factor compared to conventional computers. Its configurability allows the realization of almost arbitrary network topologies and the use of widely varied neuronal and synaptic parameters. Fixed-pattern noise inherent to analog circuitry is reduced by calibration routines. An integrated development environment allows neuroscientists to operate the device without any prior knowledge of neuromorphic circuit design. As a showcase for the capabilities of the system, we describe the successful emulation of six different neural networks which cover a broad spectrum of both structure and functionality.
Near-infrared imaging spectroscopy for counterfeit drug detection (2011)

Pharmaceutical counterfeiting is a significant issue in the healthcare community as well as for the pharmaceutical
industry worldwide. The use of counterfeit medicines can result in treatment failure or even death. A rapid
screening technique such as near infrared (NIR) spectroscopy could aid in the search for and identification of
counterfeit drugs. This work presents a comparison of two laboratory NIR imaging systems and the chemometric
analysis of the acquired spectroscopic image data. The first imaging system utilizes a NIR liquid crystal tuneable
filter and is designed for the investigation of stationary objects. The second imaging system utilizes a NIR imaging
spectrograph and is designed for the fast analysis of moving objects on a conveyor belt. Several drugs in form of
tablets and capsules were analyzed. Spectral unmixing techniques were applied to the mixed reflectance spectra
to identify constituent parts of the investigated drugs. The results show that NIR spectroscopic imaging can be
used for contact-less detection and identification of a variety of counterfeit drugs.
Pivotal Advances: High-mobility group box 1 protein—a cytokine with a role in cardiac repair (2006)

The nuclear protein high-mobility group box 1 (HMGB1) has been largely characterized for its role in inflammation. However, HMGB1 released by inflammatory cells, as well as by necrotic cells, may also act as a signal of tissue damage and participate in tissue repair by recruiting stem cells to the injury site. The emergence of this function has focused the interest on HMGB1 as a molecule with an active role in tissue regeneration. We recently demonstrated that HMGB1 administration in a mouse model of myocardial infarction activates cardiac stem cells and promotes their differentiation into cardiomyocytes. The regenerative effect results in the improvement of cardiac function. In this review, we highlight the beneficial role of HMGB1 and discuss growth factor-based therapeutic approaches for the treatment of myocardial infarction.
Generation of Pancreatic Hormone-Expressing Islet-Like Cell Aggregates from Murine Adipose Tissue-Derived Stem Cells (2009)

The success of cell replacement therapy for diabetes depends on the availability and generation of an adequate number of islets, preferably from an autologous origin. Stem cells are now being probed for the generation of physiologically competent, insulin-producing cells. In this investigation, we explored the potential of adipose tissue-derived stem cells (ASCs) to differentiate into pancreatic hormone-expressing islet-like cell aggregates (ICAs). We initiated ASC culture from epididymal fat pads of Swiss albino mice to obtain mesenchymal cells, murine epididymal (mE)-ASCs. Subsequent single-cell cloning resulted in a homogeneous cell population with a CD29(+)CD44(+)Sca-1(+) surface antigen expression profile. We formulated a 10-day differentiation protocol to generate insulin-expressing ICAs from mE-ASCs by progressively changing the differentiation cocktail on day 1, day 3, and day 5. Our stage-specific approach successfully differentiated mesodermic mE-ASCs into definitive endoderm (cells expressing Sox17, Foxa2, GATA-4, and cytokeratin [CK]-19), then into pancreatic endoderm (cells expressing pancreatic and duodenal homeobox [PDX]-1, Ngn3, NeuroD, Pax4, and glucose transporter 2), and finally into cells expressing pancreatic hormones (insulin, glucagon, somatostatin). Fluorescence-activated cell sorting analysis showed that day 5 ICAs contained 64.84% +/- 7.03% PDX-1(+) cells, and in day 10 mature ICAs, 48.17% +/- 3% of cells expressed C-peptide. Day 10 ICAs released C-peptide in a glucose-dependent manner, exhibiting in vitro functionality. Electron microscopy of day 10 ICAs revealed the presence of numerous secretory granules within the cell cytoplasm. Calcium alginate-encapsulated day 10 ICAs (1,000-1,200), when transplanted i.p. into streptozotocin-induced diabetic mice, restored normoglycemia within 2 weeks. The data presented here demonstrate the feasibility of using ASCs as a source of autologous stem cells to differentiate into the pancreatic lineage.
Photoelectrocatalytic Water Splitting: Significance of Cocatalysts, Electrolyte, and Interfaces (2016)

The efficiency of photoelectrocatalytic (PEC) water splitting is limited by the serious recombination of photogenerated charges, high overpotential, and sluggish kinetics of surface reaction. Herein we describe the recent progress on engineering the electrode–electrolyte and semiconductor–cocatalyst interfaces with cocatalysts, electrolytes, and interfacial layers (interlayers) to increase the PEC efficiency. Introducing cocatalysts has been demonstrated to be the most efficient way to lower the reaction barrier and promote charge injection to the reactants. In addition, it has been found that electrolyte ions can influence the surface catalysis remarkably. Electrolyte cations on the surface can influence the water splitting and backward reactions, and anions may take part in the proton transfer processes, indicating that fine-tuning of the electrolyte parameters turns out to be an important strategy for enhancing the PEC efficiency. Moreover, careful modification of the interface between the cocatalysts and the semiconductor via suitable interlayers is critical for promoting charge separation and transfer, which can indirectly influence the surface catalysis. The mechanisms of surface catalysis are assumed to involve transfer of photogenerated holes to the surface active sites to form high-valent species, which then oxidize the water molecules. Many key scientific issues about the generation of photovoltage, the separation, storage, and transfer of carriers, the function of cocatalysts, the roles of electrolyte ions, and the influences of other parameters during PEC water splitting will be discussed in detail with some perspective views.
Pentafluorphenylioddifluorid: alternative Darstellungsmethoden, Molekülstruktur und Eigenschaften (2000)

Es wird die Darstellung von C6F5IF2 (1) aus C6F5I (2) durch oxidative Fluorierung mit ClF, CF3OCl, BrF5, C6F5BrF2 und C6F5BrF4 beschrieben. Höchste Reinheit und Ausbeute an 1 wurde durch eine modifizierte Tieftemperaturfluorierung mit F2 erhalten. Die Thermolyse von 1 lieferte Perfluoriodcyclohexadien-1,4 und Perfluoriodcyclohexen neben 2. Die Röntgenstrukturanalyse von 1 zeigt dessen Fluoriddonor- und Fluoridakzeptoreigenschaft. 1 wird spektroskopisch charakterisiert durch NMR (19F, 13C), IR und Ra. Diskutiert wird der Einfluß der Änderung der Oxidationszahl von Iod in 2, 1 und C6F5IF4 (3) auf strukturelle und spektroskopische Ergebnisse. Die Geometrien und Ladungsverteilungen im Energieminimum wurden für 1, 2 und verwandte Moleküle berechnet (RHF, LANL2DZ). Pentafluorophenyliodine(III) Compounds. 3 Pentafluorophenyliodinedifluoride: Alternative Preparations, Molecular Structure, and Properties The formation of C6F5IF2 (1) by oxidative fluorination of C6F5I (2) using ClF, CF3OCl, BrF5, C6F5BrF2, and C6F5BrF4 is described. Highest purity and yield of 1 was achieved by a modified low temperature fluorination with F2. Thermolysis of 1 delivered perfluoroiodocyclohexadiene-1,4 and perfluoroiodocyclohexene besides 2. X-ray structural analysis of 1 exhibits the fluoride donor and acceptor ability. 1 is spectroscopically characterized by NMR (19F, 13C), IR and Ra. The influence of the change in the oxidation number of iodine in 2, 1 and C6F5IF4 (3) on spectroscopic and structural results will be discussed. Minimum energy geometries and charge distributions are calculated (RHF, LANL2DZ) for 1, 2 and related compounds.
Wavefront Aberration of the Eye (1991)

The concept of monochromatic wavefront aberration is discussed in relation to ray aberration, and methods for its measurement in the case of the eye are described. Examples are given of the measured aberration in individual eyes: in general the aberration falls within the Rayleigh quarter-wavelength criterion for pupil diameters less than 2 to 3 mm but significantly degrades image quality for larger pupils. The use of wavefront data to explore both the modulation and phase transfer functions of the eye as a function of pupil diameter and focus is described, together with typical results. Potential applications to clinical problems such as the effects of contact lenses, intraocular implants, refractive surgery, and pathology on the optical quality of the eye are outlined.
Impaired neuropathic pain responses in mice lacking the chemokine receptor CCR2 (2003)

Mice lacking the chemokine receptor chemotactic cytokine receptor 2 (CCR2) have a marked attenuation of monocyte recruitment in response to various inflammatory stimuli and a reduction of inflammatory lesions in models of demyelinating disease. In the present study, we compared nociceptive responses in inflammatory and neuropathic models of pain in CCR2 knockout and wild-type mice. In acute pain tests, responses were equivalent in CCR2 knockout and wild-type mice. In models of inflammatory pain, CCR2 knockout mice showed a 70% reduction in phase 2 of the intraplantar formalin-evoked pain response but only a modest (20-30%) and nonsignificant reduction of mechanical allodynia after intraplantar Freund's adjuvant (CFA). In a model of neuropathic pain, the development of mechanical allodynia was totally abrogated in CCR2 knockout mice. CFA administration induced marked up-regulation of CCR2 mRNA in the skin and a moderate increase in the sciatic nerve and dorsal root ganglia (DRG). In response to nerve ligation, persistent and marked up-regulation of CCR2 mRNA was evident in the nerve and DRG. Disruption of Schwann cells in response to nerve lesion resulted in infiltration of CCR2-positive monocytes/macrophages not only to the neuroma but also to the DRG. Chronic pain also resulted in the appearance of activated CCR2-positive microglia in the spinal cord. Collectively, these data suggest that the recruitment and activation of macrophages and microglia peripherally and in neural tissue may contribute to both inflammatory and neuropathic pain states. Accordingly, blockade of the CCR2 receptor may provide a novel therapeutic modality for the treatment of chronic pain.
Prospects for immunotherapy of malignant disease (2003)

The majority of T cell-recognized tumour antigens in humans are encoded by genes that are also present in normal tissues. Low levels of gene expression in normal cells can lead to the inactivation of high-avidity T cells by immunological tolerance mechanisms. As a consequence, low-avidity T cell responses in patients are often inadequate in providing tumour protection. Recently, several technologies have been developed to overcome tolerance, allowing the isolation of high-affinity, HLA-restricted receptors specific for tumour-associated peptide epitopes. Furthermore, transfer of HLA-restricted antigen receptors provides an opportunity to empower patient T cells with new tumour-reactive specificities that cannot be retrieved from the autologous T cell repertoire.
Treatment of ovarian cancer by targeting the tumor stem cell-associated carbohydrate antigen, Sialyl-Thomsen-nouveau (2018)

Recurrent ovarian cancer (OvCa) is thought to result in part from the inability to eliminate rare quiescent cancer stem cells (CSCs) that survive cytotoxic chemotherapy and drive tumor resurgence. The Sialyl-Thomsen-nouveau antigen (STn) is a carbohydrate moiety present on protein markers of CSCs in pancreatic, colon, and gastric malignancies. We have demonstrated that human OvCa cell lines contain varying levels of cells that independently express either STn or the ovarian CSC marker CD133. Here we determine co-expression of STn and CD133 in a subset of human OvCa cell lines. Analyses of colony and sphere forming capacity and of response to standard-of-care cytotoxic therapy suggest a subset of OvCa STn<sup>+</sup> cells display some CSC features. The effect of the anti-STn antibody-drug conjugates (ADCs) S3F-CL-MMAE and 2G12-2B2-CL-MMAE on OvCa cell viability <i>in vitro</i> and <i>in vivo</i> was also assessed. Treatment with S3F-CL-MMAE reduced the viability of two of three OvCa cell lines <i>in vitro</i> and exposure to either S3F-CL-MMAE or 2G12-2B2-CL-MMAE reduced OVCAR3-derived xenograft volume <i>in vivo</i>, depleting STn<sup>+</sup> tumor cells. In summary, STn<sup>+</sup> cells demonstrate some stem-like properties and specific therapeutic targeting of STn in ovarian tumors may be an effective clinical strategy to eliminate both STn<sup>+</sup> CSC and STn<sup>+</sup> non-CSC populations.