gebhart/patrepeval huggingface dataset:
System calibration method for Fourier ptychographic microscopy (2017)

Fourier ptychographic microscopy (FPM) is a recently proposed computational imaging technique with both high-resolution and wide field of view. In current FPM imaging platforms, systematic error sources come from aberrations, light-emitting diode (LED) intensity fluctuation, parameter imperfections, and noise, all of which may severely corrupt the reconstruction results with similar artifacts. Therefore, it would be unlikely to distinguish the dominating error from these degraded reconstructions without any preknowledge. In addition, systematic error is generally a mixture of various error sources in the real situation, and it cannot be separated due to their mutual restriction and conversion. To this end, we report a system calibration procedure, termed SC-FPM, to calibrate the mixed systematic errors simultaneously from an overall perspective, based on the simulated annealing algorithm, the LED intensity correction method, the nonlinear regression process, and the adaptive step-size strategy, which involves the evaluation of an error metric at each iteration step, followed by the re-estimation of accurate parameters. The performance achieved both in simulations and experiments demonstrates that the proposed method outperforms other state-of-the-art algorithms. The reported system calibration scheme improves the robustness of FPM, relaxes the experiment conditions, and does not require any preknowledge, which makes the FPM more pragmatic.
A Region of Vitamin K-dependent Protein S That Binds to C4b Binding Protein (C4BP) Identified Using Bacteriophage Peptide Display Libraries (1997)

Vitamin K-dependent protein S, a blood coagulation inhibitor, interacts with the C4b-binding protein (C4BP) in human plasma with high affinity (KD = 0.1 nM). Identification of a portion of protein S that binds to C4BP has been approached using random libraries of 6- and 15-mer peptides displayed on bacteriophage surfaces. Bacteriophage binding to the beta-chain of C4BP were selected in several rounds of affinity purification with intervening amplification in E. coli. Homology searches of the affinity purified peptide sequences against protein S led to the identification of four regions in protein S that were similar to several of the selected peptides. These regions were synthesized as linear peptides and tested in inhibition experiments. Only one distinct peak (around position 450) was observed when the homology scores versus human protein S sequence were averaged over all affinity purified peptides. A synthetic peptide comprising residues 439-460 in human protein S was found to inhibit protein S binding to C4BP. The same result was found with two overlapping peptides (residues 447-468 and 435-468, respectively) in a second set of synthetic peptides. Direct binding of the peptides to C4BP was inferred from titrations monitored by recording the near UV circular dichroism spectra or the polarization of tryptophan fluorescence. The results suggest that residues 447-460 constitute a portion of protein S that is important for the interaction with C4BP. These findings may have implications for patients suffering from thrombosis, due to the lack of free protein S, by directing the design of drugs that disrupt protein S binding to C4BP.
Mice Lacking Ataxin-1 Display Learning Deficits and Decreased Hippocampal Paired-Pulse Facilitation (1998)

Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disorder characterized by ataxia, progressive motor deterioration, and loss of cerebellar Purkinje cells. To investigate SCA1 pathogenesis and to gain insight into the function of the SCA1 gene product ataxin-1, a novel protein without homology to previously described proteins, we generated mice with a targeted deletion in the murine Sca1 gene. Mice lacking ataxin-1 are viable, fertile, and do not show any evidence of ataxia or neurodegeneration. However, Sca1 null mice demonstrate decreased exploratory behavior, pronounced deficits in the spatial version of the Morris water maze test, and impaired performance on the rotating rod apparatus. Furthermore, neurophysiological studies performed in area CA1 of the hippocampus reveal decreased paired-pulse facilitation in Sca1 null mice, whereas long-term and post-tetanic potentiations are normal. These findings demonstrate that SCA1 is not caused by loss of function of ataxin-1 and point to the possible role of ataxin-1 in learning and memory.
The Molecular Basis of Celmer's Rules:  The Stereochemistry of the Condensation Step in Chain Extension on the Erythromycin Polyketide Synthase (1997)

Modular polyketide synthases (PKSs), for example, the 6-deoxyerythronolide B synthase (DEBS) responsible for synthesis of the aglycone core of the macrolide antibiotic erythromycin, generate an impressive diversity of asymmetric centers in their polyketide products. However, as noted by Celmer, macrolides have the same absolute configuration at all comparable stereocenters. Understanding how the stereochemistry of chain extension in controlled is therefore crucial to determining the common mechanism of action of these enzymes. We aimed to elucidate the molecular basis of Celmer's rules through in vitro studies with DEBS 1-TE, a bimodular derivative of DEBS from Saccharopolyspora erythraea, which uses (2S)-methylmalonyl-coenzyme. A to produce both D- and L-methyl centers in its triketide lactone product. We show here that condensation of (2S)-methylmalonyl-CoA in module 2 proceeds with decarboxylative inversion without cleavage of the C-H bond adjacent to the methyl group; in contrast, in module 1 the chain extension process involves loss of the hydrogen attached to C-2 of the methylmalonyl-CoA precursor. The production of the D-methyl center in module 2 without loss of hydrogen from the asymmetric center of the (2S)-methylmalonyl-CoA establishes that condensation takes place with inversion of configuration as in fatty acid biosynthesis. The loss of the key hydrogen from the (2S)-methylmalonyl-CoA to produce the L-methyl center generated in module 1 implies that an additional obligatory epimerization step takes place in that module. The nature and timing of the epimerization remain to be established.
The asialoglycoprotein receptor is a potential liver-specific receptor for Marburg virus (1995)

The liver is one of the main target organs of Marburg virus (MBG), a filovirus causing severe haemorrhagic fever with a high fatality rate in humans and non-human primates. MBG grown in certain cells does not contain neuraminic acid, but has terminal galactose on its surface glycoprotein. This observation indicated that the asialoglycoprotein receptor (ASGP-R) of hepatocytes may serve as a receptor for MBG in the liver. Binding studies revealed that the attachment of MBG to ASGP-R-expressing HepG2 cells, but not to ASGP-R-negative E6 Vero cells, has the characteristics of ligand binding to the ASGP-R: binding is dependent on calcium and is inhibited by excess asialofetuin and by anti-ASGP-R antiserum. Asialofetuin and the specific antiserum also inhibited MBG infection of HepG2 cells. In addition, it was shown that expression of ASGP-R cDNA in NIH 3T3 cells enhanced the susceptibility of these cells to MBG infection 4.5-fold. Interaction of MBG with the hepatic ASGP-R could thus explain the marked hepatotropism of the virus.
Use of Nondefective Adenovirus-Simian Virus 40 Hybrids for Mapping the Simian Virus 40 Genome (1973)

A series of viable recombinants between adenovirus 2 (Ad2) and simian virus 40 (SV40) (nondefective Ad2-SV40 hybrids) have been isolated. The members of this series (designated Ad2(+)ND(1) through Ad2(+)ND(5)) differ from one another in the early SV40-specific antigens and the SV40-specific RNA species which they induce in infected cells. They also contain different amounts of SV40 DNA as shown by RNA-DNA hybridization techniques. We have examined the structure of the DNA molecules from these hybrids, using electron microscope heteroduplex mapping techniques. Each hybrid was found to contain a single segment of SV40 DNA of characteristic size covalently inserted at a unique location in the adenovirus 2 DNA molecule. The SV40 segments of the various hybrids formed an overlapping series with a common end point. When the results of the electron microscopic study were combined with data on antigen induction, it was found that a self-consistent map could be constructed which related specific regions of the SV40 genome to the induction of specific antigens. The order of these early SV40 antigen inducing regions in the SV40 DNA segments contained in the nondefective hybrids is: U antigen, tumor specific transplantation antigen, and T antigen with the U antigen region being nearest the common end point.
Improving Binding Affinity and Stability of Peptide Ligands by Substituting Glycines with D‐Amino Acids (2013)

Improving the binding affinity and/or stability of peptide ligands often requires testing of large numbers of variants to identify beneficial mutations. Herein we propose a type of mutation that promises a high success rate. In a bicyclic peptide inhibitor of the cancer-related protease urokinase-type plasminogen activator (uPA), we observed a glycine residue that has a positive ϕ dihedral angle when bound to the target. We hypothesized that replacing it with a D-amino acid, which favors positive ϕ angles, could enhance the binding affinity and/or proteolytic resistance. Mutation of this specific glycine to D-serine in the bicyclic peptide indeed improved inhibitory activity (1.75-fold) and stability (fourfold). X-ray-structure analysis of the inhibitors in complex with uPA showed that the peptide backbone conformation was conserved. Analysis of known cyclic peptide ligands showed that glycine is one of the most frequent amino acids, and that glycines with positive ϕ angles are found in many protein-bound peptides. These results suggest that the glycine-to-D-amino acid mutagenesis strategy could be broadly applied.
Embryonic stem cells differentiate into insulin-producing cells without selection of nestin-expressing cells (2004)

We present a new strategy for the differentiation of embryonic stem (ES) cells into insulin-producing cells via a multi-step process without selection and induction of nestin-positive cells. During ES cell differentiation, transcript levels of genes characteristic of early and mature beta cells including Pdx1, Pax4, insulin and islet amyloid pancreatic peptide are up regulated. Islet-like clusters are characterized by expression of C-peptide, insulin and partially cytokeratin 19 as well as by ion channel activity similar to that found in embryonic beta cells. Cells of islet-like clusters show glucose-dependent insulin release at terminal stage. At an intermediate stage, nestin is partially co-expressed with C-peptide and cytokeratin 19, whereas islet-like clusters at the terminal stage are nestin-negative. We conclude that expression of nestin and cytokeratin 19 is a normal property of ES cells preceding differentiation into C-peptide/insulin-producing cells without any selection for nestin-positive phenotypes.
Patterned Paper as a Platform for Inexpensive, Low‐Volume, Portable Bioassays (2007)

By the book: A method for patterning paper with photoresist to create well-defined, millimeter-sized channels comprising hydrophilic paper bounded by hydrophobic polymer is described. This type of patterned paper is a prototype of a class of low-cost, portable, and technically simple platforms for running multiplexed bioassays with microliter volumes of a single biological sample. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z603817_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Ambulatory management of common forms of anemia. (1999)

Anemia is a prevalent condition with a variety of underlying causes. Once the etiology has been established, many forms of anemia can be easily managed by the family physician. Iron deficiency, the most common form of anemia, may be treated orally or, rarely, parenterally. Vitamin B12 deficiency has traditionally been treated with intramuscular injections, although oral and intranasal preparations are also available. The treatment of folate deficiency is straightforward, relying on oral supplements. Folic acid supplementation is also recommended for women of child-bearing age to reduce their risk of neural tube defects. Current research focuses on folate's role in reducing the risk of premature cardiovascular disease.
Cortical and subcortical blood flow effects of subthalamic nucleus stimulation in PD (2003)

These data suggest that STN stimulation increases firing of STN output neurons, which increases inhibition of thalamocortical projections, ultimately decreasing blood flow in cortical targets. STN stimulation appears to drive, rather than inhibit, STN output neurons.
The Microsoft Interactive TV System: An Experience Report (1997)

This paper describes the Microsoft Interactive Television (MITV) system. An overview of the different components of the system is presented. The development process is described. Finally, experiences and lessons learned from the system are presented. The system is designed to be able to provide traditional television service, video-on-demand service, and custom interactive applications, such as interactive shopping services, to subscriber bases scaling from a few hundred subscribers up through major metropolitan areas. An early version of the system was deployed in a trial of 100 subscribers in the Redmond, Washington area with TCI and Viacom from April, 1995 to early 1997 using PCs to emulate set-top boxes; a trial of 298 subscribers was deployed from March 1996 to April 1997 by NTT and NEC in Yokosuka, Japan using clientpremises set-top boxes. From initial conception in early 1993 thorough the trial deployments, an eventual staff of over 200 people evolved the design and implementati...
Metabolic Modulation of Glioblastoma with Dichloroacetate (2010)

Solid tumors, including the aggressive primary brain cancer glioblastoma multiforme, develop resistance to cell death, in part as a result of a switch from mitochondrial oxidative phosphorylation to cytoplasmic glycolysis. This metabolic remodeling is accompanied by mitochondrial hyperpolarization. We tested whether the small-molecule and orphan drug dichloroacetate (DCA) can reverse this cancer-specific metabolic and mitochondrial remodeling in glioblastoma. Freshly isolated glioblastomas from 49 patients showed mitochondrial hyperpolarization, which was rapidly reversed by DCA. In a separate experiment with five patients who had glioblastoma, we prospectively secured baseline and serial tumor tissue, developed patient-specific cell lines of glioblastoma and putative glioblastoma stem cells (CD133(+), nestin(+) cells), and treated each patient with oral DCA for up to 15 months. DCA depolarized mitochondria, increased mitochondrial reactive oxygen species, and induced apoptosis in GBM cells, as well as in putative GBM stem cells, both in vitro and in vivo. DCA therapy also inhibited the hypoxia-inducible factor-1alpha, promoted p53 activation, and suppressed angiogenesis both in vivo and in vitro. The dose-limiting toxicity was a dose-dependent, reversible peripheral neuropathy, and there was no hematologic, hepatic, renal, or cardiac toxicity. Indications of clinical efficacy were present at a dose that did not cause peripheral neuropathy and at serum concentrations of DCA sufficient to inhibit the target enzyme of DCA, pyruvate dehydrogenase kinase II, which was highly expressed in all glioblastomas. Metabolic modulation may be a viable therapeutic approach in the treatment of glioblastoma.
CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDY OF THE FARNESYL DIPHOSPHATE SYNTHASE FROM TRYPANOSOMA BRUCEI (2004)

Farnesyl diphosphate synthase (FPPS) catalyses the formation of farnesyl diphosphate from dimethylallyl diphosphate and isopentenyl diphosphate and is an RNAi-validated drug target in Trypanosoma brucei, the causative agent of African sleeping sickness. A T. brucei FPPS (390 amino acids) has been expressed in Escherichia coli and the recombinant protein has been crystallized in the absence and presence of the bisphosphonate inhibitor minodronate. Diffraction data were collected at 100 K using synchrotron radiation from both crystal types. Crystals obtained in the absence of minodronate belong to space group I222, with unit-cell parameters a = 61.43, b = 118.12, c = 120.04 A, while crystals grown in the presence of minodronate belong to space group C2, with unit-cell parameters a = 131.98, b = 118.10, c = 63.25 A, beta = 112.48 degrees. An initial model of the drug-free protein has been built using a homology model with the molecular-replacement method and refined to 3.3 A resolution. It shows mostly helical structure and resembles the structure of avian farnesyl diphosphate synthase, but with the addition of two loop regions.
Pregnancy Maintenance and Parturition: The Role of Prostaglandin in Manipulating the Immune and Inflammatory Response (1994)

PREGNANCY represents a delicate balance between the requirements of the growing fetus and the maternal immune system that could potentially reject the semi-allogeneic fetal ‘graft’ (1). This balance requires an immune tolerance of the fetal tissue and a local suppression of an inflammatory response, but at the time of parturition a selective use of the inflammatory response could provide an effective mechanism for delivering the baby (2). The inflammatory response can be regarded as the effector arm of the immune system, which can be activated independently. In nonreproductive tissue, glucocorticoids afford control. However, during pregnancy and particularly in the uterus, it is likely that progesterone with its immunosuppressive and anti-inflammatory properties (3) contributes to the regulation of inflammatory-type responses. The prominent role of progesterone in maintaining pregnancy is demonstrated by the action of antiprogesterone steroids such as RU486 (Mifepristone) that can disrupt pregnancy at any stage (4–6) and, used together with prostaglandins (PGs), provide an effective method of inducing abortion.
Waveguide Integrated Balanced Photodetectors for Coherent Receivers (2017)

This paper presents a brief review of waveguide integrated balanced photodetectors for coherent receivers and describes some of their recent progresses. Waveguide integrated balanced photodetectors and balanced photodiodes (PD) monolithically integrated to InP-based coherent receiver photonic integrated circuits (PIC) are discussed. On one hand, the devices focus on high-end market for long-haul transmission, and on the other hand on short reach transmission for data centers. In this paper, also a balanced photodetector with the highest ever reported 3-dB bandwidth of 115 GHz is demonstrated. Moreover, a low-power concept for a homodyne receiver PIC with balanced avalanche PD is emphasized to introduce phase modulation formats to data center transmissions.
Experimental Cedar Pollinosis in Rhesus Monkeys (1990)

In order to develop an experimental model for human cedar pollinosis, 4 rhesus monkeys (Macaca mulatta) were subcutaneously immunized with crude cedar pollen antigen, which contained 1.0 microgram or 10 micrograms protein with aluminium hydroxide gel, six times every month. All 4 animals showed immediate-type cutaneous reactivity. Serum IgE antibody responses against the pollen antigen, as quantitated by the Prausnitz-Küstner reaction, were seen in 3 of 4 monkeys. Radioallergosorbent test scores increased in 2 monkeys and remained at higher levels throughout the study. Histamine release from leukocytes was positive in all animals. In conjunctival provocation tests, they showed clinical signs such as eye-scratching after the antigen was dropped into their eyes. This reaction is similar to that observed in humans and suggests this animal model might be useful in studying human cedar pollinosis.
Ontology design patterns for the semantic business processes (2009)

This paper discusses two research paradigms: the first one is based on using the Meta-Object Facility (MOF) to support any kind of metadata, whereas the second one emphasizes the role of the Ontology Design Patterns (ODPs) to support knowledge transformation between the source and the target models. More precisely, in this paper we represent the Business Process ODP, which reflects both the syntax and semantics of business process specification and brings an abstract solution to the typical problem of designing and modelling semantic business processes.
3DNBS: A Data De-duplication Disk-Based Network Backup System (2009)

Traditionally, backup and archiving have been performed on tapes. With the rapid advances in disk storage technology witnessed in recent years, it becomes practical to use disks other than tape libraries as backend storage device for a backup system. For such a disk-based system, storage space efficiency is essential. Since traditional backup method cannot eliminate redundancies during backup, a new data de-duplication backup technique should be developed to provide more efficient data storage at the system. This paper describes the design and performance evaluation of a data de-duplication disk-based network backup system,called 3DNBS. 3DNBS breaks files into variable sized chunks using content-defined chunking (CDC) for the purpose of duplication detection. Chunks are indexed and addressed by hashing their content, which leads to intrinsically single instance storage. Experimental results show that in comparison with traditional backup method such as Bacula, 3DNBS presents dramatic reduction in required storage space on various workloads. By eliminating duplicated data, 3DNBS also reduces the size of data to be transmitted, hence reducing time to perform backup in a bandwidth constraint environment.