gebhart/patrepeval huggingface dataset:
Image processing techniques for identifying Mycobacterium tuberculosis in Ziehl-Neelsen stains. (2008)

Worldwide, laboratory technicians tediously read sputum smears for tuberculosis (TB) diagnosis. We demonstrate proof of principle of an innovative computational algorithm that successfully recognizes Ziehl-Neelsen (ZN) stained acid-fast bacilli (AFB) in digital images. Automated, multi-stage, color-based Bayesian segmentation identified possible 'TB objects', removed artifacts by shape comparison and color-labeled objects as 'definite', 'possible' or 'non-TB', bypassing photomicrographic calibration. Superimposed AFB clusters, extreme stain variation and low depth of field were challenges. Our novel method facilitates electronic diagnosis of TB, permitting wider application in developing countries where fluorescent microscopy is currently inaccessible and unaffordable. We plan refinement and validation in the future.
The Archetype γ-Class Carbonic Anhydrase (Cam) Contains Iron When Synthesized in Vivo (2009)

A recombinant protein overproduction system was developed in Methanosarcina acetivorans to facilitate biochemical characterization of oxygen-sensitive metalloenzymes from strictly anaerobic species in the Archaea domain. The system was used to overproduce the archetype of the independently evolved gamma-class carbonic anhydrase. The overproduced enzyme was oxygen sensitive and had full incorporation of iron instead of zinc observed when overproduced in Escherichia coli. This, the first report of in vivo iron incorporation for any carbonic anhydrase, supports the need to reevaluate the role of iron in all classes of carbonic anhydrases derived from anaerobic environments.
Minimum torque ripple, maximum efficiency excitation of brushless permanent magnet motors (1994)

Permanent magnet motors are usually driven in one of two ways. Sinusoidal currents are applied when the motor has a sinusoidal back EMF, and rectangular currents are applied when the back EMF has a trapezoidal shape. If implemented perfectly, each of these drive schemes is capable of producing ripple-free torque, which is desirable in many applications. However, in reality, permanent magnet motors never exhibit perfectly sinusoidal or trapezoidal back EMFs. Moreover, the power electronics used to drive the motor often has limitations that keep it from producing the required current waveform, especially as speed or load torque increases. In addition to these limitations, a permanent magnet motor often exhibits parasitic cogging torque that directly contributes to torque ripple. This work explores the relationships between motor current and back EMF, and identifies minimum torque ripple, maximum efficiency current excitations that can be implemented with finite bandwidth power electronics (current controlled VSI).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Enhanced immunostimulatory activity of cyclic dinucleotides on mouse cells when complexed with a cell‐penetrating peptide or combined with CpG (2015)

Recognition of pathogen-derived nucleic acids by immune cells is critical for the activation of protective innate immune responses. Bacterial cyclic dinucleotides (CDNs) are small nucleic acids that are directly recognized by the cytosolic DNA sensor STING (stimulator of IFN genes), initiating a response characterized by proinflammatory cytokine and type I IFN production. Strategies to improve the immune stimulatory activities of CDNs can further their potential for clinical development. Here, we demonstrate that a simple complex of cylic-di-GMP with a cell-penetrating peptide enhances both cellular delivery and biological activity of the cyclic-di-GMP in murine splenocytes. Furthermore, our findings establish that activation of the TLR-dependent and TLR-independent DNA recognition pathways through combined use of CpG oligonucleotide (ODN) and CDN results in synergistic activity, augmenting cytokine production (IFN-α/β, IL-6, TNF-α, IP-10), costimulatory molecule upregulation (MHC class II, CD86), and antigen-specific humoral and cellular immunity. Results presented herein indicate that 3'3'-cGAMP, a recently identified bacterial CDN, is a superior stimulator of IFN genes ligand than cyclic-di-GMP in human PBMCs. Collectively, these findings suggest that the immune-stimulatory properties of CDNs can be augmented through peptide complexation or synergistic use with CpG oligonucleotide and may be of interest for the development of CDN-based immunotherapeutic agents.
Surgical Education in the Third Millennium (2001)

From the Department of Surgical Sciences, University of Milano Medical School, Milano, Italy. Correspondence: Alberto Peracchia, Department of Surgical Sciences, University of Milano, Via F. Sforza 35, I-20122 Milano, Italy. E-mail: [email protected] Accepted for publication April 2001.
NiMoO<sub>4</sub>@Co<sub>3</sub>O<sub>4</sub> Core–Shell Nanorods: In Situ Catalyst Reconstruction toward High Efficiency Oxygen Evolution Reaction (2021)

Abstract The sluggish kinetics of the oxygen evolution reaction (OER) is the bottleneck for the practical exploitation of water splitting. Here, the potential of a core–shell structure of hydrous NiMoO 4 microrods conformally covered by Co 3 O 4 nanoparticles via atomic layer depositions is demonstrated. In situ Raman and synchrotron‐based photoemission spectroscopy analysis confirms the leaching out of Mo facilitates the catalyst reconstruction, and it is one of the centers of active sites responsible for higher catalytic activity. Post OER characterization indicates that the leaching of Mo from the crystal structure, induces the surface of the catalyst to become porous and rougher, hence facilitating the penetration of the electrolyte. The presence of Co 3 O 4 improves the onset potential of the hydrated catalyst due to its higher conductivity, confirmed by the shift in the Fermi level of the heterostructure. In particular NiMoO 4 @Co 3 O 4 shows a record low overpotential of 120 mV at a current density of 10 mA cm −2 , sustaining a remarkable performance operating at a constant current density of 10, 50, and 100 mA cm −2 with negligible decay. Presented outcomes can significantly contribute to the practical use of the water‐splitting process, by offering a clear and in‐depth understanding of the preparation of a robust and efficient catalyst for water‐splitting.
The molecular pathophysiology of pain: abnormal expression of sodium channel genes and its contributions to hyperexcitability of primary sensory neurons (1999)

Although hyperexcitability and/or increased baseline sensitivity of primary sensory neurons following nerve injury can lead to abnormal burst activity associated with pain, the molecular mechanisms that contribute to it are not fully understood. Early studies demonstrated that, following axonal injury, neurons can display changes in excitability suggesting increased sodium channel expression. Consistent with this, abnormal accumulations of sodium channels have been observed at the tips of injured axons. But we now know that nearly a dozen distinct sodium channels are encoded by different genes, raising the question, what types of sodium channels underlie hyperexcitability of primary sensory neurons following injury? My laboratory has used molecular, electrophysiological, and pharmacological techniques to answer this question. Our studies have demonstrated that multiple sodium channels, with distinct physiological properties, are expressed within small dorsal root ganglion (DRG) neurons, which include nociceptive cells. Several DRG and trigeminal neuron-specific sodium channels have now been cloned and sequenced. There is a dramatic change in sodium channel expression in DRG neurons, with down-regulation of the SNS/PN3 and NaN sodium channel genes and up-regulation of previously silent Type III sodium channel gene, following injury to the axons of these cells. These changes in sodium channel gene expression can produce electrophysiological changes in DRG neurons which poise them to fire spontaneously or at inappropriate high frequencies. We have also observed changes in sodium channel gene expression in experimental models of inflammatory pain. The dynamic nature of sodium channel gene expression in DRG neurons, and the changes which occur in sodium channel and sodium current expression in these cells following axonal injury and in inflammatory pain models, suggest that abnormal expression of sodium channels contributes to the molecular pathophysiology of pain.
Intraocular epiretinal prosthesis to restore vision in blind humans (2008)

Visual sensations in blind patients suffering from retinal degenerations may be restored by electrical stimulation of retinal neurons using implantable microelectrode arrays. The EPI-RET-3 project was initiated to evaluate a wireless intraocular retinal implant system for human use in terms of safety and efficiency. The implant is a remotely controlled fully intraocular prosthesis consisting of a receiver and a stimulator module. The stimulator is placed onto the retina's surface. Data and energy are transmitted via an inductive link from outside the eye to the implant. The EPI-RET-3 device was implanted into six legally blind patients with Retinitis Pigmentosa (RP) for a period of four weeks. The surgery was performed without complications. The implants were activated on days 7, 14 and 27 after implantation. All patients reported visual sensations such as dots, arcs, or lines of different colours and intensities. The required stimulation thresholds were found to be very low. Implantation of the wireless EPI-RET-3 device is safe and the system is suitable to elicit visual sensations in blind RP patients. Major problems in the design and fabrication of a prosthesis for artificial vision could be solved in this approach.
High hydrostatic pressure treatment generates inactivated mammalian tumor cells with immunogeneic features (2010)

Most of the classical therapies for solid tumors have limitations in achieving long-lasting anti-tumor responses. Therefore, treatment of cancer requires additional and multimodal therapeutic strategies. One option is based on the vaccination of cancer patients with autologous inactivated intact tumor cells. The master requirements of cell-based therapeutic tumor vaccines are the: (a) complete inactivation of the tumor cells; (b) preservation of their immunogenicity; and (c) need to remain in accordance with statutory provisions. Physical treatments like freeze-thawing and chemotherapeutics are currently used to inactivate tumor cells for vaccination purposes, but these techniques have methodological, therapeutic, or legal restrictions. For this reason, we have proposed the use of a high hydrostatic pressure (HHP) treatment (p >or= 100 MPa) as an alternative method for the inactivation of tumor cells. HHP is a technique that has been known for more than 100 years to successfully inactivate micro-organisms and to alter biomolecules. In the studies here, we show that the treatment of MCF7, B16-F10, and CT26 tumor cells with HHP >or= 300 MPa results in mainly necrotic tumor cell death forms displaying degraded DNA. Only CT26 cells yielded a notable amount of apoptotic cells after the application of HHP. All tumor cells treated with >or= 200 MPa lost their ability to form colonies in vitro. Furthermore, the pressure-inactivated cells retained their immunogenicity, as tested in a xenogeneic as well as syngeneic mouse models. We conclude that the complete tumor cell inactivation, the degradation of the cell's nuclei, and the retention of the immunogeneic potential of these dead tumor cells induced by HHP favor the use of this technique as a powerful and low-cost technique for the inactivation of tumor cells to be used as a vaccine.
Compartmentalization in membrane rafts defines a pool of N‐cadherin associated with catenins and not engaged in cell–cell junctions in melanoma cells (2007)

Melanoma progression is associated with changes in adhesion receptor expression, in particular upregulation of N-cadherin which promotes melanoma cell survival and invasion. Plasma membrane lipid rafts contribute to the compartmentalization of signaling complexes thereby regulating their function, but how they may affect the properties of adhesion molecules remains elusive. In this study, we addressed the question whether lipid rafts in melanoma cells may contribute to the compartmentalization of N-cadherin. We show that a fraction of N-cadherin in a complex with catenins is associated with cholesterol/sphingolipid-rich membrane microdomains in aggressive melanoma cells in vitro and experimental melanomas in vivo. Partitioning of N-cadherin in membrane rafts is not modulated by growth factors and signaling pathways relevant to melanoma progression, is not necessary for cell-cell junctions' establishment or maintenance, and is not affected by cell-cell junctions' and actin cytoskeleton disruption. These results reveal that two independent pools of N-cadherin exist on melanoma cell surface: one pool is independent of lipid rafts and is engaged in cell-cell junctions, while a second pool is localized in membrane rafts and does not participate in cell-cell adhesions. Targeting to membrane rafts may represent a previously unrecognized mechanism regulating N-cadherin function in melanoma cells.
Personal photo browser that can classify photos by participants and situations (2012)

This paper demonstrates a photo browser which rearranges photos referring to the persons who were close to the photographer when the photos were taken by consulting Bluetooth device detection information. Most of Bluetooth devices accompany their owners. Each photo is tagged with Bluetooth device-IDs which were detected around the moment when it was taken. Employing the tag information, the system classifies the user's photo archive into a layered cluster tree in terms of tag similarity, and shows its user the photos of her-selected cluster on either a map or timelines.
Membrane array–based differential profiling of platelets during storage for 52 miRNAs associated with apoptosis (2009)

Overall, these results confirm the fact that miRNAs do exist in PLTs, and among 52 apoptosis-specific miRNAs studied, only a few selected miRNAs did perturb during PLT storage. Future experimental evaluation of these miRNA-target mRNA interactions will provide new insights into the molecular mechanisms of PLT storage-associated lesions.
Sensitivity improvements in uncooled microbolometer FPAs (1999)

Raytheon IRCOE has developed a family of uncooled, microbolometer FPAs. These FPAs have been designed to address commercial and high-performance military applications. The SB-151 is a high-sensitivity 320 X 240 FPA with 50 micrometers pixels. The SB-151 FPA has been fabricated with several microbolometer pixel designs that allow optimization of either sensitivity or response time. Noise equivalent temperature difference (NETD) values as low as 8.6 mK have been measured for the SB-151 FPAs with f/1 optics. NETD values less than 25 mK have been measured for FPAs with thermal time constants of approximately 18 msec.
Pyrolysis, theory and industrial practice (1983)

This book is useful for the study of pyrolysis from two perspectives: theory and industrial practice. Topics included are thermal decompositions and reactions of methane pyrolysis of ethane and propane, pyrolysis of n-butane, thermal reaction of olefins and diolefins, pyrolysis of heavy hydrocarbons, formation of aromatics, hydrogenolysis of toluene, mathematical modeling of hydrocarbon pyrolysis reactions, nonpetroleum feedstocks, formation and gasification of coke, surface reactions in pyrolysis units, pyrolysis furnace design, laboratory reactors for pyrolysis, and economic considerations in the design and operation of conventional pyrolysis furnaces.
Editorial (2012)

In this essay I propose to facilitate a dialogue between the thoughts of conceptual artist and philosopher, Daya Krishna, and the work of literary artist, Vikas Swarup. The central concept that will be “interrogated” in this dialogue is that of knowledge. I will apply my understanding of Daya Krishna’s conceptualization of the knowledge enterprise on to Vikas Swarup’s attitude toward knowledge as embodied in his 2005 novel, Q & A. This exercise serves to create a context in which conceptions of knowledge from diverse fields (hardcore philosophy and popular culture) can be in dialogue with one another, and thereby enhance meaning. Daya Krishna observes that the loss of certainty and proof in our postmodern age erodes the concept of knowledge. He alternately suggests new indicators with which to define knowledge, indicators which factor in chance and probability, and take into account inherent moral qualities of knowledge. I argue that this alternative model of knowledge finds an expression in Swarup’s novel.
Enhanced fluorescence in a nanoporous waveguide and its quantitative analysis (2012)

Fluorescence behavior was examined for fluorophore-labeled protein (BSA-AF) adsorbed on the nanopore surface of a nanoporous waveguiding film. The waveguiding film has a bilayer structure of a porous anodic alumina (PAA) layer on a metallic aluminum (Al) layer, and this structure allows efficient interaction of fluorophores entrapped in the nanoporous waveguiding film with a hotspot of the enhanced electromagnetic field of the waveguide modes. Fluorescence response of BSA-AF depends on the enhanced field within the waveguiding film and the enlarged adsorbed amount in the PAA layer where most of the light is confined. Enhancement of the field in the waveguiding film can be controlled by the refractive index of the PAA layer and enlargement of the pore size efficiently affects the enhancement of the fluorescence response. Compared to the film without a PAA layer, the PAA/Al film exhibits more than 140-fold larger fluorescence response due to the large adsorption capacity of the PAA nanopores and the enhanced field formed by the waveguide modes in the PAA layer with a low refractive index.
A new method to retrieve phase information for equiangular fan beam differential phase contrast computed tomography (2013)

Theoretical calculations and numerical simulations confirm both feasibility and validity of the RP method under fan beam illumination. Because this method is simple, fast, and releases a relatively low dose, the authors believe that this research is very useful for the x-ray phase contrast imaging applications in clinical diagnosis, bioresearch, and industrial nondestructive testing.
Intersite Differences in Weight Growth Velocity of Extremely Premature Infants (2002)

Variation in nutrition explained much of the difference in growth among the NICUs studied. Mean intake of calories and protein failed to meet recommended levels, and the average growth in only 1 NICU approximated intrauterine growth standards. Increasing nutritional intake into the recommended ranges, in particular of protein, may increase growth of extremely premature infants up to or above intrauterine rates.
Direct cloning of yeast genes from an ordered set of lambda clones in Saccharomyces cerevisiae by recombination in vivo. (1993)

Abstract We describe a technique that facilitates the isolation of yeast genes that are difficult to clone. This technique utilizes a plasmid vector that rescues lambda clones as yeast centromere plasmids. The source of these lambda clones is a set of clones whose location in the yeast genome has been determined by L. Riles et al. in 1993. The Escherichia coli-yeast shuttle plasmid carries URA3, ARS4 and CEN6, and contains DNA fragments from the lambda vector that flank the cloned yeast insert. When yeast is cotransformed with linearized plasmid and lambda clone DNA, Ura+ transformants are obtained by a recombination event between the lambda clone and the plasmid vector that generates an autonomously replicating plasmid containing the cloned yeast DNA sequences. Genes whose genetic map positions are known can easily be identified and recovered in this plasmid by testing only those lambda clones that map to the relevant region of the yeast genome for their ability to complement the mutant phenotype. This technique facilitates the isolation of yeast genes that resist cloning either because (1) they are underrepresented in yeast genomic libraries amplified in E. coli, (2) they provide phenotypes that are too marginal to allow selection of the gene by genetic complementation or (3) they provide phenotypes that are laborious to score. We demonstrate the utility of this technique by isolating three genes, GAL83, SSN2 and MAK7, each of which presents one of these problems for cloning.
Synthesis, characterisation and reactivity of germanium(ii) amidinate and guanidinate complexes (2008)

Reactions of lithium salts of the bulky guanidinate ligands, [ArNC(NR2)NAr](-) (NR2 = N(C6H11)2 (Giso-) and cis-NC5H8Me2-2,6 (Pipiso-); Ar = C6H3Pri2-2,6), with GeCl2.dioxane afforded the heteroleptic germylenes, [(Giso)GeCl] and [(Pipiso)GeCl], the former of which was structurally characterised. The further reactivity of these and the related complexes, [(Piso)GeCl] and [(Priso)GeCl] (Piso- = [ArNC(Bu(t))NAr]-, Priso- = [ArNC(NPri2)NAr]-) has been investigated. Salt elimination reactions have yielded the new monomeric complexes, [(Piso)Ge(NPri2)] and [(Piso)GeFeCp(CO)2], whilst a ligand displacement reaction afforded the heterometallic species, [(Piso)Ge(Cl)(W(CO)5)]. Chloride abstraction from [(Priso)GeCl] with GaCl3 has given the structurally characterised contact ion pair, [(Priso)Ge][GaCl4]. In addition, the inconclusive outcome of a number of attempts to reduce the germanium halide complexes are discussed.
Sites of interaction in the complex between beta- and gamma-subunits of transducin. (1990)

Transducin, the guanine nucleotide-binding regulatory protein in rod outer segments, is a heterotrimer consisting of alpha-, beta-, and gamma-subunits. Activation of the photoreceptor, rhodopsin, by light, results in activation of transducin which cleaves to form transducin alpha. GTP and a complex of beta gamma-subunits. We have investigated the point(s) of contact between the subunits of transducin by analyzing for the formation of intersubunit disulfide bond(s) in the presence of copper phenanthroline. The formation of a new species with an apparent molecular mass of 43 kDa was observed which had resulted from the formation of a disulfide bond between the beta- and gamma-subunits. The amino acid residues participating in the disulfide bond were identified as Cys-25 in the beta-subunit and Cys-36 and/or Cys-37 in the gamma-subunit. Thus, these cysteine residues and, probably, some of the adjacent amino acid residues form a point of contact between the beta- and gamma-subunits of transducin in the stable complex.
Protein-ligand interaction prediction: an improved chemogenomics approach (2008)

All data and algorithms are available as Supplementary Material.
P‐120: Volume Holographic Technology for the Viewing Angle Compensation of TN‐LCDs (2003)

Abstract Thanks to holographic technology, the hybrid holographic compensators offer interesting properties for the versatility of the compensation design as well as for product integration. The adaptability of the hybrid holographic compensator is demonstrated through the implementation of the compensator on two avionic displays.
Crystallization and preliminary X-ray analysis of a NADPH 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2001)

NADPH 2-ketopropyl-coenzyme M (2-mercaptoethanesulfonate) oxidoreductase/carboxylase is the terminal enzyme in a metabolic pathway that results in the conversion of propylene to the central metabolite acetoacetate. This enzyme is an FAD-containing enzyme that is a member of the NADPH:disulfide oxidoreductase family of enzymes and catalyzes the cleavage and carboxylation of 2-ketopropyl-coenzyme M to form acetoacetate and coenzyme M. Crystallization trials have revealed that the highest diffraction quality crystals (better that 2.0 A resolution) could be achieved when the substrate or product of the reaction was added to the enzyme in a stoichiometric excess.