gebhart/patrepeval huggingface dataset:
Outcomes of Moral Case Deliberation - the development of an evaluation instrument for clinical ethics support (the Euro-MCD) (2014)

A tentative instrument has been developed that seems to cover main outcomes of Moral Case Deliberation. The next step will be to test the Euro-MCD in a field study.
Synthesis and Antibacterial Evaluation of Certain Quinolone Derivatives (2001)

A number of 7-substituted quinolone derivatives were synthesized and evaluated for antibacterial and cytotoxic activities. Preliminary results indicated that most compounds tested in this study demonstrated better activity against methicillin-resistant Staphylococcus aureus than norfloxacin. Among them, 1-(4-amino-2-fluorophenyl)-6-fluoro-1,4-dihydro-7-[4-[2-(4-methoxyphenyl)-2-hydroxyiminoethyl]-1-piperazinyl]-4-oxo-3-quinolinecarboxylic acid (11d) and its ketone precursor 10d exhibited significant activities against Klebsiella pneumoniae, methicillin-resistant S. aureus, erythromycin- and ampicillin-resistant Streptococcus pneumoniae, and vancomycin-resistant Enterococcus faecalis. Due to strong cytotoxicities of 11d (a mean log GI(50) of -5.40), compound 10d, with good antibacterial activities and low cytotoxicities (a mean log GI(50) of -4.67), is a more potential drug candidate.
Event-Driven Real-Time Audio Processing with GPGPUs (2011)

Development of real-time audio processing applications for GPGPUs is not without challenges. Parallel processing of audio signals is often constrained by serial dependencies within or between algorithms. On GPGPUs, insufficient data pressure further limits the attainable performance improvements, as it causes inactivity of the GPU cores. In this paper, we analyze the limits of audio processing on GPGPUs and present an approach based on event-driven scheduling, that maximizes data pressure to favour performance improvements. We also present recent enhancements of Audio n-Genie, an open-source development environment for audio-processing applications. By combining Audio n-Genie and the proposed approach, we show that it is possible to increase audio processing speed-up.
Gene Conversion of Sialic Acid Binding Domains in CD33-Related Siglecs by Adjacent Pseudogenes: A Novel Mechanism To Change Sialic Acid Binding Specificity. (2004)

Abstract Siglecs (sialic acid-binding immunoglobulin superfamily lectins) are a family of cell surface receptors involved in regulating the immune response. The CD33-Related Siglecs (CD33rSiglecs, namely Siglec-3, -5 through -11 and -XII in humans) are a subgroup of these molecules found primarily on cells of the innate immune system. All are type-1 transmembrane proteins with an N-terminal sialic acid-recognizing V-set domain followed by a variable number of C-2 set domains, a transmembrane region and a cytosolic C-terminal domain that includes two tyrosine-based signaling motifs. Available data suggest an inhibitory signaling role in the innate immune response, mediated by recognition of host sialic acids as “self”. Nine of the 13 known primate Siglec genes along with 14 Siglec pseudogenes comprise the CD33-related Siglec gene cluster on human chromosome 19. Gene conversion is a mechanism for copying part of a genomic sequence into another, contributing to genetic diversity. Pseudogenes are known to play role in generating functional diversity of related genes (e.g., antibody diversity via gene conversion in chickens). We recently analyzed genomic sequences of the CD33-related Siglec gene cluster in three primates (human, chimpanzee and baboon) and found evidence for rapid evolution in this gene family (Angata et al., PNAS, in press). Additional evolutionary studies using distance-based phylogenetic trees shows evidence for three partial gene conversions between Siglec genes and adjacent Siglec pseudogenes. All three involve the coding regions for extracellular domains that mediate sialic acid recognition, and two involve a pseudogene converting a known Siglec gene. Functional analyses using recombinant proteins show marked differences in sialic acid-binding properties between the converted Siglec and its non-converted ortholog. These findings suggest that gene conversion with pseudogenes has contributed to the rapid functional evolution of the Siglecs, and provides a novel mechanism for changing sialic acid binding specificity. We hypothesize that this mechanism allows for rapid evolutionary adjustments in the recognition of endogenous sialic acids as “self”, a potential factor in controlling the innate immune response.
Comparison of Plasma Compartment versus  Two Methods for Effect Compartment–controlled Target-controlled Infusion for Propofol (2000)

Effect compartment-controlled TCI can be safely applied in clinical practice. A biophase model combining the Marsh kinetics and a time to peak effect of 1.6 min accurately predicted the time course of propofol drug effect.
The Wave2 scaffold Hem-1 is required for transition of fetal liver hematopoiesis to bone marrow (2018)

The transition of hematopoiesis from the fetal liver (FL) to the bone marrow (BM) is incompletely characterized. We demonstrate that the Wiskott-Aldrich syndrome verprolin-homologous protein (WAVE) complex 2 is required for this transition, as complex degradation via deletion of its scaffold Hem-1 causes the premature exhaustion of neonatal BM hematopoietic stem cells (HSCs). This exhaustion of BM HSC is due to the failure of BM engraftment of Hem-1<sup>-/-</sup> FL HSCs, causing early death. The Hem-1<sup>-/-</sup> FL HSC engraftment defect is not due to the lack of the canonical function of the WAVE2 complex, the regulation of actin polymerization, because FL HSCs from Hem-1<sup>-/-</sup> mice exhibit no defects in chemotaxis, BM homing, or adhesion. Rather, the failure of Hem-1<sup>-/-</sup> FL HSC engraftment in the marrow is due to the loss of c-Abl survival signaling from degradation of the WAVE2 complex. However, c-Abl activity is dispensable for the engraftment of adult BM HSCs into the BM. These findings reveal a novel function of the WAVE2 complex and define a mechanism for FL HSC fitness in the embryonic BM niche.
Neutron and temperature-resolved synchrotron X-ray powder diffraction study of akaganéite (2003)

Rietveld refinements using neutron powder diffraction data were used to locate H atom positions and obtain a more precise crystal structure refinement for akaganéite [Fe3+7.6Ni2+0.4O6.35 (OH)9.65Cl1.25·nH2O]. Difference Fourier maps clearly showed H atoms positions near those O atoms at the midpoints of the tunnel edges. The O-H vectors point toward the Cl sites at the center of the tunnel, and weak hydrogen bonds likely form between the framework O atoms and Cl. The Cl position is near the center of a prism defined by the eight hydroxyl H atoms. The Cl atoms fill ~2/3 of the tunnel sites, suggesting an ordering scheme in a given tunnel with every third tunnel site vacant. Such an arrangement allows the Cl anions to increase their separation distance along a tunnel by displacing away from one another toward their respective adjacent vacancies. The Fe-O octahedra in akaganéite are distorted with Fe-(O, OH) distances ranging from 1.94 to 2.13 Å and show three longer and three shorter Fe-O distances; as expected the longer distances are associated with the OH- anions.
Economical and rapid manufacturing of lateral flow immunosensor using fountain pens and gold colloidal solution (2015)

Lateral flow assay is a simple and rapid diagnostic tool and consequently has been widely used in both academia and industry.
Experimental investigation and kinetic-theory-based model of a rapid granular shear flow (2008)

An experimental investigation of an idealized rapidly sheared granular flow was performed to test the predictions of a model based on the kinetic theory of dry granular media. Glass ballotini beads were placed in an annular shear cell and the lower boundary rotated to induce a shearing motion in the bed. A single particle was tracked using the positron emission particle tracking (PEPT) technique, a method that determines the location of a particle through the triangulation of gamma photons emitted by a radioactive tracer particle. The packing fraction and velocity fields within the three-dimensional flow were measured and compared to the predictions of a model developed using the conservation and balance equations applicable to dissipative systems, and solved incorporating constitutive relations derived from kinetic theory. The comparison showed that kinetic theory is able to capture the general features of a rapid shear flow reasonably well over a wide range of shear rates and confining pressures.
Motion correction for separate mandibular and cranial movements in cone beam CT reconstructions (2023)

The proposed algorithm consistently enhances the visual quality of motion impaired cone beam computed tomography scans, thus eliminating the need for a re-scan in certain cases, considerably lowering radiation dosage for the patient. It can flexibly be used with differently sized regions of interest and is even applicable to local tomography.
Kombination von Ultraschall‐ und Druckwellenverfahren zur innovativen Regenerierung von Brunnen (2014)

Abstract Die Effektivität von Brunnenregenerierungen kann dadurch gesteigert werden, dass Ultraschall‐ und Druckwellenverfahren kombiniert angewandt werden. Durch theoretische Analysen wird gezeigt, dass die Wirktiefen der beiden Verfahren unterschiedlich sind. Während das Ultraschallverfahren stark im Bereich des Brunnenfilters wirkt, reicht die Wirkung des Druckwellenverfahrens in den Kiesfilter bis zur Bohrlochwand sowie in den angrenzenden Grundwasserleiter hinein. Die Verbreitung der Signale in der Brunnenumgebung wurde numerisch modelliert. Durch diese theoretischen Analysen, verknüpft mit Experimenten im Labor und Gelände, konnte bewiesen werden, dass durch die Verfahrenskombination höhere Wirkungsgrade bei der Brunnenregenerierung erreicht werden können, als bei der alleinigen Anwendung von Ultraschall. Combination of ultrasound and shockwaves for innovative regeneration of wells. The effectiveness of regeneration of wells can be enhanced if ultrasound and shockwaves are used during the same treatment. It is theoretically shown that the two methods have different depths of impact. Whereas the ultrasonic method has a strong impact on the area of the well screen, the impact of the shock waves is focused on the gavel pack, the wall of the well and the adjacent aquifer. The propagation of the signals in the formation near the well was modeled numerical. By a theoretical analysis combined with experiments in lab and field it was proven that the regeneration of wells using a combination of ultrasound and shockwaves is much more effective than the regeneration by means of ultrasound only.
ASSOCIATION BETWEEN MUTATIONS IN PLASMODIUM FALCIPARUM CHLOROQUINE RESISTANCE TRANSPORTER AND P. FALCIPARUM MULTIDRUG RESISTANCE 1 GENES AND IN VIVO AMODIAQUINE RESISTANCE IN P. FALCIPARUM MALARIA–INFECTED CHILDREN IN NIGERIA (2006)

This study investigated the association between Plasmodium falciparum chloroquine resistance transporter (pfcrt) T76 and P. falciparum multidrug resistance gene 1 (pfmdr1) Y86 alleles and in vivo amodiaquine (AQ) resistance, as well as the clearance of parasites harboring these two alleles in children treated with AQ in southwest Nigeria. One hundred one children with acute uncomplicated P. falciparum malaria infections were treated with the standard dosage of AQ and followed-up for 28 days. Blood samples were collected on filter paper samples at enrollment and during follow-up for identification of parasite genotypes and pfcrt and pfmdr1 mutations using polymerase chain reaction and restriction fragment length polymorphism approaches. Parasitologic assessment of response to treatment showed that 87% and 13% (RI) of patients were cured and failed treatment, respectively. Although infections in patients were polyclonal (as determined by merozoite surface protein 2 genotyping), the presence of both mutants pfcrtT76 and pfmdr1Y86 alleles in parasites is associated with in vivo AQ resistance (odds ratio = 7.58, 95% confidence interval = 1.58-36.25, P = 0.006) and is selected by the drug in children who failed AQ treatment. Treatment failure with the combination of mutant pfcrtT76 and pfmdr1Y86 alleles as well as the ability of patients to clear these resistant parasites is dependent on age, suggesting a critical role of host immunity in clearing AQ-resistant P. falciparum. The combination of mutant pfcrtT76 and pfmdr1Y86 alleles may be useful markers for monitoring the development and spread of AQ resistance, when combining this drug with other antimalarials for treatment of malaria in Africa.
Research on VOCs Treatment of Electrophoresis Coating Process (2020)

Abstract The coating process is the main source of VOCs emissions in the aluminium profile industry. The electrophoretic coating process is a surface processing method widely used by aluminium profile companies. However, the electrophoretic coating process generates a large amount of exhaust gas, and the main component of the exhaust gas is VOCs. This paper combined with the monitoring of the exhaust gas treatment project of an electrophoresis coating workshop of a large aluminium profile company, and found that the main component is xylene. The exhaust gas treatment process uses “activated carbon adsorption + spray absorption” and more than 97% of emissions could be achieved.
The effects of 2nd-order feature interactions in predicting human gaze (2010)

How do features interact to guide human gaze? Models of human attention have assumed a linear combination of features to construct a final saliency map that drives human overt/covert attention. We asked what role, if any, do second order feature interactions play in attracting attention. We examined the eye movements of 8 subjects while they watched videos containing natural and synthetic scenes. A set of five low-level feature channels including Color (C), Intensity (I), Orientation (O), Flicker (F) and Motion (M) using center-surround differences were computed for each of 46,489 video frames shown to the subjects. A total of 11,430 saccades were analyzed. We compared 4 models including i) simple unweighted sum of 1st-order terms, i.e., C, I, O, F, M; ii) a weighted linear sum of 1st-order terms; iii) unweighted sum of 1st-order and all 2nd-order multiplicative feature interaction terms (e.g., CC, CI, CO, CF, CM, etc.); and iv) a weighted linear combination of 1st and 2nd order terms. For the weighted combinations, the weights were learned using a genetic algorithm (GA) that optimizes a cost function defined as the difference between the distribution of human saccade end points and salient locations as computed by the respective models. The optimal solution was found from a large search space of size 2^20 for the model incorporating 1st order terms and 2^80 for the model incorporating both 1st and 2nd order terms respectively. We found that the optimized 1st order model performed significantly better than all other models (p<0.05). Further we found that models using 2nd-order interactions did not improve the predicitive power of a model in explaining eye movements of human subjects.
Transitive Steiner and Kirkman triple systems of order 27 (1992)

There are 71 Steiner triple systems of order 27 whose automorphism groups are point-transitive, and there are 248 transitive Kirkman triple systems of order 27. Computational methods used to find these designs are outlined. The designs and some of their properties are presented.
INTERFERON-GAMMA AND EPITHELIAL CELL ACTIVATION IN SJÖGREN'S SYNDROME (1995)

We have examined the hypothesis that interferon-gamma (IFN-gamma) and its interaction with epithelium may play a role in the perpetuation of inflammation in Sjögren's syndrome (SS). Labial salivary gland primary cell cultures from 16 patients with primary SS (pSS) and eight cultures from patients with SS symptoms but histologically normal biopsies were examined for expression of HLA-DR and cytoplasmic La (SS-B). Epithelial HLA-DR expression was found in 80% of cultures from pSS patients and 38% of those from patients not fulfilling diagnostic criteria. Cytoplasmic La was detected in 50 and 38% of cultures, respectively. Treatment of 14 of the cultures with IFN-gamma increased HLA-SR and cytoplasmic La expression above that of untreated cultures. Depletion of IFN-gamma using neutralizing antibody had the reverse effect. These findings suggest that the perpetuation of chronic inflammation of pSS may be due to the induction of HLA-DR and La antigen expression on epithelial cells by IFN-gamma.
Sustained TNF production by central nervous system infiltrating macrophages promotes progressive autoimmune encephalomyelitis (2016)

Sustained TNF production by infiltrating macrophages associated with progressive EAE exacerbates disease severity by promoting inflammation and disruption of BBB integrity, thereby counteracting establishment of an anti-inflammatory environment required for disease remission.
Carbon Nanotubes Enabled Laser 3D Printing of High-Performance Titanium with Highly Concentrated Reinforcement (2020)

Zero- to two-dimensional nanomaterials have been incorporated into metal-matrices to improve the strength of metals, but challengingly, high-volume-fraction nanomaterials are difficult to disperse uniformly in metal matrices, severely degrading the ductility of conventionally processed metals. Here, a considerably dense uniform dispersion of <i>in situ</i> formed nanoscale lamellar TiC reinforcement (16.1 wt %) in Ti matrix is achieved through laser-tailored 3D printing and complete reaction of Ti powder with a small amount (1.0 wt %) of carbon nanotubes (CNTs). An enhanced tensile strength of 912 MPa and an outstanding fracture elongation of 16% are simultaneously achieved for laser-printed components, showing a maximum 350% improvement in "product of strength and elongation" compared with conventional Ti. <i>In situ</i> nanoscale TiC reinforcement favors the formation of ultrafine equiaxed Ti grains and metallurgically coherent interface with minimal lattice misfit between TiC lamellae and Ti matrix. Our approach hopefully provides a feasible way to broaden structural applications of CNTs in load-bearing Ti-based engineering components via laser-tailored reorganization with Ti.
One-Shot Learning for Periocular Recognition: Exploring the Effect of Domain Adaptation and Data Bias on Deep Representations (2023)

One weakness of machine-learning algorithms is the need to train the models for a new task. This presents a specific challenge for biometric recognition due to the dynamic nature of databases and, in some instances, the reliance on subject collaboration for data collection. In this paper, we investigate the behavior of deep representations in widely used CNN models under extreme data scarcity for One-Shot periocular recognition, a biometric recognition task. We analyze the outputs of CNN layers as identity-representing feature vectors. We examine the impact of Domain Adaptation on the network layers' output for unseen data and evaluate the method's robustness concerning data normalization and generalization of the best-performing layer. We improved state-of-the-art results that made use of networks trained with biometric datasets with millions of images and fine-tuned for the target periocular dataset by utilizing out-of-the-box CNNs trained for the ImageNet Recognition Challenge and standard computer vision algorithms. For example, for the Cross-Eyed dataset, we could reduce the EER by 67% and 79% (from 1.70% and 3.41% to 0.56% and 0.71%) in the Close-World and Open-World protocols, respectively, for the periocular case. We also demonstrate that traditional algorithms like SIFT can outperform CNNs in situations with limited data or scenarios where the network has not been trained with the test classes like the Open-World mode. SIFT alone was able to reduce the EER by 64% and 71.6% (from 1.7% and 3.41% to 0.6% and 0.97%) for Cross-Eyed in the Close-World and Open-World protocols, respectively, and a reduction of 4.6% (from 3.94% to 3.76%) in the PolyU database for the Open-World and single biometric case.
Model for Effects of RF Bias Frequency and Waveform on Si Damaged-Layer Formation during Plasma Etching (2011)

We investigated damaged-layer formation on the Si substrate surface induced by high-energy ion bombardment during plasma processing, by focusing on ion energy distribution function (IEDF). We introduced a modified range theory for the projection of incident ions and applied the model to damaged-layer formation under various plasma conditions – various rf bias frequencies and waveforms, furthermore their single- or dual-frequency bias configurations. Damaged-layer thickness and residual defect site density after the wet-etch process following the plasma treatment were simulated. The IEDF having more high-energy ions induces the formation of thicker damaged layer than in the case of a monochromatic ion energy when the average ion energies are the same. However, we found that, owing to the stochastic effect on the ion-projected range, the effects of bias frequency and the waveform were suppressed, i.e., the thickness of the damaged layer and the density of residual defect sites are weakly dependent on IEDFs under the same average incident ion energy. The present findings obtained by the model prediction are significant and useful for designing bias configurations for future plasma processes.
Bone Repair: High‐Performance Thiol–Ene Composites Unveil a New Era of Adhesives Suited for Bone Repair (Adv. Funct. Mater. 26/2018) (2018)

Adhesives suitable for fracture fixation can unfold a paradigm shift toward personalized bone repairs. In article number 1800372, Michael Malkoch and co-workers describe a surgically feasible adhesive system that capitalizes on visible light thiol–ene coupling chemistry. Preclinical validation, performed via fiber-reinforced adhesive patch methodology, reveals an unprecedented fixation strength that surpasses commercial dental systems or clinically used K-wires and matches metal plates and screw implants.
Migrating into Genomics with the Neural Crest (2014)

Neural crest cells are a fascinating embryonic cell type, unique to vertebrates, which arise within the central nervous system but emigrate soon after its formation and migrate to numerous and sometimes distant locations in the periphery. Following their migratory phase, they differentiate into diverse derivatives ranging from peripheral neurons and glia to skin melanocytes and craniofacial cartilage and bone. The molecular underpinnings underlying initial induction of prospective neural crest cells at the neural plate border to their migration and differentiation have been modeled in the form of a putative gene regulatory network. This review describes experiments performed in my laboratory in the past few years aimed to test and elaborate this gene regulatory network from both an embryonic and evolutionary perspective. The rapid advances in genomic technology in the last decade have greatly expanded our knowledge of important transcriptional inputs and epigenetic influences on neural crest development. The results reveal new players and new connections in the neural crest gene regulatory network and suggest that it has an ancient origin at the base of the vertebrate tree.