gebhart/patrepeval huggingface dataset:
Identification and Characterization of Arabidopsis Indole-3-Butyric Acid Response Mutants Defective in Novel Peroxisomal Enzymes (2008)

Genetic evidence suggests that indole-3-butyric acid (IBA) is converted to the active auxin indole-3-acetic acid (IAA) by removal of two side-chain methylene units in a process similar to fatty acid beta-oxidation. Previous studies implicate peroxisomes as the site of IBA metabolism, although the enzymes that act in this process are still being identified. Here, we describe two IBA-response mutants, ibr1 and ibr10. Like the previously described ibr3 mutant, which disrupts a putative peroxisomal acyl-CoA oxidase/dehydrogenase, ibr1 and ibr10 display normal IAA responses and defective IBA responses. These defects include reduced root elongation inhibition, decreased lateral root initiation, and reduced IBA-responsive gene expression. However, peroxisomal energy-generating pathways necessary during early seedling development are unaffected in the mutants. Positional cloning of the genes responsible for the mutant defects reveals that IBR1 encodes a member of the short-chain dehydrogenase/reductase family and that IBR10 resembles enoyl-CoA hydratases/isomerases. Both enzymes contain C-terminal peroxisomal-targeting signals, consistent with IBA metabolism occurring in peroxisomes. We present a model in which IBR3, IBR10, and IBR1 may act sequentially in peroxisomal IBA beta-oxidation to IAA.
High-performance polysilicon air-gap thin film transistor on low-temperature substrates (2003)

Three-dimensional polysilicon microstructures, as cantilevers or bridges, give new opportunities to increase the application field of polycrystalline silicon. Polysilicon devices with new functions can be imagined. Air-gap thin film transistors can be built from polysilicon bridges for example. They use a highly doped polysilicon bridge as gate; the gate insulator is the air or any other ambience. Then, these devices can be used as ambience sensors including chemical or biological sensors. They are very interesting as they are deposited on any substrate. Moreover, their main interest is their full compatibility with the microelectronics technology on glass performed at temperature lower than 600°C and developed first for the flat panel displays addressing. Fully integrated sensing systems are then imaginable. Here we present a low temperature process (< 600 °C) to built air-gap-polysilicon-thin-film-transistor with high mechanical and electrical performance. The transistor-active-layer is made of Low Pressure Chemical Vapor Deposition (LPCVD) undoped polysilicon while the suspended gate is made of LPCVD highly doped polysilicon. Deposition and annealing conditions of the doped polysilicon has first optimized to obtain high mechanical performance for the polysilicon micro-bridges. Hence, an optimal tensile stress to obtain longer bridges has been found. The mechanical stress has been determined from micro-Raman analysis. Then, air-gap transistors with 500 nm thick air-gap as gate insulator have been designed and fabricated. The transistor channel is 7-μm long and 7-μm wide, with a 15-μm long and 10-μm wide bridge. Their subthreshold slope, threshold voltage, and field effect mobility are 0.22 V/dec, 2.4 V and 130 cm<sup>2</sup>/V.sec respectively. These parameters are comparable to that of the best polysilicon thin film transistors with thin silicon dioxide (100 nm) as gate insulator. Then, these transistors are interesting as electronic devices firstly. Moreover they can be involved in ambience sensors. Indeed, they are checked as oxygen sensor in a preliminary experiment. Transistor characteristics are measured in air ambience, then in oxygen and finally in air. The electrical parameters have shown a considerable dependence on the ambience with an excellent recovering after removing oxygen.
An ultrasound-based system for temperature distribution measurements in injection moulding: system design, simulations and off-line test measurements in water (2013)

The polymer melt temperature in the screw ante-chamber of an injection moulding machine influences a number of parameters during the polymer process and therefore the final product quality. For measurement of this temperature, a sensor must be non-invasive (because of the axial moved screw during the injection of the plasticized polymer into the mould) and withstand the high pressure (>1000 bar) and temperature (>200 °C) during the injection moulding process. It is well known that the temperature of the polymer melt in the screw ante-chamber is inhomogeneous, and for that reason the sensor system must be able to measure the temperature spatially resolved. Due to the fact that sound velocity is temperature dependent, we developed a non-invasive tomography system using the transit times of ultrasonic pulses along different sound paths for calculating the temperature distribution in a polymer melt. Simulation results and example experiments at a test measurement setup are shown. Moreover, different strategies for the ultrasonic probe design (buffer rods, generation of wide beam angle) are discussed. The results of the proposed system are important for the validation of numerical simulations, a better understanding of the plasticizing process and can be used for the input of a novel temperature control system.
TREM-1 and its potential ligands in non-infectious diseases: from biology to clinical perspectives (2017)

Triggering receptor expressed on myeloid cells-1 (TREM-1) is expressed on the majority of innate immune cells and to a lesser extent on parenchymal cells. Upon activation, TREM-1 can directly amplify an inflammatory response. Although it was initially demonstrated that TREM-1 was predominantly associated with infectious diseases, recent evidences shed new light into its role in sterile inflammatory diseases. Indeed, TREM-1 receptor and its signaling pathways contribute to the pathology of several non-infectious acute and chronic inflammatory diseases, including atherosclerosis, ischemia reperfusion-induced tissue injury, colitis, fibrosis and cancer. This review, aims to give an extensive overview of TREM-1 in non-infectious diseases, with the focus on the therapeutic potential of TREM-1 intervention strategies herein. In addition, we provide the reader with a functional enrichment analysis of TREM-1 signaling pathway and potential TREM-1 ligands in these diseases, obtained via in silico approach. We discuss pre-clinical studies which show that TREM-1 inhibition, via synthetic soluble TREM-1 protein mimickers, is effective in treating (preventing) specific inflammatory disorders, without significant effects on antibacterial response. Further research aimed at identifying specific TREM-1 ligands, in different inflammatory disorders, is required to further unravel the role of this receptor, and explore new avenues to modulate its function.
Synthesis, characterization, and application of Ag nanostructures (2008)

Noble metal nanoparticles (NPs) have been used for many centuries; however their properties were not truly scrutinized until Michael Farady's investigations in the 1850's. Advances in the field of nanotechnology over the last three decades have enabled insights into the properties of materials as their dimensions are reduced to the nanoscale. The repercussions of these insights are seen in many modern applications. \tIn this dissertation, properties of novel nanostructures based on Ag NPs are presented and discussed. The exceptional optical properties of Ag NPs stem from the collective oscillations of the conduction electrons known as plasmon resonances. The excitation of plasmon resonances leads to the strongest known interaction of light with matter as compared to any known organic or inorganic chromophore. \tA novel type of nanostructure, composed of Ag NPs capped with various materials and termed asymmetric hybrid nanoparticles (AHNs) was proposed and implemented. The concept of AHNs allows the addition of new properties to nanoparticles. Metals and dielectric materials were used as caps, imparting strong effects on the plasmon resonances of the AHNs. Multilayer AHNs were fabricated to render magnetic properties to Ag NPs. \tThe AHN concept led to the development of a novel type of optical labels. The labels are based on the surface enhanced Raman scattering (SERS) phenomenon from organic molecules sandwiched between Ag core and Ag cap. The observed strong SERS is well suited for multiplexed assays with optical detection. The structures were also used for fundamental SERS investigations. An alternative enhancement mechanism termed plasmon-induced electronic coupling was proposed from the results. \tCapitalizing on their large cross-section for the interaction with light, Ag NPs were also investigated as optical labels based on light scattering. Ag NPs were encapsulated in silica shells, modified with amine functionalities, followed by conjugation with neutravidin molecules. Neutravidin offers a scaffold for attaching biotinylated biomolecules including antibodies. Silica shells provided nearly complete protection of Ag core in saline solutions often used in bioanalytical applications. The ongoing work focused on the application of these labels to flow cytometry.
Serological typing of Branhamella catarrhalis strains on the basis of lipopolysaccharide antigens (1990)

A total of 302 strains of Branhamella catarrhalis from different parts of the world were serologically typed according to their lipopolysaccharide (LPS) antigenicity. For this purpose, an inhibition enzyme-linked immunosorbent assay was developed using the following reagents: antisera raised against whole bacterial suspensions for a panel of 16 serotype strains and LPS prepared from these strains by phenol extraction. Antisera were absorbed with whole bacterial suspensions of the B. catarrhalis strains to be tested. The residual activity of the sera against the homologous LPS was determined by means of an enzyme-linked immunosorbent assay, using microdilution plates coated with LPS. Strains which gave greater than 90% reduction of activity were considered to carry the same LPS type as the serotype strain. It was shown that 93.4% of the strains tested carried one of three possible LPS types. LPS of B. catarrhalis are the rough type and have an apparent Mr of 5,500, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Tumor budding as a potential histopathological biomarker in colorectal cancer: Hype or hope? (2012)

Colorectal cancer (CRC), the third most commonly diagnosed type of cancer in men and women worldwide is recognized as a complex multi-pathway disease, an observation sustained by the fact that histologically identical tumors may have different outcome, including various response to therapy. Therefore, particularly in early and intermediate stage (stages II and III, respectively) CRC, there is a compelling need for biomarkers helpful of selecting patients with aggressive disease that might benefit from adjuvant and targeted therapy. Histopathological examination shows that likely other solid tumors the development and progression of human CRC is not only determined by genetically abnormal cells, but also by intricate interactions between malignant cells and the surrounding microenvironment. This has led to reconsider the features of tumor microenvironment as potential predictive and prognostic biomarkers. Among the histopathological biomarkers, tumor budding (i.e., the presence of individual cells and small clusters of tumor cells at the tumor invasive front) has received much recent attention, particularly in the setting of CRC. Although its acceptance as a reportable factor has been held back by a lack of uniformity with respect to qualitative and quantitative aspects, tumor budding is now considered as an independent adverse prognostic factor in CRC that may allow for stratification of patients into risk categories more meaningful than those defined by tumor-node-metastasis staging alone, and also potentially guide treatment decisions, especially in T2-T3 N0 (stage II) CRCs.
Time-optimal motion planning for robots (2010)

At the practical application of robots, the part processing time has a key role. The part processing time is an idea borrowed from manufacturing technology. In robotics it mostly means that the robots tool-centre point should go along some given path and the tool orientation in every point should also have the given values. These two requirements have to be satisfied at the same time. In the present paper we propose a method which provides the motion in every point of the path with the possible maximum velocity. In fact, we divide the path to transient and cruising parts and require the maximum velocities only for this second part. The given motion is called “Time-optimal cruising motion”. We demonstrate on an example the simplicity of the approach. Using the parametric method of motion planning, we give the equations for determining time-optimal motions. Not only the translation motions of tool-centre points but, also the orientation motions of tools may be optimally planned. The time-optimal motion planning is also possible for free paths (PTP motions). A general approach for this problem is proposed, too. In the paper, some parts are devoted to the deeper understanding of the optimization problems.
New leaders in dentistry: dental students. (2010)

Leadership opportunities for dental students have opened dramatically in recent decades because of the humanistic approach to education that shares responsibility for learning between students and faculty and that values mutual respect. Technology has also had an effect because it creates instant access and global communities. This new student leadership is most apparent in the American Student Dental Association (ASDA), which recently developed a White Paper on ethics, assisted in the establishment of Student Professionalism and Ethics Clubs at schools, and is developing a policy on unsupervised dental care. Students are also demonstrating leadership in research; in dual degrees that enhance teaching and policy; and in community service and outreach.
A fabrication technique for microlens array with high fill-factor and small radius of curvature (2008)

In this paper, we report a technique for microlens array (MLA) fabrication based on lithography and thermal reflow process. The boundary of MLA was defined by a thin photoresist (PR) layer. Then, the second thick PR cylinders were patterned inside the micro-holes from the first PR layer. MLA was formed after reflowing the second think PR cylinders. In the previous processes, the gaps between the thick PR cylinders were large due to the diffraction effect. To increase the fill-factor, some residual PR between the cylinders makes the PR flow outward. But the PR cylinders merge together easily due to inexact reflow time and temperature distribution. It results in small radius of curvature and low uniformity. In our work, the first thin PR became a limiting wall so that no cylinders merge together even at over reflow time. Therefore, both the uniformity and the radius of curvature can be well controlled. Besides, the gap is small and the fill-factor is very high due to the diffraction effect is not significant at first thin PR layer. The results show that the gaps are only 2 um and the radius of curvature is approximately 24 um for MLA with 50 um in pitch and hexagonal arrangement.
Efficient grinding of high-performance materials (2008)

A significant driver in research activities of manufacturers and university institutions is the improvement of productivity in abrasive machining processes. This paper gives an insight into innovative grinding concepts, which have demonstrated significant potential for specific machining tasks. Examples of numerical simulations of abrasive processes, which improve knowledge regarding the fundamental process principles are given. In addition, high-performance cutting tools that could be realised enabled by the latest developments in grinding and preparation technologies are discussed.
QoS Transparency for Native IP Networks (2006)

This paper addresses the issue of QoS internetwork-operability when an ISP's or MSO's native IP network serves as transit or backbone to business customers whose sites span various geographic regions. The QoS interworking mechanism described in this paper is also applicable for VoIP peering among MSOs and/or ISPs. In addition, a mechanism is proposed in this paper to obtain appropriate QoS treatment in an egress router (egress PE4) when the ISP/MSO has an MPLS-enabled network. Due to penultimate hop popping (PHP), packets arrive at the egress PE of a MPLS network as native IP packets. Because of this a mechanism to preserve original QoS information of a packet across a network boundary, while allowing the ISP/MSO to key on its own marking for PHB (per hop behavior) determination, is clearly needed
A sequential decoder for linear block codes with a variable bias-term metric (1998)

A sequential decoder for linear block codes that performs maximum-likelihood soft-decision decoding is described. The decoder uses a metric computed from a lower bound on the cost of the unexplored portion of the code tree. It is shown that for certain block codes the average computational complexity of this metric is superior to that of the Fano metric. A new function, the cumulative column distance function, is introduced for linear block codes. This function is an important factor that determines the average computational effort of a sequential decoder for a linear block code with an arbitrary maximum-likelihood metric. Simulation results show that a sequential decoder for linear block codes with a fast growing cumulative column distance function achieves a low computational complexity, a result analogous to that for convolutional codes.
[Research on the polymorphism of heart fatty acid-binding protein gene in Shanxi pig breeds and their crossbred populations using PCR-RFLP]. (2005)

The genetic variation in 5' - upstream (Hinf I -RFLP)and the second intron (Hinf I *-RFLP, Hae III-RFLP)of heart fatty acid-binding protein(H-FABP)gene were detected with PCR-RFLP in 286 pigs including Mashen, Shanxi white pig and their crossbred populations. The results showed as follows: (1)Mashen presented only DD genotype while other populations varied,and Mashen crossbred populations had only 2 genotypes(DD, Dd) at the Hae III-RFLP site; (2)At the Hinf I -RFLP site of the 5' -upstream region, the crossbred population of Shanxi white pig and Duroc presented only HH genotype while other populations varied. Frequency of h allele in Mashen was 0.9727. (3)At the Hinf I *-RFLP site of the second intron, only Mashen presented 2 genotypes (BB, Bb), and frequency of B allele was 0.9667. (4)At the Hae III-RFLP and Hinf I *-RFLP sites, all populations were in Hardy-weinberg equilibrium.
Oligomeric and polymeric aggregates formed by proteins containing expanded polyglutamine (2003)

Neurological diseases resulting from proteins containing expanded polyglutamine (polyQ) are characteristically associated with insoluble neuronal inclusions, usually intranuclear, and neuronal death. We describe here oligomeric and polymeric aggregates formed in cells by expanded polyQ. These aggregates are not dissociated by concentrated formic acid, an extremely effective solvent for otherwise insoluble proteins. Perinuclear inclusions formed in cultured cells by expanded polyQ can be completely dissolved in concentrated formic acid, but a soluble protein oligomer containing the expanded polyQ and released by the formic acid is not dissociated to monomer. In Huntington's disease, a formic acid-resistant oligomer is present in cerebral cortex, but not in cerebellum. Cortical nuclei contain a polymeric aggregate of expanded polyQ that is insoluble in formic acid, does not enter polyacrylamide gels, but is retained on filters. This finding shows that the process of polymerization is more advanced in the cerebral cortex than in cultured cells. The resistance of oligomer and polymer to formic acid suggests the participation of covalent bonds in their stabilization.
Modulation of the hyperpolarization-activated current (If) by calcium and calmodulin in the guinea-pig sino-atrial node (2003)

The aim of this study was to investigate possible regulation of the hyperpolarization-activated current (I(f)) by cytosolic calcium in guinea-pig sino-atrial (SA) node cells. Isolated SA node cells were superfused with physiological saline solution (36 degrees C) and the perforated patch voltage-clamp technique used to record I(f) activated by hyperpolarizing voltage steps. A 10-min loading of SA node cells with the calcium chelator BAPTA (using 10 microM BAPTA-AM) significantly reduced the amplitude of I(f) at all potentials studied (69+/-8% at -80 mV, n=6). BAPTA loading also shifted the voltage of half-activation (V(h)) of the conductance from -83+/-2 mV in control to -93+/-2 mV in BAPTA (n=6) without significantly altering the slope of activation. The calmodulin antagonists W-7 (10 microM), calmidazolium (25 microM) and ophiobolin A (20 microM) caused similar reductions in I(f) amplitude (73+/-4, 86+/-9 and 59+/-6% at -80 mV, n=6, 5 and 4, respectively) and shifts in V(h) (11+/-3, 14+/-3 and 8+/-2 mV). In cells pre-treated with W-7, exposure to BAPTA caused no further reduction in current amplitude (n=6). I(f) current amplitude was unaffected by the calmodulin dependent kinase (CaMKII) inhibitor KN-93 (1 microM) although this CaMKII inhibition did reduce L-type calcium by 48+/-19% at 0 mV (n=3). These results are consistent with a role for calcium and calmodulin in the regulation of I(f), via a mechanism that is independent of CaMKII. Alterations in intracellular calcium during the cardiac cycle may be involved in fine tuning the voltage-dependent properties of I(f) and may thus determine its relative contribution to pacemaking in the SA node.
Multiplexed Sequence Encoding: A Framework for DNA Communication (2016)

Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.
Anonymity and Security in Public Internet Forums (2006)

In this paper, we first introduce the privacy and security requirements in public forums, which include anonymity, traceability, impossibility of impersonation, unforgeability, verifiability, fairness, easy anonymity revocation, and un-involvement of authorities. We then propose an anonymous and secure forum protocol based on a concept of alias certificate with detailed analysis to show that our scheme satisfies all these requirements. In particular, participants only need to register once with the authorities and the authorities are not involved during message postings, yet the anonymity of participants and the traceability of malicious information can be achieved. This can greatly increase the usability and efficiency as participants often post messages frequently.