gebhart/patrepeval huggingface dataset:
Fatigue improvement of welded bridge details in stainless steel using High-Frequency Mechanical Impact treatment (2018)

This paper reports the results from fatigue testing on welded non-load-carrying transverse attachments made of C-Mn (S460) and stainless (LDX2101) steels. The tests are done on 40 mm thick specimens in as-welded and HFMI-treated specimens. Measurements on weld toe radius and weld residual stresses are also reported. The results show that the improvement of fatigue strength that can be achieved by HFMI-treatment on welded LDX2101 steel is similar to what is obtained for equivalent C-Mn steels. Also in the as-welded condition do these two types of steel show similar fatigue strength. HFMI-treatment gives more than 5 steps increase in fatigue strength for both steels, which is higher than what specified, for example by the recommendations of the International Institute of Welding.
Lipid Segregation Explains Selective Toxicity of a Series of Fragments Derived from the Human Cathelicidin LL-37 (2009)

The only human cathelicidin, the 37-residue peptide LL-37, exhibits antimicrobial activity against both gram-positive and gram-negative bacteria. We studied the ability of several fragments of LL-37, exhibiting different antimicrobial activities, to interact with membranes whose compositions mimic the cytoplasmic membranes of gram-positive or of gram-negative bacteria. These fragments are as follows: KR-12, the smallest active segment of LL-37, with the sequence KRIVQRIKDFLR, which exhibits antimicrobial activity only against gram-negative bacteria; a slightly smaller peptide, RI-10, missing the two cationic residues at the N and C termini of KR-12, which has been shown not to have any antimicrobial activity; a longer peptide, GF-17, which shows antimicrobial activity against gram-positive as well as gram-negative bacteria; and GF-17D3, with 3 D-amino-acid residues, which is also selective only for gram-negative bacteria. Those fragments with the capacity to cluster anionic lipids away from zwitterionic lipids in a membrane exhibit selective toxicity toward bacteria containing zwitterionic as well as anionic lipids in their cytoplasmic membranes but not toward bacteria with only anionic lipids. This finding allows for the prediction of the bacterial-species selectivity of certain agents and paves the way for designing new antimicrobials targeted specifically toward gram-negative bacteria.
Expansion of Smartwatch Touch Interface from Touchscreen to Around Device Interface Using Infrared Line Image Sensors (2015)

Touchscreen interaction has become a fundamental means of controlling mobile phones and smartwatches. However, the small form factor of a smartwatch limits the available interactive surface area. To overcome this limitation, we propose the expansion of the touch region of the screen to the back of the user's hand. We developed a touch module for sensing the touched finger position on the back of the hand using infrared (IR) line image sensors, based on the calibrated IR intensity and the maximum intensity region of an IR array. For complete touch-sensing solution, a gyroscope installed in the smartwatch is used to read the wrist gestures. The gyroscope incorporates a dynamic time warping gesture recognition algorithm for eliminating unintended touch inputs during the free motion of the wrist while wearing the smartwatch. The prototype of the developed sensing module was implemented in a commercial smartwatch, and it was confirmed that the sensed positional information of the finger when it was used to touch the back of the hand could be used to control the smartwatch graphical user interface. Our system not only affords a novel experience for smartwatch users, but also provides a basis for developing other useful interfaces.
Seventh Workshop on Exploiting Semantic Annotations in Information Retrieval (ESAIR'14) (2014)

There is an increasing amount of structure on the Web as a result of modern Web languages, user tagging and annotation, emerging robust NLP tools, and an ever growing volume of linked data. These meaningful, semantic, annotations hold the promise to significantly enhance information access, by enhancing the depth of analysis of today's systems. The goal of the ESAIR'14 workshop remains to advance the general research agenda on this core problem, with an explicit focus on one of the most challenging aspects to address in the coming years. The main remaining challenge is on the user's side - the potential of rich document annotations can only be realized if matched by more articulate queries exploiting these powerful retrieval cues - and a more dynamic approach is emerging by exploiting new forms of query autosuggest. How can the query suggestion paradigm be used to encourage searcher to articulate longer queries, with concepts and relations linking their statement of request to existing semantic models? How do entity results and social network data in "graph search" change the classic division between searchers and information and lead to extreme personalization - are you the query? How to leverage transaction logs and recommendation, and how adaptive should we make the system? What are the privacy ramifications and the UX aspects - how to not creep out users?
Quantitative photoacoustics to measure single cell melanin production and nanoparticle attachment (2015)

Photoacoustics can be used as a label-free spectroscopic method of identifying pigmented proteins and characterizing their intracellular concentration over time in a single living cell. The authors use a microscopic laser irradiation system with a 5 ns, Q-switched laser focused onto single cells in order to collect photoacoustic responses of melanoma cells from the HS936 cell line and gold nanoparticle labeled breast cancer cells from the T47D cell line. The volume averaged intracellular concentration of melanin is found to range from 29-270 mM for single melanoma cells and the number of gold nanoparticles (AuNP) is shown to range from 850-5900 AuNPs/cell. Additionally, the melanin production response to UV-A light stimulus is measured in four melanoma cells to find a mass production rate of 5.7 pg of melanin every 15 min.
Pathway Proteomics and Chemical Proteomics Team Up in Drug Discovery (2007)

Over the last 5 years, impressive technical advances in mass spectrometry-based analysis of proteins have enabled the parallel analysis of subproteomes and entire proteomes, thus triggering the departure from the traditional single gene-single protein-single target paradigm. Today, immunoaffinity chromatography as well as generic purification methods employing engineered composite affinity tags make streamlined identification of protein complexes as molecular machines possible. In addition, use of stable isotope techniques in protein mass spectrometry allows for the characterization of protein complex composition and posttranslational modifications in an increasingly quantitative fashion. Together, these methodologies allow the elucidation of medically relevant biological pathways, and the study of the interaction of their protein components with therapeutic agents, on a much larger scale. The present review discusses some of the current experimental strategies, with a focus on applications in neurobiology.
Microsatellite status and cell cycle associated markers in rectal cancer patients undergoing a combined regimen of 5-FU and CPT-11 chemotherapy and radiotherapy. (2004)

We conclude that a molecular profile characterized by high microsatellite instability with loss of mismatch repair protein expression and p21WAF1/C1PI is predictive of an improved response to neoadjuvant treatment with 5-FU, CPT-11 and radiation therapy.
Sensing Characteristics of Arc-Induced Long Period Gratings in Polarization-Maintaining Panda Fiber (2017)

We present and discuss an investigation of the sensing features of long period gratings fabricated in a polarization-maintaining Panda optical fiber, by means of the electric arc discharge technique. In particular, the investigation regards the resonant wavelength shift of first three cladding modes as function of three environmental parameters, such as strain, temperature, and surrounding medium refractive index. We also investigate and discuss the variations of the sensing behavior as a function of the polarization input state. The achieved results show that the sensitivity of each resonant wavelength to environmental parameters is modulated by the cladding mode order and by polarization input light, with some appealing characteristics. For instance, the lowest order cladding mode in slow polarization state is practically insensitive to temperature and surrounding refractive index, but sensitive to strain. Temperature and strain sensitivities show opposite signs with the input light polarization. Sensitivity to surrounding refractive index is higher in the case of fast polarization state. These results represent a concrete perspective of the possibility that this device can act as a 3-parameter sensor.
Fabrication of Green Diatomite/Chitosan-Based Hybrid Foams with Dye Sorption Capacity (2020)

The latest tendency of the scientific community regards the development of different classes of green materials able to solve pollution problems caused by industrial and human activity. In this paper, chitosan and diatomite were used to produce a broad-spectrum hybrid adsorbent, either in powder or in monolithic form for environmental pollutant removal. Diatomite-chitosan-based powders and porous diatomite-chitosan hybrids were prepared and characterized by chemical-physical, thermal and morphological analysis. Moreover, their adsorbent capacity towards anionic dye (Indigo Carmine) was also evaluated. Obtained data showed that chitosan improves the adsorption capacity of both systems, increasing the uptake of dye in both diatomite-chitosan systems.
The Context Theory as Applied to the Decoding of the Initiator tRNA by Escherichia coli Ribosomes (1982)

The involvement of nucleotides adjacent to the termination codons in tRNA during the suppression of termination has been formulated as the 'context theory' by Bossi and Roth (1980) [Nature (Lond.) 286, 123-127]. The finding that U-U-G functions as an initiator codon has revived the discussion on the participation of the nucleotides flanking the initiator triplet in the decoding of initiator tRNA (context theory of initiation by the ribosome). We compared the capacity of oligonucleotides cognate to the anticodon loop of formylmethionine tRNA, such as A-U-G, A-U-G-A and U-A-U-G-A, to enhance the formation of the 30-S and 70-S ribosomal initiation complexes. Three different methods were used to determine the apparent binding constants and the stoichiometries of the respective complexes: adsorption of the complexes to nitrocellulose filters, equilibrium dialysis, and velocity sedimentation. We found that in the 30-S ribosomal initiation complex and in the presence of initiation factor 2 and GTP, formylmethionyl-tRNA is preferentially decoded by more than three mRNA bases. With the 70-S ribosome, however, once initiation factor 2 had been released, A-U-G represented the most effective codon to direct the formylmethionyl-tRNA to the peptidyl site. An extended initiator sequence may either give additional stability to the 30-S initiation complex or may allow for an ambiguity by one base pair in the decoding of the initiator tRNA.
The effect of graft‐versus‐host disease on outcomes after allogeneic stem cell transplantation for refractory lymphoblastic lymphoma in children and young adults (2019)

Our results suggest that the occurrence of aGVHD may be associated with better outcomes in patients with relapsed/refractory LBL who undergo allogeneic transplantation.
Harmonic Characteristics of Rectifier Substations and Their Impact on Audio Frequency Track Circuits (2013)

This report describes the basic operation of substation rectifier equipment and the modes of possible interference with audio frequency track circuits used for train detection, cab signaling, and vehicle speed control. It also includes methods of estimating EM noise received by track circuits from substation operation.
Efficient Screening of Combinatorial Peptide Libraries by Spatially Ordered Beads Immobilized on Conventional Glass Slides (2019)

Screening of one-bead-one-compound (OBOC) libraries is a proven procedure for the identification of protein-binding ligands. The demand for binders with high affinity and specificity towards various targets has surged in the biomedical and pharmaceutical field in recent years. The traditional peptide screening involves tedious steps such as affinity selection, bead picking, sequencing, and characterization. Herein, we present a high-throughput "<i>all-on-one chip</i>" system to avoid slow and technically complex bead picking steps. On a traditional glass slide provided with an electrically conductive tape, beads of a combinatorial peptide library are aligned and immobilized by application of a precision sieve. Subsequently, the chip is incubated with a fluorophore-labeled target protein. In a fluorescence scan followed by matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry, high-affinity binders are directly and unambiguously sequenced with high accuracy without picking of the positive beads. The use of an optimized ladder sequencing approach improved the accuracy of the de-novo sequencing step to nearly 100%. The new technique was validated by employing a FLAG-based model system, identifying new peptide binders for the monoclonal M2 anti-FLAG antibody, and was finally utilized to search for IgG-binding peptides. In the present format, more than 30,000 beads can be screened on one slide.
Embrittlement Properties of Aluminum Alloys 7075 and 6061 in High-Pressure Gaseous Hydrogen (2009)

SSRT (slow strain-rate technique) tests were carried out using smooth- or notched-tensile specimen of aluminum alloy plates 7075-T6 and 6061-T6 in gaseous hydrogen under high-pressure 70 or 85MPa, as compared with in 90% relative humidity air under atmospheric pressure. For 7075 the humid air caused a significant embrittlement, leading to intergranular cracking, while in contrast the high-pressure hydrogen gas resulted in little embrittlement, where the transgranular fracture mode attributed to hydrogen effect was however observed, showing an enhancement of void coalescence. The result indicates that high-pressre gaseous hydrogen is much less severe to provide hydrogen to aluminum materials than humid air. On the other hand, 6061 was found to be immune to hydrogen embrittlement in either environment. It was then comprehended that the aluminum alloys represented a series of change in fracture mode from transgranular to intergranular with increase in hydrogen concentration.
Immunogenicity of IpaC-Hybrid Proteins Expressed in theShigella flexneri2a Vaccine Candidate SC602 (1998)

We have investigated the capacity of live attenuated Shigella flexneri strains to act as vectors for the induction of local and systemic antibody responses against heterologous epitopes. The S. flexneri IpaC antigen was selected as a carrier protein into which the C3 neutralizing epitope of the poliovirus VP1 protein was inserted in eight sites distributed along IpaC. The resulting IpaC-C3 hybrid proteins were expressed from recombinant plasmids in the S. flexneri 2a vaccine candidate, SC602. Their production was similar to that of wild-type IpaC. All of the hybrid proteins but one were secreted as efficiently as wild-type IpaC. Immunization of mice with each of the recombinant SC602 derivatives reveals that one construct is able to induce serum and local anti-C3 antibodies, showing that at least one permissive site of insertion within IpaC can be defined. Furthermore, mouse-to-mouse variability in the anti-C3 response indicates that the amount of hybrid proteins produced in the host by SC602 should be improved for optimal use of S. flexneri live attenuated strains as mucosal vectors for foreign epitopes.
Exponential expressivity in deep neural networks through transient chaos (2016)

We combine Riemannian geometry with the mean field theory of high dimensional chaos to study the nature of signal propagation in deep neural networks with random weights. Our results reveal a phase transition in the expressivity of random deep networks, with networks in the chaotic phase computing nonlinear functions whose global curvature grows exponentially with depth, but not with width. We prove that this generic class of random functions cannot be efficiently computed by any shallow network, going beyond prior work that restricts their analysis to single functions. Moreover, we formally quantify and demonstrate the long conjectured idea that deep networks can disentangle exponentially curved manifolds in input space into flat manifolds in hidden space. Our theoretical framework for analyzing the expressive power of deep networks is broadly applicable and provides a basis for quantifying previously abstract notions about the geometry of deep functions.
CYP-Dependent Metabolism of PF9601N, A New Monoamine Oxidase-B Inhibitor, by C57BL / 6 Mouse and Human Liver Microsomes (2007)

The observed favourable metabolic profile may suggest suitability of PF9601N for clinical use.
Compound 3K, a Specific Pyruvate Kinase M2 Inhibitor, Induces Autophagic Cell Death through the Disruption of the Glycolytic Pathway in Ovarian Cancer Cells (2020)

Ovarian cancer is the common cause of death among gynecological cancers. Although ovarian cancer initially responds to chemotherapy, the frequent recurrence in patients remains a therapeutic challenge. Pyruvate kinase M2 (PKM2) plays a pivotal role in regulating cancer cell survival. However, its therapeutic roles remain unclear. Here, we investigated the anticancer effects of compound 3K, a specific PKM2 inhibitor, on autophagic and apoptotic pathway regulation in SK-OV-3 (PKM2-overexpressing human ovarian adenocarcinoma cell line). The anticancer effect of compound 3K was examined using the MTT and colony formation assay in SK-OV-3. The results of tissue microarray showed that PKM2 expression positively correlated with the severity of the tumor. Moreover, the expression of pro-apoptotic proteins increased in SK-OV-3 following compound 3K treatment. Compound 3K induced AMPK activation, which was accompanied by the inhibition of mTOR. Additionally, this compound inhibited glycolysis, resulting in reduced proliferation in SK-OV-3. Compound 3K treatment suppressed tumor progression in vivo xenograft model. Our findings suggest that the inhibition of PKM2 by compound 3K affected Warburg effects and induced autophagic cell death. Therefore, the use of specific PKM2 inhibitors to block the glycolytic pathway and target cancer cell metabolism represents a promising therapeutic approach for treating PKM2-overexpressing ovarian cancer.
WE‐C‐116‐10: Univariate, Multivariate, and Nonlinear Uncertainty Quantification for Magnetic Resonance‐Guided Laser Induced Thermal Therapy (2013)

Purpose: MR‐guided laser‐induced thermal therapy (MRgLITT) is an emerging minimally invasive neurosurgical tool being explored as a treatment alternative for conditions such as motion disorder, radiation necrosis, and intracranial metastases. The primary goal is to reduce complications and normal tissue morbidity associated with conventional surgery. Computational models are being investigated to aid prospective LITT planning; however, accuracy is undermined by imprecise and non‐patient specific knowledge of parameters. This work explores incorporating uncertainty quantification (UQ) of temperature output from the stochastic Pennes bioheat transfer equation (BHT). Methods: A five parameter (perfusion, thermal conductivity, optical absorption, optical scattering) stochastic BHT LITT model was used. Parameters were considered to be uniform distributions with ranges informed by literature values. Generalized polynomial chaos (gPC) was employed to calculate spatio‐temporal, voxel‐wise functions of the output temperature distributions for UQ. BHT parameter sensitivity in linear and nonlinear models was explored in silico using univariate gPC. Retrospective analysis of MR thermography (MRTI) from both phantom and MRgLITT in normal canine brain in vivo (n=4) was explored using multivariate gPC. Isotherms, temporal and linear profiles were reported. Results: Univariate simulations demonstrated that optical parameters explained the majority of model variance (peak standard deviation: anisotropy 3.75 °C, absorption 2.94 °C, scattering 1.84 °C, conductivity 1.42 °C, and perfusion 0.94 °C). Linear model variance enclosed nonlinear model variance. Mean temperature and 95% confidence interval from multivariate simulations correlated well with measured heating even near the applicator. Conclusion: gPC may provide robust and relatively fast UQ facilitating useful prospective LITT planning in brain tissue despite imprecise knowledge of parameters. The faster linear simulation approximated the nonlinear simulation without excessive variance. Further, the computational burden was reduced with minimal accuracy loss by including only the most sensitive parameters. Subsequent work includes applying stochastic BHT to retrospective human brain tumor LITT.
Resistance to antiangiogenic therapy is directed by vascular phenotype, vessel stabilization, and maturation in malignant melanoma (2013)

Angiogenesis is not only dependent on endothelial cell invasion and proliferation, it also requires pericyte coverage of vascular sprouts for stabilization of vascular walls. Clinical efficacy of angiogenesis inhibitors targeting the vascular endothelial growth factor (VEGF) signaling pathway is still limited to date. We hypothesized that the level of vessel maturation is critically involved in the response to antiangiogenic therapies. To test this hypothesis, we evaluated the vascular network in spontaneously developing melanomas of MT/ret transgenic mice after using PTK787/ZK222584 for anti-VEGF therapy but also analyzed human melanoma metastases taken at clinical relapse in patients undergoing adjuvant treatment using bevacizumab. Both experimental settings showed that tumor vessels, which are resistant to anti-VEGF therapy, are characterized by enhanced vessel diameter and normalization of the vascular bed by coverage of mature pericytes and immunoreactivity for desmin, NG-2, platelet-derived growth factor receptor beta, and the late-stage maturity marker alpha smooth muscle actin. Our findings emphasize that the level of mural cell differentiation and stabilization of the vascular wall significantly contribute to the response toward antiangiogenic therapy in melanoma. This study may be useful in paving the way toward a more rational development of second generation antiangiogenic combination therapies and in providing, for the first time, a murine model to study this.
Project team building to improve the safety culture and prevention of electrical incidents (2017)

In the past, and currently, general contractors (GC) have been known to push the schedule to a point where a subcontractor (Sub) may overlook or deliberately take short cuts to meet deadlines. Taking a step back and looking at the larger picture, the goal for every project should be to build it safely, efficiently, and with quality, whether you are the GC or a Sub. The question we have to ask ourselves is “If the objectives of two companies run parallel then why is there so much resistance to working together as a team”. This paper will present some of the “best practices”, innovative ideas, and electrical summits that have been developed to help overcome the barriers between GC and Subs. To be clear, there are no “quick fixes” or a “magic pill” that a company can implement to solve this problem. A successful safety culture in a company requires a commitment starting at the top, and on a jobsite it starts with a GC taking the time to understand the process and facilitate a team environment.