gebhart/patrepeval huggingface dataset:
Integrated fiducial sample mount and software for correlated microscopy (2014)

A novel sample mount design with integrated fiducial marks and software for assisting operators in easily and efficiently locating points of interest established in previous analytical sessions is described. The sample holder and software were evaluated with experiments to demonstrate the utility and ease of finding the same points of interest in two different microscopy instruments. Also, numerical analysis of expected errors in determining the same position with errors unbiased by a human operator was performed. Based on the results, issues related to acquiring reproducibility and best practices for using the sample mount and software were identified. Overall, the sample mount methodology allows data to be efficiently and easily collected on different instruments for the same sample location.
New Sulfur-Containing Polyarsenicals from the New Caledonian Sponge Echinochalina bargibanti (2018)

Arsenicin A (C₃H₆As₄O₃) was isolated from the New Caledonian poecilosclerid sponge <i>Echinochalina bargibanti</i>, and described as the first natural organic polyarsenic compound. Further bioguided fractionation of the extracts of this sponge led us to isolate the first sulfur-containing organic polyarsenicals ever found in Nature. These metabolites, called arsenicin B and arsenicin C, are built on a noradamantane-type framework that is characterized by an unusual As⁻As bonding. Extensive NMR measurements, in combination with mass spectra, enabled the assignment of the structure for arsenicin B (C₃H₆As₄S₂) as <b>2</b>. The scarcity of arsenicin C and its intrinsic chemical instability only allowed the collection of partial spectral data, which prevented the full structural definition. After the extensive computational testing of several putative structures, structure <b>3</b> was inferred for arsenicin C (C₃H₆As₄OS) by comparing the experimental and density functional theory (DFT)-calculated ¹H and <sup>13</sup>C NMR spectra. Finally, the absolute configurations of <b>2</b> and <b>3</b> were determined with a combined use of experimental and time-dependent (TD)-DFT calculated electronic circular dichroism (ECD) spectra and observed specific rotations. These findings pose great challenges for the investigation of the biosynthesis of these metabolites and the cycle of arsenic in Nature. Arsenicins B and C showed strong antimicrobial activities, especially against <i>S. aureus</i>, which is comparable to the reference compound gentamycin.
MetroViz: Visual Analysis of Public Transportation Data (2015)

Understanding the quality and usage of public transportation resources is important for schedule optimization and resource allocation. Ridership and adherence are the two main dimensions for evaluating the quality of service. Using Automatic Vehicle Location (AVL), Automatic Passenger Count (APC), and Global Positioning System (GPS) data, ridership data and adherence data of public transportation can be collected. In this paper, we discuss the development of a visualization tool for exploring public transportation data. We introduce "map view" and "route view" to help users locate stops in the context of geography and route information. To visualize ridership and adherence information over several years, we introduce "calendar view" - a miniaturized calendar that provides an overview of data where users can interactively select specific days to explore individual trips and stops ("trip subview" and "stop subview"). MetroViz was evaluated via a series of usability tests that included researchers from the Center for Advanced Transportation Technology (CATT) and students from the University of Maryland - College Park in which test participants used the tool to explore three years of bus transit data from Blacksburg, Virginia.
4 and 7 GHz solidly mounted thickness extension mode bulk acoustic wave resonators using 36°Y LiNbO3 (2023)

Abstract This paper describes 4 and 7 GHz solidly-mounted structure bulk acoustic wave resonators (SM-BAWRs) using LiNbO 3 (LN) thin plates. A Bragg reflector solidly supports the LN thin plate. The two kinds of SM-BAWRs use thickness extension mode in 0.81 and 0.5 μ m thick 36°Y LNs. The Bragg reflector is made of Al or SiO 2 , and Ta films. The 0.81 μ m thick LN SM-BAWRs with each acoustic layer thickness 0.23 wavelength ( λ ), which is almost optimum thickness, exhibited resonance frequency ( f r ) of 3.84 GHz, antiresonance frequency ( f a ) of 4.17 GHz, a bandwidth of 8.4%, an impedance ( Z ) ratio of 54 dB, and coupling factor k t 2 of 17.7%. Despite using an acoustic film 0.12 λ much thinner than the optimum thickness, SM-BAWR using the 0.5 μ m thick LN exhibited f r of 6.86 GHz, f a of 7.15 GHz, and Z ratio of 37 dB. Those results suggest a high potential for this device.
Riechen: Normale Funktion und Störungen (2005)

Im Folgenden wird eine Übersicht zu normalen und pathologischen Abläufen beim Riechen gegeben. Im Mittelpunkt der Arbeit stehen olfaktorische Störungen und deren in der neurologischen Praxis relevante Ursachen. Zuverlässige klinische Riechtests sowie objektivierende Messmethoden und Verfahren der klinischen Riechforschung werden vorgestellt. Neben den etablierten Therapieverfahren bei sinunasal bedingten Riechstörungen werden auch Ansätze zur pharmakologischen Therapie bei posttraumatischen und postviralen Riechdefiziten diskutiert.
Natural Language Interface for Process Mining Queries in Healthcare (2022)

Recently, the needs of data required for data analysis are becoming more diversified, and research on data extraction and analysis methods has been continuously made in order to effectively respond to various needs. Process mining is a solution that analyzes various system logs built by companies or healthcare institutions so that they can be used for process improvement. From the process model extracted from the system logs, it is possible not only to grasp the exact flow of the current business process, but also to acquire additional information such as repetitive execution of activities in the process where the bottleneck occurs in the business process flow. The manufacturing industry has made great efforts to improve the process management, and as many companies are paying attention to big data these days, various data-related technologies are emerging in the healthcare industry as well to properly provide patients with the care needed. Process mining tools allow users to pull data by programming in a process mining query language using the APIs provided with the process mining tool, or by manually creating reusable analytical documents using user friendly tool. However, these tasks require the users to be familiar with the query language APIs and understand the data model and its relationships with respect to creating analytical documents. This paper proposes a methodology that allows users to easily extract desired data through natural language interface, which relieves nonprofessional users of the burden of programming in a process mining query language. The process mining query engine with natural language interface presented in this paper consists of four major components. Among them, the natural language processing pipeline that not only extracts intermediate representation of entities used when constructing a process mining query language report from natural language queries, but also effectively extracts a query hint from the context of natural language query. The query hint is used to select a process-specific function from the library that fits the context of the user query while transforming a natural language query into a process mining query report. The method proposed in this study has the advantage of being able to roughly grasp the process state for the user just by entering a query in natural language. The proposed system provides users with four query process options. That is, the user 1) retrieves intermediate representation of entities and query hints from the NLP pipeline, 2) retrieves the process mining query language from the query language generator, 3) submits the query language to the process mining engine and execute the query, 4) retrieves description of intermediate representation of entity and query hints in natural language to confirm that the query is processed correctly. The contents proposed in this paper were constructed and executed, and the query reports in process mining query language programmatically generated by the proposed query engine were also executed in a process mining engine and the query results were verified.
Physics-Guided Sparse Identification of Nonlinear Dynamics for Prediction of Vehicle Cabin Occupant Thermal Comfort (2022)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Thermal cabin comfort is the largest consumer of battery energy second only to propulsion in Battery Electric Vehicles (BEV’s). Accurate prediction of thermal comfort in the vehicle cabin with fast turnaround times will allow engineers to study the impact of various thermal comfort technologies and develop energy efficient Heating, Ventilation and Air Conditioning (HVAC) systems. In this study a novel data-driven model based on physics-guided Sparse Identification of Nonlinear Dynamics (SINDy) method was developed to predict Equivalent Homogeneous Temperature (EHT), Mean Radiant Temperature (MRT) and cabin air temperature under transient conditions and drive cycles. EHT is a recognized measure of the total heat loss from the human body that can be used to characterize highly non-uniform thermal environments such as a vehicle cabin. The SINDy model was trained on drive cycle data from Climatic Wind Tunnel (CWT) for a representative Battery Electric Vehicle. The performance of the trained model was evaluated on drive cycle data from a Coldbox test for the same vehicle. Based on a physics-based transient lumped cabin comfort model three state variables (EHT, MRT and cabin air temperature) and four control inputs were chosen to develop the SINDy model. In addition to the control inputs, interaction terms between the different control inputs were also included. Despite training with limited data (two trajectories of different time lengths) the model learned the dynamics of the vehicle cabin and was able to predict EHT, MRT and cabin air temperature for a new set of control inputs reasonably well. The SINDy model can be used for predictions of thermal comfort under transient conditions with significantly lower turnaround times compared to physics-based simulations. It is an alternative to black box models by providing insights into the mechanisms driving a dynamical system.&lt;/div&gt;&lt;/div&gt;
L and S band low-loss filters using SAW resonators (1994)

This paper describes L and S band low-loss filters using one-port SAW resonators in a ladder circuit structure. Four kinds of filters were developed. Three types have a wide frequency band, with fractional bandwidth of about 4%. A 36° y-x LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> substrate was used for these. The last type of filter has a narrow frequency band, with 0.03% of fractional bandwidth, and used an ST-cut quartz substrate. To design these ladder type SAW filters, several important factors were considered, the static capacitance of IDT, the period of IDT and film thickness. For fabrication, i-line stepper and reactive ion etching was used to delineate fine IDT patterns with line and gap width of 0.4 to 0.7 μm. Minimum insertion losses of 2 dB were obtained for the three wide band filters. The insertion loss of the narrow band filter was 6 dB. The input and output impedance of these filters were 50 Ω. The filters were mounted in 3 mm×3 mm×1 mm or 3.8 mm×3.8 mm×1.5 mm SMT packages
온도응력을 고려한 토공구간 급속경화궤도의 거동 분석 (2015)

급속경화궤도는 자갈궤도에 급속경화 모르타르를 충진하여 콘크리트 궤도화 하는 공법으로 자갈궤도의 유지보수비 절감 및 강도 증진을 위해 개발되었다. 급속경화궤도는 무근 콘크리트 슬래브 구조물이므로 허용인장응력을 필히 고려해야 한다. 현재 콘크리트 도로 포장 분야에서는 콘크리트 슬래브와 보조기층 사이의 마찰특성과 온도응력에 관한 연구는 다양하게 이루어져 왔으나,...
Focus on the physics of biofilms (2015)

Bacteria are the smallest and most abundant form of life. They have traditionally been considered as primarily planktonic organisms, swimming or floating in a liquid medium, and this view has shaped many of the approaches to microbial processes, including for example the design of most antibiotics. However, over the last few decades it has become clear that many bacteria often adopt a sessile, surface-associated lifestyle, forming complex multicellular communities called biofilms. Bacterial biofilms are found in a vast range of environments and have major consequences on human health and industrial processes, from biofouling of surfaces to the spread of diseases. Although the study of biofilms has been biologists' territory for a long time, a multitude of phenomena in the formation and development of biofilms hinges on physical processes. We are pleased to present a collection of research papers that discuss some of the latest developments in many of the areas to which physicists can contribute a deeper understanding of biofilms, both experimentally and theoretically. The topics covered range from the influence of physical environmental parameters on cell attachment and subsequent biofilm growth, to the use of local probes and imaging techniques to investigate biofilm structure, to the development of biofilms in complex environments and the modeling of colony morphogenesis. The results presented contribute to addressing some of the major challenges in microbiology today, including the prevention of surface contamination, the optimization of biofilm disruption methods and the effectiveness of antibiotic treatments.
The ‘true’ l‐xylulose reductase of filamentous fungi identified in Aspergillus niger (2010)

L-Xylulose reductase is part of the eukaryotic pathway for l-arabinose catabolism. A previously identified L-xylulose reductase in Hypocrea jecorina turned out to be not the 'true' one since it was not upregulated during growth on L-arabinose and the deletion strain showed no reduced L-xylulose reductase activity but instead lost the D-mannitol dehydrogenase activity. In this communication we identified the 'TRUE'L-xylulose reductase in Aspergillus niger. The gene, lxrA (JGI177736), is upregulated on L-arabinose and the deletion results in a strain lacking the NADPH-specific L-xylulose reductase activity and having reduced growth on l-arabinose. The purified enzyme had a K(m) for L-xylulose of 25 mM and a nu(max) of 650 U/mg.
Diagnosing Advanced Persistent Threats: A Position Paper. (2015)

When a computer system is hacked, analyzing the root-cause (for example entry-point of penetration) is a diagnostic process. An audit trail, as defined in the National Information Assurance Glossary, is a securityrelevant chronological (set of) record(s), and/or destination and source of records that provide evidence of the sequence of activities that have affected, at any time, a specific operation, procedure, or event. After detecting an intrusion, system administrators manually analyze audit trails to both isolate the root-cause and perform damage impact assessment of the attack. Due to the sheer volume of information and low-level activities in the audit trails, this task is rather cumbersome and time intensive. In this position paper, we discuss our ideas to automate the analysis of audit trails using machine learning and model-based reasoning techniques. Our approach classifies audit trails into the high-level activities they represent, and then reasons about those activities and their threat potential in real-time and forensically. We argue that, by using the outcome of this reasoning to explain complex evidence of malicious behavior, we are equipping system administrators with the proper tools to promptly react to, stop, and mitigate attacks.
Molecular Dynamics Study of Bulk Properties of Polycrystalline NiTi (2021)

Molecular dynamics (MD) simulations were carried out to study the bulk polycrystalline properties of NiTi. Thermally driven phase transitions of NiTi between martensite and austenitewere simulated using single crystalline simulation domains. With external stress boundary conditions, MD simulation successfully predicted experimentally observed phase transformation temperatures of bulk polycrystalline. Elastic characteristics of NiTi martensite were simulated using polycrystalline simulation domains that consist of realistic disorientations and grain boundary structures. The existence of grain disorientation and grain boundary lowered the potential energy of the simulation domain, which led to more realistic elastic modulus prediction. Analysis of simulation domains that predicted realistic bulk polycrystalline properties showed that the major difference between single crystalline and polycrystalline structures is atomic stress distribution.
Metamaterial CRLH Structure-based Balun for Common-Mode Current Indicator (2014)

We proposed a new PCB-type 'common-mode current(<TEX>$I_c$</TEX>) and differential-mode current(<TEX>$I_d$</TEX>) detector' working for fast detection of <TEX>$I_c$</TEX> and <TEX>$I_d$</TEX> from the differential-mode signaling, with miniaturization effect and possibility of cheaper fabrication. In order to realize this device, we suggest a branch-line-coupler balun having a composite right- and left-handed(CRLH) one-layer microstrip phase-shifting line as compact as roughly <TEX>${\lambda}_g/14$</TEX>. The presented balun obviously is different from the conventional bent-&-folded delay lines or slits on the ground for coupling the lines on the top and bottom dielectrics. As we connect the suggested balun output ports of the differential-mode signal lines via the through-port named U and coupled-port named L, <TEX>$I_c$</TEX> and <TEX>$I_d$</TEX> will appear at port <TEX>${\Delta}$</TEX> and port <TEX>${\Sigma}$</TEX> of the present device, in order. The validity of the design scheme is verified by the circuit-and numerical electromagnetic analyses, and the dispersion curve proving the metamaterial characteristics of the geometry. Besides, the examples of the <TEX>$I_c$</TEX> and <TEX>$I_d$</TEX> indicator are observed as the even and odd modes in differential-mode signal feeding. Also, the proposed device is shown to be very compact, compared with the conventional structure.
Protease activity in the larval stage of the parasitoid wasp, Eulophus pennicornis (Nees) (Hymenoptera: Eulophidae); effects of protease inhibitors (1999)

Hymenopteran, parasitoid wasps have good potential for use in integrated pest management (IPM); for example, the gregarious ectoparasitoid, Eulophus pennicornis, has been suggested as a biological control agent for larvae of the tomato moth (Lacanobia oleracea L.). However, the processes by which such parasitic larvae are able to utilize the nutritional resource provided by the host have been little studied. Protease activity was present in E. pennicornis larvae, and characterization of the enzymes responsible for proteolysis was performed using a range of synthetic substrates and specific inhibitors. Serine protease enzymes was both trypsin- and chymotrypsin-like activities were present. A range of plant-derived serine protease inhibitors was tested for activity against these enzymes. Certain inhibitors, notably soybean Kunitz inhibitor (SKTI), inhibited enzyme activity by > 80% at < 10(-5) M. When SKTI was fed to L. oleracea larvae in an artificial diet, the inhibitor was subsequently detected within the larval haemolymph, showing that protease inhibitors in the host diet can be delivered to a parasitoid via the host haemolymph. If transgenic plants expressing foreign protease inhibitors for protection against insect pests are to form a component of IPM systems, possible adverse effects, whether direct or indirect, of transgene expression on parasitoids like E. pennicornis should be considered.
Infant milk formulas differ regarding their allergenic activity and induction of T-cell and cytokine responses (2016)

Our results show that certain CM formulas without allergenic and low proinflammatory properties can be identified and they may also explain different outcomes obtained in clinical studies using CM formulas.
ChemInform Abstract: Efficient and Versatile Synthesis of Dipeptide Isosteres Containing γ‐or δ‐Lactams. (1989)

Abstract Alkylation of the oxazolidinone (I) with allyl bromide (III), followed by alkaline hydrolysis and esterification with diazomethane (IV), yields the ester (V) which is converted to the aldehyde (VI) by ozonolysis.
A Novel Method for Continuous Synthesis of ZnO Tetrapods (2015)

In this work we propose a novel continuous method for zinc oxide tetrapod (ZnO-T) synthesis based on the combustion of micron-sized Zn particles in an air atmosphere. A stable geometry of ZnO-T structures produced over a wide synthesis temperature range in gram quantities was obtained. Stable growth conditions were determined by self-sustainable combustion around the Zn particle, as supported by thermodynamic analysis. ZnO-Ts had a high crystallinity, an average leg diameter of 15 ± 5 nm, and a length of 200 ± 100 nm. A practical application of ZnO-Ts decorated by Au nanoparticles and attached using DNA strands is investigated. The applicability of the synthesized ZnO-Ts for fast and efficient scintillation was also demonstrated, as ZnO-Ts showed an increased yield of the fast component of luminescence.
Ultrasensitive fluorescence detection of DNA (1992)

We have shown that a number of polycationic highly fluorescent dyes form complexes with double-stranded DNA (dsDNA) which are stable to electrophoresis and have characterized in detail such dsDNA complexes with TOTO (1,1[prime]-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene]-quinolinium tetraiodide) and oxazole yellow dimer (YOYO; an analogue of TOTO with a benzo-1,3-oxazole in place of the benzo-1,3-thiazole). TOTO and YOYO are virtually non-fluorescent in solution, but form highly fluorescent complexes with dsDNA, up to a maximum dye to DNA bp ratio of 1:4, with >1000-fold fluorescence enhancement. We have developed an assay using YOYO for the quantitation of single-stranded and dsDNA in solution applicable over a range of DNA concentrations from 0.5 to 100 ng per ml. The fluorescent dsDNA-dye complexes allow detection of dsDNA on agarose and acrylamide gels with picogram sensitivity. We have applied these complexes in multiplex mapping experiments for accurate sizing and quantitation of restriction fragments. We have shown that in gel shift experiments the stable dsDNA-dye complexes can be used to detect heteroduplex-Muts complexes with a sensitivity comparable to radioisotopic detection.
Chronic Myeloid Leukemia (1999)

In the past decade clinical and laboratory studies have led to important new insights into the biology of chronic myeloid leukemia (CML). Basic science has defined the molecular pathogenesis of CML as unregulated signal transduction by a tyrosine kinase. Clinical science has demonstrated that it is curable through immune-mediated elimination of leukemia cells by allogeneic T lymphocytes.Clinical FeaturesCML is a malignant clonal disorder of hematopoietic stem cells that results in increases in not only myeloid cells but also erythroid cells and platelets in peripheral blood and marked myeloid hyperplasia in the bone marrow (Figure 1A, Figure 1B, andFigure 1C). . . .
Using ceramic membranes for the separation of hydrogen produced by dehydrogenation of perhydro-m-terphenyl (2014)

The efficiency of a variety of ceramic membranes for the purification of hydrogen obtained by dehydrogenation of perhydro-m-terphenyl in a catalytic flow reactor from vapors of initial hydrocarbons and dehydrogenation products is investigated.