gebhart/patrepeval huggingface dataset:
The Utility of Breath Analysis in the Diagnosis and Staging of Parkinson’s Disease (2022)

Breath analysis shows potential for PD diagnostics and monitoring. Both off-line and on-line sensor systems were easy to do and provided comparable results which will enable this technique to be easily adopted in clinic if larger studies confirm our findings.
MicroRNAs in Diagnosis and Prognosis in Cancer: What Does the Future Hold? (2010)

In cancer, miRNAs have the capacity to target a multitude of biological processes, such as proliferation and angiogenesis, that are critical to tumor growth and progression."
Multicenter International Study of the Consensus Immunoscore for the Prediction of Relapse and Survival in Early-Stage Colon Cancer (2023)

Background: The prognostic value of Immunoscore was evaluated in Stage II/III colon cancer (CC) patients, but it remains unclear in Stage I/II, and in early-stage subgroups at risk. An international Society for Immunotherapy of Cancer (SITC) study evaluated the pre-defined consensus Immunoscore in tumors from 1885 AJCC/UICC-TNM Stage I/II CC patients from Canada/USA (Cohort 1) and Europe/Asia (Cohort 2). METHODS: Digital-pathology is used to quantify the densities of CD3+ and CD8+ T-lymphocyte in the center of tumor (CT) and the invasive margin (IM). The time to recurrence (TTR) was the primary endpoint. Secondary endpoints were disease-free survival (DFS), overall survival (OS), prognosis in Stage I, Stage II, Stage II-high-risk, and microsatellite-stable (MSS) patients. RESULTS: High-Immunoscore presented with the lowest risk of recurrence in both cohorts. In Stage I/II, recurrence-free rates at 5 years were 78.4% (95%-CI, 74.4−82.6), 88.1% (95%-CI, 85.7−90.4), 93.4% (95%-CI, 91.1−95.8) in low, intermediate and high Immunoscore, respectively (HR (Hi vs. Lo) = 0.27 (95%-CI, 0.18−0.41); p < 0.0001). In Cox multivariable analysis, the association of Immunoscore to outcome was independent (TTR: HR (Hi vs. Lo) = 0.29, (95%-CI, 0.17−0.50); p < 0.0001) of the patient’s gender, T-stage, sidedness, and microsatellite instability-status (MSI). A significant association of Immunoscore with survival was found for Stage II, high-risk Stage II, T4N0 and MSS patients. The Immunoscore also showed significant association with TTR in Stage-I (HR (Hi vs. Lo) = 0.07 (95%-CI, 0.01−0.61); P = 0.016). The Immunoscore had the strongest (69.5%) contribution χ2 for influencing survival. Patients with a high Immunoscore had prolonged TTR in T4N0 tumors even for patients not receiving chemotherapy, and the Immunoscore remained the only significant parameter in multivariable analysis. CONCLUSION: In early CC, low Immunoscore reliably identifies patients at risk of relapse for whom a more intensive surveillance program or adjuvant treatment should be considered.
A 20-Gene Set Predictive of Progression to Severe Dengue (2019)

There is a need to identify biomarkers predictive of severe dengue. Single-cohort transcriptomics has not yielded generalizable results or parsimonious, predictive gene sets. We analyzed blood samples of dengue patients from seven gene expression datasets (446 samples, five countries) using an integrated multi-cohort analysis framework and identified a 20-gene set that predicts progression to severe dengue. We validated the predictive power of this 20-gene set in three retrospective dengue datasets (84 samples, three countries) and a prospective Colombia cohort (34 patients), with an area under the receiver operating characteristic curve of 0.89, 100% sensitivity, and 76% specificity. The 20-gene dengue severity scores declined during the disease course, suggesting an infection-triggered host response. This 20-gene set is strongly associated with the progression to severe dengue and represents a predictive signature, generalizable across ages, host genetic factors, and virus strains, with potential implications for the development of a host response-based dengue prognostic assay.
Electrode stabilizing materials (2023)

An electrolyte includes a polar aprotic solvent; an alkali metal salt; and an electrode stabilizing compound that is a monomer, which when polymerized forms an electrically conductive polymer. The electrode stabilizing compound is a thiophene, a imidazole, a anilines, a benzene, a azulene, a carbazole, or a thiol. Electrochemical devices may incorporate such electrolytes.
Passive acoustic localization of the Atlantic bottlenose dolphin using whistles and echolocation clicks (1993)

A method for localization and tracking of calling marine mammals was tested under realistic field conditions that include noise, multipath, and arbitrarily located sensors. Experiments were performed in two locations using four and six hydrophones with captive Atlantic bottlenose dolphins (Tursiops truncatus). Acoustic signals from the animals were collected in the field using a digital acoustic data acquisition system. The data were then processed off-line to determine relative hydrophone positions and the animal locations. Accurate hydrophone position estimates are achieved by pinging sequentially from each hydrophone to all the others. A two-step least-squares algorithm is then used to determine sensor locations from the calibration data. Animal locations are determined by estimating the time differences of arrival of the dolphin signals at the different sensors. The peak of a matched filter output or the first cycle of the observed waveform is used to determine arrival time of an echolocation click. Cross correlation between hydrophones is used to determine inter-sensor time delays of whistles. Calculation of source location using the time difference of arrival measurements is done using a least-squares solution to minimize error. These preliminary experimental results based on a small set of data show that realistic trajectories for moving animals may be generated from consecutive location estimates.
Effect of flow rate and blood cellular elements on the efficiency of red blood cell targeting to collagen-coated surfaces. (1984)

The effect of bloodstream factors (flow rate and blood cellular elements) on the behavior of an experimental system simulating drug targeting to injured sites of vessel walls was studied. The system consisted of red blood cells carrying antibody to type I human collagen (drug carrier) and plastic tube with a collagen-coated inner surface (target). The tube was perfused with a 0.5% (v/v) suspension of 51Cr-labeled red blood cells at different linear flow rates and the red blood cell binding to the tube was determined by gamma-counting. It was demonstrated that an increase in the linear flow rate from 0 to 2 cm/s leads at first to increase of red blood cell binding from 2 X 10(5) to 7 X 10(5) cells/cm2 and then to the decrease of binding back to 2 X 10(5) cells/cm2. In the presence of 50% (v/v) of intact red blood cells the binding continuously increases from 2 X 10(5) to 2.5 X 10(6) cells/cm2 without a subsequent drop. On the basis of the obtained results it is concluded that the behavior of the systems for drug targeting in simple in vitro models can drastically differ from the conditions present in vivo.
<title>Micromachined VO<formula><inf><roman>2</roman></inf></formula>-based uncooled IR bolometric detector arrays with integrated CMOS readout electronics</title> (1996)

Uncooled IR bolometric detectors fabricated using surface silicon micromachining are presented. The detector fabrication process employs a polyamide sacrificial layer, and a VO<SUB>2</SUB> thermistor layer exhibiting a thermal coefficient of resistance on the order of -3 percent/degrees C. Detector sizes are 100 micrometers X 100 micrometers and 50 micrometers X 50 micrometers , and 64 X 64 and 128 X 128 pixel arrays are fabricate. The detectors exhibit responsivities of up to 15 000 VW<SUP>-1</SUP>, normalized detectivities typically exceeding 10<SUP>8</SUP> cm Hz<SUP>1/2</SUP>W<SUP>-1</SUP>, and response times below 20 ms. Three integrated readout circuit designs for 64 X 64 and 128 X 128 pixel detector arrays, fabricated using a standard 1.5 micrometers CMOS process,a re described. These circuits include several test and detector nonuniformity correction features and can operate in either self scanning mode at a rate of 30 frames per second, or in the random access mode in which column and row addresses are input directly.
Overflow metabolism and growth cessation in Clostridium thermocellum DSM1313 during high cellulose loading fermentations (2017)

As a model thermophilic bacterium for the production of second-generation biofuels, the metabolism of Clostridium thermocellum has been widely studied. However, most studies have characterized C. thermocellum metabolism for growth at relatively low substrate concentrations. This outlook is not industrially relevant, however, as commercial viability requires substrate loadings of at least 100 g/L cellulosic materials. Recently, a wild-type C. thermocellum DSM1313 was cultured on high cellulose loading batch fermentations and reported to produce a wide range of fermentative products not seen at lower substrate concentrations, opening the door for a more in-depth analysis of how this organism will behave in industrially relevant conditions. In this work, we elucidated the interconnectedness of overflow metabolism and growth cessation in C. thermocellum during high cellulose loading batch fermentations (100 g/L). Metabolic flux and thermodynamic analyses suggested that hydrogen and formate accumulation perturbed the complex redox metabolism and limited conversion of pyruvate to acetyl-CoA conversion, likely leading to overflow metabolism and growth cessation in C. thermocellum. Pyruvate formate lyase (PFL) acts as an important redox valve and its flux is inhibited by formate accumulation. Finally, we demonstrated that manipulation of fermentation conditions to alleviate hydrogen accumulation could dramatically alter the fate of pyruvate, providing valuable insight into process design for enhanced C. thermocellum production of chemicals and biofuels. Biotechnol. Bioeng. 2017;114: 2592-2604. © 2017 Wiley Periodicals, Inc.
Development of Crawler Drive Assist Unit for Wheelchair (2003)

手動式の車椅子を積雪路面上で使用すると車輪が埋まって走行が困難になる。本研究では、一般的な手動式車椅子に装着可能で、積雪路面においても高い走行性能が得られることを目的とした、ゴムクローラを用いた電動式の補助動力ユニットを試作した。装置は車椅子の座席下部に配置され、ハンドル操作によって操舵の他、雪面を的確に捉えられるようにゴムクローラのピッチングが可能な構成となっている。本装置について開発過程を報告する。
Measurement of electronic splitting in PbS quantum dots by two-dimensional nonlinear spectroscopy (2012)

Quantum dots exhibit rich and complex electronic structure that makes them ideal for studying the basic physics of semiconductors in the intermediate regime between bulk materials and single atoms. The remarkable nonlinear optical properties of these nanostructures make them strong candidates for photonics applications. Here, we experimentally probe changes in the fine structure on ultrafast timescales of a colloidal solution of PbS quantum dots through their nonlinear optical response despite extensive inhomogeneous spectral broadening. Using continuum excitation and detection, we observe electronic coupling between nearly degenerate exciton states split by intervalley scattering at low exciton occupancy and a sub-100 fs frequency shift presumably due to phonon-assisted transitions. At high excitation intensities, we observe multi-exciton effects and sharp absorbance bands indicative of exciton-exciton coupling. Our experiments directly probe the nonlinear optical response of nearly degenerate quantum confined nanostructures with femtosecond temporal resolution despite extensive line broadening caused by the finite size distribution found in colloidal solutions.
Synthesis and Properties of 9,9′-Diaryl-4,5-diazafluorenes. A New Type of Electron-Transporting and Hole-Blocking Material in EL Device (2004)

Abstract The title compounds were prepared and investigated for electron-transporting and hole-blocking materials in organic electroluminescent (EL) devices. EL efficiencies of the phosphorescent devices indicated high performance of hole-blocking ability in the compounds. A maximum external efficiency of 18% was achieved and a maximum power luminous efficiency was over 45 Lm W−1.
High Speed Spectral Domain Phase Microscopy for Quantitative Cell Surface and Cytoplasmic Flow Measurements (2006)

We demonstrate cellular applications for high-speed SDPM using a system with 19kHz maximum line-rate. Two-dimensional phase B-scan images taken at 13Hz show flow sensitivity in a single-celled organism.
Cyclooctanoid Ring Systems from Mixed Acetals via Heteroatom-Assisted [1,2]-Shift of Oxonium Ylides (2003)

Cyclic mixed acetals with pendant diazoketone side chains undergo efficient rearrangement to ether-bridged cyclooctanoid systems upon treatment with Cu(hfacac)2. This result demonstrates that heterosubstituted carbons are suitable migrating groups for the Stevens [1,2]-shift of oxonium ylides. In the case of a mixed thioacetal, the resulting sulfide served as a trigger for cleavage of the bridging ether through one of two complementary strategies, furnishing a bicyclo[6.3.0]octene product with an angular hydroxyl group.
Minimally invasive versus open surgery for degenerative lumbar pathologies:a systematic review and meta-analysis (2022)

Minimally invasive techniques are a remarkably interesting option to traditional open surgeries, as these procedures showed a significant reduction in blood loss, hospitalization time, complications, and surgical costs.
Dynamics of Silica-Supported Catalysts Determined by Combining Solid-State NMR Spectroscopy and DFT Calculations (2008)

The molecular dynamics of a series of organometallic complexes covalently bound to amorphous silica surfaces is determined experimentally using solid-state nuclear magnetic resonance (NMR) spectroscopy and density functional theory calculations (DFT). The determination is carried out for a series of alkylidene-based catalysts having the general formula [([triple bond]SiO)M(ER)(=CH(t)Bu)(R')] (M = Re, Ta, Mo or W; ER = C(t)Bu, NAr or CH2(t)Bu; R' = CH2(t)Bu, NPh2, NC4H4). Proton-carbon dipolar coupling constants and carbon chemical shift anisotropies (CSA) are determined experimentally by solid-state NMR. Room-temperature molecular dynamics is quantified through order parameters determined from the experimental data. For the chemical shift anisotropy data, we validate and use a method that integrates static values for the CSA obtained computationally by DFT, obviating the need for low-temperature measurements. Comparison of the room-temperature data with the calculations shows that the widths of the calculated static limit dipolar couplings and CSAs are always greater than the experimentally determined values, providing a clear indication of motional averaging on the NMR time scale. Moreover, the dynamics are found to be significantly different within the series of molecular complexes, with order parameters ranging from <S(z)> = 0.5 for [([triple bond]SiO)Ta(=CH(t)Bu)(CH2(t)Bu)2] and [([triple bond]SiO)Re([triple bond]C(t)Bu)(=CH(t)Bu)(CH2(t)Bu)] to <S(z)> = 0.9 for [([triple bond]SiO)Mo([triple bond]NAr)(=CH(t)Bu)(R') with R' = CH2(t)Bu, NPh2, NC4H4. The data also show that the motion is not isotropic and could be either a jump between two sites or more likely restricted librational motion. The dynamics are discussed in terms of the molecular structure of the surface organometallic complexes, and the orientation of the CSAs tensor at the alkylidene carbon is shown to be directly related to the magnitude of the alpha-alkylidene CH agostic interation.
System Architecture for Mobile-phone-readable RF Memory Tags (2010)

Abstract — We have developed an open architecture platform for implementing passive radio-frequency identification (RFID) tags with a mass memory. Purposes for such mass memory tags are, e.g., multimedia files embedded in advertisements or logged sensor data on a low-power sensor node. In the proposed architecture, a mobile phone acts as the reader that can read or write the memory of these RFID tags. The architecture is designed so that development path to a full Network on Terminal Architecture (NoTA) is feasible. The wireless reading speed of the mass memory tags, demonstrated to be 112 Mbit/s, is in range that a 3-minute VGA size video can be loaded from the tag to the phone in less than 10 s.
A 4H-SiC phonon polariton enhanced hybrid waveguide (2016)

This endeavor investigates the use of 4H-SİC surface phonon polariton (SPhP) to hybridize the mode of a ridge waveguide in a practical design. Applications for hybrid SPhP modes are in the fields of photonic integrated circuits (PIC) and in sensing in the mid to long infrared (IR).
Small is Beautiful and Smart (2013)

Remote monitoring and remote control in military, wildlife, and urban environments are just some of the practical applications that have been made possible by the emergence of wireless embedded sensor networks. More recently, these wireless sensor networks have enabled remote sensing and remote monitoring of the environment of the human body. These devices have been realized in applications ranging from heavy duty military suits to single sensor wireless health systems.
Molecular elements in FGF19 and FGF21 defining KLB/FGFR activity and specificity (2018)

We report here the ability of short C-terminal peptides to bind KLB and function as antagonists of FGF19 and 21 actions. These proteins maintain high conservation of sequence in those residues central to KLB binding. An FGF21 chimeric protein possessing an optimized C-terminal sequence proved to be a super-agonist in delivery of beneficial metabolic effects in obese mice.
Hierarchical Density-Based Clustering for Multi-Represented Objects (2005)

In recent years, the complexity of data objects in data mining applications has increased as well as their plain numbers. As a result, there exist various feature trans-formations and thus multiple object representations. For example, an image can be described by a text annotation, a color histogram and some texture features. To cluster thesemulti-represented objects, dedicated datamining al-gorithms have been shown to achieve improved results. In this paper, we will therefore introduce a method for hi-erarchical density-based clustering of multi-represented objects which is insensitive w.r.t. the choice of parame-ters. Furthermore, we will introduce a theoretical model that allows us to draw conclusions about the interaction of representations. Additionally, we will show how these conclusions can be used for defining a suitable combina-tion method for multiple representations. To back up the usability of our proposed method, we present encourag-ing results for clustering a real world image data set that is described by 4 different representations. 1.
A Unified Cryptographic Protocol Logic (1996)

Abstract : We present a logic for analyzing cryptographic protocols. This logic is based on a unification of four of its predecessors in the BAN family of logics, namely those given in [GNY90], [AT91], [vO93b], and BAN itself [BAN89]. The logic herein captures the desirable features of its predecessors and more; nonetheless, as a logic it is relatively simple and simple to use. We also present a model-theoretic semantics, and we prove soundness for the logic with respect to that semantics. We illustrate the logic by applying it to the Needham- Schroeder protocol, revealing that BAN analysis of it may lead to inappropriate conclusions in some settings. We also use the logic to analyze two key agreement protocols, examining an attack on one of them.
An <em>ex vivo</em> experimental system to track fluorescent nanoparticles inside skeletal muscle (2022)

The development of novel nanoconstructs for biomedical applications requires the assessment of their biodistribution, metabolism and clearance in single cells, organs and entire organisms in a living environment. To reduce the number of in vivo experiments performed and to refine the methods used, in accordance with the 3Rs principle, this work proposes an ex vivo experimental system to monitor, using fluorescence microscopy, the distribution of nanoparticles in explanted murine skeletal muscle maintained in a bioreactor that can preserve the structural and functional features of the organ for long periods of time. Fluorescently-labelled liposomes and poly(lactide-co-glycolide) (PLGA)-based nanoparticles were injected into the intact soleus muscle (in the distal region close to the tendon) immediately after explants, and their distribution was analysed at increasing incubation times in cross cryosections from the proximal region of the belly. Both nanocarriers were clearly recognized in the muscle and were found to enter and migrate inside the myofibres, whereas their migration in the connective tissue seemed to be limited. In addition, some fluorescent signals were observed inside the macrophages, demonstrating the physiological clearance of the nanocarriers that did not enter the myofibres. Our ex vivo system therefore provides more information than previous in vitro experiments on cultured muscle cells, highlighting the need for the appropriate functionalization of nanocarriers if myofibre targeting is to be improved.
Incidence of specialist natural enemies of Rhopalosiphum padi (L.) (Horn., Aphididae) on oats in monocrops and mixed intercrops with faba bean (1990)

Abstract Field experiments were conducted in southern Finland in 1981–1985. Shoots of oat, Avena sativa , were sampled in monocrops and mixed intercrops of oats and faba bean, Vicia faba , in order to estimate the densities of bird cherry‐oat aphid, Rhopalosiphum padi , its coccinellid and syrphid predators, parasitized (mummified) aphids and aphids killed by fungal pathogens. Over seasons and sites, the densities of the natural enemies on shoots did not correlate with the peak aphid densities except in the case of syrphid larvae, for which a positive correlation was found. The incidences of the natural enemies on oat shoots were not significantly affected by mixed cropping, but increased peak densities of R. padi were accompanied by a lowered ratio of specific natural enemies to aphids in the mixtures. The mechanisms possibly influencing the numbers or efficiency of natural enemies in diversified crops, as compared to monocrops, were discussed. Zusammenfassung Zum Einfluß spezialisierter natürlicher Feinde von Rhopalosiphum padi (L.) (Horn., Aphididae) in Hafermonokulturen und in Hafer‐Bohnen‐Mischkulturen In Finnland wurden von 1981 bis 1985 Haferschößlinge in Mono‐ und Mischkulturen (Hafer, Avena sativa und Bohnen, Vicia faba ) entnommen, um sowohl die Dichte von Rhopalosiphum padi zu bestimmen als auch die Häufigkeit der Räuber (Coccinelidae, Syrphidae), der parasitierten (mummifizierten) und der verpilzten Läuse zu bestimmen. In den verschiedenen Jahren und Untersuchungsgebieten konnte keine Korrelation zwischen den natürlichen Feinden und Populationshöhepunkten von R. padi festgestellt werden. Eine Ausnahme bildeten die Syrphidenlarven, deren Dichte positiv mit jener der Läuse korrelierte. Das Auftreten natürlicher Feinde auf Haferschößlingen wurde nicht signifikant durch Mischkulturen beeinflußt, aber eine ansteigende R. padi ‐Dichte wurde von einem abnehmenden Verhältnis spezialisierter Feinde zu Läusen in Mischkulturen gekennzeichnet. Die Mechanismen, die die Zahl oder Wirksamkeit natürlicher Feinde in Mischkulturen im Vergleich zu Monokulturen beeinflussen, werden diskutiert.
Reflections about Judea Pearl and his Contributions (2012)

It’s an honor to have been invited to share reflections about Judea Pearl and his contributions. Being asked to talk about Judea in front of this home audience is an interesting request as most people here understand and appreciate Judea’s work—and many of you know him well personally. Judea has been the heart and soul of a revolution in the use of probabilistic representations in AI and in computer science more broadly.  His intellectual contributions and clear writing have also provided other disciplines with insights and building blocks, with influences in econometrics, statistics, and the philosophy of science.