gebhart/patrepeval huggingface dataset:
New Approaches to Target T-ALL (2014)

Acute lymphoblastic leukemia is the most common malignancy in children. Although it is now curable in 80-90% of cases, patients with T-cell acute lymphoblastic leukemia (T-ALL) experience a higher frequency of induction failure and early relapse. Despite aggressive treatment approaches, including transplantation and new salvage regimens, most children with relapsed T-ALL will not be cured. As such, we are in need of new targeted therapies for the disease. Recent advances in the molecular characterization of T-ALL have uncovered a number of new therapeutic targets. This review will summarize recent advancements in the study of inhibiting the NOTCH1, PI3K-AKT, and Cyclin D3:CDK4/6 pathways as therapeutic strategies for T-ALL. We will focus on pre-clinical studies supporting the testing of small-molecule inhibitors targeting these proteins and the rationale of combination therapies. Moreover, epigenetic approaches to modulate T-ALL are rapidly emerging. Here, we will discuss the data supporting the role of bromodomain and extra-terminal bromodomain inhibitors in human T-ALL.
An Augmented Lagrangian Approach for Decentralized Supply Chain Planning for Multiple Companies (2005)

Coordination and optimization of supply chain planning among multiple companies have widely been received much attention from viewpoints of global supply chain management. Conventional system for supply chain planning is configured on the assumption that correct information for entire company is available by sharing the detailed information among multiple companies. It is required to generate a near optimal plan for multiple companies without sharing the confidential information such as inventory costs, set up costs and due date penalties among competing companies. In this paper, we propose a framework of a distributed supply chain planning for multiple companies by using an augmented Lagrangian relaxation approach. The proposed method features that a feasible solution can be derived without using the entire information by exchanging the data which is not directly related to cost data. From the computational experiments, it has been shown that the average gap between the solution derived by the proposed method and an optimal solution is within 1% of the performance index even though only the local information is used to derive a solution for each company
Analysis of building deformation in landslide area using multisensor PSInSAR™ technique (2014)

Buildings are sensitive to movements caused by ground deformation. The mapping both of spatial and temporal distribution, and of the degree of building damages represents a useful tool in order to understand the landslide evolution, magnitude and stress distribution. The high spatial resolution of space-borne SAR interferometry can be used to monitor displacements related to building deformations. In particular, PSInSAR technique is used to map and monitor ground deformation with millimeter accuracy. The usefulness of the above mentioned methods was evaluated in San Fratello municipality (Sicily, Italy), which was historically affected by landslides: the most recent one occurred on 14th February 2010. PSInSAR data collected by ERS 1/2, ENVISAT, RADARSAT-1 were used to study the building deformation velocities before the 2010 landslide. The X-band sensors COSMO-SkyMed and TerraSAR-X were used in order to monitor the building deformation after this event. During 2013, after accurate field inspection on buildings and structures, damage assessment map of San Fratello were created and then compared to the building deformation velocity maps. The most interesting results were obtained by the comparison between the building deformation velocity map obtained through COSMO-SkyMed and the damage assessment map. This approach can be profitably used by local and Civil Protection Authorities to manage the post-event phase and evaluate the residual risks.
Evidence of surface acoustic wave band gaps in the phononic crystals created on thin plates (2006)

Phononic structures and acoustic band gaps based on bulk materials have been researched in length in the past decades. However, few investigations have been performed on phononic structures in thin plates to form surface acoustic wave (SAW) band gaps. In this letter, we report a new type of phononic crystals manufactured by patterning periodical air-filled holes in thin plates. We confirmed the existence of SAW band gaps in the created phononic crystals through laser ultrasonics measurements. Wide multiple SAW band gaps and special structures, such as narrow pass bands within a band gap were observed experimentally.
Improvement of Force-Sensor-Based Heart Rate Estimation Using Multichannel Data Fusion (2014)

The aim of this paper is to present and evaluate algorithms for heartbeat interval estimation from multiple spatially distributed force sensors integrated into a bed. Moreover, the benefit of using multichannel systems as opposed to a single sensor is investigated. While it might seem intuitive that multiple channels are superior to a single channel, the main challenge lies in finding suitable methods to actually leverage this potential. To this end, two algorithms for heart rate estimation from multichannel vibration signals are presented and compared against a single-channel sensing solution. The first method operates by analyzing the cepstrum computed from the average spectra of the individual channels, while the second method applies Bayesian fusion to three interval estimators, such as the autocorrelation, which are applied to each channel. This evaluation is based on 28 night-long sleep lab recordings during which an eight-channel polyvinylidene fluoride-based sensor array was used to acquire cardiac vibration signals. The recruited patients suffered from different sleep disorders of varying severity. From the sensor array data, a virtual single-channel signal was also derived for comparison by averaging the channels. The single-channel results achieved a beat-to-beat interval error of 2.2% with a coverage (i.e., percentage of the recording which could be analyzed) of 68.7%. In comparison, the best multichannel results attained a mean error and coverage of 1.0% and 81.0%, respectively. These results present statistically significant improvements of both metrics over the single-channel results (p < 0.05).
Switch energy requirements for first- and second-order perturbations in asymmetric quantum box optical switches (1997)

We have studied the limits to the switching energy of electrically controlled optical absorption switches. Investigating a case with intraband transitions in asymmetric quantum boxes, it is shown that linear Stark shift allows switch energies of the optical switches that are comparable to the thermal noise limit at 300 K at least up to 30 GHz, provided boxes with very narrow absorption linewidth can be fabricated. This is several orders of magnitude lower energy than required by quadratic Stark shift in a similar, symmetric structure.
Large Language Model Programs (2023)

In recent years, large pre-trained language models (LLMs) have demonstrated the ability to follow instructions and perform novel tasks from a few examples. The possibility to parameterise an LLM through such in-context examples widens their capability at a much lower cost than finetuning. We extend this line of reasoning and present a method which further expands the capabilities of an LLM by embedding it within an algorithm or program. To demonstrate the benefits of this approach, we present an illustrative example of evidence-supported question-answering. We obtain a 6.4\% improvement over the chain of thought baseline through a more algorithmic approach without any finetuning. Furthermore, we highlight recent work from this perspective and discuss the advantages and disadvantages in comparison to the standard approaches.
A multiresolution study of two-dimensional scattering by metallic cylinders (1996)

The application of wavelet transforms in method of moments (MoM) solutions for scattering problems is extended to cases involving metallic cylinders whose periphery contains a variety of length-scale features ranging from smoothly varying large-scale features (characterized by a radius of curvature of several wavelengths) to rapidly varying small scale ones (characterized by a radius of curvature that is small compared with the wavelength). The basic idea is to first consider a periodic extension of the equivalent current in the arc-length variable with a period identical to the scatterer circumference, and then to expand this representation using a set of periodic wavelets derived from a conventional basis of wavelets by a periodic extension. Using a Galerkin method and subsequently applying a threshold operation, a substantial reduction in the number of elements of the moment-method matrix is attained without virtually affecting the solution accuracy. The proposed extension is illustrated by a numerical analysis of TM (transverse magnetic) and TE (transverse electric) scattering from a cylinder of elliptic cross section. A thorough study is carried out showing how the solution accuracy improves with increasing resolution level, and how this accuracy is affected by a thresholding process which renders the moment matrix sparsely populated.
Fabrication technology of hard x-ray aspherical mirror optics and application to nanospectroscopy (2004)

We developed ultra-precise fabrication system for x-ray optics, which combined numerically controlled plasma CVM and EEM. In this system, nanometer order form accuracy having atomic order roughness is achieved. And there are no deformed layers on the surface because these fabrication processes utilizes chemical reaction. So, this system is effective for not only reflective optics but also for diffractive optics. Recently, elliptical mirrors having less than 3 nm form accuracy are fabricated by utilizing the above system, and K-B arrangement microfocusing unit for installation of these mirrors are developed. In this unit, micro x-ray beam having the size of 180 (V)×90(H) nm<sup>2</sup> is achieved at 15 keV. By scanning irradiation of the micro x-ray beam and by detecting x-ray fluorescence, inside structures of some mammalian cells are observed with resolution of 0.2 &mu;m.
The XDOS binary code conversion system (2003)

The XDOS binary code conversion system takes the binary images of programs that were written to run on the IBM PC and converts them into programs that will run on a number of different computers that use the Unix operating system. The author discusses the use of automatic and human-aided conversion techniques, the techniques used to analyze programs, optimizations that are performed during conversion, run-time strategies, and the relative performance of converted code. It is shown that the XDOS binary code conversion system has proved to be an effective solution to the problem of running PC programs on Unix-based computers. It is able to produce converted applications that are well integrated into the Unix environment and that provide excellent performance in a multiuser environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design of unequal H-plane waveguide-power dividers for array applications (2002)

We present design data for H-plane waveguide power dividers. Such a power divider is generally used in the feed networks of waveguide antenna arrays. The power divider is a H-plane waveguide T-junction with two irises, the first to split the incoming power from port 1 to ports 2 and 3, and the second to match the input port. An integral equation moment method analysis procedure for such a structure was developed, and then used to generate some design data. Although H-plane T-junctions have been analyzed previously, no design data, to the authors' knowledge, has yet been published for the double-iris H-plane T-junction configuration.
Parametric Study of Influence of Profile Geometry on Structural Performance of Buried Profile-Wall Pipe (2006)

A study at Utah State University examined the performance of buried high-density polyethylene profile-wall pipe to provide guidance for its proper design. One aspect of this effort was a parametric study of various pipe profiles through use of linear, three-dimensional finite element models. An experimental portion of this project showed that pipes that performed well in buried tests also performed well in parallel-plate tests. This paper summarizes the results of a parametric study of profile-wall pipes in parallel-plate tests. Among the several profile features examined were pipe profile height, profile curvature, wall angle, rib width, and wall thicknesses. In the completed parametric studies, a single dimension was varied while most of the remaining parameters were maintained at constant values. To simplify the analysis, this effort was limited to linear finite element models: the displacements are assumed to be small and the material linear elastic. The small displacement assumption was accurate for the estimation of stiffness at 5% deflection but may not represent buckling correctly. Linear static and linear buckling analysis results are presented. One of the most significant conclusions from this study was that the arch curvature or profile shape had a significant effect on the stability of profile-wall pipe. Plots showing the influence of parameters such as profile height, shape, and thickness on pipe stiffness and buckling are presented.
Efficient and novel method for surface oxidation of polypropylene in the solid phase using microwave irradiation (2000)

The oxidation of polypropylene in the solid phase in the presence of potassium permanganate was carried out using microwave irradiation. The oxidation was achieved at time intervals of 20, 40, 60, and 90 s. According to the data available from FTIR spectroscopy, the vinylic and carbonyl groups are observed on the polymer surface. It is noteworthy that by using this method of oxidation we have saved energy and time and also less pollution has been entered into the environment by minimum oxidant consumption with maximum efficiency. © 20001 John Wiley & Sons, Inc. J Appl Polym Sci 79: 1317–1323, 2001
A Stereoselective Route to Hydroxyethylamine Dipeptide Isosteres (2000)

An efficient synthesis of stereodefined hydroxyethylamine dipeptide isosteres has been developed, utilizing a syn-selective Grignard addition and reductive amination as the key reactions.
Order sets utilization in a clinical order entry system. (2003)

An order set is a predefined template that has been utilized in the standard care of hospitals for many years. While in the past, it took the form of pen and paper, today, it is, indeed, electronic. Within order sets are distinct ordering patterns that may yield fruitful results for clinicians and informaticians, alike. Protocols like there electronic counterpart, order sets, provide an 'indication' identifying the clinical scenario of the patient's condition when the ordering event occurred. This 'indication' is rarely captured by individual orders, and provides difficult challenges to developers of information systems. While mandating an 'indication' be entered for every medication or lab order makes the job much more tasking on the physician provider, it is appealing to researchers and accountants. We have attempted to bypasses that consideration by identifying ordering patterns that predict diagnostic related codes (DRGs) and diagnostic codes which would greatly facilitate the information gathering process and still provide a flexible and user friendly physician interface.
Low-voltage organic electroluminescent devices using pin structures (2002)

We have realized a small-molecule organic light-emitting diode where the intrinsic emitter layer is sandwiched by n- and p-doped transport layers with appropriate blocking layers. The diodes based on this pin concept have exponential forward characteristics up to comparatively high current densities. The diodes reach high brightness at very low operating voltage: for instance, 1000 cd/m2 at a voltage of 2.9 V. Despite the highly doped transport layers, the devices reach very high efficiency for the given emitter system up to high brightness.
Engineering Hyperactive Variants of Human Deoxyribonuclease I by Altering Its Functional Mechanism (1997)

Human deoxyribonuclease I (DNase I), an enzyme used to treat cystic fibrosis patients, has been engineered to more effectively degrade double-stranded DNA to lower molecular weight fragments by altering its functional mechanism from the native single-stranded nicking pathway to a much more efficient one which results in increased double-stranded scission. By introducing positively charged amino acids at DNase I positions that can interact favorably with the proximal negatively charged phosphate groups of the DNA, we have created a hyperactive variant with approximately 35-fold higher DNA-degrading activity relative to wild type. This enhancement can be attributed to both a decrease in Km and an increase in Vmax. Furthermore, unlike wild-type DNase I, the hyperactive variants are no longer inhibited by physiological saline. Replacement of the same positions with negatively charged amino acids greatly reduced DNA cleavage activity, consistent with a repulsive effect with the neighboring DNA phosphates. In addition, these variants displayed similar activities toward a small synthetic substrate, p-nitrophenyl phenylphosphonate, suggesting that the difference in DNA cleavage activity is due to the interaction of the engineered charged residues with the DNA phosphate backbone rather than any change in catalytic machinery. Finally, experiments involving the repair of DNase I digested DNA with T4 DNA ligase and the Klenow fragment of DNA polymerase I suggest that single-stranded gaps are introduced by the hyperactive variants. Thus, the increased functional activity of the hyperactive variants may be explained in part by a shift toward a processive DNA nicking mechanism, which leads to a higher frequency of double-stranded breaks.
SEGMENTED SECONDARY LINEAR RELUCTANCE MOTOR: ANALYTICAL AND EXPERIMENTAL RESULTS (1977)

ABSTRACT The segmented secondary linear reluctance motor is analyzed using a permeance function approach. The basic assumptions are iron linearity and current excitation. The resulting analytical equations are implemented for numerical computation. The numerical results are compared with experimental results which are obtained from a 2 pole, 37 m/s laboratory model linear reluctance motor.
Scanning Tunneling Microscopy Study of Silicide Structure on Si(110) Surface (1998)

Surface structures of Ni-deposited Si(110) after annealing at various temperatures have been investigated using scanning tunneling microscopy (STM). After deposition of a few monolayers (ML) of Ni at room temperature, Ni clusters cover the surface homogeneously, where initial stripe patterns of up and down terraces, characteristic of Si(110)-“16 ×2”, are still visible. After annealing above 400°C, NiSi 2 islands with (1 ×1) periodicity grow on the Si substrate showing various Ni-induced reconstructions. Detailed STM images of the surface of the islands have revealed that paired bright protrusions are randomly distributed on the (1 ×1) terrace. We have proposed a structural model where adjacent Si atoms in the NiSi 2 (110) surface form dimers in the [001] direction forming a (1 ×1) terrace, on which pairs of dimers are located at geometrically identical sites on the next grown NiSi 2 layer.
Crystallographic observation of 'induced fit' in a cryptophane host–guest model system (2010)

Cryptophane-A, comprised of two cyclotriguaiacylenes joined by three ethylene linkers, is a prototypal organic host molecule that binds reversibly to neutral small molecules via London forces. Of note are trifunctionalized, water-soluble cryptophane-A derivatives, which exhibit exceptional affinity for xenon in aqueous solution. In this paper, we report high-resolution X-ray structures of cryptophane-A and trifunctionalized derivatives in crown-crown and crown-saddle conformations, as well as in complexes with water, methanol, xenon or chloroform. Cryptophane internal volume varied by more than 20% across this series, which exemplifies 'induced fit' in a model host-guest system.
Supplementary Fig. S1 legend from Induction of programmed cell death in ErbB2/HER2-expressing cancer cells by targeted delivery of apoptosis-inducing factor (2023)

Supplementary Fig. S1 legend from Induction of programmed cell death in ErbB2/HER2-expressing cancer cells by targeted delivery of apoptosis-inducing factor
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set (2017)

The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multitude of different methods have been reported and evaluated, such as target fishing, nearest neighbor similarity-based methods, and Quantitative Structure Activity Relationship (QSAR)-based protocols. However, such studies are typically conducted on different datasets, using different validation strategies, and different metrics. In this study, different methods were compared using one single standardized dataset obtained from ChEMBL, which is made available to the public, using standardized metrics (BEDROC and Matthews Correlation Coefficient). Specifically, the performance of Naïve Bayes, Random Forests, Support Vector Machines, Logistic Regression, and Deep Neural Networks was assessed using QSAR and proteochemometric (PCM) methods. All methods were validated using both a random split validation and a temporal validation, with the latter being a more realistic benchmark of expected prospective execution. Deep Neural Networks are the top performing classifiers, highlighting the added value of Deep Neural Networks over other more conventional methods. Moreover, the best method ('DNN_PCM') performed significantly better at almost one standard deviation higher than the mean performance. Furthermore, Multi-task and PCM implementations were shown to improve performance over single task Deep Neural Networks. Conversely, target prediction performed almost two standard deviations under the mean performance. Random Forests, Support Vector Machines, and Logistic Regression performed around mean performance. Finally, using an ensemble of DNNs, alongside additional tuning, enhanced the relative performance by another 27% (compared with unoptimized 'DNN_PCM'). Here, a standardized set to test and evaluate different machine learning algorithms in the context of multi-task learning is offered by providing the data and the protocols. Graphical Abstract .
Ductus ejaculatorius peptide 99B (DUP99B), a novel Drosophila melanogaster sex‐peptide pheromone (2002)

We have characterized a glycosylated, 31 amino-acid peptide of 4932 Da isolated from Drosophila melanogaster males. The mature peptide contains a sugar moiety of 1184 Da at a NDT consensus glycosylation site and a disulfide bond. It is synthesized in the male ejaculatory duct via a 54 amino-acid precursor containing an N-terminal signal peptide and Arg-Lys at the C-terminus which is cleaved off during maturation. The gene contains an intron of 53 bp and is localized in the cytological region 99B of the D. melanogaster genome. The peptide is therefore named DUP99B (for ductus ejaculatorius peptide, cytological localization 99B). The C-terminal parts of mature DUP99B and D. melanogaster sex-peptide (ACP70A) are highly homologous. Injected into virgin females, DUP99B elicits the same postmating responses as sex-peptide (increased oviposition, reduced receptivity). These effects are also induced by de-glycosylated native peptide or synthetic DUP99B lacking the sugar moiety. Presence of the glycosyl group, however, decreases the amount needed to elicit the postmating responses. Homologies in the coding regions of the two exons of DUP99B and sex-peptide, respectively, suggest that the two genes have evolved by gene duplication. Thus, we consider these two genes to be members of the new sex-peptide gene family.