gebhart/patrepeval huggingface dataset:
Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning (2021)

<i>Goal:</i> Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used method for comparative analysis of biological genomes. We intend to propose a novel pairwise sequence alignment method using deep reinforcement learning to break out the old pairwise alignment algorithms. <i>Methods:</i> We defined the environment and agent to enable reinforcement learning in the sequence alignment system. This novel method, named DQNalign, can immediately determine the next direction by observing the subsequences within the moving window. <i>Results:</i> DQNalign shows superiority in the dissimilar sequence pairs that have low identity values. And theoretically, we confirm that DQNalign has a low dimension for the sequence length in view of the complexity. <i>Conclusions:</i> This research shows the application method of deep reinforcement learning to the sequence alignment system and how deep reinforcement learning can improve the conventional sequence alignment method.
Atomic Force Microscope Active Optical Probe for Single-Molecule Imaging and Time-Resolved Optical Spectroscopy (DOE SBIR Phase II/IIA Final Report) (2022)

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Reverse‐phase liquid chromatography/electrospray‐ionization Fourier‐transform mass spectrometry in the analysis of peptides (1994)

Abstract Electrospray ionization (ESI) in combination with Fourier‐transform mass spectrometry (FTMS) gives both highly accurate mass analysis of peptides with external calibration and high resolution for charge‐state determination of an ion from the naturally occurring isotopic peaks. Liquid chromatographic (LC) separation of peptides is important for the analysis of complex mixtures. High‐resolution, high accuracy measurement of the molecular ions of the mix of peptides has been achieved with LC/ESI‐FTMS. Examples are given to show both the reproducibility of mass accuracy over replicate analyses and to show the utility of broadband analysis of a gradient separation of peptides. The high mass accuracy and resolution of FTMS was uncompromised for the direct analysis of chromatography peaks.
The Design and Fabrication of the East African Trial Leveraged Freedom Chair (2010)

This ð document ð presents ð the ð design ð process, ð analysis, ð and ð fabrica7on ð used ð to ð create ð a ð prototype ð Leveraged ð Freedom ð Chair ð (LFC) ð for ð trial ð in ð East ð Africa. ð The ð LFC ð is ð a ð lever�괂Ġpowered, ð wheelchair�괂Ġbased ð mobility ð aid ð designed ð specifically ð for ð use ð in ð the ð developing ð world. ð Its ð drivetrain ð op7mally ð converts ð upper ð body ð in ð a ð wide ð range ð of ð terrains, ð giving ð the ð LFC ð opera7onal ð capabili7es ð that ð extend ð beyond ð those ð of ð currently ð available ð mobility ð products. ð All ð of ð the ð moving ð parts ð in ð the ð LFC ð are ð made ð from ð bicycle ð components, ð which ð allow ð it ð to ð be ð manufactured ð and ð repaired ð anywhere ð in ð the ð developing ð world. ð In ð August ð 2009, ð eight ð LFC ð prototypes ð were ð produced ð in ð Kenya ð for ð $195.28 ð each, ð affirming ð that ð the ð chair ð can ð be ð built ð using ð local ð tools ð and ð materials ð for ð the ð same ð price ð as ð exis7ng ð mobility ð aids. ð
ZoneZoom (2004)

ZoneZoom is an input technique that lets users traverse large information spaces on smartphones. Our technique ZoneZoom, segments a given view of an information space into nine sub-segments, each of which is mapped to a key on the number keypad of the smartphone. This segmentation can be hand-crafted by the information space author or dynamically created at run-time. ZoneZoom supports "spring-loaded" view shifting which allows users to easily "glance" at nearby areas and then quickly return to their current view. Our ZoneZoom technique lets users gain an overview and compare information from different parts of a dataset. SmartPhlow is an optimized application for browsing a map of local-area road traffic conditions.
Supplementary Figure 1 from Impact of Intrinsic Affinity on Functional Binding and Biological Activity of EGFR Antibodies (2023)

&lt;p&gt;PDF file, 450KB, Biphasic distribution of the increase in binding affinity for conversion from monovalent to bivalent forms for antibodies with different intrinsic affinities.&lt;/p&gt;
Supplementary Table 4 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules (2023)

&lt;p&gt;Supplementary Table 4&lt;/p&gt;
Signal remodulation PON without power sacrifice using PolSK (2008)

We propose and demonstrate a novel signal remodulation scheme using PolSK with high extinction-ratio. Error-free was achieved in a 20km reach 10Gb/s DWDM-PON without dispersion compensation.
Syngas production from methane dry reforming via optimization of tungsten trioxide-promoted mesoporous γ-alumina supported nickel catalyst (2022)

Syngas production via dry reforming of methane was conducted over 5 wt%Ni + xWO3/γ-Al2O3 (x = 1, 3, 5, 7, or 9 wt%) catalysts at 700 °C and ambient pressure for 7.5 h in a tubular fixed-bed reactor. Textural, morphological, and catalytic properties were investigated in relation to the weight percent of tungsten trioxide loading. The physicochemical properties of the catalysts were evaluated using XRD, N2-physisorption, TGA, H2-TPR, CO2-TPD, NH3-TPD, SEM, EDX, and Raman techniques. N2-physisorption analysis showed that tungsten trioxide promoter had a minor impact on the textural properties upon varying its weight percentage loading. With increasing tungsten trioxide loading, the total amount of reducible NiO-interacting species was increased over the catalyst surface. 5Ni+5WO3/γ-Al2O3 catalyst showed stable 79% CH4 conversions and 83% CO2 conversion with the lowest carbon deposition due to the presence of stable metallic Ni species (derived from reducible NiAl2O4 and NiWOAl), the highly acidic sites, and moderate basic sites.
The Effect of Muscle Contraction Level on the Cervical Vestibular Evoked Myogenic Potential (cVEMP): Usefulness of Amplitude Normalization (2013)

Because cVEMP amplitude did not typically grow proportionally with muscle contraction level, amplitude normalization did not lead to stable cVEMP amplitudes or asymmetry ratios across varying muscle contraction levels. Until we better understand the relationships between muscle contraction level, surface electromyography (EMG) estimates of muscle contraction level, and cVEMP amplitude, the application of normalization methods to correct cVEMP amplitude appears unjustified.
Impact of the CABG SYNTAX score on all-cause death at 10 years: a SYNTAX Extended Survival (SYNTAXES) substudy (2021)

International audience
Rationale and Methodology for a Population-Based Study of Eye Diseases in Malay People: The Singapore Malay Eye Study (SiMES) (2007)

This study provides population-based data on the prevalence of and risk factors for age-related eye diseases in people of Malay ethnicity in Singapore. Data from this study allow further understanding of the etiology and impact of eye diseases in this ethnic group.
Data from External Validation of a Multiplex Urinary Protein Panel for the Detection of Bladder Cancer in a Multicenter Cohort (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Because of the faltering sensitivity and/or specificity, urine-based assays currently have a limited role in the management of patients with bladder cancer. The aim of this study was to externally validate our previously reported protein biomarker panel from multiple sites in the United States and Europe.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; This multicenter external validation study included a total of 320 subjects (bladder cancer = 183). The 10 biomarkers (IL8, MMP9, MMP10, SERPINA1, VEGFA, ANG, CA9, APOE, SDC1, and SERPINE1) were measured using commercial ELISA assays in an external laboratory. The diagnostic performance of the biomarker panel was assessed using receiver operator curves (ROC) and descriptive statistical values.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Utilizing the combination of all 10 biomarkers, the area under the ROC for the diagnostic panel was noted to be 0.847 (95% confidence interval, 0.796–0.899), outperforming any single biomarker. The multiplex assay at optimal cutoff value achieved an overall sensitivity of 0.79, specificity of 0.79, positive prediction value of 0.73, and negative prediction value of 0.84 for bladder cancer classification. Sensitivity values of the diagnostic panel for high-grade bladder cancer, low-grade bladder cancer, muscle invasive bladder cancer, and non-muscle invasive bladder cancer were 0.81, 0.90, 0.95, and 0.77, respectively.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Urinary levels of the biomarker panel enabled discrimination of patients with bladder cancer and controls, and the levels of biomarker subsets were associated with advancing tumor grade and stage.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Impact:&lt;/b&gt; If proven to be reliable, urinary diagnostic biomarker assays can detect bladder cancer in a timely manner such that the patient can expect improvements in overall survival and quality of life. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 23(9); 1804–12. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Phase I study of epirubicin, cisplatin and capecitabine plus matuzumab in previously untreated patients with advanced oesophagogastric cancer (2008)

To evaluate the safety, tolerability, efficacy, pharmacokinetics and pharmacodynamics of the humanised antiepidermal growth factor receptor monoclonal antibody matuzumab combined with epirubicin, cisplatin and capecitabine (ECX) in patients as first-line treatment for advanced oesophagogastric cancer that express epidermal growth factor receptor (EGFR). This was a phase I dose escalation study of matuzumab at 400 and 800 mg weekly and 1200 mg every 3 weeks combined with ECX (epirubicin 50 mg m(-2), cisplatin 60 mg m(-2) on day 1 and capecitabine 1000 mg m(-2) daily). Patients were treated until disease progression, unacceptable toxicity or for a maximum of eight cycles. Twenty-one patients were treated with matuzumab at three different dose levels (DLs) combined with ECX. The main dose-limiting toxicity (DLT) was grade 3 lethargy at 1200 mg matuzumab every 3 weeks and thus 800 mg matuzumab weekly was the maximum-tolerated dose (MTD). Other common toxicities included rash, nausea, stomatitis and diarrhoea. Pharmacokinetic evaluation demonstrated that the coadministration of ECX did not alter the exposure of matuzumab. Pharmacodynamic studies on skin biopsies demonstrated inhibition of the EGFR pathway. Objective response rates of 65% (95% confidence interval (CI): 43-82), disease stabilisation of 25% (95% CI: 11-47) and a disease control rate (CR + PR + SD) of 90% were achieved overall. The MTD of matuzumab in combination with ECX was 800 mg weekly, and at this DL it was well-tolerated and showed encouraging antitumour activity. At the doses evaluated in serial skin biopsies, matuzumab decreased phosphorylation of EGFR and MAPK, and increased phosphorylation of STAT-3.
Supplementary Table 1 from Selective Down-Regulation of Glioma-Associated Oncogene 2 Inhibits the Proliferation of Hepatocellular Carcinoma Cells (2023)

Supplementary Table 1 from Selective Down-Regulation of Glioma-Associated Oncogene 2 Inhibits the Proliferation of Hepatocellular Carcinoma Cells
Spektrale Photon-Counting Computertomografie für Mehrphasen-Leberdiagnostik mit zwei Kontrastmitteln (2017)

Wir präsentieren einen neues Untersuchungsprotokoll für Leberdiagnostik für zwei Kontrastmittel (KM) und spektrale Photon-Counting Computertomografie (SPCCT) mit nur einem Scan.
Shout out (2010)

A useful approach for enabling computers to automatically create new content is utilizing the text, media, and information already present on the World Wide Web. The newly created content is known as "machine-generated content". For example, a machine-generated content system may create a multimedia news show with two animated anchors presenting a news story; one anchor reads the news story with text taken from an existing news article, and the other anchor regularly interrupts with his or her own opinion about the story. In this paper, we present such a system, and describe in detail its strategy for autonomously extracting and selecting the opinions given by the second anchor.
A Blockage Model for the Open Area Mm-wave Device-to-Device Environment (2019)

A significant portion of the 5th generation of wireless networks will operate in the mm-wave bands. One of the several challenges associated with mm-wave propagation is to overcome shadowing due to signal blockage caused by environmental objects. Particularly susceptible are nodes in a device-to-device network that typically operate at low power and in a blockage prone environment such as crowded open areas. In this work, we provide an insight into the effect of blockages on the signal quality for an open area device-to-device scenario. We propose a blockage model based on the homogeneous Poisson Point Process. The model provides the average signal attenuation as a soft metric that quantifies the extent of blockage. This not only indicates whether the signal is blocked but also measures how much the signal is attenuated due to one or more blockers. The analytical results are confirmed with the help of Monte Carlo simulations for real-world blocker placement in the environment.
Consensus extraction from heterogeneous detectors to improve performance over network traffic anomaly detection (2011)

Network operators are continuously confronted with malicious events, such as port scans, denial-of-service attacks, and spreading of worms. Due to the detrimental effects caused by these anomalies, it is critical to detect them promptly and effectively. There have been numerous softwares, algorithms, or rules developed to conduct anomaly detection over traffic data. However, each of them only has limited descriptions of the anomalies, and thus suffers from high false positive/false negative rates. In contrast, the combination of multiple atomic detectors can provide a more powerful anomaly capturing capability when the base detectors complement each other. In this paper, we propose to infer a discriminative model by reaching consensus among multiple atomic anomaly detectors in an unsupervised manner when there are very few or even no known anomalous events for training. The proposed algorithm produces a perevent based non-trivial weighted combination of the atomic detectors by iteratively maximizing the probabilistic consensus among the output of the base detectors applied to different traffic records. The resulting model is different and not obtainable using Bayesian model averaging or weighted voting. Through experimental results on three network anomaly detection datasets, we show that the combined detector improves over the base detectors by 10% to 20% in accuracy.
Syntheses and Characterizations of One-Dimensional Coordination Polymers Generated from Cadmium Nitrate and Bipyridine Ligands (1999)

Two new one-dimensional organic/inorganic composite polymers were synthesized by the reaction of Cd(NO3)2·4H2O with 1,2-bis(4-pyridyl)ethyne or trans-1,2-bis(4-pyridyl)ethene in several solvent systems. [Cd(NO3)2(1,2-bis(4-pyridyl)ethyne)1.5]n (1), which has an infinite one-dimensional structure with interpenetrating molecular ladders, was obtained by reacting Cd(NO3)2·4H2O with 1,2-bis(4-pyridyl)ethyne in a methylene chloride/methanol solvent system. It crystallized in the monoclinic space group C2/c (No. 15), with a = 20.713(3) Å, b = 17.450(2) Å, c = 14.451(3) Å, β = 129.203(8)°, Z = 8. [Cd(NO3)2(1,2-bis(4-pyridyl)ethene)1.5]n (2) was generated from the reaction of Cd(NO3)2·4H2O with the trans-1,2-bis(4-pyridyl)ethene ligand in an ethanol/water system. It has a novel infinite non-interpenetrating zigzag chain structure which is made up of trans-1,2-bis(4-pyridyl)ethene−Cd−trans-1,2-bis(4-pyridyl)ethene−Cd−trans-1,2-bis(4-pyridyl)ethene building units. Compound 2 crystallized in the triclinic space group P1̄ (No. 2), with a = 10.725(2) Å, b = 10.814(2) Å, c = 9.517(2) Å, α = 104.21(2)°, β = 94.60(1)°, γ = 106.62(1)°, Z = 2. In compound 1, the Cd(II) centers lie in a heptacoordinate environment, while in compound 2, the Cd(II) atoms adopt an octahedral geometry. The two kinds of polymer structures are based on a T-shape and a linear building block, respectively. [Cd(NO3)2(1,2-bis(4-pyridyl)ethane)1.5]n (3) was also synthesized by the reaction of Cd(NO3)2·4H2O with the 1,2-bis(4-pyridyl)ethane ligand in a methylene chloride/methanol system. Polymer 3 forms square units, which are linked through the two Cd(II) centers to give infinite linear chains. The synthesis of compound 3 was reported by Fujita (Fujita, M. J. Chem. Soc., Chem. Commun. 1994, 1977) using a different solvent system.
Induction of anaerobic gene expression in Rhodobacter capsulatus is not accompanied by a local change in chromosomal supercoiling as measured by a novel assay (1989)

In the photosynthetic bacterium Rhodobacter capsulatus, the enzyme DNA gyrase has been implicated in the expression of genes for anaerobic metabolic processes such as nitrogen fixation and photosynthesis. To assess the involvement of supercoiling in anaerobic gene expression, we have developed an assay to detect in vivo changes in superhelicity of small regions of the bacterial chromosome. Our method is based on the preferential intercalaction of psoralen into supercoiled versus relaxed DNA, and we have demonstrated the sensitivity of the assay in vivo on chromosomal regions from 2 to 10 kilobases in size. In experiments with inhibitors of gyrase, the reactivity of individual chromosomal fragments to psoralen decreases by a factor of 1.8 compared with DNA from control cultures. We used our assay to determine whether there is a change in superhelicity near the genes coding for essential proteins for photosynthesis upon a shift from respiratory to anaerobic photosynthetic growth. For comparison, we also examined a restriction fragment containing the fbc operon, which codes for the subunits of cytochrome bc1, a membrane-bound electron transport complex utilized during both aerobic and anaerobic photosynthetic growth. During this shift in growth conditions, the puf and puh mRNAs, coding for structural polypeptides of the photosynthetic apparatus, underwent a six- to eightfold induction, while the amount of mRNA from the fbc locus remained constant. However, we detected no change in the superhelicity of either the genes for photosynthesis or those for the bc1 complex during this metabolic transition. Our data thus do not support a model in which stable changes in chromosomal superhelicity regulate anaerobic gene expression. We suggest instead that the requirement for DNA gyrase in the transcription of photosynthesis genes results from the requirement for a swivel near heavily transcribed regions of the chromosome.
Synthesis of three‐dimensional Co/ CoO /N‐doped carbon nanotube composite for zinc air battery (2021)

Development of bifunctional electrocatalysts for oxygen electrocatalytic reactions is significant in improving the performance of Zn-air batteries. Among all candidates, transition metal compounds and carbon nanotube composites have attracted considerable attention owing to their great catalytic activities. Herein, three-dimensional (3D) macroporous carbon nanotube (CNT) microspheres interconnected with thorn-like N-doped CNT surrounding Co/CoO ([email protected]/CoO-bC) are synthesized via spray pyrolysis, followed by N-doped CNT growth and oxidation. Hierarchical nanohybrids with porous N-doped CNT-network and Co/CoO catalysts are rationally designed and applied as an efficient oxygen electrocatalyst. The porous carbon backbone exhibits high electrical conductivity with robust corrosion resistance. In addition, interconnected N-doped CNTs wrapping Co/CoO nanocatalysts exhibit enhanced catalytic properties as compared to commercial Pt/C and RuO2 in alkaline media. [email protected]/CoO-bC exhibits a robust cycle stability, higher power density, and lower polarization potential difference when applied as the oxygen electrode in a rechargeable Zn-air battery, in comparison to commercial Pt/C-RuO2 mixed powders.
Stereotactic Body Radiation Therapy for Prostate Cancer: What is the Appropriate Patient-Reported Outcome for Clinical Trial Design? (2015)

Following prostate SBRT, clinically significant urinary symptoms are more common than bowel symptoms. Our prostate SBRT treatment protocol meets the RTOG 0938 criteria for moving forward to a Phase III trial comparing it to conventionally fractionated radiation therapy. Notably, between 12 and 36 months, the proportion of patients reporting a significant decrease in both EPIC urinary and bowel domain scores declined, suggesting a late improvement in these symptom domains. Further investigation is needed to elucidate (1) which EPIC domains bear the greatest influence on post-treatment quality of life and (2) at what time point PRO endpoint(s) should be assessed.
Volumetric characterization of ultrasonic transducers for gas flow metering (2013)

The design of ultrasonic gas flowmeters requires a thorough three dimensional characterization of the acoustic sound field. For large pipe flowmeters, such as used for flare gas metering, the transducers are operated at frequencies ranging from 20 kHz up to 150 kHz. Thus, in this work we use a commercially available calibrated 1/8-inch microphone, mounted on a 3D positioning system for performing volumetric measurements in a volume of up to 1×1×1 m. By using proper corrections in terms of angular and free-field response of the microphone, the measurement system is efficient and delivers around 30000 measurements in about only eight hours. The data then is visualized in form of 3D figures or various slices to extract all relevant information. The system has been used to identify non-uniform velocity profiles in capacitive micromachined ultrasonic transducers (CMUTs), operating in permanent contact mode. Further, the system can be used to investigate the effect of various acoustic boundary conditions the transducers are facing when mounted inside transducer port cavities and it can be used for general model validation purpose.
Data Mining Techniques for Personalization. (2000)

This paper discusses an overview of data mining techniques for personalization. It discusses some of the standard techniques which are used in order to adapt and increase the ability of the system to tailor itself to specific user behavior. We discuss several such techniques such as collaborative filtering, content based methods, and content based collaborative filtering methods. We examine the specific applicability of these techniques to various scenarios and the broad advantages of each in specific situations. 1
Hepatitis B virus genotype has no impact on hepatitis B e antigen seroconversion after lamivudine treatment (2003)

HBeAg seroconversion after treatment by lamivudine was not influenced by the HBV genotype.