gebhart/patrepeval huggingface dataset:
Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora (2018)

Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time-consuming and costly. Here, we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimizing DNA extraction from a challenging plant tissue as a case study. Following the workflow illustrated, we were able to reliably and repeatedly obtain >6.5 Gb of long-read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls and suggestions of how to adapt it to other tissue types, will be useful to others who plan to establish long-read sequencing in their own laboratories.
Predictors of heart rate variability and its prognostic significance in chronic kidney disease (2011)

This study draws attention to the importance of HRV as a relatively under recognized predictor of adverse cardiovascular and renal outcomes in patients with nondialysis CKD. Whether interventions that improve HRV will improve these outcomes in this high-risk population deserves further study.
Halogen bonding-based crystal engineering: from Borromean links to homochiral double helices (2006)

The halogen bonding (XB) (i.e. the attractive interaction where halogens work as electron density acceptors) is a particularly robust and directional noncovalent interaction [1]. Thanks to these properties, effective tectons tailored to XB-based crystal engineering could be successfully developed. In this communication, it will be shown how the judicious choice of electron donor and acceptor modules enables the fine control of the structural and functional properties of the formed supramolecular architectures. Topologies as complex as Borromean links [2] and homochiral double helices (figure) can be planned in a rational way [3].
Noninvasive Follow-up Imaging of Ruptured Pediatric Brain AVMs Using Arterial Spin-Labeling (2022)

Our results contribute data on the role of noninvasive arterial spin-labeling monitoring of the response to treatment or follow-up after obliteration of pediatric AVMs. Future research may help to better delineate how arterial spin-labeling can assist in decisions regarding the optimal timing for DSA.
Enhancing Lempel-Ziv codes using an on-line variable length binary encoding (2002)

Summary form only given. The LZW algorithm is the most popular dictionary-based adaptive text compression scheme [Welch 1984]. In the LZW algorithm, a changing dictionary contains common strings that have been encountered so far in the text. The motivation for the present research is to explore an on-line variable-length binary encoding. We apply this encoding to LZW codes for remedy of the problem that we discussed in Acharya and Mukherjee [1995]. We call it the LZWAJ algorithm.
Ultra-wideband radar methods and techniques of medical sensing and imaging (2005)

Ultra-wideband radar holds great promise for a variety of medical applications. We have demonstrated the feasibility of using ultra-wideband sensors for detection of internal injuries, monitoring of respiratory and cardiac functions, and continuous non-contact imaging of the human body. Sensors are low-power, portable, and do not require physical contact with the patient. They are ideal for use by emergency responders to make rapid diagnosis and triage decisions. In the hospital, vital signs monitoring and imaging application could improve patient outcomes. In this paper we present an overview of ultra-wideband radar technology, discuss key design tradeoffs, and give examples of ongoing research in applying ultra-wideband technology to the medical field.
ChemInform Abstract: Efficient One‐Pot Synthesis of 2′‐Deoxyribonucleoside 3′‐O‐ and 5′‐O‐ Phosphorodithioates (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Light emission from thermally oxidized silicon nanoparticles (1994)

Light emission characteristics from silicon nanoparticles consisting of a crystalline core encased in an amorphous oxide shell are presented. The particles were thermally oxidized in the open atmosphere at 800 °C for times from 5 to 160 min in order to decrease the Si core dimensions. Photoluminescence spectra, at low excitation levels, reveal that the light emission shifts to shorter wavelengths as the oxidation time is increased. At high excitation levels, photoluminescence spectra show little or no shift. These results indicate that there are at least two mechanisms involved with light emission from Si nanoparticles, one associated with quantum size effects and another which is independent of size distribution.
Third-Harmonic-Type Modulation Minimizing the DC-Link Energy Storage Requirement of Isolated Phase-Modular Three-Phase PFC Rectifier Systems (2023)

A three-phase ac/dc converter with high-frequency isolation can be realized as a monolithic three-phase or as a phase-modular system by combining three single-phase Power Factor Correction (PFC) rectifier modules with individual isolated dc-dc converters. Advantageously, for a phase-modular system the module configuration can be changed depending on the instantaneous input-output voltage ratio (i.e., a star-(Y)- or a delta-(Δ)-arrangement such that wide voltage ranges can be covered without a massive over-dimensioning of the main power components. However, the main disadvantage of a phase-modular converter realization is the fact that the input power of each PFC rectifier module pulsates at twice the mains frequency (which is inherent to single-phase power conversion) such that large dc-link capacitors are required. Recent literature predicts a substantial power pulsation reduction enabled by means of third-(3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> )-harmonic injection modulation which is applicable for the Y-connection (where a common-mode (CM) / zero-sequence (ZS) voltage is injected), and for the Δ-connection of the three single-phase PFC rectifier modules (where a CM / ZS current is injected). This changes the distribution of the power flow in the three-phase system and the power pulsation is shifted to higher frequencies. This paper experimentally verifies and extends the dc-link energy storage requirement reduction of the 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> -harmonic injection modulation concept: In a first step, the derivation of the harmonic injection concept is recapitulated and suitable control methods are discussed for both CM voltage (Y-arrangement) and CM current (Δ-arrangement) injection. Further, an alternative CM voltage injection strategy with simplified reference generation based only on the instantaneous grid voltage measurements is presented and compared to the pure 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> -harmonic injection modulation. Measurement results obtained from a 6 kW prototype reveal a dc-link voltage variation and/or energy buffering reduction by up to 38.6 % enabled by the harmonic injection modulation compared to conventional operation without 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> -harmonic injection modulation.
ChemInform Abstract: Cu‐Free Click Cycloaddition Reactions in Chemical Biology (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
First report on the synthesis and structural studies of trans -Phakellistatin 18: a rotamer of marine natural product phakellistatin 18 (2022)

Phakellistatin peptides from marine organisms are the sources of proline-rich cyclic peptides with reported significant antitumor activities. Phakellistatin 18 (<b>1</b>), reported from marine sponge <i>Phakellia fusca</i>, contains three proline-peptide linkages in <i>cis</i> form. We attempted the total synthesis of natural product <b>1</b> through solution-phase macrocyclization approach, as a result, the synthetic cyclic peptide <b>2</b> was obtained as a rotamer of natural product having all three proline residues in <i>trans</i>-conformation. Here, we describe the synthesis, structural, and cytotoxicity studies of <i>trans</i>-Phakellistatin 18 (<b>2</b>), and its analog [Ala<sup>1,3,6</sup>]-Phakellistatin 18 (<b>3</b>). Detailed NMR studies were carried out to characterize the synthesized peptides, and anti-cancer screening was performed by using MTT assay. The synthetic <i>trans</i>-Phakellistatin 18 (<b>2</b>) (IC<sub>50</sub>=67.5 ± 2.938 µM) showed comparable cytotoxicity against HepG2 cancer cell line with standard drug doxorubicin (IC<sub>50</sub>=63.88 ± 6.48 µM). Here, the first synthetic and structural studies on <i>trans</i>-Phakellistatin 18 (<b>2</b>), and its anticancer screening against HepG2 cell line was reported.
Active Multifunctional Microelectromechanical System Metadevices: Applications in Polarization Control, Wavefront Deflection, and Holograms (2016)

Metasurfaces have provided a novel route to control the local phase of electromagnetic radiation through subwavelength scatterers where the properties of each element remain passive. A passive metasurface design can only achieve a specific functionality as it is extremely challenging to reconfigure each element that contributes toward the control of the radiation. In this work, the authors propose a different scheme based on microelectromechanical system (MEMS) to reconfigure the resonance and radiation phase via control of each dipolar element. The suspension angle of the individual bimorph cantilever in air can be precisely controlled through electrostatic actuation that determines the operative phase diagram of the metadevice. The dynamic polarization conversion is demonstrated through global control. In addition, it is proposed that a multifunctional operation such as dynamic wavefront deflection and rewritable holographic display can be accomplished by using 1D and 2D control of the cantilever array when each cantilever in the MEMS metadevice array is uniformly and accurately controlled in the large‐area samples. Such a rewritable proposition can enable myriad of applications of MEMS‐based metadevices in polarization‐division multiplexing and dynamic flat lenses.
One‐Pot Synthesis of Highly Substituted Polyheteroaromatic Compounds by Rhodium(III)‐Catalyzed Multiple CH Activation and Annulation (2014)

Abstract A new method for the synthesis of highly substituted naphthyridine‐based polyheteroaromatic compounds in high yields proceeds through rhodium(III)‐catalyzed multiple CH bond cleavage and CC and CN bond formation in a one‐pot process. Such highly substituted polyheteroaromatic compounds have attracted much attention because of their unique π‐conjugation, which make them suitable materials for organic semiconductors and luminescent materials. Furthermore, a possible mechanism, which involves multiple chelation‐assisted ortho CH activation, alkyne insertion, and reductive elimination, is proposed for this transformation.
Os(II) Based Green to Red Phosphors: A Great Prospect for Solution‐Processed, Highly Efficient Organic Light‐Emitting Diodes (2012)

Abstract Preparation and characterization of a new class of emissive Os(II) complexes ( 1 – 5 ) have been achieved using 3‐(thiazol‐2‐yl), 3‐(benzothiazol‐2‐yl), 3‐(imidazol‐2‐yl) and 3‐(benzimidazol‐2‐yl) azole chelates, together with the incorporation of one diphosphine ancillary for satisfying the octahedral coordination arrangement. The resulting Os(II) complexes, except for 5 , all show bright emission spanning visible region from green to saturated red, and their structural versus spectroscopic properties have been comprehended by absorption/emission together with computational approaches. Subsequently, a series of solution‐processed OLEDs using 1 – 4 as the dopant were successfully fabricated, demonstrating excellent device performances with external quantum efficiency (EQE) of 15%, current efficiency exceeding 48 cd/A, and power conversion efficiency up to 50 lm/W. Complex 4 is the only Os(II) based phosphor so far suitable for the fabrication of highly efficient green‐emitting OLEDs.
Neural networks in articulatory speech analysis/synthesis (1991)

A major difficulty in articulatory analysis/synthesis is the estimation of vocal-tract parameters from input speech. The use of neural networks to extract these parameters is more attractive than codebook look-up due to the lower computational complexity. For example, a multilayer perceptron (MLP) with two hidden layers, trained and evaluated on a small data set was shown to perform a reasonable mapping of acousticto-geometric parameters. Increasing the training data, however, revealed ambiguity in the mapping that could not be resolved by a single network. This paper addresses the problem using an assembly of MLP's, each designated to a specific region in the articulatory space. Training data were generated by randomly sampling the parameters of an articulatory model of the vocal system. The resultant vocal-tract shapes were clustered into 128 regions, and an MLP with one hidden layer was assigned to each of these regions for mapping 18 cepstral coefficients into ten tract areas, and a nasalization parameter. Networks were selected by dynamic programming, and were used to control a time-domain articulatory synthesizer. After training, significant perceptual and objective improvements were achieved relative to using a single MLP. Comparable performance to codebook look-up with dynamic programming was obtained. This model, however, requires only 4% of the storage needed for the codebook, and performs the mapping faster by a factor of 20.
Crystal structure of (E)-7-t-Butyl-5-methoxy-3-[(E)-2'-methoxy-5',5'-dimethyl-4'-oxohex-2'-enylidene]benzofuran-2(3H)-one (1977)

The crystal structure of (E)-7-t-butyl-5-methoxy-3-[(E)-2?-methoxy- 5?,5?-dimethyl-4?-oxohex-2?enylidene]benzofuran-2(3H)-one, C22H28O5 (see preceding paper), has been determined by single-crystal X-ray diffraction at 295(1) K and refined by least squares to a residual of 0.067 (3735 ?observed? reflections). Crystals are triclinic, Pi, a 14.955(7), b 13.142(5), c 10.910(3) ?, a 85.76(3), ß 85.67(3), ? 80.12(3)°, Z 4.
A NUMERICAL AND EXPERIMENTAL STUDY OF TURBULENT BOUNDARY LAYER WITH ROD-ROUGHENED WALL (2007)

The effects of surface roughness on a turbulent boundary layer (TBL) were investigated using direct numerical simulations (DNS) and particle image velocimetry (PIV). The roughness elements used were periodically arranged two-dimensional spanwise rods, and the roughness height was k/δ=0.05 for DNS and k/δ=0.0165, 0.032 for PIV. In PIV measurements, the friction velocity uτ for smooth and rough walls was estimated by fitting of mean velocity profile. Introduction of the roughness elements increased the wake strength and the turbulent stress not only in the roughness sublayer but also in the outer layer. This indicates the existence of interaction between inner and outer layers. Iso-contours of mean velocities and Reynolds stresses in the roughness sublayer obtained by PIV measurements show a good agreement with DNS results.
Poly(amino acids) as a potent self-adjuvanting delivery system for peptide-based nanovaccines (2020)

To be optimally effective, peptide-based vaccines need to be administered with adjuvants. Many currently available adjuvants are toxic, not biodegradable; they invariably invoke adverse reactions, including allergic responses and excessive inflammation. A nontoxic, biodegradable, biocompatible, self-adjuvanting vaccine delivery system is urgently needed. Herein, we report a potent vaccine delivery system fulfilling the above requirements. A peptide antigen was coupled with poly-hydrophobic amino acid sequences serving as self-adjuvanting moieties using solid-phase synthesis, to produce fully defined single molecular entities. Under aqueous conditions, these molecules self-assembled into distinct nanoparticles and chain-like aggregates. Following subcutaneous immunization in mice, these particles successfully induced opsonic epitope-specific antibodies without the need of external adjuvant. Mice immunized with entities bearing 15 leucine residues were able to clear bacterial load from target organs without triggering the release of soluble inflammatory mediators. Thus, we have developed a well-defined and effective self-adjuvanting delivery system for peptide antigens.
On the selection of a host compound for efficient host–guest light-emitting electrochemical cells (2015)

Reversible electrochemical doping capacity is a fundamental criterion for an efficient and functional host–guest LEC.
Assessing the quality of untraditional water sources for irrigation purposes in Al-Qalubiya Governorate, Egypt (2020)

Limited freshwater coupled with the ever-growing population has forced the farmers in Egypt to reuse untraditional water sources for irrigation purposes. However, a precise evaluation of such water quality is necessary to avoid potential risks. The current work aimed at verifying the potentiality of reusing agricultural drainage water (ADW) and mixed wastewater (MWW) for irrigation in Al-Qalubiya Governorate. The study based on the considerations set by FAO 29 and 47 guidelines besides the Egyptian code of practice (ECP 501/2015) for wastewater reuse for irrigation. Twenty water samples were collected along Sindwa drain (agricultural drainage water) and Shibin El-Qanater drain (mixed wastewater), ten samples from each. Another ten samples of the Nile freshwater (NFW) were collected nearby the previously water samples from El-Sharaqua canal. The three different locations of sample collection sites showed variable ranges of pH, dissolved and suspended solids, soluble ions, and trace elements. However, they were generally lower than the maximum allowable limits set by FAO guidelines and ECP 501/2015, except NO3– and Mn in the ADW. On the other hand, the fecal coliforms in the ADW and MWW were beyond the safe limits. Based on the ECP 501/2015 the NFW is recommended for irrigating crops of Group B (e.g. dry cereal crops and cooked and processed vegetables, fruit crops and medicinal plants), while the ADW and MWW are recommended for crops of Group D (e.g. bio-charcoal crops, bio-diesel fuel crops, cellulose production crops, and timber trees).
A syntenin inhibitor blocks endosomal entry of SARS-CoV-2 and a panel of RNA viruses (2022)

Abstract Viruses are dependent on interactions with host factors in order to efficiently establish an infection and replicate. Targeting such interactions provides an attractive strategy to develop novel antivirals. Syntenin is a protein known to regulate the architecture of cellular membranes by its involvement in protein trafficking, and has previously been shown to be important for HPV infection. Here we show that a highly potent and metabolically stable peptide inhibitor that binds to the PDZ1 domain of syntenin inhibits SARS-CoV-2 infection by blocking the endosomal entry of the virus. Furthermore, we found that the inhibitor also hampered chikungunya infection, and strongly reduced flavivirus infection, which are completely dependent on receptor mediated endocytosis for their entry. In conclusion, we have identified a novel pan-viral inhibitor that efficiently target a broad range of RNA viruses.
Virus-triggered exacerbation in allergic asthmatic children: neutrophilic airway inflammation and alteration of virus sensors characterize a subgroup of patients (2017)

This multicenter prospective study was approved by the regional investigational review board (ref: 08/07).
Improved Luminous Efficiency of Organic Light-Emitting Diodes by Carrier Trapping Dopants (2001)

We propose a carrier trapping (CT) dopant method to improve the luminous efficiency of organic light-emitting diodes (OLEDs). The CT dopant did not emit light itself, but adjusted the charge balance in the OLEDs. The cell structure of the OLED in the experiment was as follows: Indium tin oxide (ITO)/hole transport layer (50 nm, 2TNATA)/emitting layer (20 nm, NPB+5% rubrene)/electron transport layer (30 nm, Alq+4% CT dopant)/MgIn. (2TNATA: 4,4 ′ ,4 ′′ -Tris(N-(2-naphthyl)-N-phenyl-amino)-triphenylamine, NPB; N,N ′ -Di(naphthalen-1-yl)-N,N ′ -diphenyl-benzidine). 4,4 ′ -Bis(carbazol-9-yl)-biphenyl (CBP) was used as a CT dopant. This cell had a yellow emission originating from the rubrene with the luminous efficiency of 8.7 cd/A at a current density of 10 mA/cm 2 . On the other hand, when the CT dopant was not used, the luminous efficiency was 7.5 cd/A. The luminous efficiency was improved by the CT dopant method.
Relative efficiency of human Langerhans´ cells and blood derived dendritic cells as antigen-presenting cells (1985)

T4 cells recognize antigens together with HLA class II molecules in the membrane of antigen-presenting cells (APC). The magnitude of the induced T cell response is in part dependent upon the APC's amount of MHC-class II molecules. Langerhans' dendritic cells (LC) express 50-100 times more HLA-DR molecules than monocytes (Mo) and blood derived dendritic cells (DC). We report here that LC are more efficient APC than DC from the same donor, indicating that the APC capacity of dendritic cells isolated from different organs is correlated to their expression of HLA class II gene products.