gebhart/patrepeval huggingface dataset:
miEAA 2.0: Integrating multi-species microRNA enrichment analysis and workflow management systems (2020)

Abstract Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from Homo sapiens, Mus musculus , and Rattus norvegicus . To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miR-Base miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualisations such as heatmaps and running sum curves with background distributions. Lastly, additional methods to correct for multiple hypothesis testing were implemented. We demonstrate the new features using case studies for human kidney cancer and mouse samples. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2 .
Chronic wound diagnostic for matrix metalloproteinase (2009)

Acute wound healing is a highly complex process that is regulated in large part by the integrated actions of several key classes of proteins, including growth factors, receptors, proteases, and extracellular matrix components. Molecular analyses of chronic wound biopsies and fluids have identified several proteins whose levels are dramatically altered compared to acute healing wounds. Specifically, high levels of matrix metalloproteinases (MMPs) in wound fluids and biopsies have been reported to correlate with poor healing of chronic wounds and to decrease as chronic wounds began to heal. At present, clinicians do not have a way to readily obtain this useful information. This critical absence has led to the development of a prototype device that can be used by wound care providers at the point-of-care to rapidly measure MMP activity in swab samples of wound fluid. The measurement of MMP activity should provide critical information on the healing trajectory of the wound and if the wound bed is adequately prepared for advanced biological therapies such as recombinant growth factors and engineered skin substitutes.
Preservative-free Treatment in Glaucoma: Who, when, and why? (2013)

This review provides an up-to-date account of the literature regarding preservatives and the eye, as well as suggestions and recommendations on to when to use preservative-free antiglaucoma treatment.
Kondo effect in quantum dots coupled to ferromagnetic leads: effect of noncollinear magnetization (2007)

We study the Kondo effect in a quantum dot coupled to two noncollinear ferromagnetic leads. First, we study the spin splitting δε = ε↓ − ε↑ in the quantum dot by the tunnel coupling to the ferromagnetic leads, using the Poor man’s scaling method. The spin splitting takes place in an intermediate direction between magnetic moments in the two leads. δε ∝ p cos(θ/2), where p is the spin polarization in the leads and θ is the angle between the magnetic moments; spin splitting is maximal in the parallel alignment of two ferromagnets (θ = 0) and minimal in the antiparallel alignment (θ = π). Second, we calculate the Kondo temperature TK. The scaling calculation yields an analytical expression of TK as a function of θ and p,TK(θ,p), when δε ≪ TK. When δε is relevant, we evaluate TK(δε,θ,p) using the slave‐boson mean‐field method. The Kondo resonance is split into two by finite δε, which results in the suppression of Kondo effect.
Evaluation of a position sensitive avalanche photodiode for PET (2003)

A gamma ray detector for PET, consisting of an array of mixed lutetium oxyorthosilicate (MLS) scintillator crystals coupled to a position sensitive avalanche photodiode (PSAPD), was evaluated. The scintillator array was constructed from individual MLS crystals with dimensions of 1.5 mm /spl times/ 1.5 mm /spl times/ 15 mm. The assembled 7 /spl times/ 7 array, including intercrystal reflector material, had a pitch of 1.79 mm. The low noise, high gain PSAPD had dimensions of 14 mm /spl times/ 14 mm. Peaks associated with each of the 49 scintillator crystals were readily identifiable in flood histograms, and most of the crystals demonstrated energy resolution in the range of 15% to 20% at 511 keV. Measurements of the timing of the PSAPD in coincidence with a fast-scintillator/PMT detector indicated a timing resolution of approximately 4 ns. The operating characteristics and design attributes, such as compactness and reduced readout channel requirements, of the PSAPD make it attractive for high resolution PET applications.
Comparative Study of SC-FDMA and OFDMA Using Turbo SIC Considering Soft-Symbol Estimate for MIMO SDM (2014)

This paper presents a comparative study of single-carrier (SC)-frequency division multiple access (FDMA) and OFDMA using turbo soft interference cancellation (SIC) from the viewpoint of throughput for multiple-input multiple-output (MIMO) spatial division multiplexing (SDM). In turbo SIC, interference from other transmission streams is generated based on the log-likelihood ratio (LLR) at the turbo decoder output and subtracted from the received signal iteratively associated with a linear minimum mean-square error (LMMSE) filter. Hence, we compare the throughput performance levels of methods for generating soft-symbol estimates of other streams based on the extrinsic LLR and the a posteriori LLR at the Max-Log-MAP decoder output. We show by computer simulation the difference in performance of turbo SIC based on the a posteriori LLR and extrinsic LLR from the viewpoints of the average block error rate and throughput. We also show that the OFDMA yields superior throughput performance compared to SC-FDMA with 16QAM and 64QAM schemes when using turbo SIC for 2-by-2 to 8-by-8 MIMO SDM.
Remote-Controlled Monitoring of Flying Pests with an Electrostatic Insect Capturing Apparatus Carried by an Unmanned Aerial Vehicle (2021)

The purpose of the study was to construct an electrostatic insect-capturing apparatus that could be applied to a drone (quadcopter). For this purpose, a double-charged dipolar electric field screen (DD-screen) was constructed using oppositely charged insulator tubes that was then attached to a drone. For charging, the inner surface of the tubes was coated with a conductive paste and then linked to a negative or positive voltage generator. The opposite charges of the tubes formed an electric field between them and created an attractive force to capture insects that entered the field. The DD-screen constructed here was sufficiently light to enable its attachment to a drone. The screen was hung from the drone perpendicular to the direction of drone movement, so as to receive the longitudinal airflow produced by the movement of the drone. It was positioned 1.8 m below the drone body to avoid the influence of the downward slipstream generated by the rotating propellers. Eventually, the drone was able to conduct a stable flight, with sufficient endurance, and captured airborne insects carried by an airflow of 8 m/s during the flight. This study, therefore, provides an experimental basis for establishing a new method for conducting trap-based monitoring of airborne insects during remote-controlled flight through operation of a DD-screen attached to a drone.
Microstructure and Phase Behavior of Block Copoly(ether ester) Thermoplastic Elastomers (2001)

The microstructure of segmented block copoly(ether esters) composed of poly(tetramethylene oxide) (PTMO) “soft” blocks and poly(butylene terephthalate) (PBT) “hard” blocks was investigated. A variety of analytical techniques, including 13C solid-state NMR, infrared spectroscopy, dynamical mechanical analysis, dielectric spectroscopy, differential scanning calorimetry, and transmission electron microscopy, were applied. The samples vary in the amount (35−60 wt %) and block length (1000−2000 g/mol) of the soft component. It is generally assumed in the literature that copoly(ether esters) have a two-phase structure consisting of a crystalline PBT phase surrounded by an amorphous phase which is a homogeneous mixture of PTMO soft segments and amorphous PBT segments. Our experimental results reveal that the amorphous phase is not a homogeneous mixture of “hard” and “soft” segments but consists of a highly mobile “PTMO-rich phase” and a less mobile “PBT/PTMO mixed phase”. The extent of microphase separation in the amorphous phase appeared to be strongly dependent on the block length and composition. Those samples that revealed a strong microphase separation showed strain-induced crystallization of the soft segments upon mechanical deformation.
Power Efficient Scheduling Algorithms for Real-time Tasks on Multi-mode Microcontrollers (2018)

Mobile smart devices are advancing with stronger demands of high energy efficiency and longer battery life. Utilizing energy-efficient microcontroller units in a mobile device for always-on functionalities has proven to be an effective solution. MCUs have the ability to switch between different running modes dynamically enabling them to have outstanding low power performance while performing real-time sensing tasks. Besides hardware optimization, balancing energy efficiency and quality of service on a MCU lies within a well-designed scheduling algorithm. In this paper, we formally define, model and derive a proper scheduling algorithm that guarantees the hard real-time task set's schedulability and minimizes power consumption. Our findings provide an approach of calculating the MCUs resource shutdown schedule, i.e., the shutdown period and the standby time in each period, under Earliest Deadline First and Rate Monotonic scheduler. However, periodically shutting down the MCU may be a simplified way of implementing real-time scheduling on a MCU but not necessarily the optimal approach. Therefore, we further use a simulation to evaluate the performance gap of the periodic shutdown method and the optimal shutdown method with respect to the power savings.
Synthesis and Structural Characterization of Novel Thulium(III) Cyclic Organohydroborate Complex with a Weak Agostic Interaction (THF)3Tm{(μ-H)2(BC8H14) }3 (2009)

Preparation of (THF) 3Tm{(µ-H)2BC8H14} 3. In the drybox 275.3 mg (1.0 mmol) of TmCl3 and 480.3 mg (3.0 mmol) of K(H2BC8H14) were put into a flask. After degassing, 30 mL of THF was transferred into the flask at -78 o C. The solution was warmed to room temperature and stirred for 24 hours. During this process the solution turned cloudy due to the formation of KCl which was removed by filtration. Volatile components were removed by means of dynamic high vacuum leaving a white solid. The solid was redissolved in ether and the solution was filtered to remove impurities. A white solid (THF)3Tm- {(µ-H)2BC8H14}3 was obtained in 65% yield upon removal of the solvent under vacuum. Crystal, suitable for X-ray diffrac- tion, was obtained by crystallization from toluene. IR (KBr) 2922(s), 2856(s), 1702(m), 1660(m), 1446(m), 1012(m), 670(m) cm -1 .
Task‐Specific Ionic Liquids as Reaction Media for the Cobalt‐Catalyzed Cyclotrimerization Reaction of Arylethynes. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Bases of biocontrol: Sequence predicts synthesis and mode of action of agrocin 84, the Trojan Horse antibiotic that controls crown gall (2006)

Agrobacterium radiobacter K84, used worldwide to biocontrol crown gall disease caused by Agrobacterium tumefaciens, produces an antiagrobacterial compound called agrocin 84. We report the nucleotide sequence of pAgK84, a 44.42-kb plasmid coding for production of this disubstituted adenine nucleotide antibiotic. pAgK84 encodes 36 ORFs, 17 of which (agn) code for synthesis of or immunity to agrocin 84. Two genes, agnB2 and agnA, encode aminoacyl tRNA synthetase homologues. We have shown that the toxic moiety of agrocin 84 inhibits cellular leucyl-tRNA synthetases and AgnB2, which confers immunity to the antibiotic, is a resistant form of this enzyme. AgnA, a truncated homologue of asparaginyl tRNA synthetase could catalyze the phosphoramidate bond between a precursor of the methyl pentanamide side group and the nucleotide. We propose previously undescribed chemistry, catalyzed by AgnB1, to generate the precursor necessary for this phosphoramidate linkage. AgnC7 is related to ribonucleotide reductases and could generate the 3'-deoxyarabinose moiety of the nucleoside. Bioinformatics suggest that agnC3, agnC4, and agnC6 contribute to maturation of the methyl pentanamide, whereas agnC2 may produce the glucofuranose side group bound to the adenine ring. AgnG is related to bacterial exporters. An agnG mutant accumulated agrocin 84 intracellularly but did not export the antibiotic. pAgK84 is transmissible and encodes genes for conjugative DNA processing but lacks a type IV secretion system, suggesting that pAgK84 transfers by mobilization. By sequence analysis, the deletion engineered into pAgK1026 removed the oriT and essential tra genes, confirming the enhanced environmental safety of this modified form of pAgK84.
LTE-WiFi Link Aggregation at Femtocell Base Station (2014)

In this paper, we propose the architecture and an algorithm of LTE-WiFi Link Aggregation (LA) provided by an LTE femtocell base station. The link aggregation simultaneously uses both an LTE link and a WiFi link in order to improve the throughput of an IP traffic flow. Our proposed LA architecture is transparent to any application and supports multiple PDN (Packet Data Network) connections for a mobile operator's Evolved Packet Core (EPC) and Local IP Access (LIPA) in a home network. For the above purposes, any application transmits/receives IP packets to/from an LA control module in a terminal via two virtual network layer device TUNs, for EPC and LIPA. Our proposed LA algorithm distributes a TCP traffic flow to LTE and WiFi links based on the Modulation and Coding Scheme (MCS) and Physical Resource Block (PRB) usage of the LTE link. We have shown in an experimental evaluation that the TCP traffic flows to PC and Android terminals make use of the available bandwidth of LTE and WiFi links by using our proposed algorithm.
Tau seeds are subject to aberrant modifications resulting in distinct signatures (2021)

The prion-like spread of tau pathology could underlie a spectrum of clinical syndromes including Alzheimer's disease (AD). Although evidence indicates that tau is transmissible, it is unclear how pathogenic tau seeds are processed in neurons. Here, we analyze fibrillar wild-type and disease-associated P301L tau seeds by using in vitro and neuronal assays. We show that P301L seeds are uniquely modified by post-translational modifications (PTMs) within the microtubule-binding region (MTBR). Although these modifications do not alter tau seed trafficking or localization, acetylated tau variants show accelerated tau aggregation, enhanced tau PTM priming, and prion-like templating. To explain the enhanced tau seed acetylation, we demonstrate that P301L seeds undergo auto-acetylation. Moreover, tau acts generally to inhibit HDAC6 deacetylase activity by preventing HDAC6 phosphorylation, leading to increased substrate acetylation. Our study highlights complex post-translational regulation of transmissible tau seeds and provides insight into the biological properties of tau strains in AD and other tauopathies.
Probing the binding site of novel selective positive allosteric modulators at the M1 muscarinic acetylcholine receptor (2018)

Subtype-selective allosteric modulation of the M<sub>1</sub> muscarinic acetylcholine (ACh) receptor (M<sub>1</sub> mAChR) is an attractive approach for the treatment of numerous disorders, including cognitive deficits. The discovery of benzyl quinolone carboxylic acid, BQCA, a selective M<sub>1</sub> mAChR positive allosteric modulator (PAM), spurred the subsequent development of newer generation M<sub>1</sub> PAMs representing diverse chemical scaffolds, different pharmacodynamic properties and, in some instances, improved pharmacokinetics. Key exemplar molecules from such efforts include PF-06767832 (N-((3R,4S)-3-hydroxytetrahydro-2H-pyran-4-yl)-5-methyl-4-(4-(thiazol-4-yl)benzyl)pyridine-2-carboxamide), VU6004256 (4,6-difluoro-N-(1S,2S)-2-hydroxycyclohexyl-1-((6-(1-methyl-1H-pyrazol-4-yl)pyridine-3-yl)methyl)-1H-indole-3-carboxamide) and MIPS1780 (3-(2-hydroxycyclohexyl)-6-(2-((4-(1-methyl-1H-pyrazol-4-yl)-benzyl)oxy)phenyl)pyrimidin-4(3H)-one). Given these diverse scaffolds and pharmacodynamics, the current study combined pharmacological analysis and site-directed mutagenesis to explore the potential binding site and function of newer M<sub>1</sub> mAChR PAMs relative to BQCA. Interestingly, the mechanism of action of the novel PAMs was consistent with a common model of allostery, as previously described for BQCA. Key residues involved in the activity of BQCA, including Y179 in the second extracellular loop (ECL) and W400<sup>7.35</sup> in transmembrane domain (TM) 7, were critical for the activity of all PAMs tested. Overall, our data indicate that structurally distinct PAMs share a similar binding site with BQCA, specifically, an extracellular allosteric site defined by residues in TM2, TM7 and ECL2. These findings provide valuable insights into the structural basis underlying modulator binding, cooperativity and signaling at the M<sub>1</sub> mAChR, which is essential for the rational design of PAMs with tailored pharmacological properties.
Figure S6 from Poly (ADP) Ribose Glycohydrolase Can Be Effectively Targeted in Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Figure S6 describes cleaved caspase 3 expression and quantitation of H2AX foci in MIA PaCa-2 after combination of PDDX-001 and oxaliplatin.&lt;/p&gt;
Speckle Tracking in 3D Echocardiography with Motion Coherence (2007)

Tracking of speckles in echocardiography enables the study of myocardium deformation, and thus can provide insights about heart structure and function. Most of the current methods are based on 2D speckle tracking, which suffers from errors due to through-plane decorrelation. Speckle tracking in 3D overcomes such limitation. However, 3D speckle tracking is a challenging problem due to relatively low spatial and temporal resolution of 3D echocardiography. To ensure accurate and robust tracking, high level spatial and temporal constraints need to be incorporated. In this paper, we introduce a novel method for speckle tracking in 3D echocardiography. Instead of tracking each speckle independently, we enforce a motion coherence constraint, in conjunction with a dynamic model for the speckles. This method is validated on in vivo porcine hearts, and is proved to be accurate and robust.
Presence of EBV‐DNA sequences in nasopharyngeal cells of individuals without IgA‐VCA antibodies (1983)

Exfoliated nasopharyngeal (NP) cells from 62 normal Cantonese Chinese having IgA/VCA antibodies for more than a year and from 39 similar persons without IgA/VCA antibodies, were tested for the presence of EBV/DNA sequences by spot followed by blot hybridization tests, using the cloned internal repeat of B95-8 viral DNA as probe. Thirteen out of 62 specimens from IgA/VCA-positive (21%) and six out of 39 specimens (15.4%) from IgA/VCA-negative individuals were found to contain EBV/DNA sequences. Forty-six cases (20 IgA/VCA-positive and 26 IgA/VCA-negative) were followed a year later for EBV/DNA sequences and EBV serology. Half of the individuals having EBV/DNA sequences in their exfoliated NP cells in 1981 did not have detectable EBV sequences a year later, and to out of 15 negative individuals became EBV/DNA-positive. There was no obvious correlation between EBV/DNA detectability and EBV serology. (We conclude that the best marker for NPC risk remains the increasing IgA/VCA and/or EA antibody titers.
Strong coupling and hybridization of Frenkel and Wannier-Mott excitons in an organic-inorganic optical microcavity (2006)

We demonstrate strong exciton-photon coupling and photon-mediated hybridization between the Frenkel and Wannier-Mott excitons of an organic-inorganic hybrid optical microcavity. Hybridization occurs between the Frenkel excitons of the small molecular weight organic tetraphenylporphyrin and the Wannier-Mott excitons of InGaP quantum wells. This mixed state consists of 10% Frenkel and Wannier-Mott exciton and 80% cavity photon character, and persists up to temperatures of $100\phantom{\rule{0.3em}{0ex}}\mathrm{K}$.
The Authors Respond (2020)

To the Editor: We thank Penning de Vries et al1 for the illustration of optimal subgroup selection for treatment in the case of ties. In our article,2 we had addressed this setting of ties by referring the reader to the formal treatment given in Luedke and van der Laan3–5 in our eAppendix; (https://links.lww.com/EDE/B466). The discussion in our main article was intended to focus on the simpler cases to keep the exposition as accessible as possible, but it is indeed good to have these matters more explicitly discussed in the epidemiologic literature. Tyler J. VanderWeeleDepartments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, [email protected]Mark J. van der LaanDepartment of Biostatistics, University of California, Berkeley, CARonald C. KesslerDepartment of Health Care Policy, Harvard Medical School, Boston, MA
Tandem Mass Spectrometry for the Direct Assay of Enzymes in Dried Blood Spots: Application to Newborn Screening for Mucopolysaccharidosis II (Hunter Disease) (2006)

This newly developed tandem mass spectrometry assay has the potential to be adopted for newborn screening of Hunter syndrome. This method also has the potential to be carried out in multiplex fashion to assay several different enzymes relevant to lysosomal storage diseases that are assayed in a single infusion into the mass spectrometer.
Measurement of the FSR of a high finesse etalon with 2.5 kHz accuracy using a narrow-linewidth frequency swept laser (2010)

Measurement of the FSR of an etalon having finesse of 1000 with 7 digits of accuracy or 2.5 kHz. A modified PDH technique is used in conjunction with a frequency swept, narrowlinewidth CW laser. © 2010 Optical Society of America.