gebhart/patrepeval huggingface dataset:
SagB Glucosaminidase Is a Determinant of Staphylococcus aureus Glycan Chain Length, Antibiotic Susceptibility, and Protein Secretion (2016)

Staphylococcus aureus is thought to secrete proteins across the plasma membrane via the Sec pathway; however, protein transport across the cell wall envelope has heretofore not been studied. We report that S. aureus sagB mutants generate elongated peptidoglycan strands and display defects in protein secretion as well as aberrant excretion of cytoplasmic proteins. These results suggest that the thick peptidoglycan layer of staphylococci presents a barrier for protein secretion and that SagB appears to extend the Sec pathway across the cell wall envelope.
Assessing the Adequacy of Endoscopically Tied Knots: A Functional Approach (2005)

This system is a reliable model for testing intracorporeal knots tied endoscopically. A three-half-hitches square knot with 3/0 nylon, tied using a flexible endoscope and knot-tightening cap, can withstand pressure up to 200 mm Hg.
Coupled Dictionary Learning for Multi-Contrast MRI Reconstruction (2018)

Medical imaging tasks often involve multiple contrasts, such as T1-and T2-weighted magnetic resonance imaging (MRI) data. These contrasts capture information associated with the same underlying anatomy and thus exhibit similarities. In this paper, we propose a Coupled Dictionary Learning based multi-contrast MRI reconstruction (CDLMRI) approach to leverage an available guidance contrast to restore the target contrast. Our approach consists of three stages: coupled dictionary learning, coupled sparse denoising, and k-space consistency enforcing. The first stage learns a group of dictionaries that capture correlations among multiple contrasts. By capitalizing on the learned adaptive dictionaries, the second stage performs joint sparse coding to denoise the corrupted target image with the aid of a guidance contrast. The third stage enforces consistency between the denoised image and the measurements in the k-space domain. Numerical experiments on the retrospective under-sampling of clinical MR images demonstrate that incorporating additional guidance contrast via our design improves MRI reconstruction, compared to state-of-the-art approaches.
A Sensitive Micro Conductometric Ethanol Sensor Based on an Alcohol Dehydrogenase-Gold Nanoparticle Chitosan Composite (2023)

In this paper, a microconductometric sensor has been designed, based on a chitosan composite including alcohol dehydrogenase-and its cofactor-and gold nanoparticles, and was calibrated by differential measurements in the headspace of aqueous solutions of ethanol. The role of gold nanoparticles (GNPs) was crucial in improving the analytical performance of the ethanol sensor in terms of response time, sensitivity, selectivity, and reproducibility. The response time was reduced to 10 s, compared to 21 s without GNPs. The sensitivity was 416 µS/cm (<i>v</i>/<i>v</i>%)<sup>-1</sup> which is 11.3 times higher than without GNPs. The selectivity factor versus methanol was 8.3, three times higher than without GNPs. The relative standard deviation (RSD) obtained with the same sensor was 2%, whereas it was found to be 12% without GNPs. When the air from the operator's mouth was analyzed just after rinsing with an antiseptic mouthwash, the ethanol content was very high (3.5 <i>v</i>/<i>v</i>%). The background level was reached only after rinsing with water.
A study on reduction of electromagnetic coupling between symmetric antennas using even-odd mode analysis (2023)

We propose a method for reducing electromagnetic coupling between two monopole antennas for MIMO communications that do not use any lumped element components. In the past, the decoupling method for connecting antennas required two steps, decoupling and matching, in order, and used lumped element components for each step. The previous design method using even-odd mode analysis also uses one lumped element component between antennas. The proposed method of this paper also uses even-odd mode analysis, but the decoupling condition can be set independently for each mode, and both decoupling and matching can be designed simultaneously, without using lumped element components. The decoupling effect was confirmed by simulation and measurement.
Cover Feature: Dumbbell‐Shaped T8‐POSS with Functional Organic Linker (Eur. J. Inorg. Chem. 27/2019) (2019)

The Cover Feature shows two dumbbell-shaped molecules based on T8 cage-like silsesquioxanes which are independently bridged by a symmetrical malonamide (MAL) and a non-symmetrical urea-thiourea (UT) organic linker. Both compounds are formed favorably by using fluoride ion as catalyst. Although it has a symmetrical linker, MAL is only monofunctional, and it is therefore represented as the “beast”. In contrast, UT has two functionalities, promising more advantageous properties, and is therefore the “beauty”, despite its non-symmetrical linker. More information can be found in the Full Paper by M. Wong Chi Man, C. Sanchez et al.
Incomplete sensitivities in design and control of fluidic channels (2001)

Control of distributed systems has various industrial applications, as it is often desired to keep complex multi-disciplinary systems in some given state. Definition or parameteri-zation of control space is the first main issue we face when formulating a control problem. Usually, one wishes to keep the parameterization space dimension as small as possible to limit the complexity of the problem. In addition, for any control approach to be effective, it should be realizable during the time the system is still controllable. Computational cost is therefore another critical issue. Our aim in this paper is to discuss alternative remedies for these two problems. We discuss the behavior of an electrokinetic microchan-nel system where the control variables include both the geometry of the microchannels and the temporal control of potentials. In a real system, the geometric control is achieved by the realization of etched microchannel structures using microlithography techniques. Flow control is accomplished by applying electric potentials along microchannels. We discuss the behavior of our design and control platform for two complementary classes of problems: the situation where the number of controls is small (a potential field) and where the number of controls is large (the geometry of a microchannel turn).
Non-oncology drugs are a source of previously unappreciated anti-cancer activity (2019)

ABSTRACT Anti-cancer uses of non-oncology drugs have been found on occasion, but such discoveries have been serendipitous and rare. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. To accomplish this, we used PRISM, which involves drug treatment of molecularly barcoded cell lines in pools. Relative barcode abundance following treatment thus reflects cell line viability. We found that an unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines. Moreover, the killing activity of the majority of these drugs was predictable based on the molecular features of the cell lines. Follow-up of several of these compounds revealed novel mechanisms. For example, compounds that kill by inducing PDE3A-SLFN12 complex formation; vanadium-containing compounds whose killing is dependent on the sulfate transporter SLC26A2; the alcohol dependence drug disulfiram, which kills cells with low expression of metallothioneins; and the anti-inflammatory drug tepoxalin, whose killing is dependent on high expression of the multi-drug resistance gene ABCB1. These results illustrate the potential of the PRISM drug repurposing resource as a starting point for new oncology therapeutic development. The resource is available at https://depmap.org .
Supplementary Figures 1-3 from Heat Shock Protein 60 Regulation of the Mitochondrial Permeability Transition Pore in Tumor Cells (2023)

Supplementary Figures 1-3 from Heat Shock Protein 60 Regulation of the Mitochondrial Permeability Transition Pore in Tumor Cells
Representing social structures in UML (2001)

From a software engineering perspective, agent systems are a specialization of object-oriented (00) systems, in which individual objects have their own threads of control and their own goals. Engineering such systems is most naturally approached as an extensions of object-oriented systems engineering. In particular, the Unified Modeling Language (UML) can be naturally extended to Agent UML (AUML) [5] to support the distinctive requirements of multi- agent systems. One such requirement results from the correspondence between multi-agent systems and social systems. We combine several existing organizational models for agents, including AALAADIN, dependency theory, interaction protocols, and holonics, in a general theoretical framework [9].
Physical Pseudo Random Function in Radio Frequency Sources for Security (2009)

There is tremendous market potential for location-based
services (LBS), enabled by the rapid growth in the
numbers of personal navigation devices and GPS-enabled
mobile handsets. One of the major difficulties for LBS
applications is accurate and reliable indoor positioning
caused by the difficulty of acquiring and tracking GPS
satellite signals in the absence of a clear unobstructed
path between the satellite and the user. An alternative
approach is to use terrestrial signal sources, such as
cellular transmitters, TV or FM broadcast, or Wi-Fi access points. However, it is difficult to achieve
accuracies comparable to outdoor GPS, since either the
time resolution is inferior (for time-of-arrival methods) or
the signal propagation characteristics are unknown or
poorly modeled (for received signal strength methods).

Multiple RF signals can be used together to compute a
location tag, which is a form of physical pseudo random
function. There is no need to synchronize the different
systems either on the transmitter or the receiver ends.
The usable parameters for location tag generation include
signal strength, time-of-arrival, and RF signal phase
information. Increased parameter diversity, greater RF
signal variety, and more transmitter numbers all increase
the information entropy in the derived tags and improve
position estimation robustness. The tradeoff of using
many location parameters is the reduction in tag
reproducibility as RF signals are contaminated by noises
and biases.

The analytical results then are applied to real data sets.
The use of location tags and a fuzzy extractor is
investigated in an office building, a parking structure, and
a soccer field on the campus of Stanford University. We
show that under ideal conditions, the position tag based
approached can achieve an accuracy of 3~6 meters in an
indoor environment. Furthermore, the usage of location
tags is not restricted to positioning; many other
applications include equipment tracking, object
identification, and data access control for security
services, etc.
Generation and characterization of cloned T helper cell lines for anti-DNA responses in NZB.H-2bm12 mice (1992)

We have previously demonstrated that the introduction of the bm12 mutation into NZB mice results in animals that spontaneously produce high titer IgG autoantibodies to dsDNA. The observation that NZB.H-2bm12 develop lupus although NZB.H-2b control mice do not, provides a unique system to study the role of Th cells in the production of antibodies to dsDNA. We have isolated, in the absence of a known stimulating autoantigen, a series of seven autoreactive T cell clones that provide help in vitro for the production of IgG anti-dsDNA antibodies by syngeneic B cells. The data on these seven cloned T cell lines was compared to two cloned T cell lines specific for keyhole limpet hemocyanin. The seven cloned T cell lines, coined clones 19D, 23G, 410F, 410H, C1, C15, and C52 all show significant help in vitro for production of IgM and IgG antibodies to ssDNA and dsDNA; antibody levels increased 7- to 30-fold compared to cultures without T cells. Clones C1, C15, and C52 were furthered studied and were shown to provide help for IgM antihistone and anti-OVA responses but provided significantly less help for IgG antibodies. In contrast, keyhole limpet hemocyanin-specific cloned T cell lines TK2 and TK5 provided help for IgM antibodies to ssDNA, dsDNA, and histone, but failed to significantly increase IgG antibodies to ssDNA, dsDNA, or histone. The cloned T cell lines were restricted to H-2bm12 and proliferated only in response to APC from NZB.H-2bm12 and B6.C-H-2bm12 but not NZB.H-2b or NZB.H-2d mice; their in vitro helper activity was inhibited by antibodies to class II. All cloned T cell lines expressed Thy-1, CD5, and TCR-alpha/beta. Three of the seven clones used TCR-V beta 4. However, the V beta expression of the four remaining autoreactive T cell clones could not be determined. All of the autoreactive cloned T cell lines produce significant IL-4 but no detectable IL-2 or IFN-gamma. We believe that HPLC-purified peptides eluted from I-Abm12 molecules from APC can potentially provide insight on the putative autoantigen.
Structural Disorder in the Complex of Human Pregnane X Receptor and the Macrolide Antibiotic Rifampicin (2005)

The human nuclear xenobiotic receptor, pregnane X receptor (PXR), detects a variety of structurally distinct endogenous and xenobiotic compounds and controls expression of genes central to drug and cholesterol metabolism. The macrolide antibiotic rifampicin, a front-line treatment for tuberculosis, is an established PXR agonist and, at 823 Da, is one of the largest known ligands for the receptor. We present the 2.8 A crystal structure of the ligand-binding domain of human PXR in complex with rifampicin. We also use structural and mutagenesis data to examine the origins of the directed promiscuity exhibited by the PXRs across species. Three structurally flexible loops adjacent to the ligand-binding pocket of PXR are disordered in this crystal structure, including the 200-210 region that is part of a sequence insert novel to the promiscuous PXRs relative to other members of the nuclear receptor superfamily. The 4-methyl-1-piperazinyl ring of rifampicin, which would lie adjacent to the disordered protein regions, is also disordered and not observed in the structure. Taken together, our results indicate that one wall of the PXR ligand-binding cavity can remain flexible even when the receptor is in complex with an activating ligand. These observations highlight the key role that structural flexibility plays in PXR's promiscuous response to xenobiotics.
Genetics and Epigenetics of the TET-ETS Translocation Network (2009)

In the present paper we review the translocation network involving TET and ETS family members with special focus on the Ewing family of tumors. FUS (fusion, involved in t(12;16) in malignant liposarcoma = TLS, Translocated in liposarcoma), EWSR1 (Ewing sarcoma breakpoint region 1) and TAF15 (TATA box-binding protein-associated factor, 68-KD) are the three human members of the TET family of RNA binding proteins. In addition, two EWSR1 pseudogenes are present in the human genome. TET family members are involved in several oncogenic gene fusions. Five of the 18 known fusion partners belong to the E26 (E twenty-six, ETS) family of transcription factors. Gene fusions between TET or ETS family members and other fusion partners link these gene fusions to a large network of oncogenic gene rearrangements.
Neuromorphic computing with memristors: devices and architectures (Conference Presentation) (2019)

The future acceleration of many computational workloads is expected to depend on novel architectures, circuits, and devices. We describe an effort utilizing the analog and non-volatile nature of memristor crossbar arrays to accelerate matrix operations, which underpin many applications in image and signal processing, neural networks, and scientific computations. Significant performance gains and energy reductions over purely digital systems are forecasted based on our work. We describe our studies in the understanding of tantalum oxide-based memristors, integration with CMOS circuits, fine programming control over memristors, compact SPICE models of the device dynamics, and experimental implementations of matrix-heavy operations, including machine learning. We also describe applications that take advantage of the neuron-like behavior in memristor devices, in addition to the above synapse-like functions. This work begins with investigations of niobium oxide-based systems, and interesting dynamics observed based on positive feedback coupling to the electronic transport. These devices are utilized in the construction of a computing system to solve optimization problems such as the traveling salesmen problem.
Diversity of MMSE MIMO Receivers (2012)

In most multiple-input multiple-output (MIMO) systems, the family of waterfall error curves, calculated at different spectral efficiencies, are asymptotically parallel at high signal-to-noise ratio. In other words, most MIMO systems exhibit a single diversity value for all fixed rates. The MIMO minimum mean square error (MMSE) receiver does not follow this pattern and exhibits a varying diversity in its family of error curves. This paper analyzes this interesting behavior of the MMSE MIMO receiver and produces the MMSE MIMO diversity at all rates. The diversity of the quasi-static flat-fading MIMO channel consisting of any arbitrary number of transmit and receive antennas is fully characterized, showing that full spatial diversity is possible if and only if the rate is within a certain bound which is a function of the number of antennas. For other rates, the available diversity is fully characterized. At sufficiently low rates, the MMSE receiver has a diversity similar to the maximum likelihood receiver (maximal diversity), while at high rates, it performs similarly to the zero-forcing receiver (minimal diversity). Linear receivers are also studied in the context of the MIMO multiple-access channel. Then, the quasi-static frequency selective MIMO channel is analyzed under zero-padding and cyclic-prefix (CP) block transmissions and MMSE reception, and lower and upper bounds on diversity are derived. For the special case of SIMO under CP, it is shown that the aforementioned bounds are tight.
Photostimulated luminescence in Tl-doped NH 4 Br translucent ceramics synthesized by SPS (2021)

Abstract We have prepared Tl-doped NH 4 Br translucent ceramics by spark-plasma sintering and evaluated their photoluminescence (PL) and photostimulated luminescence (PSL) properties. In PL, two luminescence peaks appeared due to 3 P 1 → 1 S 0 transitions of Tl + and off-center self-trapped excitons (STEs) localized around Tl + in all the samples. In PSL, the 0.1%–3% Tl-doped samples showed luminescence related to the off-center STEs around 500 nm by stimulation light at 630 nm. When correlations between exposure dose and PSL intensity were examined, we confirmed that the 0.1%–1% and 3% Tl-doped samples showed linear responses over ranges of 10–10 000 and 1–10 000 mGy, respectively.
ChemInform Abstract: NATURE OF THE NOVEL C15H15 LIGAND IN (W(CO)2(η5‐C5H5)(η3‐C15H15)) (1980)

Abstract Eine Strukturuntersuchung der als W(CO) 2 (C 5 H5 )4 formulierten Verbindung zeigte, daß es sich dabei um die Titelverbindung handelt, die mit Z=8 in der Raumgruppe P2 1 /c kristallisiert und einen neuen Liganden enthält, bei dem ein fünfgliedriger Ring in einer Allyl‐ähnlichen Art an W n3‐gebunden ist, während die beiden verbleibenden C‐Atome dieses Rings Bindungen zu den beiden anderen CsHs ‐Dienen haben.
Smart Grid Last-Mile Communications Model and Its Application to the Study of Leased Broadband Wired-Access (2013)

This paper addresses the modeling of specific Smart Grid (SG) communication requirements from a data networking research perspective, as a general approach to the study of different access technologies suitable for the last mile (LM). SGLM networks serve customers' Energy Services Interfaces. From functional descriptions of SG, a traffic model is developed. It is then applied to the study of an access architecture based on leased lines from local broadband access providers. This permits consideration of the potential starvation of domestic traffic, which is avoided by applying well-known traffic management techniques. From previous results obtained for a purpose-built WiMAX SGLM network, the intuition that a leased broadband access yields lower latencies is verified. In general, the proposed traffic model simplifies the design of benchmarks for the comparison of candidate access technologies.
Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie (2023)

<i>Microcystis</i> spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, <i>Microcystis</i> genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that <i>Microcystis</i> produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of <i>Microcystis</i> BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. <b>IMPORTANCE</b> <i>Microcystis</i> spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by <i>Microcystis</i> remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural <i>Microcystis</i> populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.
[M + Fe − 5H]2− peptide ion composition verified by Fourier transform mass spectrometry accurate mass and tandem mass spectrometry analyses (2000)

Previously, the unusual ion composition [M + Fe - 5H]2- had been proposed as the major species observed when a gamma-carboxy glutamate-containing glyco-peptide was analyzed with electrospray ionization in the negative ionization mode. The sequence assignment of this highly post-translationally modified peptide was based on the mass analysis using a quadrupole ion trap together with information from both Edman and DNA sequencing. Because there was little precedent for the loss of five protons from a ferric cationized peptide, we utilized Fourier transform mass spectrometry accurate mass and tandem mass spectrometry analyses to verify the peptide ion composition.