gebhart/patrepeval huggingface dataset:
Alkylated Dihydroxybenzoic Acid as a MALDI Matrix Additive for Hydrophobic Peptide Analysis (2012)

Hydrophobic peptides are generally difficult to detect using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) because the majority of MALDI matrixes are hydrophilic and therefore have a low affinity for hydrophobic peptides. Here, we report on a novel matrix additive, o-alkylated dihydroxybenzoic acid (ADHB), which is a 2,5-dihydroxybenzoic acid (DHB) derivative incorporating a hydrophobic alkyl chain on a hydroxyl group to improve its affinity for hydrophobic peptides, thereby improving MALDI-MS sensitivity. The addition of ADHB to the conventional matrix α-cyano-4-hydroxycinnamic acid (CHCA) improved the sensitivity of hydrophobic peptides 10- to 100-fold. The sequence coverage of phosphorylase b digest was increased using ADHB. MS imaging indicated that hydrophobic peptides were enriched in the rim of a matrix/analyte dried spot when ADHB was used. In conclusion, the addition of ADHB to the standard matrix led to improved sensitivity of hydrophobic peptides by MALDI-MS.
N‐Heterocyclic‐Carbene‐Catalyzed Synthesis of 2‐Aryl Indoles (2014)

A convergent and efficient transition-metal-free catalytic synthesis of 2-aryl-indoles has been developed. The interception of a highly reactive and transient aza-ortho-quinone methide by an acyl anion equivalent generated through N-hetereocyclic carbene catalysis is central to this successful strategy. High yields and a wide scope as well as the streamlined synthesis of a kinase inhibitor are reported.
Further characterization of<i>Shigella sonnei</i>live vaccine candidates WRSs2 and WRSs3-plasmid composition, invasion assays and Sereny reactions (2011)

Shigella sonnei live vaccine candidates WRSs2 and WRSs3 are principally attenuated by the loss of the virG(icsA) gene that prevents bacterial spread. In addition both strains lack enterotoxin SenA and a paralog SenB. WRSs3 also has a deletion in the gene encoding MsbB2. Both of these vaccine candidates are expected to be improved safer versions of WRSS1 that only lacked the virG(icsA) gene and was reactogenic in volunteer trials. During the construction of WRSs2 and WRSs3, segments of the virulence plasmid spanning two FRT sites were found to be inverted in orientation. These inversions have been analysed to show that the overall composition of the plasmid is unaltered. Furthermore, characterization of WRSs2 and WRSs3 in a cell culture and in an animal model have conclusively demonstrated that the segment inversions per se do not adversely affect the behavior of these vaccine candidates and pose no increased safety risk for human evaluation.
Developments in polymer materials for electroluminescence (2002)

In the last few years industrial research into materials fulfilling the needs of the fledgling OLED display industry have intensified considerably. At Covion we have developed a range of polymers based on phenyl-PPV derivatives which are now being commercially exploited in the first polymer LED applications. These materials have been developed systematically with the demanding requirements of the devices (e.g., high efficiency and lifetime) and the industrial applicability (e.g. processibility, reproducibility and reliability of supply) in mind. However due to market forces, such as the introduction of 3rd generation mobile communication technology, there will be an immediate demand for materials for full color OLED displays. In this paper we will report on progress in the development of Red, Green and Blue (RGB) materials at Covion. The requirements for the different colors vary depending on band gap (amongst others) and therefore the challenges for each color are different. The experience gained in understanding the important structure-property relationships in the phenyl-PPVs has been used to develop these new RGB materials.
Multi-channel power allocation for device-to-device communication underlaying cellular networks (2016)

In underlay device-to-device (D2D) communication, a D2D pair reuses the cellular spectrum and creates interference to regular cellular users. Optimal operation requires joint consideration for the achieved D2D rate and the added interference to cellular users. Most existing work on D2D rate maximization concerns only the simplified scenario where the D2D pair has access to a single channel or resource block. In this work, we present an optimization solution to allocate the D2D transmission power over multiple channels, to maximize the sum rate between D2D and cellular users, under a sum-power constraint on the D2D transmitter and minimum SINR guarantees at each RB for all cellular users. The proposed optimization is applicable to both uplink and downlink cellular spectrum sharing. Our simulation studies further shed light into how the maximum sum rate is impacted by the available D2D power and the SINR guarantees.
Detection of low back pain using pH level-dependent imaging of the intervertebral disc using the ratio of R<sub>1ρ</sub>dispersion and −OH chemical exchange saturation transfer (RROC) (2014)

RROC imaging is a promising pH level dependent MRI technique that has the potential to be a noninvasive imaging tool to detect painful IVDs in vivo.
Adaptation of data fusion-based speaker verification models (2003)

This paper presents methods for adapting models in a data fusion-based speaker verification system. The models that are used in the data fusion system are the neural tree network (NTN), dynamic time warping (DTW), and hidden Markov model (HMM). The models provide information based on discriminant information, distortion. measurements, and probabilistic evaluation, respectively. The parameters of these models are updated during the adaptation process using verification data. This allows the models to track changes in the users voice over time and additionally allows the technology to supplement the typically limited data obtained at enrollment. The adaptation algorithms are evaluated for both cases where the data is known to come from the correct user and not known to come from the correct user. For the case where the adaptation data is not known to come from the correct user, threshold criteria is used for determining if the adaptation should occur or not. Experiments were performed on voice data collected within landline telephony, wireless telephony, and multimedia environments. The adaptation lead to a 20% relative reduction on the equal error rate.
In-vivo study of non-invasive thrombolysis by histotripsy in a porcine model (2009)

Thrombolysis is currently performed using either thrombolytic drugs or catheter-based interventions, both of which have significant associated risks. Previously, it was demonstrated that histotripsy cavitation ultrasound therapy can break down blood clots rapidly in-vitro guided by imaging feedback. This study is an initial evaluation of histotripsy's ability to non-invasively dissolve clots in-vivo. A venous thrombosis model was developed using two balloon catheters inserted into the femoral vein of porcine subjects, then injecting thrombin in an occluded region of the vessel between the balloons. Both partially and fully occlusive clots were formed, with average length of 2 cm. Treatment was performed using a 1 MHz, spherically focused transducer coupled to the legs of the subject by a water bath. Therapy consisted of 5 cycle ultrasound pulses delivered at a rate of 1 kHz with a peak negative focal pressure (p-) of 14-19 MPa. The treatment was guided by ultrasound imaging. We were able to easily visualize clots on a B-Mode image, and target them such that the bubble cloud generated by histotripsy was entirely within the vessel. Histotripsy was able to break down the clots, as indicated by a reduction of echogenicity within the vessel walls, and in some cases improved flow through the vessel on color Doppler imaging. Vessels showed minimal damage post-treatment. These results indicate that histotripsy has potential to be an effective noninvasive thrombolysis technique.
Low-Complexity Robust Beamforming for a Moving Source (2020)

This paper addresses the problem of robust beamforming for a moving source. To cope with the source movement, the regularization (or diagonal loading) parameter needs to be adjusted regularly. The need for repeatedly finding an adequate value of the regularization parameter increases the overall computational complexity. This paper proposes a simple and efficient initialization of Newton's method to find the regularization parameter. The regularization parameter is chosen to minimize the mean-squared-error (MSE) of a regularized least-squares (RLS) problem by solving a certain function. We exploit some properties of this function to develop the method. Simulation results demonstrate that the proposed initialization method can reduce the runtime by 75%.
Improved signal processing technique leads to more robust Self Diagnostic Accelerometer System (2010)

The self diagnostic accelerometer (SDA) is a sensor system designed to actively monitor the health of an accelerometer. In this case an accelerometer is considered healthy if it can be determined that it is operating correctly and its measurements may be relied upon. The SDA system accomplishes this by actively monitoring the accelerometer for a variety of failure conditions including accelerometer structural damage, an electrical open circuit, and most importantly accelerometer detachment. In recent testing of the SDA system in emulated engine operating conditions it has been found that a more robust signal processing technique was necessary. An improved accelerometer diagnostic technique and test results of the SDA system utilizing this technique are presented here. Furthermore, the real time, autonomous capability of the SDA system to concurrently compensate for effects from real operating conditions such as temperature changes and mechanical noise, while monitoring the condition of the accelerometer health and attachment, will be demonstrated.
Monomeric and Polymeric Phenothiazine Photosensitizers for Photoinitiated Cationic Polymerization (2002)

The syntheses of several phenothiazine compounds bearing cationically polymerizable vinyl, vinyl ether and epoxide groups are described. These monomers were rapidly and efficiently polymerized or copolymerized by UV irradiation in the presence of onium salt photoinitiators. In addition, the monomers simultaneously function as efficient photosensitizers for the photolysis of the onium salts. In this article, the use of these polymerizable photosensitizers for the photopolymerizations of epoxide and vinyl ether monomers is reported. The inclusion of a small amount of the monomeric photosensitizer is effective in markedly accelerating the cationic photopolymerization of the bulk monomer. Polymers prepared by the polymerization of the monomeric phenothiazine photosensitizers also exhibit excellent photosensitization activity when used in combination with diaryliodonium, triarylsulfonium, and dialkylphenacylsulfonium salt photoinitiators.
Soft-decision Reed-Solomon decoding strategies for code group identification and frame synchronization in UMTS WCDMA (2003)

In UMTS WCDMA, the secondary synchronization channel uses (15,3) comma-free Reed-Solomon codes for code group identification and frame synchronization. Each code symbol of Reed-Solomon code sequence is chosen from 16 different Hadamard codes of 256 chips. After receiving a code signal of 256 chips, it is sent into correlation bank to measure the correlation values between the receiving code signal and 16 Hadamard codes. Using the 16 correlation values, we determine the hard-decision symbol value and evaluate the reliability value. Then, we apply the generalized minimum distance like (GMD-like) decoding algorithm to decode the code sequence of 15 hard-decision code symbols and corresponding reliability vector. Moreover, we can receive next 15 code symbols of the next frame and then update the symbol values as well as reliability values to further improve the performance. Also, we find a simple property to detect the frame boundary after the Reed-Solomon decoder return a cyclic-shift code sequence. These decoding strategies, compared with the method used before, need less computation and less memory. It is shown in simulations that they achieve good performance with reasonable time delay for more receiving information.
Detection in antisera of antibodies that cross-react with herpes simplex virus type 1 glycoprotein gC (1983)

Herpes simplex virus type 1 (HSV-1) glycoprotein gC was purified by affinity chromatography with an immunosorbent column containing monoclonal antibody to HSV-1 gC, and its reactivity with rabbit antisera was measured by enzyme-linked immunosorbent assay and sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of radioimmunoprecipitates. Positive reactions were detected between HSV-1 gC and rabbit hyperimmune antisera to both HSV-1 and HSV-2. Electrophoretic analysis also revealed reactivity between the rabbit antisera and peptides of HSV-1 gC generated by partial digestion with trypsin. These findings indicate that HSV-1 gC has one or more cross-reactive or type-common determinants that are readily detected, and therefore, the presence of antibodies reacting with HSV-1 gC in sera may not necessarily be indicative of an earlier infection with HSV-1.
Inhibition of herpes simplex virus type 1 ribonucleotide reductase by substituted tetrapeptide derivatives (1993)

It is known that peptides corresponding to the C-terminus of the small subunit of herpes simplex virus type 1 and 2 ribonucleotide reductase can inhibit enzymatic activity by preventing the association of the enzyme's two subunits. In a quest for smaller, more potent inhibitors, we have conducted a structure activity investigation based on the pentapeptide H-Val-Val-Asn-Asp-Leu-OH. Potency increases of up to 4000 times (IC50 0.18 microM) have been achieved in an enzymatic assay by a combination of modifying the N-terminal valine to a diethylacetyl group, adding a methyl group to the beta-carbon of the adjacent valine, dialkylating the asparagine side-chain nitrogen and dimethylating the beta-carbon of the aspartic acid residue. In addition the relative contribution of various inhibitor functionalities to inhibitor potency has been investigated.
Functional Characterization of the Two Alcohol Oxidase Genes from the Yeast <i>Pichia pastoris</i> (1989)

In Pichia pastoris, alcohol oxidase (AOX) is the first enzyme in the methanol utilization pathway and is encoded by two genes, AOX1 and AOX2. The DNA and predicted amino acid sequences of the protein-coding portions of the genes are closely homologous, whereas flanking sequences share no homology. The functional roles of AOX1 and AOX2 in the metabolism of methanol were examined. Studies of strains with disrupted AOX genes revealed that AOX1 was the major source of methanol-oxidizing activity in methanol-grown P. pastoris. The results of two types of experiments each suggested that the difference in AOX activity contributed by the two genes was a consequence of sequences located 5' of the protein-coding portions of the genes. First, the coding portion of AOX2 was able to functionally substitute for that of AOX1 when placed under the control of AOX1 regulatory sequences. Second, when labeled oligonucleotide probes specific for the 5' nontranslated region of each gene were used, it was apparent that the steady-state level of AOX1 mRNA was much higher than that of AOX2. Except for the difference in the amount of mRNA present, the two genes appeared to be regulated in the same manner. A physiological reason for the existence of AOX2 was sought but was not apparent.
Long-range surface-plasmon waveguide sensors with μ-fluidic channel (2009)

Long-range surface-plasmon waveguide sensors consisting of asymmetric double metal-films, a resonance grating and μ-fluidic channel sandwiched between the metal layers are described. 10-6 index resolution and sub-nm detection limit for sensing biomolecules are achievable.
SkimpyStash: RAM Space Skimpy Key-Value Store on Flash (2011)

We present SkimpyStash, a RAM space skimpy key-value store on flash, designed for high throughput server applications. The distinguishing feature of SkimpyStash is the design goal of extremely low RAM footprint at about 1 (+/- 0.5) byte per key-value pair, which is more aggressive than earlier designs. By being RAM space frugal, SkimpyStash can accommodate larger flash drive capacities for storing and indexing key-value pairs. SkimpyStash uses a hash table directory in RAM to index key-value pairs stored in a log-structure on flash. To break the barrier of a flash pointer (say, 4 bytes) worth of RAM overhead per key, it “moves” most of the pointers that locate each key-value pair from RAM to flash itself. This is realized by (i) resolving hash table collisions using linear chaining, where multiple keys that resolve (collide) to the same hash table bucket are chained in a linked list, and (ii) storing the linked lists on flash itself with a pointer in each hash table bucket in RAM pointing to the beginning record of the chain on flash, hence incurring multiple flash reads per lookup. Two further techniques are used to improve performance: (iii) two-choice based load balancing to reduce wide variation in bucket sizes (hence, chain lengths and associated lookup times), and a bloom filter in each hash table directory slot in RAM to disambiguate the choice during lookup, and (iv) compaction procedure to pack bucket chain records contiguously onto flash pages so as to reduce flash reads during lookup. The average bucket size is the critical design parameter that serves as a powerful knob for making a continuum of tradeoffs between low RAM usage and low lookup latencies. SkimpyStash can be used as a high throughput persistent key-value storage layer for a broad range of server class applications. We use real-world data traces from two data center applications, namely, Xbox LIVE Primetime online multi-player game and inline storage deduplication, to drive and evaluate the design of SkimpyStash on commodity server platforms. SkimpyStash provides throughputs from few 10,000s to upwards of 100,000 get-set operations/sec on the evaluated applications.
Expiratory time constant for determinations of plateau pressure, respiratory system compliance, and total resistance (2013)

We found the ƬE method was just as good as the EIP method for determining Pplt, Crs, and Rtot for various modes of ventilatory support for patients with acute respiratory failure. It is unclear if the ƬE method can be generalized to patients with chronic obstructive lung disease. ƬE is determined during passive deflation of the lungs without the need for changing the ventilatory mode and disrupting a patient's breathing. The ƬE method obviates the need to apply an EIP, allows for continuous and automatic surveillance of inspiratory Pplt so it can be maintained ≤ 30 cm H₂O for lung protection and patient safety, and permits real time assessments of pulmonary mechanics.
Molecular cloning and characterization of the hblA gene encoding the B component of hemolysin BL from Bacillus cereus (1993)

Previous evidence suggests that hemolysin BL, which consists of a binding component, B, and two lytic components, L1 and L2, is the enterotoxin responsible for the diarrheal form of gastroenteritis caused by food-borne strains of Bacillus cereus. To prove that hemolysin BL and the enterotoxin are the same requires large amounts of these components free of other B. cereus proteins. For this purpose, we sought to clone the gene encoding the B component and to express it in Escherichia coli. A partial genomic library was constructed and a 29-base, 1,152-fold-degenerate oligonucleotide probe, designed from the N-terminal amino acid sequence of the B component, was used to identify recombinant clones containing the gene. Detection of gene products reactive with a monoclonal antibody specific for the B component and analysis of the nucleotide sequence confirmed that isolated clones, reactive with the oligonucleotide probe, did contain the gene encoding the B component. The protein, expressed in E. coli, apparently from the B. cereus promoter, produces a ring-shaped zone of hemolysis when combined with purified L components from B. cereus, a reaction typical of hemolysin BL. Northern (RNA) blot analysis of B. cereus RNA showed a large (5.1-kb) transcript which hybridized with a 500-bp probe internal to the B-component-coding sequence, suggesting that the hblA gene encoding the B component may be transcribed as part of a polycistronic message, possibly including the structural genes for the two lytic components. Higher levels of expression and disruption of the hblA gene are being pursued to resolve whether hemolysin BL is indeed the enterotoxin.
Targeting Glycolytic Metabolism in Cancer (2018)

Tumors exhibit high glucose uptake and glycolysis even in the presence of oxygen ( i.e. the Warburg effect) and this metabolic phenotype serves to satisfy their increased requirement for energy and biosynthetic intermediates. Tumor glucose metabolism is stimulated in part by fructose‐2,6‐bisphosphate (F26BP) , which is the product of a family of 6‐phosphofructo‐2‐kinase/fructose‐2,6‐bisphosphatases (PFKFB1–4) and activates a key rate‐limiting enzyme in glycolysis, 6‐phosphofructo‐1‐kinase (PFK‐1). We have found that the PFKFB4 family member is over‐expressed in human tumors and highly induced by HIF‐1α and that silencing PFKFB4 expression markedly reduced F26BP, glucose metabolism, cell survival and the growth of xenograft tumors in vivo. Using virtual screening, we recently discovered a novel small molecule inhibitor of PFKFB4, 5MPN , that selectively inhibits recombinant PFKFB4 activity, and decreases glucose metabolism, proliferation and tumor growth and have now identified a 5MPN derivative that is significantly more effective at decreasing glucose metabolism and proliferation in cancer cells and markedly reduces the growth of established tumors in vivo, without systemic toxicity. Since our previous studies have determined the PFKFB3 family member to be a dominant source of F26BP in cancer cells and additionally have demonstrated co‐expression of the PFKFB4 and PFKFB3 enzymes in multiple patient‐derived cancers, we compared the effects of silencing PFKFB4 and PFKFB3 in human cancer cell lines in vitro. We unexpectedly found that PFKFB4 expression is increased by PFKFB3 silencing, suggesting that PFKFB4 may compensate for decreased PFKFB3 expression and activity. Importantly, an inhibitor of PFKFB3 (PFK158) is currently in Phase I trials and compensation by PFKFB4 may limit the clinical efficacy of this and other PFKFB3 inhibitors. We then examined the effects of simultaneous silencing of PFKFB4 and PFKFB3 on cancer cell lines and observed that co‐knockdown led to a significant decrease in cell viability and glycolysis and a near‐complete abrogation of anchorage independent growth in vitro and, additionally, found that simultaneous small molecule inhibition of the PFKFB4 and PFKFB3 enzymes in vitro resulted in a synergistic decrease in cell viability. Taken together, our data indicate that targeting PFKFB4 may be a valid therapeutic option against cancer and strongly support the further development of PFKFB4 small molecule inhibitors as well as the co‐targeting of PFKFB4 and PFKFB3 as potential strategies for the treatment of cancer. Support or Funding Information NIH REACH Program Kentucky Lung Cancer Research Program This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .