gebhart/patrepeval huggingface dataset:
Effects of mutations in glycosylation sites and disulphide bonds on processing, CD4-binding and fusion activity of human immunodeficiency virus envelope glycoproteins (1991)

Site-directed mutagenesis was used to study the biological significance of a disulphide bridge and two N-linked oligosaccharides in the CD4-binding region of the envelope glycoproteins of human immunodeficiency virus type 1. Mutagenesis was performed in a phage M13 system at sites corresponding to the cysteine residue (amino acid 402) and the asparagine residues (390 and 447) of the env gene. The mutated env gene was inserted into a recombinant vaccinia virus under the control of the vaccinia virus 7.5K promoter and the expression of mutated env proteins was analysed by SDS-PAGE, a conventional indirect immunofluorescence assay and by a fluorescence-activated cell sorter. Cysteine 402 was found to be essential for the specific cleavage of gp160 into gp120 and gp41, and for intracellular transport of the protein to the cell surface. CD4-binding and syncytium formation assays demonstrated that the disulphide bridge of cysteine 402 stabilized a conformation essential for receptor binding as well as syncytium formation by CD4+ cells. No altered biological activity compared to that of the wild-type proteins could be detected for the mutant proteins lacking the N-glycosylation sites. These data show that the two conserved glycans attached to asparagine residues 390 and 447 do not play any active role in the formation of the disulphide bridge involving cysteine 402 or in the maintenance of an active conformation of the protein, despite their location within the functionally important CD4-binding region.
Transient Changes in Serum CEA, CA19-9, CRP, YKL-40, and IL-6 during Adjuvant Chemotherapy and Survival of Patients with Colorectal Cancer (2023)

Serum carcinoembryonic antigen (CEA) is frequently monitored to detect colorectal cancer (CRC) recurrence after surgery. The clinical significance of transiently increased CEA during adjuvant chemotherapy is poorly understood. Serum CEA, CA19-9, CRP, YKL-40, and IL-6 were measured before, during, and after adjuvant 5-fluorouracil-based chemotherapy in the randomised LIPSYT study population. The biomarker kinetic patterns were classified into three groups: no increase, a transient increase (≥10% increase followed by a decrease), and a persistent increase during the adjuvant treatment, and the associations of these patterns with disease free-survival (DFS) and overall survival (OS) were investigated by using Cox regression analyses. The findings were validated in two single-centre cohorts that received modern adjuvant chemotherapy. A transient increase in CEA occurred in about a half of the patients during chemotherapy, in all the cohorts. The patients with a transient increase had a roughly similar DFS and OS to the patients with no increase, and a more favourable survival compared to the patients with a persistent increase. In the LIPSYT cohort, the hazard ratio was 0.21 for DFS (CI<sub>95%</sub> 0.07-0.66) and 0.24 for OS (CI<sub>95%</sub> 0.08-0.76). Transient increases in CA19-9 and YKL-40 tended to be associated with a favourable survival. A transient increase in CEA during adjuvant chemotherapy is associated with a favourable survival when compared with a persistent increase.
Fiber-based architecture for NFV cloud databases (2017)

The telco industry is gradually shifting from using monolithic software packages deployed on custom hardware to using modular virtualized software functions deployed on cloudified data centers using commodity hardware. This transformation is referred to as Network Function Virtualization (NFV). The scalability of the databases (DBs) underlying the virtual network functions is the cornerstone for reaping the benefits from the NFV transformation. This paper presents an industrial experience of applying shared-nothing techniques in order to achieve the scalability of a DB in an NFV setup. The special combination of requirements in NFV DBs are not easily met with conventional execution models. Therefore, we designed a special shared-nothing architecture that is based on cooperative multi-tasking using user-level threads (fibers). We further show that the fiber-based approach outperforms the approach built using conventional multi-threading and meets the variable deployment needs of the NFV transformation. Furthermore, fibers yield a simpler-to-maintain software and enable controlling a trade-off between long-duration computations and real-time requests.
Gold Redox Catalytic Cycles for the Oxidative Coupling of Alkynes (2011)

Au(I)/Au(III) catalytic cycles are catalytically competent to perform the oxidative coupling of alkynes in the homogeneous phase at room temperature and without any protecting atmosphere. Selectfluor as oxidant, wet acetonitrile as solvent, and sodium carbonate as base are the reagents of choice. Both aromatic and alkyl alkynes can be coupled, and mechanistic studies reveal that at least two gold species having different oxidation states are implicated in the key step of the coupling.
Segmentation of ophthalmic optical coherence tomography images using graph cuts (2010)

We describe an efficient approach for the automated segmentation of pathological/morphological structures in ophthalmic Spectral Domain Optical Coherence Tomography (SDOCT) images. In this algorithm, image pixels are treated as nodes of a graph with edge weights assigned to associate pairs of pixels. The weights vary according to the distances, brightness differences, and feature variations between pixel pairs. Cuts through the graph with minimum accumulated weights correspond to morphological layer boundaries. This approach has been applied to SDOCT images with encouraging results and thus forms an adaptable framework for the segmentation of many different ophthalmic structures.
Linear-array ultrasonic waveguide transducer for under sodium viewing. (2010)

In this report, we first present the basic design of a low-noise waveguide and its performance followed by a review of the array transducer technology. The report then presents the concept and basic designs of arrayed waveguide transducers that can apply to under-sodium viewing for in-service inspection of fast reactors. Depending on applications, the basic waveguide arrays consist of designs for sideway and downward viewing. For each viewing application, two array geometries, linear and circular, are included in design analysis. Methods to scan a 2-D target using a linear array waveguide transducer are discussed. Future plan to develop a laboratory array waveguide prototype is also presented.
The novel hypoxia-targeted anticancer agent AQ4N is not subject to multi-drug resistance mediated by PGP/MDR1 (2005)

525 AQ4N (banoxantrone; 1,4-Bis{[2-(dimethylamino)ethyl]amino}-5,8-dihydroxyanthracene-9,10-dione bis-N-oxide) is a novel therapeutic agent that targets the treatment-resistant hypoxic fraction of tumors. AQ4N is a highly soluble and penetrating prodrug that is enzymatically reduced to a cytotoxic DNA-binding agent, AQ4, preferentially in conditions of low oxygen tension. Combination therapy using AQ4N in addition to radiation and/or chemotherapy targets both the oxygenated and hypoxic regions of tumors, increasing effectiveness of treatment in preclinical models. AQ4N is well-tolerated in man and is currently in Phase I clinical trial. A major contributor to acquired drug resistance is the multi-drug resistance phenotype (MDR) caused by overexpression of ABC family transmembrane protein pumps. Substrates for MDR include anthracyclines (eg daunorubicin) and anthracenediones (eg mitoxantrone). We have investigated whether AQ4N and AQ4, which are structurally related to mitoxantrone, are substrates for the prototypical MDR protein PGP/MDR1. The intrinsic fluorescence of these molecules was used to directly evaluate transport by PGP using flow cytometry. The measurement of steady state levels in MDR1-positive cell lines revealed no sensitivity to the PGP inhibitor verapamil for AQ4, in contrast to a 3-5-fold increase for mitoxantrone (indicative of cellular accumulation). Direct measurements of efflux from isogenically matched PGP-overexpressing cells confirmed no verapamil-dependent efflux of AQ4, contrasting sharply with a dramatic efflux of mitoxantrone and daunorubicin. Survival assays using the MDR1-positive cells revealed no differential toxicity of AQ4 or AQ4N compared to the control parental cell lines, whereas mitoxantrone showed reduced sensitivity in the PGP-overexpressing line, demonstrating a functional relevance of the efflux observations. The potential roles of other transmembrane pumps in transport of AQ4, and the significance of these findings in in vivo models are also under further investigation. These data suggest that AQ4N is not a substrate for MDR, which is one of the major barriers to the effectiveness of anthraquinones and other agents. AQ4N is also effective under conditions of hypoxia, another well-known characteristic of treatment resistant tumours. Taken together, these features indicate significant clinical potential, and the utility of AQ4N, both as monotherapy and in combination with established regimes, is under evaluation in a range of Phase I trials.
Tuberculous Cold Abscess of the Corpus Cavernosum:A Case Report (1990)

A rare case of tuberculous cold abscess of the corpus cavernosum is presented. The only presenting symptom was obstructive urinary symptoms caused by external compression of the urethra by the abscess. Diagnosis was reached after surgical drainage and specific antituberculosis therapy led to a satisfactory conclusion.
Fused Tree WDM With High Wavelength Isolation Over Wide Wavelength Range (1987)

A tree configuration single-mode fiber wavelength division multiplexer (WDM) is proposed and demonstrated. This configuration is similar to tree topology single-mode star couplers which have been reported. Both theoretical analysis and experimental data show that a tree WDM can easily achieve a very high wavelength isolation over a wide wavelength range aroun 1300 nm and 1520 nm. The wavelength isolations measured in our experiment are greater than 28 dB both from 1255 nm to 1335 nm (80 nm-wide range, 41 dB at 1305 nm) and from 1490 nm to 1565 nm (75 nm-wide range). The insertion losses are 0.7 dB at 1300 nm and 1.1 dB at 1550 nm.
Exploring Chemical Space with Organometallics: Ruthenium Complexes as Protein Kinase Inhibitors (2007)

Complementing organic elements with a metal center provides new opportunities for building three-dimensional structures with unique and defined shapes. Such access to unexplored chemical space may lead to the discovery of molecules with unprecedented properties. Along these lines, this account article describes our successful design of highly potent and selective ruthenium-based inhibitors for the protein kinases GSK-3 and Pim-1 by using the class of indolocarbazole alkaloids as a lead structure. The described ruthenium complexes are kinetically inert scaffolds in which the ruthenium has the function to organize the orientation of the organic ligands in the three-dimensional space.
A Digital Requantizer With Shaped Requantization Noise That Remains Well Behaved After Nonlinear Distortion (2007)

A major problem in oversampling digital-to-analog converters and fractional-N frequency synthesizers, which are ubiquitous in modern communication systems, is that the noise they introduce contains spurious tones. The spurious tones are the result of digitally generated, quantized signals passing through nonlinear analog components. This paper presents a new method of digital requantization called successive requantization, special cases of which avoids the spurious tone generation problem. Sufficient conditions are derived that ensure certain statistical properties of the quantization noise, including the absence of spurious tones after nonlinear distortion. A practical example is presented and shown to satisfy these conditions.
Bright Circularly Polarized Soft X-ray Harmonics for Static and Dynamic X-ray Magnetic Circular Dichroism (2016)

We present the first circularly polarized harmonics in the soft X-ray region, enabling the first X-ray magnetic circular dichroism measurements and spin dynamics in rare earth elements such as Gd on a tabletop.
Indole 6 Carboxaldehyde Prevents Oxidative Stress-Induced Mitochondrial Dysfunction, DNA Damage and Apoptosis in C2C12 Skeletal Myoblasts (2020)

Indole-6-carboxaldehyde (I6CA) is an indole derivative derived from the brown algae Sargassum thunbergii, and some pharmacological activity is known, but the antioxidant effect of I6CA has not been reported. In the present study, the protective capacity of I6CA against oxidative stress-induced cytotoxicity in C2C12 skeletal myoblasts was investigated. I6CA's effect on hydrogen peroxide (H2O2)-disrupted cell viability, mitochondrial function, and intracellular ATP level was measured. Furthermore, I6CA's potency to reduce H2O2-induced DNA damage, reactive oxygen species (ROS) generation, AMP-activated protein kinase (AMPK) activation and apoptosis was monitored. The results indicate that preincubation of cells with I6CA prior to H2O2 stimulation resulted in significant inhibition of cytotoxicity and DNA damage associated with the inhibition of ROS generation. In addition, H2O2-induced loss of mitochondrial membrane potential and cytosolic release of cytochrome c were significantly protected in the presence of I6CA. I6CA also attenuated the decrease in ATP content by H2O2 and restored H2O2-induced activation of AMPK, indicating that I6CA maintains energy metabolism through the preservation of mitochondrial function while eliminating the ROS generated by H2O2. Furthermore, I6CA rescued C2C12 cells from H2O2-triggered apoptosis, as evidenced by reduced caspase-3 activation, PARP degradation and DNA fragmentation. Collectively, our findings conclude that I6CA effectively protected C2C12 myoblasts against oxidative damage, at least in part, by preventing mitochondrial-dependent pathway through scavenging excessive ROS. The research was supported by the Basic Science Research Program through the National Research Foundation of Korea grant funded by the Korea government (2018R1A2B2005705).
Observation of internal x-ray wave fields during Bragg diffraction with an application to impurity lattice location (1974)

By a simple extension of a previous experimental technique we demonstrate how the detailed standing-wave features of the internal x-ray wave field during the diffraction process may be observed even when a strong reflection occurs. The preliminary results reported here indicate that dynamical diffraction may be developed as a useful lattice-location technique in nearly perfect crystals.
An 18 b 5 MS/s SAR ADC with 100.2 dB dynamic range (2014)

This paper presents an 18 bit 5 MS/s SAR ADC. It has a dynamic range of 100.2 dB, SNR of 99 dB, INL of ±2 ppm and DNL of ±0.4 ppm. It has currently the lowest noise floor of any monolithic Nyquist converter relative to the full scale input (21.9 nV/√Hz, ±5V full scale) known to the author, all of this is achieved with an ADC core power of 30.52 mW giving a Schreier figure of merit of 179.3 dB [1]. Architectural choices such as the use of a residue amplifier are outlined that enable the high sample rate, low noise and power efficiency. The design is implemented on 0.18 µm CMOS with MIM capacitors and both 1.8 V and 5 V MOS devices. An LVDS interface is used to transfer the ADC result off chip.
A Pan-Cancer Assessment of RB1/TP53 Co-Mutations (2022)

Nearly all tumors have multiple mutations in cancer-causing genes. Which of these mutations act in tandem with other mutations to drive malignancy and also provide therapeutic vulnerability? To address this fundamental question, we conducted a pan-cancer screen of co-mutation enrichment (looking for two genes mutated together in the same tumor at a statistically significant rate) using the AACR-GENIE 11.0 data (AACR, Philadelphia, PA, USA). We developed a web tool for users to review results and perform ad hoc analyses. From our screen, we identified a number of such co-mutations and their associated lineages. Here, we focus on the <i>RB1/TP53</i> co-mutation, which we discovered was the most frequently observed co-mutation across diverse cancer types, with particular enrichment in small cell carcinomas, neuroendocrine carcinomas, and sarcomas. Furthermore, in many cancers with a substantial fraction of co-mutant tumors, the presence of concurrent <i>RB1/TP53</i> mutations is associated with poor clinical outcomes. From pan-cancer cell line multi-omics and functional screening datasets, we identified many targetable co-mutant-specific molecular alterations. Overall, our analyses revealed the prevalence, cancer type-specificity, clinical significance, and therapeutic vulnerabilities of the <i>RB1/TP53</i> co-mutation in the pan-cancer landscape and provide a roadmap forward for future clinical translational research.
The Proteinase-Activated Receptor 2 Is Involved in Nociception (2001)

The proteinase-activated receptor 2 is expressed on a subset of primary afferent neurons and may participate in the neurogenic component of inflammation. We hypothesized that this receptor may also play a role in neuronal sensitization and contribute to the pathogenesis of pain in inflammatory conditions such as pancreatitis. Using a specific proteinase-activated receptor 2 activating peptide, we found evidence of such sensitization in vitro in the form of enhanced capsaicin- and KCl-evoked release of calcitonin gene-related peptide, a marker for nociceptive signaling. We then demonstrated that injection of the proteinase-activated receptor 2 activating peptide into the pancreatic duct can activate and sensitize pancreas-specific afferent neurons in vivo, as measured by Fos expression in the dorsal horn of the spinal cord. These observations suggest that proteinase-activated receptor 2 contributes to nociceptive signaling and may provide a novel link between inflammation and pain.
Re-Weighted Learning for Sparsifying Deep Neural Networks (2018)

This paper addresses the topic of sparsifying deep neural networks (DNN's). While DNN's are powerful models that achieve state-of-the-art performance on a large number of tasks, the large number of model parameters poses serious storage and computational challenges. To combat these difficulties, a growing line of work focuses on pruning network weights without sacrificing performance. We propose a general affine scaling transformation (AST) algorithm to sparsify DNN's. Our approach follows in the footsteps of popular sparse recovery techniques, which have yet to be explored in the context of DNN's. We describe a principled framework for transforming densely connected DNN's into sparsely connected ones without sacrificing network performance. Unlike existing methods, our approach is able to learn sparse connections at each layer simultaneously, and achieves comparable pruning results on the architecture tested.
Analysis of the Human Head Interaction in Handset Antennas with Slotted Ground Planes (2012)

The interaction between the human head and handset antennas needs to be taken into account, since mobile phones have to be functional, and, at the same time, guarantee biological compatibility. The present research analyzed the performance of several handset antennas with different slotted ground planes in free space and also in the presence of the human head. The main objective was to compare the measured bandwidth and efficiency in both environments (free space and human interaction), and the impact on the measured SAR (Specific Absorption Rate) of such antennas as functions of the slot configuration in the ground plane and the antenna's location. Results showed that slots may be useful for increasing bandwidth and efficiency while keeping similar SAR values compared to the non-slotted ground plane. Changing the antenna's location was a good way to achieve a significant SAR reduction. In some cases, when the antenna was at the lower edge of the ground plane (down position), the SAR could be reduced by a factor of two. Impedance, efficiency, and radiation patterns were measured and analyzed with a phantom head in order to understand the human head's effect on the antenna's performance. Although all antennas suffered from changes, shorted-end slots were more robust for human interaction than open-ended slots.
Power and Load Optimization in Interference-Coupled Non-Orthogonal Multiple Access Networks (2018)

Towards energy savings in large-scale nonorthogonal multiple access (NOMA) networks, we investigate power and load optimization for multi-cell and multi-carrier NOMA systems in this paper. To capture the coupling relation of mutual interference among cells, firstly, we extend a load-coupling model from orthogonal multiple access (OMA) to NOMA networks. Next, with this analytical tool, we formulate the considered optimization problem in NOMA-based load-coupled systems, where optimizing load, power, and determining decoding order are the key aspects in the optimization. Theoretically, we prove that the minimum network energy consumption can be achieved by using all the time-frequency resources in each cell to deliver users' demand. To achieve the optimal load and enable efficient power optimization, we develop a power-adjustment algorithm. Numerical results demonstrate promising energy-saving gains of NOMA over OMA in large-scale cellular networks, in particular for the high-demand and resource-limited scenarios.
Successful development and implementation of a practical proactive resistance management plan for Bt cotton in Australia (2021)

This article describes the design and > 20 years of effective implementation of a proactive resistance-management plan for transgenic Bacillus thuringiensis (Bt) cotton that targets Helicoverpa armigera (Hübner) and Helicoverpa punctigera (Wallengren) in Australia, considering pest biology and ecology, insights from resistance-evolution modelling, and the importance of the human component to effective implementation. This is placed in the context of processes associated with adaptive resource management. Bt cotton has provided Australian cotton growers with technology to manage Helicoverpa species that previously challenged the industry's viability, while at the same time resulting in no detectable changes in the resistance allele frequency in field populations of either Helicoverpa species in eastern Australia. This is the most long-lived and successful global example of a proactive resistance management plan for an insect pest. Six key learnings important to the successful development and implementation of a proactive transgenic-crop resistance management plan are: the programme has to have a strong science base; there has to be broad stakeholder support at all levels; there has to be a strong implementation programme; the plan needs to be supported by auditing and enforced remediation of deviations from the mandated resistance management plan; A programme of rigorous and on-going resistance allele monitoring; an attitude of continuous improvement for all aspects of the resistance management plan. The lessons learnt from the deployment of Bt cotton in Australia are relevant globally and provide important guidelines for the deployment of transgenic crops for insect control wherever they are grown. © 2021 Society of Chemical Industry.