gebhart/patrepeval huggingface dataset:
Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability (2016)

Gastric cancer is not a single disease, and its subtype classification is still evolving. Next-generation sequencing studies have identified novel genetic drivers of gastric cancer, but their use as molecular classifiers or prognostic markers of disease outcome has yet to be established. In this study, we integrated somatic mutational profiles and clinicopathologic information from 544 gastric cancer patients from previous genomic studies to identify significantly mutated genes (SMG) with prognostic relevance. Gastric cancer patients were classified into regular (86.8%) and hypermutated (13.2%) subtypes based on mutation burden. Notably, TpCpW mutations occurred significantly more frequently in regular, but not hypermutated, gastric cancers, where they were associated with APOBEC expression. In the former group, six previously unreported (XIRP2, NBEA, COL14A1, CNBD1, ITGAV, and AKAP6) and 12 recurrent mutated genes exhibited high mutation prevalence (≥3.0%) and an unexpectedly higher incidence of nonsynonymous mutations. We also identified two molecular subtypes of regular-mutated gastric cancer that were associated with distinct prognostic outcomes, independently of disease staging, as confirmed in a distinct patient cohort by targeted capture sequencing. Finally, in diffuse-type gastric cancer, CDH1 mutation was found to be associated with shortened patient survival, independently of disease staging. Overall, our work identified previously unreported SMGs and a mutation signature predictive of patient survival in newly classified subtypes of gastric cancer, offering opportunities to stratify patients into optimal treatment plans based on molecular subtyping. Cancer Res; 76(7); 1724-32. ©2016 AACR.
Rhesus Macaque Resistance to Mucosal Simian Immunodeficiency Virus Infection Is Associated with a Postentry Block in Viral Replication (2002)

Elucidation of the host factors which influence susceptibility to human immunodeficiency virus or simian immunodeficiency virus (SIV) infection and disease progression has important theoretical and practical implications. Rhesus macaque 359, a vaccine control animal, resisted two successive intravaginal challenges with SIV(mac251) and failed to seroconvert. Here, after an additional intrarectal SIVmac32H challenge, macaque 359 remained highly resistant to infection. Viral RNA (10(6) copies/ml) was observed in plasma only at week 2 postchallenge. Virus isolation and proviral DNA were positive only once at week eight postchallenge. The animal remained seronegative and cleared SIV in vivo. Its blood and lymph node cells obtained at 49 weeks after intrarectal challenge did not transmit SIV to a naive macaque. We found that the resistance of macaque 359 to SIV infection was not due to a high level of CD8(+) suppressor activity but to an inherent resistance of its CD4(+) T cells. To elucidate the basis for the unusually strong resistance of macaque 359 to SIV infection in vivo and in vitro, we investigated early events of viral infection and replication in CD4(+) cells of macaque 359, including expression and mutation screening of SIV coreceptors and analysis of viral entry and reverse transcription. Mutation screening revealed no genetic alteration in SIV coreceptors. PCR analysis revealed a significant delay in production of early in vitro reverse transcription intermediates in macaque 359 cells compared to susceptible controls, but cell fusion assays showed that SIV entered the CD4(+) CCR5(+) cells of macaque 359 as readily as cells of macaques susceptible to SIV infection. Our results suggest that the resistance of macaque 359 to SIV infection is due to a postentry block in viral replication and implicate a cellular inhibitory mechanism in its CD4(+) T cells. Identification of this host mechanism will help further elucidate the biochemistry of reverse transcription and may suggest therapeutic strategies. Determining the prevalence of this host resistance mechanism among macaques may lead to better design of SIV pathogenesis and vaccine studies.
Rattling of Oxygen Ions in a Sub-Nanometer-Sized Cage Converts Terahertz Radiation to Visible Light (2017)

A simple and robust approach to visualization of continuous wave terahertz (CW-THz) light would open up opportunities to couple physical phenomena that occur at fundamentally different energy scales. Here we demonstrate how nanoscale cages of Ca<sub>12</sub>Al<sub>14</sub>O<sub>33</sub> crystal enable conversion of CW-THz radiation to visible light. These crystallographic cages are partially occupied with weakly bonded oxygen ions and give rise to a narrow conduction band that can be populated with localized, yet mobile electrons. CW-THz light excites a nearly stand-alone rattling motion of the encaged oxygen species, which promotes electron transfer from them to the neighboring vacant cages. When the power of CW-THz light reaches tens of watts, the coupling between forced rattling in the confined space, electronic excitation and ionization of oxygen species, and corresponding recombination processes result in emission of bright visible light.
BIRC6 Targeting as Potential Therapy for Advanced, Enzalutamide-Resistant Prostate Cancer (2016)

<b>Purpose:</b> Enzalutamide resistance has emerged as a major problem in the management of castration-resistant prostate cancer (CRPC). Research on therapy resistance of CRPCs has primarily focused on the androgen receptor pathway. In contrast, there is limited information on antiapoptotic mechanisms that may facilitate the treatment resistance. The inhibitor of apoptosis proteins (IAP) family is well recognized for its role in promoting treatment resistance of cancers by inhibiting drug-induced apoptosis. Here, we examined whether BIRC6, an IAP family member, has a role in enzalutamide resistance of CRPCs and could provide a therapeutic target for enzalutamide-resistant CRPC.<b>Experimental Design:</b> Use of enzalutamide-resistant CRPC models: (i) the transplantable, first high-fidelity LTL-313BR patient-derived enzalutamide-resistant CRPC tissue xenograft line showing primary enzalutamide resistance, (ii) MR42D and MR49F CRPC cells/xenografts showing acquired enzalutamide resistance. Specific BIRC6 downregulation in these models was produced using a <i>BIRC6</i>-targeting antisense oligonucleotide (ASO-6w2). Gene expression was determined by qRT-PCR and gene expression profiling. Molecular pathways associated with growth inhibition were assessed via gene enrichment analysis.<b>Results:</b> Of eight IAPs examined, BIRC6 was the only one showing elevated expression in both enzalutamide-resistant CRPC models. Treatment with ASO-6w2 markedly suppressed growth of LTL-313BR xenografts and increased tumor apoptosis without inducing major host toxicity. Pathway enrichment analysis indicated that GPCR and matrisome signaling were the most significantly altered pathways. Furthermore, ASO-6w2 inhibited expression of prosurvival genes that were upregulated in the LTL-313BR line.<b>Conclusions:</b><i>BIRC6</i> targeting inhibited the growth of enzalutamide-resistant CRPC models and may represent a new option for clinical treatment of advanced, enzalutamide-resistant prostate cancer. <i>Clin Cancer Res; 23(6); 1542-51. ©2016 AACR</i>.
Discussion on ‘Linear Real-time Rate Control’ (2007)

(2007). Discussion on ‘Linear Real-time Rate Control’. HKIE Transactions: Vol. 14, No. 3, pp. 50-51.
Badapple: promiscuity patterns from noisy evidence (2016)

Badapple is a method for rapidly identifying likely promiscuous compounds via associated scaffolds. Badapple generates a score associated with a pragmatic, empirical definition of promiscuity, with the overall goal to identify "false trails" and streamline workflows. Unlike methods reliant on expert curation of chemical substructure patterns, Badapple is fully evidence-driven, automated, self-improving via integration of additional data, and focused on scaffolds. Badapple is robust with respect to noise and errors, and skeptical of scanty evidence.
Peripheral Nerve Vein Wrapping For Intractable Lower Extremity Pain (2000)

Vein wrapping of lower extremity peripheral nerves is most effective in relieving symptoms related to adhesive neuralgia and less beneficial in the presence of intraneural damage. Although symptoms are rarely relieved completely, vein wrapping typically results in a substantial improvement in symptoms related to scar entrapment of peripheral nerves.
Force-controlled spatial manipulation of viable mammalian cells and micro-organisms by means of FluidFM technology (2010)

The FluidFM technology uses microchanneled atomic force microscope cantilevers that are fixed to a drilled atomic force microscope cantilevers probeholder. A continuous fluidic circuit is thereby achieved extending from an external liquid reservoir, through the probeholder and the hollow cantilever to the tip aperture. In this way, both overpressure and an underpressure can be applied to the liquid reservoir and hence to the built-in fluidic circuit. We describe in this letter how standard atomic force microscopy in combination with regulated pressure differences inside the microchanneled cantilevers can be used to displace living organisms with micrometric precision in a nondestructive way. The protocol is applicable to both eukaryotic and prokaryotic cells (e.g., mammalian cells, yeasts, and bacteria) in physiological buffer. By means of this procedure, cells can also be transferred from one glass slide to another one or onto an agar medium.
Modeling Carbon Nanotube Entanglement Load Transfer: Implications for Lightweight Aerospace Structures (2023)

Carbon nanotube assemblies such as fibers and sheets are an emerging lightweight material class with potential to enable aerospace structures beyond what is achievable with existing materials. Load transfer within these materials can be attributed to a combination of cohesion, static friction, covalent cross-links, and entanglements. Of these mechanisms, entanglements are the least studied or understood and are not well defined when applied to nanotube materials. In this work, an entanglement is defined with sufficient detail for molecular models to be built and tested. Non-reactive models where the covalent bond topology does not change and reactive models where covalent bonds can form and break were developed. In both model types, entanglement load transfer was observed and can be attributed to buckles (i.e., wrinkles) that form under bending compression. In non-reactive models, there are energy barriers to restructure the shape of the buckles, while reactive models formed covalent bonds at the high-curvature edges of the buckles. Reactive models produced an average load transfer approximately 14 times greater than non-reactive models due to these covalent bonds.
Supplemental Tables 1 & 2 from An Integrated Molecular Analysis of Lung Adenocarcinomas Identifies Potential Therapeutic Targets among TTF1-Negative Tumors, Including DNA Repair Proteins and Nrf2 (2023)

&lt;p&gt;Supplemental Tables 1 &amp; 2. Table 1: Significant protein changes between TTF1-low and -high tumors in PROSPECT. Table 2: Significant protein changes between TTF1-low and -high tumors in TCGA.&lt;/p&gt;
An entropy approach for evaluating an urban rainfall network: an operative case of study (2010)

Hydrological models, that are the base of operational forecasting systems, require an accuracy that is strongly dependent on the quality and quantity of the input information, represented by the rainfall depth. The finer the space-time rainfall resolution, the higher the accuracy of the hazard nowcasting. In this framework, an optimum raingauge network is essential in prediction of flash flood events: the density of raingauge networks represents infact a key parameter for proper observations of rainfall fields. &#13;\nOn the basis that a raingauge network is characterized by an exchange of information, the informative entropy approach is used as a measure of the information content of rainfall data provided by raingauges. In this work the heuristic entropy is a tool for evaluating the optimum number of raingauges in the case study network. This approach is very useful in designing and managing raingauge networks because it can lead to determine the optimum number of raingauges, not only in terms of gained accuracy of rainfall information and flood prediction, but also in terms of money savings. In fact raingauges providing redundant information could be removed. &#13;\nIn this work, results of the application of this methodology to the high density raingauge network of the urban area of Rome, are presented.
Immunotherapy of prostate cancer using novel synthetic DNA vaccines targeting multiple tumor antigens (2021)

Prostate cancer is a prevalent cancer in men and consists of both indolent and aggressive phenotypes. While active surveillance is recommended for the former, current treatments for the latter include surgery, radiation, chemo and hormonal therapy. It has been observed that the recurrence in the treated patients is high and results in castration resistant prostate cancer for which treatment options are limited. This scenario has prompted us to consider immunotherapy with synthetic DNA vaccines, as this approach can generate antigen-specific tumor-killing immune cells. Given the multifocal and heterogeneous nature of prostate cancer, we hypothesized that synthetic DNA vaccines targeting different prostate specific antigens are likely to induce broader and improved immunity who are at high risk as well as advanced clinical stage of prostate cancer, compared to a single antigen approach. Utilizing a bioinformatics approach, synthetic enhanced DNA vaccine (SEV) constructs were generated against STEAP1, PAP, PARM1, PSCA, PCTA and PSP94. Synthetic enhanced vaccines for prostate cancer antigens were shown to elicit antigen-specific immune responses in mice and the anti-tumor activity was evident in a prostate tumor challenge mouse model. These studies support further evaluation of the DNA tools for immunotherapy of prostate cancer and perhaps other cancers.
Multivalent Cyclic RGD Conjugates for Targeted Delivery of Small Interfering RNA (2011)

We have designed, synthesized, and tested conjugates of chemically modified luciferase siRNA (Luc-siRNA) with bi-, tri-, and tetravalent cyclic(arginine-glycine-aspartic) (cRGD) peptides that selectively bind to the αvβ3 integrin. The cellular uptake, subcellular distribution, and pharmacological effects of the cRGD-conjugated Luc-siRNAs compared to those of unconjugated controls were examined using a luciferase reporter cassette stably transfected into αvβ3 positive M21(+) human melanoma cells. The M21(+) cells exhibited receptor-mediated uptake of cRGD-siRNA conjugates but not of unconjugated control siRNA. The fluorophore-tagged cRGD-siRNA conjugates were taken up by a caveolar endocytotic route and primarily accumulated in cytosolic vesicles. The bi-, tri-, and tetravalent cRGD conjugates were taken up by M21(+) cells to approximately the same degree. However, there were notable differences in their pharmacological effectiveness. The tri- and tetravalent versions produced progressive, dose-dependent reductions in the level of luciferase expression, while the bivalent version had little effect. The basis for this divergence of uptake and effect is currently unclear. Nonetheless, the high selectivity and substantial "knock down" effects of the multivalent cRGD-siRNA conjugates suggest that this targeting and delivery strategy deserves further exploration.
Correlation of Collapse Forces Determined by Lateral Force AFM with Damage Generation due to Physical Cleaning Processes (2011)

Four types of silicon FINs on SiO2 were used as test structures for damage analysis: amorphous Si (a-Si), annealed Si (a*-Si), as-deposited poly-Si (p-Si) and crystalline silicon (c-Si). The collapse of single FINs was analyzed by lateral force AFM measurement and the damage due to a physical cleaning process was optically evaluated in parallel. The number of damaged FINs and the collapse force were compared. We observed a clear correlation between the damage counts and structure strengths. For both megasonic and spray cleaning techniques the damage decreases in the order a-Si > poly-Si > a*-Si > c-Si. The collapse forces increase in the same order 0.5 mN (a-Si) < 0.8 mN (poly-Si) < 1.0 mN (a*-Si) < 1.6 mN (c-Si). This remarkable correlation can be explained by structure and interface strength. The collapse behavior of a-Si FINs is also different from poly-Si FINs. a-Si FINs delaminate, break at one end, bend and finally break at the other end creating long fragments, as observed by AFM. Poly-Si and a*-Si FINs break at two ends simultaneously and create smaller fragments. This mechanism was also confirmed by detailed classification of the defects generated by physical forces during a cleaning process using physical forces.
Local delivery of Simvastatin from calcium phosphate cement (2012)

INTRODUCTION: Locally applied simvastatin (SV) is known to stimulate bone formation [l, 2]. However, the lack of suitable delivery systems has restricted its clinical use. In the present study a novel approach of using calcium phosphate cement (CPC) as potential drug carrier for simvastatin was evaluated. A release study was performed to measure the release kinetics. In addition, an in vitro study with human osteosarcoma cell line MG-63 was done to assess the effect of SV on bone formation.
Discriminating between Drugs and Nondrugs by Prediction of Activity Spectra for Substances (PASS) (2001)

Using the computer system PASS (prediction of activity spectra for substances), which predicts simultaneously several hundreds of biological activities, a training set for discriminating between drugs and nondrugs is created. For the training set, two subsets of databases of drugs and nondrugs (a subset of the World Drug Index, WDI, vs the Available Chemicals Directory, ACD) are used. The high value of prediction accuracy shows that the chemical descriptors and algorithms used in PASS provide highly robust structure-activity relationships and reliable predictions. Compared to other methods applied in this field, the direct benchmark undertaken with this paper showed that the results obtained with PASS are in good accordance with these approaches. In addition, it has been shown that the more specific drug information used in the training set of PASS, the more specific discrimination between drug and nondrug can be obtained.
Characterization and optimization of infrared poly SiGe bolometers (1999)

In this paper, we present a complete characterization of poly SiGe bolometers. Devices having different dimensions and different geometry have been fabricated. The dependence of the low-frequency noise and of the temperature coefficient of resistance (TCR) on resistivity in poly SiGe has been measured and modeled. The impact of resistivity, bias voltage, thermal conductance, thickness, and dimensions of the active element on the device performance has been investigated. It has been demonstrated that, by using the appropriate absorber and by optimizing the device parameters, poly SiGe bolometers are suitable for realizing high-performance focal plane arrays (FPA's).
Cloning and Sequence Analysis of the trpB, trpA and 3' trpC(F) Genes of Vibrio metschnikovii Strain RH530 (1994)

The genes, trpB, trpA and 3’ trpC(F) of Vibrio metschnikovii strain RH530 were cloned and sequenced. The trpB and trpA genes had open reading frames of 1,173 bp and 804 bp encoding 391 and 268 amino acids, respectively. The trpB and trpA genes had conventional ribosome-binding sequences and overlapped with each other by one nucleotide, suggesting that these two genes are translationally coupled. 115 nucleotide upstream the trpB start codon, tjere was an incomplete open reading frame of the 3’-end of the trpC(F). The amino acid sequences of trpB, trpA and trpC(F) of V. metschnikovii RH530 had identities of 64.2%, 82.4% and 73.7% respectively, for those of V. parahaemolyticus; 58.7%, 72.3% and 54.9%, respectively, for Salmonella typhimurium; and 42.6%. 54.1% and 12.5%, respectively, for brevibacterium lactofermentum. The genetic organization of these genes, especially in the noncoding region between trpC(F) and trpB, was distinct from that of Enterobacteriaceae.
Impact of Crystal Size on the Acidity and the Involved Interactions Studied by Conventional and Innovative Techniques (2017)

A series of β-zeolites with different sizes have been synthesized. Their size range from 10 μm to a few nanometers. The acidity measurement (i.e number, strength and location) were carried out by so-called conventional techniques: adsorption followed by infrared spectroscopy of various basic probe molecules (CO, C2H4, pyridine) and model reaction (n-hexane cracking). The extreme crystal downsize lowers the acid strength. These results are confirmed also by using an innovative technique: the reversed-flow inverse chromatography (RF-IGC). The involvement of the external and internal zeolitic species depend on the adsorbed molecules and the operating conditions: (i) the high content of extra-framework aluminum enhance the n-hexane cracking activity owing to the exaltation of the Brønsted sites strength, and (ii) the RF-IGC technique show an important involvement of the silanol groups (mainly present on the nanosized zeolite) in lateral interactions with ethylene.
Distributed consensus-based demodulation: algorithms and error analysis (2010)

This paper deals with distributed demodulation of space-time transmissions of a common message from a multi-antenna access point (AP) to a wireless sensor network. Based on local message exchanges with single-hop neighboring sensors, two algorithms are developed for distributed demodulation. In the first algorithm, sensors consent on the estimated symbols. By relaxing the finite-alphabet constraints on the symbols, the demodulation task is formulated as a distributed convex optimization problem that is solved iteratively using the method of multipliers. Distributed versions of the centralized zero-forcing (ZF) and minimum mean-square error (MMSE) demodulators follow as special cases. In the second algorithm, sensors iteratively reach consensus on the average (cross-) covariances of locally available per-sensor data vectors with the corresponding AP-to-sensor channel matrices, which constitute sufficient statistics for maximum likelihood demodulation. Distributed versions of the sphere decoding algorithm and the ZF/MMSE demodulators are also developed. These algorithms offer distinct merits in terms of error performance and resilience to non-ideal inter-sensor links. In both cases, the per-iteration error performance is analyzed, and the approximate number of iterations needed to attain a prescribed error rate are quantified. Simulated tests verify the analytical claims. Interestingly, only a few consensus iterations (roughly as many as the number of sensors), suffice for the distributed demodulators to approach the performance of their centralized counterparts.