gebhart/patrepeval huggingface dataset:
Technologies, Products, and Economic Viability of a Sugarcane Biorefinery in Brazil (2016)

The production of chemicals from renewable lignocellulosic raw materials is expected to become an important productive chain globally. With the recent implementation of the first industrial plants, rapid and significant advances are expected to occur in terms of revenue, technology, and productivity. It is still not possible to determine which biomasses, technologies, products, and companies will thrive in this new sector; however, some industries can already be highlighted. We believe that Brazil will play a prominent role in this industry due to its current dominance in sugarcane ethanol and because it has abundant land and a suitable climate for growing lignocellulosic materials. This article shows how Braskem seeks to understand this new sector and discusses some of the factors that will determine the characteristics of this new industrial environment. In addition, different levels of integration in value chain model, which is a key element for the future of chemical production from renewables, are analyzed and discussed in this work. Five different biorefinery designs are proposed, from conventional Ethanol production to fully integrated plants that produce two chemicals, ethanol and raw sugar, from both sugarcane biomass and juice. Braskem's method for evaluation of renewable chemicals is presented and applied to estimate the capital expenditures (CAPEX) and operational expenditures (OPEX) for each case. An early-stage economic evaluation is performed, and the results of the different approaches are compared. From all analyzed cases, a fully integrated biorefinery producing two chemicals from biomass, ethanol and sugar, showed the best results, which show the potential of integrated chemical production in a biorefinery in Brazil.
Deciphering the Plasma Proteome of Type 2 Diabetes (2020)

With an estimated prevalence of 463 million affected, type 2 diabetes represents a major challenge to health care systems worldwide. Analyzing the plasma proteomes of individuals with type 2 diabetes may illuminate hitherto unknown functional mechanisms underlying disease pathology. We assessed the associations between type 2 diabetes and >1,000 plasma proteins in the Cooperative Health Research in the Region of Augsburg (KORA) F4 cohort (<i>n</i> = 993, 110 cases), with subsequent replication in the third wave of the Nord-Trøndelag Health Study (HUNT3) cohort (<i>n</i> = 940, 149 cases). We computed logistic regression models adjusted for age, sex, BMI, smoking status, and hypertension. Additionally, we investigated associations with incident type 2 diabetes and performed two-sample bidirectional Mendelian randomization (MR) analysis to prioritize our results. Association analysis of prevalent type 2 diabetes revealed 24 replicated proteins, of which 8 are novel. Proteins showing association with incident type 2 diabetes were aminoacylase-1, growth hormone receptor, and insulin-like growth factor-binding protein 2. Aminoacylase-1 was associated with both prevalent and incident type 2 diabetes. MR analysis yielded nominally significant causal effects of type 2 diabetes on cathepsin Z and rennin, both known to have roles in the pathophysiological pathways of cardiovascular disease, and of sex hormone-binding globulin on type 2 diabetes. In conclusion, our high-throughput proteomics study replicated previously reported type 2 diabetes-protein associations and identified new candidate proteins possibly involved in the pathogenesis of type 2 diabetes.
Rapid ultrasonic isothermal amplification of DNA with multiplexed melting analysis – applications in the clinical diagnosis of sexually transmitted diseases (2014)

We describe a nucleic acid testing (NAT) platform for infectious disease diagnostics at the point-of-care, using surface acoustic waves (SAW) to perform a multiplexed loop-mediated isothermal amplification (LAMP) test for sexually transmitted diseases. The ultrasonic actuation not only enables faster NAT reactions but also provides a route towards integrating low-cost, low-power molecular diagnostics into disposable sensors.
Standard recognising self organizing map based cognitive radio transceiver (2010)

Cognitive Radio (CR) Systems have transceivers with the ability to adjust their operating parameters after observing the results in order to decide to operate in a specific radio configuration, expecting to move the radio towards some optimized operational state. Framed within this statement, this p
Towards computer-supported face-to-face knowledge sharing (2006)

Although a lot of systems provide co-located collaboration support, few existing technologies provide support for fluid knowledge sharing. To fluidly share our knowledge in co-located environments, each person's digital experience should be merged and presented on a collaborative display device such as a face-to-face tabletop display. For capturing concrete requirements for such face-to-face fluid knowledge sharing, we built a prototype system that presents merged multi-users' Web browsing histories on a tabletop display. We experimented with our prototype in an exhibition and collected over 100 filled questionnaires and informal observations.
PASSIVE Q-SWITCHING OF A CO2 LASER USING A MIXTURE OF SF6 AND C2F3Cl GASES (1969)

Passive Q-switching of a CO2 laser operating at 10.6 μ has been achieved with a mixture of sulfur hexafluoride and chlorotrifluoroethylene gases contained in a gas cell placed within the resonator. Use of chlorotrifluoroethylene gas to suppress spurious oscillations eliminates the need to use dispersive optical elements in the resonator.
Inhibition of the Peroxygenase Lytic Polysaccharide Monooxygenase by Carboxylic Acids and Amino Acids (2022)

Lytic polysaccharide monooxygenases (LPMOs) are widely distributed in fungi, and catalyze the oxidative degradation of polysaccharides such as cellulose. Despite their name, LPMOs possess a dominant peroxygenase activity that is reflected in high turnover numbers but also causes deactivation. We report on the influence of small molecules and ions on the activity and stability of LPMO during catalysis. Turbidimetric and photometric assays were used to identify LPMO inhibitors and measure their inhibitory effect. Selected inhibitors were employed to study LPMO activity and stability during cellulose depolymerization by HPLC and turbidimetry. It was found that the fungal metabolic products oxalic acid and citric acid strongly reduce LPMO activity, but also protect the enzyme from deactivation. QM calculations showed that the copper atom in the catalytic site could be ligated by bi- or tridentate chelating compounds, which replace two water molecules. MD simulations and QM calculations show that the most likely inhibition pattern is the competition between the inhibitor and reducing agent in the oxidized Cu(II) state. A correlation between the complexation energy and the IC<sub>50</sub> values demonstrates that small, bidentate molecules interact strongest with the catalytic site copper and could be used by the fungus as physiological effectors to regulate LPMO activity.
P4‐039: A NOVEL HISTONE DEACETYLASE 6 (HDAC6) INHIBITOR TO MITIGATE TAU PATHOLOGY IN ALZHEIMER'S DISEASE (2019)

Accumulating evidence endorses HDAC6 inhibitors as potential therapeutics to rescue tau pathology in neurodegenerative disorders, including Alzheimer's disease (AD). However, the currently available HDAC6 inhibitors have limited brain penetration and relatively short duration of action. Herein, we show that WT36-87, a novel HDAC6 inhibitor, is highly potent, brain penetrant, and has sustained HDAC6 inhibitory effects. We treated iHEK-Tau cells (human embryonic kidney-293 cells that express wild-type 0N4R human tau upon exposure to tetracycline) with increasing concentrations of WT36-87 for 4 hours to determine IC50 for HDAC6 inhibition. Then, treated iHEK-Tau cells were collected, lysed with RIPA buffer, and lysates were assessed by western blot. For in-vivo studies, rTg4510 tau transgenic mice were injected intraperitoneally (I.P.) with 60mg/kg or beta-cyclodextrin sulfobutyl ether Na salt vehicle, then brain and liver tissues were collected after 75 minutes of injection. Collected tissues were lysed by RIPA buffer to proceed with western blot. iHEK-Tau cells treated with increasing concentrations of WT36-87 show a gradual accumulation of acetyl groups on K40 of alpha-tubulin, a well-established marker for HDAC6 inhibition. The gradual enhancement of alpha-tubulin acetylation follows a sigmoidal dose-response relationship with an EC50 of 20nM. Regarding tau post-translational modifications, WT36-87 shows remarkable increase in tau acetylation at K280 that peaks at 10nM (2.3-fold increase over vehicle, p < 0.05) and strong reduction in tau phosphorylation at S262 that reaches its lowest at 30nM (42% lower than vehicle, p < 0.05). In-vivo studies demonstrated significant increases in acetylated tubulin. In addition, the brains of treated rTg4510 mice show 35% increase in the acetylation of beta-catenin (another marker of HDAC6 activity) 75 minutes after I.P. injection (p < 0.05). Liver acetylated tubulin also increased significantly after I.P. administration of WT36-87. WT36-87 is a highly potent HDAC6 inhibitor that has effective brain penetration. Further experiments will be conducted to test the capacity of WT36-87 to rescue tau pathology and behavioral deficit in rTg4510 mice as an AD animal model. Supported by AG058283.
A Graph-Theoretic Analysis of Information Value (2013)

We derive qualitative relationships about the informational relevance of variables in graphical decision models based on a consideration of the topology of the models. Specifically, we identify dominance relations for the expected value of information on chance variables in terms of their position and relationships in influence diagrams. The qualitative relationships can be harnessed to generate nonnumerical procedures for ordering uncertain variables in a decision model by their informational relevance.
High-Speed Coherent Transmission Using Advanced Photonics in Terahertz Bands (2015)

A terahertz-wave communication system directly connected to an optical fiber network is promising for application to future mobile backhaul and fronthaul links. The possible broad bandwidth in the terahertz band is useful for high-speed signal transmission as well as radio-space encapsulation to the high-frequency carrier. In both cases, the low-latency feature becomes important to enhance the throughput in mobile communication and is realized by waveform transport technology without any digital-signal-processing-based media conversion. A highly precise optical frequency comb signal generated by optical modulation and the vector signal demodulation technology adopted from advanced optical fiber communication technologies help perform modulation and demodulation with impairment compensation at just the edges of the link. Terahertz wave, radio over fiber, waveform transport, coherent detection, multilevel modulation, radio on radio.
Synthesis of cyclosporine. Total syntheses of ‘cyclosporin A’ and ‘cyclosporin H’, two fungal metabolites isolated from the species Tolypocladium inflatum GAMS (1984)

Abstract The heptapeptide H‐MeBmt‐Abu‐Sar‐MeLeu‐Val‐MeLeu‐Ala‐OBzl ( 20 ) was synthesized for coupling with the previously described cyclosporine tetrapeptide sequence Boc‐ D ‐Ala‐MeLeu‐MeVal‐OH ( 21 ). The product of the coupling, the undecapeptide Boc‐ D ‐Ala‐MeLeu‐MeLeu‐MeVal‐MeBmt‐abu‐Sar‐MeLeu‐Val‐MeLeu‐Ala‐OBzl ( 22 ), was then deprotected and cyclized to cyclosporine ( 1 ). The tetrapeptide diastereoisomer Boc‐ D ‐ala‐MeLeu‐MeLeu‐ D ‐MeVAl‐OH ( 23 ) could also be used as a starting material to produce selectively the desired undecapeptide 22 . In this case, the N ‐methyl‐ D ‐valine unit, was selectively isomerized to the L‐from by using the appropriate condensing agent. The diastereoisomeric undecapeptide Boc‐ D ‐ala‐MeLeu‐MeLeu‐ D ‐MeVal‐MeBmt‐Abu‐Sar‐MeLeu‐Val‐MeLeuAla‐OBzl ( 24 ) was also synthesized starting from 21 by using the mixed pivalic anhydride method to selectively invert the configuration of the N ‐methyl‐ L ‐valine. The structure of the undecapeptide 24 was confirmed by deprotection and cyclization to ‘cyclosporin H’, a natural product known to have the structure [ D ‐MeVal 11 ]cyclosporine ( 2 ).
dPV: An End-to-End Differentiable Solar-Cell Simulator (2021)

We introduce dPV, an end-to-end differentiable photovoltaic (PV) cell simulator based on the drift-diffusion model and Beer-Lambert law for optical absorption. dPV is programmed in Python using JAX, an automatic differentiation (AD) library for scientific computing. Using AD coupled with the implicit function theorem, dPV computes the power conversion efficiency (PCE) of an input PV design as well as the derivative of the PCE with respect to any input parameters, all within comparable time of solving the forward problem. We show an example of perovskite solar-cell optimization and multi-parameter discovery, and compare results with random search and finite differences. The simulator can be integrated with optimization algorithms and neural networks, opening up possibilities for data-efficient optimization and parameter discovery.
Supplementary Data from Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Table 3&lt;/p&gt;
Metabolic Imaging of Glutamine in Cancer (2017)

Glucose and glutamine are the most abundant nutrients for producing energy and building blocks in normal and tumor cells. Increased glycolysis in tumors, the Warburg Effect, is the basis for <sup>18</sup>F-FDG PET imaging. Cancer cells can also be genetically reprogrammed to use glutamine. 5-<sup>11</sup>C-(2<i>S</i>)-glutamine and <sup>18</sup>F-(2<i>S</i>,4<i>R</i>)4-fluoroglutamine may be useful complementary tools to measure changes in tumor metabolism. In glioma patients, the tracer <sup>18</sup>F-(2<i>S</i>,4<i>R</i>)4-fluoroglutamine showed tumor-to-background contrast different from that of <sup>18</sup>F-FDG and differences in uptake in glioma patients with clinical progression of disease versus stable disease (tumor-to-brain ratio > 3.7 in clinically active glioma tumors, minimal or no specific uptake in clinically stable tumors). These preliminary results suggest that <sup>18</sup>F-(2<i>S</i>,4<i>R</i>)4-fluoroglutamine PET may be a new tool for probing in vivo metabolism of glutamine in cancer patients and for guiding glutamine-targeted therapeutics. Further studies of uptake mechanism, and comparison of kinetics for <sup>18</sup>F-(2<i>S</i>,4<i>R</i>)4-fluoroglutamine versus the <sup>11</sup>C-labeled native glutamine, will be important and enlightening.
Structural identification of metabolites produced by the NodB and NodC proteins of Rhizobium leguminosarum (1994)

The Rhizobium nodulation genes nodABC are involved in the synthesis of lipo-chitin oligosaccharides. We have analysed the metabolites which are produced in vivo and in vitro by Rhizobium strains which express the single nodA, nodB and nodC genes or combinations of the three. In vivo radioactive labelling experiments, in which D-[1-14C]-glucosamine was used as a precursor, followed by mass spectrometric analysis of the purified radiolabelled metabolic products, showed that Rhizobium strains that only express the combination of the nodB and nodC genes do not produce lipo-chitin oligosaccharides but instead produce chitin oligomers (mainly pentamers) which are devoid of the N-acetyl group on the non-reducing terminal sugar residue (designated NodBC metabolites). Using the same procedure we have shown that when the nodL gene is expressed in addition to the nodBC genes the majority of metabolites contain an additional O-acetyl substituent on the non-reducing terminal sugar residue (designated NodBCL metabolites). The NodBC and NodBCL metabolites purified after in vivo labelling were compared with the radiolabelled metabolites produced in vitro by Rhizobium bacterial cell lysates to which UDP-N-acetyl-D-[U-14C]-glucosamine was added using thin-layer chromatography. The results show that the lysates of strains which expressed the nodBC or nodBCL genes can also produce NodBC and NodBCL metabolites. The same results were obtained when the NodB and NodC proteins were produced separately in two different strains. On the basis of these and other recent results, we propose that NodB is a chitin oligosaccharide deacetylase, NodC an N-acetylglucosaminyltransferase and, by default, NodA is involved in lipid attachment.
Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis viniferaL.) (1996)

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.
Data from An Anti–Transforming Growth Factor β Antibody Suppresses Metastasis via Cooperative Effects on Multiple Cell Compartments (2023)

&lt;div&gt;Abstract&lt;p&gt;Overexpression of transforming growth factor β (TGF-β) is frequently associated with metastasis and poor prognosis, and TGF-β antagonism has been shown to prevent metastasis in preclinical models with surprisingly little toxicity. Here, we have used the transplantable 4T1 model of metastatic breast cancer to address underlying mechanisms. We showed that efficacy of the anti–TGF-β antibody 1D11 in suppressing metastasis was dependent on a synergistic combination of effects on both the tumor parenchyma and microenvironment. The main outcome was a highly significant enhancement of the CD8+ T-cell–mediated antitumor immune response, but effects on the innate immune response and on angiogenesis also contributed to efficacy. Treatment with 1D11 increased infiltration of natural killer cells and T cells at the metastatic site, and enhanced expression of coactivators (NKG2D) and cytotoxic effectors (perforin and granzyme B) on CD8+ T cells. On the tumor cells, increased expression of an NKG2D ligand (Rae1γ) and of a death receptor (TNFRSF1A) contributed to enhanced immune cell-mediated recognition and lysis. The data suggest that elevated TGF-β expression in the tumor microenvironment modulates a complex web of intercellular interactions that aggregately promote metastasis and progression. TGF-β antibodies reverse this effect, and the absence of a major effect of TGF-β antagonism on any one cell compartment may be critical for a good therapeutic window and the avoidance of autoimmune complications. [Cancer Res 2008;68(10):3835–43]&lt;/p&gt;&lt;/div&gt;
METRICS (2000)

We describe METRICS, a system to recover design productivity via new infrastructure for design process optimization. METRICS seeks to treat system design and implementation as a science, rather than an art. A key precept is that measuring a design process is a prerequisite to optimizing it and continuously achieving maximum productivity. METRICS (i) unobtrusively gathers characteristics of design artifacts, design process, and communications during the system development effort, and (ii) analyzes and compares that data to analogous data from prior efforts. METRICS infrastructure consists of (i) a standard metrics schema, along with metrics transmittal capabilities embedded directly into EDA tools or into wrappers around tools; (ii) a metrics data warehouse and metrics reports; (iii) data mining and visualization capabilities for project prediction, tracking, and diagnosis. We give experiences and insights gained from development and deployment of METRICS within a leading SOC design flow.
Antimicrobial Peptides: Cooperative Approaches to Protection (2005)

Reports of cationic antimicrobial peptides (CAPs) have become standard fare in research literature. But with several hundred peptides described to date, the investigator who tries to navigate the proposed models of their activity is only treated to a generous serving of incongruencies. Rather than acting in isolation as antimicrobial molecules, CAPs also may synergize with other molecules of innate immunity and modulate both innate and adaptive immune systems, thus providing a link between the various mechanisms that result in host protection.
Supplementary Figure 3 from Reexpression of Tumor Suppressor, sFRP1, Leads to Antitumor Synergy of Combined HDAC and Methyltransferase Inhibitors in Chemoresistant Cancers (2023)

&lt;p&gt;PDF file, 130K, sFRP1 re-expression in cancer cells inhibits Wnt signaling.&lt;/p&gt;
Usnic acid: a non-genotoxic compound with anti-cancer properties (2005)

The majority of human tumors bear inactive p53 or cellular factors that down-regulate the expression and activity of the p53 network. Therefore, finding therapies that are effective in such tumors is of great interest. Usnic acid, a normal component of lichens, showed activity against the wild-type p53 breast cancer cell line MCF7 as well as the non-functional p53 breast cancer cell line MDA-MB-231 and the lung cancer cell line H1299 (null for p53). In MCF7 cells treated with usnic acid, although there was an accumulation of p53 and p21 proteins, the transcriptional activity of p53 remained unaffected. We also found that there was no phosphorylation of p53 at Ser15 after treatment of MCF7 cells with usnic acid, suggesting that the oxidative stress and disruption of the normal metabolic processes of cells triggered by usnic acid does not involve DNA damage. The property of usnic acid as a non-genotoxic anti-cancer agent that works in a p53-independent manner makes it a potential candidate for novel cancer therapy.