gebhart/patrepeval huggingface dataset:
A Rationally Designed Hsp70 Variant Rescues the Aggregation-Associated Toxicity of Human IAPP in Cultured Pancreatic Islet β-Cells (2018)

Molecular chaperones are key components of the protein homeostasis system against protein misfolding and aggregation. It has been recently shown that these molecules can be rationally modified to have an enhanced activity against specific amyloidogenic substrates. The resulting molecular chaperone variants can be effective inhibitors of protein aggregation in vitro, thus suggesting that they may provide novel opportunities in biomedical and biotechnological applications. Before such opportunities can be exploited, however, their effects on cell viability should be better characterised. Here, we employ a rational design method to specifically enhance the activity of the 70-kDa heat shock protein (Hsp70) against the aggregation of the human islet amyloid polypeptide (hIAPP, also known as amylin). We then show that the Hsp70 variant that we designed (grafted heat shock protein 70 kDa-human islet amyloid polypeptide, GHsp70-hIAPP) is significantly more effective than the wild type in recovering the viability of cultured pancreatic islet &beta;-cells RIN-m5F upon hIAPP aggregation. These results indicate that a full recovery of the toxic effects of hIAPP aggregates on cultured pancreatic cells can be achieved by increasing the specificity and activity of Hsp70 towards hIAPP, thus providing evidence that the strategy presented here provides a possible route for rationally tailoring molecular chaperones for enhancing their effects in a target-dependent manner.
Diffuse large B‐cell lymphoma: 2019 update on diagnosis, risk stratification, and treatment (2019)

This review will focus on differential treatment of DLBCL up-front and at the time of relapse by COO and molecular features.
Audio stream classification for multimedia database search (2013)

Search and retrieval of huge archives of Multimedia data is a challenging task. A classification step is often used to reduce the number of entries on which to perform the subsequent search. In particular, when new entries of the database are continuously added, a fast classification based on simple threshold evaluation is desirable. In this work we present a CART-based (Classification And Regression Tree [1]) classification framework for audio streams belonging to multimedia databases. The database considered is the Archive of Ethnography and Social History (AESS) [2], which is mainly composed of popular songs and other audio records describing the popular traditions handed down generation by generation, such as traditional fairs, and customs. The peculiarities of this database are that it is continuously updated; the audio recordings are acquired in unconstrained environment; and for the non-expert human user is difficult to create the ground truth labels. In our experiments, half of all the available audio files have been randomly extracted and used as training set. The remaining ones have been used as test set. The classifier has been trained to distinguish among three different classes: speech, music, and song. All the audio files in the dataset have been previously manually labeled into the three classes above defined by domain experts.
Harnessing the reverse cholesterol transport pathway to favor differentiation of monocyte-derived APCs and antitumor responses (2023)

Lipid and cholesterol metabolism play a crucial role in tumor cell behavior and in shaping the tumor microenvironment. In particular, enzymatic and non-enzymatic cholesterol metabolism, and derived metabolites control dendritic cell (DC) functions, ultimately impacting tumor antigen presentation within and outside the tumor mass, dampening tumor immunity and immunotherapeutic attempts. The mechanisms accounting for such events remain largely to be defined. Here we perturbed (oxy)sterol metabolism genetically and pharmacologically and analyzed the tumor lipidome landscape in relation to the tumor-infiltrating immune cells. We report that perturbing the lipidome of tumor microenvironment by the expression of sulfotransferase 2B1b crucial in cholesterol and oxysterol sulfate synthesis, favored intratumoral representation of monocyte-derived antigen-presenting cells, including monocyte-DCs. We also found that treating mice with a newly developed antagonist of the oxysterol receptors Liver X Receptors (LXRs), promoted intratumoral monocyte-DC differentiation, delayed tumor growth and synergized with anti-PD-1 immunotherapy and adoptive T cell therapy. Of note, looking at LXR/cholesterol gene signature in melanoma patients treated with anti-PD-1-based immunotherapy predicted diverse clinical outcomes. Indeed, patients whose tumors were poorly infiltrated by monocytes/macrophages expressing LXR target genes showed improved survival over the course of therapy. Thus, our data support a role for (oxy)sterol metabolism in shaping monocyte-to-DC differentiation, and in tumor antigen presentation critical for responsiveness to immunotherapy. The identification of a new LXR antagonist opens new treatment avenues for cancer patients.
Recent Chemotherapy Reduces the Sensitivity of [18F]Fluorodeoxyglucose Positron Emission Tomography in the Detection of Colorectal Metastases (2005)

These results indicate that FDG-PET scanning should be interpreted in the context of concurrent cytotoxic therapy. FDG-PET scanning results may also be useful in assessment of response to such cytotoxic therapies.
Abstract 2854: CRISPR knockout of HuR in pancreatic cancer cells causes a xenograft lethal phenotype (2016)

Abstract Pancreatic ductal adenocarcinoma (PDA) is the most prevalent type of pancreatic cancer and will soon become the second leading cause of cancer related deaths in the U.S. Studies show that the nuclear localized mRNA-binding protein HuR (ELAVL1) is activated in PDA cells, with cytoplasmic translocation associated with increased tumor size and poor prognosis. Previous in vitro and in vivo studies have established HuR's role as a PDA cell survival mechanism. Thus, we explored the phenotypic effect of completely eliminating HuR expression from PDA cells through the use of clustered, regularly interspaced, short palindromic repeat (CRISPR)/Cas9 technology to target and disrupt the HuR genomic sequence. Since INDELs are induced randomly, we designed 3 gRNAs to target HuR at different loci. Gene disruption was determined via sequencing and validated through protein and mRNA expression, where homozygous knockouts (HuR−/−) had undetectable HuR expression as compared to wild-type (HuR+/+), heterozygotes (HuR+/−), and CRISPR/Cas9 negative control. Sanger sequencing confirmed homozygous knockouts with a frame shift mutation on both alleles. When HuR knockout cells were exposed to chemotherapeutic stress including mitomycin C, oxaliplatin, and gemcitabine, no HuR expression (nuclear or cytoplasmic) was detected via immunofluorescence. Phenotypically, HuR−/− cells resulted in increased apoptosis and necrosis as measured via trypan blue assay, and accordingly, had increased caspase 3 activity, a marker of a cell death. HuR−/− cells, when treated with mitomycin C, oxaliplatin, gemcitabine, and glucose deprivation exhibited decreased long and short-term cell survival as compared to control cells. HuR−/− cells, pulse-labeled with bromodeoxyurdine (BrdU), had a higher proportion of cells in S phase and fewer cells in G2/M phase. HuR deletion enhanced premature mitotic entry thereby preventing efficient repair of DNA damage, leading to cell death. Importantly, CRISPR knockout of HuR showed marked impairment in tumor growth in mouse xenografts. The differences in median tumor volume with HuR−/- xenografts was significant as compared to xenografts in mice with HuR(+/+) cells (0.0 mm3 vs 378.0 mm3, P &amp;lt; 0.005). Taken together with our past work in patient samples, this pre-clinical model demonstrates that HuR is essential for PDA growth in vivo. Future work will develop strategies to target HuR either as a monotherapy or in combination with other chemotherapies. Citation Format: Edwin Cheung, Shruti Lal, Mahsa Zarei, Nicole C. Mambelli-Lisboa, Saswati Chand, Carmella Romeo, Kevin O’Hayer, Eric Londin, Joseph A. Cozzitorto, Charles J. Yeo, Jordan M. Winter, Jonathan R. Brody. CRISPR knockout of HuR in pancreatic cancer cells causes a xenograft lethal phenotype. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2854.
Realistic tenant traces for enterprise DBaaS (2013)

The benchmarking of databases is an involved topic to which cloud computing adds another level of complexity. For example, benchmarking of multi-tenant on-demand applications requires modeling tenants' dynamic behavior over time. This paper provides two methodologies for simulating realistic tenant behavior in enterprise on-demand scenarios. The methods cover the cases that no or not enough real-world tenant traces are available.
Thermal Degradation and Stabilization of Polyvinyl Chloride (1968)

各種の安息香酸金属塩を添加して, ポリ塩化ビニルの熱分解を粉末状態, あるいはシクロヘキサノール, フタル酸ジブチルなどの溶媒中で行ない, 塩素原子脱離量, 分解体およびその臭素付加体の紫外, 可視吸収スペクトルから吸光度比およびエステル結合生成量を求め, エステル化の条件, エステル化度と熱分解度の関係などを検討した。カドミウム, 鉛の安息香酸塩はすべての分解系でエステル結合を生成し, シクロヘキサノール中ではナトリウム, アルミニウム塩のエステル結合生成能は著しく, いずれも着色は完全に阻止される。しかしシクロヘキサノール中ではエステル結合生成能のいかんにかかわらず, いずれの金属のカルボン酸塩によっても着色, 不溶化は長時間にわたって阻止され, エステル化反応, 塩化水素不活性化反応がカルボン酸塩の安定剤効果のすべてでないことがわかる。またエステル結合を含む熱分解体を金属塩の存在しない系て再加熱すると著しく急速に濃色化するが, 他の諸結果にも鑑みてこの反応の主たる起点はエステル結合というよりもむしろ不安定な不飽和構造 (nの小さい-(CH=CH) n-CHCl～) と推測し, カルボン酸金属塩によるイオン的な塩化水素脱離とエステル結合生成反応機構を提示し, ラジカル連鎖的塩化水素脱離反応に対する金属塩の抑制効果を示唆した。
[Salt and cancer]. (2010)

Besides cardiovascular disease, a high salt intake causes other adverse health effects, i.e., gastric and some other cancers, obesity (risk factor for many cancer sites), Meniere's disease, worsening of renal disease, triggering an asthma attack, osteoporosis, exacerbation of fluid retention, renal calculi, etc. Diets containing high amounts of food preserved by salting and pickling are associated with an increased risk of cancers of the stomach, nose and throat. Because gastric cancer is still the most common cancer in some countries (especially in Japan), its prevention is one of the most important aspects of cancer control strategy. Observations among Japanese immigrants in the U.S.A. and Brazil based on the geographic differences, the trend in cancer incidence with time, and change in the incidence patterns indicate that gastric cancer is closely associated with dietary factors such as the intake of salt and salted food. The findings of many epidemiological studies suggest that high dietary salt intake is a significant risk factor for gastric cancer and this association was found to be strong in the presence of Helicobacter (H.) pylori infection with atrophic gastritis. A high-salt intake strips the lining of the stomach and may make infection with H. pylori more likely or may exacerbate the infection. Salting, pickling and smoking are traditionally popular ways of preparing food in Japan and some parts of Asia. In addition to salt intake, cigarette smoking and low consumption of fruit and vegetables increase the risk of stomach cancer. However, it is not known whether it is specifically the salt in these foods or a combination of salt and other chemicals that can cause cancer. One study identified a mutagen in nitrite-treated Japanese salted fish, and chemical structure of this mutagen suggests that it is derived from methionine and that salt and nitrite are precursors for its formation. Working under conditions of heat stress greatly increased the workers' salt excretion through perspiration. Workers exposed to heat stress consumed as much as 13-38 g salt daily. As salt strongly enhances and promotes chemical gastric carcinogenesis and H. pylori infection in both humans and animals, there is an association between work, salt intake, and development of stomach cancer. Reducing salt intake, especially during pregnancy, also reduces the risk of developing breast cancer and many other diseases, as well as obesity. The risk of most cancers is reduced by losing weight. The geographical data and analyses currently available suggest that road salt (road salting in winter) may be associated with elevated mortality from cancer of the breast, lung, esophagus, throat, larynx, large intestine, rectum and bladder. There is no available literature on the health impacts of road salt. The cause and effect relationships cannot be established without further studies.
The Interplay between Mutasynthesis and Semisynthesis: Generation and Evaluation of an Ansamitocin Library (2011)

Working hand in hand! The synthetic power of three mutant strains that produce ansamitocin and geldanamycin is combined with chemical synthesis, thus leading to 27 new ansamitocin derivatives. Structure–activity studies show that the N of the carbinolamide moiety is not important for cytotoxic activity but the α orientation of the OH group at C9 is key [see structures; chemical synthesis (red), mutasynthesis (blue), biosynthesis (black)]. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Viruses Causing Common Respiratory Infection in Man. IV. Reoviruses and Adenoviruses (1973)

Journal Article Viruses Causing Common Respiratory Infection in Man. IV. Reoviruses and Adenoviruses Get access George Gee Jackson, George Gee Jackson From the Department of Medicine, Abraham Lincoln School of Medicine, University of Illinois College of Medicine, Chicago, Illinois Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert Lee Muldoon Robert Lee Muldoon From the Department of Medicine, Abraham Lincoln School of Medicine, University of Illinois College of Medicine, Chicago, Illinois Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 128, Issue 6, December 1973, Pages 811–866, https://doi.org/10.1093/infdis/128.6.811 Published: 01 December 1973
Soft-Acting, Noncontact Gripping Method for Ultrathin Wafers Using Distributed Bernoulli Principle (2018)

The handling of ultrathin wafers (<;100 μm thickness) is a challenging task since these are among the thinnest and most fragile materials. This paper provides a soft-acting and noncontact gripping technology for ultrathin wafer based on the distributed Bernoulli principle, and also proposes an experimental measurement method for evaluating the performance. A distributed Bernoulli gripper for ultrathin wafers is designed, and the characteristics of the gripper are studied via theoretical analysis and experiments. Three performance indices for evaluating the properties of the soft gripping: deformation, vibration, and stress are presented. Through measurement experiments, the effects of the key operational parameters consisting of air flow rate and gap height on the performance indices are investigated. Based on the experimental data, the appropriate parameters settings are obtained. The comparison to present grippers reveals that the proposed gripping technology is superior in soft gripping thin and fragile materials. This paper provides guidance for implementing the distributed Bernoulli principle in practical applications of soft-acting and noncontact gripping for thin and fragile materials.
An investigation of the influence of nozzle aspect ratio on the velocity field of turbulent plane jet (2004)

The effect of nozzle aspect ratio (w/H) (major axis to minor axis ratio) on the velocity field of a turbulent plane jet is investigated using a hot-wire anemometer. The aspect ratios investigated were in the range 10 &lt; w/H
Effect of avocadofurans on larval survival, growth, and food preference of the generalist herbivore, Spodoptera exigua (1999)

Abstract We examined the effect of two avocadofurans, 2‐(pentadecyl)furan and 2‐(heptadecyl)furan, from avocado idioblast oil cells on maturation and larval feeding behavior of a generalist insect herbivore, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae). Experiments were conducted using two larval sizes: early‐stadium larvae refer to those larvae from experiments initiated with neonates while late‐stadium larvae refer to those larvae from experiments initiated with third instars. In order to use selected sublethal doses for developmental and behavioral studies on early‐ and late‐stadium larvae, log‐dose probit lines were determined using diet incorporation bioassays. Both avocadofurans had similar toxicities to early‐stadium larvae [ LC 50 = 2.2 and 1.9 μmoles/g of diet for 2‐(pentadecyl)furan and 2‐(heptadecyl)furan, respectively] and late‐stadium larvae ( LC 50 = 3.0 and 3.4 μmoles/g of diet, respectively). In diet bioassays extending from egg hatch to adult emergence, the avocadofurans significantly prolonged larval developmental times and reduced S. exigua pupal weights. In 7 d no‐choice bioassays initiated with cohorts of newly‐molted third instars, the avocadofurans significantly reduced larval weights at various sublethal concentrations (below LC 50 values). To test larval feeding deterrence effects of these avocadofurans, choice tests were conducted using early and older instar larvae. A significantly higher proportion of early‐stadium larvae preferred control diet over diet treated with either avocadofuran at several sublethal concentrations. Similarly, choice tests with late‐stadium larvae showed greater proportions of larvae on control diet than treated diet even at concentrations below the LC 50 . Moreover, late‐stadium larvae consumed significantly more of the control diet than the treated diet. Thus, the avocadofurans may act as feeding deterrents as well as toxicants in plant protection against non‐adapted insect herbivores.
A strategy for increasing an in vivo flux by genetic manipulations. The tryptophan system of yeast (1992)

Decreases in enzyme activity often have little effect on the flux carried by the pathway. Similarly, up-modulation of single genes, and hence of the dependent enzyme concentrations, is frequently found to be ineffective in increasing the flux in the pathway in which the enzyme occurs. This insensitivity to enzyme variation is demonstrated experimentally for five separate enzymes in the tryptophan synthesis system of yeast, first by down-modulation of the gene dose and secondly by increasing the dose using multi-copy vectors. Such a lack of response is discussed in terms of the concepts of metabolic control analysis. When these five enzymes, however, were simultaneously increased by a multi-copy vector carrying all five genes, a substantial elevation of the flux to tryptophan was observed. These findings revealed a new phenomenon, namely the more than additive effects on the flux of simultaneous elevations of several enzyme activities.
Using Sound Feedback to Help Blind People Navigate (2018)

People can generate mental representations of one physical magnitude (e.g., distance) in terms of another (e.g., pitch). Capitalizing on this ability, we developed a system that could help visually impaired people navigate by presenting them with sounds of lower or higher pitch according to their distance from objects that they gaze at. Eight blind-folded participants completed a Hebb-Williams Maze with the system and twelve blind-folded participants completed the maze without it. Both groups completed the maze five times. We found that participants completed the maze faster in the last three trials compared to the first trial. There were no differences between the groups in the pace of improvement and in the time to complete the maze. However, participants who used the system made less errors in the maze than participants who did not use it. Our findings indicate that the system can potentially assist visually impaired people navigate. The contribution of the system to navigation will be further investigated with larger number of participants and with more extensive training.
Impact of Flue Gas Desulfurization Gypsum and Manure Application on Transfer of Potentially Toxic Elements to Plants, Soil, and Runoff (2018)

There are concerns regarding the fate of nutrients from surface application of animal manure. One approach to reduce losses of P is to treat manure with industrial byproducts such as flue gas desulfurization (FGD) gypsum. However, concerns regarding potentially toxic elements contributed to the environment have arisen based on previous element-rich forms of FGD gypsum that included fly ash, whereas "new" FGD gypsum without fly ash is much lower in contaminants. This study examined the impact of FGD gypsum application on soil, plants, and runoff when applied alone or with poultry litter (PL) to soil. The study consisted of a plant response study (four rates of FGD gypsum of 0, 2.2, 4.4, and 8.9 Mg ha and four rates of PL of 0, 4.4, 8.9, and 13.4 Mg ha) and a rainfall simulation study (3.4 Mg PL ha with four rates of FGD gypsum of 0, 2.2, 4.4, and 8.9 Mg ha and controls). Plant, soil, and runoff samples were analyzed for As, Ba, Be, Ca, Cd, Ba, Co, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, P, Pb, Sb, Se, Tl, V, and Zn. Results indicated that FGD gypsum application would not result in increased potentially toxic elements in plants, soil, or runoff. In addition, the application of FGD gypsum significantly reduced P, As, and Fe concentrations in runoff, indicating that FGD gypsum can reduce the negative impact of manure surface application on surface water degradation.
Generalized Multicell Switched-Inductor and Switched-Capacitor Z-Source Inverters (2012)

Traditional voltage-source inverter is limited by its only voltage step-down operation, while current-source inverter is limited by its only current step-down mode. In order to add an extra boosting flexibility while keeping the number of active semiconductors unchanged, voltage-type and current-type Z-source inverters were earlier proposed. These new classes of inverters are generally more robust and less sensitive to electromagnetic noises. However, their boosting capabilities are somehow compromised by high component stresses and poorer spectral performances caused by low modulation ratios. Their boosting gains are, therefore, limited in practice. To overcome these shortcomings, the generalized switched-inductor and switched-capacitor Z-source inverters are proposed, whose extra boosting abilities and other advantages have already been verified in simulation and experiment.