gebhart/patrepeval huggingface dataset:
Staphylococcal Enterotoxins B and C (1997)

Abstract The staphylococcal enterotoxins (SEs) are a subgroup of related protein exotoxins in the pyrogenic toxin (PT) family produced by Staphylococcus aureus and Streptococcus pyogenes (1). Like other members of the PT family, the SEs are superantigens and elaborate a set of biological activities linked to their ability to stimulate cells of the immune system (2). These activities contribute to their ability to induce toxic shock syndrome, immunosuppression, and probably other diseases (3). However, as is evident from the fact that they are designated as enterotoxins, the SEs are distinguishable from other members of the PT family by their ability to induce gastroenteritis when ingested. Hence, they are the causative agents in staphylococcal food poisoning (SFP), a very common form of food-associated gastroenteritis in the United States and worldwide (4).
Imaging of Neuronal Activity in Awake Mice by Measurements of Flavoprotein Autofluorescence Corrected for Cerebral Blood Flow (2018)

Green fluorescence imaging (e.g., flavoprotein autofluorescence imaging, FAI) can be used to measure neuronal activity and oxygen metabolism in living brains without expressing fluorescence proteins. It is useful for understanding the mechanism of various brain functions and their abnormalities in age-related brain diseases. However, hemoglobin in cerebral blood vessels absorbs green fluorescence, hampering accurate assessments of brain function in animal models with cerebral blood vessel dysfunctions and subsequent cerebral blood flow (CBF) alterations. In the present study, we developed a new method to correct FAI signals for hemoglobin-dependent green fluorescence reductions by simultaneous measurements of green fluorescence and intrinsic optical signals. Intrinsic optical imaging enabled evaluations of light absorption and scatters by hemoglobin, which could then be applied to corrections of green fluorescence intensities. Using this method, enhanced flavoprotein autofluorescence by sensory stimuli was successfully detected in the brains of awake mice, despite increases of CBF, and hemoglobin interference. Moreover, flavoprotein autofluorescence could be properly quantified in a resting state and during sensory stimulation by a CO<sub>2</sub> inhalation challenge, which modified vascular responses without overtly affecting neuronal activities. The flavoprotein autofluorescence signal data obtained here were in good agreement with the previous findings from a condition with drug-induced blockade of cerebral vasodilation, justifying the current assaying methodology. Application of this technology to studies on animal models of brain diseases with possible changes of CBF, including age-related neurological disorders, would provide better understanding of the mechanisms of neurovascular coupling in pathological circumstances.
Immunity to Murine Sarcoma Virus-Induced Tumors (1974)

Abstract Experiments have been performed to examine the immune status in animals carrying tumors which are in their progressive phase of growth. Unfractionated spleen or lymph node cells of BALB/c mice, inoculated 10 to 14 days previously with murine sarcoma virus (MSV), have no demonstrable immunity in vitro to MSV-viral antigens. On fractionation of the spleen cells from such animals, however, large and small cells can be detected which react in well defined assays for immunity in this system. A cell population of intermediate size is capable of suppressing this activity. Treatment of the suppressing cell population with anti-θ or anti-immunoglobulin antiserum has provided data to suggest that the suppression is caused by a cell with immunoglobulin moieties on its surface. Moreover, evidence is presented to show that this suppression is nonspecific, in that the induction of protein synthesis in thymus-associated (T) cells in response to the mitogen phytohemagglutinin (PHA) is also suppressed by a cell with the above characteristics. The significance of these findings in relation to the status of growth of the tumor in the host is discussed.
File transfer system by a hidden ID signaling using camera in smart devices: Easy file sharing between computers and smart devices (2016)

A technique has been developed that allows a smart device to capture a video of a computer screen with its built-in camera and then, using a hidden ID signaling, automatically download the file shown onscreen. The computer displays communication metadata necessary to send a file to a smart device (e.g. the computer's IP address) as a series of color transitions that are nearly imperceptible to humans. The smart device uses a proprietary camera application to capture a video of the computer's screen and read this communication metadata, with which it then accesses the computer and downloads a file. This system implements a simple interface for transferring files between computers and smart devices, a task that has suffered from usability issues for years. In this paper, the system that have been developed and evaluated for its applicability in practical use case is described.
Surface states at unrelaxed ZnO(1010) (1980)

The electronic structure of an ideal ZnO(101̄0) surface has been studied using a tight-binding approach, with the surface modeled in a semi-infinite geometry. It is found that the surface states follow the band edge very closely due to the ionic character of the surface. Moreover, the close spacing between Zn 3d and O 2p levels produces a small but not negligible amount of d character in the surface states.
ChemInform Abstract: Pheromone Synthesis. Part 165. A New Synthesis of (3S,7R,8E,10E)‐3,7,9‐ Trimethyl‐8,10‐dodecadien‐6‐one, the Major Component of the Sex Pheromone of the Maritime Pine Scale. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cynanchum atratum Ameliorates Airway Inflammation via Maintaining Alveolar Barrier and Regulating Mast Cell-Mediated Inflammatory Responses (2019)

Asthma is a common allergic airway inflammatory disease, characterized by abnormal breathing due to bronchial inflammation. Asthma aggravates the patient's quality of life and needs continuous pharmacological treatment. Therefore, discovery of drugs for the treatment of asthma is an important area of human health. The aim of the present study was to evaluate whether <i>Cynanchum atratum</i> extract (CAE) modulates the asthma-like allergic airway inflammation and to study its possible mechanism of action using ovalbumin (OVA)-induced airway inflammation and lipopolysaccharide (LPS)-induced acute lung injury (ALI) in mice, as well as a mast cell-based <i>in vitro</i> model. The histological analysis showed that CAE reduced the airway constriction and immune cell infiltration. CAE also inhibited release of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>β</mml:mi></mml:math>-hexosaminidase and expression of inflammatory cytokines such as tumor necrosis factor (TNF)-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>α</mml:mi></mml:math>, interleukin (IL)-4, and IL-5 in bronchoalveolar lavage fluid and lung tissues. In addition, CAE reduced the OVA-specific immunoglobulin (Ig) E, total IgE, IgG1, and IgG2a levels in the serum. In the LPS-induced ALI model, CAE suppressed the LPS-induced lung barrier dysfunction and the release of proinflammatory cytokines. Because allergic airway inflammatory responses are associated with the activation of mast cells, RBL-2H3 cells were used to evaluate the underlying mechanism of CAE effects. In RBL-2H3 cells, CAE down-regulated release of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>β</mml:mi></mml:math>-hexosaminidase and histamine by reducing the intracellular calcium influx. In addition, CAE suppressed the expression of proinflammatory cytokines by inhibiting nuclear translocation of nuclear factor-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>κ</mml:mi></mml:math>B. Taken together, our findings suggest that CAE may help in the prevention or treatment of airway inflammatory diseases.
The Approximate Capacity of Half-Duplex Line Networks (2020)

This paper investigates the problem of characterizing the capacity of Half-Duplex (HD) line networks, where a source node communicates to a destination node through a multihop path of N relays. If the relays operate in Full-Duplex (FD), it is well known that the capacity of the line network equals the minimum among the point-to-point link capacities in the path. In contrast, this paper considers a different case where the relays operate in HD. In the first part of the paper, it is shown that the approximate capacity (optimal up to a constant additive gap that only depends on the number of nodes in the network) of an HD N-relay line network equals half the minimum of the harmonic means of the point-to-point link capacities of each two consecutive links in the path. It is then proved that the N +1 listen/transmit states (out of the 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sup> possible ones) sufficient to characterize the approximate capacity can be found in linear time. In the second part of the paper, it is shown that the problem of finding the path that has the largest HD approximate capacity in a network that can be represented as a graph is NP-hard. However, if the number of cycles in the network is polynomial in the number of nodes, then a polynomial-time algorithm can indeed be designed.
Analysis and Prediction of Helix Shift Errors in Homology Modeling (2006)

High sequence identity between two proteins (e.g. > 60%) is a strong evidence for high structural similarity. However, internal shifts in one of the two proteins can sometimes give rise to unexpectedly high structural differences. This, in turn, causes unreliable structure predictions when two such proteins are used in homology modeling. Here, we perform a computational analysis of helix shifts and we show that their occurrence can be predicted with statistical learning methods. Our results indicate that helix shifts increase the RMS error by factor 2.6 compared to those protein pairs without a helix shift. Although helix shifts are rare (1.6% of helices and a commensurately higher number of proteins are affected), they therefore pose a significant problem for reliable structure prediction systems. In this paper, we prototype a new approach for model quality assessment and demonstrate that it can successfully warn against helix shifts. A support vector machine trained on a wide range of sequence and structure properties predicts the occurrence of helix shifts with a sensitivity of 74.2% and a specificity of 83.6%. On an equalized test dataset, this corresponds to an accuracy of 78.9%. Projected to the full dataset, it translates to an accuracy of 83.4%. Our analysis shows that helix shift detection is a valuable building block for highly reliable structure prediction systems. Furthermore, the statistical learning based approach to helix shift detection that we employ here is orthogonal to well-established model quality assessment methods (which use geometric constraint checking or mean force potentials). Therefore, a further increase of prediction accuracy is expected from the combination of these methods.
Application of electrical treatments in alcoholic solvent for polyphenols extraction from grape seeds (2011)

The polyphenols extraction from grape seeds was studied. In order to increase the polyphenols yield and the extraction kinetics, three different pre-treatments were applied on grape seeds: pulsed electric fields (PEF) (8–20 kV/cm, 0–20 ms), high-voltage electrical discharges (HVED) (10 kA/40 kV, 1 ms) and grinding (180 W, 40 s). These electrical treatments can damage cell membranes (PEF/HVED) and cell walls (HVED) thus accelerating the compounds extraction but have different effects on the product fragmentation. The diffusion was then performed after pre-treatment with a mixture of water and ethanol. The PEF efficiency was improved when the treatment was performed at 50 °C in the presence of ethanol. PEF-assisted diffusion was then compared to HVED-assisted diffusion and to diffusion of ground grape seeds. These two pre-treatments increased both the extraction kinetics and the maximum polyphenols yield. For both cases, the final polyphenols content was 9 g GAE/100 g DM after 15 min of extraction with grinding and after 60 min with HVED. When PEF were applied in a suspension containing ethanol, the maximum polyphenols yield was also reached after 60 min. The subsequent solid–liquid separation was faster with PEF as compared to ground and HVED-treatments.
ChemInform Abstract: A PARTIAL HOMO‐FAVORSKII REARRANGEMENT IN THE DITERPENE SERIES (1983)

Abstract Aus (Ia) erhält man über die Zwischenstufen (Ib)‐(Ie) sowie (II) das Cyclobutanon (III), das durch Kieselgel in das Isomere (IV) umlagert wird.
Cedrol, a Sesquiterpene Isolated from Juniperus chinensis, Inhibits Human Colorectal Tumor Growth associated through Downregulation of Minichromosome Maintenance Proteins (2022)

Cedrol, a sesquiterpene alcohol, isolated from <i>Juniperus chinensis</i> has been reported to inhibit minichromosome maintenance (MCM) proteins as cancer biomarkers in human lung cancer in vitro. In the present study, we investigated the anti-cancer activity of cedrol in vitro and in vivo using human colorectal cancer HT29 cells and a human colorectal tumor xenograft model. Cedrol inhibited MCM protein expression and cell growth in HT29 cells, which are associated with G1 arrest and the induction of apoptosis. We demonstrated that cedrol effectively reduced HT29 tumor growth without apparent weight loss in a human tumor xenograft model. Compared with vehicle- and adriamycin-treated tumor tissues, cedrol induced changes in the tumor tissue structure, resulting in a reduced cell density within the tumor parenchyma and reduced vascularization. Moreover, the expression of MCM7, an important subunit of MCM helicase, was significantly suppressed by cedrol in tumor tissue. Collectively, these results suggest that cedrol may act as a potential anti-cancer agent for colorectal cancer by inhibiting MCM protein expression and tumor growth.
Pulvinatal, a Novel Bioactive Metabolite from the Basidiomycete Nidularia pulvinata (Schw.) Fr. (1997)

Pulvinatal (1) was isolated from fermentations of Nidularia pulvinata as an inducer of differentiation of HL-60 promyelocytic leukemia cells. Its structure was elucidated by spectroscopic methods. In addition, N. pulvinata was found to produce 2,4,5-trihydroxy-6-methyl-benzenecarbaldehyde (2) and orsellinic acid (3). Pulvinatal exhibits weak antifungal and only marginal cytotoxic activities.
New Lightweight Cement Formulation for Shallow Oil and Gas Wells (2020)

The use of lightweight pozzolanic aggregates as partial replacement of cement results in low-density cement systems. Such systems ensure effective zonal isolation in zones where low equivalent circulating densities are required. However, low pozzolanic materials, such as fly ash and ground granulated blast furnace slag (GGBFS), have poor early-age strength development and long set times, especially when used in high volume, that is, exceeding 50% by weight of cement. The objective of this study is to develop a lightweight oil- and gas-well cement recipe with enhanced properties employing the synergism that exist among fly ash, GGBFS, and silica fume. The experimental work was per laboratory procedure outlined by American Petroleum Institute. Portland class G cement and the aluminosilicate materials were admixed in water to form a 13.5 ppg slurry. Chemical admixtures were used to facilitate the dissolution of reactive components in the pozzolanic materials and the hydration process. The experimental investigations were done at 150 <sup>°</sup>F and an ambient pressure of 1500 psi. The newly developed lightweight recipe exhibited excellent rheological and mechanical properties, having a wait-on-cement time for about 4 h and a 24 h sonic strength of 3116 psi, at 150 <sup>°</sup>F and 1500 psi. The thickening time was approximately 4 h (70 Bc). This slurry will be ideal in zones that would require a low hydrostatic slurry column and rapid gel strength development.
Torque-Controlled Lightweight Arms and Articulated Hands: Do We Reach Technological Limits Now? (2004)

In this paper we briefly address DLR’s (German Aerospace Center) background in space robotics by hand of corresponding milestone projects including systems on the International Space Station. We then discuss the key technologies needed for the development of an artificial “robonaut” generation with mechatronic ultra-lightweight arms and multifingered hands. The third arm generation is nearly finished now, approaching the limits of what is technologically achievable today with respect to light weight and power losses. In a similar way DLR’s second generation of artificial four-fingered hands was a big step towards higher reliability, manipulability and overall performance.
Metal-organic-supramolecular polymers based on halogen bonding: unprecedented polymers with tunable properties (2010)

The role of halogen bonding (XB) in metal-containing crystal structures has been recently reviewed and the focus was on the wide variety of metal-ligand moieties that exhibit propensity to form XB thus inducing designed structural, conductive and magnetic properties [1,2]. Halogen bonding (XB) is any D•••X-Y interaction wherein X is an electrophilic halogen atom (Lewis acid, halogen bonding donor), D is an electron density donor (Lewis base, halogen bonding acceptor) and Y is C, N, halogen, etc. [3]. If a metal bears ligands suitable to behave as donor site the interaction with XB acceptor, a network in a supramolecular architecture originates. Despite the virtually unlimited opportunities this type of flexible metal-ligand adducts opens to crystal engineering, few such systems have been reported in the literature.
Addendum to Food Additives and Contaminants 2002, 19, 492-501 Migration of monomers from liquid crystalline poly(p -hydroxybenzoic acid-co-2-hydroxy-6-naphthoic acid) (2003)

Liquid-crystalline co-polyesters (e.g. a random copolyester based on p-hydroxybenzoic acid (HBA) and 2-hydroxy-6-naphthoic acid (HNA) known as Vectra A950) offer good barrier properties, but for food-contact use they require overall and specific migration testing. For Vectra A950 films, the highest overall migration level obtained was 2.3 mg x dm(-2) (13.8 mg x kg(-1)) in olive oil (10 days at 40 degrees C), well below the EC limit of 10 mg dm(-2) (60 mg x kg(-1)). The highest specific migration of HBA was 15.2 microg x dm(-2) (91.2 microg x kg(-1)) in olive oil (2 h at 175 degrees C). In this case, the migration level was well below the EC limit of 10 mg dm(-2) (60 mg x kg(-1)). For HNA, the highest value obtained was 4.3 microg x dm(-2) (26 microg x kg(-1)) in 10% ethanol (4 h at 100 degrees C), well below the specific migration limit (SML = 50 microg x kg(-1)). The results obtained shows that even at these severe conditions, the migration values comply with the new European Union Directive 2002/72/EC, which regulates plastic materials and articles for food contact use. In addition, the polymer Vectra A950 complies with Food Contact Notification (FCN) No. 103 of the United States Food and Drug Administration (FDA). Vectra A950 is therefore permitted for food-contact use both in the European Union and the USA.
Abstract 1798: Effective lymphoma and leukemia therapy with epratuzumab (anti-CD22 IgG) conjugated to SN-38 (Emab-SN-38), with enhanced activity in combination with veltuzumab (anti-CD20 IgG) (2011)

Abstract A number of B-cell malignancies, including lymphomas (NHL) and leukemia (ALL), can be treated effectively with antibodies, but these usually are combined with chemotherapy to enhance efficacy. We conjugated SN-38, a topoisomerase I inhibitor with nanomolar potency, to an anti-CD22 IgG (6:1 SN-38:IgG) by coupling to the tert-hydroxy group on the lactone ring of SN-38. This inhibits formation of the inactive carboxylate, a common problem with irinotecan, its prodrug, but the linker allows the active SN-38 to be released slowly from the IgG (∼50% decouples every 1 to 1.5 days) in serum or in the acidic environment of the lysosome. In vitro, Emab-SN-38 had nanomolar potency against a number of human NHL and ALL cell lines. Specific (as compared to an irrelevant anti-CEACAM5-SN-38 conjugate) and enhanced anti-tumor activity were demonstrated in mice bearing Ramos (Burkitt NHL), WSU-FSCCL (follicular NHL), or 697 (ALL) when compared to the unconjugated antibody (anti-CD22 or anti-CD20) alone or when combined with irinotecan. For example, animals bearing 0.3 to 0.8 cm3 Ramos xenografts treated with 3.75 mg/kg of an irrelevant immunoconjugate (54.5 µg/kg SN-38 equivalents) progressed to 3.0 cm3 in 1.0 week (median), while Emab-SN-38-treated animals had a median time to progression (TTP) of 4.05 weeks (P = 0.003) and 3/10 cures. Increasing the Emab-SN-38 dose to 12.5 mg/kg improved TTP to &amp;gt;12 weeks with 7/10 cures, while the irrelevant conjugate's TTP was just 3.5 wk (P = 0.023). Improvements in TTP and cures were also found for the Emab-SN-38 in FSCCL and 697. Additionally, in Ramos and FSCCL, the anti-tumor response was enhanced by co-treating animals with veltuzumab. For example, median survival in animals treated 5 days after IV implantation of FSCCL was &amp;gt;161 days for Emab-SN-38 + veltuzumab vs. 63 days and 91 days for Emab-SN-38 alone and veltuzumab alone, respectively (untreated, 42 days). Importantly, these treatments were tolerated without toxicity, with other studies showing tolerability in mice at doses of 1500 mg/kg. These data suggest the Emab-SN-38 is a potent, minimally toxic therapeutic in both NHL and ALL, with the added value when combined with anti-CD20 antibody therapy for enhanced responses. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1798. doi:10.1158/1538-7445.AM2011-1798
Anton 3 (2021)

Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution over its predecessor, Anton 2 (the current state of the art), and is over 100-fold faster than any other currently available supercomputer, thereby enabling broad new avenues of research on critical questions in biology and drug discovery. This speedup means that a 512-node Anton 3 simulates a million atoms at over 100 microseconds per day. Furthermore, Anton 3 attains this performance while consuming an order of magnitude less energy per simulated microsecond than any other machine. Like its predecessors, Anton 3 was designed from the ground up around a new custom chip to best exploit the capabilities offered by new technologies. We present here the main architectural and algorithmic developments that were necessary to achieve such significant advances.