gebhart/patrepeval huggingface dataset:
Highly Selective Acetate Aldol Additions Using Mesityl-Substituted Chiral Auxiliaries (2006)

[reaction: see text] Highly diastereoselective acetate aldol additions using chlorotitanium enolates of mesityl-substituted N-acetyloxazolidinethione and N-acetylthiazolidinethione auxiliaries are reported. These additions proceed in high yields and diastereoselectivities (93:7 to 98:2) for aliphatic, aromatic, and ,-unsaturated aldehydes. Double diastereoselective acetate aldol additions are also reported and are found to proceed in high yields and diastereoselectivities (90:10 to 97:3).
Interferon gamma in cancer immunotherapy (2018)

Immune system can recognize self vs transformed self. That is why cancer immunotherapy achieves notable benefits in a wide variety of cancers. Recently, several papers reported that immune checkpoint blockade therapy led to upregulation of IFNγ and in turn clearance of tumor cells. In this review, we conducted an extensive literature search of recent 5-year studies about the roles of IFNγ signaling in both tumor immune surveillance and immune evasion. In addition to well-known functions, IFNγ signaling also induces tumor ischemia and homeostasis program, resulting in tumor clearance and tumor escape, respectively. The yin and the yang of IFNγ signaling are summarized. Thus, this review helps us to comprehensively understand the roles of IFNγ in tumor immunity, which contributes to better design and management of clinical immunotherapy approaches.
Detection of human papillomavirus-related squamous cell carcinoma cytologically and by in situ hybridization in fine-needle aspiration biopsies of cervical metastasis (2008)

NKSCC in metastatic cervical lymph nodes predicted positive HPV-ISH and was strongly suggestive of an oropharyngeal primary tumor.
Do Species and Nature Have Rights (1992)

an organism.Our deepest folly is the notion that we are in charge of the place, that we own it and can somehow run it.We are a living part of Earth's life, owned and operated by the Earth, probably specialized for functions on its behalf that we have not yet
Adipocytes Exhibit Abnormal Subcellular Distribution and Translocation of Vesicles Containing Glucose Transporter 4 and Insulin-Regulated Aminopeptidase in Type 2 Diabetes Mellitus: Implications Regarding Defects in Vesicle Trafficking (2001)

Insulin resistance in type 2 diabetes is due to impaired stimulation of the glucose transport system in muscle and fat. Different defects are operative in these two target tissues because glucose transporter 4 (GLUT 4) expression is normal in muscle but markedly reduced in fat. In muscle, GLUT 4 is redistributed to a dense membrane compartment, and insulin-mediated translocation to plasma membrane (PM) is impaired. Whether similar trafficking defects are operative in human fat is unknown. Therefore, we studied subcellular localization of GLUT4 and insulin-regulated aminopeptidase (IRAP; also referred to as vp165 or gp160), which is a constituent of GLUT4 vesicles and also translocates to PM in response to insulin. Subcutaneous fat was obtained from eight normoglycemic control subjects (body mass index, 29 +/- 2 kg/m2) and eight type 2 diabetic patients (body mass index, 30 +/- 1 kg/m2; fasting glucose, 14 +/- 1 mM). In adipocytes isolated from diabetics, the basal 3-O-methylglucose transport rate was decreased by 50% compared with controls (7.1 +/- 2.9 vs. 14.1 +/- 3.7 mmol/mm2 surface area/min), and there was no increase in response to maximal insulin (7.9 +/- 2.7 vs. 44.5 +/- 9.2 in controls). In membrane subfractions from controls, insulin led to a marked increase of IRAP in the PM from 0.103 +/- 0.04 to 1.00 +/- 0.33 relative units/mg protein, concomitant with an 18% decrease in low-density microsomes and no change in high-density microsomes (HDM). In type 2 diabetes, IRAP overall expression in adipocytes was similar to that in controls; however, two abnormalities were observed. First, in basal cells, IRAP was redistributed away from low-density microsomes, and more IRAP was recovered in HDM (1.2-fold) and PM (4.4-fold) from diabetics compared with controls. Second, IRAP recruitment to PM by maximal insulin was markedly impaired. GLUT4 was depleted in all membrane subfractions (43-67%) in diabetes, and there was no increase in PM GLUT4 in response to insulin. Type 2 diabetes did not affect the fractionation of marker enzymes. We conclude that in human adipocytes: 1) IRAP is expressed and translocates to PM in response to insulin; 2) GLUT4 depletion involves all membrane subfractions in type 2 diabetes, although cellular levels of IRAP are normal; and 3) in type 2 diabetes, IRAP accumulates in membrane vesicles cofractionating with HDM and PM under basal conditions, and insulin-mediated recruitment to PM is impaired. Therefore, in type 2 diabetes, adipocytes express defects in trafficking of GLUT4/IRAP-containing vesicles similar to those causing insulin resistance in skeletal muscle.
<title>Adaptive sampling for atomic force microscopy</title> (2006)

In atomic force microscopy, a 3-D image of a substrate is obtained. With the total number of samples remains constant, there is a trade-off between the size of the scanned image and the resolution. For the scanning mechanism, the time needed to image an area depends mainly on the number of samples and the size of the image. It is desirable to improve the imaging speed with limited impact to the effective resolution of the portion of the substrate that is of interested. To improve the imaging speed, there are two options: 1) increase the data process rate or 2) reduce the amount of data. One key issue for reducing the amount of data is to maintain acceptable image fidelity. To address this issue, we need to classify the sample area into regions based on importance. For high importance regions, a higher resolution is needed. For regions of less importance, a coarse sample density is employed. In this study, we propose a new adaptive sampling scheme that is leveraged from image compression. By adapting the sampling resolution to the substrate profile, the proposed method can decrease the scanning time by reducing the amount of data while maintaining the desired image fidelity.
May-Flies of Fall Creek (1911)

The following paper is a preliminary study of the ecology of the May-flies in the streams about Ithaca, N. Y., more especially in Fall Creek. In these, as in most fresh water streams, the nymphs of this order are abundant. In Fall Creek they are the dominant insects of the stream during the months of April, May and June, and by their fine adaptations to diverse environments they offer a satisfying :field of study to any brook traveler. The nymphs may be easily secured, but only imagoes exist in most collections, and these usually as dried distorted specimens whose life-histories are little known. The winged or aerial life lasts but a few days at most; the nymphal or aquatic life may extend over two or three years. The imago exhibits great specialization of parts concerned with reproduction and more striking atrophy of other parts than may be seen any where else among insects. Imagoes of all the groups are remarkably alike in superficial appearance. The nymphs, on the other hand, display a series of adaptations as diverse as their environments. Only by rearing specimens from nymphal to adult life may these two stages be linked together. Many of the life-histories of those species found in Eastern North America have been made known. It has been with the hope of adding to the number of these life-histories, as well as with the purpose of gaining more knowledge of the habits of those already known, that this study has been begun. The earlier American workers, Say, Hagen and Walsh* scarcely took up the rearing of nymphs but by their descriptive work they laid the foundation for the life-history studies which have followed. Berryt ’03 reared and described the nymphs of Habrophlebia americana Banks, (which nymph is not a Habrophlebia but a typical Leptophlebia), Blasturus cupidus Say, and Callibaetis ferruginea Walsh. A note on the nymphs of the genus Tricorythus was published by Cockerell and Gill ’06. The largest number of life-histories of Eastern North American forms has been written by Professor James G. Needham in Bulletins 47, 68, and 86 of the New York State Museum, and includes the following species: * Walsh, B. D. On the pupa of the Ephemerinous genus Baetisca Walsh Proceed. of the Ent. Soc. of Philadelphia. 1864. pp. 200-206. * Walsh, D. B. List of the Pseudoneuroptera of Illinois. Proceedings of the Natural Sciences of Philadelphia. 1862.
Bacteriocins as Potential Therapeutic Approaches in the Treatment of Various Cancers: A Review of In Vitro Studies (2022)

Cancer is regarded as one of the most common and leading causes of death. Despite the availability of conventional treatments against cancer cells, current treatments are not the optimal treatment for cancer as they possess the possibility of causing various unwanted side effects to the body. As a result, this prompts a search for an alternative treatment without exhibiting any additional side effects. One of the promising novel therapeutic candidates against cancer is an antimicrobial peptide produced by bacteria called bacteriocin. It is a non-toxic peptide that is reported to exhibit potency against cancer cell lines. Experimental studies have outlined the therapeutic potential of bacteriocin against various cancer cell lines. In this review article, the paper focuses on the various bacteriocins and their cytotoxic effects, mode of action and efficacies as therapeutic agents against various cancer cell lines.
Uptake, Retention, and Biotransformation of Corticosteroids in the Lung and Airways (2001)

Dr. Hochhaus: Your results are very exciting, demonstrating the need for further evaluating how regional deposition affects pulmonary selectivity. I would like to add that in addition to the these effects, other biopharmaceutical factors should also be considered. There has been a development towards solutionbased inhalation delivery systems. Despite higher deposition efﬁciency, these devices might be less beneﬁcial, as the pulmonary residence time of drug given as solution might be too short to induce distinct pulmonary selectivity. I will talk tommorrrow about some of these ﬁndings.
New active-gyrator circuit (1974)

Ideal passive gyrators can be made using two operational amplifiers, and it has been proved that they cannot be made with only one amplifier. However, this latter proof led to the discovery that an ideal active gyrator can be made with only one amplifier. A circuit for doing this is presented here, and its behaviour when used in an inductance-simulating mode is analysed.
An X-Ray Photoelectron Spectroscopic Study of Copper Chromite Catalysts (1979)

A series of copper chromite catalysts have been studied by x-ray photoelectron spectroscopy. The data indicate that in the as-received form the copper is present as a mixture of Cu(OH) 2 and CuO. After calcination at 500 °C only CuO is present. The chromium is present as Cr +3 and Cr +4 when no promoter is added. When a BaO promoter is added, the Cr +6 is stabilized. Calcination at 500°C for varying periods of time alter the relative amounts of Cr +3 and Cr +6 on the catalytic surface. In addition, the relative amounts of the various oxidation states are a function of calcination temperature. At a calcination temperature of 240°C a Cr +5 surface species is reproducibly observed in one of the catalysts.
Simulation on endurance characteristic of charge trapping memory (2013)

A comprehensive simulation method for endurance reliability issues in charge trapping memory is developed. For this purpose, a practical algorithm is carefully designed to investigate the cycling performance of charge trapping memory. The models that account for the generation of substrate/tunneling oxide interface trapped charge and oxide trapped charge are incorporated into the simulation. The influence of these models on flat-band voltage evolution under programing/erasing cycling is investigated in detail, thus providing insight into the mechanism of the endurance issues in charge trapping memory.
Mycoplasma fermentans simplifies our view of the catalytic core of ribonuclease P RNA. (1996)

The catalytic RNA moiety of (eu)bacterial RNase P is responsible for cleavage of the 5' leader sequence from precursor tRNAs. We report the sequence, the catalytic properties, and a phylogenetic-comparative structural analysis of the RNase P RNA from Mycoplasma fermentans, at 276 nt the smallest known RNase P RNA. This RNA is noteworthy in that it lacks a stem-loop structure (helix P12) that was thought previously to be universally present in bacterial RNase P RNAs. This finding suggests that helix P12 is not required for catalytic activity in vivo. In order to test this possibility in vitro, the kinetic properties of M. fermentans RNase P RNA and a mutant Escherichia coli RNase P RNA that was engineered to lack helix P12 were determined. These RNase P RNAs are catalytically active with efficiencies (Kcat/Km) comparable to that of native E. coli RNase P RNA. These results show that helix P12 is dispensable in vivo in some organisms, and therefore is unlikely to be essential for the mechanism of RNase P action. The notion that all phylogenetically volatile structures in RNase P RNA are dispensable for the catalytic mechanism was tested. A synthetic RNA representing the phylogenetic minimum RNase P RNA was constructed by deleting all evolutionarily variable structures from the M. fermentans RNA. This simplified RNA (Micro P RNA) was catalytically active in vitro with approximately 600-fold decrease in catalytic efficiency relative to the native RNA.
Comparative molecular similarity indices analyses (CoMSIA) and hologram quantitative structure activity relationship (HQSAR) on the fungicial activity of 2-N-benzyl-5-phenoxy-3-isothiazolone derivatives against phytophthora blight fungus (2002)

Two different QSAR methods, the comparative molecular similarity indices analyses (CoMSIA) and hologram quantitative structure activity relationship (HQSAR) are studied for the fungicidal activities () of 2-N-benzyl-5-phenoxy-3-isothiazolone derivatives against sensitive (SPC: 95CC7105) and resisitive (RPC: 95CC7303) phytophthora blight fungus (Phytaphthora capsici). According to the findings from these QSAR investigation, the cross-validation value, and Pearson correlation coefficient, in the two methods were CoMSIA: RPC; , SPC; and HQSAR: RPC; , SPC; , respectively. Therefore, the two models of comparative statistical significance were obtained. From the CoMSIA contour maps, the important factors for selective fungicidal activity against RPC are to be expected that the lower hydrophobic and not bulkiness substituent as hydrogen bonding acceptor have to introduce to meta and para-position (C1-C6) on the phenoxy moiety. And the results of prediction suggest that HQSAR method showed higher fungicidal activity than CoMSIA method.
Effect of MDV3100, a novel androgen receptor signaling inhibitor, on cell proliferation and tumor size in an apocrine breast cancer xenograft model. (2012)

3072 Background: MDV3100, a new androgen receptor (AR) signaling inhibitor, has demonstrated therapeutic effects in men with post-docetaxel prostate cancer (AFFIRM). AR is also expressed in the majority of breast cancers. Molecular profiling of estrogen receptor negative (ER-) breast cancer classifies this disease into basal and molecular apocrine subtypes. Apocrine breast cancer represents ~50% of ER- tumors and is characterized by a steroid response gene signature that includes AR expression. Here we report the effects of MDV3100 on the growth of the ER-/AR+ breast cancer cell line MDA-MB-453 in tissue culture and in an in vivo xenograft mouse model. Methods: MDA-MB-453 cells were maintained in 5% complete or 5% charcoal-stripped serum supplemented with dihydrotestosterone (CSS-DHT). The DHT induced nuclear translocation of AR was determined by subcellular fractionation followed by western blot. AR target gene expression was measured by qPCR. To generate a mouse xenograft model, 5-6 wk old female NOD-SCID-IL2Rgc–/– mice were injected ortotopically with 6x10 6 MDA-MB-453 cells into the fourth inguinal gland and were administered exogenous DHT (12.5 mg in a 60 day release pellet) or control pellets. When tumor size reached 100 mm 3 , mice were treated with 10 mg/kg/day MDV3100 or vehicle (0.5% methocel solution) by oral gavage for 33 days. Results: Viability of MDA-MB-453 cells treated with 10 uM MDV3100 was reduced by 10% after 3 days and 27% after 6 days. Treatment with 25 uM MDV3100 reduced cell viability by 27% after 3 days and 36% after 6 days. Similar results were obtained when cells maintained in CSS-DHT were treated with MDV3100. Treatment with MDV3100 blocked DHT-induced nuclear translocation and concordantly reduced the expression of AR-targets fatty acid synthase, prolactin receptor, and gross cystic disease protein-15. In the xenograft model, MDV3100 inhibited tumor growth by 78% as compared to tumors treated with vehicle. Conclusions: MDV3100 reduced cell proliferation in apocrine cell lines. MDV3100 also suppressed exogenous DHT-induced growth of ER-/AR+ tumors in vivo. These results support the evaluation of MDV3100 as a treatment for apocrine tumors.
Key management and link-layer security of wireless sensor networks : energy-efficient attack and defense (2005)

The relentless miniaturization of computers and advances in radio-based communications have given rise to a new exciting technology: wireless sensor networks (WSNs). A WSN is a network consisting of numerous small, low-cost, independent sensor nodes that communicate through wireless means. These sensor nodes are self-contained units composed primarily of a microcontroller, a radio, a battery, one or more sensors and some interconnecting circuits. As such, the sensor nodes have limited computing power and energy supply, and instead of performance, they are frequently operated with energy efficiency in mind. Sensor nodes are meant to be deployed without a pre-configured topology and operated unattended, but radio communications enable them to organize themselves. When data are available through their sensors, radio communications allow the data to be distributed across the network. For monitoring-type applications, e.g. monitoring of natural habitats, this presents unprecedented sensing scale and resolution. For other types of applications, at the same time providing a transparent interface between human activities and the surroundings, WSNs integrate seamlessly with the environment. As with other technologies, WSN is not without its perils. When data are circulated in an unattended network, they might be leaked against the interests of the concerned parties. Operation-wise, there should be some means to ensure the availability of the service provided by the network, as well as a way to discriminate between legal and malicious requests to avoid executing tasks that might be disruptive to the network itself. This is where security comes in. These problems are largely categorized as information security and security against denial-of-service (DoS) attacks, and they are the foci of this thesis. The common thread that permeates through these two areas is energy efficiency. While security can be gained by tamper-proofing the hardware, increasing the computational power of the sensor nodes and so on, practical WSN security is a balancing act that is constantly in search of the highest level of protection that can be squeezed out of the judicious use of limited resources. The thesis is divided into two parts. The first part of the thesis concerns defense-oriented issues: design, implementation and key management. The second part of the thesis looks at attack-oriented issues: link-layer jamming attacks.
Discovery of a 29-Amino-Acid Reactive Abiotic Peptide for Selective Cysteine Arylation (2017)

The regio- and chemoselective modification of proteins or peptides with chemical reagents is often challenging. One approach to overcome this problem involves identifying abiotic polypeptide sequences that react with specific small molecules. Toward this goal, we profiled ∼5 × 10<sup>13</sup> randomized 30-mer peptides using mRNA display and high-throughput sequencing in search of polypeptides that can undergo cysteine arylation with a water-soluble perfluoroarene. Within this vast chemical space, we discovered a cysteine-containing sequence with a second-order rate constant of 0.29 M<sup>-1</sup> s<sup>-1</sup> for arylation. An N- and C-terminal truncation reduced the reaction rate, as did the addition of denaturants. When the reactive peptide was covalently fused to the enzyme Sortase A, we observed regiospecific arylation at a single cysteine site, leaving the enzyme's active site cysteine unchanged. Taken together, these results demonstrate that long polypeptides of defined sequence, when matched with the appropriate reactive group, can be used for selective arylation of cysteine in water.
Effects of Nitrogen Supplements on Degradation of Aspen Wood Lignin and Carbohydrate Components by <i>Phanerochaete chrysosporium</i> (1983)

A supplement of KH(2)PO(4), MgSO(4), CaCl(2), trace elements, and thiamine accelerated the initial rate of aspen wood decay by Phanerochaete chrysosporium but did not increase the extent of lignin degradation. Asparagine, casein hydrolysate, and urea supplements (1% added N) strongly inhibited lignin degradation and weight loss. The complex nitrogen sources peptone and yeast extract stimulated lignin degradation and weight loss. Albumen and NH(4)Cl had intermediate effects. Conversion of [C]lignin to CO(2) and water-soluble materials underestimated lignin degradation in the presence of the complex N sources. The highest ratio of lignin degradation to total weight loss and the largest increase in cellulase digestibility occurred during the decay of unsupplemented wood. Rotting of aspen wood by P. chrysosporium gives smaller digestibility increases than have been found with some other white-rot fungi.
Novel delayed pulse techniques for stimulated Raman scattering (1993)

The outputs of two independent, incoherent lasers are spatially overlapped in a Raman-active medium. When the probes are separated in time, the stimulated Raman scattering (SRS) efficiency of the delayed pulse is increased from 14 to 27%. This occurs because of the presence of the decaying coherent excitation induced by the SRS of the first pulse. The influence of saturable losses is removed by prepulsing the medium before applying the pulse pair. The temporal evolution of the enhancement and phase-matching conditions are investigated. Surprisingly, the pulses interact only when they are separated in time, with the enhancement vanishing when they are temporally overlapped. The outputs of several independent lasers may be combined to generate significantly higher SRS efficiencies, without increasing the pump intensity incident on the medium. The technique provides a means for recovering efficient SRS in the transient (short-pulse) regime.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>