gebhart/patrepeval huggingface dataset:
Bulk-solvent correction in large macromolecular structures (2005)

The estimation of the bulk-solvent contribution to the diffraction of a macromolecular crystal makes use of a solvent mask which delimits the bulk-solvent regions in the crystal. It is shown that the way this mask is usually defined in CNS contains a bias which can lead to absurd results in the case of very large structures, where the calculations can only be made on relatively coarse grids. A modified procedure is described and applied to 70S ribosome data at 5.5 A resolution. The B factor affecting the bulk solvent is also discussed. Even in this case of very high and widely variable atomic B factors, it seems sufficient to consider a constant and isotropic B factor for the bulk solvent. This is initially set to the average value of the atomic B factor, but can be refined.
Synthesis and Photochemical Properties of pH Responsive Tris-Cyclometalated Iridium(III) Complexes That Contain a Pyridine Ring on the 2-Phenylpyridine Ligand (2013)

In our previous publication, it was reported that fac-Ir(atpy)3 3 (atpy = 2-(5'-amino-4'-tolyl)pyridine), which contains three amino groups at the 5'-position of the atpy ligands, exhibits a pH-dependent change in the color of the emitted radiation. Aqueous solution of 3 shows a weak red emission (at around 613 nm) under neutral or basic conditions, but the emission color changes to green (at around 530 nm) under acidic conditions, where the NH2 group is protonated to become an electron-withdrawing (NH3)(+) group. In this manuscript, we report on the preparation of some new pH-responsive Ir(III) complexes; fac-Ir(4Pyppy)3 5 and fac-Ir(3Pyppy)3 6 that contain three pyridyl groups at the 5'-position of the 2-phenylpyridine (ppy) ligand, and Ir(4Pyppym)3 7 and Ir(3Pyppym)3 8 that contain a pyridyl group at the same position of the 2-phenylpyrimidine (ppym) ligand. The introduction of three pyridyl groups on iodinated Ir(ppy)3 and Ir(ppym)3 was achieved via Suzuki-Miyaura cross-coupling reaction assisted by microwave irradiation. Solutions of the acid-free Ir(III) complexes 5, 6, 7, and 8 showed a strong green emission (at around 500 nm) in dimethylsulfoxide (DMSO). Protonation of three pyridyl groups of 5 and 7 causes a significant red-shift in the emission wavelength (at around 600 nm) with a decrease in emission intensity. The pH-dependent emission change of these complexes is also discussed. The generation of singlet oxygen ((1)O2) by the photoirradiation of the Ir complexes 5 and 6 was evidenced by the decomposition of 1,3-diphenylisobenzofuran (DPBF), the oxidation of thioanisole, and the oxidation of 2,2,5,5-tetramethyl-3-pyrroline-3-carboxamide (TPC). The induction of necrosis-like cell death of HeLa-S3 cells upon photoirradiation of 5 at 465 nm is also reported.
Hydroxyapatite coating improves fixation of pedicle screws (2002)

We investigated the effects of hydroxyapatite (HA) coating on the purchase of pedicle screws. A total of 23 consecutive patients undergoing lumbar fusion was randomly assigned to one of three treatment groups. The first received uncoated stainless-steel screws, the second screws which were partly coated with HA, and the third screws which were fully coated. The insertion torque was recorded. After 11 to 16 months, 21 screws had been extracted. The extraction torque was recorded. Radiographs were taken to assess fusion and to detect loosening of the screws. At removal, the extraction torques exceeded the upper limit of the torque wrench (600 Ncm) for many HA-coated screws. The calculated mean extraction torque was 29 ± 36 Ncm for the uncoated group, 447 ± 114 Ncm for the partly-coated group and 574 ± 52 Ncm for the fully-coated group. There were significant differences between all three groups (p < 0.001). There were more radiolucent zones surrounding the uncoated screws than the HA-coated screws (p < 0.001). HA coating of pedicle screws resulted in improved fixation with reduced risk of loosening of the screws.
Effects of<i>Silybum marianum</i>on serum hepatitis C virus RNA, alanine aminotransferase levels and well‐being in patients with chronic hepatitis C (2006)

S. marianum is well tolerated in subjects with CHC, but does significantly affect serum HCV RNA, alanine aminotransferase levels, quality of life or psychological well-being in subjects with this condition.
Profiling of Substrates for Zinc‐dependent Lysine Deacylase Enzymes: HDAC3 Exhibits Decrotonylase Activity In Vitro (2012)

Systematic screening of the activities of the eleven human zinc-dependent lysine deacylases against a series of fluorogenic substrates as well as kinetic evaluation revealed substrates for screenings of histone deacetylases HDAC10 and HDAC11 at reasonably low enzyme concentrations. Furthermore, HDAC3 in complex with nuclear receptor corepressor 1 (HDAC3-NCoR1) was shown to harbor decrotonylase activity in vitro.
Pert as an Aid to Logic Design (1966)

A new application is presented for pert, the well-known statistical project-scheduling method. Using PERT, the logic designer could circumvent usually unrealistic worst-case criteria. He substitutes a formalized statistical method which determines (1) expected or most probable delays, (2) critical timing paths, (3) timing slack allowable between various inputs, and (4) probability of achieving an output by a certain time. From these data the designer can make a meaningful judgment regarding the reliability of his system. Significantly, he may achieve high reliability without being forced to resort to worst-case design.
Hematopoietic rescue via T-cell-dependent, endogenous granulocyte-macrophage colony-stimulating factor induced by the pineal neurohormone melatonin in tumor-bearing mice. (1994)

We investigated whether melatonin can affect tumor growth and/or hematopoiesis in mice transplanted with Lewis lung carcinoma and treated with cyclophosphamide or etoposide. These agents were injected i.p. for 5 days at two different cumulative doses (cyclophosphamide, 40 and 160 mg/kg body weight; etoposide, 20 and 40 mg/kg body weight) from day 8 through day 12 after tumor transplantation. Melatonin was injected s.c. at a dose of 1 mg/kg body weight/day, from day 8 throughout the experiments and from days 8 through 12 or from day 13 onwards. Melatonin did not influence tumor growth but selectively counteracted bone marrow toxicity when administered together with the cancer chemotherapy compounds without interfering with their anticancer action. In vitro, melatonin proved to counteract apoptosis in bone marrow cells incubated with etoposide. Such protection was reflected by an increased frequency of granulocyte/macrophage-colony forming units but not of the pluripotent spleen-colony forming units. The effect of melatonin was neutralized by anti-granulocyte/macrophage-colony-stimulating factor monoclonal antibodies. When athymic, T-cell-deficient mice were used as bone marrow donors, melatonin did not exert any protective effect. This suggested that melatonin is able to stimulate the endogenous production of granulocyte/macrophage-colony-stimulating factor via bone marrow T-cells. Due to the well known lack of toxic and undesirable side effects of melatonin, these findings might have a straightforward clinical application.
Measurements, analysis, and modeling of BitTorrent-like systems (2005)

Existing studies on BitTorrent systems are single-torrent based, while more than 85% of all peers participate in multiple torrents according to our trace analysis.In addition, these studies are not sufficiently insightful and accurate even for single-torrent models, due to some unrealistic assumptions.Our analysis of representative Bit-Torrent traffic provides several new findings regarding the limitations of BitTorrent systems: (1) Due to the exponentially decreasing peer arrival rate in reality, service availability in such systems becomes poor quickly, after which it is difficult for the file to be located and downloaded.(2) Client performance in the BitTorrentlike systems is unstable, and fluctuates widely with the peer population.(3) Existing systems could provide unfair services to peers, where peers with high downloading speed tend to download more and upload less.In this paper, we study these limitations on torrent evolution in realistic environments.Motivated by the analysis and modeling results, we further build a graph based multi-torrent model to study inter-torrent collaboration.Our model quantitatively provides strong motivation for inter-torrent collaboration instead of directly stimulating seeds to stay longer.We also discuss a system design to show the feasibility of multi-torrent collaboration.
Real-time quantification of wild-type contaminants in glyphosate tolerant soybean (2009)

In principle this approach could be successfully applied to any transgenic event, provided that the wild-type sequence is conserved and single copy. The main advantages of the assay here described derive from its applicability to bulk samples, which would allow to increase the number of single seeds or plants forming the analytical sample, thus improving accuracy and throughput while containing costs. For these reasons this application of quantitative PCR could represent a useful tool in agricultural biotechnology.
Reduced Feedback Designs for SDMA-OFDMA Systems (2009)

In SDMA-OFDMA wireless communication systems, the feedback load increases with the number of users, subcarriers and antennas in the cell. In this paper, we propose two efficient reduced feedback algorithms by selecting the clusters at the user side. For each cluster, we select the users according to their norm and their orthogonality. We evaluate the performance of the user selection algorithms considering the quantization effect. We also design a specific codebook design to quantize CSI for the proposed criterion.
The anti-malarial artesunate is also active against cancer (2001)

Artesunate (ART) is a semi-synthetic derivative of artemisinin, the active principle of the Chinese herb Artemisia annua. ART reveals remarkable activity against otherwise multidrug-resistant Plasmodium falciparum and P. vivax malaria. ART has now been analyzed for its anti-cancer activity against 55 cell lines of the Developmental Therapeutics Program of the National Cancer Institute, USA. ART was most active against leukemia and colon cancer cell lines (mean GI50 values: 1.11+/-0.56 microM and 2.13+/-0.74 microM , respectively). Non-small cell lung cancer cell lines showed the highest mean GI50 value (25.62+/-14.95 microM) indicating the lowest sensitivity towards ART in this test panel. Intermediate GI50 values were obtained for melanomas, breast, ovarian, prostate, CNS, and renal cancer cell lines. Importantly, a comparison of ART's cytotoxicity with those of other standard cytostatic drugs showed that ART was active in molar ranges comparable to those of established anti-tumor drugs. Furthermore, we tested CEM leukemia sub-lines resistant to either doxorubicin, vincristine, methotrexate, or hydroxyurea which do not belong to the N.C.I. screening panel. None of these drug-resistant cell lines showed cross resistance to ART. To gain insight into the molecular mechanisms of ART's cytotoxicity, we used a panel of isogenic Saccaromyces cerevisiae strains with defined genetic mutations in DNA repair, DNA checkpoint and cell proliferation genes. A yeast strain with a defective mitosis regulating BUB3 gene showed increased ART sensitivity and another strain with a defective proliferation-regulating CLN2 gene showed increased ART resistance over the wild-type strain, wt644. None of the other DNA repair or DNA check-point deficient isogenic strains were different from the wild-type. These results and the known low toxicity of ART are clues that ART may be a promising novel candidate for cancer chemotherapy.
A theoretical study of the contrast recovery and variance of MAP reconstructions from PET data (1999)

We examine the spatial resolution and variance properties of PET images reconstructed using maximum a posteriori (MAP) or penalized-likelihood methods. Resolution is characterized by the contrast recovery coefficient (CRC) of the local impulse response. Simplified approximate expressions are derived for the local impulse response CRC's and variances for each voxel. Using these results we propose a practical scheme for selecting spatially variant smoothing parameters to optimize lesion detectability through maximization of the local CRC-to-noise ratio in the reconstructed image.
Characteristics of TiN gate metal-oxide-semiconductor field effect transistors (1983)

We have investigated the compatibility of TiN gate electrodes with standard metal-oxide-semiconductor (MOS) processing. Measurements were performed on MOS capacitors to determine the metal work function, flat-band voltage, total interface charge density, mobile oxide charge density, oxide leakage current, and breakdown field. The measurement of the threshold voltage as a function of back bias on TiN gate MOS field effect transistors has revealed device characteristics which compare well with those of standard polysilicon gate devices.
The structure of starch can be manipulated by changing the expression levels of starch branching enzyme IIb in rice endosperm (2004)

When the starch branching enzyme IIb (BEIIb) gene was introduced into a BEIIb-defective mutant, the resulting transgenic rice plants showed a wide range of BEIIb activity and the fine structure of their amylopectins showed considerable variation despite having the two other BE isoforms, BEI and BEIIa, in their endosperm at the same levels as in the wild-type. The properties of the starch granules, such as their gelatinization behaviour, morphology and X-ray diffraction pattern, also changed dramatically depending on the level of BEIIb activity, even when this was either slightly lower or higher than that of the wild-type. The over-expression of BEIIb resulted in the accumulation of excessive branched, water-soluble polysaccharides instead of amylopectin. These results imply that the manipulation of BEIIb activity is an effective strategy for the generation of novel starches for use in foodstuffs and industrial applications.
Reorganization of Cytoskeleton and Transient Activation of Ca<sup>2+</sup> Channels in Mesenchymal Stem Cells Cultured on Silicon Nanowire Arrays (2013)

Tissue engineering combines biological cells and synthetic materials containing chemical signaling molecules to form scaffolds for tissue regeneration. Mesenchymal stem cells (MSCs) provide an attractive source for tissue engineering due to their versatility of multipotent differentiation. Recently, it has been recognized that both chemical and mechanical stimulations are essential mediators of adhesion and differentiation of MSCs. While significant progress has been made on the understanding of chemical regulatory factors within the extracellular matrix, the effects of mechanical stimulation exerted by nanomaterials on MSCs and the underlying mechanisms are less well-known. The present study showed that the adhesion, proliferation, and differentiation of MSCs cultured on vertically aligned silicon nanowire (SiNW) arrays were significantly different from those on flat silicon wafer and control substrates. The interactions between MSCs and the SiNW arrays caused the stem cells to preferentially differentiate toward osteocytes and chondrocytes but not adipocytes in the absence of supplementary growth factors. Our study demonstrated that Ca(2+) ion channels were transiently activated in MSCs upon mechanical stimulation, which eventually led to activation of Ras/Raf/MEK/ERK signaling cascades to regulate adhesion, proliferation, and differentiation of MSCs. The stretch-mediated transient Ca(2+) ion channel activation and cytoskeleton reorganization during stem cell-nanowire interaction may be early events of lineage-specific potentiation of MSCs in determining the fates of mesenchymal stem cells cultured on microenvironments with specific mechanical properties.
Improving Robot Controller Transparency Through Autonomous Policy Explanation (2017)

Shared expectations and mutual understanding are critical facets of teamwork. Achieving these in human-robot collaborative contexts can be especially challenging, as humans and robots are unlikely to share a common language to convey intentions, plans, or justifications. Even in cases where human co-workers can inspect a robot's control code, and particularly when statistical methods are used to encode control policies, there is no guarantee that meaningful insights into a robot's behavior can be derived or that a human will be able to efficiently isolate the behaviors relevant to the interaction. We present a series of algorithms and an accompanying system that enables robots to autonomously synthesize policy descriptions and respond to both general and targeted queries by human collaborators. We demonstrate applicability to a variety of robot controller types including those that utilize conditional logic, tabular reinforcement learning, and deep reinforcement learning, synthesizing informative policy descriptions for collaborators and facilitating fault diagnosis by non-experts.
Myocardial Oxygenation During High Work States in Hearts With Postinfarction Remodeling (1999)

Thus, the decrease of PCr/ATP during dobutamine infusion is not the result of insufficient myocardial oxygen availability. Furthermore, in CHF hearts, the low basal PCr/ATP and the attenuated response to dobutamine occurred in the absence of myocardial hypoxia, indicating that the HEP and contractile abnormalities were not the result of insufficient oxygen availability.
Anti-TOSO antibody treatment promotes T cell activation-induced cell death （AICD） in vitro and in vivo (2014)

T 房间导致激活的房间死亡(AICD ) ，那包含调停船边交货的 apoptosis 的正式就职，为有免疫力的动态平衡的维护是很重要的。TOSO 第一在长期的淋巴球的白血病被描述为调停船边交货的 apoptosis 和 overexpressed 的一个禁止者。最近， TOSO 作为 IgM FcR 被识别。在这研究，我们生产了能堵住 IgM 的绑定到 TOSO 并且发现 T 房间 apoptosis 否定地在 T 房间激活期间与 TOSO 表示被相关的 anti-TOSO monoclonal 抗体(mAb ) 。有堵住 mAb 的 anti-TOSO 的激活的 T 房间的处理支持了 T 房间 AICD 在在 xenogeneic-GVHD 的 vitro AICD 模型，和处理，有抗体的老鼠也增加了激活的 T 房间的敏感到导致船边交货的 apoptosis，它被 c-FLIPL 表示的减小和 AP-1 的起来规定伴随复杂。在摘要，我们的数据在 T 房间 AICD 显示 TOSO 的 anti-apoptotic 效果并且为 hematologic 恶意和有免疫力的混乱的处理开创新治疗学的前景。
Asymmetric Growth in Polyelectrolyte Multilayers (2013)

Radioactive counterions were used to track the ratio of positive to negative polymer repeat units within a polyelectrolyte multilayer made from poly(diallyldimethylammonium chloride), PDADMAC, and poly(styrene sulfonate), PSS. For this widely employed pair of "linearly" assembled polyelectrolytes it was found that the accepted model of charge overcompensation for each layer is incorrect. In fact, overcompensation at the surface occurs only on the addition of the polycation, whereas PSS merely compensates the PDADMAC. After the assembly of about a dozen layers, excess positive sites begin to accrue in the multilayer. Treating the surface as a reaction-diffusion region for pairing of polymer charges, a model profile was constructed. It is shown that different reaction-diffusion ranges of positive and negative polyelectrolyte charge lead to a blanket of glassy, stoichiometric complex growing on top of a layer of rubbery, PDADMAC-rich complex. Though overcompensation and growth was highly asymmetric with respect to the layer number, entirely conventional "linear" assembly of the multilayer was observed. The impact of asymmetric growth on various properties of multilayers is discussed.
Use of non-Rayleigh statistics for the identification of tumors in ultrasonic B-scans of the breast (1993)

A model for the scattering of ultrasound from breast tissue is proposed. The model is based on the use of non-Rayleigh statistics, specifically the K distribution to describe the backscattered echo from the tissue. A multiparameter test based on this model has been designed to characterize the tissue. The data from the B-scan images of the breasts of 6 different patients were analyzed using this model. The results indicate that the non-Rayleigh statistics seem to be useful in characterizing and identifying malignant, benign, and normal tissue regions.
Nuclear Factor (NF)-κB-dependent Thyroid Hormone Receptor β1 Expression Controls Dendritic Cell Function via Akt Signaling (2009)

Despite considerable progress in our understanding of the interplay between immune and endocrine systems, the role of thyroid hormones and their receptors in the control of adaptive immunity is still uncertain. Here, we investigated the role of thyroid hormone receptor (TR) beta(1) signaling in modulating dendritic cell (DC) physiology and the intracellular mechanisms underlying these immunoregulatory effects. Exposure of DCs to triiodothyronine (T(3)) resulted in a rapid and sustained increase in Akt phosphorylation independently of phosphatidylinositol 3-kinase activation, which was essential for supporting T(3)-induced DC maturation and interleukin (IL)-12 production. This effect was dependent on intact TR beta(1) signaling as small interfering RNA-mediated silencing of TR beta(1) expression prevented T(3)-induced DC maturation and IL-12 secretion as well as Akt activation and I kappaB-epsilon degradation. In turn, T(3) up-regulated TR beta(1) expression through mechanisms involving NF-kappaB, suggesting an autocrine regulatory loop to control hormone-dependent TR beta(1) signaling. These findings were confirmed by chromatin immunoprecipitation analysis, which disclosed a new functional NF-kappaB consensus site in the promoter region of the TRB1 gene. Thus, a T(3)-induced NF-kappaB-dependent mechanism controls TR beta(1) expression, which in turn signals DCs to promote maturation and function via an Akt-dependent but PI3K-independent pathway. These results underscore a novel unrecognized target that regulates DC maturation and function with critical implications in immunopathology at the cross-roads of the immune-endocrine circuits.
Epigenetic approaches to psychiatric disorders. (2010)

Psychiatric diseases place a tremendous burden on affected individuals, their caregivers, and the health care system. Although evidence exists for a strong inherited component to many of these conditions, dedicated efforts to identify DNA sequence-based causes have not been exceptionally productive, and very few pharmacologic treatment options are clinically available. Many features of psychiatric diseases are consistent with an epigenetic dysregulation, such as discordance of monozygotic twins, late age of onset, parent-of-origin and sex effects, and fluctuating disease course. In recent years, experimental technologies have significantly advanced, permitting in-depth studies of the epigenome and its role in maintenance of normal genomic functions, as well as disease etiopathogenesis. Here, we present an epigenetic explanation for many characteristics of psychiatric disease, review the current literature on the epigenetic mechanisms involved in major psychosis, Alzheimer's disease, and autism spectrum disorders, and describe some future directions in the field of psychiatric epigenomics.
Thromboxane receptor stimulation inhibits adenylate cyclase and reduces cyclic AMP‐mediated inhibition of ADP‐evoked responses in fura‐2‐loaded human platelets (1992)

Stimulation of human platelets with the thromboxane A2 analogue, U46619, after treatment with prostaglandin E1 or forskolin, reduced the inhibition of ADP-evoked Mn2+ influx and the release of Ca2+ from intracellular stores. U46619 decreased the elevated concentration of 3',5'-cyclic AMP in platelets that were pretreated with prostaglandin E1. These results suggest that occupation of prostaglandin H2/thromboxane A2 receptors, like those for other agonists, inhibits adenylate cyclase activity, which can contribute to the promotion of platelet activation.