gebhart/patrepeval huggingface dataset:
MUDiff: Unified Diffusion for Complete Molecule Generation (2023)

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph structure or on 3D geometric structure, which is not sufficient to represent a complete molecule as 2D graph captures mainly topology while 3D geometry captures mainly spatial atom arrangements. Combining these representations is essential to better represent a molecule. In this paper, we present a new model for generating a comprehensive representation of molecules, including atom features, 2D discrete molecule structures, and 3D continuous molecule coordinates, by combining discrete and continuous diffusion processes. The use of diffusion processes allows for capturing the probabilistic nature of molecular processes and exploring the effect of different factors on molecular structures. Additionally, we propose a novel graph transformer architecture to denoise the diffusion process. The transformer adheres to 3D roto-translation equivariance constraints, allowing it to learn invariant atom and edge representations while preserving the equivariance of atom coordinates. This transformer can be used to learn molecular representations robust to geometric transformations. We evaluate the performance of our model through experiments and comparisons with existing methods, showing its ability to generate more stable and valid molecules. Our model is a promising approach for designing stable and diverse molecules and can be applied to a wide range of tasks in molecular modeling.
Additional file 1 of Implementation of nationwide screening of pregnant women for HTLV-1 infection in Japan: analysis of a repeated cross-sectional study (2020)

Additional file 1. Screening and pregnant women by region in Japan, n (%).Number of screening and Birth and still birth in population by region (Hokkaido and Tohoku, Kanto, Chubu and Tokai, Kinki, Chugoku and Shikoku, Kyusyu and Okinawa) and by year (2011, 2013, 2015).
American Headache Society Committee for Headache Education: ACHE (2010)

Abstract ACHE strives to provide cutting edge, credible information on all treatments, instil hope and a sense of belonging, raise public awareness of the serious nature of headache disorders, and most of all to dispel the myth of ‘You have to learn to live with it.’
The facts about FireWire [serial communication bus] (1997)

Aimed today at consumer electronics applications, the author describes FireWire, a fast, cheap, self-configuring serial bus which may eventually consign parallel buses to the scrap heap of history. Flexibility and ease of use are among the bus's strongest points. A device may be plugged into any other conveniently located device-whether energised or not-just so long as no closed loops are formed.
The Natural Antimicrobial Enzyme Lysozyme is Up-Regulated in Gastrointestinal Inflammatory Conditions (2014)

The cells that line the mucosa of the human gastrointestinal tract (GI, that is, oral cavity, oesophagus, stomach, small intestine, large intestine, and rectum) are constantly challenged by adverse micro-environmental factors, such as different pH, enzymes, and bacterial flora. With exception of the oral cavity, these microenvironments also contain remnant cocktails of secreted enzymes and bacteria from upper organs along the tract. The density of the GI bacteria varies, from 103/mL near the gastric outlet, to 1010/mL at the ileocecal valve, to 1011 to 1012/mL in the colon. The total microbial population (ca. 1014) exceeds the total number of cells in the tract. It is, therefore, remarkable that despite the prima facie inauspicious mixture of harmful secretions and bacteria, the normal GI mucosa retains a healthy state of cell renewal. To counteract the hostile microenvironment, the GI epithelia react by speeding cell exfoliation (the GI mucosa has a turnover time of two to three days), by increasing peristalsis, by eliminating bacteria through secretion of plasma cell-immunoglobulins and by increasing production of natural antibacterial compounds, such as defensin-5 and lysozyme. Only recently, lysozyme was found up-regulated in Barrett's oesophagitis, chronic gastritis, gluten-induced atrophic duodenitis (coeliac disease), collagenous colitis, lymphocytic colitis, and Crohn's colitis. This up-regulation is a response directed to the special types of bacteria recently detected in these diseases. The aim of lysozyme up-regulation is to protect individual mucosal segments to chronic inflammation. The molecular mechanisms connected to the crosstalk between the intraluminal bacterial flora and the production of lysozyme released by the GI mucosae, are discussed. Bacterial resistance continues to exhaust our supply of commercial antibiotics. The potential use of lysozyme to treat infectious diseases is receiving much attention.
The Arab World (2011)

There is no escape from the responsibility of leadership. It is not our choice to accept it or not. It is, rather, imposed on us…Iraq can make this nation rise and can be its center post of its big abode. There are smaller posts, but it must always be Iraq that feels the responsibility, and feels it is the central support post of the Arab nation. If Iraq falls, then the entire Arab nation will fall.– Saddam Hussein, circa 1980–1981
Preimplantation development of mouse embryos in KSOM: Augmentation by amino acids and analysis of gene expression (1995)

Simplex optimization has generated several media that have improved the development of mouse preimplantation embryos in vitro. One objective of this study was to compare the development of preimplantation mouse embryos in one of these computer-optimized media, KSOM, with embryos that developed in vivo, in terms of the relative abundances of specific mRNAs involved in metabolism, transcription, and cell proliferation. First, however, since studies have indicated an improvement of other simple embryo culture media by addition of amino acids, the effects of the addition of amino acids to KSOM (KSOM/AA) on preimplantation development were assessed. We find that addition of both essential and nonessential amino acids to KSOM augments development in vitro, as compared to development supported by KSOM without amino acids. This augmentation is observed starting at the blastocyst stage, and is associated with increased rate of development to the blastocyst stage, increased frequency of hatching, and increased number of cells in the blastocysts. Reverse-transcription PCR was then used to assess the relative abundance of mRNAs for actin, glyceraldehyde-3-phosphate dehydrogenase, Na+, K(+)-ATPase, Sp1, TATA box-binding protein TBP, IGF-I, IGF-II, IGF-I receptor, and IGF-II receptor in embryos that developed in vivo and in vitro using KSOM/AA. Eight out of 9 of these mRNAs were present in the 8-cell embryos and blastocysts raised in KSOM/AA in amounts that were indistinguishable from those in embryos that developed in vivo. It is concluded that KSOM/AA provides an environment in which preimplantation mouse embryos can undergo development that is quantitatively similar to that occurring in vivo.
The use of extracorporeal devices for trauma resuscitation and life support (1994)

Although emergency cardiopulmonary bypass for cardiac resuscitation is not currently in widespread use for trauma patients, extracorporeal membrane oxygenation has been used for many years to support gas exchange in traumatic respiratory failure and dialysis has been used to support renal function. Modern improvements promise renewed interest in these extracorporeal support techniques.
Src Homology 2 Domain-Containing Inositol-5-Phosphatase 1 (SHIP1) Negatively Regulates TLR4 Mediated LPS Signaling through Phosphatase Activity and PI3K Independent Mechanism. (2004)

Abstract Lipopolysaccharide (LPS) is a cell wall component of Gram negative bacteria. LPS activates immune cells and triggers production of proinflammatory cytokines and other mediators through Toll-like receptor (TLR) 4. Src homology (SH) 2 domain-containing inositol-5-phosphatase 1 (SHIP1) plays important roles in negatively regulating the activation of immune cells primarily via phosphoinositide 3-kinase (PI3K) pathway by catalyzing PI3K product PtdIns-3,4,5P3 into PtdIns-3,4P2. However, little is known about the role of SHIP1 in TLR4-mediated LPS responses. We investigated the role of SHIP1 in LPS-induced MAPKs activation and IkappaB-alpha degradation by overexpression and RNA interfering experiments. SHIP1 becomes tyrosine phosphorylated and membrane translocated upon LPS stimulation in RAW264.7 macrophages. Stable SHIP1 transfection inhibits LPS-induced TNF-alpha and IL-6 production by 60% and 70% respectively. Transient SHIP1 transfection inhibits LPS-induced phospharylation of extracellular signal-regulated kinase (ERK1/2), p38, c-Jun NH2-terminal kinase (JNK) and degradation of IkappaB-alpha by about 20%, 50%, 40% and 40% respectively at the time point of 20 min after LPS stimulation. Disruption of SHIP1 phosphatase activity enhances LPS-induced activation of Akt, a downstream molecule of PI3K pathway, but fails to reverse SHIP1 mediated inhibition of LPS-induced activation of MAPKs and degradation of IkappaB-alpha. Consistently, LY 294002 and Wortmannin sufficiently inhibit LPS-induced Akt activation but can not diminish SHIP1 mediated inhibition of LPS-induced activation of MAPKs and degradation of IkappaB-alpha. On the contrary, SHIP1-specific RNA interfering inhibits SHIP1 expression and enhances LPS-induced phospharylation of ERK1/2, p38, JNK and degradation of IkappaB-alpha by about 2.6, 2.6, 3.0 and 8.0-fold respectively at the time point of 20 min after LPS stimulation. Even in the presence of LY 294002, SHIP1 RNA interfering could increase LPS-induced IL-6 production. Furthermore, SHIP1 overexpression nearly completely abolished TLR4 reconstitution conferred LPS responsiveness in COS7 cells. These results demonstrated that SHIP1 negatively regulates LPS responses in macrophage via phosphatase activity and PI3K-independent mechanism.
Stress induced birefringence of glass-to-metal bonded components (2020)

We report on the stress induced birefringence of 10 mm BK7 cubes bonded to 15 mm x 15 mm x 5 mm aluminium coupons using ultrashort pulse laser welding, hydroxide catalysis bonding, and an optical adhesive using a standard approach used in industry. It was observed that ultrashort pulse laser welding results in a low level of stress induced birefringence within an 85% optical aperture of the 10 mm cube. These levels are suitable for use in photography and microscopy applications as defined by the relevant ISO standard for permissible stress induced birefringence limits in optics. Hydroxide catalysis bonding was shown to approach and possibly exceed this limit, however, it must be noted that the bonding area of the hydroxide catalysis samples greatly exceeds that of the welding and adhesive bonded samples by a factor of 20 and thus will likely experience grater mechanical stress from defects on the metal surface. The induced stress in the adhesively bonded samples was found to be well-confined, with the retardation falling below the maximum acceptable limits for microscopy type applications of 10 nm/cm retardation within 0.5 - 1 mm of the glass-metal interface for the majority of samples tested. The hydroxide catalysis and ultrashort pulse laser welded samples have a significant increase in retardation in the region directly above the bonded surface compared to the adhesively bonded samples. This retardation decays rapidly as a function of distance from the bonded interface. In the case of ultrashort pulse laser welded samples, optimisation of the welding parameters has been shown to control the level of retardation within the interface region, thus reducing the overall effect of the weld on the bulk optic.
Endogenous Opiate Receptor Ligand: Electrically Induced Release in the Guinea Pig Ileum (1977)

Opiate receptors mediate the electrically evoked inhibition of the myenteric plexus-longitudinal muscle preparation of the guinea pig ileum. The electrically induced activation of the opiate receptor was produced by a prolonged simulation at 10 hertz and provides the first evidence that an endogenous opiate receptor ligand is released by nerve stimulation. The specificity of the phenomenon was demonstrated by the reversal obtained with the narcotic antagonists naloxone, naltrexone, and GPA 1843; GPA 1847, the (+)-isomer of 1843, did not cause reversal. The model system described should be useful for the study of the storage, synthesis, and release of endorphins.
The CD8 T Cell Compartment Plays a Dominant Role in the Deficiency of Brown-Norway Rats to Mount a Proper Type 1 Immune Response (2002)

Differential cytokine production by T cells plays an important role in regulating the nature of an immune response. In the rat, Brown-Norway (BN) and Lewis (LEW) strains differ markedly in their susceptibility to develop either type 1 or type 2-mediated autoimmune manifestations. BN rats are susceptible to type 2-dependent systemic autoimmunity, while LEW rats are resistant. Conversely, type 1-mediated, organ-specific autoimmune disease can be easily induced in LEW, but not in BN, rats. The mechanisms involved in the differential development of type 1 and type 2 immune responses by these two strains are still unknown. In the present study we analyzed the contributions of APC, CD4 and CD8 T cells, and MHC molecules in the difference between LEW and BN rats to develop a type 1 immune response. First, we show that the defect of BN T cells to produce type 1 cytokines in vitro does not require the presence of APC and, by using an APC-independent stimulation assay, we have localized the defect within the T cell compartment. Both CD4 and CD8 T cells are involved in the defect of BN rats to develop a type 1 immune response with a major contribution of the CD8 T cell compartment. This defect is associated with an increase in the type 2 cytokine IL-4 in both BN T cell populations, but neutralization of this cytokine does not restore this defect. Finally, by using MHC congenic rats, we show that the MHC haplotype is not involved in the defect of BN T cells to mount a proper type 1 cytokine response.
Influence by hypothyroidism on the level of sex hormones in blood and their intracrine content in the tumor in rats with Guerin’s carcinoma (2023)

The aim of our research work was to study the level of sex steroids in blood, the tumor and the perifocal zone in rats of both sexes with Guerin’s carcinoma against the background of hypothyroidism. Materials and methods. The experiment was performed in 110 outbred rats of both sexes. Hypothyroidism was induced in animals for 30 days with Mercazolil medication, and then Guerin’s carcinoma was transplanted (the main group). The reference groups included animals with an independent growth of Guerin’s carcinoma and with independent hypothyroidism, as well as intact animals (the norm). On the 18th day of the tumor growth, the animals were sacrificed, and, using standard RIA kits, in the serum, the tumor homogenates and the perifocal zone, the levels of estradiol (E2), testosterone (T) and progesterone (P4) were determined. Results. In comparison with intact animals, hypothyroidism caused an increase in the blood content of E2 in animals of both sexes by 2.2-2.4 times and T by 1.4-16 times, and P4 by 1.7 times only in females, but recorded was a decrease therein in males by 2.4 times. The growth of Guerin’s carcinoma resulted in a 2.5-5.5-fold decrease in E2 in blood of the animals of both sexes, an increase in T by 2.1 times and P4 by 3 times in the females, but a decrease in T by 2.6 times without changing P4 in the males. In the main group, in the animals of both sexes, similarly to the processes in hypothyroidism, the level of E2 and P4 increased by 1.4-1.6 times, and in females also T by 4.4 times, compared with the intact animals. Conclusion. Hypothyroidism and the growth of Guerin’s carcinoma changed E2 in different directions in animals of both sexes the level of sex hormones in blood and shifted the steroid balance in the tumor and its perifocal zone. In the females of the main group, the saturation of the tumor with estrogens, androgens and progesterone decreased, while in the males, on the contrary, the concentration of steroids increased.
Renal replacement therapy in the critically ill (2012)

Specific research on RRT timing will be mandatory in the next few years: a standard definition of timing will certainly help to shed new light on how to improve RRT patients' outcome. Dialytic dose of continuous RRT has been recently and definitely standardized to 20-25 ml/kg per hour (dialysis or hemofiltration), however, application to clinical practice still needs to be improved and new evidence on net ultrafiltration prescription showed that fluid balance may be as important as blood purification in critically ill patients with renal dysfunction. Special settings such as septic RRT, pediatric RRT, and RRT during extracorporeal membrane oxygenation recently achieved important results and new applications in clinical practice with important consequences for technical improvement and future care of these patients.
Migration of breast cancer cells into reconstituted type I collagen gels assessed via a combination of frozen sectioning and azan staining (2014)

This study sought to devise a way to assess the infiltration of cancer cells in model stromal tissues. Human breast carcinoma MDA-MB-231 cells were loaded on the surface of a type I collagen gel in the well of 8-well chamber slide and allowed to migrate into the gel. The gel was then subjected to frozen sectioning and staining. Azan staining facilitated satisfactory microscopic observation of cancer cells migrating into the collagen gel. Cell migration was promoted by the presence of fetal calf serum in the gel. In contrast, the proportion of cells remaining on the gel surface increased in the presence of galardin, a matrix metalloproteinase inhibitor. Moreover, the distance of cell migration from the gel surface was significantly shorter depending on the concentration of galardin. Observation of cancer cell migration into reconstituted type I collagen gel with a combination of frozen sectioning and azan staining is a useful way to assess the ability of individual cancer cells to migrate and to evaluate how effectively pharmaceuticals inhibit the first step of invasion.
Location of Deuterium Positions in the Proton-Conducting Perovskite BaCe0.4Zr0.4Sc0.2O2.90·xD2O by Neutron Powder Diffraction (2008)

Structural studies from X-ray and high-resolution neutron powder diffraction data collected on deuterated and nondeuterated BaCe0.4Zr0.4Sc0.2O2.9·x(D2O) have been carried out. Although X-ray diffraction suggested that a sample of the nominal composition was single phase cubic, neutron diffraction showed the structure as single phase orthorhombic in the space group Pbnm. The structural distortion can be related to the determination of accurate oxygen positions in the structure by neutron diffraction. Rietveld refinement of the neutron diffraction data and subsequent Fourier nuclear density maps have proved to be successful in locating the deuterium (D) positions despite the low occupancies present, with a final composition of BaCe0.4Zr0.4Sc0.2O2.90·0.10(D2O) and the D position associated with the O1 position in the Ba-containing plane. TGA analysis in dry air on the deuterated sample shows the 0.70% weight loss for heating from room temperature to 900 °C which corresponds to the D2O loss of 0.10/formula unit. The unit-cell volume for the deuterated phase was found to be higher than the nondeuterated phase (i.e., dry) at 295 K, i.e., V = 311.59(5) Å3 compared with 310.91(5) Å3. The O1−D distance was found to be 1.06(1) Å. The presence of anisotropic displacements for oxygen was observed during the refinement.
CROSS-PHYSICAL DEPENDENCE LIABILITY OF PSYCHOTROPICDRUGS IN RATS DEPENDENT ON BARBITURATES (1983)

Rats were rendered physically dependent on phénobarbital by phenobarbital-admixed foods. Barbital, phénobarbital, ethanol, diazepam, nitrazepam, meprobamate,methaqualone, chlorpromazine, diphenylhydantoin, mephenesin, reserpine and Clonidinewere cross-administered to evaluate the mode of suppression of withdrawal signs andcross-physical dependence liability. The drugs were administered several times duringthe period from 17–18 hr (when withdrawal signs began to appear) to about 48 hr afterthe withdrawal of phénobarbital. From the mode of suppression and severity of relapsedwithdrawal signs, the se drugs were classified into the following 3 types: Type I: drugssuppressing withdrawal signs of phénobarbital (WSP) almost completely and followedby the relapse of severe WSP. Type 11 - a : drugs suppressing WSP partially and followedby the relapse of moderate WSP. Type ll-b: drugs suppressing WSP partially andfollowed by the relapse of only mild or practically no signs. Type III (lll-a and -b):drugs practically failing to suppress or rather aggravate WSP. Consequently, we foundthat it was possible to evaluate precisely the cross-physical dependence on sedative-hypnotics by means of investigation for the method of suppression of WSP and therelapse of such signs upon their withdrawal.
The frequency-doubled copper vapour laser - An alternative source for high repetition rate micro-machining (1993)

We report on the output characteristics of a high repetition rate, high beam quality UV source, based on a frequency doubled copper vapour laser (CVL), and present preliminary results on the precision drilling of thin polymer films.
A Distinctive Load Feature Extraction Based on Fryze's Time-domain Power Theory (2016)

The performance of a nonintrusive load monitoring (NILM) system heavily depends on the uniqueness of the preferred load signature (LS) extracted from each appliance. Some electrical characteristics, such as instantaneous current waveform (CW), instantaneous power waveform, current harmonic, and voltage-current (V-I) trajectory have been proposed as appliance features in the literature. However, in some situations, these LSs cannot effectively distinguish different loads apart. In this paper, a time-domainbased advanced power theory is used to decompose the load current into the active and nonactive orthogonal components. Then, two new LSs have been established based on the nonactive component of the load current, namely, the nonactive CW (if) and the voltage-nonactive current (V-If ) characteristics curve. Simulation and experimental tests show that both of these features can distinguish different appliances. Hence, the proposed LSs can significantly enhance the existing NILM systems.
Direct Fingerprinting on Multicasting Compressed Video (2005)

A video fingerprint is a kind of digital watermark used in digital video for tracking pirate copies in a multi-user environment. Different users receive the same video with different watermarks designed for uniquely identifying designated users. As a value-added business service, fingerprinting is independent from video compression. In current fingerprinting schemes, a compressed video has to be decoded once for every user in order to add on individual fingerprints. Then the video is encoded again before the dispatch. However, the multiple decode/re-encode operations can result in poor system performance. In this paper, we propose a new integrated fingerprint algorithm, which can be applied directly to the compressed video without decoding/reencoding. Our experiments show that the performance of fingerprinting improved with no compromise to the robustness.