gebhart/patrepeval huggingface dataset:
Transcriptomic landscape regulated by the 14 types of bone morphogenetic proteins (BMPs) in lineage commitment and differentiation of mesenchymal stem cells (MSCs) (2019)

Mesenchymal stem cells (MSCs) are ubiquitously-existing multipotent progenitors that can self-renew and differentiate into multiple lineages including osteocytes, chondrocytes, adipocytes, tenocytes and myocytes. MSCs represent one of the most commonly-used adult progenitors and serve as excellent progenitor cell models for investigating lineage-specific differentiation regulated by various cellular signaling pathways, such as bone morphogenetic proteins (BMPs). As members of TGFβ superfamily, BMPs play diverse and important roles in development and adult tissues. At least 14 BMPs have been identified in mammals. Different BMPs exert distinct but overlapping biological functions. Through a comprehensive analysis of 14 BMPs in MSCs, we demonstrated that BMP9 is one of the most potent BMPs in inducing osteogenic differentiation of MSCs. Nonetheless, a global mechanistic view of BMP signaling in regulating the proliferation and differentiation of MSCs remains to be fully elucidated. Here, we conducted a comprehensive transcriptomic profiling in the MSCs stimulated by 14 types of BMPs. Hierarchical clustering analysis classifies 14 BMPs into three subclusters: an osteo/chondrogenic/adipogenic cluster, a tenogenic cluster, and BMP3 cluster. We also demonstrate that six BMPs (e.g., BMP2, BMP3, BMP4, BMP7, BMP8, and BMP9) can induce I-Smads effectively, while BMP2, BMP3, BMP4, BMP7, and BMP11 up-regulate Smad-independent MAP kinase pathway. Furthermore, we show that many BMPs can upregulate the expression of the signal mediators of Wnt, Notch and PI3K/AKT/mTOR pathways. While the reported transcriptomic changes need to be further validated, our expression profiling represents the first-of-its-kind to interrogate a comprehensive transcriptomic landscape regulated by the 14 types of BMPs in MSCs.
The use of percentage change from baseline as an outcome in a controlled trial is statistically inefficient: a simulation study (2001)

Percentage change from baseline should not be used in statistical analysis. Trialists wishing to report this statistic should use another method, such as ANCOVA, and convert the results to a percentage change by using mean baseline scores.
RESEARCH ON IMPROVEMENT OF STRENGTH OF EPS LIGHT AGGREGATE CONCRETE (2009)

This paper presents how lightweight concrete is made by using worn-out EPS foam granules as light aggregate, and Portland cement as coagulate material, an experiment which involves exploration of the method of making hulls in the mixing process by using an admixture of different reinforcing materials, the method of still resting of hulls, and the method of improving the strength of EPS light aggregate concrete.
Molecular architecture and biorecognition processes of the cystine knot protein superfamily: part I. The glycoprotein hormones (2000)

In this review article, the reader is introduced to recent advances in our knowledge on a subset of the cystine knot superfamily of homo- and hetero-dimeric proteins, from the perspective of the endocrine glycoprotein hormone family of proteins: follitropin (FSH), Iutropin (LH), thyrotropin. (TSH) and chorionic gonadotropin (CG). Subsequent papers will address the structure-function behaviour of other members of this increasingly significant family of proteins, including various members of the transforming growth factor-beta (TGF-beta) family of proteins, the activins, inhibins, bone morphogenic growth factor, platelet derived growth factor-beta, nerve growth factor and more than 35 other proteins with similar topological features. In the present review article, specific emphasis has been placed on advances with the glycoprotein hormones (GPHs) that have facilitated greater insight into their physiological functions, molecular structures and most importantly the basis of the molecular recognition events that lead to the formation of hetero-dimeric structures as well as their specific and selective recognition by their corresponding receptors and antibodies. Thus, this review article focuses on the structural motifs involved in receptor recognition and the current techniques available to identify these regions, including the role of immunological methodology, peptide fragment design and synthesis and mutagenesis to delineate their structure-function relationships and molecular recognition behaviour.
Streamlined Synthesis of Phosphatidylinositol (PI), PI3P, PI3,5P<sub>2</sub>, and Deoxygenated Analogues as Potential Biological Probes (2006)

Highly direct total syntheses of phosphatidylinositol (PI), phosphatidylinositol-3-phosphate (PI3P), phosphatidylinositol-3,5-bisphosphate (PI3,5P2), and a range of deoxygenated versions are reported. Each synthesis is carried out to deliver the target in optically pure form. The key step for each synthesis is a catalytic asymmetric phosphorylation reaction that affects desymmetrization of an appropriate myo-inositol precursor. Elaboration to each target compound is then carried out employing a diversity-oriented strategy from the common precursors. In addition to three natural products, several additional streamlined total syntheses of deoxygenated PI analogues are reported. These syntheses set the stage for high-precision biological investigations of polar headgroup/biological target interactions of these membrane-associated signaling molecules.
A Convenient Synthesis of N‐Substituted 1,6‐Dihydro‐3(2H)‐Pyridinones (1984)

Abstract N‐Substituted 1,6‐dihydro‐3(2H)‐pyridinones have been synthesised from N‐substituted piperidine‐3,5‐diones via the methyl enol ethers. Reduction of the latter with sodium borohydride (NaBH 4 ) is described.
On throughput estimation with TXOP sharing in IEEE 802.11ah networks (2016)

Nowadays the concept of the Internet of Things (IoT) becomes more and more popular. However, state-of-the-art wireless technologies do not meet the IoT requirements for low power consumption and big number of simultaneously connected devices. To meet IoT requirements, IEEE 802.11 Working Group is developing a new low-power long-range Wi-Fi, called HaLow, which is described in the new IEEE 802.11ah amendment to the Wi-Fi standard. To increase the network coverage and decrease power consumption of sensors, the new amendment introduces relaying. A part of this mechanism is TXOP sharing, which hastens two-hop frame exchange. In this paper, we develop the first analytical model of relaying with TXOP sharing in IEEE 802.11ah networks, which allows estimating network throughput.
Different Width and Tightening System: Emergency Tourniquets on Distal Limb Segments (2015)

All four designs can be effective on distal limb segments, the SWATT doing so with the lowest pressures and least pressure losses over time. The pressure change from Occlusion to Completion varies by tourniquet tightening system and can involve a pressure decrease with the windlass tightening systems. Pressure losses occur in as little as 120 seconds following Completion and so can loss of Occlusion. This is especially true for nonelastic strap tourniquet designs.
FASTM: A Log-based Hardware Transactional Memory with Fast Abort Recovery (2009)

Version management, one of the key design dimensions of hardware transactional memory (HTM) systems, defines where and how transactional modifications are stored. Current HTM systems use either eager or lazy version management. Eager systems that keep new values in-place while they hold old values in a software log, suffer long delays when aborts are frequent because the pre-transactional state is recovered by software. Lazy systems that buffer new values in specialized hardware offer complex and inefficient solutions to handle hardware overflows, which are common in applications with coarse-grain transactions. In this paper, we present FASTM, an eager log-based HTM that takes advantage of the processorpsilas cache hierarchy to provide fast abort recovery. FASTM uses a novel coherence protocol to buffer the transactional modifications in the first level cache and to keep the non-speculative values in the higher levels of the memory hierarchy. This mechanism allows fast abort recovery of transactions that do not overflow the first level cache resources. Contrary to lazy HTM systems, committing transactions do not have to perform any actions in order to make their results visible to the rest of the system. FASTM keeps the pre-transactional state in a software-managed log as well, which permits the eviction of speculative values and enables transparent execution even in the case of cache overflow. This approach simplifies eviction policies without degrading performance, because it only falls back to a software abort recovery for transactions whose modified state has overflowed the cache. Simulation results show that FASTM achieves a speed-up of 43% compared to LogTM-SE, improving the scalability of applications with coarse-grain transactions and obtaining similar performance to an ideal eager HTM with zero-cost abort recovery.
Quadratic dynamical decoupling: Universality proof and error analysis (2011)

We prove the universality of the generalized QDD${}_{{N}_{1}{N}_{2}}$ (quadratic dynamical decoupling) pulse sequence for near-optimal suppression of general single-qubit decoherence. Earlier work showed numerically that this dynamical decoupling sequence, which consists of an inner Uhrig DD (UDD) and outer UDD sequence using ${N}_{1}$ and ${N}_{2}$ pulses, respectively, can eliminate decoherence to $O({T}^{N})$ using $O({N}^{2})$ unequally spaced ``ideal'' (zero-width) pulses, where $T$ is the total evolution time and $N={N}_{1}={N}_{2}$. A proof of the universality of QDD has been given for even ${N}_{1}$. Here we give a general universality proof of QDD for arbitrary ${N}_{1}$ and ${N}_{2}$. As in earlier proofs, our result holds for arbitrary bounded environments. Furthermore, we explore the single-axis (polarization) error suppression abilities of the inner and outer UDD sequences. We analyze both the single-axis QDD performance and how the overall performance of QDD depends on the single-axis errors. We identify various performance effects related to the parities and relative magnitudes of ${N}_{1}$ and ${N}_{2}$. We prove that using QDD${}_{{N}_{1}{N}_{2}}$ decoherence can always be eliminated to $O({T}^{\mathrm{min}{{N}_{1},{N}_{2}}})$.
Tumor necrosis factor, alone or in combination with IL-2, but not IFN-gamma, is associated with macrophage killing of Mycobacterium avium complex. (1988)

Organisms belonging to the Mycobacterium avium complex (MAC) are the most common bacterial pathogens in patients with AIDS but factors associated with the activation of cellular defense mechanisms against this atypical mycobacterium have not been defined. Peritoneal macrophages harvested from a chronic MAC infection in C57 black mice are able to kill approximately 86% of intracellular MAC in contrast to 0 to 20% killing by unstimulated human and mouse macrophages in vitro. The availability of human rTNF-alpha, rIFN-gamma, and rIL-2 permitted evaluation of the role of each of these lymphokines/monokines, alone or in combination, in activating macrophages in vitro to kill MAC. Human monocyte-derived macrophages were cultured in vitro, stimulated with rIL-2, rIFN-gamma, or rTNF, and then infected with MAC (serovars 1 and 8). Mouse peritoneal macrophages were harvested, cultured in vitro, and stimulated with rIFN-gamma. rTNF (10(4) U/ml) was associated with a modest increase of intracellular killing of MAC (58 +/- 5%) even when utilized 24 or 48 h after macrophage infection or when administered for 5 consecutive days after infection (78.1 +/- 4%). Both human and murine IFN-gamma were associated with increased intracellular growth of MAC (32 +/- 4% for murine and 38 +/- 3% for human macrophages). However, intracellular killing (53 +/- 6% compared with control) was observed after 6 days of treatment with IFN-gamma. This latter effect was fully blocked by anti-TNF antibody, whereas rIL-2 alone did not augment the intracellular killing of MAC by human macrophages. rTNF plus either rIFN-gamma or rIL-2 triggered significant increases in superoxide anion production, but subsequent MAC killing was no greater than with rTNF alone. Treatment of macrophages with 10 U/ml of rTNF followed by rIL-2 (200 U/ml) was associated with 68% of intracellular killing. TNF seems to be an important monokine, promoting activation of mycobactericidal mechanisms in human macrophages.
I2-Catalyzed Oxidative Condensation of Aldoses with Diamines: Synthesis of Aldo-Naphthimidazoles for Carbohydrate Analysis (2010)

A novel method for the conversion of unprotected and unmodified aldoses to aldo-imidazoles has been developed. Using iodine as a catalyst in acetic acid solution, a series of mono- and oligosaccharides, including those containing carboxyl and acetamido groups, undergo an oxidative condensation reaction with aromatic vicinal diamines at room temperature to give the corresponding aldo-imidazole products in high yields. No cleavage of the glycosidic bond occurs under the mild reaction conditions. The compositional analysis of saccharides is commonly realized by capillary electropheresis of the corresponding aldo-imidazole derivatives, which are easily synthesized by the reported iodine-promoted oxidative condensation. In addition, a series of aldo-imidazoles were determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze molecular weight and ion intensity. The diamine-labeled saccharides showed enhanced signals in MALDI-TOF MS. The combined use of aldoimidazole derivatization and mass spectrometric analysis thus provides a rapid method for identification of saccharides, even when less than 1 pmol of saccharide is present in the sample. These results can be further applied to facilitate the isolation and analysis of novel saccharides.
A strategy for construction of industrial strains of distiller's yeast (1995)

A procedure was developed for construction of industrial strains of distiller's yeast (Saccharomyces cerevisiae). It includes several steps: construction of congenic genetically marked haploid strains of opposite mating types starting from an industrial strain of hybrid nature, integrative transformation of the above haploid strains with a DNA fragment containing an expression cassette responsible for new technological facilities, and hybridization of transformants and isolation of final industrial homozygous strains under experimental conditions simulating commercial fermentation processes. This strategy permits the generation of strains that have desirable characteristics of traditional races of distiller's yeast along with new technological facilities determined by the particular expression cassette. Using this procedure, we have constructed an industrial strain with improved amylolytic activity. (c) 1995 John Wiley & Sons, Inc.
The Effects of Basic Fibroblast Growth Factor and Doxorubicin on Cultured Human Skin Fibroblasts: Relevance to Wound Healing (1992)

Abstract The effects of basic fibroblast growth factor (bFGF) and doxorubicin on cultured human skin fibroblasts were examined in order to determine their relevance to wound healing. bFGF is shown to stimulate fibroblast collagenase production per cell, and this effect in vitro seems to be one explanation for its efficacy in wound healing. Doxorubicin inhibited not only fibroblast proliferation but also collagen production by inactivating prolyl hydroxylase. This result may explain the reduced wound healing in patients undergoing treatment with doxorubicin. These studies indicate the importance of assessing the effects of growth factors on matrix metabolism in order to understand their roles in wound healing.
Quantitative assessment of the lumbar spinal canal by computed tomography. (1980)

An experimentally validated simple standardized method for making precise measurements of the spinal canal directly from the video display of a CT scanner is described. Using this method, normal values for anteroposterior diameter, interpediculate distance, and cross-sectional area of the lumbar spinal canal have been determined in a series of 60 adults. A careful study of canal configuration combined with the prudent use of the normal values should allow the CT diagnosis of lumbar spinal stenosis to be made with a high level of confidence.
Ring-substituted 4-Hydroxy-1H-quinolin-2-ones: Preparation and Biological Activity (2009)

In the study, a series of twelve ring-substituted 4-hydroxy-1H-quinolin-2-one derivatives were prepared. The procedures for synthesis of the compounds are presented. The compounds were analyzed using RP-HPLC to determine lipophilicity and tested for their photosynthesis-inhibiting activity using spinach (Spinacia oleracea L.) chloroplasts. All the synthesized compounds were also evaluated for antifungal activity using in vitro screening with eight fungal strains. For all the compounds, the relationships between the lipophilicity and the chemical structure of the studied compounds are discussed, as well as their structure-activity relationships (SAR).
The Thiocarboxanilide Nonnucleoside Inhibitor UC781 Restores Antiviral Activity of 3′-Azido-3′-Deoxythymidine (AZT) against AZT-Resistant Human Immunodeficiency Virus Type 1 (1999)

N-[4-Chloro-3-(3-methyl-2-butenyloxy)phenyl]-2-methyl-3-furanca rbothioamide (UC781) is an exceptionally potent nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase. We found that a 1:1 molar combination of UC781 and 3'-azido-3'-deoxythymidine (AZT) showed high-level synergy in inhibiting the replication of AZT-resistant virus, implying that UC781 can restore antiviral activity to AZT against AZT-resistant HIV-1. Neither the nevirapine plus AZT nor the 2',5'-bis-O-(t-butyldimethylsilyl)-3'-spiro-5"-(4"-amino-1",2"-oxathi ole- 2",2"-dioxide plus AZT combinations had this effect. Studies with purified HIV-1 reverse transcriptase (from a wild type and an AZT-resistant mutant) showed that UC781 was a potent inhibitor of the pyrophosphorolytic cleavage of nucleotides from the 3' end of the DNA polymerization primer, a process that we have proposed to be critical for the phenotypic expression of AZT resistance. Combinations of UC781 plus AZT did not act in synergy to inhibit the replication of either wild-type virus or UC781-resistant HIV-1. Importantly, the time to the development of viral resistance to combinations of UC781 plus AZT is significantly delayed compared to the time to the development of resistance to either drug alone.
The fucosyltransferase FucT-VII regulates E-selectin ligand synthesis in human T cells. (1996)

Selectin-ligands on T cells contribute to the recruitment of circulating cells into chronic inflammatory lesions in the skin and elsewhere. This report provides the first evidence that a single fucosyltransferase, termed FucT-VII, controls the synthesis of E-selectin ligands in human T-lymphoblasts. The FucT-IV transferase (the ELFT enzyme), in contrast constructs lower avidity E-selectin ligands and requires enzyme levels found only in myeloid cells. Treatment of Jurkat cells with phorbol myristate acetate increased the expression of sialylated Lewis(x)-related sLe(x)related epitopes and induced the synthesis of E-selectin ligands functional at physiologic levels of linear shear-stress. Northern analysis revealed a parallel increase in the steady-state levels FucT-VII mRNA, but there were no increases in the two other leukocyte-associated fucosyltransferases (FucT-IV and VI). The stable transfection of the FucT-VII gene into Jurkat cells induced high levels of the sLe(x)-related epitopes and the synthesis of E-selectin ligands which equal or exceeded the avidity of those on circulating lymphocytes. The growth of T-lymphoblasts under conditions which induced expression of the sLe(x,a) epitopes increased the level of FucT-VII mRNA, the synthesis of sialylated-Lewis(x) structures by cell-free extracts and the synthesis of E-selectin ligands equal in avidity to those on FucT-VII transfectants. In contrast, neither the mRNA levels nor activities of the FucT-IV and VI enzymes increased in association with E-selectin ligand synthesis in T-lymphoblasts. Myeloid cell lines, unlike lymphoblasts, expressed high levels of both the FucT-VII and IV enzymes in conjunction with E-selectin ligands raising the possibility that both enzymes contributed to ligand synthesis. FucT-IV transfected Jurkat cells synthesized low avidity ligands for E-selectin but only in association with CDw65 (VIM-2) carbohydrate epitope. Only blood neutrophils and myeloid cell lines expressed this epitope at the levels associated with E-ligand synthesis in the transfectants. In contrast, native Jurkat cells, blood monocytes, blood lymphocytes, and cultured T-lymphoblasts expressed low levels or none. We conclude that FucT-VII is a principal regulator of E-selectin ligand synthesis in human T-lymphoblasts while both FucT-VII and FucT-IV may direct ligand synthesis in some myeloid cells.
<title>Nonlinear distributed feedback structures for optical sensor protection</title> (2000)

We analyze the intensity-dependent optical response of passive optical limiters realized using distributed feedback structures which consist of alternating layers of materials possessing opposite Kerr nonlinearities. By elaborating an analytical model and employing numerical simulations, we explore device performance with respect to key requirements for passive optical limiter deployment. We prove that the proposed limiting mechanism results in complete clamping of transmitted intensity to a sensor-safe limiting value, independent of incident intensity. We provide a direct analytical expression for this limiting intensity in terms of structural and material parameters.
Cloning and expression <i>in vitro</i> of human xanthine dehydrogenase/oxidase (1996)

To study the expression of human xanthine dehydrogenase/oxidase (hXDH/XO), we cloned the cDNA covering its complete coding sequence and characterized it by translation in vitro in rabbit reticulocyte lysates and by transient expression in COS-1 cells. Two specific protein products with approximate molecular masses of 150 and 130 kDa were detected in both expression systems. These products are compatible with the molecular sizes of XDH/XO, and these peptides also showed immunoreactivity with polyclonal anti-hXDH antibodies. Significant XDH/XO enzyme activity (277 +/- 54 pmol/min per mg of protein) was measured in lysates of transfected COS cells, whereas in control transfections the activities were below the detection limit of our assay (0.2 pmol/min per mg of protein). The COS cells expressed the enzyme predominantly (89.8 +/- 0.3%) in the dehydrogenase form.
Nitrogen and Phosphate Recovery from Source-Separated Urine by Dosing with Magnesite and Zeolite (2015)

There is increasing interest in source separation and treatment of urine so as to recover nitrogen and phosphate more efficiently than treating combined wastewater. Although previous studies primarily focused on struvite precipitation for the recovery of phosphorus, the composition of urine changes during storage. The present study compared the precipitation conditions for fresh urine and hydrolyzed urine. The optimal conditions for struvite crystallization were obtained from orthogonal experiment and single-factor optimization. The pH of fresh urine should be adjusted to around 9.5-10.0 to make the reaction thorough, while this was unnecessary for hydrolyzed urine. To reduce cost, magnesite was selected as an alternative for pure MgO, which presented similar efficiency for phosphate recovery. About 92.4% of phosphorus and 87.2% of ammonia-nitrogen were recovered from urine when adding 2.5 g/L of magnesite and 375 g/L of zeolite to get struvite crystals and nitrogen-rich zeolite as a slow-release fertilizer.