gebhart/patrepeval huggingface dataset:
Determination of the Free-Energy Change for Repair of a DNA Phosphodiester Bond (2000)

The repair of phosphodiester bonds in nicked DNA is catalyzed by DNA ligases. Ligation is coupled to cleavage of a phosphoanhydride bond in a nucleotide cofactor resulting in a thermodynamically favorable process. A free energy value for phosphodiester bond formation was calculated using the reversibility of the T4 DNA ligase reaction. The relative number of DNA nicks to phosphodiester bonds in a circular plasmid DNA, formed during this reaction at fixed concentrations of ATP to AMP and PP(i), was quantified. At 25 degrees C, pH 7, the equilibrium constant (K(eq)) for the ligation reaction is 3.89 x 10(4) m. This value corresponds to a standard free energy (DeltaG degrees ') of -6.3 kcal mol(-1). By subtracting the known energy contribution due to hydrolysis of ATP to AMP and PP(i), DeltaG degrees ' for the hydrolysis of a DNA phosphodiester bond is -5.3 kcal mol(-1).
Modulation of the proliferation and differentiation of human mesenchymal stem cells by copper (2002)

Copper plays important functional roles in bone metabolism and turnover. It is known that it is essential for normal growth and development of the skeleton in humans and in animals. Although at present the exact role that copper plays in bone metabolism is unknown, bone abnormalities are a feature of severe copper deficiency. Osteoblasts are derived from mesenchymal stem cells (MSCs) present in bone marrow stroma, which are able to differentiate into bone, adipocytes, and other cell phenotypes. Excess adipogenesis in postmenopausal women may occur at the expense of osteogenesis and, therefore, may be an important factor in the fragility of postmenopausal bone. The purpose of this study was to evaluate whether an increase of the extracellular concentration of copper affects the ability of MSCs to differentiate into osteoblasts or adipocytes. The results showed that copper modified both the differentiation and the proliferative activity of MSCs obtained from postmenopausal women. Copper (50 microM) diminished the proliferation rate of MSCs, increasing their ability to differentiate into the osteogenic and the adipogenic lineages. Copper induced a 2-fold increase in osteogenic differentiation of MSCs, measured as a increase in calcium deposition. Copper (5 and 50 microM) diminished the expression of alkaline phosphatase (50 and 80%, respectively), but induced a shift in the expression of this enzyme to earlier times during culture. Copper also induced a 1.3-fold increase in the adipogenic differentiation of MSCs. It is concluded that copper stimulates MSC differentiation, and that this is preferentially towards the osteogenic lineage.
Chemistry and Biochemistry of Microbial α‐Glucosidase Inhibitors (1981)

Abstract α‐Glucosidases are among the most important carbohydrate‐splitting enzymes. They catalyze the hydrolysis of α‐glucosidic linkages. Their substrates are—depending on their specificity—oligo‐ and polysaccharides. Microbial inhibitors of α‐amylases and other mammalian intestinal carbohydrate‐splitting enzymes studied during the last few years have aroused medical interest in the treatment of metabolic diseases such as diabetes. Moreover, they extend the spectrum of microbial secondary metabolites which comprises an enormous variety of structures. They also contribute considerably to a better understanding of the mechanism of action of α‐glucosidases. These inhibitors belong to different classes of substances. Those studied most thoroughly are microbial α‐glucosidase inhibitors which are members of a homologous series of pseudooligosaccharides of the general formula (4) . They all have a core in common which is essential for their inhibitory action, a pseudodisaccharide residue consisting of an unsaturated cyclitol unit, and a 4‐amino‐4,6‐dideoxy‐ glucose unit. The—in many respects—most interesting representative of this homologous series is acarbose (5) , a pseudotetrasaccharide exhibiting a very pronounced inhibitory effect on intestinal α‐glucosidases such as sucrase, maltase and glucoamylase. The present paper will review this new field of microbial α‐glucosidase inhibitors which has been studied with particular intensity during the past ten years.
Absence of epidermal growth factor receptor expression in squamous cell carcinoma of the uterine cervix is an indicator of limited tumor disease. (1999)

The expression of growth factors is considered as an important diagnostic and prognostic feature in tumor pathology. We investigated the value of the immunohistochemical EGF-receptor expression (EGF-R) in 30 squamous cell carcinomas of the uterine cervix, treated by radical hysterectomy and lymphadenectomy according to the Wertheim-Meigs-Okabayashi technique. Immunohistochemical reactions were performed on 4 microm sections from paraffin-embedded tissue, using an indirect peroxidase method. The staining results were evaluated semiquantitatively as negative (n=9; 30%) or as slightly, moderately or severely positive (n=21; 70%). The EGF-R-negative tumors were found in less advanced tumor stages. None had invaded into the parametrium (100%), eight were staged as T1 (89%), seven as N0 (78%), and seven showed no evidence for lymphangiosis carcinomatosa (78%). The respective values for the EGF-R-positive tumors ranged from 52% to 67%. However, only the difference in parametral invasion (EGF-R-negative: 0%, EGF-R-positive: 38%) was statistically significant (p=0.0306), probably due to the small number of cases. The EGF-R-expression was not correlated to histomorphological tumor grading. The results of this study indicate an inverse correlation between EGF-R expression and tumor spread. Assuming that this trend could be confirmed by a larger group of patients, immunostaining for EGF-R in a tumor biopsy could be useful to adapt surgical strategies and adjuvant therapy in the individual patient. Moreover, the EGF-R is an interesting target for immunotherapeutic approaches in squamous cell cervical carcinoma.
Anticoccidial derivatives of 6-azauracil. 1. Enhancement of activity by benzylation of nitrogen-1. Observations on the design of nucleotide analogs in chemotherapy (1977)

Benzylation of 6-azauracil at N-1 (which corresponds to the point of attachment of the ribose phosphate unit in pyrimidine nucleotides) has been found to augment its anticoccidial activity fourfold. The high potency of 1-benzyl-6-azauracil is ascribed to a combination of intrinsic activity, efficient oral absorption, and a moderate rate of excretion. Metabolism experiments using 1-benzyl-6-azauracil labeled with 14C in the heterocycle and (separately) in the side chain showed that, in the drug accounted for, no cleavage had occurred. Additional activity increases were achieved by introducing small, electron-withdrawing substituents in the meta and/or para position(s) of the benzyl group. One of the most active derivaties, 1-(3-cyanobenzyl)-6-azauracil, is about 16 times as potent as 6-azauracil.
Pituitary-adrenal-gonadal responses to high-intensity resistance exercise overtraining (1998)

Weight-trained men [OT; n = 11; age = 22.0 +/- 0.9 (SE) yr] resistance trained daily at 100% one-repetition maximum (1-RM) intensity for 2 wk, resulting in 1-RM strength decrements and in an overtrained state. A control group (Con; n = 6; age = 23.7 +/- 2.4 yr) trained 1 day/wk at a low relative intensity (50% 1 RM). After 2 wk, the OT group exhibited slightly increased exercise-induced testosterone (preexercise = 26.5 +/- 1.3 nmol/l, postexercise = 29.1 +/- 5.9 nmol/l) and testosterone-to-cortisol ratio (preexercise = 0. 049 +/- 0.007 nmol/l, postexercise = 0.061 +/- 0.006 nmol/l) and decreased exercise-induced cortisol (preexercise = 656.1 +/- 98.1 nmol/l, postexercise = 503.1 +/- 39.7 nmol/l). Serum concentrations for growth hormone and plasma peptide F [preproenkephalin (107-140)] were similar for both groups throughout the overtraining period. This hormonal profile is distinctly different from what has been previously reported for other types of overtraining, indicating that high-relative-intensity resistance exercise overtraining may not be successfully monitered via circulating testosterone and cortisol. Unlike overtraining conditions with endurance athletes, altered resting concentrations of pituitary, adrenal, or gonadal hormones were not evident, and exercise-induced concentrations were only modestly affected.
Stereoselectivity of Macrocyclic Ring-Closing Olefin Metathesis (2000)

[reaction: see text] Macrocyclic ring-closing olefin metathesis using ruthenium catalyst 3 was performed to produce a 14-membered lactone. The E/Z ratio of lactone was high regardless of the R group (auxiliary) or the initial alkene stereochemistry. A kinetic study demonstrates that the high E/Z ratio is due to secondary metathesis reactions that isomerize the product to the thermodynamic E/Z ratio.
<i>P<scp>orphyromonas gingivalis</scp></i> L<scp>ipopolysaccharide</scp> S<scp>ignaling in</scp> G<scp>ingival</scp> F<scp>ibroblasts</scp>–CD14 <scp>and</scp> T<scp>oll-like</scp> R<scp>eceptors</scp> (2002)

Periodontal disease is the major cause of adult tooth loss and is commonly characterized by a chronic inflammation caused by infection of oral bacteria. Porphyromonas gingivalis (P. gingivalis) is one of the suspected periodontopathic bacteria and is frequently isolated from the periodontal pockets of patients with chronic periodontal disease. The lipopolysaccharide (LPS) of P. gingivalis is a key factor in the development of periodontitis. Gingival fibroblasts, which are the major constituents of gingival connective tissue, may directly interact with bacteria and bacterial products, including LPS, in periodontitis lesions. It is suggested that gingival fibroblasts play an important role in the host responses to LPS in periodontal disease. P. gingivalis LPS enhances the production of inflammatory cytokines such as interleukin (IL)-1, IL-6, IL-8, and tumor necrosis factor alpha (TNF-alpha) in gingival fibroblasts. However, the receptor that binds with P. gingivalis LPS on gingival fibroblasts remained unknown for many years. Recently, it was demonstrated that P. gingivalis LPS binds to gingival fibroblasts. It was also found that gingival fibroblasts express CD14, Toll-like receptor 4 (TLR4), and myeloid differentiation primary response gene 88 (MyD88). P. gingivalis LPS treatment of gingival fibroblasts activates several intracellular proteins, including protein tyrosine kinases, and up-regulates the expression of monocyte chemoattractant protein-1 (MCP-1), extracellular signal-regulated kinase 1 (ERK1), and signal-regulated kinase 2 (ERK2), IL-1 receptor-associated kinase (IRAK), nuclear factor-kappaB (NF-kappaB), and activating protein-1 (AP-1). These results suggest that the binding of P. gingivalis LPS to CD14 and TLR4 on gingival fibroblasts activates various second-messenger systems. In this article, we review recent findings on the signaling pathways induced by the binding of P. gingivalis LPS to CD14 and Toll-like receptors (TLRs) in gingival fibroblasts.
Simple, Chemoselective Hydrogenation with Thermodynamic Stereocontrol (2014)

Few methods permit the hydrogenation of alkenes to a thermodynamically favored configuration when steric effects dictate the alternative trajectory of hydrogen delivery. Dissolving metal reduction achieves this control, but with extremely low functional group tolerance. Here we demonstrate a catalytic hydrogenation of alkenes that affords the thermodynamic alkane products with remarkably broad functional group compatibility and rapid reaction rates at standard temperature and pressure.
Influence of Post-CMP Cleaning on Cu Interconnects and TDDB Reliability (2005)

The etching amount of Cu wires produced by post-chemical-mechanical polishing cleaning was studied. By using polyvinyl alcohol brush cleaning, the cleaning strength concentrates on the center chip of the wafer, which leads to the erosion of Cu interconnects. The etching depths of isolated Cu wires and dense Cu wires were compared. The surface on the isolated Cu wires is etched deeply because of the nonliner diffusion of the solution and the difference between the friction strengths of both wire patterns. These etching depths were improved by optimizing the brush formation, the rotation speed of the roller and the brush, and by using organic-acids. With respect to the dependence of time-dependent dielectric breakdown (TDDB) lifetime on waiting time, there is a difference between the diluted hydrofluoric-acid (DHF) and organic-acid solutions. The TDDB lifetime for the DHF cleaning is similar until after a waiting time of ten days, whereas the TDDB lifetimes for organic-acids are similar until after a waiting time of four days.
Proteomic analysis of <b><i>Helicobacter pylori</i></b> cellular proteins fractionated by ammonium sulfate precipitation (2008)

Among 1590 ORFs in the Helicobacter pylori genome, >250 have been identified as authentic genes by proteomic analysis. Low-abundance proteins need to be enriched to a minimal amount for MALDI-TOF analysis and salt precipitation has generally been used for protein enrichment. Here, a whole-cell extract of H. pylori strain 26695 was subjected to protein fractionation with stepwise concentrations of ammonium sulfate and the proteins were displayed by 2-DE. The protein spots were quantified using PDQUEST software and identified by peptide fingerprinting. The 2-DE profiles and intensities of individual protein spots differed among the protein fractions. Out of the 98 identified proteins, 61 were found in the stepwise ammonium sulfate fractions but not in the whole-cell extract. Out of these, 37 proteins, including KdsA, were found exclusively in a single fraction. In contrast, GroEL, UreA, UreB, TrxA, NapA, and FldA were ubiquitously present in all fractions. Iron-containing proteins such as NapA, SodB, CeuE, and Pfr were found predominantly in the 100% saturated ammonium sulfate precipitate. Additionally, 29 proteins were newly identified in this study. These data will facilitate the preparation of significant H. pylori proteins, as well as provide information about low-abundance proteins.
Breast cancer immunotherapy: Current status and future prospects (1996)

The development of an immunotherapeutic approach to cancer is the concern for many immunologists, but despite the impressive progress over the past decade, such as the identification of tumour antigens and antigenic peptides as potential targets, there are still many obstacles in eliciting an effective immune response to eradicate cancer. Mucins have attracted interest as potential targets for immunotherapy in the development of vaccines for cancers expressing Mucin1 (MUC1; e.g. breast, pancreas, ovary etc.). All of the identified targets for cancer, including MUC1, are normal proteins; however MUC1 expressed on tumours can be considered as tumour specific due to their overexpression, altered glycosylation and its ubiquitous distribution on the cell surface rather than at the secretory pole in adenocarcinomas. These observations have led to the development of several different approaches to immunize against breast cancer using synthetic carbohydrates or peptides conjugated to carriers and given together with a variety of adjuvants to elicit the appropriate immune response. Mannan, a polymannose carbohydrate isolated from the cell wall of yeast, is an appropriate and effective protein carrier for eliciting a cellular (T1-type) or humoral (T2-type) immune response depending on the mode of conjugation (oxidized or reduced). In addition, mannan holds promise and opens many avenues as a carrier for vaccine development for other antigens. Several clinical trials are in progress to evaluate the immunogenicity of MUC1 and its suitability as to use for immunotherapy/vaccine for breast cancer.
Improving offline evaluation of contextual bandit algorithms via bootstrapping techniques (2014)

In many recommendation applications such as news recommendation, the items that can be rec- ommended come and go at a very fast pace. This is a challenge for recommender systems (RS) to face this setting. Online learning algorithms seem to be the most straight forward solution. The contextual bandit framework was introduced for that very purpose. In general the evaluation of a RS is a critical issue. Live evaluation is of- ten avoided due to the potential loss of revenue, hence the need for offline evaluation methods. Two options are available. Model based meth- ods are biased by nature and are thus difficult to trust when used alone. Data driven methods are therefore what we consider here. Evaluat- ing online learning algorithms with past data is not simple but some methods exist in the litera- ture. Nonetheless their accuracy is not satisfac- tory mainly due to their mechanism of data re- jection that only allow the exploitation of a small fraction of the data. We precisely address this issue in this paper. After highlighting the limita- tions of the previous methods, we present a new method, based on bootstrapping techniques. This new method comes with two important improve- ments: it is much more accurate and it provides a measure of quality of its estimation. The latter is a highly desirable property in order to minimize the risks entailed by putting online a RS for the first time. We provide both theoretical and ex- perimental proofs of its superiority compared to state-of-the-art methods, as well as an analysis of the convergence of the measure of quality.
Investigation of the block ACK scheme in wireless ad hoc networks (2006)

Abstract A Block Transmission and Acknowledgement (BTA) scheme, also called Block ACK, has been proposed in the IEEE 802.11e wireless local area networks (WLAN) specification to improve efficiency of the medium access control layer. The idea of the BTA scheme is to transmit multiple data frames followed by only one acknowledgement frame in a transmission block. In this paper, we present a theoretical model to evaluate the saturation throughput for the BTA scheme under error channel conditions in the ad hoc mode, validated with simulations. We show some advantages of BTA over the legacy MAC, and analyze how to select a proper number of frames for each transmission block. Results show that BTA is particularly effective in very high‐speed wireless networks, and it is important that the number of frames in each block is negotiated before transmissions to provide better efficiency. Copyright © 2006 John Wiley & Sons, Ltd.
Dielectric constant measurement of thin films by differential time-domain spectroscopy (2000)

We present a theoretical model and preliminary experimental results on the dielectric constant measurement of thin films by using differential time-domain spectroscopy. This technique greatly reduces the minimum measurable thickness, and it promises the dielectric constant measurement of μm-thick thin films with the frequency range from GHz to THz.
Belated Recognition for Work Flow Entrepreneurs: A Case of Selective Perception and Amnesia in Management Thought (1995)

Recent trends, such as reengineering, require work flow entrepreneurship. Important principles about these practices were recognized in post-World War II field research, but by the 1970s this work suffered neglect. Amnesia was caused by deeply held assumptions of scientific management, and by a search within business schools for academic legitimacy at the expense of praxis, which skewed the perspectives with which organizations were viewed.
Chemistry of Soluble β-Diketiminatoalkaline-Earth Metal Complexes with M−X Bonds (M = Mg, Ca, Sr; X = OH, Halides, H) (2011)

Victor Grignard's Nobel Prize-winning preparation of organomagnesium halides (Grignard reagents) marked the formal beginning of organometallic chemistry with alkaline earth metals. Further development of this invaluable synthetic route, RX+Mg→RMgX, with the heavier alkaline earth metals (Ca and Sr) was hampered by limitations in synthetic methodologies. Moreover, the lack of suitable ligands for stabilizing the reactive target molecules, particularly with the more electropositive Ca and Sr, was another obstacle. The absence in the literature, until just recently, of fundamental alkaline earth metal complexes with M-H, M-F, and M-OH (where M is the Group 2 metal Mg, Ca, or Sr) bonds amenable for organometallic reactions is remarkable. The progress in isolating various unstable compounds of p-block elements with β-diketiminate ligands was recently applied to Group 2 chemistry. The monoanionic β-diketiminate ligands are versatile tools for addressing synthetic challenges, as amply demonstrated with alkaline earth complexes: the synthesis and structural characterization of soluble β-diketiminatocalcium hydroxide, β-diketiminatostrontium hydroxide, and β-diketiminatocalcium fluoride are just a few examples of our contribution to this area of research. To advance the chemistry beyond synthesis, we have investigated the reactivity and potential for applications of these species, for example, through the demonstration of dip coating surfaces with CaCO(3) and CaF(2) with solutions of the calcium hydroxide and calcium fluoride complexes, respectively. In this Account, we summarize some recent developments in alkaline earth metal complex chemistry, particularly of Mg, Ca, and Sr, through the utilization of β-diketiminate ligands. We focus on results generated in our laboratory but give due mention to work from other groups as well. We also highlight the closely related chemistry of the Group 12 element Zn, as well as the important chemistry developed by other groups using the complexes we have reported. Although Mg and Ca are more abundant in living organisms, no other metal has as many biological functions as Zn. Thus Zn, the nontoxic alternative to the heavier Group 12 elements Cd and Hg, occupies a unique position ripe for further exploration.
25-Hydroxycholecalciferol in Poultry Nutrition (1995)

Vitamin D is a complex of secosteroids that must undergo metabolic alterations to reach optimal biological activity. The parent compounds 1) ergocalciferol (D2) and 2) cholecalciferol (D3) can be synthesized in the leaves of many plants or in the skin of most animals, respectively. Transport of vitamin D steroids after absorption is associated with vitamin D binding proteins (DBP). In general, the relative binding affinities of the vitamin D steroids are: 25-hydroxy vitamin D3 [25-(OH)D3] = 24,25-dihydroxy vitamin D3 [24,25-(OH)2D3] = 25,26-dihydroxy vitamin D3 [25,26-(OH)2D3] > 25-hydroxy vitamin D2 (25-(OH)D2) > 1,25-dihydroxy vitamin D3 [1,25-(OH)2D3] > vitamin D3. The DBP in poultry does not bind D2 forms effectively, and therefore poultry can not use this form of vitamin D adequately. The concentration of 25-(OH)D3 in blood seems to be well correlated with dietary vitamin D intake or exposure to ultraviolet light. The 1 alpha hydroxylase enzyme in the kidney is subject to negative feedback regulation and is critical for formation of the active metabolite 1,25-(OH)2D3. The intracellular vitamin D receptor (VDR) specifically binds 1,25-(OH)2D3 and is necessary for cellular action. Increased levels of two to three orders of magnitude are required for 25-(OH)D3 to compete with 1,25-(OH)2D3 for binding on VDR. Feeding studies with 25-(OH)D3 suggest it has nearly twice the activity of vitamin D3. Hatchability studies have shown that 25-(OH)D3 supports good fertility and hatchability, whereas hens fed only 1,25-(OH)2D3 did not have normal hatchability. Likewise, 1,25-(OH)2D3 seems to reach toxic levels at dietary concentrations only two to three times optimal dietary levels whereas feeding 25-(OH)D3 for extended periods at levels 8 to 10 times requirement seems to have no adverse effects. It seems that 25-(OH)D3 is the most active metabolite of vitamin D3, ultimately capable of supporting both cellular functions and embryonic development in chickens and turkeys when fed as the sole source of vitamin D3.
Testing for the D zygosity with three different methods revealed altered <i>Rhesus boxes</i> and a new weak D type (2003)

A PCR-SSP method with internal control was established for the detection of the hybrid Rhesus box. Polymorphisms in the downstream Rhesus box may interfere with the detection of RHD.