gebhart/patrepeval huggingface dataset:
ATP Citrate Lyase Knockdown Induces Growth Arrest and Apoptosis through Different Cell- and Environment-Dependent Mechanisms (2012)

ATP citrate lyase (ACLY) is a cytosolic enzyme that catalyzes generation of acetyl-CoA, which is a vital building block for fatty acid, cholesterol, and isoprenoid biosynthesis. ACLY is upregulated in several types of cancer, and its inhibition induces proliferation arrest in certain cancer cells. As ACLY is involved in several pathways, its downregulation may affect multiple processes. Here, we have shown that short hairpin RNA-mediated ACLY silencing in cell lines derived from different types of cancers induces proliferation, cell-cycle arrest, and apoptosis. However, this antiproliferative effect of ACLY knockdown was observed only when cells were cultivated under lipid-reduced growth conditions. Proliferation arrest induced by ACLY silencing was partially rescued by supplementing the media with fatty acids and/or cholesterol. This indicates that the ACLY knockdown-mediated growth arrest might be the result of either fatty acid or cholesterol starvation or both. In the absence of ACLY, the cancer cells displayed elevated expression of sterol regulatory element binding protein-regulated downstream genes involved in de novo fatty acid and cholesterol biosynthesis. Furthermore, ACLY suppression resulted in elevated expression of acyl-CoA synthetase short-chain family member 2 (ACSS2), an enzyme that also produces acetyl-CoA using acetate as a substrate. Acetate supplementation partially rescued the cancer cells from ACLY suppression-induced proliferation arrest. We also observed that the absence of ACLY enhanced ACSS2-dependent lipid synthesis. These findings provide new insights into the role of ACLY in cancer cell growth and give critical information about the effects of ACLY silencing on different pathways. This information is crucial in understanding the possible application of ACLY inhibition in cancer therapeutics.
A Fluorescence Affinity Hollow Fiber Sensor for Continuous Transdermal Glucose Monitoring (2000)

A novel concept of a fluorescence affinity hollow fiber sensor for transdermal glucose monitoring is demonstrated. The glucose-sensing principle is based on the competitive reversible binding of a mobile fluorophore-labeled Concanavalin A (Con A) to immobile pendant glucose moites inside of intensely colored Sephadex beads. The highly porous beads (molecular weight cutoff of 200 kDa) were colored with two red dyes, Safranin O and Pararosanilin, selected to block the excitation and spectrum of the fluorophore Alexa488. The sensor consists of the dyed beads and Alexa488-Con A confined inside a sealed, small segment of a hollow fiber dialysis membrane (diameter 0.5 mm, length 0.5 cm, molecular weight cutoff 10 kDa). In the absence of glucose, the majority of Alexa488-Con A resides inside the colored beads bound to fixed glucose. Thus, excitation light at 490 nm impinging on the sensor is strongly absorbed by the dyes, resulting in a drastically reduced fluorescence emission at 520 nm from the Alexa488-Con A residing within the beads. However, when the hollow fiber sensor is exposed to glucose, glucose diffuses through the membrane into the sensor chamber and competitively displaces Alexa 488-Con A molecules from the glucose residues of the Sephadex beads. Thus, Alexa 488-Con A appears in the void space outside of the beads and is fully exposed to the excitation light, and a strong increase in fluorescence emission at 520 nm is measured. At a medium to high loading degree of Sephadex with Alexa488-Con A (10 mg mL(-1) bead suspension), the absolute fluorescence increase due to 20 mM glucose was very large. It exceeded the response of other sensor devices based on FRET by a factor of 50 (Meadows and Schultz Anal. Chim. Acta 1993, 280, 21-30; Russell et al. Anal. Chem. 1999, 71, 3126-3132). The new sensor featured a glucose detection range extending from 0.15 to 100 mM, exhibiting the strongest dynamic signal change from 0.2 to 30 mM. It showed a reasonably fast response time (4-5 min). The combination of all the beneficial sensor features makes this sensor extremely attractive for future in vivo implantation studies for glucose monitoring in subdermal tissue.
Mental-organic framework derived CuO hollow spheres as high performance anodes for sodium ion battery (2016)

Hollow cupric oxide (CuO) spheres are successfully prepared via annealing a mental-organic framework precursor (HKUST-1). As novel anode materials for sodium ion batteries, the as-prepared CuO delivers high initial reversible capacity of 612 mAh g−1 and good capacity retention of 83% after 50 cycles with superior rate capability.
The Role of AMP-Activated Protein Kinase in Obesity (2008)

AMP-activated protein kinase (AMPK) is a major regulator of energy metabolism at both the cell and at the whole body level. Numerous genetic and obesity models as well as human studies have suggested a role for AMPK in the physiological regulation of fatty acid and glucose metabolism, and in the regulation of appetite. Changes in AMPK activity have been reported in obesity, type 2 diabetes, the metabolic syndrome and cardiovascular disease, which jointly represent a major health and economical problem worldwide. Whether AMPK changes are one of the causes or the consequence of these pathological conditions remains a matter of debate, but AMPK clearly represents a major potential pharmacological target in the treatment of these conditions.
Size and shape-controlled synthesis of Ru nanocrystals (2018)

Abstract Mastery over the size/shape of nanocrystals (NCs) enables control of their properties and enhancement of their usefulness for a given application. Within the past decades, the development of wet-chemistry methods leads to the blossom of research in noble metal nanomaterials with tunable sizes and shapes. We herein would prefer to devote this chapter to introduce the solution-based methods for size and shape-controlled synthesis of ruthenium (Ru) NCs, which can be summarized into five categories: (i) Synthesis of spherical Ru NCs; (ii) synthesis of one-dimensional (1D) Ru NCs, e.g. wires and rods; (iii) synthesis of two-dimensional (2D) Ru NCs, e.g. nanoplates; (iv) synthesis of Ru NCs with hollow interiors and (v) synthesis of Ru NCs with other morphologies, e.g. chains, dendrites and branches. We aim at highlighting the synthetic approaches and growth mechanisms of these types of Ru NCs. We also introduce the detailed characterization tools for analysis of Ru NCs with different sizes/shapes. With respect to the creation of great opportunities and tremendous challenges due to the accumulation in noble metal nanomaterials, we briefly make some perspectives for the future development of Ru NCs so as to provide the readers a systematic and coherent picture of this promising field. We hope this reviewing effort can provide for technical bases for effectively designing and producing Ru NCs with enhanced physical/chemical properties. Graphical Abstract : The solution-based methods for size and shape-controlled synthesis of ruthenium nanocrystals as well as the mechanisms behind them are extensively reviewed.
All screen printed mass produced Silicon Ink selective emitter solar cells (2010)

The Innovalight Cougar™ Platform is a portfolio of simple to implement technologies that, when combined with Innovalight Silicon Ink, enables the manufacture of a selective emitter solar cell with a non-masking single-step diffusion. Innovalight Silicon Ink is a highly engineered silicon nanoparticle colloidal dispersion, implemented for both high volume ink-jet and screen-print deposition, and further optimized to be produced and delivered in commercial volumes. With the addition of an industrial high throughput screen printing system, used to deposit and dry the Silicon Ink, the Cougar Platform requires the same tools and materials used in a standard screen printed solar cell manufacturing line. Consequently, the Cougar Platform improves the efficiency of standard screen printed solar cells by about 1% absolute at a manufacturing cost lower (in terms of $/W) than that of conventional homogeneous emitter front-contact solar cells. Cell efficiencies, on 125mm × 125mm Cz-Si wafers, of up to 19% have been recorded for Cougar cells processed initially at the Innovalight 10MW pilot line. Mass production data coming from the JA Solar manufacturing site, demonstrate median cells efficiencies of 18.6%.
Microbial β-Glucosidases: Cloning, Properties, and Applications (2002)

Beta-glucosidases constitute a major group among glycosylhydrolase enzymes. Out of the 82 families classified under glycosylhydrolase category, these belong to family 1 and family 3 and catalyze the selective cleavage of glucosidic bonds. This function is pivotal in many crucial biological pathways, such as degradation of structural and storage polysaccharides, cellular signaling, oncogenesis, host-pathogen interactions, as well as in a number of biotechnological applications. In recent years, interest in these enzymes has gained momentum owing to their biosynthetic abilities. The enzymes exhibit utility in syntheses of diverse oligosaccharides, glycoconjugates, alkyl- and aminoglucosides. Attempts are being made to understand the structure-function relationship of these versatile biocatalysts. Earlier reviews described the sources and properties of microbial beta-glucosidases, yeast beta-glucosidases, thermostable fungal beta-glucosidase, and the physiological functions, characteristics, and catalytic action of native beta-glucosidases from various plant, animal, and microbial sources. Recent efforts have been directed towards molecular cloning, sequencing, mutagenesis, and crystallography of the enzymes. The aim of the present article is to describe the sources and properties of recombinant beta-glucosidases, their classification schemes based on similarity at the structural and molecular levels, elucidation of structure-function relationships, directed evolution of existing enzymes toward enhanced thermostability, substrate range, biosynthetic properties, and applications.
2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference (2003)

This document reflects a process whereby a group of experts and opinion leaders revisited the 1992 sepsis guidelines and found that apart from expanding the list of signs and symptoms of sepsis to reflect clinical bedside experience, no evidence exists to support a change to the definitions. This lack of evidence serves to underscore the challenge still present in diagnosing sepsis in 2003 for clinicians and researchers and also provides the basis for introducing PIRO as a hypothesis-generating model for future research.
Morphological instability of crystals grown from thin aqueous solution films with a free surface (1995)

Abstract Morphological instability has been studied experimentally in the growth from dilute Ba(NO3)2aqueous solution of crystal films with free surfaces. The observation of transitions from faceted crystal to dendrite, and then to fractal-like patterns is presented. The micro-morphologies of these patterns are investigated. It is suggested that the competition between the step movement and the solute transfer in the growth of thin films determines the stability of the faceted crystal comers. The fractal-like pattern is attributed to random successive nucleation, which is induced by the decrease of the nucleation barrier at high supersaturation and the disturbance caused by the competition between surface-tension-gradient and wetting effects.
Invariant NKT Cell Reconstitution in Pediatric Leukemia Patients Given HLA-Haploidentical Stem Cell Transplantation Defines Distinct CD4+ and CD4− Subset Dynamics and Correlates with Remission State (2011)

Immune reconstitution plays a crucial role on the outcome of patients given T cell-depleted HLA-haploidentical hematopoietic stem cell transplantation (hHSCT) for hematological malignancies. CD1d-restricted invariant NKT (iNKT) cells are innate-like, lipid-reactive T lymphocytes controlling infections, cancer, and autoimmunity. Adult mature iNKT cells are divided in two functionally distinct CD4(+) and CD4(-) subsets that express the NK receptor CD161 and derive from thymic CD4(+)CD161(-) precursors. We investigated iNKT cell reconstitution dynamics in 33 pediatric patients given hHSCT for hematological malignancies, with a follow-up reaching 6 y posttransplantation, and correlated their emergence with disease relapse. iNKT cells fully reconstitute and rapidly convert into IFN-γ-expressing effectors in the 25 patients maintaining remission. CD4(+) cells emerge earlier than the CD4(-) ones, both displaying CD161(-) immature phenotypes. CD4(-) cells expand more slowly than CD4(+) cells, though they mature with significantly faster kinetics, reaching full maturation by 18 mo post-hHSCT. Between 4 and 6 y post-hHSCT, mature CD4(-) iNKT cells undergo a substantial expansion burst, resulting in a CD4(+)<CD4(-) NKT cell ratio similar to that found in healthy adults. In contrast with patients maintaining remission, iNKT cells failed to reconstitute in all eight patients experiencing disease relapse. These findings define the peripheral dynamics of human iNKT cells and suggest a contribution of these cells to maintain remission, possibly via early IFN-γ provision. Adoptive transfer of donor-derived iNKT cells into HLA-haploidentical patients failing to reconstitute these cells might represent a novel therapeutic option to prevent leukemia recurrence.
Adriamycin‐mediated nitration of manganese superoxide dismutase in the central nervous system: insight into the mechanism of chemobrain (2006)

Adriamycin (ADR), a potent anti-tumor agent, produces reactive oxygen species (ROS) in cardiac tissue. Treatment with ADR is dose-limited by cardiotoxicity. However, the effect of ADR in the other tissues, including the brain, is unclear because ADR does not pass the blood-brain barrier. Some cancer patients receiving ADR treatment develop a transient memory loss, inability to handle complex tasks etc., often referred to by patients as chemobrain. We previously demonstrated that ADR causes CNS toxicity, in part, via systemic release of cytokines and subsequent generation of reactive oxygen and nitrogen species (RONS) in the brain. Here, we demonstrate that treatment with ADR led to an increased circulating level of tumor necrosis factor-alpha in wild-type mice and in mice deficient in the inducible form of nitric oxide (iNOSKO). However, the decline in mitochondrial respiration and mitochondrial protein nitration after ADR treatment was observed only in wild-type mice, not in the iNOSKO mice. Importantly, the activity of a major mitochondrial antioxidant enzyme, manganese superoxide dismutase (MnSOD), was reduced and the protein was nitrated. Together, these results suggest that NO is an important mediator, coupling the effect of ADR with cytokine production and subsequent activation of iNOS expression. We also identified the mitochondrion as an important target of ADR-induced NO-mediated CNS injury.
Overcoming the screening-induced performance limits of nanowire biosensors: A simulation study on the effect of electro-diffusion flow (2008)

Device-level simulation capabilities have been developed to self-consistently model the Si-nanowire (NW) biosensor systems. Our numerical study demonstrates that by introducing electro-diffusion current flow in the electrolyte solutions, the electrostatic screening of the biological charge can be significantly suppressed; an improvement of the sensed signal strength by >ap10X is indicated. Based on such an operation principle, the screening-induced performance limits on Si-NW biosensors can be overcome.
Computer-aided stepwise service creation environment for intelligent network (2003)

A computer-aided service creation environment (CSCE) which supports easier graphical and stepwise specification descriptions corresponding to various skill levels of service designers and generates service logic programs (SLPs) for the intelligent network is presented. CSCE is mainly composed of a stepwise service specification description conversion system, intelligent editors (IEDs), and an automatic specification verification system. The service specification is described by a layered service specification description language (LSDL) or SDL. IEDs provide service designers with a sophisticated man-machine interface. Three tests are conducted on the described specification and generated SLP. The effectiveness of CSCE is demonstrated by the results of SLPs created for five new practical services.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Water–ice phase transition probed by Raman spectroscopy (2011)

Abstract Raman spectroscopy was used to study the liquid–solid water phase transition. Special attention was devoted to the OHstretching band of the Raman spectrum, which shows monotonous changes in the temperature range between 10 and − 15 °C. The interpretation of this spectral change, as well as a careful analysis of its integrated scattered intensity, led to a spectral marker that allows the determination of the water phase (liquid or solid), and the efficient identification of the liquid–solid phase transition itself. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Production of Transgenic Sheep (2003)

The production of transgenic sheep has proven difficult compared to the mouse and lower animals. The work load is far greater and the rates of success far less by most criteria. However, the benefits to human and animal health and agricultural productivity are potentially enormous (Ward and Nancarrow, Chapter 5) and support for the continuation of the work is assured. Unfortunately, the low rate of transgenesis for sheep, at about 1% of injected, transferred embryos, means that investigation of the regulation of expression of the transgenes, their phenotypic effects, and optimization of the fusion gene constructs, all of utmost importance to the agricultural industry, can seldom be addressed. We know now that the mouse may not be a good model for the sheep, an example being the ovine metallothioneinovine growth hormone fusion gene, GH9, for which expression and phenotypic effects were quite different for sheep and mice. In sheep, pronuclear microinjection of several hundred copies of the foreign gene into embryos is the only published method used to regularly produce transgenics and it will be the standard by which future methods for incorporation of the transgene are judged.
Effect of Ovarian Hormones on Glucose Metabolism in Mouse Soleus Muscle (1985)

The effects of ovarian steroid hormones on insulin binding and insulin-stimulated glucose metabolism were studied in soleus muscles isolated from groups of ovariectomized adult female mice treated orally for 10 weeks with replacement doses of 17 beta-estradiol (E2) (5 micrograms/kg X day) and progesterone (P) (1 mg/kg X day) alone and in combination. Groups of intact and ovariectomized mice were also treated with placebo. Total muscle insulin binding at 0.17 nM insulin was reduced by 32% in ovariectomized mice, and this effect was partially reversed by each of the sex steroid treatments. Ovariectomy was associated with a decrease (29%) in insulin-stimulated 2-deoxyglucose uptake, while E2 alone produced a 2-fold increase in insulin-stimulated 2-deoxyglucose uptake, glucose oxidation, and glycogenesis. P alone did not significantly alter these parameters of glucose metabolism, but P antagonized the effects of E2 when the two hormones were administered in combination. The results provide evidence that E2 promotes insulin-mediated glucose uptake and utilization in skeletal muscle. The data also indicate that E2 and P exert different effects at postreceptor sites of the insulin effector pathway.
Synthetic Nerve Guide Implants in Humans: A Comprehensive Survey (2006)

To treat longer defects, further implant development is needed, a goal that could be achieved, for example, by more closely imitating the intact nerve architecture and regulatory cell-cell interactions.
Analysis of Epitopes on Dengue Virus Envelope Protein Recognized by Monoclonal Antibodies and Polyclonal Human Sera by a High Throughput Assay (2012)

Our analyses have implications for epitope-specific diagnostics and epitope-based dengue vaccines. This high throughput method has tremendous application for mapping both intra and interdomain epitopes recognized by human mAbs and polyclonal sera, which would further our understanding of humoral immune responses to DENV at the epitope level.
Prediction of Physicochemical Parameters by Atomic Contributions (1999)

We present a new atom type classification system for use in atom-based calculation of partition coefficient (log P) and molar refractivity (MR) designed in part to address published concerns of previous atomic methods. The 68 atomic contributions to log P have been determined by fitting an extensive training set of 9920 molecules, with r2 = 0.918 and σ = 0.677. A separate set of 3412 molecules was used for the determination of contributions to MR with r2 = 0.997 and σ = 1.43. Both calculations are shown to have high predictive ability.
Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage (2017)

Taken together, these findings provide guidance for the design of HDR donor vectors and the selection of HDR-enhancing factors for applications in genome research and precision medicine.
“Transcription physiology” of pigment formation in melanocytes: central role of MITF (2010)

Melanin production is the primary mechanism protecting human skin against the UV light-induced damage. The polymeric compound melanin is synthesized within melanocytes in the specialized subcellular organelles, termed melanosomes, which are then transferred to surrounding keratinocytes. The genes for melanin synthesis and deposition are coordinately expressed in melanocytes. The transcription factor MITF, which has been reported to activate more than 25 genes in pigment cells, has emerged as an essential regulator not only for melanocyte development, proliferation and survival, but also for the expression of enzymes and structural proteins ensuring the production of melanin. MITF is a transcriptional activator of several genes which encode melanosome-localized proteins involved both in melanin synthesis and in melanosome biogenesis and transport, including genes whose mutations are associated with human oculocutaneous and ocular forms of albinism. Here, we outline the mechanisms of transcriptional regulation of genes associated with the biosynthesis of melanin in melanocytes and melanoma cells. MITF is crucial in this process, while several other factors seem to have only an auxiliary role to play under specific circumstances.
The index influenza A virus subtype H5N1 isolated from a human in 1997 differs in its receptor-binding properties from a virulent avian influenza virus (2004)

To gain insight into the events that occur when avian influenza viruses are transmitted to humans, the receptor-binding properties of the index H5N1 influenza virus isolated from a human in 1997 and the A/turkey/Ontario/7732/66 (H5N9) virus were compared, by using a haemadsorption assay. Cells expressing the haemagglutinin (HA) of the human isolate were adsorbed by both chicken red blood cells (RBCs) and human RBCs; those expressing the avian virus HA were only adsorbed by chicken RBCs. These results indicate that human and avian influenza virus H5 HAs differ in their recognition of sialyloligosaccharides on the RBCs of different animal species. Mutational analyses indicated that differences in both the oligosaccharide chains and in the amino acid sequences around the HA receptor-binding site were responsible for this difference in receptor binding. These data further support the concept that alteration in receptor recognition is important for replication of avian viruses in humans.