gebhart/patrepeval huggingface dataset:
Acute Myeloid Leukemia Is Characterized by Wnt Pathway Inhibitor Promoter Methylation. (2008)

Abstract The Wnt pathway contributes to a stem-cell like phenotype in a variety of cancer subtypes. Nuclear localization of non-phosphorylated, active β-catenin is a surrogate marker for Wnt pathway activation and has been associated with adverse outcome in patients with acute myeloid leukemia (AML). Wnt pathway inhibitors including APC, DKK1, DKK3, LKB1/STK11, RASSF1A, RUNX3, SFRP1, SFRP2, SFRP4, SFRP5, SOX17, and WIF1 contain extensive promoter region CpG islands. Wnt pathway inhibitors are silenced by promoter methylation in many malignancies including lung cancer, colon cancer and acute lymphoid leukemias. To determine if methylation of these Wnt pathway inhibitors is present in AML, we evaluated leukemia cell lines (i.e., K562, HNT34, KG1, KG1A, U937, and HL60) for evidence of promoter methylation. Additionally, 188 AML patient (median age 61 years) samples from the Johns Hopkins Hospital leukemia tumor bank were assessed for the presence of Wnt pathway inhibitor methylation. All samples were bisulfite treated and evaluated for promoter methylation using methylation specific PCR. Diagnostic samples from a subgroup of patients with normal cytogenetics (n=73) who received high dose induction therapy were evaluated for potential associations between methylation of individual Wnt pathway inhibitor genes or total number of methylated genes and event free or overall survival. RESULTS: Extensive promoter methylation of the Wnt pathway inhibitor genes was observed in leukemia cell lines. Of the primary leukemia samples, 85% had at least one methylated gene. Promoter methylation of Wnt inhibitors was common in these samples with the following frequencies: DKK1 (16%;30/188), DKK3 (8%;15/188), RUNX3 (27%;50/188), SFRP1 (34%;63/188), SFRP2 (66%;124/188), SFRP4 (9%;16/188), SFRP5 (54%;102/188), SOX17 (29%;54/188), and WIF1 (32%;61/188). This is among the first comprehensive evaluations of Wnt pathway inhibitor methylation in primary samples from AML patients. The frequency of methylation seen here is comparable to that observed in established tumor suppressor genes in patients with AML, including p15INK4B, SOCS1 and CDH1. In marked contrast with epithelial tumors, methylation of APC (2%;2/108) and RASSF1A (0%;0/188) was rare. LKB1/STK11 methylation was also uncommon (2%;2/108). Previous reports have associated Wnt pathway activation with poor prognosis. In our treated patients with normal cytogenetics, no correlation was observed between methylation of Wnt pathway inhibitors and event free or overall survival. In conclusion, in patients with AML (a) there is a high frequency of Wnt pathway inhibitor methylation; (b) Wnt pathway inhibitor methylation is distinct from that observed in epithelial malignancies; and (c) methylation of Wnt pathway genes does not correlate with adverse clinical outcome.
Structure of anionic salmon trypsin in a second crystal form (1995)

Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at 1.83 A, resolution. The crystals are orthorhombic and belong to space group P2(1)2(1)2 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 A. The present structure has been compared to salmon trypsin as it appears in a previously reported crystal form (ST-IIA) with cell dimensions a = 61.95, b = 84.33 and c = 39.11 A [Smalås & Hordvik (1993). Acta Cryst. D49, 318-330]. The presence of a sulfate group involved in several hydrogen bonds to active-site residues, and the location of an additional benzamidine site in the crystal lattice, are the most striking differences between the present and the previous structure. Superposition of main-chain atoms in the two structures give an overall r.m.s. difference of 0.26 A, with the main differences located to areas with different molecular packing. The overall coordinate error is estimated to be between 0.20 and 0.25 A, by the method of Luzzati.
Modeling and Speed Control for a Doubly-Salient Special Machine Employing a High-Fidelity Plant Model (2022)

Analytical modeling and evaluation of field-oriented control for a high-power density three-phase doubly-salient special machine are presented in this paper. The special machine contains 12 modular concentrated coils and 12 PMs in the stator and 10 pole protrusions in the rotor. The machine has been designed to operate at a rated torque of 42Nm at a base speed of 5000rpm. A generalized dynamic torque equation and an analytical model for the proposed special machine are established. The dynamic model has been used to realize an equivalent circuit by applying the synchronous reference frame theory. A high-fidelity plant model of the special machine has been developed using FEA software, and the machine characteristics have been imported into motor drive simulation software for speed control analysis. A field-oriented control technique for the special machine in synchronous reference frame has been implemented to regulate the speed over a wide range in both constant torque and field weakening regimes for electric vehicle traction applications. Stability analysis for the controller has been presented and verified by simulations in continuous domain.
Materials and Fabrication Methods for High Temperature Micro-Magnetic Machines for Micro-Turbine Power Generation (2003)

This paper presents recent advances in the development of materials and fabrication methods for high temperature (400 - 900 C) magnetic micro-machine for electrical power generation. Suitable materials and material compatibility issues are identified for the device conductors, magnetic cores, and bulk structure. Two fabrication methods for encapsulating electroplated structures inside fusion bonded silicon wafers are presented. These fabrication techniques enable the integration of thick conductive and magnetic materials into multi-wafer silicon MEMS devices. Electrical tests verify the integrity of electroplated Cu conductors after wafer bond annealing and mechanical tests confirm that the presence of the metal does not adversely affect the bond strength. Preliminary results of electrodeposited ferromagnetic Fe-Co materials are also discussed.
Abstract 1036: Cellular phenotypes of a novel series of 3-phosphoglycerate dehydrogenase inhibitors (2016)

Abstract PHGDH (3-phosphoglycerate dehydrogenase) is the first enzyme branching from glycolysis into the serine synthetic pathway and it oxidizes 3-phosphoglycerate into phospho-hydroxypyruvate using nicotinamide adenine dinucleotide (NAD) as cofactor.[1] Increases in PHGDH expression at both mRNA and protein levels have been observed in nearly 70% of estrogen receptor-negative breast cancers; in addition a fraction of malignant breast and melanoma cells are dependent on elevated expression of 3-phosphoglycerate dehydrogenase (PHGDH).[2] Furthermore, serine starvation has been shown to have a dramatic effect on tumor growth during in vivo mouse xenograft experiments.[3] PHGDH has been a target of interest in the pharma/biotech industry for several years since the initial reports in early 2012 of its relevance in cancer2 where PHGDH amplified and overexpressing cancer cell lines have been shown to possess unique sensitivity to PHGDH knockdown that cannot be rescued by nutritional serine. The mechanisms underlying these studies have been subject to intense investigation but remain unclear. We have been able to successfully identify first in class small molecule inhibitors of this target with nanomolar cellular potency, high degree of selectivity and oral bioavailability. In several cancer cell lines, these compounds inhibited glucose derived serine flux with nanomolar median inhibitory concentrations without significantly affecting glucose derived lactate. These compounds also inhibited glucose derived serine in animal studies and have the potential to be highly useful tools for understanding the role of PHGDH in tumor progression. The data presented here will provide unexpected insights on the role of PHGDH in serine biosynthesis and the dependency of cancer cells on PHGDH catalytic function. References [1] Snell, K. Enzymes of serine metabolism in normal, developing and neoplastic rat tissues. Advances in enzyme regulation. 1984; 22:325-400. [2] Cantor, J.R.; Sabatini, D. M. Cancer Cell Metabolism: One Hallmark, Many Faces, Cancer Discovery. 2012; 2(10):881-898. [3] Maddocks et al., Serine starvation induces stress and p53-dependent metabolic remodeling in cancer cells Nature, 2013, 493(7433):542-6 Citation Format: Nello Mainolfi, Adam Friedman, Mikel P. Moyer, Vipin Suri, Mark Manfredi. Cellular phenotypes of a novel series of 3-phosphoglycerate dehydrogenase inhibitors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1036.
Blind detection for disparity-coherent stereo video watermarking (2014)

Stereo video content calls for new watermarking strategies, e.g. to achieve robustness against virtual view synthesis. Prior works focused either on inserting the watermark in an invariant domain or on guaranteeing that the watermarks introduced in the left and right views are coherent with the disparity of the scene. However, the first approach raises fidelity issues while the second requires side information at detection i.e. the detector is not blind. In this paper, we propose a new blind detection procedure for disparity-coherent watermarks. In a nutshell, the detector relies on cross-correlation to aggregate the scattered pieces of the embedded reference watermark pattern rather than warping the reference pattern according to the parameters of the current view prior to detection. Reported experimental results indicate that this revisited detector successfully manages to retrieve embedded watermarks even after lossy compression.
The Mitsunobu Reaction of Tetrachlorophthalimide (1999)

Tetrachlorophthalimide is shown to be an excellent agent for Mitsunobu displacement of primary hydroxyl groups in a wide variety of substrates. Secondary alcohols also react readily, except in carbohydrate derivatives where there is a low rate of success. In a competition experiment between phthalimide and its tetrachloro counterpart, there was no trace of a product from the former.
Error-Prediction LDPC and Error-Recovery Schemes for Highly Reliable Solid-State Drives (SSDs) (2013)

Highly reliable solid-state drives (SSDs) with error-prediction low-density parity-check (EP-LDPC) and error-recovery schemes are proposed. Since the reliability of the nand flash memory of the SSD is seriously degraded as the scaling, the conventional error-correction scheme is becoming useless. Thus, LDPC error-correcting code (ECC) is considered to be the next-generation ECC for SSD. However, many read cycles are required and the LDPC scheme consumes an unacceptably long read time. To solve this problem, the proposed EP-LDPC scheme realizes the 7 × fewer sequential read cycles than the conventional LDPC scheme. Instead of reading repeatedly, the EP-LDPC scheme estimates errors from VTH, write/erase cycles, data-retention time, and inter-cell coupling information. The bit error rate (BER) estimation is based on the prerecorded table which stores the relations among write/erase cycles, data-retention time, neighboring cell data, and BER. As a result, the acceptable data-retention time of the SSD increases by more than 10 ×. Additionally, the proposed error-recovery scheme is executed and reduces the bit error if the BER of the data exceeds the error-correction capability of EP-LDPC scheme. Program-disturb error-recovery pulse and data-retention error-recovery pulse reduce the BER of the nand flash memory by 76% and 56%, respectively.
Subretinal Gene Therapy of Mice With Bardet-Biedl Syndrome Type 1 (2013)

In a knock-in model of BBS1, subretinal delivery of AAV-Bbs1 rescues BBSome formation and rhodopsin localization, and shows a trend toward improved ERG. BBS is challenging to treat with gene therapy due to the stoichiometry of the BBSome protein complex and overexpression toxicity.
Detailed routing with advanced flexibility and in compliance with self-aligned double patterning constraints (2013)

In this paper, we propose a new flexible routing method for Self-Aligned Double Patterning (SADP). SADP is one of the most promising candidates for patterning sub-20 nm node advanced technology but wafer images must satisfy tighter constraints than litho-etch-litho-etch process. Previous SADP routing methods require strict constraints induced from the relation between mandrel and trim patterns, so design freedom is unexpectedly lost. Also these methods assume to form narrow patterns by trimming process without consideration of resolution limit of optical lithography. The proposed method realizes flexible SADP routing with dynamic coloring requiring no decomposition to extract mandrel patterns and no worries about coloring conflicts. The proposed method uses realizable trimming process only for insulation of patterns. The effectiveness of the proposed method is confirmed in the experimental comparisons.
Block Polymer (2017)

IUPAC recommendations on source-based nomenclature for single-strand polymers have so far addressed its application mainly to copolymers, non-linear polymers and polymer assemblies, and within generic source-based nomenclature of polymers. In this document, rules are formulated for devising a satisfactory source-based name for a polymer, whether homopolymer or copolymer, which are as clear and rigorous as possible. Thus, the source-based system for naming polymers is presented in a totality that serves as a user-friendly alternative to the structure-based system of polymer nomenclature. In addition, because of their widespread and established use, recommendations for the use of traditional names of polymers are also elaborated.
XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair (2011)

The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts nonhomologous end joining functions has been enigmatic. Here, we report the XLF-XRCC4 complex crystal structure in combination with biophysical and mutational analyses to define the XLF-XRCC4 interactions. Crystal and solution structures plus mutations characterize alternating XRCC4 and XLF head domain interfaces forming parallel super-helical filaments. XLF Leu-115 ("Leu-lock") inserts into a hydrophobic pocket formed by XRCC4 Met-59, Met-61, Lys-65, Lys-99, Phe-106, and Leu-108 in synergy with pseudo-symmetric β-zipper hydrogen bonds to drive specificity. XLF C terminus and DNA enhance parallel filament formation. Super-helical XLF-XRCC4 filaments form a positively charged channel to bind DNA and align ends for efficient ligation. Collective results reveal how human XLF and XRCC4 interact to bind DNA, suggest consequences of patient mutations, and support a unified molecular mechanism for XLF-XRCC4 stimulation of DNA ligation.
Organocatalytic Asymmetric 5‐Hydroxyisoxazolidine Synthesis: A Highly Enantioselective Route to β‐Amino Acids. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Artificial intelligence for gastroenterology: Singapore artificial intelligence for Gastroenterology Working Group Position Statement (2023)

These series of Position Statements point out the salient issues to maintain the trust between care provider and care receivers, and to legitimize the use of a non-human tool in healthcare delivery. It is based on fundamental principles such as respect, autonomy, privacy, responsibility, and justice. Enforcing the use of AI without considering these factor risk damaging the doctor-patient relationship.
Stable Silver Nanoparticles Immobilized in Mesoporous Silica (2003)

Silver nanoparticles have been produced by γ-irradiation of silver solution in optically transparent inorganic mesoporous silica. The reduction of Ag+ within the matrix is brought about by hydrated electrons and hydroalkyl radicals generated during the radiolysis of the 2-propanol solution. The particles formed within the silica matrix were studied by electron microscopy, nitrogen sorption measurements, and absorption spectroscopy. The particles were mostly confined and dispersed in the pores of the mesoporous hosts. Absorption spectra show that the mean Ag clusters size increases with the irradiation dose. At high dose, agglomerated large particles are formed. In contrast, at a given dose, the effect of the dose rate has been clearly demonstrated to lower the cluster size. The silver particles within the silica matrix are stable in the presence of oxygen for at least several months.
The Capsular Polysaccharide of Staphylococcus aureus Is Attached to Peptidoglycan by the LytR-CpsA-Psr (LCP) Family of Enzymes (2014)

Envelope biogenesis in bacteria involves synthesis of intermediates that are tethered to the lipid carrier undecaprenol-phosphate. LytR-CpsA-Psr (LCP) enzymes have been proposed to catalyze the transfer of undecaprenol-linked intermediates onto the C6-hydroxyl of MurNAc in peptidoglycan, thereby promoting attachment of wall teichoic acid (WTA) in bacilli and staphylococci and capsular polysaccharides (CPS) in streptococci. S. aureus encodes three lcp enzymes, and a variant lacking all three genes (Δlcp) releases WTA from the bacterial envelope and displays a growth defect. Here, we report that the type 5 capsular polysaccharide (CP5) of Staphylococcus aureus Newman is covalently attached to the glycan strands of peptidoglycan. Cell wall attachment of CP5 is abrogated in the Δlcp variant, a defect that is best complemented via expression of lcpC in trans. CP5 synthesis and peptidoglycan attachment are not impaired in the tagO mutant, suggesting that CP5 synthesis does not involve the GlcNAc-ManNAc linkage unit of WTA and may instead utilize another Wzy-type ligase to assemble undecaprenyl-phosphate intermediates. Thus, LCP enzymes of S. aureus are promiscuous enzymes that attach secondary cell wall polymers with discrete linkage units to peptidoglycan.
Estimated Phytate Intake Is Associated with Bone Mineral Density in Mediterranean Postmenopausal Women (2023)

The main objective of this work was to explore the association of dietary phytate intake with bone mineral density (BMD) in a Mediterranean population of postmenopausal women. For this purpose, a cross-sectional analysis of 561 women aged 55-75 years with overweight/obesity and metabolic syndrome from a Mediterranean area and with data on dual-energy X-ray absorptiometry (DXA) scans in femur and lumbar spine was performed. Estimated phytate intake was calculated using a validated food frequency questionnaire. Our results indicated that phytate intake was associated with BMD [β(95%CI) per each 25 mg/100 kcal] in femoral neck [0.023(0.060-0.040) g/cm<sup>2</sup>], femoral Ward's triangle [0.033(0.013-0.054) g/cm<sup>2</sup>], total femur [0.018(0.001-0.035) g/cm<sup>2</sup>], and all the analyzed lumbar spine sites [L1-L4: 0.033(0.007-0.059) g/cm<sup>2</sup>] after adjusting for potential confounders. The sensitivity analysis showed that phytate intake was directly associated with lumbar spine BMD in women younger than 66 years, with a body mass index higher than 32.6 kg/cm<sup>2</sup> and without type 2 diabetes (all <i>p</i>-for interactions < 0.05). The overall results indicated that phytate, a substance present in food as cereals, legumes and nuts, was positively associated with BMD in Mediterranean postmenopausal women. Phytate may have a protective effect on bone resorption by adsorbing on the surfaces of HAP. Nevertheless, large, long-term, and randomized prospective clinical studies must be performed to assess the possible benefits of phytate consumption on BMD in postmenopausal women.
Interesterification of Vegetable Oils with Methyl or Ethyl Acetate Catalysed by Tin Compounds (2013)

The interesterification of rapeseed oil was performed in a batch reactor changing the reaction temperature in the interval 120-210 °C and using several tin (II) compounds as catalysts and methyl or ethyl acetate as acyl acceptors. The yields in esters and triacetin increased with the reaction temperature. An important parameter to optimize was the acyl donor to oil molar ratio: too low values seemed to be detrimental while too high values does not alter significantly the values of yields in esters and triacetin. The ester yields were also affected by the nature of the alkyl acetate since the methyl homologue led to higher values of this parameter with respect to the ethyl one at similar operative conditions. The best performances of the interesterification of rapeseed oil were obtained with tin(II) octoate and tin(II) chloride.
Modeling and performance of a polarization active imager at λ=806 nm (1999)

We present the modeling and the performances of a Polarization Active Imager at (lambda) equals 806 nm. The device is operating in a monostatic configuration, using a semiconductor laser to illuminate the target and a telescope to create the image on a CCD matrix. Dual images (intensity and polarization degree) of different scenes are obtained by a new method (only 2 images acquisition) and analyzed, showing the experimental validation of this concept. The application of this active imager to the detection of target buried in the background (same reflectivity but different polarization degree) is proposed.
A Modified Three-Port Bidirectional LLC Resonant Converter for Renewable Power Systems (2021)

This paper proposes a new three-port bidirectional LLC resonant converter that interfaces with one PV panel and one battery energy storage system (BESS). The topology is a combination of a boost circuit and a half-bridge LLC circuit with five active switches on the primary side and a full-bridge rectifier composed of four switches on the secondary side. This topology allows the two sources to share the same resonant tank for transferring energy to the load and allows to store the extra energy from the load back into the battery without additional circuit components. In the forward operation, a phase-shift pulse width modulation (PWM) control is employed to implement independent maximum power point tracking (MPPT) for PV panel and the converter voltage gain is controlled by varying the switching frequency as in a traditional LLC resonant converter. In the backward operation, the switching frequency is fixed at resonant frequency. A simulation study was carried out in LTspice software to validate the operating principles of the proposed topology. The PV input voltage range is selected to be 25 V to 40 V and the battery nominal voltage is 50 V with an output voltage regulated at 200 V DC.
Primary versus early secondary referral to a specialized neurotrauma center in patients with moderate/severe traumatic brain injury: a CENTER TBI study (2021)

Across Europe, substantial practice variation exists in the proportion of secondarily referred TBI patients at SNCs that is not explained by case mix. Within SNCs early secondary referral does not seem to impact functional outcome and survival after stabilisation in a non-specialised hospital. Future research should identify which patients with TBI truly benefit from direct transportation.