gebhart/patrepeval huggingface dataset:
A synthetic diphosphoinositol phosphate analogue of inositol trisphosphate (2018)

Diphosphoinositol phosphates (PP-InsPs) are inositol phosphates (InsPs) that contain PP (diphosphate) groups. Converting a phosphate group in an InsP into a diphosphate has been reported to enhance affinity for some binding proteins. We synthesised 1-PP-Ins(4,5)P<sub>2</sub>, the first diphosphate analogue of the intracellular signalling molecule InsP<sub>3</sub>, and examined its effects on InsP<sub>3</sub> receptors, which are intracellular Ca<sup>2+</sup> channels. 1-PP-Ins(4,5)P<sub>2</sub> was indistinguishable from InsP<sub>3</sub> in its ability to bind to and activate type 1 InsP<sub>3</sub> receptors, indicating that the diphosphate modification of InsP<sub>3</sub> affected neither affinity nor efficacy. Nevertheless, 1-PP-Ins(4,5)P<sub>2</sub> is the most potent 1-phosphate modified analogue of InsP<sub>3</sub> yet identified. PP-InsPs are generally hydrolysed by diphosphoinositol phosphate phosphohydrolases (DIPPs), but 1-PP-Ins(4,5)P<sub>2</sub> was not readily metabolised by human DIPPs. Differential scanning fluorimetry showed that 1-PP-Ins(4,5)P<sub>2</sub> stabilises DIPP proteins, but to a lesser extent than naturally occurring substrates 1-PP-InsP<sub>5</sub> and 5-PP-InsP<sub>5</sub>. The non-hydrolysable InsP<sub>7</sub> analogues 1-PCP-InsP<sub>5</sub> and 5-PCP-InsP<sub>5</sub> showed comparable stabilising abilities to their natural counterparts and may therefore be promising substrate analogues for co-crystallisation with DIPPs.
Weight Change in Breast Cancer Survivors Compared to Cancer-Free Women: A Prospective Study in Women at Familial Risk of Breast Cancer (2015)

Our findings provide support for the development of weight gain interventions for young breast cancer survivors with a familial risk.
The genomic and evolutionary landscapes of anaplastic thyroid carcinoma (2023)

Abstract Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas and multi-region whole-genome sequencing. Anaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Specific cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. We unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas, and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.
Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drives rapid and potent immunogenicity capable of single-dose protection (2022)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines may target epitopes that reduce durability or increase the potential for escape from vaccine-induced immunity. Using synthetic vaccinology, we have developed rationally immune-focused SARS-CoV-2 Spike-based vaccines. Glycans can be employed to alter antibody responses to infection and vaccines. Utilizing computational modeling and in vitro screening, we have incorporated glycans into the receptor-binding domain (RBD) and assessed antigenic profiles. We demonstrate that glycan-coated RBD immunogens elicit stronger neutralizing antibodies and have engineered seven multivalent configurations. Advanced DNA delivery of engineered nanoparticle vaccines rapidly elicits potent neutralizing antibodies in guinea pigs, hamsters, and multiple mouse models, including human ACE2 and human antibody repertoire transgenics. RBD nanoparticles induce high levels of cross-neutralizing antibodies against variants of concern with durable titers beyond 6 months. Single, low-dose immunization protects against a lethal SARS-CoV-2 challenge. Single-dose coronavirus vaccines via DNA-launched nanoparticles provide a platform for rapid clinical translation of potent and durable coronavirus vaccines.
2-D images for biopsy guidance and 3-D images for treatment planning and monitoring of prostate cancer based upon spectrum analysis and neural-network classification (2003)

Spectrum analysis of ultrasonic echo signals has been showing potential for distinguishing cancerous from non-cancerous prostate tissues. Recently, using neural networks to classify tissue from spectrum analysis results has provided a powerful basis for imaging, guiding biopsies, and planning, executing, and monitoring therapy. ROC curves derived from leave-one-out evaluations of neural-network classifier performance have an area of 0.87/spl plusmn/0.04 compared to an area of 0.64/spl plusmn/0.04 for B-mode methods, which implies significantly superior differentiation of cancerous from non-cancerous prostate tissue.
PI3K Signaling Through the Dual GTPase–Activating Protein ARAP3 Is Essential for Developmental Angiogenesis (2010)

One function of phosphoinositide 3-kinase α (PI3Kα), which generates the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P(3)], is its regulation of angiogenesis in the developing embryo and in pathological situations. ARAP3 is a PtdIns(3,4,5)P(3)- and Rap-activated guanosine triphosphatase (GTPase)-activating protein (GAP) for the small GTPases RhoA and Arf6. Here, we show that deleting Arap3 in the mouse caused embryonic death in mid-gestation due to an endothelial cell-autonomous defect in sprouting angiogenesis. Explants taken at a developmental stage at which no defect was yet present reproduced this phenotype ex vivo, demonstrating that the defect was not secondary to hypoxia, placental defects, or organ failure. In addition, knock-in mice expressing an ARAP3 point mutant that cannot be activated by PtdIns(3,4,5)P(3) had angiogenesis defects similar to those of Arap3(-/-) embryos. Our work delineates a previously unknown signaling pathway that controls angiogenesis immediately downstream of PI3Kα through ARAP3 to the Rho and Arf family of small GTPases.
Mechanisms and potential immune tradeoffs of accelerated coral growth induced by microfragmentation (2022)

Microfragmentation is the act of cutting corals into small pieces (~1 cm<sup>2</sup>) to accelerate the growth rates of corals relative to growth rates observed when maintaining larger-sized fragments. This rapid tissue and skeletal expansion technique offers great potential for supporting reef restoration, yet the biological processes and tradeoffs involved in microfragmentation-mediated accelerated growth are not well understood. Here we compared growth rates across a range of successively smaller fragment sizes in multiple genets of reef-building corals, <i>Orbicella faveolata</i> and <i>Montastraea cavernosa</i>. Our results confirm prior findings that smaller initial sizes confer accelerated growth after four months of recovery in a raceway. <i>O. faveolata</i> transcript levels associated with growth rate include genes encoding carbonic anhydrase and glutamic acid-rich proteins, which have been previously implicated in coral biomineralization, as well as a number of unannotated transcripts that warrant further characterization. Innate immunity enzyme activity assays and gene expression results suggest a potential tradeoff between growth rate after microfragmentation and immune investment. Microfragmentation-based restoration practices have had great success on Caribbean reefs, despite widespread mortality among wild corals due to infectious diseases. Future studies should continue to examine potential immune tradeoffs throughout the microfragmentation recovery period that may affect growout survival and disease transmission after outplanting.
Design considerations for devices based upon small SOI waveguides (2005)

With the increased desire to miniaturise devices in silicon photonics comes increased difficulty in producing polarisation independent devices whilst maintaining monomode behaviour. In this paper we discuss the design of such devices, and report supportive experimental results.
A Smaller, Faster, and More Energy-Efficient Complementary STT-MRAM Cell Uses Three Transistors and a Ground Grid: More Is Actually Less (2016)

Spin-transfer torque magnetoresistance random access memory is a major contender for static random access memory replacement in embedded caches at advanced fin field effect transistor nodes. It suffers, however, from the low resistance difference between the bistable states of the magnetic tunnel junction (MTJ). Variability on MTJ resistance and access transistors makes reliable read-out even more challenging. This triggered the use of complementary cells for low level caches needing high performance. This paper, focusing on the lower level caches, shows an improved 3T 2MTJ cell with a ground grid and a novel three transistor read and write operation to improve area density, sense margin, write performance, and write energy consumption. Despite the cell's three transistors, the improved array configuration reduces the cell area by 22% as compared with the 2T 2MTJ cell, making it only 55% larger than a 1T 1MTJ cell. The novel mismatch tolerant read operation uses all three transistors and increases the sense margin by up to 88%. The novel variation resilient write operation also uses all three transistors and takes advantage of the inherent MTJ characteristics and complementary operation of the cell. This increases the write performance by 2× and reduces the write energy by 3× compared with the 2T 2MTJ cell and by 1.5× compared with the 1T 1MTJ cell.
Correction: H2S Increases Survival During Sepsis: Protective Effect of CHOP Inhibition (2014)

Ferlito, M., Q. Wang, W. B. Fulton, P. M. Colombani, L. Marchionni, K. Fox-Talbot, N. Paolocci, and C. Steenbergen. 2014. H2S increases survival during sepsis: protective effect of CHOP inhibition. J . Immunol . 192: [1806–1814][1].

In the title, the abbreviation “H2S” should have been
In Vitro Bioactivity of Injectable Ceramic Orthopaedic Cements (2006)

The objective of this paper is to investigate and compare the in vitro bioactivity of three injectable cements for orthopaedic applications. The cements were all based on chemically bonded ceramics technology; calcium phosphate (Norian SRS), and experimental versions of calcium silicate and calcium aluminate cements. The cements were mixed with their respective liquids and were after setting stored in phosphate buffered saline at 37 °C for time periods of 1h, 24 h, 7 days and 30 days. After storage the samples were analysed with scanning electron microscopy (SEM), thin film X-Ray diffraction (TF-XRD) and energy dispersive spectroscopy (EDS) for the presence of possible apatite on the sample surface. The SEM and EDX analyses showed that surface films containing Ca and P (along with the other atoms present in the materials) were formed on all materials. Thus reactions with the storage medium had occurred. The TF-XRD analysis confirmed the presence of apatite for the calcium phosphate cement and the calcium aluminate cement. On the calcium silicate cement most of the surface zone seemed to be amorphous with only broad peaks corresponding to apatite. Thus all the tested materials showed signs of in vitro bioactivity.
Identification of a novel insect neuropeptide, CNMa and its receptor (2014)

To identify ligands for orphan GPCRs, we searched novel neuropeptide genes in the Drosophila melanogaster genome. Here, we describe CNMa, a novel cyclic neuropeptide that is a highly potent and selective agonist for the orphan GPCR, CG33696 (CNMaR). Phylogenetic analysis revealed that arthropod species have two paralogous CNMaRs, but many taxa retain only one. Drosophila CNMa potently activates CNMaR-2 from Apis mellifera, suggesting both receptors are functional. Although CNMa is conserved in most arthropods, Lepidoptera lack the CNMa gene. However, they retain the CNMaR gene. Bombyx CNMaR showed low sensitivity to Drosophila CNMa, hinting toward the existence of additional CNMaR ligand(s).
Novel Fast Degradable Thermosensitive Polymeric Micelles Based on PEG-block-poly(N-(2-hydroxyethyl)methacrylamide-oligolactates) (2005)

The aim of this study was to design a thermosensitive polymeric micelle system with a relatively fast degradation time of around 1 day. These micelles are of interest for the (targeted) delivery of biologically active molecules. Therefore, N-(2-hydroxyethyl)methacrylamide-oligolactates (HEMAm-Lac(n)()) were synthesized and used as building blocks for biodegradable (block co) polymers. p(HEMAm-Lac(2)) is a thermosensitive polymer with a cloud point (CP) of 22 degrees C which could be lowered by copolymerization with HEMAm-Lac(4). The block copolymer PEG-b-((80%HEMAm-Lac(2))-(20%HEMAm-Lac(4))) self-assembled into compact spherical micelles with an average size of 80 nm above the CP of the thermosensitive block (6 degrees C). Under physiological conditions (pH 7.4; 37 degrees C), the micelles started to swell after 4 h and were fully destabilized within 8 h due to hydrolysis of the lactate side chains. Rapidly degrading thermosensitive polymeric micelles based on PEG-b-((80%HEMAm-Lac(2))-(20%HEMAm-Lac(4))) have attractive features as a (targeted) drug carrier system for therapeutic applications.
The Effects of Water on β-d-Xylose Condensation Reactions (2009)

Car-Parrinello-based ab initio molecular dynamics simulations (CPMD) combined with metadynamics (MTD) simulations were used to determine the reaction energetics for the beta-D-xylose condensation reaction to form beta-1,4-linked xylobiose in a dilute acid solution. Protonation of the hydroxyl group on the xylose molecule and the subsequent breaking of the C-O bond were found to be the rate-limiting step during the xylose condensation reaction. Water and water structure was found to play a critical role in these reactions due to the proton's high affinity for water molecules. The reaction free energy and reaction barrier were determined using CPMD-MTD. We found that solvent reorganization due to proton partial desolvation must be taken into account in order to obtain the correct reaction activation energy. Our calculated reaction free energy and reaction activation energy compare well with available experimental results.
(Trifluormethylthioamino)borane, IV. Darstellung und Eigenschaften von [(CF3S)2N]nBX3–n mit n 3; n = 2, X Cl, Br, N3 und n = 1, X N3 (1985)

Abstract Umsetzungen von Hg[N(SCF 3 ) 2 ] 2 ( 4a ) mit BBr 3 , B(SCF 3 ) 3 und BCl 3 führen in abnehmenden Ausbeuten zu B[N(SCF 3 ) 2 ] 3 ( 1 ). Das thermisch stabile 1 ist eine sehr schwache Lewis‐Säure und hydrolyseempfindlich. Setzt man 4a bzw. (CH 3 ) 3 SiN 3 mit (CF 3 S) 2 NBX 2 um, so erhält man [(CF 3 S) 2 N] 2 BX (X  Cl, Br, 2a , b ) bzw. (CF 3 S) 2 NB(N 3 ) 2 ( 3c ). Aus 2a , b und (CH 3 ) 3 SiN 3 erhält man [(CF 3 S) 2 N] 2 BN 3 ( 2c ). Reaktionen von [(CF 3 S) 2 N] n E n [E  Hg, n = 2; (CH 3 ) 3 Sn, (CH 3 ) 3 Si und CF 3 S, n = 1, 4a–d ] mit BX (X′  F, Cl, Br, SCF 3 ) werden im Hinblick auf eine Mehrfach‐Substitution am Bor untersucht. Empirisch ermittelte relative Reaktivitäten der Element‐Stickstoffbindung und Substitutionsreihen von Borverbindungen bezüglich Hg II ‐Verbindungen werden angegeben. Spektroskopische Daten der neu hergestellten Verbindungen werden diskutiert.
Robust i-vector based adaptation of DNN acoustic model for speech recognition (2015)

In the past, conventional i-vectors based on a Universal Background Model (UBM) have been successfully used as input features to adapt a Deep Neural Network (DNN) Acoustic Model (AM) for Automatic Speech Recognition (ASR). In contrast, this paper introduces Hidden Markov Model (HMM) based ivectors that use HMM state alignment information from an ASR system for estimating i-vectors. Further, we propose passing these HMM based i-vectors though an explicit non-linear hidden layer of a DNN before combining them with standard acoustic features, such as log filter bank energies (LFBEs). To improve robustness to mismatched adaptation data, we also propose estimating i-vectors in a causal fashion for training the DNN, restricting the connectivity among hidden nodes in the DNN and applying a max-pool non-linearity at selected hidden nodes. In our experiments, these techniques yield about 5-7% relative word error rate (WER) improvement over the baseline speaker independent system in matched condition, and a substantial WER reduction for mismatched adaptation data.
Single‐Face/All‐cis Arene Hydrogenation by a Supported Single‐Site d0 Organozirconium Catalyst (2016)

Abstract The single‐site supported organozirconium catalyst Cp*ZrBz 2 /ZrS (Cp*=Me 5 C 5 , Bz=benzyl, ZrS=sulfated zirconia) catalyzes the single‐face/all‐cis hydrogenation of a large series of alkylated and fused arene derivatives to the corresponding all‐cis‐cyclohexanes. Kinetic/mechanistic and DFT analysis argue that stereoselection involves rapid, sequential H 2 delivery to a single catalyst‐bound arene face, versus any competing intramolecular arene π‐face interchange.
13 C NMR Studies of the Interaction of Gold(I) Thiomalate with 6-Mercaptopurine and Its Derivatives (2002)

The interaction of gold(I) thiomalate, [Autm] n with thiolated nucleosides, 6-mercaptopurine (6-MP), 6-mercaptopurine-9- g - D -riboside (6-MPR) and 2-amino-6-mercaptopurine-9- g - D -riboside (2-A-6-MPR) has been studied by 1 H and 13 C NMR spectroscopy. It has been observed that these thiolated purine bases break the [Autm] n polymer and form complexes of the type $[\rangle \!{\rm C} {{\hskip -1.7pt \openup -13pt \eqalign{\displaystyle{-\!\!-}\cr\displaystyle{-\!\!-}}\hskip -1.7pt}}\hbox{{\rm S}-{\rm Au-tm}]}$
Ruthenium Olefin Metathesis Catalysts Bearing Carbohydrate-Based N-Heterocyclic Carbenes (2009)

Ru-based olefin metathesis catalysts containing carbohydrate-derived NHCs from glucose and galactose were synthesized and characterized by NMR spectroscopy. 2D-NMR spectroscopy revealed the presence of Ru-C (benzylidene) rotamers at RT and the rate of rotation was measured using magnetization transfer and VT-NMR spectroscopy. The catalysts were found to be effective at ring-opening metathesis polymerization (ROMP), ring closing metathesis (RCM), cross metathesis (CM), and asymmetric ring opening cross metathesis (AROCM) and showed surprising selectivity in both CM and AROCM.
Disseminated Gonococcal Infection in Elderly Patients (1987)

No AccessJournal of UrologyInfections and Antibiotics1 Mar 1987Disseminated Gonococcal Infection in Elderly Patients P.H.L.M. Geelhoed-Duyvestijn, J.W.M. van der Meer, A.T. Lichtendahl-Bernards, C.J. Mulder, K.A.E. Meyers, and J.T. Poolman P.H.L.M. Geelhoed-DuyvestijnP.H.L.M. Geelhoed-Duyvestijn More articles by this author , J.W.M. van der MeerJ.W.M. van der Meer More articles by this author , A.T. Lichtendahl-BernardsA.T. Lichtendahl-Bernards More articles by this author , C.J. MulderC.J. Mulder More articles by this author , K.A.E. MeyersK.A.E. Meyers More articles by this author , and J.T. PoolmanJ.T. Poolman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)44111-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Disseminated Gonococcal Infection in Elderly Patients." The Journal of Urology, 137(3), p. 585 © 1987 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 137Issue 3March 1987Page: 585 Advertisement Copyright & Permissions© 1987 by The American Urological Association Education and Research, Inc.MetricsAuthor Information P.H.L.M. Geelhoed-Duyvestijn More articles by this author J.W.M. van der Meer More articles by this author A.T. Lichtendahl-Bernards More articles by this author C.J. Mulder More articles by this author K.A.E. Meyers More articles by this author J.T. Poolman More articles by this author Expand All Advertisement Loading ...
Vision in the Small: Reconstructing the Structure of Protein Macromolecules from Cryo-Electron Micrographs (2006)

Single particle reconstruction using Cryo-Electron Microscopy (cryo-EM) is an emerging technique in structural biology for estimating the 3-D structure (density) of protein macromolecules. Unlike tomography where a large number of images of a specimen can be acquired, the number of images of an individual particle is limited because of radiation damage. Instead, the specimen consists of identical copies of the same protein macro-molecule embedded in vitreous ice at random and unknown 3-D orientations. Because the images are extremely noisy, thousands to hundreds-of-thousands of projections are needed to achieve the desired resolution of 5A. Along with differences of the imaging modality compared to photographs, single particle reconstruction provides a unique set of challenges to existing computer vision algorithms. Here, we introduce the challenge and opportunity of reconstruction from transmission electron micrographs, and briefly describe our contributions in areas of particle detection, contrast transfer function (CTF) estimation, and initial 3-D model construction. Reconstructing the Structure of Protein Macromolecules One of the most exciting challenges for biology today is understanding the molecular machinery of the cell as a working, dynamic system. Critical to this understanding is determining the 3-D structure of protein macromolecules, a task that is often accomplished using x-ray crystallography. The technique of cryo electron microscopy (cryo-EM) has a unique role to play in addressing this challenge as it can provide structural information of large macromolecular complexes in a variety of conformational and compositional states while preserved under close to physiological conditions. Traditionally the methods for cryo-EM have been time consuming and labor intensive, involving data acquisition, analysis and averaging of thousands to hundreds of thousands of images (views) of the individual macro-molecular complexes. Thus, over the last few years there has been considerable interest and substantial effort devoted to developing automated methods to improve the accuracy, robustness, ease of use, and throughput of cryo-EM [1, 2, 3, 12, 15, 17], and this abstract considers three aspects originally presented in [9, 10, 11]. 1
A Simple Architecture for Computing Moments and Orientation of an Image (2002)

In this paper, a new methodology for computing orientation of a gray-tone image by the method of moments is described. Orientation is an essential feature needed in many image processing and pattern recognition tasks. Computation of moments is accomplished by a new projection method that leads to a fast algorithm of determining orientation. Using a simple architecture, the proposed algorithm can be implemented as a special purpose VLSI chip. The hardware cost of the proposed design is significantly lower compared to that of the existing architecture.
Early Detection for Li-Ion Batteries Thermal Runaway Based on Gas Sensing (2019)

During battery storage and transport, thermal runaway is a critical issue for battery safety. For cells stored in a 55 gallon (0.208 m3) drum, a single cell thermal runaway can heat up neighboring cells, causing a chain reaction of thermal runaway propagation. It is important to detect a thermal runway event before it propagates to other cells and becomes difficult to extinguish. This paper presents a Li-ion batteries thermal runaway early detection method based on gas sensing. By monitoring CO2 concentrations, which is produced at early stage of battery thermal runaway, early detection at cell failures are possible. The simulation shows much faster response of gas sensing comparing to conventional surface temperature sensing. While the surface temperature sensing approach fails to detect thermal runaway before it propagates to other cells, the gas sensing approach detects the event ahead of thermal runaway propagation.