gebhart/patrepeval huggingface dataset:
The novel driver gene ASAP2 is a potential druggable target in pancreatic cancer (2021)

Targeting mutated oncogenes is an effective approach for treating cancer. The 4 main driver genes of pancreatic ductal adenocarcinoma (PDAC) are KRAS, TP53, CDKN2A, and SMAD4, collectively called the "big 4" of PDAC, however they remain challenging therapeutic targets. In this study, ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 (ASAP2), one of the ArfGAP family, was identified as a novel driver gene in PDAC. Clinical analysis with PDAC datasets showed that ASAP2 was overexpressed in PDAC cells based on increased DNA copy numbers, and high ASAP2 expression contributed to a poor prognosis in PDAC. The biological roles of ASAP2 were investigated using ASAP2-knockout PDAC cells generated with CRISPR-Cas9 technology or transfected PDAC cells. In vitro and in vivo analyses showed that ASAP2 promoted tumor growth by facilitating cell cycle progression through phosphorylation of epidermal growth factor receptor (EGFR). A repositioned drug targeting the ASAP2 pathway was identified using a bioinformatics approach. The gene perturbation correlation method showed that niclosamide, an antiparasitic drug, suppressed PDAC growth by inhibition of ASAP2 expression. These data show that ASAP2 is a novel druggable driver gene that activates the EGFR signaling pathway. Furthermore, niclosamide was identified as a repositioned therapeutic agent for PDAC possibly targeting ASAP2.
Hyperopic shift following corneal graft rejection in a patient with keratoconus: A case report (2023)

Abstract Background Penetrating keratoplasty (PK) is the dominant technique for visual restoration of corneal blindness worldwide. Corneal graft rejection and refractive errors are common postoperative issues of it, but correlation between these complications was seldom reported. To the author’s knowledge, this is the first reported case describing hyperopic change following post-penetrating keratoplasty graft rejection. Case presentation A 15-year-old female undergoing PK for advanced keratoconus in the left eye. Postoperatively, the graft was clear and her corrected distance visual acuity (CDVA) improved to 20/20. Corneal topography revealed anterior chamber depth (ACD) of 5.87 mm and keratometry readings of 42.4/46.1 diopters (D). However, decreasing visual acuity to counting fingers was noted after twelve months. Slit-lamp biomicroscopic examination showed stromal edema and mutton-fat keratic precipitates infiltration. Corneal graft rejection was diagnosed and CDVA resumed to 20/20 within one month after intensive topical and high-dose systemic steroid administration. Four years later, corneal topography revealed an ACD of 2.98 mm and keratometry readings of 42.4/45.1 D with spherical equivalence of + 1.25 D. Clinically and topographically, the corneal graft demonstrated a process of flattening before and after the episode of graft rejection. Conclusions Graft rejection may cause hyperopic shift in patients with keratoconus after PK.
Molecular Tools for the Study of ADP‐Ribosylation: A Unified and Versatile Method to Synthesise Native Mono‐ADP‐Ribosylated Peptides (2021)

ADP-ribosylation (ADPr), as a post-translational modification, plays a crucial role in DNA-repair, immunity and many other cellular and physiological processes. Serine is the main acceptor for ADPr in DNA damage response, whereas the physiological impact of less common ADPr-modifications of cysteine and threonine side chains is less clear. Generally, gaining molecular insights into ADPr recognition and turn-over is hampered by the availability of homogeneous, ADP-ribosylated material, such as mono-ADP-ribosylated (MARylated) peptides. Here, a new and efficient solid-phase strategy for the synthesis of Ser-, Thr- and Cys-MARylated peptides is described. ADP-ribosylated cysteine, apart from being a native post-translational modification in its own right, proved to be suitable as a stabile bioisostere for ADP-ribosylated serine making it a useful tool to further biochemical research on serine ADP-ribosylation. In addition, it was discovered that the Streptococcus pyogenes encoded protein, SpyMacroD, acts as a Cys-(ADP-ribosyl) hydrolase.
Major Changes of von Willebrand Factor Multimer Distribution in Cirrhotic Patients with Stable Disease or Acute Decompensation (2018)

Characteristic changes of VWF parameters are seen in ST cirrhosis. In AD patients, highly increased VWF and reduced ADAMTS13 activity could be found, along with the presence of ULMWM, which are possible markers and contributors of the disease progression.
Co-Designing Multi-Packet Reception, Network Coding, And MAC Using A Simple Predictive Model (2010)

We design a cross-layer approach to optimize the joint use of multi-packet reception and network coding, in order to relieve congestion.We construct a model for the behavior of the 802.11MAC and apply it to several key canonical topology components and their extensions to any number of nodes.The results obtained from this model match the available experimental results, which are for routing and opportunistic network coding, with fidelity.Using this model, we show that fairness allocation by the MAC can seriously impact performance; hence, we devise a new MAC that not only substantially improves throughput relative to the current 802.11MAC, but also provides fairness to flows of information rather than to nodes.We show that the proper combination of network coding, multi-packet reception, and our new MAC protocol achieves super-additive throughput gains of up to 6.3 times that of routing alone with the use of the standard 802.11MAC.Finally, we extend the model to analyze the asymptotic behavior of our new MAC as the number of nodes increases.
The enzymatic basis for production by human neutrophils (1982)

O-.2 production is the first step in the generation of a group of powerful microbicidal oxidants by neutrophils. The production of O-.2 is catalyzed by a membrane-bound, NADPH-preferring flavoprotein oxidase, a conclusion supported by much evidence including the discovery of a new form of chronic granulomatous disease caused by a mutation affecting that oxidase directly. Also involved in the O-.2-forming reaction is a b-type cytochrome; the role of this cytochrome is as yet undefined, though it does not appear to be on the direct route of electron transfer between NADPH and oxygen. It has been postulated that quinones too participate in the O-.2-forming reaction, but further work is necessary to define their role more fully.
Mobility Performance Enhancements Based on Radio Link Quality for LTE-Advanced Heterogeneous Networks (2013)

Heterogeneous networks (HetNets) can provide higher capacity and user throughput than homogeneous networks in Long Term Evolution (LTE)-Advanced systems. However, because of increased interference from neighboring cells and the characteristics of the embedded small cells, handover performance is impacted adversely, especially when the user equipment (UE) moves at medium or high speeds. In this paper, to improve mobility performance, we propose two schemes, i.e., 1) using wideband signal-to-interference noise ratio (SINR) as the handover metric and 2) emergency attaching. The schemes can enhance mobility performance since handovers are performed based on the quality of the radio link. Importantly, the two schemes compliment rather than contradict each other. System-level simulations show that both the individual proposed schemes and the joint schemes can improve mobility performance significantly.
Pulsed laser ablation and deposition of thin films (2003)

Pulsed laser ablation is a simple, but versatile, experimental method that finds use as a means of patterning a very diverse range of materials, and in wide areas of thin film deposition and multi-layer research. Superficially, at least, the technique is conceptually simple also, but this apparent simplicity hides a wealth of fascinating, and still incompletely understood, chemical physics. This overview traces our current physico-chemical understanding of the evolution of material from target ablation through to the deposited film, addressing the initial laser-target interactions by which solid material enters the gas phase, the processing and propagation of material in the plume of ejected material, and the eventual accommodation of gas phase species onto the substrate that is to be coated. It is intended that this Review be of interest both to materials scientists interested in thin film growth, and to chemical physicists whose primary interest is with more fundamental aspects of the processes of pulsed laser ablation and deposition.
Infrared laser velocity modulation spectrum of the ν3 fundamental band of HBBr+ (1999)

The infrared absorption spectrum of the ν3 (B–Br stretching) mode of HBBr+ has been observed using a tunable diode laser and velocity modulation spectroscopy. The ion was formed in an ac glow discharge through a flowing mixture of H2 and BBr3. Thirty-three transitions of H11B79Br+ and the same number of lines of the H11B81Br+ isotopomer have been assigned. The band origins and rotational constants are H11B79Br+: ν0=937.5696(13) cm−1, B0=0.461 822(42) cm−1, and B1=0.459 254(41) cm−1. H11B81Br+: ν0=936.0554(11) cm−1, B0=0.460 330(45) cm−1, and B1=0.457 778(43) cm−1. Ab initio calculations of the band origins and the internuclear distances have been performed using the GAUSSIAN 94 package. The calculated values are in highly satisfactory agreement with the experimental results.
Joint uncertainty decoding with the second order approximation for noise robust speech recognition (2009)

Joint uncertainty decoding has recently achieved promising results by integrating the front-end uncertainty into the back-end in a mathematically consistent framework. In this paper, joint uncertainty decoding is compared with the widely used vector Taylor series (VTS). We show that the two methods are identical except that joint uncertainty decoding applies the Taylor expansion on each regression class whereas VTS applies it to each HMM mixture. The relatively rougher expansion points used in joint uncertainty decoding make it computationally cheaper than VTS but inevitably worse on recognition accuracy. To overcome this drawback, this paper proposes an improved joint uncertainty decoding algorithm which employs second-order Taylor expansion on each regression class in order to reduce the expansion errors. Special considerations are further given to limit the overall computational cost by adopting different number of regression classes for different orders in the Taylor expansion. Experiments on the Aurora 2 database show that the proposed method is able to beat VTS on recognition accuracy and computational cost with relative improvement up to 6% and 60%, respectively.
ChemInform Abstract: Halogen Exchange During Complex Formation Between an N‐Halogensuccinimide and a Quaternary Ammonium Halide. (1986)

Abstract When N‐chlorosuccinimide (I) and the ammonium bromide (II) were dissolved in Chloroform containing 10% MeOH and diethyl ether was then added, the Complex (III) was obtained (62% yield).
TnseqDiff: identification of conditionally essential genes in transposon sequencing studies (2017)

We describe a new, efficient method for identifying conditionally essential genes in Tn-Seq experiments with high detection sensitivity and specificity. It is implemented as TnseqDiff function in R package Tnseq and can be installed from the Comprehensive R Archive Network, CRAN.
A monoclonal anti-human platelet antibody: a new platelet aggregating substance (1985)

A monoclonal anti-human platelet antibody, TP82, is described, which caused irreversible aggregation of platelets in association with the release of adenosine triphosphate or [14C] serotonin, and which inhibited ristocetin-induced agglutination. Immunofluorescence assay showed that the antibody binds to platelets, megakaryocytes, and common acute lymphoblastic leukemia cells. The antibody (IgG1) immunoprecipitated a polypeptide of 23,000 daltons with an isoelectric point of about 7.0. The aggregation induced by the purified antibody and/or F(ab')2 fragments occurred in platelet-rich plasma and with washed platelets, but not with formalin-fixed washed platelets. TP82- induced aggregation was completely inhibited by disodium ethylendiaminotetraacetate, diltiazem, W-7, PGE1, and several metabolic inhibitors. At a concentration of apyrase or CP/CPK, which inhibited adenosine 5-diphosphate-induced aggregation. TP82-induced aggregation was only partially affected. Thrombin was not required for the antibody- mediated effects, since two thrombin inhibitors failed to block the reaction. The antibody, at least at a high concentration, induced platelet aggregation by a mechanism almost independent of thromboxane A2 formation, since cyclooxygenase inhibitors had little inhibitory effect on aggregation. TP82 monoclonal antibody is a new platelet- aggregating substance that interacts with a low-molecular-weight binding site on the platelet membrane.
164. The preparation of N 4-carboxyacylsulphonamides. Part II. The synthesis of N 4-phthalylsulphanilamide derivatives (1948)

C. W. Picard, E. Reid, J. Reynolds and D. E. Seymour, J. Chem. Soc., 1948, 821 DOI: 10.1039/JR9480000821
Stereochemically Reliable Syntheses of Pachastrissamine and Its 2-epi-Congener via Oxazolidinone Precursors from an Established Starting Material N-tert-Butoxycarbonyl-Protected Phytosphingosine (2012)

Efficient, stereochemically unambiguous, total syntheses of pachastrissamine and its 2-<i>epi</i>-congener from the readily available common precursor (1<i>R</i>)-1-{(4<i>S</i>,5<i>S</i>)-2-oxo-4-[(trityl­oxy)methyl]-1,3-oxazolidin-5-yl}pentadecyl methanesulfonate are reported. Syntheses of (3a<i>S</i>,6<i>R</i>,6a<i>R</i>)- and (3a<i>S</i>,6<i>S</i>,6a<i>R</i>)-6-tetradecylhexahydro-2<i>H</i>-cyclopenta[<i>d</i>][1,3]oxazol-2-one by this route have unambiguously resolved a dispute over the structures of these products.
Separating the second harmonic response of tissue and microbubbles using bispectral analysis (2012)

The second harmonic generation in medical ultrasound is either caused by tissue or ultrasound contrast agents. The conventional signal processing techniques cannot separate the harmonic response from microbubbles and tissue. The second order spectral analysis, commonly known as the frequency analysis, is the most common way of evaluating the microbubble response. Although frequency analysis can estimate the power spectrum effectively, it suppresses the phase relation between the frequency components. In this study, bispectral analysis is used to evaluate the microbubble response and separate the second harmonic generated by tissue and microbubbles via the phase coupling between fundamental and harmonic components.
ChemInform Abstract: exo‐2‐(Pyridazin‐4‐yl)‐7‐azabicyclo[2.2.1]heptanes: Syntheses and Nicotinic Acetylcholine Receptor Agonist Activity of Potent Pyridazine Analogues of (.+‐.)‐Epibatidine. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
New leads in cancer therapeutics: a keynote address. (2000)

The main problems in cancer chemotherapy are related to the fact that the available drugs are not specific nor selective enough in their anticancer action. Therefore, even a low degree of resistance at the target tumor level is sufficient to impart clinical resistance because the dose of drug cannot be increased sufficiently to overcome it without incurring unacceptable toxicity. In the face of the above mentioned difficulties, several directions of research are being currently pursued towards developing more effective and selective treatments of cancer. These include: 1) continuing traditional approaches of drug discovery stemming from lead chemical structures and in many cases utilizing combinational chemistry followed by suitable screening efforts; 2) Increasing the antitumor effectiveness of available drugs through: a) making it possible to increase drug dose intensity by protecting normal tissues from limiting toxicity through genetic manipulation or combination with such agents as GM-CSF or IL15; b) attempting to increase the specificity of drug delivery through the administration of agents encapsulated in suitable liposome or conjugated with appropriate antibodies or cytokines; c) increasing the sensitivity of target tumor to a drug by specific metabolic modulations as it was done, for example, in the case of combinations of fluoropyrimidines with leukovorin; 3) counteracting resistance to drugs through genetic and/or epigenetic approaches aimed at modifying, for example, mechanisms of drug uptake or retention or at reducing anti-apoptotic mechanisms; 4) attempting to improve biotherapeutic treatments, for example, utilizing novel therapeutic vaccines or antibodies, or treatments based on intervention on angiogenesis or on intercellular or cell-matrix relationships; 5) continuing efforts to develop more effective and selective combination treatments with drugs, biologicals or different modalities; and, 6) developing new treatments based on intervention at novel molecular targets which have an essential role in the physio-pathology of the cancer cell. The latter approach is the main subject of this address.
Oxidative Single-Electron Transfer Activation of σ-Bonds in Aliphatic Halogenation Reactions (2000)

The reactions of a series of structurally related large-ring propellanes with iodine monochloride were studied experimentally and computationally. In the case of 1,3-dehydroadamantane (1) and [3.3.1]propellane (2) free-radical addition was observed. [3.3.2]Propellane (3) and 3,6-dehydrohomoadamantane (4), which are less prone to radical attack, selectively form products of formal double nucleophilic (oxidative) addition, e.g., dichloro (in ICl/CH2Cl2), dimethoxy (in ICl/CH3OH), and diacetamino (in ICl/CH3CN) derivatives under otherwise identical conditions. Single-electron transfer pathways involving the alkane radical cations are proposed for the activation step for aliphatic hydrocarbons with relatively low oxidation potentials such as cage alkanes. Similar mechanisms are postulated for the activation of the tertiary C−H bonds of adamantane based on H/D-kinetic isotope effect data. The latter compare well to the kH/kD value for hydrogen atom loss from the adamantane radical cation (measured 2.78 ± 0.21 and computed 2.0) and differ considerably from the kinetic isotope effects for electrophilic C−H bond activations (i.e., hydride abstraction) or for loss of a proton from a hydrocarbon radical cation (kH/kD = 1.0−1.4; computed 1.4). Hence, the reactions of alkanes with elementary halogens and other weak electrophiles (but strong oxidizers) do not necessarily involve three-center two-electron species but rather occur via successive single-electron oxidation steps. Upon C−C or C−H fragmentation, the incipient alkane radical cations are trapped by nucleophiles.
Does Prior Percutaneous Endoscopic Gastrostomy Alter Post‐operative Outcome After Esophagectomy (2014)

Percutaneous endoscopic gastrostomy before esophagectomy is safe and does not adversely impact post-operative outcomes.
Morphing electroadhesive interface to manipulate uncooperative objects (2014)

The possibility of handling uncooperative objects, i.e. objects not equipped with any features that can aid their manipulation, is of particular interest for both terrestrial and space robotic applications. In this framework, this paper deals with the development and testing of a smart material substrate, which can be integrated into an end-effector device, where morphing and electro-adhesive capabilities are combined to allow the manipulation of uncooperative objects of different shapes and materials. Compliance and adhesion properties are obtained by creating a conductive pattern of electrodes embodied on the surface of a polymeric substrate. On one hand, the polymeric material, activated by a change in temperature, can adapt to any shape when it is heated, and maintain the deformed shape after being cooled, even when the load is removed, becoming compliant with the objects surface. On the other hand, the conductive pattern is responsible for the adhesive effect: when a high voltage is applied, the electric field generated induces an opposite charge on the objects surface establishing reversible attraction forces. Furthermore, the conductive pattern could be used to activate the morphing behaviour when the manipulator and the target object come into contact. A resistiveelectroadhesive pad is realized and some tests are performed to verify the heating behavior of the electrodes and the electroadhesion forces achievable. Morphing tests are also performed to verify the ability of the polymeric substrate to maintain the deformed shape after cooling.
Marinitoga hydrogenitolerans sp. nov., a novel member of the order Thermotogales isolated from a black smoker chimney on the Mid-Atlantic Ridge (2005)

A novel, thermophilic, anaerobic bacterium that is able to tolerate hydrogen was isolated from a deep-sea hydrothermal chimney collected at the Rainbow field on the Mid-Atlantic Ridge. Cells were rod-shaped and surrounded by a sheath-like outer structure (toga); they were weakly motile by means of a polar flagellum. They appeared singly, in pairs or in short chains. They grew at 35-65 degrees C (optimum 60 degrees C), pH 4.5-8.5 (optimum pH 6.0) and 10-65 g sea salts l(-1) (optimum 30-40 g l(-1)). The isolate was organotrophic, and able to grow on various carbohydrates or complex proteinaceous substrates. Growth was not inhibited under 100 % hydrogen or in the presence of 2 % oxygen in the gas phase. The isolate reduces sulfur, although sulfur reduction is not required for growth. The fermentation products identified on glucose were acetate, ethanol, formate, hydrogen and CO(2). The G + C content of the genomic DNA was 28 +/- 1 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the genus Marinitoga, order Thermotogales, in the bacterial domain. On the basis of the 16S rRNA gene sequence comparisons and physiological characteristics, the isolate is considered to represent a novel species, for which the name Marinitoga hydrogenitolerans sp. nov. is proposed. The type strain is AT1271(T) (=DSM 16785(T) = JCM 12826(T)).
Salinomycin exerts anti‐colorectal cancer activity by targeting the β‐catenin/T‐cell factor complex (2019)

Our study suggested that salinomycin could suppress the growth of colorectal cancer by disrupting the β-catenin/TCF complex and thus may be a promising agent for colorectal cancer treatment.