gebhart/patrepeval huggingface dataset:
Highly Sensitive and Exceptionally Wide Dynamic Range Detection of Ammonia Gas by Indium Hexacyanoferrate Nanoparticles Using FTIR Spectroscopy (2018)

Ammonia gas is useful but caustic; thus, its concentration is monitored depending on applications. We prepared indium hexacyanoferrate nanoparticles (InHCF-NPs, HCF = [Fe<sup>II</sup>(CN)<sub>6</sub>]<sup>4-</sup>) with average diameter around 8 nm by simple reaction at room temperature between In cations and HCF anions, and we found the unique functionality of InHCF-NPs which were capable of highly sensitive (16 ppb) and exceptionally wide range (190000, 16 ppb -0.3%) detection of ammonia gas within 6 min by IR measurements. Slope changes of the IR peak ratio of adsorbed ammonium over CN moieties in the InHCF framework indicated a good log-log linear correlation along gas concentrations, in which a wide dynamic range over 10<sup>5</sup> was realized for the first time in the field of ammonia gas detection.
Gentamicin induces a lysosomal phospholipidosis in cultured rat fibroblast [proceedings]. (1978)

On behalf of American Magazine , Ida M. Tarbell requests permission for Arnold Genthe to photograph Theodore Roosevelt for an article on the presidential candidates.
Data from Amivantamab (JNJ-61186372), an Fc Enhanced EGFR/cMet Bispecific Antibody, Induces Receptor Downmodulation and Antitumor Activity by Monocyte/Macrophage Trogocytosis (2023)

&lt;div&gt;Abstract&lt;p&gt;Small molecule inhibitors targeting mutant EGFR are standard of care in non–small cell lung cancer (NSCLC), but acquired resistance invariably develops through mutations in EGFR or through activation of compensatory pathways such as cMet. Amivantamab (JNJ-61186372) is an anti-EGFR and anti-cMet bispecific low fucose antibody with enhanced Fc function designed to treat tumors driven by activated EGFR and/or cMet signaling. Potent &lt;i&gt;in vivo&lt;/i&gt; antitumor efficacy is observed upon amivantamab treatment of human tumor xenograft models driven by mutant activated EGFR, and this activity is associated with receptor downregulation. Despite these robust antitumor responses &lt;i&gt;in vivo&lt;/i&gt;, limited antiproliferative effects and EGFR/cMet receptor downregulation by amivantamab were observed &lt;i&gt;in vitro&lt;/i&gt;. Interestingly, &lt;i&gt;in vitro&lt;/i&gt; addition of isolated human immune cells notably enhanced amivantamab-mediated EGFR and cMet downregulation, leading to antibody dose-dependent cancer cell killing. Through a comprehensive assessment of the Fc-mediated effector functions, we demonstrate that monocytes and/or macrophages, through trogocytosis, are necessary and sufficient for Fc interaction-mediated EGFR/cMet downmodulation and are required for &lt;i&gt;in vivo&lt;/i&gt; antitumor efficacy. Collectively, our findings represent a novel Fc-dependent macrophage-mediated antitumor mechanism of amivantamab and highlight trogocytosis as an important mechanism of action to exploit in designing new antibody-based cancer therapies.&lt;/p&gt;&lt;/div&gt;
Cartridge Filtration (2017)

This chapter focuses on the field of cartridge filtration presented within the context of a filter classification scheme. Cartridge filters can be classified on the basis of removal mechanism, design and construction, or application. Testing and evaluation is an important aspect of cartridge filtration. Resin-bonded media are made from a slurry of fiber and resin molded into the shape of an element. Resin-bonded media are made from slurries of fibers and resins. Unconsolidated media are used as loose assemblages of fibers or particles held together by a woven sock. Inorganic, synthetic, and natural fibers are all available for the production of filter media. Filter media, such as cellulose paper, non woven fabrics, or flat membranes, can be pleated and oriented around a supporting center tube. The ends of the medium are typically held in end caps by an adhesive. Sintered metal filter media are manufactured from metal powder or wire.
Mechanical Stimulation Enhances the Production of BMP-2 in Ossifying Rat Bone Marrow Organ Cultures (2009)

Bone marrow is a reservoir of mesenchymal stem cells and osteoprogenitors. It was previously shown [1, 2] and we have recently verified that in vitro cultures of bone marrow undergo osteogenesis without addition of osteoinductive stimulants. We hypothesized that the in vitro ossifying bone marrow organ culture system can be used as a model to investigate the dynamics of the osteogenesis process and its mechanoresponsiveness in terms of expression of key osteoinductive factors. The outcomes of these studies can be used to develop more effective tissue engineered substitutes for bone regeneration by the utilization of multiple osteogenic factors with complex/sequential delivery mechanisms.
A monoclonal antibody to a conserved sequence in the extracellular domain recognizes the angiotensin II AT1 receptor in mammalian target tissues (1993)

We have generated hybridomas which secrete monoclonal antibodies to the AT1 subtype of the angiotensin II receptor (AT1 receptor). These were obtained after immunization of Balb C/c mice with synthetic peptides representing sequences from either the extracellular domain (residues 8-17) or the intracellular domain (residues 229-237) of the AT1 receptor. Hybridoma populations were first screened for the production of antibodies which bound to rat liver cells. Further selection, and cloning by limiting dilution, was carried out for antibodies which bound specifically to rat adrenal glomerulosa cells. Confirmation that the antibody designated 6313/G2 interacted with the angiotensin II receptor was obtained using COS-7 cells transfected with AT1A receptor cDNA. In particular, the initial characterization of 6313/G2 showed specific immunofluorescence of vascular endothelium.
Varied poly(A) site efficiency in the adenovirus major late transcription unit. (1992)

Regulation of adenovirus major late transcription unit (MLTU) mRNA biosynthesis involves poly(A) site selection between five available sites, L1 through L5. The 5' proximal site completely dominates during early infection, whereas all five sites are used during late infection with L3 being favored slightly over the others. Previous studies have shown this early to late poly(A) switch will occur in the absence of MLTU-specific splicing patterns and hinges in large part on the character of the first poly(A) site. We have used in vitro assays to characterize basic features of the L1 and L3 pre-mRNAs which may help define how processing at poly(A) sites is controlled. We have found that L1 is 5-10-fold less efficient than L3 as a substrate for RNA cleavage. A primary difference between the L1 and L3 sites lies in the kinetics of their use, with cleavage at L3 occurring at twice the rate of cleavage at L1. In addition, L1 is 20-fold less effective than L3 in competing for processing factors. To investigate the sequence elements that contribute to poly(A) site efficiency, we have used competition assays in which the competitor RNAs lack upstream or downstream elements.
Surgical Treatment of Adult Degenerative Scoliosis (2014)

The rapid increase of elderly population has resulted in increased prevalence of adult scoliosis. Adult scoliosis is divided into adult idiopathic scoliosis and adult degenerative scoliosis. These two types of scoliosis vary in patient age, curve pattern and clinical symptoms, which necessitate different surgical indications and options. Back pain and deformity are major indications for surgery in adult idiopathic scoliosis, whereas radiating pain to the legs due to foraminal stenosis is what often requires surgery in adult degenerative scoliosis. When selecting a surgical method, major symptoms and underlying medical diseases should be carefully evaluated, not only to relieve symptoms but also to minimize postoperative complications. Surgical options for adult degenerative scoliosis include: decompression alone; decompression and limited short fusion; and decompression coupled with long fusion and correction of deformity. Decompression and limited short fusion can be applied to patients with a small Cobb's angle and normal sagittal imbalance. For those with a large Cobb's angle and positive sagittal imbalance, long fusion with correction of deformity is required. When long fusion is applied, a careful decision regarding the extent of fusion level should be made when selecting L5 or S1 as the distal fusion level and T10 or the thoracolumbar junction as the proximal fusion level. For the fusion extending to the sacrum, restoration of sagittal balance and rigid fixation with additional iliac screws should be considered. Any surgical procedures for adult degenerative scoliosis are known to have relatively high occurrences of complications; therefore, risks and benefits should be meticulously considered before selecting a surgical procedure.
RNAi-mediated gene silencing of highly expressed genes in the industrial fungi Trichoderma reesei and Aspergillus niger (2009)

RNA interference utilizes small interfering RNAs of 20–25 nucleotides processed from double-stranded RNA to initiate sequence-specific digestion of the cognate messenger RNA. We sought to investigate whether use of RNAi could be extended to industrially important filamentous fungi by determining if suppression of highly expressed fungal genes can be achieved and then maintained during growth in liquid media. Aspergillus niger and Trichoderma reesei are capable of secreting abundant amounts of amyloglucosidase and cellobiohydrolase II (CEL6A), respectively. A vector directing expression of a T. reesei cel6a hairpin RNA was used to transform T. reesei strain RutC30. Greater than 50% of transformants displayed some measure of CEL6A suppression, with a portion of these transformants appearing to be fully suppressed. Steady-state levels of cel6a-specific mRNA in these transformants, determined by Northern blots, paralleled extracellular yields of CEL6A visualized by SDS-PAGE. Decreased steady-state levels of cel6A-specific mRNA were confirmed using quantitative RT-PCR. In addition, cel6a-specific siRNAs were identified in transformants exhibiting decreased levels of cel6a mRNA and CEL6A protein, confirming RNAi as the process responsible for achieving gene silencing. Furthermore, RNAi-mediated gene silencing was maintained throughout both a seven-day fermentation and continuous growth over 35 days in shake flasks. Efficient gene silencing was also accomplished in A. niger, where apparently complete suppression of the amyloglucosidase (glaA) gene was achieved. These results demonstrate the robustness and stability of RNAi in T. reesei and A. niger and support the utility of this technology for strain development programs and functional genomics studies in these and possibly other industrial fungal strains.
Learning Compatibility Across Categories for Heterogeneous Item Recommendation (2016)

Identifying relationships between items is a key task of an online recommender system, in order to help users discover items that are functionally complementary or visually compatible. In domains like clothing recommendation, this task is particularly challenging since a successful system should be capable of handling a large corpus of items, a huge amount of relationships among them, as well as the high-dimensional and semantically complicated features involved. Furthermore, the human notion of "compatibility" to capture goes beyond mere similarity: For two items to be compatible---whether jeans and a t-shirt, or a laptop and a charger---they should be similar in some ways, but systematically different in others. In this paper we propose a novel method, Monomer, to learn complicated and heterogeneous relationships between items in product recommendation settings. Recently, scalable methods have been developed that address this task by learning similarity metrics on top of the content of the products involved. Here our method relaxes the metricity assumption inherent in previous work and models multiple localized notions of 'relatedness,' so as to uncover ways in which related items should be systematically similar, and systematically different. Quantitatively, we show that our system achieves state-of-the-art performance on large-scale compatibility prediction tasks, especially in cases where there is substantial heterogeneity between related items. Qualitatively, we demonstrate that richer notions of compatibility can be learned that go beyond similarity, and that our model can make effective recommendations of heterogeneous content.
Calcium-Myristoyl Tug Is a New Mechanism for Intramolecular Tuning of Calcium Sensitivity and Target Enzyme Interaction for Guanylyl Cyclase-activating Protein 1 (2012)

Guanylyl cyclase-activating protein 1 (GCAP1), a myristoylated Ca(2+) sensor in vision, regulates retinal guanylyl cyclase (RetGC). We show that protein-myristoyl group interactions control Ca(2+) sensitivity, apparent affinity for RetGC, and maximal level of cyclase activation. Mutating residues near the myristoyl moiety affected the affinity of Ca(2+) binding to EF-hand 4. Inserting Phe residues in the cavity around the myristoyl group increased both the affinity of GCAP1 for RetGC and maximal activation of the cyclase. NMR spectra show that the myristoyl group in the L80F/L176F/V180F mutant remained sequestered inside GCAP1 in both Ca(2+)-bound and Mg(2+)-bound states. This mutant displayed much higher affinity for the cyclase but reduced Ca(2+) sensitivity of the cyclase regulation. The L176F substitution improved affinity of myristoylated and non-acylated GCAP1 for the cyclase but simultaneously reduced the affinity of Ca(2+) binding to EF-hand 4 and Ca(2+) sensitivity of the cyclase regulation by acylated GCAP1. The replacement of amino acids near both ends of the myristoyl moiety (Leu(80) and Val(180)) minimally affected regulatory properties of GCAP1. N-Lauryl- and N-myristoyl-GCAP1 activated RetGC in a similar fashion. Thus, protein interactions with the central region of the fatty acyl chain optimize GCAP1 binding to RetGC and maximize activation of the cyclase. We propose a dynamic connection (or "tug") between the fatty acyl group and EF-hand 4 via the C-terminal helix that attenuates the efficiency of RetGC activation in exchange for optimal Ca(2+) sensitivity.
Mosaic and non-mosaic protocadherin 19 mutation leads to neuronal hyperexcitability in zebrafish (2021)

Abstract Epilepsy is one of the most common neurological disorders. The X-linked gene PCDH19 is associated with sporadic and familial epilepsy in humans, typically with early-onset clustering seizures and intellectual disability in females but not in so-called ‘carrier’ males, suggesting that mosaic PCDH19 expression is required to produce epilepsy. To characterize the role of loss of PCDH19 function in epilepsy, we generated zebrafish with truncating pcdh19 variants. Evaluating zebrafish larvae for electrophysiological abnormalities, we observed hyperexcitability phenotypes in both mosaic and non-mosaic pcdh19 +/- and pcdh19 -/- mutant larvae. Thus, we demonstrate that the key feature of epilepsy—network hyperexcitability—can be modeled effectively in zebrafish, even though overt spontaneous seizure-like swim patterns were not observed. Further, zebrafish with non-mosaic pcdh19 mutation displayed reduced numbers of inhibitory interneurons suggesting a potential cellular basis for the observed hyperexcitability. Our findings in both mosaic and non-mosaic pcdh19 mutant zebrafish challenge the prevailing theory that mosaicism governs all PCDH19-related phenotypes and point to interneuron-mediated mechanisms underlying these phenotypes.
Ni-Catalyzed Traceless, Directed C3-Selective C–H Borylation of Indoles (2020)

A highly efficient and general protocol for traceless, directed C3-selective C-H borylation of indoles with [Ni(IMes)<sub>2</sub>] as the catalyst is reported. Activation and borylation of N-H bonds by [Ni(IMes)<sub>2</sub>] is essential to install a Bpin moiety at the N-position as a traceless directing group, which enables the C3-selective borylation of C-H bonds. The N-Bpin group which is formed is easily converted <i>in situ</i> back to an N-H group by the oxidative addition product of [Ni(IMes)<sub>2</sub>] and <i>in situ</i>-generated HBpin. The catalytic reactions are operationally simple, allowing borylation of a variety of substituted indoles with B<sub>2</sub>pin<sub>2</sub> in excellent yields and with high selectivity. The C-H borylation can be followed by Suzuki-Miyaura cross-coupling of the C-borylated indoles in an overall two-step, one-pot process providing an efficient method for synthesizing C3-functionalized heteroarenes.
106th Congress (2000)

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Sequencing of the CHST6 gene in Czech macular corneal dystrophy patients supports the evidence of a founder mutation (2007)

Four different CHST6 missense mutations, of which p.C165Y is novel, were identified. Allelic association of the c.[484C>G; 599T>G] in six probands out of eight, as well as occurrence of this particular allele in a heterozygous state in one healthy control individual, supports a common founder effect for MCD in the Czech Republic.
Complete stereospecific determination of conjugated linoleic acids in triacylglycerol of milk-fat (2004)

We analyzed two kinds of dairy fat differing in their contents of cis9, trans11-conjugated linoleic acid (cis9,trans 11-CLA or rumenic acid), and determined the positional distribution of this CLA-isomer within the three sn- positions of the triacylglycerol. In the high rumenic acid fat (HR), the CLA-isomers amounted to 2.1% of total fatty acids, and 0.8% in the low rumenic acid fat (LR). Over 90% of the total CLA-isomers were in the form of rumenic acid, with an identical isomeric CLA distribution in both fats. The two fats differed mainly with regards to their contents in palmitic acid, alpha-linolenic acid, and isomers of trans-C 18:1. Conversely, our stereospecific determination indicates that the positional distribution of rumenic acid is preserved among both types of fat, and is more specific for the sn-3 position of the triacylglycerol (54 to 64% of the total rumenic acid). Such a positional distribution is believed to be nutritionally relevant.
Commissioning of CMS Forward Hadron Calorimeters with Upgraded Multi-anode PMTs and $u$TCA Readout (2017)

The high flux of charged particles interacting with the CMS Forward Hadron Calorimeter PMT windows introduced a significant background for the trigger and offline data analysis. During Long Shutdown 1, all of the original PMTs were replaced with multi-anode, thin window photo- multiplier tubes. At the same time, the back-end electronic readout system was upgraded to μ TCA readout. The experience with commissioning and calibration of the Forward Hadron Calorimeter is described as well as the μTCA system. The upgrade was successful and provided quality data for Run 2 data-analysis at 13 TeV.
A study of privacy policy enforcement in access control models (2010)

Internet has gained huge popularity over the last decade. It offers its users reliable, efficient and exciting online services. However, the users reveal a lot of their personal information by using these services. Websites that collect information state their practices with data in their privacy policies. However, it is difficult to ensure if the policies are enforced properly in their practices. This can lead to unintentional leakage of private information to unauthorized parties and thus increase the chance of private data to be misused. Taking the help of legal systems is expensive, time consuming and cannot compensate the loss completely. Therefore, an effective way to protect privacy is to use privacy policy to control data access. In this paper, we review some distinguished research works that address this problem. We also discuss the completeness of the privacy definition used in these works.
A model-driven approach for the extraction of network access-control policies (2012)

Network security constitutes a critical concern when developing and maintaining nowadays corporate information systems. Firewalls are a key element of network security by filtering the traffic of the network in compliance with a number of access control rules that enforce a given security policy. Unfortunately, once implemented, and due to the complexity of firewall configuration languages and the underlying network topology, knowing which security policy is actually being enforced by the network system is a complex and time consuming task that requires low-level and, often, vendor-specific expertise. In an always-evolving context, where security policies are often updated to respond to new security requirements, this discovery phase becomes critical since it could hamper the proper evolution of the system and compromise its security. To tackle this problem, our approach generates an abstract model of the firewall configurations in a network that facilitates the understanding and evolution of network security policies.