gebhart/patrepeval huggingface dataset:
Characterization of a Tn4351-generated hemin uptake mutant of Porphyromonas gingivalis: evidence for the coordinate regulation of virulence factors by hemin (1995)

The ability of Porphyromonas gingivalis to acquire iron in the iron-limited environment of the host is crucial to the colonization of this organism. We report here on the isolation and characterization of a transpositional insertion mutant of P. gingivalis A7436 (designated MSM-3) which is defective in the utilization and transport of hemin. P. gingivalis MSM-3 was selected on the basis of its nonpigmented phenotype on anaerobic blood agar following mutagenesis with the Bacteroides fragilis transposon Tn4351. P. gingivalis MSM-3 grew poorly when supplied with hemin as a sole source of iron; however, growth was observed with hemoglobin or inorganic iron. P. gingivalis MSM-3 grown in either hemin-replete or hemin-depleted conditions bound and transported less [14C]hemin or [59Fe]hemin than did the parent strain. At 4 h, P. gingivalis MSM-3 grown in hemin-replete conditions transported only 10,000 pmol of hemin per mg of protein, or 14% of the amount transported by P. gingivalis A7436. Unlike P. gingivalis A7436, hemin binding and transport by P. gingivalis MSM-3 were not tightly regulated by hemin or iron. Examination of P. gingivalis MSM-3 cultures by electron microscopy revealed an overproduction of membrane vesicles, and determination of the dry weight of purified vesicles indicated that P. gingivalis MSM-3 produced twice as much membrane vesicles as did strain A7436. Extracellular vesicles isolated from P. gingivalis MSM-3 also were found to express increased hemolytic and trypsin-like protease activities compared with the parent strain. When inoculated into subcutaneous chambers implanted in mice, P. gingivalis MSM-3 was highly infectious and more invasive than the parent strain, as indicated by secondary lesion formation and death. Taken together, these results indicate that the decreased transport of hemin by P. gingivalis MSM-3 results in the increased expression of several virulence factors which may be coordinately regulated by hemin.
Self-Assembly of Discrete Organometallic−Organic Hybrid Supramolecular Arrays from Ferrocenyl Dipyridines and Terephthalic and Trimesic Acids (2002)

Reactions of ferrocenyl dipyridines (1a,b) with terephthalic (2) and trimesic acid (4) form [2+2] and [3+2] supramolecular assemblies 3 and 5, respectively. Crystallographic analyses reveal that they are stabilized by cooperative noncovalent interactions involving multiple hydrogen-bonding and π−π interactions.
Design and Total Synthesis of a Superior Family of Epothilone Analogues, which Eliminate Xenograft Tumors to a Nonrelapsable State (2003)

Unusually promising profiles of antitumor activity are displayed by 26-trifluoro-(E)-9,10-dehydro-dEpoB (1), the design and practical total synthesis of which is described. This compound promotes tumor shrinkage and disappearance in human xenografts in nude mice at well-tolerated doses, with complete remission for over two months and early rapid recovery of body weight to the pretreatment control levels. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z52361_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Barometric measurement of tidal volume: effects of pattern and nasal temperature (1980)

The accuracy of the formula derived by Drorbaugh and Fenn (Pediatrics 16: 81-86, 1955) for calculating tidal volume (VT) from the phasic pressure change measured when an animal breathes in a closed chamber has recently been challenged. Epstein and Epstein (Respir. Physiol. 32: 105-120, 1978) argue that the formula may underestimate VT by up to 30% and predict that the error increases as the ratio of inspiratory duration (TI) to total breath duration (Ttot) increases, and as the expired temperature at the nares (TN) increases. To test their theory, I measured VT in anesthetized rats by the barometric technique and by conventional pneumotachography simultaneously. TN was varied from ambient to body temperature by passing a variable current through the pneumotachograph heater; TI/Ttot was varied by changing FICO2 and by selecting different rats. The predictions were confirmed. A factor is derived for retrospectively correcting VT estimated by the Drorbaugh-Fenn formula. It requires knowledge of TN and TI/Ttot and reduces the error between experiments to under 20% and within each experiment to about 5%. To facilitate its use, TN was measured in rat, rabbit, cat, man, and infant pigtail monkey.
In-depth analysis of the membrane and cytosolic proteome of red blood cells (2006)

In addition to transporting oxygen and carbon dioxide to and from the tissues, a range of other functions are attributed to red blood cells (RBCs) of vertebrates. Diseases compromising RBC performance in any of these functions warrant in-depth study. Furthermore, the human RBC is a vital host cell for the malaria parasite. Much has been learned from classical biochemical approaches about RBC composition and membrane organization. Here, we use mass spectrometry (MS)-based proteomics to characterize the normal RBC protein profile. The aim of this study was to obtain the most complete and informative human RBC proteome possible by combining high-accuracy, high-sensitivity protein identification technology (quadrupole time of flight and Fourier transform MS) with selected biochemical procedures for sample preparation. A total of 340 membrane proteins and 252 soluble proteins were identified, validated, and categorized in terms of subcellular localization, protein family, and function. Splice isoforms of proteins were identified, and polypeptides that migrated with anomalously high or low apparent molecular weights could be grouped into either ubiquitinylated, partially degraded, or ester-linked complexes. Our data reveal unexpected complexity of the RBC proteome, provide a wealth of data on its composition, shed light on several open issues in RBC biology, and form a departure point for comprehensive understanding of RBC functions.
Targeting HER3 using mono- and bispecific antibodies or alternative scaffolds (2016)

The human epidermal growth factor receptor 3 (HER3) has in recent years been recognized as a key node in the complex signaling network of many different cancers. It is implicated in de novo and acquired resistance against therapies targeting other growth factor receptors, e.g., EGFR, HER2, and it is a major activator of the PI3K/Akt signaling pathway. Consequently, HER3 has attracted substantial attention, and is today a key target for drugs in clinical development. Sophisticated protein engineering approaches have enabled the generation of a range of different affinity proteins targeting this receptor, including antibodies and alternative scaffolds that are either mono- or bispecific. Here, we describe HER3 and its role as a key tumor target, and give a comprehensive review of HER3-targeted proteins currently in development, including discussions on the opportunities and challenges of targeting this receptor.
Reading digits in natural images with unsupervised feature learning (2024)

Detecting and reading text from natural images is a hard computer vision task that is central to a variety of emerging applications. Related problems like document character recognition have been widely studied by computer vision and machine learning researchers and are virtually solved for practical applications like reading handwritten digits. Reliably recognizing characters in more complex scenes like photographs, however, is far more difficult: the best existing methods lag well behind human performance on the same tasks. In this paper we attack the problem of recognizing digits in a real application using unsupervised feature learning methods: reading house numbers from street level photos. To this end, we introduce a new benchmark dataset for research use containing over 600,000 labeled digits cropped from Street View images. We then demonstrate the difficulty of recognizing these digits when the problem is approached with hand-designed features. Finally, we employ variants of two recently proposed unsupervised feature learning methods and find that they are convincingly superior on our benchmarks. 1
Biomarkers for the Clinical Use of PD-1/PD-L1 Inhibitors in Non–Small-Cell Lung Cancer (2016)

The refinement of existing biomarkers and identification of novel predictive biomarkers will be key to ensuring the effective and safe use of these agents. Since most patients still do not benefit from these agents, it is critical to continue to work to define the select patient population who will derive durable benefit from PD-1/PD-L1 inhibition and identify markers that could have predictive value for combination therapies that could expand the population who benefit.
Granulocytes as active participants in acute myocardial ischemia and infarction. (1987)

The classical picture of the polymorphonuclear leukocyte--antimicrobal activities and participation in the inflammatory reaction--appears now to be expanded. It has been recognized that this cell may be highly injurious to other cells, has a propensity to be trapped in the capillary network, and may occlude microvascular pathways. The classical hypothesis that the granulocytes appear in the ischemic or postischemic myocardium as response to the associated inflammatory reaction may have to be revised. Instead, the granulocyte may actually be the key factor causing the inflammation. An array of future studies is needed to clarify the events step by step. Important aspects are the activation and degranulation sequence in the ischemic myocardium, the form and extent of injury caused by the oxygen free radicals and lysosomal enzymes, the source and nature of chemotactic substances, particularly in human forms of myocardial ischemia, and the degree to which granulocytes cause or magnify the injury.
Considerations for the use of testosterone with systemic chemotherapy in prostatic cancer (1982)

Among 52 patients with metastatic adenocarcinoma of the prostate who were treated with exogenous testosterone, 45 (87%) experienced unfavorable subjective and/or objective responses. These unfavorable responses were elicited more frequently and after shorter treatment periods in patients in symptomatic relapse following endocrine therapy than in untreated patients or patients in remission following endocrine therapy. Serious morbidity or mortality, seemingly due to the testosterone administration, occurred in eight cases (15%). It is not known if the action of chemotherapeutic agents will be enhanced by concurrent testosterone therapy but any such investigation should be undertaken with extreme caution.
Fatal pneumonia with terminal emaciation in nude mice caused by pneumonia virus of mice. (1988)

Athymic nude mice used as sentinel animals in a mouse holding room died of pneumonia 17 to 32 weeks after being placed in the room. Lesions in the pulmonary parenchyma consisted of monocytic exudate, epithelial cell necrosis, hemorrhage, fibrin deposition and interstitial fibrosis. Septal edema, septal cell necrosis and septal capillary stasis were common, but there was limited sloughing of bronchial lining epithelium. Indirect fluorescence microscopy (IFA) of lung sections using pneumonia virus of mice (PVM) antibody was positive. The pneumonia and IFA results were reproduced in euthymic mice inoculated experimentally with lung suspension from naturally infected mice or with tissue culture fluid from cultures infected with American Type Culture Collection PVM. The lungs of a naturally infected nude mouse were studied by transmission electron microscopy. Virus growth was found on Type II alveolar epithelium and on poorly differentiated replacement alveolar epithelium. Virus particles appeared as long exophytic filaments containing one to six linearly arranged nucleocapsids. Inclusion bodies and intracellular virus structures were not observed.
Brain-stem modulation of the response properties of cells in the cat's perigeniculate nucleus (1994)

Transmission through the lateral geniculate nucleus is facilitated following activation of the cholinergic input from the brain stem, which is thought to reflect activity patterns seen during arousal. One of the underlying mechanisms is the suppression of inhibitory circuits local to the lateral geniculate nucleus. However, evidence exists that some visually driven inhibitory inputs to geniculate nucleus. preserved or even enhanced under conditions of arousal, and during electrical activation of the parabrachial region of the brain stem. We have therefore reexamined the effect of brain-stem activation on the visual responses of one group of local inhibitory inputs to geniculate relay cells, those emanating from the adjacent perigeniculate nucleus. We recorded single perigeniculate cells in anesthetized, paralyzed cats. Axons innervating the lateral geniculate and perigeniculate nuclei from the parabrachial region of the brain stem were electrically activated, and the effect of this activation was assessed on both spontaneous and visually evoked responses. Visual stimulation consisted of sinusoidally modulated sine-wave gratings of varying spatial and temporal frequency. For the great majority of perigeniculate cells (32 of 40), brain-stem activation inhibited spontaneous activity, while one cell was excited, three showed a mixed effect and four were unaffected. Nevertheless, the responses of most cells (30 of 40) were facilitated when brain-stem activation was paired with certain spatio-temporal patterns of visual stimulation. Spatial tuning curves were constructed for 17 cells and temporal tuning curves for 14, before and during parabrachial activation. The responses of any one cell could be facilitated, unchanged, or suppressed, depending on the visual stimulus used. In some cases, this substantially modified the cell's spatial and temporal tuning properties. We conclude that activation of the brain stem disinhibits geniculate relay cells in the absence of visual stimulation, but it has the potential to enhance either the magnitude or specificity of visually driven inhibition arising from the perigeniculate nucleus.
Confirmation of the presence of Mycobacterium tuberculosis and other mycobacteria in mycobacterial growth indicator tubes (MGIT) by multiplex strand displacement amplification (1997)

Multiplex strand displacement amplification (mSDA) is capable of amplifying three distinct DNA sequences simultaneously. These include sequences present in most genera of mycobacteria, a sequence specific for Mycobacterium tuberculosis, and an internal control. mSDA was used to detect the presence of these target sequences in 154 (72 positive, 76 negative, and 6 failed) clinical specimens cultured in the mycobacterial growth indicator tube (MGIT) system. A wide variety of specimen types were processed and cultured. Once these cultures were deemed positive by MGIT fluorescence or were deemed negative after 8 weeks of incubation, MGIT culture aliquots were processed for mSDA analyses. A chemiluminescent microwell assay was used to detect the amplified products. The procedure was relatively simple and took less than 6 h to complete. The sensitivity of mSDA for detecting acid-fast bacilli was 96.4% compared to that of MGIT culture. Sensitivity and specificity were 97.2 and 96.1%, respectively, when all clinical criteria were considered. mSDA was shown to be a rapid and effective method for confirming the presence of M. tuberculosis and other mycobacteria in positive MGIT cultures.
Betacellulin: a mitogen from pancreatic beta cell tumors (1993)

Betacellulin, a member of the epidermal growth factor family, has been identified in the conditioned medium of cell lines derived from mouse pancreatic beta cell tumors. Betacellulin is a 32-kilodalton glycoprotein that appears to be processed from a larger transmembrane precursor by proteolytic cleavage. The carboxyl-terminal domain of betacellulin has 50 percent sequence similarity with that of rat transforming growth factor alpha. Betacellulin is a potent mitogen for retinal pigment epithelial cells and vascular smooth muscle cells.
Human phosvitin/casein kinase type II. Molecular cloning and sequencing of full‐length cDNA encoding subunit beta (1989)

Phosvitin/casein kinase type II is an ubiquitous, highly conserved enzyme consisting of subunits alpha, alpha' and beta. Subunit beta, presumably serving regulatory functions, was prepared from human placenta and the amino acid sequence of a protease digestion peptide was determined. The deduced nucleotide sequence was employed for the synthesis of a mixture of 20mers as a hybridization probe to screen a lambda gt10 HeLa cell cDNA library for clones encoding subunit beta. A full-length clone consisting of 1013 bp was isolated and the sequence of both strands determined. The deduced amino acid sequence of the largest open reading frame encodes 215 amino acid residues predicting a maximum Mr of 24925. The nucleotide sequence of the human beta subunit shows a similarity of 75% to that of Drosophila melanogaster and the deduced amino acid sequence a similarity of 88% and 97% to that of D. melanogaster and bovine lung, respectively. No further protein sequence currently known exhibits any notable similarity. Using a 537-bp restriction fragment of the cDNA clone representing 80% of the coding region, a 1-kb subunit-beta transcript was detected by Northern hybridization in total RNA prepared from human epithelial cells and placenta as well as from bovine heart suggesting a single transcript of the beta-subunit gene and also demonstrating high similarity also between the human and bovine nucleotide sequences. The same restriction fragment was used as the probe to indicate in Southern hybridizations that the corresponding genomic DNA contains at least one intron of roughly 2.5 kb in length and presumably is a single copy gene.
Reversible Photolabilization of NO from Chromium(III)-Coordinated Nitrite. A New Strategy for Nitric Oxide Delivery (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTReversible Photolabilization of NO from Chromium(III)-Coordinated Nitrite. A New Strategy for Nitric Oxide DeliveryMalcolm De Leo and Peter C. FordView Author Information Department of Chemistry, University of California Santa Barbara, California 93106 Cite this: J. Am. Chem. Soc. 1999, 121, 9, 1980–1981Publication Date (Web):February 20, 1999Publication History Received9 November 1998Published online20 February 1999Published inissue 1 March 1999https://pubs.acs.org/doi/10.1021/ja983875ahttps://doi.org/10.1021/ja983875arapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views574Altmetric-Citations71LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Anions,Photodissociation,Quantum yield,Solution chemistry,Transition metals Get e-Alerts
α 1 and α 2 Ca 2+ channel subunit expression in human neuronal and small cell carcinoma cells (1994)

Monoclonal antibodies that recognize skeletal muscle dihydropyridine-sensitive calcium channel subunits were used to identify similar proteins in neuronal and small cell carcinoma cell lines. alpha 1-related proteins were detected by FACS analysis on the surface of human neuroblastoma (IMR 32) and small cell carcinoma (DMS 273 and DMS 114) cell lines. alpha 1-like polypeptides from these cells were isolated and partially characterized. The polypeptides exhibit an M(r) similar to that of the L-type channel alpha 1 subunit and are recognized by two distinct anti-alpha 1 mAbs. The data provide biochemical evidence for structural similarities between the alpha 1 subunit of small cell carcinoma and neuronal cell lines. Similarly, an alpha 2-like protein was characterized from these cells. Because alpha 2 is a subunit shared by many subtypes of calcium channels, these data suggest that subunits other than the pore-forming alpha 1 subunit may play an important role in the etiology of Lambert-Eaton syndrome. We demonstrate directly that small cell carcinoma and a cell line derived from peripheral neurons share L-type calcium channel-related proteins and a protein common to many voltage-gated calcium channel subtypes. These data support a model that proposes that cross-reactivity of anti-tumor cell antibodies with presynaptic elements, possibly calcium channels, plays a role in the development of Lambert-Eaton syndrome.
Ultrafast Gates for Single Atomic Qubits (2010)

We demonstrate single-qubit operations on a trapped atom hyperfine qubit using a single ultrafast pulse from a mode-locked laser. We shape the pulse from the laser and perform a π rotation of the qubit in less than 50 ps with a population transfer exceeding 99% and negligible effects from spontaneous emission or ac Stark shifts. The gate time is significantly shorter than the period of atomic motion in the trap (Ω(Rabi)/ν(trap)>10(4)), demonstrating that this interaction takes place deep within the strong excitation regime.
Studies on the Mode of Action of Polyoxins (1971)

(1) Chitin-UDP acetylglucosaminyltransferase (E. C. 2. 4. 1. 16., chitin synthetase) in the cell-free system from phytopathogenic fungus Piricularia oryzae, and effects of various polyoxins and related compounds on the enzyme activity were studied. Polyoxins A_??_M, polyoxin A derivatives, polyoxin C derivatives, 5'-amino-5'-deoxyuridine, uridine and thy-midine inhibited equally the incorporation of N-acetylglucosamine (G1cNAc) from UDP-N-acetylglucosamine (UDP-G1cNAc) into chitin. (2) Competition between the above inhibitors and UDP-G1cNAc was observed by kinetic studies. The Km for UDP-G1cNAc was determined to be 3.3×10-3M and the Ki values for polyoxins A_??_M, except polyoxin C, were found to be in the range of 3.3×10-5M to 3.4×10-6M. For polyoxin C, 5'-amino-5'-deoxyuridine and uridine, the Ki values of 2.7×10-3M, 8.0×10-3M and 3.0×10-3M were given, respectively. The inhibitor constants for other related compounds were also calculated. (3) The values of binding affinity, -ΔG, for formation of substrate- or inhibitor-enzyme complexes were calculated from the Km or Ki values. In addition, partial binding affinities, -Δg, for certain moieties or groups of polyoxins were estimated from the -ΔG. For instance, the -ΔG values for UDP-GlcNAc and polyoxin L were 5.7 kcal/mole and 9.2 kcal/mole, respectively. And the -Δg values for the nucleoside moiety (part I*), the car-bamylpolyoxamic acid moiety (part II*) and the carboxyl group* at C5' position of polyoxin L were 5.2, 3.5 and 0.7 kcal/mole, respectively. (4) From the results obtained, the mechanism of action and relation between chemical structure and competitive inhibition of chitin synthetase were discussed.