gebhart/patrepeval huggingface dataset:
The molecular machinery for secretion is conserved from yeast to neurons. (1993)

A variety of approaches have been utilized to identify and characterize the molecules that mediate vesicular trafficking along the secretory pathway. Two approaches that have been particularly fruitful include the genetic dissection of the yeast secretory pathway and the biochemical characterization of proteins involved in the synaptic vesicle membrane trafficking in the mammalian nerve terminal. The recent convergence of these approaches suggests that common mechanisms may underlie a wide variety of vesicle-mediated transport steps. We discuss the results that support this possibility and propose a model for synaptic vesicle docking and fusion that incorporates evolutionarily conserved elements that may be part of a constitutive fusion machinery and specialized elements that may mediate regulatory events that are specific to the process of neurotransmitter release.
Insertion of a New Transcriptional Unit into the Genome of Mouse Hepatitis Virus (1999)

The subgenomic mRNAs of the coronavirus mouse hepatitis virus (MHV) are composed of a leader sequence, identical to the 5' 70 nucleotides of the genome, joined at distant downstream sites to a stretch of sequence that is identical to the 3' end of the genome. The points of fusion occur at intergenic sequences (IGSs), loci on the genome that contain a tract of sequence homologous to the 3' end of the leader RNA. We have constructed a mutant of MHV-A59 containing an extra IGS inserted into the genome immediately downstream of the 3'-most gene, that encoding the nucleocapsid (N) protein. We show that in cells infected with the mutant, there is synthesis of an additional leader-containing subgenomic RNA of the predicted size. Our study demonstrates that (i) an IGS can be a sufficient cis-acting element to dictate MHV transcription, (ii) the relative efficiency of an IGS must be influenced by factors other than the nucleotides immediately adjacent to the 5'AAUCUAAAC3' core consensus sequence or its position relative to the 3' end of the genome, (iii) a downstream IGS can exert a polar attenuating effect on upstream IGSs, and (iv) unknown factors prevent the insertion of large exogenous elements between the N gene and the 3' untranslated region of MHV. These results confirm and extend conclusions previously derived from the analysis of defective interfering RNAs.
Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage (2003)

We present a multifactorial, multistep approach called genomic convergence that combines gene expression with genomic linkage analysis to identify and prioritize candidate susceptibility genes for Parkinson's disease (PD). To initiate this process, we used serial analysis of gene expression (SAGE) to identify genes expressed in two normal substantia nigras (SN) and adjacent midbrain tissue. This identified over 3700 transcripts, including the three most abundant SAGE tags, which did not correspond to any known genes or ESTs. We developed high-throughput bioinformatics methods to map the genes corresponding to these tags and identified 402 SN genes that lay within five large genomic linkage regions, previously identified in 174 multiplex PD families. These genes represent excellent candidates for PD susceptibility alleles and further genomic convergence and analyses.
Phage Acm1-mediated transduction in the facultatively methanol-utilizing Acetobacter methanolicus MB 58/4 (1993)

Phage Acm1, generally virulent for the acidophilic facultatively methanol-utilizing strain of Acetobacter methanolicus MB 58/4, is also capable of lysogenizing its host strain at a low rate. Using amino acid-auxotrophic mutants of A. methanolicus MB 58/4 as recipient strains, transduction of His, Leu and Tyr markers could be demonstrated in this system. The ability to prepare transducing lysates by propagation of phage Acm1 on the prototrophic donor strain A. methanolicus MB 58/4, the transduction of three different markers as well as the efficiency of transduction, and the occurrence of permutations in the phage genome indicate that phage Acm1 mediates generalized transduction. Phage Acm1 might be a useful tool in genetic studies of methylotrophic A. methanolicus.
Signaling through the lymphotoxin beta receptor induces the death of some adenocarcinoma tumor lines. (1996)

Surface lymphotoxin (LT) is a heteromeric complex of LT-alpha and LT-beta chains that binds to the LT-beta receptor (LT-beta-R), a member of the tumor necrosis factor (TNF) family of receptors. The biological function of this receptor-ligand system is poorly characterized. Since signaling through other members of this receptor family can induce cell death, e.g., the TNF and Fas receptors, it is important to determine if similar signaling events can be communicated via the LT-beta-R. A soluble form of the surface complex was produced by coexpression of LT-alpha and a converted form of LT-beta wherein the normally type II LT-beta membrane protein was changed to a type I secreted form. Recombinant LT-alpha 1/beta 2 was cytotoxic to the human adenocarcinoma cell lines HT-29, WiDr, MDA-MB-468, and HT-3 when added with the synergizing agent interferon (IFN) gamma. When immobilized on a plastic surface, anti-LT-beta-R monoclonal antibodies (mAbs) induced the death of these cells, demonstrating direct signaling via the LT-beta-R. Anti-LT-beta-R mAbs were also identified that inhibited ligand-induced cell death, whereas others were found to potentiate the activity of the ligand when added in solution. The human WiDr adenocarcinoma line forms solid tumors in immunocompromised mice, and treatment with an anti-LT-beta-R antibody combined with human IFN-gamma arrested tumor growth. The delineation of a biological signaling event mediated by the LT-beta-R opens a window for further studies on its immunological role, and furthermore, activation of the LT-beta-R may have an application in tumor therapy.
Cloning, Sequencing, and Expression of anEscherichia coliAcid Phosphatase/Phytase Gene (appA2) Isolated from Pig Colon (1999)

Bacterial strains were isolated from the pig colon to screen for phytase and acid phosphatase activities. Among 93 colonies, Colony 88 had the highest activities for both enzymes and was identified as an Escherichia coli strain. Using primers derived from the E. coli pH 2.5 acid phosphatase appA sequence (Dassa et al. (1990), J. Bacteriol. 172, 5497-5500), we cloned a 1482 bp DNA fragment from the isolate. In spite of 95% homology between the sequenced gene and the appA, 7 amino acids were different in their deduced polypeptides. To characterize the properties and functions of the encoded protein, we expressed the coding region of the isolated DNA fragment and appA in Pichia pastoris, respectively, as r-appA2 and r-appA. The recombinant protein r-appA2, like r-appA and the r-phyA phytase expressed in Aspergillus niger, was able to hydrolyze phosphorus from sodium phytate and p-nitrophenyl phosphate. However, there were distinct differences in their pH profiles, Km and Vmax for the substrates, specific activities of the purified enzymes, and abilities to release phytate phosphorus in soybean meal. In conclusion, the DNA fragment isolated from E. coli in pig colon seems to encode for a new acid phosphatase/phytase and is designated as E. coli appA2.
Conformationally restricted thrombin inhibitors resistant to proteolytic digestion (1992)

A new type of thrombin exo-site inhibitor has been designed with enhanced inhibitory potency and increased metabolic stability. With the aid of the model of the structure of the thrombin-hirudin fragment complex [Yue, S.-Y., DiMaio, J., Szewczuk, Z., Purisima, E. O., Ni, F., & Konishi, Y. (1992) Protein Eng. 5, 77-85], cyclic analogs of the hirudin fragment (hirudin55-65) were designed and synthesized. In these analogs, the side chains of appropriately substituted residues, 58 and 61, were joined in order to restrict the conformation of the inhibitor. An analog with an 18-membered lactam ring showed higher antithrombin activity (IC50 = 0.57 microM) than the corresponding analogs with 17- or 16-membered rings and was 2-fold more potent than its linear counterpart. Even 4-fold greater enhancement was obtained when a shorter fragment, hirudin 55-62, was cyclized. This cyclization not only improved the potency but, more importantly, dramatically increased the resistance to proteolytic digestion. Remarkable enhancement of stability to proteolysis was observed for peptide bonds located in the exocyclic linear peptide segments. These results are discussed using molecular modeling.
Standing temperature waves on electrically heated catalytic ribbons (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStanding temperature waves on electrically heated catalytic ribbonsLance Lobban, Georgios Philippou, and Dan LussCite this: J. Phys. Chem. 1989, 93, 2, 733–736Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://doi.org/10.1021/j100339a045RIGHTS & PERMISSIONSArticle Views64Altmetric-Citations45LEARN 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 InReddit PDF (479 KB) Get e-Alerts
<title>Frequency-channel-based visual models as quantitative quality measures in halftoning</title> (1993)

The recent proliferation of digital binary output devices, such as laser printers and facsimile machines, has brought increased attention to high quality halftone reproduction. A question that often arises in halftone research is how to evaluate the quality of halftone images using a quantitative quality metric. Such metrics would allow objective evaluation, could be incorporated in halftoning algorithms, in addition to being independently reproducible. Given that halftoning introduces unique types of distortions and the display medium (a hardcopy device) is different than that of conventional image processing applications (a CRT display), it becomes necessary to develop visual models specifically for halftoning applications. In this paper, frequency-domain visual models are investigated as to their suitability for the formulation of quantitative quality metrics specifically for halftoning applications. Two types of frequency-domain models are investigated: models that utilize a simple contrast-sensitivity function and models that utilize multiple independent narrowband channels. The quantitative quality metric for both types of models is formulated as a weighted frequency domain error. Since the ultimate judges of image quality are human viewers, the success of the quantitative measures is assessed by comparing their results with the results of a psychovisual test performed on halftone images.
Intersubunit signal transmission in integrins by a receptor-like interaction with a pull spring (2004)

The function of some multidomain proteins is regulated by interdomain communication. We use second-site suppressor cysteine mutations to test a hypothesis on how the inserted (I)-like domain in the integrin beta-subunit regulates ligand binding by the neighboring I domain in the integrin alpha-subunit [Huth, J. R., Olejniczak, E. T., Mendoza, R., Liang, H., Harris, E. A., et al. (2000) Proc. Natl. Acad. Sci. USA 97, 5231-5236; and Alonso, J. L., Essafi, M., Xiong, J. P., Stehle, T. & Arnaout, M. A. (2002) Curr. Biol. 12, R340-R342]. The hypothesis is that an interaction between the beta I-like metal ion-dependent adhesion site (MIDAS) and an intrinsic ligand in the linker following the alpha I domain, Glu-310, exerts a pull that activates the alpha I domain. Individual mutation of alpha(L) linker residue Glu-310 or beta(2) MIDAS residues Ala-210 or Tyr-115 to cysteine abolishes I domain activation, whereas the double mutation of alpha(L)-E310C with either beta(2)-A210C or beta(2)-Y115C forms a disulfide bond that constitutively activates ligand binding. The disulfide-bonded mutant is resistant to small molecule antagonists that bind to the beta I-like domain near its interface with the alpha I domain and inhibit communication between these domains but remains susceptible to small molecule antagonists that bind underneath the I domain alpha 7-helix and certain allosteric antagonistic antibodies. Thus, the alpha 7-helix and its linker are better modeled as a pull spring than a bell rope. The results suggest that alpha(L) residue Glu-310, which is universally conserved in all I domain-containing integrins, functions as an intrinsic ligand for the beta I-like domain, and that when integrins are activated, the beta I-like MIDAS binds to Glu-310, pulls the spring, and thereby activates the alpha I domain.
Donor age‐related differences in PBPC mobilization with rHuG–CSF (2001)

The administration of rHuG-CSF to donors <18 years old leads to CD34+ cell mobilization in a pattern similar to that observed in adults. Greater age was associated with a more frequent requirement for more than one apheresis to achieve a similar number of CD34+ cells.
Two-Point Fluorescence Detection and Automated Fraction Collection Applied to Constant Denaturant Capillary Electrophoresis (2000)

Constant denaturant capillary electrophoresis (CDCE) has been shown to be a sensitive method to detect point mutations in DNA sequences of 100-bp lengths. Here, we report a significant modifications for the instrumental setup that allows a highly accurate prediction of the elution time of DNA fragments from the capillary and an efficient collection of separated fractions. Fluorescently labeled DNA fragments of TP53 exon 8 wild-type and two mutants (base pair number 14480 and 14525) are detected at two separate points of the same capillary. This permits the precise calculation of the fragment velocity after separation in the heated zone because, at room temperature, all DNA fragments of the same length have the same velocity. Such precision permits the selective collection of separated fragments using an automated fraction collector for additional CDCE analysis or sequencing. Also, the two-point detection allows one to rapidly distinguish between double-stranded and single-stranded DNA fragments of the same length, a process that cannot be achieved with a one-point detection system alone. Both modifications greatly improve the procedure to detect novel mutations by means of CDCE.
INCARCERATION SYNDROME AFTER CEREBRAL VASCULAR ACCIDENT: CASE REPORT (2022)

The case reported brings the discussion about the Imprisonment Syndrome, a rare neurological disease, characterized by complete paralysis of all voluntary muscles, with the exception, usually, of those that control the eyes, presented by a 55-year-old patient after an episode of Vascular Accident. Ischemic Cerebral Stroke (CVA). With involvement of the basilar artery, the patient manifests anarthria and follows individualized treatment. The information was obtained from a review of medical records and literature.
Evaluation of HTTP-based request-response streams for internet video streaming (2011)

Adaptive video streaming based on TCP/HTTP is becoming popular because of its ability to adapt to changing network conditions. We present an in-depth experimental analysis of the use of HTTP-based request-response streams for video streaming. In this scheme, video fragments are fetched by a client from the server, in smaller units called chunks, potentially via multiple parallel HTT P requests (TCP connections). A model for the achievable throughput is formulated.The model is validated by a broad range of streaming experiments, including an evaluation of TCP-friendliness.
Inhaled nitric oxide attenuates pulmonary hypertension and improves lung growth in infant rats after neonatal treatment with a VEGF receptor inhibitor (2004)

VEGF plays a critical role during lung development and is decreased in human infants with bronchopulmonary dysplasia. Inhibition of VEGF receptors in the newborn rat decreases vascular growth and alveolarization and causes pulmonary hypertension (PH). Nitric oxide (NO) is a downstream mediator of VEGF, but whether the effects of impaired VEGF signaling are due to decreased NO production is unknown. Therefore, we sought to determine whether impaired VEGF signaling downregulates endothelial NO synthase (eNOS) expression in the developing lung and whether inhaled NO (iNO) decreases PH and improves lung growth after VEGF inhibition. Newborn rats received a single dose of SU-5416 (a VEGF receptor inhibitor) or vehicle by subcutaneous injection and were killed up to 3 wk of age for assessments of right ventricular hypertrophy (RVH), radial alveolar counts (RAC), lung eNOS protein, and NOx production in isolated perfused lungs (IPL). Neonatal treatment with SU-5416 increased RVH in infant rats and reduced RAC. Compared with controls, SU-5416 reduced lung eNOS protein expression by 89% at 5 days (P < 0.01). IPL studies from day 14 rats demonstrated increased baseline pulmonary artery pressure and lower perfusate NOx concentration after SU-5416 treatment. Importantly, iNO treatment prevented the increase in RVH and improved RAC after SU-5416 treatment. We conclude that treatment of neonatal rats with SU-5416 downregulates lung eNOS expression and that iNO therapy decreases PH and improves lung growth after SU-5416 treatment. We speculate that decreased NO production contributes to PH and decreases distal lung growth caused by impaired VEGF signaling.
Solution structure of a DNA-binding domain from HMG1 (1993)

We have determined the tertiary structure of box 2 from hamster HMG1 using bacterial expression and 3D NMR. The all alpha-helical fold is in the form of a V-shaped arrowhead with helices along two edges and one rather flat face. This architecture is not related to any of the known DNA binding motifs. Inspection of the fold shows that the majority of conserved residue positions in the HMG box family are those involved in maintaining the tertiary structure and thus all homologous HMG boxes probably have essentially the same fold. Knowledge of the tertiary structure permits an interpretation of the mutations in HMG boxes known to abrogate DNA binding and suggests a mode of interaction with bent and 4-way junction DNA.
TGFβ signaling in cartilage development and maintenance (2014)

Members of the transforming growth factor beta (TGFβ) superfamily of secreted factors play essential roles in nearly every aspect of cartilage formation and maintenance. However, the mechanisms by which TGFβs transduce their effects in cartilage in vivo remain poorly understood. Mutations in several TGFβ family members, their receptors, extracellular modulators, and intracellular transducers have been described, and these usually impact the development of the cartilaginous skeleton. Furthermore, genome-wide association studies have linked components of the (TGFβ) superfamily to susceptibility to osteoarthritis. This review focuses on recent discoveries from genetic studies in the mouse regarding the regulation of TGFβ signaling in developing growth plate and articular cartilage, as well as the different modes of crosstalk between canonical and noncanonical TGFβ signaling. These new insights into TGFβ signaling in cartilage may open new prospects for therapies that maintain healthy articular cartilage.
Kernel principal component analysis (1999)

A new method for performing a nonlinear form of Principal Component Analysis is proposed. By the use of integral operator kernel functions, one can efficiently compute principal components in highdimensional feature spaces, related to input space by some nonlinear map; for instance the space of all possible d-pixel products in images. We give the derivation of the method and present experimental results on polynomial feature extraction for pattern recognition.
Evaluation of experimentally induced Fusobacterium necrophorum infections in mice (1977)

Two strains of mice, Swiss Webster and DBA/2Cr, were injected intraperitoneally or intravenously with varying dosages of Fusobacterium necrophorum. The ability to eliminate the infection was assessed by quantitative enumeration of the organisms present in the blood, liver, and spleen, Three- to 4-week-old DBA/2Cr mice were highly resistant to both routes of injection. The intraperitoneal injection of older mice failed to demonstrate a dose-effect relationship whereas an intravenous injection of as few as 10(4) cells of F. necrophorum produced progressively necrotic leg abscesses, apparently involving the lymphonodus ischiadicus which filters the site of injection. Mortality was increased with sensitization by a previous sublethal injection. Also, an ethanol-killed cell vaccine delayed the onset of lethal infection, whereas repeated sublethal live cell injections provided nonspecific protection since mice vaccinated with the growth medium were equally protected. The development of leg abscesses after intravenous injection visibly demonstrated the pathogenicity of F. necrophorum and may provide a suitable model for the evaluation of vaccines and the effectiveness of antibiotics.
Environment‐dependent growth inhibition of human epidermal keratinocytes by recombinant human transforming growth factor‐beta (1989)

Transforming growth factor-beta (TGF-beta) purified from platelets is a potent growth inhibitor of several normal epithelial cell types in culture. In contrast, some carcinoma cell lines derived from tumors of these same tissues are resistant to this factor. Using recombinant human TGF-beta, the authors have confirmed these results with six normal human epidermal keratinocyte strains and four human epidermal squamous carcinoma cell lines. However, the sensitivity of normal cells to TGF-beta was found to depend on the culture conditions. When grown in a specialized nutrient medium supplemented with pituitary extract, keratinocytes were completely inhibited by the addition of 0.3 ng/ml TGF-beta. In contrast, when their growth was supported by cocultivation with 3T3 fibroblast feeder cells, 30- to 100-fold higher concentrations of TGF-beta were required to achieve comparable growth inhibition. This differential sensitivity occurred despite the fact that in both culture systems TGF-beta in the culture medium had a half-life of about 50 minutes, becoming tightly bound to the surface of the culture dish. Bound TGF-beta proved to be biologically active and stable for about a week in the absence of 3T3 feeder cells. Incubating 3T3 cells on TGF-beta-coated dishes, however, resulted in nearly quantitative removal and degradation of the TGF-beta within 2 days, permitting normal rates of keratinocyte growth. The binding of TGF-beta to surfaces and the ability of fibroblasts to attenuate its inhibitory activity for epithelial cells must be considered when evaluating in vitro models and in planning strategies for the use of this factor in vivo.