gebhart/patrepeval huggingface dataset:
Alignments and Comparative Profiles of Picornavirus Genera (2014)

Genome connoisseurs are always looking for new methods to tweak the data, especially in sequence regions where good fits are harder to achieve or recognize. The previous capsid alignments were based on superimposition of virion crystal structure hydrogen-bonding maps, then extended by multiple, reiterative pairwise comparisons to include similar related sequences. With the HMMER program suite full-length picornavirus genome hidden Markov model (HMM)-profiles (lengths of 8,000 to 9,000 bases) were calculated from the previous alignments. The alignments were checked for consistency, and then refined mathematically and heuristically to (i) maximize the number of matched bases and encoded amino acids, (ii) minimize the location and frequency of indels (insertions/deletions), and (iii) emphasize the conservation of homologous features such as catalytic sites and proteolytic cleavage sites. The current iterations now include genome-length alignments for the seven most populous picornaviral genera (Enterovirus, Rhinovirus, Cardiovirus, Aphthovirus, Hepatovirus, Parechovirus, and Teschovirus) and extend over 173 different strains, providing formats for about 1,000,000 bases. The correlate polyprotein alignments, derived by translation of the aligned RNAs, include about 291,000 amino acids. For eukaryotes, there is very little information about the specific pressures that might shape a given lineage. Certainly, the symmetrical methylation of CG dinucleotides has a unique structural significance in many higher DNA genomes, reducing the value and frequency of this sequence in coding regions.
Infection by Human Immunodeficiency Virus — CD4 is Not Enough (1996)

The interaction between the human immunodeficiency virus (HIV) and its cellular target once seemed fairly simple: the virus attached to the CD4 molecule on the cell surface, entered the cell, and began its replicative cycle.1 However, in the past few years, research has turned up surprising evidence that the virus can bind to cells by means of receptors other than CD4. These alternative receptors include galactosylceramide on brain and bowel cells and, when the virus has formed a complex with antibody, Fc receptors. Binding through Fc receptors can actually enhance viral infection.1 Recent studies of the early events in HIV . . .
Nucleophilic Reactivity (1963)

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML ...Read More
Mechanism of leakage current reduction of tantalum oxide capacitors by titanium doping (2007)

In this letter, the authors will point out that defect states related to oxygen vacancies in tantalum oxide capacitors can be suppressed by titanium doping, resulting in significant leakage current reduction. The theory is that titanium forms an acceptor which can move at high temperature and neutralize other donors. However, defect states which cannot be suppressed by titanium doping were detected. These are explained by H2O-related contamination occurring at low temperature (&lt;400°C) during the cooling down period.
Is readability compatible with accuracy ? From Neuro-Fuzzy to Lazy Learning (1998)

info:eu-repo/semantics/published
Chemical strategies for tagging and imaging the proteome (2011)

Proteomic visualization serves as a complement to proteomic identification. In recent years, chemical biologists have made rapid progress developing new methods to tag and image defined sets of proteins. These researchers have requisitioned cellular machinery to place small, reactive analogues into biomolecules. The analogue has been labeled subsequently using a selective ligation reaction. Many groups have demonstrated the efficacy of the copper-catalyzed or strain-promoted azide-alkyne ligation; both enable rapid and precise labeling in complex biological mixtures. This review provides an overview of the methods which have been optimized to tag and fluorophore-label biomolecules for imaging subsets of the proteome in bacterial and mammalian cells. With the approaches described herein, it should be possible to image cells as they undergo changes over time.
Telomere-binding Protein TRF2 Binds to and Stimulates the Werner and Bloom Syndrome Helicases (2002)

Werner syndrome is a human premature aging disorder displaying cellular defects associated with telomere maintenance including genomic instability, premature senescence, and accelerated telomere erosion. The yeast homologue of the Werner protein (WRN), Sgs1, is required for recombination-mediated lengthening of telomeres in telomerase-deficient cells. In human cells, we report that WRN co-localizes and physically interacts with the critical telomere maintenance protein TRF2. This interaction is mediated by the RecQ conserved C-terminal region of WRN. In vitro, TRF2 demonstrates high affinity for WRN and for another RecQ family member, the Bloom syndrome protein (BLM). TRF2 interaction with either WRN or BLM results in a notable stimulation of their helicase activities. Furthermore, the WRN and BLM helicases, partnered with replication protein A, actively unwind long telomeric duplex regions that are pre-bound by TRF2. These results suggest that TRF2 functions with WRN, and possibly BLM, in a common pathway at telomeric ends.
Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus (2020)

Currently, the expansion of the novel human respiratory coronavirus (known as SARS-CoV-2 [severe acute respiratory syndrome coronavirus 2], COVID-2019 [coronavirus disease 2019], or 2019-nCoV [2019 novel coronavirus]) has stressed the need for therapeutic alternatives to alleviate and stop this new epidemic. The previous epidemics of infections by high-morbidity human coronaviruses, such as SARS-CoV in 2003 and the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, prompted the characterization of compounds that could be potentially active against the currently emerging novel coronavirus, SARS-CoV-2. The most promising compound is remdesivir (GS-5734), a nucleotide analog prodrug currently in clinical trials for treating Ebola virus infections. Remdesivir inhibited the replication of SARS-CoV and MERS-CoV in tissue cultures, and it displayed efficacy in nonhuman animal models. In addition, a combination of the human immunodeficiency virus type 1 (HIV-1) protease inhibitors lopinavir/ritonavir and interferon beta (LPV/RTV-IFN-β) was shown to be effective in patients infected with SARS-CoV. LPV/RTV-IFN-β also improved clinical parameters in marmosets and mice infected with MERS-CoV. Remarkably, the therapeutic efficacy of remdesivir appeared to be superior to that of LPV/RTV-IFN-β against MERS-CoV in a transgenic humanized mouse model. The relatively high mortality rates associated with these three novel human coronavirus infections, SARS-CoV, MERS-CoV, and SARS-CoV-2, have suggested that proinflammatory responses might play a role in the pathogenesis. It remains unknown whether the generated inflammatory state should be targeted. Therapeutics that target the coronavirus alone might not be able to reverse highly pathogenic infections. This minireview aims to provide a summary of therapeutic compounds that have shown potential in fighting SARS-CoV-2 infections.
Nucleocytoplasmic Shuttling of BZR1 Mediated by Phosphorylation Is Essential in<i>Arabidopsis</i>Brassinosteroid Signaling (2007)

Phytohormone brassinosteroids (BRs) play critical roles in plant growth and development. BR acts by modulating the phosphorylation status of two key transcriptional factors, BRI1 EMS SUPPRESSOR1 and BRASSINAZOLE RESISTANT1 (BZR1), through the action of BRASSINOSTEROID INSENSITIVE1/BRI1 ASSOCIATED RECEPTOR KINASE1 receptors and a GSK3 kinase, BRASSINOSTEROID INSENSITIVE2 (BIN2). It is still unknown how the perception of BR at the plasma membrane connects to the expression of BR target genes in the nucleus. We show here that BZR1 functions as a nucleocytoplasmic shuttling protein and GSK3-like kinases induce the nuclear export of BZR1 by modulating BZR1 interaction with the 14-3-3 proteins. BR-activated phosphatase mediates rapid nuclear localization of BZR1. Besides the phosphorylation domain for 14-3-3 binding, another phosphorylation domain in BZR1 is required for the BIN2-induced nuclear export of BZR1. Mutations of putative phosphorylation sites in two distinct domains enhance the nuclear retention of BZR1 and BR responses in transgenic plants. We propose that the spatial redistribution of BZR1 is critical for proper BR signaling in plant growth and development.
On-line C-arm Calibration intrinsèque "On-line" d'un C-arm par une méthode de détection de droite avec la transformée de Radon (2015)

Les ``C-arm'' sont des systémes de radiologie interventionnelle fréquemment utilisés en salle d'opération ou au lit du patient. Des images 3D des structures anatomiques internes peuvent être calculées à partir de multiples radiographies acquises sur un ``C-arm mobile'' et isocentrique décrivant une trajectoire généralement circulaire autour du patient. Pour cela, la géométrie conique d'acquisition de chaque radiographie doit être précisément connue. Malheureusement, les C-arm se déforment en général au cours de la trajectoire. De plus leur motorisation engendre des oscillations non reproductibles. Ils doivent donc être calibrés au cours de l'acquisition. Ma thèse concerne la calibration intrinsèque d'un C-arm à partir de la détection de la projection du collimateur de la source dans les radiographies.Nous avons développé une méthode de détection de la projection des bords linéaires du collimateur. Elle surpasse les méthodes classiques comme le filtre de Canny sur données simulées ou réelles. La précision que nous obtenons sur l'angle et la position (phi,s) des droites est de l'ordre de: phi{RMS}=+/- 0.0045 degrees et s{RMS}=+/- 1.67 pixels. Nous avons évalué nos méthodes et les avons comparés à des méthodes classiques de calibration dans le cadre de la reconstruction 3D.
Changes of Depressive Symptoms and Nutritional Indices after Antidepressant Treatment in the Patients with Chronic Hemodialysis and Depression. (2008)

Purpose : Depression is common in patients with chronic renal failure on maintenance hemodialysis, though success rate of treatment is low. This study aimed to investigate the features and severity of the depressive symptoms and nutritional indices, and significant changes after antidepressant treatment. Methods : The authors assessed 45 patients. Diagnosis of depression was made using DSM-IV-TR and the depressive symptoms were evaluated using Hamilton Rating Scale for Depression via semi- structured interview. Subjective global assessment, anthropometric measurements and nutritional indices such as Kt/V, nPCR were examined. Depressive patients were treated for 8 weeks with SSRI (citalopram), and all the variables were examined again after the treatment. Results : 19 (42.2%) patients were diagnosed as depression. Nutritional status was not different between patients with depression and those without depression. Compared to non-depressed patients, depressed patients showed significantly higher depressed mood, guilty feeling, suicide idea, psychic and somatic anxiety, lower work and activities, psychomotor retardation, sleep disturbances, general somatic symptoms and hypochondriasis. After antidepressant treatment, depressed mood, guilty feeling, suicide idea, psychic anxiety, initial insomnia, middle insomnia, early awakening, work and activities and general somatic symptoms were improved significantly. TSF (p
Further Investigation of the Stabilization of β‐Cristobalite (1994)

Chemical stabilization of β‐cristobalite has been achieved using two methods: (1) incorporating “stuffing” cations Na, Ca, Cu, and Sr into the cavities in the tectosilicate framework, as previously reported, and (2) without “stuffing” cations, by substituting AlPO 4 into the framework. XRD, TEM, FTIR, DSC, and solid‐state variable‐temperature 29 Si NMR confirm that stabilization occurs by both methods. Dynamic disorder, characteristic of the β‐cristobalite structure above the α↔β phase transition, was observed via TEM in the NaAlO 2 ‐, CaAl 2 O 4 ‐, and CuAl 2 O 4 ‐stabilized cristobalites at room temperature. For AlPO 4 ‐stabilized material intergrowths of AlPO 4 regions with a tridymite‐type structure suppress the β‐ ↔α‐cristobalite phase transition.
Modeling & Simulation of Complex Adaptive System——A Traffic Simulation System (2004)

Traffic system is a complex adaptive system (CAS). Intuited by CAS theory, we present a decentralized multi-agent based dynamic traffic simulation system with SWARM platform. We develop the traffic systems from bottom up, where vehicles and traffic signals are defined as agents. The interaction of these individual agents are simulated on a road map, thus leading to emergent patterns of traffic dynamics. Cellular Automaton is used to simulate the traffic flow and an evolutionary design is applied to self-organized control of the traffic signals. Furthermore, we compare the control approach if we join the forecast mechanism with the pure self-organized control method. From the experimental results, it can be concluded that the performance of the former approach is much superior to the latter one in that it can reduce the traffic jam.
Bactericidal effect of amoxicillin on Helicobacter pylori in an in vitro model using epithelial cells (1991)

The treatment of Helicobacter pylori with antimicrobial agents has largely been ineffective, and susceptibility results are in disagreement with those obtained by standard in vitro testing. The bactericidal effect of amoxicillin was tested in an in vitro model by using sessile bacteria attached to HEp-2 cells; this bactericidal effect was compared with that against planktonic bacteria. Viable cell counts were performed by standard procedures after 1, 6, and 24 h of contact with the antibiotic at different concentrations. A bactericidal effect (99.9% killing) was observed against sessile bacteria after 24 h with concentrations of only 10, 1, and 0.1 mg/liter, while against planktonic bacteria it was also noted at concentrations of 0.01 and 0.001 mg/liter, and the effect was observed after 6 h with the three highest concentrations. When the results for five strains were studied by analysis of variance at 6 and 24 h, the main variable was the antibiotic concentration, followed by the culture conditions, e.g., planktonic or sessile bacteria, the strain tested, and the time of contact. A decreased pH of 5.4 did not affect the action of amoxicillin. The bactericidal effect of the combination of amoxicillin and metronidazole was additive against sessile H. pylori.
Distinguishing right from left colon by the pattern of gene expression. (2003)

Distinct epidemiological and clinicopathological characteristics of colorectal carcinomas (CRCs) based on their anatomical location suggest different risk factors and pathways of transformation associated with proximal and distal colon carcinogenesis. These differences may reflect distinct biological characteristics of proximal and distal colonic mucosa, acquired in embryonic or postnatal development, that determine a differential response to uniformly distributed environmental factors. Alternatively, the differences in the epidemiology of proximal and distal CRCs could result from the presence of different procarcinogenic factors in the ascending versus descending colon, acting on cells with either similar or distinct biological characteristics. We applied cDNA microarray technology to explore the possibility that mucosal epithelium from adult proximal and distal colon can be distinguished by their pattern of gene expression. In addition, gene expression was studied in fetal (17-24 weeks gestation) proximal and distal colon. More than 1000 genes were expressed differentially in adult ascending versus descending colon, with 165 genes showing >2-fold and 49 genes showing >3-fold differences in expression. With almost complete concordance, biopsies of adult colonic epithelium can be correctly classified as proximal or distal by gene expression profile. Only 87 genes were expressed differently in ascending and descending fetal colon, indicating that, although anatomically relevant differences are already established in embryonic colon, additional changes in gene expression occur in postnatal development.
<i>Yarrowia lipolytica</i> Mutants Devoid of Pyruvate Carboxylase Activity Show an Unusual Growth Phenotype (2005)

We have cloned and characterized the gene PYC1, encoding the unique pyruvate carboxylase in the dimorphic yeast Yarrowia lipolytica. The protein putatively encoded by the cDNA has a length of 1,192 amino acids and shows around 70% identity with pyruvate carboxylases from other organisms. The corresponding genomic DNA possesses an intron of 269 bp located 133 bp downstream of the starting ATG. In the branch motif of the intron, the sequence CCCTAAC, not previously found at this place in spliceosomal introns of Y. lipolytica, was uncovered. Disruption of the PYC1 gene from Y. lipolytica did not abolish growth in glucose-ammonium medium, as is the case in other eukaryotic microorganisms. This unusual growth phenotype was due to an incomplete glucose repression of the function of the glyoxylate cycle, as shown by the lack of growth in that medium of double pyc1 icl1 mutants lacking both pyruvate carboxylase and isocitrate lyase activity. These mutants grew when glutamate, aspartate, or Casamino Acids were added to the glucose-ammonium medium. The cDNA from the Y. lipolytica PYC1 gene complemented the growth defect of a Saccharomyces cerevisiae pyc1 pyc2 mutant, but introduction of either the S. cerevisiae PYC1 or PYC2 gene into Y. lipolytica did not result in detectable pyruvate carboxylase activity or in growth on glucose-ammonium of a Y. lipolytica pyc1 icl1 double mutant.
Noninvasive Measurement of Intra-Aneurysmal Pressure and Flow Pattern Using Phase Contrast with Vastly Undersampled Isotropic Projection Imaging (2007)

PC-VIPR can provide anatomic as well as noninvasive quantitative and qualitative hemodynamic information in the canine aneurysm model. The PC-VIPR intra-aneurysmal pressure measurements correlated well with catheter measurements.
Characterization and classification of lupus patients based on plasma thermograms (2017)

Plasma thermograms constitute an additional biomarker which may help improve diagnosis of SLE patients, particularly when coupled with standard diagnostic testing. Differences in thermograms according to patient sex, ethnicity, clinical and environmental factors are important considerations for application of thermograms in a clinical setting.
16-QAM Optical Packet Switching with Real-time Self-homodyne Detection using Polarization-multiplexed Pilot-carrier (2012)

We first demonstrated 20-Gbit/s 16-QAM optical packet switching and real-time detection. The modulated optical packets and pilot-carriers were simultaneously generated from a prototype pilot-carrier vector modulator and detected by simple self-homodyne receivers. Error-free operation was confirmed by a real-time error count using a packet BERT.
BIM Based Virtual Environment for Fire Emergency Evacuation (2014)

Recent building emergency management research has highlighted the need for the effective utilization of dynamically changing building information. BIM (building information modelling) can play a significant role in this process due to its comprehensive and standardized data format and integrated process. This paper introduces a BIM based virtual environment supported by virtual reality (VR) and a serious game engine to address several key issues for building emergency management, for example, timely two-way information updating and better emergency awareness training. The focus of this paper lies on how to utilize BIM as a comprehensive building information provider to work with virtual reality technologies to build an adaptable immersive serious game environment to provide real-time fire evacuation guidance. The innovation lies on the seamless integration between BIM and a serious game based virtual reality (VR) environment aiming at practical problem solving by leveraging state-of-the-art computing technologies. The system has been tested for its robustness and functionality against the development requirements, and the results showed promising potential to support more effective emergency management.
Effects of Soluble CD4 on Simian Immunodeficiency Virus Infection of CD4-Positive and CD4-Negative Cells (1999)

A soluble form of the CD4 receptor (sCD4) can either enhance or inhibit the infection of cells by simian immunodeficiency virus (SIV) and human immunodeficiency virus. We investigated the basis for these varying effects by studying the entry of three SIV isolates into CD4-positive and CD4-negative cells expressing different chemokine receptors. Infection of CD4-negative cells depended upon the viral envelope glycoproteins and upon the chemokine receptor, with CCR5 and gpr15 being more efficient than STRL33. Likewise, enhancement of infection by sCD4 was observed when CCR5- and gpr15-expressing target cells were used but not when those expressing STRL33 were used. The sCD4-mediated enhancement of virus infection of CD4-negative, CCR5-positive cells was related to the sCD4-induced increase in binding of the viral gp120 envelope glycoprotein to CCR5. Inhibitory effects of sCD4 could largely be explained by competition for virus attachment to cellular CD4 rather than other detrimental effects on virus infectivity (e.g., disruption of the envelope glycoprotein spike). Consistent with this, the sCD4-activated SIV envelope glycoprotein intermediate on the virus was long-lived. Thus, the net effect of sCD4 on SIV infectivity appears to depend upon the degree of enhancement of chemokine receptor binding and upon the efficiency of competition for cellular CD4.
Effects of extremely low frequency electromagnetic field (EMF) on collagen type I mRNA expression and extracellular matrix synthesis of human osteoblastic cells (1998)

Human osteoblastic cells were grown in a three-dimensional (3-D) cell culture model and used to test the effects of a 20 Hz sinusoidal electromagnetic field (EMF; 6 mT and 113 mV/cm max) on collagen type I mRNA expression and extracellular matrix formation in comparison with the effects of growth factors. The cells were isolated from trabecular bone of a healthy individual (HO-197) and from a patient presenting with myositis ossificans (MO-192) and grown in a collagenous sponge-like substrate. Maximal enhancement of collagen type I expression after EMF treatment was 3.7-fold in HO-197 cells and 5.4-fold in MO-192 cells. Similar enhancement was found after transforming growth factor-β (TGF-β) and insulin-like growth factor-I (IGF-I) treatment. Combined treatment of the cells with EMF and the two growth factors TGF-β and IGF-I did not act synergistically. MO-192 cells produced an osteoblast-characteristic extracellular matrix containing collagen type I, alkaline phosphatase, and osteocalcin, together with collagen type III, TP-1, and TP-3, two epitopes of an osteoblastic differentiation marker. The data suggest that the effects of EMFs on osteoblastic differentiation are comparable to those of TGF-β and IGF-I. We conclude that EMF effects in the treatment of skeletal disorders and in orthopedic adjuvant therapy are mediated via enhancement of collagen type I mRNA expression, which may lead to extensive extracellular matrix synthesis. Bioelectromagnetics 19:222–231, 1998. © 1998 Wiley-Liss, Inc.
Voice-on-Target: A New Approach to Tactical Networking and Unmanned Systems Control via the Voice Interface to the SA Environment (2009)

Center for Network Innovation and Experimentation (CENETIX) Publication