gebhart/patrepeval huggingface dataset:
Beta-glucoside permease represses the bgl operon of Escherichia coli by phosphorylation of the antiterminator protein and also interacts with glucose-specific enzyme III, the key element in catabolite control. (1990)

The beta-glucoside (bgl) operon of Escherichia coli is subject to both positive control by transcriptional termination/antitermination and negative control by the beta-glucoside-specific transport protein, an integral membrane protein known as enzyme IIBgl. Previous results led us to speculate that enzyme IIBgl exerts its negative control by phosphorylating and thereby inactivating the antiterminator protein, BglG. Specifically, our model postulated that the transport protein enzyme IIBgl exhibits protein-phosphotransferase activity in the absence of beta-glucosides. We now present biochemical evidence that the phosphorylation of protein BglG does indeed occur in vivo and that it is accompanied by the loss of antitermination activity. BglG persists in the phosphorylated state in the absence of beta-glucosides but is rapidly dephosphorylated when beta-glucosides become available for transport. Our data also suggested specific interactions between the beta-glucoside transport protein and the glucose-specific enzyme III (enzyme IIIGlc), a component of glucose transport and a key element in regulation of catabolite repression. These observations indicate that enzyme IIIGlc may, in conjunction with enzyme IIBgl, modulate the transport of beta-glucosides and the phosphorylation of the antiterminator protein. In the absence of both sugars, when the catabolite-controlled promoter of the operon is derepressed, enzyme IIIGlc may mediate tight repression of antitermination.
Analogs of Synthetic Melanin Polymers for Specific Imaging Applications (1994)

Williams RF, Siegle RL, Pierce BL, Floyd LJ. Analogs of synthetic melanin polymers for specific imaging applications. Invest Radiol 1994;29:S116–S119.
Contributions of amplitude measurement in QCM sensors (1996)

The characteristics of the amplifier and the feedback loop of a quartz crystal series oscillating circuit are investigated. The fact that the change of the vibration amplitude of the quartz crystal is proportional to the change of its motional resistance is derived. The concept of a characteristic damping coefficient is introduced and the behavior of a quartz crystal vibrating in liquids is analyzed. The experiment shows that the effect of mass loading can be distinguished from that of the liquid damping of a quartz crystal microbalance (QCM) sensor in liquids by simultaneously measuring the amplitude and the frequency change.
Plug flow cytometry: An automated coupling device for rapid sequential flow cytometric sample analysis (1999)

Background: The tools for high throughput flow cytometry have been limited in part because of the requirement that the samples must flow under pressure. We describe a simple system for sampling repetitively from an open vessel. Methods: Under computer control, the sample is loaded into a sample loop in a reciprocating eight-way valve by the action of a syringe. When the valve position is switched, the plug of sample in the sample loop is transported to the flow cytometer by a pressure-driven fluid line. By coupling the plug-forming capability to a second multi-port valve, samples can be delivered sequentially from separate vessels. Results: The valve is able to deliver samples at rates ranging up to about 9 samples per minute. Each plug of sample has uniform delivery characteristics with a reproducible coefficient of variation (CV). Even at the highest sampling rate, carryover between samples is limited. Conclusions: Plug-flow flow cytometry has the potential to automate the delivery of small samples from unpressurized sources at rates compatible with many screening and assay applications. Cytometry 37:156–159, 1999. © 1999 Wiley-Liss, Inc.
Outbreak of jaundice and hemorrhagic fever in the Southeast of Brazil in 2001: Detection and molecular characterization of yellow fever virus (2002)

Between January and March 2001, an outbreak of jaundice and hemorrhagic fever occurred in the state of Minas Gerais, Southeast region of Brazil, in which a mortality rate of 53% was reported. Seroconversion, virus isolation, histopathological and immunohistochemical findings, and reverse transcription-polymerase chain reaction (RT-PCR) identified yellow fever virus (YFV) as the etiological agent responsible for the outbreak. Partial nucleotide sequence analysis from a fragment of the YFV genome spanning parts of nonstructural (NS) 5 gene and 3' noncoding region (3' UTR) showed that the YFV involved in this outbreak belongs to South American genotype I and differs from the Brazilian virus identified in 1996.
Single-Camera Basketball Tracker through Pose and Semantic Feature Fusion (2019)

Tracking sports players is a widely challenging scenario, specially in single-feed videos recorded in tight courts, where cluttering and occlusions cannot be avoided. This paper presents an analysis of several geometric and semantic visual features to detect and track basketball players. An ablation study is carried out and then used to remark that a robust tracker can be built with Deep Learning features, without the need of extracting contextual ones, such as proximity or color similarity, nor applying camera stabilization techniques. The presented tracker consists of: (1) a detection step, which uses a pretrained deep learning model to estimate the players pose, followed by (2) a tracking step, which leverages pose and semantic information from the output of a convolutional layer in a VGG network. Its performance is analyzed in terms of MOTA over a basketball dataset with more than 10k instances.
STUDY ON SUBGENUS XORIDES (HYMENOPTERA: ICHNEU‐MONIDAE) FROM NORTH CHINA (1998)

Abstract This papa deals with nine species of Xorides (Xorides ) collected in North China, of which three are new to the science, namely Xorides (X.) furcatus sp. nov., X . (X.) hirtus sp. nov. and X. (X.) aculeatus sp.nov., three, are new records, X. (X.) brachylabis , X. (X.) praecato‐rius , X. (X.1 sepulchralis , and the other three species already known in China, X. (X.) sapporen‐sis, X . (X.1 erigentis, X . (X.) hingganensis .
Advanced Heart Failure Treated with Continuous-Flow Left Ventricular Assist Device (2009)

Treatment with a continuous-flow left ventricular assist device in patients with advanced heart failure significantly improved the probability of survival free from stroke and device failure at 2 years as compared with a pulsatile device. Both devices significantly improved the quality of life and functional capacity. (ClinicalTrials.gov number, NCT00121485.)
Structural and dynamic properties of a new type of discotic nematic compounds (1989)

Abstract Thermodynamic, structural and dynamical properties of a new type of discotic compounds, a hydrocarbon without any heteroatoms, displaying a nematic discotic phase have been investigated by means of X-ray diffraction, electro-optical relaxation, and calorimetric studies. Of particular interest are the strength of the first order nematic—isotropic phase transition and the nature of the orientational fluctuations in the isotropic phase. The short range positional order was found to be biaxial in both the isotropic and the nematic phase. The isotropic phase displays strong pretransitional effects originating from orientational fluctuations in the neighbourhood of the transition to the nematic phase. The character of these pretransitional effects differs from that found for calamitic systems in that the number of correlated molecules g 2 is extremely large, of the order of 600 at the clearing temperature and the electro-optical relaxation time is very large, caused by the large value of g 2.
A samarium doped visible glass laser operating at 651nm (1988)

Laser emission at 651nm has been observed from samarium3+ doped silica optical fibre in a Fabry-Perot type laser cavity. The laser operates in cw and Q-switched modes when pumped with 488nm light at room temperature.
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2011)

Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. PEAKS DB achieves significantly improved accuracy and sensitivity over two other commonly used software packages. Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of overconfidence that exists in the conventional target decoy method for certain types of peptide identification software.
CD137, implications in immunity and potential for therapy (2009)

CD137 is a member of the TNF receptor family and a potent T cell costimulatory molecule. Crosslinking of CD137 on activated T cells has shown promise in enhancing anti-tumor immune responses in murine models, and agonistic anti-CD137 antibodies are currently being tested in phase I clinical trials. Surprisingly, these very same agonistic anti-CD137 antibodies have also been found to ameliorate autoimmune disease under certain circumstances. At the current state of knowledge these circumstances cannot be clearly defined. Therefore, anti-CD137 antibodies in man will need to be used with caution. CD137 ligand is expressed by antigen presenting cells. Antagonistic anti-CD137 ligand antibodies have shown efficacy in dampening disease in murine autoimmune models. A similar effect would be expected from antagonistic anti-CD137 antibodies, soluble CD137, or any other compound interfering with CD137 / CD137 ligand interaction. CD137 ligand is expressed as a transmembrane protein on the cell surface and it too can transmit signals into antigen presenting cells. Agonistic anti-CD137 ligand antibodies or a recombinant CD137 protein could stimulate the activity of antigen presenting cells.
Aminozuckersynthesen, XIII Zum Mechanismus des nucleophilen Ersatzes von Methansulfonylgruppen. Die gleichzeitige Bildung von D‐Gulosamin‐ und D‐Galaktosamin‐Derivaten aus Glucosamin‐Derivaten (1965)

Abstract Benzyl‐ N ‐cbo‐3‐ O ‐acetyl‐4.6‐di‐ O ‐mesyl‐α‐ D ‐glucosaminid geht beim Erhitzen mit Kaliumacetat in Eisessig/Acetanhydrid in ein Gemisch von Benzyl‐ N ‐cbo‐3.4.6‐tri‐ O ‐acetyl‐α‐ D ‐galaktosaminid und Benzyl‐4.6‐di‐ O ‐acetyl‐α‐ D ‐gulopyranosido[2.3:4′.5′]oxazolidon‐(2′) über. Ein möglicher Mechanismus dieser Umsetzung wird diskutiert.
Floor Identification Using Magnetic Field Data with Smartphone Sensors (2019)

Floor identification plays a key role in multi-story indoor positioning and localization systems. Current floor identification systems rely primarily on Wi-Fi signals and barometric pressure data. Barometric systems require installation of additional standalone sensors to perform floor identification. Wi-Fi systems, on the other hand, are vulnerable to the dynamic environment and adverse effects of path loss, shadowing, and multipath fading. In this paper, we take advantage of a pervasive magnetic field to compensate for the limitations of these systems. We employ smartphone sensors to make the proposed scheme infrastructure free and cost-effective. We use smartphone magnetic sensors to identify the floors in a multi-story building with improved accuracy. Floor identification is performed with user activities of <i>normal walking</i>, <i>call listening</i>, and <i>phone swinging</i>. Various machine learning techniques are leveraged to identify user activities. Extensive experiments are performed to evaluate the proposed magnetic-data-based floor identification scheme. Additionally, the impact of device heterogeneity on floor identification is investigated using Samsung Galaxy S8, LG G6, and LG G7 smartphones. Research results demonstrate that the magnetic floor identification outperforms barometric and Wi-Fi-enabled floor detection techniques. A floor change module is incorporated to further enhance the accuracy of floor identification.
MANF: A Novel Endoplasmic Reticulum Stress Response Protein—The Role in Neurological and Metabolic Disorders (2021)

The mesencephalic astrocyte-derived neurotrophic factor (MANF), also named as arginine-rich protein (ARP) or arginine-rich mutated in early-stage tumors (ARMET), is a novel evolutionary conserved protein related to unfolded protein response. Growing evidence suggests that MANF critically involves in many ER stress-related diseases with a protective effect. Here, we review the function of MANF based on its structure in neurological and metabolic disorders and summarize its potential applications in disease diagnosis and therapies.
THE CROSSFLOW INJECTION TECHNIQUE: AN IMPROVEMENT OF THE ETHANOL INJECTION METHOD (2002)

A novel scalable liposome preparation technique for pharmaceutical application is presented. Previous experiments have shown that the concept of continuous crossflow injection is a promising approach. For the characterization of the process, we focus on the influencing parameters like the lipid concentration, the injection hole diameter, the injection pressure, the buffer flow rate, and system performance. These experiments demonstrate that the injection hole diameter and the system performance do not influence the vesicle forming process and that a minimum of buffer flow rate is required to affect batch homogeneity. In contrast, strongly influencing parameters are lipid concentration in combination with increasing injection pressures. After exceeding the upper pressure limit of the linear range, where injection velocities remain constant, the vesicle batches are narrowly distributed, also when injecting higher lipid concentrations. Reproducibility and scalability data show similar results with respect to vesicle size and size distribution and demonstrate the stability and robustness of the novel continuous liposome preparation technique.
Human‐Serum Matrix Supports Undifferentiated Growth of Human Embryonic Stem Cells (2005)

One of the most frequently used matrices for feeder-free growth of undifferentiated human embryonic stem cells (hESCs) is Matrigel, which supports attachment and growth of undifferentiated hESCs in the presence of mouse embryonic fibroblast-conditioned medium. Unfortunately, application of Matrigel or medium conditioned by mouse embryonic feeder cells is not ideal for potential medical application of hESCs because xenogeneic pathogens can be transmitted through culture conditions. We demonstrate here that human serum as matrix and medium conditioned by differentiated hESCs reduce exposure of hESCs to animal ingredients and provide a safer direction toward completely animal-free conditions for application, handling, and understanding of hESC biology. At the same time, hESCs grown under these conditions maintain all hESC features after prolonged culture, including the developmental potential to differentiate into representative tissues of all three embryonic germ layers, unlimited and undifferentiated proliferative ability, and maintenance of normal karyotype.
Intracellular expression of an antibody fragment-neutralizing p21 ras promotes tumor regression. (1998)

Mutated ras genes are found in a large number of human tumors and, therefore, constitute one of the primary targets for cancer treatment. Microinjection of the neutralizing anti-Ras monoclonal antibody Y13-259 was previously reported to induce transient phenotypic reversion of ras-transformed rodent fibroblasts in vitro. We have prepared a single-chain Fv fragment (scFv) derived from Y13-259, and here, we show that intracellular expression of the scFv led to the specific inhibition of the Ras signaling pathway in Xenopus laevis oocytes and NIH3T3 fibroblasts. Moreover, neutralizing Ras with the scFv specifically promoted apoptosis in vitro in human cancer cells but not in untransformed cells. As a step toward cancer gene therapy, we finally demonstrated that intratumor transduction of HCT116 colon carcinoma cells with the anti-Ras scFv using an adenoviral vector elicited sustained tumor regression in nude mice.
Biomimetic approach to potential benzodiazepine receptor agonists and antagonists (1984)

Several beta-carbolines, isoquinolines, imidazopyridines , and canthin -6-ones prepared in biomimetic fashion were tested for their ability to bind to the benzodiazepine receptor. Methyl isoquinoline-3-carboxylate, methyl 6,7- dimethoxyisoquinoline -3-carboxylate (3b) 1-phenyl-3- carbomethoxyimidazopyridine , (6B,) and canthin -6- one ( 13a ) bound with moderate affinities, while 2- carbomethoxycanthin -6- one ( 13b ) bound to benzodiazepine receptors with an affinity comparable to several pharmacologically active benzodiazepines. The potency of 13b suggests that the benzodiazepine receptor(s) can tolerate substitution at positions 1 and 9 of a beta-carboline without loss of activity if the substituents are trigonal and maintain a planar topography. Moreover, displacement of the carbonyl group by two atoms from the aromatic ring (C) of the beta-carboline skeleton caused a marked decrease in binding to the benzodiazepine receptor. This observation supports the hypothesis that maximum binding affinity of beta-carbolines is achieved when the carbonyl group at position 3 is attached directly to the aromatic pyridine ring.
Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays (2009)

Identification of protein targets of post-translational modification is an important analytical problem in biology. Protein microarrays exposed to cellular extracts could offer a rapid and convenient means of identifying modified proteins, but this kind of biochemical assay, unlike DNA microarrays, depends on a faithful reconstruction of in vivo conditions. Over several years, concentrated cellular extracts have been developed, principally for cell cycle studies that reproduce very complex cellular states. We have used extracts that replicate the mitotic checkpoint and anaphase release to identify differentially regulated poyubiquitination. Protein microarrays were exposed to these complex extracts, and the polyubiquitinated products were detected by specific antibodies. We expected that among the substrates revealed by the microarray should be substrates of the anaphase promoting complex (APC). Among 8,000 proteins on the chip, 10% were polyubiquitinated. Among those, we found 11 known APC substrates (out of 16 present on the chip) to be polyubiquitinated. Interestingly, only 1.5% of the proteins were differentially ubiquitinated on exit from the checkpoint. When we arbitrarily chose 6 proteins thought to be involved in mitosis from the group of differentially modified proteins, all registered as putative substrates of the APC, and among 4 arbitrarily chosen non-mitotic proteins picked from the same list, 2 were ubiquitinated in an APC-dependent manner. The striking yield of potential APC substrates from a simple assay with concentrated cell extracts suggests that combining microarray analysis of the products of post-translational modifications with extracts that preserve the physiological state of the cell can yield information on protein modification under various in vivo conditions.
Low molecular weight dextran sulfate prevents complement activation and delays hyperacute rejection in pig‐to‐human xenotransplantation models (2001)

Dextran sulfate of 5000 molecular weight (DXS 5000) is known to block complement activation as well as the intrinsic coagulation cascade by potentiation of C inhibitor. The effect of DXS 5000 on hyperacute rejection (HAR) was tested in pig-to-human xenotransplantation models. For in vitro testing, a cytotoxicity assay was used with the pig kidney cell line PK15 as target cells and fresh, undiluted human serum as antibody and complement source. Ex vivo pig lung perfusion was chosen to assess DXS 5000 in a physiologic model. Pig lungs were perfused with fresh, citrate-anticoagulated whole human blood to which 1 or 2 mg/ml DXS 5000 were added; the lungs were ventilated and the blood de-oxygenated. Pulmonary vascular resistance (PVR) and blood oxygenation (deltapO2) were monitored throughout the experiment. Autologous pig blood and human blood without DXS 5000 served as controls. In the PK 15 assay DXS 5000 led to a complete, dose-dependent inhibition of human serum cytotoxicity with an average IC50 of 43 +/- 18 microg/ml (n=8). Pig lungs perfused with untreated human blood (n=2) underwent HAR within 105 +/- 64 min, characterized by increased PVR, decrease of deltapO2, and generalized edema. Microscopically, capillary bleeding as well as deposition of human antibodies, complement and fibrin could be observed. Addition of DXS 5000 (n=4) prolonged lung survival to 170 +/- 14 min for 1 mg/ml and 250 +/- 42 min for 2 mg/ml. and PVR values as well as edema formation were comparable to control lungs that were perfused with autologous pig blood (n=2). Activation of complement (activation products in serum, deposition on lung tissue) and the coagulation system (fibrin monomers) were significantly diminished as compared to human blood without DXS 5000. Binding of anti-Gal antibodies was not influenced, and in vitro experiments showed no evidence of complement depletion by DXS 5000. In conclusion, DXS 5000 is an efficient complement inhibitor in pig-to-human xenotransplantation models and therefore a candidate for complement-inhibitory/anti-inflammatory therapy either alone or in combination with other substances and warrants further investigation.
Isolation and partial characterization of lumican and decorin from adult chicken corneas. A keratan sulfate-containing isoform of decorin is developmentally regulated. (1992)

The proteoglycans extracted from adult chicken were initially purified by DEAE-chromatography. Digestion of these proteoglycans with chondroitinase ABC generated a single 40-kDa core protein while digestion with keratanase generated a single 52-kDa core protein. Digestion with both enzymes combined, however, increased the amount of 40-kDa core protein produced. This suggested that the 40-kDa core protein exists with chondroitin/dermatan sulfate (C/DS) side chains alone and with both C/DS and keratan sulfate (KS) side chains. The proteoglycan fraction was initially digested with chondroitinase ABC, and the M(r) = 40,000 core protein derived from proteoglycans containing C/DS side chains alone was isolated. Amino-terminal sequencing showed it to be the chick cognate of decorin. The remaining proteoglycans were then digested with keratanase, and both the 40-kDa core protein and the 52-kDa core proteins derived from KS-containing proteoglycans were purified. The M(r) = 40,000 core protein derived from proteoglycans containing both C/DS and KS side chains had the same amino-terminal sequence as decorin and cross-reacted with antibodies to decorin. Sequence from the 52-kDa core protein derived from KS-containing proteoglycans showed it to be lumican. The results of this study suggest that adult chick corneas contain two isoforms of decorin: one containing C/DS side chains and the other, a hybrid, containing both C/DS and KS side chains. Embryonic corneas did not contain the hybrid isoform of decorin. These results suggest that different post-translational modifications occur to the decorin gene product during corneal development and maturation.