gebhart/patrepeval huggingface dataset:
Fluorine-18 labeled PSMA-targeted phosphoramidate inhibitors as potential PET imaging agents for prostate cancer (2013)

441 Objectives Prostate-specific membrane antigen (PSMA), a transmembrane protein commonly found on the tumor cell surface of late-stage, androgen-independent and metastatic prostate cancer, is an ideal biomarker for staging and targeted therapy. Previously reported FB-LW-54 (IC50 = 14 nM) is an 18F labelled irreversible phosphoramidate PSMA inhibitor, which demonstrated promising in vivo results in LNCaP tumor bearing mice [1]. Three more stable phosphoramidate-based PSMA inhibitor analogues with similar binding affinity as FB-LW-54 (TG97, AH-TG97 and AH2-TG97) were synthesized for radiolabeling with 18F-flourobenzamide (18FB) for PET imaging applications. Methods Succinimidyl [18F]fluorobenzoate (SFB) prosthetic group was prepared successfully either manually in lab or the Neptis box. SFB conjugation to the three analogues was carried out at pH 9.5, 37 °C for 10 min, purified by reversed phase HPLC and concentrated for in vivo studies. PET imaging (1 and 2 h) and biodistribution studies (1, 2 h and blocked with 250 ug LW-54) were performed using nude mice with 22RV1 (PSMA+) and PC3 (PSMA-) xenograft. Results SFB conjugation to the PSMA inhibitor analogues was accomplished in 27-45% radiochemical yields. Tumor uptake ranged between 1.7-2.4 %ID/g and can retain up to 2h. Minimal uptake in the non-target organs and rapid clearance from blood was noted. High uptake was observed in the mice kidneys as expected due to its normal expression. But PSMA expression in human kidney has not been identified. PSMA specificity was demonstrated in the tumor and kidneys by LW-54 blocking (56-93% uptake decrease). Conclusions We have successfully radiolabeled three PSMA-targeted analogues for mice xenografts ([18F]FB-TG97, [18F]FB-AH-TG97 and [18F]FB-AH2-TG97) and demonstrated their specificity. [18F]FB-AH-TG97 exhibited the highest tumor uptake with exceptional clearance in 22RV1 tumor bearing mice. Research Support Supported by DOD W81XWH-11-1-0464 (SFD) and W81XWH-11-1-0191 (LW) NIH 5R01CA140617 (CB).
Potentially Probiotic Lactobacillus Strains Derived from Food Intensify Crystallization Caused by Proteus mirabilis in Urine (2020)

Proteus mirabilis is a common cause of infectious urolithiasis. The first stage in the formation of urinary stones is the crystallization of mineral salts in the urine induced by urease activity of this microorganism. Lactobacillus spp. are an important component of the human microbiota and in large quantities occur in foods. Regardless of their origin, those with probiotic properties are proposed as an alternative to antibiotic therapy in the treatment of urinary tract infections. The aim of the study was to check the effect of selected Lactobacillus plantarum and Lactobacillus brevis strains on crystallization caused by P. mirabilis in an in vitro experiment. It has been confirmed that selected Lactobacillus strains have antibacterial properties and colonize the urinary tract epithelium. During 24-h incubation of bacterial cultures, containing P. mirabilis and individual Lactobacillus strains, in synthetic urine, bacterial viability (CFU/mL), pH, and crystallization were determined. Crystallization was assessed quantitatively and qualitatively using AAS and XRD techniques as well as phase-contrast microscopy. It has been shown that in the presence of selected Lactobacillus strains, the culture pH increases faster, especially after 8 h of incubation, compared with the pure P. mirabilis culture. An increase in pH reduces the viability of P. mirabilis; however, in the presence of some lactobacilli, the uropathogen grows more intensively. The presence of Lactobacillus also affected crystallization by increasing its intensity, and the resulting crystals were larger in size. Tested L. plantarum and L. brevis strains could therefore accelerate the formation of urinary stones and development of infection.
Multi-agent Trajectory Prediction with Fuzzy Query Attention (2020)

Trajectory prediction for scenes with multiple agents and entities is a challenging problem in numerous domains such as traffic prediction, pedestrian tracking and path planning. We present a general architecture to address this challenge which models the crucial inductive biases of motion, namely, inertia, relative motion, intents and interactions. Specifically, we propose a relational model to flexibly model interactions between agents in diverse environments. Since it is well-known that human decision making is fuzzy by nature, at the core of our model lies a novel attention mechanism which models interactions by making continuous-valued (fuzzy) decisions and learning the corresponding responses. Our architecture demonstrates significant performance gains over existing state-of-the-art predictive models in diverse domains such as human crowd trajectories, US freeway traffic, NBA sports data and physics datasets. We also present ablations and augmentations to understand the decision-making process and the source of gains in our model.
ChemInform Abstract: Substituted Dihydrobenzopyran and Dihydrobenzofuran Thiazolidine‐2,4‐ diones as Hypoglycemic Agents. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enhancing the Electrical and Optoelectronic Performance of Nanobelt Devices by Molecular Surface Functionalization (2007)

By functionalizing the surfaces of ZnO nanobelts (NBs) with a thin self-assembled molecular layer, the electrical and optoelectronic performances of a single NB-based device are drastically improved. For a single NB-based device, due to energy band tuning and surface modification, the conductance was enhanced by 6 orders of magnitude upon functionalization; a coating molecule layer has changed a Schottky contact into an Ohmic contact without sophisticated deposition of multilayered metals. A functionalized NB showed negative differential resistance and exhibited huge improved photoconductivity and gas sensing response. The functionalized molecular layer also greatly reduced the etching rate of the ZnO NBs by buffer solution, largely extending their life time for biomedical applications. Our study demonstrates a new approach for improving the physical properties of oxide NBs and nanowires for device applications.
Phenylalanine Biosynthesis in Arabidopsis thaliana (2007)

There is much uncertainty as to whether plants use arogenate, phenylpyruvate, or both as obligatory intermediates in Phe biosynthesis, an essential dietary amino acid for humans. This is because both prephenate and arogenate have been reported to undergo decarboxylative dehydration in plants via the action of either arogenate (ADT) or prephenate (PDT) dehydratases; however, neither enzyme(s) nor encoding gene(s) have been isolated and/or functionally characterized. An in silico data mining approach was thus undertaken to attempt to identify the dehydratase(s) involved in Phe formation in Arabidopsis, based on sequence similarity of PDT-like and ACT-like domains in bacteria. This data mining approach suggested that there are six PDT-like homologues in Arabidopsis, whose phylogenetic analyses separated them into three distinct subgroups. All six genes were cloned and subsequently established to be expressed in all tissues examined. Each was then expressed as a Nus fusion recombinant protein in Escherichia coli, with their substrate specificities measured in vitro. Three of the resulting recombinant proteins, encoded by ADT1 (At1g11790), ADT2 (At3g07630), and ADT6 (At1g08250), more efficiently utilized arogenate than prephenate, whereas the remaining three, ADT3 (At2g27820), ADT4 (At3g44720), and ADT5 (At5g22630) essentially only employed arogenate. ADT1, ADT2, and ADT6 had k(cat)/Km values of 1050, 7650, and 1560 M(-1) S(-1) for arogenate versus 38, 240, and 16 M(-1) S(-1) for prephenate, respectively. By contrast, the remaining three, ADT3, ADT4, and ADT5, had k(cat)/Km values of 1140, 490, and 620 M(-1) S(-1), with prephenate not serving as a substrate unless excess recombinant protein (>150 microg/assay) was used. All six genes, and their corresponding proteins, are thus provisionally classified as arogenate dehydratases and designated ADT1-ADT6.
Syntactic graphs: a representation for the union of all ambiguous parse trees (1989)

In this paper, we present a new method of representing the &amp;apos;surface syntactic structure of a sentence. Trees have usually been used in linguistics and natural language processing to represent syntactic structures of a sentence. A tree structure shows only one possible syntactic parse of a sentence, but in order to choose a correct parse, we need to examine all possible tree structures one by one. Syntactic graph representation makes it possible to represent all possible surface syntactic relations in one directed graph (DG). Since a syntactic graph is expressed in terms of a set of triples, higher level semantic processes can access any part of the graph directly without navigating the whole structure. Further- more, since a syntactic graph represents the union of all possible syntactic readings of a sentence, it is fairly easy to focus on the syntactically ambiguous points. In this paper, we introduce the basic idea of syntactic graph representation and discuss its various properties. We claim that a syntactic graph carries complete syntactic information provided by a parse forest--the set of all possible parse trees
In vitromethylation of CpG-rich islands (1989)

CpG islands are distinguishable from the bulk of vertebrate DNA for being unmethylated and CpG-rich. Since CpG doublets are the specific target of eukaryotic DNA methyltransferases, CpG-rich sequences might be expected to be good methyl-accepting substrates in vitro, despite their unmethylated in vivo condition. This was tested using a partially purified DNA-methyltransferase from human placenta and several cloned CpG-rich or CpG-depleted sequences. The efficiency of methylation was found to be proportional to the CpG content for CpG-depleted regions, which are representative of the bulk genome. However, methylation was much less efficient for CpG frequencies higher than 1 in 12 nucleotides, reaching only 60% of the expected level. That suggests that the close CpG spacing typical of CpG-islands somehow inhibits mammalian DNA methyltransferase. The implications of these findings on the in vivo pattern of DNA methylation are discussed.
Streptococcus mutansfructosyltransferase interactions with glucans (2004)

Streptococcus mutans utilizes sucrose to synthesize glucans by glucosyltransferase and fructans by fructosyltransferase (FTF). Antibodies raised against a recombinant FTF were used to study S. mutans FTF secretion. Low amounts of cell-free FTF were found in culture of S. mutans grown with sucrose, while an increase in bacteria displaying cell surface FTF was detected. FTF added to S. mutans cultures was adsorbed to bacteria grown with sucrose but not to bacteria grown with glucose or fructose or to a gtf inactivated mutant grown with sucrose. Recombinant FTF was found to have high affinity for glucans suggesting that fructans and glucans are an integral part of the polysaccharide matrix of oral biofilms.
Two separate continually online-trained neurocontrollers for excitation and turbine control of a turbogenerator (2002)

This paper presents the design of two separate continually online trained (COT) neurocontrollers for excitation and turbine control of a turbogenerator connected to the infinite bus through a transmission line. These neurocontrollers augment/replace the conventional automatic voltage regulator and the turbine governor of a generator. A third COT artificial neural network is used to identify the complex nonlinear dynamics of the power system. Results are presented to show that the two COT neurocontrollers can control turbogenerators under steady-state as well as transient conditions and, thus, allow turbogenerators to operate more closely to their steady-state stability limits.
Robotic Handling of Compliant Food Objects by Robust Learning from Demonstration (2018)

The robotic handling of compliant and deformable food raw materials, characterized by high biological variation, complex geometrical 3D shapes, and mechanical structures and texture, is currently in huge demand in the ocean space, agricultural, and food industries. Many tasks in these industries are performed manually by human operators who, due to the laborious and tedious nature of their tasks, exhibit high variability in execution, with variable outcomes. The introduction of robotic automation for most complex processing tasks has been challenging due to current robot learning policies. A more consistent learning policy involving skilled operators is desired. In this paper, we address the problem of robot learning when presented with inconsistent demonstrations. To this end, we propose a robust learning policy based on Learning from Demonstration (LfD) for robotic grasping of food compliant objects. The approach uses a merging of RGB-D images and tactile data in order to estimate the necessary pose of the gripper, gripper finger configuration and forces exerted on the object in order to achieve effective robot handling. During LfD training, the gripper pose, finger configurations and tactile values for the fingers, as well as RGB-D images are saved. We present an LfD learning policy that automatically removes inconsistent demonstrations, and estimates the teacher's intended policy. The performance of our approach is validated and demonstrated for fragile and compliant food objects with complex 3D shapes. The proposed approach has a vast range of potential applications in the aforementioned industry sectors.
Cytokine and cytokine storm after SARS-CoV-2 infection (2020)

A review Cytokines are a diverse group of small mol proteins or peptides that are secreted by cells for the purpose of intercellular delivery signaling and communication, which play an important role in the immune system by regulating both the intensity and duration of the immune response During infection, the triggering of the inflammatory response, especially through the production of cytokines, is essential for the early elimination of pathogens However, cytokines are intense secreted and released during a hyper inflammatory state that may trigger a dangerous condition known as (or hypercytokinemia), resulting in uncontrolled inflammation in tissues and key organs Cytokine storms are closely related to influenza, sepsis/septic shock and acute respiratory distress syndrome, which ultimately lead to multiple organ failure This review outlines the classification and biol functions of cytokines, the clinic and damage mechanism of cytokine storms, and treatment of 2019 novel coronavirus (2019-nCoV), which provides guidance for the prevention and treatment of cytokine storm syndrome
Immunology, Treatment and Public Health Aspects of Subarachnoid Hemorrhage (2020)

Patients with subarachnoid hemorrhage undergoing interventional embolization of aneurysms can reduce the impact on immune function, decrease the adverse reactions caused by treatments, shorten the length of hospital stay and fully improve the efficacy.
Physico-chemical determinants of soluble intrabody expression in mammalian cell cytoplasm (2010)

Soluble antibody fragments are desirable not only as potential therapeutic and diagnostic agents for extracellular targets but also as 'intrabodies' for functional genomics, proteomics and gene therapy inside cells. However, antibody fragments are notoriously aggregation-prone when expressed intracellularly, due in part to unfavorable redox potential and macromolecular crowding in cell cytoplasm. Only a small proportion of intrabodies are soluble in cytoplasm and little is known about the sequence determinants that confer such stability. By comparing the cytoplasmic expression of several related human single-chain variable fragments and camelid V(HH)s in mammalian cells, we report that intrabody solubility is highly influenced by CDR content and is improved by an overall negative charge at cytoplasmic pH and reduced hydrophilicity. We hypothesize that ionic repulsion and weak hydrophobic interactions compensate, to different extents, for impaired disulfide bond formation in cytoplasm, thereby decreasing the risk for intrabody aggregation. As proof of principle, we demonstrate that the soluble expression of an aggregation-prone positively charged intrabody is modestly enhanced via cis or trans acidification using highly charged peptide tags (3XFLAG tag, SV40 NLS). These findings suggest that simple sequence analysis and electrostatic manipulation may aid in predicting and engineering solubility-enhanced intrabodies from antibody libraries for intracellular use.
Progressive 2-pass decoder for real-time broadcast news captioning (2002)

This paper describes a 2-pass decoder that progressively outputs the latest available results used for real-time closed captioning of Japanese broadcast news. The decoder practically eliminates the disadvantage of multiple-pass decoders that delay a decision until the end of a sentence. During the first pass of search the proposed decoder periodically executes the second pass that rescores partial N-best word sequences up to that time. If the rescored best word sequence has words in common with the previous one, that part is regarded as likely to be correct and is decided to be a part of the final result. This method is not theoretically optimal but makes a quick response with a negligible increase in word errors. In a recognition experiment on Japanese broadcast news, the decoder worked with an average decision delay of 554 msec for each word and degraded word accuracy only by 0.22%.
Adaptive CMOS predistortion linearizer for fiber-optic links (2003)

Nonlinearity in the electrical-to-optical conversion limits the dynamic range for transmitting analog and multilevel signals over fiber-optic channels. We describe a complementary metal-oxide-semiconductor (CMOS) predistortion linearizer that extends the dynamic range of both direct and externally modulated links. The linearizer achieves 13-24-dB suppression for both second- and third-order distortions.
Binding and leakage of barium in alginate microbeads (2012)

Microbeads of alginate crosslinked with Ca(2+) and/or Ba(2+) are popular matrices in cell-based therapy. The aim of this study was to quantify the binding of barium in alginate microbeads and its leakage under in vitro and accumulation under in vivo conditions. Low concentrations of barium (1 mM) in combination with calcium (50 mM) and high concentrations of barium (20 mM) in gelling solutions were used for preparation of microbeads made of high-G and high-M alginates. High-G microbeads accumulated barium from gelling solution and contained higher concentrations of divalent ions for both low- and high-Ba exposure compared with high-G microbeads exposed to calcium solely and to high-M microbeads for all gelling conditions. Although most of the unbound divalent ions were removed during the wash and culture steps, leakage of barium was still detected during storage. Barium accumulation in blood and femur bone of mice implanted with high-G beads was found to be dose-dependent. Estimated barium leakage relevant to transplantation to diabetic patients with islets in alginate microbeads showed that the leakage was 2.5 times lower than the tolerable intake value given by WHO for high-G microbeads made using low barium concentration. The similar estimate gave 1.5 times higher than is the tolerable intake value for the high-G microbeads made using high barium concentration. To reduce the risk of barium accumulation that may be of safety concern, the microbeads made of high-G alginate gelled with a combination of calcium and low concentration of barium ions is recommended for islet transplantation.
Current perspectives on the role of IL-17 in autoimmune disease (2010)

Until recently, autoimmune diseases had been categorized as either Th1- or Th2-mediated diseases. However, the discovery of a novel subset of helper T cells producing interleukin (IL)-17, ie, Th17 cells, changed this paradigm. Currently, IL-17 and Th17 cells are implicated in many autoimmune diseases, such as rheumatoid arthritis, psoriasis, multiple sclerosis, and inflammatory bowel diseases. Such conclusions were initially drawn from observations in animal models of autoimmune diseases, and accumulating data from clinical research also support the involvement of IL-17 in human diseases as well. Reagents targeting Th17-related molecules have been under clinical investigation for some diseases but have not always been effective in controlling disease activity. Consistent with this, it has become evident that there are substantial differences in the development of Th17 cells and in the way they function in autoimmune diseases between humans and experimental animals. Thus, further investigation is needed before we can draw any conclusions about the importance of IL-17 and Th17 cells in human autoimmune diseases.
Fiabilidad y validez de la version española del Inventario para la Depresión de Beck de 1978 en pacientes con trastornos psicológicos (1999)

Data on reliability and validity are provided of the application of the Spanish version of the 1978 Version of the Beck Depression Inventory (BDI; Beck, Rush, Shaw and Emery, 1979), to a sample of 338 outpatients suffering from various psychopathological diagnosis according to DSM-III-R (APA. 1987/1988). Alpha reliability coefficient was high (.90). Also, criterion validity indixes were fair: patients with depressive disorders scored significantly higher than did those with anxiety or schizophrenic disorders. Discriminant analysis of BDI items revealed that a sub - set of symptoms (Sadness, Dissatisfaction and Fatigability) correctly sorted 88% of patients as depressive or non depressive. Nevertheless, analysis of diagnosis accuracy showed that not a single cut-off score proved sensitive enough to allow a differential diagnosis. Therefore, it is concluded that the Spanish BDI version is a valid tool to detect and quantify depressive symptoms in patients, but it is a poor instrument for differential diagnoses