gebhart/patrepeval huggingface dataset:
Blood‐based protein biomarkers for stroke differentiation: A systematic review (2017)

Computed tomography (CT) scan is the mainstay for diagnosis of stroke; but the facility of CT scan is not easily available. A blood-based biomarker approach is required to distinguish ischemic stroke (IS) from hemorrhagic stroke (HS) in pre-hospital settings.To conduct a systematic review of diagnostic utility of blood biomarkers for differential diagnosis of stroke.A comprehensive literature search was carried out till March 7, 2017 in PubMed, Cochrane, Medline, OVID, and Google Scholar databases. Methodological quality of each study was assessed using the modified Quality Assessment of Diagnostic Accuracy Studies questionnaire.Eighteen studies were identified relevant to our systematic review. Ten single biomarkers and seven panels of different biomarkers were identified which showed potential for differentiating IS and HS. Activated Protein C- Protein C Inhibitor Complex (APC-PCI) (sensitivity-96%), Glial Fibrillary Acidic Protein (GFAP) (specificity-100%) and a panel of APC-PCI & GFAP (sensitivity- 71%) and Retinol Binding Protein 4 (RBP4) & GFAP (specificity- 100%) were found to have high sensitivity and specificity for differentiating the two stroke types.Our systematic review does not recommend the use of any blood biomarker for clinical purposes yet based on the studies conducted till date.
Laughter, crying and sadness in ALS (2017)

This study identifies associations of PBA and additionally finds PBA (especially crying-predominant PBA) more prevalent in women with ALS. Although the two self-report instruments (CNS-LS and PHQ-9) discriminate well between PBA and depression, there is significant overlap between depression and crying in PBA. Studies of PBA should stratify for gender, examine crying and laughter as separate outcomes and adjust for depression.
Molecular phylogeny of the mycorrhizal desert truffles (<i>Terfezia</i>and<i>Tirmania</i>), host specificity and edaphic tolerance (2002)

Terfezia and Tirmania, so called desert truffles, are mycorrhizal fungi mostly endemic to arid and semi-arid areas of the Mediterranean Region, where they are associated with Helianthemum species. The aim of this work was to study the phylogenetic relationships in these pezizalean hypogeous fungi. The restriction fragment length polymorphism (RFLP) and DNA sequences of internal transcribed spacers (ITS) of the nuclear rDNA were studied for several morphological species, Terfezia arenaria, T. boudieri, T. claveryi, T. leptoderma, T. terfezioides (=Mattirolomyces terfezioides), Tirmania nivea and T. pinoyi. The sequences were analyzed with distance and parsimony methods. Phylogenetic analyses indicated a close genetic relationship between Tirmania and Terfezia. They may have arisen from a single evolutionary lineage of pezizalean fungi that developed the hypogeous habit as an adaptation to heat and drought in Mediterranean ecosystems. This analysis also supports the re-establishment of the genus Mattirolomyces. The genera Tirmania and Terfezia were monophyletic, and morphological species corresponded to phylogenetic species. The Tirmania clade comprises desert truffles with smooth spores and amyloid asci, which were found in deserts. The Terfezia clade grouped species found in semi-arid habitats having ornamented and spherical spores. These species are adapted to exploit different types of soil (either acid or basic soils) in association with specific hosts (either basophilous or acidophilous species). Although other factors might also play a role, host specialization and edaphic tolerances (fungus and/or host tolerances) might be the key in the species diversity of these genera.
The use of disposable double spacer and self-aligned cobalt silicide for LDD MOSFET fabrication (1991)

The use of a disposable double spacer of silicon-nitride/amorphous-silicon to fabricate lightly-doped-drain (LDD) MOSFETs with just two masking steps compared to four in the conventional oxide spacer LDD FET is discussed. The alpha -Si spacer is disposed of after it has been used to pattern the nitride. The nitride acts as a second spacer to block low-energy source/drain (S/D) implants and to shift LDD implants away from the gate edge. Self-aligned metallization can be realized using the nitride as silicidation barrier.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of Humidity on Scintillation Performance in Na and Tl Activated CsI Crystals (2014)

Time dependent photoluminescence and radioluminescence for sodium (Na) and thallium (Tl) activated cesium iodide (CsI) single crystals exposed to 50% and 75% relative humidity (RH) has been investigated. These results indicate that Tl activated crystals are more robust than the Na activated crystals against humidity induced scintillation degradation. The development of “etching pits” and “inactive” domains are the characteristics of deteriorated Na activated CsI crystals. These “inactive” domains, bearing a resemblance to a polycrystalline appearance beneath the crystal surface, can be readily detected by a 250 nm light emitting diode. These features are commonly observed at the corners and deep scratched areas where moisture condensation is more likely to occur. Mechanisms contributing to the scintillation degradation in Na activated CsI crystals were investigated by Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). ToF-SIMS depth profiles indicate that Na has been preferentially diffused out of CsI crystal, leaving the Na concentration in these “inactive” domains below its scintillation threshold.
Generation of Neutralizing Antipeptide Antibodies to the Enzymatic Domain of <i>Pseudomonas aeruginosa</i> Exotoxin A (1998)

Burn patients suffer a break in the physical barrier (skin), which, when combined with their generalized state of immunodeficiency, creates an open window for opportunistic infections, mainly with Pseudomonas aeruginosa. Infection of the burn wound has always been a major factor in retardation of wound healing, and sepsis remains the leading cause of death in burn patients. Because studies have shown that topical treatment with antiexotoxin A (ETA) antibodies significantly increases survival in rats infected with toxin-producing strains of P. aeruginosa, we examined 11 synthetic peptides encompassing 12 to 45 amino acid (aa) residues, representing what were predicted by computer analysis to be the most hydrophilic and antigenic regions of ETA. These synthetic peptides were injected into rabbits for antibody production. Different groups of rabbits were immunized with a combination of peptides, with each combination representing one of the three distinct domains of ETA. Animals immunized with various peptide combinations produced peptide-specific antibodies that exhibited cross-reactivity to ETA. Two major epitopes were identified on the ETA molecule by experiments with peptide-specific antibodies in enzyme-linked immunosorbent assay and immunoprecipitation. One of these epitopes was located in the translocation domain (II) (aa 297 to 310), while the other was mapped to the last 13 aa residues at the carboxy-terminal end of the enzymatic domain (III) (aa 626 to 638). Of these two regions, the epitope in the enzymatic domain induced a much higher level of neutralizing antibodies that abrogated the cytotoxic activity of ETA in vitro. Antibodies to this epitope blocked the ADP-ribosyltransferase activity of ETA and appeared to interfere with binding of the substrate elongation factor 2 to the enzymatic active site of the ETA molecule. We conclude that polyclonal, as well as monoclonal, antibodies to short peptides, representing small regions of ETA, may have therapeutic potential in passive immunization or topical treatment of burn patients infected with toxin-producing strains of P. aeruginosa.
Control of a GaAs monolithic Ka-band phase shifter using a high-speed optical interconnect (1990)

The use of a high-speed optical interconnect in the control of a Ka-band GaAs monolithic phase shifter is described. A 16-b serial control signal was used to modulate the output of a laser transmitter, and the transmitted optical signal was detected and demultiplexed into 16 parallel electrical outputs using a high-speed hybrid GaAs optoelectronic integrated circuit. Four of the parallel output lines were interfaced to the 4-b phase shifter, and high-speed, optically controlled switching of the phase shifter was observed at clock frequencies to 30 MHz using an interferometric technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Neuropathological findings in autism (2004)

Autism is currently viewed as a largely genetically determined neurodevelopmental disorder, although its underlying biological causes remain to be established. In this review, we examine the available neuropathological literature on autism and discuss the findings that have emerged. Classic neuropathological observations are rather consistent with respect to the limbic system (nine of 14 studied cases showed increased cell packing density and smaller neuronal size), the cerebellum (21 of 29 studied cases showed a decreased number of Purkinje cells, and in all of five cases that were examined for age-related morphological alterations, these changes were found in cerebellar nuclei and inferior olive) and the cerebral cortex (>50% of the studied cases showed features of cortical dysgenesis). However, all reported studies had to contend with the problem of small sample sizes, the use of quantification techniques not free of bias and assumptions, and high percentages of autistic subjects with comorbid mental retardation (at least 70%) or epilepsy (at least 40%). Furthermore, data from the limbic system and on age-related changes lack replication by independent groups. It is anticipated that future neuropathological studies hold great promise, especially as new techniques such as design-based stereology and gene expression are increasingly implemented and combined, larger samples are analysed, and younger subjects free of comorbidities are investigated.
Replicated procedure call (1984)

A new mechanism for constructing highly available distributed programs is described. It combines remote procedure call with replication of program modules for fault tolerance.The set of replicas of a module is called a troupe. In a program constructed from troupes, what appears to the programmer as a single inter-module procedure call results in a replicated procedure call. A distributed program constructed in this way will continue to function as long as at least one member of each troupe survives.The semantics of replicated procedure calls and troupes are defined and algorithms are presented that support these semantics.
Design as a Means of Exploring the Emotional Component of Scent (2019)

As more is being discovered about the physiological and psychological mechanisms that govern our relationship with odour, designers are starting to experiment with technologies that might deliver scent in more meaningful ways. This paper explores this forgotten sense through the documentation of a number of research projects that look at scent in relation to the body, fashion, ritual and emotion. Whilst engagement with the visual remains the most significant area for designers, some of the most notable design incorporates a sensitivity to its impact on more neglected sensory stimuli. Tactile interfaces, which have long been explored in design research and education, are finally getting the attention they deserve through developments in wearable technology and the increasing willingness of textile and fashion designers to explore their potential. Similarly, the importance of sound in interface and interaction is becoming a more familiar area of investigation. Evidence suggests that exploring the link between smell and emotion might be an even more fruitful area of development, given its significant role in the triggering of emotional responses. Despite this, the sense of smell has only recently become a respectable subject of serious study, and has received only the most transitory mention in the proceedings of the <em>Design & Emotion</em> Conferences to date. Odours drive our emotions, warn us of danger, influence our body chemistry and steep us in luxury. Since smell signals have a direct access to the emotional centres of the brain, the emotional shading of our lives are influenced by the smells around us. In this paper the authors discuss new forms of aroma delivery that go beyond passive microencapsulated techniques to incorporate microfluidic delivery systems that dispense a selection of fragrances to trigger human emotions, convey information and enhance wellbeing through olfaction stimulation of the autonomic nervous system. In addition, a number of design proposals are presented which demonstrate how designers are able to envision completely new modes of interaction with scent- producing devices. These range from objects that exploit the performative component of scent application to the creation of an individual, smart, interactive “scent-bubble” around the user that can be constantly modified according to mood, environment or time of day.
On the localness of software (2014)

The n-gram language model, which has its roots in statistical natural language processing, has been shown to successfully capture the repetitive and predictable regularities (“naturalness") of source code, and help with tasks such as code suggestion, porting, and designing assistive coding devices. However, we show in this paper that this natural-language-based model fails to exploit a special property of source code: localness. We find that human-written programs are localized: they have useful local regularities that can be captured and exploited. We introduce a novel cache language model that consists of both an n-gram and an added “cache" component to exploit localness. We show empirically that the additional cache component greatly improves the n-gram approach by capturing the localness of software, as measured by both cross-entropy and suggestion accuracy. Our model’s suggestion accuracy is actually comparable to a state-of-the-art, semantically augmented language model; but it is simpler and easier to implement. Our cache language model requires nothing beyond lexicalization, and thus is applicable to all programming languages.
Antibody recognition of the type 14 pneumococcal capsule. Evidence for a conformational epitope in a neutral polysaccharide. (1989)

Oligosaccharides consisting of one or more tetrasaccharide repeating units were derived from the capsular polysaccharide of type 14 pneumococcus (Pn14) by endo-beta-galactosidase digestion. The relative affinity of anticapsular antibody binding to derivative oligosaccharides of different chain lengths was measured in a Pn 14 ELISA inhibition assay. The concentration of inhibiting antigen required to achieve 50% inhibition of IgG binding increased progressively from 5.6 x 10(-4) M to 7.0 x 10(-11) M as the inhibiting saccharide chain length increased from 1 tetrasaccharide repeating unit to 2,500 repeating units. These data indicate that antibodies directed against the Pn14 polysaccharide recognize a conformational epitope fully expressed only in high molecular weight forms of the antigen. Similar results were found for inhibition of Fab fragment binding, suggesting that recognition of the conformational epitope is largely dependent on the intrinsic affinity of the Fab combining region. Unlike previously reported polysaccharides for which conformational epitopes have been described, the Pn14 polysaccharide does not contain negatively charged residues, indicating that expression of conformational determinants is not limited to acidic polysaccharides. Antibody recognition of conformational epitopes may be a common mechanism by which the host immune response discriminates between bacterial polysaccharides and host oligosaccharides of similar structure.
Transient MicroRNA Expression Enhances Myogenic Potential of Mouse Embryonic Stem Cells (2018)

MicroRNAs (miRNAs) are known regulators of various cellular processes, including pluripotency and differentiation of embryonic stem cells (ESCs). We analyzed differentiation of two ESC lines-D3 and B8, and observed significant differences in the expression of miRNAs and genes involved in pluripotency and differentiation. We also examined if transient miRNA overexpression could serve as a sufficient impulse modulating differentiation of mouse ESCs. ESCs were transfected with miRNA Mimics and differentiated in embryoid bodies and embryoid body outgrowths. miRNAs involved in differentiation of mesodermal lineages, such as miR145 and miR181, as well as miRNAs regulating myogenesis (MyomiRs)-miR1, miR133a, miR133b, and miR206 were tested. Using such approach, we proved that transient overexpression of molecules selected by us modulated differentiation of mouse ESCs. Increase in miR145 levels upregulated Pax3, Pax7, Myod1, Myog, and MyHC2, while miR181 triggered the expression of such crucial myogenic factors as Myf5 and MyHC2. As a result, the ability of ESCs to initiate myogenic differentiation and form myotubes was enhanced. Premature expression of MyomiRs had, however, an adverse effect on myogenic differentiation of ESCs. Stem Cells 2018;36:655-670.
Production Technologies for Reduced Alcoholic Wines (2011)

The production and sale of alcohol-reduced wines, and the lowering of ethanol concentration in wines with alcohol levels greater than acceptable for a specific wine style, poses a number of technical and marketing challenges. Several engineering solutions and wine production strategies that focus upon pre- or postfermentation technologies have been described and patented for production of wines with lower ethanol concentrations than would naturally arise through normal fermentation and wine production techniques. However, consumer perception and acceptance of the sensory quality of wines manufactured by techniques that utilize thermal distillation for alcohol removal is generally unfavorable. This negative perception from consumers has focused attention on nonthermal production processes and the development or selection of specific yeast strains with downregulated or modified gene expression for alcohol production. The information presented in this review will allow winemakers to assess the relative technical merits of each of the technologies described and make decisions regarding implementation of novel winemaking techniques for reducing ethanol concentration in wine.
Integrating purposive vision with deliberative and reactive planning: engineering support for robotic applications (1998)

We propose a multi-agent vision-based architecture to solve complex sensor-based planning tasks. A test bed implementation, with skills such as vision and collision avoidance, was used to run experiments in the proposed architecture. We demonstrate experimentally how the system can execute successfully complex assembly plans while dealing with unpredictable events and imprecise information, with no significant cost in run-time efficiency. Such experiments provided important insights about vision and planning and on how to build real world robotic systems.
Impact of the spheroid model complexity on drug response (2015)

Pharmaceutical investigators are searching for preclinical models closely resembling the original cancer and predicting clinical outcome. This study compares drug response of three in vitro 3D-drug screening models with different complexity. Tumor cell line spheroids were generated from the cell lines Caco-2, DLD-1, COLO 205, HT-29 and HCT-116, and treated with clinically relevant combination therapies, namely 5-FU/oxaliplatin (FO), 5-FU/irinotecan (FI) and the molecular drugs Cetuximab, Trastuzumab, Vorinostat and Everolimus. Treatment results were compared with spheroids originated from tumor cell lines (Caco-2, DLD-1) co-cultured with stromal cells (PBMCs, cancer-associated fibroblasts of colorectal origin) and spheroids directly prepared from colon cancer tissues. Different microenvironment compositions altered the tumor cell line spheroid response patterns. Adding PBMCs increased resistance to FO treatment by 10-15% in Caco-2 and DLD-1 spheroids but decreased resistance to FI by 16% in DLD-1 spheroids. Fibroblast co-cultures decreased resistance to FI in Caco-2 spheroids by 38% but had no impact on FO. Treatment of colon cancer tissue spheroids revealed three distinct response pattern subgroups not detectable in 3D cell lines models. The cancer tissue spheroid model mimics both tumor characteristics and the stromal microenvironment and therefore is an invaluable screening model for pharmaceutical drug development.
The acid-catalysed synthesis of 7-azaindoles from 3-alkynyl-2-aminopyridines and their antimicrobial activity (2013)

The synthesis of 7-azaindoles from 3-alkynyl-2-aminopyridines using acidic conditions, namely, a mixture of trifluoroacetic acid (TFA) and trifluoroacetic anhydride (TFAA), is described. This methodology resulted in the synthesis of fifteen 7-azaindoles, with most containing substituents at the 2- and 5-positions. The majority of these were tested for antimicrobial activity against a range of bacteria and yeasts. The 7-azaindoles displayed the best activity against the yeasts, particularly against Cryptococcus neoformans, where activities as low as 3.9 μg ml(-1) were observed.
Evaluating pointwise reliability of machine learning prediction (2022)

Interest in Machine Learning applications to tackle clinical and biological problems is increasing. This is driven by promising results reported in many research papers, the increasing number of AI-based software products, and by the general interest in Artificial Intelligence to solve complex problems. It is therefore of importance to improve the quality of machine learning output and add safeguards to support their adoption. In addition to regulatory and logistical strategies, a crucial aspect is to detect when a Machine Learning model is not able to generalize to new unseen instances, which may originate from a population distant to that of the training population or from an under-represented subpopulation. As a result, the prediction of the machine learning model for these instances may be often wrong, given that the model is applied outside its "reliable" space of work, leading to a decreasing trust of the final users, such as clinicians. For this reason, when a model is deployed in practice, it would be important to advise users when the model's predictions may be unreliable, especially in high-stakes applications, including those in healthcare. Yet, reliability assessment of each machine learning prediction is still poorly addressed. Here, we review approaches that can support the identification of unreliable predictions, we harmonize the notation and terminology of relevant concepts, and we highlight and extend possible interrelationships and overlap among concepts. We then demonstrate, on simulated and real data for ICU in-hospital death prediction, a possible integrative framework for the identification of reliable and unreliable predictions. To do so, our proposed approach implements two complementary principles, namely the density principle and the local fit principle. The density principle verifies that the instance we want to evaluate is similar to the training set. The local fit principle verifies that the trained model performs well on training subsets that are more similar to the instance under evaluation. Our work can contribute to consolidating work in machine learning especially in medicine.