gebhart/patrepeval huggingface dataset:
Inferring Neuronal Network Connectivity from Spike Data: A Temporal Data Mining Approach (2008)

Understanding the functioning of a neural system in terms of its underlying circuitry is an important problem in neuroscience. Recent developments in electrophysiology and imaging allow one to simultaneously record activities of hundreds of neurons. Inferring the underlying neuronal connectivity patterns from such multi-neuronal spike train data streams is a challenging statistical and computational problem. This task involves finding significant temporal patterns from vast amounts of symbolic time series data. In this paper we show that the frequent episode mining methods from the field of temporal data mining can be very useful in this context. In the frequent episode discovery framework, the data is viewed as a sequence of events, each of which is characterized by an event type and its time of occurrence and episodes are certain types of temporal patterns in such data. Here we show that, using the set of discovered frequent episodes from multi-neuronal data, one can infer different types of connectivity patterns in the neural system that generated it. For this purpose, we introduce the notion of mining for frequent episodes under certain temporal constraints; the structure of these temporal constraints is motivated by the application. We present algorithms for discovering serial and parallel episodes under these temporal constraints. Through extensive simulation studies we demonstrate that these methods are useful for unearthing patterns of neuronal network connectivity.
Not all tags are created equal: Learning flickr tag semantics for global annotation (2009)

Large collaborative datasets offer the challenging opportunity of creating systems capable of extracting knowledge in the presence of noisy data. In this work we explore the ability to automatically learn tag semantics by mining a global georeferenced image collection crawled from Flickr with the aim of improving an automatic annotation system. We are able to categorize sets of tags as places, landmarks, and visual descriptors. By organizing our dataset of more than 1.69 million images using a quadtree we can efficiently find geographic areas with sufficient density to provide useful results for place and landmark extraction. Precision-recall curves for our techniques compared with previous existing work used to identify place tags and manual groundtruth landmark annotation show the merit of our methods applied on a world scale.
Spatial keyframing for performance-driven animation (2005)

This paper introduces spatial keyframing, a technique for performance-driven character animation. In traditional temporal keyframing, key poses are defined at specific points in time: i.e., we define a map from a set key times to the configuration space of the character and then extend this map to the entire timeline by interpolation. By contrast, in spatial keyframing key poses are defined at specific key positions in a 3D space where the character lives; the mapping from the 3D space to the configuration space is again defined by interpolation. The user controls a character by adjusting the position of a control cursor in the 3D space; the pose of the character is given as a blend of nearby key poses. The user thus can make expressive motion in real time and the resulting motion can be recorded and interpreted as an animation sequence. Although similar ideas are present in previous systems, our system is unique in that the designer can quickly design a new set of keyframes from scratch, and make an animation without motion capture data or special input devices. Our technique is especially useful for imaginary characters other than human figures because we do not rely on motion-capture data. We also introduce several applications of the basic idea and give examples showing the expressiveness of the approach.
Functional analyses of PAU genes in Saccharomyces cerevisiae (2009)

PAU genes constitute the largest gene family in Saccharomyces cerevisiae, with 24 members mostly located in the subtelomeric regions of chromosomes. Little information is available about PAU genes, other than expression data for some members. In this study, we systematically compared the sequences of all 24 members, examined the expression of PAU3, PAU5, DAN2, PAU17 and PAU20 in response to stresses, and investigated the stability of all Pau proteins. The chromosomal localization, synteny and sequence analyses revealed that PAU genes could have been amplified by segmental and retroposition duplication through mechanisms of chromosomal end translocation and Ty-associated recombination. The coding sequences diverged through nucleotide substitution and insertion/deletion of one to four codons, thus causing changes in amino acids, truncation or extension of Pau proteins. Pairwise comparison of non-coding regions revealed little homology in flanking sequences of some members. All 24 PAU promoters contain a TATA box, and 22 PAU promoters contain at least one copy of the anaerobic response element and the aerobic repression motif. Differential expression was observed among PAU3, PAU5, PAU17, PAU20 and DAN2 in response to stress, with PAU5 having the highest capacity to be induced by anaerobic conditions, low temperature and wine fermentations. Furthermore, Pau proteins with 124 aa were less stable than those with 120 or 122 aa. Our results indicate that duplicated PAU genes have been evolving, and the individual Pau proteins might possess specific roles for the adaptation of S. cerevisiae to certain environmental stresses.
Cloxacepride and related compounds: a new series of orally active antiallergic compounds (1983)

4-[[(p-Chlorophenoxy)acetyl]amino]-5-chloro-2-methoxy-N-[2-(diethylamino)ethyl]benzamide (cloxacepride, 1), exhibited substantial oral antiallergic potential in a reaginic PCA test in rats over a wide range of antigenic challenge times. Available reference compounds with oral activity, such as doxantrazole and 7-(2-hydroxyethoxy)-9-oxoxanthene-2-carboxylic acid (AH 7725, 4), were active only when administered 15 min before challenge: 4, in particular, was not consistent in effect. Oral ED50 values for cloxacepride of 46-49 mg/kg were comparable to that of theophylline and to an intravenous injection of 2 mg/kg of disodium chromoglycate (DSCG) followed by immediate challenge. Following oral ED50 doses, 1 showed slower onset and longer duration of action than theophylline. The absence of inhibition of systemic anaphylaxis and of antihistaminic activity suggests specific effect or reaginic antigen antibody reactions. Structure-activity relationships of various chemical modifications were investigated and discussed in terms of essential substituents.
Neuronal Phosphoproteins: Physiological and Clinical Implications (1984)

The presence of a great variety of neuron-specific phosphoproteins in nervous tissue supports the view that protein phosphorylation plays many roles in neuronal function. The physiological significance of several of these phosphoproteins has already been established. Some neuronal phosphoproteins have been detected throughout the entire nervous system, whereas the distribution of others is limited to one or a few neuronal cell types. These various neuron-specific phosphoproteins are proving of value in the study of the physiology, anatomy, developmental biology, and pathophysiology of the nervous system.
Surface acoustic wave enabled pipette on a chip (2016)

Mono-disperse droplet formation in microfluidic devices allows the rapid production of thousands of identical droplets and has enabled a wide range of chemical and biological studies through repeat tests performed at pico-to-nanoliter volume samples. However, it is exactly this efficiency of production which has hindered the ability to carefully control the location and quantity of the distribution of various samples on a chip - the key requirement for replicating micro well plate based high throughput screening in vastly reduced volumetric scales. To address this need, here, we present a programmable microfluidic chip capable of pipetting samples from mobile droplets with high accuracy using a non-contact approach. Pipette on a chip (PoaCH) system selectively ejects (pipettes) part of a droplet into a customizable reaction chamber using surface acoustic waves (SAWs). Droplet pipetting is shown to range from as low as 150 pL up to 850 pL with precision down to tens of picoliters. PoaCH offers ease of integration with existing lab on a chip systems as well as a robust and contamination-free droplet manipulation technique in closed microchannels enabling potential implementation in screening and other studies.
Measurement of Ether Phospholipids in Human Plasma with HPLC–ELSD and LC/ESI–MS After Hydrolysis of Plasma with Phospholipase A<sub>1</sub> (2016)

Ethanolamine ether phospholipid (eEtnGpl) and choline ether phospholipid (eChoGpl) are present in human plasma or serum, but the relative concentration of the ether phospholipids in plasma is very low as compared to those in other tissues. Nowadays, measurement of ether phospholipids in plasma depends on tandem mass spectrometry (LC/MS/MS), but a system for LC/MS/MS is generally too expensive for usual clinical laboratories. Treatment of plasma with phospholipase A1 (PLA1) causes complete hydrolysis of diacylphospholipids, but ether phospholipids remain intact. After the treatment of plasma with PLA1, both eEtnGpl and eChoGpl are detected as independent peaks by high-performance liquid chromatography with evaporative light scattering detection (HPLC-ELSD). The same sample used for HPLC-ELSD can be applied to detect eEtnGpl and eChoGpl with electrospray ionization mass spectrometry. Presence of alkylacylphospholipids in both eChoGpl and eEtnGpl in human plasma was indicated by sequential hydrolysis of plasma with PLA1 and hydrochloric acid.
Mass Spectra of 2-Substituted Diethyl Malonate Derivatives (1999)

Addition of Grignard derivatives to diethyl ethoxymethylene malonate generates 2-substituted diethyl malonate derivatives. This paper reports the mass spectral data for these derivatives.
Regulation of Transposition in Bacteria (1990)

Bacterial transposons are subject to a variety of regulatory processes that affect the quantity, quality, and timing of transposition events. Many of these processes seem specifically designed to provide features that favor the evolutionary success of the element. The most important conclusion reached from the identification and characterization of these regulatory mechanisms is that transposable elements are not mechanistic accidents of recent origin, but instead are highly evolved entities that have adapted to their ecological niche with a degree of sophistication comparable to that exhibited by plasmids and bacterial viruses.
A component architecture for an extensible, highly integrated context-aware computing infrastructure (2003)

Ubiquitous context-aware computing systems present several challenges in their construction. Principal among them is the tradeoff between easily providing new context-aware services to users and the tight integration of those services, as demanded by the small form factor of the devices typically found in ubiquitous computing environments. Performance issues further complicate the management of this tradeoff. Mechanisms have been proposed and toolkits developed for aiding the construction of context-aware systems, but there has been little consideration of how to specialize, organize, and compose these mechanisms to meet the above requirements. We motivate and describe a software architecture that provides the desired integration and extensibility of services in a context-aware application infrastructure. A key result is the fissioning of intuitive class organizations, both across layers and within layers, to achieve the required integration of services and separation of concerns.
Stem cell factor protects erythroid precursor cells from chemotherapeutic agents via up-regulation of BCL-2 family proteins (2003)

Suppression of red blood cell production is a common complication of chemotherapy, causing anemia in a significant number of cancer patients. We have evaluated the sensitivity of human hematopoietic progenitors and erythroid precursor cells to chemotherapeutic drugs and found that probasophilic erythroblasts represent the stage of erythroid differentiation more vulnerable to the cytotoxic effects of myelosuppressive agents. Stem cell factor (SCF) supports proliferation and survival of early hematopoietic cells by binding to the c-kit receptor. In unilineage erythropoietic culture of CD34+ progenitors, short-term pretreatment of immature erythroid precursors with SCF results in protection from apoptosis induced by chemotherapeutic agents and restores normal proliferation and differentiation after removal of the cytotoxic stimulus. The levels of drug-induced caspase processing are significantly reduced in erythroblasts treated with SCF, indicating that activation of the c-kit receptor generates antiapoptotic signals acting before amplification of the caspase cascade. Accordingly, we found that SCF up-regulates Bcl-2 and Bcl-X L in erythroid precursors and that exogenous expression of these proteins protects erythroblasts from caspase activation and death induced by chemotherapeutic agents. These results suggest a possible mechanism for SCF-mediated protection of erythroid precursor cells from apoptosis and may contribute to devise new strategies for prevention and treatment of chemotherapy-induced anemia.
Ocaratuzumab, an Fc-engineered antibody demonstrates enhanced antibody-dependent cell-mediated cytotoxicity in chronic lymphocytic leukemia (2014)

Chronic lymphocytic leukemia (CLL) is common in both developed and developing nations where the need for inexpensive and convenient administration of therapy is apparent. Ocaratuzumab is a novel Fc-engineered humanized IgG1 anti-CD20 monoclonal antibody (mAb) designed for effective antibody-dependent cell-mediated cytotoxicity (ADCC) at very low concentrations that may facilitate sub-cutaneous (vs. intravenous) dosing. Here, we report ocaratuzumab's potency against CLL cells. In vitro assessment of ocaratuzumab's direct cytotoxicity (DC), complement-dependent cytotoxicity (CDC), antibody-dependent cellular phagocytosis (ADCP), and ADCC was performed on CLL cells. Ocaratuzumab induced DC, CDC, and ADCP similarly to rituximab or ofatumumab (anti-CD20 mAbs). However, ocaratuzumab showed an advantage in NK cell-mediated ADCC over these antibodies. In allogeneic ADCC, [E:T (effector:target) ratios = 25:1, 12:1, 6:1], ocaratuzumab (10 µg/mL) improved ADCC by ~3-fold compared with rituximab or ofatumumab (P<0.001 all tested E:T ratios). Notably, the superiority of ocaratuzumab-induced ADCC was observed at low concentrations (0.1-10 ug/ml; P<0.03; allogeneic assays). In extended allogeneic ADCC E:T titration, ocaratuzumab (0.1 µg/mL) demonstrated 19.4% more cytotoxicity than rituximab (E:T = 0.38:1; P = 0.0066) and 21.5% more cytotoxicity than ofatumumab (E:T = 1.5:1; P = 0.0015). In autologous ADCC, ocaratuzumab (10 µg/mL) demonstrated ~1.5-fold increase in cytotoxicity compared with rituximab or ofatumumab at all E:T ratios tested (E:Ts = 25:1,12:1,6:1; all P<0.001). Obinutuzumab, a glyco-engineered anti-CD20 mAb, showed no improvement in ADCC activity compared with ocaratuzumab. The enhanced ADCC of ocaratuzumab suggests that it may be effective at low concentrations. If supported by clinical investigation, this feature could potentially allow for subcutaneous dosing at low doses that could expand the potential of administering chemoimmunotherapy in developing countries.
Feeding Symptoms, Dietary Patterns, and Growth in Young Children With Autism Spectrum Disorders (2010)

ASD children showed feeding symptoms from infancy and had a less varied diet from 15 months, but energy intake and growth were not impaired.
A machine learning approach to live migration modeling (2017)

Live migration is one of the key technologies to improve data center utilization, power efficiency, and maintenance. Various live migration algorithms have been proposed; each exhibiting distinct characteristics in terms of completion time, amount of data transferred, virtual machine (VM) downtime, and VM performance degradation. To make matters worse, not only the migration algorithm but also the applications running inside the migrated VM affect the different performance metrics. With service-level agreements and operational constraints in place, choosing the optimal live migration technique has so far been an open question. In this work, we propose an adaptive machine learning-based model that is able to predict with high accuracy the key characteristics of live migration in dependence of the migration algorithm and the workload running inside the VM. We discuss the important input parameters for accurately modeling the target metrics, and describe how to profile them with little overhead. Compared to existing work, we are not only able to model all commonly used migration algorithms but also predict important metrics that have not been considered so far such as the performance degradation of the VM. In a comparison with the state-of-the-art, we show that the proposed model outperforms existing work by a factor 2 to 5.
Traumatic brain injury in the elderly: A level 1 trauma centre study (2015)

This descriptive study provides a better understanding of characteristics and outcome of different age groups of patients with TBI all over 65 years old in Montreal, Canada.
Recent advances in techniques of male and female sterilization. (1975)

Advances in sterilization toward the goal of simple painless inexpensive methods of permanent contraception until fertility is desired with a reasonable possibility of reversal are discussed. Vasectomy as performed today is described with attention to refinements of existing methods some promising instant sterility others suggesting reversibility. In men intravasal devices that would block sperm transport and that could later be removed are being investigated. These may be combined with chemically active agents such as copper. Some investigators have concentrated on pharmacologically induced sterility through sustained-release steroid implants or spermicidal agents such as chlorohydrin or cyproterone acetate applied directly with the scrotum. A neurological blocking substance that would mimic the effects of lumbar sympathectomy where sexual potency is preserved with total azoospermia is being sought. Attempts have been made to isolate the autoimmunizing factor that causes sperm agglutinating antibodies after vasectomy in at least 30% of men. In women culdoscopy and hysteroscopy have been investigated as alternative approaches to laparoscopy for tubal interruption. Mechanical barriers such as tubal plugs or caps for the fimbriae or ovaries have been under development. Sustained-release steroid hormones or endometrium-ablating substances could be implanted in the uterus. Another potential method considered is immunization against antigens specific to embryonic tissue placental tissue semen or hormones produced during pregnancy.(AUTHORS MODIFIED)
Intrathecally Administered Natural Human Fibroblast Interferon Reduces Exacerbations of Multiple Sclerosis (1987)

A randomized, double-blinded, placebo-controlled, two-year multicenter study demonstrated that natural human fibroblast interferon (interferon beta) administered intrathecally (IT) is effective in reducing the exacerbations of exacerbating-remitting multiple sclerosis (MS). The mean reduction in exacerbation rate of 34 patients with MS who received interferon beta administered IT was significantly greater during the study than that of 35 control patients who received placebo. The prestudy exacerbation rates were comparable for both patients who received interferon beta and control patients, but the exacerbation rate of patients receiving interferon beta at the end of the study was significantly lower than that of the control patients. Interferon beta was administered by nine or ten lumbar punctures for the first six months of the study, and observations were continued for two years. In 95% of the recipients, interferon beta therapy was well tolerated, and the side effects experienced were clearly acceptable for the benefits achieved. Low doses of indomethacin dramatically reduced the toxicity of interferon beta therapy and played an important role in successful double blinding. This study confirms a preliminary report on 20 patients that initially suggested that interferon beta administered IT was of benefit in patients with MS. The number of treatments was fewer and the dosage of interferon beta administered was less in the present study than in the preliminary one. It is possible that even fewer treatments with lower doses of interferon beta administered might provide a similar degree of prophylaxis against exacerbations.
Inside Cover: Polyoxometalates Made of Gold: The Polyoxoaurate [Au<sup>III</sup><sub>4</sub>As<sup>V</sup><sub>4</sub>O<sub>20</sub>]<sup>8−</sup> (Angew. Chem. Int. Ed. 10/2010) (2010)

A brand new line of gold jewelry has been designed in the world of polyoxometalate chemistry. In their Communication on page 1886 ff, U. Kortz et al. identify the first discrete inorganic polyoxoaurate [AuIII4AsV4O20]8− with a tetrameric structure and square-planar coordinated AuIII ions linked by oxo and arsenate bridging ligands (see structure; Au yellow, As blue, O red). The facile open-beaker synthetic procedure appears to be a convenient and general method for making a variety of gold-based inorganic oxo complexes. Mr. Rami Al-Oweini (PhD Student, Jacobs University) is thanked for his creative design.
Dipeptidyl Peptidase-4 Inhibitor (2014)

Recent advances in incretin biology have led to the development of a new class of oral anti-diabetic drugs. To date, there are two known incretin hormones, glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), of which the former is a more important therapeutic target for type 2 diabetes. GLP-1 is secreted by intestinal L-cells in response to oral nutrient intake, and it stimulates insulin secretion and suppresses glucagon secretion in a glucose-dependent manner. However, both GLP-1 and GIP are rapidly degraded by dipeptidyl peptidase-4 (DPP-4), a multifunctional type II transmembrane glycoprotein. Thus, several DPP-4 inhibitors with different pharmacologic features are now available and can be used either as monotherapy or in combination with other anti-diabetic agents for the treatment of type 2 diabetes. In both therapeutic regimens, DPP-4 inhibitors have been shown to reduce hemoglobin A1c levels by approximately 0.5-0.8%. In clinical trials, DPP-4 inhibitors were generally well-tolerated, posed a low risk of hypoglycemia, and did not increase body weight. Despite some reports of a possible increased risk of pancreatitis with GLP-1 receptor agonists and DPP-4 inhibitors, no causal associations have been found. Recent randomized controlled clinical trials have shown that DPP-4 inhibitors did not increase or decrease the rates of major adverse cardiovascular events in patients with type 2 diabetes at high risk of cardiovascular disease, even though this class of anti-diabetic agents had various salutary effects in many studies involving animals or healthy and diabetic humans. Additional studies will be required to resolve these disparate conclusions. (Korean J Med 2014;87:1-8)