gebhart/patrepeval huggingface dataset:
Iterative Divergent/Convergent Doubling Approach to Linear Conjugated Oligomers. A Rapid Route to a 128 A Long Potential Molecular Wire (1994)

Described is the synthesis of oligo(2-ethylphenylene-ethynylene)s and oligo(2-(3'ethylheptyl)phenylene-ethynylene)s via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, and octamer of the ethyl derivative and the monomer, dimer, tetramer, octamer, and 16-mer of the ethylheptyl derivative. The 16-mer is 128 A long. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers verses the random coils of polystyrene. These differences become quite apparent at the octamer stage. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.
Advanced Thread Synchronization for Multithreaded MPI Implementations (2017)

Concurrent multithreaded access to the Message Passing Interface (MPI) is gaining importance to support emerging hybrid MPI applications. The interoperability between threads and MPI, however, is complex and renders efficient implementations nontrivial. Prior studies showed that threads waiting for communication progress (waiting threads) often interfere with others (active threads) and degrade their progress. This situation occurs when both classes of threads compete for the same MPI resource and ownership passing to waiting threads does not guarantee communication to advance. The best-known practical solution prioritizes active threads and adapts first-in-first-out arbitration within each class. This approach, however, suffers from residual wasted resource acquisitions (waste) and ignores data locality, thus resulting in poor scalability. In this work, we propose thread synchronization improvements to eliminate waste while preserving data locality in a production MPI implementation. First, we leverage MPI knowledge and a fast synchronization method to eliminate waste and accelerate progress. Second, we rely on a cooperative progress model that dynamically elects and restricts a single waiting thread to drive a communication context for improved data locality. Third, we prioritize active threads and synchronize them with a locality-preserving lock that is hierarchical and exploits unbounded bias for high throughput. Results show significant improvement in synthetic microbenchmarks and two MPI+OpenMP applications.
Glial cell fate specification modulated by the bHLH gene <i>Hes5</i>in mouse retina (2000)

Neurons and glial cells differentiate from common precursors. Whereas the gene glial cells missing (gcm) determines the glial fate in Drosophila, current data about the expression patterns suggest that, in mammals, gcm homologues are unlikely to regulate gliogenesis. Here, we found that, in mouse retina, the bHLH gene Hes5 was specifically expressed by differentiating Müller glial cells and that misexpression of Hes5 with recombinant retrovirus significantly increased the population of glial cells at the expense of neurons. Conversely, Hes5-deficient retina showed 30-40% decrease of Müller glial cell number without affecting cell survival. These results indicate that Hes5 modulates glial cell fate specification in mouse retina.
Gene Expression Differences in Peripheral Blood of Parkinson’s Disease Patients with Distinct Progression Profiles (2016)

The prognosis of neurodegenerative disorders is clinically challenging due to the inexistence of established biomarkers for predicting disease progression. Here, we performed an exploratory cross-sectional, case-control study aimed at determining whether gene expression differences in peripheral blood may be used as a signature of Parkinson's disease (PD) progression, thereby shedding light into potential molecular mechanisms underlying disease development. We compared transcriptional profiles in the blood from 34 PD patients who developed postural instability within ten years with those of 33 patients who did not develop postural instability within this time frame. Our study identified >200 differentially expressed genes between the two groups. The expression of several of the genes identified was previously found deregulated in animal models of PD and in PD patients. Relevant genes were selected for validation by real-time PCR in a subset of patients. The genes validated were linked to nucleic acid metabolism, mitochondria, immune response and intracellular-transport. Interestingly, we also found deregulation of these genes in a dopaminergic cell model of PD, a simple paradigm that can now be used to further dissect the role of these molecular players on dopaminergic cell loss. Altogether, our study provides preliminary evidence that expression changes in specific groups of genes and pathways, detected in peripheral blood samples, may be correlated with differential PD progression. Our exploratory study suggests that peripheral gene expression profiling may prove valuable for assisting in prediction of PD prognosis, and identifies novel culprits possibly involved in dopaminergic cell death. Given the exploratory nature of our study, further investigations using independent, well-characterized cohorts will be essential in order to validate our candidates as predictors of PD prognosis and to definitively confirm the value of gene expression analysis in aiding patient stratification and therapeutic intervention.
Protective vaccination with promastigote surface antigen 2 from Leishmania major is mediated by a TH1 type of immune response (1995)

Leishmania major promastigote surface antigen-2 complex (PSA-2) comprises a family of three similar but distinct polypeptides. The three PSA-2 polypeptides were purified from cultured promastigotes by a combination of detergent phase separation and monoclonal antibody affinity chromatography. Intraperitoneal vaccination of C3H/He mice with PSA-2 with Corynebacterium parvum as an adjuvant resulted in complete protection from lesion development after challenge infection with virulent L. major. Significant protection was also obtained in the genetically susceptible BALB/cH-2k and BALB/c mice. One of the PSA-2 genes was cloned and expressed in both Escherichia coli and Leishmania mexicana promastigotes. Vaccination with the recombinant PSA-2 purified from E. coli did not confer protection, in contrast to the L. mexicana-derived recombinant PSA-2, which provided excellent protection. CD4+ T cells isolated from the spleens of vaccinated mice produced large amounts of gamma interferon but no detectable interleukin 4 upon stimulation with PSA-2 in vitro. Limiting dilution analysis showed a marked increase in the precursor frequency of PSA-2-specific gamma interferon-secreting CD4+ T cells. No substantial change in precursor frequency was observed for interleukin 4-secreting T cells in the vaccinated mice. A CD4+ PSA-2 specific T-cell line generated from splenocytes of a vaccinated mouse produces a cytokine pattern consistent with a TH1 phenotype. Intravenous injection of this line into naive mice reduced significantly the parasite burden upon challenge infection. Taken together, the data suggest that vaccination with PSA-2 induces a TH1 type of immune response which protects mice from L. major infection. Moreover, a single recombinant PSA-2 polypeptide derived from a genomic clone can also vaccinate, provided that the structural form of the antigen is near native.
REAL-TIME PCR BASED FOOD PATHOGEN DETECTION ON A CENTRIFUGAL MICROFLUIDIC FOIL DISK INCLUDING POSITIVE- AND NO-TEMPLATE-CONTROLS (2011)

We designed and evaluated a novel microfluidic structure for the real-time PCR based detection of six common food pathogens on a centrifugal microfluidic foil disk, including onboard positive- and no-template-controls for each of the targets. The microfluidic design enables for geometric multiplexed PCR in a standard centrifugal real-time PCR thermocycler. The limit of detection was 0.1 pg target DNA what corresponds to 17-56 DNA copies per PCR reaction.
Prevalence and Risk Factors for Workplace Bullying (2017)

Abstract The prevalence of workplace bullying depends on many factors: how bullying is measured and the definition used, the timeframe, the geographic area, the gender ratio of the employees, and so on. Risk factors are most often found in the psychosocial work environment. How the work is organized, the type of leader and leadership quality, and the social climate of the work groups are all aspects that under the right conditions may turn into risk factors for workplace bullying. Vulnerability factors such as being a minority (e.g., being a woman in a male work group or vice versa, being handicapped, or being of a different ethnicity from the majority) or having depression may also be potential risk factors.
A neural model of the motor control system (2015)

In this thesis I present the Recurrent Error-driven Adaptive Control Hierarchy (REACH);\na large-scale spiking neuron model of the motor cortices and cerebellum of the motor control system. The REACH model consists of anatomically organized spiking neurons that control a nonlinear three-link arm to perform reaching and handwriting, while being able to adapt to unknown changes in arm dynamics and structure. I show that the REACH model accounts for data across 19 clinical and experimental studies of the motor control system. These data includes a mix of behavioural and neural spiking activity, across normal and damaged subjects performing adaptive and static tasks.\n\nThe REACH model is a dynamical control system based on modern control theoretic methods, specifically operational space control, dynamic movement primitives, and nonlinear adaptive control. The model is implemented in spiking neurons using the Neural Engineering Framework (NEF). \n\nThe model plans trajectories in end-effector space, and transforms these commands into joint torques that can be sent to the arm simulation. Adaptive components of the model are able to compensate for unknown kinematic or dynamic system parameters, such\nas arm segment length or mass. Using the NEF the adaptive components of the system\ncan be seeded with approximations of the system kinematics and dynamics, allowing faster convergence to stability. Stability proofs for nonlinear adaptation methods implemented in distributed systems with scalar output are presented.\n\nBy implementing the motor control model in spiking neurons, biological constraints such\nas neurotransmitter time-constants and anatomical connectivity can be imposed, allowing\nfurther comparison to experimental data for model validation. The REACH model is compared to clinical data from human patients as well as neural recording from monkeys\nperforming reaching experiments. The REACH model represents a novel integration of\ncontrol theoretic methods and neuroscientific constraints to specify a general, adaptive,\nbiologically plausible motor control algorithm.
Pictorial Applications For Range Sensing Cameras (1988)

The acquisition of range information allows real-world scenes to be manipulated in ways traditionally restricted to computer-generated images. This paper will describe lighting, focus, and other changes upon real scenes, describe some of the implications of range sensing to efficient coding of image sequences, and outline some new research into passive range sensing cameras which use focus information to infer distance.
Good stream ciphers are hard to design (2005)

Cipher systems are commonly subdivided into block ciphers and stream ciphers. In the application, block ciphers require, as their name indicates, large blocksizes. Contrastingly, stream ciphers can operate on data units as small as a bit or a character, a fact that has greatly contributed to their popularity. In this paper a survey of the different approaches to the design of stream cipher systems is presented. Examples are used to illustrate the results that can be obtained.
Axis2, Middleware for Next Generation Web Services (2006)

Axis2, the next generation of Apache Web services middleware, is an effort to re-architecture Apache Web service stack to incorporate the changes in Web services. Among many improvements, Axis2 provides first class messaging and SOAP extension supports together with a novel lightweight streaming based XML processing model. The architecture is build on top of a simple and extensible core that provides the basic abstractions for the rest of the system. We present the design and the thought process behind the key abstractions by breaking down the architecture into three topics, XML processing model, extensible SOAP processing model and messaging framework. This paper explains the overall architecture while concentrating on the three topics, and demonstrate how they all fit together to yield Axis2
Flow response and microstructure of polymers reinforced with discontinuous fibers (1993)

The reinforcement of plastics with fibers has been practiced for many years. Only recently have long discontinuous fibers been compounded with thermoplastics by the method of pultrusion which preserves fiber length while promoting wetting of each fiber by the matrix polymer. Reinforcement of linear polymers with high strength fibers enhances physical properties and creates formable thermoplastic composites. Conventional compounding of fiber and polymer in a pelletizing extruder creates pellets. These are typically cylindrical, about 3 × 3 mm; containing fibers with a length distribution averaging 0.3 mm (but always < 3 mm). In distinction to such “short fiber” (SF) materials, greater fiber length can be achieved by the process of pultrusion. In this technology, continuous tows of fiber are wetted by molten polymer, “pultruded” through a die; and chopped to any desired length. The resulting pellets are typically 3 mm diameter, 12 mm long, and contain 30 to 60 weight percent of fibers with l/d ≥ 700. These long fiber (LF) pellets can be processed e.g. by injection molding, to give parts with net shape and good dimensional tolerances, high stiffness, tensile, and impact strength. In order to understand the distribution of discontinuous fibers in molded parts, and to comprehend the flow behavior of these non-Newtonian fiber-filled suspensions, we have examined the melt rheology of short and long fiber reinforced thermoplastics.
Kermit 2/XGIPC, an IGF1 receptor interacting protein, is required for IGF signaling in<i>Xenopus</i>eye development (2006)

GIPC is a PDZ-domain-containing protein identified in vertebrate and invertebrate organisms through its interaction with a variety of binding partners including many membrane proteins. Despite the multiple reports identifying GIPC, its endogenous function and the physiological significance of these interactions are much less studied. We have previously identified the Xenopus GIPC homolog kermit as a frizzled 3 interacting protein that is required for frizzled 3 induction of neural crest in ectodermal explants. We identified a second Xenopus GIPC homolog, named kermit 2 (also recently described as an IGF receptor interacting protein and named XGIPC). Despite its high amino acid similarity with kermit, kermit 2/XGIPC has a distinct function in Xenopus embryos. Loss-of-function analysis indicates that kermit 2/XGIPC is specifically required for Xenopus eye development. Kermit 2/XGIPC functions downstream of IGF in eye formation and is required for maintaining IGF-induced AKT activation. A constitutively active PI3 kinase partially rescues the Kermit 2/XGIPC loss-of-function phenotype. Our results provide the first in vivo loss of function analysis of GIPC in embryonic development and also indicate that kermit 2/XGIPC is a novel component of the IGF pathway, potentially functioning through modulation of the IGF1 receptor.
Elevation of <i>N</i>-(Carboxymethyl)valine Residue in Hemoglobin of Diabetic Patients (2001)

We established an assay method for CMV-Hb and confirmed the presence of CMV-Hb in circulating erythrocytes. CMV-Hb was more prevalent in diabetic patients than in healthy subjects. Furthermore, it was significantly higher in patients with diabetic nephropathy, suggesting that the presence of CMV-Hb may be a valuable marker for the progression of diabetic nephropathy.
Novel Reliability-Based Hybrid ARQ Technique (2009)

In this paper we propose a novel technique for hybrid automatic repeat request (HARQ) systems where turbo codes are used as the forward error correction (FEC) techniques. This technique uses the histogram of the soft values generated by the turbo decoder to control the size and the contents of the retransmissions needed when the packet can not be decoded correctly. These soft values represent the reliabilities of the information bits; hence the proposed technique is a reliability-based (RB) HARQ technique. The proposed technique is compared to the conventional RBHARQ and the conventional rate compatible punctured turbo (RCPT) codes, and is shown to achieve higher throughput and/or less number of transmissions.
TL1A/DR3 axis involvement in the inflammatory cytokine network during pulmonary sarcoidosis (2015)

These data suggest that TL1A/DR3 interactions are part of the extended and complex immune-inflammatory network that characterizes sarcoidosis during its active phase and may contribute to the pathogenesis and to the progression of the disease.
Specific measurement of angiotensin metabolites and in vitro generated angiotensin II in plasma. (1986)

Combining high-performance liquid chromatography with radioimmunoassay enabled the precise measurement of different angiotensins and their metabolites in plasma. Peptides were extracted from 2 ml of plasma by reversible adsorption to phenylsilyl-silica, separated by isocratic high-performance liquid chromatography, and quantitated by radioimmunoassay using a sensitive but suitably cross-reacting angiotensin II antiserum. For the C-terminal angiotensin II metabolites (2-8)heptapeptide, (3-8)hexapeptide, and (4-8)pentapeptide, overall recoveries of 10 fmol peptide added to 1 ml of plasma were (mean +/- SD), 74 +/- 6, 68 +/- 8, and 67 +/- 11%, respectively. The detection limit for these peptides in plasma was 0.2 fmol/ml. Blanks were below the detection limits. In eight seated normal subjects treated for 4 days with enalapril, 20 mg p.o., q.d., angiotensin II metabolites tended to decrease during the 4 postdrug hours. However, their cumulated concentration in relation to octapeptide increased from 54 to 163% on Day 1 and from 62 to 103% on Day 4. After 4 hours of converting enzyme inhibition with enalapril there was still a close correlation between plasma renin activity and angiotensin-(1-8)octapeptide level (r = 0.83, p less than 0.05) and between blood angiotensin I and angiotensin-(1-8)octapeptide levels (r = 0.86, p less than 0.01). Adding angiotensin I in vitro raised the angiotensin-(1-8)octapeptide levels after incubation at 4 degrees C for 4 hours. Thus, immunoreactive "angiotensin II" does not disappear after converting enzyme inhibition largely because of the cumulated contribution of cross-reacting metabolites and partly because of in vitro generation of true angiotensin II.
Control of power quality in inverter-based distributed generation (2003)

Power quality is an important additional service of inverter-based interfaces for distributed generators. In grid connected applications the power quality depends on the harmonic content of the current injected at the point of common coupling. By careful design of the power converter and its output filter the switching frequency components in the output current spectrum can be reduced to low levels. The effect of the harmonic distortion of the grid voltage on the output current can be minimised by using an appropriate inverter control strategy. Conventional control methods (manipulation of inverter voltage magnitude and phase) offer active and reactive power control, but not the control of the output current quality. This paper describes a new choice of control structure and explains the interaction between the applied control loops. The inverter is used to control the current in the first element of an LCL filter. A further controller is wrapped around this loop to control power export to the grid. The usefulness of this arrangement in providing big power quality is emphasised. Experimental results from a 10 kVA prototype are used to evaluate the distortion rejection properties and the regulation of active and reactive power control. The results show high quality of generated power and excellent transient and steady state-response to both active and reactive power demands.
Brain Steroidogenesis Mediates Ethanol Modulation of GABA<sub>A</sub>Receptor Activity in Rat Hippocampus (2004)

An interaction with the GABA type A (GABA(A)) receptor has long been recognized as one of the main neurochemical mechanisms underlying many of the pharmacological actions of ethanol. However, more recent data have suggested that certain behavioral and electrophysiological actions of ethanol are mediated by an increase in brain concentration of neuroactive steroids that results from stimulation of the hypothalamic-pituitary-adrenal (HPA) axis. Neuroactive steroids such as 3alpha-hydroxy-5alpha-pregnan-20-one (3alpha,5alpha-THP) are, in fact, potent and efficacious endogenous positive modulators of GABA(A) receptor function. Because neurosteroids can be synthesized de novo in the brain, we have investigated whether ethanol might affect both neurosteroid synthesis and GABA(A) receptor function in isolated rat hippocampal tissue. Here, we show that ethanol increases the concentration of 3alpha,5alpha-THP as well as the amplitude of GABA(A) receptor-mediated IPSCs recorded from CA1 pyramidal neurons in isolated hippocampal slices. These effects are shared by the neurosteroid precursor progesterone, the peripheral benzodiazepine receptor-selective agonist CB34, and gamma-hydroxybutyrate, all of which are known to increase the formation of neuroactive steroids in plasma and in the brain. The action of ethanol on GABA(A) receptor-mediated IPSC amplitude is biphasic, consisting of a rapid, direct effect on GABA(A) receptor activity and an indirect effect that appears to be mediated by neurosteroid synthesis. Furthermore, ethanol affects GABA(A) receptor activity through a presynaptic action, an effect that is not dependent on neurosteroid formation. These observations suggest that ethanol may modulate GABA(A) receptor function through an increase in de novo neurosteroid synthesis in the brain that is independent of the HPA axis. This novel mechanism may have a crucial role in mediating specific central effects of ethanol.