gebhart/patrepeval huggingface dataset:
Amyloid-β peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease (2016)

The amyloid-β peptide (Aβ) is a key protein in Alzheimer's disease (AD) pathology. We previously reported in vitro evidence suggesting that Aβ is an antimicrobial peptide. We present in vivo data showing that Aβ expression protects against fungal and bacterial infections in mouse, nematode, and cell culture models of AD. We show that Aβ oligomerization, a behavior traditionally viewed as intrinsically pathological, may be necessary for the antimicrobial activities of the peptide. Collectively, our data are consistent with a model in which soluble Aβ oligomers first bind to microbial cell wall carbohydrates via a heparin-binding domain. Developing protofibrils inhibited pathogen adhesion to host cells. Propagating β-amyloid fibrils mediate agglutination and eventual entrapment of unatttached microbes. Consistent with our model, Salmonella Typhimurium bacterial infection of the brains of transgenic 5XFAD mice resulted in rapid seeding and accelerated β-amyloid deposition, which closely colocalized with the invading bacteria. Our findings raise the intriguing possibility that β-amyloid may play a protective role in innate immunity and infectious or sterile inflammatory stimuli may drive amyloidosis. These data suggest a dual protective/damaging role for Aβ, as has been described for other antimicrobial peptides.
Algorithm for Generating All Optimal 16-QAM BI-STCM-ID Labelings (2015)

This paper focuses on 16-QAM labelings of bit-interleaved space-time coded modulation with iterative decoding (BI-STCM-ID). What is contributed is an algorithm to generate (with no random search) optimal labelings for BI-STCM-ID systems with any number of transmit- and receive antennas, transmitting over Rayleigh fading channel. Along with the algorithm, a couple of corollaries are brought, which give an account of the optimal labelings’ features. Having a complete set of optimal 16-QAM BI-STCM-ID labelings at hand, it is possible to advance research on labeling diversity scheme by finding all such labeling pairs that—if applied to a system with two different labeling maps within adjacent transmit streams—bring maximum asymptotic coding gain .
Monocular Relative Depth Perception with Web Stereo Data Supervision (2018)

In this paper we study the problem of monocular relative depth perception in the wild. We introduce a simple yet effective method to automatically generate dense relative depth annotations from web stereo images, and propose a new dataset that consists of diverse images as well as corresponding dense relative depth maps. Further, an improved ranking loss is introduced to deal with imbalanced ordinal relations, enforcing the network to focus on a set of hard pairs. Experimental results demonstrate that our proposed approach not only achieves state-of-the-art accuracy of relative depth perception in the wild, but also benefits other dense per-pixel prediction tasks, e.g., metric depth estimation and semantic segmentation.
Phrenic Long-Term Facilitation Requires Spinal Serotonin Receptor Activation and Protein Synthesis (2002)

Respiratory long-term facilitation (LTF) is a form of serotonin-dependent plasticity induced by intermittent hypoxia. LTF is manifested as a long-lasting increase in respiratory amplitude (and frequency) after the hypoxic episodes have ended. We tested the hypotheses that LTF of phrenic amplitude requires spinal serotonin receptor activation and spinal protein synthesis. A broad-spectrum serotonin receptor antagonist (methysergide) or protein synthesis inhibitors (emetine or cycloheximide) were injected intrathecally in the cervical spinal cord of anesthetized rats. Control rats, injected with vehicle (artificial CSF), exhibited an augmented phrenic burst amplitude after three 5 min episodes of hypoxia (78 +/- 15% above baseline, 60 min after hypoxia; p < 0.05), indicating LTF. Pretreatment with methysergide, emetine, or cycloheximide attenuated or abolished phrenic LTF (20 +/- 4, 0.2 +/- 11, and 20 +/- 2%, respectively; all p > 0.05). With protein synthesis inhibitors, phrenic LTF differed from control by 15 min after intermittent hypoxia. As an internal control against unintended drug distribution, we measured respiratory LTF in hypoglossal (XII) motor output. At 60 min after intermittent hypoxia, all treatment groups exhibited similar XII LTF (artificial CSF, 44 +/- 10%; methysergide, 40 +/- 5%; emetine, 35 +/- 9%; and cycloheximide, 57 +/- 29%; all p < 0.05), suggesting that drugs were restricted at effective doses to the spinal cord. We conclude that phrenic LTF requires spinal serotonin receptor activation and protein synthesis. Serotonin receptors on phrenic motoneuron dendrites may induce new protein synthesis, thereby giving rise to phrenic LTF.
IMMUNOLOGICAL ASPECTS OF ALZHEIMER DISEASE: A REVIEW (1987)

Clinical and neuropathological similarities between Alzheimer disease and the transmissible spongiform encephalopathies have sparked intensive investigation of the role of nearly every arm of the immune system in the etiology and pathogenesis of Alzheimer disease. These endeavors have yielded intriguing results but no clear-cut answers. Studies of humoral and cellular immune function in patients with dementia of the Alzheimer type (DAT), immunohistochemical examinations of Alzheimer brain tissue and HLA typing of both sporadic and familial DAT are reviewed. Sporadic DAT appears to be associated with the complement allotype C4B2 in the major histocompatibility complex, which is linked very closely to HLA. Mechanisms for the role of complement in the pathogenesis of DAT are postulated.
A Control Strategy for Intelligent Stamp Forming Tooling (2011)

This paper describes the development and implementation of closed-loop control for oval stamp forming tooling using MATLAB®’s SIMULINK® and the dSPACE®CONTROLDESK®. A traditional PID controller was used for the blank holder pressure and an advanced controller utilizing fuzzy logic combining a linear quadratic gauss controller and a bang–bang controller was used to control draw bead position. The draw beads were used to control local forces near the draw beads. The blank holder pressures were used to control both wrinkling and local forces during forming. It was shown that a complex, advanced controller could be modeled using MATLAB’s SIMULINK and implemented in DSPACE CONTROLDESK. The resulting control systems for blank holder pressures and draw beads were used to control simultaneously local punch forces and wrinkling during the forming operation thereby resulting in a complex control strategy that could be used to improve the robustness of the stamp forming processes.
Oxidatively modified proteins as plasma biomarkers in breast cancer (2013)

Specific PTMs in individual proteins may be useful for distinguishing between women with breast cancer and those with benign breast disease. These oxidative changes in plasma proteins may reflect redox changes in breast cancer. Additional studies on oxidative modifications in individual proteins are warranted.
New Fluoroprostaglandin F2.ALPHA. Derivatives with Prostanoid FP-Receptor Agonistic Activity as Potent Ocular-Hypotensive Agents (2003)

To find new prostanoid FP-receptor agonists possessing potent ocular-hypotensive effects with minimal side effects, we evaluated the agonistic activities of newly synthesized prostaglandin F(2alpha) derivatives for the prostanoid FP-receptor both in vitro and in vivo. The iris constrictions induced by the derivatives and their effects on melanin content were examined using cat isolated iris sphincters and cultured B16 melanoma cells, respectively. The effects of derivative ester forms on miosis and intraocular pressure (IOP) were evaluated in cats and cynomolgus monkeys, respectively. Of these derivatives, 6 out of 12 compounds were more potent iris constrictors, with EC(50) values of 0.6 to 9.4 nM, than a carboxylic acid of latanoprost (EC(50)=13.6 nM). A carboxylic acid of latanoprost (100 microM) significantly increased the melanin content of cultured B16 melanoma cells, but some 15,15-difluoro derivatives, such as AFP-157 and AFP-172, did not. Topically applied AFP-168, AFP-169 and AFP-175 (isopropyl ester, methyl ester and ethyl ester forms, respectively, of AFP-172) induced miosis in cats more potently than latanoprost. AFP-168 (0.0005%) reduced IOP to the same extent as 0.005% latanoprost (for at least 8 h). These findings indicate that 15,15-difluoroprostaglandin F(2alpha) derivatives, especially AFP-168, have more potent prostanoid FP-receptor agonistic activities than latanoprost. Hence, AFP-168 may be worthy of further evaluation as an ocular-hypotensive agent.
N-acyl-homoserine lactone-mediated regulation of phenazine gene expression by Pseudomonas aureofaciens 30-84 in the wheat rhizosphere (1997)

Pseudomonas aureofaciens 30-84 is a soilborne bacterium that colonizes the wheat rhizosphere. This strain produces three phenazine antibiotics which suppress take-all disease of wheat by inhibition of the causative agent Gaeumannomyces graminis var. tritici. Phenazines also enhance survival of 30-84 within the wheat rhizosphere in competition with other organisms. Expression of the phenazine biosynthetic operon is controlled by the phzR/phzI N-acyl-homoserine lactone (AHL) response system (L. S. Pierson III et al., J. Bacterial 176:3966-3974, 1994; D. W. Wood and L. S. Pierson III, Gene 168:49-53, 1996). By using high-pressure liquid chromatography coupled with high-resolution mass spectrometry, the AHL produced by PhzI has now been identified as N-hexanoyl-homoserine lactone (HHL). In addition, the ability of HHL to serve as an interpopulation signal molecule in the wheat rhizosphere has been examined by using isogenic reporter strains. Disruption of phzI reduced expression of the phenazine biosynthetic operon 1,000-fold in the wheat rhizosphere. Coinoculation of an isogenic strain which produced the endogenous HHL signal restored phenazine gene expression in the phzI mutant to wild-type levels in situ. These results demonstrate that HHL is required for phenazine expression in situ and is an effective interpopulation signal molecule in the wheat rhizosphere.
“CLASSIC NMR”: An In‐Situ NMR Strategy for Mapping the Time‐Evolution of Crystallization Processes by Combined Liquid‐State and Solid‐State Measurements (2014)

A new in-situ NMR strategy (termed CLASSIC NMR) for mapping the evolution of crystallization processes is reported, involving simultaneous measurement of both liquid-state and solid-state NMR spectra as a function of time. This combined strategy allows complementary information to be obtained on the evolution of both the solid and liquid phases during the crystallization process. In particular, as crystallization proceeds (monitored by solid-state NMR), the solution state becomes more dilute, leading to changes in solution-state speciation and the modes of molecular aggregation in solution, which are monitored by liquid-state NMR. The CLASSIC NMR experiment is applied here to yield new insights into the crystallization of m-aminobenzoic acid.
An analysis of the Burrows—Wheeler transform (2001)

The Burrows—Wheeler Transform (also known as Block-Sorting) is at the base of compression algorithms that are the state of the art in lossless data compression. In this paper, we analyze two algorithms that use this technique. The first one is the original algorithm described by Burrows and Wheeler, which, despite its simplicity outperforms the Gzip compressor. The second one uses an additional run-length encoding step to improve compression. We prove that the compression ratio of both algorithms can be bounded in terms of the k th order empirical entropy of the input string for any k ≥ 0. We make no assumptions on the input and we obtain bounds which hold in the worst case that is for every possible input string. All previous results for Block-Sorting algorithms were concerned with the average compression ratio and have been established assuming that the input comes from a finite-order Markov source.
A review of technologies for transporting heavy crude oil and bitumen via pipelines (2013)

Heavy crude oil and bitumen resources are more than double the conventional light oil reserves worldwide. Heavy crude oil and bitumen production is on average twice as capital and energy intensive as the production of conventional oil. This is because of their extremely low mobility due to high viscosity at reservoir conditions alongside the presence of undesirable components such as asphaltenes, heavy metals and sulphur making it more challenging to produce, transport as well as refine. It is well know that pipelines are the most convenient means of transporting crude oil from the producing field to the refinery. However, moving heavy crude oil and bitumen is extremely challenging because of their inability to flow freely. As such, without prior reduction in the heavy crude oil and bitumen viscosity, transportation via pipeline is difficult. This is because of the huge energy (i.e. high pumping power) required to overcome the high-pressure drop in the pipeline due to their high viscosity at reservoir conditions. To reduce this high-pressure drop and cost of transportation, several technologies have been proposed to improve the flow properties of the heavy crude oil and bitumen through pipelines. In this study, different technologies are reviewed and the advantages and disadvantages of each technology are highlighted with the view that the review will provide direction for improvement and development of novel technologies for bitumen and heavy oil transportation via pipelines.
Canonical structures of short CDR‐L3 in antibodies (2014)

Despite sequence diversity, five out of six hypervariable loops in antibodies assume a limited number of conformations called canonical structures. Their correct identification is essential for successful prediction of antibody structure. This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database. Antibodies with the eight-residue CDR-L3 represent the second most common type of antibodies after those with the nine-residue CDR-L3. We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set. In most cases, the canonical structure is defined by the absence or presence and position of a proline residue within the CDR.
Self-limited underdense microplasmas in bulk silicon induced by ultrashort laser pulses (2014)

Two-photon ionization by focused femtosecond laser pulses initiates the development of micrometer-scale plasmas in the bulk of silicon. Using pump-and-probe transmission microscopy with infrared light, we investigate the space-time characteristics of these plasmas for laser intensities up to 1012 W/cm2. The measurements reveal a self-limitation of the excitation at a maximum free-carrier density of ≅1019 cm−3, which is more than one order of magnitude below the threshold for permanent modification. The plasmas remain unchanged in the ∼100 ps timescale revealing slow carrier kinetics. The results underline the limits in local control of silicon dielectric permittivity, which are inherent to the use of single near-infrared ultrashort Gaussian pulses.
Role of conformational sampling in computing mutation‐induced changes in protein structure and stability (2010)

The prediction of changes in protein stability and structure resulting from single amino acid substitutions is both a fundamental test of macromolecular modeling methodology and an important current problem as high throughput sequencing reveals sequence polymorphisms at an increasing rate. In principle, given the structure of a wild-type protein and a point mutation whose effects are to be predicted, an accurate method should recapitulate both the structural changes and the change in the folding-free energy. Here, we explore the performance of protocols which sample an increasing diversity of conformations. We find that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that the resolution of the force field is matched to the resolution of the sampling method. Methods involving backbone sampling can in some cases closely recapitulate the structural changes accompanying mutations but not surprisingly tend to do more harm than good in cases where structural changes are negligible. Analysis of the outliers in the stability change calculations suggests areas needing particular improvement; these include the balance between desolvation and the formation of favorable buried polar interactions, and unfolded state modeling.
Protection Solutions to Reduce Arc-Flash Hazards (2008)

In this paper, we include some important industry definitions of arc flash and ways of measuring arc-flash hazards. We then examine the use of existing technologies, including digital relays and communications capabilities, to implement reduced trip times using instantaneous overcurrent relays, a fast bus trip scheme, differential schemes, and light detection. We use a typical industrial switchgear lineup as an example of how to implement these schemes. Finally, we quantify the levels to which we can reduce arc-flash energy and its impact on safety.
Self-learning of inverse kinematics for feedforward control of intracardiac robotic ablation catheters (2015)

This paper investigates the self-learning of inverse kinematics for the feed-forward control of a robot to position intracardiac catheters. Cardiac ablation is routinely performed to treat Atrial Fibrillation, and requires a catheter be accurately positioned in the heart, by hand or by a robot, under feedback control. This is typically a slow process and methods to reduce procedure times are needed. To investigate our proposed method, a robotic system to manipulate a standard intracardiac catheter was constructed. To safely develop our proposed learning system, a comprehensive dataset was collected using a magnetic tracking system to measure the catheter tip positions versus robot actuator positions. Initially, the robot began with no model of its kinematics. A Genetic Algorithm was used to decide on the next actuator sequence that would reduce the uncertainty in a Feedforward Neural Network (FFNN) based inverse kinematic model. An automated iterative process was followed where the robot would perform virtual experiments, to grow its knowledge of its inverse kinematics. After 791 learning cycles the final analysis revealed that the complete inverse kinematic relationship has been explored with the given constraints. A validation dataset indicated the learned FFNN model was able to predict x, y and z positions of the catheter tip to within ±0.17 mm, ±0.73 mm and ±0.62 mm, respectively. The robot successfully self-learned its inverse kinematic model using the proposed methodology. Future work is required to investigate the influence of disturbances on positioning accuracy.
Inhibition of heme oxygenase-1 increases responsiveness of melanoma cells to ALA-based photodynamic therapy (2007)

Based on the observation that 5-aminolevulinic acid (ALA) induces the expression of heme oxygenase-1 (HO-1) in cultured melanoma cells, the role of HO-1 on the effectiveness of 5-aminolevulinic acid-based photodynamic therapy (ALA-PDT) was examined. Transcriptional activation of the HO-1 gene is considered to be an adaptive response to oxidative and cellular stress and confers a protective capacity against cell and tissue injury, which could affect the responsiveness to ALA-PDT. A time-dependent accumulation (0-16 h) of protoporphyrin IX (PPIX) within melanoma cells was seen after incubation with ALA (0.5 mM ALA). Over the same time interval, a significant increase (up to 25-fold) in HO-1 protein expression was observed. Thus, the production and degradation of PPIX (via heme by HO-1) were simultaneously enhanced, leading to a reduced intracellular concentration of the photodynamically active substance PPIX. Diminishing HO-1 activity by the HO-1 inhibitor tin protoporphyrin IX (SnPPIX) significantly enhanced the formation of PPIX up to 1.8 fold. A further strong increase in HO-1 protein expression (up to 128-fold) was seen after ALA-PDT treatment. Induction of HO-1 is an essential step in the 'rescue response' of tumor cells. The pharmacological inhibition of HO-1 activity by SnPPIX leads to a considerable increase in the sensitivity of tumor cells to ALA-PDT treatment. At low radiation doses (0.42 J/cm(2)), the percentages of death cells increased significantly from 7.3+/-1.3% to 43.7+/-6.4%. This effect could be further intensified by cellular depletion of HO-1 mRNA by siRNA. The combination of pharmacological inactivation of HO-1 with gene silencing led to an increase in the death rate of up to 54.1+/-8.6%. The results presented indicate that HO-1 can play a protective role against ALA-PDT mediated cytotoxicity so that a specific inhibition of HO-1 activity and/or expression might be used to increase the efficacy of ALA-based photodynamic therapy.
ADHD in adults: what the science says (2008)

Introduction. History and Prevalence of ADHD in Adults. Diagnostic Criteria for ADHD in Adults. Defining ADHD in Adults: Making the Diagnosis in the UMASS and Milwaukee Studies. DSM Symptom Utility and the Issue of Age of Onset. Impairment in Major Life Activities. Identifying New Symptoms of ADHD in Adulthood. Comorbid Psychiatric Disorders and Psychological Maladjustment. Educational and Occupational Functioning. Drug Use and Antisocial Behavior. Health, Lifestyle, Money Management, and Driving. Sex, Dating and Marriage, Parenting, and Psychological Adjustment of Offspring. Neuropsychological Functioning. Summary, Conclusions, and Treatment Implications.
Effects of <i>Apis mellifera</i> Propolis on the Activities of Streptococcal Glucosyltransferases in Solution and Adsorbed onto Saliva–Coated Hydroxyapatite (2000)

Propolis, a resinous hive product collected by Apis mellifera bees, has been used for thousands of years in folk medicine. Ethanolic extracts of propolis (EEP) have been shown to inhibit the activity of a mixture of crude glucosyltransferase (Gtf) enzymes in solution. These enzymes synthesize glucans from sucrose, which are important for the formation of pathogenic dental plaque. In the present study, the effects of propolis from two different regions of Brazil on the activity of separate, purified Gtf enzymes in solution and on the surface of saliva-coated hydroxyapatite (sHA) beads were evaluated. The EEP from Minas Gerais (MG; Southeastern Brazil) and Rio Grande do Sul (RS; Southern Brazil) were tested for their ability to inhibit the enzymes GtfB (synthesis of insoluble glucan), GtfC (insoluble/soluble glucan) and GtfD (soluble glucan). The effects of propolis on Gtf from Streptococcus sanguis (soluble glucan synthesis) was also explored. The EEP from both regions effectively inhibited the activity of all Gtfs in solution (75-95%) and on the surface of sHA beads (45-95%) at concentrations between 0.75 and 3.0 mg of propolis/ml. However, the two samples of propolis showed different levels of inhibition on each of the enzymes tested. In general, EEP RS demonstrated a significantly higher inhibitory activity on GtfB and C activities (both solution and surface assays) than EEP MG at concentrations between 0.047 and 0.187 mg/ml (p<0.05). EEP MG, on the other hand, exhibited a greater inhibitory effect on the activities of surface GtfD (at 0.375, 0.75 and 1.5 mg/ml) and S. sanguis Gtf (at 1.5 and 3.0 mg/ml; p<0.05). These data indicate that EEP is a potent inhibitor of Gtf enzymes in solution and adsorbed on an experimental pellicle; however, its effect on Gtf activity is variable depending on the geographical origin of the propolis samples. There is a need to identify the active compounds of propolis.