gebhart/patrepeval huggingface dataset:
Reorganization of Synaptic Connections and Perineuronal Nets in the Deep Cerebellar Nuclei ofPurkinje Cell DegenerationMutant Mice (2015)

The perineuronal net (PN) is a subtype of extracellular matrix appearing as a net-like structure around distinct neurons throughout the whole CNS. PNs surround the soma, proximal dendrites, and the axonal initial segment embedding synaptic terminals on the neuronal surface. Different functions of the PNs are suggested which include support of synaptic stabilization, inhibition of axonal sprouting, and control of neuronal plasticity. A number of studies provide evidence that removing PNs or PN-components results in renewed neurite growth and synaptogenesis. In a mouse model for Purkinje cell degeneration, we examined the effect of deafferentation on synaptic remodeling and modulation of PNs in the deep cerebellar nuclei. We found reduced GABAergic, enhanced glutamatergic innervations at PN-associated neurons, and altered expression of the PN-components brevican and hapln4. These data refer to a direct interaction between ECM and synapses. The altered brevican expression induced by activated astrocytes could be required for an adequate regeneration by promoting neurite growth and synaptogenesis.
Primaquine-tolerant vivax malaria in Thailand (1997)

(1997). Primaquine-tolerant vivax malaria in Thailand. Annals of Tropical Medicine & Parasitology: Vol. 91, No. 8, pp. 939-943.
The Approach to the Evaluation and Surgical Treatment of Mechanical Hip Pain in the Young Patient (2013)

The mechanical causes of hip pain in a young athlete often reflect a complex combination of static and dynamic factors. A comprehensive diagnostic approach is paramount to the development of a rational treatment strategy that will address all underlying pathologic factors. The goals of this paper are to highlight the pertinent biomechanical factors of the hip joint in femoroacetabular impingement and to discuss the clinical history, physical examination, and radiographic findings that are essential to formulating a proper diagnosis and an effective treatment plan. In addition, the current literature and reported outcomes of femoroacetabular impingement surgery in athletic patients are reviewed.
3D Monte-Carlo simulations of multipactor in dielectric-loaded accelerating structures (2012)

In this paper, results of three-dimensional Monte-Carlo simulations of multipactor in dielectric-loaded accelerating structures are presented. Results are compared with available experimental data. Good agreement between theory and experiment is observed for all structures under study. Some results of multipactor suppression by an external magnetic field are shown and discussed.
LIPOSUCTION CANNULA DESIGN PROBLEMS (1989)

Hospital of the University of Pennsylvania 2 Maloney Building 3600 Spruce Street Philadelphia, Pa. 19104
Transient receptor potential vanilloid 4 (2010)

The critical discovery in the past two decades of the transient receptor potential (TRP) superfamily of ion channels has revealed the potential mechanisms by which cells sense diverse stimuli beyond the prototypical "five senses," identifying ion channels that are gated by heat, cold, mechanical loading, osmolarity, and other physical and chemical stimuli. TRP vanilloid 4 (TRPV4) is a Ca(2+)-permeable nonselective cation channel that appears to play a mechanosensory or osmosensory role in several musculoskeletal tissues. In articular cartilage, TRPV4 exhibits osmotic sensitivity, controlling cellular volume recovery, and other physiologic responses to osmotic stress. TRPV4 is expressed in both osteoblasts and osteoclasts, and the absence of TRPV4 prevents disuse-induced bone loss. TRPV4 activation promotes chondrogenesis by inducing SOX9 transcription, whereas a TRPV4 gain-of-function mutation leads to a developmental skeletal dysplasia, suggesting a critical role for TRPV4 in skeletal development. These studies provide mounting evidence for a regulatory role for the sensory channel TRPV4 in control of musculoskeletal tissues.
Human Antimicrobial Peptides and Proteins (2014)

As the key components of innate immunity, human host defense antimicrobial peptides and proteins (AMPs) play a critical role in warding off invading microbial pathogens. In addition, AMPs can possess other biological functions such as apoptosis, wound healing, and immune modulation. This article provides an overview on the identification, activity, 3D structure, and mechanism of action of human AMPs selected from the antimicrobial peptide database. Over 100 such peptides have been identified from a variety of tissues and epithelial surfaces, including skin, eyes, ears, mouths, gut, immune, nervous and urinary systems. These peptides vary from 10 to 150 amino acids with a net charge between -3 and +20 and a hydrophobic content below 60%. The sequence diversity enables human AMPs to adopt various 3D structures and to attack pathogens by different mechanisms. While α-defensin HD-6 can self-assemble on the bacterial surface into nanonets to entangle bacteria, both HNP-1 and β-defensin hBD-3 are able to block cell wall biosynthesis by binding to lipid II. Lysozyme is well-characterized to cleave bacterial cell wall polysaccharides but can also kill bacteria by a non-catalytic mechanism. The two hydrophobic domains in the long amphipathic α-helix of human cathelicidin LL-37 lays the basis for binding and disrupting the curved anionic bacterial membrane surfaces by forming pores or via the carpet model. Furthermore, dermcidin may serve as ion channel by forming a long helix-bundle structure. In addition, the C-type lectin RegIIIα can initially recognize bacterial peptidoglycans followed by pore formation in the membrane. Finally, histatin 5 and GAPDH(2-32) can enter microbial cells to exert their effects. It appears that granulysin enters cells and kills intracellular pathogens with the aid of pore-forming perforin. This arsenal of human defense proteins not only keeps us healthy but also inspires the development of a new generation of personalized medicine to combat drug-resistant superbugs, fungi, viruses, parasites, or cancer. Alternatively, multiple factors (e.g., albumin, arginine, butyrate, calcium, cyclic AMP, isoleucine, short-chain fatty acids, UV B light, vitamin D, and zinc) are able to induce the expression of antimicrobial peptides, opening new avenues to the development of anti-infectious drugs.
Optimization parameter design of a circular e + e − Higgs factory (2013)

In this paper we will show a general method of how to make an optimized parameter design of a circular e+e-Higgs Factory by using analytical expression of maximum beam-beam parameter and beamstrahlung beam lifetime started from given design goal and technical limitations. A parameter space has been explored. Based on beam parameters scan and RF parameters scan, a set of optimized parameter designs for 50 km Circular Higgs Factory (CHF) with different RF frequency was proposed.
Mechanical analysis of extrapulmonary volume displacements in the thorax and abdomen (1989)

Currently, the effect of intrathoracoabdominal, extrapulmonary volume displacements (Vep) are not well understood. Various clinical conditions can lead to volume displacements caused by gas or liquid accumulations. To analyze the pressure and volume changes that occur by Vep, we used a mathematical model of chest wall and lung mechanics that accounts for static changes associated with rib cage, diaphragm, abdomen, and lungs. By solving the model equations, we obtained simulations of the pleural and abdominal displacements that clearly differentiate the mechanisms involved. When abdominal displacement occurs, the reduction in lung volume is less than that caused by an equal displacement in pleural space. Abdominal displacement produces an increased pressure that expands the rib cage significantly, whereas pleural displacement does not produce a comparable action. Furthermore, our model predicts the conditions under which the work of inspiration is expected to increase as a consequence of these displacements. Finally, an important distinction is predicted between abdominal displacements caused by gas or liquid accumulation. Although an abdominal gas displacement tends to decrease the resting lung volume, the weight effect of a liquid displacement tends to increase the resting lung volume by pulling down the diaphragm.
Relationship between polymorphism of SOCS-3 and dyslipidemia in China Xinjiang Uygur (2015)

We investigated the relationship between the polymorphism of SOCS-3 and dyslipidemia of people from Uygur in Xinjiang, China. This cross-sectional study included 1379 participants in a Hetian Xinjiang Uygur population who were 30-70 years of age and were not from interracial marriages of 3 generations; all subjects were genotyped (909 dyslipidemia subjects, 470 healthy subjects). Allele (P = 0.002) and genotype (P = 0.003) frequencies of the distribution of rs12953258 was significantly different between dyslipidemia and control groups. Between the total cholesterol abnormal and control groups, high-density lipoprotein cholesterol abnormal and control groups, triglycerides abnormal and control groups, the frequencies of genotype in rs12953258 were significantly different (P = 0.007, 0.012, 0.0004, respectively). Based on the logistic regression analysis, genotype CA and AA of rs12953258 were independent and risk factors for dyslipidemia in Uygur (CC vs CA; odds ratio = 1.48, 95% confidence interval = 1.11-1.98, P = 0.008), (CC vs AA; odds ratio = 2.48, 95% confidence interval1.07-5.79, P = 0.035). Genotype AA of rs12953258 merged with subjects whose waist-to-hip ratio was abnormal, indicating the presence of dyslipidemia. The frequency of haplotype 4(H4) A-G-C in the dyslipidemia group was higher than in the control group (8.44 vs 5.37%, P = 0.003). rs12953258 site of the SOCS-3 gene showed a close relationship with dyslipidemia in Uygur. Combining genotype AA with subjects whose waist-to-hip ratios were abnormal will increase prevalence of dyslipidemia obviously.
A Classification-Based Polyphonic Piano Transcription Approach Using Learned Feature Representations. (2011)

[TODO] Add abstract here.
An efficient cost model for optimization of nearest neighbor search in low and medium dimensional spaces (2004)

Existing models for nearest neighbor search in multidimensional spaces are not appropriate for query optimization because they either lead to erroneous estimation or involve complex equations that are expensive to evaluate in real-time. This article proposes an alternative method that captures the performance of nearest neighbor queries using approximation. For uniform data, our model involves closed formulae that are very efficient to compute and accurate for up to 10 dimensions. Further, the proposed equations can be applied on nonuniform data with the aid of histograms. We demonstrate the effectiveness of the model by using it to solve several optimization problems related to nearest neighbor search.
The Absence of Retroelement Activity Is Characteristic for Childhood Acute Leukemias and Adult Acute Lymphoblastic Leukemia (2022)

Retroelements (RE) have been proposed as important players in cancerogenesis. Different cancer types are characterized by a different level of tumor-specific RE insertions. In previous studies, small cohorts of hematological malignancies, such as acute myeloid leukemia, multiple myeloma, and chronic lymphocytic leukemia have been characterized by a low level of RE insertional activity. Acute lymphoblastic leukemia (ALL) in adults and childhood acute leukemias have not been studied in this context. We performed a search for new RE insertions (Alu and L1) in 44 childhood ALL, 14 childhood acute myeloid leukemia, and 14 adult ALL samples using a highly sensitive NGS-based approach. First, we evaluated the method sensitivity revealing the 1% detection threshold for the proportion of cells with specific RE insertion. Following this result, we did not identify new tumor-specific RE insertions in the tested cohort of acute leukemia samples at the established level of sensitivity. Additionally, we analyzed the transcription levels of active L1 copies and found them increased. Thus, the increased transcription of active L1 copies is not sufficient for overt elevation of L1 retrotranspositional activity in leukemia.
Power quality data analysis based on a state-wide monitoring system in China (2018)

This paper presents the analysis of power quality data obtained from a state-wide monitoring system in China in two aspects, one for benchmarking using power quality statistics, and the other for harmonic characteristics identification using waveform data. First, based on three-minute-interval power quality monitoring data, two metrics are proposed to measure the scale and severity of limit-exceeding occurrences of monitoring points, therefore, power quality performance in different spatial and temporal dimensions can be quantified and compared. Then, a coupled harmonic admittance identification method based on voltage and current measurements is proposed. The effectiveness of the method is verified through comparisons with Norton model-based method using historical waveform data from the monitoring system.
InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data (2020)

High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the 'interactome sequencing' approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/.
CORTICAL EVOKED RESPONSES FROM THE PERINEAL NERVE (1999)

A cortical evoked response from the perineal nerve can be elicited reliably at the ventral penis. This neural pathway is independent of the dorsal nerve of the penis. The study of perineal somatic innervation may prove important in understanding the physiology of ejaculatory and erectile dysfunction.
Beyond anticoagulant: Heparin as a potential anti-cancer agent (2014)

Heparin has been in the market since the last six decades due to its potential anticoagulantÂ property. The mechanism of its anti-coagulation effect is well established. Along with itsÂ anticoagulant activity the other activity that is gathering a lot of importance now-a-days is itsÂ ability to arrest the progression of tumors specially some solid forms of tumors such as small cellÂ lung carcinoma and pancreatic tumors. The chemically modified and light molecular weightÂ fractions of heparin have been found to be more active in countering tumor progression. In thisÂ review we discuss a brief history of this versatile biomolecule with its clinical data andÂ postulated mechanism of action as per recent studies. This review also highlighted the approachÂ of heparin-conjugated nanoparticles to achieve targeted drug delivery with synergistic responseÂ in tumor cells.
Cloning and Biochemical Characterization of a Novel Carbendazim (Methyl-1 H -Benzimidazol-2-ylcarbamate)-Hydrolyzing Esterase from the Newly Isolated Nocardioides sp. Strain SG-4G and Its Potential for Use in Enzymatic Bioremediation (2010)

A highly efficient carbendazim (methyl-1H-benzimidazol-2-ylcarbamate, or MBC)-mineralizing bacterium was isolated from enrichment cultures originating from MBC-contaminated soil samples. This bacterium, Nocardioides sp. strain SG-4G, hydrolyzed MBC to 2-aminobenzimidazole, which in turn was converted to the previously unknown metabolite 2-hydroxybenzimidazole. The initial steps of this novel metabolic pathway were confirmed by growth and enzyme assays and liquid chromatography-mass spectrometry (LC-MS) studies. The enzyme responsible for carrying out the first step was purified and subjected to N-terminal and internal peptide sequencing. The cognate gene, named mheI (for MBC-hydrolyzing enzyme), was cloned using a reverse genetics approach. The MheI enzyme was found to be a serine hydrolase of 242 amino acid residues. Its nearest known relative is an uncharacterized hypothetical protein with only 40% amino acid identity to it. Codon optimized mheI was heterologously expressed in Escherichia coli, and the His-tagged enzyme was purified and biochemically characterized. The enzyme has a K(m) and k(cat) of 6.1 muM and 170 min(-1), respectively, for MBC. Radiation-killed, freeze-dried SG-4G cells showed strong and stable MBC detoxification activity suitable for use in enzymatic bioremediation applications.
Nutrition and Nutritional Supplements and Osteoarthritis (2008)

• There are numerous mechanisms by which micronutrients might be expected to influence the development or progression of osteoarthritis, but there has been insufficient research to draw definitive conclusions • One observational study suggested a protective effect of vitamin C for progression of osteoarthritis of the knee. Intake of vitamin E and β-carotene bore no relationship to osteoarthritis incidence or progression in that study, suggesting that the mechanism of benefit of vitamin C may be mediated through nonantioxidant properties • Clinical trials of vitamins E, C, and A and selenium have produced negative or inconsistent results • Epidemiological data for vitamin D in the treatment of symptoms and structural progression of osteoarthritis are conflicting. A randomized controlled trial is currently underway to address the efficacy of vitamin D in both the treatment of symptoms and structural progression in osteoarthritis. • Epidemiological data for vitamin K as a disease modifying micronutrient in osteoarthritis are conflicting. Randomized controlled trials are currently underway to address the efficacy of vitamin K in both the treatment of symptoms and structural progression in osteoarthritis. • There have been numerous positive clinical trials of glucosamine and chondroitin products for OA that have shown them to be well tolerated; however, interpretation of these trials is clouded by issues of biological plausibility, heterogeneity, publication bias, inconsistent results and methodological problems.
Group-velocity dispersion emulator using a time lens (2021)

We report a novel method to continuously track the temporal evolution of an arbitrary complex waveform as it propagates through a group-velocity dispersion medium by using a single-frequency-driven phase modulator. The proposed method exploits the fact that the frequency spectrum of a given (input) waveform, following a suitable sinusoidal temporal phase modulation, exhibits the same shape as that of a dispersed version of the same temporal waveform after propagation through a prescribed amount of dispersion. In experiments, we track the dispersion-induced temporal evolution of different optical picosecond pulsed waveforms by tuning the frequency and/or amplitude of the phase modulation signal and observing the resulting shapes in the optical frequency domain. A good agreement is obtained between the measured spectra and predicted temporal shapes of the propagating waveform for different amounts of dispersion. Moreover, the method is successfully applied on a chirped optical pulse to find the optimal pulse compression conditions.
[Antigenicity and physicochemical properties of two human NR1a polypeptides related to activation of NMDA receptor]. (2002)

Both human NR1a polypeptides related to activation of NMDA receptor, P1 and P2, have a certain amount of antigenic sites. Compared with P1, P2 may be of higher antigenicity, and may be more easily used as a molecular target in immunization intervention to control the activation of NMDAR.
Scale selection for anisotropic scale-space: application to volumetric tumor characterization (2004)

A unified approach for treating the scale selection problem in the anisotropic scale-space is proposed. The anisotropic scale-space is a generalization of the classical isotropic Gaussian scale-space by considering the Gaussian kernel with a fully parameterized analysis scale (bandwidth) matrix. The "maximum-over-scales" and the "most-stable-over-scales" criteria are constructed by employing the "L-normalized scale-space derivatives", i.e., response-normalized derivatives in the anisotropic scale-space. This extension allows us to directly analyze the anisotropic (ellipsoidal) shape of local structures. The main conclusions are (i) the norm of the /spl gamma/- and L-normalized anisotropic scale-space derivatives with a constant /spl gamma/ =1/2 are maximized regardless of the signal's dimension iff the analysis scale matrix is equal to the signal's covariance and (ii) the most-stable-over-scales criterion with the isotropic scale-space outperforms the maximum-over-scales criterion in the presence of noise. Experiments with 1D and 2D synthetic data confirm the above findings. 3D implementations of the most-stable-over-scales methods are applied to the problem of estimating anisotropic spreads of pulmonary tumors shown in high-resolution computed-tomography (HRCT) images. Comparison of the first- and second-order methods shows the advantage of exploiting the second-order information.
Structure in Neural Activity during Observed and Executed Movements Is Shared at the Neural Population Level, Not in Single Neurons (2020)

In multiple cortical areas, including the motor cortex, neurons have similar firing rate statistics whether we observe or execute movements. These "congruent" neurons are hypothesized to support action understanding by participating in a neural circuit consistently activated in both observed and executed movements. We examined this hypothesis by analyzing neural population structure and dynamics between observed and executed movements. We find that observed and executed movements exhibit similar neural population covariation in a shared subspace capturing significant neural variance. Further, neural dynamics are more similar between observed and executed movements within the shared subspace than outside it. Finally, we find that this shared subspace has a heterogeneous composition of congruent and incongruent neurons. Together, these results argue that similar neural covariation and dynamics between observed and executed movements do not occur via activation of a subpopulation of congruent single neurons, but through consistent temporal activation of a heterogeneous neural population.
Primary Structure of Escherichia coli Glutamine Synthetase (1971)

Abstract A 21-member tryptic peptide containing covalently bound adenylic acid has been isolated by gel filtration and ion exchange chromatography from Escherichia coli glutamine synthetase. The amino acid sequence of the peptide is [see PDF for sequence] Analysis of a thermolysin fragment of the heneicosapeptide containing uniformly labeled 14C-AMP revealed that the radioactivity of the ribose moiety of the AMP is released from the peptide along with tyrosine during the Edman degradation. This establishes that tyrosine is the amino acid residue to which the AMP is covalently bound.
ChemInform Abstract: Nucleophilic Addition to N‐Alkoxyamides (2014)

Abstract Review: 9 refs.