gebhart/patrepeval huggingface dataset:
Structure and function of the healthy pre-adolescent pediatric gut microbiome (2015)

Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.
Evaluation of Snail Consumption by Black Buffalo (2018)

Abstract Bolbophorous damnificus is a digenetic trematode that causes economic loss for commercial catfish producers by decreasing adult growth rates and increasing mortality in juvenile catfish Ictalurus spp. Efforts to control B. damnificus mainly center around control of an intermediate host, the Ram's Horn Snail Planorbella trivolvis. Black Buffalo Ictiobus niger is a catostomid fish species documented to consume mollusks and, therefore, is a potential control option; however, gastropod consumption by this species has not been documented. Thus, experiments were conducted to (1) evaluate Ram's Horn Snail consumption by Black Buffalo at juvenile and adult life stages and (2) determine whether juvenile Black Buffalo are able to consume sizes of snails typically found in catfish ponds. Nine wild-caught adult Black Buffalo and 56 captively reared juveniles (age 1) were used in this study. No snails were consumed in adult or juvenile experiments, thus suggesting Black Buffalo do not have the capacity to reduce incidence of B. damnificus through direct consumption of Ram's Horn Snails.
A review of machine learning techniques using decision tree and support vector machine (2016)

In this paper, the brief survey of data mining classification by using the machine learning techniques is presented. The machine learning techniques like decision tree and support vector machine play the important role in all the applications of artificial intelligence. Decision tree works efficiently with discrete data and SVM is capable of building the nonlinear boundaries among the classes. Both of these techniques have their own set of strengths which makes them suitable in almost all classification tasks.
Predicting Negative Emotions Based on Mobile Phone Usage Patterns: An Exploratory Study (2016)

We developed a system capable of predicting negative emotions based on mobile phone usage patterns. This system has potential for ecological momentary intervention (EMI) for depressive disorders by automatically recognizing negative emotions and providing people with preventive treatments before it escalates to clinical depression.
Comparison of Advanced Detection Techniques for QPSK Signals in Super-Nyquist WDM Systems (2014)

We compare the performance of detecting quadrature-phase-shift-keying (QPSK) in a super-Nyquist wavelength division multiplexing system as a QPSK and quadrature duobinary (QDB) signal using maximum likelihood sequence estimation (MLSE) and maximum a posteriori (MAP) criterion with both simulations and experiments. Three different detection schemes are studied: 1) QPSK detection with a multitap linear equalizer followed by a MLSE or MAP detector; 2) QPSK detection with only a MLSE or MAP detector; and 3) QDB detection with a MLSE or MAP detector, where a multitap linear equalizer and a delay-&-add operation are placed before the MLSE/MAP detector to convert a QPSK signal to a QDB signal. Our simulations and experiments show that the QDB detection with multitap MLSE does not provide better performance than that with two-tap MLSE, and the QDB detection with two-tap MLSE has better filtering tolerance than the QPSK detection with linear equalization followed by a multitap MLSE/MAP detector.
Gene Expression and Biological Significance of Hexokinase in Erythroid Cells (2002)

Red blood cells (RBCs) express two hexokinase (HK) isoforms, HK-I and HK-R. Both isozymes are generated from the HK-I gene by use of an alternate promoter. Gene structure and exon-intron organization of the HK-I gene have been elucidated from a sequence of three contiguous genomic clones localized at human chromosome 10. The sequence spans about 131 kb, and consists of 25 exons, which include 6 testis- and 1 erythroid-specific exons. HK-R has been shown as an erythroid-specific isozyme whose expression is turned on in the early erythroid-progenitors and is significantly induced during their differentiation. HK-R unfolds major HK activity in immature RBCs and is rapidly degraded during the maturation process. HK-I has a porin-binding domain in its N-terminus. Recent studies have shown that HK isozymes with a porin-binding domain play a role in mitochondrial integrity, suggesting that HK-I-deficient erythroid cells might be eliminated by apoptosis. It is most likely that RBCs are most labile as a result of HK-I/R deficiency since the HK-I gene but not the other isozyme genes are expressed in fetal and adult RBCs.
Low-Rank Factorization of Determinantal Point Processes for Recommendation (2016)

Determinantal point processes (DPPs) have garnered attention as an elegant probabilistic model of set diversity. They are useful for a number of subset selection tasks, including product recommendation. DPPs are parametrized by a positive semi-definite kernel matrix. In this work we present a new method for learning the DPP kernel from observed data using a low-rank factorization of this kernel. We show that this low-rank factorization enables a learning algorithm that is nearly an order of magnitude faster than previous approaches, while also providing for a method for computing product recommendation predictions that is far faster (up to 20x faster or more for large item catalogs) than previous techniques that involve a full-rank DPP kernel. Furthermore, we show that our method provides equivalent or sometimes better predictive performance than prior full-rank DPP approaches, and better performance than several other competing recommendation methods in many cases. We conduct an extensive experimental evaluation using several real-world datasets in the domain of product recommendation to demonstrate the utility of our method, along with its limitations.
Acute increase of α-synuclein inhibits synaptic vesicle recycling evoked during intense stimulation (2014)

Parkinson's disease is associated with multiplication of the α-synuclein gene and abnormal accumulation of the protein. In animal models, α-synuclein overexpression broadly impairs synaptic vesicle trafficking. However, the exact steps of the vesicle trafficking pathway affected by excess α-synuclein and the underlying molecular mechanisms remain unknown. Therefore we acutely increased synuclein levels at a vertebrate synapse and performed a detailed ultrastructural analysis of the effects on presynaptic membranes. At stimulated synapses (20 Hz), excess synuclein caused a loss of synaptic vesicles and an expansion of the plasma membrane, indicating an impairment of vesicle recycling. The N-terminal domain (NTD) of synuclein, which folds into an α-helix, was sufficient to reproduce these effects. In contrast, α-synuclein mutants with a disrupted N-terminal α-helix (T6K and A30P) had little effect under identical conditions. Further supporting this model, another α-synuclein mutant (A53T) with a properly folded NTD phenocopied the synaptic vesicle recycling defects observed with wild type. Interestingly, the vesicle recycling defects were not observed when the stimulation frequency was reduced (5 Hz). Thus excess α-synuclein impairs synaptic vesicle recycling evoked during intense stimulation via a mechanism that requires a properly folded N-terminal α-helix.
Activity of the Distal Positive Element of the Peripherin Gene Is Dependent on Proteins Binding to an Ets-like Recognition Site and a Novel Inverted Repeat Site (1996)

The peripherin gene, encoding a neuron-specific intermediate filament protein, is transcriptionally induced when PC12 cells begin to terminally differentiate into neurons in response to nerve growth factor. Previously we identified two regulatory sequences of the peripherin gene: a proximal negative element (centered at -173), which prevents peripherin expression in undifferentiated PC12 cells, and a distal positive region (-2660 to -2308) necessary for full induction of peripherin in differentiated PC12 cells (Thompson, M., Lee, E. Lawe, D., Gizang-Ginsberg, E., and Ziff, E. (1992) Mol. Cell. Biol. 12,2501-2513). Here we define a distal positive element (DPE, -2445 to -2337) within the distal positive region. Methylation interference footprinting of the DPE identified DNA-protein contact points at a novel inverted repeat sequence (AACCACTGGTT) and an Ets-like recognition sequence (CAGGAG). Functional analysis using site-directed mutagenesis demonstrates that both sites are necessary for the activity of the DPE. In addition, ternary complex formation at the DPE is dependent on both sites. Antibody competition assays confirm that an Ets family member participates in the DNA-protein complex. We have indirect evidence that the inverted repeat binding protein and the Ets-related protein interact directly with each other. Finally, we demonstrate that the DPE is constitutively active and that neuron-specific regulation of peripherin expression may be due to interaction with distal and proximal negative regulatory elements.
Intelligent network overview (1993)

The International Consultative Committee for Telephone and Telegraph (CCITT) program of work that addresses global international intelligent network (IN) standards and a framework for the standardized evolution of IN are described. Bell Communication Research's (Bellcore's) IN work, referred to as the Advanced Intelligent Network (AIN), is also discussed in relation to the CCITT IN Recommendations. In addition, IN activities of the European Telecommunications Standards Institute (ETSI) and the Telecommunications Technology Committee (TTC) of Japan are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Specificity of humoral and cellular immune response against recombinant particles of nucleocapsid protein of human hepatitis B virus in rabbits. (1998)

Nucleocapsid (core) protein of hepatitis B virus (HBcAg) induces potent cellular and humoral responses that have a clear protective potential. Rabbits were immunized by particles formed by recombinant molecules of HBcAg carrying N-terminally inserted heterologous sequences. Specificity of humoral and cellular immune response against HBcAg and selection of HBcAg epitopes was surveyed. Immunological properties of the recombinant particles were similar to those of the original HBcAg. Recombinant particles were not toxic to the peripheral blood mononuclear cells (PBMC) of non-immune or HBcAg-immunized animals ex vivo. Proliferative response of PBMC (T-lymphocytes) to HBcAg in immunized animals increased in a concentration-dependent manner in the broad interval of HBcAg concentrations (10-104 ng/ml). On the contrary, a narrow bell-shaped HBcAg dose-dependence curve was earlier observed for T-lymphocytes of donors immune to HBV after natural infection that was probably due to the cytotoxic effect of HBcAg on the expressing cells. Specificity of humoral and cellular immune response against HBcAg particles in the immunized animals and in natural infection with hepatitis B virus (HBV) was compared. Immunization with recombinant HBcAg particles induced potent anti-HBcAg antibody responses: high (up to 2.107) titers of anti-HBcAg antibodies were reached. Appearance of anti-HBcAg antibodies was in every case preceded by an increasing T-cell response to the whole protein and HBcAg-derived peptides, thus mimicking immune responses during acute HBV infection in humans. A predominant universal (haplotype-independent) T-helper cell epitope (amino acid residues (aa) 61-85 of HBcAg (p61-85)) was recognized by T-cells of all animals. Transient antibody response against p61-85 was recorded during the early stages of immunization in spite of the fact that a major B-cell epitope localized in this region is supposed to be purely conformational. A sequence representing another cluster of immunodominant T-cell epitopes of mice and HBV infected humans, aa 121-140 (p121-140), was not immunogenic on the T-cell level. However, it appeared to be a potent B-cell immunogen, despite a common assumption that HBcAg and p121-140 are not cross-reactive at the B-cell level. A possibility that anti-p121-140 antibodies were induced by an exposed region of the native particulate HBcAg and not by the denatured protein molecules, was confirmed by recognition of the particulate HBcAg by antibodies specific to synthetic peptides representing aa 120-140 of HBcAg. The data point to the exposition of aa 121-140 on the surface of the particles.
Ventilation of Red Sea Water with respect to chlorofluorocarbons (1999)

Chlorofluorocarbon (CFC) measurements were made in the northwestern Indian Ocean in August‐September 1995 as part of the World Ocean Circulation Experiment Hydrographic Program Section I1. The data in the Gulf of Aden section from this expedition provide information on the mixing processes that affect Red Sea Water (RSW) as it flows from its source into the open northwestern Indian Ocean. Combining measurements by Rhein et al. [1997] with the outcome from a two‐end‐member mixing model results in an estimate of 65–70% saturation for the CFCs in the RSW end‐member at Bab el Mandeb. A boundary condition that may be more applicable to ocean models is given by the CFC content of RSW after its initial diapycnal descent along the continental slope in the western Gulf of Aden. Entrainment of water containing lower amounts of CFCs produces RSW that has CFC saturations of 20–50% once RSW has settled at its depth of neutral buoyancy. Apparent p CFC ages at Bab el Mandeb and after the separation of RSW from the bottom are 12–13 and 18–27 years, respectively. As RSW continues eastward through the Gulf of Aden as an isopycnal flow, horizontal eddy diffusion plays an important role in further diluting RSW, which is characterized by a maximum in salinity and a positive anomaly in CFC concentrations. Horizontal eddy diffusion parameters estimated from tracer conservation in a box model of the central and eastern Gulf of Aden range from 0.2 × 10 4 to 2.0 × 10 4 m 2 s −1 . As other observations show, eddy diffusion is presumably enhanced in this part of the ocean.
SOUND RETRIEVAL FROM VOICE IMITATION QUERIES IN COLLABORATIVE DATABASES (2014)

The retrieval of sounds in large databases can benefit from novel paradigms that exploit human-computer interaction. This work introduces the use of non-speech voice imitations as input queries in a large user-contributed sound repository. We address first the analysis of the human voice properties when imitating sounds. Second, we study the automatic classification of voice imitations in clusters by means of user experiments. Finally, we present an evaluation that demonstrates the potential of a content-based classification using voice imitations as input queries. Future perspectives for using voice interfaces in sound assets retrieval are exposed.
Understanding and Predicting Gun Barrel Erosion (2005)

The Australian Defence Force will soon have to contend with gun barrel erosion issues arising from the use of new low-vulnerability gun propellants, the acquisition of new ammunition and gun systems, and possible modifications to existing propelling charge designs. A critical, technical review of advances is gun barrel erosion research, mitigation, and assessment over the last fifteen years is presented. Known and postulated erosion mechanisms, obtained through recent experimental and numerical modelling work, are described and contrasted. New approaches to erosion mitigation and updated knowledge of existing methods are reviewed. Also included is an assessment of the utility of the various erosion modelling and experimental techniques, and notes on their possible use of defence applications in Australia.
50.3: Image Qualitu Considerations in Bi‐Sinusoidally Scanned Retinal Scanning Display Systems (2002)

Abstract System design considerations for a bi‐sinusoidally scanned retinal scanning display (RSD) system are investigated. Results show that fundamental limitations on the temporal and spatial sampling frequency are imposed by limitations on the maximum achievable horizontal scan frequency. Spatial and temporal image artifacts are studied using simulations and an experiment prototype.
Efficient Interleukin-21 Production by Optimization of Codon and Signal Peptide in Chinese Hamster Ovarian Cells (2019)

Interleukin-21 is a common γ-chain cytokine that controls the immune responses of B cells, T cells, and natural killer cells. Targeting IL-21 to strengthen the immune system is promising for the development of vaccines as well as anti-infection and anti-tumor therapies. However, the practical application of IL-21 is limited by the high production cost. In this study, we improved IL-21 production by codon optimization and selection of appropriate signal peptide in CHO-K1 cells. Codon-optimized or non-optimized human IL-21 was stably transfected into CHO-K1 cells. IL-21 expression was 10-fold higher for codon-optimized than non-optimized IL-21. We fused five different signal peptides to codon-optimized mature IL-21 and evaluated their effect on IL-21 production. The best result (a 3-fold increase) was obtained using a signal peptide derived from human azurocidin. Furthermore, codon-optimized IL-21 containing the azurocidin signal peptide promoted IFN-γ secretion and STAT3 phosphorylation in NK-92 cells similar to codon-optimized IL-21 containing original signal peptide. Collectively, these results indicate that codon optimization and azurocidin signal peptides provide an efficient approach for the high-level production of IL-21 as a biopharmaceutical.
Intestinal Fibrosis in Crohns Disease: Medical Treatment or Surgery? (2010)

Crohn's disease (CD) is a chronic panenteric disease of unknown aethiology tending to progress, inspite medical or surgical treatment. Intestinal fibrosis is among the most common complications of CD, resulting in stricture formation in the small intestine and colon. About 75% of CD patients will undergo surgery at least once over the course of their disease and fibrotic strictures represents the main indication for surgery and the first cause of hospitalization and costs for CD patients. Clinical management of intestinal strictures depends on the type of stricture: inflammatory strictures are treated medically and are usually responsive to treatment, while fibrotic strictures require surgery. Clinical decisions regarding the right treatment choice for such conditions require proper knowledge on what to expect from the emerging drug strategies and surgical techniques. To achieve optimal results in patients management an approach combining the expertise of both gastroenterologist and colorectal surgeon is essential. This review aims at providing clinicians with an overview on fibrotic strictures in CD patients particular focus will be placed on the principal imaging modalities, and the medical, endoscopic and surgical treatment options with relative indications, according to the most recent evidence available.
Transient behavior of self-assembled quantum dots formed by atomic layer epitaxy technique (2004)

We investigated the effects of carrier dynamics on the temperature dependence of the photoluminescence (PL) of an InGaAs dots-in-a-well (DWELL) structure. The quantum dots (QDs) were formed by the atomic layer epitaxy (ALE) technique alternately supplying InAs and GaAs sources. It was found from the PL measurements at various temperatures that the DWELL structure was accomplished through the generation process of the intermediate layer between the quantum well (QW) and the QDs during the formation of the QDs inside a QW. The thermal quenching equations on the basis of the rate equation model can be explained by the carrier dynamics, which included in the radiative recombination, the carrier thermal escape and the carrier capture process occurring in these three layers, i.e. QW, QD and the intermediate layer.
Structural Role of Counterions Adsorbed on Self-Assembled Peptide Nanotubes (2011)

Among noncovalent forces, electrostatic ones are the strongest and possess a rather long-range action. For these reasons, charges and counterions play a prominent role in self-assembly processes in water and therefore in many biological systems. However, the complexity of the biological media often hinders a detailed understanding of all the electrostatic-related events. In this context, we have studied the role of charges and counterions in the self-assembly of lanreotide, a cationic octapeptide. This peptide spontaneously forms monodisperse nanotubes (NTs) above a critical concentration when solubilized in pure water. Free from any screening buffer, we assessed the interactions between the different peptide oligomers and counterions in solutions, above and below the critical assembly concentration. Our results provide explanations for the selection of a dimeric building block instead of a monomeric one. Indeed, the apparent charge of the dimers is lower than that of the monomers because of strong chemisorption. This phenomenon has two consequences: (i) the dimer-dimer interaction is less repulsive than the monomer-monomer one and (ii) the lowered charge of the dimeric building block weakens the electrostatic repulsion from the positively charged NT walls. Moreover, additional counterion condensation (physisorption) occurs on the NT wall. We furthermore show that the counterions interacting with the NTs play a structural role as they tune the NTs diameter. We demonstrate by a simple model that counterions adsorption sites located on the inner face of the NT walls are responsible for this size control.
Enhancing compression rate by just-noticeable distortion model for H.264/AVC (2009)

In this paper, we proposed an algorithm to enhance compression rate for the H.264/AVC. The properties of human visual system are utilized to reduce the bit rate without introducing noticeable visual distortion. The just-noticeable distortion (JND) threshold for every block in a frame is computed, and non-zero coefficients are removed if their magnitudes are less than the JND thresholds. Experimental results show that bit rate can be reduced by as much as 50% without degradation in visual quality.
Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage (2017)

Understanding mechanisms of coevolution between nuclear and mitochondrial (mt) genomes is a defining challenge in eukaryotic genetics. The angiosperm genus Silene is a natural system to investigate the causes and consequences of mt mutation rate variation because closely related species have highly divergent rates. In Silene species with fast-evolving mtDNA, nuclear genes that encode mitochondrially targeted proteins (N-mt genes) are also fast-evolving. This correlation could indicate positive selection to compensate for mt mutations, but might also result from a recent relaxation of selection. To differentiate between these interpretations, we used phylogenetic and population-genetic methods to test for positive and relaxed selection in three classes of N-mt genes (oxidative phosphorylation genes, ribosomal genes, and "RRR" genes involved in mtDNA recombination, replication, and repair). In all three classes, we found that species with fast-evolving mtDNA had: 1) elevated dN/dS, 2) an excess of nonsynonymous divergence relative to levels of intraspecific polymorphism, which is a signature of positive selection, and 3) no clear signals of relaxed selection. "Control" genes exhibited comparatively few signs of positive selection. These results suggest that high mt mutation rates can create selection on N-mt genes and that relaxed selection is an unlikely cause of recent accelerations in the evolution of N-mt genes. Because mt-RRR genes were found to be under positive selection, it is unlikely that elevated mt mutation rates in Silene were caused by inactivation of these mt-RRR genes. Therefore, the causes of extreme increases in angiosperm mt mutation rates remain uncertain.