gebhart/patrepeval huggingface dataset:
The Body-wide Transcriptome Landscape of Disease Models (2018)

Virtually all diseases affect multiple organs. However, our knowledge of the body-wide effects remains limited. Here, we report the body-wide transcriptome landscape across 13-23 organs of mouse models of myocardial infarction, diabetes, kidney diseases, cancer, and pre-mature aging. Using such datasets, we find (1) differential gene expression in diverse organs across all models; (2) skin as a disease-sensor organ represented by disease-specific activities of putative gene-expression network; (3) a bone-skin cross talk mediated by a bone-derived hormone, FGF23, in response to dysregulated phosphate homeostasis, a known risk-factor for kidney diseases; (4) candidates for the signature activities of many more putative inter-organ cross talk for diseases; and (5) a cross-species map illustrating organ-to-organ and model-to-disease relationships between human and mouse. These findings demonstrate the usefulness and the potential of such body-wide datasets encompassing mouse models of diverse disease types as a resource in biological and medical sciences. Furthermore, the findings described herein could be exploited for designing disease diagnosis and treatment.
Life History and Descriptions of Immatures of the Dictyopharid Planthopper Phylloscelis pallescens (Homoptera: Fulgoroidea) (1995)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Molecular Determinants and Dynamics of Hepatitis C Virus Secretion (2012)

The current model of hepatitis C virus (HCV) production involves the assembly of virions on or near the surface of lipid droplets, envelopment at the ER in association with components of VLDL synthesis, and egress via the secretory pathway. However, the cellular requirements for and a mechanistic understanding of HCV secretion are incomplete at best. We combined an RNA interference (RNAi) analysis of host factors for infectious HCV secretion with the development of live cell imaging of HCV core trafficking to gain a detailed understanding of HCV egress. RNAi studies identified multiple components of the secretory pathway, including ER to Golgi trafficking, lipid and protein kinases that regulate budding from the trans-Golgi network (TGN), VAMP1 vesicles and adaptor proteins, and the recycling endosome. Our results support a model wherein HCV is infectious upon envelopment at the ER and exits the cell via the secretory pathway. We next constructed infectious HCV with a tetracysteine (TC) tag insertion in core (TC-core) to monitor the dynamics of HCV core trafficking in association with its cellular cofactors. In order to isolate core protein movements associated with infectious HCV secretion, only trafficking events that required the essential HCV assembly factor NS2 were quantified. TC-core traffics to the cell periphery along microtubules and this movement can be inhibited by nocodazole. Sub-populations of TC-core localize to the Golgi and co-traffic with components of the recycling endosome. Silencing of the recycling endosome component Rab11a results in the accumulation of HCV core at the Golgi. The majority of dynamic core traffics in association with apolipoprotein E (ApoE) and VAMP1 vesicles. This study identifies many new host cofactors of HCV egress, while presenting dynamic studies of HCV core trafficking in infected cells.
Human Evolutionary Genetics (2019)

Human Evolutionary Genetics is a groundbreaking text which for the first time brings together molecular genetics and genomics to the study of the origins and movements of human populations. Starting with an overview of molecular genomics for the non-specialist (which can be a useful review for those with a more genetic background), the book shows how data from the post-genomic era can be used to examine human origins and the human colonisation of the planet, richly illustrated with genetic trees and global maps. For the first time in a textbook, the authors outline how genetic data and the understanding of our origins which emerges, can be applied to contemporary population analyses, including genealogies, forensics and medicine.
Effect of Ti Substitution for Mn on the Structure of LiNi[sub 0.5]Mn[sub 1.5−x]Ti[sub x]O[sub 4] and Their Electrochemical Properties as Lithium Insertion Material (2004)

The effect of Ti substitution for Mn on the structure and electrochemical properties of the was studied. The was successfully synthesized at 900°C by solid-state reaction method. Additional annealing was used for the ordering of transition metals in octahedral sites. X-ray diffraction (XRD) and selected-area electron diffraction study clearly showed that Ti substitution leads to the disordering of the transition metals and consequently lowers the symmetry from primitive simple cubic structure to face-centered spinel Electron diffraction patterns of the showed stacking faults which came from the localized incorporation of Ti atoms in the lattice. exhibited higher operating voltages, faster lithium ion diffusion, and better rate capability than Ti-free confirmed by electrochemical tests including galvanostatic intermittent titration technique measurement. In addition, ex situ XRD data of the delithiated 0.3, and 0.5) showed that phase transition was suppressed with increasing Ti content. A large amount of Ti substitution in however, exhibited low discharge capacity, which would be due to the blocking migration pathway of electrons by the ions in octahedral sites. © 2004 The Electrochemical Society. All rights reserved.
Biotin Status and Its Correlation with Other Biochemical Parameters in the Elderly People of Japan (1998)

Although serum biotin levels are not affected by aging, the serum biotin levels of elderly people vary greatly.
Fibroblast growth factor‐2 over‐rides insulin‐like growth factor‐I induced proliferation and cell survival in human neuroblastoma cells (2003)

The insulin-like growth factor (IGF) system is a key regulator of cell growth, survival and differentiation, and these functions are co-modulated by other growth factors including fibroblast growth factor-2 (FGF-2). To investigate IGF/FGF interactions in neuronal cells, we employed neuroblastoma cells (SK-N-MC). In serum free conditions proliferation of the SK-N-MC cells was promoted by IGF-I (25 ng/ml), but blunted by FGF-2 (50 ng/ml). IGF-I-induced proliferation was abolished in the presence of FGF-2 even when IGF-I was used at 100 ng/ml. In addition to our previously described FGF-2 induced proteolytic cleavage of IGFBP-2, we found that FGF-2 increased IGFBP-6 levels in conditioned medium (CM) without affecting IGFBP-6 mRNA abundance. Modulation of IGFBP-2 and -6 levels were not significant mechanisms involved in the blockade of IGF-I action since the potent IGF-I analogues [QAYL]IGF-I and des(1-3)IGF-I (minimal IGFBP affinity) were unable to overcome FGF-2 inhibition of cell proliferation. FGF-2 treated cells showed morphological differentiation expressing the TUJ1 neuronal marker while cells treated with IGF-I alone showed no morphological change. When IGF-I was combined with FGF-2, however, cell morphology was indistinguishable from that seen with FGF-2 alone. FGF-2 inhibited proliferation and enhanced differentiation was also associated with a 70% increase in cell death. Although IGF-I alone was potently anti-apoptotic (60% decreased), IGF-I was unable to prevent apoptosis when administrated in combination with FGF-2. Gene-array analysis confirmed FGF-2 activation of the intrinsic and extrinsic apoptotic pathways and blockade of IGF anti-apoptotic signaling. FGF-2, directly and indirectly, overcomes the proliferative and anti-apoptotic activity of IGF-I by complex mechanisms, including enhancement of differentiation and apoptotic pathways, and inhibition of IGF-I induced anti-apoptotic signalling. Modulation of IGF binding protein abundance by FGF-2 does not play a significant role in inhibition of IGF-I induced mitogenesis.
The concept and realization of context-based content delivery of NGSON (2012)

An explosively increasing number of multimedia contents including video, music, and pictures will be the main driver for data explosion in the next decade. However, the current IP network does not have enough capabilities to support smart content delivery that enables a network to enhance end-to-end quality and fair usage of network resources for every user while optimizing network traffic for ISPs, and to present a collaborative way for a content provider. In order to realize smart content delivery, NGSON, which has recently finished standards on its functional architecture, includes important implications like context-based routing and content delivery. In this article, we focus on smart content delivery using context information called context-based content delivery (CBCD). We present experiences with implementing and evaluating the concept as a new feature of the NGSON standard. Experiment results show that a network provider could achieve over 30 percent backbone traffic reduction by realizing the CBCD concept.
Self-weighing in weight gain prevention and weight loss trials (2005)

Results support the idea that daily weighing is valuable to individuals trying to lose weight or prevent weight gain. Daily self-weighing should be emphasized in clinical and public health messages about weight control. Experimental studies on the effects of weighing frequency in these contexts are recommended.
A Multi-layer Bidirectional Transformer Encoder for Pre-trained Word Embedding: A Survey of BERT (2020)

Language modeling is the task of assigning a probability distribution over sequences of words that matches the distribution of a language. A language model is required to represent the text to a form understandable from the machine point of view. A language model is capable to predict the probability of a word occurring in the context-related text. Although it sounds formidable, in the existing research, most of the language models are based on unidirectional training. In this paper, we have investigated a bi-directional training model-BERT (Bidirectional Encoder Representations from Transformers). BERT builds on top of the bidirectional idea as compared to other word embedding models (like Elmo). It practices the comparatively new transformer encoder-based architecture to compute word embedding. In this paper, it has been described that how this model is to be producing or achieving state-of-the-art results on various NLP tasks. BERT has the capability to train the model in bi-directional over a large corpus. All the existing methods are based on unidirectional training (either the left or the right). This bi-directionality of the language model helps to obtain better results in the context-related classification tasks in which the word(s) was used as input vectors. Additionally, BERT is outlined to do multi-task learning using context-related datasets. It can perform different NLP tasks simultaneously. This survey focuses on the detailed representation of the BERT- based technique for word embedding, its architecture, and the importance of this model for pre-training purposes using a large corpus.
Detecting the onset of hyper-reflexive bladder contractions from pudendal nerve electrical activity (2005)

Individuals with spinal cord injury or neurological disorders may develop involuntary bladder contraction at low volumes (bladder hyper-reflexia), which can lead to significant health problems. Current devices can eliminate nascent contractions through continuous stimulation, but do not have a means to detect the onset of bladder contraction to stimulate conditionally. The objective of this study is to determine the relationship between the electrical activity of the pudendal nerve (PNT) and hyper-reflexive bladder contraction, and to use the relationship to develop an algorithm to detect the onset of a bladder contraction. Bladder pressure and PNT ENG were recorded in six intact male cats. There were bursts of neuronal activity in the PNT during bladder contractions. An algorithm was developed to detect the onset of a bladder contraction using the PNT ENG activity. The algorithm calculated the onset of bladder contraction on average 2.8 seconds after the contraction started with an average increase in pressure of 14.0 cmH2O. There existed a phasic relationship between the bladder and the PNT ENG, which enabled the algorithm to detect the onset of a bladder contraction. The PNT ENG can be used as a trigger to deliver conditional inhibitory stimulation of the bladder.
Among 46 Near Full Length HIV Type 1 Genome Sequences from Rakai District, Uganda, Subtype D and AD Recombinants Predominate (2002)

The impact of HIV-1 genetic diversity on candidate vaccines is uncertain. To minimize genetic diversity in the evaluation of HIV-1 vaccines, vaccine products must be matched to the predominant subtype in a vaccine cohort. To that end, full genome sequencing was used to detect and characterize HIV-1 subtypes and recombinant strains from individuals in Rakai District, Uganda. DNA extracted from peripheral blood mononuclear cells (PMBC) was PCR amplified using primers in the long terminal repeats (LTRs) to generate nearly full length genomes. Amplicons were directly sequenced with dye terminators and automated sequencers. Sequences were phylogenetically analyzed and recombinants were detected and mapped with distance scan and bootscan. Among 46 sequences, 54% were subtype D, 15% were subtype A, and 30% were recombinant. All recombinants were individually unique, and most combined subtypes A and D. Subtype D comprised more than 70% of all the HIV-1 genomes in Rakai when both pure subtypes and recombinants were considered. Candidate vaccines based on HIV-1 subtype D would be appropriate for evaluation in Rakai District, Uganda.
Size-Dependent Electrocatalytic Activity of Gold Nanoparticles on HOPG and Highly Boron-Doped Diamond Surfaces (2011)

Gold nanoparticles were prepared by electrochemical deposition on highly oriented pyrolytic graphite (HOPG) and boron-doped, epitaxial 100-oriented diamond layers. Using a potentiostatic double pulse technique, the average particle size was varied in the range from 5 nm to 30 nm in the case of HOPG as a support and between < 1 nm and 15 nm on diamond surfaces, while keeping the particle density constant. The distribution of particle sizes was very narrow, with standard deviations of around 20% on HOPG and around 30% on diamond. The electrocatalytic activity towards hydrogen evolution and oxygen reduction of these carbon supported gold nanoparticles in dependence of the particle sizes was investigated using cyclic voltammetry. For oxygen reduction the current density normalized to the gold surface (specific current density) increased for decreasing particle size. In contrast, the specific current density of hydrogen evolution showed no dependence on particle size. For both reactions, no effect of the different carbon supports on electrocatalytic activity was observed.
Predicted band structures of III-V semiconductors in the wurtzite phase (2010)

While non-nitride III-V semiconductors typically have a zinc-blende structure, they may also form wurtzite crystals under pressure or when grown as nanowhiskers. This makes electronic structure calculation difficult since the band structures of wurtzite III-V semiconductors are poorly characterized. We have calculated the electronic band structure for nine III-V semiconductors in the wurtzite phase using transferable empirical pseudopotentials including spin-orbit coupling. We find that all the materials have direct gaps. Our results differ significantly from earlier ab initio calculations, and where experimental results are available (InP, InAs, and GaAs) our calculated band gaps are in good agreement. We tabulate energies, effective masses, and linear and cubic Dresselhaus zero-field spin-splitting coefficients for the zone-center states. The large zero-field spin-splitting coefficients we find may facilitate the development of spin-based devices.
Nonabsorbing-mirror (NAM) CDH-LOC diode lasers (1984)

CDH-LOC lasers with lateral and transverse mode control in nonabsorbing mirror regions are realised by a single etch-and-regrowth cycle. The maximum achieved peak-pulsed output power (100 ns) and catastrophic-optical-damage (power-density) levels are 1.5 W and (20–30) MW/cm2, respectively. A linear power density of 200 mW/μm is reached at catastrophic damage. Fundamental-mode operation is obtained to 80 mW in narrow beams (θ∥≅7°; θ⟂≅15°).
Electroporation for Drug and Gene Delivery in the Clinic: Doctors Go Electric (2008)

Electroporation is a unique system for drug and gene delivery, as it is possible to very specifically target certain tissues within the body with whatever drug, gene, isotope, or other product is desired in a specific situation. An increasing number of clinical trials are being launched, and sophistication of equipment and protocols continues. This chapter reviews present knowledge from clinical trials, describes important issues in the patient management when using electroporation, and outlines future perspectives of the technology.
Nonoxidative Conversion of Methane in a Dielectric Barrier Discharge Reactor: Prediction of Reaction Performance Based on Neural Network Model (2014)

The nonoxidative conversion of CH4 into H2 and higher hydrocarbons has been performed in a coaxial dielectric barrier discharge reactor at atmospheric pressure and low temperatures. The effect of discharge power, gas flow rate, and excitation frequency on the reaction performance of the plasma methane conversion is investigated. A three-layer back-propagation artificial neural network (ANN) model has been developed and trained to simulate and predict the complex plasma chemical reaction in terms of the conversion of CH4, the selectivity and yield of gas products, and the energy efficiency of the plasma process. A good agreement between the experimental and simulated results is achieved. The ANN model shows that the maximum CH4 conversion of 36% can be obtained at a discharge power of 75 W with a high selectivity of C2H6 (42.4%). In this study, the discharge power is found to be the most influential parameter with a relative weight of 45–52% for the plasma nonoxidative coupling of methane, while the excitation frequency of the plasma system is the least important parameter affecting the plasma process. The results successfully demonstrate that the well-trained ANN model can accurately simulate and predict a complex plasma chemical reaction.
Low Latency Pipelined Circular CORDIC (2005)

The pipelined CORDIC with linear approximation to rotation has been proposed to achieve reductions in delay, power and area; however, the schemes for rotation (multiplication) and vectoring (division) complicate implementation in a single unit. In this work, we improve the linear approximation scheme, leading to a unified implementation for rotation and vectoring where fully parallel tree multipliers are used instead of the second half of CORDIC iterations. We also combine the linear approximation to rotation with the scale factor compensation so that the compensation is performed concurrently with the rotation process. Comparison with other designs is also provided.
Metabolic cycling without cell division cycling in respiring yeast (2011)

Despite rapid progress in characterizing the yeast metabolic cycle, its connection to the cell division cycle (CDC) has remained unclear. We discovered that a prototrophic batch culture of budding yeast, growing in a phosphate-limited ethanol medium, synchronizes spontaneously and goes through multiple metabolic cycles, whereas the fraction of cells in the G1/G0 phase of the CDC increases monotonically from 90 to 99%. This demonstrates that metabolic cycling does not require cell division cycling and that metabolic synchrony does not require carbon-source limitation. More than 3,000 genes, including most genes annotated to the CDC, were expressed periodically in our batch culture, albeit a mere 10% of the cells divided asynchronously; only a smaller subset of CDC genes correlated with cell division. These results suggest that the yeast metabolic cycle reflects a growth cycle during G1/G0 and explains our previous puzzling observation that genes annotated to the CDC increase in expression at slow growth.
Detection of 5-bromodeoxyuridine (BrdUrd) incorporation by monoclonal antibodies: role of the DNA denaturation step. (1985)

Immunochemical detection of cells that incorporate 5-bromodeoxyuridine (BrdUrd) requires prior denaturation of DNA in situ to make BrdUrd binding sites accessible to the antibodies. A technique is described in which the DNA denaturation step is facilitated by a) prior dissociation of histones from DNA and b) the use of low ionic strength buffer in which the cells are suspended during heating. Dissociation of histones is achieved by cell treatment with 0.08N HCl at 0 degree C, which a) increases accessibility of DNA to propidium iodide (and following the denaturation to the antibodies); b) lowers stability of DNA to thermal denaturation; c) decreases differences between various cell types due to variability in chromatin structure; and d) ensures more complete DNA denaturation. Cell heating (80-95 degrees C) at low ionic strength (1 mM Na+) eliminates the need for formamide and results in extensive and rapid DNA denaturation. The method was applied in Friend leukemia, L1210 and HL-60 cell lines, and to bone marrow, experimental animal tumor and primary human tumor cells.
Economic Systems and Rates of Polygyny (1990)

This paper examines the roles of primary subsistence base and women's contributions to food production in the etiology of polygyny. Cross-cultural data from the Ethonographic Atlas are employed. Polygyny is differentiated into categories of absent (monogamy only), occasional (less than 20% of all marriages), and frequent (20% or more of all marriages). The results show that polygyny is very likely to be allowed, but infrequently practiced, in exploitative and incipient agriculture economies. It is most likely to be widespread in herding and extensive agriculture economies, but decreases in" frequency as agricultural technology develops further. These patterns are explained by variation in the roles of men and women in subsistence production.in combination with variation in the labor-intensiveness of subsistence activities.
Modified LDLs are internalized by macrophages in part via macropinocytosis (1999)

Macrophage foam cell formation in vitro requires uptake of modified low density lipoproteins (LDL) such as acetylated LDL (AcLDL) and moderately oxidized LDL (OxLDL). Macrophages incubated with AcLDL and OxLDL, but not LDL, showed increased membrane ruffling as seen with time-lapse phase contrast video light microscopy. Modified LDLs stimulated circular membrane ruffles between 2 and 10 min after incubation. These membrane ruffles were readsorbed into the plasma membrane between 5 and 15 min later. Phase-bright macropinosomes formed at the base of the stimulated membrane ruffles. The fluid-phase marker lucifer yellow labeled the modified LDL stimulated macropinosomes. Modified LDLs stimulate fluid-phase uptake by 1.5-fold to threefold as measured with 14C-sucrose uptake. Transmission electron microscopy showed that gold conjugated AcLDL and OxLDL bound preferentially to membrane ruffles and were present in macropinosomes (diameter >0.2 pm) underneath these membrane ruffles. AcLDL and OxLDL were also present in clathrin-coated pits and endosomes. These studies suggest that modified lipoproteins stimulate macropinocytosis. AcLDL and OxLDL are partially internalized by macropinocytosis and partially internalized via clathrin-coated pit endocytosis.
Endothelial Nitric Oxide Synthase Stimulates Aneurysm Growth in Aged Mice (2008)

eNOS expression is reduced in both aged human and aged mouse endothelium and eNOS expression is linked to aneurysm expansion in aged but not young adult mice. These findings support the relevance of age-associated changes in eNOS expression in clinical aneurysmal disease.