gebhart/patrepeval huggingface dataset:
The role of dendritic cells and their immunometabolism in rheumatoid arthritis (2023)

Dendritic cells (DCs) play crucial roles in the pathogenesis of rheumatoid arthritis (RA), a prototypic autoimmune disease characterized by chronic synovitis and joint destruction. Conventional dendritic cells (cDCs) with professional antigen-presenting functions are enriched in the RA synovium. In the synovium, the cDCs are activated and show both enhanced migratory capacities and T cell activation in comparison with peripheral blood cDCs. Plasmacytoid dendritic cells, another subtype of DCs capable of type I interferon production, are likely to be tolerogenic in RA. Monocyte-derived dendritic cells (moDCs), once called "inflammatory DCs", are localized in the RA synovium, and they induce T-helper 17 cell expansion and enhanced proinflammatory cytokine production. Recent studies revealed that synovial proinflammatory hypoxic environments are linked to metabolic reprogramming. Activation of cDCs in the RA synovium is accompanied by enhanced glycolysis and anabolism. In sharp contrast, promoting catabolism can induce tolerogenic DCs from monocytes. Herein, we review recent studies that address the roles of DCs and their immunometabolic features in RA. Immunometabolism of DCs could be a potential therapeutic target in RA.
Decreased Heterogeneity of Capillary Plasma Flow in the Rat Whisker-Barrel Cortex during Functional Hyperemia (1996)

The pattern of capillary plasma perfusion was investigated in the rat brain during functional activation. Functional hyperemia was induced in the left whisker-barrel cortex by deflection of the right mystacial vibrissae for 2 min at frequencies of 1-7 Hz. Rats were decapitated under anesthesia 3-4 s after i.v. bolus injection of Evans blue dye. The steep increase of the arterial dye concentration ensures that divergent capillary plasma transit times result in unequal intracapillary dye concentrations. Plasma perfusion heterogeneity was determined from the coefficient of variation (CV) of Evans blue concentrations measured in numerous single capillaries of the whisker-barrel cortex. Functional hyperemia was quantified from measurements of CBF using the [14C]-iodoantipyrine technique in a second experimental group. CBF in the left whisker-barrel cortex increased with the stimulation frequency and was maximal at 5 Hz compared to the right side. Conversely, plasma perfusion heterogeneity decreased with stimulation frequency in a reciprocal way, being minimal at 5 Hz. Results indicate a decrease in the microcirculatory flow heterogeneity during functional hyperemia in the brain.
What makes a good bug report? (2008)

In software development, bug reports provide crucial information to developers. However, these reports widely differ in their quality. We conducted a survey among developers and users of APACHE, ECLIPSE, and MOZILLA to find out what makes a good bug report.
Design considerations for high-current photodetectors (1999)

This paper outlines the design considerations for gigahertz-bandwidth, high-current p-i-n photodiodes utilizing InGaAs absorbers. The factors being investigated are photodetector intrinsic region length, intrinsic region doping density, temperature effects, illumination spot size, illumination wavelength, frequency, and illumination direction. Space-charge calculations are used to determine optimal device geometry and conditions which maximize saturation photocurrent. A thermal model is developed to study the effects of temperature on high-current photodetector performance. The thermal and space-charge model results are combined to emphasize the importance of thin intrinsic region lengths to obtain high current. Finally, a comparison between surface-illuminated p-i-n structures and waveguide structures is made to differentiate between the problems associated with achieving high current in each structure and to outline techniques to achieve maximum performance.
Recognition of phonemes and words in singing (2010)

This paper studies the influence of n-gram language models in the recognition of sung phonemes and words. We train uni-, bi-, and trigram language models for phonemes and bi- and trigrams for words. The word-level language model is estimated from a textual lyrics database. In the recognition we use a hidden Markov model based phonetic recognizer adapted to singing voice. The models were tested on monophonic singing and on vocal lines separated from polyphonic music. On clean singing the phoneme recognition accuracies varied from 20% (no language model) to 39% (bigram) and on polyphonic music from 6% (no language model) to 20% (bigram). In word recognition, one fifth of the words were recognized in clean singing, the performance being lower on polyphonic music. We study the use of the recognition results in a query-by-singing application. Using the recognized words, we retrieve the songs by searching for the text in a text lyrics database. For the word recognition system having only 24% correct recognition rate, the first retrieved song is correct in 57% of the test cases.
Wide-color gamut multi-twist retarders (2015)

We show how highly chromatic Multi-Twist Retarder (MTR) films can be used to create a single-film color filter wherein the color may be selected only by the MTR orientation angle. By this approach, we can create multi- color images with just an MTR between polarizers. We study the design method and limits of the available color gamut possibilities in this approach, and experimentally demonstrate several designs of continuous and discrete patterns. This technique may be useful in art, displays, microscopy, and remote sensing.
Interaction of Sulfaphenazole Derivatives with Human Liver Cytochromes P450 2C:  Molecular Origin of the Specific Inhibitory Effects of Sulfaphenazole on CYP 2C9 and Consequences for the Substrate Binding Site Topology of CYP 2C9 (1996)

The effects of sulfaphenazole, 1, on typical activities catalyzed by human cytochromes P450 of the 1A, 3A, and 2C subfamilies expressed in yeast were studied. 1 acts as a strong, competitive inhibitor of CYP 2C9 (K(i) = 0.3 +/- 0.1 microM); it is much less potent toward CYP 2C8 and 2C18 (K(i) = 63 and 29 microM, respectively) and fails to inhibit CYP 1A1, 1A2, 3A4, and 2C19. From difference visible spectroscopy experiments using microsomes of yeast expressing various human P450s, 1 selectively interacts only with CYP 2C9 with the appearance of a peak at 429 nm as expected for the formation of a P450 Fe(III)-nitrogenous ligand complex (Ks = 0.4 +/- 0.1 microM). Comparative studies of the spectral interaction and inhibitory effects of twelve compounds related to 1 with CYP 2C9 showed that the aniline function of 1 is responsible for the formation of the iron-nitrogen bond of the 429 nm-absorbing complex and is necessary for the inhibitory effects of 1. The study of two new compounds synthesized during this work, in which the N-phenyl group of 1 was replaced with either an ethyl group or a 3,4-dichlorophenyl group, showed that the presence of an hydrophobic substituent at position 1 of the pyrazole function of 1 is required for a strong interaction with CYP 2C9. A model for the binding of 1 in the CYP 2C9 active site is proposed; that takes into account three major interactions that should be at the origin of the high-affinity and specific inhibitory effects of 1 toward CYP 2C9: (i) the binding of its nitrogen atom to CYP 2C9 iron, (ii) an ionic interaction of its SO2N- anionic site with a cationic residue of CYP 2C9, and (iii) an interaction of its N-phenyl group with an hydrophobic part of the protein active site.
Fake Photos in the News (2010)

Fake Photos in the News Tim Willis, Lynchburg College I can distinctly remember, from the 2004 presidential election, a picture of a young John Kerry sitting next to Jane Fonda as she was addressing an anti-Vietnam War protest.The picture was widely disseminated as part of a campaign to impugn Senator Kerry's character, and it was largely effective.Kerry would go on to lose that election; quite possibly that photograph played a role in his defeat.It is also worth noting that the picture was a fake.Ten years earlier, O
Neither Caspase‐3 nor DNA Fragmentation Factor Is Required for High Molecular Weight DNA Degradation in Apoptosis (1999)

In this paper, we show that there is a two-step process of DNA fragmentation in apoptosis; DNA is first cleaved to large fragments of 50-300 kb that are subsequently cleaved to smaller oligonucleosomes in some, but not all cells. Significantly, only the first stage is considered essential for cell death since some cells, for example human MCF7 breast carcinoma cells and human NT2 neuronal cells, do not show this behavior but still display normal nuclear morphological apoptotic changes. In cells that usually produce small fragments blocking the second (internucleosomal) stage of DNA fragmentation prevents neither nuclear condensation nor apoptosis. We are beginning to understand why the extent of DNA fragmentation during apoptosis varies enormously and why it appears to be a function of the cell type not the inducer. Presumably, this reflects the content of not only endonuclease activit(ies) but also on the ability of the cells to activate caspases, particularly caspase-3, and other proteases that may be involved in endonuclease activation. Since NT2 cells activate caspase-3, but do not correctly process DFF45, other factors must also impinge on the inevitability of that process.
Amino acid composition of α1/α2 domains and cytoplasmic tail of MHC class I molecules determine their susceptibility to human cytomegalovirus US11‐mediated down‐regulation (2003)

During co-evolution with its host, human cytomegalovirus has acquired multiple defense mechanisms to escape from immune recognition. In this study, we focused on US11, which binds to MHC class I heavy chains and mediates their dislocation to the cytosol and subsequent degradation by proteasomes. To examine which domains of class I heavy chains are involved in this process, we constructed chimeric HLA molecules of US11-sensitive and -insensitive class I molecules (HLA-A2 and HLA-G, respectively). Pulse-chase experiments were performed to evaluate protein stability and interactions between class I heavy chains and US11. Flow cytometry was employed to assess the effect of US11 on surface expression of the different chimeras. Our results indicate that the alpha1 and alpha2 domains of HLA molecules are important for the affinity of US11 association. However, the degradation efficiency seems to rely mostly on cytosolic tail residues. We found that the nonclassical HLA-G molecule is insensitive to US11-mediated degradation solely because it lacks essential tail residues. A deletion of the last two tail residues in full-length MHC class I molecules already caused a severe reduction in degradation efficiency. Altogether, our data provide new insights into the mechanism by which US11 down-regulates MHC class I molecules.
Effect of static stretch training on neural and mechanical properties of the human plantar‐flexor muscles (2003)

To determine the contributions of neural and mechanical mechanisms to the limits in the range of motion (ROM) about a joint, we studied the effects of 30 sessions of static stretch training on the characteristics of the plantar-flexor muscles in 12 subjects. Changes in the maximal ankle dorsiflexion and the torque produced during passive stretching at various ankle angles, as well as maximal voluntary contraction (MVC) and electrically induced contractions, were recorded after 10, 20, and 30 sessions, and 1 month after the end of the training program. Reflex activities were tested by recording the Hoffmann reflex (H reflex) and tendon reflex (T reflex) in the soleus muscle. Training caused a 30.8% (P < 0.01) increase in the maximal ankle dorsiflexion. This improved flexibility was associated (r(2) = 0.88; P < 0.001) with a decrease in muscle passive stiffness and, after the first 10 sessions only, with a small increase in passive torque at maximal dorsiflexion. Furthermore, both the H- and T-reflex amplitudes were reduced after training, especially the latter (-36% vs. -14%; P < 0.05). The MVC torque and the maximal rate of torque development were not affected by training. Although the changes in flexibility and passive stiffness were partially maintained 1 month after the end of the training program, reflex activities had already returned to control levels. It is concluded that the increased flexibility results mainly from reduced passive stiffness of the muscle-tendon unit and tonic reflex activity. The underlying neural and mechanical adaptation mechanisms, however, showed different time courses.
Nifuroxazide inhibits survival of multiple myeloma cells by directly inhibiting STAT3 (2008)

Constitutive activation of the transcription factor STAT3 contributes to the pathogenesis of many cancers, including multiple myeloma (MM). Since STAT3 is dispensable in most normal tissue, targeted inhibition of STAT3 is an attractive therapy for patients with these cancers. To identify STAT3 inhibitors, we developed a transcriptionally based assay and screened a library of compounds known to be safe in humans. We found the drug nifuroxazide to be an effective inhibitor of STAT3 function. Nifuroxazide inhibits the constitutive phosphorylation of STAT3 in MM cells by reducing Jak kinase autophosphorylation, and leads to down-regulation of the STAT3 target gene Mcl-1. Nifuroxazide causes a decrease in viability of primary myeloma cells and myeloma cell lines containing STAT3 activation, but not normal peripheral blood mononuclear cells. Although bone marrow stromal cells provide survival signals to myeloma cells, nifuroxazide can overcome this survival advantage. Reflecting the interaction of STAT3 with other cellular pathways, nifuroxazide shows enhanced cytotoxicity when combined with either the histone deacetylase inhibitor depsipeptide or the MEK inhibitor UO126. Therefore, using a mechanistic-based screen, we identified the clinically relevant drug nifuroxazide as a potent inhibitor of STAT signaling that shows cytotoxicity against myeloma cells that depend on STAT3 for survival.
Three-Dimensional Video Postproduction and Processing (2011)

This paper gives an overview of the state-of-the-art in 3-D video postproduction and processing as well as an outlook to remaining challenges and opportunities. First, fundamentals of stereography are outlined that set the rules for proper 3-D content creation. Manipulation of the depth composition of a given stereo pair via view synthesis is identified as the key functionality in this context. Basic algorithms are described to adapt and correct fundamental stereo properties such as geometric distortions, color alignment, and stereo geometry. Then, depth image-based rendering is explained as the widely applied solution for view synthesis in 3-D content creation today. Recent improvements of depth estimation already provide very good results. However, in most cases, still interactive workflows dominate. Warping-based methods may become an alternative for some applications in the future, which do not rely on dense and accurate depth estimation. Finally, 2-D to 3-D conversion is covered, which is an important special area for reuse of existing legacy 2-D content in 3-D. Here various advanced algorithms are combined in interactive workflows.
Afrocentrism and Freemasonry: (De) Constructing Myths about Egypt (1996)

A review of the book - 'Not Out of Africa: How Afrocentrism became an excuse to teach myth as history' is presented. The book analyses and debates on the Afrocentric myths and truths associated with Egyptian antiquity.
Pattern of Auxin and Cytokinin Responses for Shoot Meristem Induction Results from the Regulation of Cytokinin Biosynthesis by AUXIN RESPONSE FACTOR3     (2012)

De novo organ regeneration is an excellent biological system for the study of fundamental questions regarding stem cell initiation, cell fate determination, and hormone signaling. Despite the general belief that auxin and cytokinin responses interact to regulate de novo organ regeneration, the molecular mechanisms underlying such a cross talk are little understood. Here, we show that spatiotemporal biosynthesis and polar transport resulted in local auxin distribution in Arabidopsis (Arabidopsis thaliana), which in turn determined the cytokinin response during de novo shoot regeneration. Genetic and pharmacological interference of auxin distribution disrupted the cytokinin response and ATP/ADP ISOPENTENYLTRANSFERASE5 (AtIPT5) expression, affecting stem cell initiation and meristem formation. Transcriptomic data suggested that AUXIN RESPONSE FACTOR3 (ARF3) mediated the auxin response during de novo organ regeneration. Indeed, mutations in ARF3 caused ectopic cytokinin biosynthesis via the misexpression of AtIPT5, and this disrupted organ regeneration. We further showed that ARF3 directly bound to the promoter of AtIPT5 and negatively regulated AtIPT5 expression. The results from this study thus revealed an auxin-cytokinin cross talk mechanism involving distinct intermediate signaling components required for de novo stem cell initiation and shed new light on the mechanisms of organogenesis in planta.
ChemInform Abstract: Pharmacological Profile of a Novel Synthetic Inhibitor of 3‐Hydroxy‐3‐ methylglutaryl‐coenzyme A Reductase. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED (2015)

Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences ("markers") and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred.
Optical transmittance of a two-dimensional triangular photonic lattice (1995)

The optical transmittance of a slab of a two-dimensional photonic lattice composed of a triangular array of circular rods was calculated by means of the plane-wave expansion. This method naturally gives the specular and Bragg reflectivity as well. The comparison between the band structure of the relevant infinite lattice and the calculated transmittance showed a clear correspondence concerned with band gaps. However, it also showed a null coupling between the external radiation field and an internal electromagnetic mode in addition to a considerable amount of the energy transfer to the Bragg waves. This fact implies that the simple analysis of the spectra based on the state density is insufficient.
Principles of GNSS, Inertial, and Multisensor Integrated Navigation Systems, Second Edition (2013)

This newly revised and greatly expanded edition of the popular Artech House book Principles of GNSS, Inertial, and Multisensor Integrated Navigation Systems offers you a current and comprehensive understanding of satellite navigation, inertial navigation, terrestrial radio navigation, dead reckoning, and environmental feature matching . It provides both an introduction to navigation systems and an in-depth treatment of INS/GNSS and multisensor integration. The second edition offers a wealth of added and updated material, including a brand new chapter on the principles of radio positioning and a chapter devoted to important applications in the field. Other updates include expanded treatments of map matching, image-based navigation, attitude determination, acoustic positioning, pedestrian navigation, advanced GNSS techniques, and several terrestrial and short-range radio positioning technologies. The book shows you how satellite, inertial, and other navigation technologies work, and focuses on processing chains and error sources. In addition, you get a clear introduction to coordinate frames, multi-frame kinematics, Earth models, gravity, Kalman filtering, and nonlinear filtering. Providing solutions to common integration problems, the book describes and compares different integration architectures, and explains how to model different error sources. You get a broad and penetrating overview of current technology and are brought up to speed with the latest developments in the field, including context-dependent and cooperative positioning. DVD Included: Features eleven appendices, interactive worked examples, basic GNSS and INS MATLAB simulation software, and problems and exercises to help you master the material.
A concatenated decoding scheme for (1-D) partial response with matched spectral-null coding (2002)

Since the (1-D) partial response channel has a spectral null at DC, applying 3 DC-free code raises the minimum squared Euclidean distance from 2 for the uncoded channel to 4 for the matched spectral-null coded channel. Due to the complexity of the optimal decoder, there is interest in suboptimal decoders which have roughly the same performance as the optimal decoder. For DC-free block codes, we present a sub-optimal approach which treats the channel and the code separately using a two stage decoding process. The first stage consists of a maximum-likelihood detector for the uncoded (1-D) channel. The second stage is an error-event detector which uses the DC-free block code to detect and correct minimum distance error-events.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>