gebhart/patrepeval huggingface dataset:
Role of lung iron in determining the bacterial and host struggle in cystic fibrosis (2009)

Cystic fibrosis (CF) is the most common lethal genetic disorder in Caucasian populations. It is a multiorgan system disease that affects the lungs, gastrointestinal tract, liver, and pancreas. The majority of morbidity and mortality in CF relates to chronic airway infection with a variety of bacterial species, commencing in very early infancy, which results in lung destruction and ultimately organ failure (41, 43). This review focuses on iron homeostasis in the CF lung and its role in determining the success and chronicity of Pseudomonas aeruginosa infection. There have been previous excellent reviews regarding iron metabolism in the lower respiratory tract and mechanisms of P. aeruginosa iron acquisition, and we direct readers to these articles for further background reading (31, 53, 58, 77, 96). In this review, we have brought the "two sides of the coin" together to provide a holistic overview of the relationship between host and bacterial iron homeostasis and put this information into the context of current understanding on infection in the CF lung.
Multichannel Detrended Fluctuation Analysis Reveals Synchronized Patterns of Spontaneous Spinal Activity in Anesthetized Cats (2011)

The analysis of the interaction and synchronization of relatively large ensembles of neurons is fundamental for the understanding of complex functions of the nervous system. It is known that the temporal synchronization of neural ensembles is involved in the generation of specific motor, sensory or cognitive processes. Also, the intersegmental coherence of spinal spontaneous activity may indicate the existence of synaptic neural pathways between different pairs of lumbar segments. In this study we present a multichannel version of the detrended fluctuation analysis method (mDFA) to analyze the correlation dynamics of spontaneous spinal activity (SSA) from time series analysis. This method together with the classical detrended fluctuation analysis (DFA) were used to find out whether the SSA recorded in one or several segments in the spinal cord of the anesthetized cat occurs either in a random or in an organized manner. Our results are consistent with a non-random organization of the sets of neurons involved in the generation of spontaneous cord dorsum potentials (CDPs) recorded either from one lumbar segment (DFA-α mean = 1.04[Formula: see text]0.09) or simultaneously from several lumbar segments (mDFA-α mean = 1.01[Formula: see text]0.06), where α = 0.5 indicates randomness while α = 0.5 indicates long-term correlations. To test the sensitivity of the mDFA method we also examined the effects of small spinal lesions aimed to partially interrupt connectivity between neighboring lumbosacral segments. We found that the synchronization and correlation between the CDPs recorded from the L5 and L6 segments in both sides of the spinal cord were reduced when a lesion comprising the left dorsal quadrant was performed between the segments L5 and L6 (mDFA-[Formula: see text] = 0.992 as compared to initial conditions mDFA-α = 1.186). The synchronization and correlation were reduced even further after a similar additional right spinal lesion (mDFA-α = 0.924). In contrast to the classical methods, such as correlation and coherence quantification that define a relation between two sets of data, the mDFA method properly reveals the synchronization of multiple groups of neurons in several segments of the spinal cord. This method is envisaged as a useful tool to characterize the structure of higher order ensembles of cord dorsum spontaneous potentials after spinal cord or peripheral nerve lesions.
Correction of adenosine deaminase deficiency in cultured human T and B cells by retrovirus-mediated gene transfer. (1986)

A retroviral vector called SAX, containing the cloned human cDNA for adenosine deaminase (ADA), has been constructed and used to introduce the ADA gene into cultured T- and B-lymphocyte lines derived from patients with ADA deficiency. DNA analysis showed that the SAX vector was inserted intact into the T and B cells at approximately one copy per cell. The treated cells produced the characteristic isozymes of human ADA at a level similar to normal T and B lymphocytes. It is known that ADA-deficient lymphocytes are unusually sensitive to high levels of 2'-deoxyadenosine, and this is the mechanism thought to underlie the selective lymphocytotoxicity associated with ADA deficiency in vivo. Expression of the introduced ADA gene was sufficient to reverse the hypersensitivity of these genetically deficient lymphocytes to 2'-deoxyadenosine toxicity. These results support the suggestion that retroviral vector gene-delivery systems show promise for application to human gene therapy.
Multipolar dielectrophoretic and electrorotation theory (1996)

A new dyadic tensor representation for multipolar moments is used to formulate expressions for the dielectrophoretic force and electrorotational torque exerted on lossy spherical particles by an arbitrary electric field. The new tensor expressions for the moments satisfy the requirement of symmetry. When combined with previously derived expressions for the induced moments in terms of the electric field and its derivatives, the theory accommodates electrically linear spherical particles with any type of ohmic or dielectric loss in any sinusoidally-varying electric field. The special case of a plant protoplast suspended in an aqueous medium and subjected to a traveling electric field wave is chosen to demonstrate the theory's easy adaptation to the practical planar or multi-planar microelectrode geometries now used to move, rotate, or position small particles such as biological cells.
A new common integration region (int-3) for mouse mammary tumor virus on mouse chromosome 17 (1987)

Mus musculus subsp. musculus (Czech II) mammary tumor DNA frequently contains an integrated proviral genome of the mouse mammary tumor virus (MMTV) within a specific 0.5-kilobase-pair region of the cellular genome (designated int-3). Viral integration at this site results in activation of expression of an adjacent cellular gene. We mapped int-3 to mouse chromosome 17 by analysis of PstI-restricted cellular DNAs from mouse-hamster somatic cell hybrids. Restriction analysis of cellular DNA from (C3H/OuJ X Czech II) X Czech II backcross mice established the gene order T-H-2-int-3. These results demonstrated that the int-3 locus is distinct from two other common integration regions for mouse mammary tumor virus (designated int-1 and int-2) in mammary tumor DNA and suggest that several cellular genes may be at risk for virally induced activation during mammary tumor development.
Radiation entropy flux and entropy production of the Earth system (2010)

[1] The study of the Earth's radiation entropy flux at the top of the atmosphere is reviewed with an emphasis on its estimation methods. Existing expressions for calculating radiation entropy flux scattered in different disciplines are surveyed, and their applicabilities are examined. It is found that the Earth's net radiation entropy flux estimated from these various expressions can differ substantially, more than the typical value of the entropy production rate associated with the atmospheric latent heat process. Comparison analysis shows that the commonly used expression of radiation entropy flux as the ratio of radiation energy flux to absolute temperature underestimates the Earth's radiation entropy flux by >30%. Theoretical analysis reveals that the large difference in the Earth's reflected solar radiation entropy flux among the different expressions arises mainly from the difference of the Earth's reflection properties (i.e., Lambertian or specular) assumed in these expressions. For the Earth system with typical shortwave albedo of 0.30 and longwave emissivity between 0.50 and 1.00, the Earth's net radiation entropy flux derived from the most accurate Planck's spectral expression ranges from 1.272 to 1.284 W m−2 K−1, amounting to the overall Earth's entropy production rate from 6.481 × 1014 to 6.547 × 1014 W K−1.
Androgen receptors beyond prostate cancer: an old marker as a new target (2014)

Androgen receptors (ARs) play a critical role in the development of prostate cancer. Targeting ARs results in important salutary effects in this malignancy. Despite mounting evidence that ARs also participate in the pathogenesis and/or progression of diverse tumors, exploring the impact of hormonal manipulation of these receptors has not been widely pursued beyond prostate cancer. This review describes patterns of AR expression in a spectrum of cancers, and the potential to exploit this knowledge in the clinical therapeutic setting.
Antigen-specific immunotherapy: is it a real possibility to combat T-cell-mediated autoimmunity? (1994)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Hogwild: A Lock-Free Approach to Parallelizing Stochastic Gradient Descent (2011)

Stochastic Gradient Descent (SGD) is a popular algorithm that can achieve state-of-the-art performance on a variety of machine learning tasks. Several researchers have recently proposed schemes to parallelize SGD, but all require performance-destroying memory locking and synchronization. This work aims to show using novel theoretical analysis, algorithms, and implementation that SGD can be implemented without any locking. We present an update scheme called HOGWILD! which allows processors access to shared memory with the possibility of overwriting each other's work. We show that when the associated optimization problem is sparse, meaning most gradient updates only modify small parts of the decision variable, then HOGWILD! achieves a nearly optimal rate of convergence. We demonstrate experimentally that HOGWILD! outperforms alternative schemes that use locking by an order of magnitude.
Lattice-ladder decorrelation filters developed for co-channel speech separation (2002)

The previously proposed lattice-ladder adaptive decorrelation filtering (LL-ADF) algorithm (Ken and Zhao 1999) is further studied and improved in this work, with the aim of developing a more efficient co-channel speech separation system. The effect of the joint linear predictions is first analyzed and the conversions between the lattice coefficients and the prediction and filter vectors are formulated. The implementation issues on the estimation of lattice coefficients are then discussed and the adaptation equations are further refined. Experimental results demonstrate the effectiveness of the algorithm in reducing cross-interference between co-channel speech sources as well as the significant performance improvement over the previous direct-form ADF algorithm. A simplified LL-ADF is also proposed as a compromise between computational cost and system performance.
Probiotic therapy for the prevention and treatment of Clostridium difficile-associated diarrhea: a systematic review (2005)

Studies conducted to date provide insufficient evidence for the routine clinical use of probiotics to prevent or treat CDAD. Better designed and larger studies are needed.
Endometrial Carcinoma (1996)

Uterine cancer is the fourth most frequent cancer in women, with an estimated 34,000 cases and 6000 deaths in the United States in 1996.1 It is the most curable of the 10 most common cancers in women and the most frequent and curable of the gynecologic cancers. Ninety-seven percent of all cancers of the uterus arise from the glands of the endometrium and are known as endometrial carcinomas. The remaining 3 percent of uterine cancers are sarcomas, which are not discussed here. Numerous changes in the pathological description of endometrial cancer, identification of prognostic variables, staging, and treatment have occurred . . .
PDGF Receptor and its Antagonists: Role in Treatment of PAH (2009)

Pulmonary Hypertension is a severe lung disease, which is characterized by vasoconstriction and remodelling of the vessel wall. Mostly addressing the increased vascular tone, prostacyclin and its analogues, endothelin-receptor antagonists and phosphodiesterase type 5 inhibitors have been approved for treatment of PAH and represent the current therapeutic options. Mechanistically, these vasodilators decrease pulmonary vascular resistance and reduce thereby shear stress, which is a strong proliferative stimulus per se. Beside the development of new vasodilators, current research focuses on the development of causal treatment regimens aiming a normalization of the vessel structure. Mechanistically, increased proliferation, migration and a resistance to apoptosis of vascular cells represent key events in disease progression. In this context, tyrosine kinase inhibitors like imatinib have been shown to possess reverse remodelling potential in preclinical models of pulmonary hypertension by inducing apoptosis and blocking proliferation. This book chapter describes the role of the platelet derived growth factor (PDGF) receptor and its antagonists for treatment of pulmonary hypertension.
The lymphocyte glycoprotein CD6 contains a repeated domain structure characteristic of a new family of cell surface and secreted proteins. (1991)

The isolation, characterization, and expression of a full-length cDNA encoding the human T cell glycoprotein CD6 is described. COS cells transfected with the CD6 clone express a 90-kD protein that reacts with all available anti-CD6 monoclonal antibodies. RNA blot hybridization analysis indicates that CD6 transcripts are predominantly restricted to cells in the T lineage. The predicted CD6 sequence is 468 amino acids long, with the typical features of a type I integral membrane protein. The cytoplasmic domain of CD6 contains two serine residues, one or both of which are substrates for phosphorylation during T cell activation. The extracellular domain of CD6 is significantly related to the extracellular domain of the human and mouse T cell antigen CD5, the cysteine-rich domain of the bovine and mouse type I macrophage scavenger receptor, the extracellular domain of the sea urchin spermatozoa protein that crosslinks the egg peptide speract, the mammalian complement factor 1, and the human lung tumor antigen L3. These molecules, therefore, constitute a new gene superfamily that is well conserved across species boundaries.
Two-Dimensional Phase Unwrapping: Theory, Algorithms, and Software (1998)

Introduction to Phase Unwrapping. Line Integrals, Residues, and 2-D Phase Unwrapping. Phase Data, Quality Maps, Masks, and Filters. Path-Following Methods. Minimum-Norm Methods. Comparisons and Conclusion. Appendices. Index.
Microbial Incorporation of Fatty Acids Derived From n -Alkanes Into Glycerides and Waxes (1964)

When n-alkanes with 13 to 20 carbon atoms were fed to a Nocardia closely related to N. salmonicolor, the produced cellular triglycerides and aliphatic waxes invariably contained fatty acids with an even or an odd number of carbon atoms subject to this feature of the n-alkane substrate. Beta-oxidation and C(2) addition are both operative, as evidenced by the spectra of fatty acids incorporated into the cellular lipid components. There is no distinction in the rate of microbial incorporation of the odd-or even-numbered carbon chains. The fatty acids are apparently directly derived from the long chain n-alkanes, rather than synthesized via the classic C(2)-condensation route. The alcohol component of waxes produced by the Nocardia is invariably of the same chain length as the n-alkane substrate.
Autophagy mitigates metabolic stress and genome damage in mammary tumorigenesis (2007)

Autophagy is a catabolic process involving self-digestion of cellular organelles during starvation as a means of cell survival; however, if it proceeds to completion, autophagy can lead to cell death. Autophagy is also a haploinsufficient tumor suppressor mechanism for mammary tumorigenesis, as the essential autophagy regulator beclin1 is monoallelically deleted in breast carcinomas. However, the mechanism by which autophagy suppresses breast cancer remains elusive. Here we show that allelic loss of beclin1 and defective autophagy sensitized mammary epithelial cells to metabolic stress and accelerated lumen formation in mammary acini. Autophagy defects also activated the DNA damage response in vitro and in mammary tumors in vivo, promoted gene amplification, and synergized with defective apoptosis to promote mammary tumorigenesis. Therefore, we propose that autophagy limits metabolic stress to protect the genome, and that defective autophagy increases DNA damage and genomic instability that ultimately facilitate breast cancer progression.
Senile dementia of the Alzheimer type (1983)

The prevalence of severe dementia in the United States is about 1.3 million cases, of which at least 50 to 60% are of the Alzheimer type. Severe dementia of the Alzheimer type is found rarely in a clearly dominant pattern, although often one or more relatives are affected. Down's syndrome in adults is often associated with Alzheimer changes. The diagnosis is a clinicopathological one; there is a considerable error rate in the clinical diagnosis early in the course of the disease, especially in regard to dementia in depression. The differential diagnosis involves a great many disorders, including multi-infarct dementia, tumors, subdural hematomas, and others. Physiological aspects of Alzheimer's disease include a diffusely slow electroencephalogram, reduced cerebral blood flow, and particular patterns noted on positron emission tomographic scanning. The latter technique has also demonstrated that oxygen extraction is normal in Alzheimer's disease, thus excluding ischemia from possible pathogenetic factors. Morphological changes, that is, the presence of plaques and tangles, are widely distributed in neocortex, paleocortex, and many deep gray areas down through the pontine tegmentum, but largely exclude the basal ganglia, thalamus, and substantia nigra. Numerous plaques without neocortical tangles are found in many demented persons older than 75 years. A severe loss of large neocortical neurons is characteristic of the disease. The chemical nature of the paired helical filaments that make up the neurofibrillary tangle has not yet been ascertained. Neurons are markedly deficient in the basal forebrain nuclei, and this deficiency may account for the severe diminution of choline acetyltransferase and acetylcholine in the neocortex and paleocortex. Muscarinic cholinergic receptors are present in normal amounts. Norepinephrine is reduced in some cases, and somatostatin in most. Substance P is low in severe cases. The etiology of the disorder is unknown and the role of aluminum is disputed. Management of patients with Alzheimer's disease is difficult, and neuroleptics are to be used with great caution because of their side effects. Substrate therapy has not been effective; physostigmine improves memory but is not suitable for general use. Trophic factors, gangliosides, and aluminum chelation are being investigated for use in pharmacological intervention.
Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages (2012)

CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages.
Attenuation of HIV-1 replication in macrophages by cannabinoid receptor 2 agonists (2013)

Infiltrating monocytes and macrophages play a crucial role in the progression of HIV-1 infection in the CNS. Previous studies showed that activation of the CB₂ can attenuate inflammatory responses and affect HIV-1 infectivity in T cells and microglia. Here, we report that CB₂ agonists can also act as immunomodulators on HIV-1-infected macrophages. First, our findings indicated the presence of elevated levels of CB₂ expression on monocytes/macrophages in perivascular cuffs of postmortem HIV-1 encephalitic cases. In vitro analysis by FACS of primary human monocytes revealed a step-wise increase in CB₂ surface expression in monocytes, MDMs, and HIV-1-infected MDMs. We next tested the notion that up-regulation of CB₂ may allow for the use of synthetic CB₂ agonist to limit HIV-1 infection. Two commercially available CB₂ agonists, JWH133 and GP1a, and a resorcinol-based CB₂ agonist, O-1966, were evaluated. Results from measurements of HIV-1 RT activity in the culture media of 7 day-infected cells showed a significant decrease in RT activity when the CB₂ agonist was present. Furthermore, CB₂ activation also partially inhibited the expression of HIV-1 pol. CB₂ agonists did not modulate surface expression of CXCR4 or CCR5 detected by FACS. We speculate that these findings indicate that prevention of viral entry is not a central mechanism for CB₂-mediated suppression in viral replication. However, CB₂ may affect the HIV-1 replication machinery. Results from a single-round infection with the pseudotyped virus revealed a marked decrease in HIV-1 LTR activation by the CB₂ ligands. Together, these results indicate that CB₂ may offer a means to limit HIV-1 infection in macrophages.
Role of Particle Size in Individual and Competitive Diffusion of Carboxylic Acid Derivatized Colloidal Gold Particles in Thermally Evaporated Fatty Amine Films (1999)

We have recently shown that nanocomposites of colloidal particles in a fatty lipid matrix can be grown via a diffusion process controlled by selective electrostatic interactions. In this paper, a detailed investigation of the diffusion of carboxylic acid derivatized gold colloidal particles of different sizes into thermally evaporated octadecylamine films using quartz crystal microgravimetry (QCM), transmission electron microscopy, and UV−vis absorption and Fourier transform infrared (FTIR) spectroscopies is described. The QCM kinetics of gold cluster incorporation has been analyzed in terms of a one-dimensional Fickian-type diffusion model, and it is found that the cluster diffusivity increases with decreasing cluster size. The pH at which maximum cluster incorporation in the amine occurs was found to be dependent on the cluster size as well. FTIR spectroscopy of the fatty amine-gold particle composites indicated weak coupling of the clusters to the protonated amine groups as well as interesting cluster size dependent changes in the amine and methylene antisymmetric deformations as well as the methylene scissoring bands. In a competitive diffusion process of large and small gold particles, it was observed that bigger gold particles were preferentially incorporated into the amine matrix even though the cluster diffusivity is higher for the smaller gold particles.