gebhart/patrepeval huggingface dataset:
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology (2013)

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).
Therapeutic strategies for tau mediated neurodegeneration (2012)

Based on the amyloid hypothesis, controlling β-amyloid protein (Aβ) accumulation is supposed to suppress downstream pathological events, tau accumulation, neurodegeneration and cognitive decline. However, in recent clinical trials, Aβ removal or reducing Aβ production has shown limited efficacy. Moreover, while active immunisation with Aβ resulted in the clearance of Aβ, it did not prevent tau pathology or neurodegeneration. This prompts the concern that it might be too late to employ Aβ targeting therapies once tau mediated neurodegeneration has occurred. Therefore, it is timely and very important to develop tau directed therapies. The pathomechanisms of tau mediated neurodegeneration are unclear but hyperphosphorylation, oligomerisation, fibrillisation and propagation of tau pathology have been proposed as the likely pathological processes that induce loss of function or gain of toxic function of tau, causing neurodegeneration. Here we review the strategies for tau directed treatments based on recent progress in research on tau and our understanding of the pathomechanisms of tau mediated neurodegeneration.
Scanning probe electrospray ionization for ambient mass spectrometry (2012)

The method, named scanning probe electrospray ionization (SPESI), promises to be a simple and unique approach toward direct sampling and ionization methodology.
许诺、许诺:马克思和德曼的关于言语行为、文学和政治经济学诸理论之异同 (2001)

马克思主义美学可理解为马克思本人的美学,然而也经常被理解为由马克思主义引申出来的美学理论。这一理论附属于马克思政治经济批判,也就是马克思关于劳动、生产、商品价值、周期、货币、资金、剩余价值、拜物教、阶级斗争、意识形态、上层建筑、无产阶级专政的观
Improved tomographic imaging of wavelength scanning digital holographic microscopy by use of digital spectral shaping (2007)

The technique of wavelength scanning digital holographic microscopy (WSDHM) is improved by use of a digital spectral shaping method which is used to suppress the sidelobes of the amplitude modulation function in WSDHM for non-Gaussian-shaped source spectra. Spurious structures caused by sidelobes can be eliminated in tomographic imaging and the performance of the tomographic system greatly improved. Detailed theoretical analysis is given. Both simulation and experimental results are presented to verify the idea.
Psychological Stress and Mitochondria: A Systematic Review (2018)

Overall, evidence supports the notion that acute and chronic stressors influence various aspects of mitochondrial biology, and that chronic stress exposure can lead to molecular and functional recalibrations among mitochondria. Limitations of current animal and human studies are discussed. Maladaptive mitochondrial changes that characterize this subcellular state of stress are termed mitochondrial allostatic load. Prospective studies with sensitive measures of specific mitochondrial outcomes will be needed to establish the link between psychosocial stressors, emotional states, the resulting neuroendocrine and immune processes, and mitochondrial energetics relevant to mind-body research in humans.
Optimisation of pulse parameters in vitro for in vivo electrochemotherapy. (2002)

The aim of our study was to optimise electric pulse parameters for electrochemotherapy by sampling the space of pulse parameter variables using systematic in vitro experiments. For this purpose we defined parameters that describe the effectiveness of different sets of electric pulse parameters in vitro and combined them into an objective function that characterises requirements for successful electrochemotherapy. The objective function values were calculated for all the sets of electric pulse parameters included in in vitro experiments. Similar values were grouped together by hierarchical clustering. The 'electrochemotherapeutic' effectiveness of two sets of pulse parameters (8 pulses, 100 micros, 1 Hz and 1 pulse, 1000 micros, 1 Hz), which belong to the most efficient cluster, and one set of pulse parameters (16 pulses, 20 ms, 1 Hz), which belongs to the least efficient cluster, was tested in vivo on a murine tumor model. The sets of pulse parameters from the most efficient cluster had comparable effects in vivo, while the electrochemotherapy with the set of pulse parameters from the least efficient cluster was less effective. Our results demonstrated that electric pulse parameters for effective in vivo application can be determined from in vitro experiments considering application specifications.
Bovine Mononuclear Leukocyte Subpopulations in Peripheral Blood and Mammary Gland Secretions During Lactation (1992)

Florescence flow cytometry and monoclonal antibodies were used to analyze the composition of leukocytes from peripheral blood and mammary gland secretions. Samples were obtained from Holstein dairy cows, free of IMI, at six time points during the lactation cycle. The percentage of monocytes in peripheral blood mononuclear cells varied from 15 to 31%; the lowest percentage occurred at the early nonlactation period. The percentage of T lymphocytes from mammary gland secretions varied from 16% during the periparturient period to 62% at late lactation. The B lymphocytes varied from 7% at late lactation to 25% during the periparturient period. Macrophages varied from 21 to 69%; the highest percentage occurred during the periparturient period. The mean ratio of CD4+:CD8+ T lymphocytes in the peripheral blood and mammary gland secretions was 1.53 and .85, respectively. A subpopulation of activated CD8+ T lymphocytes present in mammary gland secretions throughout the lactation cycle coexpressed a new activation molecule, ACT2. Increases in the proportion of CD8+ T lymphocytes were associated with an increase in the percentage of CD8+, ACT2+ T lymphocytes. Activated CD8+ T lymphocytes may play an important role in the regulation and expression of the local immune response to pathogens.
A lock-docking oligo(dT) primer for 5' and 3' RACE PCR. (1992)

We describe a method that can be used to obtain and sequence 3' and 5' ends of cDNA transcripts directly from PCR products. The method employs a modified oligo(dT) primer that enables it to "lock-dock" at the junction of gene-specific cDNA sequence and a natural (3') or appended (5') poly(A) tail. As a result, discrete, first-round PCR products are obtained that are easily isolated and sequenced directly.
Transition metal ions within human atherosclerotic lesions can catalyse the oxidation of low density lipoprotein by macrophages (1995)

The oxidation of low density lipoprotein (LDL) in the arterial wall may contribute to atherogenesis. The oxidation of LDL by cells usually requires catalytically active transition metal ions. We show here some that gruel samples from human advanced atherosclerotic lesions are capable of catalysing the oxidation of LDL by macrophages as measured by thiobarbituric acid-reactive substances, enhanced electrophoretic mobility and increased macrophage uptake. This catalysis could be inhibited by pretreatment of the gruel with Chelex-100, which binds transition metal ions. The presence of catalytically active transition metal ions in atherosclerotic lesions may help to explain why LDL oxidation occurs at these sites.
Inflammation and Age-Related Macular Degeneration (AMD) (2011)

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly. The cause of AMD is complex and many risk factors have been implicated including age, family history (genetics), diet, smoking, and other environmental risk factors. Over the past decade, studies has found that inflammation play a large role in the pathogenesis of age-related macular degeneration (AMD). In fact, the main genetic changes (polymorphism) associated with AMD were found to be genes that regulate inflammation, most notably complement Factor H. This review ties together many studies done over the past decade to give us new insight into the role inflammation plays in the development of AMD.
STYPANDRA IMBRICATA (“BLINDGRASS”) TOXICOSIS IN GOATS AND SHEEP—CLINICAL AND PATHOLOGIC FINDINGS IN 4 FIELD CASES (1981)

Two goats and 2 sheep from field outbreaks of Stypandra imbricata toxicosis had severe lesions in the retina, optic nerves and white matter of the central nervous system. Clinical, ophthalmoscopic, fluorescein angiographic, electroretinographic and histologic atrophy, necrosis and degeneration of axons in the optic nerves and optic tracts and status spongiosus of cerebral white matter.
Bioactive compounds produced by cyanobacteria (1996)

Cyanobacteria produce a large number of compounds with varying bioactivities. Prominent among these are toxins: hepatotoxins such as microcystins and nodularins and neurotoxins such as anatoxins and saxitoxins. Cytotoxicity to tumor cells has been demonstrated for other cyanobacterial products, including 9-deazaadenosine, dolastatin 13 and analogs. A number of compounds in cyanobacteria are inhibitors of proteases --micropeptins, cyanopeptolins, oscillapeptin, microviridin, aeruginosins --and other enzymes, while still other compounds have no recognized biological activities. In general cyclic peptides and depsipeptides are the most common structural types, but a wide variety of other types are also found: linear peptides, guanidines, phosphonates, purines and macrolides. The close similarity or identity in structures between cyanobacterial products and compounds isolated from sponges, tunicates and other marine invertebrates suggests the latter compounds may be derived from dietary or symbiotic blue-green algae.
Electronic Transport Properties of Individual Chemically Reduced Graphene Oxide Sheets (2007)

Individual graphene oxide sheets subjected to chemical reduction were electrically characterized as a function of temperature and external electric fields. The fully reduced monolayers exhibited conductivities ranging between 0.05 and 2 S/cm and field effect mobilities of 2-200 cm2/Vs at room temperature. Temperature-dependent electrical measurements and Raman spectroscopic investigations suggest that charge transport occurs via variable range hopping between intact graphene islands with sizes on the order of several nanometers. Furthermore, the comparative study of multilayered sheets revealed that the conductivity of the undermost layer is reduced by a factor of more than 2 as a consequence of the interaction with the Si/SiO2 substrate.
Slepian-Wolf Coded Nested Lattice Quantization for Wyner-Ziv Coding: High-Rate Performance Analysis and Code Design (2006)

Nested lattice quantization provides a practical scheme for Wyner-Ziv coding. This paper examines the high-rate performance of nested lattice quantizers and gives the theoretical performance for general continuous sources. In the quadratic Gaussian case, as the rate increases, we observe an increasing gap between the performance of finite-dimensional nested lattice quantizers and the Wyner-Ziv distortion-rate function. We argue that this is because the boundary gain decreases as the rate of the nested lattice quantizers increases. To increase the boundary gain and ultimately boost the overall performance, a new practical Wyner-Ziv coding scheme called Slepian-Wolf coded nested lattice quantization (SWC-NQ) is proposed, where Slepian-Wolf coding is applied to the quantization indices of the source for the purpose of compression with side information at the decoder. Theoretical analysis shows that for the quadratic Gaussian case and at high rate, SWC-NQ performs the same as conventional entropy-coded lattice quantization with the side information available at both the encoder and the decoder. Furthermore, a nonlinear minimum mean-square error (MSE) estimator is introduced at the decoder, which is theoretically proven to degenerate to the linear minimum MSE estimator at high rate and experimentally shown to outperform the linear estimator at low rate. Practical designs of one- and two-dimensional nested lattice quantizers together with multilevel low-density parity-check (LDPC) codes for Slepian-Wolf coding give performance close to the theoretical limits of SWC-NQ
Skull base and calvarial deformities: association with intracranial changes in craniofacial syndromes. (1996)

A wide range of neuroimaging abnormalities are present in the craniofacial syndromes. Some of these are clearly primary, whereas others appear to be related to the small skull base and sutural synostoses. MR venography may prove useful in defining the cause of some of the associated anomalies.
An Official ATS/ERS/JRS/ALAT Statement: Idiopathic Pulmonary Fibrosis: Evidence-based Guidelines for Diagnosis and Management (2011)

This document is an international evidence-based guideline on the diagnosis and management of idiopathic pulmonary fibrosis, and is a collaborative effort of the American Thoracic Society, the European Respiratory Society, the Japanese Respiratory Society, and the Latin American Thoracic Association. It represents the current state of knowledge regarding idiopathic pulmonary fibrosis (IPF), and contains sections on definition and epidemiology, risk factors, diagnosis, natural history, staging and prognosis, treatment, and monitoring disease course. For the diagnosis and treatment sections, pragmatic GRADE evidence-based methodology was applied in a question-based format. For each diagnosis and treatment question, the committee graded the quality of the evidence available (high, moderate, low, or very low), and made a recommendation (yes or no, strong or weak). Recommendations were based on majority vote. It is emphasized that clinicians must spend adequate time with patients to discuss patients' values and preferences and decide on the appropriate course of action.
Characterization of dull1, a Maize Gene Coding for a Novel Starch Synthase (1998)

The maize dull1 (du1) gene is a determinant of the structure of endosperm starch, and du1- mutations affect the activity of two enzymes involved in starch biosynthesis, starch synthase II (SSII) and starch branching enzyme IIa (SBEIIa). Six novel du1- mutations generated in Mutator-active plants were identified. A portion of the du1 locus was cloned by transposon tagging, and a nearly full-length Du1 cDNA sequence was determined. Du1 codes for a predicted 1674-residue protein, comprising one portion that is similar to SSIII of potato, as well as a large unique region. Du1 transcripts are present in the endosperm during the time of starch biosynthesis, but the mRNA was undetectable in leaf or root tissue. The predicted size of the Du1 gene product and its expression pattern are consistent with those of maize SSII. The Du1 gene product contains two repeated regions in its unique N terminus. One of these contains a sequence identical to a conserved segment of SBEs. We conclude that Du1 codes for a starch synthase, most likely SSII, and that secondary effects of du1- mutations, such as reduction of SBEIIa, result from the primary deficiency in this starch synthase.
Server operating systems (1996)

We introduce server operating systems, which are sets of abstractions and runtime support for specialized, high-performance server applications. We have designed and are implementing a prototype server OS with support for aggressive specialization, direct device-to-device access, an event-driven organization, and dynamic compiler-assisted ILP. Using this server OS, we have constructed an HTTP server that outperforms servers running on a conventional OS by more than an order of magnitude and that can safely timeshare the hardware platform with other applications.
Nonadhesive Alginate Hydrogels Support Growth of Pluripotent Stem Cell-Derived Intestinal Organoids (2019)

Human intestinal organoids (HIOs) represent a powerful system to study human development and are promising candidates for clinical translation as drug-screening tools or engineered tissue. Experimental control and clinical use of HIOs is limited by growth in expensive and poorly defined tumor-cell-derived extracellular matrices, prompting investigation of synthetic ECM-mimetics for HIO culture. Since HIOs possess an inner epithelium and outer mesenchyme, we hypothesized that adhesive cues provided by the matrix may be dispensable for HIO culture. Here, we demonstrate that alginate, a minimally supportive hydrogel with no inherent cell instructive properties, supports HIO growth in vitro and leads to HIO epithelial differentiation that is virtually indistinguishable from Matrigel-grown HIOs. In addition, alginate-grown HIOs mature to a similar degree as Matrigel-grown HIOs when transplanted in vivo, both resembling human fetal intestine. This work demonstrates that purely mechanical support from a simple-to-use and inexpensive hydrogel is sufficient to promote HIO survival and development.
Formation of 8-hydroxydeoxyguanosine in liver DNA of rats following long-term exposure to a peroxisome proliferator. (1989)

The mechanism by which nongenotoxic peroxisome proliferators induce hepatocellular carcinomas in rats and mice remains intriguing. The available experimental evidence suggests that the proliferation of peroxisomes and induction of peroxisome-associated enzymes results in oxidative stress which then leads to tumorigenesis. However, so far no direct evidence for oxidative DNA damage in livers of peroxisome proliferator-treated animals has been established. In the present study we have examined the DNA obtained from the livers of rats treated with ciprofibrate, a potent peroxisome proliferator, for variable periods of time for 8-hydroxydeoxyguanosine (8-OH-dG), an adduct that results from the damage of DNA caused by hydroxyl radical. Administration of ciprofibrate in diet at a concentration of 0.025% for 16, 28, 36, or 40 weeks resulted in progressive increases in the levels of 8-OH-dG. At 16, 28, and 40 weeks of ciprofibrate treatment, the 8-OH-dG in the liver DNA was significantly increased as compared to controls. This increase in 8-OH-dG levels is attributed to persistent peroxisome proliferation resulting from chronic ciprofibrate treatment as no increase in 8-OH-dG was found in liver DNA of rats that received a single large dose of ciprofibrate. The results of this study clearly demonstrate, for the first time, that persistent proliferation of peroxisomes leads to specific oxidative DNA damage.
Oxygen Diffusion and Permeability in Alkylaminothionylphosphazene Films Intended for Phosphorescence Barometry Applications (2000)

This paper describes the application of a technique based on luminescence quenching to measure the diffusivity and permeability of molecular oxygen in a series of poly(n-alkylaminothionylphosphazenes) (CnPTP) and in un-cross-linked high molecular weight PDMS. The glass transition temperatures (Tg) of these polymers decrease from 4 °C for n = 2 to −18 °C for n = 6. Experiments performed on thin films of these highly permeable polymers show that oxygen diffusivity is sensitive to the microstructure of these polymers and that the diffusion coefficient for oxygen increases as Tg decreases. In contrast, the oxygen solubility in these polymers is not very sensitive to the nature of the alkyl substituent. Both the oxygen diffusion coefficient DO2 and the oxygen solubility SO2 are smaller for this series of polymers than for PDMS.
The Incidence and Epidemiology of Hepatocellular Carcinoma: A Global and Regional Perspective (2010)

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, and the burden of this devastating cancer is expected to increase further in coming years. The collection and analysis of epidemiologic HCC data will play a critical role in guiding future disease prevention strategies and optimizing patient management. Previous epidemiologic studies have highlighted striking global variations in the incidence of HCC, which is particularly high in much of east Asia and sub-Saharan Africa, and lower, but on the increase, in North America and most of Europe. This variation appears to be related to the complex etiology of HCC, with different risk factors, primarily infection with hepatitis B or hepatitis C virus, responsible for driving HCC incidence rates in different regions. Although previous studies have contributed considerably to the knowledge of HCC epidemiology, there are limitations associated with the currently available data, which arise from studies performed at different times in the past, using varying methodologies, and with diverse patient populations. A new and global approach to the study of HCC epidemiology is required if HCC disease prevention and treatment strategies are to be adequately directed and supported in coming years.
Functional diversity of bitter taste receptor TAS2R16 in primates (2012)

In mammals, bitter taste is mediated by TAS2R genes, which belong to the large family of seven transmembrane G protein-coupled receptors. Because TAS2Rs are directly involved in the interaction between mammals and their dietary sources, it is likely that these genes evolved to reflect species-specific diets during mammalian evolution. Here, we investigated the sensitivities of TAS2R16s of various primates by using a cultured cell expression system, and found that the sensitivity of each primate species varied according to the ligand. Especially, the sensitivity of TAS2R16 of Japanese macaques to salicin was much lower than that of human TAS2R16, which was supported by behavioural tests. These results suggest the possibility that bitter-taste sensitivities evolved independently by replacing specific amino acid residues of TAS2Rs in different primate species to adapt to food items they use.
THE ACTION OF PHLORIZIN ON THE EXCRETION OF GLUCOSE, XYLOSE, SUCROSE, CREATININE AND UREA BY MAN (1933)

Although phlorizin has been used mostly in the lower animals, its administration to man is
Potential Contribution of a Novel Antifibrotic Factor, Hepatocyte Growth Factor, to Prevention of Myocardial Fibrosis by Angiotensin II Blockade in Cardiomyopathic Hamsters (2000)

Here, we demonstrated that Ang II blockade prevented myocardial fibrosis in the cardiomyopathic hamster, accompanied by a significant increase in cardiac HGF. Overall, increase in local HGF expression may participate in the prevention of myocardial injury by Ang II blockade through its antifibrotic action.