gebhart/patrepeval huggingface dataset:
Microbial Communities and Chemosynthesis in Yellowstone Lake Sublacustrine Hydrothermal Vent Waters (2011)

Five sublacustrine thermal spring locations from 1 to 109 m water depth in Yellowstone Lake were surveyed by 16S ribosomal RNA gene sequencing in relation to their chemical composition and dark CO(2) fixation rates. They harbor distinct chemosynthetic bacterial communities, depending on temperature (16-110°C) and electron donor supply (H(2)S <1 to >100 μM; NH(3) <0.5 to >10 μM). Members of the Aquificales, most closely affiliated with the genus Sulfurihydrogenibium, are the most frequently recovered bacterial 16S rRNA gene phylotypes in the hottest samples; the detection of these thermophilic sulfur-oxidizing autotrophs coincided with maximal dark CO(2) fixation rates reaching near 9 μM C h(-1) at temperatures of 50-60°C. Vents at lower temperatures yielded mostly phylotypes related to the mesophilic gammaproteobacterial sulfur oxidizer Thiovirga. In contrast, cool vent water with low chemosynthetic activity yielded predominantly phylotypes related to freshwater Actinobacterial clusters with a cosmopolitan distribution.
Antimicrobial Peptides in Health and Disease (2002)

Microbes surround us. However, most of the time we are unaware of them. Our epithelial surfaces, which provide the physical barrier separating us from the environment, are usually free of signs of a battle taking place. Over the past several years, we have come to realize that the epithelium is capable of mounting its own battery of defensive chemicals, which are more extensive, more potent, and more exquisitely regulated than initially appreciated. I am referring not to the constituents of fluids, such as tears, saliva, and sweat, that are secreted onto the surface of epithelia, but to antimicrobial peptides, the . . .
V2O5 Nano‐Electrodes with High Power and Energy Densities for Thin Film Li‐Ion Batteries (2011)

Abstract Nanostructured V 2 O 5 thin films have been prepared by means of cathodic deposition from an aqueous solution made from V 2 O 5 and H 2 O 2 directly on fluorine‐doped tin oxide coated (FTO) glasses followed by annealing at 500°C in air, and studied as film electrodes for lithium ion batteries. XPS results show that the as‐deposited films contained 15% V 4+ , however after annealing all the vanadium is oxidized to V 5+ . The crystallinity, surface morphology, and microstructures of the films have been investigated by means of XRD, SEM, and AFM. The V 2 O 5 thin film electrodes show excellent electrochemical properties as cathodes for lithium ion intercalation: a high initial discharge capacity of 402 mA h g −1 and 240 mA h g −1 is retained after over 200 cycles with a discharging rate of 200 mA g −1 (1.3 C). The specific energy density is calculated as 900 W h kg −1 for the 1 st cycle and 723 W h kg −1 for the 180 th cycle when the films are tested at 200 mA g −1 (1.3 C). When discharge/charge is carried out at a high current density of 10.5 A g −1 (70 C), the thin film electrodes retain a good discharge capacity of 120 mA h g −1 , and the specific power density is over 28 kW kg −1 .
Kunjin Virus Replicon Vectors for Human Immunodeficiency Virus Vaccine Development (2003)

We have previously demonstrated the ability of the vaccine vectors based on replicon RNA of the Australian flavivirus Kunjin (KUN) to induce protective antiviral and anticancer CD8+ T-cell responses using murine polyepitope as a model immunogen (I. Anraku, T. J. Harvey, R. Linedale, J. Gardner, D. Harrich, A. Suhrbier, and A. A. Khromykh, J. Virol. 76:3791-3799, 2002). Here we showed that immunization of BALB/c mice with KUN replicons encoding HIV-1 Gag antigen resulted in induction of both Gag-specific antibody and protective Gag-specific CD8+ T-cell responses. Two immunizations with KUNgag replicons in the form of virus-like particles (VLPs) induced anti-Gag antibodies with titers of > or =1:10,000. Immunization with KUNgag replicons delivered as plasmid DNA, naked RNA, or VLPs induced potent Gag-specific CD8+ T-cell responses, with one immunization of KUNgag VLPs inducing 4.5-fold-more CD8+ T cells than the number induced after immunization with recombinant vaccinia virus carrying the gag gene (rVVgag). Two immunizations with KUNgag VLPs also provided significant protection against challenge with rVVgag. Importantly, KUN replicon VLP vaccinations induced long-lasting immune responses with CD8+ T cells able to secrete gamma interferon and to mediate protection 6 to 10 months after immunization. These results illustrate the potential value of the KUN replicon vectors for human immunodeficiency virus vaccine design.
Technical advances in the Naval Meteorology and Oceanography program (2005)

The challenge of the Naval Meteorology and Oceanography Command is to assess and predict the world's most diverse operating environment and translate its impact on military defense areas - aviation, maritime operations, expeditionary/special operations and undersea/surface/mine operations. The command seeks continual improvement in its core competencies to provide meteorology and oceanography geospatial information -in order to provide safety of navigation and turn environmental information into combat power. In recent years, the Navy has reinvigorated its METOC program through advanced training programs, numeric modeling, state of the art survey ships, airborne lidar surveys, autonomous underwater vehicles and rapidly deployable fleet survey teams. This presentation describes the role of new technologies in Navy Oceanography.
A critical review of sanitary provisions in medium to large shopping malls (2012)

﻿This research explores the current situation of the Sanitary Provision in medium to large shopping malls. It outlines the develop process on the Sanitary Provision Ratio in Hong Kong, the History, Development and the Current Situation. This research also studies how the relationships between sanitary provisions and the operation / performance of shopping malls. The research involves a review of relationship between the revenue or the customer satisfying rate and the sanitary provision.&#13;\n&#13;\nThe researcher tries to make suggestions for sanitary provision in future shopping mall and compare the benefit with the falter reasons. The benefit is quantified to the revenue &amp; customer service in particular shopping mall while comparing to the expense on offering a better sanitary provision facility. After the comparison, suggestions would be drawn on the form of sanitary provision in the future shopping mall in order to achieve a balance between Cost (extra installation on the sanitary provision) and Benefit (Good impression from the customer and Shopping Mall Revenue).
Potential application of in vivo imaging of impaired lymphatic duct to evaluate the severity of pressure ulcer in mouse model (2014)

Ischemia-reperfusion (IR) injury is a cause of pressure ulcer. However, a mechanism underlying the IR injury-induced lymphatic vessel damage remains unclear. We investigated the alterations of structure and function of lymphatic ducts in a mouse cutaneous IR model. And we suggested a new method for evaluating the severity of pressure ulcer. Immunohistochemistry showed that lymphatic ducts were totally vanished by IR injury, while blood vessels were relatively preserved. The production of harmful reactive oxygen species (ROS) was increased in injured tissue. In vitro study showed a high vulnerability of lymphatic endothelial cells to ROS. Then we evaluated the impaired lymphatic drainage using an in vivo imaging system for intradermally injected indocyanine green (ICG). The dysfunction of ICG drainage positively correlated with the severity of subsequent cutaneous changes. Quantification of the lymphatic duct dysfunction by this imaging system could be a useful strategy to estimate the severity of pressure ulcer.
Bleomycin-induced Pulmonary Fibrosis in Rats: Biochemical Demonstration of Increased Rate of Collagen Synthesis 1, 2 (1980)

The net rate of collagen synthesis in short-term lung explant cultures from rats was examined during a period of 4 wk after administration of a single intratracheal dose of bleomycin. After a delay of 3 to 4 days, the net rate of collagen synthesis was significantly increased over that in untreated control animals. This increase was sustained during approximately 10 days and subsequently returned to normal or below normal values. The increased rate of collagen synthesis could not be explained by increased free radioactive proline pools or by age differences among the animals. The period of increased rate of collagen synthesis preceded the detectable increases in lung collagen content, as we have reported previously.
Cells need safety valves (2009)

In Escherichia coli, the role of lacA, the third gene of the lactose operon, has remained an enigma. I suggest that its role is the consequence of the need for cells to have safety valves that protect them from the osmotic effect created by their permeases. Safety valves allow them to cope with the buildup of osmotic pressure under accidental transient conditions. Multidrug resistance (MDR) efflux, thus named because of our anthropocentrism, is ubiquitous. Yet, the formation of simple leaks would result in futile influx/efflux cycles. Versatile modification enzymes with low sensitivity solve the problem if the modified metabolite is the one exported by MDR permeases. This may account for the pervasive presence of acetyltransferases, such as LacA, associated to acetyl-metabolite exporters. This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells.
Gene expression profile in the salivary glands of primary Sjögren's syndrome patients before and after treatment with rituximab (2010)

Our results demonstrate the ability to elaborate a set of genes predictive of rituximab efficacy and highlight the importance of studying the differential expression of B cell and IFN pathway signaling molecules in relation to the response to anti-CD20 treatment. A randomized controlled study is currently ongoing to confirm these results.
Support vector regression and classification based multi-view face detection and recognition (2002)

A support vector machine-based multi-view face detection and recognition framework is described. Face detection is carried out by constructing several detectors, each of them in charge of one specific view. The symmetrical property of face images is employed to simplify the complexity of the modelling. The estimation of head pose, which is achieved by using the support vector regression technique, provides crucial information for choosing the appropriate face detector. This helps to improve the accuracy and reduce the computation in multi-view face detection compared to other methods. For video sequences, further computational reduction can be achieved by using a pose change smoothing strategy. When face detectors find a face in frontal view, a support vector machine-based multi-class classifier is activated for face recognition. All the above issues are integrated under a support vector machine framework. Test results on four video sequences are presented, among them the detection rate is above 95%, recognition accuracy is above 90%, average pose estimation error is around 10/spl deg/, and the full detection and recognition speed is up to 4 frames/second on a Pentium II 300 PC.
Topological representation model for image database query (2005)

Search algorithms in image databases usually return k nearest neighbours (kNN) of an image according to a similarity measure. This approach presents some anomalies and is based on assumptions that are not always satisfied. We have examined the causes of these anomalies and we have concluded that image query models have to exploit topological properties rather than the similarity degree. This paper proposes a topological model based on neighbourhood graphs built on automatically extracted image features. Each image is represented as a feature vector in R p and stands for a node in the neighbourhood graph. The graph exploration corresponds to database browsing, the neighbours of a node represent similar images. In order to perform query by example, the query image is represented as a R p feature vector and inserted in the graph by locally updating the neighbourhood graph. The topology of an image database is more informative than a similarity measure usually applied in content based image retrieval, as proved by our experiments. A prototype of a visualization and query tool called Smart Image Query (SIQ) is also introduced.
De Novo Lymph Node Formation in Chronic Inflammation of the Human Leg (2002)

Organized lymphoid tissue is the first line of antigenic defense. Recruited by antigen located in the non-lymphoid tissues, the infiltrating lymphocytes often organize themselves as follicle-like structures that contain germinal centers, similar to those in secondary lymphoid follicles of lymph nodes. These extranodal tertiary lymphoid follicles are found in various autoimmune diseases. We investigated 153 patients with protracted lymph stasis of the lower limb, caused by lymphatic damage incurred through soft tissue bacterial inflammation or mechanical trauma of soft tissues and bones. In 10% of patients with post-inflammatory, and in 25% with post-traumatic lymph stasis, "newly-formed" lymph nodes were detected by means of lymphoscintigraphy. They were located along the large calf and thigh veins. Although scattered nodes are normally detected in these areas, the number and total mass of visualized nodes substantially exceeded those seen in healthy subjects. The calculated surface area of "newly formed" nodes attained 50-70% of the area of ipsilateral inguinal nodes. Histological evaluation of nodal biopsy specimens in three such patients revealed, in one, a lymph node structure without differentiation into cortical and medullary areas, and in a second, a follicle-like structure within a dilated lymph vessel. Lymph clot removed from another dilated vessel contained a lymphocyte/dendritic cell aggregate. The "newly formed" nodes likely originate from primordial lymphoid follicles and/or lymphoid cell aggregates formed in response to chronic stimulation by microbial products and self-antigens from the damaged tissues. Detection of "newly-formed" lymph nodes in the limb is evidence of an ongoing inflammatory process and requires appropriate therapy.
Reaction of N-trimethylsilyl benzil monoimine with simple lithium ester enolates. A synthetic tool for the regioselective one-pot preparation of novel polyfunctional pyrrolines (1990)

Sequential treatment of benzil with lithium hexarnethyldisilylamide and simple α-lithiated esters leads, in a regioselective one-pot process, to the polyfunctional pyrrolines(4)–(8), depending on the nature of the enolate and on the experimental conditions. A reasonable explanation for the observed results is discussed. In addition, the reaction of 2,5-dihydro-5-hydroxy-4,5-diphenyl-2-oxo-1H-pyrrole-3-carbonitrile with sodium hydroxide has been reinvestigated and the structure of the previously described product corrected.
Guanylyl cyclases, nitric oxide, natriuretic peptides, and airway smooth muscle function (2003)

Airway smooth muscle (ASM) plays an important role in asthma pathophysiology through its contractile and proliferative functions. The cyclic nucleotides adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP) are second messengers capable of mediating the effects of a variety of drugs and hormones. There is a large body of evidence to support the hypothesis that cAMP is a mediator of the ASM's relaxant effects of drugs, such as beta2-adrenoceptor agonists, in human airways. Although most attention has been paid to this second messenger and the signal transduction pathways it activates, recent evidence suggests that cGMP is also an important second messenger in ASM with important relaxant and antiproliferative effects. Here, we review the regulation and function of cGMP in ASM and discuss the implications for asthma pathophysiology and therapeutics. Recent studies suggest that activators of soluble and particulate guanylyl cyclases, such as nitric oxide donors and natriuretic peptides, have both relaxant and antiproliferative effects that are mediated through cGMP-dependent and cGMP-independent pathways. Abnormalities in these pathways may contribute to asthma pathophysiology, and therapeutic manipulation may complement the effects of beta2-adrenoceptor agonists.
Bilateral subthalamic stimulation for Parkinson's disease by using three-dimensional stereotactic magnetic resonance imaging and electrophysiological guidance (2000)

At evaluation 6 months after surgery, continuous STN stimulation was shown to have improved parkinsonian motor disability by 64% and 78% in the "off' and "on" medication states, respectively. Antiparkinsonian drug treatment was reduced by 70% in 10 patients and withdrawn in two patients. The severity of levodopa-induced dyskinesias was reduced by 83% and motor fluctuations by 88%. Continuous high-frequency stimulation of the STN applied through electrodes implanted with the aid of 3D MR imaging and electrophysiological guidance is a safe and effective therapy for patients suffering from severe, advanced levodopa-responsive PD.
Structure−Activity Modifications of the HIV-1 Inhibitors (+)-Calanolide A and (−)-Calanolide B (1996)

The delta 7,8 olefinic linkages within (+)-calanolide A(1) and (-)-calanolide B(2) were catalytically reduced to determine impact on the anti-HIV activity of the parent compounds. In addition, a series of structure modifications of the C-12 hydroxyl group in (-)-calanolide B was made to investigate the importance of that substituent to the HIV-1 inhibitory activity of these coumarins. A total of 14 analogs were isolated or prepared and compared to (+)-calanolide A and (-)-calanolide B in the NCI primary anti-HIV assay. While none of the compounds showed activity superior to the two unmodified leads, some structure-activity requirements were apparent from the relative anti-HIV potencies of the various analogs.
Conjugated azoalkenes. Part 14. Synthesis of new 1-amino- and 1,2-diaminopyrrole derivatives by reaction of some conjugated azoalkenes with activated methylene compounds RCH2Ac and RCH2CN (R = aryl, heteroaryl) (1993)

1-Amino- and 1,2-diamino-pyrrole derivatives are obtained in high yield by reaction of conjugated azoalkenes with ketones and cyanides containing methylene groups further activated by a 4-nitrophenyl, 2-fluorophenyl, benzothiazol-2-yl or benzimidazol-2-yl group. In some cases the heterocycles can be prepared in a one flask procedure, while in others a two step sequence is required, namely, formation of the 1, 4-conjugate adduct and then cyclization. Reaction of 2,4-dichloro- and 2,3,6-trichlorophenylacetonitrile with the azoalkenes gave the 1,4-conjugate adducts, but these could not be successfully cyclized.
Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients (2009)

Together with our earlier report, these findings may shed light on the biological basis of TESI and may help identify patients at increased risk of this potentially serious adverse event.
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre (2007)

Structural and functional annotation of the large and growing database of genomic sequences is a major problem in modern biology. Protein structure prediction by detecting remote homology to known structures is a well-established and successful annotation technique. However, the broad spectrum of evolutionary change that accompanies the divergence of close homologues to become remote homologues cannot easily be captured with a single algorithm. Recent advances to tackle this problem have involved the use of multiple predictive algorithms available on the Internet. Here we demonstrate how such ensembles of predictors can be designed in-house under controlled conditions and permit significant improvements in recognition by using a concept taken from protein loop energetics and applying it to the general problem of 3D clustering. We have developed a stringent test that simulates the situation where a protein sequence of interest is submitted to multiple different algorithms and not one of these algorithms can make a confident (95%) correct assignment. A method of meta-server prediction (Phyre) that exploits the benefits of a controlled environment for the component methods was implemented. At 95% precision or higher, Phyre identified 64.0% of all correct homologous query-template relationships, and 84.0% of the individual test query proteins could be accurately annotated. In comparison to the improvement that the single best fold recognition algorithm (according to training) has over PSI-Blast, this represents a 29.6% increase in the number of correct homologous query-template relationships, and a 46.2% increase in the number of accurately annotated queries. It has been well recognised in fold prediction, other bioinformatics applications, and in many other areas, that ensemble predictions generally are superior in accuracy to any of the component individual methods. However there is a paucity of information as to why the ensemble methods are superior and indeed this has never been systematically addressed in fold recognition. Here we show that the source of ensemble power stems from noise reduction in filtering out false positive matches. The results indicate greater coverage of sequence space and improved model quality, which can consequently lead to a reduction in the experimental workload of structural genomics initiatives.
Recombinant human tumor necrosis factor does not inhibit lipoprotein lipase in primary cultures of isolated human adipocytes (1988)

Previous studies have demonstrated that cachectin/tumor necrosis factor (TNF) inhibits lipoprotein lipase (LPL) activity in cultures of 3T3-L1 cells. To determine whether TNF also inhibits LPL in human adipocytes, primary cultures of isolated human adipocytes were exposed to a spectrum of concentrations of recombinant human TNF. TNF concentrations up to 1000 pM had no effect on either LPL activity or LPL immunoreactive mass in the human adipocytes. Specific binding of 125I-labeled TNF was demonstrated in human adipocytes, and a TNF concentration of 100 pM competed for approximately 50% of the 125I-labeled TNF binding sites. In contrast, the same TNF in the same concentrations progressively inhibited LPL activity and immunoreactive mass in 3T3-L1 cells. Thus, human adipocytes respond to TNF in a different manner than 3T3-L1 cells. TNF may not cause the cachexia of cancer or chronic infection by directly inhibiting LPL in adipose tissue.
Electronic and Steric Optimization of Fluorogenic Probes for Biomolecular Imaging (2017)

Fluorogenic probes are invaluable tools for spatiotemporal investigations within live cells. In common fluorogenic probes, the intrinsic fluorescence of a small-molecule fluorophore is masked by esterification until entry into a cell, where endogenous esterases catalyze the hydrolysis of the masking groups, generating fluorescence. The susceptibility of masking groups to spontaneous hydrolysis is a major limitation of these probes. Previous attempts to address this problem have incorporated auto-immolative linkers at the cost of atom economy and synthetic adversity. Here, we report on a linker-free strategy that employs adventitious electronic and steric interactions in easy-to-synthesize probes. We find that X···C═O n→π* interactions and acyl group size are optimized in 2',7'-dichlorofluorescein diisobutyrate. This probe is relatively stable to spontaneous hydrolysis but is a highly reactive substrate for esterases both in vitro and in cellulo, yielding a bright, photostable fluorophore with utility in biomolecular imaging.