gebhart/patrepeval huggingface dataset:
Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health (2016)

The colon is inhabited by a dense population of microorganisms, the so-called "gut microbiota," able to ferment carbohydrates and proteins that escape absorption in the small intestine during digestion. This microbiota produces a wide range of metabolites, including short chain fatty acids (SCFA). These compounds are absorbed in the large bowel and are defined as 1-6 carbon volatile fatty acids which can present straight or branched-chain conformation. Their production is influenced by the pattern of food intake and diet-mediated changes in the gut microbiota. SCFA have distinct physiological effects: they contribute to shaping the gut environment, influence the physiology of the colon, they can be used as energy sources by host cells and the intestinal microbiota and they also participate in different host-signaling mechanisms. We summarize the current knowledge about the production of SCFA, including bacterial cross-feedings interactions, and the biological properties of these metabolites with impact on the human health.
Digital position determination system for electron microscopy (2005)

The precise determination of object positions within a specimen grid is important for many applications in electron microscopy. For example, real-time position determination is necessary for current statistical approaches and the efficient mapping and relocation of objects. Unfortunately, precise real-time position determination is not available on many older electron microscopes with manual stage controls. This report demonstrates the cost-effective and flexible implementation of a digital position determination system that can be adapted to many hand-operated electron microscopes. A customized solution that includes the hardware and software to accomplish position determination is presented. Lists of required parts, instructions for building the hardware, and descriptions of the developed programs are included. Two LED-photodiode assemblies detect x and y movements via an optical wheel that is in physical contact with the mechanical x and y stage control elements. These detector assemblies are interfaced with an integrated circuit that converts movement information into serial port-compatible signals, which are interpreted by a computer with specialized software. Two electron microscopes, a Philips CM12 (S)TEM and a Philips 201 TEM, were equipped with the described digital position determination system. The position fidelity and position fidelity after reloading of grids were determined for both microscopes. The determined position deviation was 1.06 microm in the x axis and 0.565 microm in the y axis for the Philips CM12 (S)TEM, and 0.303 microm in the x axis and 0.545 microm in the y axis for the Philips 201 TEM. After reloading and computational realigning, the determined average position variation was 2.66 microm in the x axis and 2.61 microm in the y axis for the Philips CM12 (S)TEM, and 1.13 microm in the x axis and 1.27 microm in the y axis for the Philips 201 TEM.
Trajectory triangulation over conic section (1999)

We consider the problem of reconstructing the 3D coordinates of a moving point seen from a monocular moving camera, i.e., to reconstruct moving objects from line-of-sight measurements only. The task is feasible only when same constraints are placed on the shape of the trajectory of the moving point. We coin the family of such tasks as "trajectory triangulation". In this paper we focus on trajectories whose shape is a conic-section and show that generally 9 views are sufficient for a unique reconstruction of the moving point and fewer views when the conic is a known type (like a circle in 3D Euclidean space for which 7 views are sufficient). Experiments demonstrate that our solutions are practical. The paradigm of Trajectory Triangulation in general pushes the envelope of processing dynamic scenes forward. Thus static scenes become a particular case of a more general task of reconstructing scenes rich with moving objects (where an object could be a single point).
Prevention is the key. (1996)

As a pediatrician two of the most frequent questions that I have encountered have been: 'What is your area ofconcent-
Immediate Inflammatory Responses to Adenovirus-Mediated Gene Transfer in Rat Salivary Glands (1996)

Although replication-deficient adenoviruses can efficiently transfer genes to the salivary glands, the current vectors precipitate an immediate, transient decrease in salivary function. To study the cause of this salivary hypofunction, 10(6)-10(10) plaque-forming units (pfu) of the vector AdCMV beta gal were delivered by retrograde ductal infusion to the submandibular glands (SMGs) of rats. Microscopic analysis of infected glands showed a dose-related, rapidly developing inflammatory response, which at the highest amount of virus was characterized by a predominantly neutrophil-containing infiltrate, focal necrosis, and edema. Moreover, the glands of nude rats developed similar morphologic changes to those of immunocompetent rats. After 3 days, the volume of stimulated saliva secreted from SMGs receiving AdCMV beta gal (6.75 x 10(9) pfu) was approximately 20% that of controls. UV-inactivated virus caused a similar decrease in saliva output. We evaluated to what extent the anti-inflammatory glucocorticoid, dexamethasone, could suppress inflammation and preserve salivary function. Three days after infusion with a high dose of AdCMV beta gal (6.75 x 10(9) pfu), the glands from dexamethasone-treated animals showed markedly less inflammation and no necrosis. Furthermore, there was no significant difference in the average amount of saliva secreted from the infected glands (105 +/- 17 microliters) compared to the control glands (123 +/- 18 microliters). In addition, dexamethasone extended the expression of beta-galactosidase in the SMGs. These results suggest that the adenovirus-mediated acute inflammation in rat SMG is responsible for diminished gland function and transgene expression. Furthermore, we demonstrate a useful role for glucocorticoids in controlling acute inflammation during experimental gene transfer with current adenovirus vectors.
Preparation of Poly (Schiff base) (1969)

ポリシッフ塩基はテレフタルアルデヒドまたはイソフタルアルデヒドなどのジアルデヒドと2,4-ジヒドラジノ-6-フェニル-s-トリアジン,2,4-ジヒドラジノ-6-フェニル-s-トリアジン,イソシンコメロン酸ヒドラジド,ジピコリン酸ヒドラジド,シュウ酸ヒドラジドまたは炭酸ヒドラジドなどのジヒドラジノ化合物を処理することにより合成された。ジヒドラジノ化合物とジアルデヒドを非プロトン系極性溶媒中で混合し,ポリシッフ塩基が溶媒から少しずつ沈殿した。ポリシッフ塩基の固有粘度はDMSOまたはNMP中で0.11～0.94dl/gである。この高分子は非プロトン系極性溶媒に可溶であるが,他の有機溶媒に溶解しない。ポリマーは350～400℃,窒素気流中で熱分解する。ポリシッフ塩基の熱安定性はすぐれていない。これらポリマーのモデル化合物はベンズァルデヒドとヒドラジノ化合物より合成された。ポリシッフ塩基はモデル化合物の赤外線スペクトルにより確かめた。
Using column dependency to compress tables (2004)

Large amounts of business data are kept in tables of fixed-length records. Columns in such a table may be functionally dependent on one another, resulting in low overall information content. This paper shows how to exploit this source of information redundancy to compress table data. Experiments with a wide variety of massive tables including telecom data and stock quotes show that this technique compresses table data well, up to 48:1 or even 100:1 reduction in some cases.
Efficient generation of stable bispecific IgG1 by controlled Fab-arm exchange (2013)

The promise of bispecific antibodies (bsAbs) to yield more effective therapeutics is well recognized; however, the generation of bsAbs in a practical and cost-effective manner has been a formidable challenge. Here we present a technology for the efficient generation of bsAbs with normal IgG structures that is amenable to both antibody drug discovery and development. The process involves separate expression of two parental antibodies, each containing single matched point mutations in the CH3 domains. The parental antibodies are mixed and subjected to controlled reducing conditions in vitro that separate the antibodies into HL half-molecules and allow reassembly and reoxidation to form highly pure bsAbs. The technology is compatible with standard large-scale antibody manufacturing and ensures bsAbs with Fc-mediated effector functions and in vivo stability typical of IgG1 antibodies. Proof-of-concept studies with HER2×CD3 (T-cell recruitment) and HER2×HER2 (dual epitope targeting) bsAbs demonstrate superior in vivo activity compared with parental antibody pairs.
HIV-1 Membrane Fusion Mechanism:  Structural Studies of the Interactions between Biologically-Active Peptides from gp41 (1996)

Two synthetic peptides corresponding to sequences in HIV-1LAI gp41, (aa558-595) and T20 (aa 643-678), are strong inhibitors of HIV-1 viral fusion, having EC50 values of 1 microgram/mL and 1 ng/mL, respectively. Previous work suggested that T21 forms a coiled-coil structure in PBS solution, while T20 is primarily nonhelical, and that the inhibitory action of these peptides occurs after the interaction between the viral gp120 protein and the cellular CD4 receptor [Wild, C.T., Shugars, D. C., Greenwell, T. K., McDanal, C. B., Matthews, T. J. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 9770 and references therein]. The current study uses sedimentation equilibrium (SE), circular dichroism (CD), and viral-fusion assays to quantitatively investigate peptide structure and peptide-peptide interactions. SE analyses of T21 (1-100 microM) indicate that the peptide self associates via a monomer/dimer/tetramer equilibrium; in addition, T20 is monomeric in the range of 1-10 microM and exhibits a complicated monomer/tetramer equilibrium between 20 and 100 microM. Singular value decomposition analyses of the CD spectra of T21 and T20 indicate that the helical content of these peptides in PBS solution is 90% and 20%, respectively. A structural interaction between the two peptides is detected by CD at several concentration ratios of T20:T21. These experiments emphasize that T20 interacts specifically with the tetrameric form of T21. Truncated forms of T20 also exhibit structural interactions with T21 at varying concentration ratios. The ability of T20 and the truncated peptides to interact structurally with tetrameric T21 correlates with antiviral activity. Implications of these findings are discussed in terms of proposed mechanisms of membrane fusion inhibition and the structural changes which occur in gp41 during membrane fusion.
A generic new platform for topological quantum computation using semiconductor heterostructures (2009)

We show that a film of a semiconductor such as GaAs, in which s-wave superconductivity and a Zeeman splitting are induced by proximity effect, supports zero-energy Majorana fermion modes in the ordinary vortex excitations. The key to the topological order is the existence of spin-orbit coupling, coexisting with proximity-induced s-wave superconductivity. Since time reversal symmetry is explicitly broken, the edge of the film constitutes a chiral Majorana wire. The heterostructure we propose -- a semiconducting thin film sandwiched between an s-wave superconductor and a magnetic insulator -- is a generic system which can be used as the platform for topological quantum computation by virtue of the existence of non-Abelian Majorana fermions.
Isolation, cloning and expression of a multifunctional O‐methyltransferase capable of forming 2,5‐dimethyl‐4‐methoxy‐3(2H)‐furanone, one of the key aroma compounds in strawberry fruits (2002)

Strawberry fruits contain an uncommon group of key aroma compounds with a 2,5-dimethyl-3(2H)-furanone structure. Here, we report on the methylation of 2,5-dimethyl-4-hydroxy-3(2H)-furanone (DMHF) to 2,5-dimethyl-4-methoxy-3(2H)-furanone (DMMF) by a S-adenosyl-L-methionine dependent O-methyltransferase, the cloning of the corresponding cDNA and characterization of the encoded protein. Northern-hybridization indicated that the Strawberry-OMT specific transcripts accumulated during ripening in strawberry fruits and were absent in root, petiole, leaf and flower. The protein was functionally expressed in E. coli and exhibited a substrate specificity for catechol, caffeic acid, protocatechuic aldehyde, caffeoyl CoA and DMHF. A common structural feature of the accepted substrates was a o-diphenolic structure also present in DMHF in its dienolic tautomer. FaOMT is active as a homodimer and the native enzyme shows optimum activity at pH 8.5 and 37 degrees C. It does not require a cofactor for enzymatic activity. Due to the expression pattern of FaOMT and the enzymatic activity in the different stages of fruit ripening we suppose that FaOMT is involved in lignification of the achenes and the vascular bundles in the expanding fruit. In addition, it is concluded that the Strawberry-OMT plays an important role in the biosynthesis of strawberry volatiles such as vanillin and DMMF.
The Association Between Serum Folate Levels and Periodontal Disease in Older Adults: Data from the National Health and Nutrition Examination Survey 2001/02 (2006)

A low serum folate level was independently associated with periodontal disease in older adults. The results suggest that serum folate levels, important indicators of periodontal disease in older adults, may provide an important clinical target for intervention to promote oral health.
TACS--A Demand Assignment System for FLEETSAT (1979)

The UHF FLEETSATCOM system provides a substantial resource to support important communication needs of the U.S. Navy and other Department of Defense users. Because of the significant investment being made in this system, there is strong motivation to examine techniques that make efficient usage of its components. This paper reports on one such effort, the Terminal Access Control System (TACS) that was developed at the M.I.T. Lincoln Laboratory. TACS utilizes time division multiple access (TDMA) to derive up to nine 2400 bit/s circuits from each of the several 25-kHz-wide frequency channels available on the FLEETSAT satellites. Using TACS, access to these circuits would be controlled in real time by a central control station in response to user demand. This application of demand assignment further multiplies the number of subscribers that can use the system by a significant factor. A description of the access control techniques and efficiency of performance is provided. A master control station and subscriber unit were constructed and used in an extensive laboratory test program.
Reduction of polysaccharide production in Pseudomonas aeruginosa biofilms by bismuth dimercaprol (BisBAL) treatment (1999)

Microorganisms in biofilms, cells attached to a surface and embedded in secreted insoluble extracellular polymers, are recalcitrant to chemical biocides and antibiotics. When Pseudomonas aeruginosa ERC1 biofilms were treated continuously with 1 x MIC of bismuth dimercaprol (BisBAL), biofilm density determined by both total cell counts and viable cell counts increased during the first 30 h period then decreased thereafter. After 120 h of treatment there was an approximate 3-log reduction in viable cell areal density compared with the untreated control. Per-cell total polysaccharide production was significantly reduced in biofilms exposed to 12.5 microM BisBAL compared with the untreated control. In biofilm cultures, 1 x MIC of BisBAL did not initially kill attached cells but was enough to reduce polysaccharide production. As treatment proceeded, the normalized polysaccharide content was reduced and those cells attached became susceptible to 1 x MIC of BisBAL.
Functional genomic screening identifies dual leucine zipper kinase as a key mediator of retinal ganglion cell death (2013)

Glaucoma, a major cause of blindness worldwide, is a neurodegenerative optic neuropathy in which vision loss is caused by loss of retinal ganglion cells (RGCs). To better define the pathways mediating RGC death and identify targets for the development of neuroprotective drugs, we developed a high-throughput RNA interference screen with primary RGCs and used it to screen the full mouse kinome. The screen identified dual leucine zipper kinase (DLK) as a key neuroprotective target in RGCs. In cultured RGCs, DLK signaling is both necessary and sufficient for cell death. DLK undergoes robust posttranscriptional up-regulation in response to axonal injury in vitro and in vivo. Using a conditional knockout approach, we confirmed that DLK is required for RGC JNK activation and cell death in a rodent model of optic neuropathy. In addition, tozasertib, a small molecule protein kinase inhibitor with activity against DLK, protects RGCs from cell death in rodent glaucoma and traumatic optic neuropathy models. Together, our results establish a previously undescribed drug/drug target combination in glaucoma, identify an early marker of RGC injury, and provide a starting point for the development of more specific neuroprotective DLK inhibitors for the treatment of glaucoma, nonglaucomatous forms of optic neuropathy, and perhaps other CNS neurodegenerations.
Selective Covalent Protein Immobilization: Strategies and Applications (2009)

A wide range of biologically mediated methods and important applications of site-specific protein immobilization are discussed, through the culmination of a major multidisciplinary research effort spanning molecular biology. The study focused the attention on oriented protein immobilization methodology that allow defined attachment of proteins with uniform orientation at the bioactive site. The study include enzyme-mediated attachment to a small-molecule immobilizing ligand and the development of genetically encoded protein tags for immobilization. The advent of high-density array printing technology and improved methods for high-throughput production and purification of large number of proteins that allowed the preparation of protein microarrays. The development of proteome chip technology is used to probe an entire collection of proteins for specific function of biochemistry.
Identification of DNA Basepairing via Tunnel-Current Decay (2007)

We propose a new approach for reading the sequence of a DNA molecule passing between electrodes on a nanopore, using hydrogen bond-mediated tunneling signals. The base-electrode interaction is modeled using a nucleo-base-functionalized STM probe that is pulled away from a nucleoside monolayer. Watson-Crick recognition results in slow decay of the tunnel current, which is uniquely characteristic of the basepair in over half the reads. Thirteen independent reads would yield the desired 99.99% accuracy.
An efficient system for high‐level expression and easy purification of authentic recombinant proteins (2004)

Expression of recombinant proteins as fusions to the eukaryotic protein ubiquitin has been found to significantly increase the yield of unstable or poorly expressed proteins. The benefit of this technique is further enhanced by the availability of naturally occurring deubiquitylating enzymes, which remove ubiquitin from the fusion product. However, the versatility of the system has been constrained due to the lack of a robust, easily purified deubiquitylating enzyme. Here we report the development of an efficient expression system, utilizing the ubiquitin fusion technique, which allows convenient high yield and easy purification of authentic protein. An Escherichia coli vector (pHUE) was constructed for the expression of proteins as histidine-tagged ubiquitin fusions, and a histidine-tagged deubiquitylating enzyme to cleave these fusions was expressed and purified. The expression system was tested using several proteins varying in size and complexity. These results indicate that this procedure will be suitable for the expression and rapid purification of a broad range of proteins and peptides, and should be amenable to high-throughput applications.
An Insect Olfactometer (1926)

Journal Article An Insect Olfactometer Get access N. E. McIndoo N. E. McIndoo Ph. D. Entomologist, Fruit Insect Investigations, Bureau of Entomology, United States Department of Agriculture, Washington, D. C. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 19, Issue 3, 1 June 1926, Pages 545–571, https://doi.org/10.1093/jee/19.3.545 Published: 01 June 1926
2-DE analysis indicates that Acinetobacter baumannii displays a robust and versatile metabolism (2009)

This work indicates that A. baumannii has a versatile and robust metabolism and also reveal a number of proteins that may play a key role in the mechanism of drug resistance and virulence. The data obtained complements earlier reports of A. baumannii proteome and provides new tools to increase our knowledge on the protein expression profile of this pathogen.
Properties and reactions of ylidenemalononitriles (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProperties and reactions of ylidenemalononitrilesFillmore FreemanCite this: Chem. Rev. 1980, 80, 4, 329–350Publication Date (Print):August 1, 1980Publication History Published online1 May 2002Published inissue 1 August 1980https://pubs.acs.org/doi/10.1021/cr60326a004https://doi.org/10.1021/cr60326a004research-articleACS PublicationsRequest reuse permissionsArticle Views1259Altmetric-Citations278LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Hyder - A Transactional Record Manager for Shared Flash (2011)

Hyder supports reads and writes on indexed records within classi-cal multi-step transactions. It is designed to run on a cluster of servers that have shared access to a large pool of network-addressable raw flash chips. The flash chips store the indexed records as a multiversion log-structured database. Log-structuring leverages the high random I/O rate of flash and automatically wear-levels it. Hyder uses a data-sharing architecture that scales out without partitioning the database or application. Each transac-tion executes on a snapshot, logs its updates in one record, and broadcasts the log record to all servers. Each server rolls forward the log against its locally-cached partial-copy of the last committed state, using optimistic concurrency control to determine whether each transaction commits. This paper explains the architecture of the overall system and its three main components: the log, the index, and the roll-forward algorithm. Simulations and prototype measurements are presented that show Hyder can scale out to support high transaction rates. 1.
Cardiac autonomic nerve fiber regeneration in chronic heart failure: Do Akt gene-transduced mesenchymal stem cells promote repair?*☆ (2010)

AbstractBACKGROUND:Transplantation of Akt-over-expressing mesenchymal stem cells (Akt-MSCs) has been shown to repair infarcted myocardium and improve cardiac function. However, little is known about the therapeutic effects of Akt-MSCs on cardiac autonomic neuropathy in chronic heart failure (CHF).OB