jimnoneill/paper-to-field-training huggingface dataset:
Immunologic properties and therapeutic efficacy of a multivalent epitope‐based vaccine against four Helicobacter pylori adhesins (urease, Lpp20, HpaA, and CagL) in Mongolian gerbils

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Abstract Background Therapeutic vaccination is a desirable alternative for controlling Helicobacter pylori ( H. pylori ) infection. Attachment to the gastric mucosa is the first step in establishing bacterial colonization, and adhesins, which are on the surface of H. pylori , play a pivotal role in binding to human gastric mucosa. Materials and Methods In the present study, we constructed a multivalent epitope‐based vaccine named CFA dE with seven carefully selected antigenic fragments from four H. pylori adhesins (urease, Lpp20, HpaA and CagL). The specificity, immunogenicity and ability to produce neutralizing antibodies of CFA dE were evaluated in BALB /c mice. After that, its therapeutic efficacy and protective immune mechanisms were explored in H. pylori ‐infected Mongolian gerbils. Results The results indicated that CFA dE could induce comparatively high levels of specific antibodies against urease, Lpp20, HpaA and CagL. Additionally, oral therapeutic immunization with CFA dE plus polysaccharide adjuvant ( PA ) significantly decreased H. pylori colonization compared with oral immunization with urease plus PA , and the protection was correlated with IgG and sIgA antibody and antigen‐specific CD 4 + T cells. Conclusions This study indicated that the multivalent epitope‐based vaccine, which targeted multiple adhesins in adherence of H. pylori to the gastric mucosa, is more effective than the univalent vaccine targeting urease only. This multivalent epitope‐based vaccine may be a promising therapeutic candidate vaccine against H. pylori infection.
Evaluation of osteoporosis using radiographic hip geometry, compared with dual energy X-ray absorptiometry (DXA) as the standard

Field: Medicine (Health Sciences)

Osteoporotic hip fracture is associated with high mortality and morbidity and often results in a loss of mobility and independence. Osteoporosis is diagnosed by measuring bone mineral density (BMD, g cm -2 ), a measure of the amount of mineral in a bone. Although BMD continues to serve well it does not fully account for bone strength and only partially accounts for the risk of hip fracture. The shape and structure of the proximal femur also helps to determine how forces act in the hip in a fall and their measurement can aid the prediction of hip fracture. In this study, the geometrical variables of the right proximal femur in a total number of fifty Indian women were measured from digital x-ray images, and these results were compared with BMD values of the proximal femur measured by Dual energy x-ray absorptiometry (DXA) for same set of women, as a standard. Results obtained by this proposed approach explored how they were related with BMD and anthropometric factors such as body-height, and body-weight. In this study, it was found that 34% and 20% of the study Indian women were found to have osteoporosis and osteopenia respectively. The mean values of thickness of the medial shaft cortex (SC) as well as lesser trochanter thickness of the medial cortex (NC) and width of the acetabular bone (AW) were lesser in the osteoporotic Indian women than in normal Indian women. These values were found to be decreased by -21%, -11%, and -18% respectively, when comparing to normal Indian women. Simple radiograph hip geometry measurements are useful in the evaluation of osteoporosis.
Extremophiles as a Source of Biotechnological Products

Field: Agricultural and Biological Sciences (Life Sciences)

Extremophile and extremozyme capabilities to uphold catalytic actions under extreme situations open up a varied array of biotechnological applications. Extremophiles are a rich supply of biocatalysts used for innumerable purposes. Bioactive molecules and enzymes isolated from organisms inhabiting risky environments being used in biological innovation pipelines and pharmaceutical have positive claims. The species biodiversity has favourable reservoir of the unexploited amalgams with biotechnological significance. Prospective solicitations of extremozymes, chiefly as catalysis of multistep progressions, quorum sensing, bioremediation, biofuel, biodiversity and prospecting, biomining, and genetic technology are explored. To boost the biotechnological uses of extremozymes, research and development efforts are needed to address hurdles such as extremophile culture, gene expression in host cells, and extremozyme bioprocessing. Extremophiles can be a resource for innovative biotechnological comprising industrial biotechnology, agriculture, medical, food, and environmental biotechnology.
Probing the thermodynamics and kinetics of ethylene carbonate reduction at the electrode–electrolyte interface with molecular simulations

Field: Chemistry (Physical Sciences)

Understanding the formation of the solid–electrolyte interphase (SEI) in lithium-ion batteries is an ongoing area of research due to its high degree of complexity and the difficulties encountered by experimental studies. Herein, we investigate the initial stage of SEI growth, the reduction reaction of ethylene carbonate (EC), from both a thermodynamic and a kinetic approach with theory and molecular simulations. We employed both the potential distribution theorem and the Solvation Method based on Density (SMD) to EC solvation for the estimation of reduction potentials of Li+, EC, and Li+-solvating EC (s-EC) as well as reduction rate constants of EC and s-EC. We find that solvation effects greatly influence these quantities of interest, particularly the Li+/Li reference electrode potential in EC solvent. Furthermore, we also compute the inner- and outer-sphere reorganization energies for both EC and s-EC at the interface of liquid EC and a hydroxyl-terminated graphite surface, where total reorganization energies are predicted to be 76.6 and 88.9 kcal/mol, respectively. With the computed reorganization energies, we estimate reduction rate constants across a range of overpotentials and show that EC has a larger electron transfer rate constant than s-EC at equilibrium, despite s-EC being more thermodynamically favorable. Overall, this manuscript demonstrates how ion solvation effects largely govern the prediction of reduction potentials and electron transfer rate constants at the electrode–electrolyte interface.
Successful treatment of Budd-Chiari Syndrome with Balloon Dilatation Angioplasty

Field: Medicine (Health Sciences)

A 62-year-old woman was admitted because of prolonged jaundice. After examination of contrast enhanced computed tomography images, she was diagnosed with Budd-Chiari syndrome due to a short obstruction of the hepatic portion of the inferior vena cava. She received endovascular angioplasty using a catheter with a balloon 14 mm in diameter. After balloon dilatation angioplasty of the obstructed inferior vena cava, favourable antegrade blood flow was restored. Then, oral warfarin therapy was started to prevent restenosis by thrombus formation. Contrast-enhanced computed tomography images taken four months after treatment revealed no restenosis of the inferior vena cava. This report is significant because it presents an effective and minimally invasive strategy for treating Budd-Chiari syndrome. Balloon dilatation angioplasty should be considered as the first choice of treatment if an obstruction is short and located in the major trunk of the hepatic vein or inferior vena cava.
Detectors for slowly extracted heavy ions at the GSI facility

Field: Physics and Astronomy (Physical Sciences)

The beam currents of the high energy heavy ion beam, extracted from the SIS at the GSI, Darmstadt, are routinely determined with three types of detectors: Scintillation counters in the range up to 10 pps, ionization chambers (between 10 and 10 pps) and secondary electron monitors (between 10 and 10 pps). The performance of these devices, and in particular the high intensity limits of the ionization chamber are discussed. As an application, the time structure of the slowly extracted spill is measured with the scintillators, which give a non-integrating, dead time free analyzing system in the frequency domain. 1 PARTICLE CURRENTS OF SLOWLY EXTRACTED IONS The GSI heavy ion facility can deliver the whole spectrum of heavy ions in a wide energy range. Using the heavy ion synchrotron SIS, ions from p to U can be accelerated to energies from 50 MeV/u to 2 GeV/u. The number of stored particles in the SIS ranges between 10 for rare isotopes and a few times 10 for e.g. Ne. Most of the experiments use the slow extraction mode with a spill length between 0.5 s and 10 s. This is equivalent to about 10 pps (particles per second) and 10 pps, or, expressed in electrical current between 0.1 pA and 100 nA. These low, quasi dc currents cannot be measured with standard current transformers. Instead, other techniques are used: Low numbers of extracted ions are counted directly with plastic scintillators. For an intermediate range of particles gas filled ionization chambers (IC) are used. Since several decades this device is used for proton and heavy ion beams e.g. at CERN[1], LBL[2] and KEK [3]. As shown below, there is a drop of the efficiency (here called saturation) for particle rates higher than about 10 pps for heavy ions (depending on the ion species). To cover also the higher intensity range, secondary electron monitors (SEM) are used. Again, these devices are used since a long time e.g. at CERN[4]. Their current output is about three orders of magnitude lower compared to the ionization chamber and also their absolute precision is about a factor of 2 lower than for the IC.
Investigation of laser induced air breakdown thresholds at 1064, 532, 355, 266 and 248nm

Field: Physics and Astronomy (Physical Sciences)

Laboratory air is one most popular transparent medium for high power laser beam propagation. Its threshold of laser induced breakdown is one of the key characters for the high power laser system. The thresholds of laser induced air breakdown under laboratory condition were measured using 1064, 532, 355, 266 and 248nm short pulse laser. The focal spot varies from 50μ m to 150μ m which achieved using a lens with 117mm focal length. The measured breakdown thresholds range from 3.2×1010W/cm2 to 5.1×1011W/cm2, depending on the wavelength. It is confirmed that the KrF laser induced air breakdown threshold should be 3.2×1010W/cm2, which is almost 1 order of magnitude higher than the reported value of 2.7 ×109W/cm2 .The measurements indicate multi-photon ionization is the dominant mechanism since the air breakdown thresholds at 1064, 532, 355, 266 and 248nm seemed well-agreed with the scale law of λ2.
Tribbles pseudokinase 3 promotes enterovirus A71 infection via dual mechanisms

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Enterovirus A71 (EV-A71) is the main pathogen causing hand, foot and mouth disease (HFMD) in children and occasionally associated with neurological diseases such as aseptic meningitis, brainstem encephalitis (BE) and acute flaccid paralysis. We report here that cellular pseudokinase tribbles 3 (TRIB3) facilitates the infection of EV-A71 via dual mechanisms. In one hand, TRIB3 maintains the metabolic stability of scavenger receptor class B member 2 (SCARB2), the bona fide receptor of EV-A71, to enhance the infectious entry and spreading of the virus. On the other hand, TRIB3 facilitates the replication of EV-A71 RNA in a SCARB2-independent manner. The critical role of TRIB3 in EV-A71 infection and pathogenesis was further demonstrated in vivo in mice. In comparison to wild-type C57BL/6 mice, EV-A71 infection in TRIB3 knockdown mice (Trib3+/−) resulted in significantly lower viral loads in muscular tissues and reduced lethality and severity of clinical scores and tissue pathology. In addition, TRIB3 also promoted the replication of coxsackievirus B3 (CVB3) and coxsackievirus A16 (CVA16) in vitro. In conclusion, our results suggest that TRIB3 is one of key host cellular proteins required for the infection and pathogenesis of EV-A71 and some other human enteroviruses and may thus be a potential therapeutic target for combating the infection of those viruses.
The System of Divine Manifestation in The Ibn ‘Arabian School of Thought

Field: Arts and Humanities (Social Sciences)

<div><p>One of the fundamental problems of Theoretical Mysticism is the explanation of the world as being something other than God after having accepted the Unity of Existence. This paper seeks to present, after having explained certain necessary premises, the theory of manifestation as one that can explain and analyze multiplicity.</p><p>In this article we especially seek to solidify the relation of such claims to mystics in general and to the adherents of the Ibn ‘Arabian school of thought in particular. This is especially important because in some of the works of many specialists in this ﬁeld we ﬁnd that some unrealistic claims have been deﬁnitively attributed in to the Great Sheikh. The only way to counteract such false claims, in any ﬁeld, including Theoretical Mysticism, is to make it binding upon ourselves to delve into the views of others in a cautious way. We must take the apparent meanings of the sayings of the mystics as a proof in this matter. Therefore the method of research of the writer of this article is to relate the sayings of the Great Sheikh and his commentators while commentating upon and analyzing them as well.</p><p> </p></div>
Statice limonium Linnaeus, 1753, spec. nov.

Field: Agricultural and Biological Sciences (Life Sciences)

Statice limonium, spec. nov. 2. Statice caule nudo paniculato tereti, foliis laevibus. Statice caule nudo ramoso. Hort. cliff. 115. Fl. suec. 254. Gron. virg. 150. Roy. lugdb. 192. Limonium maritimum majus. Bauh. pin. 192. β. Limonium maritimum minus, oleae folio. Bauh. pin. 192. γ. Statice foliis obverse-ovatis glabris, caule nudo ramoso. Sauv. monsp.15. Limonium parvum, bellidis minoris folio. Bauh. pin. 192. δ. Limonium maritimum minimum. Bauh. pin. 192. prodr. 99. Bocc. sic. 25. t.19. Habitat in Europae & Virginiae maritimis. ♃
Traditional use and conservation of the “calaverita” Laelia anceps subsp. dawsonii f. chilapensis Soto-Arenas at Chilapa, Guerrero, México

Field: Agricultural and Biological Sciences (Life Sciences)

Mexico lodges a heritage of traditional knowledge on use, management and conservation of a great vari- ety of genetic resources tie to its culture and idiosyn- crasy (Davis et al. 1994; Toledo 1991). That heritage is protected in the memory of the indigenous and rural villages of the country, which by means of the daily practice and oral transmission of their customs, have allowed several species to survive, among them some orchids of the genus Laelia (Halbinger and Soto 1997, Toledo 1991).
Identification and Sequence Composition Characterization of Chondroitin Sulfate-Binding Peptides through Peptide Array Screening

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Chondroitin sulfate (CS) is an important glycosaminoglycan that has been implicated in several disease processes, such as cancer and spinal cord injury. However, few studies have characterized CS-binding protein and peptide sequences for diagnostic and therapeutic use. In this study, peptide array screening, affinity capillary electrophoresis, and statistical analysis were used to both identify and characterize C6S-binding peptides for sequence composition. The compositional characterization results showed that Phe, Arg, and Tyr all had a significantly high rate of occurrence in the "high binding" affinity peptides, while tryptophan and lysine were significantly underrepresented in this population. Peptides modified with alanine point mutations for Phe, Arg, and Tyr all had lower C6S-binding affinities than the original peptides, demonstrating that these amino acids are all important for C6S binding. Several peptides were designed that substituted Arg for Lys and Phe or Tyr for Trp to create peptides with higher binding affinity. The peptides with the Arg substitution all had improved binding affinities while the Phe/Tyr substitution decreased C6S-binding affinity. Further analysis showed that the increased occurrence of Phe and Tyr in the "high affinity" peptides was dependent upon their positions both within the peptide sequence and in relation to other critical amino acids. Finally, a motif (ABBAA) was suggested for C6S-binding peptides where A represents any aromatic amino acid and B any basic amino acid. The results demonstrate that the methodology developed in this study for sequence composition analysis is an effective technique for the characterization of the interaction between peptides and CS.
Enhancement of antroquinonol production via the overexpression of 4 - hydroxybenzoate polyprenyltransferase biosynthesis-related genes in Antrodia cinnamomea

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

This dataset contains the digitized treatments in Plazi based on the original journal article Liu, Xiaofeng, Xia, Yongjun, Zhang, Yao, Liang, Lihong, Xiong, Zhiqiang, Wang, Guangqiang, Song, Xin, Ai, Lianzhong (2021): Enhancement of antroquinonol production via the overexpression of 4 - hydroxybenzoate polyprenyltransferase biosynthesis-related genes in Antrodia cinnamomea. Phytochemistry (112677) 184: 1-9, DOI: 10.1016/j.phytochem.2021.112677, URL: http://dx.doi.org/10.1016/j.phytochem.2021.112677
Depth Variance of Organic Matter Respiration Stoichiometry in the Subtropical North Atlantic and the Implications for the Global Oxygen Cycle

Field: Environmental Science (Physical Sciences)

Abstract Climate warming likely drives ocean deoxygenation, but models still cannot fully explain observed declines in oxygen. One unconstrained parameter is the oxygen demand per carbon respired for complete remineralization of organic matter (i.e., the total respiration quotient, r Σ‐O2:C ). Here, we tested if r Σ‐O2:C declined with depth by quantifying suspended concentrations of particulate organic carbon (POC), particulate organic nitrogen (PON), particulate organic phosphorus (POP), particulate chemical oxygen demand (PCOD), and total oxygen demand (Σ‐O 2 = PCOD + 2PON) down to a depth of 1,000 m in the Sargasso Sea. The respiration quotient ( r ‐O2:C = PCOD:POC) and total respiration quotient ( r Σ‐O2:C = Σ‐O 2 :POC) declined with depth in the euphotic zone, but increased vertically in the disphotic zone. C:N and r Σ‐O2:N changed with depth, but surface values were similar to values at 1,000 m. C:P, N:P, and r Σ‐O2:P mostly decreased with depth. We hypothesize that r Σ‐O2:C is linked to multiple environmental factors that change with depth, such as phytoplankton community structure and the preferential production/removal of biomolecules. Using a global model, we show that the global distribution of dissolved oxygen is equally sensitive to r ‐O2:C varying between surface biomes versus vertically during remineralization. Additionally, adjusting the model's r ‐O2:C with depth to match our observations resulted in less dissolved oxygen throughout the upper ocean. Most of this loss occurred in the tropical Pacific thermocline, where oxygen models underestimate deoxygenation the most. This study aims to improve our understanding of biological oxygen demand as warming‐induced deoxygenation continues.
Bioenergetics of lactic acid bacteria: cytoplasmic pH and osmotolerance

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Lactic acid bacteria maintain a cytoplasm that is more alkaline than the medium, but whose pH decreases as the medium is acidified during growth and fermentation.Streptococci generally acidify the cytoplasm from approximately pH 7.6 to 5.7 (external pH 4.5) before growth and then fermentation cease.The internal enzyme machinery of these anaerobic fermenters thus tolerates a fairly wide range in internal proton concentration.Lactobacilli tolerate a significantly more acidic cytoplasmic pH of 4.4 (external pH 3.5).However, when the cytoplasmic pH decreases below a threshold pH, which depends on the organism, cellular functions are inhibited.Fermentation end-products, such as organic acids or alcohols, exert their deleterious effects by bringing about acidification of the cytoplasm below the permissible pH.Organic acids, which act as protonophores, or solvents, which perturb membrane phospholipids, at high concentrations increase the inward leak of H + so that H + efflux is not rapid
Novel Microemulsion Breaker System Remove Drill-in-Fluids Filter Cake and Remediate Near Wellbore Damage to Enhance Productivity of Horizontal Wells of Offshore Sabah, Malaysia

Field: Energy (Physical Sciences)

Abstract In a case study of four wells located in offshore Sabah Malaysia, a field application using microemulsion technology to develop a customized in-situ breaker solution enhanced production rate by removing oil-based mud (OBM) and synthetic based mud (SBM) filter cake and remediating near-wellbore damage. All wells were completed as open–hole horizontal wells. Key challenges of the field are the multiple sand layers interbedded with intra-reservoir shale intervals necessitating a complex well trajectory and an operational preference for drilling with SBM drill-in fluid (SBM DIF). Lower than expected production rates were associated a water-impermeable SBM DIF filter cake and solids residue resulting from a conventional breaker system being unable to fully remove emulsion damage and effectively disrupt the filtercake. A series of laboratory tests for return permeability using formation cores from the offset wells and ceramic discs were completed as part of a feasibility study prior to field trials of the new microemulsion breaker system - a customized formulation consisting of a proprietary surfactant blend, organic acid, corrosion inhibitor and brine designed to remove the damage caused by the SBM DIF and restore open-hole flow conditions. The new breaker system has ultra-low interfacial tension which, when pumped into the open-hole section and allowed to soak for a sufficient period of time, diffuses into the rock matrix and forms an in-situ microemulsion completely and uniformly cleaning the near wellbore environment of SBM DIF residue, dispersing solids and leaving all surfaces water-wet. Laboratory results described in this paper show that the customized microemulsion breaker has the capability to remove SBM DIF filter cake, remediate emulsion damage caused by SBM-DIF, and restores the rock matrix back to its original permeability and predrilled state. All four wells in this field application have exceeded their expected production rate. The customized microemulsion breaker is the major contributing factor.
Use of Na{sup 24} in a circulation study on a patient believed to have impaired circulation in the left leg

Field: Medicine (Health Sciences)

This report describes a diagnostic study utilizing sodium 24 on a patient with a vascular disorder in a left lower extremity. Five cc. of normal saline containing 50 microcuries of radioactive sodium were injected into the left antecubital vein. Radioactivity was determined at the soles of both feet for 30 seconds until the counts had levelled off and the exchange of sodium had apparently reached equilibrium. Circulation time from arm to foot was measured and was found to be 30 seconds in both extremities.
Leadership in online learning in higher education: Why instructional designers for online learning should lead the way

Field: Social Sciences (Social Sciences)

With the increase in demand for online education at the university level has also come the “recognition that in order to be effective, such programs cannot simply be on-line replicas of the instruction delivered in classrooms” (Reiser, 2001, p. 64). An environment of collaboration with a shared vision is needed to bring faculty expertise together with online learning design and technological expertise. This article addresses why and how instructional designers should lead the way.