gebhart/patrepeval huggingface dataset:
The first 1000 cultured species of the human gastrointestinal microbiota (2014)

The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
Reviewing the Effects of l-Leucine Supplementation in the Regulation of Food Intake, Energy Balance, and Glucose Homeostasis (2015)

Leucine is a well-known activator of the mammalian target of rapamycin (mTOR). Because mTOR signaling regulates several aspects of metabolism, the potential of leucine as a dietary supplement for treating obesity and diabetes mellitus has been investigated. The objective of the present review was to summarize and discuss the available evidence regarding the mechanisms and the effects of leucine supplementation on the regulation of food intake, energy balance, and glucose homeostasis. Based on the available evidence, we conclude that although central leucine injection decreases food intake, this effect is not well reproduced when leucine is provided as a dietary supplement. Consequently, no robust evidence indicates that oral leucine supplementation significantly affects food intake, although several studies have shown that leucine supplementation may help to decrease body adiposity in specific conditions. However, more studies are necessary to assess the effects of leucine supplementation in already-obese subjects. Finally, although several studies have found that leucine supplementation improves glucose homeostasis, the underlying mechanisms involved in these potential beneficial effects remain unknown and may be partially dependent on weight loss.
Application of Copper-Decoration Method to Characterize As-Grown Czochralski-Silicon (1992)

Czochralski-silicon wafers having ring-likely distributed stacking faults (ring-SFs) were investigated by means of copper decoration. The size and density of copper precipitates were measured by X-ray transmission topography and preferential etching. In the outer region of the ring-SFs, electrical properties (recombination lifetime of minority carriers, the dielectric breakdown strength) were found to be excellent. On the other hand, in the inner region of the ring-SFs electrical properties were degraded. These phenomena may be explained by the large defects which remain in the center region of the ingot.
A CBP derivative as bipolar host for performance enhancement in phosphorescent organic light-emitting diodes (2012)

N,N′-Dicarbazolyl-4,4′-biphenyl (CBP) is one of the most successful uni-polar host materials for phosphorescent organic light-emitting diodes (PhOLEDs). We report the synthesis and properties of one novel CBP derivative, CBP-CN, with two cyano groups (CN) at the 3-site of carbazole rings. The strong electron-withdrawing CN group was introduced with the expectation to promote electron-injecting/-transporting abilities and to achieve bipolar features for CBP-CN. In comparison with the parent CBP, CBP-CN possesses lowered HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) levels and dramatically increased Tg (glass transition temperature, 162 °C), but unaltered HOMO–LUMO band gap and triplet energy (2.69 eV). Green and red PhOLEDs were fabricated with CBP-CN as hosts for traditional iridium phosphors. The maximum luminance efficiency (ηL) of 80.61 cd A−1 (23.13%) was achieved for the green PhOLED, and 10.67 cd A−1 (15.54%) for the red one, which represent efficiency increases of 25–33% compared with those of the best devices with CBP host and are even among the best data for phosphorescent OLEDs reported so far. The theoretical calculation and the carrier-only devices investigation confirmed that the electron-injecting/-transporting character and the bipolar nature of CBP-CN should be responsible for the performance enhancements.
Influence of particle agglomeration on the catalytic activity of carbon-supported Pt nanoparticles in CO monolayer oxidation (2004)

Fuel cell electrocatalysts usually feature high noble metal contents, and these favour particle agglomeration. In this paper a variety of synthetic approaches (wet chemical deposition, electrodeposition and electrodeposition on chemically preformed Pt nuclei) is employed to shed light on the influence of nanoparticle agglomeration on their electrocatalytic properties. Pt loading on model glassy carbon (GC) support is increased systematically from 1.8 to 10.6 μg Pt cm−2 and changes in the catalyst structure are followed by transmission electron microscopy. At low metal loadings (≤5.4 μg Pt cm−2) isolated single crystalline Pt nanoparticles are formed on the support surface by wet chemical deposition from H2PtCl4 precursor. An increase in the metal loading results, first, in a systematic increase of the average diameter of isolated Pt nanoparticles and, second, in coalescence of nanoparticles and formation of particle agglomerates. This behaviour is in line with the previous observations on carbon-supported noble metal fuel cell electrocatalysts. The catalytic activity of Pt/GC electrodes is tested in CO monolayer oxidation. In agreement with the previous studies (F. Maillard, M. Eikerling, O. V. Cherstiouk, S. Schreier, E. Savinova and U. Stimming, Faraday Discuss., 2004, 125, 357), we find that the reaction is strongly size sensitive, exhibiting an increase of the reaction overpotential as the particle size decreases below ca. 3 nm. At larger particle sizes the dependence levels off, the catalytic activity of particles with diameters above 3 nm approaching that of polycrystalline Pt. Meanwhile, Pt agglomerates show remarkably enhanced catalytic activity in comparison to either isolated Pt nanopraticles or polycrystalline Pt foil, catalysing CO monolayer oxidation at ca. 90 mV lower overpotential. Enhanced catalytic activity of Pt agglomerates is ascribed to high concentration of surface defects. CO stripping voltammograms from Pt/GC electrodes, comprising Pt agglomerates along with isolated single crystalline Pt nanoparticles from 2 to 6 nm size, feature double voltammetric peaks, the more negative corresponding to CO oxidation on Pt agglomerates, while the more positive to CO oxidation on isolated Pt nanoparticles. It is shown that CO stripping voltammetry provides a fingerprint of the particle size distribution and the extent of particle agglomeration in carbon-supported Pt catalysts.
Chromium and parenteral nutrition. (1995)

Studies involving patients on total parenteral nutrition (TPN) led to conclusive documentation of the essential role of Cr in human nutrition. These patients developed severe diabetic symptoms including glucose intolerance, weight loss, impaired energy utilization, and nerve and brain disorders that were refractory to insulin. After addition of Cr to TPN fluids, diabetic symptoms were alleviated, and exogenous insulin was no longer required. Cr intake by healthy subjects consuming average Westernized diets is suboptimal; if these subjects experience severe physical trauma or other forms of stress, Cr status may be overtly compromised. Recommendations for daily Cr supplementation of 10-20 micrograms for patients on short-term TPN (< or = 1-3 mos) appear to be adequate. Stable patients on long-term TPN may receive ample Cr from that present in TPN fluids. Because of the variable nature of contaminating Cr, Cr intake and losses of TPN patients should be monitored.
Functional expression in Escherichia coli of proteins B and C from soluble methane monooxygenase of Methylococcus capsulatus (Bath) (1992)

Methylococcus capsulatus (Bath) uses a soluble methane monooxygenase (sMMO) to catalyse the oxidation of methane to methanol. sMMO is comprised of three components; A, B and C. Protein C (the reductase) transfers electrons from NADH to protein A (the hydroxylase) which contains the active site, and protein B regulates this electron flow. The five genes encoding the sMMO proteins and their subunits are clustered and have been cloned in Escherichia coli. A DNA fragment containing mmoB, the gene encoding protein B, was subcloned into pT7-5, a plasmid of the T7 RNA polymerase promoter expression system. Upon induction, E. coli expressed protein B which was fully functional after purification. The gene encoding protein C, mmoC, was amplified with unique restriction sites at each end using the polymerase chain reaction and then subcloned into pT7-7 (a plasmid similar to pT7-5 but containing its own ribosome-binding site and ATG start codon). Protein C expressed in E. coli was also found to be functional. This is the first report of the functional expression of methanotroph methane monooxygenase genes in a heterologous host and represents a significant step forward in our analysis of the assembly and catalysis of sMMO.
Expression of a plant protein by Neurospora crassa (1997)

Heterologous expression of plant genes may serve as an important alternative for producing plant proteins. We have investigated the ability of the fungus Neurospora crassa to secrete zeamatin, a protein produced by Zea mays. Zeamatin was induced after being fused to glucoamylase, an extracellular hydrolase produced by N. crassa. Glucoamylase induction and other culture parameters were monitored in untransformed N. crassa grown in shaken liquid culture. A DNA plasmid, pGEZ, was constructed by inserting zeamatin-encoding cDNA into an expression cassette containing the promoter, a truncated open reading frame, and the terminator sequence of the N. crassa glucoamylase gene. Zeamatin-encoding cDNA was modified at the N terminus to include a kex-2 protease site, allowing cleavage of the chimeric product in the secretory pathway. Strains containing the chimeric gene construct were grown in liquid culture and induced for glucoamylase and zeamatin production. Zeamatin antibody detected a protein in a Western blot of concentrated culture supernatants that comigrated with authentic zeamatin. Secreted zeamatin was active in inhibiting the growth of Candida albicans in an agar diffusion assay, indicating that zeamatin had been correctly synthesized, processed, and secreted by N. crassa.
SyM-BBB: a microfluidic blood brain barrier model (2012)

Current techniques for mimicking the Blood-Brain Barrier (BBB) largely use incubation chambers (Transwell) separated with a filter and matrix coating to represent and to study barrier permeability. These devices have several critical shortcomings: (a) they do not reproduce critical microenvironmental parameters, primarily anatomical size or hemodynamic shear stress, (b) they often do not provide real-time visualization capability, and (c) they require a large amount of consumables. To overcome these limitations, we have developed a microfluidics based Synthetic Microvasculature model of the Blood-Brain Barrier (SyM-BBB). The SyM-BBB platform is comprised of a plastic, disposable and optically clear microfluidic chip with a microcirculation sized two-compartment chamber. The chamber is designed in such a way as to permit the realization of side-by-side apical and basolateral compartments, thereby simplifying fabrication and facilitating integration with standard instrumentation. The individually addressable apical side is seeded with endothelial cells and the basolateral side can support neuronal cells or conditioned media. In the present study, an immortalized Rat Brain Endothelial cell line (RBE4) was cultured in SyM-BBB with a perfusate of Astrocyte Conditioned Media (ACM). Biochemical analysis showed upregulation of tight junction molecules while permeation studies showed an intact BBB. Finally, transporter assay was successfully demonstrated in SyM-BBB indicating a functional model.
Synthesis and Characterization of Elastin-Mimetic Protein Gels Derived from a Well-Defined Polypeptide Precursor (2000)

To elucidate the effects of uniformity of molecular architecture on gel properties, a protein polymer based on the elastin-mimetic repeat sequence [(Val-Pro-Gly-Val-Gly)4(Val-Pro-Gly-Lys-Gly)], 1 (Lys-25), was synthesized using genetic engineering and microbial protein expression. The regularly placed lysine residues in poly(Lys-25) underwent selective reaction with electrophilic cross-linkers under mild conditions in either dimethyl sulfoxide or aqueous phosphate buffer to afford solvent-swollen networks. Chemical derivatization and spectroscopic investigations of the cross-linking reaction indicated that approximately 85% of the lysine residues reacted with the cross-linker. The protein hydrogel exhibited reversible, temperature-dependent expansion and contraction with an estimated midpoint temperature for the phase transition at 35 °C. Scanning electron microscopy (SEM) investigations indicated profound differences in morphology between protein gels prepared in organic vs aqueous solution.
Caspases, Apoptosis, and Alzheimer Disease: Causation, Correlation, and Confusion (2001)

Extensive neuron loss occurs in Alzheimer disease (AD) brain and some authors have speculated that dysregulation of apoptotic death pathways is etiologically responsible for the disease. Apoptosis is regulated in mammalian cells by a family of cysteine proteases called caspases. At least 7 different caspases (caspases 1, 2, 3, 6, 8, 9, and 12) have been implicated in regulating neuronal cell death in response to amyloid beta (A beta) exposure in vitro, in animal models of neurodegenerative diseases, and in AD brain itself. Despite this seemingly impressive array of data implicating caspases and apoptosis as etiologic factors in AD, the direct involvement of caspase-dependent neuronal apoptosis in AD pathogenesis remains uncertain. Alternative explanations for some findings, contradictory experimental observations, and lack of morphologically convincing apoptotic neurons in the vast majority of AD brains has led to the revised hypothesis that apoptosis-associated molecular events cause neuronal dysfunction in the absence of, or prior to, neuronal death. Unfortunately, this new view renders the term "apoptosis-associated" functionally meaningless since it bears no relationship with apoptotic death and fails to focus scientific investigation on the molecular insults that trigger the "apoptosis-associated" response in AD neurons. On balance, an etiologic role for caspases in AD is far from proven. It remains possible, however, that caspase-dependent neuronal death contributes to AD neuron loss and thus, caspase inhibition offers some hope for extending AD neuron survival so that other agents, targeting upstream events, may delay or reverse primary AD pathology.
Translating natural language utterances to search queries for SLU domain detection using query click logs (2012)

Logs of user queries from a search engine (such as Bing or Google) together with the links clicked provide valuable implicit feedback to improve statistical spoken language understanding (SLU) models. However, the form of natural language utterances occurring in spoken interactions with a computer differs stylistically from that of keyword search queries. In this paper, we propose a machine translation approach to learn a mapping from natural language utterances to search queries. We train statistical translation models, using task and domain independent semantically equivalent natural language and keyword search query pairs mined from the search query click logs. We then extend our previous work on enriching the existing classification feature sets for input utterance domain detection with features computed using the click distribution over a set of clicked URLs from search engine query click logs of user utterances with automatically translated queries. This approach results in significant improvements for domain detection, especially when detecting the domains of user utterances that are formulated as natural language queries and effectively complements to the earlier work using syntactic transformations.
Promotion of experimental liver metastasis by tumor necrosis factor (1995)

Models for experimental metastasis were established to investigate the influence of rmTNF on tumor-colony formation in the liver. Highly metastatic lymphoma tumor cells were either injected i.v. or inoculated s.c. to form spontaneous metastases. In both systems, administration of rmTNF to the animals led to significant enhancement of the number of liver metastases in comparison with control groups. The number of metastatic tumor-cell colonies at an early stage of metastasis was increased, as well as the number of surface metastases in a late stage. Consequently, TNF-treated animals revealed a higher mortality. The optimal time for TNF to exert this metastasis-enhancing effect was found to be 7 days after tumor inoculation. In vitro adhesion of the lymphoma tumor cells to a mouse endothelioma cell line was strongly inhibited by monoclonal antibodies interfering with the interaction of VCAM-1 with VLA-4. These results support and extend earlier results with a fibrosarcoma lung colonization model. In addition, they show that stimulation of the immune system in tumor-bearing hosts activates tumor-promoting pathways, in addition to having possible beneficial effects.
Polarity and transport properties of rabbit kidney proximal tubule cells on collagen IV-coated porous membranes (1995)

A high degree of functional polarity has been obtained in primary cultures of rabbit kidney proximal tubule cells grown on collagen IV-coated porous membranes. Tight confluency was attained 6 days after seeding and maintained for at least 6 more days, as shown by analysis of paracellular inulin diffusion. From day 6 onward, L-lactate, ammonia, and D-glucose concentration gradient and a pH difference of approximately 1 unit developed between the two nutrient medium compartments. Confluent monolayers expressed organic ion transport properties higher than those formerly reported for other cell models. Transcellular transport of 20 microM tetraethylammonium was directed from basal to apical compartment and was specifically inhibited by mepiperphenidol (1 mM). Unidirectional transport of 2.4 microM p-aminohippurate also occurred from basal to apical compartment, was saturable, and specifically inhibited by probenecid (1 mM). These results suggest that rabbit kidney proximal tubule cells, cultured under the experimental conditions described here, may be a useful model for the in vitro study of highly polarized renal transport processes.
Rescue of Transgenic Alzheimer’s Pathophysiology by Polymeric Cellular Prion Protein Antagonists (2019)

Cellular prion protein (PrP<sup>C</sup>) binds the scrapie conformation of PrP (PrP<sup>Sc</sup>) and oligomeric β-amyloid peptide (Aβo) to mediate transmissible spongiform encephalopathy (TSE) and Alzheimer's disease (AD), respectively. We conducted cellular and biochemical screens for compounds blocking PrP<sup>C</sup> interaction with Aβo. A polymeric degradant of an antibiotic targets Aβo binding sites on PrP<sup>C</sup> with low nanomolar affinity and prevents Aβo-induced pathophysiology. We then identified a range of negatively charged polymers with specific PrP<sup>C</sup> affinity in the low to sub-nanomolar range, from both biological (melanin) and synthetic (poly [4-styrenesulfonic acid-co-maleic acid], PSCMA) origin. Association of PSCMA with PrP<sup>C</sup> prevents Aβo/PrP<sup>C</sup>-hydrogel formation, blocks Aβo binding to neurons, and abrogates PrP<sup>Sc</sup> production by ScN2a cells. We show that oral PSCMA yields effective brain concentrations and rescues APPswe/PS1ΔE9 transgenic mice from AD-related synapse loss and memory deficits. Thus, an orally active PrP<sup>C</sup>-directed polymeric agent provides a potential therapeutic approach to address neurodegeneration in AD and TSE.
Inhibition of Human Immunodeficiency Virus-1 (HIV-1) Replication After Transduction of Granulocyte Colony-Stimulating Factor–Mobilized CD34+ Cells From HIV-1–Infected Donors Using Retroviral Vectors Containing Anti–HIV-1 Genes (1997)

Transfer of "anti-HIV-1 genes" into hematopoietic stem cells of human immunodeficiency virus-1 (HIV-1)-infected individuals may be a potent therapeutic approach to render mature cells arising from transduced stem cells resistant to the destructive events associated with HIV-1 infection. To determine the feasibility of gene therapy for acquired immunodeficiency syndrome in individuals already infected with HIV-1, granulocyte colony-stimulating factor mobilized peripheral blood CD34+ cells were isolated from HIV-1-infected individuals and transduced with retroviral vectors containing three different anti-HIV-1-genes: the Rev binding domain of the Rev Responsive Element (RRE decoy) (L-RRE-neo), a double hammerhead ribozyme vector targeted to cleave the tat and rev transcripts (L-TR/TAT-neo), and the trans-dominant mutant of rev (M10) (L-M10-SN). As a control, a vector mediating only neomycin resistance (LN) was used. After 3 days of transduction on allogeneic stroma in the presence of stem cell factor, interleukin-6 (IL-6), and IL-3, the cultures were G418-selected, and then challenged with HIV-1(JR-FL) and a primary HIV-1 isolate. Compared with the control cultures, the L-RRE-neo-, L-TR/TAT-neo-, and L-M10-SN-transduced cultures displayed up to 1,000-fold inhibition of HIV-1 replication after challenge with HIV-1(JR-FL) and the primary HIV-1 isolate. Growth of the hematopoietic cells in long-term bone marrow culture was not perturbed by the presence of any of the anti-HIV-1 genes. This study shows that anti-HIV-1 genes can be introduced into CD34+ cells from individuals already infected with HIV-1, and strongly inhibit HIV-1 replication in primary monocytes derived from the CD34+ progenitors.