gebhart/patrepeval huggingface dataset:
Pulsed Field Capillary Electrophoresis of Multikilobase Length Nucleic Acids in Dilute Methyl Cellulose Solutions (1994)

Pulsed field capillary gel electrophoresis in dilute methyl cellulose solutions is used to separate nucleic acid fragments in the size range 75-23,000 base pairs. Field inversion is shown to increase resolution for fragments longer than about 500 base pairs. Methyl cellulose solutions as dilute as 0.01% can be used. Intermolecular hydrogen bonding is suggested as the cause of apparent cellulose fiber entanglement at concentrations below the calculated entanglement limit. The 1-kb DNA ladder and the lambda DNA/HindIII restriction fragment mixtures are each baseline resolved in a 28-cm capillary in less than 9 min at 180 V/cm (dc component).
The Hexahistidine Motif of Host-Defense Protein Human Calprotectin Contributes to Zinc Withholding and Its Functional Versatility (2016)

Human calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is an abundant host-defense protein that is involved in the metal-withholding innate immune response. CP coordinates a variety of divalent first-row transition metal ions, which is implicated in its antimicrobial function, and its ability to sequester nutrient Zn(II) ions from microbial pathogens has been recognized for over two decades. CP has two distinct transition-metal-binding sites formed at the S100A8/S100A9 dimer interface, including a histidine-rich site composed of S100A8 residues His17 and His27 and S100A9 residues His91 and His95. In this study, we report that CP binds Zn(II) at this site using a hexahistidine motif, completed by His103 and His105 of the S100A9 C-terminal tail and previously identified as the high-affinity Mn(II) and Fe(II) coordination site. Zn(II) binding at this unique site shields the S100A9 C-terminal tail from proteolytic degradation by proteinase K. X-ray absorption spectroscopy and Zn(II) competition titrations support the formation of a Zn(II)-His6 motif. Microbial growth studies indicate that the hexahistidine motif is important for preventing microbial Zn(II) acquisition from CP by the probiotic Lactobacillus plantarum and the opportunistic human pathogen Candida albicans. The Zn(II)-His6 site of CP expands the known biological coordination chemistry of Zn(II) and provides new insight into how the human innate immune system starves microbes of essential metal nutrients.
Expression of Angiogenic Factors Vascular Endothelial Growth Factor and Interleukin-8/CXCL8 Is Highly Responsive to Ambient Glutamine Availability (2004)

Vascular endothelial growth factor (VEGF) and interleukin-8/CXCL8 (IL-8) are prominent pro-angiogenic and pro-metastatic proteins that represent negative prognostic factors in many types of cancer. Hypoxia is thought to be the primary environmental cause of VEGF and IL-8 expression in solid tumors. We hypothesized that a lack of nutrients other than oxygen could stimulate the expression of these factors and previously demonstrated that expression of VEGF and IL-8 is responsive to amino acid deprivation. In the present study, we examined the effect of glutamine availability on the expression of these factors as well as the role of transcription factors NFkappaB and activating protein-1 (AP-1) in the response of TSE human breast carcinoma cells to glutamine deprivation. VEGF and IL-8 secretion and mRNA levels were dramatically induced by glutamine deprivation. mRNA stabilization contributed to this response. Glutamine deprivation increased NFkappaB (p65/p50) and AP-1 (Fra-1/c-Jun+JunD) DNA-binding activities. Blocking NFkappaB and AP-1 activation with curcumin as well as expression of dominant inhibitors, inhibitor of nuclear factor-kappaB (IkappaB) super repressor (IkappaBM), and a mutant form of c-Fos (A-Fos) demonstrated that the activation of NFkappaB and AP-1 transcription factors was necessary for the induction of IL-8 expression but dispensable for the induction of VEGF expression. A macro-array containing 111 NFkappaB target genes identified a total of 17 that were up-regulated 2-fold or more in response to glutamine deprivation. These included growth regulated oncogene alpha (GROalpha/GRO1/CXCL1), another neutrophil chemoattractant implicated in tumor angiogenesis and metastasis.
P‐75  Development of an <i>in vitro</i> test to evaluate cerumen‐dissolving properties of veterinary ear cleansing solutions (2004)

This study aimed to evaluate objectively the cleansing properties of four veterinary ear care solutions. An in vitro test was developed, based on dissolution of synthetic dog cerumen in test tubes. Artificial cerumen was produced, based on literature data, with a melting point and consistency very close to natural canine cerumen. One millilitre of test solution was poured into haemolysis tubes containing 100 mg of synthetic cerumen. Contact time was 10 min at 37°C. Moderate agitation was then applied for 10 s to mimic in vivo application. Solutions were vacuum‐filtered on filter paper and cerumen remaining in the tube or on the paper was weighed after drying. The experiment was repeated five times for each formulation. One‐way ANOVA was performed to detect differences between formulations. In order to validate the test, measurement of the solution wetting power was performed in parallel using the reference ISO 8022 method. Mean quantities of cerumen dissolved were 4.7, 6.5, 7.7, 14.7 and 23.2 mg for Cerulane ® , Otolane ® , distilled water (control), Otoclean ® and Physiological Ear Cleanser ® , respectively. The latter was the only solution that demonstrated greater ability for cerumen dissolution as compared to water ( P < 0.05). Macroscopically, Physiological Ear Cleanser ® solution became white and opaque in test tubes, reflecting the formation of an emulsion. Other solutions remained clear or only partially turbid. This cerumen dissolution test proved a practical and valuable model to assess the cleansing power of ear solutions before in vivo trials. Funding: Virbac SA.
A comparison of priority-based decentralized load balancing policies (1986)

Load balancing policies in distributed systems divide jobs into two classes; those processed at their of origination ( local jobs ) and those processed at some other site in the system after being transfered through a communication network ( remote jobs ). This paper considers a class of decentralized load balancing policies that use a threshold on the local job queue length at each host in making decisions for remote processing. They differ from each other according to how they assign priorities to each of these job classes, ranging from one providing favorable treatment to local jobs to one providing favorable treatment to remote jobs. Under each policy, the optimal load balancing problem is formulated as an optimization problem with respect to the threshold parameter. The optimal threshold is obtained numerically using matrix-geometric formulation and an iteration method. Last, we consider the effects that the job arrival process can have on performance. One expects that load balancing for systems operating in an environment of bursty job arrivals should be more beneficial than for an environment with random job arrivals. This fact is observed through numerical examples.
Use of biochemical markers of osteoarthritis to investigate the potential disease‐modifying effect of tibial plateau levelling osteotomy (2006)

Tibial plateau levelling osteotomy did not significantly alter the expression of the named candidate biomarkers. These findings reflect the limited nature of the arthrotomy or indicate that tibial plateau levelling osteotomy does not influence the progression of osteoarthritis (OA). From these studies, there is no evidence that tibial plateau levelling osteotomy affects cartilage metabolism.
<scp>l</scp>‐arginine and aminoguanidine reduce colonic damage of acetic acid‐induced colitis in rats: Potential modulation of nuclear factor‐<i>κ</i>B/p65 (2014)

The transcription factor, nuclear factor-κB (NF-κB) is a key inducer of inducible nitric oxide synthase (iNOS) gene expression. The aim of the present study was to investigate the potential protective effect of l-arginine (Arg; nitric oxide precursor) and aminoguanidine (inducible nitric oxide synthase inhibitor) against acetic acid (AA)-induced colitis in rats, and the potential role of NF-κB. Colitis was induced by intrarectal inoculation of rats with 4% acetic acid for three consecutive days. The effect of Arg and aminoguanidine on nitric oxide levels was assessed by Greiss assay and protein expression of NF-κB/p65, and inducible nitric oxide synthase was also investigated by immunohistochemistry. Slides were examined using ImageJ, and results reported as the percent area positive for each marker. Intrarectal AA caused a significant increase in bodyweight loss and colon weights. Arg at 100 mg/day for 7 days before induction of colitis diminished the changes in both bodyweight loss and colon weights. Furthermore, Arg attenuated the colonic tissues macroscopic and microscopic damage induced by acetic acid. In addition, i.p. AG 100 mg/kg given during and after induction of colitis recovered the colonic ulcerative lesion induced by AA. Arg can protect against colonic inflammation; an effect that probably be attributed to its nitric oxide-donating property, resulting in modulatory effects on the expression of NF-κB/p65 in the colon tissues. The results suggested that Arg might reduce the inflammation associated with colitis as confirmed by histopathological investigations. Arg might inhibit AA-induced colitis through the NF-κB/nitric oxide pathway.
The effect of Lactobacillus acidophilus administration upon the survival of Salmonella in randomly selected human carriers. (1983)

The influence of Lactobacillus acidophilus in milk upon carrier time of Salmonella infected humans was compared to that in a similar population which received no acidophilus milk. The participants were 132 individuals between 3 and 73 years old of both sexes. Many were carriers of more than one infective agent. None were suffering from acute gastrointestinal symptoms nor receiving medication. The participants entered the study various times after diagnosis, and consumed acidophilus milk ad libitum continuously until 3 to 5 negative feces samples were obtained. The results were compared with a control population consisting of 160 individuals who consumed neither fermented milk products nor medication. The data show that consumption of greater than 500 ml acidophilus milk shortened the duration of the Salmonella carrier state.
A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms (Tool Paper) (2022)

Blockchain has recently attracted the attention of the industry due, in part, to its ability to automate asset transfers. It requires distributed participants to reach a consensus on a block despite the presence of malicious (a.k.a. Byzantine) participants. Malicious participants exploit regularly weaknesses of these blockchain consensus algorithms, with sometimes devastating consequences. In fact, these weaknesses are quite common and are well illustrated by the flaws in various blockchain consensus algorithms [Pierre Tholoniat and Vincent Gramoli, 2019]. Paradoxically, until now, no blockchain consensus has been holistically verified. In this paper, we remedy this paradox by model checking for the first time a blockchain consensus used in industry. We propose a holistic approach to verify the consensus algorithm of the Red Belly Blockchain [Tyler Crain et al., 2021], for any number n of processes and any number f < n/3 of Byzantine processes. We decompose directly the algorithm pseudocode in two parts - an inner broadcast algorithm and an outer decision algorithm - each modelled as a threshold automaton [Igor Konnov et al., 2017], and we formalize their expected properties in linear-time temporal logic. We then automatically check the inner broadcasting algorithm, under a carefully identified fairness assumption. For the verification of the outer algorithm, we simplify the model of the inner algorithm by relying on its proven properties. Doing so, we formally verify, for any parameter, not only the safety properties of the Red Belly Blockchain consensus but also its liveness in less than 70 seconds.
Myb-Independent Macrophages: A Family of Cells That Develops with Their Tissue of Residence and Is Involved in Its Homeostasis (2013)

In most metazoans, all tissues contain phagocytes "in residence," generally termed "macrophages" in vertebrates. In contrast to myeloid cells produced continuously by the bone marrow (BM), tissue-resident macrophages develop during embryogenesis together with their tissue of residence, and persist in adulthood, independently of hematopoietic stem cells and the transcription factor Myb. They therefore represent an independent lineage from blood monocytes, dendritic cells, and monocytes/macrophages that are recruited to tissues during inflammation. Tissue-resident macrophage functions are yet to be completely defined. They all share the ability to scavenge toxic compounds, lipids, microorganisms, and dead cells and contribute to tissue remodeling, via phagocytosis and the production of growth factors. In contrast, the production of inflammatory mediators seems to be more associated with BM-derived cells. Tissue-resident macrophages and BM-derived myeloid cells thus differ in developmental origin and functions; the term "macrophages" could be reserved for Myb-independent-resident macrophages to avoid confusion. A genetic and molecular dissection of resident macrophage functions will reveal their roles in tissue metabolism and the maintenance of homeostasis independently of the extravasation of inflammatory leukocytes, and in the control of the recruitment of BM-derived cells in overt inflammation.
Acid‐catalyzed esterification of naphthenic acids (2012)

The reclamation of mining operation tailings water is of major concern to the oil sands industry. Naphthenic acids (NAs) are recognized as a major toxic component in tailings water. The acid‐catalyzed esterification of commercially prepared NAs to biodiesel was performed as a test case for the utilization of these toxic compounds. In a series of batch acid‐catalyzed esterification reactions, the influence of reaction temperature, catalyst type, catalyst concentration, and methanol to oil ratio on the esterification was investigated. The NA esterification reactions were found to be positively dependent on temperature and catalyst concentration while large methanol to oil ratios had a negative effect on the esterification. Finally, sulfuric acid was identified as a preferred catalyst for the esterification compared to p‐toluene sulfonic acid. The esterification was completed successfully at the relatively mild conditions used in commercial biodiesel production . © 2012 American Institute of Chemical Engineers Environ Prog, 32: 406‐410, 2013
Expression Quantitative Trait Loci Analysis of BAN, F3H and TT19 Genes in Brassica napus (2012)

Flavonone 3-hydroxylase (F3H), anthocyanidin reductase (ANR) encoded by BANYULS (BAN) gene and glutathione S-transferase encoded by TRANSPARENT TESTA 19 (TT19) gene are three key enzymes in flavonoid pathway, playing important roles in the synthesis and transport of anthocyanin and proanthocyanidin. However, little is known about the expression variations and the regulatory network in Brassica. In this study, we examined their expression levels in seeds of 30 days after flowering (DAF) in F7 recombinant inbred lines (RILs) derived from a cross between Brassica nap us cultivars Youyan2 (black-seeded) and GH06 (yellow-seeded), and characterized the locus-level regulatory network related to B. nap us BAN, F3H and TT19 genes. Expression quantitative trait loci (eQTL) mapping revealed five, seven and eight eQTLs for BAN, F3H and TT19 genes, respectively. Marker E4M8 was associated with qBAN-8-2 and qTT19-8-2, while marker H022L18-2 was linked with qBAN-16-4 and qF3H-16-6, implying that there might be upstream regulatory genes in E4M8 and H022L18-2 marker flanking regions. In further analysis, we identified four trans-eQTLs (qBAN-16-5, qF3H-16-5, qBAN-16-4 and qF3H-11-2) close to the location of the major QTL controlling yellow-seeded trait of B. nap us. The 200-kb flanking sequences of the four eQTL on B. rapa chromosome A09 showed well synteny to B. oleracea genome sequence and partial continuous fragment of chromosome 1 of Arabidopsis genome, suitable for candidate gene predication of eQTLs. Based on gene finding results, seven transcription factors were suggested to be the potential upstream candidate(s) controlling expression variations of BAN, F3H and TT19 genes. These results could provide a new approach for constructing regulatory pathways that contribute to complex traits, such as yellow-seeded trait.
Clinical and molecular review of atypical congenital adrenal hyperplasia (2015)

Congenital adrenal hyperplasia (CAH) is one of the most common inherited metabolic disorders. It comprises a group of autosomal recessive disorders caused by the mutations in the genes encoding for steroidogenic enzymes that involved cortisol synthesis. More than 90% of cases are caused by a defect in the enzyme 21-hydroxylase. Four other enzyme deficiencies (cholesterol side-chain cleavage, 17α-hydroxylase [P450c17], 11β-hydroxylase [P450c11β], 3β-hydroxysteroid dehydrogenase) in the steroid biosynthesis pathway, along with one cholesterol transport protein defect (steroidogenic acute regulatory protein), and one electrontransfer protein (P450 oxidoreductase) account for the remaining cases. The clinical symptoms of the different forms of CAH result from the particular hormones that are deficient and those that are produced in excess. A characteristic feature of CAH is genital ambiguity or disordered sex development, and most variants are associated with glucocorticoid deficiency. However, in the rare forms of CAH other than 21-hydroxylase deficiency so-called "atypical CAH", the clinical and hormonal phenotypes can be more complicated, and are not well recognized. This review will focus on the atypical forms of CAH, including the genetic analyses, and phenotypic correlates.
Development of Compact Ultra-Low-Field MRI System Using an Induction Coil (2017)

Ultra-low-field magnetic resonance imaging (ULF-MRI) is attractive for MRI applications such as a concurrent system of magnetoencephalography (MEG) and MRI. We are developing a compact ULF-MRI system that can be combined with a small-animal MEG system. In this paper, we developed a detection method that uses an induction coil instead of a superconducting quantum interference device for the ULF-MRI. The induction coil has advantages such as being more robust, easy to handle, and flexible for designing. We fabricated an induction coil from a copper wire with dimensions of 29 mm x 39 mm x 29 mm (inner diameter x outer diameter x length). A capacitor was connected to increase the sensitivity by the LC resonance effect. The resonance frequency was 3 kHz, and the corresponding magnetic field density for MRI measurement was 70 μT. The detection coil was integrated with the compact ULF-MRI system and placed inside a magnetically shielded box. MRI measurement was demonstrated by using water phantoms with a total volume of 5.5 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The size of the obtained image was 32 x 32 pixels for 30.2 mm x 30.2 mm. A clear shape of the water phantom was taken with this ULF-MRI system. This result shows the induction coil can be used for the compact ULF-MRI system.
Structural Control of the Excited-State Dynamics of Bis(dipyrrinato)zinc Complexes:  Self-Assembling Chromophores for Light-Harvesting Architectures (2004)

The replacement of the phenyl rings at the 5,5'-positions of a bis(dipyrrinato)zinc complex with mesityl groups transforms the molecule from a very weak emitter that deactivates rapidly after photoexcitation (Phif = 0.006; tau approximately 90 ps) to a highly fluorescent chromophore with a long-lived singlet excited state (Phif = 0.36; tau approximately 3 ns). The results demonstrate that steric constraints on aryl-ring internal rotation dramatically alter the excited-state properties of 5,5'-substituted bis(dipyrrinato)metal complexes. The insights establish the foundation for tuning the photophysical properties of these chromophores for use in diverse photochemical applications.
A Designedβ-Hairpin Containing a Natural Hydrophobic Cluster (2000)

Designer hairpins: 12-Residue peptide 1, containing D-proline, folds to form a two-stranded antiparallel β-sheet in aqueous solution, which causes clustering of the side chains of Trp 2, Tyr 4, Phe 11, and Val 13 (highlighted in the drawing). A similar cluster occurs in the folded state of the protein GB1. Thermodynamic analysis suggests that both the hydrophobic effect and intrinsic interstrand attractions contribute to β-hairpin stability.
Bio‐inspired Development of a Dual‐Mode Nanoprobe for MRI and Raman Imaging (2014)

New generation dual-mode imaging probes for MRI and Raman imaging techniques are developed, inspired by the hyper intense contrast enhancing capability in T1 -weighted MRI and characteristic Raman signal of natural melanin. MDA-MB-231cells labeled with dual-mode imaging probe are successfully detected in both T1-weighted MRI and Raman imaging.
Anomaly Detection in Satellite Communications Systems using LSTM Networks (2018)

Most satellite communications monitoring tools use simple thresholding of univariate measurements to alert the operator to unusual events [1], [2]. This approach suffers from frequent false alarms, and is moreover unable to detect sequence or multivariate anomalies [3]. Here we consider the problem of detecting outliers in high-dimensional time-series data, such as transponder frequency spectra. Long Short Term Memory (LSTM) networks are able to form sophisticated representations of such multivariate temporal data, and can be used to predict future sequences when presented with sufficient context. We report here on the utility of LSTM prediction error as a defacto measure for detecting outliers. We show that this approach significantly improves on simple threshold models, as well as on moving average and static predictors. The latter simply assume the next trace will be equal to the previous trace. The advantages of using an LSTM network for anomaly detection are twofold. Firstly, the training data do not need to be labelled. This alleviates the need to provide the model with specific examples of anomalies. Secondly, the trained model is able to detect previously unseen anomalies. Such anomalies have a degree of unpredictability that makes them stand out. LSTM networks are further able to potentially detect more nuanced sequence and multivariate anomalies. These occur when all values are within normal tolerances, but the sequence or combinations of values are themselves unusual. The technique we describe could be used in practice for alerting satellite network operators to unusual conditions requiring their attention.
Volatile fermentation products as attractants for Macrolepidoptera1 (1977)

Pure hexoses fermented in aqueous solutions proved as attractive to moths as the ordinary bait made from brown sugar, beer and baker's yeast. The attract ant properties are suggested to depend mainly on fermentation. Of 38 pure compounds (simple alcohols, acids, esters and aldehydes) present in the ordinary bait, 35 attracted Macrolepidoptera, the most efficient being ethyl alcohol, isoamyl alcohol, acetic acid and acetoin. Geometridae preferred ethyl alcohol, /1-phenethyl alcohol and acetoin. A mixture of eight compounds exhibited synergistic increase of attractiveness to Thyatiridae and Noctuidae, but not to Geometridae.