Miracle-dz/UniFAR-FTUs huggingface dataset:
Nmr studies of the molecular conformations in the linear oligopeptides H‐(L‐Ala)n‐L‐Pro‐OH

The molecular conformations of the linear oligopeptides H‐(L‐Ala)n‐L‐Pro‐OH, with n = 1,2 and 3, have been investigated. 13C nmr observation of the equilibrium between the cis and trans forms of the Ala‐Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala‐Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala‐Pro peptide bond was studied by comparison of the peptides H‐(Ala)n‐Pro‐OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from 1H nmr studies. However, the cis:trans ratio of the Ala‐Pro bond was not affected by N‐methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.
Mutations Enhancing Amino Acid Catabolism Confer a Growth Advantage in Stationary Phase

ABSTRACT Starved cultures of Escherichia coli undergo successive rounds of population takeovers by mutants of increasing fitness. These mutants express the growth advantage in stationary phase (GASP) phenotype. Previous work identified the rpoS819 allele as a GASP mutation allowing cells to take over stationary-phase cultures after growth in rich media (M. M. Zambrano, D. A. Siegele, M. A. Almirón, A. Tormo, and R. Kolter, Science 259:1757–1760, 1993). Here we have identified three new GASP loci from an aged rpoS819 strain: sgaA, sgaB, and sgaC. Each locus is capable of conferring GASP on therpoS819 parent, and they can provide successively higher fitnesses for the bacteria in the starved cultures. All four GASP mutations isolated thus far allow for faster growth on both individual and mixtures of amino acids. Each mutation confers a growth advantage on a different subset of amino acids, and these mutations act in concert to increase the overall catabolic capacity of the cell. We present a model whereby this enhanced ability to catabolize amino acids is responsible for the fitness gain during carbon starvation, as it may allow GASP mutants to outcompete the parental cells when growing on the amino acids released by dying cells.
An automatic annotation method for early esophageal cancers based on saliency guided superpixel segmentation

The annotation of Early Esophageal Cancer (EEC) in gastroscopic images is mainly performed by clinicians in clinic, In order to reduce subjective and fatigue manual annotation works, computer-aided annotation is needed for accurate diagnosis. This study develops an automatic annotation method to annotate EEC in gastroscopic images. We initially designed a new segmentation method named "Saliency Guided Superpixel Segmentation", to rapidly find the salient regions and their surrounding regions. Then, a two-step annotation strategy of EEC, which is based on the "relationships between the salient regions and EEC regions", was proposed. The first step is to detect the salient EEC regions and the second step is the left unsalient EEC regions. Finally, the two kinds of lesion regions are combined together to obtain the annotation results. 267 EEC images and 285 normal images were used to validate the proposed method. The experimental results show that, the detection rate and Dice similarity coefficients of our method were 97.14% and 74.53%, respectively. Compared with other patch-based or superpixel-based state-of-the-art methods, our method showed better performance. Thus, it has a good prospect for clinical application.
The Methodius Corpus of Rhetorical Discourse Structures and Generated Texts

Using the Methodius Natural Language Generation (NLG) System, we have created a corpus which consists of a collection of generated texts which describe ancient Greek artefacts. Each text is linked to two representations created as part of the NLG process. The first is a content plan, which uses rhetorical relations to describe the high-level discourse structure of the text, and the second is a logical form describing the syntactic structure, which is sent to the OpenCCG surface realization module to produce the final text output. In recent work, White and Howcroft (2015) have used the SPaRKy restaurant corpus, which contains similar combination of texts and representations, for their research on the induction of rules for the combination of clauses. In the first instance this corpus will be used to test their algorithms on an additional domain, and extend their work to include the learning of referring expression generation rules. As far as we know, the SPaRKy restaurant corpus is the only existing corpus of this type, and we hope that the creation of this new corpus in a different domain will provide a useful resource to the Natural Language Generation community.
Induction of microglial apoptosis by corticotropin‐releasing hormone

Neuropeptides are short‐chain peptides found in brain tissue, some of which function as neurotransmitters and others as hormones. Neuropeptides may directly or indirectly modulate glial functions in the CNS. In the present study, effects of various neuropeptides on the viability and inflammatory activation of cultured microglia were investigated. Vasoactive intestinal peptide, substance P, cholecystokinin and neuropeptide Y did not affect microglial cell viability, whereas corticotropin‐releasing hormone (CRH) induced a classical apoptosis of mouse microglia in culture as shown by nuclear condensation and fragmentation, terminal deoxynucleotidyl transferase dUTP nick‐end labeling, and cleavage of caspase 3 and poly(ADP‐ribose) polymerase protein. CRH, however, did not influence nitric oxide production or expression of inflammatory genes including those encoding cytokines and chemokines, indicating that CRH did not affect the inflammatory activation of microglia. The CRH‐induced microglial apoptosis appeared to involve a mitochondrial pathway and reactive oxygen species, based on the mitochondrial membrane potential change, caspase 9 activation and sensitivity to antioxidants. Taken together, our results indicate that the stress neuropeptide CRH may regulate neuroinflammation by inducing the apoptosis of microglia, the major cellular source of inflammatory mediators in the CNS.
Efficient nonviral gene delivery into primary lymphocytes from rats and mice

A rapid method for efficient gene delivery into primary rodent lymphocytes would greatly facilitate the study of signaling and metabolic pathways in untransformed hematopoietic cells as well as the validation of gene expression and targeting strategies before the generation of knockout or knock‐down animals. Here, we report that species‐adapted nucleofection procedures combined with optimized cultivation conditions render proliferating primary T cells, B cells, and natural killer cells from widely used rat and mouse strains susceptible to high‐level gene delivery. As a result, transgene expression levels were enhanced ? 10‐ to 370‐fold over established protocols. The effectiveness of the nucleofection approach for functional analyses was demonstrated by specific down‐regulation of CD4 cell surface molecules by either transient expression of the endocytosis‐inducing Nef protein from human immunodeficiency virus or by specific gene silencing mediated by small interfering RNA. In conclusion, this species‐adapted procedure for nonviral gene delivery renders primary rodent lymphocytes accessible to rapid functional ex vivo studies, which until now have not been feasible. Furthermore, nucleofection may aid the advancement of therapeutic nonviral gene delivery approaches.
An Architecture of Content-Centric Networking over Protocol-Oblivious Forwarding

Traditional Internet based on the IP routing has an innate deficiency when facing up with large numbers of concurrent distribution of video and other media content. Software-Defined Networking (SDN) and OpenFlow protocol try to improve data transfer efficiency and flexibility by separating the forwarding layer and control layer, and the content-based routing idea proposed by Content-Centric Networking (CCN), provides a possible direction for the evolution of the Internet. However, the current implementations of SDN-based CCN still rely on IP-based routing and lack of engineering realization. Protocol-Oblivious Forwarding (POF) protocol is an extension on OpenFlow protocol, supporting any network layer packet with user-defined format. A new content-centric network architecture POF- CCN is designed and implemented in this paper. Guided route principle and Bloom Filter structure are adopted in POF-CCN, to condense the content cache name into a limited size so as to look up content quickly. A prototype system is deployed in real network environment and test results prove the feasibility of the architecture.
The clinical use of colistin in patients with cystic fibrosis

Colistin is a cationic polypeptide antibiotic from the polymyxin family that was first introduced in 1962 but abandoned in the early 1970s because of initial reports of severe toxicities. However, a recent increase in the prevalence of multidrug resistant (MDR) Pseudomonas aeruginosa and the lack of novel agents in development calls for a need to re-examine the role of colistin therapy in patients with cystic fibrosis. Current data supports the use of intravenous colistimethate for the treatment of acute pulmonary exacerbations involving MDR P. aeruginosa and inhaled therapy for initial colonization. The frequency of nephrotoxicity and severity of neurotoxicity seem to be substantially less than previously believed. In addition, recent pharmacokinetic and pharmacodynamic data suggests new intravenous dosing regimens may enhance efficacy while minimizing toxicities; such regimens deserve further evaluation. Pre- and post-treatment spirometry is recommended at initiation of inhaled colistin therapy to identify sensitized individuals. Judicious use of colistin where the benefits have been clearly documented will retain this as a useful agent in the management of P. aeruginosa infections in patients with cystic fibrosis.
Tools for Handwriting and Grasp Patterns Used

Asha V. Asher OBJECTIVE. Classroom teachers teach handwriting, but when problems arise, students are referred to occupational therapy for remediation. This study, conducted by occupational therapists, reviews handwriting instruction by classroom teachers in one school district. METHOD. Teachers from kindergarten through grade 6 were asked to complete an open-ended questionnaire regarding handwriting instruction. RESULTS. Teachers differed in their methods of instruction, including in the programs and paper used, and practice provided. Teachers of grades 5 and 6 had to continue to review handwriting instruction, because all students could not fluently use handwriting as a tool of expression. CONCLUSION. Elementary students need structured instruction to develop the motor skill of writing. School-based occupational therapists can support effective handwriting instruction by interpreting information from motor learning theory pertaining to instruction and practice, which supports acquisition, transfer, and retention of handwriting skills. They also need to be cognizant of prior handwriting instruction when addressing handwriting difficulties.
Difference in Mass Analysis Using Labeled Lysines (DIMAL-K)

Here we describe an original strategy for unbiased quantification of protein expression called difference in mass analysis using labeled lysine (K) (DIMAL-K). DIMAL-K is based on the differential predigestion labeling of lysine residues in complex protein mixtures. The method is relevant for proteomic analysis by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. Protein labeling on lysine residues uses two closely related chemical reagents, S-methyl thioacetimidate and S-methyl thiopropionimidate. Using protein standards, we demonstrated that 1) the chemical labeling was quantitative, specific, and rapid; 2) the differentially labeled proteins co-migrated on two-dimensional gels; and 3) the identification by mass fingerprinting and the relative quantification of the proteins were possible from a single MALDI-TOF mass spectrum. The power of the method was tested by comparing and quantifying the secretion of proteins in normal and proinflammatory astrocytic secretomes (20 μg). We showed that DIMAL-K was more sensitive and accurate than densitometric image analysis and allowed the detection and quantification of novel proteins.
Lysyl oxidase‐like 2 (LOXL2) oxidizes trimethylated lysine 4 in histone H3

Methylation of histone H3 lysine 4 is linked to active transcription and can be removed by LSD1 or the JmjC domain‐containing proteins by amino‐oxidation or hydroxylation, respectively. Here we describe that its deamination can be catalyzed by lysyl oxidase‐like 2 protein (LOXL2), presenting an unconventional chemical mechanism for H3K4 modification. Infrared spectroscopy and mass spectrometry analyses demonstrated that recombinant LOXL2 specifically deaminates trimethylated H3K4. Moreover, by regulating H3K4me3 deamination, LOXL2 activity is linked with the transcriptional control of the CDH1 gene. These results reveal the existence of further H3 modification as well as a novel mechanism for H3K4me3 demethylation.
Observations on adrenergic innervation of dog heart.

The adrenergic innervation of the dog heart was studied by a histochemical fluorescence technique. The SA and AV nodes are extensively innervated by adrenergic fibers. Certain parts of the atria, auricles, and ventricles show a rich adrenergic innervation, while other parts of the same tissues are very deficient, suggesting that the sympathetic innervation to the heart is "patchy. " The adrenergic innervation of the Purkinje cells is likewise very sparse, large numbers of cells showing no adrenergic innervation at all. It is suggested that the adrenergically innervated Purkinje cells exhibit a form of "pacemaker" activity.
Melting temperature of tungsten from two ab initio approaches

We have calculated the melting temperature of tungsten by two ab initio approaches. The first approach can be divided into two steps. In the first step, we simulate a large coexisting solid and liquid system by the classical embedded-atom method potential and obtain an approximate melting temperature. In the second step, we compute the accurate melting temperature by performing the ab initio free-energy corrections. The second approach is to perform a direct ab initio molecular-dynamics simulation for the coexisting solid and liquid system using the constant particle number, pressure, and enthalpy ensemble. In the second approach, the simulation is carried out entirely using a density-functional theory Hamiltonian, and no other approximations are imposed. However, the simulation is performed using a relatively small supercell. The results obtained from two ab initio approaches can provide a check for each other. Our results show that they are in good agreement with each other and also in reasonably good agreement with the experimental value.
Some fundamental limitations in the control of two-mass systems

In this paper fundamental limitations in the control of two-mass systems are discussed, giving particular emphasis to the role of the minimum-phase lightly damped zeros of the system. Cheap control theory for SITO (Single Input Two Outputs) systems is used to quantify performance limitations on the class of all the stabilizing controllers, even allowing arbitrarily high control effort. These fundamental limitations arise even if all the transfer functions of the systems are stable and minimum phase, and are strictly related to the minimum phase zeros near the imaginary axis. Use of recent results on the best tracking performance achievable under control effort constraint confirms the limiting effect of such zeros.
A test of insulator interactions in Drosophila

Insulators are a class of elements that define independent domains of gene function. The Drosophila gypsy insulator is proposed to establish regulatory isolation by forming loop domains that constrain interactions between transcriptional control elements. This supposition is based upon the observation that insertion of a single gypsy insulator between an enhancer and promoter blocks enhancer function, while insertion of two gypsy insulators promotes enhancer bypass and activation of transcription. To investigate this model, we determined whether non‐gypsy insulators interacted with each other and with the gypsy insulator. Pairs of scs or scs′ insulators blocked enhancer function. Further, an intervening scs insulator did not block gypsy insulator interactions. Taken together, these data suggest that not all Drosophila insulators interact, with this property restricted to some insulators, such as gypsy. Three gypsy insulators inserted between an enhancer and promoter blocked enhancer function, indicating that gypsy insulator interactions may be restricted to pairs. Our studies imply that formation of loop domains may represent one of many mechanisms used by insulators to impart regulatory isolation.
Characterization and quantitation of concanavalin a binding by plasma membrane enriched fractions from soybean root.

The binding of concanavalin A (Con A) to soybean root membranes in plasma membrane enriched fractions (recovered from the 34/45% interface of simplified discontinuous sucrose density gradients) was studied using a radiochemical assay employing tritiated ((3)H)-Con A. The effect of lectin concentration, time, and membrane protein concentration on the specific binding of (3)H-Con A by the membranes was evaluated. Kinetic analyses showed that Con A will react with membranes in that fraction in a characteristic and predictable manner. The parameters for an optimal and standard binding assay were established. Maximal binding occurred with Con A concentrations in the range of 8 to 16% of the total membrane protein with incubation times greater than 40 min at 22 C. Approximately 10(15) molecules of (3)H-Con A were bound per microgram of membrane protein at saturation. Binding was reversible. Greater than 92% of the total Con A bound at saturation was released by addition of alpha-methyl mannoside.A major peak of (3)H-Con A binding was also observed in fractions recovered from the 25/30% interface of a complex discontinuous sucrose density gradient when membranes were isolated in the absence of Mg(2+). When high Mg(2+) was present in the isolation and gradient media, the peak was shifted to a fraction recovered from the 34/38% sucrose interface. These results suggest that Con A binding sites are also present on membranes of the endoplasmic reticulum. The amount of Con A bound by endoplasmic reticulum membranes was at least twice the amount bound by membranes in plasma membrane enriched fractions when binding was compared on a per unit membrane protein basis. In contrast, mitochondrial inner membranes, which equilibrate at the same density as plasma membranes, had little ability to bind the lectin.
The application of polysaccharide-based nanogels in peptides/proteins and anticancer drugs delivery

Abstract Finding adequate carriers for proteins/peptides and anticancer drugs delivery has become an urgent need, owing to the growing number of therapeutic macromolecules and the increasing amount of cancer incidence. Polysaccharide-based nanogels have attracted interest as carriers for proteins/peptides and anticancer drugs because of their characteristic properties like biodegradability, biocompatibility, stimuli-responsive behaviour, softness and swelling to help achieve a controlled, triggered response at the target site. In addition, the groups of the polysaccharide backbone are able to be modified to develop functional nanogels. Some polysaccharides have the intrinsic ability to recognise specific cell types, allowing the design of targeted drug delivery systems through receptor-mediated endocytosis. This review is aimed at describing and exploring the potential of polysaccharides that are used in nanogels which can help to deliver proteins/peptides and anticancer drugs.
Gendered Pathways From Child Abuse to Adult Crime Through Internalizing and Externalizing Behaviors in Childhood and Adolescence

Gender differences in externalizing and internalizing pathways from child abuse to adult crime were examined across four waves of an extended longitudinal study (N = 186 males and 170 females) using multiple-group structural equation modeling. Results show that child abuse was associated with both internalizing and externalizing behaviors in the elementary school years for both males and females. However, gender differences were found such that internalizing behaviors increased the risk of adult crime for females only, and externalizing behaviors increased the risk of adult crime for males only. Internalizing behaviors among males actually lessened the risk of adult crime, and externalizing behaviors were unrelated to adult crime among females. Findings confirm distinct pathways leading from child abuse to later crime for males and females, which is important for prevention and intervention strategies.
Extended Real Model of Kalman Filter for Time-Varying Harmonics Estimation

The effective harmonics estimation for measuring power signals has become an important issue in the power quality assessment. By reviewing those commonly used Kalman filter-based models, some limitations for harmonics estimation can be observed. In this paper an extended real model of Kalman filter combined with a resetting mechanism for accurately tracking time-varying harmonic components of power signals is presented. The usefulness of the proposed algorithm is demonstrated by a simple laboratory setup with LabVIEW program and the dedicated hardware for harmonics monitoring. Results show that the proposed method can achieve more accurate and robust measurement of harmonic amplitudes and phase angles for the time-varying power signals among compared methods while the uncertainty testing performances required by IEC standard 61000-4-30 are satisfied.