cssi/SciSciGPT-SciSciNet huggingface dataset:
Natural Variability in S-Adenosylmethionine (SAM)-Dependent Riboswitches: S-Box Elements in Bacillus subtilis Exhibit Differential Sensitivity to SAM In Vivo and In Vitro

Riboswitches are regulatory systems in which changes in structural elements in the 5' region of the nascent RNA transcript (the "leader region") control expression of the downstream coding sequence in response to a regulatory signal in the absence of a trans-acting protein factor. The S-box riboswitch, found primarily in low-G+C gram-positive bacteria, is the paradigm for riboswitches that sense S-adenosylmethionine (SAM). Genes in the S-box family are involved in methionine metabolism, and their expression is induced in response to starvation for methionine. S-box genes exhibit conserved primary sequence and secondary structural elements in their leader regions. We previously demonstrated that SAM binds directly to S-box leader RNA, causing a structural rearrangement that results in premature termination of transcription at S-box leader region terminators. S-box genes have a variety of physiological roles, and natural variability in S-box structure and regulatory response could provide additional insight into the role of conserved S-box leader elements in SAM-directed transcription termination. In the current study, in vivo and in vitro assays were employed to analyze the differential regulation of S-box genes in response to SAM. A wide range of responses to SAM were observed for the 11 S-box-regulated transcriptional units in Bacillus subtilis, demonstrating that S-box riboswitches can be calibrated to different physiological requirements.
Clustering on subspaces and sparse representation of signals

In many practical problems the data X under consideration (given as (m /spl times/ N)-matrix) is of the form X = AS, where the matrices A and S with dimensions m /spl times/ n and n /spl times/ N respectively (often called mixing matrix or dictionary and source matrix) are unknown (m /spl les/ n < N). Under some conditions, we can recover A and S uniquely (up to scaling and permutation), such that S is r-sparse in sense that each column of S has at most m - r nonzero elements. In this paper we consider the case r /spl ges/ 2 and develop an algorithm for clustering over subspaces, which is essential for identification of the mixing matrix A. The idea of this clustering is the same as in the k-mean clustering problem, but instead of balls, here we cluster oven subspaces with co-dimension r. The problem is to find subspaces with co-dimension r such that the sum of the distances from given data points to them is minimal. For identification of the source matrix, we apply a special source recovery algorithm. We illustrate our algorithms with an example. We note that our method is quite general, since the sparseness conditions could be obtained with some preprocessing methods and no independence conditions for the source signals are imposed (in contrast to independent component analysis).
Comparison of Heparin Therapy for ≤48 Hours to >48 Hours in Unstable Angina Pectoris

Of 450 consecutive patients with unstable angina admitted to a tertiary care, university-based medical center over a 24-month period, 334 were administered heparin and aspirin for some length of time. Two groups of 98 patients matched for acuity and gender at baseline were treated with either 48 hours (group 2) of heparin. The acuity model used in this study incorporates 6 factors: age, recent myocardial infarction, treatment with intravenous nitroglycerin, previous therapy with beta blockers or calcium antagonists, baseline ST depression, and diabetes. Despite similar risks and overall clinical outcome, group 2 had significantly more myocardial infarction or death after 48 hours than group 1 (p = 0.01). In part, this was due to a delay in the performance of coronary angiography (2.8 +/- 1.4 vs 3.5 +/- 15 days, p = 0.01), coronary intervention (2.7 +/- 1.8 vs 5.1 +/- 2.3 days, p = 0.01), and bypass surgery (3.8 +/- 3.6 vs 7.0 +/- 5.6 days, p = 0.02). There was no difference between groups regarding the success of coronary intervention (90% vs 88%, p = NS). Heparin duration was influenced by the finding of intracoronary thrombus or ulceration on angiography before revascularization, as each finding was seen more often in group 2 (thrombus, 12% vs 24%; ulceration, 38% vs 60%). These results suggest that the optimal duration of heparin therapy is up to 48 hours after admission in unstable angina; a longer time period is associated with increased adverse consequences.
Selectional restriction and semantic priming effects in normals and Broca's aphasics

Three experiments explored the extent to which patterns of abnormal comprehension in Broca’s aphasia can be attributed to a disruption of information encoded in the selectional restrictions of verbs. An auditory lexical decision paradigm was used to examine sensitivity to selectional restriction relations between verbs and their noun arguments as well as to associative semantic relations. Experiment I explored these effects at the lexical level. Experiment II examined these effects in a simple syntactic context, and Experiment III compared these effects in grammatical and ungrammatical sentence contexts. Both normal and Broca’s aphasic subjects showed sensitivity to selectional restrictions and semantic associates in both lexical and sentential contexts. However, although Broca’s aphasics did show sensitivity to selectional restriction information associated with verbs, unlike normal subjects they failed to show a selection restriction effect in ungrammatical sentences, suggesting that access to selectional restriction information was less stable than access to semantic associative information. Implications of the results for normals and Broca’s aphasics are discussed in relation to parallel and serial theories of sentence processing and to lexically based theories of aphasic language comprehension deficits. q 2005 Elsevier Ltd. All rights reserved.
Age-progressed images may harm recognition of missing children by increasing the number of plausible targets

Age progression, often used to help find missing children, is a technique whereby an outdated photograph of an individual is used to generate an updated image of that individual. Despite its importance, few empir- ical psychological studies have tested the utility of age progression. The current studies had two purposes: (1) to empirically test the effectiveness of a computerized age-progression system (APRILage); and (2) to examine how the presentation of an age-progressed image changes observers' decision-making strate- gies. Presenting participants with an age-progressed image in addition to an outdated image resulted in fewer target recognitions and more mistaken non-target 'recognitions' (Study 1; N = 135), led participants to assign fewer confidence points to the actual target and more confidence points to non-targets (Study 2; N = 231), and increased, rather than decreased, the number of plausible targets (Study 3; N = 88). Results are explained within a multidimensional face-space conceptualization of facial recognition.
Barriers reported among patients with breast and cervical abnormalities in the patient navigation research program: impact on timely care.

Abstract Background Patient navigation (PN) is a system-level strategy to decrease cancer mortality rates by reducing barriers to cancer care. Barriers to resolution among participants in the PN intervention arm with a breast or cervical abnormality in the Patient Navigation Research Program and navigators' actions to address those barriers were examined. Methods Data from seven institutions (2005–2010) included 1,995 breast and 1,194 cervical patients. A stratified Cox proportional hazards regression model was used to examine the effects of barriers on time to resolution of an abnormal screening test or clinical finding. Findings The range of unique barriers was 0 to 12 and 0 to 7 among participants with breast and cervical abnormalities, respectively. About two thirds of breast and one half of cervical participants had at least one barrier resulting in longer time to diagnostic resolution among breast (adjusted hazard ratio [HR], 0.744; p p Conclusions Having a barrier resulted in a delay in diagnostic resolution of an abnormal screening test or clinical finding. Health care systems can use these findings to improve existing PN programs or when developing new programs.
Characterization of Genes Responsible for the CO-Linked Hydrogen Production Pathway in Rubrivivax gelatinosus

Upon exposure to carbon monoxide, the purple nonsulfur photosynthetic bacterium Rubrivivax gelatinosus produces hydrogen concomitantly with the oxidation of CO according to the equation CO + H2O ↔ CO2 + H2. Yet little is known about the genetic elements encoding this reaction in this organism. In the present study, we use transposon mutagenesis and functional complementation to uncover three clustered genes, cooL, cooX, and cooH, in Rubrivivax gelatinosus putatively encoding part of a membrane-bound, multisubunit NiFe-hydrogenase. We present the complete amino acid sequences for the large catalytic subunit and its electron-relaying small subunit, encoded by cooH and cooL, respectively. Sequence alignment reveals a conserved region in the large subunit coordinating a binuclear [NiFe] center and a conserved region in the small subunit coordinating a [4Fe-4S] cluster. Protein purification experiments show that a protein fraction of 58 kDa molecular mass could function in H2 evolution mediated by reduced methyl viologen. Western blotting experiments show that the two hydrogenase subunits are detectable and accumulate only when cells are exposed to CO. The cooX gene encodes a putative Fe-S protein mediating electron transfer to the hydrogenase small subunit. We conclude that these three Rubrivivax proteins encompass part of a membrane-bound, multisubunit NiFe-hydrogenase belonging to the energy-converting hydrogenase (Ech) type, which has been found among diverse microbes with a common feature in coupling H2 production with proton pumping for energy generation.
Royal scaling for factor matrices, yes or no ?

It is suggested that factor matrices be scaled for presentation—not just computation—so that the test vectors in the common factor space all become and remain of unit-length, the termini of which all lie on the surface of a unit hypersphere. This implies that factor matrices representing uncorrelated (“orthogonal”) factors are row-normalized. [Factor matrices representing correlated (“oblique”) factors would also have test vectors of unit-length, but the row vectors in such a matrix would not be normalized because of the nonorthogonality of such vectors.]
A generalized message-passing mechanism for communicating sequential processes

Bidirectional message-passing (bi-io), a novel symmetric communication mechanism for concurrent processes, is introduced and developed. The mechanism is symmetric in the sense that, in one atomic action, a message is transmitted in each direction between two processes. For some applications (tree structure, systolic arrays) this method is shown to have several advantages over conventional synchronization and communication primitives (mainly conciseness of programs, absence of certain types of deadlock). The mechanism is rigorously defined with a CSP-like syntax and a weakest-precondition semantics. Two systolic arrays are developed using bidirectional message-passing: a matrix-vector multiplier and a palindrome recognizer. >
Structural Analysis and Dynamics of Retinal Chromophore in Dark and Meta I States of Rhodopsin from 2H NMR of Aligned Membranes

Rhodopsin is a prototype for G protein-coupled receptors (GPCRs) that are implicated in many biological responses in humans. A site-directed (2)H NMR approach was used for structural analysis of retinal within its binding cavity in the dark and pre-activated meta I states. Retinal was labeled with (2)H at the C5, C9, or C13 methyl groups by total synthesis, and was used to regenerate the opsin apoprotein. Solid-state (2)H NMR spectra were acquired for aligned membranes in the low-temperature lipid gel phase versus the tilt angle to the magnetic field. Data reduction assumed a static uniaxial distribution, and gave the retinylidene methyl bond orientations plus the alignment disorder (mosaic spread). The dark-state (2)H NMR structure of 11-cis-retinal shows torsional twisting of the polyene chain and the beta-ionone ring. The ligand undergoes restricted motion, as evinced by order parameters of approximately 0.9 for the spinning C-C(2)H(3) groups, with off-axial fluctuations of approximately 15 degrees . Retinal is accommodated within the rhodopsin binding pocket with a negative pre-twist about the C11=C12 double bond that explains its rapid photochemistry and the trajectory of 11-cis to trans isomerization. In the cryo-trapped meta I state, the (2)H NMR structure shows a reduction of the polyene strain, while torsional twisting of the beta-ionone ring is maintained. Distortion of the retinal conformation is interpreted through substituent control of receptor activation. Steric hindrance between trans retinal and Trp265 can trigger formation of the subsequent activated meta II state. Our results are pertinent to quantum and molecular mechanics simulations of ligands bound to GPCRs, and illustrate how (2)H NMR can be applied to study their biological mechanisms of action.
Synaptic organization of individual neurons in the macaque lateral geniculate nucleus.

Parvocellular and magnocellular neurons in the dorsal lateral geniculate nucleus of macaque monkeys were recorded electrophysiologically and then injected with HRP. The injected neurons were examined with the electron microscope. Synaptic terminals contacting the dendrites of individual neurons were classified and the synapses counted to estimate the number and distribution of each type over the entire dendritic tree. Seven parvocellular and 2 magnocellular neurons were analyzed. Two of the parvocellular neurons had presynaptic dendrites and no axons. These interneurons had electro-physiological characteristics much like those of relay neurons with the exception that their receptive field center responses had the opposite sign; i.e., they had OFF centers, while most neurons around them had ON centers. All of the relay neurons had similar types and distributions of terminal contacts. However, the distribution of each synaptic type along the dendrites of an individual neuron was not homogeneous. Retinal and F terminals were located predominantly on proximal dendrites whereas RSD terminals, either from the cortex and/or brain stem, predominated on the intermediate and distal dendrites. Parvocellular neurons were estimated to have about 500 total synapses on their dendritic trees, while magnocellular neurons had about 3000 total synapses on their dendritic trees. The retinal terminals making synaptic contacts with magnocellular neurons were also presynaptic to terminals containing flattened vesicles; these latter terminals also had synapses onto the magnocellular neuron's dendrites. Such a synaptic arrangement is called a triadic arrangement, or triad. Parvocellular neurons rarely had such triadic arrangements. In comparing these data with those of the cat, it was concluded that the major synaptic difference between relay cell types in both species (Class 1/Class 2 cells for the cat and parvo/magno cells for the monkey) was the frequent occurrence of triads for Class 2 cells and magnocellular cells versus the infrequent occurrence of triads for Class 1 cells and parvocellular cells. Although these triadic arrangements have been studied for over 2 decades, their function has yet to be determined, but probably relates to inhibition of retina signals at dendrites of magnocellular neurons in the monkey and Class 2 cells in the cat.
AKT activation by N-cadherin regulates beta-catenin signaling and neuronal differentiation during cortical development

During cerebral cortical development, neural precursor-precursor interactions in the ventricular zone neurogenic niche coordinate signaling pathways that regulate proliferation and differentiation. Previous studies with shRNA knockdown approaches indicated that N-cadherin adhesion between cortical precursors regulates β-catenin signaling, but the underlying mechanisms remained poorly understood. Here, with conditional knockout approaches, we find further supporting evidence that N-cadherin maintains β-catenin signaling during cortical development. Using shRNA to N-cadherin and dominant negative N-cadherin overexpression in cell culture, we find that N-cadherin regulates Wnt-stimulated β-catenin signaling in a cell-autonomous fashion. Knockdown or inhibition of N-cadherin with function-blocking antibodies leads to reduced activation of the Wnt co-receptor LRP6. We also find that N-cadherin regulates β-catenin via AKT, as reduction of N-cadherin causes decreased AKT activation and reduced phosphorylation of AKT targets GSK3β and β-catenin. Inhibition of AKT signaling in neural precursors in vivo leads to reduced β-catenin-dependent transcriptional activation, increased migration from the ventricular zone, premature neuronal differentiation, and increased apoptotic cell death. These results show that N-cadherin regulates β-catenin signaling through both Wnt and AKT, and suggest a previously unrecognized role for AKT in neuronal differentiation and cell survival during cortical development.
Comparative ultrastructure of lipid storage sites in femaleEuchaeta marina andPleuromamma xiphias (Copepoda: Calanoida)

FemaleEuchaeta marina (Prestandrea, 1833) have one large, thin-walled lipid sac, whereas femalePleuromamma xiphias (Giesbrecht, 1889) have two separate and morphologically distinct lipid storage sites. One lipid site inP. xiphias corresponds to the mesenteric tissue that surrounds the anterior region of the midgut. The morphology of these cells resembles that of mammalian brown adipocytes. The cytoplasm is filled with extensive smooth endoplasmic reticulum, numerous mitochondria and several deposits of intracellular lipid. The second lipid site ofP. xiphias lies in the posterior region of the metasome and resembles the thin-walled lipid sac ofE. marina. Both lie adjacent to, but are not contiguous with, the narrow mesenteric tissue surrounding the last region of the midgut. Both sacs contain a single, large deposit of intracellular lipid enclosed by a very thin rim of cytoplasm and resemble mammalian white adipocytes. The different habitats and reproductive processes of these two copepod species may relate to the observed variations in lipid cell morphology. The reserve lipid inE. marina plays a primary role in reproduction and is linked closely with the continuous cycle of oocytic maturation. The lipids synthesized and stored byP. xiphias, a strong vertical migrator, may be influenced by food availability, a function of their mesopelagic habitat. The primary role of the reserve lipids in this copepod may be to provide energy during migrations and between feeding periods, with relatively less lipid being allocated to reproduction.
Atypical hepatocellular adenoma–like neoplasms with β-catenin activation show cytogenetic alterations similar to well-differentiated hepatocellular carcinomas

The distinction of hepatocellular adenoma from well-differentiated hepatocellular carcinoma (HCC) arising in noncirrhotic liver can be challenging, particularly when tumors histologically resembling hepatocellular adenoma occur in unusual clinical settings such as in a man or an older woman or show focal atypical morphologic features. In this study, we examine the morphologic, immunohistochemical, and cytogenetic features of hepatocellular adenoma-like neoplasms occurring in men, women 50 years or older or younger than 15 years, and/or those with focal atypia (small cell change, pseudogland formation, and/or nuclear atypia), designated atypical hepatocellular neoplasms, where the distinction of hepatocellular adenoma versus HCC could not be clearly established. Immunohistochemistry was performed for β-catenin, glutamine synthetase, and serum amyloid A in 31 hepatocellular adenomas, 20 well-differentiated HCCs, and 40 atypical hepatocellular neoplasms. Chromosomal gains/losses had previously been determined in 37 cases using comparative genomic hybridization or fluorescence in situ hybridization. β-Catenin activation was observed in 35% of atypical hepatocellular neoplasms compared with 10% of typical hepatocellular adenomas (P < .05) and 55% of well-differentiated HCCs (P = .14). Cytogenetic changes typically observed in HCC were present in all atypical hepatocellular neoplasms with β-catenin activation. β-Catenin activation in atypical hepatocellular neoplasms was also associated with atypical morphologic features. Follow-up data were limited, but adverse outcome was observed in 2 atypical hepatocellular neoplasms with β-catenin activation (1 recurrence, 1 metastasis); transition to areas of HCC was observed in 1 case. The similarity in morphologic and cytogenetic features of β-catenin-activated hepatocellular adenoma-like tumors and HCC suggests that the former tumors represent an extremely well-differentiated variant of HCC.
High sensitivity PCR assay in plastic micro reactors

Small volume operation and rapid thermal cycling have been subjects of numerous reports in micro reactor chip development. Sensitivity aspects of the micro PCR reactor have not been studied in detail, however, despite the fact that detection of rare targets or trace genomic material from clinical and/or environmental samples has been a great challenge for microfluidic devices. In this study, a serpentine shaped thin (0.75 mm) polycarbonate plastic PCR micro reactor was designed, constructed, and tested for not only its rapid operation and efficiency, but also its detection sensitivity and specificity, in amplification of Escherichia coli (E. coli) K12-specific gene fragment. At a template concentration as low as 10 E. coli cells (equivalent to 50 fg genomic DNA), a K12-specific gene product (221 bp) was adequately amplified with a total of 30 cycles in 30 min. Sensitivity of the PCR micro reactor was demonstrated with its ability to amplify K12-specific gene from 10 cells in the presence of 2% blood. Specificity of the polycarbonate PCR micro reactor was also proven through multiplex PCR and/or amplification of different pathogen-specific genes. This is, to our knowledge, the first systematic study of assay sensitivity and specificity performed in plastic, disposable micro PCR devices.
Border-crossers' nephropathy: the risk of coming to America

Immigrants attempting to cross the border often wander for days without food or water, subsequently developing acute kidney injury (AKI) secondary to rhabdomyolysis. In this article, we describe ou...
A novel clofarabine bridge strategy facilitates allogeneic transplantation in patients with relapsed/refractory leukemia and high-risk myelodysplastic syndromes.

A novel clofarabine bridge strategy facilitates allogeneic transplantation in patients with relapsed/refractory leukemia and high-risk myelodysplastic syndromes
Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities.
Evaluating The Strategic Implications Of Japanese IT Offshore Outsourcing In China And India

Many studies have been done on the market, managerial and technological factors that impact IT outsourcing decisions. However, few of these studies have looked at institutional and cultural factors influencing various approaches to outsourcing. Developments in Japanese IT software outsourcing make it an excellent sector for studying the impact of such institutional and cultural factors. This qualitative study looks at the contrasting motivations behind IT outsourcing to India and China in order to gain insights into what the Japanese firms consider the key success factors for IT software offshore outsourcing. Preliminary indications are that old business relations, trust, language requirements, cultural similarity and the ability to capture certain idiosyncratic business practices and routines are essential factors driving Japanese IT outsourcing decisions.
Analysis of potential factors allowing coexistence in a sexual/asexual minnow complex

The northern redbelly dace (Chrosomus eos) and the finescale dace (C. neogaeus) have hybridized to produce an all-female, asexual hybrid (C. eos-neogaeus) that reproduces by sperm-limited parthenogenesis (gynogenesis). However, in this system, gynogenesis is not 100 % efficient; triploid females are occasionally formed which reproduce as sexuals, producing nuclear males and females of the paternal species (generally C. eos). Thus, the asexual lineage continually produces occasional males that can serve as a sperm source. Because (almost) all hybrid offspring are females, the hybrid population has the potential to grow more quickly and even outcompete the sexuals, thus eliminating their own sperm source. The current research uses behavioral testing, ovarian analyses, and modeling to examine three hypotheses for the maintenance of the sexual/asexual complex: male discrimination against hybrid females, fecundity differences between sexual and asexual females, and production of nuclear male sexuals from the asexual lineage. Results suggest that males do not discriminate against asexual females, and that both sexual and asexual females have similar fecundities, eliminating these hypotheses as potential coexistence mechanisms. However, computer simulations of population growth support the hypothesis that occasional triploidy within the hybrid population supplies enough breeding males to maintain the sexual/asexual complex.
Nanotechnology: Development of practical systems and nano-micro-macro integration

There are strong nanotechnology research programs across the world with every conceivable application in all economic sectors. Basic discoveries have progressed at an amazing pace, as evidenced by the accumulation of publications in the literature. At present, the development of practical systems and commercial products is the next big challenge. Nanoscale is not a human scale. In many cases, development of practical systems demands seamless integration of nano-micro-macro to produce scaled components and processes. While the ultimate vision in nanotechnology may be an entirely bottom-up approach to building systems, it is unrealistic to expect this to happen anytime in the foreseeable future. Only realistic possibility to achieve tangible results in a reasonable time frame, before the stakeholders run out of patience, is to use nanomaterials in a hybrid approach that involves a systematic nano-micro-macro integration. Such an approach will also allow us to utilize the existing infrastructure in the micro area (MEMS, microelectronics) from the last couple of decades, which would make economic sense. This talk will expand on this theme on product and system development using nanomaterials and nanotechnology. Examples will include a carbon nanotube (CNT) based chemical sensor that has been tested for monitoring air quality in the crew cabin in the International Space Station in 2009 and further developed for security applications; a CNT based biosensor for water quality monitoring and health monitoring; CNT-based X-ray tubes for security and other applications; supercapacitors, and several other developments we have been working on for the last 5–8 years. The author thanks all past and present NASA Ames colleagues for their contributions to the application development efforts, especially Jing Li, Yijiang Lu, Jessica Koehne, Cattien Nguyen, Jinwoo Han, Beomsok Kim, Ami Hannon and Michael Oye.
The Treatment of Pre-Acquisition Contingencies and Bargain Purchases: Proposed Changes to APB 16

In their article "Accounting for a Bargain Purchase in a Business Combination" DeMoville and Petrie (D&P) point out that application of APB 16 to some bargain purchase transactions can result in misleading information related to the reported values for non-current assets. This paper extends the D&P study by advancing another treatment consistent with other reasons. A review of the causes of bargain purchaases is appropriate since cause should dictate the accounting treatment. The current standard and both (D&P and this paper) proposed treatments seem to have a place in accounting for acquisitions.
Emerging Issues in Duoethnography.

AbstractDuoethnography is a relatively new research method in which two participants interrogate the cultural contexts of autobiographical experiences in order to gain insight into their current perspectives on and experience of issues related to personal and professional identities. Commonly explored themes include race, gender, pedagogy, professional practice, or sexual identity. While borrowing from other qualitative methods, duoethnography is distinctive in its emphasis on the researchers as the site of the research and on the interacting narratives. This paper attempts to assess the state of the method in relation to the basic tenets established in earlier work. Among the specific recommendations are that future duoethnographers consider establishing an integral methodological core without becoming prescriptive; that the role and relationships of participants be more clearly defined; and that researchers explore ways of making conversations transparent enough to witness the transformative process tha...
Scientific Realism and Components: The Case of Classical Astronomy

L'A. defend contre l'anti-realisme de Van Fraassen le realisme de l'astronomie classique heritee de Proclus, concernant le mouvement planetaire et ses composantes en un epicycle et un deferent, ou en un mouvement excentrique, dont le caractere non-observable souleve le probleme a la fois epistemique et rationnel de la justification de la croyance en leur realite et en leur capacite a sauver les phenomenes
The allosteric regulatory mechanism of the E. coli MetNI methionine ABC transporter

The MetNI methionine importer of Escherichia coli, an ATP Binding Cassette (ABC) transporter, uses the energy of ATP binding and hydrolysis to catalyze the high affinity uptake of D- and L-methionine. Early in vivo studies showed that the uptake of external methionine is repressed by the level of the internal methionine pool, a phenomenon termed transinhibition. Our understanding of MetNI mechanism has thus far been limited to a series of crystal structures in an inward facing conformation. To understand the molecular mechanism of transinhibition, we studied the kinetics of ATP hydrolysis using detergent-solubilized MetNI. We find that transinhibition is due to noncompetitive inhibition by L-methionine, much like a negative feedback loop. Thermodynamic analyses revealed two allosteric methionine binding sites per transporter. This quantitative analysis of transinhibition, the first to our knowledge for a structurally defined transporter, builds upon the previously proposed structurally based model for regulation. This mechanism of regulation at the transporter activity level could be applicable to not only ABC transporters but other types of membrane transporters as well.
The study of the method for determination of cyanide in water by flow injection analysis

[Objective] To establish a method for determination of cyanide in water by flow injection analysis(FIA).[Methods] Cyanide in water was detected by FIA,and the best experimental conditions were chosen.[Results] Under the best conditions,the linear range was 2.0-200.0 μg/L,and the detection limit of the method was 0.39 μg/L,with the relative standard deviations(RSD) of the determination of standard solution being 0.74%-3.19%.For analysis of water,this method obtained the satisfactory result,and the average recovery was 95.8%-106.1%.As compared with national standard methods as isonicotinic acid-barbituric acid spectrophotometry,flow injection analysis showed no significant difference in determination.[Conclusion] This method is sensitive and suitable for the determination of cyanide in water.
A new hybrid simulated annealing algorithm and its application

In this paper,multilayer feedforward neural networks model is framed to solve the problem in nonlinear system identification and prediction.To train the weights of NN,it proposed a new hybrid algorithm consisting of Powell algorithm and simulated annealing algorithm with adaptive cooling schedule.The main parameters in the cooling schedule are initial value and the attenuation function of control parameter(fictive temperature) in the algorithm.The whole iteration is divided into several stages.When each stage ends,according to NN model errors,the next stage's tempering temperature,the parameter of attenuation function of fictive temperature,and initial value of iterative step-length are adaptively modified.The above hybrid algorithm has strongly global and local search property and identification precision is remarkably raised.The validity of the scheme is proved by its applications.
Changes of calcitonin gene-related peptide and nerve growth factor in human dental pulp tissues following orthodontic force

AIM:To examine the expression of calcitonin gene-related peptide(CGRP) and nerve growth factor(NGF) in human dental pulp tissues in the early stage following orthodontic force.METHODS:Twerty patients were randomly assigned to the control,1 d,3 d,7 d and 15 d group.According to Derringer methods,orthodontic force(in the range of 0.5-1N in a mesial and extrusive direction) was applied to the upper first premolars of the test groups.The test teeth were extracted at the indicated time.Immunohistochemical method(SABC method) was utilized to localize and examine the expression of CGRP and NGF in the paraffin section of decalcifying dental tissue.Average optical density(AOD) of the positive cells was analyzed quantitatively by image analysis system.RESULTS:Strong CGRP expression and weak NGF expression were observed in the control group.One day after orthodontic force,CGRP expression decreased significantly(P 0.05),but on day 3,its expression significantly increased(P 0.05).NGF expression increased obviously 1 d after orthodontic forces(P 0.05),reached maximum 3 d post-orthodontic force addition(P 0.05) and decreased afterwards.On 15 d post-orthodontic force addition,CGRP and NGF expressions were the same as in the control group.CONCLUSION:CGRP and NGF are up-regulated in human dental pulp tissues following orthodontic force and it is suggested that CGRP and NGF may play a role in the pain reaction and pulp restoration in the early stage of orthodontic treatment.
LES/RANS Modeling of Aero-Optical Effects in a Supersonic Cavity Flow

Abstract : A hybrid Large Eddy simulation / Reynolds-Averaged Navier-Stokes turbulence model is applied to compute the wavefront aberrations in an optical beam passing through a supersonic open cavity flow. The turbulence model blends a RANS-type closure near solid walls with a subgrid model in the free-stream based on the ratios of estimated inner and outer turbulent length scales. The cavity geometry is modeled using an immersed boundary method, and an auxiliary flat plate simulation is performed to replicate the effects of the wind-tunnel boundary layer on the computed optical path difference. Two-dimensional proper orthogonal decomposition modes of the optical wavefront are computed; these compare favorably with wind tunnel data despite uncertainties about inflow turbulence levels and boundary layer thicknesses over the wind tunnel window. Dynamic mode decomposition of a planar wavefront spanning the entire cavity reveals that wavefront distortions are driven by shear layer oscillation at the Rossiter frequencies; these disturbances create eddy shocklets that propagate into the free-stream and create additional optical path disturbances.
Effects of template aging on facial recognition

"Facial recognition revenues are projected to grow from $34.4m in 2002 to $429.1m in 2007 and are expected to comprise approximately 10% of the entire biometric market" (International Biometric Group, Facial Recognition Market, 2003). With biometrics becoming a more viable solution to today's verification and identification needs as "customers deploy it for criminal and civil identification applications" (International Biometric Group, Facial Recognition Market, 2003), it is increasingly important to understand all of the factors that affect performance of biometric systems. One factor is the changing of an individual's biometric template over time. The resolution of this factor is the goal of template updating. Template updating falls into one of two categories, template aging or template improvement. While template updating attempts to mitigate change and compensate for it in a biometric template (Jain, et al., 2003, p.3), it is not fully understood how it affects the performance of a biometric system. This research will attempt to answer the question to what extent does template aging affect biometric system performance in an unattended facial recognition identification setting.
Deficit Irrigation as a Strategy to Cope with Declining Groundwater Supplies: Experiences from Kansas

The High Plains aquifer shown in Fig. 3.1 underlies 453,248 km2 in parts of eight states (Nebraska, Texas, Kansas, Colorado, New Mexico, Oklahoma, Wyoming, and South Dakota) making it the biggest aquifer in North America (Fig. 3.1). The predominant formation in the High Plains aquifer is the Ogallala Formation of the Miocene/Pliocene age (Sophocleous 2012), thus this aquifer is commonly referred to as the Ogallala aquifer. This predominantly unconfined aquifer comprises of silt, sand, gravel and clay, and varies in saturated thickness and permeability (Buchanan et al. 2009). For example, the predevelopment aquifer thickness and depth to water in Kansas varies from 15 m to over 90 m, and 8 m to over 105 respectively (High Plain Atlas). Most of the water from the aquifer is paleo or fossil water associated with the events of the last ice age when glaciers covered the Great Plains.
Eight-Year Long-Term Survival of an Advanced Gastric Cancer Patient Treated by Multidisciplinary Therapy Including Repeated Surgery and Metronomic Chemotherapy

A 69-year-old male, who had gastric cancer with extensive intra-abdominal lymph node metastasis, received palliative distal gastrectomy. He underwent repeated resection of metachronous right and left adrenal metastatic lesions 2 years and 5.3 years after the initial operation, respectively. The patient also experienced right femoral bone metastasis and IVC tumour thrombus 2.9 years and 6.6 years after the initial surgery, which were treated by radiation therapy. The slowly progressive tumour status was maintained by continuation of metronomic chemotherapy including S-1 as a key drug, and a total of 8-year long-term survival was achieved. Although rare, some selected patients with advanced gastric cancer have a chance of long-term survival, like the current case. The efficacy of multidisciplinary therapy for far advanced gastric cancer patients, especially an important role of repeated surgery and metronomic chemotherapy, was discussed.
Toward an Understanding of the Excitonic Structure of the CP47 Antenna Protein Complex of Photosystem II Revealed via Circularly Polarized Luminescence.

Identification of the lowest energy pigments in the photosynthetic CP47 antenna protein complex of Photosystem II (PSII) is essential for understanding its excitonic structure, as well as excitation energy pathways in the PSII core complex. Unfortunately, there is no consensus concerning the nature of the low-energy state(s), nor chlorophyll (Chl) site energies in this important photosynthetic antenna. Although we raised concerns regarding the estimations of Chl site energies obtained from modeling studies of various types of CP47 optical spectra [Reinot, T; et al., Anal. Chem. Insights 2016, 11, 35–48] recent new assignments imposed by the shape of the circularly polarized luminescence (CPL) spectrum [Hall, J.; et al., Biochim. Biophys. Acta 2016, 1857, 1580–1593] necessitate our comments. We demonstrate that other combinations of low-energy Chls provide equally good or improved simultaneous fits of various optical spectra (absorption, emission, CPL, circular dichroism, and nonresonant hole-burned spectr...
Desistance under the Microscope: The Definition and Measurement of Desistance in Modern Criminology

What is desistance from crime? How do you know it when you see it? How does one measure it in research? As with any budding area of research, understanding what a concept means and how to operationally define it are vital. There remains some ambiguity with respect to (a) what desistance is and (b) how to measure it in research. For example, is desistance the absence of crime after 10 years? Can a person who was never seriously criminal really desist? If desistance is a process rather than the point at which one stops for good, how do researchers capture that process? In this chapter, Rocque reviews and charts various definitions of desistance and illustrates the consequences of having no standard measurement or analytic strategy when trying to come to grips with conclusions from desistance research. Conceptualization (e.g., what is desistance) varies both within the literature as well as the way it is measured and analyzed. Based on this review, five ‘lessons’ for desistance research are presented. Rocque recommends that criminology standardize basic concepts such as desistance and measurement strategies.
Dispersion immune change of soliton repetition rate in a silicon-nitride microresonator

We show soliton-self-frequency-shift (SSFS) in a SiN microresonator dominates the change of soliton repetition rate relative to thermal effects. The SSFS-induced repetition rate change with detuning is not directly dependent on the dispersion.
Dynamic Characteristics of Green Sandstone Subjected to Repetitive Impact Loading: Phenomena and Mechanisms

A split Hopkinson pressure bar apparatus driven by a pendulum hammer was used to perform uniaxial compression tests to examine the degradation process of green sandstone subjected to repetitive impact loading. The acoustic characteristics, dissipated energy, deformation characteristics, and microstructure evolution were investigated. The representative stress–strain curve can be broken into five stages that were characterized by changes in the axial strain response during impact loading. Both the ultrasonic wave velocity and cumulative dissipated energy exhibited obvious three-stage behavior with respect to the impact number. As the impact number increased, more than one peak was observed in the frequency spectra, and the relative weight of the peak frequency increased in the low-frequency range. According to the evolution of the ultrasonic wave velocity, the degradation process was divided into three stages. By comparing the intact stage I and early stage II microcrack development patterns, the initiation of new cracks and elongation of existing cracks were identified as the main degradation mechanisms. Furthermore, a slight increase in the number of cracks was observed, and microcrack lengths steadily increased. Moreover, due to the low level of microcrack damage, the deformation mechanism was mainly characterized by volume compression during impact loading. In late stage II, the main degradation mechanism was the elongation of existing cracks. Additionally, as microcracks accumulated in the rock samples, cracks were arranged parallel to the loading direction, which led to volume dilation. In stage III, microcracks continued to elongate nearly parallel to the loading direction and then linked to each other, which led to intense degradation in the rock samples. In this stage, rock sample deformation was mainly characterized by volume dilation during impact loading. Finally, rock samples were split into blocks with fractures oriented subparallel to the loading direction. These results can improve the understanding of the stability evaluations of rock structures subjected to repetitive impact loading.
Manipulating tree crown structure to promote old-growth characteristics in second-growth redwood forest canopies

Abstract In old-growth Sequoia sempervirens forests, reiterated trunks and limbs provide required habitat elements for specialized arboreal species, including an endangered seabird, Brachyramphus marmoratus. The oldest second-growth redwood forests—established after 19th century logging—lack species dependent on complex structure, presumably because redwoods maintain simple, model-conforming crowns for centuries unless damaged by wind or fire. We imposed a factorial experiment on 24 redwoods 59–75 m tall in six second-growth forests to determine if trunk reiteration and limb formation can be induced by removing treetops (topping) and branch tips (tipping) to disrupt apical control. We also increased light availability in the upper crown by pruning branches. After intensively mapping trunks and branches and imposing treatments, we re-mapped trees three years later to quantify growth increments. Topping stimulated trunk reiteration from the cut, and reiterated tops gained height more rapidly than controls. Tipping also stimulated trunk reiteration from branches, especially when combined with topping, resulting in formation of limbs (i.e., branches giving rise to reiterated trunks). Pruning had consistently negative effects on trunk and branch growth increments even after accounting for post-treatment variation in leaf area and light availability, suggesting that photosynthate was diverted to compartmentalization of wounds. Strategic injury of trees may have long-term conservation value in second-growth redwood forests if limbs can be initiated high enough in the crown to persist as trees approach maximum height. Topping and tipping treatments should be combined with silvicultural thinning of neighboring trees to increase light availability far more than can be achieved by pruning.