Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a Cellobiose Utilization Gene Cluster with Cryptic β-Galactosidase Activity in Vibrio fischeri

ABSTRACT Cellobiose utilization is a variable trait that is often used to differentiate members of the family Vibrionaceae. We investigated how Vibrio fischeri ES114 utilizes cellobiose and found a cluster of genes required for growth on this β-1,4-linked glucose disaccharide. This cluster includes genes annotated as a phosphotransferase system II (celA, celB, and celC), a glucokinase (celK), and a glucosidase (celG). Directly downstream of celCBGKA is celI, which encodes a LacI family regulator that represses cel transcription in the absence of cellobiose. When the celCBGKAI gene cluster was transferred to cellobiose-negative strains of Vibrio and Photobacterium, the cluster conferred the ability to utilize cellobiose. Genomic analyses of naturally cellobiose-positive Vibrio species revealed that V. salmonicida has a homolog of the celCBGKAI cluster, but V. vulnificus does not. Moreover, bioinformatic analyses revealed that CelG and CelK share the greatest homology with glucosidases and glucokinases in the phylum Firmicutes. These observations suggest that distinct genes for cellobiose utilization have been acquired by different lineages within the family Vibrionaceae. In addition, the loss of the celI regulator, but not the structural genes, attenuated the ability of V. fischeri to compete for colonization of its natural host, Euprymna scolopes, suggesting that repression of the cel gene cluster is important in this symbiosis. Finally, we show that the V. fischeri cellobioase (CelG) preferentially cleaves β-d-glucose linkages but also cleaves β-d-galactose-linked substrates such as 5-bromo-4-chloro-3-indolyl-β-d-galactoside (X-gal), a finding that has important implications for the use of lacZ as a marker or reporter gene in V. fischeri.
Relationships between retinal axonal and neuronal measures and global central nervous system pathology in multiple sclerosis.

OBJECTIVE To determine the relationships between conventional and segmentation-derived optical coherence tomography (OCT) retinal layer thickness measures with intracranial volume (a surrogate of head size) and brain substructure volumes in multiple sclerosis (MS). DESIGN Cross-sectional study. SETTING Johns Hopkins University, Baltimore, Maryland. PARTICIPANTS A total of 84 patients with MS and 24 healthy control subjects. MAIN OUTCOME MEASURES High-definition spectral-domain OCT conventional and automated segmentation-derived discrete retinal layer thicknesses and 3-T magnetic resonance imaging brain substructure volumes. RESULTS Peripapillary retinal nerve fiber layer as well as composite ganglion cell layer+inner plexiform layer thicknesses in the eyes of patients with MS without a history of optic neuritis were associated with cortical gray matter (P=.01 and P=.04, respectively) and caudate (P=.04 and P=.03, respectively) volumes. Inner nuclear layer thickness, also in eyes without a history of optic neuritis, was associated with fluid-attenuated inversion recovery lesion volume (P=.007) and inversely associated with normal-appearing white matter volume (P=.005) in relapsing-remitting MS. As intracranial volume was found to be related with several of the OCT measures in patients with MS and healthy control subjects and is already known to be associated with brain substructure volumes, all OCT-brain substructure relationships were adjusted for intracranial volume. CONCLUSIONS Retinal measures reflect global central nervous system pathology in multiple sclerosis, with thicknesses of discrete retinal layers each appearing to be associated with distinct central nervous system processes. Moreover, OCT measures appear to correlate with intracranial volume in patients with MS and healthy control subjects, an important unexpected factor unaccounted for in prior studies examining the relationships between peripapillary retinal nerve fiber layer thickness and brain substructure volumes.
ON THE STRUCTURE OF GRAPHS WHICH ARE LOCALLY INDISTINGUISHABLE FROM A LATTICE

For each integer $d\geqslant 3$ , we obtain a characterization of all graphs in which the ball of radius $3$ around each vertex is isomorphic to the ball of radius 3 in $\mathbb{L}^{d}$ , the graph of the $d$ -dimensional integer lattice. The finite, connected graphs with this property have a highly rigid, ‘global’ algebraic structure; they can be viewed as quotient lattices of $\mathbb{L}^{d}$ in various compact $d$ -dimensional orbifolds which arise from crystallographic groups. We give examples showing that ‘radius 3’ cannot be replaced by ‘radius 2’, and that ‘orbifold’ cannot be replaced by ‘manifold’. In the $d=2$ case, our methods yield new proofs of structure theorems of Thomassen [‘Tilings of the Torus and Klein bottle and vertex-transitive graphs on a fixed surface’, Trans. Amer. Math. Soc. 323 (1991), 605–635] and of Márquez et al. [‘Locally grid graphs: classification and Tutte uniqueness’, Discrete Math. 266 (2003), 327–352], and also yield short, ‘algebraic’ restatements of these theorems. Our proofs use a mixture of techniques and results from combinatorics, geometry and group theory.
Differences in Resilience by Acculturation Strategies: A Study with Qiang Nationality Following 2008 Chinese Earthquake

A number of studies have assessed the association between acculturation and resilience following atraumatic event. This study examines the relationship between acculturation strategies and resilience among the Qiang nationality following the 2008 Chinese earthquake. We found evidence that there are four acculturation strategies (integration, assimilation, separation and marginalization) based on the Qiang’s cultural identity status. We also assessed resilience among this sample, using the Connor-DavidsonResilience Scale (CD-RISC). Correlation analysis results indicated that most dimensions of the Qiang cultural identities have positive relationships with participants’ scores on CD-RISC dimensions of tenacity, strength and optimism. And regression analyses indicated that most of the cultural identity dimensions can predict resilience. The four acculturation strategies are also predictive of resilience: those with an Integration strategy have greater resilience than those pursuing marginalization; those pursuing assimilation and separation have intermediate levels of resilience.
Associations of spontaneous self-affirmation with health care experiences and health information seeking in a national survey of US adults

Objective: Self-affirming – such as by reflecting on one’s strengths and values – reduces defensiveness to threatening information, reduces negative effects of stereotype threat and promotes prosociality. These outcomes may promote physical health, highlighting a need to examine the role of self-affirmation in medical and health contexts. Design: Data were collected as part of the nationally representative, cross-sectional, 2013 Health Information National Trends Survey. Items were completed by 2731 respondents. Main Outcome Measures: Respondents answered questions about spontaneous self-affirmation tendencies, perceptions of providers and health care, involvement in medical appointments, health information seeking and engagement in medical research. Results: Spontaneous self-affirmation was associated with more positive perceptions of communication with one’s provider, better perceived quality of care, greater likelihood of asking questions in a medical appointment, greater information seeking for oneself and multiple indices of surrogate information seeking (i.e. seeking information for others). Four of eight significant associations remained significant when controlling for optimism. The associations of self-affirmation with aspects of the patient–provider relationship were not modified by factors likely to be associated with stereotype threat (e.g. race or BMI). Conclusion: Spontaneous self-affirmation was related to positive outcomes in health contexts. Experimental research is needed to further explore the causal nature of these associations.
An exploration of the current working relationship between the educational psychologist and the young offender in England

The purpose of this study was to explore the current working relationship between the Educational Psychologist and the Young Offender in England. It aimed to identify the work EPs have done with YOs in the previous year and to explore the Educational Psychologist’s perceptions of the characteristics they perceive as necessary for a successful relationship with a young offender. A mixed methods approach was applied whereby both quantitative and qualitative data was collected. Online questionnaires were sent to all Principal Educational Psychologists in England with the intention of the questionnaire being passed on to all Educational Psychologists within their local education authority. 47 Educational Psychologists took part in the quantitative stage, with 21 participants that were able to complete the questionnaire having worked with young offenders in the previous year. The qualitative data was collected through interviews from a sample of 8 participants. The findings suggest that the majority of Educational Psychologists’ work is commissioned by schools and Youth Offending Teams requesting support for young offenders with social, emotional and behavioural difficulties, to increase engagement, attendance, to assess their levels of need and to decrease reoffending. The participants reported that the most commonly used approach was that of solution focused. Looking at the characteristics that are necessary for a successful relationship between the Educational Psychologist and the young offender, using thematic analysis, 4 overarching themes emerged specific to the young offender and 9 specific to the Educational Psychologist. In conclusion this study achieved both its aims of conducting a survey to explore what a number of educational psychologists have done with young offenders over the previous year and to identify characteristics that the Educational Psychologists perceived to be necessary for a successful relationship with a young offender.
A Proteomic Approach for Identification of Secreted Proteins during the Differentiation of 3T3-L1 Preadipocytes to Adipocytes*

We have undertaken a systematic proteomic approach to purify and identify secreted factors that are differentially expressed in preadipocytes versus adipocytes. Using one-dimensional gel electrophoresis combined with nanoelectrospray tandem mass spectrometry, proteins that were specifically secreted by 3T3-L1 preadipocytes or adipocytes were identified. In addition to a number of previously reported molecules that are up- or down-regulated during this differentiation process (adipsin, adipocyte complement-related protein 30 kDa, complement C3, and fibronectin), we identified four secreted molecules that have not been shown previously to be expressed differentially during the process of adipogenesis. Pigment epithelium-derived factor, a soluble molecule with potent antiangiogenic properties, was found to be highly secreted by preadipocytes but not adipocytes. Conversely, we found hippocampal cholinergic neurostimulating peptide, neutrophil gelatinase-associated lipocalin, and haptoglobin to be expressed highly by mature adipocytes. We also used liquid chromatography-based separation followed by automated tandem mass spectrometry to identify proteins secreted by mature adipocytes. Several additional secreted proteins including resistin, secreted acidic cysteine-rich glycoprotein/osteonectin, stromal cell-derived factor-1, cystatin C, gelsolin, and matrix metalloprotease-2 were identified by this method. To our knowledge, this is the first study to identify several novel secreted proteins by adipocytes by a proteomic approach using mass spectrometry.
Ten-Year Follow-Up Study of Patients with Dissociative Identity Disorder

Abstract Lit tie fol low-up data has been pub lished on in di vid u als with dissociative iden tity dis or der (DID). In this study, DID was di agnosed in 25 pa tients by two sea soned dissociative dis or der clinician/researchers be ginning in 1986. The initial evaluationin cludedacomprehensive med i cal and psy chi at ric eval u a tion and Min ne sota Multiphasic Per sonal ity In ven tory (MMPI). A ten-year fol low-up eval u a tion in eluded the Dissociative Experi ences Scale, Ci vil ian Mis sis sippi PTSD Scale, Beck Inventory for De pres sion, Life Ex pe ri ences Sur vey, the MMPI Hypochondriasis scale, and a dissociative dis or ders fol low-up ques tion naire. The pa tients were also asked to write a nar ra tive about their life and treatment since intake. Twelve patients provided follow-up data. Of these twelve, six ul ti mately achieved full in te gra tion of their per son al ity states, although two of them subsequently dissociated into alter personality states again. The two teen-aged pa tients achieved full in te gra tion within two years, while the older pa tients took con sid er ably Ion ger. Of the patients who elected to con tinue in treat ment for their dissociative dis or der and who con tinued to dis so ci ate into al ter per son al ity states, all have experienced major symptomatic improvement in both dissociative and non-dissociative symptomatology. Of the two therapy dropouts, both con tinue to have dissociative symp toms at fol low-up. We con elude that treatmentforDIDfollowingtreatmentguidelinespromulgated by the International Societyforthe Study of Dis so ciation brings about symptomatic im prove merit in both dissociative and non-dissociative symp toms. Ig noring symp toms of dis so ci a tion, as has been ad vo cated by some, resuits in no im prove ment.
Real and Nominal Wage Rigidity in a Model of Equal-Treatment Contracting

Following insights by Bewley (1999a), this paper analyses a model with downward rigidities in which firms cannot pay discriminate based on a year of entry to a firm, and develops an equilibrium model of wages and unemployment. We solve for the dynamics of wages and unemployment under conditions of downward wage rigidity, where forward looking firms take into account these constraints. Using simulated productivity data based on the post-war US economy, we analyse the ability of the model to match certain stylised labour market facts.
A Salt-Inducible Mn-Catalase (KatB) Protects Cyanobacterium from Oxidative Stress

A salt-inducible Mn-catalase from Anabaena plays a vital role in combating oxidative and salinity stress. Catalases, enzymes that detoxify H2O2, are widely distributed in all phyla, including cyanobacteria. Unlike the heme-containing catalases, the physiological roles of Mn-catalases remain inadequately characterized. In the cyanobacterium Anabaena, pretreatment of cells with NaCl resulted in unusually enhanced tolerance to oxidative stress. On exposure to H2O2, the NaCl-treated Anabaena showed reduced formation of reactive oxygen species, peroxides, and oxidized proteins than the control cells (i.e. not treated with NaCl) exposed to H2O2. This protective effect correlated well with the substantial increase in production of KatB, a Mn-catalase. Addition of NaCl did not safeguard the katB mutant from H2O2, suggesting that KatB was indeed responsible for detoxifying the externally added H2O2. Moreover, Anabaena deficient in KatB was susceptible to oxidative effects of salinity stress. The katB gene was strongly induced in response to osmotic stress or desiccation. Promoter-gfp analysis showed katB to be expressed only in the vegetative cells but not in heterocysts. Biochemically, KatB was an efficient, robust catalase that remained active in the presence of high concentrations of NaCl. Our findings unravel the role of Mn-catalase in acclimatization to salt/oxidative stress and demonstrate that the oxidative stress resistance of an organism can be enhanced by a simple compound such as NaCl.
Maintenance of remission following 2 years of standard treatment then dose reduction with abatacept in patients with early rheumatoid arthritis and poor prognosis

Objectives To evaluate maintenance of response while reducing intravenous abatacept dose from ∼10 mg/kg to ∼5 mg/kg in patients with early rheumatoid arthritis (RA) who achieved disease activity score (DAS)28 (erythrocyte sedimentation rate, ESR) <2.6. Methods This 1-year, multinational, randomised, double-blind substudy evaluated the efficacy and safety of ∼10 mg/kg and ∼5 mg/kg abatacept in patients with early RA with poor prognosis who had reached DAS28 (ESR) <2.6 at year 2 of the AGREE study. The primary outcome was time to disease relapse (defined as additional disease-modifying antirheumatic drugs, ≥2 courses high-dose steroids, return to open-label abatacept ∼10 mg/kg, or DAS28 (C reactive protein) ≥3.2 at two consecutive visits). Results 108 patients were randomised (∼10 mg/kg, n=58; ∼5 mg/kg, n=50). Three and five patients, respectively, discontinued, and four per group returned to open-label abatacept. Relapse over time and the proportion of patients relapsing were similar in both groups (31% (∼10 mg/kg) vs 34% (∼5 mg/kg); HR: 0.87 (95% CI 0.45 to 1.69)). Mean steady-state trough serum concentration for the ∼10 mg/kg group was 20.3–24.1 µg/mL, compared with 8.8–12.0 µg/mL for the ∼5 mg/kg group. Conclusions This exploratory study suggests that abatacept dose reduction may be an option in patients with poor prognosis early RA who achieve DAS28 (ESR) <2.6 after ≥1 year on abatacept (∼10 mg/kg). Trial registration number NCT00989235.
Attachment Theory and Family Functioning: Expectations and Congruencies

SynopsisQuestionnaire measures of attachment style, family functioning, and beliefs about self and others were taken from 193 adults. A principal components factor analysis of IS attachment items revealed a two factor solution to the attachment construct - Closeness and Anxiety. The three previously described attachment styles (Hazan & Shaver, 1987) were plotted on a grid using these two dimensions as axes. Measures of family functioning and mental models separated the secure from insecure attachment styles. Secure subjects scored higher on the family intimacy scale, were more democratic in their parenting style, and reported less conflict than insecure subjects. Secure subjects also reported themselves as easy to get to know and expressed more confidence in themselves and others. Insecure subjects generally disagreed that they were easy to get to know and expressed doubts about themselves and the likelihood of others liking them. Avoidant subjects scored lower on the family scales than the Anxious/ambiva.
Emotions as Learning Enhancers of Foreign Language Learning Motivation

The present article reports on a study that explores the effects of the emotional experiences of Mexican language learners on their motivation to learn English. In this qualitative research we present how emotions impact the motivation of university language learners in south Mexico. Results suggest that emotions, both negative and positive, contribute to enhancing and diminishing motivation. Although negative emotions may be considered detrimental to foreign language learning, the findings of this study show that negative emotions serve as learning enhancers. Results also evidence that Mexican language learners perceive negative emotions as positive for their language learning process. En este articulo se presenta una investigacion en la que se exploran los efectos que causan las experiencias emocionales en la motivacion de estudiantes mexicanos al aprender ingles. Con base en un estudio cualitativo se presenta como las emociones inciden en la motivacion de estudiantes universitarios en el sur de Mexico. Los resultados sugieren que las emociones, tanto positivas como negativas, contribuyen a potenciar y disminuir su motivacion. Se encontro que a pesar de que las emociones negativas pueden afectar el aprendizaje de una lengua extranjera, estas actuan incluso como potenciadoras del aprendizaje. Los resultados tambien indican que los estudiantes mexicanos perciben las emociones negativas como positivas en su proceso de aprendizaje.
A robust method for identifying a deterministic jitter model in a total jitter distribution

A new method for identifying a deterministic jitter (DJ) model in a total jitter (TJ) distribution is introduced in this paper. The new method is based on the characteristic function and identifies the DJ model from the given TJ PDF contaminated by an unknown DJ PDF. Benchmark testing using sinusoidal jitter provides validation of the new method for high-performance identification of the DJ model. Experiments on a variety of TJ PDFs also validate the very low false alarm probability of the new method.
Personal exposures of children to nitrogen dioxide relative to concentrations in outdoor air

OBJECTIVES To investigate the relation between fluctuations in personal exposure to nitrogen dioxide (NO2) in school children and changes in outdoor NO2 concentrations. METHODS 114 Asthmatic school children aged 7–12 years were recruited from the Southampton area. Weekly average personal exposures to NO2 were measured over a 13 month period with passive diffusion tubes. At the same time, outdoor NO2 concentrations were monitored at a fixed site in the centre of Southampton. Correlations between weekly personal exposures and mean outdoor concentrations during the same periods were examined. RESULTS Mean duration of follow up was 32 weeks. Measurements of weekly mean personal NO2 exposures were generally low and ranged from 0.7 to 496 μg/m3 with a geometric mean of 17 μg/m3. Substantial variation in personal exposures occurred between children and more especially within individual children from week to week. Daily outdoor concentrations of NO2 ranged from 4.3 to 29.8 μg/m3, with a geometric mean of 12.3 μg/m3. There was no evidence of seasonal variation in outdoor concentrations. No significant correlation was found between each child's weekly mean personal exposures to NO2 and mean outdoor concentrations for the corresponding periods. CONCLUSION At low outdoor NO2 concentrations, fluctuations in NO2in outdoor air as measured at a central monitoring station do not contribute importantly to variations in personal exposure when averaged over a week.
Efficient Shape Matching using Vector Extrapolation

We propose the adoption of a vector extrapolation technique to accelerate convergence of correspondence problems under the quadratic assignment formulation for attributed graph matching (QAP). In order to capture a broad range of matching scenarios, we provide a class of relaxations of the QAP under elastic net constraints. This allows us to regulate the sparsity/complexity trade-off which is inherent to most instances of the matching problem, thus enabling us to study the application of the acceleration method over a family of problems of varying difficulty. The validity of the approach is assessed by considering three different matching scenarios; namely, rigid and non-rigid three-dimensional shape matching, and image matching for Structure from Motion. As demonstrated on both real and synthetic data, our approach leads to an increase in performance of up to one order of magnitude when compared to the standard methods.