Miracle-dz/UniFAR-FTUs huggingface dataset:
A simple and rapid method for the preparation of gram-negative bacterial genomic DNA.

Two major protocols for the preparation of bacterial genomic DNA have been commonly used (1, 2). These methods provided powerful means of preparing genomic DNA; however, both of them are rather complex and time-consuming. Presented here is a simple and rapid method for extraction of bacterial genomic DNA. This method is effective in producing digestible genomic DNA from a variety of gram-negative bacteria, including those of the genera Xanhomonas, Pseudomonase, Agrobacterium, and Rhizobium. All of them normally produce copious amounts of polysaccharides (2, 3), the most common problem affecting DNA purity, which can inhibit the activity of many molecular biological enzymes (2). The method also has several advantages of not requiring any enzymes for expensive cell lysis materials. It requires only one chloroform extraction, and the entire process can be accomplished within one hour.
GROUNDED THEORY or GROUNDED DATA?: the PRODUCTION of POWER and KNOWLEDGE in ETHNOGRAPHIC RESEARCH

This paper concerns my own reflections on ethnographic research with Indigenous students studying at university. I began the research by using the methodology of interpretive ethnography to discover what constitutes success for Indigenous students studying at university. But after some unflattering critiques of my initial interpretation of the data, I returned to the drawing board to reflect on the methods that I had used to organise and structure the data in my interpretation. This led me to the critical ethnographers who helped me to look back on my initial positioning to see things that I could not see before. The paper consists of critical reflections on how power and knowledge are produced through the ethnographer's methodology to suggest that knowledge is not just found in the field or in the data but is also negotiated and produced through the relation between the participant and ethnographer. It is this relation that governs how the data are collected and what the ethnographer can find.
Ataxia‐telangiectasia, cancer and the pathobiology of the ATM gene

Ataxia‐telangiectasia (A‐T) is a pleiotropic inherited disease characterized by neurodegeneration, cancer, immunodeficiencies, radiation sensitivity, and genetic instability. Although A‐T homozygotes are rare, the A‐T gene may play a role in sporadic breast cancer and leukemia. ATM, the gene responsible for A‐T, is homologous to several cell cycle checkpoint genes from other organisms. ATM is thought to play a crucial role in a signal transduction network that modulates cell cycle checkpoints, genetic recombination, apoptosis, and other cellular responses to DNA damage. New insights into the pathobiology of A‐T have been provided by the creation of Atm−/− mice and by in vitro studies of ATM function. Analyses of ATM mutations in A‐T patients and in sporadic tumors suggest the existence of two classes of ATM mutation: null mutations that lead to A‐T and dominant negative missense mutations that may predispose to cancer in the heterozygous state.
Distinctive features and natural classes in phonological theory

1. I want in this paper to draw attention again to the theoretical basis of the use of distinctive features in generative phonology, and with that in mind, to consider what improvements can be made. One function of distinctive features is to provide a formal means of expressing the notion of a NATURAL CLASS (cf. Harms, 1968: 26), such that a phonological rule which applies to a natural class of segments may be expressed in a simpler way than a rule applying to some other class of segments. Distinctive features, and notational devices and conventions, are intended to capture this notion of simplicity so that by examining a formalized rule one may discover, counting the symbols in it according to a set of values provided, at least whether the rule is simpler than a comparable rule, if not its simplicity in any absolute sense. It is also intended that the set of features should be a substantive universal of language, though, as Harms' examples (1968: 23–38), drawn from various people's analyses of various languages, show, it cannot yet be seen that there is a tendency towards agreement on which these might be, as Harms himself (38) is aware. He sees the problem, however, in these terms: The basic set of features can be viewed as a hypothesis about language, subject to empirical validation. Arguments for adding new features to the list or for altering the basic features must demonstrate the inadequacy of the basic hypothesis. Such arguments, however, cannot be based upon an appeal to the simplicity metric, for the features themselves are elements in the simplicity metric. Phonemic solutions that do not assume the same set of features cannot be compared in terms of simplicity. The claim must be that one solution provides a more reasonable hypothesis of the phonological structure of the language in question.
An Evaluation of Family-Centered Rounds in the PICU: Room for Improvement Suggested by Families and Providers*

Objective: To identify areas for improvement in family-centered rounds from both the family and provider perspectives. Design: Prospective, cross-sectional mixed-methods study, including an objective measure (direct observation of family-centered rounds) and subjective measures (surveys of English-speaking families and providers) of family-centered rounds. Setting: PICU in a single, tertiary children’s hospital. Subjects: Families of children admitted to the PICU, physicians, and nurses. Interventions: None. Measurements and Main Results: Two hundred thirty-two family-centered round encounters were observed over a 10-week period. Family-centered round encounters averaged 10.5 minutes per child. Multivariable regression analysis revealed that family presence was independently associated with length of family-centered rounds (p < 0.002) despite family talk time accounting for an average of 25 seconds (4%) of the encounter. Non–English-speaking families were less likely to attend family-centered rounds compared with English-speaking families even when physically present at the patient’s bedside (p < 0.001). Most commonly families and providers agreed that family-centered rounds keep the family informed and reported positive statements about family presence on family-centered rounds; however, PICU fellows did not agree that families provided pertinent information and nurses reported that family presence limited patient discussions. The primary advice families offered providers to improve family-centered rounds was to be more considerate and courteous, including accommodating family schedules, minimizing distractions, and limiting computer viewing. Conclusions: Family presence increased the length of family-centered rounds despite a small percentage of time spoken by families, suggesting longer rounds are due to changes in provider behavior when families are present. Also, non–English-speaking families may need more support to be able to attend and benefit from family-centered rounds. Lastly, in an era of full family-centered rounds acceptance, families and most providers, except fellows, report benefit from family presence during family-centered rounds. However, providers should be aware of the perception of their behaviors to optimize the experience for families.
Social Exclusion: More Important to Human Females Than Males

Theoretical models based on primate evidence suggest that social structure determines the costs and benefits of particular aggressive strategies. In humans, males more than females interact in groups of unrelated same-sex peers, and larger group size predicts success in inter-group contests. In marked contrast, human females form isolated one-on-one relationships with fewer instrumental benefits, so social exclusion constitutes a more useful strategy. If this model is accurate, then human social exclusion should be utilized by females more than males and females should be more sensitive to its occurrence. Here we present four studies supporting this model. In Study 1, using a computerized game with fictitious opponents, we demonstrate that females are more willing than males to socially exclude a temporary ally. In Study 2, females report more actual incidents of social exclusion than males do. In Study 3, females perceive cues revealing social exclusion more rapidly than males do. Finally, in Study 4, females’ heart rate increases more than males’ in response to social exclusion. Together, results indicate that social exclusion is a strategy well-tailored to human females’ social structure.
Novel immunodeficiency data servers

The Internet contains scientific information in increasing amounts. It is possible to obtain the latest information, and Web services can easily be maintained and updated. We have set up three Internet services on immunodeficiencies. Immunodeficiency-related mutation infor mation is available in immunodeficiency mutation databases (IDbases). Currently 14 registries are distributed, including information about Bloom syndrome (BLMbase), X-linked agammaglobulinemia (BTKbase), X-linked and autosomal recessive chronic granulomatous diseases (CYBBbase for X-linked CGD, CYBAbase for p22(phox) deficiency, NCF1base for p47(phox) deficiency, NCF2base for p67(phox) deficiency), CD3gamma and CD3epsilon deficiencies (CD3Gbase, CD3Ebase), X-linked hyper-IgM syndrome (CD40Lbase), T-B+ severe combined immunodeficiency (JAK3base), V(D)J recombination defects (RAG1base, RAG2base), X-linked lymphoproliferative syndrome (SH2D1Abase), and ZAP-70 deficiency (ZAP70base). Information on laboratories analysing the genetic defects is collected to IDdiagnostics registry. Due to the rareness of immunodeficiencies there are very few laboratories performing genetic diagnostics. Such laboratories are listed in IDdiagnostics and physicians can use the registry to find a suitable laboratory for their diagnostic needs. Immunodeficiency Resource (IDR) is a comprehensive integrated knowledge base for all the information on immunode ficiencies, including clinical, biochemical, genetic, structural and computational data and analyses. All three services are available at http: //www.uta. fi/imt/bioinfo/.
Research challenges in wireless networks of biomedical sensors

Implanted biomedical devices have the potential to revolutionize medicine. Smart sensors, which are created by combining sensing materials with integrated circuitry, are being considered for several biomedical applications such as a glucose level monitor or a retina prosthesis. These devices require the capability to communicate with an external computer system (base station) via a wireless interface. The limited power and computational capabilities of smart sensor based biological implants present research challenges in several aspects of wireless networking due to the need for having a bio-compatible, fault-tolerant, energy-efficient, and scalable design. Further, em bedding thesesensors in humans add additional requirements. For example, the wireless networking solutions should be ultra-safe and reliable, work trouble-free in different geographical locations (although implants are typically not expected to move; they shouldn't restrict the movements of their human host), and require minimal maintenance. This necessitates application-specific solutions which are vastly different from traditional solutions. In this paper, we describe the potential of biomedical smart sensors. We then explain the challenges for wireless networking of human-embedded smart sensor arrays and our preliminary approach for wireless networking of a retina prosthesis. Our aim is to motivate vigorous research in this area by illustrating the need for more application-specific and novel approaches toward developing wireless networking solutions for human-implanted smart sensors.
Distributed Content Based Video Identification in Peer-to-Peer Networks: Requirements and Solutions

In this paper, we first discuss the essential requirements for a fingerprint (perceptual hash)-based distributed video identification system in peer-to-peer (P2P) networks in comparison with traditional central database implementations of fingerprints. This discussion reveals that first, fingerprint sizes of existing video fingerprint methods are not compatible with the cache sizes of current P2P clients; second, fingerprint extraction durations during a query are not at tolerable levels for a user in the network; third, the repetitive patterns in the extracted fingerprints avoid the uniform distribution of storage and traffic load among the peers; and finally, the existing methods do not provide a solution to synchronize the fingerprint extraction from the shared video and queried video. In order to solve the mentioned requirements, we propose a baseline method using only the difference of video frame means, which decreases the fingerprint sizes to typical cache sizes, by increasing the granularity levels from seconds to minutes. We then develop a novel algorithm which utilizes reference points on one-dimensional frame mean sequence for the synchronization of fingerprint extraction. This algorithm is extended with a hierarchical decoding approach based on Gaussian scales, which only decodes a subset of video frames without needing a full decoding. Finally, an analysis on the effect of design parameters to the fingerprint probability distribution is performed to avoid repetitive patterns. Our ultimate solution reduces the fingerprint sizes into kilobytes, extraction time to seconds, and search duration into milliseconds, and achieves about 90% detection rates with 1–4 min granularities, while enabling a fair distribution of storage load among the peers at the same time.
Phosphorylation of a NAC Transcription Factor by a Calcium/Calmodulin-Dependent Protein Kinase Regulates Abscisic Acid-Induced Antioxidant Defense in Maize1[OPEN]

The maize protein kinase ZmCCaMK phosphorylates the ZmNAC84 transcription factor at Ser113 during abscisic acid-induced antioxidant. Calcium/calmodulin-dependent protein kinase (CCaMK) has been shown to play an important role in abscisic acid (ABA)-induced antioxidant defense and enhance the tolerance of plants to drought stress. However, its downstream molecular events are poorly understood. Here, we identify a NAC transcription factor, ZmNAC84, in maize (Zea mays), which physically interacts with ZmCCaMK in vitro and in vivo. ZmNAC84 displays a partially overlapping expression pattern with ZmCCaMK after ABA treatment, and H2O2 is required for ABA-induced ZmNAC84 expression. Functional analysis reveals that ZmNAC84 is essential for ABA-induced antioxidant defense in a ZmCCaMK-dependent manner. Furthermore, ZmCCaMK directly phosphorylates Ser-113 of ZmNAC84 in vitro, and Ser-113 is essential for the ABA-induced stimulation of antioxidant defense by ZmCCaMK. Moreover, overexpression of ZmNAC84 in tobacco (Nicotiana tabacum) can improve drought tolerance and alleviate drought-induced oxidative damage of transgenic plants. These results define a mechanism for ZmCCaMK function in ABA-induced antioxidant defense, where ABA-produced H2O2 first induces expression of ZmCCaMK and ZmNAC84 and activates ZmCCaMK. Subsequently, the activated ZmCCaMK phosphorylates ZmNAC84 at Ser-113, thereby inducing antioxidant defense by activating downstream genes.
Regulation of ATG 6 / Beclin-1 homologs by abiotic stresses and hormones in rice ( Oryza sativa L . )

Autophagy, a complex and conserved mechanism, serving as a defense response in all eukaryotic organisms, is regulated by several proteins, among which ATG proteins are the most important due to their involvement in autophagosome formation. ATG6/Beclin-1 proteins, reported to be essential for autophagosome formation and assigned as a conserved domain, were subjected to database searches. We found three homologs in the rice (Oryza sativa) genome. A phylogeny tree was constructed to establish their across species relationship, which divided them into three distinct groups; two for plants, i.e., monocots and dicots, and one for animals. Evolutionary study of this family by critical amino acid conservation analysis revealed significant functional divergence. The finding of important stress-related cis-acting elements in the promoter region of rice ATG6 genes demonstrated their involvement in 3677 Regulation of ATG6 homologs by abiotic stresses and hormones ©FUNPEC-RP www.funpecrp. com.br Genetics and Molecular Research 11 (4): 3676-3687 (2012) abiotic stress responses. Furthermore, expression profiling of rice ATG6 genes based on microarray data, as well as by semi-quantitative RTPCR, showed differential expression when subjected to different stresses suggesting the involvement of OsATG6 genes in abiotic stresses (heat, cold and drought) and hormone (abscisic acid) responses. Analysis of co-expressed genes showed that most of them annotated to DNA repair pathways and proteolysis, etc. Collectively, these results suggest the involvement of OsATG6 genes in different stresses, and provide a basis for further functional studies to investigate the biological mechanism of action of these genes under abiotic stresses.
Commerce international et salaires relatifs: les enseignements des modèles d'équilibre général calculables

Cet article etudie les enseignements des modeles d'equilibre general calculables quant a l'impact sur les salaires relatifs d'un choc de politique commerciale ou d'un choc exogene de commerce international. Les simulations presentees confirment que, en s'appuyant sur un cadre d'analyse "realiste", l'ordre de grandeur de cet impact est generalement faible.
Analysis of the module-voltage fluctuations of the Modular Multilevel Converter at variable speed drive applications

For medium-voltage drives multilevel converters are advantageous to reduce the insulation stress of the windings of the machine. State of the art are multilevel converters as Diode Clamped Converter, Imbricated Cell Converter or Stacked H-Bridge Converter with a low number of levels limited by the restrictions in practical construction. The Modular Multilevel Converter is not limited in the number of levels. Its modularity allows a nearly unlimited cascading of sub-modules and therewith of voltage levels at the same complexity in construction. The challenges of this topology used as drive converter are the AC fluctuations of the sub-module voltages rising with sinking output frequency. This paper derives analytically equations for the module-voltage fluctuations for two different controls using the converter in the whole speed range. The results are analysed and compared to simulation results.
Training of affect recognition in schizophrenia: Neurobiological correlates

Abstract Recently, a standardized program for training of affect recognition (TAR) was developed which has demonstrated efficacy and specificity with respect to behavioral performance. The effects of the TAR on the cerebral correlates were evaluated using repeated fMRI event-related measurements in a group of schizophrenia patients (n=10) before and after TAR treatment six weeks apart. A second patient group without training (n=10, treatment as usual, TAU) as well as healthy subjects (n=10) were investigated at equivalent time points. Schizophrenia patients were shown to be differentially impaired in the identification of the emotional aspects of facial expressions (but not age discrimination) when compared with healthy participants. A specific improvement in the increased number of correct identifications was observed in trained patients only. In parallel, an increase in activation was noted in the left middle and superior occipital lobe, the right inferior and superior parietal cortex, and the inferior frontal cortex bilaterally in TAR patients compared to the TAU group. These activation changes in TAR patients correlated with their behavioral improvement, further corroborating the positive effect of training. Specific training effects are seen to correspond with cerebral effects, probably reflecting a more efficient use of attentional, perceptual, or cognitive strategies.
Mothers’ and Fathers’ Perceptions of Mutuality in Middle Childhood: The Domain of Intimacy

This study investigated parents’ experiences of closeness in their interactions with their children in middle childhood. Structured, open-ended interviews were conducted with mothers and fathers from 23 families (46 participants) with children aged between 7 and 11 years (M = 9.2 years). Qualitative analyses indicated that parents’ experiences of close interactions were consistent with an underlying construct of parent—child intimacy. Parents reported that they experienced closeness predominantly during interactions where they perceived mutuality and shared pleasure. Parents were strategic in creating both intimate interactions and contexts for intimacy. Children were perceived to contribute to intimacy by initiating and responding to parental bids for intimate interactions.
Testing the k^3 Component in the Primordial Perturbation Power Spectrum

Well-known causality arguments show that events occurring at the end of inflation, associated with reheating or preheating, could contribute a blue component to the spectrum of primordial curvature perturbations, with the dependence k 3. We explore the possibility that they could be observably large in current CMB, LSS, and Lyman-α data. We find that a k 3 component with a cutoff at some maximum k can modestly improve the fits (∆χ 2 = 1.4, 5.4) of the low multipoles (ℓ ∼ 10 − 50) or the second peak (ℓ ∼ 540) of the CMB angular spectrum when the three-year WMAP data are used. Moreover, the results from WMAP are consistent with the CBI, ACBAR, 2dFGRS, and SDSS data when they are included in the analysis. Including the SDSS galaxy clustering power spectrum, we find weak positive evidence for the k 3 component at the level of ∆χ 2 ′ = 2.4, with the caveat that the nonlinear evolution of the power spectrum may not be properly treated in the presence of the k 3 distortion. To investigate the high-k regime, we use the Lyman-α forest data (LUQAS, Croft et al., and SDSS Lyman-α); here we find evidence at the level ∆χ 2 ′ = 3.8. We give constraints on the ratio between the k 3 component and the nearly scale-invariant component, r σ < 1.5 over the range of wavenumbers 2.3 × 10 −3 Mpc −1 < k < 8.2 Mpc −1. We also discuss theoretical models which could lead to the k 3 effect, including ordinary hybrid inflation, and double D-term inflation models.
Semantic relatedness and first-second language effects in the bilingual brain: a brain mapping study*

Behavioural studies investigating word processing in bilinguals generally report faster response times (RTs) for first (L1) than for second (L2) language words. To examine the locus of this language effect, this study used behavioural data and event-related potentials (ERPs) collected from bilinguals while performing a semantic categorisation task on visual word pairs. RTs revealed both language and semantic relatedness effects. Spatio-temporal analysis of ERP map series showed that the semantic effect was explained by a condition-specific map segment occurring during the N400 component. The language effect was primarily explained by a map segment that started at ~170 ms and covered the period of the P2 component, that was longer in L2 than in L1 and whose duration correlated with RTs. Source localisation showed that this early segment involved the bilateral occipito-temporal regions including the fusiform area. These findings indicate that ERPs differentiated L1 and L2 during early word recognition steps.