Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a Mannose Utilization System in Bacillus subtilis

ABSTRACT The mannose operon of Bacillus subtilis consists of three genes, manP, manA, and yjdF, which are responsible for the transport and utilization of mannose. Upstream and in the same orientation as the mannose operon a regulatory gene, manR, codes for a transcription activator of the mannose operon, as shown in this study. Both mannose operon transcription and manR transcription are inducible by mannose. The presence of mannose resulted in a 4- to 7-fold increase in expression of lacZ from the manP promoter (PmanP ) and in a 3-fold increase in expression of lacZ from the manR promoter (PmanR ). The transcription start sites of manPA-yjdF and manR were determined to be a single A residue and a single G residue, respectively, preceded by −10 and −35 boxes resembling a vegetative σA promoter structure. Through deletion analysis the target sequences of ManR upstream of PmanP and PmanR were identified between bp −80 and −35 with respect to the transcriptional start site of both promoters. Deletion of manP (mannose transporter) resulted in constitutive expression from both the PmanP and PmanR promoters, indicating that the phosphotransferase system (PTS) component EIIMan has a negative effect on regulation of the mannose operon and manR. Moreover, both PmanP and PmanR are subject to carbon catabolite repression (CCR). By constructing protein sequence alignments a DNA binding motif at the N-terminal end, two PTS regulation domains (PRDs), and an EIIA- and EIIB-like domain were identified in the ManR sequence, indicating that ManR is a PRD-containing transcription activator. Like findings for other PRD regulators, the phosphoenolpyruvate (PEP)-dependent phosphorylation by the histidine protein HPr via His15 plays an essential role in transcriptional activation of PmanP and PmanR . Phosphorylation of Ser46 of HPr or of the homologous Crh protein by HPr kinase and formation of a repressor complex with CcpA are parts of the B. subtilis CCR system. Only in the double mutant with an HPr Ser46Ala mutation and a crh knockout mutation was CCR strongly reduced. In contrast, PmanR and PmanP were not inducible in a ccpA deletion mutant.
The Embedded Neuron, the Enactive Field?

The concept of the receptive field, first articulated by Hartline, is central to visual neuroscience. The receptive field of a neuron encompasses the spatial and temporal properties of stimuli that activate the neuron, and, as Hubel and Wiesel conceived of it, a neuron’s receptive field is static. This makes it possible to build models of neural circuits and to build up more complex receptive fields out of simpler ones. Recent work in visual neurophysiology is providing evidence that the classical receptive field is an inaccurate picture. The receptive field seems to be a dynamic feature of the neuron. In particular, the receptive field of neurons in V1 seems to be dependent on the properties of the stimulus. In this paper, we review the history of the concept of the receptive field and the problematic data. We then consider a number of possible theoretical responses to these data.
Overcoming uncertainty of roadside sensors with smart adaptive traffic congestion analysis system

Real time traffic congestion degree is useful information in assisting decision making of drivers. It can also be a factor for calculating other traffic information. The congestion degree can be usually calculated on the basis of sensors installed along roads. It is possible that the sensory data can be lost due to potentially unreliable communication or faulty sensors, leading to lost of important traffic data. In this paper, we propose both adaptive traffic congestion analysis system architecture as well as a novel traffic congestion estimation algorithm that can compensate missing sensory data. An ability to provide traffic condition of road segments at all time is feasible. Unlike other existing methods, our approach aims not to rely on only traffic data from sensors, but utilize discoverable external context instead. The promising experiment result and analysis are reported in this paper. In addition, the context attribute correlation analysis is also discussed.
Comparison and Prognostic Analysis of Adjuvant Radiotherapy versus Salvage Radiotherapy for Treatment of Radically Resected Locally Advanced Esophageal Squamous Cell Carcinoma

Objective. To compare adjuvant radiotherapy and salvage radiotherapy after radical resection for treatment of esophageal squamous cell carcinoma (ESCC). Methods. Data from 155 patients with locally advanced ESCC who underwent radical resection and received postoperative radiotherapy from 2005 to 2011 were reviewed. Seventy-nine patients received adjuvant radiotherapy and 76 received salvage radiotherapy after locoregional recurrence. Results. The median disease-free survival (DFS) and overall survival (OS) were significantly higher in the adjuvant radiotherapy group than the salvage radiotherapy group (DFS 25.73 months versus 10.73 months, P < 0.001; OS 33.33 months versus 26.22 months, P = 0.006). The independent prognostic factors for DFS were performance status (PS) before radiotherapy and pathological stage in the adjuvant radiotherapy group, compared with lymph node metastasis, tumor location, and adjuvant chemotherapy in the salvage radiotherapy group. The independent prognostic factors for OS were age and PS in both groups. No differences in median DFS and OS between the groups were observed in patients aged > 65 years or with PS ≥ 2. Conclusion. Compared to salvage radiotherapy, postoperative adjuvant radiotherapy can prolong DFS and OS for patients with radically resected local advanced ESCC but cannot improve survival for patients aged > 65 years or with PS ≥ 2.
Differential Item Functioning (DIF) and the Mini-Mental State Examination (MMSE): Overview, Sample, and Issues of Translation

Background:Various forms of differential item functioning (DIF) in the Mini-Mental State Examination (MMSE) have been identified. Items have been found to perform differently for individuals of different educational levels, racial/ethnic groups, and/or of groups whose first language is not English. The articles in this section illustrate the use of different methods to examine DIF in relation to English and Spanish language administration of the MMSE. Objectives:The aim of this article is to provide a context for interpretation of the findings contained in the following set of papers examining DIF in the MMSE. Methods:The performance of the MMSE, when administered in English and Spanish, was reviewed. “Translation” has been discussed in the context of measurement bias, illustrating the variability in Spanish translations. Presented are the readability of the MMSE, description of the translation method, the study design and sample for the data set used, together with treatment of missing data, and model assumptions related to the analyses described in the accompanying set of papers examining DIF. Conclusions:The examination of item bias in cognitive impairment assessment instruments has practical and theoretical implications in the context of health disparities. Considerable DIF has been identified in the MMSE. A critical factor that may contribute to measurement bias is language translation and conversion. Once DIF has been established consistently in a measure, decisions regarding adjustments proceed. Perhaps the development of guidelines for appropriate adjustments for DIF correction in self-reported measures represents the next challenge in addressing measurement equivalence in crosscultural research.
In situ Quantification of Ammonium Sulfate in Single Aerosol Droplets by Means of Laser Trapping and Raman Spectroscopy

Noncontact levitation in air of single micrometer-sized water droplets containing ammonium sulfate was successful by a laser trapping technique. The trapping laser beam was also used simultaneously as an excitation light source for the Raman spectroscopy of trapped droplets. Raman scattering of the symmetric stretching vibration of the SO_4^2– anion and the OH stretching vibrations of H_2O were observed at 980 and 3420 cm^–1, respectively. The intensity ratio of these two Raman peaks was linearly proportional to the ammonium sulfate concentration in water. Therefore, the in situ quantification of ammonium sulfate in single aerosol droplets was achieved by means of laser trapping and Raman spectroscopy. To the best of our knowledge, this study is the first experimental observation of the independence of ammonium sulfate concentrations of aerosol water droplets to those of the mother solutions under constant relative humidity conditions.
Integrating fisheries approaches and household utility models for improved resource management

Natural resource management is littered with cases of overexploitation and ineffectual management, leading to loss of both biodiversity and human welfare. Disciplinary boundaries stifle the search for solutions to these issues. Here, I combine the approach of management strategy evaluation, widely applied in fisheries, with household utility models from the conservation and development literature, to produce an integrated framework for evaluating the effectiveness of competing management strategies for harvested resources against a range of performance metrics. I demonstrate the strengths of this approach with a simple model, and use it to examine the effect of manager ignorance of household decisions on resource management effectiveness, and an allocation tradeoff between monitoring resource stocks to reduce observation uncertainty and monitoring users to improve compliance. I show that this integrated framework enables management assessments to consider household utility as a direct metric for system performance, and that although utility and resource stock conservation metrics are well aligned, harvest yield is a poor proxy for both, because it is a product of household allocation decisions between alternate livelihood options, rather than an end in itself. This approach has potential far beyond single-species harvesting in situations where managers are in full control; I show that the integrated approach enables a range of management intervention options to be evaluated within the same framework.
Prediction of disordered regions in proteins based on the meta approach

MOTIVATION Intrinsically disordered regions in proteins have no unique stable structures without their partner molecules, thus these regions sometimes prevent high-quality structure determination. Furthermore, proteins with disordered regions are often involved in important biological processes, and the disordered regions are considered to play important roles in molecular interactions. Therefore, identifying disordered regions is important to obtain high-resolution structural information and to understand the functional aspects of these proteins. RESULTS We developed a new prediction method for disordered regions in proteins based on the meta approach and implemented a web-server for this prediction method named 'metaPrDOS'. The method predicts the disorder tendency of each residue using support vector machines from the prediction results of the seven independent predictors. Evaluation of the meta approach was performed using the CASP7 prediction targets to avoid an overestimation due to the inclusion of proteins used in the training set of some component predictors. As a result, the meta approach achieved higher prediction accuracy than all methods participating in CASP7.
Comprehensive Analysis of MGMT Promoter Methylation: Correlation with MGMT Expression and Clinical Response in GBM

O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR = 5.23, 95% CI [2.089–13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR = 3.076, 95% CI [1.301–7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting.
Language and Social Interaction: Taking Stock and Looking Forward

The Language and Social Interaction Division of the International Communication Association attracts a membership from a wide range of disciplines. The unifying concern of language and social interaction (LSI) researchers is to understand how communication works through the empirical study of everyday language use and talk in social interaction. This essay, along with Sanders, Fitch, and Pomerantz’s contribution to this volume in Chapter 17, describes the distinctive features of LSI research. This chapter sketches four major approaches to the field: conversation analysis, ethnography of communication, discourse analysis, and language and social psychology. The present state of theory and research is considered under the broad headings of power and identity, central concerns of LSI researchers. The tensions that emerge as a result of the different perspectives and commitments of LSI scholars are considered, and a research agenda aimed at resolving these tensions is outlined.
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements

CpG methylation is a key component of the epigenome architecture that is associated with changes in gene expression without a change to the DNA sequence. Since the first reports on deregulation of DNA methylation, in diseases such as cancer, and the initiation of the Human Epigenome Project, an increasing need has arisen for a detailed, high-throughput and quantitative method of analysis to discover and validate normal and aberrant DNA methylation profiles in large sample cohorts. Here we present an improved protocol using base-specific fragmentation and MALDI-TOF mass spectrometry that enables a sensitive and high-throughput method of DNA methylation analysis, quantitative to 5% methylation for each informative CpG residue. We have determined the accuracy, variability and sensitivity of the protocol, implemented critical improvements in experimental design and interpretation of the data and developed a new formula to accurately measure CpG methylation. Key innovations now permit determination of differential and allele-specific methylation, such as in cancer and imprinting. The new protocol is ideally suitable for detailed DNA methylation analysis of multiple genomic regions and large sample cohorts that is critical for comprehensive profiling of normal and diseased human epigenomes.
Towards controller-aided multimedia dissemination in Named Data Networking

Software Defined Networking (SDN) and Named Data Networking (NDN) are two topics which have received lots of attention in the networking research community in recent years. While both have emerged independently from each other we believe that their core features can be well aligned to each other. Hence combining both may hold potential benefits for network operators. In this paper we investigate the advantage of having a central SDN controller which is aware of the complete topology of an underlying NDN network. In our approach we use the controller for routing Interests for names unknown to the forwarding elements and to find alternative routes in case of link congestion. Another advantage of SDN is the ability to analyze and control the network on an application-layer component which communicates with the controller. This allows the development of application-aware networks that support the specific needs of the applications that use them. As an example use case we assumed a network whose main purpose is to disseminate multimedia content with Zipf-distributed popularity among users. Having an application layer which knows about content popularity statistics we improve the dissemination of multimedia content by instructing dedicated nodes in the network to prefetch content which is expected to become popular in their geographical region or autonomous system (AS) in the near future. The aim of this approach is to reduce the distance to potential consumers and reduce the load of the core network.
Adaptive CMMSE receivers for space-time block coded MIMO CDMA systems

A technique that can suppress multiple access interference (MAI) in space-time block coded (STBC) multiple-input multiple-output (MIMO) CDMA systems is developed. The proposed scheme, called the constrained minimum mean square error (CMMSE) receiver, is an extension of our method (see Hong, S.C. et al., Proc. VTC'02 Spring, 2002) to MIMO systems. The proposed CMMSE receiver for STBC systems has the identical complexity and rate of convergence as those of the CMMSE receiver for a SISO system, irrespective of the number of transmission antennas. Closed-form expressions for signal-to-interference-and-noise ratio (SINR) of the proposed and conventional maximum likelihood (ML) receivers are derived. As a result, it is shown that the proposed CMMSE receiver can provide significant performance improvement over the existing ML receiver.
Implementing Cyber Physical social Systems for smart cities: A semantic web perspective

Aim of the paper is to give a demonstration of the main Cyber-Physical-Systems (CPSs) and social networking facilities used to implement an ubiquitous city platform called Wi-City-Plus provided with mobile and centralized decision support systems (DSSs) taking advantage of all the data of city interest, including social data, and those sensed by networked monitoring devices. In particular, the paper adopts a semantic web approach that allow us to model such data by a suitable ontology specifically designed to support the main user scenarios in smart cities and to implement both the technical interoperability and the service integration envisaged by the CPS ideal model.
A 340-GHz Heterodyne Receiver Front End in 40-nm CMOS for THz Biomedical Imaging Applications

A low-power and high-performance 340-GHz heterodyne receiver front end (RFE) optimized for terahertz (THz) biomedical imaging applications is proposed in this paper. The THz RFE consists of an on-chip patch antenna, a single-balanced mixer, and a triple-push harmonic oscillator. The oscillator adopts a proposed harmonic oscillator architecture which can provide differential output by extracting output signals from the same current loop without any additional balun required. The mixer biased in the subthreshold region is designed not only to have high conversion gain and low noise figure by choosing the output intermediate frequency well above the flicker-noise corner frequency, but the required local oscillator (LO) power can also be as low as -11 dBm. Such a low demand on the LO power makes the proposed mixer very suitable for THz applications in which the achievable LO power is very limited. The impact of unavoidable slots for passing design rule checks on the performance of an on-chip patch antenna is also presented. The proposed THz RFE is implemented in a 40-nm digital complementary metal-oxide-semiconductor technology. The measured voltage conversion gain is -1.7 dB at 335.8 GHz, while the mixer and the oscillator only consume 0.3 and 52.8 mW, respectively, from a 1.1 V supply. The proposed THz RFE is employed to set up a THz transmissive imaging system which can provide spatial resolution of 1.4 mm.
Human Dignity In Bioethics And Biolaw

1. Human Dignity and Human Rights: Human Dignity as Empowerment 2. Human Dignity and the New Bioethics: Human Dignity as Constraint 3. Dignity, Human Dignity, and Dignified Conduct 4. The Principle of Generic Consistency and Its Justification 5. Kant and Gewirth 6. Dignity, Rights, and Virtue under the Principle of Generic Consistency 7. Being Born with Dignity: Selecting the Genetic Characteristics of Offspring 8. Living with Dignity I: Ownership and Commodification of the Human Body and Its Parts 9. Living wih Dignity II: Patents and Contracts 10. Living with Dignity III: Prolonging Life, Denying Death, and Cosmetic Augmentation 11. Dying with Dignity Bibliography
Cognitive Behavioural Prevention of Suicide in Psychosis: A treatment manual

This practical and informative text lays out the product of a number of years of clinical research into suicide behaviour and its prevention. While the focus is on non-affective psychosis and the schizophrenia-spectrum disorders, the mechanisms underlying suicide behaviour in this group may well underlie or at least influence suicide behaviour in other disorders. The authors describe methods of assessment through individual formulation, and a cognitive behavioural intervention through case studies, to reduce the risk of suicide.This book argues that:� Suicide behaviour lies on a cognitive-behavioural continuum from ideation, through intention to action. � Mechanisms based on biased information processing systems, the development of suicide schema, and appraisal styles are likely to be fruitful in explaining suicidal thoughts and behaviours. � A psychological theory of suicide behaviour is needed in order to develop a mechanism of suicide and to understand the components of suicidal thoughts and behaviours. � Suicide risk can be reduced through the use of the intervention methods described within the text Cognitive Behavioural Prevention of Suicide in Psychosis evaluates practical applications of contemporary research on this topic, and will therefore be of interest to practitioners, post-graduates in training, and researchers studying suicide and/or psychosis.